Query 038591
Match_columns 82
No_of_seqs 213 out of 1093
Neff 8.6
Searched_HMMs 46136
Date Fri Mar 29 12:34:17 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/038591.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/038591hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PHA01976 helix-turn-helix prot 99.8 4.7E-18 1E-22 90.9 7.2 58 21-78 3-60 (67)
2 PF12844 HTH_19: Helix-turn-he 99.7 5.4E-18 1.2E-22 89.9 6.2 57 22-78 1-57 (64)
3 PF01381 HTH_3: Helix-turn-hel 99.7 9.7E-18 2.1E-22 86.5 5.7 54 25-78 1-54 (55)
4 COG1476 Predicted transcriptio 99.7 2.4E-17 5.1E-22 88.3 6.3 57 23-79 4-60 (68)
5 TIGR03070 couple_hipB transcri 99.7 1.2E-16 2.6E-21 82.6 7.8 56 21-76 3-58 (58)
6 PRK06424 transcription factor; 99.7 2.7E-16 5.8E-21 95.5 8.1 59 22-80 86-144 (144)
7 PRK08359 transcription factor; 99.7 3.6E-16 7.9E-21 97.5 7.8 59 22-80 87-145 (176)
8 PF13560 HTH_31: Helix-turn-he 99.7 2.5E-16 5.5E-21 83.7 5.1 59 22-80 3-62 (64)
9 PRK09726 antitoxin HipB; Provi 99.7 1.2E-15 2.7E-20 85.8 7.9 57 22-78 14-70 (88)
10 TIGR00270 conserved hypothetic 99.6 8.1E-16 1.7E-20 94.4 7.2 58 22-79 71-128 (154)
11 PRK09706 transcriptional repre 99.6 1E-15 2.3E-20 91.9 7.3 58 21-78 6-63 (135)
12 TIGR02607 antidote_HigA addict 99.6 1.1E-14 2.4E-19 79.7 7.6 57 21-77 5-62 (78)
13 PRK13890 conjugal transfer pro 99.6 1.2E-14 2.5E-19 86.1 7.2 58 21-78 6-63 (120)
14 PRK09943 DNA-binding transcrip 99.6 9.4E-15 2E-19 91.6 7.2 58 21-78 8-65 (185)
15 PRK08154 anaerobic benzoate ca 99.6 8.1E-15 1.8E-19 98.2 6.2 70 10-79 15-87 (309)
16 TIGR02684 dnstrm_HI1420 probab 99.6 8.5E-15 1.8E-19 82.7 5.2 60 16-77 28-87 (89)
17 PF13443 HTH_26: Cro/C1-type H 99.5 1.8E-14 4E-19 76.0 5.7 56 24-79 1-57 (63)
18 PRK10072 putative transcriptio 99.5 5.9E-14 1.3E-18 80.2 7.6 56 21-77 34-89 (96)
19 TIGR02612 mob_myst_A mobile my 99.5 1.3E-13 2.8E-18 84.4 7.1 56 22-77 27-84 (150)
20 PRK04140 hypothetical protein; 99.5 1.4E-13 3.1E-18 92.6 7.5 57 22-78 128-184 (317)
21 smart00530 HTH_XRE Helix-turn- 99.4 1.2E-12 2.6E-17 65.3 6.8 54 25-78 2-55 (56)
22 KOG3398 Transcription factor M 99.4 1.4E-12 3.1E-17 76.8 7.0 78 3-80 48-133 (135)
23 cd00093 HTH_XRE Helix-turn-hel 99.4 3E-12 6.4E-17 64.3 7.0 56 23-78 2-57 (58)
24 TIGR03830 CxxCG_CxxCG_HTH puta 99.4 2.9E-12 6.3E-17 75.7 7.3 62 17-79 62-123 (127)
25 COG1813 Predicted transcriptio 99.4 2.4E-12 5.3E-17 79.3 7.1 58 22-79 81-138 (165)
26 PHA00542 putative Cro-like pro 99.3 5.2E-11 1.1E-15 66.2 8.3 54 20-73 18-72 (82)
27 COG2944 Predicted transcriptio 99.3 3.2E-11 7E-16 69.5 6.9 49 17-65 41-89 (104)
28 PRK10856 cytoskeletal protein 99.3 2.5E-11 5.3E-16 82.3 7.0 58 21-78 15-78 (331)
29 PF13744 HTH_37: Helix-turn-he 99.2 5.1E-11 1.1E-15 65.9 5.6 56 22-77 20-76 (80)
30 COG3620 Predicted transcriptio 99.2 8.8E-11 1.9E-15 72.4 6.9 52 22-73 7-58 (187)
31 COG3093 VapI Plasmid maintenan 99.1 4.2E-10 9.1E-15 64.7 6.4 57 21-77 10-67 (104)
32 PRK13355 bifunctional HTH-doma 99.1 5.3E-10 1.2E-14 79.1 7.5 57 22-78 5-66 (517)
33 PRK02866 cyanate hydratase; Va 99.0 2E-09 4.4E-14 65.5 7.3 57 22-78 7-63 (147)
34 smart00352 POU Found in Pit-Oc 99.0 4.6E-09 1E-13 57.3 7.0 46 22-69 13-64 (75)
35 PF07022 Phage_CI_repr: Bacter 98.9 6.5E-10 1.4E-14 59.4 2.4 53 24-77 2-56 (66)
36 TIGR00673 cynS cyanate hydrata 98.9 1E-08 2.3E-13 62.6 7.6 56 22-77 10-65 (150)
37 COG3655 Predicted transcriptio 98.9 6E-09 1.3E-13 56.6 5.6 58 22-79 4-62 (73)
38 COG1709 Predicted transcriptio 98.9 3.1E-09 6.8E-14 68.2 4.7 52 21-72 28-80 (241)
39 PF13413 HTH_25: Helix-turn-he 98.9 9.6E-09 2.1E-13 54.4 5.4 55 24-78 1-61 (62)
40 COG1395 Predicted transcriptio 98.8 1.4E-08 3E-13 68.2 6.5 56 22-77 127-182 (313)
41 COG1396 HipB Predicted transcr 98.8 8.2E-08 1.8E-12 52.0 7.3 56 22-77 3-59 (120)
42 PF08667 BetR: BetR domain; I 98.7 1.1E-07 2.4E-12 58.0 6.1 59 20-78 5-67 (147)
43 PHA01083 hypothetical protein 98.6 2.3E-07 5E-12 56.4 5.9 56 23-78 5-62 (149)
44 cd01392 HTH_LacI Helix-turn-he 98.5 3.6E-07 7.9E-12 46.1 5.2 41 38-78 2-45 (52)
45 COG5499 Predicted transcriptio 98.5 4.3E-07 9.2E-12 52.7 5.2 55 22-77 62-116 (120)
46 PF00356 LacI: Bacterial regul 98.5 1.1E-06 2.5E-11 43.8 5.9 42 35-76 1-45 (46)
47 COG1426 Predicted transcriptio 98.5 8.3E-07 1.8E-11 59.3 6.6 59 21-79 4-68 (284)
48 PF08965 DUF1870: Domain of un 98.3 5.6E-06 1.2E-10 48.8 6.7 51 22-72 3-55 (118)
49 COG3636 Predicted transcriptio 98.3 1.9E-06 4.1E-11 49.1 4.5 54 22-77 40-93 (100)
50 smart00354 HTH_LACI helix_turn 98.2 6E-06 1.3E-10 44.4 5.7 44 34-77 1-47 (70)
51 TIGR01321 TrpR trp operon repr 98.2 8.9E-06 1.9E-10 46.3 5.9 47 22-68 42-90 (94)
52 COG4800 Predicted transcriptio 98.2 1.1E-05 2.3E-10 49.0 6.5 54 18-72 14-67 (170)
53 COG2522 Predicted transcriptio 98.1 1.5E-05 3.3E-10 47.1 5.6 34 26-60 16-49 (119)
54 PF13693 HTH_35: Winged helix- 98.0 2E-05 4.3E-10 43.4 4.8 55 22-79 4-58 (78)
55 COG3423 Nlp Predicted transcri 98.0 7.2E-05 1.6E-09 40.9 6.6 59 18-79 6-64 (82)
56 PRK08099 bifunctional DNA-bind 98.0 2.2E-05 4.8E-10 54.7 5.8 47 32-78 2-49 (399)
57 TIGR02147 Fsuc_second hypothet 97.9 4.3E-05 9.4E-10 50.9 5.5 48 33-80 27-75 (271)
58 PF13384 HTH_23: Homeodomain-l 97.7 8.6E-05 1.9E-09 37.0 4.2 31 24-56 10-40 (50)
59 PRK10344 DNA-binding transcrip 97.7 0.0005 1.1E-08 38.8 7.1 58 19-79 7-64 (92)
60 PRK09526 lacI lac repressor; R 97.7 0.00015 3.2E-09 48.4 5.6 47 32-78 4-53 (342)
61 TIGR01481 ccpA catabolite cont 97.7 0.0002 4.3E-09 47.5 6.1 45 34-78 2-49 (329)
62 PRK10014 DNA-binding transcrip 97.6 0.00022 4.8E-09 47.5 6.4 47 32-78 5-54 (342)
63 PRK09492 treR trehalose repres 97.6 0.00023 4.9E-09 47.0 6.1 46 33-78 4-52 (315)
64 PHA00675 hypothetical protein 97.6 0.00019 4.1E-09 39.3 4.6 37 22-58 28-64 (78)
65 PF02796 HTH_7: Helix-turn-hel 97.6 0.00019 4E-09 35.4 4.3 34 22-56 11-44 (45)
66 PRK10703 DNA-binding transcrip 97.6 0.00023 5E-09 47.5 6.1 44 34-77 2-48 (341)
67 PRK11303 DNA-binding transcrip 97.6 0.00024 5.2E-09 47.1 6.1 44 34-77 1-50 (328)
68 TIGR02405 trehalos_R_Ecol treh 97.6 0.00026 5.7E-09 46.8 6.2 45 34-78 2-49 (311)
69 PRK10727 DNA-binding transcrip 97.6 0.00024 5.2E-09 47.6 6.1 45 34-78 2-49 (343)
70 TIGR02844 spore_III_D sporulat 97.6 0.00075 1.6E-08 37.4 7.0 50 23-73 10-60 (80)
71 PF14549 P22_Cro: DNA-binding 97.6 0.00021 4.5E-09 37.5 4.3 42 31-76 8-49 (60)
72 PRK14987 gluconate operon tran 97.6 0.00019 4.2E-09 47.7 5.2 46 33-78 5-53 (331)
73 TIGR03879 near_KaiC_dom probab 97.6 0.00047 1E-08 37.5 5.7 40 28-69 27-66 (73)
74 TIGR02293 TAS_TIGR02293 putati 97.6 0.00054 1.2E-08 41.1 6.5 54 18-71 21-74 (133)
75 PF04814 HNF-1_N: Hepatocyte n 97.5 0.00039 8.5E-09 43.8 5.8 51 22-72 120-170 (180)
76 PRK10401 DNA-binding transcrip 97.5 0.00042 9.2E-09 46.4 6.2 44 34-77 2-48 (346)
77 PF00157 Pou: Pou domain - N-t 97.5 0.00086 1.9E-08 36.7 6.2 47 22-70 13-65 (75)
78 TIGR02417 fruct_sucro_rep D-fr 97.4 0.00058 1.2E-08 45.3 5.9 44 35-78 1-50 (327)
79 PHA02591 hypothetical protein; 97.4 0.00053 1.1E-08 37.7 4.5 31 25-55 51-81 (83)
80 PF13936 HTH_38: Helix-turn-he 97.4 0.00028 6.2E-09 34.6 3.2 31 24-55 12-42 (44)
81 PF13412 HTH_24: Winged helix- 97.4 0.00056 1.2E-08 33.8 4.3 33 23-55 7-39 (48)
82 COG1609 PurR Transcriptional r 97.4 0.00079 1.7E-08 45.7 6.1 44 34-77 1-47 (333)
83 PRK03975 tfx putative transcri 97.4 0.00034 7.4E-09 42.5 3.9 46 30-76 18-66 (141)
84 COG5606 Uncharacterized conser 97.3 0.00062 1.3E-08 38.1 4.2 57 22-78 30-87 (91)
85 COG4197 Uncharacterized protei 97.3 0.00021 4.6E-09 40.4 2.2 44 35-78 14-59 (96)
86 PRK10339 DNA-binding transcrip 97.2 0.00049 1.1E-08 45.8 4.0 44 34-77 2-50 (327)
87 PRK10423 transcriptional repre 97.2 0.0012 2.6E-08 43.7 5.6 41 37-77 2-45 (327)
88 cd04762 HTH_MerR-trunc Helix-T 97.1 0.001 2.2E-08 32.2 3.7 23 34-56 1-23 (49)
89 PF08535 KorB: KorB domain; I 97.1 0.00067 1.5E-08 38.2 3.1 25 31-55 1-25 (93)
90 PF06056 Terminase_5: Putative 97.1 0.00089 1.9E-08 34.9 3.1 26 31-56 11-36 (58)
91 PF05269 Phage_CII: Bacterioph 97.0 0.00011 2.5E-09 41.5 -0.5 46 30-79 20-65 (91)
92 PF02954 HTH_8: Bacterial regu 97.0 0.0027 5.8E-08 30.7 4.4 33 22-54 7-39 (42)
93 TIGR00721 tfx DNA-binding prot 97.0 0.0019 4.1E-08 39.1 4.6 26 31-56 19-44 (137)
94 PF12728 HTH_17: Helix-turn-he 97.0 0.0016 3.4E-08 32.5 3.6 28 34-61 2-29 (51)
95 TIGR01764 excise DNA binding d 96.9 0.0023 5E-08 31.0 3.6 27 34-60 2-28 (49)
96 PF07037 DUF1323: Putative tra 96.9 0.0013 2.7E-08 38.9 2.8 22 34-55 1-22 (122)
97 PF13518 HTH_28: Helix-turn-he 96.8 0.0042 9.2E-08 30.7 4.4 24 32-55 11-34 (52)
98 PF00325 Crp: Bacterial regula 96.8 0.0021 4.5E-08 29.6 2.7 23 33-55 2-24 (32)
99 cd04761 HTH_MerR-SF Helix-Turn 96.8 0.0034 7.4E-08 30.7 3.7 23 34-56 1-23 (49)
100 PF10668 Phage_terminase: Phag 96.8 0.0021 4.7E-08 33.7 3.0 24 33-56 22-45 (60)
101 cd04764 HTH_MlrA-like_sg1 Heli 96.7 0.006 1.3E-07 32.0 4.8 22 34-55 1-22 (67)
102 PF00376 MerR: MerR family reg 96.7 0.0017 3.6E-08 31.0 2.4 23 35-57 1-23 (38)
103 PF04545 Sigma70_r4: Sigma-70, 96.7 0.0063 1.4E-07 30.2 4.6 29 27-55 14-42 (50)
104 TIGR02531 yecD_yerC TrpR-relat 96.7 0.0037 8E-08 35.2 3.9 27 30-56 47-73 (88)
105 PF08279 HTH_11: HTH domain; 96.7 0.0037 8E-08 31.5 3.7 32 24-55 5-37 (55)
106 PF02001 DUF134: Protein of un 96.6 0.0039 8.5E-08 36.2 3.8 35 22-56 44-80 (106)
107 COG1356 tfx Transcriptional re 96.6 0.0025 5.4E-08 38.2 2.7 28 29-56 19-46 (143)
108 cd01104 HTH_MlrA-CarA Helix-Tu 96.5 0.0048 1E-07 32.3 3.5 22 34-55 1-22 (68)
109 PRK08558 adenine phosphoribosy 96.5 0.015 3.2E-07 38.1 6.3 41 33-73 23-63 (238)
110 PF04218 CENP-B_N: CENP-B N-te 96.5 0.0024 5.3E-08 32.5 2.1 34 23-56 11-45 (53)
111 PF02376 CUT: CUT domain; Int 96.4 0.036 7.8E-07 31.1 6.6 58 22-79 15-79 (87)
112 PF04967 HTH_10: HTH DNA bindi 96.4 0.0066 1.4E-07 31.1 3.2 24 32-55 22-45 (53)
113 PRK01381 Trp operon repressor; 96.4 0.0094 2E-07 34.2 4.2 53 22-74 42-96 (99)
114 cd04763 HTH_MlrA-like Helix-Tu 96.4 0.0052 1.1E-07 32.4 3.0 22 34-55 1-22 (68)
115 PF13411 MerR_1: MerR HTH fami 96.3 0.0051 1.1E-07 32.3 2.8 23 34-56 1-23 (69)
116 PF05225 HTH_psq: helix-turn-h 96.3 0.01 2.2E-07 29.2 3.7 35 23-58 7-41 (45)
117 cd00569 HTH_Hin_like Helix-tur 96.2 0.01 2.2E-07 26.2 3.2 24 31-54 19-42 (42)
118 PRK15418 transcriptional regul 96.2 0.01 2.2E-07 40.4 4.4 52 24-75 20-84 (318)
119 PRK13698 plasmid-partitioning 96.2 0.013 2.8E-07 40.1 4.8 35 22-56 164-199 (323)
120 PF13404 HTH_AsnC-type: AsnC-t 96.2 0.02 4.3E-07 27.8 4.3 31 22-52 6-36 (42)
121 smart00422 HTH_MERR helix_turn 96.2 0.012 2.6E-07 30.8 3.8 22 34-55 1-22 (70)
122 TIGR02044 CueR Cu(I)-responsiv 96.2 0.0097 2.1E-07 35.3 3.7 46 34-79 1-63 (127)
123 cd01109 HTH_YyaN Helix-Turn-He 96.1 0.0096 2.1E-07 34.5 3.6 22 34-55 1-22 (113)
124 COG1342 Predicted DNA-binding 96.1 0.0089 1.9E-07 34.1 3.2 34 22-55 36-71 (99)
125 COG2390 DeoR Transcriptional r 96.1 0.012 2.7E-07 40.2 4.4 54 22-75 15-81 (321)
126 PF01527 HTH_Tnp_1: Transposas 96.1 0.0021 4.6E-08 34.4 0.6 32 23-55 14-45 (76)
127 PF01047 MarR: MarR family; I 96.1 0.012 2.5E-07 30.0 3.3 33 23-55 7-39 (59)
128 cd04781 HTH_MerR-like_sg6 Heli 96.0 0.012 2.6E-07 34.5 3.6 46 34-79 1-62 (120)
129 PF04552 Sigma54_DBD: Sigma-54 96.0 0.0015 3.3E-08 40.5 -0.3 46 31-76 47-92 (160)
130 PRK09744 DNA-binding transcrip 96.0 0.033 7.2E-07 30.3 4.9 36 35-73 12-47 (75)
131 COG2842 Uncharacterized ATPase 96.0 0.028 6E-07 38.1 5.5 55 22-76 8-62 (297)
132 smart00550 Zalpha Z-DNA-bindin 95.9 0.027 5.9E-07 29.9 4.4 33 23-55 10-44 (68)
133 cd06171 Sigma70_r4 Sigma70, re 95.9 0.032 7E-07 26.9 4.5 26 30-55 23-48 (55)
134 PF13022 HTH_Tnp_1_2: Helix-tu 95.9 0.0089 1.9E-07 36.4 2.7 25 33-57 34-58 (142)
135 TIGR00180 parB_part ParB-like 95.9 0.042 9.2E-07 34.5 5.9 48 22-70 109-156 (187)
136 COG1513 CynS Cyanate lyase [In 95.9 0.079 1.7E-06 32.0 6.6 56 22-77 10-65 (151)
137 smart00421 HTH_LUXR helix_turn 95.8 0.016 3.4E-07 28.6 3.2 25 31-55 16-40 (58)
138 PF01418 HTH_6: Helix-turn-hel 95.8 0.034 7.4E-07 30.1 4.7 40 25-64 26-65 (77)
139 COG1318 Predicted transcriptio 95.8 0.017 3.6E-07 36.3 3.8 32 28-59 56-87 (182)
140 cd01105 HTH_GlnR-like Helix-Tu 95.8 0.021 4.5E-07 31.8 3.8 23 33-55 1-23 (88)
141 TIGR02054 MerD mercuric resist 95.8 0.023 4.9E-07 33.7 4.1 47 33-79 3-66 (120)
142 cd04773 HTH_TioE_rpt2 Second H 95.8 0.019 4.1E-07 33.2 3.8 23 34-56 1-23 (108)
143 cd04784 HTH_CadR-PbrR Helix-Tu 95.8 0.018 3.9E-07 34.0 3.7 46 34-79 1-63 (127)
144 PRK04217 hypothetical protein; 95.7 0.032 6.9E-07 32.6 4.5 30 26-55 51-80 (110)
145 PRK10227 DNA-binding transcrip 95.7 0.022 4.7E-07 34.3 3.9 23 34-56 1-23 (135)
146 cd01108 HTH_CueR Helix-Turn-He 95.7 0.021 4.6E-07 33.8 3.7 23 34-56 1-23 (127)
147 PF13545 HTH_Crp_2: Crp-like h 95.7 0.017 3.7E-07 30.7 3.1 24 32-55 27-50 (76)
148 smart00420 HTH_DEOR helix_turn 95.7 0.047 1E-06 26.6 4.5 31 25-55 6-36 (53)
149 PF13551 HTH_29: Winged helix- 95.7 0.024 5.2E-07 32.1 3.8 26 30-55 8-34 (112)
150 PF05930 Phage_AlpA: Prophage 95.7 0.0043 9.4E-08 31.2 0.6 28 34-61 4-31 (51)
151 cd04777 HTH_MerR-like_sg1 Heli 95.6 0.025 5.4E-07 32.5 3.8 22 34-55 1-22 (107)
152 KOG3802 Transcription factor O 95.6 0.018 4E-07 40.3 3.7 48 22-71 212-265 (398)
153 PF08281 Sigma70_r4_2: Sigma-7 95.6 0.035 7.7E-07 27.7 4.0 31 25-55 18-48 (54)
154 TIGR03764 ICE_PFGI_1_parB inte 95.6 0.029 6.4E-07 37.3 4.5 42 32-73 135-181 (258)
155 PF08220 HTH_DeoR: DeoR-like h 95.6 0.027 5.9E-07 28.9 3.6 32 24-55 5-36 (57)
156 PF00165 HTH_AraC: Bacterial r 95.6 0.023 5.1E-07 27.1 3.1 31 31-61 6-36 (42)
157 TIGR02047 CadR-PbrR Cd(II)/Pb( 95.6 0.022 4.8E-07 33.8 3.6 22 34-55 1-22 (127)
158 PRK13749 transcriptional regul 95.5 0.026 5.6E-07 33.5 3.7 47 33-79 3-66 (121)
159 PRK09413 IS2 repressor TnpA; R 95.5 0.04 8.6E-07 32.4 4.5 26 30-55 26-51 (121)
160 PRK15002 redox-sensitivie tran 95.5 0.027 5.9E-07 34.7 3.9 51 29-79 7-73 (154)
161 PF01371 Trp_repressor: Trp re 95.5 0.059 1.3E-06 30.2 4.9 34 22-55 36-71 (87)
162 PF12802 MarR_2: MarR family; 95.5 0.029 6.3E-07 28.6 3.5 33 23-55 9-43 (62)
163 cd00092 HTH_CRP helix_turn_hel 95.5 0.064 1.4E-06 27.6 4.8 24 32-55 24-47 (67)
164 cd04789 HTH_Cfa Helix-Turn-Hel 95.5 0.03 6.6E-07 32.0 3.8 23 34-56 2-24 (102)
165 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 95.5 0.04 8.7E-07 27.8 3.8 29 28-56 15-43 (50)
166 cd01107 HTH_BmrR Helix-Turn-He 95.5 0.029 6.3E-07 32.3 3.7 23 34-56 1-23 (108)
167 PRK00118 putative DNA-binding 95.4 0.051 1.1E-06 31.5 4.6 30 26-55 26-55 (104)
168 PF13011 LZ_Tnp_IS481: leucine 95.4 0.058 1.3E-06 30.2 4.7 26 30-55 22-47 (85)
169 PF13613 HTH_Tnp_4: Helix-turn 95.4 0.022 4.8E-07 28.8 2.8 28 28-55 14-41 (53)
170 cd01106 HTH_TipAL-Mta Helix-Tu 95.4 0.032 6.9E-07 31.8 3.8 22 34-55 1-22 (103)
171 smart00419 HTH_CRP helix_turn_ 95.4 0.027 6E-07 27.1 3.0 24 32-55 7-30 (48)
172 PF02042 RWP-RK: RWP-RK domain 95.4 0.057 1.2E-06 27.5 4.2 30 25-54 7-36 (52)
173 PRK09514 zntR zinc-responsive 95.4 0.034 7.3E-07 33.6 3.9 23 34-56 2-24 (140)
174 TIGR02043 ZntR Zn(II)-responsi 95.4 0.032 6.9E-07 33.3 3.8 23 34-56 2-24 (131)
175 cd04765 HTH_MlrA-like_sg2 Heli 95.4 0.022 4.8E-07 32.5 3.0 22 34-55 1-22 (99)
176 cd04768 HTH_BmrR-like Helix-Tu 95.4 0.034 7.4E-07 31.4 3.7 23 34-56 1-23 (96)
177 cd04772 HTH_TioE_rpt1 First He 95.3 0.036 7.7E-07 31.5 3.8 23 34-56 1-23 (99)
178 PRK15043 transcriptional regul 95.3 0.039 8.5E-07 36.4 4.4 46 33-78 3-65 (243)
179 TIGR01610 phage_O_Nterm phage 95.3 0.025 5.3E-07 32.0 3.0 26 30-55 44-69 (95)
180 cd04774 HTH_YfmP Helix-Turn-He 95.3 0.038 8.2E-07 31.3 3.8 22 34-55 1-22 (96)
181 smart00351 PAX Paired Box doma 95.3 0.055 1.2E-06 32.0 4.6 25 31-55 31-55 (125)
182 PF09339 HTH_IclR: IclR helix- 95.3 0.018 4E-07 28.8 2.2 31 25-55 9-40 (52)
183 cd04788 HTH_NolA-AlbR Helix-Tu 95.3 0.04 8.7E-07 31.1 3.8 22 34-55 1-22 (96)
184 PRK04132 replication factor C 95.2 0.041 8.9E-07 42.0 4.7 43 36-78 420-462 (846)
185 cd04775 HTH_Cfa-like Helix-Tur 95.2 0.041 8.9E-07 31.4 3.8 22 34-55 2-23 (102)
186 cd04786 HTH_MerR-like_sg7 Heli 95.2 0.036 7.9E-07 33.2 3.6 22 34-55 1-22 (131)
187 PF14590 DUF4447: Domain of un 95.1 0.23 4.9E-06 30.0 6.8 44 19-62 6-49 (166)
188 PRK10840 transcriptional regul 95.1 0.098 2.1E-06 32.8 5.7 61 20-80 151-216 (216)
189 PRK11891 aspartate carbamoyltr 95.1 0.039 8.4E-07 39.2 4.1 35 22-56 5-39 (429)
190 cd04782 HTH_BltR Helix-Turn-He 95.1 0.046 9.9E-07 30.9 3.7 46 34-79 1-63 (97)
191 cd00592 HTH_MerR-like Helix-Tu 95.1 0.047 1E-06 30.7 3.7 22 34-55 1-22 (100)
192 COG3415 Transposase and inacti 95.1 0.029 6.2E-07 34.1 3.0 26 30-55 18-43 (138)
193 COG3311 AlpA Predicted transcr 95.1 0.047 1E-06 29.5 3.5 31 34-64 14-44 (70)
194 COG1191 FliA DNA-directed RNA 95.0 0.052 1.1E-06 35.9 4.3 33 23-55 202-234 (247)
195 cd04766 HTH_HspR Helix-Turn-He 95.0 0.049 1.1E-06 30.4 3.6 22 34-55 2-23 (91)
196 COG1522 Lrp Transcriptional re 95.0 0.065 1.4E-06 32.1 4.4 32 22-53 11-42 (154)
197 PF07638 Sigma70_ECF: ECF sigm 95.0 0.073 1.6E-06 33.3 4.7 33 23-55 141-173 (185)
198 cd00131 PAX Paired Box domain 94.9 0.041 8.9E-07 32.8 3.3 25 31-55 31-55 (128)
199 cd01111 HTH_MerD Helix-Turn-He 94.9 0.056 1.2E-06 31.2 3.8 23 34-56 1-23 (107)
200 cd01279 HTH_HspR-like Helix-Tu 94.9 0.057 1.2E-06 30.6 3.7 22 34-55 2-23 (98)
201 PRK10458 DNA cytosine methylas 94.8 0.15 3.2E-06 36.6 6.5 48 28-75 24-80 (467)
202 PF12840 HTH_20: Helix-turn-he 94.8 0.061 1.3E-06 27.7 3.5 32 23-54 14-45 (61)
203 COG0789 SoxR Predicted transcr 94.8 0.04 8.8E-07 32.0 3.0 22 34-55 1-22 (124)
204 cd04780 HTH_MerR-like_sg5 Heli 94.8 0.065 1.4E-06 30.3 3.8 23 34-56 1-23 (95)
205 PF13309 HTH_22: HTH domain 94.7 0.031 6.8E-07 29.4 2.2 21 35-55 44-64 (64)
206 PRK13752 putative transcriptio 94.7 0.06 1.3E-06 32.7 3.7 23 33-55 7-29 (144)
207 cd01282 HTH_MerR-like_sg3 Heli 94.6 0.072 1.6E-06 30.9 3.8 22 34-55 1-22 (112)
208 PF01978 TrmB: Sugar-specific 94.6 0.065 1.4E-06 28.1 3.3 33 23-55 12-44 (68)
209 PF13542 HTH_Tnp_ISL3: Helix-t 94.6 0.14 3E-06 25.3 4.4 22 34-55 28-49 (52)
210 cd06170 LuxR_C_like C-terminal 94.6 0.063 1.4E-06 26.4 3.2 25 31-55 13-37 (57)
211 PF13730 HTH_36: Helix-turn-he 94.5 0.058 1.2E-06 27.0 2.9 21 35-55 27-47 (55)
212 cd04769 HTH_MerR2 Helix-Turn-H 94.5 0.052 1.1E-06 31.6 3.0 22 34-55 1-22 (116)
213 cd04783 HTH_MerR1 Helix-Turn-H 94.5 0.05 1.1E-06 32.1 3.0 22 34-55 1-22 (126)
214 smart00497 IENR1 Intron encode 94.5 0.077 1.7E-06 26.3 3.3 24 35-58 19-42 (53)
215 cd04770 HTH_HMRTR Helix-Turn-H 94.5 0.052 1.1E-06 31.8 3.0 22 34-55 1-22 (123)
216 cd04767 HTH_HspR-like_MBC Heli 94.5 0.08 1.7E-06 31.4 3.7 23 34-56 2-24 (120)
217 PRK13182 racA polar chromosome 94.5 0.065 1.4E-06 33.7 3.5 22 34-55 1-22 (175)
218 PRK11169 leucine-responsive tr 94.4 0.071 1.5E-06 32.8 3.6 32 22-53 17-48 (164)
219 TIGR03697 NtcA_cyano global ni 94.4 0.05 1.1E-06 33.5 3.0 24 32-55 142-165 (193)
220 PF01022 HTH_5: Bacterial regu 94.4 0.063 1.4E-06 26.3 2.7 30 25-55 8-37 (47)
221 TIGR01950 SoxR redox-sensitive 94.4 0.055 1.2E-06 32.8 3.0 22 34-55 2-23 (142)
222 smart00346 HTH_ICLR helix_turn 94.3 0.14 3.1E-06 27.9 4.4 30 25-54 11-41 (91)
223 PF09048 Cro: Cro; InterPro: 94.3 0.049 1.1E-06 28.4 2.2 33 25-59 6-38 (59)
224 cd04787 HTH_HMRTR_unk Helix-Tu 94.3 0.063 1.4E-06 32.0 3.0 22 34-55 1-22 (133)
225 PRK00430 fis global DNA-bindin 94.2 0.17 3.8E-06 28.7 4.7 34 22-55 57-90 (95)
226 PF00196 GerE: Bacterial regul 94.2 0.058 1.3E-06 27.5 2.5 26 30-55 15-40 (58)
227 cd01110 HTH_SoxR Helix-Turn-He 94.2 0.092 2E-06 31.7 3.7 22 34-55 2-23 (139)
228 PF13556 HTH_30: PucR C-termin 94.2 0.22 4.8E-06 25.6 4.7 39 31-80 10-48 (59)
229 PRK01905 DNA-binding protein F 94.1 0.2 4.4E-06 27.2 4.7 34 22-55 39-72 (77)
230 cd04776 HTH_GnyR Helix-Turn-He 94.1 0.11 2.4E-06 30.5 3.7 22 34-55 1-22 (118)
231 PF00440 TetR_N: Bacterial reg 94.0 0.12 2.5E-06 25.2 3.3 25 31-55 14-38 (47)
232 PRK12469 RNA polymerase factor 94.0 0.025 5.5E-07 40.6 1.1 45 32-76 368-412 (481)
233 TIGR02885 spore_sigF RNA polym 94.0 0.15 3.2E-06 32.7 4.6 28 29-56 195-222 (231)
234 TIGR01636 phage_rinA phage tra 94.0 0.19 4.1E-06 30.1 4.7 35 33-74 100-134 (134)
235 cd04779 HTH_MerR-like_sg4 Heli 93.9 0.078 1.7E-06 31.9 3.0 22 34-55 1-22 (134)
236 PRK11512 DNA-binding transcrip 93.9 0.18 3.9E-06 30.1 4.6 34 22-55 43-76 (144)
237 cd04785 HTH_CadR-PbrR-like Hel 93.9 0.12 2.7E-06 30.5 3.8 22 34-55 1-22 (126)
238 PF00126 HTH_1: Bacterial regu 93.9 0.25 5.3E-06 25.3 4.5 35 35-80 15-49 (60)
239 PRK11179 DNA-binding transcrip 93.9 0.16 3.4E-06 30.9 4.3 34 20-53 10-43 (153)
240 TIGR00122 birA_repr_reg BirA b 93.8 0.21 4.7E-06 26.2 4.3 27 29-55 9-35 (69)
241 PRK13918 CRP/FNR family transc 93.8 0.074 1.6E-06 33.0 2.9 24 32-55 148-171 (202)
242 TIGR02395 rpoN_sigma RNA polym 93.8 0.023 5E-07 40.2 0.6 45 32-76 317-361 (429)
243 smart00344 HTH_ASNC helix_turn 93.7 0.22 4.8E-06 28.1 4.6 34 22-55 6-39 (108)
244 TIGR02051 MerR Hg(II)-responsi 93.7 0.084 1.8E-06 31.1 2.9 21 35-55 1-21 (124)
245 PF10078 DUF2316: Uncharacteri 93.7 0.32 7E-06 27.4 5.0 36 22-57 12-47 (89)
246 PRK13413 mpi multiple promoter 93.6 0.11 2.4E-06 32.8 3.4 32 24-56 164-195 (200)
247 PRK11753 DNA-binding transcrip 93.6 0.091 2E-06 32.8 3.0 23 33-55 168-190 (211)
248 PF07453 NUMOD1: NUMOD1 domain 93.5 0.12 2.6E-06 24.0 2.7 19 35-53 18-36 (37)
249 PRK05932 RNA polymerase factor 93.5 0.03 6.5E-07 40.0 0.8 45 32-76 342-386 (455)
250 smart00345 HTH_GNTR helix_turn 93.5 0.12 2.7E-06 25.7 2.9 22 34-55 20-42 (60)
251 PRK09954 putative kinase; Prov 93.5 0.18 3.9E-06 34.4 4.5 34 22-55 6-39 (362)
252 PF06322 Phage_NinH: Phage Nin 93.5 0.2 4.4E-06 26.3 3.7 30 27-56 10-39 (64)
253 COG2512 Predicted membrane-ass 93.4 0.14 3.1E-06 34.0 3.9 34 22-55 198-232 (258)
254 PF04297 UPF0122: Putative hel 93.4 0.09 2E-06 30.3 2.5 27 30-56 30-56 (101)
255 COG3413 Predicted DNA binding 93.3 0.12 2.5E-06 33.1 3.2 23 33-55 178-200 (215)
256 TIGR02392 rpoH_proteo alternat 93.3 0.11 2.3E-06 34.4 3.1 23 33-55 236-258 (270)
257 PRK05572 sporulation sigma fac 93.3 0.23 5E-06 32.4 4.6 28 29-56 214-241 (252)
258 PF01325 Fe_dep_repress: Iron 93.2 0.12 2.6E-06 26.8 2.6 26 30-55 19-44 (60)
259 PF08280 HTH_Mga: M protein tr 93.2 0.28 6E-06 25.2 4.0 32 24-55 10-41 (59)
260 smart00342 HTH_ARAC helix_turn 93.2 0.29 6.4E-06 25.6 4.3 24 33-56 1-24 (84)
261 TIGR03209 P21_Cbot clostridium 93.1 0.15 3.2E-06 30.1 3.3 24 28-51 118-141 (142)
262 cd04790 HTH_Cfa-like_unk Helix 93.1 0.19 4.1E-06 31.4 3.8 22 34-55 2-23 (172)
263 PF04703 FaeA: FaeA-like prote 93.1 0.2 4.3E-06 26.4 3.3 30 26-55 7-37 (62)
264 COG1974 LexA SOS-response tran 93.1 0.18 3.8E-06 32.4 3.7 49 27-76 6-54 (201)
265 PRK11608 pspF phage shock prot 93.1 0.23 5.1E-06 33.8 4.5 34 22-55 288-321 (326)
266 TIGR02985 Sig70_bacteroi1 RNA 93.0 0.31 6.8E-06 28.8 4.7 28 28-55 124-151 (161)
267 PRK09480 slmA division inhibit 93.0 0.1 2.2E-06 32.0 2.6 28 32-59 29-56 (194)
268 PRK11161 fumarate/nitrate redu 93.0 0.12 2.5E-06 33.0 2.9 23 33-55 184-206 (235)
269 TIGR02394 rpoS_proteo RNA poly 93.0 0.18 3.8E-06 33.6 3.8 44 31-78 240-283 (285)
270 TIGR02937 sigma70-ECF RNA poly 93.0 0.15 3.2E-06 29.5 3.1 25 31-55 124-148 (158)
271 PRK13509 transcriptional repre 92.9 0.26 5.6E-06 32.4 4.4 32 24-55 10-41 (251)
272 TIGR02702 SufR_cyano iron-sulf 92.8 0.29 6.4E-06 31.0 4.5 33 23-55 5-37 (203)
273 PRK06759 RNA polymerase factor 92.8 0.35 7.7E-06 28.7 4.6 28 28-55 117-144 (154)
274 PRK08215 sporulation sigma fac 92.8 0.3 6.5E-06 32.0 4.6 28 29-56 221-248 (258)
275 PF07471 Phage_Nu1: Phage DNA 92.7 0.081 1.8E-06 33.0 1.8 23 33-55 2-24 (164)
276 PRK09391 fixK transcriptional 92.7 0.14 3.1E-06 32.8 3.0 22 33-54 179-200 (230)
277 PRK06596 RNA polymerase factor 92.7 0.15 3.2E-06 34.1 3.1 24 32-55 247-270 (284)
278 PF01710 HTH_Tnp_IS630: Transp 92.7 0.34 7.4E-06 28.3 4.3 35 21-55 58-93 (119)
279 PRK11924 RNA polymerase sigma 92.7 0.23 4.9E-06 30.0 3.7 26 30-55 138-163 (179)
280 PRK00215 LexA repressor; Valid 92.6 0.32 6.8E-06 30.8 4.5 25 31-55 21-46 (205)
281 PRK10411 DNA-binding transcrip 92.6 0.3 6.5E-06 31.9 4.5 32 24-55 9-40 (240)
282 PRK15320 transcriptional activ 92.6 0.15 3.3E-06 33.1 3.0 26 30-55 176-201 (251)
283 TIGR02974 phageshock_pspF psp 92.5 0.33 7.1E-06 33.2 4.6 34 22-55 294-327 (329)
284 TIGR02337 HpaR homoprotocatech 92.5 0.3 6.5E-06 28.2 3.9 34 22-55 31-64 (118)
285 PRK12427 flagellar biosynthesi 92.4 0.37 7.9E-06 31.3 4.6 27 29-55 195-221 (231)
286 TIGR02999 Sig-70_X6 RNA polyme 92.4 0.42 9.1E-06 29.2 4.7 27 29-55 146-172 (183)
287 PRK12519 RNA polymerase sigma 92.3 0.24 5.2E-06 30.7 3.6 27 29-55 153-179 (194)
288 COG2973 TrpR Trp operon repres 92.3 0.89 1.9E-05 26.1 5.5 51 22-72 47-99 (103)
289 TIGR02980 SigBFG RNA polymeras 92.3 0.39 8.4E-06 30.7 4.6 27 29-55 190-216 (227)
290 PRK15411 rcsA colanic acid cap 92.3 0.23 5E-06 31.5 3.5 37 20-56 138-175 (207)
291 PRK07037 extracytoplasmic-func 92.3 0.45 9.7E-06 28.6 4.6 28 28-55 120-147 (163)
292 PHA01082 putative transcriptio 92.2 0.11 2.5E-06 30.9 1.9 31 31-61 28-58 (133)
293 PRK11361 acetoacetate metaboli 92.2 0.35 7.6E-06 33.8 4.6 34 22-55 419-452 (457)
294 smart00418 HTH_ARSR helix_turn 92.2 0.41 8.8E-06 23.7 3.8 25 31-55 8-32 (66)
295 PRK09652 RNA polymerase sigma 92.2 0.44 9.5E-06 28.8 4.5 27 29-55 140-166 (182)
296 PF06892 Phage_CP76: Phage reg 92.1 1.1 2.4E-05 27.8 6.2 50 22-73 11-62 (162)
297 PF09012 FeoC: FeoC like trans 92.0 0.29 6.3E-06 25.8 3.2 31 24-54 4-35 (69)
298 TIGR01818 ntrC nitrogen regula 92.0 0.4 8.6E-06 33.6 4.7 34 22-55 428-461 (463)
299 TIGR02947 SigH_actino RNA poly 92.0 0.13 2.8E-06 32.0 2.1 27 29-55 143-169 (193)
300 TIGR02850 spore_sigG RNA polym 91.9 0.42 9.2E-06 31.2 4.5 25 31-55 220-244 (254)
301 PRK13869 plasmid-partitioning 91.9 0.42 9.2E-06 33.5 4.7 43 32-74 47-101 (405)
302 PRK11511 DNA-binding transcrip 91.9 0.45 9.7E-06 28.0 4.2 30 32-61 24-53 (127)
303 TIGR02393 RpoD_Cterm RNA polym 91.8 0.42 9.2E-06 30.9 4.4 26 31-56 194-219 (238)
304 TIGR03453 partition_RepA plasm 91.8 0.39 8.4E-06 33.3 4.4 43 32-74 32-86 (387)
305 PRK09639 RNA polymerase sigma 91.7 0.52 1.1E-05 28.3 4.5 28 27-55 122-149 (166)
306 PRK09047 RNA polymerase factor 91.7 0.53 1.2E-05 28.1 4.5 27 29-55 118-144 (161)
307 PRK15090 DNA-binding transcrip 91.7 0.36 7.8E-06 31.6 4.0 33 23-55 18-50 (257)
308 COG1309 AcrR Transcriptional r 91.7 0.14 3.1E-06 30.0 2.0 27 32-58 31-57 (201)
309 PRK15115 response regulator Gl 91.7 0.38 8.3E-06 33.6 4.3 34 22-55 400-433 (444)
310 PRK14165 winged helix-turn-hel 91.7 0.2 4.4E-06 32.6 2.7 25 31-55 19-43 (217)
311 COG5484 Uncharacterized conser 91.6 0.21 4.4E-06 33.4 2.7 27 31-57 17-43 (279)
312 smart00347 HTH_MARR helix_turn 91.6 0.54 1.2E-05 25.6 4.2 34 22-55 13-46 (101)
313 PRK08583 RNA polymerase sigma 91.5 0.54 1.2E-05 30.7 4.7 27 29-55 217-243 (257)
314 PRK10365 transcriptional regul 91.5 0.5 1.1E-05 32.8 4.8 34 22-55 407-440 (441)
315 PF01710 HTH_Tnp_IS630: Transp 91.5 0.22 4.8E-06 29.1 2.6 24 32-55 17-40 (119)
316 TIGR02989 Sig-70_gvs1 RNA poly 91.5 0.61 1.3E-05 27.8 4.6 26 29-54 123-148 (159)
317 PRK08301 sporulation sigma fac 91.4 0.27 5.8E-06 31.6 3.2 25 31-55 196-220 (234)
318 PRK10219 DNA-binding transcrip 91.4 1.3 2.8E-05 25.0 5.7 26 32-57 20-45 (107)
319 PRK15201 fimbriae regulatory p 91.4 0.33 7.1E-06 31.0 3.3 37 20-56 134-171 (198)
320 PRK10046 dpiA two-component re 91.3 0.26 5.6E-06 31.3 3.0 23 33-55 177-199 (225)
321 TIGR02329 propionate_PrpR prop 91.3 0.5 1.1E-05 34.4 4.7 34 22-55 492-525 (526)
322 PRK13919 putative RNA polymera 91.3 0.61 1.3E-05 28.6 4.6 27 29-55 147-173 (186)
323 PRK09642 RNA polymerase sigma 91.3 0.63 1.4E-05 27.9 4.6 28 28-55 117-144 (160)
324 PRK07408 RNA polymerase sigma 91.3 0.58 1.3E-05 30.7 4.6 27 29-55 215-241 (256)
325 TIGR03613 RutR pyrimidine util 91.2 0.24 5.2E-06 30.7 2.7 29 32-60 27-55 (202)
326 PRK12529 RNA polymerase sigma 91.2 0.71 1.5E-05 28.4 4.8 28 28-55 138-165 (178)
327 PRK06986 fliA flagellar biosyn 91.2 0.55 1.2E-05 30.3 4.5 27 29-55 196-222 (236)
328 PRK12537 RNA polymerase sigma 91.2 0.62 1.4E-05 28.7 4.5 28 28-55 144-171 (182)
329 COG1508 RpoN DNA-directed RNA 91.2 0.15 3.3E-06 36.4 1.9 43 34-76 331-373 (444)
330 cd07377 WHTH_GntR Winged helix 91.1 0.36 7.8E-06 24.4 2.9 21 35-55 27-47 (66)
331 PF11268 DUF3071: Protein of u 91.1 0.38 8.3E-06 30.2 3.5 36 19-55 56-91 (170)
332 PF07750 GcrA: GcrA cell cycle 91.0 0.38 8.2E-06 29.9 3.4 30 24-54 10-40 (162)
333 COG2197 CitB Response regulato 91.0 0.31 6.7E-06 31.2 3.1 38 19-56 148-186 (211)
334 PRK12423 LexA repressor; Provi 91.0 0.68 1.5E-05 29.4 4.6 32 22-53 12-46 (202)
335 TIGR01884 cas_HTH CRISPR locus 91.0 0.62 1.3E-05 29.5 4.4 33 23-55 147-179 (203)
336 cd00090 HTH_ARSR Arsenical Res 91.0 0.8 1.7E-05 23.3 4.2 30 25-55 13-42 (78)
337 PRK13832 plasmid partitioning 90.9 0.91 2E-05 33.2 5.6 33 22-55 108-140 (520)
338 PRK12534 RNA polymerase sigma 90.9 0.65 1.4E-05 28.6 4.5 28 28-55 148-175 (187)
339 COG1595 RpoE DNA-directed RNA 90.9 0.43 9.4E-06 29.4 3.6 28 28-55 138-165 (182)
340 TIGR02366 DHAK_reg probable di 90.9 0.3 6.6E-06 29.7 2.9 35 23-57 10-47 (176)
341 cd08316 Death_FAS_TNFRSF6 Deat 90.9 1.6 3.4E-05 24.9 5.6 37 22-58 8-45 (97)
342 PRK12547 RNA polymerase sigma 90.9 0.76 1.6E-05 27.8 4.6 28 28-55 123-150 (164)
343 PRK07122 RNA polymerase sigma 90.8 0.61 1.3E-05 30.8 4.5 27 29-55 227-253 (264)
344 COG4565 CitB Response regulato 90.8 0.48 1E-05 31.0 3.8 25 31-55 171-195 (224)
345 PRK09649 RNA polymerase sigma 90.8 0.66 1.4E-05 28.7 4.4 28 28-55 141-168 (185)
346 PRK09645 RNA polymerase sigma 90.8 0.76 1.6E-05 27.9 4.6 28 28-55 129-156 (173)
347 PRK07500 rpoH2 RNA polymerase 90.8 0.32 7E-06 32.6 3.2 25 32-56 244-268 (289)
348 TIGR02959 SigZ RNA polymerase 90.8 0.81 1.7E-05 27.9 4.7 28 28-55 111-138 (170)
349 PF13463 HTH_27: Winged helix 90.7 0.39 8.5E-06 24.7 2.9 31 25-55 9-40 (68)
350 COG3355 Predicted transcriptio 90.7 0.74 1.6E-05 27.6 4.3 34 22-55 30-64 (126)
351 TIGR01889 Staph_reg_Sar staphy 90.7 0.7 1.5E-05 26.4 4.1 24 32-55 42-65 (109)
352 TIGR02915 PEP_resp_reg putativ 90.7 0.6 1.3E-05 32.6 4.5 34 22-55 407-440 (445)
353 PRK12523 RNA polymerase sigma 90.7 0.82 1.8E-05 27.8 4.7 28 28-55 130-157 (172)
354 PRK11302 DNA-binding transcrip 90.7 0.56 1.2E-05 30.8 4.2 36 30-65 31-66 (284)
355 PRK10923 glnG nitrogen regulat 90.6 0.62 1.3E-05 32.8 4.6 34 22-55 431-464 (469)
356 PRK15008 HTH-type transcriptio 90.6 0.29 6.2E-06 30.9 2.7 36 32-67 37-72 (212)
357 PRK09975 DNA-binding transcrip 90.6 0.27 5.8E-06 30.8 2.5 28 32-59 30-57 (213)
358 COG1654 BirA Biotin operon rep 90.6 0.86 1.9E-05 25.1 4.2 21 34-54 20-40 (79)
359 PRK03573 transcriptional regul 90.5 0.35 7.6E-06 28.8 2.9 32 24-55 36-68 (144)
360 PRK12511 RNA polymerase sigma 90.5 0.55 1.2E-05 29.2 3.9 27 29-55 123-149 (182)
361 PRK10402 DNA-binding transcrip 90.5 0.3 6.4E-06 31.2 2.7 23 33-55 169-191 (226)
362 smart00342 HTH_ARAC helix_turn 90.5 0.99 2.1E-05 23.5 4.4 26 30-55 47-73 (84)
363 cd04778 HTH_MerR-like_sg2 Heli 90.4 0.52 1.1E-05 30.6 3.8 23 34-56 2-24 (219)
364 PRK12530 RNA polymerase sigma 90.4 0.8 1.7E-05 28.5 4.5 28 28-55 145-172 (189)
365 PRK13719 conjugal transfer tra 90.4 1.1 2.4E-05 29.2 5.2 51 20-70 144-199 (217)
366 TIGR00637 ModE_repress ModE mo 90.4 0.93 2E-05 25.8 4.4 35 34-79 17-51 (99)
367 PRK12532 RNA polymerase sigma 90.4 0.52 1.1E-05 29.3 3.7 27 29-55 148-174 (195)
368 PRK05803 sporulation sigma fac 90.4 0.38 8.3E-06 31.0 3.1 24 32-55 194-217 (233)
369 COG2771 CsgD DNA-binding HTH d 90.3 0.83 1.8E-05 23.0 3.9 28 29-56 15-42 (65)
370 PRK10141 DNA-binding transcrip 90.3 0.89 1.9E-05 26.8 4.4 30 25-54 22-51 (117)
371 PRK13777 transcriptional regul 90.3 0.64 1.4E-05 29.5 4.0 33 22-54 48-80 (185)
372 TIGR02479 FliA_WhiG RNA polyme 90.3 0.84 1.8E-05 29.1 4.6 27 29-55 187-213 (224)
373 PRK12513 RNA polymerase sigma 90.3 0.42 9.1E-06 29.7 3.2 25 31-55 153-177 (194)
374 PRK10668 DNA-binding transcrip 90.3 0.24 5.2E-06 31.1 2.1 28 33-60 31-58 (215)
375 PRK11050 manganese transport r 90.3 0.71 1.5E-05 28.1 4.1 25 31-55 49-73 (152)
376 PRK12524 RNA polymerase sigma 90.2 0.86 1.9E-05 28.4 4.6 28 28-55 147-174 (196)
377 PRK15424 propionate catabolism 90.2 0.67 1.4E-05 33.9 4.5 34 22-55 499-532 (538)
378 TIGR02846 spore_sigmaK RNA pol 90.2 0.41 8.9E-06 30.8 3.2 24 32-55 193-216 (227)
379 TIGR02954 Sig70_famx3 RNA poly 90.2 0.83 1.8E-05 27.6 4.4 28 28-55 130-157 (169)
380 PRK11475 DNA-binding transcrip 90.1 0.45 9.8E-06 30.4 3.3 37 20-56 135-172 (207)
381 PRK12516 RNA polymerase sigma 90.1 0.91 2E-05 28.3 4.6 28 28-55 127-154 (187)
382 PRK09647 RNA polymerase sigma 90.1 0.91 2E-05 28.7 4.6 28 28-55 149-176 (203)
383 PF09862 DUF2089: Protein of u 90.1 0.68 1.5E-05 27.2 3.7 30 24-54 41-70 (113)
384 PRK10430 DNA-binding transcrip 90.0 0.37 8E-06 30.8 2.8 24 32-55 177-200 (239)
385 COG1349 GlpR Transcriptional r 89.9 0.52 1.1E-05 31.1 3.5 30 23-52 9-38 (253)
386 TIGR03384 betaine_BetI transcr 89.9 0.37 8E-06 29.4 2.7 28 32-59 27-54 (189)
387 TIGR02983 SigE-fam_strep RNA p 89.9 0.84 1.8E-05 27.3 4.2 28 28-55 121-148 (162)
388 KOG1168 Transcription factor A 89.9 0.15 3.3E-06 34.7 1.0 34 22-55 223-265 (385)
389 PF04760 IF2_N: Translation in 89.9 0.098 2.1E-06 26.3 0.1 42 33-74 3-53 (54)
390 TIGR02950 SigM_subfam RNA poly 89.9 0.48 1.1E-05 28.1 3.1 24 32-55 120-143 (154)
391 PRK05911 RNA polymerase sigma 89.8 0.93 2E-05 29.8 4.7 27 29-55 217-243 (257)
392 TIGR02941 Sigma_B RNA polymera 89.8 0.89 1.9E-05 29.6 4.6 28 28-55 216-243 (255)
393 PRK09641 RNA polymerase sigma 89.8 0.63 1.4E-05 28.5 3.7 26 30-55 149-174 (187)
394 PF08822 DUF1804: Protein of u 89.8 1.1 2.3E-05 28.1 4.6 46 23-68 9-56 (165)
395 PRK09508 leuO leucine transcri 89.8 1.2 2.7E-05 29.5 5.3 37 33-80 36-72 (314)
396 TIGR02952 Sig70_famx2 RNA poly 89.7 1.1 2.3E-05 26.9 4.6 28 28-55 133-160 (170)
397 TIGR02997 Sig70-cyanoRpoD RNA 89.7 0.83 1.8E-05 30.7 4.4 25 31-55 267-291 (298)
398 PRK05602 RNA polymerase sigma 89.7 0.92 2E-05 27.9 4.4 28 28-55 139-166 (186)
399 PRK10434 srlR DNA-bindng trans 89.7 0.59 1.3E-05 30.8 3.6 32 23-54 9-40 (256)
400 PRK12514 RNA polymerase sigma 89.7 1 2.2E-05 27.5 4.5 27 29-55 141-167 (179)
401 PF05043 Mga: Mga helix-turn-h 89.6 0.45 9.8E-06 26.0 2.7 46 23-76 20-65 (87)
402 PRK06930 positive control sigm 89.6 1.1 2.4E-05 27.9 4.6 28 28-55 125-152 (170)
403 TIGR02835 spore_sigmaE RNA pol 89.5 0.5 1.1E-05 30.5 3.2 24 32-55 197-220 (234)
404 PRK12528 RNA polymerase sigma 89.5 1.2 2.6E-05 26.7 4.6 28 28-55 124-151 (161)
405 PRK09392 ftrB transcriptional 89.5 0.43 9.3E-06 30.4 2.8 22 33-54 173-194 (236)
406 PRK12536 RNA polymerase sigma 89.4 0.81 1.8E-05 28.1 4.0 27 29-55 141-167 (181)
407 PRK12682 transcriptional regul 89.4 0.72 1.6E-05 30.5 3.9 47 23-80 4-52 (309)
408 PRK12525 RNA polymerase sigma 89.4 0.9 1.9E-05 27.6 4.1 26 29-54 130-155 (168)
409 PRK10906 DNA-binding transcrip 89.4 0.73 1.6E-05 30.4 3.9 29 25-53 11-39 (252)
410 PRK05022 anaerobic nitric oxid 89.4 0.91 2E-05 32.7 4.6 34 22-55 470-503 (509)
411 TIGR02984 Sig-70_plancto1 RNA 89.3 1.2 2.6E-05 27.2 4.7 27 29-55 152-178 (189)
412 PRK09483 response regulator; P 89.3 1.6 3.5E-05 26.7 5.3 45 30-74 160-208 (217)
413 PRK12542 RNA polymerase sigma 89.3 1.1 2.4E-05 27.6 4.5 28 28-55 133-160 (185)
414 PRK10681 DNA-binding transcrip 89.3 0.88 1.9E-05 29.9 4.2 33 23-55 11-43 (252)
415 PRK11202 DNA-binding transcrip 89.3 0.29 6.3E-06 30.7 1.9 29 32-60 31-59 (203)
416 PRK09640 RNA polymerase sigma 89.2 0.62 1.3E-05 28.8 3.3 26 30-55 147-172 (188)
417 PRK12527 RNA polymerase sigma 89.1 1.3 2.8E-05 26.5 4.6 28 28-55 116-143 (159)
418 TIGR02431 pcaR_pcaU beta-ketoa 89.1 0.85 1.8E-05 29.6 4.0 31 25-55 15-46 (248)
419 COG2963 Transposase and inacti 89.1 1.2 2.7E-05 25.5 4.3 32 24-55 15-47 (116)
420 PRK11923 algU RNA polymerase s 89.1 1.1 2.4E-05 27.7 4.4 28 28-55 149-176 (193)
421 PF05732 RepL: Firmicute plasm 89.0 0.45 9.7E-06 29.6 2.5 21 34-54 76-96 (165)
422 PRK12526 RNA polymerase sigma 89.0 1.2 2.7E-05 28.0 4.6 27 29-55 165-191 (206)
423 PRK12545 RNA polymerase sigma 89.0 1.2 2.6E-05 28.0 4.6 28 28-55 150-177 (201)
424 PRK10100 DNA-binding transcrip 88.9 0.97 2.1E-05 29.0 4.2 26 31-56 168-193 (216)
425 PRK14996 TetR family transcrip 88.9 0.37 8E-06 29.8 2.2 28 32-59 27-54 (192)
426 COG2826 Tra8 Transposase and i 88.9 0.57 1.2E-05 32.1 3.1 33 22-55 13-45 (318)
427 PRK10188 DNA-binding transcrip 88.9 2.7 5.9E-05 27.4 6.3 43 31-73 192-238 (240)
428 PRK12518 RNA polymerase sigma 88.9 0.61 1.3E-05 28.3 3.1 25 31-55 134-158 (175)
429 PRK09834 DNA-binding transcrip 88.9 1.1 2.3E-05 29.5 4.4 32 24-55 16-48 (263)
430 PHA02535 P terminase ATPase su 88.8 0.49 1.1E-05 35.0 3.0 24 33-56 18-41 (581)
431 PRK00767 transcriptional regul 88.8 0.53 1.2E-05 28.9 2.8 29 32-60 28-56 (197)
432 TIGR02948 SigW_bacill RNA poly 88.8 0.82 1.8E-05 27.9 3.7 27 29-55 148-174 (187)
433 PF06971 Put_DNA-bind_N: Putat 88.7 0.99 2.1E-05 22.7 3.3 21 32-52 27-47 (50)
434 PRK09648 RNA polymerase sigma 88.7 1.4 3E-05 27.2 4.7 27 29-55 151-177 (189)
435 PRK09802 DNA-binding transcrip 88.7 0.81 1.8E-05 30.4 3.8 32 23-54 21-52 (269)
436 PHA00738 putative HTH transcri 88.7 1.2 2.6E-05 26.0 4.0 32 23-54 16-47 (108)
437 PRK12533 RNA polymerase sigma 88.7 0.81 1.8E-05 29.4 3.7 27 29-55 146-172 (216)
438 TIGR03826 YvyF flagellar opero 88.6 1.3 2.7E-05 27.0 4.2 51 26-76 37-91 (137)
439 PRK11557 putative DNA-binding 88.6 1.4 3E-05 29.0 4.8 36 29-64 26-61 (278)
440 PRK14845 translation initiatio 88.5 1.3 2.9E-05 34.9 5.2 50 22-76 324-373 (1049)
441 PF01726 LexA_DNA_bind: LexA D 88.5 1.4 3E-05 23.2 3.9 33 23-55 13-48 (65)
442 PRK06288 RNA polymerase sigma 88.4 1.4 3.1E-05 29.0 4.8 28 28-55 223-250 (268)
443 PRK12515 RNA polymerase sigma 88.4 1.5 3.2E-05 27.1 4.7 28 28-55 142-169 (189)
444 PRK09638 RNA polymerase sigma 88.4 0.71 1.5E-05 28.0 3.2 26 30-55 139-164 (176)
445 cd08804 Death_ank2 Death domai 88.3 2.5 5.5E-05 23.3 5.1 34 23-56 5-38 (84)
446 PRK12517 RNA polymerase sigma 88.3 0.94 2E-05 28.2 3.7 28 28-55 139-166 (188)
447 PF12116 SpoIIID: Stage III sp 88.3 0.96 2.1E-05 25.1 3.3 48 26-73 12-60 (82)
448 PRK04424 fatty acid biosynthes 88.3 0.88 1.9E-05 28.7 3.6 33 23-55 11-43 (185)
449 PRK09646 RNA polymerase sigma 88.3 1.4 3.1E-05 27.3 4.6 28 28-55 153-180 (194)
450 PRK11388 DNA-binding transcrip 88.3 1.1 2.4E-05 33.1 4.5 34 22-55 593-626 (638)
451 PRK09637 RNA polymerase sigma 88.3 0.99 2.1E-05 27.9 3.8 27 29-55 118-144 (181)
452 cd06571 Bac_DnaA_C C-terminal 88.3 1.2 2.7E-05 24.6 3.9 33 23-55 34-67 (90)
453 PRK12546 RNA polymerase sigma 88.2 1 2.2E-05 28.2 3.8 28 28-55 124-151 (188)
454 PRK12522 RNA polymerase sigma 88.2 0.97 2.1E-05 27.5 3.7 27 29-55 131-157 (173)
455 PRK12520 RNA polymerase sigma 88.2 1.6 3.4E-05 27.0 4.7 27 29-55 143-169 (191)
456 PRK15482 transcriptional regul 88.1 1.5 3.1E-05 29.1 4.7 38 29-66 30-67 (285)
457 PRK06811 RNA polymerase factor 88.1 1.6 3.4E-05 27.1 4.6 27 29-55 143-169 (189)
458 PRK07921 RNA polymerase sigma 87.9 0.69 1.5E-05 31.7 3.1 24 33-56 282-305 (324)
459 TIGR01565 homeo_ZF_HD homeobox 87.9 0.72 1.6E-05 23.9 2.5 35 23-57 14-56 (58)
460 PRK09210 RNA polymerase sigma 87.9 0.67 1.4E-05 32.2 3.1 24 33-56 325-348 (367)
461 PRK12540 RNA polymerase sigma 87.9 1.1 2.5E-05 27.7 3.9 27 29-55 123-149 (182)
462 PF00046 Homeobox: Homeobox do 87.8 0.86 1.9E-05 22.7 2.8 21 36-56 30-50 (57)
463 PRK12541 RNA polymerase sigma 87.8 1.2 2.6E-05 26.7 3.9 28 28-55 123-150 (161)
464 PRK11337 DNA-binding transcrip 87.8 1.2 2.6E-05 29.5 4.2 36 31-66 44-79 (292)
465 TIGR03454 partition_RepB plasm 87.7 1.3 2.9E-05 30.5 4.4 39 30-68 174-212 (325)
466 PRK11569 transcriptional repre 87.7 1.3 2.7E-05 29.4 4.2 33 23-55 32-65 (274)
467 PRK08295 RNA polymerase factor 87.7 0.8 1.7E-05 28.6 3.1 26 30-55 167-192 (208)
468 PRK05657 RNA polymerase sigma 87.7 0.73 1.6E-05 31.5 3.1 25 31-55 280-304 (325)
469 TIGR02939 RpoE_Sigma70 RNA pol 87.7 1 2.3E-05 27.5 3.6 27 29-55 150-176 (190)
470 COG1737 RpiR Transcriptional r 87.6 1.2 2.6E-05 29.7 4.1 28 30-57 33-60 (281)
471 PRK10086 DNA-binding transcrip 87.6 1.3 2.9E-05 29.3 4.3 37 33-80 28-64 (311)
472 PRK10163 DNA-binding transcrip 87.6 1.4 3E-05 29.2 4.3 33 23-55 29-62 (271)
473 PRK03601 transcriptional regul 87.5 1.3 2.9E-05 28.8 4.2 37 33-80 15-51 (275)
474 PRK12543 RNA polymerase sigma 87.4 1.8 3.9E-05 26.5 4.6 28 28-55 128-155 (179)
475 COG1321 TroR Mn-dependent tran 87.4 1.4 3E-05 27.1 4.0 24 32-55 23-46 (154)
476 PRK09415 RNA polymerase factor 87.4 1.1 2.5E-05 27.4 3.7 27 29-55 139-165 (179)
477 PRK10870 transcriptional repre 87.4 0.86 1.9E-05 28.4 3.1 32 23-54 59-92 (176)
478 PRK07405 RNA polymerase sigma 87.4 0.78 1.7E-05 31.2 3.1 25 32-56 275-299 (317)
479 PRK07670 RNA polymerase sigma 87.4 1.7 3.8E-05 28.3 4.7 28 28-55 212-239 (251)
480 PF14174 YycC: YycC-like prote 87.3 0.57 1.2E-05 23.6 1.8 20 59-78 5-24 (53)
481 COG2207 AraC AraC-type DNA-bin 87.3 3.3 7.1E-05 23.2 5.4 30 32-61 35-64 (127)
482 PRK09644 RNA polymerase sigma 87.3 1.1 2.4E-05 27.0 3.5 27 29-55 120-146 (165)
483 PRK12531 RNA polymerase sigma 87.2 1.7 3.7E-05 27.0 4.4 26 29-54 153-178 (194)
484 PRK06704 RNA polymerase factor 87.2 1.1 2.4E-05 29.2 3.6 27 28-54 127-153 (228)
485 PRK10820 DNA-binding transcrip 87.1 1.5 3.3E-05 31.8 4.6 33 22-55 476-508 (520)
486 PF10743 Phage_Cox: Regulatory 87.0 1.5 3.3E-05 24.6 3.6 28 33-60 12-39 (87)
487 PF02082 Rrf2: Transcriptional 87.0 0.68 1.5E-05 25.2 2.3 22 34-55 26-47 (83)
488 TIGR02943 Sig70_famx1 RNA poly 87.0 2 4.4E-05 26.6 4.7 28 28-55 142-169 (188)
489 PRK09651 RNA polymerase sigma 87.0 1.5 3.3E-05 26.7 4.0 27 29-55 131-157 (172)
490 PRK12539 RNA polymerase sigma 86.8 1.9 4E-05 26.6 4.4 27 29-55 143-169 (184)
491 PRK12512 RNA polymerase sigma 86.8 2 4.3E-05 26.3 4.5 27 29-55 143-169 (184)
492 PRK05901 RNA polymerase sigma 86.7 1.5 3.3E-05 31.9 4.4 25 32-56 466-490 (509)
493 PRK09643 RNA polymerase sigma 86.7 1.8 4E-05 26.9 4.4 27 28-54 145-171 (192)
494 PRK13756 tetracycline represso 86.6 0.62 1.3E-05 29.7 2.2 36 33-68 24-59 (205)
495 PRK11922 RNA polymerase sigma 86.5 1 2.2E-05 29.0 3.2 25 31-55 163-187 (231)
496 PRK12538 RNA polymerase sigma 86.5 1.6 3.5E-05 28.3 4.1 28 28-55 182-209 (233)
497 PRK11886 bifunctional biotin-- 86.4 1.6 3.4E-05 29.5 4.2 32 23-54 8-39 (319)
498 PRK10216 DNA-binding transcrip 86.4 1.9 4.1E-05 28.7 4.5 35 35-80 24-58 (319)
499 PRK12535 RNA polymerase sigma 86.4 1.3 2.9E-05 27.8 3.6 27 29-55 145-171 (196)
500 PRK15369 two component system 86.4 2.8 6.1E-05 25.0 5.0 27 30-56 161-187 (211)
No 1
>PHA01976 helix-turn-helix protein
Probab=99.76 E-value=4.7e-18 Score=90.89 Aligned_cols=58 Identities=28% Similarity=0.476 Sum_probs=55.8
Q ss_pred CHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcc
Q 038591 21 TPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRV 78 (82)
Q Consensus 21 ~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e 78 (82)
.+.+|+.+|+..|+||.+||+.+|+++++|++||+|...|+.+.+.+||++|||++++
T Consensus 3 ~~~rl~~~R~~~glt~~~lA~~~gvs~~~v~~~e~g~~~p~~~~l~~ia~~l~v~~~~ 60 (67)
T PHA01976 3 FAIQLIKARNARAWSAPELSRRAGVRHSLIYDFEADKRLPNLKTLLRLADALGVTLDW 60 (67)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHHCcCHHH
Confidence 4789999999999999999999999999999999999999999999999999999875
No 2
>PF12844 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_A 2XIU_B 2GZU_B 2XJ3_A 1UTX_A 2XI8_B 3F6W_C 3EUS_B.
Probab=99.75 E-value=5.4e-18 Score=89.94 Aligned_cols=57 Identities=32% Similarity=0.493 Sum_probs=49.4
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcc
Q 038591 22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRV 78 (82)
Q Consensus 22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e 78 (82)
|.+|+.+|+..|+||.+||+.+|+++++|++||+|...|+...+.+||++|||++++
T Consensus 1 G~~lk~~r~~~~lt~~~~a~~~~i~~~~i~~~e~g~~~~~~~~l~~i~~~~~v~~~~ 57 (64)
T PF12844_consen 1 GERLKELREEKGLTQKDLAEKLGISRSTISKIENGKRKPSVSTLKKIAEALGVSLDE 57 (64)
T ss_dssp HHHHHHHHHHCT--HHHHHHHHTS-HHHHHHHHTTSS--BHHHHHHHHHHHTS-HHH
T ss_pred CHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCcCCCHHHHHHHHHHhCCCHHH
Confidence 689999999999999999999999999999999999999999999999999999875
No 3
>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=99.73 E-value=9.7e-18 Score=86.49 Aligned_cols=54 Identities=35% Similarity=0.487 Sum_probs=49.9
Q ss_pred HHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcc
Q 038591 25 IQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRV 78 (82)
Q Consensus 25 lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e 78 (82)
|+.+|+..|+||.+||+.+|+|+++|++||+|...|+.+.+.+||++|||++++
T Consensus 1 ik~~r~~~gls~~~la~~~gis~~~i~~~~~g~~~~~~~~~~~ia~~l~~~~~~ 54 (55)
T PF01381_consen 1 IKELRKEKGLSQKELAEKLGISRSTISRIENGKRNPSLDTLKKIAKALGVSPEY 54 (55)
T ss_dssp HHHHHHHTTS-HHHHHHHHTS-HHHHHHHHTTSSTSBHHHHHHHHHHHTSEHHH
T ss_pred CHHHHHHcCCCHHHHHHHhCCCcchhHHHhcCCCCCCHHHHHHHHHHHCCCHHH
Confidence 688999999999999999999999999999999999999999999999999864
No 4
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=99.72 E-value=2.4e-17 Score=88.31 Aligned_cols=57 Identities=19% Similarity=0.309 Sum_probs=54.5
Q ss_pred HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCccc
Q 038591 23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVK 79 (82)
Q Consensus 23 ~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e~ 79 (82)
.+++.+|...|+||.+||+.+|||++||..||+|+..|++....+||+.|++++++.
T Consensus 4 nk~k~~R~~~~ltQ~elA~~vgVsRQTi~~iEkgky~Psl~La~kia~~f~~~iedI 60 (68)
T COG1476 4 NKLKELRAELGLTQEELAKLVGVSRQTIIAIEKGKYNPSLELALKIARVFGKTIEDI 60 (68)
T ss_pred hHHHHHHHHhCcCHHHHHHHcCcCHHHHHHHHcCCCCchHHHHHHHHHHhCCCHHHH
Confidence 489999999999999999999999999999999999999999999999999998763
No 5
>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=99.71 E-value=1.2e-16 Score=82.60 Aligned_cols=56 Identities=21% Similarity=0.310 Sum_probs=53.6
Q ss_pred CHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 038591 21 TPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKL 76 (82)
Q Consensus 21 ~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~ 76 (82)
.+.+|+.+|+..|+||.+||+.+|+|+++|++||+|...|+.+.+.+|+++||+++
T Consensus 3 ~~~~l~~~r~~~gltq~~lA~~~gvs~~~vs~~e~g~~~~~~~~~~~i~~~lgv~l 58 (58)
T TIGR03070 3 IGMLVRARRKALGLTQADLADLAGVGLRFIRDVENGKPTVRLDKVLRVLDALGLEL 58 (58)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHcCCCC
Confidence 37899999999999999999999999999999999999999999999999999985
No 6
>PRK06424 transcription factor; Provisional
Probab=99.68 E-value=2.7e-16 Score=95.54 Aligned_cols=59 Identities=34% Similarity=0.487 Sum_probs=57.3
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcccc
Q 038591 22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVKI 80 (82)
Q Consensus 22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e~~ 80 (82)
+.+|+.+|+.+||||.+||+.+|+++++|++||+|...|+.+.+.+|+++||+++.|++
T Consensus 86 g~~Ir~lRe~~GLSQ~eLA~~iGvs~stIskiE~G~~~Ps~~~l~kLa~~Lgvsl~e~~ 144 (144)
T PRK06424 86 AELVKNARERLSMSQADLAAKIFERKNVIASIERGDLLPDIKTARKLEKILGITLIEKA 144 (144)
T ss_pred HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHhCCCCCCCC
Confidence 89999999999999999999999999999999999999999999999999999999864
No 7
>PRK08359 transcription factor; Validated
Probab=99.67 E-value=3.6e-16 Score=97.50 Aligned_cols=59 Identities=15% Similarity=0.241 Sum_probs=57.0
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcccc
Q 038591 22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVKI 80 (82)
Q Consensus 22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e~~ 80 (82)
+.+|+.+|+.+||||.+||..+|++.++|++||+|...|+.+.+.+||++|||++.+..
T Consensus 87 ~~rIkeaRe~kglSQeeLA~~lgvs~stI~~iE~G~~~Ps~~~l~kLak~l~VsL~e~~ 145 (176)
T PRK08359 87 AERVYEAIQKSGLSYEELSHEVGLSVNDLRRIAHGEYEPTIKEAKKLERYFKIKLIERV 145 (176)
T ss_pred HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCCCcCCCHHHHHHHHHHhCCcccccc
Confidence 99999999999999999999999999999999999999999999999999999997753
No 8
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=99.65 E-value=2.5e-16 Score=83.70 Aligned_cols=59 Identities=27% Similarity=0.456 Sum_probs=51.0
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCC-CCCHHHHHHHHHHhCCCCcccc
Q 038591 22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKA-VPNQTVLAKMEKAIGVKLRVKI 80 (82)
Q Consensus 22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~-~p~~~~~~~la~~lgv~~~e~~ 80 (82)
|..|+.+|+..|+||.++|+.+|+|+++|++||+|.. .|+.+.+.+||.+||+++++.+
T Consensus 3 g~~lr~~R~~~gls~~~lA~~~g~s~s~v~~iE~G~~~~p~~~~l~~l~~~l~~~~~~~~ 62 (64)
T PF13560_consen 3 GRRLRRLRERAGLSQAQLADRLGVSQSTVSRIERGRRPRPSPDTLQRLARALGVPPDERA 62 (64)
T ss_dssp HHHHHHHHHCHTS-HHHHHHHHTS-HHHHHHHHTTSSSS-BHHHHHHHHHHTT--HHHHH
T ss_pred HHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCCHHHHHHHHHHHCcCHHHHc
Confidence 6889999999999999999999999999999999999 5999999999999999988754
No 9
>PRK09726 antitoxin HipB; Provisional
Probab=99.65 E-value=1.2e-15 Score=85.79 Aligned_cols=57 Identities=18% Similarity=0.323 Sum_probs=55.0
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcc
Q 038591 22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRV 78 (82)
Q Consensus 22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e 78 (82)
+.+|+.+|...|+||.+||+.+|+++++|++||+|...|+.+.+.+||++|||+++-
T Consensus 14 ~~~lk~~R~~~gltq~elA~~~gvs~~tis~~e~g~~~ps~~~l~~ia~~lgv~~~~ 70 (88)
T PRK09726 14 ANAMKLVRQQNGWTQSELAKKIGIKQATISNFENNPDNTTLTTFFKILQSLELSMTL 70 (88)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCHHHHHHHHHHcCCCcch
Confidence 889999999999999999999999999999999999999999999999999999764
No 10
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=99.64 E-value=8.1e-16 Score=94.41 Aligned_cols=58 Identities=31% Similarity=0.472 Sum_probs=56.4
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCccc
Q 038591 22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVK 79 (82)
Q Consensus 22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e~ 79 (82)
+.+|+.+|+.+||||.+||+.+|+++++|++||+|...|+.+.+.+|+++||+++++.
T Consensus 71 g~~Ir~~Re~~glSqeeLA~~lgvs~s~IsriE~G~~~Ps~~~l~kLa~~Lgvsl~el 128 (154)
T TIGR00270 71 GIIIRREREKRGWSQEQLAKKIQEKESLIKKIENAEIEPEPKVVEKLEKLLKIKLREQ 128 (154)
T ss_pred HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHhCCCHHHH
Confidence 8999999999999999999999999999999999999999999999999999999773
No 11
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=99.64 E-value=1e-15 Score=91.88 Aligned_cols=58 Identities=22% Similarity=0.262 Sum_probs=55.5
Q ss_pred CHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcc
Q 038591 21 TPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRV 78 (82)
Q Consensus 21 ~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e 78 (82)
.|.+|+.+|...|+||.+||+.+|||+++|++||+|...|+.+.+.+||++|||+++.
T Consensus 6 ~g~rlk~~R~~~gltq~~lA~~~gvs~~~is~~E~g~~~p~~~~l~~la~~l~vs~~~ 63 (135)
T PRK09706 6 LGQRIRYRRKQLKLSQRSLAKAVKVSHVSISQWERDETEPTGKNLFALAKALQCSPTW 63 (135)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHHCcCHHH
Confidence 4899999999999999999999999999999999999999999999999999999763
No 12
>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=99.59 E-value=1.1e-14 Score=79.70 Aligned_cols=57 Identities=16% Similarity=0.154 Sum_probs=54.5
Q ss_pred CHHHHH-HHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCc
Q 038591 21 TPRQIQ-RARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLR 77 (82)
Q Consensus 21 ~~~~lk-~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~ 77 (82)
.|++|+ .+|+..|+|+.+||+.+|+++++|++||+|...|+.+.+.+||++|||+++
T Consensus 5 ~g~~i~~~~~~~~~~t~~~lA~~~gis~~tis~~~~g~~~~~~~~~~~l~~~l~v~~~ 62 (78)
T TIGR02607 5 PGEILREEFLEPLGLSIRALAKALGVSRSTLSRIVNGRRGITADMALRLAKALGTSPE 62 (78)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHcCCCHH
Confidence 478999 899999999999999999999999999999999999999999999999975
No 13
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=99.57 E-value=1.2e-14 Score=86.10 Aligned_cols=58 Identities=19% Similarity=0.283 Sum_probs=54.8
Q ss_pred CHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcc
Q 038591 21 TPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRV 78 (82)
Q Consensus 21 ~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e 78 (82)
.+.+|+.++..+|+||.+||+.+|+|+++|++||+|...|+.+.+.+||++||+++++
T Consensus 6 ~~~~l~~ll~~~Glsq~eLA~~~Gis~~~is~iE~g~~~ps~~~l~kIa~aL~v~~~~ 63 (120)
T PRK13890 6 FFTNVLRLLDERHMTKKELSERSGVSISFLSDLTTGKANPSLKVMEAIADALETPLPL 63 (120)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHHCCCHHH
Confidence 4788999999999999999999999999999999999999999999999999997654
No 14
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=99.57 E-value=9.4e-15 Score=91.59 Aligned_cols=58 Identities=22% Similarity=0.283 Sum_probs=55.9
Q ss_pred CHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcc
Q 038591 21 TPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRV 78 (82)
Q Consensus 21 ~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e 78 (82)
.+.+|+.+|+.+|+||.+||+.+|+|+++|++||+|...|+...+.+||++||+++++
T Consensus 8 ~g~~l~~~R~~~glt~~elA~~~gis~~~is~~E~g~~~p~~~~l~~ia~~l~v~~~~ 65 (185)
T PRK09943 8 PGKRLSEIRQQQGLSQRRAAELSGLTHSAISTIEQDKVSPAISTLQKLLKVYGLSLSE 65 (185)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCHHH
Confidence 4899999999999999999999999999999999999999999999999999999865
No 15
>PRK08154 anaerobic benzoate catabolism transcriptional regulator; Reviewed
Probab=99.56 E-value=8.1e-15 Score=98.20 Aligned_cols=70 Identities=19% Similarity=0.250 Sum_probs=60.9
Q ss_pred hhhccCCCCCCC---HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCccc
Q 038591 10 MRKLDEGTEPDT---PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVK 79 (82)
Q Consensus 10 ~~~~~~~~~~~~---~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e~ 79 (82)
|+.+..+...|. |.+|+.+|+.+|+||.+||+.+|+|+++|++||+|...|+.+.+.+||++|||++++.
T Consensus 15 ~~~~~~~~~~~~~~~g~rl~~~R~~~gltq~~lA~~~gvs~~~i~~~E~g~~~ps~~~l~~ia~~l~v~~~~l 87 (309)
T PRK08154 15 MTGAAAEEAPFLAALGERVRTLRARRGMSRKVLAQASGVSERYLAQLESGQGNVSILLLRRVARALGCSLADL 87 (309)
T ss_pred CCCCccchHHHHHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCCHHHHHHHHHHhCCCHHHH
Confidence 333444444443 9999999999999999999999999999999999999999999999999999998753
No 16
>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=99.56 E-value=8.5e-15 Score=82.65 Aligned_cols=60 Identities=23% Similarity=0.320 Sum_probs=54.6
Q ss_pred CCCCCCHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCc
Q 038591 16 GTEPDTPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLR 77 (82)
Q Consensus 16 ~~~~~~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~ 77 (82)
....+.+..|+.+|+..|+|| ||+++||++++|++||+|...|+.+.+.+||++||+++.
T Consensus 28 ~~~~~~~~~l~~~r~~~glSq--LAe~~GIs~stLs~iE~g~~~Ps~~tL~kI~~aLgi~l~ 87 (89)
T TIGR02684 28 GDPAYIAHALGYIARARGMTQ--LARKTGLSRESLYKALSGKGNPTFDTILKVTKALGLKLT 87 (89)
T ss_pred CCHHHHHHHHHHHHHHCChHH--HHHHHCCCHHHHHHHHcCCCCCCHHHHHHHHHHcCCcee
Confidence 344455889999999999995 999999999999999999999999999999999999875
No 17
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=99.55 E-value=1.8e-14 Score=76.02 Aligned_cols=56 Identities=23% Similarity=0.310 Sum_probs=43.5
Q ss_pred HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCC-CCCCHHHHHHHHHHhCCCCccc
Q 038591 24 QIQRARLGKKMSQPDLANQINQRPQVVSEYENGK-AVPNQTVLAKMEKAIGVKLRVK 79 (82)
Q Consensus 24 ~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~-~~p~~~~~~~la~~lgv~~~e~ 79 (82)
+|+.++..+|+|+.+||+.+|++++++++|.+|. ..|+.+.+.+||.+|||+++|.
T Consensus 1 ~L~~~m~~~~it~~~La~~~gis~~tl~~~~~~~~~~~~~~~l~~ia~~l~~~~~el 57 (63)
T PF13443_consen 1 KLKELMAERGITQKDLARKTGISRSTLSRILNGKPSNPSLDTLEKIAKALNCSPEEL 57 (63)
T ss_dssp HHHHHHHHTT--HHHHHHHHT--HHHHHHHHTTT-----HHHHHHHHHHHT--HHHC
T ss_pred CHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhcccccccHHHHHHHHHHcCCCHHHH
Confidence 5889999999999999999999999999999998 7999999999999999999874
No 18
>PRK10072 putative transcriptional regulator; Provisional
Probab=99.54 E-value=5.9e-14 Score=80.18 Aligned_cols=56 Identities=18% Similarity=0.298 Sum_probs=52.3
Q ss_pred CHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCc
Q 038591 21 TPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLR 77 (82)
Q Consensus 21 ~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~ 77 (82)
.+..|+.+|...|+||.+||+.+|+|.+||++||+|.+.|+...+. +++++|++|.
T Consensus 34 ~~~eik~LR~~~glTQ~elA~~lGvS~~TVs~WE~G~r~P~~~~l~-Ll~~L~~~P~ 89 (96)
T PRK10072 34 SFTEFEQLRKGTGLKIDDFARVLGVSVAMVKEWESRRVKPSSAELK-LMRLIQANPA 89 (96)
T ss_pred ChHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHH-HHHHHhhCHH
Confidence 5778999999999999999999999999999999999999999954 9999999983
No 19
>TIGR02612 mob_myst_A mobile mystery protein A. Members of this protein family are found in mobization-related contexts more often than not, including within a CRISPR-associated gene region in Geobacter sulfurreducens PCA, and on plasmids in Agrobacterium tumefaciens and Coxiella burnetii, always together with mobile mystery protein B, a member of the Fic protein family (pfam02661). This protein is encoded by the upstream member of the gene pair and belongs to a family of helix-turn-helix DNA binding proteins (pfam01381).
Probab=99.49 E-value=1.3e-13 Score=84.36 Aligned_cols=56 Identities=20% Similarity=0.229 Sum_probs=52.4
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCC--CCCHHHHHHHHHHhCCCCc
Q 038591 22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKA--VPNQTVLAKMEKAIGVKLR 77 (82)
Q Consensus 22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~--~p~~~~~~~la~~lgv~~~ 77 (82)
..+|+.+|...||||.+||+.+|||+++|++||+|.. .|+.+.+.+||++|||++.
T Consensus 27 ~~~Ir~~R~~lGmTq~eLAerlGVS~~tIs~iE~G~~~~~psl~~L~kIA~aLgv~~~ 84 (150)
T TIGR02612 27 EGWVRAIRKALGMSGAQLAGRLGVTPQRVEALEKSELSGTVTLKTLRAAAEALDCTFV 84 (150)
T ss_pred HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCCCHHHHHHHHHHcCCCHH
Confidence 5789999999999999999999999999999999975 4899999999999999964
No 20
>PRK04140 hypothetical protein; Provisional
Probab=99.48 E-value=1.4e-13 Score=92.58 Aligned_cols=57 Identities=26% Similarity=0.352 Sum_probs=55.0
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcc
Q 038591 22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRV 78 (82)
Q Consensus 22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e 78 (82)
|.+|+.+|+..||||.+||+.+|+|+++|++||+|...|+.+.+.+|+++||+++.+
T Consensus 128 GerLk~lRe~~GlSq~eLA~~lGVSr~tIskyE~G~~~Ps~e~~~kLa~~Lgv~l~~ 184 (317)
T PRK04140 128 GDVLREAREELGLSLGELASELGVSRRTISKYENGGMNASIEVAIKLEEILDVPLTK 184 (317)
T ss_pred HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCChHH
Confidence 999999999999999999999999999999999999999999999999999998644
No 21
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=99.43 E-value=1.2e-12 Score=65.33 Aligned_cols=54 Identities=33% Similarity=0.500 Sum_probs=51.0
Q ss_pred HHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcc
Q 038591 25 IQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRV 78 (82)
Q Consensus 25 lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e 78 (82)
|+.+|...++|+.+||+.+|+++.+|++|++|...|+.+.+..++++||++++.
T Consensus 2 i~~~~~~~~~s~~~la~~~~i~~~~i~~~~~~~~~~~~~~~~~i~~~~~~~~~~ 55 (56)
T smart00530 2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDE 55 (56)
T ss_pred HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHhCCChhh
Confidence 677899999999999999999999999999999999999999999999999864
No 22
>KOG3398 consensus Transcription factor MBF1 [Transcription]
Probab=99.41 E-value=1.4e-12 Score=76.83 Aligned_cols=78 Identities=50% Similarity=0.709 Sum_probs=70.8
Q ss_pred ccchhhhhhhccCCCCCCC--------HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCC
Q 038591 3 TAGAVINMRKLDEGTEPDT--------PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGV 74 (82)
Q Consensus 3 ~~~~~~~~~~~~~~~~~~~--------~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv 74 (82)
.-+.+++.+++|++.+... |..|...|..+||||++||.+++=.++.|..||+|+..|+...+.++.++|||
T Consensus 48 q~~~~~~t~klD~etE~~~~~~v~~~Vg~aIq~aR~~KgmsqkDLA~kInekpqVv~dyEsGrAIpNqqil~kmEraLgv 127 (135)
T KOG3398|consen 48 QHPSTQSTAKLDRETEELGHDRVPLEVGKAIQQARAQKGMSQKDLAQKINEKPQVIQDYESGRAIPNQQILSKMERALGV 127 (135)
T ss_pred cCCcccchhhccccccccccccccHHHHHHHHHHHHhccccHHHHHHHHccCchhhhhHhccccCchHHHHHHHHHHhce
Confidence 3456788899988777664 89999999999999999999999999999999999999999999999999999
Q ss_pred CCcccc
Q 038591 75 KLRVKI 80 (82)
Q Consensus 75 ~~~e~~ 80 (82)
.++.++
T Consensus 128 Klrgk~ 133 (135)
T KOG3398|consen 128 KLRGKN 133 (135)
T ss_pred eccccc
Confidence 988765
No 23
>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=99.40 E-value=3e-12 Score=64.31 Aligned_cols=56 Identities=32% Similarity=0.504 Sum_probs=52.6
Q ss_pred HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcc
Q 038591 23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRV 78 (82)
Q Consensus 23 ~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e 78 (82)
..|+.++...|+|+.++|..+|+++.+|++|++|...|+...+..|++.||++++.
T Consensus 2 ~~l~~~~~~~~~s~~~~a~~~~~~~~~v~~~~~g~~~~~~~~~~~i~~~~~~~~~~ 57 (58)
T cd00093 2 ERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDE 57 (58)
T ss_pred hHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCChhh
Confidence 56888899999999999999999999999999999999999999999999998764
No 24
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=99.38 E-value=2.9e-12 Score=75.72 Aligned_cols=62 Identities=24% Similarity=0.327 Sum_probs=55.0
Q ss_pred CCCCCHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCccc
Q 038591 17 TEPDTPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVK 79 (82)
Q Consensus 17 ~~~~~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e~ 79 (82)
...+.+..|+.+|...|+||.+||+.+|+++++|++||+|...|+.. +..+++.|+++++..
T Consensus 62 ~~~~~~~~i~~~r~~~gltq~~lA~~lg~~~~tis~~e~g~~~p~~~-~~~l~~~l~~~p~~l 123 (127)
T TIGR03830 62 DGLLTPPEIRRIRKKLGLSQREAAELLGGGVNAFSRYERGEVRPSKA-LDKLLRLLDKHPELL 123 (127)
T ss_pred cCCcCHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCCCCCCCHH-HHHHHHHHHHChHHH
Confidence 34556899999999999999999999999999999999999888865 688889999998653
No 25
>COG1813 Predicted transcription factor, homolog of eukaryotic MBF1 [Transcription]
Probab=99.38 E-value=2.4e-12 Score=79.32 Aligned_cols=58 Identities=38% Similarity=0.570 Sum_probs=56.4
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCccc
Q 038591 22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVK 79 (82)
Q Consensus 22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e~ 79 (82)
+++|+.+|+.+||||++||.+++++.+.|.+||+|...|+...+.+|.++||+.+.++
T Consensus 81 ~e~Ir~ARE~~G~SqedLA~ki~ek~svI~~iE~g~~~P~~~~akkLEk~LgIkL~e~ 138 (165)
T COG1813 81 GERIREAREKRGLSQEDLAAKLKEKVSVIRRIERGEATPNIKVAKKLEKLLGIKLVEK 138 (165)
T ss_pred HHHHHHHHHHcCCCHHHHHHHhcccHHHHHHHHhcccCccHHHHHHHHHHhCceeeee
Confidence 8999999999999999999999999999999999999999999999999999998765
No 26
>PHA00542 putative Cro-like protein
Probab=99.28 E-value=5.2e-11 Score=66.23 Aligned_cols=54 Identities=17% Similarity=0.278 Sum_probs=48.7
Q ss_pred CCHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCC-CCCCHHHHHHHHHHhC
Q 038591 20 DTPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGK-AVPNQTVLAKMEKAIG 73 (82)
Q Consensus 20 ~~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~-~~p~~~~~~~la~~lg 73 (82)
+....+..++...|+|+.+||+.+|||+++|++||+|. ..|+.+.+.+||+++-
T Consensus 18 ~~~~~l~~~l~~~glTq~elA~~lgIs~~tIsr~e~g~~~~p~~~~l~ki~~~~~ 72 (82)
T PHA00542 18 QRPDELVCALIRAGWSQEQIADATDVSQPTICRIYSGRHKDPRYSVVEKLRHLVL 72 (82)
T ss_pred cCHHHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHcCCCCCCCHHHHHHHHHHHH
Confidence 34667888899999999999999999999999999998 5899999999999863
No 27
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=99.26 E-value=3.2e-11 Score=69.46 Aligned_cols=49 Identities=24% Similarity=0.390 Sum_probs=43.8
Q ss_pred CCCCCHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHH
Q 038591 17 TEPDTPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVL 65 (82)
Q Consensus 17 ~~~~~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~ 65 (82)
...+.+..|+.+|+..|+||.+||..+|+|.+||++||+|...|+-..+
T Consensus 41 ~~~ls~~eIk~iRe~~~lSQ~vFA~~L~vs~~Tv~~WEqGr~kPsg~Al 89 (104)
T COG2944 41 VKTLSPTEIKAIREKLGLSQPVFARYLGVSVSTVRKWEQGRKKPSGAAL 89 (104)
T ss_pred CCCCCHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHcCCcCCCCHHH
Confidence 3446699999999999999999999999999999999999999886553
No 28
>PRK10856 cytoskeletal protein RodZ; Provisional
Probab=99.25 E-value=2.5e-11 Score=82.34 Aligned_cols=58 Identities=16% Similarity=0.221 Sum_probs=53.4
Q ss_pred CHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCH------HHHHHHHHHhCCCCcc
Q 038591 21 TPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQ------TVLAKMEKAIGVKLRV 78 (82)
Q Consensus 21 ~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~------~~~~~la~~lgv~~~e 78 (82)
.|.+|+.+|+.+||||.+||+++++++++|++||+|...+.. ..+..+|++||++.++
T Consensus 15 ~G~~Lr~aRe~~GlSq~~vA~~l~l~~~~I~~iE~g~~~~~~~~tf~RGyir~yA~~lgv~~~~ 78 (331)
T PRK10856 15 TGERLRQAREQLGLTQQAVAERLCLKVSTVRDIEEDKAPADLASTFLRGYIRSYARLVHIPEEE 78 (331)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHCCCCCCChhHHHHHHHHHHHHHHHCcCHHH
Confidence 489999999999999999999999999999999999887776 4589999999999875
No 29
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=99.21 E-value=5.1e-11 Score=65.90 Aligned_cols=56 Identities=23% Similarity=0.293 Sum_probs=46.6
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcC-CCCCCHHHHHHHHHHhCCCCc
Q 038591 22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENG-KAVPNQTVLAKMEKAIGVKLR 77 (82)
Q Consensus 22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g-~~~p~~~~~~~la~~lgv~~~ 77 (82)
...|..+++..||||.++|+.+|++++.|+++++| ...++.+.+..++..+|..++
T Consensus 20 ~~~i~~~~~~~~ltQ~e~A~~lgisq~~vS~l~~g~~~~~sl~~L~~~l~aLG~~v~ 76 (80)
T PF13744_consen 20 MAAIRELREERGLTQAELAERLGISQPRVSRLENGKIDDFSLDTLLRYLEALGGRVE 76 (80)
T ss_dssp HHHHHHHHHCCT--HHHHHHHHTS-HHHHHHHHTT-GCC--HHHHHHHHHHTTEEEE
T ss_pred HHHHHHHHHHcCCCHHHHHHHHCCChhHHHHHHcCcccCCCHHHHHHHHHHcCCeEE
Confidence 56688999999999999999999999999999998 468999999999999998764
No 30
>COG3620 Predicted transcriptional regulator with C-terminal CBS domains [Transcription]
Probab=99.20 E-value=8.8e-11 Score=72.42 Aligned_cols=52 Identities=21% Similarity=0.395 Sum_probs=49.7
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhC
Q 038591 22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIG 73 (82)
Q Consensus 22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lg 73 (82)
.+-|+..|+..|+||++||+..|+|+++|.++|.|+..|.+.++.+|.++|-
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 6789999999999999999999999999999999999999999999998874
No 31
>COG3093 VapI Plasmid maintenance system antidote protein [General function prediction only]
Probab=99.11 E-value=4.2e-10 Score=64.74 Aligned_cols=57 Identities=16% Similarity=0.225 Sum_probs=52.3
Q ss_pred CHHHHHH-HHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCc
Q 038591 21 TPRQIQR-ARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLR 77 (82)
Q Consensus 21 ~~~~lk~-~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~ 77 (82)
.|+.|++ +.+..|+|+.+||+.+||++.+|+.+.+|++.++.+++.+|+++||.+++
T Consensus 10 PGEiL~eeflep~glt~~~lA~~lgV~r~~is~ling~~~iT~dmAlrL~k~fGtspe 67 (104)
T COG3093 10 PGEILREEFLEPLGLTQTELAEALGVTRNTISELINGRRAITADMALRLAKVFGTSPE 67 (104)
T ss_pred chHHHHHHHhccccCCHHHHHHHhCCCHHHHHHHHcCCcCCCHHHHHHHHHHhCCCHH
Confidence 4888855 66778999999999999999999999999999999999999999999875
No 32
>PRK13355 bifunctional HTH-domain containing protein/aminotransferase; Provisional
Probab=99.08 E-value=5.3e-10 Score=79.14 Aligned_cols=57 Identities=23% Similarity=0.364 Sum_probs=53.9
Q ss_pred HHHHHHHHHhCCCCHHHHHHHh-----CCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcc
Q 038591 22 PRQIQRARLGKKMSQPDLANQI-----NQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRV 78 (82)
Q Consensus 22 ~~~lk~~r~~~g~s~~elA~~~-----gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e 78 (82)
+.+|+.+|+..|+||.+||+.+ +|++++|++||+|+..|+.+.+..||++|||+++.
T Consensus 5 ~~rL~~~r~~~g~tq~~la~~~~~~g~~vs~~~is~~e~g~~~p~~~~l~~la~~l~v~~~~ 66 (517)
T PRK13355 5 AERLKQAMKARGLKQEDLVHAAEARGVKLGKSHISQYVSGKTGPRRDVLPFLAAILGVSEDW 66 (517)
T ss_pred HHHHHHHHHHCCCCHHHHHHHHHhccCCcCHHHHHHHHCCCCCCCHHHHHHHHHHhCcCHHH
Confidence 6899999999999999999996 69999999999999999999999999999999864
No 33
>PRK02866 cyanate hydratase; Validated
Probab=99.02 E-value=2e-09 Score=65.50 Aligned_cols=57 Identities=18% Similarity=0.176 Sum_probs=53.7
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcc
Q 038591 22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRV 78 (82)
Q Consensus 22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e 78 (82)
.+.|..+|.++|+|++++|+.+|+|+.++..++.|+..++.+.+.+||++||++.+.
T Consensus 7 ~e~Ll~AK~~kGLTw~~IA~~iG~S~v~vaaa~lGQ~~ls~e~A~kla~~LgL~~~~ 63 (147)
T PRK02866 7 TEKILAAKKEKGLTWADIAEAIGLSEVWVTAALLGQMTLPAEEAEKVAELLGLDEDA 63 (147)
T ss_pred HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHhCCCCCCHHHHHHHHHHhCCCHHH
Confidence 567899999999999999999999999999999999999999999999999988654
No 34
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=98.98 E-value=4.6e-09 Score=57.26 Aligned_cols=46 Identities=11% Similarity=0.242 Sum_probs=39.7
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhC------CCHHHHHHHHcCCCCCCHHHHHHHH
Q 038591 22 PRQIQRARLGKKMSQPDLANQIN------QRPQVVSEYENGKAVPNQTVLAKME 69 (82)
Q Consensus 22 ~~~lk~~r~~~g~s~~elA~~~g------is~~~i~~~e~g~~~p~~~~~~~la 69 (82)
+.+++..|...|+||.+||+.+| +|+++|++||+|. .+..++.+|-
T Consensus 13 ~~~lk~~R~~lGLTQ~dvA~~lg~~~g~i~SQstISR~Es~~--ls~~n~~kl~ 64 (75)
T smart00352 13 AKTFKQRRIKLGFTQADVGLALGALYGPDFSQTTICRFEALQ--LSFKNMCKLK 64 (75)
T ss_pred HHHHHHHHHHcCCCHHHHHHHhcccccCcCCHHHHHHHHhcC--ccHHHHHHHH
Confidence 89999999999999999999999 5999999999974 4566655553
No 35
>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=98.93 E-value=6.5e-10 Score=59.41 Aligned_cols=53 Identities=21% Similarity=0.355 Sum_probs=39.5
Q ss_pred HHHHHHHhCCCCH-HHHHHHhCCCHHHHH-HHHcCCCCCCHHHHHHHHHHhCCCCc
Q 038591 24 QIQRARLGKKMSQ-PDLANQINQRPQVVS-EYENGKAVPNQTVLAKMEKAIGVKLR 77 (82)
Q Consensus 24 ~lk~~r~~~g~s~-~elA~~~gis~~~i~-~~e~g~~~p~~~~~~~la~~lgv~~~ 77 (82)
.|+.+++..|++. .+||+.+|||+++|+ .|......| .+.+.+||..+||+++
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 5777888888765 699999999999999 899877676 9999999999999986
No 36
>TIGR00673 cynS cyanate hydratase. Alternate names include cyanate lyase, cyanase and cyanate hydrolase.
Probab=98.92 E-value=1e-08 Score=62.58 Aligned_cols=56 Identities=11% Similarity=0.124 Sum_probs=53.0
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCc
Q 038591 22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLR 77 (82)
Q Consensus 22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~ 77 (82)
.+.|..++.++|+|.+++|+.+|+|+..+..++.|+..++.+.+.+||++||++-+
T Consensus 10 t~~Ll~AK~~KGLTwe~IAe~iG~sevwvaaa~lGQ~~ls~e~A~kla~lLgL~~e 65 (150)
T TIGR00673 10 ADALLESKKKKGLTFADIADGLGLAEVFVAAALYGQAAAPADEARLVGAKLDLDED 65 (150)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHhCCCCCCHHHHHHHHHHhCcCHH
Confidence 57788999999999999999999999999999999999999999999999998754
No 37
>COG3655 Predicted transcriptional regulator [Transcription]
Probab=98.91 E-value=6e-09 Score=56.55 Aligned_cols=58 Identities=21% Similarity=0.212 Sum_probs=52.6
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCC-CCCCHHHHHHHHHHhCCCCccc
Q 038591 22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGK-AVPNQTVLAKMEKAIGVKLRVK 79 (82)
Q Consensus 22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~-~~p~~~~~~~la~~lgv~~~e~ 79 (82)
.-++..++..++++..+||+.+|||.++++.+.+|+ ..+.++++.+||++|.|.|.|.
T Consensus 4 ~~~l~~~l~~r~~~~~eLa~~igis~~~ls~l~~gk~k~I~~~tL~~iC~~LeCqpgDi 62 (73)
T COG3655 4 AVRLDVMLADRKISLKELAEAIGISEANLSKLKTGKVKAIRLSTLEKICKALECQPGDI 62 (73)
T ss_pred hHhHHHHHHHHhhhHHHHHHHHcccHHHHHHHHcCCcceeeHHHHHHHHHHcCCChhhe
Confidence 456788899999999999999999999999999886 4689999999999999999764
No 38
>COG1709 Predicted transcriptional regulator [Transcription]
Probab=98.89 E-value=3.1e-09 Score=68.21 Aligned_cols=52 Identities=27% Similarity=0.465 Sum_probs=48.5
Q ss_pred CHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCC-CCHHHHHHHHHHh
Q 038591 21 TPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAV-PNQTVLAKMEKAI 72 (82)
Q Consensus 21 ~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~-p~~~~~~~la~~l 72 (82)
.|+.|+.+|+..++||.|||+.+|+|++.|+.||.|++. |....+.++-.+|
T Consensus 28 pge~lrKWR~~F~vSQ~elA~~l~vSpSVISDYE~GRRk~Pg~~~vkk~V~AL 80 (241)
T COG1709 28 PGETLRKWREIFNVSQTELARELGVSPSVISDYESGRRKSPGIAFVKKFVEAL 80 (241)
T ss_pred hhHHHHHHHHHhCccHHHHHHHhCCCcceeehhhccCccCccHHHHHHHHHHH
Confidence 499999999999999999999999999999999999877 9999988887766
No 39
>PF13413 HTH_25: Helix-turn-helix domain; PDB: 2WUS_R 3FYM_A.
Probab=98.86 E-value=9.6e-09 Score=54.36 Aligned_cols=55 Identities=24% Similarity=0.375 Sum_probs=41.5
Q ss_pred HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcC--CCCCCH----HHHHHHHHHhCCCCcc
Q 038591 24 QIQRARLGKKMSQPDLANQINQRPQVVSEYENG--KAVPNQ----TVLAKMEKAIGVKLRV 78 (82)
Q Consensus 24 ~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g--~~~p~~----~~~~~la~~lgv~~~e 78 (82)
+|+.+|+.+|+|..++|..++|+.++|..+|+| ...|+. ..+..+|++||++.++
T Consensus 1 ~Lr~~R~~~glsl~~va~~t~I~~~~l~aiE~~~~~~lp~~~y~rg~lr~Ya~~Lgld~~~ 61 (62)
T PF13413_consen 1 RLREAREAKGLSLEDVAEETKISVSYLEAIENGDFDSLPSPVYARGYLRKYARFLGLDPDE 61 (62)
T ss_dssp -HHHHHHCTT--HHHHHHHCS--HHHHHHHHCT-GCCSSSHHHHHHHHHHHHHHTT--HHH
T ss_pred ChHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCcChhhCCcHHHHHHHHHHHHHHhCcCccc
Confidence 488999999999999999999999999999999 445654 3488999999998764
No 40
>COG1395 Predicted transcriptional regulator [Transcription]
Probab=98.83 E-value=1.4e-08 Score=68.22 Aligned_cols=56 Identities=23% Similarity=0.316 Sum_probs=54.3
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCc
Q 038591 22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLR 77 (82)
Q Consensus 22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~ 77 (82)
|+.|++.|++.|+|.-+||..+|+|+.+|++||+|...|+.+.+.+|-..||.++-
T Consensus 127 ge~Lre~Ree~glSlG~lA~~lgVSRktV~~YE~G~~~~sleva~kLeei~g~~iv 182 (313)
T COG1395 127 GEKLREKREEMGLSLGDLATMLGVSRKTVYKYEKGLSDASLEVALKLEEIFGEDIV 182 (313)
T ss_pred hHHHHHHHHHcCcCHHHHHHHhCccHHHHHHhccCCCCccHHHHHHHHHHhcchhh
Confidence 99999999999999999999999999999999999999999999999999998764
No 41
>COG1396 HipB Predicted transcriptional regulators [Transcription]
Probab=98.76 E-value=8.2e-08 Score=52.01 Aligned_cols=56 Identities=29% Similarity=0.503 Sum_probs=52.5
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCC-CCCHHHHHHHHHHhCCCCc
Q 038591 22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKA-VPNQTVLAKMEKAIGVKLR 77 (82)
Q Consensus 22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~-~p~~~~~~~la~~lgv~~~ 77 (82)
+.+++.+|...|+|+.++|..+|++..+++.||+|.. .|+...+..++..|+++..
T Consensus 3 ~~~~~~~r~~~~~s~~~~a~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~ 59 (120)
T COG1396 3 GERLKELRKKKGLSQEELAERLGVSRSTISRIERGRSESPSLELLARLAAALGVSLD 59 (120)
T ss_pred HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCCCHHHHHHHHHHHCCCHH
Confidence 6789999999999999999999999999999999988 9999999999999888654
No 42
>PF08667 BetR: BetR domain; InterPro: IPR013975 CheY-like phosphoacceptor (or receiver [REC]) domain is a common module in a variety of response regulators of the bacterial signal transduction systems. BetR is one of the many response regulators and is encoded mainly in Burkholderia spp. It is a N-terminal helix-turn-helix domain (HTH) and has been shown to be related to the XRE-type HTH domain (IPR001387 from INTERPRO), it has been suggested that BetR would have dimerization, protein-protein interaction, and activation/relief-of-inhibition properties [].
Probab=98.65 E-value=1.1e-07 Score=58.01 Aligned_cols=59 Identities=17% Similarity=0.161 Sum_probs=54.2
Q ss_pred CCHHHHHHHHHhCCCCH----HHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcc
Q 038591 20 DTPRQIQRARLGKKMSQ----PDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRV 78 (82)
Q Consensus 20 ~~~~~lk~~r~~~g~s~----~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e 78 (82)
...++|+.+...+|+.+ .+||+.||+|.+++++-.+|+...+...+.+|++.||+++++
T Consensus 5 ~~~erV~~Ll~~~Gi~kr~~~s~LA~iL~Is~ssa~RKL~G~~~ftl~EI~~Ia~~fgvS~d~ 67 (147)
T PF08667_consen 5 AIAERVRELLDRKGIPKRKHASELADILGISYSSAYRKLNGKSPFTLEEIKKIAKHFGVSPDE 67 (147)
T ss_pred HHHHHHHHHHHHcCCcchhhHHHHHHHHCCCHHHHHHHhcCCCCCCHHHHHHHHHHhCcCHHH
Confidence 34789999999999876 679999999999999999999999999999999999999875
No 43
>PHA01083 hypothetical protein
Probab=98.58 E-value=2.3e-07 Score=56.41 Aligned_cols=56 Identities=13% Similarity=0.280 Sum_probs=48.1
Q ss_pred HHHHHHHHhCCC-CHHHHHHHhCCCHHHHHHHHcC-CCCCCHHHHHHHHHHhCCCCcc
Q 038591 23 RQIQRARLGKKM-SQPDLANQINQRPQVVSEYENG-KAVPNQTVLAKMEKAIGVKLRV 78 (82)
Q Consensus 23 ~~lk~~r~~~g~-s~~elA~~~gis~~~i~~~e~g-~~~p~~~~~~~la~~lgv~~~e 78 (82)
+.|....+..++ +-++||..+||+++.|++|.+| ++.++.+.+..||+.+|+++.+
T Consensus 5 kLLda~K~a~~~~sdkqLA~~LGVs~q~IS~~R~G~r~~i~de~A~~LAe~aGiDp~e 62 (149)
T PHA01083 5 KLLDAYKKAKNYVQYKQIAHDLGVSPQKISKMRTGVRTYISDEEAIFLAESAGIDPEI 62 (149)
T ss_pred HHHHHHHHHHhhccHHHHHHHhCCCHHHHHHHHcCCCCCCCHHHHHHHHHHhCCCHHH
Confidence 445666666654 5589999999999999999999 9999999999999999999853
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=98.54 E-value=3.6e-07 Score=46.05 Aligned_cols=41 Identities=20% Similarity=0.249 Sum_probs=34.0
Q ss_pred HHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCCCCcc
Q 038591 38 DLANQINQRPQVVSEYENGKAVPNQTV---LAKMEKAIGVKLRV 78 (82)
Q Consensus 38 elA~~~gis~~~i~~~e~g~~~p~~~~---~~~la~~lgv~~~e 78 (82)
+||+.+|+|++||++|++|...++... +..++..||+.++.
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~~vs~~~~~~i~~~~~~l~~~~~~ 45 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKPRVSEETRERVLAAAEELGYRPNA 45 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCCCCCHHHHHHHHHHHHHhCCCCCH
Confidence 799999999999999999986666444 56688899987753
No 45
>COG5499 Predicted transcription regulator containing HTH domain [Transcription]
Probab=98.49 E-value=4.3e-07 Score=52.72 Aligned_cols=55 Identities=20% Similarity=0.233 Sum_probs=51.7
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCc
Q 038591 22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLR 77 (82)
Q Consensus 22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~ 77 (82)
-+.|+.+++..|+|+.+||..+| |.+.+|++.+|++..+.+.+.+|.+-||++.+
T Consensus 62 ve~I~t~Md~~glt~~dLa~~iG-Sks~vS~iL~~rraLTle~ikkL~q~~gIpa~ 116 (120)
T COG5499 62 VEVIRTLMDQYGLTLADLANEIG-SKSRVSNILSGRRALTLEHIKKLHQRFGIPAD 116 (120)
T ss_pred HHHHHHHHHHhCCcHHHHHHHhC-chHHHHHHHhhhhHhhHHHHHHHHHHhCcCHH
Confidence 57889999999999999999998 67999999999999999999999999999875
No 46
>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=98.47 E-value=1.1e-06 Score=43.82 Aligned_cols=42 Identities=17% Similarity=0.250 Sum_probs=33.6
Q ss_pred CHHHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCCCC
Q 038591 35 SQPDLANQINQRPQVVSEYENGKAVPNQTV---LAKMEKAIGVKL 76 (82)
Q Consensus 35 s~~elA~~~gis~~~i~~~e~g~~~p~~~~---~~~la~~lgv~~ 76 (82)
|.+|+|+.+|+|.+|||++.+|...++.++ +..+++.+|..+
T Consensus 1 Ti~dIA~~agvS~~TVSr~ln~~~~vs~~tr~rI~~~a~~lgY~p 45 (46)
T PF00356_consen 1 TIKDIAREAGVSKSTVSRVLNGPPRVSEETRERILEAAEELGYRP 45 (46)
T ss_dssp CHHHHHHHHTSSHHHHHHHHTTCSSSTHHHHHHHHHHHHHHTB-S
T ss_pred CHHHHHHHHCcCHHHHHHHHhCCCCCCHHHHHHHHHHHHHHCCCC
Confidence 578999999999999999999988887776 455566666554
No 47
>COG1426 Predicted transcriptional regulator contains Xre-like HTH domain [Function unknown]
Probab=98.45 E-value=8.3e-07 Score=59.34 Aligned_cols=59 Identities=20% Similarity=0.290 Sum_probs=50.9
Q ss_pred CHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCC--CCCH----HHHHHHHHHhCCCCccc
Q 038591 21 TPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKA--VPNQ----TVLAKMEKAIGVKLRVK 79 (82)
Q Consensus 21 ~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~--~p~~----~~~~~la~~lgv~~~e~ 79 (82)
.|++|++.|+++|||+.|+|.+++|.+.++..+|+|.. .|.. ..+..+|+++|++.++.
T Consensus 4 ~Ge~Lr~~Re~~gLsL~dva~~t~I~~~~L~aiEeg~~~~lp~~~y~rG~ir~YA~~l~ld~~~l 68 (284)
T COG1426 4 LGERLRQAREEKGLSLEDVAARTKIRKSYLRALEEGNFDKLPGPVYIRGYIRSYAKFLGLDEDEL 68 (284)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHhCccHHHHHHHhcCccccccchHHHHHHHHHHHHHhCCCHHHH
Confidence 48999999999999999999999999999999999943 3432 35789999999998753
No 48
>PF08965 DUF1870: Domain of unknown function (DUF1870); InterPro: IPR015060 This family consist of hypothetical bacterial proteins. ; PDB: 1S4K_A.
Probab=98.29 E-value=5.6e-06 Score=48.79 Aligned_cols=51 Identities=14% Similarity=0.140 Sum_probs=39.2
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhC--CCHHHHHHHHcCCCCCCHHHHHHHHHHh
Q 038591 22 PRQIQRARLGKKMSQPDLANQIN--QRPQVVSEYENGKAVPNQTVLAKMEKAI 72 (82)
Q Consensus 22 ~~~lk~~r~~~g~s~~elA~~~g--is~~~i~~~e~g~~~p~~~~~~~la~~l 72 (82)
+..|+.+|...++|+.|.|..++ ++..+..+||+|...++.+.+..+....
T Consensus 3 ~~ELqalR~~l~lt~~EaA~~Ia~~v~~~tWq~WE~G~~~IP~~Vie~l~~m~ 55 (118)
T PF08965_consen 3 NLELQALRQILGLTVEEAAYYIAQDVSSRTWQQWEKGERPIPDDVIEELLEMK 55 (118)
T ss_dssp HHHHHHHHHHTT--HHHHHHHTSSS--HHHHHHHHTTSS---HHHHHHHHHHH
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHccCCHHHHHHHHcCCCCCCHHHHHHHHHHH
Confidence 56789999999999999999999 9999999999999999998887776543
No 49
>COG3636 Predicted transcriptional regulator [Transcription]
Probab=98.28 E-value=1.9e-06 Score=49.05 Aligned_cols=54 Identities=17% Similarity=0.190 Sum_probs=46.2
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCc
Q 038591 22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLR 77 (82)
Q Consensus 22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~ 77 (82)
...+-..-...|||| +|++.|+|+..+++-.+...+|+++++.+++++||+.+.
T Consensus 40 ~~alg~var~~GMsq--vA~~aGlsRe~LYkaLS~~GNPtf~Til~V~kAlG~rl~ 93 (100)
T COG3636 40 AAALGVVARSRGMSQ--VARKAGLSREGLYKALSPGGNPTFDTILAVLKALGLRLS 93 (100)
T ss_pred HHHHHHHHHhcCHHH--HHHHhCccHHHHHHHhCCCCCCcHHHHHHHHHHcCceee
Confidence 444444556678877 999999999999999999999999999999999998653
No 50
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=98.24 E-value=6e-06 Score=44.36 Aligned_cols=44 Identities=16% Similarity=0.142 Sum_probs=36.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCCCCc
Q 038591 34 MSQPDLANQINQRPQVVSEYENGKAVPNQTV---LAKMEKAIGVKLR 77 (82)
Q Consensus 34 ~s~~elA~~~gis~~~i~~~e~g~~~p~~~~---~~~la~~lgv~~~ 77 (82)
+|+.|+|+.+|+|.+||+++.+|...++.+. +..+++.+|..++
T Consensus 1 ~t~~~iA~~~gvS~~TVSr~ln~~~~v~~~t~~~i~~~~~~~gy~~~ 47 (70)
T smart00354 1 ATIKDVARLAGVSKATVSRVLNGNGRVSEETREKVLAAMEELGYIPN 47 (70)
T ss_pred CCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHhCCCCC
Confidence 4789999999999999999999987766544 6667888887665
No 51
>TIGR01321 TrpR trp operon repressor, proteobacterial. This model represents TrpR, the repressor of the trp operon. It is found so far only in the gamma subdivision of the proteobacteria and in Chlamydia trachomatis. All members belong to species capable of tryptophan biosynthesis.
Probab=98.19 E-value=8.9e-06 Score=46.27 Aligned_cols=47 Identities=13% Similarity=0.130 Sum_probs=34.7
Q ss_pred HHHHHHHHH--hCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHH
Q 038591 22 PRQIQRARL--GKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKM 68 (82)
Q Consensus 22 ~~~lk~~r~--~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~l 68 (82)
..|+.-+.. ..++||+|+|..+|||.+||++++++-...+++.-..|
T Consensus 42 ~~R~~i~~~Ll~~~~tQrEIa~~lGiS~atIsR~sn~lk~~~~~~~~~l 90 (94)
T TIGR01321 42 GDRIRIVNELLNGNMSQREIASKLGVSIATITRGSNNLKTMDPNFKQFL 90 (94)
T ss_pred HHHHHHHHHHHhCCCCHHHHHHHhCCChhhhhHHHhhcccCCHHHHHHH
Confidence 344444432 47899999999999999999999999775554444443
No 52
>COG4800 Predicted transcriptional regulator with an HTH domain [Transcription]
Probab=98.18 E-value=1.1e-05 Score=49.01 Aligned_cols=54 Identities=17% Similarity=0.180 Sum_probs=48.3
Q ss_pred CCCCHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHh
Q 038591 18 EPDTPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAI 72 (82)
Q Consensus 18 ~~~~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~l 72 (82)
.+-++..|+.+..+.|+|..|||++.|+.++|++++.+| +.|..+++.+|-+.+
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 344588899999999999999999999999999999999 789999998887765
No 53
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=98.08 E-value=1.5e-05 Score=47.11 Aligned_cols=34 Identities=24% Similarity=0.226 Sum_probs=30.0
Q ss_pred HHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCC
Q 038591 26 QRARLGKKMSQPDLANQINQRPQVVSEYENGKAVP 60 (82)
Q Consensus 26 k~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p 60 (82)
+.++++ |+||.++|+.+|+|+++||+|.+|++.+
T Consensus 16 ~~L~ee-G~Sq~~iA~LLGltqaAVS~Yls~krg~ 49 (119)
T COG2522 16 KELIEE-GLSQYRIAKLLGLTQAAVSQYLSGKRGS 49 (119)
T ss_pred HHHHHc-CCcHHHHHHHhCCCHHHHHHHHccCCch
Confidence 455565 9999999999999999999999998774
No 54
>PF13693 HTH_35: Winged helix-turn-helix DNA-binding; PDB: 1NEQ_A 1NER_A.
Probab=98.00 E-value=2e-05 Score=43.42 Aligned_cols=55 Identities=15% Similarity=0.068 Sum_probs=41.9
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCccc
Q 038591 22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVK 79 (82)
Q Consensus 22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e~ 79 (82)
...|+.....+|+|..+||+..|++++|+++... .|....-..||+++|+++.+.
T Consensus 4 ~adI~AaL~krG~sL~~lsr~~Gl~~~tl~nal~---r~~pk~E~~IA~aLgv~P~eI 58 (78)
T PF13693_consen 4 RADIKAALRKRGTSLAALSREAGLSSSTLRNALR---RPWPKGERIIADALGVPPEEI 58 (78)
T ss_dssp HHHHHHHHCTTS--HHHHHHHHSS-HHHHHHTTT---SS-HHHHHHHHHHTTS-HHHH
T ss_pred HHHHHHHHHHcCCCHHHHHHHcCCCHHHHHHHHc---CCChHHHHHHHHHHCcCHHHh
Confidence 4567777778999999999999999999999874 556667788999999998763
No 55
>COG3423 Nlp Predicted transcriptional regulator [Transcription]
Probab=97.98 E-value=7.2e-05 Score=40.89 Aligned_cols=59 Identities=17% Similarity=0.135 Sum_probs=47.3
Q ss_pred CCCCHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCccc
Q 038591 18 EPDTPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVK 79 (82)
Q Consensus 18 ~~~~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e~ 79 (82)
......-|....+.+|+|...|+.+.|+|++|+.+.... ..|..+ ..||.++||++.|.
T Consensus 6 ~dWh~adI~A~Lkk~G~Sl~~LS~~agls~~tL~n~L~r-p~pkgE--riIA~algv~P~eI 64 (82)
T COG3423 6 QDWHPADIIAALKKKGTSLAALSREAGLSSSTLANALDR-PWPKGE--RIIADALGVPPEEI 64 (82)
T ss_pred ccCCHHHHHHHHHHccccHHHHHHHcCCCHHHHHHHHcC-CCchHH--HHHHHHhCCCHHHh
Confidence 445566677778889999999999999999999999863 344444 56899999999874
No 56
>PRK08099 bifunctional DNA-binding transcriptional repressor/ NMN adenylyltransferase; Provisional
Probab=97.97 E-value=2.2e-05 Score=54.69 Aligned_cols=47 Identities=15% Similarity=0.252 Sum_probs=43.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHcCC-CCCCHHHHHHHHHHhCCCCcc
Q 038591 32 KKMSQPDLANQINQRPQVVSEYENGK-AVPNQTVLAKMEKAIGVKLRV 78 (82)
Q Consensus 32 ~g~s~~elA~~~gis~~~i~~~e~g~-~~p~~~~~~~la~~lgv~~~e 78 (82)
.|+|..+||+.+|+|.++++++|||+ ..|+.+.+.+|+++|||+...
T Consensus 2 ~~~~~~~~~~~~~~~~~y~~~l~~~~~~~ps~~~~~~~~~~~~~~~~~ 49 (399)
T PRK08099 2 QGCTLQQVADASGMTKGYLSQLLNAKIKSPSAQKLEALHRFLGLEFPR 49 (399)
T ss_pred CCCcHHHHHHHhCCcHHHHHHHhcCCCCCccHHHHHHHHHHhCCChhh
Confidence 68999999999999999999999995 579999999999999998643
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=97.87 E-value=4.3e-05 Score=50.90 Aligned_cols=48 Identities=15% Similarity=0.207 Sum_probs=44.8
Q ss_pred CCCHHHHHHHhCCCH-HHHHHHHcCCCCCCHHHHHHHHHHhCCCCcccc
Q 038591 33 KMSQPDLANQINQRP-QVVSEYENGKAVPNQTVLAKMEKAIGVKLRVKI 80 (82)
Q Consensus 33 g~s~~elA~~~gis~-~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e~~ 80 (82)
.+|-.+||+.+|++. ++++.+++|+++++...+.+++.+||.+..|.+
T Consensus 27 ~fS~R~fa~~~G~ss~s~L~~v~~Gkr~Ls~~~~~k~a~~l~L~~~E~~ 75 (271)
T TIGR02147 27 AFSWRFFAEKAGFSSTSYLNDIIKGKKNLTKRMIPKFAEALGLDEKEAA 75 (271)
T ss_pred CcCHHHHHHHhCCCCHHHHHHHHcCCCCCCHHHHHHHHHHcCCCHHHHH
Confidence 699999999999876 999999999999999999999999999988754
No 58
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=97.74 E-value=8.6e-05 Score=37.00 Aligned_cols=31 Identities=16% Similarity=0.147 Sum_probs=22.4
Q ss_pred HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591 24 QIQRARLGKKMSQPDLANQINQRPQVVSEYENG 56 (82)
Q Consensus 24 ~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g 56 (82)
.|..+.+ |+|..++|+.+|+|++||++|.+-
T Consensus 10 ii~l~~~--G~s~~~ia~~lgvs~~Tv~~w~kr 40 (50)
T PF13384_consen 10 IIRLLRE--GWSIREIAKRLGVSRSTVYRWIKR 40 (50)
T ss_dssp HHHHHHH--T--HHHHHHHHTS-HHHHHHHHT-
T ss_pred HHHHHHC--CCCHHHHHHHHCcCHHHHHHHHHH
Confidence 3444444 999999999999999999999864
No 59
>PRK10344 DNA-binding transcriptional regulator Nlp; Provisional
Probab=97.70 E-value=0.0005 Score=38.75 Aligned_cols=58 Identities=16% Similarity=0.034 Sum_probs=46.0
Q ss_pred CCCHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCccc
Q 038591 19 PDTPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVK 79 (82)
Q Consensus 19 ~~~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e~ 79 (82)
.....-|......+|+|...|+...|++.+|+.+... .|-+.-=..||++||+.+.+.
T Consensus 7 DWH~adI~AaL~KrG~sLa~lsr~~Gls~~TL~nAL~---rp~PKgEriIA~aLGv~P~eI 64 (92)
T PRK10344 7 DWHPADIIAGLRKKGTSMAAESRRNGLSSSTLANALS---RPWPKGEMIIAKALGTDPWVI 64 (92)
T ss_pred CCCHHHHHHHHHHcCCcHHHHHHHcCCChHHHHHHHc---CCCchHHHHHHHHHCcCHHHh
Confidence 4455667777777999999999999999999999876 333344467999999998764
No 60
>PRK09526 lacI lac repressor; Reviewed
Probab=97.66 E-value=0.00015 Score=48.40 Aligned_cols=47 Identities=15% Similarity=0.026 Sum_probs=38.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCCCCcc
Q 038591 32 KKMSQPDLANQINQRPQVVSEYENGKAVPNQTV---LAKMEKAIGVKLRV 78 (82)
Q Consensus 32 ~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~---~~~la~~lgv~~~e 78 (82)
+..|.+|+|+.+|||.+|||++.||...++.++ +..+++.||..++.
T Consensus 4 ~~~ti~dIA~~aGVS~~TVSrvLn~~~~vs~~tr~rV~~~a~elgY~pn~ 53 (342)
T PRK09526 4 KPVTLYDVARYAGVSYQTVSRVLNQASHVSAKTREKVEAAMAELNYVPNR 53 (342)
T ss_pred CCCcHHHHHHHhCCCHHHHHHHhcCCCCCCHHHHHHHHHHHHHHCCCcCH
Confidence 357999999999999999999999987676655 66677778876653
No 61
>TIGR01481 ccpA catabolite control protein A. Catabolite control protein A is a LacI family global transcriptional regulator found in Gram-positive bacteria. CcpA is involved in repressing carbohydrate utilization genes [ex: alpha-amylase (amyE), acetyl-coenzyme A synthase (acsA)] and in activating genes involved in transporting excess carbon from the cell [ex: acetate kinase (ackA), alpha-acetolactate synthase (alsS)]. Additionally, disruption of CcpA in Bacillus megaterium, Staphylococcus xylosus, Lactobacillus casei and Lactocacillus pentosus also decreases growth rate, which suggests CcpA is involved in the regulation of other metabolic pathways.
Probab=97.65 E-value=0.0002 Score=47.54 Aligned_cols=45 Identities=16% Similarity=0.164 Sum_probs=37.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCCCCcc
Q 038591 34 MSQPDLANQINQRPQVVSEYENGKAVPNQTV---LAKMEKAIGVKLRV 78 (82)
Q Consensus 34 ~s~~elA~~~gis~~~i~~~e~g~~~p~~~~---~~~la~~lgv~~~e 78 (82)
.|.+|+|+.+|||.+|||++.||...++.++ +.+.++.||..++.
T Consensus 2 ~ti~dIA~~agvS~~TVSrvLn~~~~vs~~tr~rV~~~a~~lgY~pn~ 49 (329)
T TIGR01481 2 VTIYDVAREAGVSMATVSRVVNGNPNVKPATRKKVLEVIKRLDYRPNA 49 (329)
T ss_pred CcHHHHHHHhCCCHHHHHHHhCCCCCCCHHHHHHHHHHHHHHCCCCCH
Confidence 4789999999999999999999987777666 56678888887653
No 62
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=97.65 E-value=0.00022 Score=47.50 Aligned_cols=47 Identities=19% Similarity=0.135 Sum_probs=39.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHH---HHHhCCCCcc
Q 038591 32 KKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKM---EKAIGVKLRV 78 (82)
Q Consensus 32 ~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~l---a~~lgv~~~e 78 (82)
...|.+|+|+.+|||.+|||+..||...++.++-.++ ++.||..++.
T Consensus 5 ~~~Ti~dIA~~agVS~~TVSr~Ln~~~~vs~~tr~~V~~~a~elgY~p~~ 54 (342)
T PRK10014 5 KKITIHDVALAAGVSVSTVSLVLSGKGRISTATGERVNQAIEELGFVRNR 54 (342)
T ss_pred CCCcHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHhCCCcCH
Confidence 3589999999999999999999999888887775544 8888887653
No 63
>PRK09492 treR trehalose repressor; Provisional
Probab=97.62 E-value=0.00023 Score=46.97 Aligned_cols=46 Identities=15% Similarity=0.122 Sum_probs=37.9
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCCCCcc
Q 038591 33 KMSQPDLANQINQRPQVVSEYENGKAVPNQTV---LAKMEKAIGVKLRV 78 (82)
Q Consensus 33 g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~---~~~la~~lgv~~~e 78 (82)
.+|.+|+|+.+|||.+|||++.||...++.++ +.+.++.+|..++.
T Consensus 4 ~~ti~dIA~~agVS~~TVSrvLn~~~~vs~~tr~rV~~~a~elgY~pn~ 52 (315)
T PRK09492 4 KLTIKDIARLSGVGKSTVSRVLNNESGVSEETRERVEAVINQHGFSPSK 52 (315)
T ss_pred CCcHHHHHHHhCCCHHHHhHHhCCCCCCCHHHHHHHHHHHHHHCCCcCH
Confidence 47999999999999999999999987777666 44567788876653
No 64
>PHA00675 hypothetical protein
Probab=97.62 E-value=0.00019 Score=39.29 Aligned_cols=37 Identities=16% Similarity=0.109 Sum_probs=31.6
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591 22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKA 58 (82)
Q Consensus 22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~ 58 (82)
-+.|+.+++..|.|..+||..+|+|+++|++|.+|+.
T Consensus 28 V~~IR~l~~r~G~s~~~IA~~fGVsrstV~~I~~gk~ 64 (78)
T PHA00675 28 VERIRELHEVEGMSYAVLAEKFEQSKGAIAKICRYER 64 (78)
T ss_pred HHHHHHHHHhcCccHHHHHHHhCCCHHHHHHHHccch
Confidence 4556666667899999999999999999999999864
No 65
>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=97.62 E-value=0.00019 Score=35.38 Aligned_cols=34 Identities=24% Similarity=0.259 Sum_probs=24.9
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591 22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENG 56 (82)
Q Consensus 22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g 56 (82)
.+.+..++. .|+|..++|+.+|||++||++|.+.
T Consensus 11 ~~~i~~l~~-~G~si~~IA~~~gvsr~TvyR~l~~ 44 (45)
T PF02796_consen 11 IEEIKELYA-EGMSIAEIAKQFGVSRSTVYRYLNK 44 (45)
T ss_dssp HHHHHHHHH-TT--HHHHHHHTTS-HHHHHHHHCC
T ss_pred HHHHHHHHH-CCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 455666554 5699999999999999999999763
No 66
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=97.62 E-value=0.00023 Score=47.47 Aligned_cols=44 Identities=14% Similarity=0.055 Sum_probs=36.8
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCCCCc
Q 038591 34 MSQPDLANQINQRPQVVSEYENGKAVPNQTV---LAKMEKAIGVKLR 77 (82)
Q Consensus 34 ~s~~elA~~~gis~~~i~~~e~g~~~p~~~~---~~~la~~lgv~~~ 77 (82)
+|.+|+|+.+|+|.+|||++.||...++.++ +.++++.+|..++
T Consensus 2 ~Ti~dIA~~agVS~~TVSrvLn~~~~vs~~tr~~V~~~a~elgY~pn 48 (341)
T PRK10703 2 ATIKDVAKRAGVSTTTVSHVINKTRFVAEETRNAVWAAIKELHYSPS 48 (341)
T ss_pred CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHCCCcC
Confidence 4899999999999999999999977676555 6677778887664
No 67
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=97.62 E-value=0.00024 Score=47.10 Aligned_cols=44 Identities=16% Similarity=0.111 Sum_probs=36.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcCCC---CCCHHH---HHHHHHHhCCCCc
Q 038591 34 MSQPDLANQINQRPQVVSEYENGKA---VPNQTV---LAKMEKAIGVKLR 77 (82)
Q Consensus 34 ~s~~elA~~~gis~~~i~~~e~g~~---~p~~~~---~~~la~~lgv~~~ 77 (82)
+|.+|+|+.+|||.+|||++.||.. .++.++ +.+.++.||..++
T Consensus 1 ~ti~dIA~~aGVS~~TVSrvLn~~~~~~~Vs~~tr~rV~~~a~elgY~pn 50 (328)
T PRK11303 1 MKLDEIARLAGVSRTTASYVINGKAKQYRVSDKTVEKVMAVVREHNYHPN 50 (328)
T ss_pred CCHHHHHHHhCCCHHHHHHHHcCCCCCCCcCHHHHHHHHHHHHHhCCCCC
Confidence 5889999999999999999999975 466655 5566778887665
No 68
>TIGR02405 trehalos_R_Ecol trehalose operon repressor, proteobacterial. This family consists of repressors of the LacI family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gammaproteobacteria and does not include the GntR family TreR of Bacillus subtilis
Probab=97.61 E-value=0.00026 Score=46.83 Aligned_cols=45 Identities=13% Similarity=0.097 Sum_probs=36.9
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCCCCcc
Q 038591 34 MSQPDLANQINQRPQVVSEYENGKAVPNQTV---LAKMEKAIGVKLRV 78 (82)
Q Consensus 34 ~s~~elA~~~gis~~~i~~~e~g~~~p~~~~---~~~la~~lgv~~~e 78 (82)
.|.+|+|+.+|+|++|||++.||...++.++ +...++.+|..++.
T Consensus 2 ~ti~dIA~~agVS~sTVSr~Ln~~~~vs~~tr~rV~~~a~~lgY~pn~ 49 (311)
T TIGR02405 2 LTIKDIARLAGVGKSTVSRVLNNEPKVSIETRERVEQVIQQSGFVPSK 49 (311)
T ss_pred CcHHHHHHHhCCCHHHHHHHhCCCCCCCHHHHHHHHHHHHHHCCCcCH
Confidence 5899999999999999999999977666655 55567778877653
No 69
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=97.61 E-value=0.00024 Score=47.56 Aligned_cols=45 Identities=11% Similarity=0.083 Sum_probs=37.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCCCCcc
Q 038591 34 MSQPDLANQINQRPQVVSEYENGKAVPNQTV---LAKMEKAIGVKLRV 78 (82)
Q Consensus 34 ~s~~elA~~~gis~~~i~~~e~g~~~p~~~~---~~~la~~lgv~~~e 78 (82)
.|.+|+|+.+|||.+|||++.||...++.++ +.+.++.||..++-
T Consensus 2 ~ti~dIA~~aGVS~~TVSrvLn~~~~Vs~~tr~rV~~~a~elgY~pn~ 49 (343)
T PRK10727 2 ATIKDVARLAGVSVATVSRVINNSPKASEASRLAVHSAMESLSYHPNA 49 (343)
T ss_pred CCHHHHHHHhCCCHHHHHHHhCCCCCCCHHHHHHHHHHHHHHCCCCCH
Confidence 4889999999999999999999987777665 66667788877653
No 70
>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=97.61 E-value=0.00075 Score=37.35 Aligned_cols=50 Identities=8% Similarity=0.019 Sum_probs=40.7
Q ss_pred HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCC-CCCCHHHHHHHHHHhC
Q 038591 23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYENGK-AVPNQTVLAKMEKAIG 73 (82)
Q Consensus 23 ~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~-~~p~~~~~~~la~~lg 73 (82)
..+..++. ..+|..++|+.+|+|..||++..++. ..++.++-.++-.+..
T Consensus 10 ~I~e~l~~-~~~ti~dvA~~~gvS~~TVsr~L~~~~~~Vs~~Tr~rV~~aa~ 60 (80)
T TIGR02844 10 EIGKYIVE-TKATVRETAKVFGVSKSTVHKDVTERLPEINPELAEEVKEVLD 60 (80)
T ss_pred HHHHHHHH-CCCCHHHHHHHhCCCHHHHHHHhcCCCCCCCHHHHHHHHHHHc
Confidence 34455667 88999999999999999999999985 6788888777766554
No 71
>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B.
Probab=97.57 E-value=0.00021 Score=37.54 Aligned_cols=42 Identities=29% Similarity=0.276 Sum_probs=30.2
Q ss_pred hCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 038591 31 GKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKL 76 (82)
Q Consensus 31 ~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~ 76 (82)
..| ++..||+.+|||+++|++| + ..++......|..+-+-.+
T Consensus 8 ~~G-~~~~lAkalGVs~~aVs~W--~-~~IP~~ra~~Ie~~T~G~l 49 (60)
T PF14549_consen 8 YFG-GQSKLAKALGVSPQAVSQW--G-ERIPAERAYQIEKLTNGKL 49 (60)
T ss_dssp HHS-SHHHHHHHHTS-HHHHHHH--H-TS--HHHHHHHHHHTTTSS
T ss_pred HHC-CHHHHHHHHCCCHHHHHHh--c-CccCHHHHHHHHHHhCCce
Confidence 345 7899999999999999999 3 4566777788877665433
No 72
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=97.57 E-value=0.00019 Score=47.72 Aligned_cols=46 Identities=13% Similarity=0.156 Sum_probs=38.2
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCCCCcc
Q 038591 33 KMSQPDLANQINQRPQVVSEYENGKAVPNQTV---LAKMEKAIGVKLRV 78 (82)
Q Consensus 33 g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~---~~~la~~lgv~~~e 78 (82)
..|.+|+|+.+|||.+|||++.||...++.++ +.++++.||..++.
T Consensus 5 ~~ti~dIA~~agVS~~TVSrvLn~~~~vs~~tr~rV~~~a~elgY~pn~ 53 (331)
T PRK14987 5 RPVLQDVADRVGVTKMTVSRFLRNPEQVSVALRGKIAAALDELGYIPNR 53 (331)
T ss_pred CCcHHHHHHHhCCCHHHhhhhhCCCCCCCHHHHHHHHHHHHHhCCCccH
Confidence 47999999999999999999999987776665 56677888877653
No 73
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=97.56 E-value=0.00047 Score=37.53 Aligned_cols=40 Identities=20% Similarity=0.256 Sum_probs=32.0
Q ss_pred HHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHH
Q 038591 28 ARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKME 69 (82)
Q Consensus 28 ~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la 69 (82)
.|...|+|+.|+|+.+|+|+++|..+.++ .+....+.+++
T Consensus 27 ~R~~eGlS~kEIAe~LGIS~~TVk~~l~~--~~~~~~~~~~~ 66 (73)
T TIGR03879 27 AREEAGKTASEIAEELGRTEQTVRNHLKG--ETKAGGLVKLA 66 (73)
T ss_pred HHHHcCCCHHHHHHHHCcCHHHHHHHHhc--CcccchHHHHH
Confidence 36679999999999999999999999985 34444555554
No 74
>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=97.56 E-value=0.00054 Score=41.11 Aligned_cols=54 Identities=2% Similarity=-0.029 Sum_probs=44.1
Q ss_pred CCCCHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHH
Q 038591 18 EPDTPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKA 71 (82)
Q Consensus 18 ~~~~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~ 71 (82)
.-+....+..+....|++++++|..+|+|++|++++-++...++.+.-.++..+
T Consensus 21 ~Glp~~~~~~l~~~l~ls~~el~~~lgis~~Tl~R~~~~~~~Ls~~~serl~~l 74 (133)
T TIGR02293 21 RGLPIGALDRLAHLLAIGKAEIFKATGIPKATLQRRKMAHQRLSSEESDRLARV 74 (133)
T ss_pred cCCCHHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHhhcCCCCCHHHHHHHHHH
Confidence 345578888899999999999999999999999999987667776665555443
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=97.53 E-value=0.00039 Score=43.75 Aligned_cols=51 Identities=10% Similarity=0.012 Sum_probs=35.4
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHh
Q 038591 22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAI 72 (82)
Q Consensus 22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~l 72 (82)
.+.||.++..++|+|.++++.+|||.++||+|.+-....+...=..|-..|
T Consensus 120 keeIK~fl~~h~IsQ~~V~q~TGisQS~lSq~L~kGt~Mk~qKR~alY~Wy 170 (180)
T PF04814_consen 120 KEEIKAFLQQHNISQREVVQVTGISQSHLSQHLNKGTPMKEQKRRALYRWY 170 (180)
T ss_dssp HHHHHHHHHHCT--CHHHHHHHT--HHHHHHHHCTB----HHHHHHHHHHH
T ss_pred HHHHHHHHHHcCCcHHHHHHHhhhhHHHHHHHHHcCCCccHHHHHHHHHHH
Confidence 889999999999999999999999999999999755555555544444443
No 76
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=97.51 E-value=0.00042 Score=46.42 Aligned_cols=44 Identities=20% Similarity=0.224 Sum_probs=36.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCCCCc
Q 038591 34 MSQPDLANQINQRPQVVSEYENGKAVPNQTV---LAKMEKAIGVKLR 77 (82)
Q Consensus 34 ~s~~elA~~~gis~~~i~~~e~g~~~p~~~~---~~~la~~lgv~~~ 77 (82)
.|.+|+|+.+|||.+|||++.||...++.++ +.+.++.+|..++
T Consensus 2 ~ti~dIA~~aGVS~~TVSrvLn~~~~Vs~~tr~kV~~~a~elgY~pn 48 (346)
T PRK10401 2 ITIRDVARQAGVSVATVSRVLNNSALVSADTREAVMKAVSELGYRPN 48 (346)
T ss_pred CCHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCCC
Confidence 5889999999999999999999977666555 6666777887665
No 77
>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=97.50 E-value=0.00086 Score=36.66 Aligned_cols=47 Identities=11% Similarity=0.253 Sum_probs=36.6
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhC------CCHHHHHHHHcCCCCCCHHHHHHHHH
Q 038591 22 PRQIQRARLGKKMSQPDLANQIN------QRPQVVSEYENGKAVPNQTVLAKMEK 70 (82)
Q Consensus 22 ~~~lk~~r~~~g~s~~elA~~~g------is~~~i~~~e~g~~~p~~~~~~~la~ 70 (82)
+..++..|...|+||.+++..+| .|+++|+++|+ -..+...+.+|-=
T Consensus 13 a~~fk~rRi~LG~TQ~dVg~al~~~~G~~~SQttI~RFE~--L~LS~kn~~klkP 65 (75)
T PF00157_consen 13 AKEFKQRRIKLGYTQADVGAALGRLYGKEFSQTTICRFEA--LQLSFKNMCKLKP 65 (75)
T ss_dssp HHHHHHHHHHTT--HHHHHHHHHHHHSSGGSHHHHHHHHT--TTSCHHHHHHHHH
T ss_pred HHHHHHhhhhcccCHHHHhHHHHHhcCccccchhhhhhHh--cccCHHHHHHHHH
Confidence 57788999999999999999886 58999999998 4567777666543
No 78
>TIGR02417 fruct_sucro_rep D-fructose-responsive transcription factor. Members of this family belong the lacI helix-turn-helix family (pfam00356) of DNA-binding transcriptional regulators. All members are from the proteobacteria. Characterized members act as positive and negative transcriptional regulators of fructose and sucrose transport and metabolism. Sucrose is a disaccharide composed of fructose and glucose; D-fructose-1-phosphate rather than an intact sucrose moiety has been shown to act as the inducer.
Probab=97.42 E-value=0.00058 Score=45.33 Aligned_cols=44 Identities=20% Similarity=0.204 Sum_probs=35.8
Q ss_pred CHHHHHHHhCCCHHHHHHHHcCCC---CCCHHH---HHHHHHHhCCCCcc
Q 038591 35 SQPDLANQINQRPQVVSEYENGKA---VPNQTV---LAKMEKAIGVKLRV 78 (82)
Q Consensus 35 s~~elA~~~gis~~~i~~~e~g~~---~p~~~~---~~~la~~lgv~~~e 78 (82)
|.+|+|+.+|||.+|||++.||.. .++.++ +.++++.+|..++.
T Consensus 1 ti~dIA~~aGVS~~TVSrvLn~~~~~~~vs~~tr~rV~~~a~~lgY~pn~ 50 (327)
T TIGR02417 1 TLSDIAKLAGVSKTTASYVINGKAKEYRISQETVERVMAVVREQGYQPNI 50 (327)
T ss_pred CHHHHHHHhCCCHHHHHHHHcCCCCCCccCHHHHHHHHHHHHHhCCCCCH
Confidence 578999999999999999999975 466665 55678888887753
No 79
>PHA02591 hypothetical protein; Provisional
Probab=97.39 E-value=0.00053 Score=37.68 Aligned_cols=31 Identities=13% Similarity=0.179 Sum_probs=26.4
Q ss_pred HHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 25 IQRARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 25 lk~~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
+.....+.|+||.++|+.+|++..+|++|..
T Consensus 51 vA~eL~eqGlSqeqIA~~LGVsqetVrKYL~ 81 (83)
T PHA02591 51 VTHELARKGFTVEKIASLLGVSVRKVRRYLE 81 (83)
T ss_pred HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHh
Confidence 4444556899999999999999999999975
No 80
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=97.39 E-value=0.00028 Score=34.62 Aligned_cols=31 Identities=23% Similarity=0.249 Sum_probs=20.9
Q ss_pred HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 24 QIQRARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 24 ~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
.|..++ ..|+|+.++|+.+|++++||+++..
T Consensus 12 ~I~~l~-~~G~s~~~IA~~lg~s~sTV~relk 42 (44)
T PF13936_consen 12 QIEALL-EQGMSIREIAKRLGRSRSTVSRELK 42 (44)
T ss_dssp HHHHHH-CS---HHHHHHHTT--HHHHHHHHH
T ss_pred HHHHHH-HcCCCHHHHHHHHCcCcHHHHHHHh
Confidence 355554 5899999999999999999999763
No 81
>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=97.38 E-value=0.00056 Score=33.79 Aligned_cols=33 Identities=18% Similarity=0.347 Sum_probs=26.8
Q ss_pred HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 23 ~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
..|..+.+.-++|+.++|+.+|+|.++++++.+
T Consensus 7 ~Il~~l~~~~~~t~~ela~~~~is~~tv~~~l~ 39 (48)
T PF13412_consen 7 KILNYLRENPRITQKELAEKLGISRSTVNRYLK 39 (48)
T ss_dssp HHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 456778888889999999999999999998764
No 82
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=97.36 E-value=0.00079 Score=45.70 Aligned_cols=44 Identities=18% Similarity=0.191 Sum_probs=36.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCCCCc
Q 038591 34 MSQPDLANQINQRPQVVSEYENGKAVPNQTV---LAKMEKAIGVKLR 77 (82)
Q Consensus 34 ~s~~elA~~~gis~~~i~~~e~g~~~p~~~~---~~~la~~lgv~~~ 77 (82)
.|.+|+|+.+|||.+|||++.||...++.++ +.+.++.+|.-++
T Consensus 1 ~TikDVA~~AGVS~sTVSrvln~~~~Vs~eTr~kV~~a~~elgY~pN 47 (333)
T COG1609 1 ATIKDVAKLAGVSKATVSRVLNGSPYVSEETREKVLAAIKELGYRPN 47 (333)
T ss_pred CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHCCCCC
Confidence 3789999999999999999999988777665 6666777777654
No 83
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=97.36 E-value=0.00034 Score=42.55 Aligned_cols=46 Identities=13% Similarity=0.226 Sum_probs=34.0
Q ss_pred HhCCCCHHHHHHHhCCCHHHHHHHHcCCCC---CCHHHHHHHHHHhCCCC
Q 038591 30 LGKKMSQPDLANQINQRPQVVSEYENGKAV---PNQTVLAKMEKAIGVKL 76 (82)
Q Consensus 30 ~~~g~s~~elA~~~gis~~~i~~~e~g~~~---p~~~~~~~la~~lgv~~ 76 (82)
...|+||+|+|+.+|+|+++|+.||++-.. -...++ ++++.++.++
T Consensus 18 r~~GlTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~tl-~~~~~l~a~~ 66 (141)
T PRK03975 18 RERGLTQQEIADILGTSRANVSSIEKRARENIEKARETL-AFAETLNAPV 66 (141)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH-HHHHHcCCCe
Confidence 369999999999999999999999986211 112233 6777777654
No 84
>COG5606 Uncharacterized conserved small protein [Function unknown]
Probab=97.31 E-value=0.00062 Score=38.15 Aligned_cols=57 Identities=21% Similarity=0.171 Sum_probs=49.0
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCC-CCCHHHHHHHHHHhCCCCcc
Q 038591 22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKA-VPNQTVLAKMEKAIGVKLRV 78 (82)
Q Consensus 22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~-~p~~~~~~~la~~lgv~~~e 78 (82)
+..|..+.+..+++|+++|+.+||+++.+|.+.+|+. ..+.+.+.......|..++-
T Consensus 30 ~~~i~~~i~q~~l~Q~qiae~lgV~qprvS~l~~gk~~~fs~dkLvtml~~~g~ei~~ 87 (91)
T COG5606 30 MMAIKQWIEQAALSQAQIAELLGVTQPRVSDLARGKIQDFSIDKLVTMLARAGQEIDV 87 (91)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCCCchHHHHHhcchhHhhHHHHHHHHHHcCCcccc
Confidence 6677888899999999999999999999999999964 56788888888888877653
No 85
>COG4197 Uncharacterized protein conserved in bacteria, prophage-related [Function unknown]
Probab=97.27 E-value=0.00021 Score=40.39 Aligned_cols=44 Identities=20% Similarity=0.261 Sum_probs=38.9
Q ss_pred CHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhC--CCCcc
Q 038591 35 SQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIG--VKLRV 78 (82)
Q Consensus 35 s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lg--v~~~e 78 (82)
.|+.+|..+|+|+++|++|-+|.+.........|.++.+ |+..|
T Consensus 14 ~q~a~a~LLgvsp~~vnQw~~g~r~~~a~r~~aIerAt~g~Vs~~e 59 (96)
T COG4197 14 GQKALARLLGVSPPSVNQWIKGRRQVAAERALAIERATSGQVSREE 59 (96)
T ss_pred cHHHHHHHHccCchHHHHHhhheeecCcccchHHHHHhcCCccHHH
Confidence 488899999999999999999999999899999999888 65544
No 86
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=97.23 E-value=0.00049 Score=45.79 Aligned_cols=44 Identities=14% Similarity=0.145 Sum_probs=35.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcCCCC--CCHHH---HHHHHHHhCCCCc
Q 038591 34 MSQPDLANQINQRPQVVSEYENGKAV--PNQTV---LAKMEKAIGVKLR 77 (82)
Q Consensus 34 ~s~~elA~~~gis~~~i~~~e~g~~~--p~~~~---~~~la~~lgv~~~ 77 (82)
.|.+|+|+.+|||.+|||++.||... ++.++ +.++++.||..++
T Consensus 2 ~ti~dIA~~agVS~~TVSrvln~~~~~~vs~~tr~rV~~~a~~lgY~pn 50 (327)
T PRK10339 2 ATLKDIAIEAGVSLATVSRVLNDDPTLNVKEETKHRILEIAEKLEYKTS 50 (327)
T ss_pred CCHHHHHHHhCCCHHhhhhhhcCCCCCCcCHHHHHHHHHHHHHhCCCCc
Confidence 48899999999999999999998742 55444 6677888887665
No 87
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=97.20 E-value=0.0012 Score=43.70 Aligned_cols=41 Identities=15% Similarity=0.124 Sum_probs=33.9
Q ss_pred HHHHHHhCCCHHHHHHHHcCCCCCCHHH---HHHHHHHhCCCCc
Q 038591 37 PDLANQINQRPQVVSEYENGKAVPNQTV---LAKMEKAIGVKLR 77 (82)
Q Consensus 37 ~elA~~~gis~~~i~~~e~g~~~p~~~~---~~~la~~lgv~~~ 77 (82)
+|+|+.+|||.+|||++.||...++.++ +.+.++.+|..++
T Consensus 2 ~dIA~~agVS~~TVSrvLn~~~~vs~~tr~rV~~~a~~lgY~pn 45 (327)
T PRK10423 2 KDVARLAGVSTSTVSHVINKDRFVSEAITAKVEAAIKELNYAPS 45 (327)
T ss_pred hhHHHHhCCcHHHHHHHhCCCCCCCHHHHHHHHHHHHHHCCCcc
Confidence 6899999999999999999987777666 5556777887665
No 88
>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=97.15 E-value=0.001 Score=32.23 Aligned_cols=23 Identities=9% Similarity=0.297 Sum_probs=20.8
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcC
Q 038591 34 MSQPDLANQINQRPQVVSEYENG 56 (82)
Q Consensus 34 ~s~~elA~~~gis~~~i~~~e~g 56 (82)
+|..|+|+.+||+++||.+|++.
T Consensus 1 ~s~~e~a~~lgvs~~tl~~~~~~ 23 (49)
T cd04762 1 LTTKEAAELLGVSPSTLRRWVKE 23 (49)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHc
Confidence 57899999999999999999854
No 89
>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=97.11 E-value=0.00067 Score=38.19 Aligned_cols=25 Identities=16% Similarity=0.137 Sum_probs=19.1
Q ss_pred hCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 31 GKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 31 ~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
+.||||.|+|+++|.|+++|+++..
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 4799999999999999999999875
No 90
>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=97.07 E-value=0.00089 Score=34.86 Aligned_cols=26 Identities=12% Similarity=0.175 Sum_probs=23.9
Q ss_pred hCCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591 31 GKKMSQPDLANQINQRPQVVSEYENG 56 (82)
Q Consensus 31 ~~g~s~~elA~~~gis~~~i~~~e~g 56 (82)
-.|+++.++|+.+|++.+||+.|..-
T Consensus 11 ~~G~~~~eIA~~Lg~~~~TV~~W~~r 36 (58)
T PF06056_consen 11 LQGWSIKEIAEELGVPRSTVYSWKDR 36 (58)
T ss_pred HcCCCHHHHHHHHCCChHHHHHHHHh
Confidence 36999999999999999999999864
No 91
>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=97.04 E-value=0.00011 Score=41.52 Aligned_cols=46 Identities=13% Similarity=0.143 Sum_probs=35.6
Q ss_pred HhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCccc
Q 038591 30 LGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVK 79 (82)
Q Consensus 30 ~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e~ 79 (82)
.-..++|..+|+.+|++.++||+|-++ -...+..++.+|+..+.+.
T Consensus 20 rlA~~gq~~vA~~~Gv~eStISR~k~~----~~~~~a~lLa~L~~~v~~~ 65 (91)
T PF05269_consen 20 RLASVGQKKVAEAMGVDESTISRWKND----FIEKMAMLLAALELGVEDS 65 (91)
T ss_dssp HHHHHHHHHHHHHHTSSTTTHHHHHHH----HHHHHHHHHHHTTTTHHHH
T ss_pred HHHHHhhHHHHHHhCCCHHHHHHHHhh----HHHHHHHHHHHHHhccccc
Confidence 345678999999999999999999764 3456677777777766543
No 92
>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=97.01 E-value=0.0027 Score=30.74 Aligned_cols=33 Identities=9% Similarity=-0.072 Sum_probs=27.0
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591 22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYE 54 (82)
Q Consensus 22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e 54 (82)
...|....+..+.++.+.|+.+|||++|+++-.
T Consensus 7 ~~~i~~aL~~~~gn~~~aA~~Lgisr~tL~~kl 39 (42)
T PF02954_consen 7 KQLIRQALERCGGNVSKAARLLGISRRTLYRKL 39 (42)
T ss_dssp HHHHHHHHHHTTT-HHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHH
Confidence 456888889999999999999999999998753
No 93
>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=97.00 E-value=0.0019 Score=39.14 Aligned_cols=26 Identities=27% Similarity=0.350 Sum_probs=24.7
Q ss_pred hCCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591 31 GKKMSQPDLANQINQRPQVVSEYENG 56 (82)
Q Consensus 31 ~~g~s~~elA~~~gis~~~i~~~e~g 56 (82)
..|+||+|+|+.+|+|+++|+.+++.
T Consensus 19 ~~GlTq~EIAe~LgiS~stV~~~e~r 44 (137)
T TIGR00721 19 EKGLSQKEIAKELKTTRANVSAIEKR 44 (137)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHHh
Confidence 59999999999999999999999975
No 94
>PF12728 HTH_17: Helix-turn-helix domain
Probab=96.99 E-value=0.0016 Score=32.51 Aligned_cols=28 Identities=11% Similarity=0.201 Sum_probs=23.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcCCCCCC
Q 038591 34 MSQPDLANQINQRPQVVSEYENGKAVPN 61 (82)
Q Consensus 34 ~s~~elA~~~gis~~~i~~~e~g~~~p~ 61 (82)
+|..|+|+.+|||++||.+|.+....|.
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 6889999999999999999987554444
No 95
>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=96.87 E-value=0.0023 Score=31.04 Aligned_cols=27 Identities=11% Similarity=0.188 Sum_probs=23.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcCCCCC
Q 038591 34 MSQPDLANQINQRPQVVSEYENGKAVP 60 (82)
Q Consensus 34 ~s~~elA~~~gis~~~i~~~e~g~~~p 60 (82)
+|..|+|+.+|+|+++|.+|.+....|
T Consensus 2 lt~~e~a~~lgis~~ti~~~~~~g~i~ 28 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTVYRLIHEGELP 28 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHcCCCC
Confidence 688999999999999999999654444
No 96
>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=96.85 E-value=0.0013 Score=38.93 Aligned_cols=22 Identities=18% Similarity=0.306 Sum_probs=20.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 038591 34 MSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 34 ~s~~elA~~~gis~~~i~~~e~ 55 (82)
||.+|||+.+|+|++||++|-.
T Consensus 1 MT~eELA~~tG~srQTINrWvR 22 (122)
T PF07037_consen 1 MTPEELAELTGYSRQTINRWVR 22 (122)
T ss_pred CCHHHHHHHhCccHHHHHHHHH
Confidence 6899999999999999999975
No 97
>PF13518 HTH_28: Helix-turn-helix domain
Probab=96.82 E-value=0.0042 Score=30.74 Aligned_cols=24 Identities=13% Similarity=0.148 Sum_probs=22.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 32 KKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 32 ~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
.|.|..++|..+|||+++|.+|.+
T Consensus 11 ~g~s~~~~a~~~gis~~tv~~w~~ 34 (52)
T PF13518_consen 11 EGESVREIAREFGISRSTVYRWIK 34 (52)
T ss_pred cCCCHHHHHHHHCCCHhHHHHHHH
Confidence 477999999999999999999975
No 98
>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=96.79 E-value=0.0021 Score=29.61 Aligned_cols=23 Identities=22% Similarity=0.326 Sum_probs=17.9
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHc
Q 038591 33 KMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 33 g~s~~elA~~~gis~~~i~~~e~ 55 (82)
.+|..|+|+.+|+++.||++...
T Consensus 2 ~mtr~diA~~lG~t~ETVSR~l~ 24 (32)
T PF00325_consen 2 PMTRQDIADYLGLTRETVSRILK 24 (32)
T ss_dssp E--HHHHHHHHTS-HHHHHHHHH
T ss_pred CcCHHHHHHHhCCcHHHHHHHHH
Confidence 47899999999999999999764
No 99
>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=96.77 E-value=0.0034 Score=30.70 Aligned_cols=23 Identities=22% Similarity=0.264 Sum_probs=20.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcC
Q 038591 34 MSQPDLANQINQRPQVVSEYENG 56 (82)
Q Consensus 34 ~s~~elA~~~gis~~~i~~~e~g 56 (82)
+|..|+|+.+|++++||..|++-
T Consensus 1 ~~~~e~a~~~gv~~~tlr~~~~~ 23 (49)
T cd04761 1 YTIGELAKLTGVSPSTLRYYERI 23 (49)
T ss_pred CcHHHHHHHHCcCHHHHHHHHHC
Confidence 57889999999999999999864
No 100
>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=96.76 E-value=0.0021 Score=33.68 Aligned_cols=24 Identities=13% Similarity=0.368 Sum_probs=22.1
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHcC
Q 038591 33 KMSQPDLANQINQRPQVVSEYENG 56 (82)
Q Consensus 33 g~s~~elA~~~gis~~~i~~~e~g 56 (82)
+++..++|+.+|||.+||+.|-+-
T Consensus 22 ~i~lkdIA~~Lgvs~~tIr~WK~~ 45 (60)
T PF10668_consen 22 KIKLKDIAEKLGVSESTIRKWKSR 45 (60)
T ss_pred CccHHHHHHHHCCCHHHHHHHhhh
Confidence 589999999999999999999764
No 101
>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=96.75 E-value=0.006 Score=32.02 Aligned_cols=22 Identities=18% Similarity=0.439 Sum_probs=20.2
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 038591 34 MSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 34 ~s~~elA~~~gis~~~i~~~e~ 55 (82)
++..|+|+.+|||++||..|+.
T Consensus 1 ~~i~evA~~~gvs~~tlR~~~~ 22 (67)
T cd04764 1 YTIKEVSEIIGVKPHTLRYYEK 22 (67)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 4788999999999999999985
No 102
>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=96.75 E-value=0.0017 Score=30.96 Aligned_cols=23 Identities=17% Similarity=0.341 Sum_probs=19.2
Q ss_pred CHHHHHHHhCCCHHHHHHHHcCC
Q 038591 35 SQPDLANQINQRPQVVSEYENGK 57 (82)
Q Consensus 35 s~~elA~~~gis~~~i~~~e~g~ 57 (82)
|..|+|+.+|||+.||..||.-.
T Consensus 1 ti~e~A~~~gvs~~tlR~ye~~G 23 (38)
T PF00376_consen 1 TIGEVAKLLGVSPRTLRYYEREG 23 (38)
T ss_dssp EHHHHHHHHTS-HHHHHHHHHTT
T ss_pred CHHHHHHHHCCCHHHHHHHHHCC
Confidence 45789999999999999999753
No 103
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=96.73 E-value=0.0063 Score=30.19 Aligned_cols=29 Identities=14% Similarity=0.196 Sum_probs=24.4
Q ss_pred HHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 27 RARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 27 ~~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
.++-..++|..|+|+.+|+|.++|+++..
T Consensus 14 ~~~y~~~~t~~eIa~~lg~s~~~V~~~~~ 42 (50)
T PF04545_consen 14 RLRYFEGLTLEEIAERLGISRSTVRRILK 42 (50)
T ss_dssp HHHHTST-SHHHHHHHHTSCHHHHHHHHH
T ss_pred HHHhcCCCCHHHHHHHHCCcHHHHHHHHH
Confidence 34557899999999999999999999875
No 104
>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=96.71 E-value=0.0037 Score=35.18 Aligned_cols=27 Identities=11% Similarity=0.180 Sum_probs=24.8
Q ss_pred HhCCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591 30 LGKKMSQPDLANQINQRPQVVSEYENG 56 (82)
Q Consensus 30 ~~~g~s~~elA~~~gis~~~i~~~e~g 56 (82)
...|+|..++|+.+|+|++||++|.+|
T Consensus 47 l~~G~S~~eIA~~LgISrsTIyRi~R~ 73 (88)
T TIGR02531 47 LKQGKTYSDIEAETGASTATISRVKRC 73 (88)
T ss_pred HHCCCCHHHHHHHHCcCHHHHHHHHHh
Confidence 457999999999999999999999885
No 105
>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=96.70 E-value=0.0037 Score=31.53 Aligned_cols=32 Identities=9% Similarity=0.152 Sum_probs=24.6
Q ss_pred HHHHHHHhCC-CCHHHHHHHhCCCHHHHHHHHc
Q 038591 24 QIQRARLGKK-MSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 24 ~lk~~r~~~g-~s~~elA~~~gis~~~i~~~e~ 55 (82)
.|..+....+ +|..+||+.+|||..||.+..+
T Consensus 5 il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i~ 37 (55)
T PF08279_consen 5 ILKLLLESKEPITAKELAEELGVSRRTIRRDIK 37 (55)
T ss_dssp HHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHHH
T ss_pred HHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHH
Confidence 3555655554 9999999999999999998754
No 106
>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function.
Probab=96.63 E-value=0.0039 Score=36.23 Aligned_cols=35 Identities=11% Similarity=0.113 Sum_probs=29.2
Q ss_pred HHHHHHHH--HhCCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591 22 PRQIQRAR--LGKKMSQPDLANQINQRPQVVSEYENG 56 (82)
Q Consensus 22 ~~~lk~~r--~~~g~s~~elA~~~gis~~~i~~~e~g 56 (82)
.+.+..+| .-.|+||.+.|..+|||++|+.++.+.
T Consensus 44 ~dElEAiRL~D~egl~QeeaA~~MgVSR~T~~ril~~ 80 (106)
T PF02001_consen 44 VDELEAIRLVDYEGLSQEEAAERMGVSRPTFQRILES 80 (106)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHcCCcHHHHHHHHHH
Confidence 56666655 468999999999999999999999863
No 107
>COG1356 tfx Transcriptional regulator [DNA replication, recombination and repair]
Probab=96.57 E-value=0.0025 Score=38.19 Aligned_cols=28 Identities=21% Similarity=0.228 Sum_probs=25.2
Q ss_pred HHhCCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591 29 RLGKKMSQPDLANQINQRPQVVSEYENG 56 (82)
Q Consensus 29 r~~~g~s~~elA~~~gis~~~i~~~e~g 56 (82)
..++|+||+++|+.+|.++..||.+|..
T Consensus 19 lRekG~tQ~eIA~~L~TTraNvSaIEkr 46 (143)
T COG1356 19 LREKGLTQSEIARILKTTRANVSAIEKR 46 (143)
T ss_pred hhhccccHHHHHHHHccchhhHHHHHHH
Confidence 3568999999999999999999999974
No 108
>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=96.52 E-value=0.0048 Score=32.29 Aligned_cols=22 Identities=14% Similarity=0.253 Sum_probs=20.4
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 038591 34 MSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 34 ~s~~elA~~~gis~~~i~~~e~ 55 (82)
+|..|+|+.+||+++|+..|++
T Consensus 1 ~s~~eva~~~gvs~~tlr~w~~ 22 (68)
T cd01104 1 YTIGAVARLTGVSPDTLRAWER 22 (68)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 4788999999999999999996
No 109
>PRK08558 adenine phosphoribosyltransferase; Provisional
Probab=96.50 E-value=0.015 Score=38.15 Aligned_cols=41 Identities=17% Similarity=0.354 Sum_probs=35.6
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhC
Q 038591 33 KMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIG 73 (82)
Q Consensus 33 g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lg 73 (82)
-+|-+||++.+|++.+.+++|-+|...|+.+....+.+.+.
T Consensus 23 ~~ty~el~~~~g~p~~~l~RYv~g~~~P~~~~a~~~~~~l~ 63 (238)
T PRK08558 23 TYTYEELSSITGLPESVLNRYVNGHVLPSVERAREIVEKLG 63 (238)
T ss_pred ccCHHHHHHHHCCCHHHHHHHHcCCcCCCHHHHHHHHHHHH
Confidence 37999999999999999999999999999887666665444
No 110
>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=96.49 E-value=0.0024 Score=32.50 Aligned_cols=34 Identities=21% Similarity=0.258 Sum_probs=24.4
Q ss_pred HHHHHH-HHhCCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591 23 RQIQRA-RLGKKMSQPDLANQINQRPQVVSEYENG 56 (82)
Q Consensus 23 ~~lk~~-r~~~g~s~~elA~~~gis~~~i~~~e~g 56 (82)
+.+.-+ +-+.|.++.++|...||+.+||+.|...
T Consensus 11 eK~~iI~~~e~g~s~~~ia~~fgv~~sTv~~I~K~ 45 (53)
T PF04218_consen 11 EKLEIIKRLEEGESKRDIAREFGVSRSTVSTILKN 45 (53)
T ss_dssp HHHHHHHHHHCTT-HHHHHHHHT--CCHHHHHHHC
T ss_pred HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHh
Confidence 344443 2468889999999999999999999875
No 111
>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=96.40 E-value=0.036 Score=31.07 Aligned_cols=58 Identities=16% Similarity=0.143 Sum_probs=40.6
Q ss_pred HHHHHHHHHhCCCCHHHHHHHh-CCCHHHHHHHHcCCCCCCH------HHHHHHHHHhCCCCccc
Q 038591 22 PRQIQRARLGKKMSQPDLANQI-NQRPQVVSEYENGKAVPNQ------TVLAKMEKAIGVKLRVK 79 (82)
Q Consensus 22 ~~~lk~~r~~~g~s~~elA~~~-gis~~~i~~~e~g~~~p~~------~~~~~la~~lgv~~~e~ 79 (82)
...|+..+...+++|+.||+.+ |.|+.+++.+.+.-..-+. +...++-..|..+-+++
T Consensus 15 ~~~ik~~L~~~~IsQ~~Fa~~vL~rsqgtlsdlL~~PKpW~~L~~~gre~y~RM~nWL~~~e~~r 79 (87)
T PF02376_consen 15 ARRIKEWLKRNNISQRVFAKKVLNRSQGTLSDLLRKPKPWNKLKPKGREPYIRMYNWLSLPEEER 79 (87)
T ss_dssp HHHHHHHHHHTT--HHHHHHHTTSS-HHHHHHHHHSCCTTCHHHHHHHHHHHHHHHHHCSTHHHH
T ss_pred HHHHHHHHHHcCCCHHHHHHHHhccChhHHHHHhCCCCCHHHcCccccHHHHHHHHHhcCCHHHH
Confidence 6788999999999999999976 9999999999985332222 22566777776665443
No 112
>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=96.37 E-value=0.0066 Score=31.05 Aligned_cols=24 Identities=21% Similarity=0.337 Sum_probs=21.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 32 KKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 32 ~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
++.|..|||+.+|||++|++....
T Consensus 22 R~~tl~elA~~lgis~st~~~~LR 45 (53)
T PF04967_consen 22 RRITLEELAEELGISKSTVSEHLR 45 (53)
T ss_pred CcCCHHHHHHHhCCCHHHHHHHHH
Confidence 478999999999999999998764
No 113
>PRK01381 Trp operon repressor; Provisional
Probab=96.37 E-value=0.0094 Score=34.24 Aligned_cols=53 Identities=8% Similarity=0.077 Sum_probs=38.4
Q ss_pred HHHHHHHHH--hCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCC
Q 038591 22 PRQIQRARL--GKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGV 74 (82)
Q Consensus 22 ~~~lk~~r~--~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv 74 (82)
+.|++-++. .-++||.|+|..+|||..||++--+.-...+...-..|...++-
T Consensus 42 ~~R~~I~~~L~~g~~sQREIa~~lGvSiaTITRgsn~Lk~~~~~~k~~l~~~l~~ 96 (99)
T PRK01381 42 GTRVRIVEELLRGELSQREIKQELGVGIATITRGSNSLKTAPPEFKEWLEQQLLK 96 (99)
T ss_pred HHHHHHHHHHHcCCcCHHHHHHHhCCceeeehhhHHHhccCCHHHHHHHHHHhcc
Confidence 555555543 34599999999999999999998776444456666666666553
No 114
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=96.36 E-value=0.0052 Score=32.39 Aligned_cols=22 Identities=18% Similarity=0.342 Sum_probs=20.1
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 038591 34 MSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 34 ~s~~elA~~~gis~~~i~~~e~ 55 (82)
++..|+|+.+||+++||..||.
T Consensus 1 ~~i~e~A~~~gVs~~tlr~ye~ 22 (68)
T cd04763 1 YTIGEVALLTGIKPHVLRAWER 22 (68)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 4678999999999999999985
No 115
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=96.31 E-value=0.0051 Score=32.30 Aligned_cols=23 Identities=17% Similarity=0.349 Sum_probs=20.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcC
Q 038591 34 MSQPDLANQINQRPQVVSEYENG 56 (82)
Q Consensus 34 ~s~~elA~~~gis~~~i~~~e~g 56 (82)
+|..|+|+.+|||+++|..|++-
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 46789999999999999999863
No 116
>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=96.31 E-value=0.01 Score=29.22 Aligned_cols=35 Identities=23% Similarity=0.281 Sum_probs=24.7
Q ss_pred HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591 23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKA 58 (82)
Q Consensus 23 ~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~ 58 (82)
..|..++... +|+.+.|+..||+++||++..+|..
T Consensus 7 ~Ai~~v~~g~-~S~r~AA~~ygVp~sTL~~r~~g~~ 41 (45)
T PF05225_consen 7 KAIEAVKNGK-MSIRKAAKKYGVPRSTLRRRLRGKP 41 (45)
T ss_dssp HHHHHHHTTS-S-HHHHHHHHT--HHHHHHHHHHTT
T ss_pred HHHHHHHhCC-CCHHHHHHHHCcCHHHHHHHHcCCC
Confidence 3455555333 9999999999999999999998854
No 117
>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=96.20 E-value=0.01 Score=26.24 Aligned_cols=24 Identities=13% Similarity=0.194 Sum_probs=21.6
Q ss_pred hCCCCHHHHHHHhCCCHHHHHHHH
Q 038591 31 GKKMSQPDLANQINQRPQVVSEYE 54 (82)
Q Consensus 31 ~~g~s~~elA~~~gis~~~i~~~e 54 (82)
..+++..++|+.+|++.++|++|.
T Consensus 19 ~~~~s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 19 AAGESVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHhC
Confidence 468899999999999999999873
No 118
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=96.20 E-value=0.01 Score=40.39 Aligned_cols=52 Identities=10% Similarity=0.110 Sum_probs=37.1
Q ss_pred HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc-----CC--------CCCCHHHHHHHHHHhCCC
Q 038591 24 QIQRARLGKKMSQPDLANQINQRPQVVSEYEN-----GK--------AVPNQTVLAKMEKAIGVK 75 (82)
Q Consensus 24 ~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~-----g~--------~~p~~~~~~~la~~lgv~ 75 (82)
++-++-=..|+||.|+|+++|+|+.+|+++.+ |- .....+.-..|.+.||+.
T Consensus 20 ~vA~lYY~~g~tQ~eIA~~lgiSR~~VsRlL~~Ar~~GiV~I~I~~~~~~~~~Le~~L~~~fgLk 84 (318)
T PRK15418 20 RIAWFYYHDGLTQSEIGERLGLTRLKVSRLLEKGRQSGIIRVQINSRFEGCLELENALRQHFSLQ 84 (318)
T ss_pred HHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHcCcEEEEEeCCCccHHHHHHHHHHHhCCC
Confidence 34444456799999999999999999999964 31 112344556777777754
No 119
>PRK13698 plasmid-partitioning protein; Provisional
Probab=96.18 E-value=0.013 Score=40.13 Aligned_cols=35 Identities=14% Similarity=0.059 Sum_probs=30.0
Q ss_pred HHHH-HHHHHhCCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591 22 PRQI-QRARLGKKMSQPDLANQINQRPQVVSEYENG 56 (82)
Q Consensus 22 ~~~l-k~~r~~~g~s~~elA~~~gis~~~i~~~e~g 56 (82)
|... +.+....|+||++||+.+|+|+++|++..+-
T Consensus 164 A~ay~~~L~~~~~~tQeeLA~~lG~SRs~Vsn~Lrl 199 (323)
T PRK13698 164 GLRYASRLQNEFAGNISALADAENISRKIITRCINT 199 (323)
T ss_pred HHHHHHHHHHhcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 5555 5577789999999999999999999999764
No 120
>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=96.17 E-value=0.02 Score=27.75 Aligned_cols=31 Identities=13% Similarity=0.182 Sum_probs=24.3
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHH
Q 038591 22 PRQIQRARLGKKMSQPDLANQINQRPQVVSE 52 (82)
Q Consensus 22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~ 52 (82)
...|..+......|..++|+.+|+|++++.+
T Consensus 6 ~~Il~~Lq~d~r~s~~~la~~lglS~~~v~~ 36 (42)
T PF13404_consen 6 RKILRLLQEDGRRSYAELAEELGLSESTVRR 36 (42)
T ss_dssp HHHHHHHHH-TTS-HHHHHHHHTS-HHHHHH
T ss_pred HHHHHHHHHcCCccHHHHHHHHCcCHHHHHH
Confidence 4567888888999999999999999999875
No 121
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=96.16 E-value=0.012 Score=30.83 Aligned_cols=22 Identities=14% Similarity=0.185 Sum_probs=19.9
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 038591 34 MSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 34 ~s~~elA~~~gis~~~i~~~e~ 55 (82)
+|..|+|+.+|||+++|..|+.
T Consensus 1 ~s~~eva~~~gvs~~tlr~~~~ 22 (70)
T smart00422 1 YTIGEVAKLAGVSVRTLRYYER 22 (70)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 5788999999999999999964
No 122
>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=96.16 E-value=0.0097 Score=35.26 Aligned_cols=46 Identities=20% Similarity=0.307 Sum_probs=32.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcCCCC-C-----------CHHH-----HHHHHHHhCCCCccc
Q 038591 34 MSQPDLANQINQRPQVVSEYENGKAV-P-----------NQTV-----LAKMEKAIGVKLRVK 79 (82)
Q Consensus 34 ~s~~elA~~~gis~~~i~~~e~g~~~-p-----------~~~~-----~~~la~~lgv~~~e~ 79 (82)
|+..|+|+.+|||..||.-||.-.-. | +.+. +...++.+|++++|.
T Consensus 1 m~I~e~a~~~gvs~~tlRyYe~~GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI 63 (127)
T TIGR02044 1 MNIGQVAKLTGLSSKMIRYYEEKGLIPPPLRSEGGYRTYTQQHLDELRLISRARQVGFSLEEC 63 (127)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHCCCCHHHH
Confidence 57889999999999999999963222 2 1222 344566777777653
No 123
>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=96.15 E-value=0.0096 Score=34.52 Aligned_cols=22 Identities=14% Similarity=0.280 Sum_probs=20.2
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 038591 34 MSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 34 ~s~~elA~~~gis~~~i~~~e~ 55 (82)
+|..|+|+.+|||+.||..||+
T Consensus 1 ~~i~e~a~~~gvs~~tlr~ye~ 22 (113)
T cd01109 1 YTIKEVAEKTGLSADTLRYYEK 22 (113)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 5788999999999999999986
No 124
>COG1342 Predicted DNA-binding proteins [General function prediction only]
Probab=96.13 E-value=0.0089 Score=34.10 Aligned_cols=34 Identities=12% Similarity=0.055 Sum_probs=28.2
Q ss_pred HHHHHHHH--HhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 22 PRQIQRAR--LGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 22 ~~~lk~~r--~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
-+.|..+| .-.|++|.|.|.++|||++|+.+..+
T Consensus 36 ~eElEAlRLvD~~~l~QeeAA~rMgISr~Tfwr~l~ 71 (99)
T COG1342 36 IEELEALRLVDYEGLTQEEAALRMGISRQTFWRLLT 71 (99)
T ss_pred HHHHHHHHHHhHhhccHHHHHHHhcccHHHHHHHHH
Confidence 45555554 56899999999999999999999876
No 125
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=96.09 E-value=0.012 Score=40.17 Aligned_cols=54 Identities=13% Similarity=0.169 Sum_probs=40.6
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc-----C--------CCCCCHHHHHHHHHHhCCC
Q 038591 22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN-----G--------KAVPNQTVLAKMEKAIGVK 75 (82)
Q Consensus 22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~-----g--------~~~p~~~~~~~la~~lgv~ 75 (82)
..++.++--..|+||.|+|+++|||+.+|+++.+ | ......+.-..|.+.||++
T Consensus 15 ~~~~A~lYY~~gltQ~eIA~~LgiSR~~v~rlL~~Ar~~GiV~I~i~~~~~~~~~Le~~L~~~fgL~ 81 (321)
T COG2390 15 LARAAWLYYVEGLTQSEIAERLGISRATVSRLLAKAREEGIVKISINSPVEGCLELEQQLKERFGLK 81 (321)
T ss_pred HHHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCeEEEEeCCCCcchHHHHHHHHHhcCCC
Confidence 4566677778899999999999999999999964 3 1122344557777888876
No 126
>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=96.08 E-value=0.0021 Score=34.37 Aligned_cols=32 Identities=13% Similarity=0.270 Sum_probs=25.0
Q ss_pred HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 23 ~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
..|... ...|.|..++|...||++++|++|..
T Consensus 14 ~~v~~~-~~~g~sv~~va~~~gi~~~~l~~W~~ 45 (76)
T PF01527_consen 14 QAVREY-LESGESVSEVAREYGISPSTLYNWRK 45 (76)
T ss_dssp HHHHHH-HHHHCHHHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHH-HHCCCceEeeecccccccccccHHHH
Confidence 344444 34689999999999999999999975
No 127
>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=96.07 E-value=0.012 Score=29.98 Aligned_cols=33 Identities=15% Similarity=0.192 Sum_probs=27.8
Q ss_pred HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 23 ~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
..|..+....++++.+||+.+++++++++++.+
T Consensus 7 ~iL~~l~~~~~~~~~~la~~~~~~~~~~t~~i~ 39 (59)
T PF01047_consen 7 RILRILYENGGITQSELAEKLGISRSTVTRIIK 39 (59)
T ss_dssp HHHHHHHHHSSEEHHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHHcCCCCHHHHHHHHCCChhHHHHHHH
Confidence 456778888999999999999999999998864
No 128
>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=96.01 E-value=0.012 Score=34.51 Aligned_cols=46 Identities=20% Similarity=0.273 Sum_probs=32.1
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcCCC-CC----------CHHH-----HHHHHHHhCCCCccc
Q 038591 34 MSQPDLANQINQRPQVVSEYENGKA-VP----------NQTV-----LAKMEKAIGVKLRVK 79 (82)
Q Consensus 34 ~s~~elA~~~gis~~~i~~~e~g~~-~p----------~~~~-----~~~la~~lgv~~~e~ 79 (82)
|+..|+|+.+|||..||.-||+-.- .| +... +...++.+|+++++.
T Consensus 1 m~IgevA~~~gvs~~tlRyYe~~GLl~p~~~~~gyR~Y~~~~l~~l~~I~~lr~~G~~L~eI 62 (120)
T cd04781 1 LDIAEVARQSGLPASTLRYYEEKGLIASIGRRGLRRQYDPQVLDRLALIALGRAAGFSLDEI 62 (120)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCCCCCcCCCCceecCHHHHHHHHHHHHHHHcCCCHHHH
Confidence 5789999999999999999996322 22 1122 445666777777653
No 129
>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=96.00 E-value=0.0015 Score=40.49 Aligned_cols=46 Identities=13% Similarity=0.174 Sum_probs=2.0
Q ss_pred hCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 038591 31 GKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKL 76 (82)
Q Consensus 31 ~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~ 76 (82)
-.-+|++++|+.+|++.+|||+.-+|+..-+..-+.-|..+|...+
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 3468999999999999999999999987766666778888887665
No 130
>PRK09744 DNA-binding transcriptional regulator DicC; Provisional
Probab=95.98 E-value=0.033 Score=30.33 Aligned_cols=36 Identities=31% Similarity=0.483 Sum_probs=26.3
Q ss_pred CHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhC
Q 038591 35 SQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIG 73 (82)
Q Consensus 35 s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lg 73 (82)
+...+|..+|||+++|++| |...| ......|..+-+
T Consensus 12 s~~kvA~aLGIs~~AVsQW--Ge~VP-e~rA~~ie~~T~ 47 (75)
T PRK09744 12 SKTKLANAAGVRLASVAAW--GELVP-EGRAMRLQEASG 47 (75)
T ss_pred cHHHHHHHHCCCHHHHHHH--hccCc-HHHHHHHHHHhC
Confidence 6778999999999999999 65444 444455555443
No 131
>COG2842 Uncharacterized ATPase, putative transposase [General function prediction only]
Probab=95.95 E-value=0.028 Score=38.11 Aligned_cols=55 Identities=24% Similarity=0.140 Sum_probs=43.9
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 038591 22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKL 76 (82)
Q Consensus 22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~ 76 (82)
-..++++.+-.+++|..+|..+|+++.+++++.+|...-....-.+|+.+++...
T Consensus 8 ~k~~k~f~e~~~~~q~~~a~gi~~~~~~vsk~L~g~~g~~~~~~a~ia~~le~~~ 62 (297)
T COG2842 8 IKKLKEFAEFSGMCQKYLARGIGTSAPALSKYLNGYKGDYATNEAKIAAFLEKKG 62 (297)
T ss_pred HHHHHHHHHhhhhhHHHHHHHhccCchhHHHHhcCcCchHHHHHHHHHHHHcCCC
Confidence 4678888999999999999999999999999999833333445567777776554
No 132
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=95.90 E-value=0.027 Score=29.93 Aligned_cols=33 Identities=9% Similarity=0.039 Sum_probs=26.2
Q ss_pred HHHHHHHHhCC--CCHHHHHHHhCCCHHHHHHHHc
Q 038591 23 RQIQRARLGKK--MSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 23 ~~lk~~r~~~g--~s~~elA~~~gis~~~i~~~e~ 55 (82)
..|..+...-+ ++..+||+.+|++..++++...
T Consensus 10 ~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~ 44 (68)
T smart00550 10 KILEFLENSGDETSTALQLAKNLGLPKKEVNRVLY 44 (68)
T ss_pred HHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHH
Confidence 44555565545 9999999999999999998854
No 133
>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=95.90 E-value=0.032 Score=26.90 Aligned_cols=26 Identities=15% Similarity=0.262 Sum_probs=23.5
Q ss_pred HhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 30 LGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 30 ~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
-..|+++.++|+.+|++..+|++|.+
T Consensus 23 ~~~~~~~~~ia~~~~~s~~~i~~~~~ 48 (55)
T cd06171 23 FGEGLSYEEIAEILGISRSTVRQRLH 48 (55)
T ss_pred HhcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 34799999999999999999999875
No 134
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=95.89 E-value=0.0089 Score=36.36 Aligned_cols=25 Identities=8% Similarity=0.295 Sum_probs=19.8
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591 33 KMSQPDLANQINQRPQVVSEYENGK 57 (82)
Q Consensus 33 g~s~~elA~~~gis~~~i~~~e~g~ 57 (82)
..|+.++|+.+||+++|+++|-+..
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 4789999999999999999998754
No 135
>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=95.88 E-value=0.042 Score=34.51 Aligned_cols=48 Identities=15% Similarity=0.134 Sum_probs=36.2
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHH
Q 038591 22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEK 70 (82)
Q Consensus 22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~ 70 (82)
+..++.+....|+|+.++|+.+|+|+++|+++..=-. .+.+.+..+..
T Consensus 109 a~~~~~l~~~~g~s~~~iA~~lg~s~~~V~r~l~l~~-lp~~v~~~~~~ 156 (187)
T TIGR00180 109 AQAYKRLLEKFSMTQEDLAKKIGKSRAHITNLLRLLK-LPSEIQSAIPE 156 (187)
T ss_pred HHHHHHHHHHhCCCHHHHHHHHCcCHHHHHHHHHHHc-CCHHHHHHHHh
Confidence 5566666666899999999999999999999987433 44455555544
No 136
>COG1513 CynS Cyanate lyase [Inorganic ion transport and metabolism]
Probab=95.88 E-value=0.079 Score=31.99 Aligned_cols=56 Identities=18% Similarity=0.149 Sum_probs=49.6
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCc
Q 038591 22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLR 77 (82)
Q Consensus 22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~ 77 (82)
...|-...+.+|+|-.++++.+|.+...+....-|+...+.+.+.+++..||.+-+
T Consensus 10 ~~~ll~~Kk~kgLsfaDl~~~lG~~ev~vaa~~ygqa~~~~~ear~v~e~L~L~~~ 65 (151)
T COG1513 10 ADALLLAKKKKGLSFADLADGLGLAEVFVAAALYGQAALPADEARAVGEALDLDED 65 (151)
T ss_pred HHHHHHHHHhcCCcHHHHHhhcCccHHHHHHHHHhhccCCHHHHHHHHHHhCCCHH
Confidence 34555667789999999999999999999999999999999999999999998644
No 137
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=95.84 E-value=0.016 Score=28.63 Aligned_cols=25 Identities=8% Similarity=0.224 Sum_probs=23.1
Q ss_pred hCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 31 GKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 31 ~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
..|++..++|+.+|+|+++|..+..
T Consensus 16 ~~g~s~~eia~~l~is~~tv~~~~~ 40 (58)
T smart00421 16 AEGLTNKEIAERLGISEKTVKTHLS 40 (58)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 5799999999999999999999875
No 138
>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=95.84 E-value=0.034 Score=30.14 Aligned_cols=40 Identities=13% Similarity=0.129 Sum_probs=27.7
Q ss_pred HHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH
Q 038591 25 IQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTV 64 (82)
Q Consensus 25 lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~ 64 (82)
+.....-..+|..+||+.+|+|+++|.++-+.-..-+...
T Consensus 26 l~~~~~~~~~si~elA~~~~vS~sti~Rf~kkLG~~gf~e 65 (77)
T PF01418_consen 26 LENPDEIAFMSISELAEKAGVSPSTIVRFCKKLGFSGFKE 65 (77)
T ss_dssp HH-HHHHCT--HHHHHHHCTS-HHHHHHHHHHCTTTCHHH
T ss_pred HhCHHHHHHccHHHHHHHcCCCHHHHHHHHHHhCCCCHHH
Confidence 3445566789999999999999999999987555545444
No 139
>COG1318 Predicted transcriptional regulators [Transcription]
Probab=95.82 E-value=0.017 Score=36.34 Aligned_cols=32 Identities=22% Similarity=0.312 Sum_probs=29.3
Q ss_pred HHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCC
Q 038591 28 ARLGKKMSQPDLANQINQRPQVVSEYENGKAV 59 (82)
Q Consensus 28 ~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~ 59 (82)
+|...|+|.+++|+.+|.+++||.++..|...
T Consensus 56 arekag~Ti~EIAeelG~TeqTir~hlkgetk 87 (182)
T COG1318 56 AREKAGMTISEIAEELGRTEQTVRNHLKGETK 87 (182)
T ss_pred HHHHccCcHHHHHHHhCCCHHHHHHHHhcchh
Confidence 56899999999999999999999999998654
No 140
>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=95.81 E-value=0.021 Score=31.82 Aligned_cols=23 Identities=9% Similarity=0.229 Sum_probs=21.0
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHc
Q 038591 33 KMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 33 g~s~~elA~~~gis~~~i~~~e~ 55 (82)
++|..|+|+.+|||++||..||.
T Consensus 1 ~~ti~evA~~~gvs~~tLR~ye~ 23 (88)
T cd01105 1 VIGIGEVSKLTGVSPRQLRYWEE 23 (88)
T ss_pred CcCHHHHHHHHCcCHHHHHHHHH
Confidence 46889999999999999999985
No 141
>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=95.80 E-value=0.023 Score=33.66 Aligned_cols=47 Identities=17% Similarity=0.173 Sum_probs=33.1
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHcCC-CCCC-----------HHH-----HHHHHHHhCCCCccc
Q 038591 33 KMSQPDLANQINQRPQVVSEYENGK-AVPN-----------QTV-----LAKMEKAIGVKLRVK 79 (82)
Q Consensus 33 g~s~~elA~~~gis~~~i~~~e~g~-~~p~-----------~~~-----~~~la~~lgv~~~e~ 79 (82)
.+|..|||+.+|+|..||..||.-. -.|. ... +...++.+|+++++.
T Consensus 3 ~~tI~elA~~~gvs~~tlR~Ye~~GLL~p~~r~~~gyR~Y~~~~l~rL~~I~~lr~~G~~L~eI 66 (120)
T TIGR02054 3 AYTISRLAEDAGVSVHVVRDYLLRGLLHPVRRTTSGYGIFDDASLQRLRFVRAAFEAGIGLGEL 66 (120)
T ss_pred CCcHHHHHHHHCcCHHHHHHHHHCCCCCCCccCCCCCeeCCHHHHHHHHHHHHHHHcCCCHHHH
Confidence 5899999999999999999998632 2222 222 445556777777653
No 142
>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=95.79 E-value=0.019 Score=33.16 Aligned_cols=23 Identities=22% Similarity=0.426 Sum_probs=20.8
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcC
Q 038591 34 MSQPDLANQINQRPQVVSEYENG 56 (82)
Q Consensus 34 ~s~~elA~~~gis~~~i~~~e~g 56 (82)
+|..++|+.+|||+.||..||.-
T Consensus 1 ~~i~eva~~~gvs~~tlR~ye~~ 23 (108)
T cd04773 1 MTIGELAHLLGVPPSTLRHWEKE 23 (108)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC
Confidence 57899999999999999999863
No 143
>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=95.77 E-value=0.018 Score=34.03 Aligned_cols=46 Identities=13% Similarity=0.194 Sum_probs=32.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcCC-C-----------CCCHHH-----HHHHHHHhCCCCccc
Q 038591 34 MSQPDLANQINQRPQVVSEYENGK-A-----------VPNQTV-----LAKMEKAIGVKLRVK 79 (82)
Q Consensus 34 ~s~~elA~~~gis~~~i~~~e~g~-~-----------~p~~~~-----~~~la~~lgv~~~e~ 79 (82)
|+..|||+.+|||+.||.-||+-. - ..+.+. +....+.+|++++|.
T Consensus 1 m~IgevA~~~gvs~~tLRyYe~~GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI 63 (127)
T cd04784 1 MKIGELAKKTGCSVETIRYYEKEGLLPAPARSANNYRLYDEEHLERLLFIRRCRSLDMSLDEI 63 (127)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHH
Confidence 578899999999999999998632 1 222222 345556778877653
No 144
>PRK04217 hypothetical protein; Provisional
Probab=95.71 E-value=0.032 Score=32.64 Aligned_cols=30 Identities=10% Similarity=-0.018 Sum_probs=26.1
Q ss_pred HHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 26 QRARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 26 k~~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
-.++...|+|++++|+.+|+|.+||+++..
T Consensus 51 i~l~~~eGlS~~EIAk~LGIS~sTV~r~L~ 80 (110)
T PRK04217 51 LRLVDYEGLTQEEAGKRMGVSRGTVWRALT 80 (110)
T ss_pred HHHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 345566899999999999999999999876
No 145
>PRK10227 DNA-binding transcriptional regulator CueR; Provisional
Probab=95.69 E-value=0.022 Score=34.30 Aligned_cols=23 Identities=22% Similarity=0.316 Sum_probs=20.8
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcC
Q 038591 34 MSQPDLANQINQRPQVVSEYENG 56 (82)
Q Consensus 34 ~s~~elA~~~gis~~~i~~~e~g 56 (82)
|+..|||+.+|+|..||.-||+-
T Consensus 1 m~Ige~a~~~gvs~~tlRyYE~~ 23 (135)
T PRK10227 1 MNISDVAKITGLTSKAIRFYEEK 23 (135)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC
Confidence 57889999999999999999863
No 146
>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=95.69 E-value=0.021 Score=33.84 Aligned_cols=23 Identities=17% Similarity=0.208 Sum_probs=20.8
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcC
Q 038591 34 MSQPDLANQINQRPQVVSEYENG 56 (82)
Q Consensus 34 ~s~~elA~~~gis~~~i~~~e~g 56 (82)
|+..|+|+.+|||+.||..||+-
T Consensus 1 m~I~e~a~~~gvs~~tlRyYe~~ 23 (127)
T cd01108 1 MNIGEAAKLTGLSAKMIRYYEEI 23 (127)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC
Confidence 57889999999999999999863
No 147
>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=95.68 E-value=0.017 Score=30.72 Aligned_cols=24 Identities=17% Similarity=0.259 Sum_probs=21.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 32 KKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 32 ~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
..+|+.++|..+|+|+.++++..+
T Consensus 27 ~~lt~~~iA~~~g~sr~tv~r~l~ 50 (76)
T PF13545_consen 27 LPLTQEEIADMLGVSRETVSRILK 50 (76)
T ss_dssp EESSHHHHHHHHTSCHHHHHHHHH
T ss_pred ecCCHHHHHHHHCCCHHHHHHHHH
Confidence 468999999999999999998764
No 148
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=95.67 E-value=0.047 Score=26.58 Aligned_cols=31 Identities=16% Similarity=0.128 Sum_probs=25.2
Q ss_pred HHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 25 IQRARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 25 lk~~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
+..+....+++..++|+.+++++++++++..
T Consensus 6 l~~l~~~~~~s~~~l~~~l~~s~~tv~~~l~ 36 (53)
T smart00420 6 LELLAQQGKVSVEELAELLGVSEMTIRRDLN 36 (53)
T ss_pred HHHHHHcCCcCHHHHHHHHCCCHHHHHHHHH
Confidence 4445555679999999999999999988764
No 149
>PF13551 HTH_29: Winged helix-turn helix
Probab=95.66 E-value=0.024 Score=32.06 Aligned_cols=26 Identities=12% Similarity=0.277 Sum_probs=22.6
Q ss_pred HhCCC-CHHHHHHHhCCCHHHHHHHHc
Q 038591 30 LGKKM-SQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 30 ~~~g~-s~~elA~~~gis~~~i~~~e~ 55 (82)
-..|+ |..++|+.+|+|++||++|.+
T Consensus 8 ~~~g~~~~~~ia~~lg~s~~Tv~r~~~ 34 (112)
T PF13551_consen 8 LAEGVSTIAEIARRLGISRRTVYRWLK 34 (112)
T ss_pred HHcCCCcHHHHHHHHCcCHHHHHHHHH
Confidence 45688 599999999999999999954
No 150
>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=95.65 E-value=0.0043 Score=31.18 Aligned_cols=28 Identities=7% Similarity=0.167 Sum_probs=20.2
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcCCCCCC
Q 038591 34 MSQPDLANQINQRPQVVSEYENGKAVPN 61 (82)
Q Consensus 34 ~s~~elA~~~gis~~~i~~~e~g~~~p~ 61 (82)
++.+|+++.+|+|.+|+.++.+....|.
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 5678999999999999999987544543
No 151
>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=95.64 E-value=0.025 Score=32.46 Aligned_cols=22 Identities=23% Similarity=0.247 Sum_probs=20.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 038591 34 MSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 34 ~s~~elA~~~gis~~~i~~~e~ 55 (82)
|+..+||+.+|+|..||.-||.
T Consensus 1 m~Ige~a~~~gvs~~tlRyYe~ 22 (107)
T cd04777 1 MKIGKFAKKNNITIDTVRHYID 22 (107)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 5788999999999999999986
No 152
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=95.63 E-value=0.018 Score=40.25 Aligned_cols=48 Identities=10% Similarity=0.221 Sum_probs=39.5
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhC------CCHHHHHHHHcCCCCCCHHHHHHHHHH
Q 038591 22 PRQIQRARLGKKMSQPDLANQIN------QRPQVVSEYENGKAVPNQTVLAKMEKA 71 (82)
Q Consensus 22 ~~~lk~~r~~~g~s~~elA~~~g------is~~~i~~~e~g~~~p~~~~~~~la~~ 71 (82)
+..+|..|...|+||.|+...+| .|.+||.++|. -..++.++-+|-=.
T Consensus 212 AK~FKqRRIkLGfTQaDVGlALG~lyGn~FSQTTIcRFEA--LqLSFKNMCKLKPL 265 (398)
T KOG3802|consen 212 AKTFKQRRIKLGFTQADVGLALGALYGNVFSQTTICRFEA--LQLSFKNMCKLKPL 265 (398)
T ss_pred HHHHHhheeccccchhHHHHHHHhhhCcccchhhhhHhHh--hccCHHHHhhhHHH
Confidence 78888889999999999999998 69999999997 45666666555433
No 153
>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=95.62 E-value=0.035 Score=27.71 Aligned_cols=31 Identities=19% Similarity=0.113 Sum_probs=21.9
Q ss_pred HHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 25 IQRARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 25 lk~~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
+=.++-..|+|..|+|+.+|+|+++|..+..
T Consensus 18 i~~l~~~~g~s~~eIa~~l~~s~~~v~~~l~ 48 (54)
T PF08281_consen 18 IFLLRYFQGMSYAEIAEILGISESTVKRRLR 48 (54)
T ss_dssp HHHHHHTS---HHHHHHHCTS-HHHHHHHHH
T ss_pred HHHHHHHHCcCHHHHHHHHCcCHHHHHHHHH
Confidence 3345567899999999999999999998753
No 154
>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=95.62 E-value=0.029 Score=37.31 Aligned_cols=42 Identities=14% Similarity=0.228 Sum_probs=30.8
Q ss_pred CCCCHHHHHHHhCC-----CHHHHHHHHcCCCCCCHHHHHHHHHHhC
Q 038591 32 KKMSQPDLANQINQ-----RPQVVSEYENGKAVPNQTVLAKMEKAIG 73 (82)
Q Consensus 32 ~g~s~~elA~~~gi-----s~~~i~~~e~g~~~p~~~~~~~la~~lg 73 (82)
.++||.+||+.+|- |+++|++++.--..+.......|+.-+|
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 9999999987544444455455544443
No 155
>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=95.61 E-value=0.027 Score=28.88 Aligned_cols=32 Identities=16% Similarity=0.140 Sum_probs=26.8
Q ss_pred HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 24 QIQRARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 24 ~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
.+..+.+...+|..++|+.+|+|..||.+-.+
T Consensus 5 Il~~l~~~~~~s~~ela~~~~VS~~TiRRDl~ 36 (57)
T PF08220_consen 5 ILELLKEKGKVSVKELAEEFGVSEMTIRRDLN 36 (57)
T ss_pred HHHHHHHcCCEEHHHHHHHHCcCHHHHHHHHH
Confidence 45666777889999999999999999988644
No 156
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=95.60 E-value=0.023 Score=27.09 Aligned_cols=31 Identities=19% Similarity=0.195 Sum_probs=21.2
Q ss_pred hCCCCHHHHHHHhCCCHHHHHHHHcCCCCCC
Q 038591 31 GKKMSQPDLANQINQRPQVVSEYENGKAVPN 61 (82)
Q Consensus 31 ~~g~s~~elA~~~gis~~~i~~~e~g~~~p~ 61 (82)
..+++..++|..+|+|++++++...-....+
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 3579999999999999999999876443333
No 157
>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=95.60 E-value=0.022 Score=33.79 Aligned_cols=22 Identities=23% Similarity=0.326 Sum_probs=20.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 038591 34 MSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 34 ~s~~elA~~~gis~~~i~~~e~ 55 (82)
|+..|+|+.+|||..||..||+
T Consensus 1 m~I~e~a~~~gvs~~tlR~Ye~ 22 (127)
T TIGR02047 1 MKIGELAQKTGVSVETIRFYEK 22 (127)
T ss_pred CcHHHHHHHHCcCHHHHHHHHH
Confidence 5788999999999999999986
No 158
>PRK13749 transcriptional regulator MerD; Provisional
Probab=95.55 E-value=0.026 Score=33.50 Aligned_cols=47 Identities=13% Similarity=0.162 Sum_probs=33.1
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHcCC------------CCCCHHH-----HHHHHHHhCCCCccc
Q 038591 33 KMSQPDLANQINQRPQVVSEYENGK------------AVPNQTV-----LAKMEKAIGVKLRVK 79 (82)
Q Consensus 33 g~s~~elA~~~gis~~~i~~~e~g~------------~~p~~~~-----~~~la~~lgv~~~e~ 79 (82)
.+|..|||+.+|+|..||.-||.-. +..+... +...++.+|++++|.
T Consensus 3 ~~tIgelA~~~gvS~~tiR~YE~~GLl~p~~r~~~gyR~Y~~~~l~rL~~I~~~r~~G~sL~eI 66 (121)
T PRK13749 3 AYTVSRLALDAGVSVHIVRDYLLRGLLRPVACTTGGYGLFDDAALQRLCFVRAAFEAGIGLDAL 66 (121)
T ss_pred CCcHHHHHHHHCCCHHHHHHHHHCCCCCCCCcCCCCCccCCHHHHHHHHHHHHHHHcCCCHHHH
Confidence 4789999999999999999998532 1222222 344456788887664
No 159
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=95.54 E-value=0.04 Score=32.39 Aligned_cols=26 Identities=12% Similarity=0.054 Sum_probs=23.6
Q ss_pred HhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 30 LGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 30 ~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
...|.|..++|..+|||+++|++|-+
T Consensus 26 ~~~g~sv~evA~e~gIs~~tl~~W~r 51 (121)
T PRK09413 26 FEPGMTVSLVARQHGVAASQLFLWRK 51 (121)
T ss_pred HcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 45699999999999999999999965
No 160
>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional
Probab=95.51 E-value=0.027 Score=34.67 Aligned_cols=51 Identities=18% Similarity=0.322 Sum_probs=35.1
Q ss_pred HHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCC-----------CHHH-----HHHHHHHhCCCCccc
Q 038591 29 RLGKKMSQPDLANQINQRPQVVSEYENGKAVP-----------NQTV-----LAKMEKAIGVKLRVK 79 (82)
Q Consensus 29 r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p-----------~~~~-----~~~la~~lgv~~~e~ 79 (82)
+...=++..|+|+.+|||..||..||.-.-.+ +.+. +.+.++.+|++++|.
T Consensus 7 ~~~~~~~IgevAk~~gvs~~TlRyYE~~GLi~~~r~~~g~R~Y~~~~i~~L~~I~~lr~lG~sL~eI 73 (154)
T PRK15002 7 RIKALLTPGEVAKRSGVAVSALHFYESKGLITSIRNSGNQRRYKRDVLRYVAIIKIAQRIGIPLATI 73 (154)
T ss_pred hhcccccHHHHHHHHCcCHHHHHHHHHCCCCCCccCCCCCEEECHHHHHHHHHHHHHHHcCCCHHHH
Confidence 34456899999999999999999999632111 2222 445566777777653
No 161
>PF01371 Trp_repressor: Trp repressor protein; InterPro: IPR000831 The Trp repressor (TrpR) binds to at least five operators in the Escherichia coli genome, repressing gene expression. The operators at which it binds vary considerably in DNA sequence and location within the promoter; when bound to the Trp operon it recognises the sequence 5'-ACTAGT-3' and acts to prevent the initiation of transcription. The TrpR controls the trpEDCBA (trpO) operon and the genes for trpR, aroH, mtr and aroL, which are involved in the biosynthesis and uptake of the amino acid tryptophan []. The repressor binds to the operators only in the presence of L-tryptophan, thereby controlling the intracellular level of its effector; the complex also regulates Trp repressor biosynthesis by binding to its own regulatory region. TrpR acts as a dimer that is composed of identical 6-helical subunits, where four of the helices form the core of the protein and intertwine with the corresponding helices from the other subunit.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3FRW_H 3KOR_A 3SSW_N 1P6Z_N 1CO0_B 1JHG_A 1WRT_S 1WRS_R 1WRP_R 1RCS_B ....
Probab=95.51 E-value=0.059 Score=30.25 Aligned_cols=34 Identities=15% Similarity=0.197 Sum_probs=27.0
Q ss_pred HHHHHHHH--HhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 22 PRQIQRAR--LGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 22 ~~~lk~~r--~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
+.|++-++ -..|.||.++|+.+|+|..||++.-+
T Consensus 36 ~~R~~va~~lL~~g~syreIa~~tgvS~aTItRvsr 71 (87)
T PF01371_consen 36 AQRWQVAKELLDEGKSYREIAEETGVSIATITRVSR 71 (87)
T ss_dssp HHHHHHHHHHHHTTSSHHHHHHHHTSTHHHHHHHHH
T ss_pred HHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 45555544 35799999999999999999998754
No 162
>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=95.51 E-value=0.029 Score=28.59 Aligned_cols=33 Identities=18% Similarity=0.215 Sum_probs=25.6
Q ss_pred HHHHHHHHhCC--CCHHHHHHHhCCCHHHHHHHHc
Q 038591 23 RQIQRARLGKK--MSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 23 ~~lk~~r~~~g--~s~~elA~~~gis~~~i~~~e~ 55 (82)
..|..+...-+ +|+.+||+.++++++++++..+
T Consensus 9 ~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~ 43 (62)
T PF12802_consen 9 RVLMALARHPGEELTQSELAERLGISKSTVSRIVK 43 (62)
T ss_dssp HHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHH
Confidence 34555666666 8999999999999999998754
No 163
>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=95.48 E-value=0.064 Score=27.58 Aligned_cols=24 Identities=13% Similarity=0.219 Sum_probs=21.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 32 KKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 32 ~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
..+|+.++|+.+|+++++++++.+
T Consensus 24 ~~~s~~ela~~~g~s~~tv~r~l~ 47 (67)
T cd00092 24 LPLTRQEIADYLGLTRETVSRTLK 47 (67)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHH
Confidence 458999999999999999998765
No 164
>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=95.47 E-value=0.03 Score=31.99 Aligned_cols=23 Identities=17% Similarity=0.189 Sum_probs=21.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcC
Q 038591 34 MSQPDLANQINQRPQVVSEYENG 56 (82)
Q Consensus 34 ~s~~elA~~~gis~~~i~~~e~g 56 (82)
++..|+|+.+|||+.||..||+-
T Consensus 2 ~~i~eva~~~gvs~~tlR~ye~~ 24 (102)
T cd04789 2 YTISELAEKAGISRSTLLYYEKL 24 (102)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC
Confidence 67899999999999999999863
No 165
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=95.47 E-value=0.04 Score=27.83 Aligned_cols=29 Identities=14% Similarity=0.217 Sum_probs=22.9
Q ss_pred HHHhCCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591 28 ARLGKKMSQPDLANQINQRPQVVSEYENG 56 (82)
Q Consensus 28 ~r~~~g~s~~elA~~~gis~~~i~~~e~g 56 (82)
++.+.|++..++|+.+|-|+..|.+|.++
T Consensus 15 ~m~qlG~s~~~isr~i~RSr~~Ir~yl~d 43 (50)
T PF11427_consen 15 VMHQLGMSLREISRRIGRSRTCIRRYLKD 43 (50)
T ss_dssp HHHHTT--HHHHHHHHT--HHHHHHHHHS
T ss_pred HHHHhchhHHHHHHHhCccHHHHHHHhcC
Confidence 56789999999999999999999999875
No 166
>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=95.47 E-value=0.029 Score=32.33 Aligned_cols=23 Identities=13% Similarity=0.159 Sum_probs=20.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcC
Q 038591 34 MSQPDLANQINQRPQVVSEYENG 56 (82)
Q Consensus 34 ~s~~elA~~~gis~~~i~~~e~g 56 (82)
++..++|+.+|||++||..||.-
T Consensus 1 ~~i~eva~~~gis~~tlR~ye~~ 23 (108)
T cd01107 1 FTIGEFAKLSNLSIKALRYYDKI 23 (108)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHc
Confidence 47889999999999999999863
No 167
>PRK00118 putative DNA-binding protein; Validated
Probab=95.45 E-value=0.051 Score=31.48 Aligned_cols=30 Identities=17% Similarity=0.093 Sum_probs=26.1
Q ss_pred HHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 26 QRARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 26 k~~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
-.++-..|+|..++|+.+|+|++||+++..
T Consensus 26 l~L~y~eg~S~~EIAe~lGIS~~TV~r~L~ 55 (104)
T PRK00118 26 MELYYLDDYSLGEIAEEFNVSRQAVYDNIK 55 (104)
T ss_pred HHHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 345667899999999999999999999865
No 168
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=95.43 E-value=0.058 Score=30.18 Aligned_cols=26 Identities=4% Similarity=0.045 Sum_probs=23.6
Q ss_pred HhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 30 LGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 30 ~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
-+.|++..++|...|||..|.++|..
T Consensus 22 v~~g~~~a~aA~~~gVS~~Ta~kW~~ 47 (85)
T PF13011_consen 22 VEQGWPVAHAAAEFGVSRRTAYKWLA 47 (85)
T ss_pred HHcCCcHHHHHHHhCCCHHHHHHHHH
Confidence 35899999999999999999999964
No 169
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=95.43 E-value=0.022 Score=28.76 Aligned_cols=28 Identities=21% Similarity=0.166 Sum_probs=24.5
Q ss_pred HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 28 ARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 28 ~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
.+-..|.+..++|...|||++|+++|-+
T Consensus 14 ~~LR~~~~~~~La~~FgIs~stvsri~~ 41 (53)
T PF13613_consen 14 MYLRLNLTFQDLAYRFGISQSTVSRIFH 41 (53)
T ss_pred HHHHcCCcHhHHhhheeecHHHHHHHHH
Confidence 3456799999999999999999999875
No 170
>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=95.43 E-value=0.032 Score=31.80 Aligned_cols=22 Identities=9% Similarity=0.190 Sum_probs=20.1
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 038591 34 MSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 34 ~s~~elA~~~gis~~~i~~~e~ 55 (82)
+|..|+|+.+|||++||..||.
T Consensus 1 ~ti~eva~~~gvs~~tlR~ye~ 22 (103)
T cd01106 1 YTVGEVAKLTGVSVRTLHYYDE 22 (103)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 4788999999999999999975
No 171
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=95.41 E-value=0.027 Score=27.09 Aligned_cols=24 Identities=13% Similarity=0.202 Sum_probs=21.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 32 KKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 32 ~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
..+++.++|+.+|+|++++++..+
T Consensus 7 ~~~s~~~la~~l~~s~~tv~~~l~ 30 (48)
T smart00419 7 LPLTRQEIAELLGLTRETVSRTLK 30 (48)
T ss_pred eccCHHHHHHHHCCCHHHHHHHHH
Confidence 468999999999999999998764
No 172
>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=95.41 E-value=0.057 Score=27.49 Aligned_cols=30 Identities=3% Similarity=-0.011 Sum_probs=25.6
Q ss_pred HHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591 25 IQRARLGKKMSQPDLANQINQRPQVVSEYE 54 (82)
Q Consensus 25 lk~~r~~~g~s~~elA~~~gis~~~i~~~e 54 (82)
+..++.-..+++.+.|+.+||+.+++.+.-
T Consensus 7 ~~~L~~~fhlp~~eAA~~Lgv~~T~LKr~C 36 (52)
T PF02042_consen 7 LEDLSQYFHLPIKEAAKELGVSVTTLKRRC 36 (52)
T ss_pred HHHHHHHhCCCHHHHHHHhCCCHHHHHHHH
Confidence 567788899999999999999988877664
No 173
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=95.39 E-value=0.034 Score=33.61 Aligned_cols=23 Identities=22% Similarity=0.294 Sum_probs=21.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcC
Q 038591 34 MSQPDLANQINQRPQVVSEYENG 56 (82)
Q Consensus 34 ~s~~elA~~~gis~~~i~~~e~g 56 (82)
++..|+|+.+|||+.||..||.-
T Consensus 2 ~~I~e~a~~~gvs~~tlR~Ye~~ 24 (140)
T PRK09514 2 YRIGELAKLAEVTPDTLRFYEKQ 24 (140)
T ss_pred CcHHHHHHHHCcCHHHHHHHHHC
Confidence 67899999999999999999863
No 174
>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=95.38 E-value=0.032 Score=33.30 Aligned_cols=23 Identities=17% Similarity=0.231 Sum_probs=21.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcC
Q 038591 34 MSQPDLANQINQRPQVVSEYENG 56 (82)
Q Consensus 34 ~s~~elA~~~gis~~~i~~~e~g 56 (82)
++..|+|+.+|||+.||..||.-
T Consensus 2 ~~I~e~a~~~gvs~~tlR~Ye~~ 24 (131)
T TIGR02043 2 FQIGELAKLCGVTSDTLRFYEKN 24 (131)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC
Confidence 67899999999999999999863
No 175
>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=95.37 E-value=0.022 Score=32.47 Aligned_cols=22 Identities=23% Similarity=0.398 Sum_probs=20.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 038591 34 MSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 34 ~s~~elA~~~gis~~~i~~~e~ 55 (82)
+|..|+|+.+|||++|+..||.
T Consensus 1 yti~EvA~~~gVs~~tLR~ye~ 22 (99)
T cd04765 1 FSIGEVAEILGLPPHVLRYWET 22 (99)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 4778999999999999999975
No 176
>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=95.36 E-value=0.034 Score=31.38 Aligned_cols=23 Identities=9% Similarity=0.206 Sum_probs=20.8
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcC
Q 038591 34 MSQPDLANQINQRPQVVSEYENG 56 (82)
Q Consensus 34 ~s~~elA~~~gis~~~i~~~e~g 56 (82)
+|..|+|+.+|||+.||..||+-
T Consensus 1 ~ti~eva~~~gvs~~tLRyye~~ 23 (96)
T cd04768 1 LTIGEFAKLAGVSIRTLRHYDDI 23 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC
Confidence 47889999999999999999963
No 177
>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=95.34 E-value=0.036 Score=31.55 Aligned_cols=23 Identities=39% Similarity=0.492 Sum_probs=20.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcC
Q 038591 34 MSQPDLANQINQRPQVVSEYENG 56 (82)
Q Consensus 34 ~s~~elA~~~gis~~~i~~~e~g 56 (82)
++..|+|+.+|||..||..||.-
T Consensus 1 y~i~e~A~~~gvs~~tlR~Ye~~ 23 (99)
T cd04772 1 YRTVDLARAIGLSPQTVRNYESL 23 (99)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHc
Confidence 46789999999999999999863
No 178
>PRK15043 transcriptional regulator MirA; Provisional
Probab=95.33 E-value=0.039 Score=36.44 Aligned_cols=46 Identities=13% Similarity=0.238 Sum_probs=33.0
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHc--C----------CCCCCHHHHHHHH-----HHhCCCCcc
Q 038591 33 KMSQPDLANQINQRPQVVSEYEN--G----------KAVPNQTVLAKME-----KAIGVKLRV 78 (82)
Q Consensus 33 g~s~~elA~~~gis~~~i~~~e~--g----------~~~p~~~~~~~la-----~~lgv~~~e 78 (82)
-++..++|+.+|||+.|+..||. | .+..+.+.+..|. ...|+++.+
T Consensus 3 ~ytIgeVA~~~GVs~~TLR~wErr~GLL~P~Rt~~G~R~Ys~~dv~rL~~I~~l~~~G~~i~e 65 (243)
T PRK15043 3 LYTIGEVALLCDINPVTLRAWQRRYGLLKPQRTDGGHRLFNDADIDRIREIKRWIDNGVQVSK 65 (243)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHhcCCCCCccCCCCCEEECHHHHHHHHHHHHHHHcCCCHHH
Confidence 47899999999999999999983 4 2334455555554 556666654
No 179
>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain. This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.
Probab=95.33 E-value=0.025 Score=31.98 Aligned_cols=26 Identities=12% Similarity=0.054 Sum_probs=22.7
Q ss_pred HhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 30 LGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 30 ~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
....+|+.|||+.+|++++++++..+
T Consensus 44 ~~~~is~~eLa~~~g~sr~tVsr~L~ 69 (95)
T TIGR01610 44 KQDRVTATVIAELTGLSRTHVSDAIK 69 (95)
T ss_pred cCCccCHHHHHHHHCcCHHHHHHHHH
Confidence 46689999999999999999999643
No 180
>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=95.30 E-value=0.038 Score=31.32 Aligned_cols=22 Identities=14% Similarity=0.315 Sum_probs=20.2
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 038591 34 MSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 34 ~s~~elA~~~gis~~~i~~~e~ 55 (82)
++..++|+.+|+|++||..||+
T Consensus 1 ~~I~e~a~~~gvs~~tLR~ye~ 22 (96)
T cd04774 1 YKVDEVAKRLGLTKRTLKYYEE 22 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 4778999999999999999986
No 181
>smart00351 PAX Paired Box domain.
Probab=95.29 E-value=0.055 Score=32.03 Aligned_cols=25 Identities=16% Similarity=0.126 Sum_probs=22.8
Q ss_pred hCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 31 GKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 31 ~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
..|.|+.++|+.+|||++||++|.+
T Consensus 31 ~~G~s~~~iA~~~gvs~~tV~kwi~ 55 (125)
T smart00351 31 QNGVRPCDISRQLCVSHGCVSKILG 55 (125)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 3799999999999999999999954
No 182
>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=95.26 E-value=0.018 Score=28.80 Aligned_cols=31 Identities=10% Similarity=0.186 Sum_probs=23.3
Q ss_pred HHHHHH-hCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 25 IQRARL-GKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 25 lk~~r~-~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
|..+.. ..++|..|+|+.+|+++++++++.+
T Consensus 9 L~~l~~~~~~~t~~eia~~~gl~~stv~r~L~ 40 (52)
T PF09339_consen 9 LEALAESGGPLTLSEIARALGLPKSTVHRLLQ 40 (52)
T ss_dssp HHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 333433 3458999999999999999999865
No 183
>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=95.26 E-value=0.04 Score=31.10 Aligned_cols=22 Identities=14% Similarity=0.273 Sum_probs=20.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 038591 34 MSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 34 ~s~~elA~~~gis~~~i~~~e~ 55 (82)
|+..|+|+.+|+|+.||..||.
T Consensus 1 m~i~eva~~~gvs~~tlR~ye~ 22 (96)
T cd04788 1 WKIGELARRTGLSVRTLHHYDH 22 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 5788999999999999999996
No 184
>PRK04132 replication factor C small subunit; Provisional
Probab=95.22 E-value=0.041 Score=42.04 Aligned_cols=43 Identities=28% Similarity=0.484 Sum_probs=40.4
Q ss_pred HHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcc
Q 038591 36 QPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRV 78 (82)
Q Consensus 36 ~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e 78 (82)
.+++|++.||....+-.|..|++.|++..-.+||++||+++++
T Consensus 420 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 462 (846)
T PRK04132 420 RKEIAEKTGIRADRILEYIKGKRKPSLKNYIKIAKALGINLEK 462 (846)
T ss_pred HHHHHHHhCCcHHHHHHHHhcCCCccHHHHHHHHHHhcccHHH
Confidence 4789999999999999999999999999999999999999865
No 185
>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=95.21 E-value=0.041 Score=31.40 Aligned_cols=22 Identities=9% Similarity=0.194 Sum_probs=20.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 038591 34 MSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 34 ~s~~elA~~~gis~~~i~~~e~ 55 (82)
++..|+|+.+|||++||..||+
T Consensus 2 ~~i~eva~~~gvs~~tLR~ye~ 23 (102)
T cd04775 2 YTIGQMSRKFGVSRSTLLYYES 23 (102)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 6789999999999999999986
No 186
>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=95.17 E-value=0.036 Score=33.15 Aligned_cols=22 Identities=23% Similarity=0.273 Sum_probs=20.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 038591 34 MSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 34 ~s~~elA~~~gis~~~i~~~e~ 55 (82)
|+..|||+.+|||..||.-||+
T Consensus 1 m~Ige~a~~~gvs~~tLRyYE~ 22 (131)
T cd04786 1 MKIGELAKRSGMAASRIRFYEA 22 (131)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 5788999999999999999986
No 187
>PF14590 DUF4447: Domain of unknown function (DUF4447); PDB: 2OX6_B.
Probab=95.14 E-value=0.23 Score=30.03 Aligned_cols=44 Identities=16% Similarity=0.160 Sum_probs=32.6
Q ss_pred CCCHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCH
Q 038591 19 PDTPRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQ 62 (82)
Q Consensus 19 ~~~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~ 62 (82)
.+++-.++.+|...|+|..++|+..+.|..-|-.||.|....+.
T Consensus 6 glnaie~~ylr~slgl~~aqv~~l~k~se~dv~aweage~~~~~ 49 (166)
T PF14590_consen 6 GLNAIEIKYLRLSLGLTTAQVAELTKASEADVLAWEAGEKPAPG 49 (166)
T ss_dssp ---HHHHHHHHHHTT--HHHHHHHHTS-HHHHHHHHTTSS---H
T ss_pred cchHHHHHHHHHHcCCCHHHHHHhhccCHHHhhhhhccCCcCch
Confidence 34577889999999999999999999999999999999766543
No 188
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=95.13 E-value=0.098 Score=32.84 Aligned_cols=61 Identities=15% Similarity=0.218 Sum_probs=38.6
Q ss_pred CCHHHHHHHH-HhCCCCHHHHHHHhCCCHHHHHHHHcC----CCCCCHHHHHHHHHHhCCCCcccc
Q 038591 20 DTPRQIQRAR-LGKKMSQPDLANQINQRPQVVSEYENG----KAVPNQTVLAKMEKAIGVKLRVKI 80 (82)
Q Consensus 20 ~~~~~lk~~r-~~~g~s~~elA~~~gis~~~i~~~e~g----~~~p~~~~~~~la~~lgv~~~e~~ 80 (82)
+......-++ -..|+|.+|+|+.+++|..||..+.+. -...+...+..++.-.-.++.++|
T Consensus 151 Lt~rE~evl~~~~~G~s~~eIA~~l~iS~~TV~~h~~~i~~Kl~v~~~~~l~~~~~~~~~~~~~~~ 216 (216)
T PRK10840 151 LSPKESEVLRLFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVENDIALLNYLSSVTLSPADKD 216 (216)
T ss_pred CCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCCCCHHHHHHHHHHhcCCcccCC
Confidence 4444443333 357999999999999999999988754 122344444455544455555543
No 189
>PRK11891 aspartate carbamoyltransferase; Provisional
Probab=95.12 E-value=0.039 Score=39.20 Aligned_cols=35 Identities=14% Similarity=0.148 Sum_probs=31.7
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591 22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENG 56 (82)
Q Consensus 22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g 56 (82)
.+.|+.++...|||..+||+++|++..++.+|.--
T Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~wl~p 39 (429)
T PRK11891 5 QAFLRDAMRRLNMTREAFANRIGVSRRALDTWLLP 39 (429)
T ss_pred HHHHHHHHHHhCCCHHHHHHHhCCcHHhHHhhcCC
Confidence 35689999999999999999999999999999843
No 190
>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=95.11 E-value=0.046 Score=30.92 Aligned_cols=46 Identities=15% Similarity=0.230 Sum_probs=31.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc-CCC-----------CCCHHH-----HHHHHHHhCCCCccc
Q 038591 34 MSQPDLANQINQRPQVVSEYEN-GKA-----------VPNQTV-----LAKMEKAIGVKLRVK 79 (82)
Q Consensus 34 ~s~~elA~~~gis~~~i~~~e~-g~~-----------~p~~~~-----~~~la~~lgv~~~e~ 79 (82)
+|..|+|+.+|||+.||..||+ |-- ..+... +....+.+|+++.+.
T Consensus 1 ~~i~eva~~~gvs~~tlR~ye~~Gll~p~~~~~~gyR~Y~~~~~~~l~~I~~lr~~G~~l~eI 63 (97)
T cd04782 1 FTTGEFAKLCGISKQTLFHYDKIGLFKPEIVKENGYRYYTLEQFEQLDIILLLKELGISLKEI 63 (97)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCCCCCccCCCCCccCCHHHHHHHHHHHHHHHcCCCHHHH
Confidence 4788999999999999999985 321 222222 344566777777653
No 191
>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=95.09 E-value=0.047 Score=30.72 Aligned_cols=22 Identities=14% Similarity=0.249 Sum_probs=20.1
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 038591 34 MSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 34 ~s~~elA~~~gis~~~i~~~e~ 55 (82)
++..|+|+.+|+++++|..|++
T Consensus 1 ~~~~eva~~~gi~~~tlr~~~~ 22 (100)
T cd00592 1 YTIGEVAKLLGVSVRTLRYYEE 22 (100)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 5788999999999999999975
No 192
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=95.08 E-value=0.029 Score=34.08 Aligned_cols=26 Identities=15% Similarity=0.234 Sum_probs=23.6
Q ss_pred HhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 30 LGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 30 ~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
...|+|.+++|.++|+|.+|+.+|.+
T Consensus 18 ~~~G~S~re~Ak~~gvs~sTvy~wv~ 43 (138)
T COG3415 18 VGEGLSCREAAKRFGVSISTVYRWVR 43 (138)
T ss_pred HHcCccHHHHHHHhCccHHHHHHHHH
Confidence 45799999999999999999999964
No 193
>COG3311 AlpA Predicted transcriptional regulator [Transcription]
Probab=95.07 E-value=0.047 Score=29.47 Aligned_cols=31 Identities=10% Similarity=0.193 Sum_probs=25.9
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH
Q 038591 34 MSQPDLANQINQRPQVVSEYENGKAVPNQTV 64 (82)
Q Consensus 34 ~s~~elA~~~gis~~~i~~~e~g~~~p~~~~ 64 (82)
+...|++..+|+|++||+++.+....|....
T Consensus 14 lrl~ev~~~~GlSrstiYr~i~~~~FPkpvk 44 (70)
T COG3311 14 LRLPEVAQLTGLSRSTIYRLIKDGTFPKPVK 44 (70)
T ss_pred hhHHHHHHHHCccHHHHHHHHccCCCCCCee
Confidence 4567899999999999999999877776543
No 194
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=95.03 E-value=0.052 Score=35.91 Aligned_cols=33 Identities=15% Similarity=0.255 Sum_probs=27.9
Q ss_pred HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 23 ~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
..|-.+|-..++|++|+|+.+|||.++||+++.
T Consensus 202 k~Vl~l~y~eelt~kEI~~~LgISes~VSql~k 234 (247)
T COG1191 202 KLVLVLRYKEELTQKEIAEVLGISESRVSRLHK 234 (247)
T ss_pred HHHHHHHHHhccCHHHHHHHhCccHHHHHHHHH
Confidence 344456667799999999999999999999986
No 195
>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=94.99 E-value=0.049 Score=30.38 Aligned_cols=22 Identities=23% Similarity=0.212 Sum_probs=20.4
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 038591 34 MSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 34 ~s~~elA~~~gis~~~i~~~e~ 55 (82)
+|..++|+.+|||+.||..||.
T Consensus 2 ~~i~e~A~~~gvs~~tLr~ye~ 23 (91)
T cd04766 2 YVISVAAELSGMHPQTLRLYER 23 (91)
T ss_pred cCHHHHHHHHCcCHHHHHHHHH
Confidence 5788999999999999999995
No 196
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=94.98 E-value=0.065 Score=32.12 Aligned_cols=32 Identities=19% Similarity=0.319 Sum_probs=28.5
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHH
Q 038591 22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEY 53 (82)
Q Consensus 22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~ 53 (82)
-..|+.+......++.++|+.+|+|++++.+-
T Consensus 11 ~~IL~~L~~d~r~~~~eia~~lglS~~~v~~R 42 (154)
T COG1522 11 RRILRLLQEDARISNAELAERVGLSPSTVLRR 42 (154)
T ss_pred HHHHHHHHHhCCCCHHHHHHHHCCCHHHHHHH
Confidence 56788889999999999999999999998765
No 197
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=94.97 E-value=0.073 Score=33.25 Aligned_cols=33 Identities=15% Similarity=0.237 Sum_probs=26.7
Q ss_pred HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 23 ~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
.++=.++.-.|+|..|+|..+|+|+.||.+...
T Consensus 141 ~~~v~l~~~~Gls~~EIA~~lgiS~~tV~r~l~ 173 (185)
T PF07638_consen 141 RRVVELRFFEGLSVEEIAERLGISERTVRRRLR 173 (185)
T ss_pred HHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 334445667899999999999999999988654
No 198
>cd00131 PAX Paired Box domain
Probab=94.94 E-value=0.041 Score=32.79 Aligned_cols=25 Identities=20% Similarity=0.202 Sum_probs=22.9
Q ss_pred hCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 31 GKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 31 ~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
..|+|+.++|..+|||++||++|.+
T Consensus 31 ~~G~s~~~iA~~~~Vs~~tV~r~i~ 55 (128)
T cd00131 31 QSGIRPCDISRQLRVSHGCVSKILN 55 (128)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 4799999999999999999999954
No 199
>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=94.92 E-value=0.056 Score=31.24 Aligned_cols=23 Identities=22% Similarity=0.190 Sum_probs=20.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcC
Q 038591 34 MSQPDLANQINQRPQVVSEYENG 56 (82)
Q Consensus 34 ~s~~elA~~~gis~~~i~~~e~g 56 (82)
++..|+|+.+|||..||..||+-
T Consensus 1 y~Ige~A~~~gvs~~tlR~ye~~ 23 (107)
T cd01111 1 YSISQLALDAGVSVHIVRDYLLR 23 (107)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC
Confidence 47789999999999999999863
No 200
>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=94.88 E-value=0.057 Score=30.63 Aligned_cols=22 Identities=18% Similarity=0.289 Sum_probs=20.2
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 038591 34 MSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 34 ~s~~elA~~~gis~~~i~~~e~ 55 (82)
++..++|+.+|||++||..|++
T Consensus 2 ~~i~eva~~~gVs~~tLR~ye~ 23 (98)
T cd01279 2 YPISVAAELLGIHPQTLRVYDR 23 (98)
T ss_pred cCHHHHHHHHCcCHHHHHHHHH
Confidence 5788999999999999999975
No 201
>PRK10458 DNA cytosine methylase; Provisional
Probab=94.84 E-value=0.15 Score=36.62 Aligned_cols=48 Identities=17% Similarity=0.243 Sum_probs=36.2
Q ss_pred HHHhCCCCHHHHHHHhC------CCHHHHHHHHcCCCC---CCHHHHHHHHHHhCCC
Q 038591 28 ARLGKKMSQPDLANQIN------QRPQVVSEYENGKAV---PNQTVLAKMEKAIGVK 75 (82)
Q Consensus 28 ~r~~~g~s~~elA~~~g------is~~~i~~~e~g~~~---p~~~~~~~la~~lgv~ 75 (82)
.+...+++|+++|..++ .+..++.+|++|... ++...+..|-..+.-.
T Consensus 24 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 80 (467)
T PRK10458 24 EKLLEIYDVKTLAAQLNGVGENHWSRAILKRWLAGKSAWHRLSEAEFAHLQTLLPKP 80 (467)
T ss_pred HHHHHhcCHHHHHHHHhhcccCccCHHHHHHHHcCCCCCCCccHHHHHHHHHhcccC
Confidence 34557899999999997 789999999999763 3446566666665433
No 202
>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=94.83 E-value=0.061 Score=27.69 Aligned_cols=32 Identities=19% Similarity=0.159 Sum_probs=25.3
Q ss_pred HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591 23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYE 54 (82)
Q Consensus 23 ~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e 54 (82)
..|+.+....++|..++|+.+|+++++++.-.
T Consensus 14 ~Il~~L~~~~~~t~~ela~~l~~~~~t~s~hL 45 (61)
T PF12840_consen 14 RILRLLASNGPMTVSELAEELGISQSTVSYHL 45 (61)
T ss_dssp HHHHHHHHCSTBEHHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHH
Confidence 34555667789999999999999999998753
No 203
>COG0789 SoxR Predicted transcriptional regulators [Transcription]
Probab=94.80 E-value=0.04 Score=31.98 Aligned_cols=22 Identities=14% Similarity=0.170 Sum_probs=20.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 038591 34 MSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 34 ~s~~elA~~~gis~~~i~~~e~ 55 (82)
++..++|+.+|||..||.-||.
T Consensus 1 ~~I~eva~~~gvs~~tLRyYE~ 22 (124)
T COG0789 1 YTIGEVAKLTGVSVRTLRFYER 22 (124)
T ss_pred CcHHHHHHHhCCCHHHHHHHHH
Confidence 5788999999999999999986
No 204
>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=94.78 E-value=0.065 Score=30.31 Aligned_cols=23 Identities=13% Similarity=0.198 Sum_probs=20.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcC
Q 038591 34 MSQPDLANQINQRPQVVSEYENG 56 (82)
Q Consensus 34 ~s~~elA~~~gis~~~i~~~e~g 56 (82)
|+..|||+.+|+|.+||..||+-
T Consensus 1 m~I~eva~~~gvs~~tlR~Ye~~ 23 (95)
T cd04780 1 MRMSELSKRSGVSVATIKYYLRE 23 (95)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC
Confidence 57789999999999999999963
No 205
>PF13309 HTH_22: HTH domain
Probab=94.74 E-value=0.031 Score=29.44 Aligned_cols=21 Identities=14% Similarity=0.162 Sum_probs=18.8
Q ss_pred CHHHHHHHhCCCHHHHHHHHc
Q 038591 35 SQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 35 s~~elA~~~gis~~~i~~~e~ 55 (82)
+...+|+.+|||+.||++|.+
T Consensus 44 av~~vA~~L~iS~~TVY~YLr 64 (64)
T PF13309_consen 44 AVEYVAEKLGISRATVYRYLR 64 (64)
T ss_pred HHHHHHHHHCCCHHHHHHHcC
Confidence 668999999999999999863
No 206
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=94.71 E-value=0.06 Score=32.73 Aligned_cols=23 Identities=9% Similarity=0.159 Sum_probs=21.5
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHc
Q 038591 33 KMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 33 g~s~~elA~~~gis~~~i~~~e~ 55 (82)
.++..+||+.+|||..||.-||+
T Consensus 7 ~~~IgevAk~~Gvs~~TLRyYE~ 29 (144)
T PRK13752 7 NLTIGVFAKAAGVNVETIRFYQR 29 (144)
T ss_pred cccHHHHHHHHCcCHHHHHHHHH
Confidence 48999999999999999999986
No 207
>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=94.64 E-value=0.072 Score=30.88 Aligned_cols=22 Identities=23% Similarity=0.288 Sum_probs=20.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 038591 34 MSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 34 ~s~~elA~~~gis~~~i~~~e~ 55 (82)
++..|+|+.+|||+.||..||+
T Consensus 1 m~i~eva~~~gvs~~tlR~Ye~ 22 (112)
T cd01282 1 MRIGELAARTGVSVRSLRYYEE 22 (112)
T ss_pred CCHHHHHHHHCCCHHHHHHHHH
Confidence 5788999999999999999986
No 208
>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=94.63 E-value=0.065 Score=28.11 Aligned_cols=33 Identities=6% Similarity=0.005 Sum_probs=27.4
Q ss_pred HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 23 ~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
..+..+....++|..++|+.+|+++++++++.+
T Consensus 12 ~vy~~Ll~~~~~t~~eIa~~l~i~~~~v~~~L~ 44 (68)
T PF01978_consen 12 KVYLALLKNGPATAEEIAEELGISRSTVYRALK 44 (68)
T ss_dssp HHHHHHHHHCHEEHHHHHHHHTSSHHHHHHHHH
T ss_pred HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 344556677889999999999999999998764
No 209
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=94.62 E-value=0.14 Score=25.25 Aligned_cols=22 Identities=18% Similarity=0.095 Sum_probs=20.4
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 038591 34 MSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 34 ~s~~elA~~~gis~~~i~~~e~ 55 (82)
.|.+++|+.+|+|..||.++.+
T Consensus 28 ~s~~~vA~~~~vs~~TV~ri~~ 49 (52)
T PF13542_consen 28 RSFKDVARELGVSWSTVRRIFD 49 (52)
T ss_pred CCHHHHHHHHCCCHHHHHHHHH
Confidence 6999999999999999999865
No 210
>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=94.62 E-value=0.063 Score=26.44 Aligned_cols=25 Identities=8% Similarity=0.133 Sum_probs=22.9
Q ss_pred hCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 31 GKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 31 ~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
..|+|..++|+.+|+|+.+|..+..
T Consensus 13 ~~~~s~~eia~~l~~s~~tv~~~~~ 37 (57)
T cd06170 13 AEGKTNKEIADILGISEKTVKTHLR 37 (57)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 4799999999999999999999865
No 211
>PF13730 HTH_36: Helix-turn-helix domain
Probab=94.54 E-value=0.058 Score=27.02 Aligned_cols=21 Identities=24% Similarity=0.232 Sum_probs=19.5
Q ss_pred CHHHHHHHhCCCHHHHHHHHc
Q 038591 35 SQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 35 s~~elA~~~gis~~~i~~~e~ 55 (82)
|++.+|+.+|+|+.||.++.+
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~ 47 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIK 47 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 899999999999999999865
No 212
>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=94.53 E-value=0.052 Score=31.64 Aligned_cols=22 Identities=27% Similarity=0.318 Sum_probs=20.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 038591 34 MSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 34 ~s~~elA~~~gis~~~i~~~e~ 55 (82)
+|..|+|+.+|||+.||..||.
T Consensus 1 ~~ige~a~~~gvs~~tLryYe~ 22 (116)
T cd04769 1 MYIGELAQQTGVTIKAIRLYEE 22 (116)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 5788999999999999999996
No 213
>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=94.52 E-value=0.05 Score=32.13 Aligned_cols=22 Identities=14% Similarity=0.286 Sum_probs=20.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 038591 34 MSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 34 ~s~~elA~~~gis~~~i~~~e~ 55 (82)
|+..|+|+.+|||+.||..||.
T Consensus 1 m~I~e~a~~~gvs~~tlR~Ye~ 22 (126)
T cd04783 1 LTIGELAKAAGVNVETIRYYQR 22 (126)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 5788999999999999999986
No 214
>smart00497 IENR1 Intron encoded nuclease repeat motif. Repeat of unknown function, but possibly DNA-binding via helix-turn-helix motif (Ponting, unpublished).
Probab=94.52 E-value=0.077 Score=26.25 Aligned_cols=24 Identities=21% Similarity=0.201 Sum_probs=21.9
Q ss_pred CHHHHHHHhCCCHHHHHHHHcCCC
Q 038591 35 SQPDLANQINQRPQVVSEYENGKA 58 (82)
Q Consensus 35 s~~elA~~~gis~~~i~~~e~g~~ 58 (82)
|+.+.|+.+|++.++|+++.+|..
T Consensus 19 S~~eAa~~lg~~~~~I~~~~~~~~ 42 (53)
T smart00497 19 SIREAAKYLGISHSSISKYLNTGK 42 (53)
T ss_pred CHHHHHHHhCCCHHHHHHHHhCCC
Confidence 788999999999999999999854
No 215
>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=94.51 E-value=0.052 Score=31.78 Aligned_cols=22 Identities=27% Similarity=0.439 Sum_probs=20.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 038591 34 MSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 34 ~s~~elA~~~gis~~~i~~~e~ 55 (82)
+|..|+|+.+|||+.||.-||+
T Consensus 1 ~~I~eva~~~gvs~~tLRyYe~ 22 (123)
T cd04770 1 MKIGELAKAAGVSPDTIRYYER 22 (123)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 5788999999999999999986
No 216
>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=94.46 E-value=0.08 Score=31.41 Aligned_cols=23 Identities=17% Similarity=0.254 Sum_probs=20.8
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcC
Q 038591 34 MSQPDLANQINQRPQVVSEYENG 56 (82)
Q Consensus 34 ~s~~elA~~~gis~~~i~~~e~g 56 (82)
++..++|+.+|||++||..||+-
T Consensus 2 ysI~eVA~~~GVs~~TLR~wE~~ 24 (120)
T cd04767 2 YPIGVVAELLNIHPETLRIWERH 24 (120)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC
Confidence 67899999999999999999863
No 217
>PRK13182 racA polar chromosome segregation protein; Reviewed
Probab=94.46 E-value=0.065 Score=33.73 Aligned_cols=22 Identities=23% Similarity=0.480 Sum_probs=19.9
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 038591 34 MSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 34 ~s~~elA~~~gis~~~i~~~e~ 55 (82)
++..++|+.+|||+.||.+|+.
T Consensus 1 mti~evA~~lGVS~~TLRrw~k 22 (175)
T PRK13182 1 MKTPFVAKKLGVSPKTVQRWVK 22 (175)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 5788999999999999999973
No 218
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=94.44 E-value=0.071 Score=32.82 Aligned_cols=32 Identities=13% Similarity=0.233 Sum_probs=28.0
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHH
Q 038591 22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEY 53 (82)
Q Consensus 22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~ 53 (82)
-..|..+.+...+|..++|+.+|+|++++.+-
T Consensus 17 ~~IL~~Lq~d~R~s~~eiA~~lglS~~tv~~R 48 (164)
T PRK11169 17 RNILNELQKDGRISNVELSKRVGLSPTPCLER 48 (164)
T ss_pred HHHHHHhccCCCCCHHHHHHHHCcCHHHHHHH
Confidence 56778888999999999999999999997653
No 219
>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=94.43 E-value=0.05 Score=33.49 Aligned_cols=24 Identities=13% Similarity=0.235 Sum_probs=21.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 32 KKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 32 ~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
..+|+.++|..+|+++.||++..+
T Consensus 142 ~~~t~~~iA~~lG~tretvsR~l~ 165 (193)
T TIGR03697 142 LRLSHQAIAEAIGSTRVTITRLLG 165 (193)
T ss_pred CCCCHHHHHHHhCCcHHHHHHHHH
Confidence 358999999999999999999754
No 220
>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=94.37 E-value=0.063 Score=26.29 Aligned_cols=30 Identities=13% Similarity=0.161 Sum_probs=23.0
Q ss_pred HHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 25 IQRARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 25 lk~~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
|..+.. ..++..|+|+.+|+++++|++..+
T Consensus 8 l~~L~~-~~~~~~el~~~l~~s~~~vs~hL~ 37 (47)
T PF01022_consen 8 LKLLSE-GPLTVSELAEELGLSQSTVSHHLK 37 (47)
T ss_dssp HHHHTT-SSEEHHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHh-CCCchhhHHHhccccchHHHHHHH
Confidence 344444 778999999999999999998753
No 221
>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=94.37 E-value=0.055 Score=32.82 Aligned_cols=22 Identities=18% Similarity=0.268 Sum_probs=20.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 038591 34 MSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 34 ~s~~elA~~~gis~~~i~~~e~ 55 (82)
|+..|+|+.+|||+.||.-||.
T Consensus 2 ~~IgevA~~~Gvs~~tLRyYE~ 23 (142)
T TIGR01950 2 LTVGELAKRSGVAVSALHFYES 23 (142)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 6889999999999999999996
No 222
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=94.32 E-value=0.14 Score=27.91 Aligned_cols=30 Identities=7% Similarity=0.103 Sum_probs=23.9
Q ss_pred HHHHHHh-CCCCHHHHHHHhCCCHHHHHHHH
Q 038591 25 IQRARLG-KKMSQPDLANQINQRPQVVSEYE 54 (82)
Q Consensus 25 lk~~r~~-~g~s~~elA~~~gis~~~i~~~e 54 (82)
|..+-.. .++|..++|+.+|+++++++++.
T Consensus 11 l~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l 41 (91)
T smart00346 11 LRALAEEPGGLTLAELAERLGLSKSTAHRLL 41 (91)
T ss_pred HHHHHhCCCCcCHHHHHHHhCCCHHHHHHHH
Confidence 3444343 47999999999999999999884
No 223
>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=94.28 E-value=0.049 Score=28.39 Aligned_cols=33 Identities=9% Similarity=0.005 Sum_probs=24.7
Q ss_pred HHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCC
Q 038591 25 IQRARLGKKMSQPDLANQINQRPQVVSEYENGKAV 59 (82)
Q Consensus 25 lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~ 59 (82)
|.++-...| |.+.|+.+||+++.|++..+-.++
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 445555566 999999999999999999876554
No 224
>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=94.26 E-value=0.063 Score=32.03 Aligned_cols=22 Identities=32% Similarity=0.436 Sum_probs=20.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 038591 34 MSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 34 ~s~~elA~~~gis~~~i~~~e~ 55 (82)
|+..|||+.+|||+.||.-||+
T Consensus 1 m~IgE~A~~~gvs~~TLRyYE~ 22 (133)
T cd04787 1 MKVKELANAAGVTPDTVRFYTR 22 (133)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 5788999999999999999986
No 225
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=94.23 E-value=0.17 Score=28.69 Aligned_cols=34 Identities=6% Similarity=-0.086 Sum_probs=29.0
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
...|..+....+..+.+.|+.+||+++|+.+...
T Consensus 57 r~~i~~aL~~~~gn~s~AAr~LGIsRsTL~rKLk 90 (95)
T PRK00430 57 APLLDMVMQYTRGNQTRAALMLGINRGTLRKKLK 90 (95)
T ss_pred HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHH
Confidence 3457777888899999999999999999988765
No 226
>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=94.22 E-value=0.058 Score=27.46 Aligned_cols=26 Identities=19% Similarity=0.339 Sum_probs=22.1
Q ss_pred HhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 30 LGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 30 ~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
-..|.+..++|+.+|+|+.||..+.+
T Consensus 15 l~~G~~~~eIA~~l~is~~tV~~~~~ 40 (58)
T PF00196_consen 15 LAQGMSNKEIAEELGISEKTVKSHRR 40 (58)
T ss_dssp HHTTS-HHHHHHHHTSHHHHHHHHHH
T ss_pred HHhcCCcchhHHhcCcchhhHHHHHH
Confidence 45799999999999999999998754
No 227
>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=94.22 E-value=0.092 Score=31.67 Aligned_cols=22 Identities=18% Similarity=0.243 Sum_probs=20.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 038591 34 MSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 34 ~s~~elA~~~gis~~~i~~~e~ 55 (82)
++..|+|+.+|||+.||..||.
T Consensus 2 ~~I~EvA~~~Gvs~~tLRyYE~ 23 (139)
T cd01110 2 LSVGEVAKRSGVAVSALHFYEQ 23 (139)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 6889999999999999999985
No 228
>PF13556 HTH_30: PucR C-terminal helix-turn-helix domain; PDB: 3ONQ_B.
Probab=94.20 E-value=0.22 Score=25.56 Aligned_cols=39 Identities=15% Similarity=0.172 Sum_probs=29.0
Q ss_pred hCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcccc
Q 038591 31 GKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVKI 80 (82)
Q Consensus 31 ~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e~~ 80 (82)
..+.+..+.|+.++|.++|+.. .+.+|.+.+|+++++-+
T Consensus 10 ~~~~n~~~tA~~L~iHrNTl~y-----------Rl~ki~~l~g~dl~~~~ 48 (59)
T PF13556_consen 10 ENNGNISKTARALHIHRNTLRY-----------RLKKIEELLGLDLDDPE 48 (59)
T ss_dssp HTTT-HHHHHHHHTS-HHHHHH-----------HHHHHHHHHS--TTSHH
T ss_pred HcCCCHHHHHHHHCCCHHHHHH-----------HHHHHHHHHCcCCCCHH
Confidence 4678999999999999999976 56788888888887643
No 229
>PRK01905 DNA-binding protein Fis; Provisional
Probab=94.12 E-value=0.2 Score=27.19 Aligned_cols=34 Identities=6% Similarity=-0.101 Sum_probs=29.2
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
...+..+....+.++.+.|+.+||+++++++...
T Consensus 39 ~~~i~~aL~~~~gn~s~aAr~LGIsrstL~rklk 72 (77)
T PRK01905 39 KPLLEVVMEQAGGNQSLAAEYLGINRNTLRKKLQ 72 (77)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 4567778888899999999999999999988765
No 230
>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=94.07 E-value=0.11 Score=30.48 Aligned_cols=22 Identities=23% Similarity=0.498 Sum_probs=20.2
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 038591 34 MSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 34 ~s~~elA~~~gis~~~i~~~e~ 55 (82)
++..++|+.+|||..||.-||+
T Consensus 1 ~~Igeva~~~gvs~~tlRyYe~ 22 (118)
T cd04776 1 YTISELAREFDVTPRTLRFYED 22 (118)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 4678999999999999999986
No 231
>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=94.02 E-value=0.12 Score=25.23 Aligned_cols=25 Identities=16% Similarity=0.088 Sum_probs=22.1
Q ss_pred hCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 31 GKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 31 ~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
-.++|..++|+++|+++++++++-.
T Consensus 14 ~~~~s~~~Ia~~~gvs~~~~y~~f~ 38 (47)
T PF00440_consen 14 YEAVSIRDIARRAGVSKGSFYRYFP 38 (47)
T ss_dssp TTTSSHHHHHHHHTSCHHHHHHHCS
T ss_pred HHhCCHHHHHHHHccchhhHHHHcC
Confidence 4678999999999999999998754
No 232
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=94.01 E-value=0.025 Score=40.64 Aligned_cols=45 Identities=16% Similarity=0.169 Sum_probs=38.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 038591 32 KKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKL 76 (82)
Q Consensus 32 ~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~ 76 (82)
+-|+.+++|+.+|++.+|||+.-+|+..-+..-+.-|-.+|...+
T Consensus 368 kPLtlkdVAe~lglHeSTVSRa~~~KY~~tp~GifeLK~FFs~~v 412 (481)
T PRK12469 368 KPLVLRDVAEELGLHESTISRATGNKYMATPRGTFEFKHFFPRKL 412 (481)
T ss_pred cCCcHHHHHHHhCCCcchhhHHhcCceeecCCceEeHHHhhcccc
Confidence 358999999999999999999999987777777777777887554
No 233
>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=94.01 E-value=0.15 Score=32.72 Aligned_cols=28 Identities=29% Similarity=0.275 Sum_probs=24.6
Q ss_pred HHhCCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591 29 RLGKKMSQPDLANQINQRPQVVSEYENG 56 (82)
Q Consensus 29 r~~~g~s~~elA~~~gis~~~i~~~e~g 56 (82)
+-..|+|+.++|+.+|+|+.+|+++++.
T Consensus 195 ~~~~~~t~~eIA~~lgis~~~V~~~~~~ 222 (231)
T TIGR02885 195 RYFKDKTQTEVANMLGISQVQVSRLEKK 222 (231)
T ss_pred HHHcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 3346999999999999999999999864
No 234
>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=93.98 E-value=0.19 Score=30.07 Aligned_cols=35 Identities=14% Similarity=0.280 Sum_probs=30.2
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCC
Q 038591 33 KMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGV 74 (82)
Q Consensus 33 g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv 74 (82)
.+|..++|..+|+|.++++++.+ ..+.+||..||.
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 46999999999999999999976 477888888873
No 235
>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=93.91 E-value=0.078 Score=31.94 Aligned_cols=22 Identities=18% Similarity=0.217 Sum_probs=20.2
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 038591 34 MSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 34 ~s~~elA~~~gis~~~i~~~e~ 55 (82)
++..++|+.+|||+.||..||.
T Consensus 1 y~I~e~a~~~gvs~~TLR~Ye~ 22 (134)
T cd04779 1 YRIGQLAHLAGVSKRTIDYYTN 22 (134)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 4678999999999999999985
No 236
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=93.91 E-value=0.18 Score=30.14 Aligned_cols=34 Identities=6% Similarity=0.066 Sum_probs=27.4
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
...|..+...-++|+.+||+.++++++++++..+
T Consensus 43 ~~vL~~l~~~~~~t~~eLa~~l~i~~~tvsr~l~ 76 (144)
T PRK11512 43 FKVLCSIRCAACITPVELKKVLSVDLGALTRMLD 76 (144)
T ss_pred HHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3445666666789999999999999999998743
No 237
>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=93.89 E-value=0.12 Score=30.50 Aligned_cols=22 Identities=23% Similarity=0.356 Sum_probs=20.4
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 038591 34 MSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 34 ~s~~elA~~~gis~~~i~~~e~ 55 (82)
++..|+|+.+|||+.||..||.
T Consensus 1 ~~I~e~a~~~gvs~~tlR~Ye~ 22 (126)
T cd04785 1 LSIGELARRTGVNVETIRYYES 22 (126)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 5788999999999999999986
No 238
>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=93.88 E-value=0.25 Score=25.31 Aligned_cols=35 Identities=23% Similarity=0.320 Sum_probs=28.4
Q ss_pred CHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcccc
Q 038591 35 SQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVKI 80 (82)
Q Consensus 35 s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e~~ 80 (82)
|....|+.+|+|+++|++ .+..|.+.||+++-+++
T Consensus 15 s~~~AA~~l~is~~~vs~-----------~i~~LE~~lg~~Lf~r~ 49 (60)
T PF00126_consen 15 SISAAAEELGISQSAVSR-----------QIKQLEEELGVPLFERS 49 (60)
T ss_dssp SHHHHHHHCTSSHHHHHH-----------HHHHHHHHHTS-SEEEC
T ss_pred CHHHHHHHhhccchHHHH-----------HHHHHHHHhCCeEEEEC
Confidence 677799999999999998 45778888888887664
No 239
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=93.86 E-value=0.16 Score=30.88 Aligned_cols=34 Identities=12% Similarity=0.096 Sum_probs=28.9
Q ss_pred CCHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHH
Q 038591 20 DTPRQIQRARLGKKMSQPDLANQINQRPQVVSEY 53 (82)
Q Consensus 20 ~~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~ 53 (82)
+....|..+......|..++|+.+|+|++++.+-
T Consensus 10 ~D~~Il~~Lq~d~R~s~~eiA~~lglS~~tV~~R 43 (153)
T PRK11179 10 LDRGILEALMENARTPYAELAKQFGVSPGTIHVR 43 (153)
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHH
Confidence 3466778888889999999999999999997654
No 240
>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=93.83 E-value=0.21 Score=26.17 Aligned_cols=27 Identities=11% Similarity=0.094 Sum_probs=22.5
Q ss_pred HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 29 RLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 29 r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
......+..+||+.+|+|.++|++...
T Consensus 9 L~~~~~~~~eLa~~l~vS~~tv~~~l~ 35 (69)
T TIGR00122 9 LADNPFSGEKLGEALGMSRTAVNKHIQ 35 (69)
T ss_pred HHcCCcCHHHHHHHHCCCHHHHHHHHH
Confidence 445568899999999999999988754
No 241
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=93.83 E-value=0.074 Score=33.04 Aligned_cols=24 Identities=13% Similarity=0.153 Sum_probs=21.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 32 KKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 32 ~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
..+|+.++|..+|+++.+|++..+
T Consensus 148 ~~~t~~~iA~~lG~tretvsR~l~ 171 (202)
T PRK13918 148 IYATHDELAAAVGSVRETVTKVIG 171 (202)
T ss_pred ecCCHHHHHHHhCccHHHHHHHHH
Confidence 357999999999999999999754
No 242
>TIGR02395 rpoN_sigma RNA polymerase sigma-54 factor. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called sigma-54, or RpoN (unrelated to sigma 70-type factors such as RpoD/SigA). RpoN is responsible for enhancer-dependent transcription, and its presence characteristically is associated with varied panels of activators, most of which are enhancer-binding proteins (but see Brahmachary, et al., PubMed:15231786). RpoN may be responsible for transcription of nitrogen fixation genes, flagellins, pilins, etc., and synonyms for the gene symbol rpoN, such as ntrA, reflect these observations
Probab=93.79 E-value=0.023 Score=40.22 Aligned_cols=45 Identities=11% Similarity=0.155 Sum_probs=36.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 038591 32 KKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKL 76 (82)
Q Consensus 32 ~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~ 76 (82)
+-||.+++|+.+|++.+|||+.-+|+..-+..-+.-|-.+|.-.+
T Consensus 317 kPLtlkdiA~~lglheSTVSRav~~Kyi~tp~Gi~~lk~FFs~~~ 361 (429)
T TIGR02395 317 KPLTLREVAEELGLHESTISRAINNKYLQTPRGVFELKYFFSRGV 361 (429)
T ss_pred cCCcHHHHHHHhCCCccchhhhhcCceEecCCceEEHHHhcCCcc
Confidence 358999999999999999999999987666666666777776433
No 243
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=93.75 E-value=0.22 Score=28.15 Aligned_cols=34 Identities=15% Similarity=0.304 Sum_probs=27.5
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
-..|..+.....+|..++|+.+|+|++++++..+
T Consensus 6 ~~il~~L~~~~~~~~~~la~~l~~s~~tv~~~l~ 39 (108)
T smart00344 6 RKILEELQKDARISLAELAKKVGLSPSTVHNRVK 39 (108)
T ss_pred HHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 3456667777789999999999999999987643
No 244
>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=93.73 E-value=0.084 Score=31.15 Aligned_cols=21 Identities=19% Similarity=0.286 Sum_probs=19.1
Q ss_pred CHHHHHHHhCCCHHHHHHHHc
Q 038591 35 SQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 35 s~~elA~~~gis~~~i~~~e~ 55 (82)
|..|||+.+|||+.||..||.
T Consensus 1 ~I~e~a~~~gvs~~tlR~Ye~ 21 (124)
T TIGR02051 1 TIGELAKAAGVNVETIRYYER 21 (124)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 467999999999999999986
No 245
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=93.66 E-value=0.32 Score=27.43 Aligned_cols=36 Identities=17% Similarity=0.167 Sum_probs=31.1
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591 22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGK 57 (82)
Q Consensus 22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~ 57 (82)
...|++-.+..|+|..++|..+|+|...|.++.+=+
T Consensus 12 ~~ELq~nf~~~~ls~~~ia~dL~~s~~~le~vL~l~ 47 (89)
T PF10078_consen 12 RQELQANFELSGLSLEQIAADLGTSPEHLEQVLNLK 47 (89)
T ss_pred HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCC
Confidence 456777778899999999999999999999998743
No 246
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=93.61 E-value=0.11 Score=32.80 Aligned_cols=32 Identities=16% Similarity=0.353 Sum_probs=26.2
Q ss_pred HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591 24 QIQRARLGKKMSQPDLANQINQRPQVVSEYENG 56 (82)
Q Consensus 24 ~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g 56 (82)
.+..+ ...|+|..++|+.+|||++|+++|.+.
T Consensus 164 ~i~~~-~~~g~s~~~iak~lgis~~Tv~r~~k~ 195 (200)
T PRK13413 164 KIKKL-LDKGTSKSEIARKLGVSRTTLARFLKT 195 (200)
T ss_pred HHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHh
Confidence 44444 356999999999999999999999863
No 247
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=93.58 E-value=0.091 Score=32.82 Aligned_cols=23 Identities=9% Similarity=0.253 Sum_probs=21.0
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHc
Q 038591 33 KMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 33 g~s~~elA~~~gis~~~i~~~e~ 55 (82)
.+|+++||..+|+++.+++++.+
T Consensus 168 ~~t~~~lA~~lG~tr~tvsR~l~ 190 (211)
T PRK11753 168 KITRQEIGRIVGCSREMVGRVLK 190 (211)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHH
Confidence 58999999999999999999864
No 248
>PF07453 NUMOD1: NUMOD1 domain; InterPro: IPR010896 This helix-turn-helix-containing DNA-binding domain is found associated in homing nucleases [].
Probab=93.54 E-value=0.12 Score=23.98 Aligned_cols=19 Identities=21% Similarity=0.289 Sum_probs=17.5
Q ss_pred CHHHHHHHhCCCHHHHHHH
Q 038591 35 SQPDLANQINQRPQVVSEY 53 (82)
Q Consensus 35 s~~elA~~~gis~~~i~~~ 53 (82)
|..+.|+.+|++.++|+++
T Consensus 18 Si~eAa~~l~i~~~~I~~~ 36 (37)
T PF07453_consen 18 SIREAARYLGISHSTISKY 36 (37)
T ss_pred CHHHHHHHhCCCHHHHHHh
Confidence 7889999999999999876
No 249
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=93.52 E-value=0.03 Score=39.95 Aligned_cols=45 Identities=11% Similarity=0.182 Sum_probs=36.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 038591 32 KKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKL 76 (82)
Q Consensus 32 ~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~ 76 (82)
+-||++++|+.+|++.+|||+.-+|+..-+..-+.-|-.+|...+
T Consensus 342 kPLtlkdvAe~lglheSTVSRav~~Kyv~tp~Gi~~lk~FFs~~~ 386 (455)
T PRK05932 342 KPLVLKDIAEELGMHESTISRATTNKYMATPRGIFELKYFFSSAV 386 (455)
T ss_pred cCccHHHHHHHhCCCccchhhhhcCceeecCCceEEHHHhccccc
Confidence 358999999999999999999999987656556666666776544
No 250
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=93.49 E-value=0.12 Score=25.68 Aligned_cols=22 Identities=27% Similarity=0.314 Sum_probs=19.4
Q ss_pred C-CHHHHHHHhCCCHHHHHHHHc
Q 038591 34 M-SQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 34 ~-s~~elA~~~gis~~~i~~~e~ 55 (82)
+ |+.+||+.+|+|++++.+..+
T Consensus 20 l~s~~~la~~~~vs~~tv~~~l~ 42 (60)
T smart00345 20 LPSERELAAQLGVSRTTVREALS 42 (60)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHH
Confidence 5 899999999999999988653
No 251
>PRK09954 putative kinase; Provisional
Probab=93.48 E-value=0.18 Score=34.43 Aligned_cols=34 Identities=12% Similarity=0.060 Sum_probs=29.6
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
...|+.+++...+|+.++|+.+|+|+++|.+..+
T Consensus 6 ~~il~~l~~~~~~s~~~la~~l~~s~~~v~~~i~ 39 (362)
T PRK09954 6 KEILAILRRNPLIQQNEIADILQISRSRVAAHIM 39 (362)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3467888888899999999999999999998865
No 252
>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=93.47 E-value=0.2 Score=26.30 Aligned_cols=30 Identities=13% Similarity=0.210 Sum_probs=24.0
Q ss_pred HHHHhCCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591 27 RARLGKKMSQPDLANQINQRPQVVSEYENG 56 (82)
Q Consensus 27 ~~r~~~g~s~~elA~~~gis~~~i~~~e~g 56 (82)
++..+.--+|.|+|+.+++++.||.+|-..
T Consensus 10 elLi~~~GnqtEvaR~l~c~R~TVrKY~~D 39 (64)
T PF06322_consen 10 ELLIETYGNQTEVARRLGCNRATVRKYSRD 39 (64)
T ss_pred HHHHHHhCcHHHHHHHhcccHHHHHHHhcc
Confidence 333444458999999999999999999765
No 253
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=93.45 E-value=0.14 Score=34.03 Aligned_cols=34 Identities=15% Similarity=0.140 Sum_probs=30.6
Q ss_pred HHHHHHHHHhCC-CCHHHHHHHhCCCHHHHHHHHc
Q 038591 22 PRQIQRARLGKK-MSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 22 ~~~lk~~r~~~g-~s~~elA~~~gis~~~i~~~e~ 55 (82)
.+.|+.++..-| ++|.||.+.+|.|++|++++.+
T Consensus 198 ~~il~~i~~~GGri~Q~eL~r~lglsktTvsR~L~ 232 (258)
T COG2512 198 KEILDLIRERGGRITQAELRRALGLSKTTVSRILR 232 (258)
T ss_pred HHHHHHHHHhCCEEeHHHHHHhhCCChHHHHHHHH
Confidence 677888888888 9999999999999999999864
No 254
>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=93.40 E-value=0.09 Score=30.32 Aligned_cols=27 Identities=15% Similarity=0.219 Sum_probs=19.7
Q ss_pred HhCCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591 30 LGKKMSQPDLANQINQRPQVVSEYENG 56 (82)
Q Consensus 30 ~~~g~s~~elA~~~gis~~~i~~~e~g 56 (82)
-.-++|..|+|+.+|||+++|+.+.+-
T Consensus 30 y~eDlSlsEIAe~~~iSRqaV~d~ikr 56 (101)
T PF04297_consen 30 YEEDLSLSEIAEELGISRQAVYDSIKR 56 (101)
T ss_dssp CTS---HHHHHHHCTS-HHHHHHHHHH
T ss_pred HccCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 346899999999999999999998753
No 255
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=93.29 E-value=0.12 Score=33.14 Aligned_cols=23 Identities=26% Similarity=0.313 Sum_probs=20.9
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHc
Q 038591 33 KMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 33 g~s~~elA~~~gis~~~i~~~e~ 55 (82)
..+.++||+.+|||++|++...+
T Consensus 178 ~~~l~dLA~~lGISkst~~ehLR 200 (215)
T COG3413 178 RVSLKDLAKELGISKSTLSEHLR 200 (215)
T ss_pred cCCHHHHHHHhCCCHHHHHHHHH
Confidence 56999999999999999998875
No 256
>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=93.29 E-value=0.11 Score=34.42 Aligned_cols=23 Identities=17% Similarity=0.328 Sum_probs=21.9
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHc
Q 038591 33 KMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 33 g~s~~elA~~~gis~~~i~~~e~ 55 (82)
++|++++|+.+|||+.+|++++.
T Consensus 236 ~~t~~eIA~~lgvS~~~V~q~~~ 258 (270)
T TIGR02392 236 KLTLQELAAEYGVSAERIRQIEK 258 (270)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHH
Confidence 79999999999999999999986
No 257
>PRK05572 sporulation sigma factor SigF; Validated
Probab=93.27 E-value=0.23 Score=32.41 Aligned_cols=28 Identities=25% Similarity=0.273 Sum_probs=24.6
Q ss_pred HHhCCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591 29 RLGKKMSQPDLANQINQRPQVVSEYENG 56 (82)
Q Consensus 29 r~~~g~s~~elA~~~gis~~~i~~~e~g 56 (82)
+-..|+|+.++|+.+|+|+++|+++++.
T Consensus 214 ~~~~~~s~~eIA~~lgis~~~V~~~~~r 241 (252)
T PRK05572 214 RYFKDKTQSEVAKRLGISQVQVSRLEKK 241 (252)
T ss_pred HHhCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 4446999999999999999999999864
No 258
>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=93.22 E-value=0.12 Score=26.85 Aligned_cols=26 Identities=23% Similarity=0.391 Sum_probs=21.2
Q ss_pred HhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 30 LGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 30 ~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
....++..++|+.+|+|+++++...+
T Consensus 19 ~~~~v~~~~iA~~L~vs~~tvt~ml~ 44 (60)
T PF01325_consen 19 EGGPVRTKDIAERLGVSPPTVTEMLK 44 (60)
T ss_dssp CTSSBBHHHHHHHHTS-HHHHHHHHH
T ss_pred CCCCccHHHHHHHHCCChHHHHHHHH
Confidence 44678999999999999999998753
No 259
>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=93.19 E-value=0.28 Score=25.20 Aligned_cols=32 Identities=16% Similarity=0.173 Sum_probs=25.5
Q ss_pred HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 24 QIQRARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 24 ~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
.|..+-....++..++|..+|+|..+|.++.+
T Consensus 10 Ll~~L~~~~~~~~~ela~~l~~S~rti~~~i~ 41 (59)
T PF08280_consen 10 LLELLLKNKWITLKELAKKLNISERTIKNDIN 41 (59)
T ss_dssp HHHHHHHHTSBBHHHHHHHCTS-HHHHHHHHH
T ss_pred HHHHHHcCCCCcHHHHHHHHCCCHHHHHHHHH
Confidence 34555567789999999999999999998764
No 260
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=93.17 E-value=0.29 Score=25.58 Aligned_cols=24 Identities=17% Similarity=0.289 Sum_probs=19.8
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHcC
Q 038591 33 KMSQPDLANQINQRPQVVSEYENG 56 (82)
Q Consensus 33 g~s~~elA~~~gis~~~i~~~e~g 56 (82)
.+|..++|+.+|+|..++.++...
T Consensus 1 ~~~~~~la~~~~~s~~~l~~~f~~ 24 (84)
T smart00342 1 PLTLEDLAEALGMSPRHLQRLFKK 24 (84)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHH
Confidence 368889999999999998888753
No 261
>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=93.14 E-value=0.15 Score=30.14 Aligned_cols=24 Identities=21% Similarity=0.285 Sum_probs=20.8
Q ss_pred HHHhCCCCHHHHHHHhCCCHHHHH
Q 038591 28 ARLGKKMSQPDLANQINQRPQVVS 51 (82)
Q Consensus 28 ~r~~~g~s~~elA~~~gis~~~i~ 51 (82)
++--.|+|.+|+|+.+|+|.+||.
T Consensus 118 l~~~~~~s~~EIA~~l~is~~tV~ 141 (142)
T TIGR03209 118 MKFFEDMKEIDIAKKLHISRQSVY 141 (142)
T ss_pred HHHHcCCCHHHHHHHHCcCHHhhc
Confidence 445679999999999999999985
No 262
>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=93.06 E-value=0.19 Score=31.37 Aligned_cols=22 Identities=23% Similarity=0.315 Sum_probs=20.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 038591 34 MSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 34 ~s~~elA~~~gis~~~i~~~e~ 55 (82)
+|..|||+.+|||+.||..||.
T Consensus 2 ~~I~evA~~~gvs~~tLRyYe~ 23 (172)
T cd04790 2 LTISQLARQFGLSRSTLLYYER 23 (172)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 6889999999999999999986
No 263
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=93.06 E-value=0.2 Score=26.38 Aligned_cols=30 Identities=7% Similarity=0.094 Sum_probs=22.6
Q ss_pred HHHHH-hCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 26 QRARL-GKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 26 k~~r~-~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
..+.. ...++-.|+|+.+|+|..++..|.+
T Consensus 7 ~~i~~~~~p~~T~eiA~~~gls~~~aR~yL~ 37 (62)
T PF04703_consen 7 EYIKEQNGPLKTREIADALGLSIYQARYYLE 37 (62)
T ss_dssp HHHHHHTS-EEHHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHcCCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 33444 5789999999999999999998864
No 264
>COG1974 LexA SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms]
Probab=93.06 E-value=0.18 Score=32.44 Aligned_cols=49 Identities=14% Similarity=0.089 Sum_probs=43.4
Q ss_pred HHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 038591 27 RARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKL 76 (82)
Q Consensus 27 ~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~ 76 (82)
..+++.+.++.++++..|+++ ++..|.++-..++...+....+.|+..-
T Consensus 6 rrq~el~~~~~~~~~~~g~~p-s~~e~~~~~~~~s~~~~~~~l~~L~~~g 54 (201)
T COG1974 6 RRQKELLDFIRSLIKETGYPP-SIREIGDALGLASPSAIHSHLKALERKG 54 (201)
T ss_pred HHHHHHHHHHHHHHHHhCCCc-cHHHHHHhhCCCChHHHHHHHHHHhcCC
Confidence 356778899999999999999 9999999999999999999999887653
No 265
>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional
Probab=93.05 E-value=0.23 Score=33.76 Aligned_cols=34 Identities=15% Similarity=0.099 Sum_probs=29.3
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
...|..+....+.++.+.|+.+|||++|+++..+
T Consensus 288 r~~I~~aL~~~~gn~~~aA~~LGIsR~tLyrklk 321 (326)
T PRK11608 288 KELLQRSLQQAKFNQKRAAELLGLTYHQLRALLK 321 (326)
T ss_pred HHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHH
Confidence 4457777788899999999999999999998875
No 266
>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=93.05 E-value=0.31 Score=28.80 Aligned_cols=28 Identities=11% Similarity=-0.021 Sum_probs=24.0
Q ss_pred HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 28 ARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 28 ~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
++--.|+|..|+|..+|+|+++|.....
T Consensus 124 l~~~~~~~~~eIA~~lgis~~tv~~~~~ 151 (161)
T TIGR02985 124 LSRFEGKSYKEIAEELGISVKTVEYHIS 151 (161)
T ss_pred HHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3445799999999999999999998764
No 267
>PRK09480 slmA division inhibitor protein; Provisional
Probab=93.02 E-value=0.1 Score=32.05 Aligned_cols=28 Identities=14% Similarity=0.178 Sum_probs=25.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHcCCCC
Q 038591 32 KKMSQPDLANQINQRPQVVSEYENGKAV 59 (82)
Q Consensus 32 ~g~s~~elA~~~gis~~~i~~~e~g~~~ 59 (82)
.+.|..++|+.+|||+++++.+-.++..
T Consensus 29 ~~~ti~~Ia~~agvs~gt~Y~~F~~K~~ 56 (194)
T PRK09480 29 ERITTAKLAARVGVSEAALYRHFPSKAR 56 (194)
T ss_pred CccCHHHHHHHhCCCHhHHHHHCCCHHH
Confidence 5899999999999999999999887654
No 268
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=93.00 E-value=0.12 Score=32.98 Aligned_cols=23 Identities=17% Similarity=0.299 Sum_probs=20.7
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHc
Q 038591 33 KMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 33 g~s~~elA~~~gis~~~i~~~e~ 55 (82)
.+|++++|..+|+++.++++..+
T Consensus 184 ~lt~~~iA~~lG~sr~tvsR~l~ 206 (235)
T PRK11161 184 TMTRGDIGNYLGLTVETISRLLG 206 (235)
T ss_pred cccHHHHHHHhCCcHHHHHHHHH
Confidence 48999999999999999999753
No 269
>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=92.97 E-value=0.18 Score=33.60 Aligned_cols=44 Identities=11% Similarity=0.115 Sum_probs=33.4
Q ss_pred hCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcc
Q 038591 31 GKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRV 78 (82)
Q Consensus 31 ~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e 78 (82)
..|+|++|+|+.+|+|.++|..+... ....+.......+++++.
T Consensus 240 ~e~~s~~EIA~~Lgis~~tVk~~l~r----AlkkLr~~l~~~~~~~~~ 283 (285)
T TIGR02394 240 YEPATLEEVAAEVGLTRERVRQIQVE----ALKKLRRILERDGVDREA 283 (285)
T ss_pred CCCccHHHHHHHHCCCHHHHHHHHHH----HHHHHHHHHHHhhhhhhc
Confidence 56899999999999999999999864 344555555566666553
No 270
>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=92.97 E-value=0.15 Score=29.52 Aligned_cols=25 Identities=12% Similarity=0.052 Sum_probs=22.9
Q ss_pred hCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 31 GKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 31 ~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
-.|+|..++|+.+|+|+++|+++.+
T Consensus 124 ~~g~s~~eIA~~l~~s~~~v~~~~~ 148 (158)
T TIGR02937 124 LEGLSYKEIAEILGISVGTVKRRLK 148 (158)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 4699999999999999999999875
No 271
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=92.92 E-value=0.26 Score=32.42 Aligned_cols=32 Identities=6% Similarity=0.009 Sum_probs=26.5
Q ss_pred HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 24 QIQRARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 24 ~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
.++.+.+...++..|||+.+|+|..|+.+..+
T Consensus 10 Il~~l~~~~~~~~~ela~~l~vS~~TirRdL~ 41 (251)
T PRK13509 10 LLELLAQLGFVTVEKVIERLGISPATARRDIN 41 (251)
T ss_pred HHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHH
Confidence 45556666779999999999999999988754
No 272
>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=92.81 E-value=0.29 Score=31.02 Aligned_cols=33 Identities=15% Similarity=0.111 Sum_probs=27.0
Q ss_pred HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 23 ~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
..|..+...-++|+.+||+.+|+++++|++..+
T Consensus 5 ~IL~~L~~~~~~t~~eLA~~lgis~~tV~~~L~ 37 (203)
T TIGR02702 5 DILSYLLKQGQATAAALAEALAISPQAVRRHLK 37 (203)
T ss_pred HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 345666667789999999999999999988743
No 273
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=92.80 E-value=0.35 Score=28.70 Aligned_cols=28 Identities=11% Similarity=-0.100 Sum_probs=24.2
Q ss_pred HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 28 ARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 28 ~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
++--.|+|..|+|+.+|+|.++|..+..
T Consensus 117 l~~~~~~s~~EIA~~l~is~~tV~~~~~ 144 (154)
T PRK06759 117 ERFFVGKTMGEIALETEMTYYQVRWIYR 144 (154)
T ss_pred HHHhcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3445799999999999999999998864
No 274
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=92.79 E-value=0.3 Score=31.97 Aligned_cols=28 Identities=25% Similarity=0.277 Sum_probs=24.3
Q ss_pred HHhCCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591 29 RLGKKMSQPDLANQINQRPQVVSEYENG 56 (82)
Q Consensus 29 r~~~g~s~~elA~~~gis~~~i~~~e~g 56 (82)
+-..|+|+.++|+.+|+|+.+|++++..
T Consensus 221 ~~~~~~t~~eIA~~lgis~~~V~~~~~~ 248 (258)
T PRK08215 221 RFFQGKTQMEVAEEIGISQAQVSRLEKA 248 (258)
T ss_pred HHhcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 3346999999999999999999999863
No 275
>PF07471 Phage_Nu1: Phage DNA packaging protein Nu1; InterPro: IPR010906 This entry is represented by the Bacteriophage lambda, Nu1, terminase small subunit. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Terminase, the DNA packaging enzyme of bacteriophage lambda, is a heteromultimer composed of subunits Nu1 and A. The smaller Nu1 terminase subunit has a low-affinity ATPase stimulated by non-specific DNA [].; PDB: 1J9I_A.
Probab=92.74 E-value=0.081 Score=32.98 Aligned_cols=23 Identities=13% Similarity=0.382 Sum_probs=18.5
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHc
Q 038591 33 KMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 33 g~s~~elA~~~gis~~~i~~~e~ 55 (82)
.++.++||+.+|||.+||.+|..
T Consensus 2 ~vnk~~lA~i~gvS~~ti~~W~~ 24 (164)
T PF07471_consen 2 KVNKKELAEIFGVSERTIDKWQR 24 (164)
T ss_dssp EEEHHHHHHHTT--HHHHHHHTT
T ss_pred CCCHHHHHHHHCCCHHHHHHHHH
Confidence 35789999999999999999974
No 276
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=92.71 E-value=0.14 Score=32.80 Aligned_cols=22 Identities=27% Similarity=0.280 Sum_probs=20.0
Q ss_pred CCCHHHHHHHhCCCHHHHHHHH
Q 038591 33 KMSQPDLANQINQRPQVVSEYE 54 (82)
Q Consensus 33 g~s~~elA~~~gis~~~i~~~e 54 (82)
.+|+.++|..+|+++.++++..
T Consensus 179 ~lt~~~IA~~lGisretlsR~L 200 (230)
T PRK09391 179 PMSRRDIADYLGLTIETVSRAL 200 (230)
T ss_pred cCCHHHHHHHHCCCHHHHHHHH
Confidence 4799999999999999999965
No 277
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=92.68 E-value=0.15 Score=34.10 Aligned_cols=24 Identities=21% Similarity=0.267 Sum_probs=22.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 32 KKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 32 ~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
.++|+.++|+.+|||+.+|++++.
T Consensus 247 ~~~Tl~EIA~~lgvS~~rVrqi~~ 270 (284)
T PRK06596 247 DKSTLQELAAEYGVSAERVRQIEK 270 (284)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHH
Confidence 379999999999999999999986
No 278
>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=92.68 E-value=0.34 Score=28.33 Aligned_cols=35 Identities=9% Similarity=0.132 Sum_probs=28.8
Q ss_pred CHHHHHHHH-HhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 21 TPRQIQRAR-LGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 21 ~~~~lk~~r-~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
..+.|+.+- ...++|+.|+|..+|||.++|+.+..
T Consensus 58 d~~~L~~~v~~~pd~tl~Ela~~l~Vs~~ti~~~Lk 93 (119)
T PF01710_consen 58 DRDELKALVEENPDATLRELAERLGVSPSTIWRALK 93 (119)
T ss_pred cHHHHHHHHHHCCCcCHHHHHHHcCCCHHHHHHHHH
Confidence 355676664 45789999999999999999999885
No 279
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=92.68 E-value=0.23 Score=29.99 Aligned_cols=26 Identities=12% Similarity=0.047 Sum_probs=23.4
Q ss_pred HhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 30 LGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 30 ~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
...|++..++|+.+|+|+.+|.++..
T Consensus 138 ~~~~~~~~eIA~~lgis~~tv~~~~~ 163 (179)
T PRK11924 138 YVEGLSYREIAEILGVPVGTVKSRLR 163 (179)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 34699999999999999999999875
No 280
>PRK00215 LexA repressor; Validated
Probab=92.65 E-value=0.32 Score=30.76 Aligned_cols=25 Identities=24% Similarity=0.349 Sum_probs=21.3
Q ss_pred hCCCCHHHHHHHhCC-CHHHHHHHHc
Q 038591 31 GKKMSQPDLANQINQ-RPQVVSEYEN 55 (82)
Q Consensus 31 ~~g~s~~elA~~~gi-s~~~i~~~e~ 55 (82)
...+|+.|||+.+|+ +++|++++.+
T Consensus 21 ~~~~s~~ela~~~~~~~~~tv~~~l~ 46 (205)
T PRK00215 21 GYPPSRREIADALGLRSPSAVHEHLK 46 (205)
T ss_pred CCCCCHHHHHHHhCCCChHHHHHHHH
Confidence 345699999999999 9999999943
No 281
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=92.64 E-value=0.3 Score=31.94 Aligned_cols=32 Identities=16% Similarity=0.141 Sum_probs=26.9
Q ss_pred HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 24 QIQRARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 24 ~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
.+..+.+...+++.|||+.+|+|..||++..+
T Consensus 9 Il~~l~~~~~~~~~eLa~~l~VS~~TiRRdL~ 40 (240)
T PRK10411 9 IVDLLLNHTSLTTEALAEQLNVSKETIRRDLN 40 (240)
T ss_pred HHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHH
Confidence 45566677889999999999999999988754
No 282
>PRK15320 transcriptional activator SprB; Provisional
Probab=92.60 E-value=0.15 Score=33.13 Aligned_cols=26 Identities=23% Similarity=0.302 Sum_probs=23.6
Q ss_pred HhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 30 LGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 30 ~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
-..|+|++|+|+.+++|.+||+.+.+
T Consensus 176 LAkG~SNKEIAekL~LS~KTVSTYKn 201 (251)
T PRK15320 176 LSSGHPAIELAKKFGLGTKTVSIYRK 201 (251)
T ss_pred HHcCCCHHHHHHHhccchhhHHHHHH
Confidence 46799999999999999999999865
No 283
>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=92.47 E-value=0.33 Score=33.16 Aligned_cols=34 Identities=12% Similarity=0.043 Sum_probs=29.5
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
...|..+....+.++.+.|+.+|||++|+++..+
T Consensus 294 ~~~I~~aL~~~~gn~~~aA~~LGisr~tL~rklk 327 (329)
T TIGR02974 294 IELLQQALAEAQFNQRKAAELLGLTYHQLRGLLR 327 (329)
T ss_pred HHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHH
Confidence 4567777888899999999999999999998764
No 284
>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=92.46 E-value=0.3 Score=28.15 Aligned_cols=34 Identities=18% Similarity=-0.009 Sum_probs=27.6
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
...|..+....++|+.++|+.+|++++++++..+
T Consensus 31 ~~iL~~l~~~~~~t~~ela~~~~~~~~tvs~~l~ 64 (118)
T TIGR02337 31 WRILRILAEQGSMEFTQLANQACILRPSLTGILA 64 (118)
T ss_pred HHHHHHHHHcCCcCHHHHHHHhCCCchhHHHHHH
Confidence 3456666677889999999999999999988743
No 285
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=92.44 E-value=0.37 Score=31.25 Aligned_cols=27 Identities=11% Similarity=0.172 Sum_probs=24.0
Q ss_pred HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 29 RLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 29 r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
+-..|+|++++|..+|+|..+|++++.
T Consensus 195 ~~~~~~t~~EIA~~lgis~~~V~q~~~ 221 (231)
T PRK12427 195 YYQHEMSLKEIALVLDLTEARICQLNK 221 (231)
T ss_pred HHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 445699999999999999999999886
No 286
>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=92.36 E-value=0.42 Score=29.24 Aligned_cols=27 Identities=11% Similarity=0.100 Sum_probs=23.5
Q ss_pred HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 29 RLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 29 r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
+--.|+|.+|+|+.+|+|.+||.....
T Consensus 146 ~~~~g~s~~EIA~~lgis~~tVk~~l~ 172 (183)
T TIGR02999 146 RFFAGLTVEEIAELLGVSVRTVERDWR 172 (183)
T ss_pred HHHcCCCHHHHHHHhCCCHHHHHHHHH
Confidence 455799999999999999999988754
No 287
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=92.34 E-value=0.24 Score=30.70 Aligned_cols=27 Identities=15% Similarity=0.161 Sum_probs=23.7
Q ss_pred HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 29 RLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 29 r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
+--.|+|.+|+|+.+|+|.++|..+..
T Consensus 153 ~~~~g~s~~EIA~~lgis~~tV~~~l~ 179 (194)
T PRK12519 153 AYYEGLSQSEIAKRLGIPLGTVKARAR 179 (194)
T ss_pred hhhcCCCHHHHHHHhCCCHHHHHHHHH
Confidence 344699999999999999999998875
No 288
>COG2973 TrpR Trp operon repressor [Transcription]
Probab=92.33 E-value=0.89 Score=26.13 Aligned_cols=51 Identities=14% Similarity=0.218 Sum_probs=33.7
Q ss_pred HHHHHHHH--HhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHh
Q 038591 22 PRQIQRAR--LGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAI 72 (82)
Q Consensus 22 ~~~lk~~r--~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~l 72 (82)
|.+++-+. -...+||.|++..+|+|-.+|.+=-|.-...+.+.-.-+.+.+
T Consensus 47 ~~Rv~Iv~eLL~ge~sQREi~~~LgvsiAtITRGSN~LK~~~~~~k~~L~~~l 99 (103)
T COG2973 47 GTRVRIVEELLRGELSQREIAQKLGVSIATITRGSNSLKTADPEFKQWLEKVL 99 (103)
T ss_pred HHHHHHHHHHHhccccHHHHHHHhCcchhhhccchhhhccCCHHHHHHHHHHh
Confidence 55555443 3568999999999999988888744443333444445555544
No 289
>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily. This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.
Probab=92.31 E-value=0.39 Score=30.66 Aligned_cols=27 Identities=19% Similarity=0.225 Sum_probs=23.8
Q ss_pred HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 29 RLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 29 r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
+-..|+|++++|+.+|+|+++|+.+..
T Consensus 190 ~y~~~~s~~eIA~~lgis~~~v~~~~~ 216 (227)
T TIGR02980 190 RFFEDKTQSEIAERLGISQMHVSRLLR 216 (227)
T ss_pred HHhcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 334699999999999999999999875
No 290
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=92.30 E-value=0.23 Score=31.55 Aligned_cols=37 Identities=14% Similarity=0.125 Sum_probs=28.9
Q ss_pred CCHHHHHHHH-HhCCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591 20 DTPRQIQRAR-LGKKMSQPDLANQINQRPQVVSEYENG 56 (82)
Q Consensus 20 ~~~~~lk~~r-~~~g~s~~elA~~~gis~~~i~~~e~g 56 (82)
+.....+-++ -..|+|.+|+|+++++|+.||..+.+.
T Consensus 138 LT~RE~eVL~lla~G~snkeIA~~L~iS~~TVk~h~~~ 175 (207)
T PRK15411 138 LSRTESSMLRMWMAGQGTIQISDQMNIKAKTVSSHKGN 175 (207)
T ss_pred CCHHHHHHHHHHHcCCCHHHHHHHcCCCHHHHHHHHHH
Confidence 5555555543 457999999999999999999998753
No 291
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=92.27 E-value=0.45 Score=28.57 Aligned_cols=28 Identities=18% Similarity=0.152 Sum_probs=23.8
Q ss_pred HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 28 ARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 28 ~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
++--.|+|.+|+|+.+|+|..+|.....
T Consensus 120 l~~~~~~s~~EIA~~lgis~~tV~~~l~ 147 (163)
T PRK07037 120 MYRLHGETQKDIARELGVSPTLVNFMIR 147 (163)
T ss_pred HHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3455799999999999999999998743
No 292
>PHA01082 putative transcription regulator
Probab=92.24 E-value=0.11 Score=30.88 Aligned_cols=31 Identities=16% Similarity=0.259 Sum_probs=28.5
Q ss_pred hCCCCHHHHHHHhCCCHHHHHHHHcCCCCCC
Q 038591 31 GKKMSQPDLANQINQRPQVVSEYENGKAVPN 61 (82)
Q Consensus 31 ~~g~s~~elA~~~gis~~~i~~~e~g~~~p~ 61 (82)
+.|+|..|.|+.+--|..+|.+|-.|+..|+
T Consensus 28 eCgLsveeaa~LCfKsVrtVk~WD~G~~IPP 58 (133)
T PHA01082 28 ECGLSVEEAAKLCFKTVSEVKQWDAGEKIPP 58 (133)
T ss_pred ccCccHHHHHHHHHHhHHHHhhccCCCcCCh
Confidence 5799999999999999999999999987665
No 293
>PRK11361 acetoacetate metabolism regulatory protein AtoC; Provisional
Probab=92.17 E-value=0.35 Score=33.77 Aligned_cols=34 Identities=9% Similarity=-0.061 Sum_probs=29.1
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
...|..+....+.++.+.|+.+|||++|+++..+
T Consensus 419 ~~~i~~al~~~~gn~~~aA~~LGisr~tL~rkl~ 452 (457)
T PRK11361 419 KRIIMEVLEQQEGNRTRTALMLGISRRALMYKLQ 452 (457)
T ss_pred HHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHH
Confidence 4567777888899999999999999999988654
No 294
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=92.16 E-value=0.41 Score=23.73 Aligned_cols=25 Identities=16% Similarity=0.121 Sum_probs=21.8
Q ss_pred hCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 31 GKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 31 ~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
....+..++++.+|+|++++++..+
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~ 32 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLK 32 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHH
Confidence 5678999999999999999988754
No 295
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=92.15 E-value=0.44 Score=28.80 Aligned_cols=27 Identities=15% Similarity=-0.010 Sum_probs=23.6
Q ss_pred HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 29 RLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 29 r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
+--.|+|.+++|..+|+|..+|..+..
T Consensus 140 ~~~~~~s~~eIA~~lgis~~tV~~~l~ 166 (182)
T PRK09652 140 REIEGLSYEEIAEIMGCPIGTVRSRIF 166 (182)
T ss_pred HHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 335699999999999999999998765
No 296
>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=92.07 E-value=1.1 Score=27.84 Aligned_cols=50 Identities=16% Similarity=0.163 Sum_probs=37.8
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCC--CCCCHHHHHHHHHHhC
Q 038591 22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGK--AVPNQTVLAKMEKAIG 73 (82)
Q Consensus 22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~--~~p~~~~~~~la~~lg 73 (82)
-..++.+-...+ ..+||..+|++++++.+-.|.. ..++...+..|+++-|
T Consensus 11 ~~Ac~~fa~~h~--~~~lA~~lGm~~~~LrNKLNP~q~H~Lt~~el~~i~~~Tg 62 (162)
T PF06892_consen 11 DEACRAFAKNHN--MAALAERLGMNPQTLRNKLNPEQPHKLTVDELIAITDATG 62 (162)
T ss_pred HHHHHHHHHhcC--HHHHHHHhCCCHHHHHHHcCCCCCCCCCHHHHHHHHHHhC
Confidence 345566666665 5789999999999999999874 3567888888777654
No 297
>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=91.97 E-value=0.29 Score=25.82 Aligned_cols=31 Identities=23% Similarity=0.336 Sum_probs=21.4
Q ss_pred HHHH-HHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591 24 QIQR-ARLGKKMSQPDLANQINQRPQVVSEYE 54 (82)
Q Consensus 24 ~lk~-~r~~~g~s~~elA~~~gis~~~i~~~e 54 (82)
.|+. ++....+|..|||..+++++++|..+.
T Consensus 4 ~i~~~l~~~~~~S~~eLa~~~~~s~~~ve~mL 35 (69)
T PF09012_consen 4 EIRDYLRERGRVSLAELAREFGISPEAVEAML 35 (69)
T ss_dssp HHHHHHHHS-SEEHHHHHHHTT--HHHHHHHH
T ss_pred HHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHH
Confidence 3455 456667899999999999999876653
No 298
>TIGR01818 ntrC nitrogen regulation protein NR(I). This model represents NtrC, a DNA-binding response regulator that is phosphorylated by NtrB and interacts with sigma-54. NtrC usually controls the expression of glutamine synthase, GlnA, and may be called GlnL, GlnG, etc.
Probab=91.97 E-value=0.4 Score=33.62 Aligned_cols=34 Identities=6% Similarity=-0.007 Sum_probs=28.7
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
...|..+....+.++.+.|+.+|||++|+++..+
T Consensus 428 ~~~i~~al~~~~gn~~~aA~~Lgisr~tL~rkl~ 461 (463)
T TIGR01818 428 RPLLEAALQHTRGHKQEAAALLGWGRNTLTRKLK 461 (463)
T ss_pred HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHH
Confidence 3457777788899999999999999999988653
No 299
>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=91.96 E-value=0.13 Score=31.98 Aligned_cols=27 Identities=7% Similarity=-0.038 Sum_probs=23.5
Q ss_pred HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 29 RLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 29 r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
+.-.|+|..|+|+.+|+|..+|.....
T Consensus 143 ~~~~g~s~~EIA~~lgis~~tVk~~l~ 169 (193)
T TIGR02947 143 ADVEGFAYKEIAEIMGTPIGTVMSRLH 169 (193)
T ss_pred hhhcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 344599999999999999999998875
No 300
>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=91.94 E-value=0.42 Score=31.23 Aligned_cols=25 Identities=24% Similarity=0.210 Sum_probs=23.0
Q ss_pred hCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 31 GKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 31 ~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
-.|+|++++|+.+|+|+.+|+++++
T Consensus 220 ~~~~t~~eIA~~lgis~~~V~~~~~ 244 (254)
T TIGR02850 220 FEGKTQMEVAEEIGISQAQVSRLEK 244 (254)
T ss_pred cCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 4589999999999999999999986
No 301
>PRK13869 plasmid-partitioning protein RepA; Provisional
Probab=91.90 E-value=0.42 Score=33.55 Aligned_cols=43 Identities=7% Similarity=0.156 Sum_probs=34.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHc------------CCCCCCHHHHHHHHHHhCC
Q 038591 32 KKMSQPDLANQINQRPQVVSEYEN------------GKAVPNQTVLAKMEKAIGV 74 (82)
Q Consensus 32 ~g~s~~elA~~~gis~~~i~~~e~------------g~~~p~~~~~~~la~~lgv 74 (82)
+.+|..|+|+.+||+.+||..|+. |.+..+.+.+..+.+.|+-
T Consensus 47 r~ft~~e~A~~lgvs~~tlr~~~~~g~~~~~~~~~~grR~yt~~di~~lr~~l~~ 101 (405)
T PRK13869 47 RKFTSGEAARLMKISDSTLRKMTLAGEGPQPELASNGRRFYTLGQINEIRQMLAG 101 (405)
T ss_pred CCCCHHHHHHHhCcCHHHHHHHHHcCCCCCCccCCCCceeecHHHHHHHHHHHHh
Confidence 367999999999999999999953 3445677788888888863
No 302
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=91.87 E-value=0.45 Score=28.02 Aligned_cols=30 Identities=3% Similarity=-0.043 Sum_probs=24.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHcCCCCCC
Q 038591 32 KKMSQPDLANQINQRPQVVSEYENGKAVPN 61 (82)
Q Consensus 32 ~g~s~~elA~~~gis~~~i~~~e~g~~~p~ 61 (82)
..++..+||+.+|+|+.++.++.......+
T Consensus 24 ~~~sl~~lA~~~g~S~~~l~r~Fk~~~G~s 53 (127)
T PRK11511 24 SPLSLEKVSERSGYSKWHLQRMFKKETGHS 53 (127)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHCcC
Confidence 358999999999999999999987543333
No 303
>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=91.80 E-value=0.42 Score=30.90 Aligned_cols=26 Identities=12% Similarity=0.303 Sum_probs=23.6
Q ss_pred hCCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591 31 GKKMSQPDLANQINQRPQVVSEYENG 56 (82)
Q Consensus 31 ~~g~s~~elA~~~gis~~~i~~~e~g 56 (82)
..++|++++|+.+|+|+++|++++..
T Consensus 194 ~~~~t~~EIA~~lgis~~~V~q~~~~ 219 (238)
T TIGR02393 194 GRPHTLEEVGKEFNVTRERIRQIESK 219 (238)
T ss_pred CCCccHHHHHHHHCCCHHHHHHHHHH
Confidence 46799999999999999999999864
No 304
>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=91.76 E-value=0.39 Score=33.33 Aligned_cols=43 Identities=5% Similarity=0.151 Sum_probs=33.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHcC------------CCCCCHHHHHHHHHHhCC
Q 038591 32 KKMSQPDLANQINQRPQVVSEYENG------------KAVPNQTVLAKMEKAIGV 74 (82)
Q Consensus 32 ~g~s~~elA~~~gis~~~i~~~e~g------------~~~p~~~~~~~la~~lgv 74 (82)
.-+|..|+|+.+|++++||..||.- .+..+.+.+..|...+..
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 3589999999999999999999753 333466777777777654
No 305
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=91.73 E-value=0.52 Score=28.32 Aligned_cols=28 Identities=14% Similarity=0.145 Sum_probs=24.4
Q ss_pred HHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 27 RARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 27 ~~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
.++- .|++.+++|+.+|+|.++|.....
T Consensus 122 ~l~~-~g~s~~eIA~~lgis~~tV~~~i~ 149 (166)
T PRK09639 122 LLRF-SGYSYKEIAEALGIKESSVGTTLA 149 (166)
T ss_pred HHHH-cCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3455 899999999999999999998864
No 306
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=91.72 E-value=0.53 Score=28.08 Aligned_cols=27 Identities=15% Similarity=0.079 Sum_probs=23.5
Q ss_pred HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 29 RLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 29 r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
+.-.|+|.+|+|+.+|+|..+|.....
T Consensus 118 ~~~~g~s~~EIA~~lgis~~tV~~~l~ 144 (161)
T PRK09047 118 RYWEDMDVAETAAAMGCSEGSVKTHCS 144 (161)
T ss_pred HHHhcCCHHHHHHHHCCCHHHHHHHHH
Confidence 445699999999999999999998765
No 307
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=91.71 E-value=0.36 Score=31.58 Aligned_cols=33 Identities=9% Similarity=0.158 Sum_probs=26.3
Q ss_pred HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 23 ~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
..|..+.....+|..|+|+.+|++++|++++.+
T Consensus 18 ~IL~~l~~~~~l~l~eia~~lgl~kstv~Rll~ 50 (257)
T PRK15090 18 GILQALGEEREIGITELSQRVMMSKSTVYRFLQ 50 (257)
T ss_pred HHHHHhhcCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 444555455679999999999999999999854
No 308
>COG1309 AcrR Transcriptional regulator [Transcription]
Probab=91.70 E-value=0.14 Score=30.00 Aligned_cols=27 Identities=7% Similarity=-0.002 Sum_probs=23.8
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHcCCC
Q 038591 32 KKMSQPDLANQINQRPQVVSEYENGKA 58 (82)
Q Consensus 32 ~g~s~~elA~~~gis~~~i~~~e~g~~ 58 (82)
.++|..++|+.+|+++++++++..++.
T Consensus 31 ~~~t~~~Ia~~agvs~~~~Y~~f~~K~ 57 (201)
T COG1309 31 AATTVDEIAKAAGVSKGTLYRHFPSKE 57 (201)
T ss_pred CCCCHHHHHHHhCCCcchhHHHcCCHH
Confidence 468899999999999999999987754
No 309
>PRK15115 response regulator GlrR; Provisional
Probab=91.69 E-value=0.38 Score=33.56 Aligned_cols=34 Identities=6% Similarity=-0.094 Sum_probs=29.2
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
...|..+....+.++.+.|+.+|||++|+++-.+
T Consensus 400 ~~~i~~al~~~~gn~~~aA~~Lgisr~tL~rkl~ 433 (444)
T PRK15115 400 LNYLRKLLQITKGNVTHAARMAGRNRTEFYKLLS 433 (444)
T ss_pred HHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHH
Confidence 4567777888899999999999999999988765
No 310
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=91.69 E-value=0.2 Score=32.55 Aligned_cols=25 Identities=16% Similarity=0.244 Sum_probs=21.8
Q ss_pred hCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 31 GKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 31 ~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
..++|+.+||+.+++|+++++++.+
T Consensus 19 ~~~IS~~eLA~~L~iS~~Tvsr~Lk 43 (217)
T PRK14165 19 TVKISSSEFANHTGTSSKTAARILK 43 (217)
T ss_pred CCCcCHHHHHHHHCcCHHHHHHHHH
Confidence 3468999999999999999999854
No 311
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=91.62 E-value=0.21 Score=33.40 Aligned_cols=27 Identities=19% Similarity=0.378 Sum_probs=23.9
Q ss_pred hCCCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591 31 GKKMSQPDLANQINQRPQVVSEYENGK 57 (82)
Q Consensus 31 ~~g~s~~elA~~~gis~~~i~~~e~g~ 57 (82)
-.||...++|+++|||+.||..|-+..
T Consensus 17 l~gmk~~dIAeklGvspntiksWKrr~ 43 (279)
T COG5484 17 LKGMKLKDIAEKLGVSPNTIKSWKRRD 43 (279)
T ss_pred HhhccHHHHHHHhCCChHHHHHHHHhc
Confidence 357999999999999999999998643
No 312
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=91.59 E-value=0.54 Score=25.60 Aligned_cols=34 Identities=15% Similarity=0.142 Sum_probs=27.0
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
...|..+....++++.++|+.+++++++|++..+
T Consensus 13 ~~il~~l~~~~~~~~~~la~~~~~s~~~i~~~l~ 46 (101)
T smart00347 13 FLVLRILYEEGPLSVSELAKRLGVSPSTVTRVLD 46 (101)
T ss_pred HHHHHHHHHcCCcCHHHHHHHHCCCchhHHHHHH
Confidence 3455666666679999999999999999988754
No 313
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=91.54 E-value=0.54 Score=30.70 Aligned_cols=27 Identities=15% Similarity=0.207 Sum_probs=24.0
Q ss_pred HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 29 RLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 29 r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
+--.|+|+.|+|+.+|+|..+|..+..
T Consensus 217 ~~~~g~s~~eIA~~l~is~~tV~~~~~ 243 (257)
T PRK08583 217 TFIENLSQKETGERLGISQMHVSRLQR 243 (257)
T ss_pred HHhCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 345799999999999999999999875
No 314
>PRK10365 transcriptional regulatory protein ZraR; Provisional
Probab=91.54 E-value=0.5 Score=32.81 Aligned_cols=34 Identities=12% Similarity=-0.010 Sum_probs=28.7
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
...|..+....+.++.+.|+.+|||++|+++-.+
T Consensus 407 ~~~i~~~l~~~~gn~~~aa~~Lgisr~tl~rk~~ 440 (441)
T PRK10365 407 KEVILAALEKTGGNKTEAARQLGITRKTLLAKLS 440 (441)
T ss_pred HHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHhh
Confidence 4467777888899999999999999999987543
No 315
>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=91.53 E-value=0.22 Score=29.14 Aligned_cols=24 Identities=17% Similarity=0.138 Sum_probs=22.1
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 32 KKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 32 ~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
.|.|..++|...+||.+||.+|..
T Consensus 17 ~g~s~~eaa~~F~VS~~Tv~~W~k 40 (119)
T PF01710_consen 17 KGKSIREAAKRFGVSRNTVYRWLK 40 (119)
T ss_pred ccchHHHHHHHhCcHHHHHHHHHH
Confidence 488999999999999999999965
No 316
>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=91.53 E-value=0.61 Score=27.78 Aligned_cols=26 Identities=23% Similarity=0.239 Sum_probs=22.8
Q ss_pred HHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591 29 RLGKKMSQPDLANQINQRPQVVSEYE 54 (82)
Q Consensus 29 r~~~g~s~~elA~~~gis~~~i~~~e 54 (82)
+.-.|++.+|+|+.+|+|.++|....
T Consensus 123 ~~~~g~~~~eIA~~l~is~~tv~~~l 148 (159)
T TIGR02989 123 RYQRGVSLTALAEQLGRTVNAVYKAL 148 (159)
T ss_pred HHhcCCCHHHHHHHhCCCHHHHHHHH
Confidence 45579999999999999999998764
No 317
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=91.44 E-value=0.27 Score=31.59 Aligned_cols=25 Identities=20% Similarity=0.393 Sum_probs=22.5
Q ss_pred hCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 31 GKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 31 ~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
..|+|.+|+|+.+|+|..||.+...
T Consensus 196 ~eg~s~~EIA~~lgis~~tVk~~~~ 220 (234)
T PRK08301 196 GEEKTQKEVADMLGISQSYISRLEK 220 (234)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3699999999999999999998864
No 318
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=91.40 E-value=1.3 Score=24.96 Aligned_cols=26 Identities=4% Similarity=-0.078 Sum_probs=22.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591 32 KKMSQPDLANQINQRPQVVSEYENGK 57 (82)
Q Consensus 32 ~g~s~~elA~~~gis~~~i~~~e~g~ 57 (82)
..++..++|+.+|+|+.++.+..+..
T Consensus 20 ~~~~~~~lA~~~~~S~~~l~r~f~~~ 45 (107)
T PRK10219 20 QPLNIDVVAKKSGYSKWYLQRMFRTV 45 (107)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 35899999999999999999887653
No 319
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=91.36 E-value=0.33 Score=31.00 Aligned_cols=37 Identities=3% Similarity=0.006 Sum_probs=28.1
Q ss_pred CCHHHHHHHH-HhCCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591 20 DTPRQIQRAR-LGKKMSQPDLANQINQRPQVVSEYENG 56 (82)
Q Consensus 20 ~~~~~lk~~r-~~~g~s~~elA~~~gis~~~i~~~e~g 56 (82)
+......-++ -..|+|.+|+|+.+++|+.||..+-+.
T Consensus 134 LSpRErEVLrLLAqGkTnKEIAe~L~IS~rTVkth~sr 171 (198)
T PRK15201 134 FSVTERHLLKLIASGYHLSETAALLSLSEEQTKSLRRS 171 (198)
T ss_pred CCHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 4444444443 467999999999999999999987653
No 320
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=91.33 E-value=0.26 Score=31.29 Aligned_cols=23 Identities=9% Similarity=0.179 Sum_probs=21.1
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHc
Q 038591 33 KMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 33 g~s~~elA~~~gis~~~i~~~e~ 55 (82)
|+|.+|+|+.+|+|+.||.++..
T Consensus 177 g~s~~eIa~~l~iS~~Tv~~~~~ 199 (225)
T PRK10046 177 QHTAETVAQALTISRTTARRYLE 199 (225)
T ss_pred CcCHHHHHHHhCccHHHHHHHHH
Confidence 68999999999999999998864
No 321
>TIGR02329 propionate_PrpR propionate catabolism operon regulatory protein PrpR. At least five distinct pathways exists for the catabolism of propionate by way of propionyl-CoA. Members of this family represent the transcriptional regulatory protein PrpR, whose gene is found in most cases divergently transcribed from an operon for the methylcitric acid cycle of propionate catabolism. 2-methylcitric acid, a catabolite by this pathway, is a coactivator of PrpR.
Probab=91.33 E-value=0.5 Score=34.44 Aligned_cols=34 Identities=6% Similarity=-0.110 Sum_probs=29.7
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
...|....+..+.++.+.|+.+|||++|+++..+
T Consensus 492 r~~I~~aL~~~~Gn~~~aA~~LGIsRtTL~Rklk 525 (526)
T TIGR02329 492 ALAVRAALERFGGDRDAAAKALGISRTTLWRRLK 525 (526)
T ss_pred HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHh
Confidence 4567788888999999999999999999998764
No 322
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=91.33 E-value=0.61 Score=28.63 Aligned_cols=27 Identities=4% Similarity=-0.041 Sum_probs=23.7
Q ss_pred HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 29 RLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 29 r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
+--.|+|.+|+|+.+|+|..+|.....
T Consensus 147 ~~~~~~s~~eIA~~lgis~~~V~~~l~ 173 (186)
T PRK13919 147 LYYQGYTHREAAQLLGLPLGTLKTRAR 173 (186)
T ss_pred HHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 445699999999999999999998765
No 323
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=91.32 E-value=0.63 Score=27.87 Aligned_cols=28 Identities=18% Similarity=-0.008 Sum_probs=23.6
Q ss_pred HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 28 ARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 28 ~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
++--.|+|.+|+|+.+|+|.+||.....
T Consensus 117 l~~~~g~s~~EIA~~lgis~~tV~~~l~ 144 (160)
T PRK09642 117 AHYLEEKSYQEIALQEKIEVKTVEMKLY 144 (160)
T ss_pred HHHHhCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3455699999999999999999977654
No 324
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=91.25 E-value=0.58 Score=30.71 Aligned_cols=27 Identities=19% Similarity=0.245 Sum_probs=23.8
Q ss_pred HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 29 RLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 29 r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
+--.|+|++++|..+|+|..+|+++..
T Consensus 215 ~y~~~~s~~eIA~~lgvs~~~V~~~~~ 241 (256)
T PRK07408 215 VFLHDLTQKEAAERLGISPVTVSRRVK 241 (256)
T ss_pred HHHCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 334699999999999999999999976
No 325
>TIGR03613 RutR pyrimidine utilization regulatory protein R. This protein is observed in operons extremely similar to that characterized in E. coli K-12 responsible for the import and catabolism of pyrimidines, primarily uracil. This protein is a member of the TetR family of transcriptional regulators defined by the N-teminal model pfam00440 and the C-terminal model pfam08362 (YcdC-like protein, C-terminal region).
Probab=91.22 E-value=0.24 Score=30.71 Aligned_cols=29 Identities=14% Similarity=0.009 Sum_probs=24.6
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHcCCCCC
Q 038591 32 KKMSQPDLANQINQRPQVVSEYENGKAVP 60 (82)
Q Consensus 32 ~g~s~~elA~~~gis~~~i~~~e~g~~~p 60 (82)
.+.|..++|+.+|||+.+++.+-.++...
T Consensus 27 ~~~s~~~IA~~agvs~~~lY~hF~sKe~L 55 (202)
T TIGR03613 27 HGTSLEQIAELAGVSKTNLLYYFPSKDAL 55 (202)
T ss_pred ccCCHHHHHHHhCCCHHHHHHHcCCHHHH
Confidence 46899999999999999999998765443
No 326
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=91.22 E-value=0.71 Score=28.39 Aligned_cols=28 Identities=21% Similarity=0.243 Sum_probs=24.0
Q ss_pred HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 28 ARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 28 ~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
++.-.|+|.+|+|+.+|+|.+||.....
T Consensus 138 L~~~~g~s~~EIA~~lgis~~tVk~~l~ 165 (178)
T PRK12529 138 MATLDGMKQKDIAQALDIALPTVKKYIH 165 (178)
T ss_pred HHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 4456699999999999999999988764
No 327
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=91.21 E-value=0.55 Score=30.25 Aligned_cols=27 Identities=7% Similarity=0.155 Sum_probs=23.8
Q ss_pred HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 29 RLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 29 r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
+-..|+|.+|+|+.+|+|.++|..+..
T Consensus 196 ~~~~g~s~~EIA~~lgis~~tV~~~~~ 222 (236)
T PRK06986 196 YYQEELNLKEIGAVLGVSESRVSQIHS 222 (236)
T ss_pred HhccCCCHHHHHHHHCCCHHHHHHHHH
Confidence 445699999999999999999998875
No 328
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=91.17 E-value=0.62 Score=28.66 Aligned_cols=28 Identities=11% Similarity=0.146 Sum_probs=24.2
Q ss_pred HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 28 ARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 28 ~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
++--.|+|.+|+|+.+|+|.++|..+..
T Consensus 144 l~~~~~~s~~eIA~~lgis~~tV~~~l~ 171 (182)
T PRK12537 144 HAYVDGCSHAEIAQRLGAPLGTVKAWIK 171 (182)
T ss_pred HHHHcCCCHHHHHHHHCCChhhHHHHHH
Confidence 3445799999999999999999998865
No 329
>COG1508 RpoN DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription]
Probab=91.16 E-value=0.15 Score=36.41 Aligned_cols=43 Identities=16% Similarity=0.191 Sum_probs=35.1
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 038591 34 MSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKL 76 (82)
Q Consensus 34 ~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~ 76 (82)
++.+++|+.+|++.+|||+.-+++..-+..-+..|-.+|-..+
T Consensus 331 L~LrdvA~~i~~HESTISRai~nKy~~tprG~feLK~FFs~~i 373 (444)
T COG1508 331 LVLRDVADEIGMHESTISRAITNKYLATPRGLFELKYFFSSSL 373 (444)
T ss_pred ccHHHHHHHhCccHHHHHHHHhcccccCCcceeeHHHHHHHhc
Confidence 8999999999999999999999987666666666666665544
No 330
>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=91.12 E-value=0.36 Score=24.40 Aligned_cols=21 Identities=24% Similarity=0.278 Sum_probs=18.4
Q ss_pred CHHHHHHHhCCCHHHHHHHHc
Q 038591 35 SQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 35 s~~elA~~~gis~~~i~~~e~ 55 (82)
|..++|+.+|+|++++++..+
T Consensus 27 ~~~~la~~~~is~~~v~~~l~ 47 (66)
T cd07377 27 SERELAEELGVSRTTVREALR 47 (66)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 599999999999999988654
No 331
>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=91.10 E-value=0.38 Score=30.20 Aligned_cols=36 Identities=25% Similarity=0.361 Sum_probs=29.2
Q ss_pred CCCHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 19 PDTPRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 19 ~~~~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
.+.+..|+ .|...|.|..|+|+..|++...|.+|+.
T Consensus 56 ~L~PReIQ-arIRaGas~eeVA~~~G~~~~rV~rfa~ 91 (170)
T PF11268_consen 56 SLRPREIQ-ARIRAGASAEEVAEEAGVPVERVRRFAG 91 (170)
T ss_pred CCCHHHHH-HHHHCCCCHHHHHHHhCCCHHHhhhccc
Confidence 34455554 5777899999999999999999999864
No 332
>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=91.05 E-value=0.38 Score=29.89 Aligned_cols=30 Identities=13% Similarity=0.232 Sum_probs=23.4
Q ss_pred HHHHHHHhCCCCHHHHHHHhC-CCHHHHHHHH
Q 038591 24 QIQRARLGKKMSQPDLANQIN-QRPQVVSEYE 54 (82)
Q Consensus 24 ~lk~~r~~~g~s~~elA~~~g-is~~~i~~~e 54 (82)
.|+++. ..|+|..++|..|| +|+++|-..-
T Consensus 10 ~L~~lw-~~G~SasqIA~~lg~vsRnAViGk~ 40 (162)
T PF07750_consen 10 RLRKLW-AEGLSASQIARQLGGVSRNAVIGKA 40 (162)
T ss_pred HHHHHH-HcCCCHHHHHHHhCCcchhhhhhhh
Confidence 444444 47999999999999 9999876543
No 333
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=91.05 E-value=0.31 Score=31.17 Aligned_cols=38 Identities=24% Similarity=0.377 Sum_probs=28.8
Q ss_pred CCCHHHHHHHH-HhCCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591 19 PDTPRQIQRAR-LGKKMSQPDLANQINQRPQVVSEYENG 56 (82)
Q Consensus 19 ~~~~~~lk~~r-~~~g~s~~elA~~~gis~~~i~~~e~g 56 (82)
.+....+.-++ -..|+|.+|+|+++++|..||..+-+.
T Consensus 148 ~LT~RE~eVL~lla~G~snkeIA~~L~iS~~TVk~h~~~ 186 (211)
T COG2197 148 LLTPRELEVLRLLAEGLSNKEIAEELNLSEKTVKTHVSN 186 (211)
T ss_pred CCCHHHHHHHHHHHCCCCHHHHHHHHCCCHhHHHHHHHH
Confidence 34445554443 468999999999999999999887654
No 334
>PRK12423 LexA repressor; Provisional
Probab=90.96 E-value=0.68 Score=29.44 Aligned_cols=32 Identities=13% Similarity=0.050 Sum_probs=24.7
Q ss_pred HHHHHHHHHhCCC--CHHHHHHHhC-CCHHHHHHH
Q 038591 22 PRQIQRARLGKKM--SQPDLANQIN-QRPQVVSEY 53 (82)
Q Consensus 22 ~~~lk~~r~~~g~--s~~elA~~~g-is~~~i~~~ 53 (82)
-..|.......|+ |..|||+.+| .|+++++..
T Consensus 12 l~~l~~~i~~~g~~Ps~~eia~~~g~~s~~~v~~~ 46 (202)
T PRK12423 12 LAFIRERIAQAGQPPSLAEIAQAFGFASRSVARKH 46 (202)
T ss_pred HHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHH
Confidence 3456666666777 9999999999 589888754
No 335
>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=90.96 E-value=0.62 Score=29.53 Aligned_cols=33 Identities=9% Similarity=0.155 Sum_probs=25.9
Q ss_pred HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 23 ~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
..|..+....++++.++|+.+|+|++|+++..+
T Consensus 147 ~IL~~l~~~g~~s~~eia~~l~is~stv~r~L~ 179 (203)
T TIGR01884 147 KVLEVLKAEGEKSVKNIAKKLGKSLSTISRHLR 179 (203)
T ss_pred HHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHH
Confidence 444555554678999999999999999988754
No 336
>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=90.95 E-value=0.8 Score=23.26 Aligned_cols=30 Identities=13% Similarity=0.137 Sum_probs=23.3
Q ss_pred HHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 25 IQRARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 25 lk~~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
+..+.. .+++..++|+.+|++..+++++.+
T Consensus 13 l~~l~~-~~~~~~ei~~~~~i~~~~i~~~l~ 42 (78)
T cd00090 13 LRLLLE-GPLTVSELAERLGLSQSTVSRHLK 42 (78)
T ss_pred HHHHHH-CCcCHHHHHHHHCcCHhHHHHHHH
Confidence 444444 349999999999999999988764
No 337
>PRK13832 plasmid partitioning protein; Provisional
Probab=90.94 E-value=0.91 Score=33.17 Aligned_cols=33 Identities=12% Similarity=0.082 Sum_probs=27.5
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
...++.+. ..|+|+.++|..+|+|+.+|+++..
T Consensus 108 a~AfkrLi-e~G~T~EeIA~~lG~S~~~V~rlll 140 (520)
T PRK13832 108 WRAIERLV-ALGWTEEAIAVALALPVRQIRKLRL 140 (520)
T ss_pred HHHHHHHH-hcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 45556665 7999999999999999999999654
No 338
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=90.93 E-value=0.65 Score=28.57 Aligned_cols=28 Identities=11% Similarity=0.139 Sum_probs=24.0
Q ss_pred HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 28 ARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 28 ~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
++--.|+|.+|+|+.+|+|..+|.....
T Consensus 148 l~~~~g~s~~eIA~~lgis~~~v~~~l~ 175 (187)
T PRK12534 148 TAFFEGITYEELAARTDTPIGTVKSWIR 175 (187)
T ss_pred HHHHcCCCHHHHHHHhCCChhHHHHHHH
Confidence 3445799999999999999999998765
No 339
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=90.92 E-value=0.43 Score=29.42 Aligned_cols=28 Identities=14% Similarity=0.092 Sum_probs=24.3
Q ss_pred HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 28 ARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 28 ~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
++.-.|+|..|+|+.+|+|.+||.....
T Consensus 138 l~~~~gls~~EIA~~l~i~~~tVks~l~ 165 (182)
T COG1595 138 LRYLEGLSYEEIAEILGISVGTVKSRLH 165 (182)
T ss_pred hHhhcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 4555699999999999999999998875
No 340
>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=90.92 E-value=0.3 Score=29.69 Aligned_cols=35 Identities=17% Similarity=0.128 Sum_probs=26.6
Q ss_pred HHHHHHHHhC---CCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591 23 RQIQRARLGK---KMSQPDLANQINQRPQVVSEYENGK 57 (82)
Q Consensus 23 ~~lk~~r~~~---g~s~~elA~~~gis~~~i~~~e~g~ 57 (82)
..+-++..+. .+|.+++|+++|||++|++.+-..+
T Consensus 10 ~a~~~Ll~~k~~~~ITV~~I~~~AgvsR~TFY~hF~dK 47 (176)
T TIGR02366 10 KAFKDLMEVQAFSKISVSDIMSTAQIRRQTFYNHFQDK 47 (176)
T ss_pred HHHHHHHHHCCCccCCHHHHHHHhCCCHHHHHHHCCCH
Confidence 3444455555 4799999999999999999886653
No 341
>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=90.88 E-value=1.6 Score=24.95 Aligned_cols=37 Identities=5% Similarity=0.032 Sum_probs=30.1
Q ss_pred HHHHHHHHHhCCCC-HHHHHHHhCCCHHHHHHHHcCCC
Q 038591 22 PRQIQRARLGKKMS-QPDLANQINQRPQVVSEYENGKA 58 (82)
Q Consensus 22 ~~~lk~~r~~~g~s-~~elA~~~gis~~~i~~~e~g~~ 58 (82)
...|..+.+..++. -++||+.+|+|...|..++....
T Consensus 8 ~~~l~~Ia~~~~~~~wK~faR~lglse~~Id~I~~~~~ 45 (97)
T cd08316 8 SKHIPDIADVMTLKDVKKFVRKSGLSEPKIDEIKLDNP 45 (97)
T ss_pred HHhhHHHHHHcCHHHHHHHHHHcCCCHHHHHHHHHcCC
Confidence 45677777878875 58999999999999999997643
No 342
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=90.85 E-value=0.76 Score=27.79 Aligned_cols=28 Identities=11% Similarity=-0.105 Sum_probs=24.0
Q ss_pred HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 28 ARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 28 ~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
++.-.|+|.+|+|+.+|+|+.+|.....
T Consensus 123 l~~~~g~s~~eIA~~lgis~~tV~~~l~ 150 (164)
T PRK12547 123 LIGASGFSYEDAAAICGCAVGTIKSRVS 150 (164)
T ss_pred HHHHcCCCHHHHHHHhCCCHHHHHHHHH
Confidence 3445799999999999999999988765
No 343
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=90.83 E-value=0.61 Score=30.84 Aligned_cols=27 Identities=22% Similarity=0.261 Sum_probs=23.8
Q ss_pred HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 29 RLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 29 r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
+-..|+|+.++|+.+|+|..+|++++.
T Consensus 227 ~y~~~~t~~EIA~~lgis~~~V~~~~~ 253 (264)
T PRK07122 227 RFFESMTQTQIAERVGISQMHVSRLLA 253 (264)
T ss_pred HhcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 334699999999999999999999875
No 344
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=90.83 E-value=0.48 Score=30.95 Aligned_cols=25 Identities=12% Similarity=0.280 Sum_probs=22.5
Q ss_pred hCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 31 GKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 31 ~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
...+|..++|+.+|+|+.|+.+|..
T Consensus 171 ~~~~Taeela~~~giSRvTaRRYLe 195 (224)
T COG4565 171 DQELTAEELAQALGISRVTARRYLE 195 (224)
T ss_pred CCccCHHHHHHHhCccHHHHHHHHH
Confidence 4679999999999999999999864
No 345
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=90.82 E-value=0.66 Score=28.74 Aligned_cols=28 Identities=11% Similarity=-0.123 Sum_probs=24.3
Q ss_pred HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 28 ARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 28 ~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
++.-.|+|..|+|+.+|+|..+|.....
T Consensus 141 L~~~~g~s~~EIA~~lgis~~tVk~~l~ 168 (185)
T PRK09649 141 LTQLLGLSYADAAAVCGCPVGTIRSRVA 168 (185)
T ss_pred hHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 4566799999999999999999988764
No 346
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=90.81 E-value=0.76 Score=27.88 Aligned_cols=28 Identities=11% Similarity=0.052 Sum_probs=23.6
Q ss_pred HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 28 ARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 28 ~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
++.-.|+|..|+|+.+|+|..+|.....
T Consensus 129 L~~~~g~s~~EIA~~lgis~~tV~~~l~ 156 (173)
T PRK09645 129 RSYYRGWSTAQIAADLGIPEGTVKSRLH 156 (173)
T ss_pred HHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 4455699999999999999999977654
No 347
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=90.80 E-value=0.32 Score=32.58 Aligned_cols=25 Identities=12% Similarity=0.157 Sum_probs=23.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591 32 KKMSQPDLANQINQRPQVVSEYENG 56 (82)
Q Consensus 32 ~g~s~~elA~~~gis~~~i~~~e~g 56 (82)
.|+|.+|+|+.+|+|+.+|++++..
T Consensus 244 ~~~t~~EIa~~lgvs~~~V~q~~~~ 268 (289)
T PRK07500 244 DGATLEALGEELGISKERVRQIEAR 268 (289)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 5899999999999999999999863
No 348
>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=90.76 E-value=0.81 Score=27.92 Aligned_cols=28 Identities=11% Similarity=0.035 Sum_probs=24.2
Q ss_pred HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 28 ARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 28 ~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
++.-.|++.+|+|+.+|+|..+|.....
T Consensus 111 l~~~~g~s~~eIA~~lgis~~tV~~~l~ 138 (170)
T TIGR02959 111 LTELEGLSQQEIAEKLGLSLSGAKSRVQ 138 (170)
T ss_pred HHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 4456799999999999999999988764
No 349
>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=90.74 E-value=0.39 Score=24.68 Aligned_cols=31 Identities=23% Similarity=0.267 Sum_probs=22.0
Q ss_pred HHHHH-HhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 25 IQRAR-LGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 25 lk~~r-~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
|..+. ....+++.+||+.++++++++++..+
T Consensus 9 L~~l~~~~~~~t~~~l~~~~~~~~~~vs~~i~ 40 (68)
T PF13463_consen 9 LRALAHSDGPMTQSDLAERLGISKSTVSRIIK 40 (68)
T ss_dssp HHHHT--TS-BEHHHHHHHTT--HHHHHHHHH
T ss_pred HHHHHccCCCcCHHHHHHHHCcCHHHHHHHHH
Confidence 44444 56789999999999999999998754
No 350
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=90.71 E-value=0.74 Score=27.60 Aligned_cols=34 Identities=12% Similarity=0.052 Sum_probs=28.3
Q ss_pred HHHHHHHH-HhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 22 PRQIQRAR-LGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 22 ~~~lk~~r-~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
-+.+..+. ....+|..+||+.++.+++|+++..+
T Consensus 30 v~v~~~LL~~~~~~tvdelae~lnr~rStv~rsl~ 64 (126)
T COG3355 30 VEVYKALLEENGPLTVDELAEILNRSRSTVYRSLQ 64 (126)
T ss_pred HHHHHHHHhhcCCcCHHHHHHHHCccHHHHHHHHH
Confidence 45566677 57889999999999999999998754
No 351
>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=90.70 E-value=0.7 Score=26.43 Aligned_cols=24 Identities=8% Similarity=0.178 Sum_probs=21.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 32 KKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 32 ~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
.++++.+||..+++++++|++..+
T Consensus 42 ~~~t~~eL~~~l~~~~stvs~~i~ 65 (109)
T TIGR01889 42 GKLTLKEIIKEILIKQSALVKIIK 65 (109)
T ss_pred CcCcHHHHHHHHCCCHHHHHHHHH
Confidence 569999999999999999998754
No 352
>TIGR02915 PEP_resp_reg putative PEP-CTERM system response regulator. Members of this protein family share full-length homology with (but do not include) the acetoacetate metabolism regulatory protein AtoC. These proteins have a Fis family DNA binding sequence (pfam02954), a response regulator receiver domain (pfam00072), and sigma-54 interaction domain (pfam00158).
Probab=90.67 E-value=0.6 Score=32.59 Aligned_cols=34 Identities=6% Similarity=0.008 Sum_probs=28.4
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
...|..+....+.++.+.|+.+|||++|+++-.+
T Consensus 407 ~~~i~~al~~~~gn~~~aA~~Lgisr~tl~rkl~ 440 (445)
T TIGR02915 407 REAVRKAIARVDGNIARAAELLGITRPTLYDLMK 440 (445)
T ss_pred HHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHH
Confidence 3456677788899999999999999999988654
No 353
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=90.67 E-value=0.82 Score=27.83 Aligned_cols=28 Identities=14% Similarity=0.179 Sum_probs=24.2
Q ss_pred HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 28 ARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 28 ~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
++.-.|+|..|+|+.+|+|.++|.....
T Consensus 130 L~~~~g~s~~EIA~~lgis~~tV~~~l~ 157 (172)
T PRK12523 130 YNRLDGMGHAEIAERLGVSVSRVRQYLA 157 (172)
T ss_pred HHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 4455799999999999999999998764
No 354
>PRK11302 DNA-binding transcriptional regulator HexR; Provisional
Probab=90.65 E-value=0.56 Score=30.81 Aligned_cols=36 Identities=14% Similarity=0.051 Sum_probs=27.9
Q ss_pred HhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHH
Q 038591 30 LGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVL 65 (82)
Q Consensus 30 ~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~ 65 (82)
.-..+|..+||+.+|+|++||.++-+--..-+...+
T Consensus 31 ~v~~~si~~lA~~~~vS~aTv~Rf~kklG~~gf~e~ 66 (284)
T PRK11302 31 TAIHSSIATLAKMANVSEPTVNRFCRSLDTKGFPDF 66 (284)
T ss_pred HHHhcCHHHHHHHhCCCHHHHHHHHHHcCCCCHHHH
Confidence 345789999999999999999999875444444443
No 355
>PRK10923 glnG nitrogen regulation protein NR(I); Provisional
Probab=90.64 E-value=0.62 Score=32.78 Aligned_cols=34 Identities=6% Similarity=-0.025 Sum_probs=28.9
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
...|..+....+..+.+.|+.+|||++|+++-.+
T Consensus 431 ~~~i~~aL~~~~gn~~~aA~~Lgisr~tL~rkl~ 464 (469)
T PRK10923 431 RTLLTTALRHTQGHKQEAARLLGWGRNTLTRKLK 464 (469)
T ss_pred HHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHH
Confidence 3457777788899999999999999999988664
No 356
>PRK15008 HTH-type transcriptional regulator RutR; Provisional
Probab=90.61 E-value=0.29 Score=30.92 Aligned_cols=36 Identities=14% Similarity=0.040 Sum_probs=27.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHH
Q 038591 32 KKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAK 67 (82)
Q Consensus 32 ~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~ 67 (82)
.+.|..++|+.+|||..+|+.+-.++...-...+..
T Consensus 37 ~~~s~~dIA~~aGvs~gtiY~hF~sKe~L~~a~~~~ 72 (212)
T PRK15008 37 HGTRLEQIAELAGVSKTNLLYYFPSKEALYIAVLRQ 72 (212)
T ss_pred ccCCHHHHHHHhCcCHHHHHHHCCCHHHHHHHHHHH
Confidence 357899999999999999999987765444444333
No 357
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=90.61 E-value=0.27 Score=30.77 Aligned_cols=28 Identities=14% Similarity=0.063 Sum_probs=23.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHcCCCC
Q 038591 32 KKMSQPDLANQINQRPQVVSEYENGKAV 59 (82)
Q Consensus 32 ~g~s~~elA~~~gis~~~i~~~e~g~~~ 59 (82)
.++|..++|+.+|||+.|++.+-.++..
T Consensus 30 ~~~ti~~Ia~~agvsk~t~Y~~F~sKe~ 57 (213)
T PRK09975 30 SNTTLNDIADAANVTRGAIYWHFENKTQ 57 (213)
T ss_pred ccCCHHHHHHHcCCCHHHHHHHcCCHHH
Confidence 3689999999999999999999876543
No 358
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=90.59 E-value=0.86 Score=25.09 Aligned_cols=21 Identities=19% Similarity=0.137 Sum_probs=19.2
Q ss_pred CCHHHHHHHhCCCHHHHHHHH
Q 038591 34 MSQPDLANQINQRPQVVSEYE 54 (82)
Q Consensus 34 ~s~~elA~~~gis~~~i~~~e 54 (82)
.|..+||+.+|+|+.+|.+..
T Consensus 20 ~SGe~La~~LgiSRtaVwK~I 40 (79)
T COG1654 20 VSGEKLAEELGISRTAVWKHI 40 (79)
T ss_pred ccHHHHHHHHCccHHHHHHHH
Confidence 899999999999999998764
No 359
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=90.53 E-value=0.35 Score=28.77 Aligned_cols=32 Identities=16% Similarity=0.087 Sum_probs=25.0
Q ss_pred HHHHHHHh-CCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 24 QIQRARLG-KKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 24 ~lk~~r~~-~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
.|..+... -++|+.+||+.+++++++|++..+
T Consensus 36 vL~~l~~~~~~~t~~eLa~~l~~~~~tvt~~v~ 68 (144)
T PRK03573 36 TLHNIHQLPPEQSQIQLAKAIGIEQPSLVRTLD 68 (144)
T ss_pred HHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHH
Confidence 35555443 468999999999999999998753
No 360
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=90.52 E-value=0.55 Score=29.16 Aligned_cols=27 Identities=7% Similarity=-0.109 Sum_probs=23.6
Q ss_pred HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 29 RLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 29 r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
+--.|+|.+|+|+.+|+|.++|.....
T Consensus 123 ~~~eg~s~~EIA~~lgis~~tV~~~l~ 149 (182)
T PRK12511 123 VAIEGLSYQEAAAVLGIPIGTLMSRIG 149 (182)
T ss_pred HHHcCCCHHHHHHHhCcCHHHHHHHHH
Confidence 445699999999999999999998864
No 361
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=90.50 E-value=0.3 Score=31.19 Aligned_cols=23 Identities=4% Similarity=-0.113 Sum_probs=20.1
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHc
Q 038591 33 KMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 33 g~s~~elA~~~gis~~~i~~~e~ 55 (82)
.+|+.++|..+|+|+.+|++..+
T Consensus 169 ~~t~~~lA~~lG~sretvsR~L~ 191 (226)
T PRK10402 169 HEKHTQAAEYLGVSYRHLLYVLA 191 (226)
T ss_pred cchHHHHHHHHCCcHHHHHHHHH
Confidence 36899999999999999999643
No 362
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=90.47 E-value=0.99 Score=23.47 Aligned_cols=26 Identities=12% Similarity=0.073 Sum_probs=21.7
Q ss_pred HhCCCCHHHHHHHhCC-CHHHHHHHHc
Q 038591 30 LGKKMSQPDLANQINQ-RPQVVSEYEN 55 (82)
Q Consensus 30 ~~~g~s~~elA~~~gi-s~~~i~~~e~ 55 (82)
....++..++|..+|+ +++++++.-.
T Consensus 47 ~~~~~~~~~ia~~~g~~s~~~f~r~Fk 73 (84)
T smart00342 47 RDTDLSVTEIALRVGFSSQSYFSRAFK 73 (84)
T ss_pred HcCCCCHHHHHHHhCCCChHHHHHHHH
Confidence 3346999999999999 9999988764
No 363
>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=90.43 E-value=0.52 Score=30.62 Aligned_cols=23 Identities=22% Similarity=0.277 Sum_probs=21.1
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcC
Q 038591 34 MSQPDLANQINQRPQVVSEYENG 56 (82)
Q Consensus 34 ~s~~elA~~~gis~~~i~~~e~g 56 (82)
++..|||+.+|+|.++|..||.-
T Consensus 2 y~i~elA~~~Gvs~~tIR~Ye~~ 24 (219)
T cd04778 2 YRIDDLARAAGTTVRNVRAYQDR 24 (219)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC
Confidence 67899999999999999999964
No 364
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=90.40 E-value=0.8 Score=28.45 Aligned_cols=28 Identities=7% Similarity=0.005 Sum_probs=23.8
Q ss_pred HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 28 ARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 28 ~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
++.-.|+|.+|+|+.+|+|.+||.....
T Consensus 145 L~~~~g~s~~EIA~~lgis~~tVk~~l~ 172 (189)
T PRK12530 145 MREYLELSSEQICQECDISTSNLHVLLY 172 (189)
T ss_pred HHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3445699999999999999999988764
No 365
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=90.40 E-value=1.1 Score=29.20 Aligned_cols=51 Identities=12% Similarity=-0.053 Sum_probs=33.9
Q ss_pred CCHHHHHHHH-HhCCCCHHHHHHHhCCCHHHHHHHHcC----CCCCCHHHHHHHHH
Q 038591 20 DTPRQIQRAR-LGKKMSQPDLANQINQRPQVVSEYENG----KAVPNQTVLAKMEK 70 (82)
Q Consensus 20 ~~~~~lk~~r-~~~g~s~~elA~~~gis~~~i~~~e~g----~~~p~~~~~~~la~ 70 (82)
+......-++ -..|+|.+|+|+.+++|+.||..+... -...+...+..++.
T Consensus 144 LS~RE~eVL~Lia~G~SnkEIA~~L~IS~~TVk~hvs~I~~KLgv~sR~eLv~~A~ 199 (217)
T PRK13719 144 VTKYQNDVFILYSFGFSHEYIAQLLNITVGSSKNKISEILKFFGISSRDELLIILH 199 (217)
T ss_pred CCHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCHHHHHHHHH
Confidence 4444444443 457999999999999999999888653 22334444444443
No 366
>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=90.39 E-value=0.93 Score=25.79 Aligned_cols=35 Identities=17% Similarity=0.144 Sum_probs=26.4
Q ss_pred CCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCccc
Q 038591 34 MSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVK 79 (82)
Q Consensus 34 ~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e~ 79 (82)
-|....|+.+|+|++++++. +..|.+.||+++-++
T Consensus 17 gSis~AA~~L~iS~stvs~~-----------I~~LE~~lg~~Lf~R 51 (99)
T TIGR00637 17 GSISQAAKDAGISYKSAWDY-----------IRAMNNLSGEPLVER 51 (99)
T ss_pred CCHHHHHHHHCCCHHHHHHH-----------HHHHHHHhCCCeEEe
Confidence 36677999999999999874 456666777766554
No 367
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=90.36 E-value=0.52 Score=29.29 Aligned_cols=27 Identities=4% Similarity=-0.085 Sum_probs=23.5
Q ss_pred HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 29 RLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 29 r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
+.-.|+|..|+|+.+|+|..||.....
T Consensus 148 ~~~~g~s~~EIA~~lgis~~tVk~~l~ 174 (195)
T PRK12532 148 KEILGFSSDEIQQMCGISTSNYHTIMH 174 (195)
T ss_pred HHHhCCCHHHHHHHHCCCHHHHHHHHH
Confidence 455699999999999999999988764
No 368
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=90.36 E-value=0.38 Score=30.97 Aligned_cols=24 Identities=25% Similarity=0.332 Sum_probs=22.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 32 KKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 32 ~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
.|+|.+++|+.+|+|.++|.++..
T Consensus 194 e~~S~~EIA~~lgis~~tV~~~~~ 217 (233)
T PRK05803 194 KEKTQREIAKALGISRSYVSRIEK 217 (233)
T ss_pred CCcCHHHHHHHHCcCHHHHHHHHH
Confidence 578999999999999999999864
No 369
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=90.31 E-value=0.83 Score=23.02 Aligned_cols=28 Identities=11% Similarity=0.111 Sum_probs=24.1
Q ss_pred HHhCCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591 29 RLGKKMSQPDLANQINQRPQVVSEYENG 56 (82)
Q Consensus 29 r~~~g~s~~elA~~~gis~~~i~~~e~g 56 (82)
+-..|.+..++|..+++|+.||......
T Consensus 15 l~~~G~s~~eia~~l~is~~tV~~h~~~ 42 (65)
T COG2771 15 LVAQGKSNKEIARILGISEETVKTHLRN 42 (65)
T ss_pred HHHCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 4567899999999999999999887653
No 370
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=90.29 E-value=0.89 Score=26.79 Aligned_cols=30 Identities=17% Similarity=0.162 Sum_probs=23.8
Q ss_pred HHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591 25 IQRARLGKKMSQPDLANQINQRPQVVSEYE 54 (82)
Q Consensus 25 lk~~r~~~g~s~~elA~~~gis~~~i~~~e 54 (82)
|..+...-.++..++|+.+|+++++|++-.
T Consensus 22 L~~L~~~~~~~v~ela~~l~lsqstvS~HL 51 (117)
T PRK10141 22 VLLLRESGELCVCDLCTALDQSQPKISRHL 51 (117)
T ss_pred HHHHHHcCCcCHHHHHHHHCcCHHHHHHHH
Confidence 344444456899999999999999999864
No 371
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=90.28 E-value=0.64 Score=29.48 Aligned_cols=33 Identities=12% Similarity=-0.072 Sum_probs=27.0
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591 22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYE 54 (82)
Q Consensus 22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e 54 (82)
...|..+....|+||.+||+.++++++|++++.
T Consensus 48 ~~iL~~L~~~~~itq~eLa~~l~l~~sTvtr~l 80 (185)
T PRK13777 48 HHILWIAYHLKGASISEIAKFGVMHVSTAFNFS 80 (185)
T ss_pred HHHHHHHHhCCCcCHHHHHHHHCCCHhhHHHHH
Confidence 355666677789999999999999999988753
No 372
>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=90.28 E-value=0.84 Score=29.13 Aligned_cols=27 Identities=7% Similarity=0.132 Sum_probs=23.5
Q ss_pred HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 29 RLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 29 r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
+-..|+|.+|+|+.+|+|..+|..+..
T Consensus 187 ~y~~~~s~~eIA~~lgis~~tV~~~~~ 213 (224)
T TIGR02479 187 YYYEELNLKEIGEVLGLTESRVSQIHS 213 (224)
T ss_pred HHhCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 345699999999999999999998765
No 373
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=90.27 E-value=0.42 Score=29.66 Aligned_cols=25 Identities=8% Similarity=0.057 Sum_probs=22.0
Q ss_pred hCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 31 GKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 31 ~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
-.|+|..|+|+.+|+|..+|.....
T Consensus 153 ~~g~s~~EIA~~lgis~~tV~~~l~ 177 (194)
T PRK12513 153 HGDLELEEIAELTGVPEETVKSRLR 177 (194)
T ss_pred ccCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3599999999999999999987754
No 374
>PRK10668 DNA-binding transcriptional repressor AcrR; Provisional
Probab=90.27 E-value=0.24 Score=31.07 Aligned_cols=28 Identities=14% Similarity=-0.026 Sum_probs=23.8
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHcCCCCC
Q 038591 33 KMSQPDLANQINQRPQVVSEYENGKAVP 60 (82)
Q Consensus 33 g~s~~elA~~~gis~~~i~~~e~g~~~p 60 (82)
+.|..++|+.+|+|+.+++.+..++...
T Consensus 31 ~~t~~~Ia~~agvs~~tlY~~F~sKe~L 58 (215)
T PRK10668 31 ATSLADIAKAAGVTRGAIYWHFKNKSDL 58 (215)
T ss_pred cCCHHHHHHHhCCChHHHHHHCCCHHHH
Confidence 5689999999999999999998765443
No 375
>PRK11050 manganese transport regulator MntR; Provisional
Probab=90.27 E-value=0.71 Score=28.12 Aligned_cols=25 Identities=16% Similarity=0.169 Sum_probs=22.1
Q ss_pred hCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 31 GKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 31 ~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
.-++++.++|+.+++++++|+++.+
T Consensus 49 ~~~~t~~eLA~~l~is~stVsr~l~ 73 (152)
T PRK11050 49 VGEARQVDIAARLGVSQPTVAKMLK 73 (152)
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3578999999999999999999863
No 376
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=90.24 E-value=0.86 Score=28.40 Aligned_cols=28 Identities=18% Similarity=0.260 Sum_probs=24.5
Q ss_pred HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 28 ARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 28 ~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
++--.|++.+|+|+.+|+|..||.....
T Consensus 147 L~~~~g~s~~eIA~~lgis~~tV~~~l~ 174 (196)
T PRK12524 147 LRHIEGLSNPEIAEVMEIGVEAVESLTA 174 (196)
T ss_pred HHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 4455799999999999999999998875
No 377
>PRK15424 propionate catabolism operon regulatory protein PrpR; Provisional
Probab=90.23 E-value=0.67 Score=33.93 Aligned_cols=34 Identities=12% Similarity=-0.022 Sum_probs=29.7
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
...|.......+.++...|+.+|||++|+++..+
T Consensus 499 r~~I~~~L~~~~Gn~~~aA~~LGIsRtTL~RkLk 532 (538)
T PRK15424 499 AATLQQALERFNGDKTAAANYLGISRTTLWRRLK 532 (538)
T ss_pred HHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHH
Confidence 4567778888899999999999999999999875
No 378
>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=90.20 E-value=0.41 Score=30.75 Aligned_cols=24 Identities=21% Similarity=0.322 Sum_probs=21.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 32 KKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 32 ~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
.|+|.+|+|+.+|+|+++|..+.+
T Consensus 193 e~~S~~EIAe~lgis~~tV~~~~~ 216 (227)
T TIGR02846 193 RRKTQREIAKILGISRSYVSRIEK 216 (227)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHH
Confidence 689999999999999999988764
No 379
>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=90.18 E-value=0.83 Score=27.65 Aligned_cols=28 Identities=18% Similarity=0.296 Sum_probs=23.7
Q ss_pred HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 28 ARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 28 ~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
++--.|+|.+|+|+.+|+|.++|.....
T Consensus 130 l~~~~g~s~~eiA~~lgis~~tv~~~l~ 157 (169)
T TIGR02954 130 LRYYHDLTIKEIAEVMNKPEGTVKTYLH 157 (169)
T ss_pred HHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3445699999999999999999988764
No 380
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=90.08 E-value=0.45 Score=30.40 Aligned_cols=37 Identities=16% Similarity=0.305 Sum_probs=27.3
Q ss_pred CCHHHHHHHH-HhCCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591 20 DTPRQIQRAR-LGKKMSQPDLANQINQRPQVVSEYENG 56 (82)
Q Consensus 20 ~~~~~lk~~r-~~~g~s~~elA~~~gis~~~i~~~e~g 56 (82)
+......-++ -..|+|.+++|+.+++|+.||..+-..
T Consensus 135 LT~RE~eVL~ll~~G~snkeIA~~L~iS~~TV~~h~~~ 172 (207)
T PRK11475 135 LSPTEREILRFMSRGYSMPQIAEQLERNIKTIRAHKFN 172 (207)
T ss_pred CCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 4444444332 357999999999999999999887653
No 381
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=90.08 E-value=0.91 Score=28.28 Aligned_cols=28 Identities=7% Similarity=-0.089 Sum_probs=24.1
Q ss_pred HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 28 ARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 28 ~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
++.-.|+|..|+|+.+|+|..+|.....
T Consensus 127 L~~~~g~s~~EIA~~Lgis~~tVk~~l~ 154 (187)
T PRK12516 127 LVGASGFAYEEAAEICGCAVGTIKSRVN 154 (187)
T ss_pred HHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 4455799999999999999999988764
No 382
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=90.08 E-value=0.91 Score=28.74 Aligned_cols=28 Identities=11% Similarity=0.000 Sum_probs=24.2
Q ss_pred HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 28 ARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 28 ~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
++.-.|++.+|+|+.+|+|..+|.....
T Consensus 149 L~~~~g~s~~EIA~~Lgis~~tV~~~l~ 176 (203)
T PRK09647 149 LCDIEGLSYEEIAATLGVKLGTVRSRIH 176 (203)
T ss_pred HHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 4456799999999999999999988764
No 383
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=90.07 E-value=0.68 Score=27.23 Aligned_cols=30 Identities=7% Similarity=0.001 Sum_probs=22.7
Q ss_pred HHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591 24 QIQRARLGKKMSQPDLANQINQRPQVVSEYE 54 (82)
Q Consensus 24 ~lk~~r~~~g~s~~elA~~~gis~~~i~~~e 54 (82)
-|+.+....| +.+++++.+|||++||..-.
T Consensus 41 Fi~~Fi~~rG-nlKe~e~~lgiSYPTvR~rL 70 (113)
T PF09862_consen 41 FIKLFIKNRG-NLKEMEKELGISYPTVRNRL 70 (113)
T ss_pred HHHHHHHhcC-CHHHHHHHHCCCcHHHHHHH
Confidence 3444445444 89999999999999998743
No 384
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=89.96 E-value=0.37 Score=30.79 Aligned_cols=24 Identities=25% Similarity=0.273 Sum_probs=22.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 32 KKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 32 ~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
.|+|.+++|+.+|+|+.||..+.+
T Consensus 177 ~g~s~~eIA~~l~iS~~Tv~~~~~ 200 (239)
T PRK10430 177 YEFSTDELANAVNISRVSCRKYLI 200 (239)
T ss_pred CCcCHHHHHHHhCchHHHHHHHHH
Confidence 799999999999999999998865
No 385
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=89.95 E-value=0.52 Score=31.08 Aligned_cols=30 Identities=13% Similarity=0.163 Sum_probs=25.9
Q ss_pred HHHHHHHHhCCCCHHHHHHHhCCCHHHHHH
Q 038591 23 RQIQRARLGKKMSQPDLANQINQRPQVVSE 52 (82)
Q Consensus 23 ~~lk~~r~~~g~s~~elA~~~gis~~~i~~ 52 (82)
..|+.+.+..-++.+|||+.+|||..||.+
T Consensus 9 ~Il~~l~~~g~v~v~eLa~~~~VS~~TIRR 38 (253)
T COG1349 9 KILELLKEKGKVSVEELAELFGVSEMTIRR 38 (253)
T ss_pred HHHHHHHHcCcEEHHHHHHHhCCCHHHHHH
Confidence 455667777789999999999999999988
No 386
>TIGR03384 betaine_BetI transcriptional repressor BetI. BetI is a DNA-binding transcriptional repressor of the bet (betaine) regulon. In sequence, it is related to TetR (pfam00440). Choline, through BetI, induces the expression of the betaine biosynthesis genes betA and betB by derepression. The choline porter gene betT is also part of this regulon in Escherichia coli. Note that a different transcriptional regulator, ArcA, controls the expression of bet regulon genes in response to oxygen, as BetA is an oxygen-dependent enzyme.
Probab=89.93 E-value=0.37 Score=29.36 Aligned_cols=28 Identities=18% Similarity=0.293 Sum_probs=23.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHcCCCC
Q 038591 32 KKMSQPDLANQINQRPQVVSEYENGKAV 59 (82)
Q Consensus 32 ~g~s~~elA~~~gis~~~i~~~e~g~~~ 59 (82)
.+.|..++|+.+|+|..+++.+..++..
T Consensus 27 ~~~s~~~IA~~agvsk~~ly~~F~sK~~ 54 (189)
T TIGR03384 27 LDVTIAQIARRAGVSSGIISHYFGGKQG 54 (189)
T ss_pred ccCCHHHHHHHhCCCHHHHHHHcCCHHH
Confidence 3678999999999999999998765443
No 387
>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=89.92 E-value=0.84 Score=27.33 Aligned_cols=28 Identities=14% Similarity=0.149 Sum_probs=24.1
Q ss_pred HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 28 ARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 28 ~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
++--.|+|.+|+|+.+|+|.++|.....
T Consensus 121 l~~~~g~s~~eIA~~lgis~~tV~~~l~ 148 (162)
T TIGR02983 121 LRYYEDLSEAQVAEALGISVGTVKSRLS 148 (162)
T ss_pred hHHHhcCCHHHHHHHhCCCHHHHHHHHH
Confidence 3445799999999999999999998765
No 388
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=89.91 E-value=0.15 Score=34.72 Aligned_cols=34 Identities=12% Similarity=0.358 Sum_probs=30.8
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhC---------CCHHHHHHHHc
Q 038591 22 PRQIQRARLGKKMSQPDLANQIN---------QRPQVVSEYEN 55 (82)
Q Consensus 22 ~~~lk~~r~~~g~s~~elA~~~g---------is~~~i~~~e~ 55 (82)
+++.++.|...|+||.|++..+- +|++||-++|+
T Consensus 223 AErFKQRRIKLGVTQADVG~ALAnLKiPGVGsLSQSTICRFES 265 (385)
T KOG1168|consen 223 AERFKQRRIKLGVTQADVGKALANLKIPGVGSLSQSTICRFES 265 (385)
T ss_pred HHHHHhhhhhhcccHHHHHHHHHhCcCCCcccccccceeeeee
Confidence 89999999999999999998772 68999999986
No 389
>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=89.86 E-value=0.098 Score=26.35 Aligned_cols=42 Identities=14% Similarity=0.216 Sum_probs=27.9
Q ss_pred CCCHHHHHHHhCCCHHHHHHHH---cCC------CCCCHHHHHHHHHHhCC
Q 038591 33 KMSQPDLANQINQRPQVVSEYE---NGK------AVPNQTVLAKMEKAIGV 74 (82)
Q Consensus 33 g~s~~elA~~~gis~~~i~~~e---~g~------~~p~~~~~~~la~~lgv 74 (82)
+++..|||+.+|++...|-... .|. ...+.+.+..|+..||+
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 4677899999999987776665 352 23456667888888875
No 390
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.
Probab=89.85 E-value=0.48 Score=28.05 Aligned_cols=24 Identities=21% Similarity=0.142 Sum_probs=21.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 32 KKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 32 ~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
.|+|..++|+.+|+|..+|.....
T Consensus 120 ~g~s~~eIA~~lgis~~tv~~~l~ 143 (154)
T TIGR02950 120 KEFSYKEIAELLNLSLAKVKSNLF 143 (154)
T ss_pred ccCcHHHHHHHHCCCHHHHHHHHH
Confidence 489999999999999999988754
No 391
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=89.85 E-value=0.93 Score=29.81 Aligned_cols=27 Identities=7% Similarity=0.103 Sum_probs=24.0
Q ss_pred HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 29 RLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 29 r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
+-..++|..|+|..+|+|.++|++++.
T Consensus 217 ~y~e~~t~~EIA~~lgis~~~V~~~~~ 243 (257)
T PRK05911 217 YYYEELVLKEIGKILGVSESRVSQIHS 243 (257)
T ss_pred HHhcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 334699999999999999999999976
No 392
>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=89.85 E-value=0.89 Score=29.63 Aligned_cols=28 Identities=14% Similarity=0.249 Sum_probs=24.3
Q ss_pred HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 28 ARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 28 ~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
++-..|+|..|+|+.+|+|.++|..+..
T Consensus 216 l~~~~g~s~~eIA~~lgis~~~V~~~~~ 243 (255)
T TIGR02941 216 CTFEENLSQKETGERLGISQMHVSRLQR 243 (255)
T ss_pred HHHcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 3445799999999999999999998875
No 393
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=89.82 E-value=0.63 Score=28.45 Aligned_cols=26 Identities=8% Similarity=0.072 Sum_probs=22.8
Q ss_pred HhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 30 LGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 30 ~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
--.|++.+++|+.+|+|..+|.....
T Consensus 149 ~~~~~s~~eIA~~lgis~~~v~~~l~ 174 (187)
T PRK09641 149 YIEDLSLKEISEILDLPVGTVKTRIH 174 (187)
T ss_pred HhhCCCHHHHHHHHCCCHHHHHHHHH
Confidence 34699999999999999999988764
No 394
>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=89.82 E-value=1.1 Score=28.12 Aligned_cols=46 Identities=9% Similarity=0.038 Sum_probs=32.5
Q ss_pred HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcC--CCCCCHHHHHHH
Q 038591 23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYENG--KAVPNQTVLAKM 68 (82)
Q Consensus 23 ~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g--~~~p~~~~~~~l 68 (82)
..++.+----++|....|..+|||..|+.+|-.. ...-.++.+..-
T Consensus 9 ~~~R~~YV~~~~sLe~aA~~~gVs~~TarrWK~~Ak~~GDDWDk~RaA 56 (165)
T PF08822_consen 9 DAVRRAYVFDRLSLEQAAAKCGVSYATARRWKREAKAKGDDWDKARAA 56 (165)
T ss_pred HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHHHHHHcCCcHHHHHHH
Confidence 3445555557899999999999999999999752 122355554433
No 395
>PRK09508 leuO leucine transcriptional activator; Reviewed
Probab=89.80 E-value=1.2 Score=29.52 Aligned_cols=37 Identities=16% Similarity=0.225 Sum_probs=27.7
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcccc
Q 038591 33 KMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVKI 80 (82)
Q Consensus 33 g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e~~ 80 (82)
.-|....|+.+|+|+++||+ .+..|.+.||+++-+|.
T Consensus 36 ~gs~s~AA~~L~isQpavS~-----------~I~~LE~~lg~~LF~R~ 72 (314)
T PRK09508 36 EQNITRAAHNLGMSQPAVSN-----------AVARLKVMFNDELFVRY 72 (314)
T ss_pred cCCHHHHHHHhCCCHHHHHH-----------HHHHHHHhhCCCcEEEc
Confidence 34566799999999999998 45666677777765554
No 396
>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=89.72 E-value=1.1 Score=26.94 Aligned_cols=28 Identities=14% Similarity=0.285 Sum_probs=23.4
Q ss_pred HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 28 ARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 28 ~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
++--.|+|..|+|+.+|+|.++|.....
T Consensus 133 l~~~~g~s~~eIA~~l~is~~tv~~~l~ 160 (170)
T TIGR02952 133 LRFGQNLPIAEVARILGKTEGAVKILQF 160 (170)
T ss_pred HHHhcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3445699999999999999999987653
No 397
>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=89.70 E-value=0.83 Score=30.65 Aligned_cols=25 Identities=16% Similarity=0.389 Sum_probs=22.8
Q ss_pred hCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 31 GKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 31 ~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
..++|.+|+|+.+|+|+.+|.+++.
T Consensus 267 ~~~~Tl~EIa~~lgiS~erVrq~~~ 291 (298)
T TIGR02997 267 GEPLTLAEIGRRLNLSRERVRQIEA 291 (298)
T ss_pred CCCcCHHHHHHHHCcCHHHHHHHHH
Confidence 3589999999999999999999986
No 398
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=89.69 E-value=0.92 Score=27.91 Aligned_cols=28 Identities=7% Similarity=0.036 Sum_probs=24.5
Q ss_pred HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 28 ARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 28 ~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
++--.|+|..|+|+.+|+|..+|.....
T Consensus 139 l~~~~g~s~~EIA~~lgis~~tV~~~l~ 166 (186)
T PRK05602 139 LQYYQGLSNIEAAAVMDISVDALESLLA 166 (186)
T ss_pred HHHhcCCCHHHHHHHhCcCHHHHHHHHH
Confidence 3455799999999999999999999875
No 399
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=89.67 E-value=0.59 Score=30.80 Aligned_cols=32 Identities=13% Similarity=0.076 Sum_probs=25.4
Q ss_pred HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591 23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYE 54 (82)
Q Consensus 23 ~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e 54 (82)
..+..+.+...++..|||+.+|+|..||.+-.
T Consensus 9 ~Il~~L~~~~~v~v~eLa~~l~VS~~TIRRDL 40 (256)
T PRK10434 9 AILEYLQKQGKTSVEELAQYFDTTGTTIRKDL 40 (256)
T ss_pred HHHHHHHHcCCEEHHHHHHHHCCCHHHHHHHH
Confidence 34455566667999999999999999998753
No 400
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=89.66 E-value=1 Score=27.49 Aligned_cols=27 Identities=11% Similarity=0.103 Sum_probs=23.2
Q ss_pred HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 29 RLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 29 r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
+--.|+|.+|+|+.+|+|..+|.....
T Consensus 141 ~~~~g~s~~eIA~~lgis~~tV~~~l~ 167 (179)
T PRK12514 141 AYLEGLSYKELAERHDVPLNTMRTWLR 167 (179)
T ss_pred HHHcCCCHHHHHHHHCCChHHHHHHHH
Confidence 345699999999999999999988764
No 401
>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=89.64 E-value=0.45 Score=25.96 Aligned_cols=46 Identities=20% Similarity=0.166 Sum_probs=32.3
Q ss_pred HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 038591 23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKL 76 (82)
Q Consensus 23 ~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~ 76 (82)
..+..+-.....|..++|+.+++|.+|+.+..+ .+....+.+|+.+
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 445666778899999999999999999999754 4555566666655
No 402
>PRK06930 positive control sigma-like factor; Validated
Probab=89.61 E-value=1.1 Score=27.93 Aligned_cols=28 Identities=18% Similarity=0.264 Sum_probs=24.5
Q ss_pred HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 28 ARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 28 ~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
++-..|+|..++|+.+|+|.++|..+..
T Consensus 125 L~~~eg~s~~EIA~~lgiS~~tVk~~l~ 152 (170)
T PRK06930 125 MHRGYGLSYSEIADYLNIKKSTVQSMIE 152 (170)
T ss_pred HHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 3456899999999999999999999875
No 403
>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=89.50 E-value=0.5 Score=30.49 Aligned_cols=24 Identities=17% Similarity=0.303 Sum_probs=21.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 32 KKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 32 ~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
.|+|.+|+|+.+|+|..||.....
T Consensus 197 eg~s~~EIA~~Lgis~~tV~~~l~ 220 (234)
T TIGR02835 197 TEKTQKEVADMLGISQSYISRLEK 220 (234)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHH
Confidence 589999999999999999988764
No 404
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=89.49 E-value=1.2 Score=26.73 Aligned_cols=28 Identities=14% Similarity=0.169 Sum_probs=23.7
Q ss_pred HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 28 ARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 28 ~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
++--.|+|..|+|+.+|+|.+||.....
T Consensus 124 L~~~~g~s~~EIA~~l~is~~tV~~~l~ 151 (161)
T PRK12528 124 LAQVDGLGYGEIATELGISLATVKRYLN 151 (161)
T ss_pred HHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3455799999999999999999987653
No 405
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=89.46 E-value=0.43 Score=30.43 Aligned_cols=22 Identities=18% Similarity=0.155 Sum_probs=19.8
Q ss_pred CCCHHHHHHHhCCCHHHHHHHH
Q 038591 33 KMSQPDLANQINQRPQVVSEYE 54 (82)
Q Consensus 33 g~s~~elA~~~gis~~~i~~~e 54 (82)
.+|+.++|..+|+++.+|++..
T Consensus 173 ~~t~~~iA~~lG~tretvsR~l 194 (236)
T PRK09392 173 PYEKRVLASYLGMTPENLSRAF 194 (236)
T ss_pred eCCHHHHHHHhCCChhHHHHHH
Confidence 4678999999999999999975
No 406
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=89.42 E-value=0.81 Score=28.12 Aligned_cols=27 Identities=11% Similarity=-0.093 Sum_probs=23.6
Q ss_pred HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 29 RLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 29 r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
+.-.|+|.+|+|+.+|+|.++|.....
T Consensus 141 ~~~~g~s~~EIA~~l~is~~tV~~~l~ 167 (181)
T PRK12536 141 VKLEGLSVAETAQLTGLSESAVKVGIH 167 (181)
T ss_pred HHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 445799999999999999999998764
No 407
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=89.40 E-value=0.72 Score=30.52 Aligned_cols=47 Identities=15% Similarity=0.348 Sum_probs=33.9
Q ss_pred HHHHHHHH--hCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcccc
Q 038591 23 RQIQRARL--GKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVKI 80 (82)
Q Consensus 23 ~~lk~~r~--~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e~~ 80 (82)
..|+.+.. +.|.|....|+.+|+|+++||+. +..|.+.||+++-+|.
T Consensus 4 ~~L~~F~~v~~~~~s~s~AA~~L~isq~avSr~-----------I~~LE~~lg~~LF~R~ 52 (309)
T PRK12682 4 QQLRFVREAVRRNLNLTEAAKALHTSQPGVSKA-----------IIELEEELGIEIFIRH 52 (309)
T ss_pred HHHHHHHHHHHccCCHHHHHHHhcCccHHHHHH-----------HHHHHHHhCCeeEEEC
Confidence 34555543 34678999999999999999984 4566677777765553
No 408
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=89.40 E-value=0.9 Score=27.59 Aligned_cols=26 Identities=4% Similarity=0.142 Sum_probs=22.9
Q ss_pred HHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591 29 RLGKKMSQPDLANQINQRPQVVSEYE 54 (82)
Q Consensus 29 r~~~g~s~~elA~~~gis~~~i~~~e 54 (82)
+--.|+|.+|+|+.+|+|..||....
T Consensus 130 ~~~eg~s~~EIA~~l~is~~tV~~~l 155 (168)
T PRK12525 130 SQLEGLTYVEIGERLGVSLSRIHQYM 155 (168)
T ss_pred HHHcCCCHHHHHHHHCCCHHHHHHHH
Confidence 44569999999999999999998775
No 409
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=89.38 E-value=0.73 Score=30.36 Aligned_cols=29 Identities=17% Similarity=0.274 Sum_probs=23.9
Q ss_pred HHHHHHhCCCCHHHHHHHhCCCHHHHHHH
Q 038591 25 IQRARLGKKMSQPDLANQINQRPQVVSEY 53 (82)
Q Consensus 25 lk~~r~~~g~s~~elA~~~gis~~~i~~~ 53 (82)
+..+.+...++..|||+.++||..||++.
T Consensus 11 l~~l~~~~~~~~~ela~~l~vS~~TiRRd 39 (252)
T PRK10906 11 IELVKQQGYVSTEELVEHFSVSPQTIRRD 39 (252)
T ss_pred HHHHHHcCCEeHHHHHHHhCCCHHHHHHH
Confidence 44455555699999999999999999985
No 410
>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional
Probab=89.37 E-value=0.91 Score=32.73 Aligned_cols=34 Identities=9% Similarity=0.036 Sum_probs=29.8
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
...|..+.+..+..+...|+.+|||++|+++..+
T Consensus 470 r~~I~~aL~~~~gn~~~aA~~LGisr~tL~rklk 503 (509)
T PRK05022 470 RQLIRQALAQHQGNWAAAARALELDRANLHRLAK 503 (509)
T ss_pred HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHH
Confidence 4567888888999999999999999999988765
No 411
>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=89.34 E-value=1.2 Score=27.22 Aligned_cols=27 Identities=19% Similarity=0.153 Sum_probs=23.1
Q ss_pred HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 29 RLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 29 r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
+--.|++.+++|..+|+|.++|.....
T Consensus 152 ~~~~g~s~~eIA~~lgis~~~v~~~l~ 178 (189)
T TIGR02984 152 RHLEGLSFAEVAERMDRSEGAVSMLWV 178 (189)
T ss_pred HHhcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 344699999999999999999988754
No 412
>PRK09483 response regulator; Provisional
Probab=89.30 E-value=1.6 Score=26.75 Aligned_cols=45 Identities=18% Similarity=0.349 Sum_probs=32.2
Q ss_pred HhCCCCHHHHHHHhCCCHHHHHHHHcC----CCCCCHHHHHHHHHHhCC
Q 038591 30 LGKKMSQPDLANQINQRPQVVSEYENG----KAVPNQTVLAKMEKAIGV 74 (82)
Q Consensus 30 ~~~g~s~~elA~~~gis~~~i~~~e~g----~~~p~~~~~~~la~~lgv 74 (82)
-..|+|.+++|+.+++|..||..+.+. -...+...+..+|.-.|+
T Consensus 160 ~~~G~~~~~Ia~~l~is~~TV~~~~~~i~~Kl~v~~~~~l~~~a~~~~~ 208 (217)
T PRK09483 160 ITKGQKVNEISEQLNLSPKTVNSYRYRMFSKLNISGDVELTHLAIRHGL 208 (217)
T ss_pred HHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHcCCCCHHHHHHHHHHcCC
Confidence 368999999999999999999888753 122345555556555553
No 413
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=89.30 E-value=1.1 Score=27.58 Aligned_cols=28 Identities=4% Similarity=0.024 Sum_probs=23.6
Q ss_pred HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 28 ARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 28 ~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
++.-.|+|.+|+|+.+|+|.+||.....
T Consensus 133 l~~~~g~s~~EIA~~lgis~~tVk~~l~ 160 (185)
T PRK12542 133 YKVFYNLTYQEISSVMGITEANVRKQFE 160 (185)
T ss_pred HHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3455799999999999999999988653
No 414
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=89.27 E-value=0.88 Score=29.88 Aligned_cols=33 Identities=15% Similarity=0.145 Sum_probs=26.5
Q ss_pred HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 23 ~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
..+..+.....++..+||+.+|||..||.+-.+
T Consensus 11 ~I~~~l~~~~~v~v~eLa~~~~VS~~TIRRDL~ 43 (252)
T PRK10681 11 QLLQALKRSDKLHLKDAAALLGVSEMTIRRDLN 43 (252)
T ss_pred HHHHHHHHcCCCcHHHHHHHhCCCHHHHHHHHH
Confidence 345556667779999999999999999987643
No 415
>PRK11202 DNA-binding transcriptional repressor FabR; Provisional
Probab=89.26 E-value=0.29 Score=30.75 Aligned_cols=29 Identities=10% Similarity=0.029 Sum_probs=24.3
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHcCCCCC
Q 038591 32 KKMSQPDLANQINQRPQVVSEYENGKAVP 60 (82)
Q Consensus 32 ~g~s~~elA~~~gis~~~i~~~e~g~~~p 60 (82)
.++|..++|+.+|+|+.+++++..++...
T Consensus 31 ~~~si~~IA~~Agvs~~t~Y~hF~sKe~L 59 (203)
T PRK11202 31 SSLSLREVAREAGIAPTSFYRHFRDMDEL 59 (203)
T ss_pred ccCCHHHHHHHhCCCcchHHHHCCCHHHH
Confidence 35799999999999999999998765443
No 416
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=89.18 E-value=0.62 Score=28.82 Aligned_cols=26 Identities=4% Similarity=0.028 Sum_probs=22.8
Q ss_pred HhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 30 LGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 30 ~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
--.|+|.+|+|+.+|+|.++|.....
T Consensus 147 ~~~g~s~~EIA~~lgis~~tV~~~l~ 172 (188)
T PRK09640 147 FVAELEFQEIADIMHMGLSATKMRYK 172 (188)
T ss_pred HhcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 34589999999999999999998865
No 417
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=89.12 E-value=1.3 Score=26.49 Aligned_cols=28 Identities=14% Similarity=0.135 Sum_probs=23.9
Q ss_pred HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 28 ARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 28 ~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
++.-.|+|.+|+|+.+|+|.++|.....
T Consensus 116 l~~~~~~s~~eIA~~lgis~~tv~~~l~ 143 (159)
T PRK12527 116 LRKLEGLSHQQIAEHLGISRSLVEKHIV 143 (159)
T ss_pred HHHHcCCCHHHHHHHhCCCHHHHHHHHH
Confidence 4455799999999999999999988764
No 418
>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family. Member of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.
Probab=89.11 E-value=0.85 Score=29.64 Aligned_cols=31 Identities=10% Similarity=0.117 Sum_probs=24.9
Q ss_pred HHHHHH-hCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 25 IQRARL-GKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 25 lk~~r~-~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
|..+-. ..++|..|+|+.+|++++|++++.+
T Consensus 15 L~~l~~~~~~~~l~eia~~lglpksT~~RlL~ 46 (248)
T TIGR02431 15 IEAFGAERPRLTLTDVAEATGLTRAAARRFLL 46 (248)
T ss_pred HHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 444433 4679999999999999999999864
No 419
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=89.07 E-value=1.2 Score=25.53 Aligned_cols=32 Identities=6% Similarity=0.042 Sum_probs=25.7
Q ss_pred HHHHHHHhCCCCHHHHHHHhCC-CHHHHHHHHc
Q 038591 24 QIQRARLGKKMSQPDLANQINQ-RPQVVSEYEN 55 (82)
Q Consensus 24 ~lk~~r~~~g~s~~elA~~~gi-s~~~i~~~e~ 55 (82)
.+-.+....|.|..++|+..|| +.+++++|-.
T Consensus 15 ~iv~~~~~~g~sv~~vAr~~gv~~~~~l~~W~~ 47 (116)
T COG2963 15 EAVALYLRGGDTVSEVAREFGIVSATQLYKWRI 47 (116)
T ss_pred HHHHHHHhcCccHHHHHHHhCCCChHHHHHHHH
Confidence 4444556678899999999996 9999998854
No 420
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=89.05 E-value=1.1 Score=27.70 Aligned_cols=28 Identities=18% Similarity=0.001 Sum_probs=23.8
Q ss_pred HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 28 ARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 28 ~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
++--.|+|.+|+|+.+|+|+.+|.....
T Consensus 149 l~~~~g~s~~eIA~~lgis~~tv~~~l~ 176 (193)
T PRK11923 149 LREFDGLSYEDIASVMQCPVGTVRSRIF 176 (193)
T ss_pred hHHhcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3456799999999999999999988764
No 421
>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=88.99 E-value=0.45 Score=29.62 Aligned_cols=21 Identities=19% Similarity=0.234 Sum_probs=19.2
Q ss_pred CCHHHHHHHhCCCHHHHHHHH
Q 038591 34 MSQPDLANQINQRPQVVSEYE 54 (82)
Q Consensus 34 ~s~~elA~~~gis~~~i~~~e 54 (82)
+|++++|+.+|+|.+||++..
T Consensus 76 ~t~~~ia~~l~iS~~Tv~r~i 96 (165)
T PF05732_consen 76 ATQKEIAEKLGISKPTVSRAI 96 (165)
T ss_pred eeHHHHHHHhCCCHHHHHHHH
Confidence 589999999999999999874
No 422
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=88.97 E-value=1.2 Score=28.02 Aligned_cols=27 Identities=26% Similarity=0.171 Sum_probs=23.1
Q ss_pred HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 29 RLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 29 r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
+--.|+|.+|+|+.+|+|..+|.....
T Consensus 165 ~~~~g~s~~EIA~~lgis~~tV~~~l~ 191 (206)
T PRK12526 165 VYFQELSQEQLAQQLNVPLGTVKSRLR 191 (206)
T ss_pred HHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 345699999999999999999987753
No 423
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=88.96 E-value=1.2 Score=27.97 Aligned_cols=28 Identities=11% Similarity=0.007 Sum_probs=23.8
Q ss_pred HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 28 ARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 28 ~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
++.-.|+|.+|+|+.+|+|.+||.....
T Consensus 150 L~~~eg~s~~EIA~~lgis~~tVk~~l~ 177 (201)
T PRK12545 150 MREFLDFEIDDICTELTLTANHCSVLLY 177 (201)
T ss_pred HHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 3455799999999999999999987754
No 424
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=88.93 E-value=0.97 Score=29.04 Aligned_cols=26 Identities=12% Similarity=0.012 Sum_probs=23.0
Q ss_pred hCCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591 31 GKKMSQPDLANQINQRPQVVSEYENG 56 (82)
Q Consensus 31 ~~g~s~~elA~~~gis~~~i~~~e~g 56 (82)
..|+|.+|+|+.+++|..||..+...
T Consensus 168 ~~G~s~~eIA~~L~iS~~TVk~~~~~ 193 (216)
T PRK10100 168 RIGASNNEIARSLFISENTVKTHLYN 193 (216)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 45999999999999999999988753
No 425
>PRK14996 TetR family transcriptional regulator; Provisional
Probab=88.91 E-value=0.37 Score=29.78 Aligned_cols=28 Identities=11% Similarity=0.035 Sum_probs=23.7
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHcCCCC
Q 038591 32 KKMSQPDLANQINQRPQVVSEYENGKAV 59 (82)
Q Consensus 32 ~g~s~~elA~~~gis~~~i~~~e~g~~~ 59 (82)
.+.|..++|+.+|+|+.+++.+..++..
T Consensus 27 ~~tSi~~Ia~~aGvsk~~lY~~F~sK~~ 54 (192)
T PRK14996 27 AAMTVRRIASEAQVAAGQVHHHFSSAGE 54 (192)
T ss_pred hhccHHHHHHHhCCCcHHHHHHcCCHHH
Confidence 3578999999999999999999876543
No 426
>COG2826 Tra8 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]
Probab=88.90 E-value=0.57 Score=32.08 Aligned_cols=33 Identities=27% Similarity=0.321 Sum_probs=26.9
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
...|..++ ..|+|..++|+.||..++||++=..
T Consensus 13 R~~I~~l~-~~~~S~reIA~~LgRh~sTIsRElk 45 (318)
T COG2826 13 RYEIERLL-KAKMSIREIAKQLNRHHSTISRELK 45 (318)
T ss_pred HHHHHHHH-HcCCCHHHHHHHhCCCcchhhHHHh
Confidence 34455555 6799999999999999999998654
No 427
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=88.89 E-value=2.7 Score=27.41 Aligned_cols=43 Identities=19% Similarity=0.223 Sum_probs=30.5
Q ss_pred hCCCCHHHHHHHhCCCHHHHHHHHcC----CCCCCHHHHHHHHHHhC
Q 038591 31 GKKMSQPDLANQINQRPQVVSEYENG----KAVPNQTVLAKMEKAIG 73 (82)
Q Consensus 31 ~~g~s~~elA~~~gis~~~i~~~e~g----~~~p~~~~~~~la~~lg 73 (82)
..|+|..|+|..+|||..||....+. -...+...+...|-.+|
T Consensus 192 a~G~t~~eIa~~l~is~~TV~~h~~~~~~KL~~~nr~q~v~~a~~~g 238 (240)
T PRK10188 192 AEGKTSAEIAMILSISENTVNFHQKNMQKKFNAPNKTQIACYAAATG 238 (240)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCHHHHHHHHHHcC
Confidence 67999999999999999999887654 12334444444444443
No 428
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=88.88 E-value=0.61 Score=28.32 Aligned_cols=25 Identities=16% Similarity=0.089 Sum_probs=22.0
Q ss_pred hCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 31 GKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 31 ~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
-.|+|..|+|+.+|+|..+|.....
T Consensus 134 ~~g~s~~eIA~~lg~s~~tv~~~l~ 158 (175)
T PRK12518 134 LEDLPQKEIAEILNIPVGTVKSRLF 158 (175)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3599999999999999999988764
No 429
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=88.86 E-value=1.1 Score=29.53 Aligned_cols=32 Identities=9% Similarity=-0.086 Sum_probs=24.7
Q ss_pred HHHHHHHh-CCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 24 QIQRARLG-KKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 24 ~lk~~r~~-~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
.|..+-.. .++|..|+|+.+|++++|++++.+
T Consensus 16 iL~~l~~~~~~ls~~eia~~lgl~kstv~RlL~ 48 (263)
T PRK09834 16 VLRALNRLDGGATVGLLAELTGLHRTTVRRLLE 48 (263)
T ss_pred HHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 34444443 359999999999999999999853
No 430
>PHA02535 P terminase ATPase subunit; Provisional
Probab=88.81 E-value=0.49 Score=34.97 Aligned_cols=24 Identities=4% Similarity=0.300 Sum_probs=22.6
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHcC
Q 038591 33 KMSQPDLANQINQRPQVVSEYENG 56 (82)
Q Consensus 33 g~s~~elA~~~gis~~~i~~~e~g 56 (82)
|+|..++|+.+|++++||++|-.-
T Consensus 18 G~sv~eIA~~LGv~~~Tl~~W~kr 41 (581)
T PHA02535 18 GWTVAEIAEELGLKSRTIYSWKER 41 (581)
T ss_pred CCCHHHHHHHhCCChhHHHHHhcc
Confidence 999999999999999999999764
No 431
>PRK00767 transcriptional regulator BetI; Validated
Probab=88.79 E-value=0.53 Score=28.89 Aligned_cols=29 Identities=17% Similarity=0.226 Sum_probs=24.0
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHcCCCCC
Q 038591 32 KKMSQPDLANQINQRPQVVSEYENGKAVP 60 (82)
Q Consensus 32 ~g~s~~elA~~~gis~~~i~~~e~g~~~p 60 (82)
.+.|..++|+.+|+|+.+++.+..++...
T Consensus 28 ~~~s~~~Ia~~aGvs~gslY~~F~~Ke~L 56 (197)
T PRK00767 28 LDATIAQIARRAGVSTGIISHYFGGKDGL 56 (197)
T ss_pred ccCCHHHHHHHhCCCHHHHHHHhCCHHHH
Confidence 35789999999999999999998665443
No 432
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=88.78 E-value=0.82 Score=27.94 Aligned_cols=27 Identities=7% Similarity=0.115 Sum_probs=23.3
Q ss_pred HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 29 RLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 29 r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
+--.|+|.+|+|+.+|+|+.+|.....
T Consensus 148 ~~~~g~s~~eIA~~lgis~~~v~~~l~ 174 (187)
T TIGR02948 148 KYMEDLSLKEISEILDLPVGTVKTRIH 174 (187)
T ss_pred HHhcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 345699999999999999999998764
No 433
>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=88.75 E-value=0.99 Score=22.68 Aligned_cols=21 Identities=24% Similarity=0.460 Sum_probs=16.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHH
Q 038591 32 KKMSQPDLANQINQRPQVVSE 52 (82)
Q Consensus 32 ~g~s~~elA~~~gis~~~i~~ 52 (82)
..+|-.+||+.+|+++.+|.+
T Consensus 27 ~~vSS~~La~~~gi~~~qVRK 47 (50)
T PF06971_consen 27 ERVSSQELAEALGITPAQVRK 47 (50)
T ss_dssp SEE-HHHHHHHHTS-HHHHHH
T ss_pred eeECHHHHHHHHCCCHHHhcc
Confidence 457889999999999999875
No 434
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=88.74 E-value=1.4 Score=27.18 Aligned_cols=27 Identities=19% Similarity=0.266 Sum_probs=23.2
Q ss_pred HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 29 RLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 29 r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
+--.|+|..|+|+.+|+|..||.....
T Consensus 151 ~~~~g~s~~EIA~~lgis~~tV~~~l~ 177 (189)
T PRK09648 151 RVVVGLSAEETAEAVGSTPGAVRVAQH 177 (189)
T ss_pred HHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 445699999999999999999988764
No 435
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=88.71 E-value=0.81 Score=30.41 Aligned_cols=32 Identities=19% Similarity=0.138 Sum_probs=25.5
Q ss_pred HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591 23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYE 54 (82)
Q Consensus 23 ~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e 54 (82)
..+..++....++..|||+.+|||..||.+-.
T Consensus 21 ~Il~~L~~~~~vtv~eLa~~l~VS~~TIRRDL 52 (269)
T PRK09802 21 QIIQRLRQQGSVQVNDLSALYGVSTVTIRNDL 52 (269)
T ss_pred HHHHHHHHcCCEeHHHHHHHHCCCHHHHHHHH
Confidence 34455666667999999999999999997753
No 436
>PHA00738 putative HTH transcription regulator
Probab=88.71 E-value=1.2 Score=26.00 Aligned_cols=32 Identities=6% Similarity=-0.070 Sum_probs=24.7
Q ss_pred HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591 23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYE 54 (82)
Q Consensus 23 ~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e 54 (82)
..|..+...-.++..+|++.+++|+++||+-.
T Consensus 16 ~IL~lL~~~e~~~V~eLae~l~lSQptVS~HL 47 (108)
T PHA00738 16 KILELIAENYILSASLISHTLLLSYTTVLRHL 47 (108)
T ss_pred HHHHHHHHcCCccHHHHHHhhCCCHHHHHHHH
Confidence 33444554446999999999999999999864
No 437
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=88.70 E-value=0.81 Score=29.38 Aligned_cols=27 Identities=19% Similarity=0.031 Sum_probs=23.2
Q ss_pred HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 29 RLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 29 r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
+--.|+|.+|+|+.+|+|.++|.....
T Consensus 146 ~y~eg~s~~EIAe~LgiS~~tVk~~L~ 172 (216)
T PRK12533 146 RELEDMSYREIAAIADVPVGTVMSRLA 172 (216)
T ss_pred HHhcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 344699999999999999999988764
No 438
>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=88.63 E-value=1.3 Score=26.96 Aligned_cols=51 Identities=6% Similarity=0.080 Sum_probs=35.0
Q ss_pred HHHHHhCC--CCHHHHHHHhCCCHHHHHHHHcCCC-C-CCHHHHHHHHHHhCCCC
Q 038591 26 QRARLGKK--MSQPDLANQINQRPQVVSEYENGKA-V-PNQTVLAKMEKAIGVKL 76 (82)
Q Consensus 26 k~~r~~~g--~s~~elA~~~gis~~~i~~~e~g~~-~-p~~~~~~~la~~lgv~~ 76 (82)
..+|+..+ .|..++++.+||+...|.+|..-.+ . .....+..-|+--|.++
T Consensus 37 ~yLr~~p~~~ati~eV~e~tgVs~~~I~~~IreGRL~~~~~~nl~~~CE~CG~~I 91 (137)
T TIGR03826 37 KFLRKHENRQATVSEIVEETGVSEKLILKFIREGRLQLKHFPNLGYPCERCGTSI 91 (137)
T ss_pred HHHHHCCCCCCCHHHHHHHHCcCHHHHHHHHHcCCeeccCCCCCcCcccccCCcC
Confidence 44677777 8999999999999999999986422 1 22234444555555444
No 439
>PRK11557 putative DNA-binding transcriptional regulator; Provisional
Probab=88.58 E-value=1.4 Score=29.01 Aligned_cols=36 Identities=14% Similarity=0.186 Sum_probs=27.5
Q ss_pred HHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHH
Q 038591 29 RLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTV 64 (82)
Q Consensus 29 r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~ 64 (82)
-+-..+|..+||+.+|+|++||.++-+--..-....
T Consensus 26 ~~v~~~si~elA~~~~vS~aTv~Rf~kklG~~Gf~e 61 (278)
T PRK11557 26 DTARHLSSQQLANEAGVSQSSVVKFAQKLGYKGFPA 61 (278)
T ss_pred HHHHhcCHHHHHHHhCCCHHHHHHHHHHcCCCCHHH
Confidence 344579999999999999999999987533333333
No 440
>PRK14845 translation initiation factor IF-2; Provisional
Probab=88.52 E-value=1.3 Score=34.94 Aligned_cols=50 Identities=20% Similarity=0.326 Sum_probs=42.4
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCC
Q 038591 22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKL 76 (82)
Q Consensus 22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~ 76 (82)
...|+.+|...++|+.|++. +.++++.||+ ...|+.+.+..+..+|.-..
T Consensus 324 ~~el~~lr~~~~lt~~e~~~----~~~~Y~~~e~-~~~~s~~~l~~~l~~~~~~~ 373 (1049)
T PRK14845 324 NEELKRLRLLFGFTRNELSS----NIPFYSKYES-EEAPSYEILMEILNSIERGS 373 (1049)
T ss_pred HHHHHHHHHhcCcchhhccc----cchhhhhhhc-ccCCCHHHHHHHHHHHHhcC
Confidence 55789999999999988775 7899999999 88999999988888776433
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=88.48 E-value=1.4 Score=23.19 Aligned_cols=33 Identities=9% Similarity=0.074 Sum_probs=23.2
Q ss_pred HHHHHHHHhCCC--CHHHHHHHhCCC-HHHHHHHHc
Q 038591 23 RQIQRARLGKKM--SQPDLANQINQR-PQVVSEYEN 55 (82)
Q Consensus 23 ~~lk~~r~~~g~--s~~elA~~~gis-~~~i~~~e~ 55 (82)
..|.....+.|+ |..|+|+.+|++ +++|.....
T Consensus 13 ~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~ 48 (65)
T PF01726_consen 13 EFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLK 48 (65)
T ss_dssp HHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHH
T ss_pred HHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHH
Confidence 345555555555 779999999996 888887653
No 442
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=88.43 E-value=1.4 Score=28.97 Aligned_cols=28 Identities=4% Similarity=0.112 Sum_probs=23.9
Q ss_pred HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 28 ARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 28 ~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
++-..|+|..++|..+|+|.++|.+...
T Consensus 223 l~~~~~~s~~eIA~~lgis~~tV~~~~~ 250 (268)
T PRK06288 223 LYYYEDLTLKEIGKVLGVTESRISQLHT 250 (268)
T ss_pred HHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 3445699999999999999999998764
No 443
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=88.40 E-value=1.5 Score=27.09 Aligned_cols=28 Identities=7% Similarity=-0.065 Sum_probs=23.9
Q ss_pred HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 28 ARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 28 ~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
++.-.|+|.+++|+.+|+|..+|.....
T Consensus 142 l~~~~~~s~~eIA~~lgis~~tV~~~l~ 169 (189)
T PRK12515 142 LVYYHEKSVEEVGEIVGIPESTVKTRMF 169 (189)
T ss_pred HHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 3456799999999999999999987764
No 444
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=88.39 E-value=0.71 Score=28.04 Aligned_cols=26 Identities=12% Similarity=0.018 Sum_probs=22.4
Q ss_pred HhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 30 LGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 30 ~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
.-.|+|.+++|+.+|+|.++|.....
T Consensus 139 ~~~g~s~~eIA~~l~is~~~V~~~l~ 164 (176)
T PRK09638 139 HYYGYTYEEIAKMLNIPEGTVKSRVH 164 (176)
T ss_pred hhcCCCHHHHHHHHCCChhHHHHHHH
Confidence 34699999999999999999987763
No 445
>cd08804 Death_ank2 Death domain of Ankyrin-2. Death Domain (DD) of Ankyrin-2 (ANK-2) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-2, also called ankyrin-B (for broadly expressed), is required for proper function of the Na/Ca ion exchanger-1 in cardiomyocytes, and is thought to function in linking integral membrane proteins to the underlying cytoskeleton. Human ANK-2 is associated with "Ankyrin-B syndrome", an atypical arrythmia disorder with risk of sudden cardiac death. It also plays key roles in the brain and striated muscle. Loss of ANK-2 is associated with significant nervous system defects and sarcomere disorganization. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other
Probab=88.35 E-value=2.5 Score=23.29 Aligned_cols=34 Identities=9% Similarity=0.075 Sum_probs=29.5
Q ss_pred HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591 23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYENG 56 (82)
Q Consensus 23 ~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~g 56 (82)
.+|..+....|..=++||+.+|+|..-|.+++..
T Consensus 5 ~~l~~ia~~LG~dWk~LAr~Lg~se~dI~~i~~~ 38 (84)
T cd08804 5 ERLAVIADHLGFSWTELARELDFTEEQIHQIRIE 38 (84)
T ss_pred hHHHHHHHHHhhhHHHHHHHcCCCHHHHHHHHHH
Confidence 3567778888888899999999999999999875
No 446
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=88.34 E-value=0.94 Score=28.20 Aligned_cols=28 Identities=11% Similarity=0.033 Sum_probs=23.9
Q ss_pred HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 28 ARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 28 ~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
++.-.|++.+|+|..+|+|..+|.....
T Consensus 139 l~~~~g~s~~EIA~~lgis~~tV~~~l~ 166 (188)
T PRK12517 139 LQVIGGFSGEEIAEILDLNKNTVMTRLF 166 (188)
T ss_pred HHHHhCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3445699999999999999999988764
No 447
>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=88.33 E-value=0.96 Score=25.07 Aligned_cols=48 Identities=10% Similarity=0.078 Sum_probs=28.7
Q ss_pred HHHHHhCCCCHHHHHHHhCCCHHHHHHHHcCC-CCCCHHHHHHHHHHhC
Q 038591 26 QRARLGKKMSQPDLANQINQRPQVVSEYENGK-AVPNQTVLAKMEKAIG 73 (82)
Q Consensus 26 k~~r~~~g~s~~elA~~~gis~~~i~~~e~g~-~~p~~~~~~~la~~lg 73 (82)
-....+.+.|..+.|...|||.+||.+-..-. ..++......+-.+|.
T Consensus 12 ~~yIi~~~aTVR~~Ak~FGvSKSTVHkDvteRL~~in~~La~eV~~vL~ 60 (82)
T PF12116_consen 12 ANYIIETKATVRQAAKVFGVSKSTVHKDVTERLPKINPELAREVRKVLD 60 (82)
T ss_dssp HHHHHHH---HHHHHHHHTS-HHHHHHHHTTHHHHH-HHHHHHHHHHHH
T ss_pred HHHHHHcccHHHHHHHHHCCcHHHHHHHHHHHHHhcCHHHHHHHHHHHH
Confidence 34455668999999999999999999877642 2334444444444443
No 448
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=88.32 E-value=0.88 Score=28.66 Aligned_cols=33 Identities=9% Similarity=0.002 Sum_probs=26.5
Q ss_pred HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 23 ~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
..+..+....-++..+||+.+|+|..||.+=.+
T Consensus 11 ~Il~~l~~~~~~~~~~La~~~~vS~~TiRRDl~ 43 (185)
T PRK04424 11 ALQELIEENPFITDEELAEKFGVSIQTIRLDRM 43 (185)
T ss_pred HHHHHHHHCCCEEHHHHHHHHCcCHHHHHHHHH
Confidence 344556666678999999999999999988654
No 449
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=88.30 E-value=1.4 Score=27.34 Aligned_cols=28 Identities=7% Similarity=-0.001 Sum_probs=24.1
Q ss_pred HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 28 ARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 28 ~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
++--.|+|.+|+|+.+|+|..+|..+..
T Consensus 153 l~~~~~~s~~EIA~~Lgis~~tVk~~l~ 180 (194)
T PRK09646 153 LAYYGGLTYREVAERLAVPLGTVKTRMR 180 (194)
T ss_pred HHHHcCCCHHHHHHHhCCChHhHHHHHH
Confidence 3445799999999999999999988764
No 450
>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional
Probab=88.30 E-value=1.1 Score=33.09 Aligned_cols=34 Identities=9% Similarity=-0.093 Sum_probs=29.1
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
...|..+....+.++.+.|+.+|||++|+++-.+
T Consensus 593 ~~~i~~al~~~~gn~~~aA~~LGisR~TLyrklk 626 (638)
T PRK11388 593 KEAIINAAQVCGGRIQEMAALLGIGRTTLWRKMK 626 (638)
T ss_pred HHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHH
Confidence 4557777788899999999999999999998765
No 451
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=88.29 E-value=0.99 Score=27.92 Aligned_cols=27 Identities=11% Similarity=0.046 Sum_probs=23.3
Q ss_pred HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 29 RLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 29 r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
+.-.|++..|+|..+|+|..+|.....
T Consensus 118 ~~~~g~~~~EIA~~lgis~~tV~~~l~ 144 (181)
T PRK09637 118 TELEGLSQKEIAEKLGLSLSGAKSRVQ 144 (181)
T ss_pred HHhcCCCHHHHHHHhCCCHHHHHHHHH
Confidence 445799999999999999999987764
No 452
>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=88.29 E-value=1.2 Score=24.62 Aligned_cols=33 Identities=15% Similarity=0.119 Sum_probs=26.5
Q ss_pred HHHHHHHHhCCCCHHHHHHHhC-CCHHHHHHHHc
Q 038591 23 RQIQRARLGKKMSQPDLANQIN-QRPQVVSEYEN 55 (82)
Q Consensus 23 ~~lk~~r~~~g~s~~elA~~~g-is~~~i~~~e~ 55 (82)
-.+-.++...|+|..++|+.+| .+.+||+...+
T Consensus 34 ia~yl~~~~~~~s~~~Ig~~fg~r~hStV~~a~~ 67 (90)
T cd06571 34 IAMYLARELTGLSLPEIGRAFGGRDHSTVLHAVR 67 (90)
T ss_pred HHHHHHHHHhCCCHHHHHHHhCCCCHhHHHHHHH
Confidence 3345567788999999999999 99999887543
No 453
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=88.24 E-value=1 Score=28.17 Aligned_cols=28 Identities=14% Similarity=-0.028 Sum_probs=24.1
Q ss_pred HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 28 ARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 28 ~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
++.-.|+|..|+|+.+|+|..+|.....
T Consensus 124 L~~~~g~s~~EIA~~LgiS~~tVk~~l~ 151 (188)
T PRK12546 124 LVGASGFSYEEAAEMCGVAVGTVKSRAN 151 (188)
T ss_pred hHHhcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3455799999999999999999988765
No 454
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=88.20 E-value=0.97 Score=27.49 Aligned_cols=27 Identities=15% Similarity=0.032 Sum_probs=23.0
Q ss_pred HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 29 RLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 29 r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
+--.|+|.+|+|+.+|+|..+|.....
T Consensus 131 ~~~~~~s~~EIA~~lgis~~tV~~~l~ 157 (173)
T PRK12522 131 YYYEQYSYKEMSEILNIPIGTVKYRLN 157 (173)
T ss_pred HHHcCCCHHHHHHHhCCCHHHHHHHHH
Confidence 344699999999999999999988754
No 455
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=88.16 E-value=1.6 Score=27.01 Aligned_cols=27 Identities=4% Similarity=-0.021 Sum_probs=23.1
Q ss_pred HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 29 RLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 29 r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
+.-.|+|.+|+|+.+|+|.+||.....
T Consensus 143 ~~~~g~s~~EIA~~lgis~~tV~~~l~ 169 (191)
T PRK12520 143 REWLELETEEICQELQITATNAWVLLY 169 (191)
T ss_pred HHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 344699999999999999999988754
No 456
>PRK15482 transcriptional regulator MurR; Provisional
Probab=88.11 E-value=1.5 Score=29.11 Aligned_cols=38 Identities=16% Similarity=0.146 Sum_probs=29.3
Q ss_pred HHhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHH
Q 038591 29 RLGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLA 66 (82)
Q Consensus 29 r~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~ 66 (82)
-....+|..+||+.+|+|++||.++-+--..-.+..+.
T Consensus 30 ~~v~~~si~elA~~~~vS~aTv~Rf~kkLGf~Gf~efk 67 (285)
T PRK15482 30 SELKSVSSRKMAKQLGISQSSIVKFAQKLGAQGFTELR 67 (285)
T ss_pred HHHHhcCHHHHHHHhCCCHHHHHHHHHHhCCCCHHHHH
Confidence 34457999999999999999999998754444544443
No 457
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=88.07 E-value=1.6 Score=27.07 Aligned_cols=27 Identities=7% Similarity=0.059 Sum_probs=23.2
Q ss_pred HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 29 RLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 29 r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
+--.|+|.+|+|+.+|+|..+|.....
T Consensus 143 ~~~~g~s~~EIAe~lgis~~~V~~~l~ 169 (189)
T PRK06811 143 RYLLGEKIEEIAKKLGLTRSAIDNRLS 169 (189)
T ss_pred HHHccCCHHHHHHHHCCCHHHHHHHHH
Confidence 345699999999999999999988764
No 458
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=87.94 E-value=0.69 Score=31.67 Aligned_cols=24 Identities=8% Similarity=0.086 Sum_probs=22.1
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHcC
Q 038591 33 KMSQPDLANQINQRPQVVSEYENG 56 (82)
Q Consensus 33 g~s~~elA~~~gis~~~i~~~e~g 56 (82)
.+|..++|+.+|||+..|+++|..
T Consensus 282 ~~Tl~eIa~~lgvS~eRVrQIe~~ 305 (324)
T PRK07921 282 PRTLDQIGKLFGLSRERVRQIERE 305 (324)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHH
Confidence 379999999999999999999974
No 459
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class. This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam model pfam00046. It is found in both C4 and C3 plants.
Probab=87.93 E-value=0.72 Score=23.92 Aligned_cols=35 Identities=6% Similarity=0.095 Sum_probs=24.7
Q ss_pred HHHHHHHHhCCC--------CHHHHHHHhCCCHHHHHHHHcCC
Q 038591 23 RQIQRARLGKKM--------SQPDLANQINQRPQVVSEYENGK 57 (82)
Q Consensus 23 ~~lk~~r~~~g~--------s~~elA~~~gis~~~i~~~e~g~ 57 (82)
..|...-+..|+ ...+||..+|++...|.-|.++.
T Consensus 14 ~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~ 56 (58)
T TIGR01565 14 EKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNN 56 (58)
T ss_pred HHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccC
Confidence 344455556677 66888888888888887777653
No 460
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=87.93 E-value=0.67 Score=32.16 Aligned_cols=24 Identities=4% Similarity=0.095 Sum_probs=22.1
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHcC
Q 038591 33 KMSQPDLANQINQRPQVVSEYENG 56 (82)
Q Consensus 33 g~s~~elA~~~gis~~~i~~~e~g 56 (82)
++|..++|+.+|||+..|++++..
T Consensus 325 ~~tl~EIa~~lgvs~erVrQi~~~ 348 (367)
T PRK09210 325 TRTLEEVGKVFGVTRERIRQIEAK 348 (367)
T ss_pred CccHHHHHHHHCCCHHHHHHHHHH
Confidence 489999999999999999999864
No 461
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=87.91 E-value=1.1 Score=27.70 Aligned_cols=27 Identities=15% Similarity=-0.054 Sum_probs=23.6
Q ss_pred HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 29 RLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 29 r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
+-..|+|..|+|+.+|+|..+|.....
T Consensus 123 ~~~~g~s~~EIA~~Lgis~~tV~~~l~ 149 (182)
T PRK12540 123 VGASGFSYEDAAAICGCAVGTIKSRVN 149 (182)
T ss_pred HHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 445799999999999999999988765
No 462
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=87.82 E-value=0.86 Score=22.71 Aligned_cols=21 Identities=14% Similarity=0.306 Sum_probs=18.4
Q ss_pred HHHHHHHhCCCHHHHHHHHcC
Q 038591 36 QPDLANQINQRPQVVSEYENG 56 (82)
Q Consensus 36 ~~elA~~~gis~~~i~~~e~g 56 (82)
..+||..+|++...|..|...
T Consensus 30 ~~~la~~l~l~~~~V~~WF~n 50 (57)
T PF00046_consen 30 REELAKELGLTERQVKNWFQN 50 (57)
T ss_dssp HHHHHHHHTSSHHHHHHHHHH
T ss_pred cccccccccccccccccCHHH
Confidence 378999999999999999764
No 463
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=87.81 E-value=1.2 Score=26.73 Aligned_cols=28 Identities=14% Similarity=-0.094 Sum_probs=23.7
Q ss_pred HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 28 ARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 28 ~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
++.-.|+|..++|+.+|+|..+|.....
T Consensus 123 l~~~~~~s~~eIA~~lgis~~tv~~~l~ 150 (161)
T PRK12541 123 LRDYYGFSYKEIAEMTGLSLAKVKIELH 150 (161)
T ss_pred hHHhcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 4455799999999999999999987654
No 464
>PRK11337 DNA-binding transcriptional repressor RpiR; Provisional
Probab=87.75 E-value=1.2 Score=29.52 Aligned_cols=36 Identities=8% Similarity=0.108 Sum_probs=28.4
Q ss_pred hCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHH
Q 038591 31 GKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLA 66 (82)
Q Consensus 31 ~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~ 66 (82)
-..+|..+||+.+|+|+.||.++-+.-..-+...+.
T Consensus 44 v~~~si~~lA~~~~vS~aTi~Rf~kkLGf~gf~efk 79 (292)
T PRK11337 44 SEATALKDIAEALAVSEAMIVKVAKKLGFSGFRNLR 79 (292)
T ss_pred HHhcCHHHHHHHhCCChHHHHHHHHHcCCCCHHHHH
Confidence 457899999999999999999998765555554443
No 465
>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=87.75 E-value=1.3 Score=30.48 Aligned_cols=39 Identities=3% Similarity=0.034 Sum_probs=28.8
Q ss_pred HhCCCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHH
Q 038591 30 LGKKMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKM 68 (82)
Q Consensus 30 ~~~g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~l 68 (82)
...|+++.++|..+|++.++|+++..=-..++.+.+..|
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 468999999999999999999999873222333443333
No 466
>PRK11569 transcriptional repressor IclR; Provisional
Probab=87.74 E-value=1.3 Score=29.38 Aligned_cols=33 Identities=9% Similarity=0.075 Sum_probs=25.4
Q ss_pred HHHHHHHH-hCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 23 RQIQRARL-GKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 23 ~~lk~~r~-~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
..|+.+-+ ..++|..|||+.+|++++|++++.+
T Consensus 32 ~IL~~l~~~~~~~~lseia~~lglpksTv~RlL~ 65 (274)
T PRK11569 32 KLLEWIAESNGSVALTELAQQAGLPNSTTHRLLT 65 (274)
T ss_pred HHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHH
Confidence 33444433 4579999999999999999999854
No 467
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=87.70 E-value=0.8 Score=28.58 Aligned_cols=26 Identities=12% Similarity=0.156 Sum_probs=22.4
Q ss_pred HhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 30 LGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 30 ~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
--.|+|.+|+|+.+|+|+++|.....
T Consensus 167 ~~e~~s~~EIA~~lgis~~tV~~~l~ 192 (208)
T PRK08295 167 YLDGKSYQEIAEELNRHVKSIDNALQ 192 (208)
T ss_pred HHccCCHHHHHHHHCCCHHHHHHHHH
Confidence 34699999999999999999987654
No 468
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=87.67 E-value=0.73 Score=31.48 Aligned_cols=25 Identities=16% Similarity=0.155 Sum_probs=23.0
Q ss_pred hCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 31 GKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 31 ~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
..|+|.+++|..+|+|..+|.+++.
T Consensus 280 ~e~~s~~EIA~~Lgis~~tV~~~~~ 304 (325)
T PRK05657 280 YEAATLEDVAREIGLTRERVRQIQV 304 (325)
T ss_pred CCCcCHHHHHHHHCcCHHHHHHHHH
Confidence 4589999999999999999999986
No 469
>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=87.66 E-value=1 Score=27.54 Aligned_cols=27 Identities=19% Similarity=0.041 Sum_probs=23.0
Q ss_pred HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 29 RLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 29 r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
+--.|+|..|+|+.+|+|..+|.....
T Consensus 150 ~~~~~~s~~EIA~~lgis~~tv~~~l~ 176 (190)
T TIGR02939 150 RELEGLSYEDIARIMDCPVGTVRSRIF 176 (190)
T ss_pred hhhcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 345699999999999999999988764
No 470
>COG1737 RpiR Transcriptional regulators [Transcription]
Probab=87.60 E-value=1.2 Score=29.71 Aligned_cols=28 Identities=18% Similarity=0.200 Sum_probs=23.9
Q ss_pred HhCCCCHHHHHHHhCCCHHHHHHHHcCC
Q 038591 30 LGKKMSQPDLANQINQRPQVVSEYENGK 57 (82)
Q Consensus 30 ~~~g~s~~elA~~~gis~~~i~~~e~g~ 57 (82)
....+|..+||+.+|||++||.++-+--
T Consensus 33 ~~~~~si~elA~~a~VS~aTv~Rf~~kL 60 (281)
T COG1737 33 EVALLSIAELAERAGVSPATVVRFARKL 60 (281)
T ss_pred HHHHHHHHHHHHHhCCCHHHHHHHHHHc
Confidence 3456899999999999999999998753
No 471
>PRK10086 DNA-binding transcriptional regulator DsdC; Provisional
Probab=87.59 E-value=1.3 Score=29.34 Aligned_cols=37 Identities=27% Similarity=0.423 Sum_probs=29.9
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcccc
Q 038591 33 KMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVKI 80 (82)
Q Consensus 33 g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e~~ 80 (82)
--|....|+.+|+|+++||+ .+..|.+.||+++-+|+
T Consensus 28 ~gs~s~AA~~L~iSQpavS~-----------~I~~LE~~lG~~LF~R~ 64 (311)
T PRK10086 28 HQSFALAADELSLTPSAVSH-----------RINQLEEELGIKLFVRS 64 (311)
T ss_pred cCCHHHHHHHHCCCHHHHHH-----------HHHHHHHHhCCeeEEEc
Confidence 34667799999999999998 46778888888887765
No 472
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=87.57 E-value=1.4 Score=29.22 Aligned_cols=33 Identities=12% Similarity=0.062 Sum_probs=25.6
Q ss_pred HHHHHHHH-hCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 23 RQIQRARL-GKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 23 ~~lk~~r~-~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
..|..+-. ..++|..|+|+.+|++++|++++.+
T Consensus 29 ~IL~~~~~~~~~~tl~eIa~~lglpkStv~RlL~ 62 (271)
T PRK10163 29 AILQYLEKSGGSSSVSDISLNLDLPLSTTFRLLK 62 (271)
T ss_pred HHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHH
Confidence 44444433 3579999999999999999999854
No 473
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=87.47 E-value=1.3 Score=28.81 Aligned_cols=37 Identities=19% Similarity=0.193 Sum_probs=29.4
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcccc
Q 038591 33 KMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVKI 80 (82)
Q Consensus 33 g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e~~ 80 (82)
--|....|+.+|+|+++||+. +..|...||+++-+|.
T Consensus 15 ~gs~s~AA~~L~isqpavS~~-----------I~~LE~~lG~~LF~R~ 51 (275)
T PRK03601 15 TRHFGRAAESLYLTQSAVSFR-----------IRQLENQLGVNLFTRH 51 (275)
T ss_pred cCCHHHHHHHhCCChHHHHHH-----------HHHHHHHhCCceEEEC
Confidence 346677999999999999984 5677888888876664
No 474
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=87.42 E-value=1.8 Score=26.52 Aligned_cols=28 Identities=18% Similarity=0.108 Sum_probs=23.6
Q ss_pred HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 28 ARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 28 ~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
++.-.|+|.+|+|+.+|+|..+|.....
T Consensus 128 l~~~e~~s~~EIA~~lgis~~tV~~~l~ 155 (179)
T PRK12543 128 LRYLHDYSQEEIAQLLQIPIGTVKSRIH 155 (179)
T ss_pred HHHHccCCHHHHHHHHCCCHHHHHHHHH
Confidence 3455799999999999999999887754
No 475
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=87.41 E-value=1.4 Score=27.12 Aligned_cols=24 Identities=21% Similarity=0.293 Sum_probs=20.5
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 32 KKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 32 ~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
.-....++|..++|++++++.+.+
T Consensus 23 ~~~~~~diA~~L~Vsp~sVt~ml~ 46 (154)
T COG1321 23 GFARTKDIAERLKVSPPSVTEMLK 46 (154)
T ss_pred CcccHHHHHHHhCCCcHHHHHHHH
Confidence 347889999999999999988754
No 476
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=87.41 E-value=1.1 Score=27.43 Aligned_cols=27 Identities=11% Similarity=0.044 Sum_probs=23.1
Q ss_pred HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 29 RLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 29 r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
+--.|+|..|+|+.+|+|..+|.....
T Consensus 139 ~~~~g~s~~EIA~~l~is~~tv~~~l~ 165 (179)
T PRK09415 139 FYYEELSIKEIAEVTGVNENTVKTRLK 165 (179)
T ss_pred HHhcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 344699999999999999999988764
No 477
>PRK10870 transcriptional repressor MprA; Provisional
Probab=87.41 E-value=0.86 Score=28.40 Aligned_cols=32 Identities=3% Similarity=0.076 Sum_probs=24.3
Q ss_pred HHHHHHHH--hCCCCHHHHHHHhCCCHHHHHHHH
Q 038591 23 RQIQRARL--GKKMSQPDLANQINQRPQVVSEYE 54 (82)
Q Consensus 23 ~~lk~~r~--~~g~s~~elA~~~gis~~~i~~~e 54 (82)
..|..+.. ..++++.+||+.++++++++++..
T Consensus 59 ~iL~~L~~~~~~~it~~eLa~~l~l~~~tvsr~v 92 (176)
T PRK10870 59 MALITLESQENHSIQPSELSCALGSSRTNATRIA 92 (176)
T ss_pred HHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHH
Confidence 44455543 246899999999999999998764
No 478
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=87.37 E-value=0.78 Score=31.22 Aligned_cols=25 Identities=12% Similarity=0.278 Sum_probs=22.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591 32 KKMSQPDLANQINQRPQVVSEYENG 56 (82)
Q Consensus 32 ~g~s~~elA~~~gis~~~i~~~e~g 56 (82)
.++|.+|+|+.+|+|+.+|.+++..
T Consensus 275 ~~~Tl~EIa~~lgiS~erVRqi~~r 299 (317)
T PRK07405 275 QPLTLAKIGERLNISRERVRQIERE 299 (317)
T ss_pred CCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 5689999999999999999999864
No 479
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=87.37 E-value=1.7 Score=28.26 Aligned_cols=28 Identities=7% Similarity=0.188 Sum_probs=23.9
Q ss_pred HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 28 ARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 28 ~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
++-..|+|.+|+|..+|+|..+|.....
T Consensus 212 l~~~~~~s~~EIA~~lgis~~tV~~~~~ 239 (251)
T PRK07670 212 LFYKEELTLTEIGQVLNLSTSRISQIHS 239 (251)
T ss_pred HHHhcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 3445699999999999999999988764
No 480
>PF14174 YycC: YycC-like protein
Probab=87.35 E-value=0.57 Score=23.62 Aligned_cols=20 Identities=25% Similarity=0.327 Sum_probs=17.3
Q ss_pred CCCHHHHHHHHHHhCCCCcc
Q 038591 59 VPNQTVLAKMEKAIGVKLRV 78 (82)
Q Consensus 59 ~p~~~~~~~la~~lgv~~~e 78 (82)
.++.++..+|++.|||+++.
T Consensus 5 qIS~eTA~kLs~~L~vPlE~ 24 (53)
T PF14174_consen 5 QISPETAVKLSKKLGVPLEQ 24 (53)
T ss_pred ccCHHHHHHHHHHHCCcHHH
Confidence 47899999999999999863
No 481
>COG2207 AraC AraC-type DNA-binding domain-containing proteins [Transcription]
Probab=87.33 E-value=3.3 Score=23.18 Aligned_cols=30 Identities=13% Similarity=0.202 Sum_probs=24.2
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHcCCCCCC
Q 038591 32 KKMSQPDLANQINQRPQVVSEYENGKAVPN 61 (82)
Q Consensus 32 ~g~s~~elA~~~gis~~~i~~~e~g~~~p~ 61 (82)
.+++..++|..+|+|+.++.+........+
T Consensus 35 ~~~~l~~la~~~g~S~~~l~r~f~~~~g~s 64 (127)
T COG2207 35 EPLTLEDLARRLGMSRRTLSRLFKKETGTS 64 (127)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHCCC
Confidence 458999999999999999999887433333
No 482
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=87.26 E-value=1.1 Score=26.99 Aligned_cols=27 Identities=4% Similarity=-0.080 Sum_probs=23.4
Q ss_pred HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 29 RLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 29 r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
+--.|+|..|+|..+|+|..+|..+..
T Consensus 120 ~~~~g~s~~eIA~~lgis~~tv~~~l~ 146 (165)
T PRK09644 120 CDVHELTYEEAASVLDLKLNTYKSHLF 146 (165)
T ss_pred HHHhcCCHHHHHHHHCCCHHHHHHHHH
Confidence 345699999999999999999988764
No 483
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=87.21 E-value=1.7 Score=27.02 Aligned_cols=26 Identities=8% Similarity=0.020 Sum_probs=22.1
Q ss_pred HHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591 29 RLGKKMSQPDLANQINQRPQVVSEYE 54 (82)
Q Consensus 29 r~~~g~s~~elA~~~gis~~~i~~~e 54 (82)
+--.|+|.+|+|+.+|+|.++|....
T Consensus 153 ~~~eg~s~~EIA~~lgis~~tVk~rl 178 (194)
T PRK12531 153 VYLEELPHQQVAEMFDIPLGTVKSRL 178 (194)
T ss_pred HHHcCCCHHHHHHHhCcCHHHHHHHH
Confidence 44569999999999999999997654
No 484
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=87.20 E-value=1.1 Score=29.20 Aligned_cols=27 Identities=15% Similarity=-0.028 Sum_probs=22.7
Q ss_pred HHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591 28 ARLGKKMSQPDLANQINQRPQVVSEYE 54 (82)
Q Consensus 28 ~r~~~g~s~~elA~~~gis~~~i~~~e 54 (82)
++.-.|+|.+|+|+.+|+|.++|....
T Consensus 127 L~~~eg~S~~EIAe~LgiS~~tVksrL 153 (228)
T PRK06704 127 LKDVFQYSIADIAKVCSVSEGAVKASL 153 (228)
T ss_pred hHHhhCCCHHHHHHHHCcCHHHHHHHH
Confidence 344569999999999999999998764
No 485
>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional
Probab=87.09 E-value=1.5 Score=31.78 Aligned_cols=33 Identities=12% Similarity=0.092 Sum_probs=25.6
Q ss_pred HHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 22 PRQIQRARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 22 ~~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
...|..+....+ +..++|+.+|||++|+++-.+
T Consensus 476 ~~~i~~~l~~~~-~~~~aA~~LGisr~tL~rkl~ 508 (520)
T PRK10820 476 RSVLTRLYRNYP-STRKLAKRLGVSHTAIANKLR 508 (520)
T ss_pred HHHHHHHHHHCC-CHHHHHHHhCCCHHHHHHHHH
Confidence 344555555566 888999999999999998765
No 486
>PF10743 Phage_Cox: Regulatory phage protein cox; InterPro: IPR019679 Phage Cox proteins are expressed by Enterobacteria phages. The Cox protein is a 79-residue basic protein with a predicted strong helix-turn-helix DNA-binding motif. It inhibits integrative recombination and it activates site-specific excision of the HP1 genome from the Haemophilus influenzae chromosome, Hp1. Cox appears to function as a tetramer. Cox binding sites consist of two direct repeats of the consensus motif 5'-GGTMAWWWWA, one Cox tetramer binding to each motif. Cox binding interferes with the interaction of HP1 integrase with one of its binding sites, IBS5. This competition is central to directional control. Both Cox binding sites are needed for full inhibition of integration and for activating excision, because it plays a positive role in assembling the nucleoprotein complexes that produce excisive recombination, by inducing the formation of a critical conformation in those complexes [].
Probab=87.03 E-value=1.5 Score=24.62 Aligned_cols=28 Identities=18% Similarity=0.345 Sum_probs=22.8
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHcCCCCC
Q 038591 33 KMSQPDLANQINQRPQVVSEYENGKAVP 60 (82)
Q Consensus 33 g~s~~elA~~~gis~~~i~~~e~g~~~p 60 (82)
-+|...||+.+|.++++|..+-.....|
T Consensus 12 ~v~~~~FA~~IGKt~sAVr~Mi~~gKLP 39 (87)
T PF10743_consen 12 AVTYEKFAEYIGKTPSAVRKMIKAGKLP 39 (87)
T ss_pred ccCHHHHHHHHCCCHHHHHHHHHcCCCC
Confidence 5788999999999999999886544444
No 487
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=87.02 E-value=0.68 Score=25.18 Aligned_cols=22 Identities=14% Similarity=0.327 Sum_probs=19.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHc
Q 038591 34 MSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 34 ~s~~elA~~~gis~~~i~~~e~ 55 (82)
+|..++|+.+++++.++.++.+
T Consensus 26 ~s~~eiA~~~~i~~~~l~kil~ 47 (83)
T PF02082_consen 26 VSSKEIAERLGISPSYLRKILQ 47 (83)
T ss_dssp BEHHHHHHHHTS-HHHHHHHHH
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 8999999999999999999864
No 488
>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=87.01 E-value=2 Score=26.63 Aligned_cols=28 Identities=4% Similarity=-0.024 Sum_probs=23.4
Q ss_pred HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 28 ARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 28 ~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
++--.|+|.+|+|+.+|+|.++|.....
T Consensus 142 l~~~~g~s~~EIA~~lgis~~tvk~rl~ 169 (188)
T TIGR02943 142 MREVLGFESDEICQELEISTSNCHVLLY 169 (188)
T ss_pred HHHHhCCCHHHHHHHhCCCHHHHHHHHH
Confidence 3445699999999999999999987754
No 489
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=87.00 E-value=1.5 Score=26.72 Aligned_cols=27 Identities=11% Similarity=0.199 Sum_probs=23.1
Q ss_pred HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 29 RLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 29 r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
+.-.|+|..|+|+.+|+|.++|.....
T Consensus 131 ~~~~g~s~~EIA~~lgis~~tV~~~l~ 157 (172)
T PRK09651 131 SQLDGLTYSEIAHKLGVSVSSVKKYVA 157 (172)
T ss_pred hhccCCCHHHHHHHhCCCHHHHHHHHH
Confidence 344699999999999999999988764
No 490
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=86.82 E-value=1.9 Score=26.58 Aligned_cols=27 Identities=11% Similarity=-0.028 Sum_probs=23.4
Q ss_pred HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 29 RLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 29 r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
+--.|+|..|+|+.+|+|..+|.....
T Consensus 143 ~~~~g~s~~eIA~~lgis~~tV~~~l~ 169 (184)
T PRK12539 143 VKLEGLSVAEAATRSGMSESAVKVSVH 169 (184)
T ss_pred HHHcCCcHHHHHHHHCcCHHHHHHHHH
Confidence 445699999999999999999988764
No 491
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=86.79 E-value=2 Score=26.30 Aligned_cols=27 Identities=11% Similarity=-0.060 Sum_probs=23.1
Q ss_pred HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 29 RLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 29 r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
+--.|+|..|+|+.+|+|..+|.....
T Consensus 143 ~~~~g~s~~eIA~~l~is~~tV~~~l~ 169 (184)
T PRK12512 143 ISVEGASIKETAAKLSMSEGAVRVALH 169 (184)
T ss_pred HHHcCCCHHHHHHHhCCCHHHHHHHHH
Confidence 344699999999999999999988764
No 492
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=86.74 E-value=1.5 Score=31.94 Aligned_cols=25 Identities=4% Similarity=0.109 Sum_probs=22.9
Q ss_pred CCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591 32 KKMSQPDLANQINQRPQVVSEYENG 56 (82)
Q Consensus 32 ~g~s~~elA~~~gis~~~i~~~e~g 56 (82)
.++|+.++|+.+|||+..|+++|..
T Consensus 466 e~~TL~EIa~~lGVSrERVRQIe~k 490 (509)
T PRK05901 466 QPKTLDEIGQVYGVTRERIRQIESK 490 (509)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 4699999999999999999999974
No 493
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=86.68 E-value=1.8 Score=26.89 Aligned_cols=27 Identities=19% Similarity=-0.025 Sum_probs=22.9
Q ss_pred HHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591 28 ARLGKKMSQPDLANQINQRPQVVSEYE 54 (82)
Q Consensus 28 ~r~~~g~s~~elA~~~gis~~~i~~~e 54 (82)
++--.|+|.+|+|..+|+|.++|..-.
T Consensus 145 l~~~~g~s~~EIA~~lg~s~~tV~~rl 171 (192)
T PRK09643 145 AVDMQGYSVADAARMLGVAEGTVKSRC 171 (192)
T ss_pred HHHHcCCCHHHHHHHHCcCHHHHHHHH
Confidence 455679999999999999999997654
No 494
>PRK13756 tetracycline repressor protein TetR; Provisional
Probab=86.57 E-value=0.62 Score=29.72 Aligned_cols=36 Identities=8% Similarity=0.078 Sum_probs=27.0
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHH
Q 038591 33 KMSQPDLANQINQRPQVVSEYENGKAVPNQTVLAKM 68 (82)
Q Consensus 33 g~s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~l 68 (82)
++|..+||+++|+++.+++++..++...-...+..+
T Consensus 24 ~lsmr~lA~~lgv~~~slY~hf~~K~~Ll~~~~~~~ 59 (205)
T PRK13756 24 GLTTRKLAQKLGVEQPTLYWHVKNKRALLDALAIEI 59 (205)
T ss_pred cCCHHHHHHHhCCCchHHHHHcCCHHHHHHHHHHHH
Confidence 579999999999999999999876544333333333
No 495
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=86.50 E-value=1 Score=28.98 Aligned_cols=25 Identities=12% Similarity=0.113 Sum_probs=22.1
Q ss_pred hCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 31 GKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 31 ~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
-.|+|.+++|+.+|+|.++|.....
T Consensus 163 ~~g~s~~EIAe~lgis~~tVk~~l~ 187 (231)
T PRK11922 163 VEELSVEETAQALGLPEETVKTRLH 187 (231)
T ss_pred hcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 4599999999999999999988764
No 496
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=86.45 E-value=1.6 Score=28.27 Aligned_cols=28 Identities=14% Similarity=0.198 Sum_probs=24.1
Q ss_pred HHHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 28 ARLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 28 ~r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
++.-.|+|.+|+|+.+|+|..+|.....
T Consensus 182 L~~~eg~s~~EIA~~Lgis~~tVk~~l~ 209 (233)
T PRK12538 182 LSYHENMSNGEIAEVMDTTVAAVESLLK 209 (233)
T ss_pred hHHhcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 3455799999999999999999988765
No 497
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=86.43 E-value=1.6 Score=29.53 Aligned_cols=32 Identities=9% Similarity=0.026 Sum_probs=25.2
Q ss_pred HHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHH
Q 038591 23 RQIQRARLGKKMSQPDLANQINQRPQVVSEYE 54 (82)
Q Consensus 23 ~~lk~~r~~~g~s~~elA~~~gis~~~i~~~e 54 (82)
..|..+......+..+||+.+|+|+++|++..
T Consensus 8 ~il~~L~~~~~~s~~~LA~~lgvsr~tV~~~l 39 (319)
T PRK11886 8 QLLSLLADGDFHSGEQLGEELGISRAAIWKHI 39 (319)
T ss_pred HHHHHHHcCCCcCHHHHHHHHCCCHHHHHHHH
Confidence 34455555667899999999999999997753
No 498
>PRK10216 DNA-binding transcriptional regulator YidZ; Provisional
Probab=86.42 E-value=1.9 Score=28.70 Aligned_cols=35 Identities=31% Similarity=0.316 Sum_probs=27.5
Q ss_pred CHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCCCcccc
Q 038591 35 SQPDLANQINQRPQVVSEYENGKAVPNQTVLAKMEKAIGVKLRVKI 80 (82)
Q Consensus 35 s~~elA~~~gis~~~i~~~e~g~~~p~~~~~~~la~~lgv~~~e~~ 80 (82)
|....|+.+++|+++||+. +..|.+.||+++-+|.
T Consensus 24 s~t~AA~~L~iSQpavS~~-----------I~~LE~~lg~~LF~R~ 58 (319)
T PRK10216 24 SVTKAAKRMNVTPSAVSKS-----------LAKLRAWFDDPLFVNT 58 (319)
T ss_pred CHHHHHHHhCCCHHHHHHH-----------HHHHHHHhCCceEEec
Confidence 6777999999999999984 5667777777766553
No 499
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=86.41 E-value=1.3 Score=27.75 Aligned_cols=27 Identities=7% Similarity=-0.065 Sum_probs=23.4
Q ss_pred HHhCCCCHHHHHHHhCCCHHHHHHHHc
Q 038591 29 RLGKKMSQPDLANQINQRPQVVSEYEN 55 (82)
Q Consensus 29 r~~~g~s~~elA~~~gis~~~i~~~e~ 55 (82)
+.-.|+|.+|+|+.+|+|..+|.....
T Consensus 145 ~~~~g~s~~EIAe~lgis~~tV~~~l~ 171 (196)
T PRK12535 145 TQVLGYTYEEAAKIADVRVGTIRSRVA 171 (196)
T ss_pred HHHhCCCHHHHHHHhCCCHHHHHHHHH
Confidence 445699999999999999999988764
No 500
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=86.40 E-value=2.8 Score=25.03 Aligned_cols=27 Identities=15% Similarity=0.199 Sum_probs=23.6
Q ss_pred HhCCCCHHHHHHHhCCCHHHHHHHHcC
Q 038591 30 LGKKMSQPDLANQINQRPQVVSEYENG 56 (82)
Q Consensus 30 ~~~g~s~~elA~~~gis~~~i~~~e~g 56 (82)
-..|++.+++|+.+++|..||..+...
T Consensus 161 ~~~g~~~~~Ia~~l~~s~~tv~~~~~~ 187 (211)
T PRK15369 161 ITEGYTNRDIAEQLSISIKTVETHRLN 187 (211)
T ss_pred HHCCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 357899999999999999999988754
Done!