Query psy15513
Match_columns 77
No_of_seqs 113 out of 337
Neff 6.9
Searched_HMMs 46136
Date Fri Aug 16 23:14:38 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy15513.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/15513hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00292 PAX: 'Paired box' dom 99.9 8.4E-28 1.8E-32 152.3 6.7 76 1-76 29-104 (125)
2 cd00131 PAX Paired Box domain 99.9 3.8E-26 8.3E-31 144.9 8.8 76 1-76 29-104 (128)
3 smart00351 PAX Paired Box doma 99.9 1.8E-24 3.9E-29 136.6 8.7 75 2-76 30-104 (125)
4 KOG3517|consensus 99.9 2.3E-22 5E-27 140.0 3.5 76 1-76 32-107 (334)
5 COG3415 Transposase and inacti 99.8 2.8E-18 6E-23 110.4 7.7 72 4-76 20-91 (138)
6 PF01710 HTH_Tnp_IS630: Transp 99.7 1.4E-17 3E-22 104.2 6.2 67 3-76 16-82 (119)
7 KOG3862|consensus 99.7 1.1E-17 2.5E-22 117.3 4.5 76 1-76 37-112 (327)
8 PF13551 HTH_29: Winged helix- 99.6 9.4E-15 2E-19 88.3 7.5 75 1-75 7-90 (112)
9 KOG0849|consensus 99.3 1.2E-12 2.7E-17 94.7 3.3 76 1-76 27-103 (354)
10 PF13565 HTH_32: Homeodomain-l 99.2 1.7E-10 3.6E-15 66.3 6.3 54 21-76 1-59 (77)
11 PF13384 HTH_23: Homeodomain-l 99.1 2.6E-11 5.6E-16 64.8 1.1 32 2-33 14-45 (50)
12 PF13011 LZ_Tnp_IS481: leucine 98.9 4.4E-09 9.6E-14 62.9 6.7 58 3-60 23-83 (85)
13 PF13518 HTH_28: Helix-turn-he 98.9 1.9E-09 4.2E-14 57.5 3.1 32 3-34 10-41 (52)
14 PF13936 HTH_38: Helix-turn-he 98.7 1.3E-08 2.9E-13 53.7 2.4 27 2-28 17-43 (44)
15 PRK09413 IS2 repressor TnpA; R 98.6 7E-08 1.5E-12 60.3 4.5 36 2-37 26-61 (121)
16 PF02796 HTH_7: Helix-turn-hel 98.6 4E-08 8.7E-13 51.9 1.9 27 1-27 17-43 (45)
17 cd01104 HTH_MlrA-CarA Helix-Tu 98.5 1.1E-06 2.3E-11 49.1 7.1 64 6-75 1-67 (68)
18 PF06056 Terminase_5: Putative 98.2 1.2E-06 2.7E-11 48.8 2.7 33 1-33 9-41 (58)
19 cd04763 HTH_MlrA-like Helix-Tu 98.2 2.5E-05 5.5E-10 43.9 7.4 64 6-75 1-67 (68)
20 cd04762 HTH_MerR-trunc Helix-T 98.1 6.9E-06 1.5E-10 42.3 4.6 32 6-41 1-32 (49)
21 PF04218 CENP-B_N: CENP-B N-te 98.1 1.6E-06 3.4E-11 47.4 1.3 28 2-29 19-46 (53)
22 PF14493 HTH_40: Helix-turn-he 98.0 2.7E-05 5.8E-10 46.3 6.4 69 1-75 9-77 (91)
23 PF01527 HTH_Tnp_1: Transposas 97.9 8.4E-06 1.8E-10 46.3 2.5 28 3-30 21-48 (76)
24 cd04764 HTH_MlrA-like_sg1 Heli 97.9 0.00015 3.4E-09 40.4 7.2 63 6-75 1-66 (67)
25 cd04765 HTH_MlrA-like_sg2 Heli 97.9 0.00016 3.4E-09 43.9 7.7 67 6-76 1-69 (99)
26 cd01105 HTH_GlnR-like Helix-Tu 97.8 0.00015 3.2E-09 43.0 7.1 65 5-75 1-68 (88)
27 PF13411 MerR_1: MerR HTH fami 97.8 9.1E-05 2E-09 41.3 5.9 64 6-76 1-67 (69)
28 smart00422 HTH_MERR helix_turn 97.8 0.00018 4E-09 40.0 7.1 63 6-75 1-67 (70)
29 PF01325 Fe_dep_repress: Iron 97.8 2.3E-05 5E-10 43.7 3.3 38 4-41 21-58 (60)
30 COG2963 Transposase and inacti 97.8 8.5E-05 1.8E-09 45.6 5.6 37 3-39 22-59 (116)
31 cd04773 HTH_TioE_rpt2 Second H 97.8 0.00019 4E-09 44.1 7.0 66 6-75 1-67 (108)
32 PRK10141 DNA-binding transcrip 97.8 2.9E-05 6.3E-10 48.8 3.3 59 4-62 29-87 (117)
33 smart00421 HTH_LUXR helix_turn 97.8 3.8E-05 8.2E-10 40.4 3.3 30 2-31 15-44 (58)
34 cd01106 HTH_TipAL-Mta Helix-Tu 97.7 0.00033 7.2E-09 42.4 7.6 64 6-75 1-67 (103)
35 TIGR01764 excise DNA binding d 97.7 4.2E-05 9E-10 39.5 3.1 32 6-41 2-33 (49)
36 PF04703 FaeA: FaeA-like prote 97.7 4.2E-05 9.1E-10 43.2 3.2 40 4-43 14-53 (62)
37 PRK15418 transcriptional regul 97.7 3.9E-05 8.4E-10 55.0 3.7 36 3-38 27-62 (318)
38 cd01279 HTH_HspR-like Helix-Tu 97.7 0.00027 5.9E-09 42.7 6.8 65 6-75 2-68 (98)
39 cd04767 HTH_HspR-like_MBC Heli 97.7 0.00018 4E-09 45.4 6.2 64 6-75 2-67 (120)
40 cd04761 HTH_MerR-SF Helix-Turn 97.7 0.00017 3.8E-09 37.5 5.0 44 6-54 1-44 (49)
41 cd04774 HTH_YfmP Helix-Turn-He 97.7 0.00033 7.1E-09 42.3 6.8 65 6-75 1-67 (96)
42 smart00345 HTH_GNTR helix_turn 97.7 7.6E-05 1.6E-09 39.9 3.5 33 7-39 22-54 (60)
43 PF07037 DUF1323: Putative tra 97.6 0.00012 2.5E-09 46.4 4.6 55 6-60 1-56 (122)
44 PF12802 MarR_2: MarR family; 97.6 7.7E-05 1.7E-09 40.6 3.4 40 6-45 22-61 (62)
45 cd00569 HTH_Hin_like Helix-tur 97.6 3.5E-05 7.5E-10 36.4 1.7 25 2-26 18-42 (42)
46 PF00325 Crp: Bacterial regula 97.6 0.00013 2.8E-09 36.3 3.6 29 6-34 3-31 (32)
47 TIGR01321 TrpR trp operon repr 97.6 5.1E-05 1.1E-09 46.2 2.2 26 3-28 53-78 (94)
48 TIGR02531 yecD_yerC TrpR-relat 97.6 6.3E-05 1.4E-09 45.2 2.6 24 3-26 48-71 (88)
49 cd01109 HTH_YyaN Helix-Turn-He 97.5 0.001 2.2E-08 40.9 7.9 64 6-75 1-67 (113)
50 PF12728 HTH_17: Helix-turn-he 97.5 0.00013 2.9E-09 38.7 3.5 32 6-41 2-33 (51)
51 cd04770 HTH_HMRTR Helix-Turn-H 97.5 0.0012 2.5E-08 40.9 8.2 64 6-75 1-67 (123)
52 cd04766 HTH_HspR Helix-Turn-He 97.5 0.00063 1.4E-08 40.3 6.7 65 6-75 2-68 (91)
53 cd01111 HTH_MerD Helix-Turn-He 97.5 0.0009 1.9E-08 41.1 7.5 66 6-75 1-67 (107)
54 PF13412 HTH_24: Winged helix- 97.5 0.00017 3.8E-09 37.8 3.8 32 4-35 16-47 (48)
55 cd04780 HTH_MerR-like_sg5 Heli 97.5 0.00078 1.7E-08 40.6 7.0 66 6-75 1-68 (95)
56 PRK13182 racA polar chromosome 97.5 0.00063 1.4E-08 45.4 7.2 63 6-73 1-64 (175)
57 smart00420 HTH_DEOR helix_turn 97.5 0.0002 4.3E-09 37.3 3.8 36 4-39 13-48 (53)
58 PF09339 HTH_IclR: IclR helix- 97.5 0.00014 3E-09 39.0 3.2 33 4-36 17-49 (52)
59 cd06171 Sigma70_r4 Sigma70, re 97.5 0.00025 5.4E-09 36.4 4.0 29 3-31 24-52 (55)
60 PF08281 Sigma70_r4_2: Sigma-7 97.5 0.00019 4E-09 38.4 3.6 29 3-31 24-52 (54)
61 PF13613 HTH_Tnp_4: Helix-turn 97.5 0.00014 3.1E-09 39.3 3.1 28 4-31 18-45 (53)
62 cd04782 HTH_BltR Helix-Turn-He 97.5 0.0017 3.7E-08 39.0 8.0 64 6-75 1-67 (97)
63 cd04772 HTH_TioE_rpt1 First He 97.5 0.0018 3.9E-08 39.1 8.0 65 6-74 1-65 (99)
64 PRK11050 manganese transport r 97.4 0.0004 8.7E-09 44.9 5.3 37 4-40 50-86 (152)
65 cd00592 HTH_MerR-like Helix-Tu 97.4 0.0014 3.1E-08 39.0 7.4 63 6-75 1-66 (100)
66 PHA02591 hypothetical protein; 97.4 0.00012 2.7E-09 43.2 2.5 27 1-27 55-81 (83)
67 PRK00118 putative DNA-binding 97.4 8.5E-05 1.8E-09 45.9 1.8 63 3-65 31-93 (104)
68 cd04789 HTH_Cfa Helix-Turn-Hel 97.4 0.0013 2.8E-08 39.9 7.0 65 6-75 2-67 (102)
69 cd04775 HTH_Cfa-like Helix-Tur 97.4 0.0014 2.9E-08 39.8 7.0 63 6-75 2-67 (102)
70 cd06170 LuxR_C_like C-terminal 97.4 0.00024 5.2E-09 37.4 3.3 29 3-31 13-41 (57)
71 PF01047 MarR: MarR family; I 97.4 0.00017 3.6E-09 39.1 2.5 42 4-45 16-57 (59)
72 PF01022 HTH_5: Bacterial regu 97.4 0.0002 4.4E-09 37.7 2.7 34 2-35 12-45 (47)
73 cd01107 HTH_BmrR Helix-Turn-He 97.4 0.0018 3.9E-08 39.6 7.3 66 6-75 1-68 (108)
74 PRK13413 mpi multiple promoter 97.4 0.00014 3.1E-09 48.4 2.6 27 2-28 169-195 (200)
75 cd04788 HTH_NolA-AlbR Helix-Tu 97.4 0.002 4.4E-08 38.6 7.3 62 6-75 1-67 (96)
76 TIGR03879 near_KaiC_dom probab 97.4 0.00016 3.4E-09 42.2 2.3 32 4-35 31-62 (73)
77 PF08279 HTH_11: HTH domain; 97.3 0.00017 3.6E-09 38.7 2.2 29 5-33 15-43 (55)
78 PRK13749 transcriptional regul 97.3 0.0028 6.1E-08 40.0 8.0 68 5-76 3-71 (121)
79 cd00090 HTH_ARSR Arsenical Res 97.3 0.0003 6.4E-09 38.4 3.2 38 4-41 19-56 (78)
80 TIGR02054 MerD mercuric resist 97.3 0.0024 5.2E-08 40.2 7.7 68 4-75 2-70 (120)
81 cd01108 HTH_CueR Helix-Turn-He 97.3 0.0025 5.5E-08 39.9 7.7 62 6-75 1-67 (127)
82 PF05225 HTH_psq: helix-turn-h 97.3 0.00036 7.8E-09 36.9 3.1 25 4-28 14-39 (45)
83 cd01110 HTH_SoxR Helix-Turn-He 97.3 0.0022 4.7E-08 41.0 7.3 65 6-75 2-67 (139)
84 TIGR02043 ZntR Zn(II)-responsi 97.3 0.0027 5.9E-08 40.1 7.7 64 6-75 2-68 (131)
85 TIGR02044 CueR Cu(I)-responsiv 97.3 0.0031 6.7E-08 39.5 7.8 62 6-75 1-67 (127)
86 smart00346 HTH_ICLR helix_turn 97.3 0.0019 4.2E-08 37.4 6.5 59 4-64 19-77 (91)
87 cd04777 HTH_MerR-like_sg1 Heli 97.3 0.0017 3.6E-08 39.5 6.4 62 6-75 1-65 (107)
88 PF05930 Phage_AlpA: Prophage 97.3 0.00024 5.1E-09 38.2 2.3 34 6-43 4-38 (51)
89 PRK09514 zntR zinc-responsive 97.3 0.0027 5.9E-08 40.6 7.5 64 6-75 2-68 (140)
90 PF04545 Sigma70_r4: Sigma-70, 97.2 0.00074 1.6E-08 35.7 4.1 29 3-31 18-46 (50)
91 TIGR02944 suf_reg_Xantho FeS a 97.2 0.00091 2E-08 41.7 5.1 62 5-66 25-89 (130)
92 cd04783 HTH_MerR1 Helix-Turn-H 97.2 0.0038 8.2E-08 39.0 7.9 63 6-75 1-67 (126)
93 PF01381 HTH_3: Helix-turn-hel 97.2 0.0003 6.6E-09 37.5 2.5 26 3-28 7-32 (55)
94 COG2390 DeoR Transcriptional r 97.2 0.00035 7.6E-09 50.5 3.4 38 3-40 24-61 (321)
95 PRK11512 DNA-binding transcrip 97.2 0.00072 1.6E-08 42.8 4.4 43 4-46 53-95 (144)
96 smart00419 HTH_CRP helix_turn_ 97.2 0.00067 1.5E-08 34.8 3.6 34 5-38 8-41 (48)
97 cd04787 HTH_HMRTR_unk Helix-Tu 97.2 0.0038 8.1E-08 39.4 7.6 64 6-75 1-67 (133)
98 cd04768 HTH_BmrR-like Helix-Tu 97.2 0.0046 9.9E-08 37.1 7.6 64 6-75 1-67 (96)
99 cd00092 HTH_CRP helix_turn_hel 97.2 0.00087 1.9E-08 36.7 4.1 36 4-39 24-59 (67)
100 PHA00738 putative HTH transcri 97.2 0.00037 8E-09 43.4 2.8 41 5-45 26-66 (108)
101 smart00418 HTH_ARSR helix_turn 97.2 0.0012 2.7E-08 35.0 4.5 39 3-41 8-46 (66)
102 PRK10227 DNA-binding transcrip 97.1 0.0048 1E-07 39.3 7.7 66 6-75 1-67 (135)
103 cd04784 HTH_CadR-PbrR Helix-Tu 97.1 0.0043 9.3E-08 38.8 7.2 64 6-75 1-67 (127)
104 PF02082 Rrf2: Transcriptional 97.1 0.00076 1.7E-08 39.3 3.6 34 6-39 26-59 (83)
105 PF13542 HTH_Tnp_ISL3: Helix-t 97.1 0.0006 1.3E-08 36.1 2.9 24 6-29 28-51 (52)
106 cd04786 HTH_MerR-like_sg7 Heli 97.1 0.0052 1.1E-07 39.0 7.6 64 6-75 1-67 (131)
107 PF12840 HTH_20: Helix-turn-he 97.1 0.00064 1.4E-08 37.4 3.0 39 3-41 22-60 (61)
108 COG0789 SoxR Predicted transcr 97.1 0.0062 1.3E-07 37.3 7.7 66 6-75 1-67 (124)
109 smart00354 HTH_LACI helix_turn 97.1 0.0032 7E-08 35.6 5.9 43 6-64 1-43 (70)
110 TIGR02047 CadR-PbrR Cd(II)/Pb( 97.1 0.0055 1.2E-07 38.5 7.5 62 6-75 1-67 (127)
111 PF13730 HTH_36: Helix-turn-he 97.1 0.0011 2.5E-08 35.4 3.8 28 7-34 27-54 (55)
112 TIGR02051 MerR Hg(II)-responsi 97.1 0.005 1.1E-07 38.5 7.3 61 7-75 1-66 (124)
113 cd01282 HTH_MerR-like_sg3 Heli 97.1 0.0063 1.4E-07 37.4 7.6 63 6-75 1-66 (112)
114 PRK04217 hypothetical protein; 97.1 0.0011 2.3E-08 41.4 4.1 29 3-31 56-84 (110)
115 PHA00542 putative Cro-like pro 97.1 0.00046 9.9E-09 40.5 2.2 25 3-27 29-53 (82)
116 PRK11014 transcriptional repre 97.1 0.0012 2.6E-08 41.9 4.3 35 6-40 26-60 (141)
117 PF00356 LacI: Bacterial regul 97.0 0.0007 1.5E-08 36.0 2.7 40 7-62 1-40 (46)
118 PF12116 SpoIIID: Stage III sp 97.0 0.0004 8.6E-09 41.2 1.8 25 3-27 17-41 (82)
119 TIGR01889 Staph_reg_Sar staphy 97.0 0.0043 9.3E-08 37.7 6.5 56 4-59 42-100 (109)
120 cd04776 HTH_GnyR Helix-Turn-He 97.0 0.0045 9.7E-08 38.5 6.6 62 6-75 1-65 (118)
121 cd04785 HTH_CadR-PbrR-like Hel 97.0 0.0089 1.9E-07 37.4 7.9 64 6-75 1-67 (126)
122 cd07377 WHTH_GntR Winged helix 97.0 0.0014 3E-08 35.5 3.7 32 7-38 27-58 (66)
123 PRK10870 transcriptional repre 97.0 0.0042 9E-08 41.0 6.5 50 5-54 71-123 (176)
124 cd04779 HTH_MerR-like_sg4 Heli 97.0 0.0049 1.1E-07 39.4 6.6 63 6-75 1-66 (134)
125 smart00550 Zalpha Z-DNA-bindin 97.0 0.002 4.3E-08 36.5 4.3 34 5-38 22-55 (68)
126 PRK03573 transcriptional regul 97.0 0.0045 9.8E-08 38.9 6.4 42 4-45 45-86 (144)
127 TIGR00721 tfx DNA-binding prot 96.9 0.001 2.3E-08 42.9 3.3 29 3-31 19-47 (137)
128 PF00392 GntR: Bacterial regul 96.9 0.0012 2.6E-08 36.6 3.2 35 7-41 26-60 (64)
129 COG2522 Predicted transcriptio 96.9 0.00043 9.3E-09 43.8 1.4 30 1-30 18-47 (119)
130 smart00529 HTH_DTXR Helix-turn 96.9 0.0031 6.8E-08 36.9 5.1 34 7-40 1-34 (96)
131 cd04781 HTH_MerR-like_sg6 Heli 96.9 0.0069 1.5E-07 37.6 6.9 63 6-75 1-66 (120)
132 TIGR02337 HpaR homoprotocatech 96.9 0.0049 1.1E-07 37.7 6.1 54 4-57 41-97 (118)
133 TIGR03070 couple_hipB transcri 96.9 0.0011 2.4E-08 35.1 2.7 24 3-26 13-36 (58)
134 PF13443 HTH_26: Cro/C1-type H 96.9 0.00057 1.2E-08 37.4 1.5 27 1-27 6-32 (63)
135 PHA01976 helix-turn-helix prot 96.9 0.0013 2.9E-08 36.3 2.9 24 3-26 13-36 (67)
136 PRK11303 DNA-binding transcrip 96.8 0.0037 7.9E-08 43.2 5.6 44 6-62 1-44 (328)
137 PRK01381 Trp operon repressor; 96.8 0.00038 8.2E-09 42.7 0.6 26 3-28 53-78 (99)
138 TIGR03830 CxxCG_CxxCG_HTH puta 96.8 0.0028 6E-08 39.0 4.5 47 3-66 76-122 (127)
139 PF05344 DUF746: Domain of Unk 96.8 0.0023 5E-08 36.5 3.7 36 5-40 13-55 (65)
140 PF02001 DUF134: Protein of un 96.8 0.0022 4.9E-08 39.7 3.9 28 4-31 56-83 (106)
141 PF10668 Phage_terminase: Phag 96.8 0.0018 3.9E-08 36.4 3.2 26 5-30 22-47 (60)
142 PF13560 HTH_31: Helix-turn-he 96.8 0.0013 2.7E-08 36.4 2.5 25 3-27 12-36 (64)
143 cd04769 HTH_MerR2 Helix-Turn-H 96.8 0.013 2.9E-07 36.1 7.3 63 6-75 1-66 (116)
144 PRK10072 putative transcriptio 96.8 0.0015 3.2E-08 39.7 2.8 51 3-71 44-94 (96)
145 PF02954 HTH_8: Bacterial regu 96.8 0.001 2.2E-08 34.4 1.8 27 3-29 16-42 (42)
146 PRK03975 tfx putative transcri 96.8 0.0018 4E-08 41.9 3.4 30 3-32 19-48 (141)
147 COG2944 Predicted transcriptio 96.8 0.0061 1.3E-07 37.7 5.5 45 4-65 56-100 (104)
148 PF01371 Trp_repressor: Trp re 96.8 0.0017 3.6E-08 39.0 2.9 29 2-30 46-74 (87)
149 TIGR02702 SufR_cyano iron-sulf 96.7 0.0031 6.8E-08 42.2 4.6 36 3-38 13-48 (203)
150 PHA00675 hypothetical protein 96.7 0.0015 3.3E-08 38.4 2.6 33 3-36 37-69 (78)
151 PRK15002 redox-sensitivie tran 96.7 0.012 2.6E-07 38.5 7.1 62 6-75 12-77 (154)
152 TIGR00122 birA_repr_reg BirA b 96.7 0.0027 5.8E-08 35.6 3.6 32 4-35 12-43 (69)
153 COG2826 Tra8 Transposase and i 96.7 0.0024 5.3E-08 46.0 4.1 72 2-75 20-100 (318)
154 PF00196 GerE: Bacterial regul 96.7 0.0026 5.6E-08 34.6 3.4 30 3-32 16-45 (58)
155 PF01978 TrmB: Sugar-specific 96.7 0.00091 2E-08 37.4 1.5 36 4-39 21-56 (68)
156 PF13744 HTH_37: Helix-turn-he 96.7 0.0017 3.8E-08 37.7 2.7 25 3-27 29-53 (80)
157 TIGR01950 SoxR redox-sensitive 96.7 0.011 2.3E-07 38.1 6.5 63 6-75 2-67 (142)
158 PF12759 HTH_Tnp_IS1: InsA C-t 96.7 0.0013 2.7E-08 35.2 1.7 28 1-28 17-44 (46)
159 PRK11169 leucine-responsive tr 96.6 0.003 6.4E-08 41.1 3.8 67 1-67 23-104 (164)
160 PRK09652 RNA polymerase sigma 96.6 0.0036 7.8E-08 39.8 4.1 28 4-31 143-170 (182)
161 PF07638 Sigma70_ECF: ECF sigm 96.6 0.0033 7.2E-08 41.4 4.0 29 3-31 149-177 (185)
162 smart00347 HTH_MARR helix_turn 96.6 0.013 2.7E-07 33.8 6.1 52 4-55 23-77 (101)
163 cd04790 HTH_Cfa-like_unk Helix 96.6 0.021 4.6E-07 37.7 7.7 62 6-75 2-68 (172)
164 PF08220 HTH_DeoR: DeoR-like h 96.6 0.0019 4.1E-08 35.4 2.2 36 6-42 15-50 (57)
165 TIGR02985 Sig70_bacteroi1 RNA 96.6 0.0042 9.2E-08 38.6 3.9 29 3-31 127-155 (161)
166 TIGR02844 spore_III_D sporulat 96.5 0.011 2.4E-07 34.9 5.4 41 6-61 20-60 (80)
167 cd01392 HTH_LacI Helix-turn-he 96.5 0.0014 2.9E-08 34.5 1.4 18 10-27 2-19 (52)
168 PRK15043 transcriptional regul 96.5 0.015 3.3E-07 40.6 6.9 65 5-75 3-70 (243)
169 PRK06759 RNA polymerase factor 96.5 0.0046 1E-07 38.7 4.0 29 3-31 120-148 (154)
170 COG1321 TroR Mn-dependent tran 96.5 0.0042 9.2E-08 40.5 3.9 37 6-42 25-61 (154)
171 PRK14987 gluconate operon tran 96.5 0.0062 1.3E-07 42.2 4.9 22 6-27 6-27 (331)
172 PRK10014 DNA-binding transcrip 96.5 0.0079 1.7E-07 41.7 5.4 23 5-27 6-28 (342)
173 TIGR02937 sigma70-ECF RNA poly 96.5 0.0049 1.1E-07 37.3 3.9 29 3-31 124-152 (158)
174 PF13463 HTH_27: Winged helix 96.5 0.0042 9.1E-08 34.1 3.3 43 3-45 16-58 (68)
175 PF03444 HrcA_DNA-bdg: Winged 96.5 0.0092 2E-07 35.2 4.8 41 6-46 24-66 (78)
176 TIGR02607 antidote_HigA addict 96.5 0.0028 6.1E-08 35.9 2.5 26 2-27 15-40 (78)
177 PF01726 LexA_DNA_bind: LexA D 96.5 0.0072 1.6E-07 34.2 4.1 36 4-39 22-60 (65)
178 PRK11179 DNA-binding transcrip 96.5 0.0035 7.5E-08 40.3 3.2 34 3-36 20-54 (153)
179 PF09607 BrkDBD: Brinker DNA-b 96.4 0.0024 5.3E-08 35.7 2.0 24 7-30 27-50 (58)
180 PRK09642 RNA polymerase sigma 96.4 0.0057 1.2E-07 38.7 4.0 28 4-31 121-148 (160)
181 smart00344 HTH_ASNC helix_turn 96.4 0.0039 8.5E-08 37.3 3.1 63 5-67 17-91 (108)
182 TIGR02989 Sig-70_gvs1 RNA poly 96.4 0.0057 1.2E-07 38.4 4.0 28 4-31 126-153 (159)
183 PRK13919 putative RNA polymera 96.4 0.0054 1.2E-07 39.6 3.9 28 4-31 150-177 (186)
184 PRK08241 RNA polymerase factor 96.4 0.032 6.9E-07 39.5 8.1 60 4-63 168-227 (339)
185 PRK10857 DNA-binding transcrip 96.4 0.015 3.3E-07 38.2 5.9 39 6-44 26-66 (164)
186 smart00342 HTH_ARAC helix_turn 96.4 0.014 3E-07 32.3 5.0 59 6-75 2-60 (84)
187 TIGR00738 rrf2_super rrf2 fami 96.4 0.025 5.3E-07 35.0 6.6 34 5-38 25-58 (132)
188 PF08535 KorB: KorB domain; I 96.4 0.0031 6.7E-08 37.5 2.4 27 3-29 1-27 (93)
189 TIGR02010 IscR iron-sulfur clu 96.4 0.014 3.1E-07 36.7 5.5 33 6-38 26-58 (135)
190 PF14549 P22_Cro: DNA-binding 96.4 0.004 8.7E-08 34.9 2.6 19 7-25 11-29 (60)
191 PRK11924 RNA polymerase sigma 96.3 0.0067 1.5E-07 38.4 4.0 28 4-31 140-167 (179)
192 PRK12537 RNA polymerase sigma 96.3 0.0063 1.4E-07 39.5 3.8 28 4-31 148-175 (182)
193 PRK13752 putative transcriptio 96.3 0.038 8.1E-07 35.6 7.4 63 5-75 7-74 (144)
194 PRK10727 DNA-binding transcrip 96.3 0.012 2.6E-07 41.1 5.3 41 7-63 3-43 (343)
195 PF00126 HTH_1: Bacterial regu 96.3 0.0085 1.8E-07 32.8 3.7 32 3-35 12-43 (60)
196 PRK09639 RNA polymerase sigma 96.3 0.0079 1.7E-07 38.1 4.1 28 4-31 126-153 (166)
197 PF01418 HTH_6: Helix-turn-hel 96.3 0.005 1.1E-07 35.5 2.9 25 5-29 34-58 (77)
198 PF13545 HTH_Crp_2: Crp-like h 96.3 0.009 2E-07 33.5 3.9 34 5-38 28-61 (76)
199 PRK08301 sporulation sigma fac 96.3 0.0073 1.6E-07 40.8 4.1 29 3-31 196-224 (234)
200 COG3311 AlpA Predicted transcr 96.3 0.016 3.5E-07 33.5 4.9 33 6-42 14-47 (70)
201 PRK07037 extracytoplasmic-func 96.3 0.0081 1.8E-07 38.0 4.1 28 4-31 124-151 (163)
202 TIGR02999 Sig-70_X6 RNA polyme 96.3 0.008 1.7E-07 38.7 4.1 28 4-31 149-176 (183)
203 cd00093 HTH_XRE Helix-turn-hel 96.3 0.0042 9.2E-08 31.3 2.3 25 3-27 10-34 (58)
204 TIGR02960 SigX5 RNA polymerase 96.3 0.031 6.7E-07 39.2 7.3 72 4-75 157-229 (324)
205 PRK09638 RNA polymerase sigma 96.2 0.008 1.7E-07 38.4 4.0 29 4-32 141-169 (176)
206 PRK12514 RNA polymerase sigma 96.2 0.0079 1.7E-07 38.7 4.0 28 4-31 144-171 (179)
207 TIGR02947 SigH_actino RNA poly 96.2 0.008 1.7E-07 39.3 4.0 29 3-31 145-173 (193)
208 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 96.2 0.0038 8.3E-08 33.9 2.0 27 1-27 16-42 (50)
209 TIGR02983 SigE-fam_strep RNA p 96.2 0.0083 1.8E-07 37.9 3.9 28 4-31 125-152 (162)
210 TIGR01610 phage_O_Nterm phage 96.2 0.011 2.4E-07 35.4 4.2 36 3-38 45-80 (95)
211 PRK00215 LexA repressor; Valid 96.2 0.0089 1.9E-07 39.8 4.2 37 5-41 23-60 (205)
212 PRK14165 winged helix-turn-hel 96.2 0.013 2.8E-07 40.3 5.1 52 5-56 21-72 (217)
213 PRK10703 DNA-binding transcrip 96.2 0.012 2.6E-07 40.9 4.9 22 6-27 2-23 (341)
214 PRK10046 dpiA two-component re 96.2 0.0076 1.7E-07 40.1 3.8 36 5-40 177-212 (225)
215 PF09012 FeoC: FeoC like trans 96.2 0.0027 5.9E-08 35.8 1.4 34 6-39 15-48 (69)
216 smart00530 HTH_XRE Helix-turn- 96.2 0.0045 9.9E-08 30.9 2.1 24 3-26 8-31 (56)
217 PRK10423 transcriptional repre 96.2 0.012 2.7E-07 40.4 4.9 19 9-27 2-20 (327)
218 TIGR02405 trehalos_R_Ecol treh 96.2 0.0044 9.4E-08 42.8 2.6 22 6-27 2-23 (311)
219 TIGR02952 Sig70_famx2 RNA poly 96.2 0.01 2.2E-07 37.6 4.1 28 4-31 137-164 (170)
220 PRK10906 DNA-binding transcrip 96.2 0.0046 1E-07 42.9 2.7 39 4-43 17-56 (252)
221 TIGR02950 SigM_subfam RNA poly 96.2 0.0099 2.2E-07 37.1 4.0 28 4-31 120-147 (154)
222 TIGR01481 ccpA catabolite cont 96.1 0.016 3.5E-07 39.9 5.3 22 6-27 2-23 (329)
223 TIGR02954 Sig70_famx3 RNA poly 96.1 0.01 2.2E-07 37.9 4.0 28 4-31 134-161 (169)
224 PRK11920 rirA iron-responsive 96.1 0.015 3.3E-07 37.6 4.8 34 6-39 25-58 (153)
225 PRK12519 RNA polymerase sigma 96.1 0.0099 2.1E-07 38.7 4.0 28 4-31 156-183 (194)
226 cd04778 HTH_MerR-like_sg2 Heli 96.1 0.053 1.1E-06 37.2 7.7 65 6-75 2-67 (219)
227 PRK09726 antitoxin HipB; Provi 96.1 0.0062 1.3E-07 35.8 2.7 25 3-27 23-47 (88)
228 PRK09492 treR trehalose repres 96.1 0.0046 1E-07 42.4 2.4 23 6-28 5-27 (315)
229 PF07750 GcrA: GcrA cell cycle 96.1 0.0028 6.1E-08 41.7 1.2 33 1-33 14-47 (162)
230 PRK12536 RNA polymerase sigma 96.1 0.011 2.4E-07 38.3 4.0 28 4-31 144-171 (181)
231 PRK09047 RNA polymerase factor 96.1 0.011 2.4E-07 37.1 3.9 28 4-31 121-148 (161)
232 COG3355 Predicted transcriptio 96.1 0.0096 2.1E-07 38.0 3.5 36 3-38 40-75 (126)
233 TIGR03338 phnR_burk phosphonat 96.0 0.024 5.1E-07 37.5 5.5 45 6-50 35-79 (212)
234 TIGR02417 fruct_sucro_rep D-fr 96.0 0.021 4.5E-07 39.5 5.4 43 7-62 1-43 (327)
235 PRK09409 IS2 transposase TnpB; 96.0 0.024 5.2E-07 40.2 5.8 66 1-72 7-72 (301)
236 PRK13777 transcriptional regul 96.0 0.036 7.8E-07 37.2 6.4 51 4-54 58-111 (185)
237 PRK12423 LexA repressor; Provi 96.0 0.0087 1.9E-07 40.1 3.4 37 4-40 22-61 (202)
238 PRK12534 RNA polymerase sigma 96.0 0.012 2.6E-07 38.1 3.9 28 4-31 152-179 (187)
239 COG1959 Predicted transcriptio 96.0 0.024 5.1E-07 36.7 5.3 35 6-40 26-60 (150)
240 PRK09706 transcriptional repre 96.0 0.0073 1.6E-07 38.0 2.8 25 3-27 16-40 (135)
241 COG1595 RpoE DNA-directed RNA 95.9 0.014 3.1E-07 37.9 4.1 29 4-32 142-170 (182)
242 PRK09649 RNA polymerase sigma 95.9 0.014 3E-07 38.1 4.0 29 4-32 145-173 (185)
243 PRK09744 DNA-binding transcrip 95.9 0.0071 1.5E-07 35.4 2.3 26 7-39 12-37 (75)
244 PRK09526 lacI lac repressor; R 95.9 0.0084 1.8E-07 41.6 3.1 23 6-28 6-28 (342)
245 PRK12547 RNA polymerase sigma 95.9 0.015 3.3E-07 37.1 4.1 28 4-31 127-154 (164)
246 PRK09637 RNA polymerase sigma 95.9 0.014 3.1E-07 38.1 4.0 28 4-31 121-148 (181)
247 PRK09640 RNA polymerase sigma 95.9 0.015 3.2E-07 37.9 4.1 28 4-31 149-176 (188)
248 TIGR02948 SigW_bacill RNA poly 95.9 0.014 3.1E-07 37.5 3.9 29 3-31 150-178 (187)
249 PF13309 HTH_22: HTH domain 95.9 0.0051 1.1E-07 34.6 1.6 21 7-27 44-64 (64)
250 PRK06704 RNA polymerase factor 95.9 0.011 2.4E-07 40.6 3.6 63 4-68 131-193 (228)
251 PRK12530 RNA polymerase sigma 95.9 0.015 3.3E-07 38.1 4.0 28 4-31 149-176 (189)
252 PRK12511 RNA polymerase sigma 95.9 0.015 3.3E-07 38.0 4.0 28 4-31 126-153 (182)
253 smart00352 POU Found in Pit-Oc 95.9 0.01 2.2E-07 34.8 2.8 33 3-40 22-60 (75)
254 PF10654 DUF2481: Protein of u 95.8 0.0092 2E-07 37.7 2.7 31 2-32 77-107 (126)
255 PRK12528 RNA polymerase sigma 95.8 0.016 3.5E-07 36.6 4.0 28 4-31 128-155 (161)
256 PRK12513 RNA polymerase sigma 95.8 0.016 3.6E-07 37.7 4.1 29 3-31 153-181 (194)
257 PHA02535 P terminase ATPase su 95.8 0.0045 9.7E-08 47.9 1.5 28 3-30 16-43 (581)
258 COG3677 Transposase and inacti 95.8 0.006 1.3E-07 38.8 1.9 37 2-38 86-122 (129)
259 PRK12532 RNA polymerase sigma 95.8 0.016 3.5E-07 37.9 4.0 28 4-31 151-178 (195)
260 PF13404 HTH_AsnC-type: AsnC-t 95.8 0.011 2.5E-07 30.6 2.6 24 6-29 18-41 (42)
261 PRK15320 transcriptional activ 95.8 0.014 3E-07 40.5 3.6 39 2-40 176-214 (251)
262 COG1846 MarR Transcriptional r 95.8 0.013 2.8E-07 34.7 3.2 37 9-45 40-76 (126)
263 PRK12516 RNA polymerase sigma 95.8 0.017 3.8E-07 37.9 4.0 28 4-31 131-158 (187)
264 PRK13509 transcriptional repre 95.8 0.011 2.3E-07 40.9 3.2 38 4-42 17-55 (251)
265 PRK12524 RNA polymerase sigma 95.8 0.017 3.8E-07 37.9 4.0 28 4-31 151-178 (196)
266 PRK12542 RNA polymerase sigma 95.8 0.018 3.9E-07 37.4 4.0 28 4-31 137-164 (185)
267 PRK12518 RNA polymerase sigma 95.8 0.018 3.9E-07 36.8 4.0 28 4-31 135-162 (175)
268 PRK09415 RNA polymerase factor 95.8 0.018 3.8E-07 37.3 4.0 28 4-31 142-169 (179)
269 PRK03902 manganese transport t 95.8 0.017 3.7E-07 36.5 3.8 34 5-38 22-55 (142)
270 PRK15411 rcsA colanic acid cap 95.8 0.012 2.7E-07 39.4 3.3 34 2-35 149-182 (207)
271 PRK09645 RNA polymerase sigma 95.8 0.019 4.1E-07 36.7 4.0 28 4-31 133-160 (173)
272 PRK12533 RNA polymerase sigma 95.7 0.018 3.8E-07 39.0 4.0 28 4-31 149-176 (216)
273 PRK01905 DNA-binding protein F 95.7 0.012 2.6E-07 34.1 2.8 27 3-29 48-74 (77)
274 PF07900 DUF1670: Protein of u 95.7 0.11 2.4E-06 36.0 7.9 65 6-74 106-172 (220)
275 PRK09644 RNA polymerase sigma 95.7 0.018 4E-07 36.6 3.9 28 4-31 123-150 (165)
276 PRK09647 RNA polymerase sigma 95.7 0.019 4.1E-07 38.3 4.0 29 4-32 153-181 (203)
277 PF04967 HTH_10: HTH DNA bindi 95.7 0.027 5.9E-07 30.8 4.0 28 4-31 22-49 (53)
278 PRK08583 RNA polymerase sigma 95.7 0.019 4.1E-07 39.4 4.1 28 4-31 220-247 (257)
279 TIGR00637 ModE_repress ModE mo 95.7 0.076 1.6E-06 32.1 6.3 48 7-54 18-69 (99)
280 PF08822 DUF1804: Protein of u 95.7 0.021 4.5E-07 38.0 4.0 32 4-35 18-49 (165)
281 TIGR02959 SigZ RNA polymerase 95.7 0.022 4.7E-07 36.7 4.1 28 4-31 115-142 (170)
282 PRK10401 DNA-binding transcrip 95.6 0.01 2.2E-07 41.5 2.7 23 6-28 2-24 (346)
283 TIGR02957 SigX4 RNA polymerase 95.6 0.08 1.7E-06 36.9 7.1 66 4-75 123-189 (281)
284 PRK12525 RNA polymerase sigma 95.6 0.023 4.9E-07 36.4 4.1 28 4-31 133-160 (168)
285 PRK12522 RNA polymerase sigma 95.6 0.022 4.7E-07 36.5 4.0 29 4-32 134-162 (173)
286 PRK11923 algU RNA polymerase s 95.6 0.022 4.9E-07 37.0 4.0 28 4-31 153-180 (193)
287 PRK06811 RNA polymerase factor 95.6 0.022 4.8E-07 37.2 4.0 29 4-32 146-174 (189)
288 COG2452 Predicted site-specifi 95.6 0.021 4.5E-07 38.8 3.9 51 5-60 1-51 (193)
289 PF01710 HTH_Tnp_IS630: Transp 95.6 0.016 3.5E-07 35.9 3.2 28 4-31 70-97 (119)
290 PRK09906 DNA-binding transcrip 95.6 0.011 2.4E-07 40.4 2.5 31 2-33 13-43 (296)
291 PRK11013 DNA-binding transcrip 95.6 0.012 2.7E-07 40.7 2.8 47 2-51 16-63 (309)
292 PRK12682 transcriptional regul 95.6 0.013 2.8E-07 40.5 2.9 36 2-37 13-49 (309)
293 PF12844 HTH_19: Helix-turn-he 95.6 0.013 2.8E-07 31.9 2.4 25 3-27 10-34 (64)
294 TIGR03339 phn_lysR aminoethylp 95.6 0.013 2.9E-07 39.3 2.9 33 2-35 9-41 (279)
295 TIGR02980 SigBFG RNA polymeras 95.6 0.023 5E-07 38.1 4.1 28 4-31 193-220 (227)
296 COG1522 Lrp Transcriptional re 95.5 0.016 3.5E-07 36.5 3.1 30 6-35 23-52 (154)
297 PRK12529 RNA polymerase sigma 95.5 0.025 5.4E-07 36.6 4.1 28 4-31 142-169 (178)
298 PRK06930 positive control sigm 95.5 0.023 5.1E-07 37.5 4.0 29 3-31 128-156 (170)
299 COG2771 CsgD DNA-binding HTH d 95.5 0.025 5.5E-07 30.4 3.5 34 2-35 16-49 (65)
300 PRK12523 RNA polymerase sigma 95.5 0.025 5.3E-07 36.3 4.0 28 4-31 134-161 (172)
301 COG1342 Predicted DNA-binding 95.5 0.022 4.8E-07 34.9 3.5 29 4-32 48-76 (99)
302 PRK09483 response regulator; P 95.5 0.019 4E-07 36.9 3.4 33 3-35 161-193 (217)
303 PF08765 Mor: Mor transcriptio 95.5 0.024 5.2E-07 34.7 3.7 29 4-32 71-99 (108)
304 PRK06986 fliA flagellar biosyn 95.5 0.025 5.4E-07 38.3 4.1 29 3-31 198-226 (236)
305 PRK13890 conjugal transfer pro 95.5 0.011 2.3E-07 37.0 2.1 26 2-27 15-40 (120)
306 PRK05602 RNA polymerase sigma 95.5 0.026 5.7E-07 36.5 4.0 28 4-31 143-170 (186)
307 TIGR03001 Sig-70_gmx1 RNA poly 95.5 0.025 5.3E-07 39.1 4.1 28 4-31 176-203 (244)
308 PRK12520 RNA polymerase sigma 95.5 0.025 5.4E-07 36.9 3.9 28 4-31 146-173 (191)
309 PRK12541 RNA polymerase sigma 95.5 0.028 6.2E-07 35.5 4.1 28 4-31 127-154 (161)
310 PRK09641 RNA polymerase sigma 95.5 0.027 5.8E-07 36.2 4.0 28 4-31 151-178 (187)
311 PRK11414 colanic acid/biofilm 95.5 0.064 1.4E-06 35.9 6.0 45 6-50 35-79 (221)
312 PRK09834 DNA-binding transcrip 95.5 0.027 5.9E-07 38.9 4.3 36 4-39 25-60 (263)
313 TIGR02612 mob_myst_A mobile my 95.5 0.016 3.5E-07 37.8 2.9 25 3-27 36-60 (150)
314 TIGR02835 spore_sigmaE RNA pol 95.5 0.025 5.4E-07 38.4 4.0 27 4-30 197-223 (234)
315 PRK10411 DNA-binding transcrip 95.4 0.02 4.4E-07 39.4 3.6 38 4-42 17-54 (240)
316 PF00376 MerR: MerR family reg 95.4 0.015 3.3E-07 29.6 2.2 25 7-35 1-25 (38)
317 PRK12517 RNA polymerase sigma 95.4 0.028 6E-07 36.9 4.0 28 4-31 143-170 (188)
318 PRK12512 RNA polymerase sigma 95.4 0.029 6.4E-07 36.2 4.0 28 4-31 146-173 (184)
319 PRK15201 fimbriae regulatory p 95.4 0.025 5.3E-07 38.4 3.7 35 2-36 145-179 (198)
320 TIGR02939 RpoE_Sigma70 RNA pol 95.4 0.031 6.8E-07 36.0 4.1 29 3-31 152-180 (190)
321 TIGR03697 NtcA_cyano global ni 95.4 0.026 5.6E-07 36.3 3.7 33 6-38 144-176 (193)
322 TIGR02431 pcaR_pcaU beta-ketoa 95.4 0.029 6.3E-07 38.3 4.1 34 4-37 23-56 (248)
323 cd06571 Bac_DnaA_C C-terminal 95.4 0.033 7.1E-07 32.9 3.8 28 4-31 43-71 (90)
324 PRK12543 RNA polymerase sigma 95.4 0.031 6.6E-07 36.1 4.0 28 4-31 132-159 (179)
325 PRK09646 RNA polymerase sigma 95.3 0.03 6.6E-07 36.7 4.0 28 4-31 157-184 (194)
326 PRK12540 RNA polymerase sigma 95.3 0.032 7E-07 36.5 4.1 30 3-32 125-154 (182)
327 TIGR01884 cas_HTH CRISPR locus 95.3 0.03 6.5E-07 37.4 4.0 36 4-39 156-191 (203)
328 PRK12526 RNA polymerase sigma 95.3 0.03 6.6E-07 37.2 4.0 28 4-31 168-195 (206)
329 TIGR02943 Sig70_famx1 RNA poly 95.3 0.032 7E-07 36.5 4.0 28 4-31 146-173 (188)
330 COG5484 Uncharacterized conser 95.3 0.017 3.6E-07 41.0 2.7 27 4-30 18-44 (279)
331 PRK09954 putative kinase; Prov 95.3 0.023 5E-07 40.6 3.5 30 6-35 18-47 (362)
332 PF04645 DUF603: Protein of un 95.3 0.022 4.8E-07 38.2 3.2 35 1-35 14-49 (181)
333 PRK12527 RNA polymerase sigma 95.3 0.033 7.2E-07 35.1 3.9 28 4-31 120-147 (159)
334 PRK05572 sporulation sigma fac 95.3 0.032 6.9E-07 38.2 4.1 29 3-31 216-244 (252)
335 PF04297 UPF0122: Putative hel 95.3 0.033 7.1E-07 34.3 3.6 29 3-31 31-59 (101)
336 TIGR02859 spore_sigH RNA polym 95.2 0.035 7.6E-07 36.0 4.0 28 4-31 164-191 (198)
337 TIGR02479 FliA_WhiG RNA polyme 95.2 0.035 7.5E-07 37.3 4.1 29 3-31 189-217 (224)
338 PRK00430 fis global DNA-bindin 95.2 0.022 4.7E-07 34.5 2.8 26 4-29 67-92 (95)
339 PRK12539 RNA polymerase sigma 95.2 0.035 7.6E-07 36.0 4.0 28 4-31 146-173 (184)
340 PRK10163 DNA-binding transcrip 95.2 0.037 8E-07 38.5 4.3 35 4-38 39-73 (271)
341 PRK08295 RNA polymerase factor 95.2 0.036 7.8E-07 36.3 4.1 28 4-31 169-196 (208)
342 PRK05803 sporulation sigma fac 95.2 0.035 7.5E-07 37.6 4.1 27 4-30 194-220 (233)
343 PRK09651 RNA polymerase sigma 95.2 0.038 8.3E-07 35.5 4.1 28 4-31 134-161 (172)
344 PRK09464 pdhR transcriptional 95.2 0.074 1.6E-06 36.2 5.6 37 7-43 36-72 (254)
345 TIGR02325 C_P_lyase_phnF phosp 95.2 0.028 6E-07 37.8 3.5 34 7-40 34-67 (238)
346 PRK12545 RNA polymerase sigma 95.2 0.036 7.8E-07 36.7 3.9 27 4-30 154-180 (201)
347 TIGR02984 Sig-70_plancto1 RNA 95.1 0.039 8.4E-07 35.4 4.0 28 4-31 155-182 (189)
348 PRK12538 RNA polymerase sigma 95.1 0.037 8E-07 37.8 4.0 28 4-31 186-213 (233)
349 PRK09648 RNA polymerase sigma 95.1 0.041 8.9E-07 35.7 4.1 28 4-31 154-181 (189)
350 PRK12544 RNA polymerase sigma 95.1 0.039 8.4E-07 36.9 4.0 28 4-31 163-190 (206)
351 PRK12515 RNA polymerase sigma 95.1 0.042 9E-07 35.7 4.0 28 4-31 146-173 (189)
352 PRK09943 DNA-binding transcrip 95.1 0.023 5E-07 37.3 2.8 25 3-27 18-42 (185)
353 PRK10840 transcriptional regul 95.1 0.03 6.4E-07 36.8 3.4 33 3-35 163-195 (216)
354 TIGR02424 TF_pcaQ pca operon t 95.1 0.023 5E-07 38.9 2.9 33 3-36 16-49 (300)
355 TIGR00180 parB_part ParB-like 95.1 0.028 6.2E-07 37.2 3.3 27 4-30 119-145 (187)
356 PRK12546 RNA polymerase sigma 95.1 0.042 9.2E-07 36.2 4.0 30 3-32 127-156 (188)
357 PRK11753 DNA-binding transcrip 95.1 0.034 7.3E-07 36.3 3.5 32 6-37 169-200 (211)
358 PRK13348 chromosome replicatio 95.0 0.024 5.3E-07 38.7 2.9 54 3-61 15-69 (294)
359 PRK15369 two component system 95.0 0.038 8.2E-07 34.5 3.6 35 2-36 161-195 (211)
360 PRK12531 RNA polymerase sigma 95.0 0.042 9.1E-07 36.0 3.9 28 4-31 156-183 (194)
361 PRK13719 conjugal transfer tra 95.0 0.032 6.8E-07 38.6 3.4 35 2-36 155-189 (217)
362 PRK12535 RNA polymerase sigma 95.0 0.043 9.3E-07 36.3 4.0 28 4-31 148-175 (196)
363 PRK11534 DNA-binding transcrip 95.0 0.11 2.3E-06 34.8 5.9 45 6-50 31-75 (224)
364 PRK11151 DNA-binding transcrip 95.0 0.025 5.3E-07 39.0 2.9 33 2-35 13-45 (305)
365 TIGR00498 lexA SOS regulatory 95.0 0.042 9.1E-07 36.3 3.8 34 6-39 26-60 (199)
366 PRK09635 sigI RNA polymerase s 95.0 0.16 3.5E-06 35.8 7.0 66 4-75 133-199 (290)
367 TIGR02885 spore_sigF RNA polym 95.0 0.046 9.9E-07 36.8 4.1 28 4-31 198-225 (231)
368 PRK10339 DNA-binding transcrip 95.0 0.018 4E-07 39.9 2.2 23 6-28 2-24 (327)
369 PRK12684 transcriptional regul 94.9 0.023 5E-07 39.6 2.7 34 3-36 14-48 (313)
370 COG1414 IclR Transcriptional r 94.9 0.051 1.1E-06 37.5 4.3 38 4-41 18-55 (246)
371 PRK11608 pspF phage shock prot 94.9 0.021 4.6E-07 40.8 2.5 27 3-29 297-323 (326)
372 PRK13918 CRP/FNR family transc 94.9 0.039 8.4E-07 35.8 3.5 31 6-36 150-180 (202)
373 COG2345 Predicted transcriptio 94.9 0.054 1.2E-06 37.4 4.4 43 3-45 23-67 (218)
374 PRK15090 DNA-binding transcrip 94.9 0.052 1.1E-06 37.3 4.3 35 4-38 27-61 (257)
375 PF07022 Phage_CI_repr: Bacter 94.9 0.012 2.5E-07 33.0 0.9 22 7-28 14-36 (66)
376 PRK03601 transcriptional regul 94.9 0.031 6.8E-07 38.2 3.1 32 3-35 14-46 (275)
377 PRK11922 RNA polymerase sigma 94.9 0.048 1E-06 36.9 4.0 27 4-30 164-190 (231)
378 PRK11569 transcriptional repre 94.9 0.054 1.2E-06 37.7 4.3 35 4-38 42-76 (274)
379 PRK10430 DNA-binding transcrip 94.8 0.043 9.2E-07 36.8 3.7 33 3-35 176-208 (239)
380 PRK11482 putative DNA-binding 94.8 0.031 6.8E-07 39.1 3.1 46 3-51 42-88 (317)
381 smart00497 IENR1 Intron encode 94.8 0.042 9.1E-07 28.8 2.9 23 6-28 18-40 (53)
382 TIGR03418 chol_sulf_TF putativ 94.8 0.033 7.2E-07 37.9 3.1 33 2-35 13-45 (291)
383 PF07453 NUMOD1: NUMOD1 domain 94.8 0.029 6.3E-07 27.9 2.1 20 6-25 17-36 (37)
384 PRK09636 RNA polymerase sigma 94.8 0.2 4.4E-06 34.9 7.1 29 4-32 130-158 (293)
385 PRK10225 DNA-binding transcrip 94.8 0.04 8.7E-07 37.6 3.5 37 7-43 35-71 (257)
386 PRK11161 fumarate/nitrate redu 94.8 0.041 8.8E-07 36.7 3.4 33 6-38 185-217 (235)
387 TIGR02846 spore_sigmaK RNA pol 94.8 0.055 1.2E-06 36.5 4.1 28 4-31 193-220 (227)
388 PRK15431 ferrous iron transpor 94.8 0.04 8.8E-07 32.5 2.9 37 2-38 12-49 (78)
389 PRK07408 RNA polymerase sigma 94.7 0.055 1.2E-06 37.3 4.1 28 4-31 218-245 (256)
390 PRK11233 nitrogen assimilation 94.7 0.031 6.8E-07 38.6 2.9 30 3-33 14-43 (305)
391 PRK12683 transcriptional regul 94.7 0.032 7E-07 38.8 2.9 31 3-33 14-44 (309)
392 cd07153 Fur_like Ferric uptake 94.7 0.067 1.4E-06 32.3 4.0 38 4-41 15-57 (116)
393 COG1349 GlpR Transcriptional r 94.7 0.024 5.1E-07 39.4 2.2 39 3-42 16-55 (253)
394 PF14502 HTH_41: Helix-turn-he 94.7 0.062 1.3E-06 28.9 3.3 36 6-41 7-42 (48)
395 PRK10100 DNA-binding transcrip 94.7 0.047 1E-06 37.0 3.6 34 3-36 168-201 (216)
396 TIGR02018 his_ut_repres histid 94.7 0.044 9.5E-07 36.9 3.4 34 7-40 27-60 (230)
397 PRK04984 fatty acid metabolism 94.7 0.05 1.1E-06 36.7 3.7 36 7-42 33-68 (239)
398 COG2964 Uncharacterized protei 94.7 0.036 7.7E-07 38.4 2.9 25 9-33 195-219 (220)
399 PRK06424 transcription factor; 94.7 0.037 7.9E-07 35.9 2.8 25 3-27 95-119 (144)
400 PRK09391 fixK transcriptional 94.7 0.048 1E-06 36.7 3.5 32 6-37 180-211 (230)
401 TIGR02404 trehalos_R_Bsub treh 94.6 0.048 1E-06 36.7 3.5 34 7-40 26-59 (233)
402 PRK09791 putative DNA-binding 94.6 0.037 8E-07 38.0 3.0 36 2-38 17-53 (302)
403 TIGR02941 Sigma_B RNA polymera 94.6 0.063 1.4E-06 36.7 4.1 29 3-31 219-247 (255)
404 PRK10216 DNA-binding transcrip 94.6 0.038 8.1E-07 38.5 3.0 32 3-35 21-53 (319)
405 PRK09990 DNA-binding transcrip 94.6 0.072 1.6E-06 36.2 4.4 38 7-44 33-70 (251)
406 COG2197 CitB Response regulato 94.6 0.051 1.1E-06 36.6 3.5 36 2-37 160-195 (211)
407 COG1802 GntR Transcriptional r 94.6 0.14 3E-06 34.5 5.6 50 6-55 40-89 (230)
408 PRK13698 plasmid-partitioning 94.5 0.054 1.2E-06 39.4 3.8 60 3-65 174-233 (323)
409 PHA02517 putative transposase 94.5 0.094 2E-06 36.1 4.9 55 15-76 1-56 (277)
410 PRK14999 histidine utilization 94.5 0.051 1.1E-06 36.9 3.5 33 7-39 38-70 (241)
411 PRK11475 DNA-binding transcrip 94.5 0.05 1.1E-06 36.7 3.4 34 2-35 146-179 (207)
412 PRK08215 sporulation sigma fac 94.5 0.068 1.5E-06 36.7 4.1 27 4-30 224-250 (258)
413 PRK06474 hypothetical protein; 94.5 0.051 1.1E-06 36.0 3.3 33 6-38 27-60 (178)
414 TIGR02812 fadR_gamma fatty aci 94.5 0.17 3.7E-06 34.0 5.9 38 6-43 30-68 (235)
415 CHL00180 rbcR LysR transcripti 94.5 0.037 8E-07 38.2 2.7 32 3-35 18-49 (305)
416 PRK12681 cysB transcriptional 94.5 0.13 2.8E-06 36.2 5.5 33 3-35 14-46 (324)
417 TIGR02394 rpoS_proteo RNA poly 94.5 0.066 1.4E-06 37.4 4.0 29 3-31 240-268 (285)
418 PRK09643 RNA polymerase sigma 94.4 0.077 1.7E-06 34.8 4.0 28 4-31 149-176 (192)
419 PF02042 RWP-RK: RWP-RK domain 94.4 0.07 1.5E-06 29.1 3.2 24 5-28 15-38 (52)
420 TIGR02392 rpoH_proteo alternat 94.4 0.054 1.2E-06 37.6 3.4 27 4-30 235-261 (270)
421 PRK03837 transcriptional regul 94.4 0.067 1.4E-06 36.0 3.8 37 7-43 39-75 (241)
422 PRK12680 transcriptional regul 94.4 0.044 9.5E-07 38.7 3.0 33 3-35 14-46 (327)
423 PRK10421 DNA-binding transcrip 94.4 0.06 1.3E-06 36.7 3.6 37 7-43 28-64 (253)
424 PRK10079 phosphonate metabolis 94.4 0.057 1.2E-06 36.7 3.4 34 7-40 37-70 (241)
425 PRK11361 acetoacetate metaboli 94.3 0.041 9E-07 40.1 2.8 27 3-29 428-454 (457)
426 PRK10360 DNA-binding transcrip 94.3 0.065 1.4E-06 33.8 3.4 31 3-33 150-180 (196)
427 PRK09801 transcriptional activ 94.3 0.053 1.1E-06 37.8 3.2 32 3-35 19-50 (310)
428 PRK11523 DNA-binding transcrip 94.3 0.066 1.4E-06 36.5 3.6 37 7-43 34-70 (253)
429 PRK10403 transcriptional regul 94.2 0.061 1.3E-06 33.9 3.2 32 3-34 166-197 (215)
430 PRK10094 DNA-binding transcrip 94.2 0.052 1.1E-06 37.8 3.1 30 3-33 15-44 (308)
431 PRK10341 DNA-binding transcrip 94.2 0.051 1.1E-06 37.7 3.1 29 7-35 23-51 (312)
432 PRK15481 transcriptional regul 94.2 0.068 1.5E-06 38.9 3.8 36 7-42 31-66 (431)
433 TIGR02787 codY_Gpos GTP-sensin 94.2 0.096 2.1E-06 36.9 4.3 36 6-41 199-234 (251)
434 PRK12679 cbl transcriptional r 94.2 0.048 1.1E-06 38.0 2.9 34 2-35 13-47 (316)
435 TIGR03541 reg_near_HchA LuxR f 94.2 0.064 1.4E-06 36.5 3.4 32 2-33 183-214 (232)
436 PRK10434 srlR DNA-bindng trans 94.2 0.04 8.7E-07 38.2 2.4 39 3-42 16-55 (256)
437 PRK07122 RNA polymerase sigma 94.2 0.089 1.9E-06 36.6 4.1 29 3-31 229-257 (264)
438 PRK14997 LysR family transcrip 94.2 0.058 1.3E-06 36.9 3.2 46 3-51 15-61 (301)
439 PRK05911 RNA polymerase sigma 94.1 0.09 2E-06 36.3 4.1 28 4-31 220-247 (257)
440 PF05732 RepL: Firmicute plasm 94.1 0.07 1.5E-06 35.2 3.3 36 6-41 76-111 (165)
441 PF00440 TetR_N: Bacterial reg 94.1 0.087 1.9E-06 27.3 3.1 23 4-26 15-37 (47)
442 PRK10837 putative DNA-binding 94.1 0.051 1.1E-06 36.8 2.7 30 3-33 16-45 (290)
443 PRK10651 transcriptional regul 94.1 0.087 1.9E-06 33.3 3.6 33 3-35 168-200 (216)
444 PF03428 RP-C: Replication pro 94.0 0.12 2.6E-06 34.6 4.3 40 6-45 71-111 (177)
445 TIGR03020 EpsA transcriptional 94.0 0.062 1.3E-06 37.5 3.1 34 3-36 203-236 (247)
446 PRK11557 putative DNA-binding 94.0 0.063 1.4E-06 37.0 3.1 25 5-29 30-54 (278)
447 PRK07670 RNA polymerase sigma 94.0 0.1 2.2E-06 35.7 4.1 29 3-31 215-243 (251)
448 COG1725 Predicted transcriptio 93.9 0.086 1.9E-06 33.6 3.4 34 6-39 36-69 (125)
449 PRK09191 two-component respons 93.9 0.1 2.2E-06 34.8 3.9 30 4-33 103-132 (261)
450 COG2186 FadR Transcriptional r 93.9 0.093 2E-06 36.1 3.7 36 7-42 36-71 (241)
451 TIGR00270 conserved hypothetic 93.9 0.068 1.5E-06 34.9 2.9 30 3-37 80-109 (154)
452 PRK15482 transcriptional regul 93.8 0.074 1.6E-06 36.9 3.2 25 5-29 34-58 (285)
453 PRK06288 RNA polymerase sigma 93.8 0.11 2.5E-06 35.9 4.1 28 3-30 226-253 (268)
454 PRK10402 DNA-binding transcrip 93.8 0.08 1.7E-06 35.4 3.2 33 6-38 170-202 (226)
455 PRK09764 DNA-binding transcrip 93.8 0.095 2.1E-06 35.6 3.6 34 7-40 31-64 (240)
456 COG1339 Transcriptional regula 93.7 0.13 2.9E-06 35.3 4.2 34 5-38 19-52 (214)
457 PRK10082 cell density-dependen 93.7 0.083 1.8E-06 36.4 3.3 46 3-51 24-70 (303)
458 PF04552 Sigma54_DBD: Sigma-54 93.7 0.078 1.7E-06 34.9 3.0 71 6-76 50-132 (160)
459 PRK12427 flagellar biosynthesi 93.7 0.12 2.6E-06 35.2 4.0 29 3-31 197-225 (231)
460 PRK11402 DNA-binding transcrip 93.7 0.1 2.2E-06 35.4 3.5 33 7-39 35-67 (241)
461 TIGR02974 phageshock_pspF psp 93.6 0.052 1.1E-06 39.0 2.2 27 3-29 303-329 (329)
462 PRK09775 putative DNA-binding 93.6 0.087 1.9E-06 39.6 3.4 38 3-42 11-48 (442)
463 PRK09508 leuO leucine transcri 93.6 0.082 1.8E-06 36.7 3.1 32 3-35 35-67 (314)
464 PF13022 HTH_Tnp_1_2: Helix-tu 93.6 0.091 2E-06 34.2 3.0 25 6-30 35-59 (142)
465 COG1191 FliA DNA-directed RNA 93.6 0.084 1.8E-06 37.0 3.1 28 3-30 210-237 (247)
466 PHA02943 hypothetical protein; 93.6 0.2 4.4E-06 33.2 4.7 42 3-44 21-63 (165)
467 PRK10632 transcriptional regul 93.5 0.09 2E-06 36.5 3.2 28 6-33 17-44 (309)
468 PRK09935 transcriptional regul 93.5 0.15 3.3E-06 32.2 4.0 32 3-34 162-193 (210)
469 PRK10086 DNA-binding transcrip 93.5 0.088 1.9E-06 36.6 3.1 26 7-32 30-55 (311)
470 PRK04140 hypothetical protein; 93.5 0.077 1.7E-06 38.4 2.8 25 3-27 137-161 (317)
471 PRK10820 DNA-binding transcrip 93.5 0.064 1.4E-06 40.7 2.5 24 7-30 488-511 (520)
472 COG1609 PurR Transcriptional r 93.4 0.074 1.6E-06 37.9 2.7 41 7-63 2-42 (333)
473 PRK09802 DNA-binding transcrip 93.4 0.093 2E-06 36.7 3.1 36 6-42 32-67 (269)
474 TIGR02850 spore_sigG RNA polym 93.4 0.14 3.1E-06 35.1 4.0 27 4-30 221-247 (254)
475 TIGR02915 PEP_resp_reg putativ 93.4 0.071 1.5E-06 38.9 2.6 27 3-29 416-442 (445)
476 COG1737 RpiR Transcriptional r 93.4 0.067 1.5E-06 37.5 2.4 25 6-30 37-61 (281)
477 PRK11886 bifunctional biotin-- 93.4 0.14 3E-06 36.4 4.0 31 5-35 18-48 (319)
478 PF00165 HTH_AraC: Bacterial r 93.4 0.2 4.2E-06 25.3 3.6 27 3-29 6-32 (42)
479 PRK11302 DNA-binding transcrip 93.3 0.097 2.1E-06 36.0 3.1 25 5-29 34-58 (284)
480 PRK11062 nhaR transcriptional 93.3 0.099 2.1E-06 36.0 3.1 32 3-35 17-48 (296)
481 PF12964 DUF3853: Protein of u 93.3 0.064 1.4E-06 32.8 1.9 27 8-38 48-74 (96)
482 COG1710 Uncharacterized protei 93.3 0.088 1.9E-06 33.7 2.5 31 1-31 105-135 (139)
483 PRK11074 putative DNA-binding 93.3 0.1 2.2E-06 35.9 3.1 36 2-38 14-50 (300)
484 PRK07500 rpoH2 RNA polymerase 93.2 0.16 3.6E-06 35.8 4.1 29 3-31 243-271 (289)
485 PRK15092 DNA-binding transcrip 93.2 0.11 2.3E-06 36.5 3.1 43 7-51 27-70 (310)
486 TIGR02393 RpoD_Cterm RNA polym 93.2 0.17 3.6E-06 34.4 4.0 29 3-31 194-222 (238)
487 PRK06596 RNA polymerase factor 93.1 0.17 3.6E-06 35.6 4.0 27 4-30 247-273 (284)
488 PRK05657 RNA polymerase sigma 93.1 0.17 3.6E-06 36.4 4.1 29 3-31 280-308 (325)
489 PRK13870 transcriptional regul 93.0 0.18 3.8E-06 34.6 4.0 34 3-36 186-219 (234)
490 PRK03635 chromosome replicatio 93.0 0.14 3.1E-06 35.1 3.6 55 3-62 15-70 (294)
491 PRK15424 propionate catabolism 93.0 0.087 1.9E-06 40.5 2.7 28 3-30 508-535 (538)
492 PF05269 Phage_CII: Bacterioph 93.0 0.12 2.6E-06 31.3 2.7 24 7-30 25-48 (91)
493 TIGR03298 argP transcriptional 92.9 0.12 2.6E-06 35.2 3.1 55 3-62 14-69 (292)
494 PF08222 HTH_CodY: CodY helix- 92.9 0.2 4.3E-06 28.1 3.3 36 6-41 5-40 (61)
495 PF05043 Mga: Mga helix-turn-h 92.8 0.08 1.7E-06 30.6 1.8 29 3-31 28-56 (87)
496 COG2188 PhnF Transcriptional r 92.8 0.15 3.3E-06 34.8 3.4 33 7-39 33-65 (236)
497 PRK10188 DNA-binding transcrip 92.8 0.13 2.9E-06 35.3 3.1 35 2-36 191-225 (240)
498 PRK09986 DNA-binding transcrip 92.8 0.095 2.1E-06 35.6 2.4 30 3-33 20-49 (294)
499 PRK09392 ftrB transcriptional 92.8 0.17 3.6E-06 33.8 3.5 54 6-66 174-227 (236)
500 PRK09863 putative frv operon r 92.7 0.59 1.3E-05 35.7 6.8 72 3-76 15-103 (584)
No 1
>PF00292 PAX: 'Paired box' domain; InterPro: IPR001523 The paired box is a conserved 124 amino acid N-terminal domain of unknown function that usually, but not always, precedes a homeobox domain (see IPR001356 from INTERPRO) [, ]. Paired box genes are expressed in alternate segments of the developing fruit fly, the observed grouping of segments into pairs depending on the position of the segment in the segmental array, and not on the identity of the segment as in the case of homeotic genes. This implies that the genes affect different processes from those altered by homeotic genes.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 6PAX_A 1K78_E 1MDM_A 2K27_A 1PDN_C.
Probab=99.95 E-value=8.4e-28 Score=152.25 Aligned_cols=76 Identities=78% Similarity=1.323 Sum_probs=57.9
Q ss_pred CccCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHhCCCCcHHHHHHHhh
Q psy15513 1 MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGENPAMFSWEIRDRLV 76 (77)
Q Consensus 1 l~~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~pd~tl~El~~~L~ 76 (77)
|++.|+++|+||++|.||++||+||++||++||++.|++.||.+|++.+|+++.+|.++..+||.+|+|||+++|+
T Consensus 29 la~~G~rp~~Isr~l~Vs~gcVsKIl~Ry~eTGsi~Pg~iGGskprv~tp~v~~~I~~~k~enP~ifawEiR~~L~ 104 (125)
T PF00292_consen 29 LAKEGVRPCDISRQLRVSHGCVSKILSRYRETGSIRPGPIGGSKPRVATPEVVEKIEQYKRENPTIFAWEIRDRLI 104 (125)
T ss_dssp HHHTT--HHHHHHHHT--HHHHHHHHHHHHHHS-SS----S----SSS-HCHHHHHHHHHHH-TTS-HHHHHHHHH
T ss_pred HhhhcCCHHHHHHHHccchhHHHHHHHHHHHhcccCcccccCCCCCCCChHHHHHHHHHHhcCCCcchHHHHHHHH
Confidence 5789999999999999999999999999999999999999999999999999999999999999999999999985
No 2
>cd00131 PAX Paired Box domain
Probab=99.93 E-value=3.8e-26 Score=144.91 Aligned_cols=76 Identities=79% Similarity=1.327 Sum_probs=70.9
Q ss_pred CccCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHhCCCCcHHHHHHHhh
Q psy15513 1 MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGENPAMFSWEIRDRLV 76 (77)
Q Consensus 1 l~~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~pd~tl~El~~~L~ 76 (77)
|+++|+|+++||++|+||.+||++|+++|++||+++|++.||++|+..++++.++|..++++|||+|++||+++|.
T Consensus 29 ~~~~G~s~~~iA~~~~Vs~~tV~r~i~r~~e~G~v~pk~~gg~rpr~~~~~~~~~i~~~v~~~p~~Tl~El~~~L~ 104 (128)
T cd00131 29 LAQSGIRPCDISRQLRVSHGCVSKILNRYYETGSIRPGAIGGSKPRVATPEVVKKIEIYKQENPGMFAWEIRDRLL 104 (128)
T ss_pred HHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCCCCCCCCCCcCCHHHHHHHHHHHHHCCCCCHHHHHHHHH
Confidence 3578999999999999999999999999999999999999987788888888899999999999999999999874
No 3
>smart00351 PAX Paired Box domain.
Probab=99.91 E-value=1.8e-24 Score=136.56 Aligned_cols=75 Identities=75% Similarity=1.263 Sum_probs=70.9
Q ss_pred ccCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHhCCCCcHHHHHHHhh
Q psy15513 2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGENPAMFSWEIRDRLV 76 (77)
Q Consensus 2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~pd~tl~El~~~L~ 76 (77)
+++|.|.++||++||||.+||++|+++|+++|+++|+++||++|+..++++.++|.+++++|||+|++||++.|.
T Consensus 30 ~~~G~s~~~iA~~~gvs~~tV~kwi~r~~~~G~~~pk~~gg~rp~~~~~~~~~~I~~~~~~~p~~t~~el~~~L~ 104 (125)
T smart00351 30 AQNGVRPCDISRQLCVSHGCVSKILGRYYETGSIRPGAIGGSKPKVATPKVVKKIADYKQENPGIFAWEIRDRLL 104 (125)
T ss_pred HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCcCCCCCCCCccCHHHHHHHHHHHHHCCCCCHHHHHHHHH
Confidence 468999999999999999999999999999999999999988888888888999999999999999999999884
No 4
>KOG3517|consensus
Probab=99.85 E-value=2.3e-22 Score=139.96 Aligned_cols=76 Identities=68% Similarity=1.176 Sum_probs=74.0
Q ss_pred CccCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHhCCCCcHHHHHHHhh
Q psy15513 1 MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGENPAMFSWEIRDRLV 76 (77)
Q Consensus 1 l~~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~pd~tl~El~~~L~ 76 (77)
|++.|.++|||+++|.||++||+|++.||.|||++.|...||.+|++.||.++..|+++.+..|.||.|||+|+|+
T Consensus 32 LarlGiRPCDISRQLrvSHGCVSKILaRy~EtGsIlPGaIGGSkPRVTTP~VV~~IR~~Kq~DPGIFAWEIRDRLl 107 (334)
T KOG3517|consen 32 LARLGIRPCDISRQLRVSHGCVSKILARYNETGSILPGAIGGSKPRVTTPKVVKYIRSLKQRDPGIFAWEIRDRLL 107 (334)
T ss_pred HHHcCCCccchhhhhhhccchHHHHHHHhccCCcccccccCCCCCccCChhHHHHHHHhhccCCceeeehhhhhhh
Confidence 5778999999999999999999999999999999999999999999999999999999999999999999999986
No 5
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=99.76 E-value=2.8e-18 Score=110.45 Aligned_cols=72 Identities=22% Similarity=0.207 Sum_probs=65.8
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHhCCCCcHHHHHHHhh
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGENPAMFSWEIRDRLV 76 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~pd~tl~El~~~L~ 76 (77)
.|||+++||++||||.|||++|++||+++|...|.+.++++|+.+++++.+.|++.+++.. .|+.+++..|.
T Consensus 20 ~G~S~re~Ak~~gvs~sTvy~wv~r~~e~G~~l~~~~~~GrP~kl~~~q~~~l~e~~~~k~-wTl~~~~~~l~ 91 (138)
T COG3415 20 EGLSCREAAKRFGVSISTVYRWVRRYRETGLDLPPKPRKGRPRKLSEEQLEILLERLREKD-WTLKELVEELG 91 (138)
T ss_pred cCccHHHHHHHhCccHHHHHHHHHHhccccccccCccCCCCCcccCHHHHHHHHHHHhccc-chHHHHHHHHh
Confidence 7999999999999999999999999999999988888889999999998888888887765 99999998763
No 6
>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=99.72 E-value=1.4e-17 Score=104.22 Aligned_cols=67 Identities=24% Similarity=0.303 Sum_probs=58.7
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHhCCCCcHHHHHHHhh
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGENPAMFSWEIRDRLV 76 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~pd~tl~El~~~L~ 76 (77)
+.|.|+++||++|+||.+||++|++ ..++|++.|++.|+. .. +.+.|.++|++|||+|+.||++.|-
T Consensus 16 ~~g~s~~eaa~~F~VS~~Tv~~W~k-~~~~G~~~~k~r~~~----Ki--d~~~L~~~v~~~pd~tl~Ela~~l~ 82 (119)
T PF01710_consen 16 EKGKSIREAAKRFGVSRNTVYRWLK-RKETGDLEPKPRGRK----KI--DRDELKALVEENPDATLRELAERLG 82 (119)
T ss_pred HccchHHHHHHHhCcHHHHHHHHHH-hcccccccccccccc----cc--cHHHHHHHHHHCCCcCHHHHHHHcC
Confidence 5789999999999999999999999 788999999987643 22 2567999999999999999998863
No 7
>KOG3862|consensus
Probab=99.70 E-value=1.1e-17 Score=117.30 Aligned_cols=76 Identities=76% Similarity=1.279 Sum_probs=74.0
Q ss_pred CccCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHhCCCCcHHHHHHHhh
Q psy15513 1 MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGENPAMFSWEIRDRLV 76 (77)
Q Consensus 1 l~~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~pd~tl~El~~~L~ 76 (77)
||+.|+.+|+||+++.||++||++++.+|+|||+++|+..||.++++.++.+++.|-.++++||.++.||++++|.
T Consensus 37 La~~gvrpcdisrQl~vShGcvSkil~r~yEtgS~~pg~iggsk~KvAtp~Vvk~i~~~k~~n~~mfaweiR~~l~ 112 (327)
T KOG3862|consen 37 LAQNGVRPCDISRQLRVSHGCVSKILGRYYETGSIRPGVIGGSKPKVATPKVVKKIALYKRQNPTMFAWEIRDRLL 112 (327)
T ss_pred HHHcCCcchhHHHHHhhccCCchhHHHHHHHhcCcccCCCCCCccccccchHHHHHHHHhhcCcchhhhhhhhhhh
Confidence 6889999999999999999999999999999999999999999999999999999999999999999999999985
No 8
>PF13551 HTH_29: Winged helix-turn helix
Probab=99.58 E-value=9.4e-15 Score=88.27 Aligned_cols=75 Identities=31% Similarity=0.446 Sum_probs=62.7
Q ss_pred CccCCCC-HHHHHHHhccCHHHHHHHHHHHHHhc--CCCccccCCCCCCC-CCHHHHHHHHHHHHhCC-----CCcHHHH
Q psy15513 1 MAAAGVR-PCVISRQLRVSHGCVSKILNRYQETG--SIRPGVIGGSKPRV-ATPDVERRIEEYKGENP-----AMFSWEI 71 (77)
Q Consensus 1 l~~~G~s-~~~iA~rf~VS~stv~r~~~r~r~tG--~v~pk~~gg~~~~~-~~~~~~~~i~~~v~~~p-----d~tl~El 71 (77)
|+.+|++ +.+||+.||||..||++|+++|+++| .+.+...++++++. +++++.+.|.+++.++| ..|+.++
T Consensus 7 l~~~g~~~~~~ia~~lg~s~~Tv~r~~~~~~~~G~~~l~~~~~~~g~~~~~l~~~~~~~l~~~~~~~p~~g~~~~t~~~l 86 (112)
T PF13551_consen 7 LLAEGVSTIAEIARRLGISRRTVYRWLKRYREGGIEGLLPRKPRGGRPRKRLSEEQRAQLIELLRENPPEGRSRWTLEEL 86 (112)
T ss_pred HHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHcccHHHHHhccccCCCCCCCCCHHHHHHHHHHHHHCCCCCCCcccHHHH
Confidence 4568996 99999999999999999999999999 66773233345554 78999999999999999 5889998
Q ss_pred HHHh
Q psy15513 72 RDRL 75 (77)
Q Consensus 72 ~~~L 75 (77)
++.|
T Consensus 87 ~~~l 90 (112)
T PF13551_consen 87 AEWL 90 (112)
T ss_pred HHHH
Confidence 8865
No 9
>KOG0849|consensus
Probab=99.31 E-value=1.2e-12 Score=94.68 Aligned_cols=76 Identities=80% Similarity=1.337 Sum_probs=71.7
Q ss_pred CccCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCC-CCCHHHHHHHHHHHHhCCCCcHHHHHHHhh
Q psy15513 1 MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR-VATPDVERRIEEYKGENPAMFSWEIRDRLV 76 (77)
Q Consensus 1 l~~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~-~~~~~~~~~i~~~v~~~pd~tl~El~~~L~ 76 (77)
|+..|+++|.+++.+.||+.||++++.+|.+||++.|...||.+++ +.+++++.+|.++..++|++|.|||++.|+
T Consensus 27 ~a~~~~~~~~~~~~l~vs~~~~~~il~r~~~~~~i~p~~i~~~~~~~~~t~~~~~~i~~~k~~~P~~~~~~ir~~l~ 103 (354)
T KOG0849|consen 27 MAHKGIRPCVISRQLKVSHGCVSKILNRYYRTGSIRPGGIGGSKPRIVATPEVEAKIEQYKRENPAMFAWEIRDQLL 103 (354)
T ss_pred ccccccCcccchhhhhhhhHHHHhhhcccccccccccccccccccCCCCCchhHHHHHHHHhcCCcccchhhhhccc
Confidence 5678999999999999999999999999999999999999998886 888999999999999999999999999874
No 10
>PF13565 HTH_32: Homeodomain-like domain
Probab=99.15 E-value=1.7e-10 Score=66.28 Aligned_cols=54 Identities=31% Similarity=0.457 Sum_probs=45.2
Q ss_pred HHHHHHHHHHHhc-----CCCccccCCCCCCCCCHHHHHHHHHHHHhCCCCcHHHHHHHhh
Q psy15513 21 CVSKILNRYQETG-----SIRPGVIGGSKPRVATPDVERRIEEYKGENPAMFSWEIRDRLV 76 (77)
Q Consensus 21 tv~r~~~r~r~tG-----~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~pd~tl~El~~~L~ 76 (77)
||++|+++|++.| +..+++.+| +|+. ++++.+.|.+++.++|++|+.+|++.|.
T Consensus 1 Tv~rw~~ry~~~G~~gL~~~~~~~~~G-rp~~-~~e~~~~i~~~~~~~p~wt~~~i~~~L~ 59 (77)
T PF13565_consen 1 TVYRWLKRYREEGLEGLKDRKRRPRPG-RPRK-DPEQRERIIALIEEHPRWTPREIAEYLE 59 (77)
T ss_pred CHHHHHHHHHhhCchhhhcccccCCCC-CCCC-cHHHHHHHHHHHHhCCCCCHHHHHHHHH
Confidence 7999999999999 655555554 5555 7877799999999999999999999874
No 11
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=99.10 E-value=2.6e-11 Score=64.82 Aligned_cols=32 Identities=31% Similarity=0.457 Sum_probs=21.4
Q ss_pred ccCCCCHHHHHHHhccCHHHHHHHHHHHHHhc
Q psy15513 2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETG 33 (77)
Q Consensus 2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG 33 (77)
..+|+|.++||+.||||++||++|+++|+++|
T Consensus 14 ~~~G~s~~~ia~~lgvs~~Tv~~w~kr~~~~G 45 (50)
T PF13384_consen 14 LREGWSIREIAKRLGVSRSTVYRWIKRYREEG 45 (50)
T ss_dssp HHHT--HHHHHHHHTS-HHHHHHHHT------
T ss_pred HHCCCCHHHHHHHHCcCHHHHHHHHHHccccc
Confidence 34699999999999999999999999999988
No 12
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=98.95 E-value=4.4e-09 Score=62.91 Aligned_cols=58 Identities=29% Similarity=0.401 Sum_probs=41.6
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCC--CccccCCC-CCCCCCHHHHHHHHHHH
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSI--RPGVIGGS-KPRVATPDVERRIEEYK 60 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v--~pk~~gg~-~~~~~~~~~~~~i~~~v 60 (77)
++|.+..++|+.||||..|++||+.||++.|.. ..+..-+. .|..+.++.+..|.++.
T Consensus 23 ~~g~~~a~aA~~~gVS~~Ta~kW~~Ryra~G~~GL~DRSSRP~~sP~~t~~~~~~~I~~lR 83 (85)
T PF13011_consen 23 EQGWPVAHAAAEFGVSRRTAYKWLARYRAEGEAGLQDRSSRPHRSPRRTPPEVERRIIELR 83 (85)
T ss_pred HcCCcHHHHHHHhCCCHHHHHHHHHHHHHcCcccccccCCCCCCCCccCCHHHHHHHHHHh
Confidence 579999999999999999999999999999865 22222222 23344465566666553
No 13
>PF13518 HTH_28: Helix-turn-helix domain
Probab=98.88 E-value=1.9e-09 Score=57.48 Aligned_cols=32 Identities=28% Similarity=0.449 Sum_probs=30.0
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcC
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGS 34 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~ 34 (77)
.+|.|..++|+.||||.+||++|+++|.+.|.
T Consensus 10 ~~g~s~~~~a~~~gis~~tv~~w~~~y~~~G~ 41 (52)
T PF13518_consen 10 LEGESVREIAREFGISRSTVYRWIKRYREGGI 41 (52)
T ss_pred HcCCCHHHHHHHHCCCHhHHHHHHHHHHhcCH
Confidence 47889999999999999999999999999884
No 14
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=98.68 E-value=1.3e-08 Score=53.68 Aligned_cols=27 Identities=30% Similarity=0.347 Sum_probs=20.5
Q ss_pred ccCCCCHHHHHHHhccCHHHHHHHHHH
Q psy15513 2 AAAGVRPCVISRQLRVSHGCVSKILNR 28 (77)
Q Consensus 2 ~~~G~s~~~iA~rf~VS~stv~r~~~r 28 (77)
.+.|+|.++||+.||+|++||+++++|
T Consensus 17 ~~~G~s~~~IA~~lg~s~sTV~relkR 43 (44)
T PF13936_consen 17 LEQGMSIREIAKRLGRSRSTVSRELKR 43 (44)
T ss_dssp HCS---HHHHHHHTT--HHHHHHHHHH
T ss_pred HHcCCCHHHHHHHHCcCcHHHHHHHhc
Confidence 468999999999999999999999987
No 15
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=98.61 E-value=7e-08 Score=60.33 Aligned_cols=36 Identities=19% Similarity=0.187 Sum_probs=32.2
Q ss_pred ccCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCc
Q psy15513 2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP 37 (77)
Q Consensus 2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~p 37 (77)
.+.|++..++|+.||||.+|+++|+++|++.|....
T Consensus 26 ~~~g~sv~evA~e~gIs~~tl~~W~r~y~~~~~~~~ 61 (121)
T PRK09413 26 FEPGMTVSLVARQHGVAASQLFLWRKQYQEGSLTAV 61 (121)
T ss_pred HcCCCCHHHHHHHHCcCHHHHHHHHHHHhhcccccc
Confidence 457999999999999999999999999998776554
No 16
>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=98.55 E-value=4e-08 Score=51.95 Aligned_cols=27 Identities=33% Similarity=0.444 Sum_probs=21.8
Q ss_pred CccCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513 1 MAAAGVRPCVISRQLRVSHGCVSKILN 27 (77)
Q Consensus 1 l~~~G~s~~~iA~rf~VS~stv~r~~~ 27 (77)
|.++|+|..+||+.||||.+||+|+++
T Consensus 17 l~~~G~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 17 LYAEGMSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp HHHTT--HHHHHHHTTS-HHHHHHHHC
T ss_pred HHHCCCCHHHHHHHHCcCHHHHHHHHh
Confidence 457899999999999999999999975
No 17
>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=98.50 E-value=1.1e-06 Score=49.14 Aligned_cols=64 Identities=16% Similarity=0.127 Sum_probs=43.9
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHH---HHHHHhCCCCcHHHHHHHh
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRI---EEYKGENPAMFSWEIRDRL 75 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i---~~~v~~~pd~tl~El~~~L 75 (77)
+|..++|+.+|||++|+.+|.+++ |-+.|....++. +.-++.+...+ ..+.+ -++++.|+++.|
T Consensus 1 ~s~~eva~~~gvs~~tlr~w~~~~---g~~~~~r~~~~~-r~yt~~~v~~l~~i~~l~~--~g~~l~~i~~~~ 67 (68)
T cd01104 1 YTIGAVARLTGVSPDTLRAWERRY---GLPAPQRTDGGH-RLYSEADVARLRLIRRLTS--EGVRISQAAALA 67 (68)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHhC---CCCCCCcCCCCC-eecCHHHHHHHHHHHHHHH--CCCCHHHHHHHh
Confidence 578999999999999999998764 666654433222 33444444444 34443 589999998765
No 18
>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=98.21 E-value=1.2e-06 Score=48.84 Aligned_cols=33 Identities=21% Similarity=0.194 Sum_probs=29.3
Q ss_pred CccCCCCHHHHHHHhccCHHHHHHHHHHHHHhc
Q psy15513 1 MAAAGVRPCVISRQLRVSHGCVSKILNRYQETG 33 (77)
Q Consensus 1 l~~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG 33 (77)
|+-.|+++.+||+.|||+.+||+.|.+++.-.+
T Consensus 9 LY~~G~~~~eIA~~Lg~~~~TV~~W~~r~~W~~ 41 (58)
T PF06056_consen 9 LYLQGWSIKEIAEELGVPRSTVYSWKDRYKWDE 41 (58)
T ss_pred HHHcCCCHHHHHHHHCCChHHHHHHHHhhCccc
Confidence 456899999999999999999999999987544
No 19
>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=98.15 E-value=2.5e-05 Score=43.86 Aligned_cols=64 Identities=11% Similarity=0.146 Sum_probs=43.6
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHH---HHHHHHhCCCCcHHHHHHHh
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERR---IEEYKGENPAMFSWEIRDRL 75 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~---i~~~v~~~pd~tl~El~~~L 75 (77)
++..++|+.+|||.+|+..|-+.+ |-+.|....++. +.-+..+... |..+.+ .++++.|++..|
T Consensus 1 ~~i~e~A~~~gVs~~tlr~ye~~~---gl~~~~r~~~g~-R~yt~~di~~l~~i~~l~~--~g~~l~~i~~~l 67 (68)
T cd04763 1 YTIGEVALLTGIKPHVLRAWEREF---GLLKPQRSDGGH-RLFNDADIDRILEIKRWID--NGVQVSKVKKLL 67 (68)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHhc---CCCCCCcCCCCC-cccCHHHHHHHHHHHHHHH--cCCCHHHHHHHh
Confidence 478899999999999999884433 777675543333 3344434443 445544 789999998765
No 20
>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=98.14 E-value=6.9e-06 Score=42.26 Aligned_cols=32 Identities=13% Similarity=0.135 Sum_probs=26.3
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccC
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIG 41 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~g 41 (77)
++..++|+.||||.+|+.+|.++ |.+.+.+.+
T Consensus 1 ~s~~e~a~~lgvs~~tl~~~~~~----g~~~~~~~~ 32 (49)
T cd04762 1 LTTKEAAELLGVSPSTLRRWVKE----GKLKAIRTP 32 (49)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHc----CCCCceeCC
Confidence 57899999999999999999886 777554443
No 21
>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=98.07 E-value=1.6e-06 Score=47.44 Aligned_cols=28 Identities=32% Similarity=0.345 Sum_probs=22.7
Q ss_pred ccCCCCHHHHHHHhccCHHHHHHHHHHH
Q psy15513 2 AAAGVRPCVISRQLRVSHGCVSKILNRY 29 (77)
Q Consensus 2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~ 29 (77)
.+.|.|.++||+.|||+.+||+.|++..
T Consensus 19 ~e~g~s~~~ia~~fgv~~sTv~~I~K~k 46 (53)
T PF04218_consen 19 LEEGESKRDIAREFGVSRSTVSTILKNK 46 (53)
T ss_dssp HHCTT-HHHHHHHHT--CCHHHHHHHCH
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHHhH
Confidence 4689999999999999999999999863
No 22
>PF14493 HTH_40: Helix-turn-helix domain
Probab=98.04 E-value=2.7e-05 Score=46.34 Aligned_cols=69 Identities=13% Similarity=0.071 Sum_probs=58.2
Q ss_pred CccCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHhCCCCcHHHHHHHh
Q psy15513 1 MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGENPAMFSWEIRDRL 75 (77)
Q Consensus 1 l~~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~pd~tl~El~~~L 75 (77)
|+++|+|.-+||+.-+++.+||..-+-.+...|..-+-. ....++..+.|.+.++..+...+.++.+.|
T Consensus 9 l~~~G~si~eIA~~R~L~~sTI~~HL~~~~~~g~~~~~~------~~l~~e~~~~I~~~~~~~~~~~lk~i~e~l 77 (91)
T PF14493_consen 9 LFQKGLSIEEIAKIRGLKESTIYGHLAELIESGEPLDIE------ELLSEEEIKQIEDAIEKLGSEKLKPIKEAL 77 (91)
T ss_pred HHHcCCCHHHHHHHcCCCHHHHHHHHHHHHHhCCCCCHH------HhCCHHHHHHHHHHHHHcCcccHHHHHHHC
Confidence 578999999999999999999999999999999833221 346666778899999999988899988876
No 23
>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=97.92 E-value=8.4e-06 Score=46.28 Aligned_cols=28 Identities=14% Similarity=0.287 Sum_probs=25.6
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHH
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQ 30 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r 30 (77)
..|.|..++|+.+||+++|+++|+++|+
T Consensus 21 ~~g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 21 ESGESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp HHHCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred HCCCceEeeecccccccccccHHHHHHh
Confidence 4689999999999999999999999999
No 24
>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=97.88 E-value=0.00015 Score=40.42 Aligned_cols=63 Identities=16% Similarity=0.083 Sum_probs=41.2
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHH---HHHHHHhCCCCcHHHHHHHh
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERR---IEEYKGENPAMFSWEIRDRL 75 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~---i~~~v~~~pd~tl~El~~~L 75 (77)
++..++|+.+|||++|+..|-++..- ..|+..||. +.-++++... |..+.+ -.+++.|+.+.|
T Consensus 1 ~~i~evA~~~gvs~~tlR~~~~~g~l---~~~~~~~g~--R~y~~~~l~~l~~i~~l~~--~g~~l~~i~~~l 66 (67)
T cd04764 1 YTIKEVSEIIGVKPHTLRYYEKEFNL---YIPRTENGR--RYYTDEDIELLKKIKTLLE--KGLSIKEIKEIL 66 (67)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHhcCC---CCCCCCCCc--eeeCHHHHHHHHHHHHHHH--CCCCHHHHHHHh
Confidence 57889999999999999999765331 223333433 3344434443 445554 569999998765
No 25
>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=97.88 E-value=0.00016 Score=43.95 Aligned_cols=67 Identities=10% Similarity=-0.009 Sum_probs=47.6
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHH--hCCCCcHHHHHHHhh
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKG--ENPAMFSWEIRDRLV 76 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~--~~pd~tl~El~~~L~ 76 (77)
++..++|+.+|||.+|+..|-+. .|-+.|...+|+ .+.-++++...|..+.. .+-.+++.++++.|.
T Consensus 1 yti~EvA~~~gVs~~tLR~ye~~---~gli~p~r~~~g-~R~Yt~~di~~l~~I~~llr~~G~~l~~i~~~l~ 69 (99)
T cd04765 1 FSIGEVAEILGLPPHVLRYWETE---FPQLKPVKRAGG-RRYYRPKDVELLLLIKHLLYEKGYTIEGAKQALK 69 (99)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHH---cCCCCCcCCCCC-CeeeCHHHHHHHHHHHHHHHHCCCCHHHHHHHHH
Confidence 57889999999999999988544 355666544333 34455666776666553 466799999988763
No 26
>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=97.85 E-value=0.00015 Score=43.03 Aligned_cols=65 Identities=18% Similarity=0.085 Sum_probs=45.3
Q ss_pred CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHH---HHHHHHhCCCCcHHHHHHHh
Q psy15513 5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERR---IEEYKGENPAMFSWEIRDRL 75 (77)
Q Consensus 5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~---i~~~v~~~pd~tl~El~~~L 75 (77)
++++.++|+.+|||.+|+..| .+.|-+.|....++..+.-++.+... |..+.+ -++++.|+++.+
T Consensus 1 ~~ti~evA~~~gvs~~tLR~y----e~~Gll~p~r~~~~g~R~Ys~~dv~~l~~I~~Lr~--~G~sl~~i~~~l 68 (88)
T cd01105 1 VIGIGEVSKLTGVSPRQLRYW----EEKGLIKSIRSDGGGQRKYSLADVDRLLVIKELLD--EGFTLAAAVEKL 68 (88)
T ss_pred CcCHHHHHHHHCcCHHHHHHH----HHCCCCCCCccCCCCceecCHHHHHHHHHHHHHHH--CCCCHHHHHHHH
Confidence 578999999999999999998 44588887664321223344444443 445543 679999998766
No 27
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=97.84 E-value=9.1e-05 Score=41.29 Aligned_cols=64 Identities=20% Similarity=0.145 Sum_probs=45.2
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHH---HHHHHHhCCCCcHHHHHHHhh
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERR---IEEYKGENPAMFSWEIRDRLV 76 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~---i~~~v~~~pd~tl~El~~~L~ 76 (77)
|+..++|+.+|||.+|+..|.++ |-+.|....++. +.-++++... |..+.+ -.+++.|+++.|.
T Consensus 1 yti~eva~~~gvs~~tlr~y~~~----gll~~~~~~~g~-r~y~~~dv~~l~~i~~l~~--~G~sl~~I~~~l~ 67 (69)
T PF13411_consen 1 YTIKEVAKLLGVSPSTLRYYERE----GLLPPPRDENGY-RYYSEEDVERLREIKELRK--QGMSLEEIKKLLK 67 (69)
T ss_dssp EEHHHHHHHTTTTHHHHHHHHHT----TSSTTBESTTSS-EEE-HHHHHHHHHHHHHHH--TTTHHHHHHHHH-
T ss_pred CcHHHHHHHHCcCHHHHHHHHHh----cCcccccccCce-eeccHHHHHHHHHHHHHHH--CcCCHHHHHHHHc
Confidence 57889999999999999999665 668887743333 4455555554 445544 5799999998764
No 28
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=97.84 E-value=0.00018 Score=40.00 Aligned_cols=63 Identities=17% Similarity=0.106 Sum_probs=43.1
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc-ccCCCCCCCCCHHHHH---HHHHHHHhCCCCcHHHHHHHh
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPG-VIGGSKPRVATPDVER---RIEEYKGENPAMFSWEIRDRL 75 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk-~~gg~~~~~~~~~~~~---~i~~~v~~~pd~tl~El~~~L 75 (77)
++..++|+.+|||.+|+.+|.+ .|-+.|. +..++. +.-+..+.. .|..+.+ -++++.++...|
T Consensus 1 ~s~~eva~~~gvs~~tlr~~~~----~gli~~~~~~~~g~-r~y~~~dl~~l~~i~~lr~--~g~~~~~i~~~l 67 (70)
T smart00422 1 YTIGEVAKLAGVSVRTLRYYER----IGLLPPPIRTEGGY-RLYSDEDLERLRFIKRLKE--LGFSLEEIKELL 67 (70)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCccCCCCC-EecCHHHHHHHHHHHHHHH--cCCCHHHHHHHH
Confidence 5789999999999999999965 7988875 332222 233333343 3445543 568888887654
No 29
>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=97.84 E-value=2.3e-05 Score=43.75 Aligned_cols=38 Identities=29% Similarity=0.316 Sum_probs=32.4
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccC
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIG 41 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~g 41 (77)
..++..+||+.|+||++||+..++++.+.|-|.-.+-+
T Consensus 21 ~~v~~~~iA~~L~vs~~tvt~ml~~L~~~GlV~~~~y~ 58 (60)
T PF01325_consen 21 GPVRTKDIAERLGVSPPTVTEMLKRLAEKGLVEYEPYK 58 (60)
T ss_dssp SSBBHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT
T ss_pred CCccHHHHHHHHCCChHHHHHHHHHHHHCCCEEecCCC
Confidence 34889999999999999999999999999988766543
No 30
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=97.79 E-value=8.5e-05 Score=45.57 Aligned_cols=37 Identities=16% Similarity=0.142 Sum_probs=32.7
Q ss_pred cCCCCHHHHHHHhcc-CHHHHHHHHHHHHHhcCCCccc
Q psy15513 3 AAGVRPCVISRQLRV-SHGCVSKILNRYQETGSIRPGV 39 (77)
Q Consensus 3 ~~G~s~~~iA~rf~V-S~stv~r~~~r~r~tG~v~pk~ 39 (77)
+.|.+..++|+.||| +.++.++|+++|++.+...+..
T Consensus 22 ~~g~sv~~vAr~~gv~~~~~l~~W~~~~~~~~~~~~~~ 59 (116)
T COG2963 22 RGGDTVSEVAREFGIVSATQLYKWRIQLQKGGGLAFSG 59 (116)
T ss_pred hcCccHHHHHHHhCCCChHHHHHHHHHHHHcccccccC
Confidence 468899999999995 9999999999999988776653
No 31
>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=97.78 E-value=0.00019 Score=44.06 Aligned_cols=66 Identities=14% Similarity=0.049 Sum_probs=42.8
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHh-CCCCcHHHHHHHh
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGE-NPAMFSWEIRDRL 75 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~-~pd~tl~El~~~L 75 (77)
|+..++|+.+|||++|+..|-+ .|-+.|....++..+.-++.+...+.....- .-++++.||++.|
T Consensus 1 ~~i~eva~~~gvs~~tlR~ye~----~Gll~p~~~~~~g~R~Y~~~dl~~l~~I~~lr~~G~~l~~I~~~l 67 (108)
T cd04773 1 MTIGELAHLLGVPPSTLRHWEK----EGLLSPDREPETGYRVYDPSDVRDARLIHLLRRGGYLLEQIATVV 67 (108)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCcCCCCCceeeCHHHHHHHHHHHHHHHCCCCHHHHHHHH
Confidence 6889999999999999999844 5988876543222233444445443322221 2358888887655
No 32
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=97.77 E-value=2.9e-05 Score=48.76 Aligned_cols=59 Identities=15% Similarity=0.151 Sum_probs=48.0
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHh
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGE 62 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~ 62 (77)
.+++.+++|..|++|++||++-++-.++.|=|...+.|....-.+.+...+|+..++.+
T Consensus 29 ~~~~v~ela~~l~lsqstvS~HL~~L~~AGLV~~~r~Gr~~~Y~l~~~~~~~~~~~~~~ 87 (117)
T PRK10141 29 GELCVCDLCTALDQSQPKISRHLALLRESGLLLDRKQGKWVHYRLSPHIPAWAAKIIEQ 87 (117)
T ss_pred CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEEEcCEEEEEECchHHHHHHHHHHH
Confidence 35899999999999999999999999999999999888655545566566667665544
No 33
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=97.76 E-value=3.8e-05 Score=40.39 Aligned_cols=30 Identities=23% Similarity=0.259 Sum_probs=27.0
Q ss_pred ccCCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 2 AAAGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
...|+|..+||+.|+||.+||++++++.++
T Consensus 15 ~~~g~s~~eia~~l~is~~tv~~~~~~~~~ 44 (58)
T smart00421 15 LAEGLTNKEIAERLGISEKTVKTHLSNIMR 44 (58)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 347999999999999999999999998764
No 34
>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=97.75 E-value=0.00033 Score=42.36 Aligned_cols=64 Identities=19% Similarity=0.102 Sum_probs=43.8
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHH---HHHHHhCCCCcHHHHHHHh
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRI---EEYKGENPAMFSWEIRDRL 75 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i---~~~v~~~pd~tl~El~~~L 75 (77)
+++.++|+.||||++|+..|-+ .|-+.|...+++..+.-++.+...+ ..+. . -++++.|++.-+
T Consensus 1 ~ti~eva~~~gvs~~tlR~ye~----~Gll~~~~~~~~g~R~y~~~di~~l~~i~~lr-~-~g~~l~~i~~~~ 67 (103)
T cd01106 1 YTVGEVAKLTGVSVRTLHYYDE----IGLLKPSRRTENGYRLYTEEDLERLQQILFLK-E-LGFSLKEIKELL 67 (103)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCccCCCCceeeCHHHHHHHHHHHHHH-H-cCCCHHHHHHHH
Confidence 5789999999999999998865 6888775433223344555555443 3333 3 579999998765
No 35
>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=97.73 E-value=4.2e-05 Score=39.48 Aligned_cols=32 Identities=19% Similarity=0.276 Sum_probs=26.0
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccC
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIG 41 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~g 41 (77)
++..++|+.||||.+|+++|++ .|.+.+-..|
T Consensus 2 lt~~e~a~~lgis~~ti~~~~~----~g~i~~~~~g 33 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTVYRLIH----EGELPAYRVG 33 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHHH----cCCCCeEEeC
Confidence 5789999999999999999985 4777654444
No 36
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=97.72 E-value=4.2e-05 Score=43.25 Aligned_cols=40 Identities=13% Similarity=0.163 Sum_probs=33.2
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCC
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGS 43 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~ 43 (77)
.+++.+|||..||+|..+|.+|+......|.|...|.+.+
T Consensus 14 ~p~~T~eiA~~~gls~~~aR~yL~~Le~eG~V~~~~~~rG 53 (62)
T PF04703_consen 14 GPLKTREIADALGLSIYQARYYLEKLEKEGKVERSPVRRG 53 (62)
T ss_dssp S-EEHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEES-SSS
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCCCC
Confidence 5689999999999999999999999999999987665433
No 37
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=97.71 E-value=3.9e-05 Score=54.96 Aligned_cols=36 Identities=25% Similarity=0.383 Sum_probs=33.7
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG 38 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk 38 (77)
.+|+++.|||++||||+++|+|++++-|++|=|.=.
T Consensus 27 ~~g~tQ~eIA~~lgiSR~~VsRlL~~Ar~~GiV~I~ 62 (318)
T PRK15418 27 HDGLTQSEIGERLGLTRLKVSRLLEKGRQSGIIRVQ 62 (318)
T ss_pred hcCCCHHHHHHHhCCCHHHHHHHHHHHHHcCcEEEE
Confidence 579999999999999999999999999999998655
No 38
>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=97.71 E-value=0.00027 Score=42.68 Aligned_cols=65 Identities=11% Similarity=0.082 Sum_probs=45.5
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHH--hCCCCcHHHHHHHh
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKG--ENPAMFSWEIRDRL 75 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~--~~pd~tl~El~~~L 75 (77)
++..++|+.+|||.+|+..|. +.|-+.|....+ ..+.-++.+.+.+..... .+-++++.++..-|
T Consensus 2 ~~i~eva~~~gVs~~tLR~ye----~~Gli~p~r~~~-g~R~Ys~~dv~~l~~I~~L~~~~G~~l~~i~~~l 68 (98)
T cd01279 2 YPISVAAELLGIHPQTLRVYD----RLGLVSPARTNG-GGRRYSNNDLELLRQVQRLSQDEGFNLAGIKRII 68 (98)
T ss_pred cCHHHHHHHHCcCHHHHHHHH----HCCCCCCCcCCC-CCeeECHHHHHHHHHHHHHHHHCCCCHHHHHHHH
Confidence 578999999999999999994 468888843322 223455556666655443 33589999998765
No 39
>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=97.70 E-value=0.00018 Score=45.38 Aligned_cols=64 Identities=16% Similarity=0.169 Sum_probs=45.9
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHH--HhCCCCcHHHHHHHh
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYK--GENPAMFSWEIRDRL 75 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v--~~~pd~tl~El~~~L 75 (77)
++..++|+.+|||++|+..|-+. |-+.|...+|. +.-++++...|..+. ..+.++++.||++-|
T Consensus 2 ysI~eVA~~~GVs~~TLR~wE~~----GLl~p~r~~G~--R~Ys~~dv~rL~~I~~L~~e~G~~l~eI~~~L 67 (120)
T cd04767 2 YPIGVVAELLNIHPETLRIWERH----GLIKPARRNGQ--RLYSNNDLKRLRFIKKLINEKGLNIAGVKQIL 67 (120)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC----CCCCCcCCCCc--EEECHHHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence 68899999999999999988764 98988765443 334444455443222 234689999999876
No 40
>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=97.67 E-value=0.00017 Score=37.48 Aligned_cols=44 Identities=14% Similarity=0.055 Sum_probs=30.5
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHH
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVER 54 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~ 54 (77)
|+..++|+.||||.+|+.+|.++ |.+.|...+| ..+.-++++..
T Consensus 1 ~~~~e~a~~~gv~~~tlr~~~~~----g~l~~~~~~~-~~~~y~~~~v~ 44 (49)
T cd04761 1 YTIGELAKLTGVSPSTLRYYERI----GLLSPARTEG-GYRLYSDADLE 44 (49)
T ss_pred CcHHHHHHHHCcCHHHHHHHHHC----CCCCCCcCCC-CCEEeCHHHHH
Confidence 57899999999999999999644 7776654433 22334444443
No 41
>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=97.67 E-value=0.00033 Score=42.26 Aligned_cols=65 Identities=15% Similarity=0.166 Sum_probs=44.2
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHH--hCCCCcHHHHHHHh
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKG--ENPAMFSWEIRDRL 75 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~--~~pd~tl~El~~~L 75 (77)
|++.++|+++|||.+|+..|-+ .|-+.|....++ .+.-++.+...+..... +.-++++.|++.-|
T Consensus 1 ~~I~e~a~~~gvs~~tLR~ye~----~Gll~p~r~~~g-~R~Y~~~dv~~l~~I~~L~~~~G~~l~ei~~~l 67 (96)
T cd04774 1 YKVDEVAKRLGLTKRTLKYYEE----IGLVSPERSEGR-YRLYSEEDLKRLERILRLREVLGFSLQEVTHFL 67 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCcCCCC-CEEECHHHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence 5789999999999999999954 498887654332 33444445554443222 22479999998655
No 42
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=97.66 E-value=7.6e-05 Score=39.88 Aligned_cols=33 Identities=24% Similarity=0.295 Sum_probs=30.5
Q ss_pred CHHHHHHHhccCHHHHHHHHHHHHHhcCCCccc
Q psy15513 7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGV 39 (77)
Q Consensus 7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~ 39 (77)
|..++|++|+||.+||.+.+++..+.|-+...+
T Consensus 22 s~~~la~~~~vs~~tv~~~l~~L~~~g~i~~~~ 54 (60)
T smart00345 22 SERELAAQLGVSRTTVREALSRLEAEGLVQRRP 54 (60)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence 899999999999999999999999999887554
No 43
>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=97.65 E-value=0.00012 Score=46.38 Aligned_cols=55 Identities=16% Similarity=0.199 Sum_probs=42.5
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCC-CCCHHHHHHHHHHH
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR-VATPDVERRIEEYK 60 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~-~~~~~~~~~i~~~v 60 (77)
|.+.++|..+|+|.-||+||++..-=+-+..|+..||.-+- ..++.+.+||...-
T Consensus 1 MT~eELA~~tG~srQTINrWvRkegW~T~p~pGVkGGrARLIhId~~V~efi~s~~ 56 (122)
T PF07037_consen 1 MTPEELAELTGYSRQTINRWVRKEGWKTEPKPGVKGGRARLIHIDEQVREFIRSIP 56 (122)
T ss_pred CCHHHHHHHhCccHHHHHHHHHhcCceeccCCccccccceeeeecHHHHHHHHhhH
Confidence 68899999999999999999998876666777777775443 45566677776544
No 44
>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=97.64 E-value=7.7e-05 Score=40.62 Aligned_cols=40 Identities=20% Similarity=0.373 Sum_probs=33.8
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCC
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKP 45 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~ 45 (77)
+++.+||+.+++|+++|++.++++.+.|-|.-.+..++++
T Consensus 22 ~t~~~la~~l~~~~~~vs~~v~~L~~~Glv~r~~~~~D~R 61 (62)
T PF12802_consen 22 LTQSELAERLGISKSTVSRIVKRLEKKGLVERERDPGDRR 61 (62)
T ss_dssp EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE-SSSTT
T ss_pred cCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeCCCCCCC
Confidence 8999999999999999999999999999997766555543
No 45
>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=97.63 E-value=3.5e-05 Score=36.36 Aligned_cols=25 Identities=36% Similarity=0.417 Sum_probs=22.5
Q ss_pred ccCCCCHHHHHHHhccCHHHHHHHH
Q psy15513 2 AAAGVRPCVISRQLRVSHGCVSKIL 26 (77)
Q Consensus 2 ~~~G~s~~~iA~rf~VS~stv~r~~ 26 (77)
+..|.+..++|+.|+||.+||++|+
T Consensus 18 ~~~~~s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 18 LAAGESVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHhC
Confidence 3578899999999999999999985
No 46
>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=97.61 E-value=0.00013 Score=36.27 Aligned_cols=29 Identities=24% Similarity=0.350 Sum_probs=24.7
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcC
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGS 34 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~ 34 (77)
|+..|||..+|.|.-||+|.++++++.|-
T Consensus 3 mtr~diA~~lG~t~ETVSR~l~~l~~~gl 31 (32)
T PF00325_consen 3 MTRQDIADYLGLTRETVSRILKKLERQGL 31 (32)
T ss_dssp --HHHHHHHHTS-HHHHHHHHHHHHHTTS
T ss_pred cCHHHHHHHhCCcHHHHHHHHHHHHHcCC
Confidence 68899999999999999999999999884
No 47
>TIGR01321 TrpR trp operon repressor, proteobacterial. This model represents TrpR, the repressor of the trp operon. It is found so far only in the gamma subdivision of the proteobacteria and in Chlamydia trachomatis. All members belong to species capable of tryptophan biosynthesis.
Probab=97.57 E-value=5.1e-05 Score=46.19 Aligned_cols=26 Identities=19% Similarity=0.198 Sum_probs=23.5
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHH
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNR 28 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r 28 (77)
+.|+|.++||+.+|||.+||+||-+-
T Consensus 53 ~~~~tQrEIa~~lGiS~atIsR~sn~ 78 (94)
T TIGR01321 53 NGNMSQREIASKLGVSIATITRGSNN 78 (94)
T ss_pred hCCCCHHHHHHHhCCChhhhhHHHhh
Confidence 46899999999999999999998654
No 48
>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=97.57 E-value=6.3e-05 Score=45.17 Aligned_cols=24 Identities=17% Similarity=0.171 Sum_probs=22.4
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHH
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKIL 26 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~ 26 (77)
..|+|..+||+.||||.+||+||.
T Consensus 48 ~~G~S~~eIA~~LgISrsTIyRi~ 71 (88)
T TIGR02531 48 KQGKTYSDIEAETGASTATISRVK 71 (88)
T ss_pred HCCCCHHHHHHHHCcCHHHHHHHH
Confidence 579999999999999999999966
No 49
>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=97.55 E-value=0.001 Score=40.85 Aligned_cols=64 Identities=14% Similarity=0.053 Sum_probs=42.5
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHH---HHHHHHhCCCCcHHHHHHHh
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERR---IEEYKGENPAMFSWEIRDRL 75 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~---i~~~v~~~pd~tl~El~~~L 75 (77)
|+..++|+.+|||++|+..|-+ .|-+.|.+...+..+.=++.+... |..+. +-+++|.||.+-|
T Consensus 1 ~~i~e~a~~~gvs~~tlr~ye~----~gll~~~~r~~~gyR~Y~~~~l~~l~~I~~lr--~~G~sL~eI~~~l 67 (113)
T cd01109 1 YTIKEVAEKTGLSADTLRYYEK----EGLLPPVKRDENGIRDFTEEDLEWLEFIKCLR--NTGMSIKDIKEYA 67 (113)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCCcCCCCCccCCHHHHHHHHHHHHHH--HcCCCHHHHHHHH
Confidence 5789999999999999988854 588855433222223344444443 44443 3579999998755
No 50
>PF12728 HTH_17: Helix-turn-helix domain
Probab=97.55 E-value=0.00013 Score=38.66 Aligned_cols=32 Identities=25% Similarity=0.325 Sum_probs=26.2
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccC
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIG 41 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~g 41 (77)
+|..|+|..||||.+||++|+++ |.+.+-+.|
T Consensus 2 lt~~e~a~~l~is~~tv~~~~~~----g~i~~~~~g 33 (51)
T PF12728_consen 2 LTVKEAAELLGISRSTVYRWIRQ----GKIPPFKIG 33 (51)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHc----CCCCeEEeC
Confidence 57899999999999999999964 777555443
No 51
>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=97.55 E-value=0.0012 Score=40.95 Aligned_cols=64 Identities=17% Similarity=0.138 Sum_probs=42.0
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHH---HHHHHHHhCCCCcHHHHHHHh
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVER---RIEEYKGENPAMFSWEIRDRL 75 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~---~i~~~v~~~pd~tl~El~~~L 75 (77)
|++.++|+.||||.+|+.- |-+.|-+.|.....+..+.=++.+.. .|..+ .+-++++.||.+-+
T Consensus 1 ~~I~eva~~~gvs~~tLRy----Ye~~GLl~p~~r~~~gyR~Y~~~~i~~l~~I~~l--r~~G~sl~eI~~~l 67 (123)
T cd04770 1 MKIGELAKAAGVSPDTIRY----YERIGLLPPPQRSENGYRLYGEADLARLRFIRRA--QALGFSLAEIRELL 67 (123)
T ss_pred CCHHHHHHHHCcCHHHHHH----HHHCCCCCCCCCCCCCCccCCHHHHHHHHHHHHH--HHCCCCHHHHHHHH
Confidence 6789999999999999843 56679888644322222334444444 34444 34578999988654
No 52
>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=97.54 E-value=0.00063 Score=40.30 Aligned_cols=65 Identities=11% Similarity=0.053 Sum_probs=45.9
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHH--hCCCCcHHHHHHHh
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKG--ENPAMFSWEIRDRL 75 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~--~~pd~tl~El~~~L 75 (77)
++..++|+.+|||++|+..|.+ .|-+.|....+ ..+.-++.+...+..... .+-++++.+++.-|
T Consensus 2 ~~i~e~A~~~gvs~~tLr~ye~----~Gli~p~r~~~-g~R~y~~~dv~~l~~i~~L~~d~g~~l~~i~~~l 68 (91)
T cd04766 2 YVISVAAELSGMHPQTLRLYER----LGLLSPSRTDG-GTRRYSERDIERLRRIQRLTQELGVNLAGVKRIL 68 (91)
T ss_pred cCHHHHHHHHCcCHHHHHHHHH----CCCcCCCcCCC-CCeeECHHHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence 5788999999999999999964 59999865433 234455656665554433 33579999887654
No 53
>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=97.54 E-value=0.0009 Score=41.11 Aligned_cols=66 Identities=14% Similarity=-0.007 Sum_probs=46.3
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHH-hCCCCcHHHHHHHh
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKG-ENPAMFSWEIRDRL 75 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~-~~pd~tl~El~~~L 75 (77)
+++.++|+.+|||..|+..|-+. |-+.|.....+..+.-++.+..++.-... .+-++.+.||++.+
T Consensus 1 y~Ige~A~~~gvs~~tlR~ye~~----GLl~p~~r~~~g~R~Y~~~~l~~l~~I~~lr~~G~~l~~I~~~l 67 (107)
T cd01111 1 YSISQLALDAGVSVHIVRDYLLR----GLLHPVARTEGGYGLFDDCALQRLRFVRAAFEAGIGLDELARLC 67 (107)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC----CCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence 57889999999999999877655 99988544322334455656665554333 44578999988765
No 54
>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=97.54 E-value=0.00017 Score=37.80 Aligned_cols=32 Identities=22% Similarity=0.414 Sum_probs=27.4
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCC
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSI 35 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v 35 (77)
.++|..++|+.+|+|.+||++.+++..+.|=+
T Consensus 16 ~~~t~~ela~~~~is~~tv~~~l~~L~~~g~I 47 (48)
T PF13412_consen 16 PRITQKELAEKLGISRSTVNRYLKKLEEKGLI 47 (48)
T ss_dssp TTS-HHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHCcCc
Confidence 45999999999999999999999999998854
No 55
>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=97.53 E-value=0.00078 Score=40.57 Aligned_cols=66 Identities=15% Similarity=0.132 Sum_probs=47.1
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHh--CCCCcHHHHHHHh
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGE--NPAMFSWEIRDRL 75 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~--~pd~tl~El~~~L 75 (77)
|+..++|+.+|||.+|+..|.+ .|-+.|....+...+.-++.+...|.....- +=++++.|+++.+
T Consensus 1 m~I~eva~~~gvs~~tlR~Ye~----~GLl~p~~r~~~g~r~Y~~~dv~~l~~I~~L~~~~G~~l~~I~~~l 68 (95)
T cd04780 1 MRMSELSKRSGVSVATIKYYLR----EGLLPEGRRLAPNQAEYSEAHVERLRLIRALQQEGGLPISQIKEVL 68 (95)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCcCCCCCCeecCHHHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence 6789999999999999988876 5888885433222345667677766654332 2479999998765
No 56
>PRK13182 racA polar chromosome segregation protein; Reviewed
Probab=97.52 E-value=0.00063 Score=45.39 Aligned_cols=63 Identities=11% Similarity=0.038 Sum_probs=42.2
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHH-HhCCCCcHHHHHH
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYK-GENPAMFSWEIRD 73 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v-~~~pd~tl~El~~ 73 (77)
|++.++|+++|||..|+.+|.++ |.+.+.+..++. +.-++.+..+|..+. ..+-++++.+++.
T Consensus 1 mti~evA~~lGVS~~TLRrw~k~----g~L~~~R~~~G~-R~y~~~dl~~L~~I~~l~~~Gm~i~~i~~ 64 (175)
T PRK13182 1 MKTPFVAKKLGVSPKTVQRWVKQ----LNLPCEKNEYGH-YIFTEEDLQLLEYVKSQIEEGQNMQDTQK 64 (175)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHc----CCCCCCcCCCCC-EEECHHHHHHHHHHHHHHHcCCCHHHHHH
Confidence 57899999999999999999886 556444333323 334455566655443 3445677887755
No 57
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=97.52 E-value=0.0002 Score=37.28 Aligned_cols=36 Identities=22% Similarity=0.207 Sum_probs=32.5
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccc
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV 39 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~ 39 (77)
.+++..++|+.|+||.+||++.++.+.+.|-+....
T Consensus 13 ~~~s~~~l~~~l~~s~~tv~~~l~~L~~~g~i~~~~ 48 (53)
T smart00420 13 GKVSVEELAELLGVSEMTIRRDLNKLEEQGLLTRVH 48 (53)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEee
Confidence 469999999999999999999999999999887543
No 58
>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=97.50 E-value=0.00014 Score=39.00 Aligned_cols=33 Identities=21% Similarity=0.356 Sum_probs=29.3
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCC
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIR 36 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~ 36 (77)
.+++..+||+++|+++|||+|+++.+.+.|=+.
T Consensus 17 ~~~t~~eia~~~gl~~stv~r~L~tL~~~g~v~ 49 (52)
T PF09339_consen 17 GPLTLSEIARALGLPKSTVHRLLQTLVEEGYVE 49 (52)
T ss_dssp SCEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHHCcCee
Confidence 457999999999999999999999999999765
No 59
>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=97.50 E-value=0.00025 Score=36.44 Aligned_cols=29 Identities=24% Similarity=0.263 Sum_probs=26.7
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
..|++..+||..+|+|.++|++|+.+.++
T Consensus 24 ~~~~~~~~ia~~~~~s~~~i~~~~~~~~~ 52 (55)
T cd06171 24 GEGLSYEEIAEILGISRSTVRQRLHRALK 52 (55)
T ss_pred hcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 37899999999999999999999998765
No 60
>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=97.49 E-value=0.00019 Score=38.42 Aligned_cols=29 Identities=24% Similarity=0.306 Sum_probs=22.8
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
-+|+|..+||+.+|+|.++|.+|+.+-++
T Consensus 24 ~~g~s~~eIa~~l~~s~~~v~~~l~ra~~ 52 (54)
T PF08281_consen 24 FQGMSYAEIAEILGISESTVKRRLRRARK 52 (54)
T ss_dssp TS---HHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred HHCcCHHHHHHHHCcCHHHHHHHHHHHHh
Confidence 37999999999999999999999998765
No 61
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=97.49 E-value=0.00014 Score=39.34 Aligned_cols=28 Identities=14% Similarity=0.243 Sum_probs=24.9
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
.|.+-.++|.+||||+|||+||......
T Consensus 18 ~~~~~~~La~~FgIs~stvsri~~~~~~ 45 (53)
T PF13613_consen 18 LNLTFQDLAYRFGISQSTVSRIFHEWIP 45 (53)
T ss_pred cCCcHhHHhhheeecHHHHHHHHHHHHH
Confidence 5778899999999999999999988754
No 62
>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=97.47 E-value=0.0017 Score=38.99 Aligned_cols=64 Identities=17% Similarity=0.113 Sum_probs=42.7
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHH---HHHHHHHhCCCCcHHHHHHHh
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVER---RIEEYKGENPAMFSWEIRDRL 75 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~---~i~~~v~~~pd~tl~El~~~L 75 (77)
+++.++|+.+|||.+|+..|-+ .|-+.|...+.+..+.-++.+.. .|..+. .-++++.||.+.+
T Consensus 1 ~~i~eva~~~gvs~~tlR~ye~----~Gll~p~~~~~~gyR~Y~~~~~~~l~~I~~lr--~~G~~l~eI~~~l 67 (97)
T cd04782 1 FTTGEFAKLCGISKQTLFHYDK----IGLFKPEIVKENGYRYYTLEQFEQLDIILLLK--ELGISLKEIKDYL 67 (97)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCccCCCCCccCCHHHHHHHHHHHHHH--HcCCCHHHHHHHH
Confidence 5788999999999999988744 59998864322223334444433 344443 2369999998755
No 63
>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=97.45 E-value=0.0018 Score=39.11 Aligned_cols=65 Identities=17% Similarity=0.153 Sum_probs=42.7
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHhCCCCcHHHHHHH
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGENPAMFSWEIRDR 74 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~pd~tl~El~~~ 74 (77)
+++.++|+.+|||.+|+..| -+.|-+.|...+....+.=++.+..++.-...-..++.+.++++.
T Consensus 1 y~i~e~A~~~gvs~~tlR~Y----e~~Gll~~~~r~~~g~R~Y~~~~v~~l~~I~~l~~g~~l~~i~~~ 65 (99)
T cd04772 1 YRTVDLARAIGLSPQTVRNY----ESLGLIPPAERTANGYRIYTDKHIAALRAYRALLPGYGYRVAQRI 65 (99)
T ss_pred CCHHHHHHHHCcCHHHHHHH----HHcCCCCCCCcCCCCCeecCHHHHHHHHHHHHHhhCCCHHHHHHH
Confidence 36789999999999999877 446988764332222344556566665443333257888887653
No 64
>PRK11050 manganese transport regulator MntR; Provisional
Probab=97.44 E-value=0.0004 Score=44.87 Aligned_cols=37 Identities=27% Similarity=0.336 Sum_probs=33.5
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcccc
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI 40 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~ 40 (77)
.+.++.++|+.|+||+++|+++++++.+.|-+...+.
T Consensus 50 ~~~t~~eLA~~l~is~stVsr~l~~Le~~GlI~r~~~ 86 (152)
T PRK11050 50 GEARQVDIAARLGVSQPTVAKMLKRLARDGLVEMRPY 86 (152)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 5689999999999999999999999999998876553
No 65
>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=97.44 E-value=0.0014 Score=39.01 Aligned_cols=63 Identities=17% Similarity=0.157 Sum_probs=43.6
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHH---HHHHHhCCCCcHHHHHHHh
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRI---EEYKGENPAMFSWEIRDRL 75 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i---~~~v~~~pd~tl~El~~~L 75 (77)
|+..++|+.+||+.+|+..|.+ .|-+.|.+.+++. +.-+..+...+ ..+.. .++++.++...+
T Consensus 1 ~~~~eva~~~gi~~~tlr~~~~----~Gll~~~~~~~g~-r~y~~~dv~~l~~i~~l~~--~g~~~~~i~~~l 66 (100)
T cd00592 1 YTIGEVAKLLGVSVRTLRYYEE----KGLLPPERSENGY-RLYSEEDLERLRLIRRLRE--LGLSLKEIRELL 66 (100)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH----CCCcCCCcCCCCC-cccCHHHHHHHHHHHHHHH--cCCCHHHHHHHH
Confidence 5789999999999999999965 4888776544333 33444444443 34433 688998887654
No 66
>PHA02591 hypothetical protein; Provisional
Probab=97.43 E-value=0.00012 Score=43.22 Aligned_cols=27 Identities=30% Similarity=0.254 Sum_probs=24.9
Q ss_pred CccCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513 1 MAAAGVRPCVISRQLRVSHGCVSKILN 27 (77)
Q Consensus 1 l~~~G~s~~~iA~rf~VS~stv~r~~~ 27 (77)
|.+.|+|..+||..||||+.+|++++.
T Consensus 55 L~eqGlSqeqIA~~LGVsqetVrKYL~ 81 (83)
T PHA02591 55 LARKGFTVEKIASLLGVSVRKVRRYLE 81 (83)
T ss_pred HHHcCCCHHHHHHHhCCCHHHHHHHHh
Confidence 567899999999999999999999875
No 67
>PRK00118 putative DNA-binding protein; Validated
Probab=97.42 E-value=8.5e-05 Score=45.88 Aligned_cols=63 Identities=13% Similarity=0.050 Sum_probs=41.5
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHhCCC
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGENPA 65 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~pd 65 (77)
..|+|..+||+.||||.+||++++.+-+..=.=.-.+.|+-.+.....+.-+.+....+..||
T Consensus 31 ~eg~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 93 (104)
T PRK00118 31 LDDYSLGEIAEEFNVSRQAVYDNIKRTEKLLEDYEEKLHLYEKFIERNELFDKIAYLKEKYPD 93 (104)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHChHHHHHHHHHHHHHHHHHHHcccc
Confidence 479999999999999999999999987754333333445433332323333445555555554
No 68
>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=97.41 E-value=0.0013 Score=39.92 Aligned_cols=65 Identities=11% Similarity=-0.051 Sum_probs=42.6
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHH-HHhCCCCcHHHHHHHh
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEY-KGENPAMFSWEIRDRL 75 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~-v~~~pd~tl~El~~~L 75 (77)
++..++|+.+|||++|+..|-+ .|-+.|....+ ..+.=++.+.+++.-. .-.+-++++.|+++.+
T Consensus 2 ~~i~eva~~~gvs~~tlR~ye~----~Gll~~~r~~~-g~R~Y~~~~l~~l~~I~~l~~~G~~l~ei~~~l 67 (102)
T cd04789 2 YTISELAEKAGISRSTLLYYEK----LGLITGTRNAN-GYRLYPDSDLQRLLLIQQLQAGGLSLKECLACL 67 (102)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCcCCC-CCeeCCHHHHHHHHHHHHHHHCCCCHHHHHHHH
Confidence 6889999999999999986654 59998754332 2233444445443311 1234479999988754
No 69
>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=97.40 E-value=0.0014 Score=39.78 Aligned_cols=63 Identities=17% Similarity=0.050 Sum_probs=41.3
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHH---HHHHHHHhCCCCcHHHHHHHh
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVER---RIEEYKGENPAMFSWEIRDRL 75 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~---~i~~~v~~~pd~tl~El~~~L 75 (77)
++..++|+.||||++|+.-|-+ .|-+.|....++ .+.=++.+.. +|..+ .+-++++.|++..+
T Consensus 2 ~~i~eva~~~gvs~~tLR~ye~----~Gll~~~r~~~g-~R~Y~~~dl~~l~~I~~l--~~~G~~l~ei~~~~ 67 (102)
T cd04775 2 YTIGQMSRKFGVSRSTLLYYES----IGLIPSARSEAN-YRLYSEADLSRLEKIVFL--QAGGLPLEEIAGCL 67 (102)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCCCCCC-CeeeCHHHHHHHHHHHHH--HHCCCCHHHHHHHH
Confidence 6889999999999999955544 488855433222 2333333343 44455 34579999998754
No 70
>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=97.40 E-value=0.00024 Score=37.41 Aligned_cols=29 Identities=24% Similarity=0.188 Sum_probs=26.5
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
..|++..+||+.|++|.+||.+++.+.++
T Consensus 13 ~~~~s~~eia~~l~~s~~tv~~~~~~~~~ 41 (57)
T cd06170 13 AEGKTNKEIADILGISEKTVKTHLRNIMR 41 (57)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 47899999999999999999999998765
No 71
>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=97.37 E-value=0.00017 Score=39.09 Aligned_cols=42 Identities=19% Similarity=0.380 Sum_probs=35.8
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCC
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKP 45 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~ 45 (77)
.|++..++|+.++++++++++++++..+.|=+.-.+...+++
T Consensus 16 ~~~~~~~la~~~~~~~~~~t~~i~~L~~~g~I~r~~~~~D~R 57 (59)
T PF01047_consen 16 GGITQSELAEKLGISRSTVTRIIKRLEKKGLIERERDPDDRR 57 (59)
T ss_dssp SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTETT
T ss_pred CCCCHHHHHHHHCCChhHHHHHHHHHHHCCCEEeccCCCCCC
Confidence 568999999999999999999999999999997776655554
No 72
>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=97.37 E-value=0.0002 Score=37.71 Aligned_cols=34 Identities=21% Similarity=0.363 Sum_probs=29.0
Q ss_pred ccCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCC
Q psy15513 2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETGSI 35 (77)
Q Consensus 2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v 35 (77)
.+.-++.+++|+.|++|+++|++-++..++.|=|
T Consensus 12 ~~~~~~~~el~~~l~~s~~~vs~hL~~L~~~glV 45 (47)
T PF01022_consen 12 SEGPLTVSELAEELGLSQSTVSHHLKKLREAGLV 45 (47)
T ss_dssp TTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred HhCCCchhhHHHhccccchHHHHHHHHHHHCcCe
Confidence 3444889999999999999999999999998855
No 73
>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=97.36 E-value=0.0018 Score=39.58 Aligned_cols=66 Identities=14% Similarity=0.109 Sum_probs=43.8
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCC-CCCCCCCHHHHHHHHHHHH-hCCCCcHHHHHHHh
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGG-SKPRVATPDVERRIEEYKG-ENPAMFSWEIRDRL 75 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg-~~~~~~~~~~~~~i~~~v~-~~pd~tl~El~~~L 75 (77)
++..++|+.||||.+|+.-|-++ |=+.|....+ +..+.=++.+...|..... .+=++++.|+..-+
T Consensus 1 ~~i~eva~~~gis~~tlR~ye~~----GLi~p~~~~~~ngyR~Y~~~~i~~l~~I~~lr~~G~sl~~i~~l~ 68 (108)
T cd01107 1 FTIGEFAKLSNLSIKALRYYDKI----GLLKPAYVDPDTGYRYYSAEQLERLNRIKYLRDLGFPLEEIKEIL 68 (108)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHc----CCCCCCcCCCCCCccccCHHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence 57889999999999999887664 9998865321 2334445555554442222 22368999988654
No 74
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=97.36 E-value=0.00014 Score=48.35 Aligned_cols=27 Identities=26% Similarity=0.399 Sum_probs=24.8
Q ss_pred ccCCCCHHHHHHHhccCHHHHHHHHHH
Q psy15513 2 AAAGVRPCVISRQLRVSHGCVSKILNR 28 (77)
Q Consensus 2 ~~~G~s~~~iA~rf~VS~stv~r~~~r 28 (77)
...|+|..+||+.||||.+||+|+++.
T Consensus 169 ~~~g~s~~~iak~lgis~~Tv~r~~k~ 195 (200)
T PRK13413 169 LDKGTSKSEIARKLGVSRTTLARFLKT 195 (200)
T ss_pred HHCCCCHHHHHHHHCCCHHHHHHHHHh
Confidence 357999999999999999999999985
No 75
>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=97.35 E-value=0.002 Score=38.62 Aligned_cols=62 Identities=16% Similarity=0.152 Sum_probs=43.1
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcccc--CCCCCCCCCHHHH---HHHHHHHHhCCCCcHHHHHHHh
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI--GGSKPRVATPDVE---RRIEEYKGENPAMFSWEIRDRL 75 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~--gg~~~~~~~~~~~---~~i~~~v~~~pd~tl~El~~~L 75 (77)
|++.++|+.+|||.+|+..|-+ .|-+.|... +|.| .=++.+. .+|..+.+ -++++.||.+.+
T Consensus 1 m~i~eva~~~gvs~~tlR~ye~----~Gll~p~~r~~~gyR--~Y~~~~l~~l~~I~~lr~--~G~~l~eI~~~l 67 (96)
T cd04788 1 WKIGELARRTGLSVRTLHHYDH----IGLLSPSQRTEGGHR--LYDRADIRRLHQIIALRR--LGFSLREIGRAL 67 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCccCCCCce--eeCHHHHHHHHHHHHHHH--cCCCHHHHHHHH
Confidence 6789999999999999988754 698888533 3333 3344444 34555543 369999998765
No 76
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=97.35 E-value=0.00016 Score=42.17 Aligned_cols=32 Identities=22% Similarity=0.301 Sum_probs=28.0
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCC
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSI 35 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v 35 (77)
+|+|..+||+.+|||.+||..|+.+....|-+
T Consensus 31 eGlS~kEIAe~LGIS~~TVk~~l~~~~~~~~~ 62 (73)
T TIGR03879 31 AGKTASEIAEELGRTEQTVRNHLKGETKAGGL 62 (73)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHhcCcccchH
Confidence 79999999999999999999999986655543
No 77
>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=97.33 E-value=0.00017 Score=38.74 Aligned_cols=29 Identities=17% Similarity=0.284 Sum_probs=26.8
Q ss_pred CCCHHHHHHHhccCHHHHHHHHHHHHHhc
Q psy15513 5 GVRPCVISRQLRVSHGCVSKILNRYQETG 33 (77)
Q Consensus 5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG 33 (77)
.+|..++|..|+||..||.+-++..++.|
T Consensus 15 ~it~~eLa~~l~vS~rTi~~~i~~L~~~~ 43 (55)
T PF08279_consen 15 PITAKELAEELGVSRRTIRRDIKELREWG 43 (55)
T ss_dssp SBEHHHHHHHCTS-HHHHHHHHHHHHHTT
T ss_pred CcCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence 48999999999999999999999999999
No 78
>PRK13749 transcriptional regulator MerD; Provisional
Probab=97.33 E-value=0.0028 Score=40.00 Aligned_cols=68 Identities=10% Similarity=-0.058 Sum_probs=48.2
Q ss_pred CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHH-hCCCCcHHHHHHHhh
Q psy15513 5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKG-ENPAMFSWEIRDRLV 76 (77)
Q Consensus 5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~-~~pd~tl~El~~~L~ 76 (77)
.+++.++|+++|||..|+.-| -+.|=+.|-....+..+.=++.+..++.-... ..-++++.||++.|.
T Consensus 3 ~~tIgelA~~~gvS~~tiR~Y----E~~GLl~p~~r~~~gyR~Y~~~~l~rL~~I~~~r~~G~sL~eI~~ll~ 71 (121)
T PRK13749 3 AYTVSRLALDAGVSVHIVRDY----LLRGLLRPVACTTGGYGLFDDAALQRLCFVRAAFEAGIGLDALARLCR 71 (121)
T ss_pred CCcHHHHHHHHCCCHHHHHHH----HHCCCCCCCCcCCCCCccCCHHHHHHHHHHHHHHHcCCCHHHHHHHHh
Confidence 489999999999999998544 34587777544333344556666776654443 567899999998763
No 79
>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=97.33 E-value=0.0003 Score=38.37 Aligned_cols=38 Identities=21% Similarity=0.349 Sum_probs=33.3
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccC
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIG 41 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~g 41 (77)
.+++..++|+.|++|.++|++++++..+.|-+.....+
T Consensus 19 ~~~~~~ei~~~~~i~~~~i~~~l~~L~~~g~i~~~~~~ 56 (78)
T cd00090 19 GPLTVSELAERLGLSQSTVSRHLKKLEEAGLVESRREG 56 (78)
T ss_pred CCcCHHHHHHHHCcCHhHHHHHHHHHHHCCCeEEEEec
Confidence 34889999999999999999999999999988766544
No 80
>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=97.33 E-value=0.0024 Score=40.16 Aligned_cols=68 Identities=13% Similarity=0.004 Sum_probs=46.8
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHH-hCCCCcHHHHHHHh
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKG-ENPAMFSWEIRDRL 75 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~-~~pd~tl~El~~~L 75 (77)
..+++.++|+.+|||..|+.-|-+ .|=+.|.....+..+.=++.+..+|.-... ..-++++.||++-+
T Consensus 2 ~~~tI~elA~~~gvs~~tlR~Ye~----~GLL~p~~r~~~gyR~Y~~~~l~rL~~I~~lr~~G~~L~eI~~ll 70 (120)
T TIGR02054 2 NAYTISRLAEDAGVSVHVVRDYLL----RGLLHPVRRTTSGYGIFDDASLQRLRFVRAAFEAGIGLGELARLC 70 (120)
T ss_pred CCCcHHHHHHHHCcCHHHHHHHHH----CCCCCCCccCCCCCeeCCHHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence 368999999999999999876644 488887655322334455556665543333 44679999998754
No 81
>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=97.31 E-value=0.0025 Score=39.93 Aligned_cols=62 Identities=18% Similarity=0.111 Sum_probs=41.2
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcccc--CCCCCCCCCHHHHHH---HHHHHHhCCCCcHHHHHHHh
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI--GGSKPRVATPDVERR---IEEYKGENPAMFSWEIRDRL 75 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~--gg~~~~~~~~~~~~~---i~~~v~~~pd~tl~El~~~L 75 (77)
|++.++|+.+|||..|+.-|-+ .|-+.|... +|.| .=++.+... |..+ .+-++++.||++-+
T Consensus 1 m~I~e~a~~~gvs~~tlRyYe~----~GLl~~~~r~~~g~R--~Y~~~~~~~l~~I~~l--r~~G~sL~eI~~~l 67 (127)
T cd01108 1 MNIGEAAKLTGLSAKMIRYYEE----IGLIPPPSRSDNGYR--VYNQRDIEELRFIRRA--RDLGFSLEEIRELL 67 (127)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCCcCCCCce--ecCHHHHHHHHHHHHH--HHcCCCHHHHHHHH
Confidence 6889999999999999876654 488875332 3333 333434443 4444 34678999988754
No 82
>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=97.29 E-value=0.00036 Score=36.87 Aligned_cols=25 Identities=12% Similarity=0.191 Sum_probs=19.1
Q ss_pred CC-CCHHHHHHHhccCHHHHHHHHHH
Q psy15513 4 AG-VRPCVISRQLRVSHGCVSKILNR 28 (77)
Q Consensus 4 ~G-~s~~~iA~rf~VS~stv~r~~~r 28 (77)
.| +|.+++|+.|||+.+|+++.++.
T Consensus 14 ~g~~S~r~AA~~ygVp~sTL~~r~~g 39 (45)
T PF05225_consen 14 NGKMSIRKAAKKYGVPRSTLRRRLRG 39 (45)
T ss_dssp TTSS-HHHHHHHHT--HHHHHHHHHH
T ss_pred hCCCCHHHHHHHHCcCHHHHHHHHcC
Confidence 45 99999999999999999977654
No 83
>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=97.29 E-value=0.0022 Score=41.04 Aligned_cols=65 Identities=22% Similarity=0.163 Sum_probs=43.9
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHH-hCCCCcHHHHHHHh
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKG-ENPAMFSWEIRDRL 75 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~-~~pd~tl~El~~~L 75 (77)
|++.++|+.+|||.+|+..|-+. |-+.|....++ .+.=++.+..+|..... .+-++++.||++.|
T Consensus 2 ~~I~EvA~~~Gvs~~tLRyYE~~----GLl~p~r~~~g-~R~Y~~~dl~~l~~I~~lr~~G~sl~eI~~~l 67 (139)
T cd01110 2 LSVGEVAKRSGVAVSALHFYEQK----GLIASWRNAGN-QRRYPRDVLRRIAFIKVAQRLGLSLAEIAEAL 67 (139)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC----CCCCCCcCCCC-CeEECHHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence 78999999999999999877655 88887554333 23344545554332211 34568899988765
No 84
>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=97.28 E-value=0.0027 Score=40.07 Aligned_cols=64 Identities=19% Similarity=0.132 Sum_probs=42.7
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHH---HHHHHHHhCCCCcHHHHHHHh
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVER---RIEEYKGENPAMFSWEIRDRL 75 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~---~i~~~v~~~pd~tl~El~~~L 75 (77)
+++.++|+++|||..|+.-|-+. |-+.|.....+..+.=++.+.. +|..+. +-++++.|+.+-+
T Consensus 2 ~~I~e~a~~~gvs~~tlR~Ye~~----GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr--~~G~sl~eI~~~l 68 (131)
T TIGR02043 2 FQIGELAKLCGVTSDTLRFYEKN----GLIKPAGRTDSGYRLYTDEDQKRLRFILKAK--ELGFTLDEIKELL 68 (131)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC----CCCCCCCcCCCCceecCHHHHHHHHHHHHHH--HcCCCHHHHHHHH
Confidence 68999999999999999877654 9998854322222233333444 344443 4578999988755
No 85
>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=97.28 E-value=0.0031 Score=39.51 Aligned_cols=62 Identities=18% Similarity=0.159 Sum_probs=41.4
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcccc--CCCCCCCCCHHHHHH---HHHHHHhCCCCcHHHHHHHh
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI--GGSKPRVATPDVERR---IEEYKGENPAMFSWEIRDRL 75 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~--gg~~~~~~~~~~~~~---i~~~v~~~pd~tl~El~~~L 75 (77)
|+..++|+++|||..|+.-|- +.|-+.|... +|.| .=++++... |..+ ..-++++.||++.|
T Consensus 1 m~I~e~a~~~gvs~~tlRyYe----~~GLl~p~~r~~~gyR--~Y~~~~l~~l~~I~~l--r~~G~sL~eI~~~l 67 (127)
T TIGR02044 1 MNIGQVAKLTGLSSKMIRYYE----EKGLIPPPLRSEGGYR--TYTQQHLDELRLISRA--RQVGFSLEECKELL 67 (127)
T ss_pred CCHHHHHHHHCcCHHHHHHHH----HCCCCCCCCcCCCCCe--ecCHHHHHHHHHHHHH--HHCCCCHHHHHHHH
Confidence 688999999999999987554 4588877543 3333 333434443 4343 34578899988754
No 86
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=97.28 E-value=0.0019 Score=37.38 Aligned_cols=59 Identities=20% Similarity=0.282 Sum_probs=42.5
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHhCC
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGENP 64 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~p 64 (77)
.+++..+||+.++||.+||++.++.+.+.|-+...+.+| + ....+...++-..+...++
T Consensus 19 ~~~t~~~ia~~l~i~~~tv~r~l~~L~~~g~l~~~~~~~-~-y~l~~~~~~~~~~~~~~~~ 77 (91)
T smart00346 19 GGLTLAELAERLGLSKSTAHRLLNTLQELGYVEQDGQNG-R-YRLGPKVLELGQSYLSSLD 77 (91)
T ss_pred CCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeeecCCCC-c-eeecHHHHHHHHHHHhcCC
Confidence 469999999999999999999999999999997654332 2 2344444444445544443
No 87
>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=97.27 E-value=0.0017 Score=39.50 Aligned_cols=62 Identities=19% Similarity=0.233 Sum_probs=42.1
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHH---HHHHHHHHhCCCCcHHHHHHHh
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVE---RRIEEYKGENPAMFSWEIRDRL 75 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~---~~i~~~v~~~pd~tl~El~~~L 75 (77)
|++.++|+.+|||..|+.- |-+.|=+.|...+|++. =++.+. .+|..+.+- ++++.||++-+
T Consensus 1 m~Ige~a~~~gvs~~tlRy----Ye~~GLl~p~~~~g~r~--Y~~~~~~~l~~I~~lr~~--G~sL~eI~~~l 65 (107)
T cd04777 1 MKIGKFAKKNNITIDTVRH----YIDLGLLIPEKKGGQYF--FDEKCQDDLEFILELKGL--GFSLIEIQKIF 65 (107)
T ss_pred CCHHHHHHHHCcCHHHHHH----HHHCCCcCCccCCCccc--cCHHHHHHHHHHHHHHHC--CCCHHHHHHHH
Confidence 6889999999999999754 34668888876555443 233333 344444433 68999988754
No 88
>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=97.27 E-value=0.00024 Score=38.18 Aligned_cols=34 Identities=24% Similarity=0.495 Sum_probs=23.4
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCC-CccccCCC
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSI-RPGVIGGS 43 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v-~pk~~gg~ 43 (77)
++..++++.+|||.+|+++|++ .|.. .|-+.|+.
T Consensus 4 l~~~ev~~~~g~s~~ti~~~~k----~g~FP~pvklg~r 38 (51)
T PF05930_consen 4 LRIKEVAELLGVSRSTIYRLIK----DGKFPKPVKLGGR 38 (51)
T ss_dssp E-HHHHHHHHSS-HHHHHHHHH----HHH---SEESSS-
T ss_pred ccHHHHHHHHCCCHHHHHHHHh----cccCCCCEEECCC
Confidence 3678999999999999999999 3544 55556653
No 89
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=97.26 E-value=0.0027 Score=40.59 Aligned_cols=64 Identities=20% Similarity=0.155 Sum_probs=43.1
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHH---HHHHHHhCCCCcHHHHHHHh
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERR---IEEYKGENPAMFSWEIRDRL 75 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~---i~~~v~~~pd~tl~El~~~L 75 (77)
+++.++|+.+|||..|+.-|-+ .|-+.|.....+..+.=++.+... |..+ .+-++++.||++.+
T Consensus 2 ~~I~e~a~~~gvs~~tlR~Ye~----~GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~l--r~~G~sL~eI~~~l 68 (140)
T PRK09514 2 YRIGELAKLAEVTPDTLRFYEK----QGLMDPEVRTEGGYRLYTEQDLQRLRFIRRA--KQLGFTLEEIRELL 68 (140)
T ss_pred CcHHHHHHHHCcCHHHHHHHHH----CCCCCCcccCCCCCeeeCHHHHHHHHHHHHH--HHcCCCHHHHHHHH
Confidence 6889999999999999988754 498888543222223344444443 3343 34578999998765
No 90
>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=97.25 E-value=0.00074 Score=35.70 Aligned_cols=29 Identities=28% Similarity=0.361 Sum_probs=24.9
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
-.|+|..+||+.||||.++|.++.++-.+
T Consensus 18 ~~~~t~~eIa~~lg~s~~~V~~~~~~al~ 46 (50)
T PF04545_consen 18 FEGLTLEEIAERLGISRSTVRRILKRALK 46 (50)
T ss_dssp TST-SHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred cCCCCHHHHHHHHCCcHHHHHHHHHHHHH
Confidence 46899999999999999999999987653
No 91
>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial. The SUF system is an oxygen-resistant iron-sulfur cluster assembly system found in both aerobes and facultative anaerobes. Its presence appears to be a marker of oxygen tolerance; strict anaerobes and microaerophiles tend to have different FeS cluster biosynthesis systems. Members of this protein family belong to the rrf2 family of transcriptional regulators and are found, typically, as the first gene of a SUF operon. It is found only in a subset of genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role.
Probab=97.24 E-value=0.00091 Score=41.71 Aligned_cols=62 Identities=21% Similarity=0.126 Sum_probs=42.6
Q ss_pred CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccc--cCCCCCCCCC-HHHHHHHHHHHHhCCCC
Q psy15513 5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV--IGGSKPRVAT-PDVERRIEEYKGENPAM 66 (77)
Q Consensus 5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~--~gg~~~~~~~-~~~~~~i~~~v~~~pd~ 66 (77)
.+|..+||.+++||+++|.+.++..++.|=+...+ .||....... ......|.+.++..+.+
T Consensus 25 ~~s~~eia~~l~is~~~v~~~l~~L~~~Gli~~~~g~~ggy~l~~~~~~it~~~v~~~l~~~~~v 89 (130)
T TIGR02944 25 PYSAAEIAEQTGLNAPTVSKILKQLSLAGIVTSKRGVEGGYTLARAPRDITVADIVKAVEGPVAL 89 (130)
T ss_pred CccHHHHHHHHCcCHHHHHHHHHHHHHCCcEEecCCCCCChhhcCCccccCHHHHHHHHcCCCCc
Confidence 48999999999999999999999999999986543 3444331111 11233455556655543
No 92
>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=97.24 E-value=0.0038 Score=39.01 Aligned_cols=63 Identities=19% Similarity=0.185 Sum_probs=41.1
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCC-ccccCCCCCCCCCHHHHHH---HHHHHHhCCCCcHHHHHHHh
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIR-PGVIGGSKPRVATPDVERR---IEEYKGENPAMFSWEIRDRL 75 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~-pk~~gg~~~~~~~~~~~~~---i~~~v~~~pd~tl~El~~~L 75 (77)
|++.++|+.||||.+|+. -|-+.|-+. |.+..+ ..+.-++.+... |..+. +=++++.||.+-+
T Consensus 1 m~I~e~a~~~gvs~~tlR----~Ye~~GLl~~~~r~~~-gyR~Y~~~~l~~l~~I~~lr--~~G~sL~eI~~~l 67 (126)
T cd04783 1 LTIGELAKAAGVNVETIR----YYQRRGLLPEPPRPEG-GYRRYPEETVTRLRFIKRAQ--ELGFTLDEIAELL 67 (126)
T ss_pred CCHHHHHHHHCcCHHHHH----HHHHCCCCCCCCcCCC-CCeecCHHHHHHHHHHHHHH--HcCCCHHHHHHHH
Confidence 678999999999999993 335668887 443222 233444444444 44443 3468899888755
No 93
>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=97.23 E-value=0.0003 Score=37.46 Aligned_cols=26 Identities=23% Similarity=0.380 Sum_probs=21.7
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHH
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNR 28 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r 28 (77)
+.|+|..++|+.+|||+++|++|.+-
T Consensus 7 ~~gls~~~la~~~gis~~~i~~~~~g 32 (55)
T PF01381_consen 7 EKGLSQKELAEKLGISRSTISRIENG 32 (55)
T ss_dssp HTTS-HHHHHHHHTS-HHHHHHHHTT
T ss_pred HcCCCHHHHHHHhCCCcchhHHHhcC
Confidence 57999999999999999999999753
No 94
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=97.22 E-value=0.00035 Score=50.45 Aligned_cols=38 Identities=24% Similarity=0.450 Sum_probs=34.7
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcccc
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI 40 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~ 40 (77)
.+|+++.+||++||||..+|+|++++-++.|-|.-.-.
T Consensus 24 ~~gltQ~eIA~~LgiSR~~v~rlL~~Ar~~GiV~I~i~ 61 (321)
T COG2390 24 VEGLTQSEIAERLGISRATVSRLLAKAREEGIVKISIN 61 (321)
T ss_pred hcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCeEEEEeC
Confidence 57999999999999999999999999999999876543
No 95
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=97.21 E-value=0.00072 Score=42.80 Aligned_cols=43 Identities=21% Similarity=0.300 Sum_probs=38.7
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCC
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR 46 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~ 46 (77)
.|+++.++|+.++|+++||++.+++..+.|-|.-.+...+++.
T Consensus 53 ~~~t~~eLa~~l~i~~~tvsr~l~~Le~~GlI~R~~~~~DrR~ 95 (144)
T PRK11512 53 ACITPVELKKVLSVDLGALTRMLDRLVCKGWVERLPNPNDKRG 95 (144)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeccCcccCCe
Confidence 5699999999999999999999999999999988877667663
No 96
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=97.20 E-value=0.00067 Score=34.85 Aligned_cols=34 Identities=24% Similarity=0.305 Sum_probs=31.2
Q ss_pred CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513 5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG 38 (77)
Q Consensus 5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk 38 (77)
.++..++|+.+++|+++|++.++++.+.|-+...
T Consensus 8 ~~s~~~la~~l~~s~~tv~~~l~~L~~~g~l~~~ 41 (48)
T smart00419 8 PLTRQEIAELLGLTRETVSRTLKRLEKEGLISRE 41 (48)
T ss_pred ccCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence 4789999999999999999999999999998754
No 97
>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=97.20 E-value=0.0038 Score=39.45 Aligned_cols=64 Identities=14% Similarity=0.059 Sum_probs=42.3
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHH---HHHHHHHhCCCCcHHHHHHHh
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVER---RIEEYKGENPAMFSWEIRDRL 75 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~---~i~~~v~~~pd~tl~El~~~L 75 (77)
|++.++|+.+|||..|+.-| -+.|-+.|....++..+.=++.+.. +|..+. +-+++|.||++-+
T Consensus 1 m~IgE~A~~~gvs~~TLRyY----E~~GLl~p~r~~~~gyR~Y~~~~~~~l~~I~~lr--~~G~sL~eI~~~l 67 (133)
T cd04787 1 MKVKELANAAGVTPDTVRFY----TRIGLLRPTRDPVNGYRLYSEKDLSRLRFILSAR--QLGFSLKDIKEIL 67 (133)
T ss_pred CCHHHHHHHHCcCHHHHHHH----HHCCCCCCCcCCCCCeeeCCHHHHHHHHHHHHHH--HcCCCHHHHHHHH
Confidence 68899999999999998443 5679888865431222333343443 344443 4569999988765
No 98
>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=97.19 E-value=0.0046 Score=37.06 Aligned_cols=64 Identities=16% Similarity=0.033 Sum_probs=42.5
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHH---HHHHHHHhCCCCcHHHHHHHh
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVER---RIEEYKGENPAMFSWEIRDRL 75 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~---~i~~~v~~~pd~tl~El~~~L 75 (77)
++..++|+.+|||.+|+.-|-+. |-+.|.....+..+.-+..+.. .|..+.+ -++++.||++.+
T Consensus 1 ~ti~eva~~~gvs~~tLRyye~~----Gll~p~~~~~~gyR~Y~~~~l~~l~~I~~lr~--~G~~l~~I~~~l 67 (96)
T cd04768 1 LTIGEFAKLAGVSIRTLRHYDDI----GLFKPAKIAENGYRYYSYAQLYQLQFILFLRE--LGFSLAEIKELL 67 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC----CCCCCCccCCCCeeeCCHHHHHHHHHHHHHHH--cCCCHHHHHHHH
Confidence 57889999999999999877654 9998865422222333333333 3444433 469999998765
No 99
>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=97.18 E-value=0.00087 Score=36.69 Aligned_cols=36 Identities=22% Similarity=0.219 Sum_probs=32.5
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccc
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV 39 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~ 39 (77)
..++..++|..+|+|.+||++.++++.+.|-+...+
T Consensus 24 ~~~s~~ela~~~g~s~~tv~r~l~~L~~~g~i~~~~ 59 (67)
T cd00092 24 LPLTRQEIADYLGLTRETVSRTLKELEEEGLISRRG 59 (67)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecC
Confidence 358999999999999999999999999999887653
No 100
>PHA00738 putative HTH transcription regulator
Probab=97.18 E-value=0.00037 Score=43.39 Aligned_cols=41 Identities=24% Similarity=0.139 Sum_probs=37.2
Q ss_pred CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCC
Q psy15513 5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKP 45 (77)
Q Consensus 5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~ 45 (77)
.+++++++..|++|+++||+-++-.++.|=|...+.|....
T Consensus 26 ~~~V~eLae~l~lSQptVS~HLKvLreAGLV~srK~Gr~vy 66 (108)
T PHA00738 26 ILSASLISHTLLLSYTTVLRHLKILNEQGYIELYKEGRTLY 66 (108)
T ss_pred CccHHHHHHhhCCCHHHHHHHHHHHHHCCceEEEEECCEEE
Confidence 48999999999999999999999999999999998875443
No 101
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=97.17 E-value=0.0012 Score=34.97 Aligned_cols=39 Identities=23% Similarity=0.378 Sum_probs=33.6
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccC
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIG 41 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~g 41 (77)
....+..+|++.|+||.++|++.++++.+.|-+.....+
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~~g~i~~~~~~ 46 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLREAGLVESRREG 46 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHHCCCeeeeecC
Confidence 345889999999999999999999999999998755433
No 102
>PRK10227 DNA-binding transcriptional regulator CueR; Provisional
Probab=97.14 E-value=0.0048 Score=39.33 Aligned_cols=66 Identities=9% Similarity=0.069 Sum_probs=43.5
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHH-hCCCCcHHHHHHHh
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKG-ENPAMFSWEIRDRL 75 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~-~~pd~tl~El~~~L 75 (77)
|++.++|+++|||..|+.-| -+.|-+.|.....+..+.=++.+..+|.-... .+-++++.||++-+
T Consensus 1 m~Ige~a~~~gvs~~tlRyY----E~~GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sl~eI~~~l 67 (135)
T PRK10227 1 MNISDVAKITGLTSKAIRFY----EEKGLVTPPMRSENGYRTYTQQHLNELTLLRQARQVGFNLEESGELV 67 (135)
T ss_pred CCHHHHHHHHCcCHHHHHHH----HHCCCCCCcccCCCCcccCCHHHHHHHHHHHHHHHCCCCHHHHHHHH
Confidence 68899999999999998554 45588877544222234445555555543322 34579999987754
No 103
>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=97.12 E-value=0.0043 Score=38.75 Aligned_cols=64 Identities=14% Similarity=0.081 Sum_probs=41.8
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHH---HHHHHHHhCCCCcHHHHHHHh
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVER---RIEEYKGENPAMFSWEIRDRL 75 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~---~i~~~v~~~pd~tl~El~~~L 75 (77)
|++.++|+.+|||..|+.-|- +.|-+.|.....+..+.=++.+.. +|..+.+ =++++.||.+-|
T Consensus 1 m~IgevA~~~gvs~~tLRyYe----~~GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~--~G~sL~eI~~~l 67 (127)
T cd04784 1 MKIGELAKKTGCSVETIRYYE----KEGLLPAPARSANNYRLYDEEHLERLLFIRRCRS--LDMSLDEIRTLL 67 (127)
T ss_pred CCHHHHHHHHCcCHHHHHHHH----HCCCCCCCCcCCCCCeecCHHHHHHHHHHHHHHH--cCCCHHHHHHHH
Confidence 678999999999999986554 458887543322223344444454 4444433 369999988754
No 104
>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=97.12 E-value=0.00076 Score=39.27 Aligned_cols=34 Identities=26% Similarity=0.395 Sum_probs=30.7
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccc
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV 39 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~ 39 (77)
++..+||++++||++++.+++++..+.|=+...+
T Consensus 26 ~s~~eiA~~~~i~~~~l~kil~~L~~~Gli~s~~ 59 (83)
T PF02082_consen 26 VSSKEIAERLGISPSYLRKILQKLKKAGLIESSR 59 (83)
T ss_dssp BEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHhhCCeeEecC
Confidence 7999999999999999999999999999987654
No 105
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=97.11 E-value=0.0006 Score=36.13 Aligned_cols=24 Identities=33% Similarity=0.462 Sum_probs=22.6
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHH
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRY 29 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~ 29 (77)
.|..+||+.+|||.+||.+++.+|
T Consensus 28 ~s~~~vA~~~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 28 RSFKDVARELGVSWSTVRRIFDRY 51 (52)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHhh
Confidence 589999999999999999999886
No 106
>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=97.11 E-value=0.0052 Score=38.98 Aligned_cols=64 Identities=13% Similarity=0.066 Sum_probs=41.6
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHH---HHHHHHHhCCCCcHHHHHHHh
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVER---RIEEYKGENPAMFSWEIRDRL 75 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~---~i~~~v~~~pd~tl~El~~~L 75 (77)
|++.++|+++|||.+|+.-|- +.|-+.|....++..+.=++.+.. +|..+. .-+++|.||.+-|
T Consensus 1 m~Ige~a~~~gvs~~tLRyYE----~~GLl~p~~r~~~gyR~Y~~~~v~~l~~I~~lr--~~GfsL~eI~~ll 67 (131)
T cd04786 1 MKIGELAKRSGMAASRIRFYE----AEGLLSSVERSANGYRDYPPETVWVLEIISSAQ--QAGFSLDEIRQLL 67 (131)
T ss_pred CCHHHHHHHHCcCHHHHHHHH----HCCCCCCCCcCCCCCeecCHHHHHHHHHHHHHH--HcCCCHHHHHHHH
Confidence 688999999999999986654 458887743322222333343443 344433 3468999998765
No 107
>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=97.10 E-value=0.00064 Score=37.43 Aligned_cols=39 Identities=23% Similarity=0.298 Sum_probs=33.8
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccC
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIG 41 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~g 41 (77)
..+++..++|+.|+++++|+++-++...+.|=|...+.|
T Consensus 22 ~~~~t~~ela~~l~~~~~t~s~hL~~L~~aGli~~~~~g 60 (61)
T PF12840_consen 22 NGPMTVSELAEELGISQSTVSYHLKKLEEAGLIEVEREG 60 (61)
T ss_dssp CSTBEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEET
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEeccC
Confidence 567999999999999999999999999999988766544
No 108
>COG0789 SoxR Predicted transcriptional regulators [Transcription]
Probab=97.09 E-value=0.0062 Score=37.26 Aligned_cols=66 Identities=17% Similarity=0.100 Sum_probs=44.2
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHH-hCCCCcHHHHHHHh
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKG-ENPAMFSWEIRDRL 75 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~-~~pd~tl~El~~~L 75 (77)
|++.++|+.+|||..|+.-| -+.|-+.|.....+..+.=++++...+..... .+-++++.|+.+.|
T Consensus 1 ~~I~eva~~~gvs~~tLRyY----E~~GLl~p~~~~~~gyR~Ys~~dl~~l~~I~~~r~~G~~L~~I~~~l 67 (124)
T COG0789 1 YTIGEVAKLTGVSVRTLRFY----ERKGLLSPERRDEGGYRYYTPEDLELLQIIKTLRELGFSLAEIKELL 67 (124)
T ss_pred CcHHHHHHHhCCCHHHHHHH----HHcCCCCCcccCCCCceecCHHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence 57899999999999998655 45688888766532334445555444332221 24579999998866
No 109
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=97.09 E-value=0.0032 Score=35.61 Aligned_cols=43 Identities=21% Similarity=0.224 Sum_probs=30.7
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHhCC
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGENP 64 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~p 64 (77)
++..+||++.|||.+||+++++ +++. .+++..+.|.+..++..
T Consensus 1 ~t~~~iA~~~gvS~~TVSr~ln---------------~~~~-v~~~t~~~i~~~~~~~g 43 (70)
T smart00354 1 ATIKDVARLAGVSKATVSRVLN---------------GNGR-VSEETREKVLAAMEELG 43 (70)
T ss_pred CCHHHHHHHHCCCHHHHHHHHC---------------CCCC-CCHHHHHHHHHHHHHhC
Confidence 3678999999999999999882 1222 34556677777666653
No 110
>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=97.08 E-value=0.0055 Score=38.47 Aligned_cols=62 Identities=19% Similarity=0.130 Sum_probs=41.0
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcccc--CCCCCCCCCHHHH---HHHHHHHHhCCCCcHHHHHHHh
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI--GGSKPRVATPDVE---RRIEEYKGENPAMFSWEIRDRL 75 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~--gg~~~~~~~~~~~---~~i~~~v~~~pd~tl~El~~~L 75 (77)
|++.++|+.+|||..|+.-|-+ .|-+.|... +|.| .=++.+. .+|..+. .=++++.||.+.|
T Consensus 1 m~I~e~a~~~gvs~~tlR~Ye~----~GLl~~~~r~~~gyR--~Y~~~~l~~l~~I~~lr--~lG~sL~eI~~~l 67 (127)
T TIGR02047 1 MKIGELAQKTGVSVETIRFYEK----QGLLPPPARTDNNYR--VYTVGHVERLAFIRNCR--TLDMSLAEIRQLL 67 (127)
T ss_pred CcHHHHHHHHCcCHHHHHHHHH----CCCCCCCCcCCCCCC--cCCHHHHHHHHHHHHHH--HcCCCHHHHHHHH
Confidence 6789999999999999877654 588865332 3333 3334343 3444443 3468888888754
No 111
>PF13730 HTH_36: Helix-turn-helix domain
Probab=97.08 E-value=0.0011 Score=35.39 Aligned_cols=28 Identities=21% Similarity=0.373 Sum_probs=26.4
Q ss_pred CHHHHHHHhccCHHHHHHHHHHHHHhcC
Q psy15513 7 RPCVISRQLRVSHGCVSKILNRYQETGS 34 (77)
Q Consensus 7 s~~~iA~rf~VS~stv~r~~~r~r~tG~ 34 (77)
|...+|+.+|+|.+||+++++...+.|-
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~L~~~G~ 54 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKELEEKGL 54 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHCcC
Confidence 8899999999999999999999999884
No 112
>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=97.08 E-value=0.005 Score=38.47 Aligned_cols=61 Identities=15% Similarity=0.131 Sum_probs=39.9
Q ss_pred CHHHHHHHhccCHHHHHHHHHHHHHhcCCCcccc--CCCCCCCCCHHHHHH---HHHHHHhCCCCcHHHHHHHh
Q psy15513 7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI--GGSKPRVATPDVERR---IEEYKGENPAMFSWEIRDRL 75 (77)
Q Consensus 7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~--gg~~~~~~~~~~~~~---i~~~v~~~pd~tl~El~~~L 75 (77)
++.++|+.+|||+.|+.-| -+.|-+.|... +|.|. -++.+... |..+ ..-++++.||.+.|
T Consensus 1 ~I~e~a~~~gvs~~tlR~Y----e~~GLl~~~~r~~~g~R~--Y~~~~l~~l~~I~~l--~~~G~sl~eI~~~l 66 (124)
T TIGR02051 1 TIGELAKAAGVNVETIRYY----ERKGLLPEPDRPEGGYRR--YPEETVKRLRFIKRA--QELGFSLEEIGGLL 66 (124)
T ss_pred CHHHHHHHHCcCHHHHHHH----HHCCCCCCCccCCCCCEe--ECHHHHHHHHHHHHH--HHCCCCHHHHHHHH
Confidence 4689999999999999555 45688865322 44332 33434443 4444 44579999998765
No 113
>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=97.07 E-value=0.0063 Score=37.41 Aligned_cols=63 Identities=19% Similarity=0.124 Sum_probs=42.5
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHH---HHHHHHhCCCCcHHHHHHHh
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERR---IEEYKGENPAMFSWEIRDRL 75 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~---i~~~v~~~pd~tl~El~~~L 75 (77)
|++.++|+.+|||.+|+.-|-+ .|-+.|....++ .+.=++.+... |..+. .-++++.||.+.+
T Consensus 1 m~i~eva~~~gvs~~tlR~Ye~----~GLl~p~r~~~g-~R~Y~~~~~~~l~~I~~lr--~~G~sl~eI~~~l 66 (112)
T cd01282 1 MRIGELAARTGVSVRSLRYYEE----QGLLVPERSANG-YRDYDEAAVDRVRQIRRLL--AAGLTLEEIREFL 66 (112)
T ss_pred CCHHHHHHHHCCCHHHHHHHHH----CCCCCCCcCCCC-CeecCHHHHHHHHHHHHHH--HcCCCHHHHHHHH
Confidence 6789999999999999988755 498888544322 23344444443 44443 3468888888654
No 114
>PRK04217 hypothetical protein; Provisional
Probab=97.07 E-value=0.0011 Score=41.38 Aligned_cols=29 Identities=21% Similarity=0.296 Sum_probs=26.0
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
.+|+|..+||+.||||.+||++.+.+.++
T Consensus 56 ~eGlS~~EIAk~LGIS~sTV~r~L~RArk 84 (110)
T PRK04217 56 YEGLTQEEAGKRMGVSRGTVWRALTSARK 84 (110)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 37899999999999999999999987654
No 115
>PHA00542 putative Cro-like protein
Probab=97.06 E-value=0.00046 Score=40.51 Aligned_cols=25 Identities=24% Similarity=0.260 Sum_probs=23.2
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILN 27 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~ 27 (77)
+.|++..++|+.+|||+++|++|..
T Consensus 29 ~~glTq~elA~~lgIs~~tIsr~e~ 53 (82)
T PHA00542 29 RAGWSQEQIADATDVSQPTICRIYS 53 (82)
T ss_pred HCCCCHHHHHHHHCcCHHHHHHHHc
Confidence 5789999999999999999999974
No 116
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=97.05 E-value=0.0012 Score=41.94 Aligned_cols=35 Identities=17% Similarity=0.177 Sum_probs=32.2
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcccc
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI 40 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~ 40 (77)
.|..++|++|+||+.+|.+.+++....|=|...+.
T Consensus 26 ~s~~~ia~~~~is~~~vrk~l~~L~~~Glv~s~~G 60 (141)
T PRK11014 26 TSISEVTEVYGVSRNHMVKIINQLSRAGYVTAVRG 60 (141)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHHHHhCCEEEEecC
Confidence 68899999999999999999999999999977764
No 117
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=97.04 E-value=0.0007 Score=36.00 Aligned_cols=40 Identities=30% Similarity=0.280 Sum_probs=30.0
Q ss_pred CHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHh
Q psy15513 7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGE 62 (77)
Q Consensus 7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~ 62 (77)
+..+||+..|||.+||+|.+.-. ....++..+.|.+.+++
T Consensus 1 Ti~dIA~~agvS~~TVSr~ln~~----------------~~vs~~tr~rI~~~a~~ 40 (46)
T PF00356_consen 1 TIKDIAREAGVSKSTVSRVLNGP----------------PRVSEETRERILEAAEE 40 (46)
T ss_dssp CHHHHHHHHTSSHHHHHHHHTTC----------------SSSTHHHHHHHHHHHHH
T ss_pred CHHHHHHHHCcCHHHHHHHHhCC----------------CCCCHHHHHHHHHHHHH
Confidence 35799999999999999998631 12445667778777665
No 118
>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=97.04 E-value=0.0004 Score=41.21 Aligned_cols=25 Identities=16% Similarity=0.101 Sum_probs=18.1
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILN 27 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~ 27 (77)
+...+.|++|+.||||.|||.+=+.
T Consensus 17 ~~~aTVR~~Ak~FGvSKSTVHkDvt 41 (82)
T PF12116_consen 17 ETKATVRQAAKVFGVSKSTVHKDVT 41 (82)
T ss_dssp HH---HHHHHHHHTS-HHHHHHHHT
T ss_pred HcccHHHHHHHHHCCcHHHHHHHHH
Confidence 3467899999999999999998663
No 119
>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=97.03 E-value=0.0043 Score=37.74 Aligned_cols=56 Identities=13% Similarity=0.249 Sum_probs=45.0
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCC---CCHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRV---ATPDVERRIEEY 59 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~---~~~~~~~~i~~~ 59 (77)
.+++..++|..+++++++|++.+++..+.|=|.-.+...+++.. +++.-.+.+..+
T Consensus 42 ~~~t~~eL~~~l~~~~stvs~~i~~Le~kg~I~r~~~~~D~R~~~i~lT~~G~~~~~~~ 100 (109)
T TIGR01889 42 GKLTLKEIIKEILIKQSALVKIIKKLSKKGYLSKERSEDDERKVIISINKEQRSKIESL 100 (109)
T ss_pred CcCcHHHHHHHHCCCHHHHHHHHHHHHHCCCEeccCCcccCCeEEEEECHHHHHHHHHH
Confidence 45999999999999999999999999999999877777777643 556555544443
No 120
>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=97.03 E-value=0.0045 Score=38.52 Aligned_cols=62 Identities=21% Similarity=0.224 Sum_probs=43.9
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHH---HHHHhCCCCcHHHHHHHh
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIE---EYKGENPAMFSWEIRDRL 75 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~---~~v~~~pd~tl~El~~~L 75 (77)
+++.++|+.+|||..|+.-|=+ .|-+.|...+|. +.=++.+..+|. .+. +-++++.||.+.+
T Consensus 1 ~~Igeva~~~gvs~~tlRyYe~----~GLl~p~r~~gy--R~Y~~~~l~~l~~I~~lr--~~G~~L~~I~~~l 65 (118)
T cd04776 1 YTISELAREFDVTPRTLRFYED----KGLLSPERRGQT--RVYSRRDRARLKLILRGK--RLGFSLEEIRELL 65 (118)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH----CCCCCCcCCCCc--cccCHHHHHHHHHHHHHH--HCCCCHHHHHHHH
Confidence 5788999999999999876644 499999766543 344555555443 433 4579999988755
No 121
>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=97.01 E-value=0.0089 Score=37.41 Aligned_cols=64 Identities=16% Similarity=0.079 Sum_probs=40.7
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHH---HHHHHHhCCCCcHHHHHHHh
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERR---IEEYKGENPAMFSWEIRDRL 75 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~---i~~~v~~~pd~tl~El~~~L 75 (77)
|+..++|+.+|||.+|+.-|- +.|-+.|.....+..+.-++.+... |..+. +=++++.||.+-+
T Consensus 1 ~~I~e~a~~~gvs~~tlR~Ye----~~Gll~~~~r~~~g~R~Y~~~~l~~l~~I~~lr--~~G~sL~eI~~~l 67 (126)
T cd04785 1 LSIGELARRTGVNVETIRYYE----SIGLLPEPARTAGGYRLYGAAHVERLRFIRRAR--DLGFSLEEIRALL 67 (126)
T ss_pred CCHHHHHHHHCcCHHHHHHHH----HCCCCCCCCcCCCCccccCHHHHHHHHHHHHHH--HCCCCHHHHHHHH
Confidence 678999999999999987554 4588876433211223344444443 43433 4458888888654
No 122
>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=96.99 E-value=0.0014 Score=35.47 Aligned_cols=32 Identities=19% Similarity=0.260 Sum_probs=29.3
Q ss_pred CHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513 7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPG 38 (77)
Q Consensus 7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk 38 (77)
+.+++|..|+||.++|.+.++++.+.|-+...
T Consensus 27 ~~~~la~~~~is~~~v~~~l~~L~~~G~i~~~ 58 (66)
T cd07377 27 SERELAEELGVSRTTVREALRELEAEGLVERR 58 (66)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEec
Confidence 48899999999999999999999999988644
No 123
>PRK10870 transcriptional repressor MprA; Provisional
Probab=96.98 E-value=0.0042 Score=40.96 Aligned_cols=50 Identities=16% Similarity=0.187 Sum_probs=41.8
Q ss_pred CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCC---CCCHHHHH
Q psy15513 5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR---VATPDVER 54 (77)
Q Consensus 5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~---~~~~~~~~ 54 (77)
++++.++|+.++++++||++.+++..+.|=|...+...+++. .+|++-.+
T Consensus 71 ~it~~eLa~~l~l~~~tvsr~v~rLe~kGlV~R~~~~~DrR~~~v~LT~~G~~ 123 (176)
T PRK10870 71 SIQPSELSCALGSSRTNATRIADELEKRGWIERRESDNDRRCLHLQLTEKGHE 123 (176)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHH
Confidence 488899999999999999999999999999988887777664 35554333
No 124
>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=96.98 E-value=0.0049 Score=39.37 Aligned_cols=63 Identities=21% Similarity=0.175 Sum_probs=43.8
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHH---HHHHHHHhCCCCcHHHHHHHh
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVER---RIEEYKGENPAMFSWEIRDRL 75 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~---~i~~~v~~~pd~tl~El~~~L 75 (77)
+++.++|+.+|||.+|+..|- +.|-+.|....++. +.-++.+.. +|..+. +=++++.||.+.+
T Consensus 1 y~I~e~a~~~gvs~~TLR~Ye----~~GLl~p~r~~~g~-R~Y~~~~l~~l~~I~~lr--~~G~sL~eI~~~l 66 (134)
T cd04779 1 YRIGQLAHLAGVSKRTIDYYT----NLGLLTPERSDSNY-RYYDETALDRLQLIEHLK--GQRLSLAEIKDQL 66 (134)
T ss_pred CCHHHHHHHHCcCHHHHHHHH----HCCCCCCccCCCCC-eeECHHHHHHHHHHHHHH--HCCCCHHHHHHHH
Confidence 578899999999999998885 45999887653322 223333333 455553 3569999998765
No 125
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=96.97 E-value=0.002 Score=36.50 Aligned_cols=34 Identities=12% Similarity=0.252 Sum_probs=31.9
Q ss_pred CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513 5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG 38 (77)
Q Consensus 5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk 38 (77)
|++..+||+.+||+.++|.|.+..+.+.|-|...
T Consensus 22 ~~ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~~~ 55 (68)
T smart00550 22 TSTALQLAKNLGLPKKEVNRVLYSLEKKGKVCKQ 55 (68)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEec
Confidence 5999999999999999999999999999999764
No 126
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=96.96 E-value=0.0045 Score=38.92 Aligned_cols=42 Identities=10% Similarity=0.245 Sum_probs=38.0
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCC
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKP 45 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~ 45 (77)
.|.++.++|+.++++++||++.+++..+.|=|.-.+...+++
T Consensus 45 ~~~t~~eLa~~l~~~~~tvt~~v~~Le~~GlV~r~~~~~DrR 86 (144)
T PRK03573 45 PEQSQIQLAKAIGIEQPSLVRTLDQLEEKGLISRQTCASDRR 86 (144)
T ss_pred CCCCHHHHHHHhCCChhhHHHHHHHHHHCCCEeeecCCCCcC
Confidence 468999999999999999999999999999998887766666
No 127
>TIGR00721 tfx DNA-binding protein, Tfx family. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.
Probab=96.94 E-value=0.001 Score=42.86 Aligned_cols=29 Identities=28% Similarity=0.371 Sum_probs=26.1
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
..|+|..+||++||+|+++|+++.++.++
T Consensus 19 ~~GlTq~EIAe~LgiS~stV~~~e~ra~k 47 (137)
T TIGR00721 19 EKGLSQKEIAKELKTTRANVSAIEKRAME 47 (137)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHHhHHH
Confidence 58999999999999999999998887554
No 128
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=96.94 E-value=0.0012 Score=36.61 Aligned_cols=35 Identities=20% Similarity=0.178 Sum_probs=30.0
Q ss_pred CHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccC
Q psy15513 7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIG 41 (77)
Q Consensus 7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~g 41 (77)
|..++|++|+||.+||.+-+.+..+.|-+...+..
T Consensus 26 s~~~la~~~~vsr~tvr~al~~L~~~g~i~~~~~~ 60 (64)
T PF00392_consen 26 SERELAERYGVSRTTVREALRRLEAEGLIERRPGR 60 (64)
T ss_dssp -HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT
T ss_pred CHHHHHHHhccCCcHHHHHHHHHHHCCcEEEECCc
Confidence 78999999999999999999999999999777543
No 129
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=96.94 E-value=0.00043 Score=43.76 Aligned_cols=30 Identities=20% Similarity=0.356 Sum_probs=26.1
Q ss_pred CccCCCCHHHHHHHhccCHHHHHHHHHHHH
Q psy15513 1 MAAAGVRPCVISRQLRVSHGCVSKILNRYQ 30 (77)
Q Consensus 1 l~~~G~s~~~iA~rf~VS~stv~r~~~r~r 30 (77)
|.+.|+|+.+||+-||||++.||++++-.+
T Consensus 18 L~eeG~Sq~~iA~LLGltqaAVS~Yls~kr 47 (119)
T COG2522 18 LIEEGLSQYRIAKLLGLTQAAVSQYLSGKR 47 (119)
T ss_pred HHHcCCcHHHHHHHhCCCHHHHHHHHccCC
Confidence 345799999999999999999999997543
No 130
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=96.93 E-value=0.0031 Score=36.94 Aligned_cols=34 Identities=24% Similarity=0.370 Sum_probs=30.5
Q ss_pred CHHHHHHHhccCHHHHHHHHHHHHHhcCCCcccc
Q psy15513 7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI 40 (77)
Q Consensus 7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~ 40 (77)
++.++|+.|+||++||++.+++..+.|=+...+.
T Consensus 1 ~~~ela~~l~is~stvs~~l~~L~~~glI~r~~~ 34 (96)
T smart00529 1 RTSEIAERLNVSPPTVTQMLKKLEKDGLVEYEPY 34 (96)
T ss_pred CHHHHHHHhCCChHHHHHHHHHHHHCCCEEEcCC
Confidence 3679999999999999999999999998877654
No 131
>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=96.93 E-value=0.0069 Score=37.56 Aligned_cols=63 Identities=19% Similarity=0.129 Sum_probs=42.6
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHH---HHHHhCCCCcHHHHHHHh
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIE---EYKGENPAMFSWEIRDRL 75 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~---~~v~~~pd~tl~El~~~L 75 (77)
|++.++|+.+|||..|+.-|-++ |-+.|....+ ..+.=++.+..+|. .+. .=++++.|+++.+
T Consensus 1 m~IgevA~~~gvs~~tlRyYe~~----GLl~p~~~~~-gyR~Y~~~~l~~l~~I~~lr--~~G~~L~eI~~~l 66 (120)
T cd04781 1 LDIAEVARQSGLPASTLRYYEEK----GLIASIGRRG-LRRQYDPQVLDRLALIALGR--AAGFSLDEIQAML 66 (120)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC----CCCCCCcCCC-CceecCHHHHHHHHHHHHHH--HcCCCHHHHHHHH
Confidence 67899999999999999776654 8888754433 22334444455443 332 2379999998754
No 132
>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=96.92 E-value=0.0049 Score=37.67 Aligned_cols=54 Identities=15% Similarity=0.168 Sum_probs=42.2
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCC---CCCHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR---VATPDVERRIE 57 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~---~~~~~~~~~i~ 57 (77)
.+++..++|+.+++++++|++.+++..+.|=|.-.+...+++. .+|++-.+.+.
T Consensus 41 ~~~t~~ela~~~~~~~~tvs~~l~~Le~~GlI~r~~~~~D~R~~~v~LT~~G~~~~~ 97 (118)
T TIGR02337 41 GSMEFTQLANQACILRPSLTGILARLERDGLVTRLKASNDQRRVYISLTPKGQALYA 97 (118)
T ss_pred CCcCHHHHHHHhCCCchhHHHHHHHHHHCCCEEeccCCCCCCeeEEEECHhHHHHHH
Confidence 5689999999999999999999999999999987665555542 45565444333
No 133
>TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
Probab=96.89 E-value=0.0011 Score=35.06 Aligned_cols=24 Identities=13% Similarity=0.147 Sum_probs=22.5
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHH
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKIL 26 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~ 26 (77)
+.|++..++|+..|||+++|++|.
T Consensus 13 ~~gltq~~lA~~~gvs~~~vs~~e 36 (58)
T TIGR03070 13 ALGLTQADLADLAGVGLRFIRDVE 36 (58)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHH
Confidence 468999999999999999999997
No 134
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=96.88 E-value=0.00057 Score=37.40 Aligned_cols=27 Identities=33% Similarity=0.517 Sum_probs=20.9
Q ss_pred CccCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513 1 MAAAGVRPCVISRQLRVSHGCVSKILN 27 (77)
Q Consensus 1 l~~~G~s~~~iA~rf~VS~stv~r~~~ 27 (77)
|.+.|++..++|+..|||.+|+++|++
T Consensus 6 m~~~~it~~~La~~~gis~~tl~~~~~ 32 (63)
T PF13443_consen 6 MAERGITQKDLARKTGISRSTLSRILN 32 (63)
T ss_dssp HHHTT--HHHHHHHHT--HHHHHHHHT
T ss_pred HHHcCCCHHHHHHHHCcCHHHHHHHHh
Confidence 356899999999999999999999987
No 135
>PHA01976 helix-turn-helix protein
Probab=96.85 E-value=0.0013 Score=36.33 Aligned_cols=24 Identities=21% Similarity=0.166 Sum_probs=22.3
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHH
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKIL 26 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~ 26 (77)
+.|+|..++|+.+|||+++|++|.
T Consensus 13 ~~glt~~~lA~~~gvs~~~v~~~e 36 (67)
T PHA01976 13 ARAWSAPELSRRAGVRHSLIYDFE 36 (67)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHH
Confidence 478999999999999999999995
No 136
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=96.84 E-value=0.0037 Score=43.18 Aligned_cols=44 Identities=16% Similarity=0.114 Sum_probs=30.8
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHh
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGE 62 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~ 62 (77)
|+..+||+..|||.+||||.++.. +..+ ...++.++.|++.+++
T Consensus 1 ~ti~dIA~~aGVS~~TVSrvLn~~------------~~~~-~Vs~~tr~rV~~~a~e 44 (328)
T PRK11303 1 MKLDEIARLAGVSRTTASYVINGK------------AKQY-RVSDKTVEKVMAVVRE 44 (328)
T ss_pred CCHHHHHHHhCCCHHHHHHHHcCC------------CCCC-CcCHHHHHHHHHHHHH
Confidence 578999999999999999999621 0001 2345566777766665
No 137
>PRK01381 Trp operon repressor; Provisional
Probab=96.84 E-value=0.00038 Score=42.75 Aligned_cols=26 Identities=15% Similarity=0.164 Sum_probs=21.8
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHH
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNR 28 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r 28 (77)
+.++|.|+||..+|||.+||+|=-+-
T Consensus 53 ~g~~sQREIa~~lGvSiaTITRgsn~ 78 (99)
T PRK01381 53 RGELSQREIKQELGVGIATITRGSNS 78 (99)
T ss_pred cCCcCHHHHHHHhCCceeeehhhHHH
Confidence 34599999999999999999985443
No 138
>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=96.83 E-value=0.0028 Score=38.97 Aligned_cols=47 Identities=17% Similarity=0.292 Sum_probs=34.8
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHhCCCC
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGENPAM 66 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~pd~ 66 (77)
+.|++..++|+.+|+|++||++| ++|...|. . ....+..++..+|+.
T Consensus 76 ~~gltq~~lA~~lg~~~~tis~~-----e~g~~~p~-----------~-~~~~l~~~l~~~p~~ 122 (127)
T TIGR03830 76 KLGLSQREAAELLGGGVNAFSRY-----ERGEVRPS-----------K-ALDKLLRLLDKHPEL 122 (127)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHH-----HCCCCCCC-----------H-HHHHHHHHHHHChHH
Confidence 46899999999999999999999 55654432 1 134466777778754
No 139
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=96.82 E-value=0.0023 Score=36.53 Aligned_cols=36 Identities=14% Similarity=0.267 Sum_probs=30.1
Q ss_pred CCCHHHHHHHhccCHHHHHHHHHHHHH-------hcCCCcccc
Q psy15513 5 GVRPCVISRQLRVSHGCVSKILNRYQE-------TGSIRPGVI 40 (77)
Q Consensus 5 G~s~~~iA~rf~VS~stv~r~~~r~r~-------tG~v~pk~~ 40 (77)
-+|..++|+++|+++.+|.+|+..||+ +|+.+++-+
T Consensus 13 ~~s~~~Aa~~lG~~~~~v~~wv~~fR~wll~LDPSG~~E~RVR 55 (65)
T PF05344_consen 13 QISVAQAADRLGTDPGTVRRWVRMFRQWLLQLDPSGHWEARVR 55 (65)
T ss_pred cccHHHHHHHHCcCHHHHHHHHHHHHHHHHHcCCCCChHHHhh
Confidence 378999999999999999999999997 466555544
No 140
>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function.
Probab=96.81 E-value=0.0022 Score=39.74 Aligned_cols=28 Identities=18% Similarity=0.280 Sum_probs=26.2
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
.|+++.++|.+.|||.+|+.+++..-|.
T Consensus 56 egl~QeeaA~~MgVSR~T~~ril~~ARk 83 (106)
T PF02001_consen 56 EGLSQEEAAERMGVSRPTFQRILESARK 83 (106)
T ss_pred cCCCHHHHHHHcCCcHHHHHHHHHHHHH
Confidence 6899999999999999999999998775
No 141
>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=96.81 E-value=0.0018 Score=36.41 Aligned_cols=26 Identities=23% Similarity=0.247 Sum_probs=23.3
Q ss_pred CCCHHHHHHHhccCHHHHHHHHHHHH
Q psy15513 5 GVRPCVISRQLRVSHGCVSKILNRYQ 30 (77)
Q Consensus 5 G~s~~~iA~rf~VS~stv~r~~~r~r 30 (77)
++.-.+||..||||.+||.+|-.+..
T Consensus 22 ~i~lkdIA~~Lgvs~~tIr~WK~~dk 47 (60)
T PF10668_consen 22 KIKLKDIAEKLGVSESTIRKWKSRDK 47 (60)
T ss_pred CccHHHHHHHHCCCHHHHHHHhhhcc
Confidence 48999999999999999999987744
No 142
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=96.79 E-value=0.0013 Score=36.40 Aligned_cols=25 Identities=32% Similarity=0.446 Sum_probs=20.3
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILN 27 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~ 27 (77)
..|+|..++|+++|||+++|++|-+
T Consensus 12 ~~gls~~~lA~~~g~s~s~v~~iE~ 36 (64)
T PF13560_consen 12 RAGLSQAQLADRLGVSQSTVSRIER 36 (64)
T ss_dssp CHTS-HHHHHHHHTS-HHHHHHHHT
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHC
Confidence 4689999999999999999999743
No 143
>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=96.78 E-value=0.013 Score=36.06 Aligned_cols=63 Identities=16% Similarity=0.106 Sum_probs=43.7
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHH---HHHHHHhCCCCcHHHHHHHh
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERR---IEEYKGENPAMFSWEIRDRL 75 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~---i~~~v~~~pd~tl~El~~~L 75 (77)
|+..++|+.+|||+.|+.-|- +.|-+.|....+ ..+.-++.+..+ |..+. +-++++.||.+.+
T Consensus 1 ~~ige~a~~~gvs~~tLryYe----~~GLi~p~~~~~-~yR~Y~~~d~~~l~~I~~lr--~~G~sl~eI~~~l 66 (116)
T cd04769 1 MYIGELAQQTGVTIKAIRLYE----EKGLLPSPKRSG-NYRVYDAQHVECLRFIKEAR--QLGFTLAELKAIF 66 (116)
T ss_pred CCHHHHHHHHCcCHHHHHHHH----HCCCCCCCCCCC-CceeeCHHHHHHHHHHHHHH--HcCCCHHHHHHHH
Confidence 688999999999999987664 459998866554 334444545554 44443 3468899988654
No 144
>PRK10072 putative transcriptional regulator; Provisional
Probab=96.77 E-value=0.0015 Score=39.74 Aligned_cols=51 Identities=20% Similarity=0.266 Sum_probs=36.6
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHhCCCCcHHHH
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGENPAMFSWEI 71 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~pd~tl~El 71 (77)
+.|++..++|+.+|||.+||++|.+ |...|. . + . ..+.+++..+| -++.+|
T Consensus 44 ~~glTQ~elA~~lGvS~~TVs~WE~-----G~r~P~--------~--~-~-l~Ll~~L~~~P-~~~~~l 94 (96)
T PRK10072 44 GTGLKIDDFARVLGVSVAMVKEWES-----RRVKPS--------S--A-E-LKLMRLIQANP-ALSKQL 94 (96)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHc-----CCCCCC--------H--H-H-HHHHHHHhhCH-HHHHHH
Confidence 4699999999999999999999964 333332 1 2 2 33788899999 444443
No 145
>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=96.76 E-value=0.001 Score=34.37 Aligned_cols=27 Identities=22% Similarity=0.331 Sum_probs=21.8
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHH
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRY 29 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~ 29 (77)
..|-...++|+.||||.+|+++-+++|
T Consensus 16 ~~~gn~~~aA~~Lgisr~tL~~klkk~ 42 (42)
T PF02954_consen 16 RCGGNVSKAARLLGISRRTLYRKLKKY 42 (42)
T ss_dssp HTTT-HHHHHHHHTS-HHHHHHHHHHC
T ss_pred HhCCCHHHHHHHHCCCHHHHHHHHHhC
Confidence 356688999999999999999999875
No 146
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=96.76 E-value=0.0018 Score=41.89 Aligned_cols=30 Identities=30% Similarity=0.294 Sum_probs=26.7
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHHh
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQET 32 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~t 32 (77)
..|+|..+||+.||+|+++|++|.++.++.
T Consensus 19 ~~GlTq~EIAe~LGiS~~tVs~ie~ra~kk 48 (141)
T PRK03975 19 ERGLTQQEIADILGTSRANVSSIEKRAREN 48 (141)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 589999999999999999999999876553
No 147
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=96.76 E-value=0.0061 Score=37.74 Aligned_cols=45 Identities=29% Similarity=0.407 Sum_probs=35.5
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHhCCC
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGENPA 65 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~pd 65 (77)
.|+|+-+-|+.||||.+||++| |.|...|- | + +..++.+|+.+|-
T Consensus 56 ~~lSQ~vFA~~L~vs~~Tv~~W-----EqGr~kPs--g--------~--AlkLL~ivq~~p~ 100 (104)
T COG2944 56 LGLSQPVFARYLGVSVSTVRKW-----EQGRKKPS--G--------A--ALKLLRIVQNHPL 100 (104)
T ss_pred hCCCHHHHHHHHCCCHHHHHHH-----HcCCcCCC--C--------H--HHHHHHHHHhcch
Confidence 5799999999999999999999 45544432 1 2 5678999999884
No 148
>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=96.75 E-value=0.0017 Score=38.96 Aligned_cols=29 Identities=14% Similarity=0.142 Sum_probs=25.2
Q ss_pred ccCCCCHHHHHHHhccCHHHHHHHHHHHH
Q psy15513 2 AAAGVRPCVISRQLRVSHGCVSKILNRYQ 30 (77)
Q Consensus 2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r 30 (77)
...|+|.++||+.+|||.+||+|--+-..
T Consensus 46 L~~g~syreIa~~tgvS~aTItRvsr~Lk 74 (87)
T PF01371_consen 46 LDEGKSYREIAEETGVSIATITRVSRCLK 74 (87)
T ss_dssp HHTTSSHHHHHHHHTSTHHHHHHHHHHHH
T ss_pred HHCCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 45899999999999999999999766544
No 149
>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=96.75 E-value=0.0031 Score=42.16 Aligned_cols=36 Identities=17% Similarity=0.242 Sum_probs=32.7
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG 38 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk 38 (77)
..++|..++|+.|+||++||++.++++.+.|-|...
T Consensus 13 ~~~~t~~eLA~~lgis~~tV~~~L~~Le~~GlV~r~ 48 (203)
T TIGR02702 13 QGQATAAALAEALAISPQAVRRHLKDLETEGLIEYE 48 (203)
T ss_pred cCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEe
Confidence 356999999999999999999999999999999654
No 150
>PHA00675 hypothetical protein
Probab=96.74 E-value=0.0015 Score=38.44 Aligned_cols=33 Identities=21% Similarity=0.402 Sum_probs=26.4
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCC
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIR 36 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~ 36 (77)
.+|.|.-+||+.||||.|||+.+....+ =|++.
T Consensus 37 r~G~s~~~IA~~fGVsrstV~~I~~gk~-W~~~~ 69 (78)
T PHA00675 37 VEGMSYAVLAEKFEQSKGAIAKICRYER-RGQFA 69 (78)
T ss_pred hcCccHHHHHHHhCCCHHHHHHHHccch-hhhee
Confidence 4789999999999999999999876543 34443
No 151
>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional
Probab=96.74 E-value=0.012 Score=38.46 Aligned_cols=62 Identities=18% Similarity=0.153 Sum_probs=41.8
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcccc-CCCCCCCCCHHHHHH---HHHHHHhCCCCcHHHHHHHh
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI-GGSKPRVATPDVERR---IEEYKGENPAMFSWEIRDRL 75 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~-gg~~~~~~~~~~~~~---i~~~v~~~pd~tl~El~~~L 75 (77)
|++.++|+++|||..|+..| -+.|-+.|... +|+ +.-++.+..+ |..+. +=+++|.||++.|
T Consensus 12 ~~IgevAk~~gvs~~TlRyY----E~~GLi~~~r~~~g~--R~Y~~~~i~~L~~I~~lr--~lG~sL~eIk~ll 77 (154)
T PRK15002 12 LTPGEVAKRSGVAVSALHFY----ESKGLITSIRNSGNQ--RRYKRDVLRYVAIIKIAQ--RIGIPLATIGEAF 77 (154)
T ss_pred ccHHHHHHHHCcCHHHHHHH----HHCCCCCCccCCCCC--EEECHHHHHHHHHHHHHH--HcCCCHHHHHHHH
Confidence 78999999999999998665 45598888544 333 3334444443 33333 3458888888765
No 152
>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=96.74 E-value=0.0027 Score=35.60 Aligned_cols=32 Identities=19% Similarity=0.147 Sum_probs=28.9
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCC
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSI 35 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v 35 (77)
.-++..++|.+|+||.+||++-+++..+.|-.
T Consensus 12 ~~~~~~eLa~~l~vS~~tv~~~l~~L~~~g~~ 43 (69)
T TIGR00122 12 NPFSGEKLGEALGMSRTAVNKHIQTLREWGVD 43 (69)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCe
Confidence 34778999999999999999999999998875
No 153
>COG2826 Tra8 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]
Probab=96.73 E-value=0.0024 Score=46.05 Aligned_cols=72 Identities=19% Similarity=0.127 Sum_probs=49.0
Q ss_pred ccCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCC---------CccccCCCCCCCCCHHHHHHHHHHHHhCCCCcHHHHH
Q psy15513 2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETGSI---------RPGVIGGSKPRVATPDVERRIEEYKGENPAMFSWEIR 72 (77)
Q Consensus 2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v---------~pk~~gg~~~~~~~~~~~~~i~~~v~~~pd~tl~El~ 72 (77)
.+.|+|.++||++||..+|||+|=++|=+..+.. .-.+.+.-++...+++-.+.|.+.+++. +.-.+|+
T Consensus 20 ~~~~~S~reIA~~LgRh~sTIsRElkRn~~~~~Y~a~~A~~~~~~~rrr~~~k~~~~~eL~~~V~e~L~~~--wSPEQI~ 97 (318)
T COG2826 20 LKAKMSIREIAKQLNRHHSTISRELKRNRTRDIYSAVKAQERYRMLRRRRIRKLKLNPELRELVLEKLKSK--WSPEQII 97 (318)
T ss_pred HHcCCCHHHHHHHhCCCcchhhHHHhcCCccceeeHHHHHHHHHHhhcccCCcccCCHHHHHHHHHHHHhh--CCHHHHH
Confidence 4679999999999999999999988874433312 1111222344567788888888887663 5555555
Q ss_pred HHh
Q psy15513 73 DRL 75 (77)
Q Consensus 73 ~~L 75 (77)
-.|
T Consensus 98 g~l 100 (318)
T COG2826 98 GRL 100 (318)
T ss_pred HHH
Confidence 444
No 154
>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=96.73 E-value=0.0026 Score=34.57 Aligned_cols=30 Identities=23% Similarity=0.254 Sum_probs=26.3
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHHh
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQET 32 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~t 32 (77)
..|++..+||..++||.+||+..++..+..
T Consensus 16 ~~G~~~~eIA~~l~is~~tV~~~~~~i~~K 45 (58)
T PF00196_consen 16 AQGMSNKEIAEELGISEKTVKSHRRRIMKK 45 (58)
T ss_dssp HTTS-HHHHHHHHTSHHHHHHHHHHHHHHH
T ss_pred HhcCCcchhHHhcCcchhhHHHHHHHHHHH
Confidence 479999999999999999999999987764
No 155
>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=96.70 E-value=0.00091 Score=37.40 Aligned_cols=36 Identities=19% Similarity=0.261 Sum_probs=33.1
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccc
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV 39 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~ 39 (77)
.+++..+||+.+++|.++|++.++...+.|-|...+
T Consensus 21 ~~~t~~eIa~~l~i~~~~v~~~L~~L~~~GlV~~~~ 56 (68)
T PF01978_consen 21 GPATAEEIAEELGISRSTVYRALKSLEEKGLVEREE 56 (68)
T ss_dssp CHEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEc
Confidence 458999999999999999999999999999997765
No 156
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=96.69 E-value=0.0017 Score=37.68 Aligned_cols=25 Identities=24% Similarity=0.396 Sum_probs=20.3
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILN 27 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~ 27 (77)
+.|+|..++|+++|||++.|+++.+
T Consensus 29 ~~~ltQ~e~A~~lgisq~~vS~l~~ 53 (80)
T PF13744_consen 29 ERGLTQAELAERLGISQPRVSRLEN 53 (80)
T ss_dssp CCT--HHHHHHHHTS-HHHHHHHHT
T ss_pred HcCCCHHHHHHHHCCChhHHHHHHc
Confidence 5799999999999999999999875
No 157
>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=96.69 E-value=0.011 Score=38.08 Aligned_cols=63 Identities=17% Similarity=0.126 Sum_probs=42.6
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHH---HHHHHHHhCCCCcHHHHHHHh
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVER---RIEEYKGENPAMFSWEIRDRL 75 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~---~i~~~v~~~pd~tl~El~~~L 75 (77)
|++.++|+.+|||..|+.-|=+. |-+.|....++. +.=++.+.. +|..+.+ =++++.||++.+
T Consensus 2 ~~IgevA~~~Gvs~~tLRyYE~~----GLl~~~r~~~g~-R~Y~~~di~~l~~I~~lr~--~G~sL~eI~~~l 67 (142)
T TIGR01950 2 LTVGELAKRSGVAVSALHFYESK----GLITSIRNSGNQ-RRYKRDVLRRVAVIKAAQR--VGIPLATIGEAL 67 (142)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC----CCCCCccCCCCC-EEECHHHHHHHHHHHHHHH--cCCCHHHHHHHH
Confidence 68899999999999998776554 989885543332 333344443 3444432 368999998765
No 158
>PF12759 HTH_Tnp_IS1: InsA C-terminal domain; InterPro: IPR024431 This entry represents the helix-turn-helix domain found at the C-terminal of InsA.
Probab=96.65 E-value=0.0013 Score=35.22 Aligned_cols=28 Identities=29% Similarity=0.274 Sum_probs=25.0
Q ss_pred CccCCCCHHHHHHHhccCHHHHHHHHHH
Q psy15513 1 MAAAGVRPCVISRQLRVSHGCVSKILNR 28 (77)
Q Consensus 1 l~~~G~s~~~iA~rf~VS~stv~r~~~r 28 (77)
|+.+|..+|+.|+.|+||.+||.|=+|.
T Consensus 17 ma~nG~GiRdtaRvL~I~~nTVlrtLK~ 44 (46)
T PF12759_consen 17 MAFNGSGIRDTARVLKISINTVLRTLKN 44 (46)
T ss_pred HHhcCCcchhhHhHhcchHHHHHHHHhc
Confidence 5678999999999999999999988764
No 159
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=96.65 E-value=0.003 Score=41.08 Aligned_cols=67 Identities=16% Similarity=0.257 Sum_probs=45.8
Q ss_pred CccCC-CCHHHHHHHhccCHHHHHHHHHHHHHhcCCC-------ccccCCCCC---CC----CCHHHHHHHHHHHHhCCC
Q psy15513 1 MAAAG-VRPCVISRQLRVSHGCVSKILNRYQETGSIR-------PGVIGGSKP---RV----ATPDVERRIEEYKGENPA 65 (77)
Q Consensus 1 l~~~G-~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~-------pk~~gg~~~---~~----~~~~~~~~i~~~v~~~pd 65 (77)
|.++| +|..+||+++|+|.+||.+=+++..+.|-+. |.+.|-+-. .+ ..+...+.+.+.+.+.|.
T Consensus 23 Lq~d~R~s~~eiA~~lglS~~tv~~Ri~rL~~~GvI~~~~~~v~p~~lg~~~~a~v~i~~~~~~~~~~~~~~~~l~~~p~ 102 (164)
T PRK11169 23 LQKDGRISNVELSKRVGLSPTPCLERVRRLERQGFIQGYTALLNPHYLDASLLVFVEITLNRGAPDVFEQFNAAVQKLEE 102 (164)
T ss_pred hccCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEEEECHHHhCCCEEEEEEEEEcCCChHHHHHHHHHHhcCcc
Confidence 34556 9999999999999999999999999999874 444443211 01 123333445566677776
Q ss_pred Cc
Q psy15513 66 MF 67 (77)
Q Consensus 66 ~t 67 (77)
+.
T Consensus 103 V~ 104 (164)
T PRK11169 103 IQ 104 (164)
T ss_pred ee
Confidence 54
No 160
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=96.63 E-value=0.0036 Score=39.75 Aligned_cols=28 Identities=21% Similarity=0.217 Sum_probs=25.6
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
.|+|..+||..||||.+||+.++.+-+.
T Consensus 143 ~~~s~~eIA~~lgis~~tV~~~l~ra~~ 170 (182)
T PRK09652 143 EGLSYEEIAEIMGCPIGTVRSRIFRARE 170 (182)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 7999999999999999999999887654
No 161
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=96.63 E-value=0.0033 Score=41.37 Aligned_cols=29 Identities=24% Similarity=0.291 Sum_probs=26.4
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
-.|+|..+||..+|||.+||+|.++..+.
T Consensus 149 ~~Gls~~EIA~~lgiS~~tV~r~l~~aR~ 177 (185)
T PF07638_consen 149 FEGLSVEEIAERLGISERTVRRRLRRARA 177 (185)
T ss_pred HCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 37999999999999999999999988764
No 162
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=96.63 E-value=0.013 Score=33.80 Aligned_cols=52 Identities=19% Similarity=0.239 Sum_probs=39.6
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCC---CCCCHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKP---RVATPDVERR 55 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~---~~~~~~~~~~ 55 (77)
.+++..++|+.+++|+++|++.++.+.+.|-|...+.+++++ -.+++.-...
T Consensus 23 ~~~~~~~la~~~~~s~~~i~~~l~~L~~~g~v~~~~~~~~~r~~~~~lT~~g~~~ 77 (101)
T smart00347 23 GPLSVSELAKRLGVSPSTVTRVLDRLEKKGLIRRLPSPEDRRSVLVSLTEEGREL 77 (101)
T ss_pred CCcCHHHHHHHHCCCchhHHHHHHHHHHCCCeEecCCCCCCCeEEEEECHhHHHH
Confidence 358999999999999999999999999999997655444433 2345543433
No 163
>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=96.62 E-value=0.021 Score=37.66 Aligned_cols=62 Identities=16% Similarity=0.182 Sum_probs=42.1
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcccc--CCCCCCCCCHHHHH---HHHHHHHhCCCCcHHHHHHHh
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI--GGSKPRVATPDVER---RIEEYKGENPAMFSWEIRDRL 75 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~--gg~~~~~~~~~~~~---~i~~~v~~~pd~tl~El~~~L 75 (77)
+++.++|+.+|||..|+..|-+ .|-+.|... +|.| .=++.+.. .|..+ .+=++++.||+.-|
T Consensus 2 ~~I~evA~~~gvs~~tLRyYe~----~GLl~p~~r~~~gyR--~Y~~~dl~rL~~I~~l--r~~G~sL~eI~~ll 68 (172)
T cd04790 2 LTISQLARQFGLSRSTLLYYER----IGLLSPSARSESNYR--LYGERDLERLEQICAY--RSAGVSLEDIRSLL 68 (172)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCccCCCCCc--cCCHHHHHHHHHHHHH--HHcCCCHHHHHHHH
Confidence 5889999999999999877654 598888543 3333 33333333 34444 33468899988765
No 164
>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=96.57 E-value=0.0019 Score=35.38 Aligned_cols=36 Identities=25% Similarity=0.392 Sum_probs=31.1
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCC
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGG 42 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg 42 (77)
++..++|..|+||.+||.|=+....+.|-+.- ..||
T Consensus 15 ~s~~ela~~~~VS~~TiRRDl~~L~~~g~i~r-~~GG 50 (57)
T PF08220_consen 15 VSVKELAEEFGVSEMTIRRDLNKLEKQGLIKR-THGG 50 (57)
T ss_pred EEHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE-EcCE
Confidence 78999999999999999999999999997653 3444
No 165
>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=96.55 E-value=0.0042 Score=38.58 Aligned_cols=29 Identities=17% Similarity=0.113 Sum_probs=26.3
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
-.|+|..+||..||||.+||..++.+.++
T Consensus 127 ~~~~~~~eIA~~lgis~~tv~~~~~ra~~ 155 (161)
T TIGR02985 127 FEGKSYKEIAEELGISVKTVEYHISKALK 155 (161)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 36999999999999999999999988764
No 166
>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID. Members of this protein are the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if and only if the species is capable of endospore formation as occurs in the model species Bacillus subtilis. SpoIIID is a DNA binding protein that, in B. subtilis, downregulates many genes but also turns on ten genes.
Probab=96.55 E-value=0.011 Score=34.87 Aligned_cols=41 Identities=17% Similarity=0.227 Sum_probs=30.6
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHH
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKG 61 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~ 61 (77)
++..++|+.||||.+||++-+. + +.+ ...++..+.|.+.++
T Consensus 20 ~ti~dvA~~~gvS~~TVsr~L~-------------~-~~~-~Vs~~Tr~rV~~aa~ 60 (80)
T TIGR02844 20 ATVRETAKVFGVSKSTVHKDVT-------------E-RLP-EINPELAEEVKEVLD 60 (80)
T ss_pred CCHHHHHHHhCCCHHHHHHHhc-------------C-CCC-CCCHHHHHHHHHHHc
Confidence 7889999999999999999661 1 111 244667778888877
No 167
>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre
Probab=96.54 E-value=0.0014 Score=34.55 Aligned_cols=18 Identities=44% Similarity=0.506 Sum_probs=16.7
Q ss_pred HHHHHhccCHHHHHHHHH
Q psy15513 10 VISRQLRVSHGCVSKILN 27 (77)
Q Consensus 10 ~iA~rf~VS~stv~r~~~ 27 (77)
++|+++|||.+||++|++
T Consensus 2 ~lA~~~gvs~~tvs~~l~ 19 (52)
T cd01392 2 DIARAAGVSVATVSRVLN 19 (52)
T ss_pred cHHHHHCcCHHHHHHHHc
Confidence 689999999999999983
No 168
>PRK15043 transcriptional regulator MirA; Provisional
Probab=96.53 E-value=0.015 Score=40.64 Aligned_cols=65 Identities=11% Similarity=0.075 Sum_probs=44.5
Q ss_pred CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHH---HHHHHHHhCCCCcHHHHHHHh
Q psy15513 5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVER---RIEEYKGENPAMFSWEIRDRL 75 (77)
Q Consensus 5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~---~i~~~v~~~pd~tl~El~~~L 75 (77)
-+++.++|+.+|||..|+..|-++ .|-+.|....|+. +.-++++.+ +|..+.+ -++++.|+++.+
T Consensus 3 ~ytIgeVA~~~GVs~~TLR~wErr---~GLL~P~Rt~~G~-R~Ys~~dv~rL~~I~~l~~--~G~~i~eIk~ll 70 (243)
T PRK15043 3 LYTIGEVALLCDINPVTLRAWQRR---YGLLKPQRTDGGH-RLFNDADIDRIREIKRWID--NGVQVSKVKMLL 70 (243)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHh---cCCCCCccCCCCC-EEECHHHHHHHHHHHHHHH--cCCCHHHHHHHH
Confidence 478999999999999999887654 4888886543322 333344444 3445543 468888887765
No 169
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=96.52 E-value=0.0046 Score=38.68 Aligned_cols=29 Identities=17% Similarity=-0.001 Sum_probs=26.2
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
-+|+|..+||..+|||.+||..++.|-+.
T Consensus 120 ~~~~s~~EIA~~l~is~~tV~~~~~ra~~ 148 (154)
T PRK06759 120 FVGKTMGEIALETEMTYYQVRWIYRQALE 148 (154)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 37999999999999999999999988654
No 170
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=96.52 E-value=0.0042 Score=40.52 Aligned_cols=37 Identities=30% Similarity=0.448 Sum_probs=33.9
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCC
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGG 42 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg 42 (77)
++..+||+.|+||++||+..+++..+-|=|.-.|.+|
T Consensus 25 ~~~~diA~~L~Vsp~sVt~ml~rL~~~GlV~~~~y~g 61 (154)
T COG1321 25 ARTKDIAERLKVSPPSVTEMLKRLERLGLVEYEPYGG 61 (154)
T ss_pred ccHHHHHHHhCCCcHHHHHHHHHHHHCCCeEEecCCC
Confidence 7889999999999999999999999999998776655
No 171
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=96.51 E-value=0.0062 Score=42.25 Aligned_cols=22 Identities=18% Similarity=0.152 Sum_probs=20.6
Q ss_pred CCHHHHHHHhccCHHHHHHHHH
Q psy15513 6 VRPCVISRQLRVSHGCVSKILN 27 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~ 27 (77)
.+..+||+..|||.+||||.++
T Consensus 6 ~ti~dIA~~agVS~~TVSrvLn 27 (331)
T PRK14987 6 PVLQDVADRVGVTKMTVSRFLR 27 (331)
T ss_pred CcHHHHHHHhCCCHHHhhhhhC
Confidence 6889999999999999999995
No 172
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=96.50 E-value=0.0079 Score=41.75 Aligned_cols=23 Identities=22% Similarity=0.141 Sum_probs=21.3
Q ss_pred CCCHHHHHHHhccCHHHHHHHHH
Q psy15513 5 GVRPCVISRQLRVSHGCVSKILN 27 (77)
Q Consensus 5 G~s~~~iA~rf~VS~stv~r~~~ 27 (77)
.++..+||+.+|||.+||||-++
T Consensus 6 ~~Ti~dIA~~agVS~~TVSr~Ln 28 (342)
T PRK10014 6 KITIHDVALAAGVSVSTVSLVLS 28 (342)
T ss_pred CCcHHHHHHHhCCCHHHHHHHHC
Confidence 37899999999999999999986
No 173
>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=96.50 E-value=0.0049 Score=37.30 Aligned_cols=29 Identities=28% Similarity=0.335 Sum_probs=26.4
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
-.|+|..+||+.||||.++|++++++.++
T Consensus 124 ~~g~s~~eIA~~l~~s~~~v~~~~~~~~~ 152 (158)
T TIGR02937 124 LEGLSYKEIAEILGISVGTVKRRLKRARK 152 (158)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 36999999999999999999999998764
No 174
>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=96.49 E-value=0.0042 Score=34.11 Aligned_cols=43 Identities=19% Similarity=0.282 Sum_probs=32.7
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCC
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKP 45 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~ 45 (77)
...++..++|..|++++++|++.+++..+-|=|.-.+...+++
T Consensus 16 ~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~glv~~~~~~~d~R 58 (68)
T PF13463_consen 16 DGPMTQSDLAERLGISKSTVSRIIKKLEEKGLVEKERDPHDKR 58 (68)
T ss_dssp TS-BEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEEEESSCTT
T ss_pred CCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEecCCCCcCC
Confidence 4568999999999999999999999999999995554433333
No 175
>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress. Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=96.48 E-value=0.0092 Score=35.18 Aligned_cols=41 Identities=24% Similarity=0.370 Sum_probs=34.5
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCC--ccccCCCCCC
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIR--PGVIGGSKPR 46 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~--pk~~gg~~~~ 46 (77)
+.-++||+.+++|.+||.+-++...+-|-|+ |.+.||..|.
T Consensus 24 VgSk~ia~~l~~s~aTIRN~M~~Le~lGlve~~p~~s~GriPT 66 (78)
T PF03444_consen 24 VGSKTIAEELGRSPATIRNEMADLEELGLVESQPHPSGGRIPT 66 (78)
T ss_pred cCHHHHHHHHCCChHHHHHHHHHHHHCCCccCCCCCCCCCCcC
Confidence 5678899999999999999999999999996 4455665554
No 176
>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=96.47 E-value=0.0028 Score=35.86 Aligned_cols=26 Identities=27% Similarity=0.442 Sum_probs=23.3
Q ss_pred ccCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513 2 AAAGVRPCVISRQLRVSHGCVSKILN 27 (77)
Q Consensus 2 ~~~G~s~~~iA~rf~VS~stv~r~~~ 27 (77)
-+.|++..++|+.+|||.++|++|.+
T Consensus 15 ~~~~~t~~~lA~~~gis~~tis~~~~ 40 (78)
T TIGR02607 15 EPLGLSIRALAKALGVSRSTLSRIVN 40 (78)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 35789999999999999999999854
No 177
>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=96.46 E-value=0.0072 Score=34.17 Aligned_cols=36 Identities=22% Similarity=0.281 Sum_probs=30.3
Q ss_pred CCC--CHHHHHHHhccC-HHHHHHHHHHHHHhcCCCccc
Q psy15513 4 AGV--RPCVISRQLRVS-HGCVSKILNRYQETGSIRPGV 39 (77)
Q Consensus 4 ~G~--s~~~iA~rf~VS-~stv~r~~~r~r~tG~v~pk~ 39 (77)
.|+ |.+|||+.||++ .++|...++...+.|-+.-.+
T Consensus 22 ~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le~kG~I~r~~ 60 (65)
T PF01726_consen 22 NGYPPTVREIAEALGLKSTSTVQRHLKALERKGYIRRDP 60 (65)
T ss_dssp HSS---HHHHHHHHTSSSHHHHHHHHHHHHHTTSEEEGC
T ss_pred cCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCcCccCCC
Confidence 454 568999999996 999999999999999997553
No 178
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=96.46 E-value=0.0035 Score=40.28 Aligned_cols=34 Identities=18% Similarity=0.316 Sum_probs=31.1
Q ss_pred cCC-CCHHHHHHHhccCHHHHHHHHHHHHHhcCCC
Q psy15513 3 AAG-VRPCVISRQLRVSHGCVSKILNRYQETGSIR 36 (77)
Q Consensus 3 ~~G-~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~ 36 (77)
++| .|..+||+.+|+|.+||.+=+++..+.|-+.
T Consensus 20 ~d~R~s~~eiA~~lglS~~tV~~Ri~rL~~~GvI~ 54 (153)
T PRK11179 20 ENARTPYAELAKQFGVSPGTIHVRVEKMKQAGIIT 54 (153)
T ss_pred HcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCee
Confidence 455 8999999999999999999999999999774
No 179
>PF09607 BrkDBD: Brinker DNA-binding domain; InterPro: IPR018586 This DNA-binding domain is the first approx. 100 residues of the N-terminal end of Brinker. The structure of this domain in complex with DNA consists of four alpha-helices that contain a helix-turn-helix DNA recognition motif specific for GC-rich DNA. The Brinker nuclear repressor is a major element of the Drosophila Decapentaplegic morphogen signalling pathway []. ; PDB: 2GLO_A.
Probab=96.43 E-value=0.0024 Score=35.68 Aligned_cols=24 Identities=21% Similarity=0.187 Sum_probs=19.6
Q ss_pred CHHHHHHHhccCHHHHHHHHHHHH
Q psy15513 7 RPCVISRQLRVSHGCVSKILNRYQ 30 (77)
Q Consensus 7 s~~~iA~rf~VS~stv~r~~~r~r 30 (77)
+.|.+|+.|+|+..+|.+|+++--
T Consensus 27 ~~RAaarkf~V~r~~Vr~W~kqe~ 50 (58)
T PF09607_consen 27 NQRAAARKFNVSRRQVRKWRKQEE 50 (58)
T ss_dssp -HHHHHHHTTS-HHHHHHHHTTHH
T ss_pred hHHHHHHHhCccHHHHHHHHHHHH
Confidence 458899999999999999998743
No 180
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=96.42 E-value=0.0057 Score=38.65 Aligned_cols=28 Identities=18% Similarity=0.038 Sum_probs=25.4
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
.|+|..+||..||+|.+||...+.|-+.
T Consensus 121 ~g~s~~EIA~~lgis~~tV~~~l~Rar~ 148 (160)
T PRK09642 121 EEKSYQEIALQEKIEVKTVEMKLYRARK 148 (160)
T ss_pred hCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 7999999999999999999888887664
No 181
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=96.42 E-value=0.0039 Score=37.34 Aligned_cols=63 Identities=19% Similarity=0.274 Sum_probs=43.9
Q ss_pred CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCc-------cccCCCC-----CCCCCHHHHHHHHHHHHhCCCCc
Q psy15513 5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRP-------GVIGGSK-----PRVATPDVERRIEEYKGENPAMF 67 (77)
Q Consensus 5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~p-------k~~gg~~-----~~~~~~~~~~~i~~~v~~~pd~t 67 (77)
.++..++|+.+|+|.+||.+.+++..+.|-+.. ...|-+- -....+...+.+.+.+.+.|.++
T Consensus 17 ~~~~~~la~~l~~s~~tv~~~l~~L~~~g~i~~~~~~~~~~~~g~~~~~~v~i~~~~~~~~~~v~~~l~~~p~v~ 91 (108)
T smart00344 17 RISLAELAKKVGLSPSTVHNRVKRLEEEGVIKGYTAVINPKKLGLSVTAFVGVDLESPDKLEEFLEKLEKLPEVV 91 (108)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeceEEEeCHHHcCCCEEEEEEEEECChhHHHHHHHHHhCCcceE
Confidence 489999999999999999999999999998752 1112110 01111344566777788888654
No 182
>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=96.41 E-value=0.0057 Score=38.37 Aligned_cols=28 Identities=29% Similarity=0.335 Sum_probs=26.0
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
.|+|..+||+.+|||.+||...+.|-+.
T Consensus 126 ~g~~~~eIA~~l~is~~tv~~~l~Rar~ 153 (159)
T TIGR02989 126 RGVSLTALAEQLGRTVNAVYKALSRLRV 153 (159)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 6999999999999999999999988764
No 183
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=96.41 E-value=0.0054 Score=39.64 Aligned_cols=28 Identities=14% Similarity=0.113 Sum_probs=25.9
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
.|+|..+||..+|||.++|..++.|.++
T Consensus 150 ~~~s~~eIA~~lgis~~~V~~~l~ra~~ 177 (186)
T PRK13919 150 QGYTHREAAQLLGLPLGTLKTRARRALS 177 (186)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 7999999999999999999999988764
No 184
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=96.41 E-value=0.032 Score=39.53 Aligned_cols=60 Identities=17% Similarity=0.158 Sum_probs=38.1
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHhC
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGEN 63 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~ 63 (77)
.|+|..+||..||+|.+||...+.|-++.=.-.+...-+-.+......+.+.+.++++.-
T Consensus 168 ~g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~~~~~~~~~~~~~~~~~~~~v~~~~~A~ 227 (339)
T PRK08241 168 LGWSAAEVAELLDTSVAAVNSALQRARATLAERGPSAADTLREPDDPEERALLARYVAAF 227 (339)
T ss_pred hCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhhcCCCcccccCCCCChHHHHHHHHHHHHH
Confidence 799999999999999999999988877543321111111123334444555555555543
No 185
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=96.38 E-value=0.015 Score=38.16 Aligned_cols=39 Identities=21% Similarity=0.267 Sum_probs=33.8
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc--ccCCCC
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPG--VIGGSK 44 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk--~~gg~~ 44 (77)
+|..+||++++||..++.++++..++.|=|... +.||..
T Consensus 26 vs~~eIA~~~~ip~~~l~kIl~~L~~aGLv~s~rG~~GGy~ 66 (164)
T PRK10857 26 VPLADISERQGISLSYLEQLFSRLRKNGLVSSVRGPGGGYL 66 (164)
T ss_pred CcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeCCCCCCCee
Confidence 899999999999999999999999999999753 345544
No 186
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=96.38 E-value=0.014 Score=32.30 Aligned_cols=59 Identities=15% Similarity=0.152 Sum_probs=41.6
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHhCCCCcHHHHHHHh
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGENPAMFSWEIRDRL 75 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~pd~tl~El~~~L 75 (77)
.+..++|+.||+|.+++.+.+++. +| ..|+.. ......+.+..++..+ ++++.|+++.+
T Consensus 2 ~~~~~la~~~~~s~~~l~~~f~~~--~~-~s~~~~-------~~~~r~~~a~~~l~~~-~~~~~~ia~~~ 60 (84)
T smart00342 2 LTLEDLAEALGMSPRHLQRLFKKE--TG-TTPKQY-------LRDRRLERARRLLRDT-DLSVTEIALRV 60 (84)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHH--hC-cCHHHH-------HHHHHHHHHHHHHHcC-CCCHHHHHHHh
Confidence 477899999999999999998864 22 233321 1222345577788776 89999998764
No 187
>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator). This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.
Probab=96.37 E-value=0.025 Score=34.97 Aligned_cols=34 Identities=21% Similarity=0.259 Sum_probs=31.4
Q ss_pred CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513 5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG 38 (77)
Q Consensus 5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk 38 (77)
.+|..+||+.+++|.++|.++++...+.|=+...
T Consensus 25 ~~s~~eia~~~~i~~~~v~~il~~L~~~gli~~~ 58 (132)
T TIGR00738 25 PVSVKEIAERQGISRSYLEKILRTLRRAGLVESV 58 (132)
T ss_pred cCcHHHHHHHHCcCHHHHHHHHHHHHHCCcEEec
Confidence 5899999999999999999999999999988653
No 188
>PF08535 KorB: KorB domain; InterPro: IPR013741 This entry contains several KorB transcriptional repressor proteins. The korB gene is a major regulatory element in the replication and maintenance of broad host-range plasmid RK2. It negatively controls the replication gene trfA, the host-lethal determinants kilA and kilB, and the korA-korB operon []. This domain includes the DNA-binding HTH motif []. ; PDB: 1R71_C.
Probab=96.37 E-value=0.0031 Score=37.50 Aligned_cols=27 Identities=26% Similarity=0.186 Sum_probs=20.0
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHH
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRY 29 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~ 29 (77)
+.|+++.+||+++|-|+++|++.+.-.
T Consensus 1 ~~G~tq~eIA~~lGks~s~Vs~~l~Ll 27 (93)
T PF08535_consen 1 EFGWTQEEIAKRLGKSRSWVSNHLALL 27 (93)
T ss_dssp HTT--HHHHHHHTT--HHHHHHHHGGG
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 369999999999999999999987643
No 189
>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR. This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system.
Probab=96.36 E-value=0.014 Score=36.74 Aligned_cols=33 Identities=15% Similarity=0.291 Sum_probs=30.9
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPG 38 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk 38 (77)
++..+||++++||..++.+++.+.++.|=|...
T Consensus 26 ~s~~~ia~~~~ip~~~l~kil~~L~~~glv~s~ 58 (135)
T TIGR02010 26 VTLADISERQGISLSYLEQLFAKLRKAGLVKSV 58 (135)
T ss_pred CcHHHHHHHHCcCHHHHHHHHHHHHHCCceEEE
Confidence 799999999999999999999999999988653
No 190
>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B.
Probab=96.35 E-value=0.004 Score=34.87 Aligned_cols=19 Identities=26% Similarity=0.281 Sum_probs=17.1
Q ss_pred CHHHHHHHhccCHHHHHHH
Q psy15513 7 RPCVISRQLRVSHGCVSKI 25 (77)
Q Consensus 7 s~~~iA~rf~VS~stv~r~ 25 (77)
+...+|+.||||+++|+.|
T Consensus 11 ~~~~lAkalGVs~~aVs~W 29 (60)
T PF14549_consen 11 GQSKLAKALGVSPQAVSQW 29 (60)
T ss_dssp SHHHHHHHHTS-HHHHHHH
T ss_pred CHHHHHHHHCCCHHHHHHh
Confidence 6789999999999999999
No 191
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=96.34 E-value=0.0067 Score=38.37 Aligned_cols=28 Identities=29% Similarity=0.319 Sum_probs=26.0
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
.|++..+||..||+|.+||.+++.+.+.
T Consensus 140 ~~~~~~eIA~~lgis~~tv~~~~~ra~~ 167 (179)
T PRK11924 140 EGLSYREIAEILGVPVGTVKSRLRRARQ 167 (179)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 6999999999999999999999988764
No 192
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=96.32 E-value=0.0063 Score=39.49 Aligned_cols=28 Identities=21% Similarity=0.319 Sum_probs=26.1
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
.|+|..+||..||||.+||..++.|-++
T Consensus 148 ~~~s~~eIA~~lgis~~tV~~~l~ra~~ 175 (182)
T PRK12537 148 DGCSHAEIAQRLGAPLGTVKAWIKRSLK 175 (182)
T ss_pred cCCCHHHHHHHHCCChhhHHHHHHHHHH
Confidence 7999999999999999999999998764
No 193
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=96.31 E-value=0.038 Score=35.60 Aligned_cols=63 Identities=11% Similarity=0.004 Sum_probs=41.4
Q ss_pred CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcccc--CCCCCCCCCHHHHH---HHHHHHHhCCCCcHHHHHHHh
Q psy15513 5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI--GGSKPRVATPDVER---RIEEYKGENPAMFSWEIRDRL 75 (77)
Q Consensus 5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~--gg~~~~~~~~~~~~---~i~~~v~~~pd~tl~El~~~L 75 (77)
-+++.++|+++|||..|+.-|= +.|-+.|... +|.| .-++.+.. +|..+. +=+++|.||++.+
T Consensus 7 ~~~IgevAk~~Gvs~~TLRyYE----~~GLl~p~~r~~~gyR--~Y~~~~l~rl~~I~~lr--~~G~sL~eI~~ll 74 (144)
T PRK13752 7 NLTIGVFAKAAGVNVETIRFYQ----RKGLLPEPDKPYGSIR--RYGEADVTRVRFVKSAQ--RLGFSLDEIAELL 74 (144)
T ss_pred cccHHHHHHHHCcCHHHHHHHH----HCCCCCCCccCCCCCe--ecCHHHHHHHHHHHHHH--HcCCCHHHHHHHH
Confidence 3899999999999999986554 3487765433 3333 33444444 344444 3358899988755
No 194
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=96.29 E-value=0.012 Score=41.09 Aligned_cols=41 Identities=20% Similarity=0.206 Sum_probs=29.8
Q ss_pred CHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHhC
Q psy15513 7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGEN 63 (77)
Q Consensus 7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~ 63 (77)
+..+||+..|||.+||||.++. +++ ..++.++.|++.+++.
T Consensus 3 ti~dIA~~aGVS~~TVSrvLn~---------------~~~-Vs~~tr~rV~~~a~el 43 (343)
T PRK10727 3 TIKDVARLAGVSVATVSRVINN---------------SPK-ASEASRLAVHSAMESL 43 (343)
T ss_pred CHHHHHHHhCCCHHHHHHHhCC---------------CCC-CCHHHHHHHHHHHHHH
Confidence 6889999999999999999951 111 3355566676666553
No 195
>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=96.28 E-value=0.0085 Score=32.78 Aligned_cols=32 Identities=19% Similarity=0.347 Sum_probs=26.8
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCC
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSI 35 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v 35 (77)
+.| |...+|+.++||+++|++.+++..+.=.+
T Consensus 12 ~~g-s~~~AA~~l~is~~~vs~~i~~LE~~lg~ 43 (60)
T PF00126_consen 12 ETG-SISAAAEELGISQSAVSRQIKQLEEELGV 43 (60)
T ss_dssp HHS-SHHHHHHHCTSSHHHHHHHHHHHHHHHTS
T ss_pred HhC-CHHHHHHHhhccchHHHHHHHHHHHHhCC
Confidence 345 88999999999999999999999865433
No 196
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=96.28 E-value=0.0079 Score=38.06 Aligned_cols=28 Identities=21% Similarity=0.278 Sum_probs=25.9
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
.|+|..+||..||||.+||.+.+.+-+.
T Consensus 126 ~g~s~~eIA~~lgis~~tV~~~i~ra~~ 153 (166)
T PRK09639 126 SGYSYKEIAEALGIKESSVGTTLARAKK 153 (166)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 7999999999999999999999988664
No 197
>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=96.28 E-value=0.005 Score=35.46 Aligned_cols=25 Identities=8% Similarity=0.103 Sum_probs=20.2
Q ss_pred CCCHHHHHHHhccCHHHHHHHHHHH
Q psy15513 5 GVRPCVISRQLRVSHGCVSKILNRY 29 (77)
Q Consensus 5 G~s~~~iA~rf~VS~stv~r~~~r~ 29 (77)
.+|..++|+..+||++||.|+.+..
T Consensus 34 ~~si~elA~~~~vS~sti~Rf~kkL 58 (77)
T PF01418_consen 34 FMSISELAEKAGVSPSTIVRFCKKL 58 (77)
T ss_dssp T--HHHHHHHCTS-HHHHHHHHHHC
T ss_pred HccHHHHHHHcCCCHHHHHHHHHHh
Confidence 4789999999999999999999874
No 198
>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=96.28 E-value=0.009 Score=33.51 Aligned_cols=34 Identities=32% Similarity=0.382 Sum_probs=31.0
Q ss_pred CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513 5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG 38 (77)
Q Consensus 5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk 38 (77)
.++..++|..+|+|..||+|.++++++.|=+.-.
T Consensus 28 ~lt~~~iA~~~g~sr~tv~r~l~~l~~~g~I~~~ 61 (76)
T PF13545_consen 28 PLTQEEIADMLGVSRETVSRILKRLKDEGIIEVK 61 (76)
T ss_dssp ESSHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEE
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEc
Confidence 4788999999999999999999999999988743
No 199
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=96.28 E-value=0.0073 Score=40.76 Aligned_cols=29 Identities=14% Similarity=0.201 Sum_probs=25.7
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
-+|+|..+||..||||.+||.+++.+-+.
T Consensus 196 ~eg~s~~EIA~~lgis~~tVk~~~~rA~~ 224 (234)
T PRK08301 196 GEEKTQKEVADMLGISQSYISRLEKRIIK 224 (234)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 47999999999999999999999877654
No 200
>COG3311 AlpA Predicted transcriptional regulator [Transcription]
Probab=96.28 E-value=0.016 Score=33.51 Aligned_cols=33 Identities=18% Similarity=0.465 Sum_probs=25.9
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCC-CccccCC
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSI-RPGVIGG 42 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v-~pk~~gg 42 (77)
.+-.|++..+|+|.+|++|+++. |+. .|.+.||
T Consensus 14 lrl~ev~~~~GlSrstiYr~i~~----~~FPkpvklG~ 47 (70)
T COG3311 14 LRLPEVAQLTGLSRSTIYRLIKD----GTFPKPVKLGG 47 (70)
T ss_pred hhHHHHHHHHCccHHHHHHHHcc----CCCCCCeecCc
Confidence 45688999999999999999987 444 4555565
No 201
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=96.27 E-value=0.0081 Score=37.96 Aligned_cols=28 Identities=25% Similarity=0.178 Sum_probs=25.3
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
.|+|..+||+.||||.+||...+.+-+.
T Consensus 124 ~~~s~~EIA~~lgis~~tV~~~l~ra~~ 151 (163)
T PRK07037 124 HGETQKDIARELGVSPTLVNFMIRDALV 151 (163)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 6999999999999999999999877554
No 202
>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=96.27 E-value=0.008 Score=38.69 Aligned_cols=28 Identities=25% Similarity=0.134 Sum_probs=26.1
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
+|+|..+||..||||.+||...+.|-+.
T Consensus 149 ~g~s~~EIA~~lgis~~tVk~~l~Rar~ 176 (183)
T TIGR02999 149 AGLTVEEIAELLGVSVRTVERDWRFARA 176 (183)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 7999999999999999999999988765
No 203
>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=96.26 E-value=0.0042 Score=31.29 Aligned_cols=25 Identities=28% Similarity=0.409 Sum_probs=22.6
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILN 27 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~ 27 (77)
..|+|..++|+.+++|.+++++|.+
T Consensus 10 ~~~~s~~~~a~~~~~~~~~v~~~~~ 34 (58)
T cd00093 10 EKGLTQEELAEKLGVSRSTISRIEN 34 (58)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHc
Confidence 4689999999999999999999854
No 204
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 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=96.25 E-value=0.031 Score=39.18 Aligned_cols=72 Identities=17% Similarity=0.107 Sum_probs=42.3
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcccc-CCCCCCCCCHHHHHHHHHHHHhCCCCcHHHHHHHh
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI-GGSKPRVATPDVERRIEEYKGENPAMFSWEIRDRL 75 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~-gg~~~~~~~~~~~~~i~~~v~~~pd~tl~El~~~L 75 (77)
.|+|..+||..||+|.+||...+.|-+..=.-.-+.. +...+....+.+.+.+.++++.-..--+..|.+.|
T Consensus 157 ~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~~~~~~~~~~~~~~~~v~~~~~a~~~gD~~~l~~Ll 229 (324)
T TIGR02960 157 LGWRAAETAELLGTSTASVNSALQRARATLDEVGPSARDDQLAQPPSPEEQDLLERYIAAFESYDLDALTALL 229 (324)
T ss_pred hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhcccccccccCCCCCHHHHHHHHHHHHHHHcCCHHHHHHHh
Confidence 7999999999999999999999888775432211111 11111223344555555555544333344444433
No 205
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=96.24 E-value=0.008 Score=38.44 Aligned_cols=29 Identities=17% Similarity=0.189 Sum_probs=26.3
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHHh
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQET 32 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~t 32 (77)
.|+|..+||..||+|.++|...+.|-++.
T Consensus 141 ~g~s~~eIA~~l~is~~~V~~~l~ra~~~ 169 (176)
T PRK09638 141 YGYTYEEIAKMLNIPEGTVKSRVHHGIKQ 169 (176)
T ss_pred cCCCHHHHHHHHCCChhHHHHHHHHHHHH
Confidence 69999999999999999999999887653
No 206
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=96.24 E-value=0.0079 Score=38.72 Aligned_cols=28 Identities=14% Similarity=0.100 Sum_probs=25.8
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
+|+|..+||..||+|.+||...+.|-+.
T Consensus 144 ~g~s~~eIA~~lgis~~tV~~~l~Rar~ 171 (179)
T PRK12514 144 EGLSYKELAERHDVPLNTMRTWLRRSLL 171 (179)
T ss_pred cCCCHHHHHHHHCCChHHHHHHHHHHHH
Confidence 7999999999999999999999988664
No 207
>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=96.24 E-value=0.008 Score=39.26 Aligned_cols=29 Identities=21% Similarity=0.190 Sum_probs=25.9
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
-+|+|..+||..+|||.+||...+.|-+.
T Consensus 145 ~~g~s~~EIA~~lgis~~tVk~~l~Rar~ 173 (193)
T TIGR02947 145 VEGFAYKEIAEIMGTPIGTVMSRLHRGRK 173 (193)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 37999999999999999999999887654
No 208
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=96.23 E-value=0.0038 Score=33.87 Aligned_cols=27 Identities=30% Similarity=0.480 Sum_probs=20.7
Q ss_pred CccCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513 1 MAAAGVRPCVISRQLRVSHGCVSKILN 27 (77)
Q Consensus 1 l~~~G~s~~~iA~rf~VS~stv~r~~~ 27 (77)
|.+.|+|.++||++++=|..||.++++
T Consensus 16 m~qlG~s~~~isr~i~RSr~~Ir~yl~ 42 (50)
T PF11427_consen 16 MHQLGMSLREISRRIGRSRTCIRRYLK 42 (50)
T ss_dssp HHHTT--HHHHHHHHT--HHHHHHHHH
T ss_pred HHHhchhHHHHHHHhCccHHHHHHHhc
Confidence 456899999999999999999999986
No 209
>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=96.23 E-value=0.0083 Score=37.89 Aligned_cols=28 Identities=21% Similarity=0.287 Sum_probs=26.2
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
.|+|..+||..+|+|.+||..++.|-++
T Consensus 125 ~g~s~~eIA~~lgis~~tV~~~l~ra~~ 152 (162)
T TIGR02983 125 EDLSEAQVAEALGISVGTVKSRLSRALA 152 (162)
T ss_pred hcCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 7999999999999999999999998775
No 210
>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=96.23 E-value=0.011 Score=35.42 Aligned_cols=36 Identities=19% Similarity=0.127 Sum_probs=32.8
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG 38 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk 38 (77)
..++|..++|..+|+|+.||+|.++++.+.|=|...
T Consensus 45 ~~~is~~eLa~~~g~sr~tVsr~L~~Le~~GlI~r~ 80 (95)
T TIGR01610 45 QDRVTATVIAELTGLSRTHVSDAIKSLARRRIIFRQ 80 (95)
T ss_pred CCccCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeee
Confidence 357899999999999999999999999999999754
No 211
>PRK00215 LexA repressor; Validated
Probab=96.22 E-value=0.0089 Score=39.76 Aligned_cols=37 Identities=22% Similarity=0.144 Sum_probs=32.6
Q ss_pred CCCHHHHHHHhcc-CHHHHHHHHHHHHHhcCCCccccC
Q psy15513 5 GVRPCVISRQLRV-SHGCVSKILNRYQETGSIRPGVIG 41 (77)
Q Consensus 5 G~s~~~iA~rf~V-S~stv~r~~~r~r~tG~v~pk~~g 41 (77)
+.+..++|+.||+ |++||++++++..+.|-+...+.+
T Consensus 23 ~~s~~ela~~~~~~~~~tv~~~l~~L~~~g~i~~~~~~ 60 (205)
T PRK00215 23 PPSRREIADALGLRSPSAVHEHLKALERKGFIRRDPGR 60 (205)
T ss_pred CCCHHHHHHHhCCCChHHHHHHHHHHHHCCCEEeCCCC
Confidence 3588899999999 999999999999999999766533
No 212
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=96.22 E-value=0.013 Score=40.32 Aligned_cols=52 Identities=12% Similarity=0.156 Sum_probs=38.8
Q ss_pred CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHH
Q psy15513 5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRI 56 (77)
Q Consensus 5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i 56 (77)
+.|..++|+.+++|++||++++++..+.|-|.....+.+..=.+|+.-.+.+
T Consensus 21 ~IS~~eLA~~L~iS~~Tvsr~Lk~LEe~GlI~R~~~~r~~~v~LTekG~~ll 72 (217)
T PRK14165 21 KISSSEFANHTGTSSKTAARILKQLEDEGYITRTIVPRGQLITITEKGLDVL 72 (217)
T ss_pred CcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEEcCCceEEEECHHHHHHH
Confidence 5899999999999999999999999999999766543222224555434433
No 213
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=96.21 E-value=0.012 Score=40.93 Aligned_cols=22 Identities=23% Similarity=0.265 Sum_probs=20.2
Q ss_pred CCHHHHHHHhccCHHHHHHHHH
Q psy15513 6 VRPCVISRQLRVSHGCVSKILN 27 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~ 27 (77)
++..+||+..|||.+||||.++
T Consensus 2 ~Ti~dIA~~agVS~~TVSrvLn 23 (341)
T PRK10703 2 ATIKDVAKRAGVSTTTVSHVIN 23 (341)
T ss_pred CCHHHHHHHhCCCHHHHHHHHc
Confidence 3788999999999999999995
No 214
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=96.20 E-value=0.0076 Score=40.11 Aligned_cols=36 Identities=11% Similarity=0.148 Sum_probs=33.4
Q ss_pred CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcccc
Q psy15513 5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI 40 (77)
Q Consensus 5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~ 40 (77)
|++..+||+.++||..||.+.+....+.|.+...-.
T Consensus 177 g~s~~eIa~~l~iS~~Tv~~~~~~~~~~~~~~~~~~ 212 (225)
T PRK10046 177 QHTAETVAQALTISRTTARRYLEYCASRHLIIAEIV 212 (225)
T ss_pred CcCHHHHHHHhCccHHHHHHHHHHHHhCCeEEEEee
Confidence 689999999999999999999999999999977654
No 215
>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=96.20 E-value=0.0027 Score=35.83 Aligned_cols=34 Identities=24% Similarity=0.315 Sum_probs=29.2
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccc
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV 39 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~ 39 (77)
+|..++|+.|++|+.+|.-.+.++...|.|+.-.
T Consensus 15 ~S~~eLa~~~~~s~~~ve~mL~~l~~kG~I~~~~ 48 (69)
T PF09012_consen 15 VSLAELAREFGISPEAVEAMLEQLIRKGYIRKVD 48 (69)
T ss_dssp EEHHHHHHHTT--HHHHHHHHHHHHCCTSCEEEE
T ss_pred cCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEec
Confidence 8999999999999999999999999999995443
No 216
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=96.19 E-value=0.0045 Score=30.94 Aligned_cols=24 Identities=25% Similarity=0.356 Sum_probs=22.1
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHH
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKIL 26 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~ 26 (77)
..|+|..++|+.++||.+++++|.
T Consensus 8 ~~~~s~~~la~~~~i~~~~i~~~~ 31 (56)
T smart00530 8 EKGLTQEELAEKLGVSRSTLSRIE 31 (56)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHH
Confidence 578999999999999999999985
No 217
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=96.17 E-value=0.012 Score=40.43 Aligned_cols=19 Identities=32% Similarity=0.361 Sum_probs=17.9
Q ss_pred HHHHHHhccCHHHHHHHHH
Q psy15513 9 CVISRQLRVSHGCVSKILN 27 (77)
Q Consensus 9 ~~iA~rf~VS~stv~r~~~ 27 (77)
.|||+..|||.+||||.++
T Consensus 2 ~dIA~~agVS~~TVSrvLn 20 (327)
T PRK10423 2 KDVARLAGVSTSTVSHVIN 20 (327)
T ss_pred hhHHHHhCCcHHHHHHHhC
Confidence 5899999999999999996
No 218
>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=96.17 E-value=0.0044 Score=42.81 Aligned_cols=22 Identities=32% Similarity=0.347 Sum_probs=20.4
Q ss_pred CCHHHHHHHhccCHHHHHHHHH
Q psy15513 6 VRPCVISRQLRVSHGCVSKILN 27 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~ 27 (77)
++..+||+.+|||++||||.++
T Consensus 2 ~ti~dIA~~agVS~sTVSr~Ln 23 (311)
T TIGR02405 2 LTIKDIARLAGVGKSTVSRVLN 23 (311)
T ss_pred CcHHHHHHHhCCCHHHHHHHhC
Confidence 4789999999999999999995
No 219
>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=96.16 E-value=0.01 Score=37.56 Aligned_cols=28 Identities=18% Similarity=0.189 Sum_probs=26.0
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
.|+|..+||+.||||.+||...+.|-++
T Consensus 137 ~g~s~~eIA~~l~is~~tv~~~l~ra~~ 164 (170)
T TIGR02952 137 QNLPIAEVARILGKTEGAVKILQFRAIK 164 (170)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 6999999999999999999999988765
No 220
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=96.15 E-value=0.0046 Score=42.91 Aligned_cols=39 Identities=26% Similarity=0.319 Sum_probs=33.4
Q ss_pred CC-CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCC
Q psy15513 4 AG-VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGS 43 (77)
Q Consensus 4 ~G-~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~ 43 (77)
.| ++..++|++|+||..||.|.+....+.|-+. +-+||-
T Consensus 17 ~~~~~~~ela~~l~vS~~TiRRdL~~Le~~g~l~-r~~GGa 56 (252)
T PRK10906 17 QGYVSTEELVEHFSVSPQTIRRDLNDLAEQNKIL-RHHGGA 56 (252)
T ss_pred cCCEeHHHHHHHhCCCHHHHHHHHHHHHHCCCEE-EecCCE
Confidence 44 7899999999999999999999999999874 456663
No 221
>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=96.15 E-value=0.0099 Score=37.08 Aligned_cols=28 Identities=21% Similarity=0.071 Sum_probs=26.0
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
+|+|..+||..||||.+||...+.|.+.
T Consensus 120 ~g~s~~eIA~~lgis~~tv~~~l~Ra~~ 147 (154)
T TIGR02950 120 KEFSYKEIAELLNLSLAKVKSNLFRARK 147 (154)
T ss_pred ccCcHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 7999999999999999999999988764
No 222
>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=96.14 E-value=0.016 Score=39.95 Aligned_cols=22 Identities=32% Similarity=0.409 Sum_probs=20.2
Q ss_pred CCHHHHHHHhccCHHHHHHHHH
Q psy15513 6 VRPCVISRQLRVSHGCVSKILN 27 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~ 27 (77)
++..+||+..|||.+||||.++
T Consensus 2 ~ti~dIA~~agvS~~TVSrvLn 23 (329)
T TIGR01481 2 VTIYDVAREAGVSMATVSRVVN 23 (329)
T ss_pred CcHHHHHHHhCCCHHHHHHHhC
Confidence 4678999999999999999995
No 223
>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=96.12 E-value=0.01 Score=37.89 Aligned_cols=28 Identities=18% Similarity=0.194 Sum_probs=26.1
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
.|+|..+||..||||.+||...+.|-+.
T Consensus 134 ~g~s~~eiA~~lgis~~tv~~~l~Ra~~ 161 (169)
T TIGR02954 134 HDLTIKEIAEVMNKPEGTVKTYLHRALK 161 (169)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 6999999999999999999999998765
No 224
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=96.12 E-value=0.015 Score=37.64 Aligned_cols=34 Identities=29% Similarity=0.208 Sum_probs=31.4
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccc
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV 39 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~ 39 (77)
++..+||++++||++++.|+++..++.|=|...+
T Consensus 25 ~s~~eIA~~~~is~~~L~kIl~~L~~aGlv~S~r 58 (153)
T PRK11920 25 SRIPEIARAYGVSELFLFKILQPLVEAGLVETVR 58 (153)
T ss_pred CcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeec
Confidence 6899999999999999999999999999886655
No 225
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=96.11 E-value=0.0099 Score=38.72 Aligned_cols=28 Identities=18% Similarity=0.229 Sum_probs=25.8
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
.|++..+||..||+|.+||..++.|.+.
T Consensus 156 ~g~s~~EIA~~lgis~~tV~~~l~Ra~~ 183 (194)
T PRK12519 156 EGLSQSEIAKRLGIPLGTVKARARQGLL 183 (194)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 7999999999999999999999988664
No 226
>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=96.11 E-value=0.053 Score=37.21 Aligned_cols=65 Identities=15% Similarity=0.089 Sum_probs=47.8
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHH-hCCCCcHHHHHHHh
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKG-ENPAMFSWEIRDRL 75 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~-~~pd~tl~El~~~L 75 (77)
+++.++|+..|||.+||.-|-++ |-+.|....+ ..+.-++.|.+.|.-... ....+++.+|.+.|
T Consensus 2 y~i~elA~~~Gvs~~tIR~Ye~~----GLL~p~r~~~-~~r~Y~~~~v~rL~~I~~l~~~G~~L~~I~~~l 67 (219)
T cd04778 2 YRIDDLARAAGTTVRNVRAYQDR----GLLPPPRRRG-RVAIYNDSHLARLRLINQLLERGYTLAHIAELL 67 (219)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC----CCCCCcccCC-CCcccCHHHHHHHHHHHHHHHCCCCHHHHHHHH
Confidence 68899999999999998776544 8887754433 334667778877765555 34678999998765
No 227
>PRK09726 antitoxin HipB; Provisional
Probab=96.10 E-value=0.0062 Score=35.83 Aligned_cols=25 Identities=12% Similarity=0.318 Sum_probs=23.2
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILN 27 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~ 27 (77)
+.|++..++|++.|||+++|++|.+
T Consensus 23 ~~gltq~elA~~~gvs~~tis~~e~ 47 (88)
T PRK09726 23 QNGWTQSELAKKIGIKQATISNFEN 47 (88)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHC
Confidence 4689999999999999999999976
No 228
>PRK09492 treR trehalose repressor; Provisional
Probab=96.08 E-value=0.0046 Score=42.43 Aligned_cols=23 Identities=30% Similarity=0.323 Sum_probs=21.3
Q ss_pred CCHHHHHHHhccCHHHHHHHHHH
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNR 28 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r 28 (77)
++..+||+.+|||.+||||.++.
T Consensus 5 ~ti~dIA~~agVS~~TVSrvLn~ 27 (315)
T PRK09492 5 LTIKDIARLSGVGKSTVSRVLNN 27 (315)
T ss_pred CcHHHHHHHhCCCHHHHhHHhCC
Confidence 68899999999999999999974
No 229
>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=96.08 E-value=0.0028 Score=41.72 Aligned_cols=33 Identities=33% Similarity=0.392 Sum_probs=28.1
Q ss_pred CccCCCCHHHHHHHhc-cCHHHHHHHHHHHHHhc
Q psy15513 1 MAAAGVRPCVISRQLR-VSHGCVSKILNRYQETG 33 (77)
Q Consensus 1 l~~~G~s~~~iA~rf~-VS~stv~r~~~r~r~tG 33 (77)
|..+|+|..+||++|| ||.+.|+--+.|..=.+
T Consensus 14 lw~~G~SasqIA~~lg~vsRnAViGk~hRlgL~~ 47 (162)
T PF07750_consen 14 LWAEGLSASQIARQLGGVSRNAVIGKAHRLGLSG 47 (162)
T ss_pred HHHcCCCHHHHHHHhCCcchhhhhhhhhcccccc
Confidence 4579999999999999 99999998888874333
No 230
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=96.07 E-value=0.011 Score=38.27 Aligned_cols=28 Identities=14% Similarity=0.121 Sum_probs=25.8
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
+|+|..+||+.||||.+||...+.+-++
T Consensus 144 ~g~s~~EIA~~l~is~~tV~~~l~rar~ 171 (181)
T PRK12536 144 EGLSVAETAQLTGLSESAVKVGIHRGLK 171 (181)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 7999999999999999999999988664
No 231
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=96.06 E-value=0.011 Score=37.09 Aligned_cols=28 Identities=14% Similarity=0.153 Sum_probs=25.4
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
.|+|..+||..||||.+||...+.|-+.
T Consensus 121 ~g~s~~EIA~~lgis~~tV~~~l~ra~~ 148 (161)
T PRK09047 121 EDMDVAETAAAMGCSEGSVKTHCSRATH 148 (161)
T ss_pred hcCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 7999999999999999999999887654
No 232
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=96.05 E-value=0.0096 Score=37.98 Aligned_cols=36 Identities=17% Similarity=0.159 Sum_probs=32.0
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG 38 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk 38 (77)
+.+++.-+||..++.|.|||+|-+++.-+.|=|.-.
T Consensus 40 ~~~~tvdelae~lnr~rStv~rsl~~L~~~GlV~Re 75 (126)
T COG3355 40 NGPLTVDELAEILNRSRSTVYRSLQNLLEAGLVERE 75 (126)
T ss_pred cCCcCHHHHHHHHCccHHHHHHHHHHHHHcCCeeee
Confidence 355899999999999999999999999999998433
No 233
>TIGR03338 phnR_burk phosphonate utilization associated transcriptional regulator. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Polaromonas, Burkholderia, Ralstonia and Verminephrobacter.
Probab=96.02 E-value=0.024 Score=37.53 Aligned_cols=45 Identities=24% Similarity=0.265 Sum_probs=36.9
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCH
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATP 50 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~ 50 (77)
.+-.++|++||||.++|..-+++....|=|...|..|-.-...+.
T Consensus 35 L~e~~La~~lgVSRtpVReAL~~L~~eGlv~~~~~~G~~V~~~~~ 79 (212)
T TIGR03338 35 LNESDIAARLGVSRGPVREAFRALEEAGLVRNEKNRGVFVREISL 79 (212)
T ss_pred ecHHHHHHHhCCChHHHHHHHHHHHHCCCEEEecCCCeEEecCCH
Confidence 566789999999999999999999999999888766544344443
No 234
>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=96.02 E-value=0.021 Score=39.50 Aligned_cols=43 Identities=19% Similarity=0.145 Sum_probs=29.7
Q ss_pred CHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHh
Q psy15513 7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGE 62 (77)
Q Consensus 7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~ 62 (77)
+..+||+..|||.+||||.++. .+......++.++.|.+.+++
T Consensus 1 ti~dIA~~aGVS~~TVSrvLn~-------------~~~~~~vs~~tr~rV~~~a~~ 43 (327)
T TIGR02417 1 TLSDIAKLAGVSKTTASYVING-------------KAKEYRISQETVERVMAVVRE 43 (327)
T ss_pred CHHHHHHHhCCCHHHHHHHHcC-------------CCCCCccCHHHHHHHHHHHHH
Confidence 4679999999999999999952 000012445567777777666
No 235
>PRK09409 IS2 transposase TnpB; Reviewed
Probab=96.02 E-value=0.024 Score=40.22 Aligned_cols=66 Identities=29% Similarity=0.316 Sum_probs=42.6
Q ss_pred CccCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHhCCCCcHHHHH
Q psy15513 1 MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGENPAMFSWEIR 72 (77)
Q Consensus 1 l~~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~pd~tl~El~ 72 (77)
|..+|++...+++.||||.|+.++|++++..- . ..+ ..+.....+..+.|.++.+++|..=..-|.
T Consensus 7 ~~~~~~~v~~lC~~l~VsRs~yY~~~~r~~~~--~-~~~---~~~~~~~~~l~~~I~~i~~~~~~yG~Rri~ 72 (301)
T PRK09409 7 LIARGWGVSLVSRCLRVSRAQLHVILRRTDDW--M-DGR---RSRHTDDTDVLLRIHHVIGELPTYGYRRVW 72 (301)
T ss_pred HHhcCCcHHHHHHhcCcChHHhhhhccccccc--c-ccc---cccCcchHHHHHHHHHHHHhCccCCHHHHH
Confidence 45678999999999999999999999986521 1 111 011122234456677777777765444333
No 236
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=96.02 E-value=0.036 Score=37.18 Aligned_cols=51 Identities=14% Similarity=0.055 Sum_probs=41.9
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCC---CCCHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR---VATPDVER 54 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~---~~~~~~~~ 54 (77)
.|+++.++|+.++++++||++.+++..+.|=|.-.+...+++. .+|+.-.+
T Consensus 58 ~~itq~eLa~~l~l~~sTvtr~l~rLE~kGlI~R~~~~~DrR~~~I~LTekG~~ 111 (185)
T PRK13777 58 KGASISEIAKFGVMHVSTAFNFSKKLEERGYLTFSKKEDDKRNTYIELTEKGEE 111 (185)
T ss_pred CCcCHHHHHHHHCCCHhhHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHH
Confidence 6899999999999999999999999999999987766666663 35554343
No 237
>PRK12423 LexA repressor; Provisional
Probab=96.00 E-value=0.0087 Score=40.13 Aligned_cols=37 Identities=22% Similarity=0.185 Sum_probs=32.5
Q ss_pred CCC--CHHHHHHHhc-cCHHHHHHHHHHHHHhcCCCcccc
Q psy15513 4 AGV--RPCVISRQLR-VSHGCVSKILNRYQETGSIRPGVI 40 (77)
Q Consensus 4 ~G~--s~~~iA~rf~-VS~stv~r~~~r~r~tG~v~pk~~ 40 (77)
.|. |.+++|+.|| +|+++|++.+++..+.|-+...+.
T Consensus 22 ~g~~Ps~~eia~~~g~~s~~~v~~~l~~L~~~G~l~~~~~ 61 (202)
T PRK12423 22 AGQPPSLAEIAQAFGFASRSVARKHVQALAEAGLIEVVPN 61 (202)
T ss_pred cCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCCCEEecCC
Confidence 454 8999999999 599999999999999999976654
No 238
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=95.99 E-value=0.012 Score=38.13 Aligned_cols=28 Identities=14% Similarity=0.157 Sum_probs=26.2
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
.|+|..+||..||||.++|...+.|-+.
T Consensus 152 ~g~s~~eIA~~lgis~~~v~~~l~Rar~ 179 (187)
T PRK12534 152 EGITYEELAARTDTPIGTVKSWIRRGLA 179 (187)
T ss_pred cCCCHHHHHHHhCCChhHHHHHHHHHHH
Confidence 7999999999999999999999998765
No 239
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=95.99 E-value=0.024 Score=36.69 Aligned_cols=35 Identities=20% Similarity=0.303 Sum_probs=32.0
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcccc
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI 40 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~ 40 (77)
+|..+||.+.+||++++.|++...++-|=|...+.
T Consensus 26 ~s~~~IA~~~~is~~~L~kil~~L~kaGlV~S~rG 60 (150)
T COG1959 26 VSSAEIAERQGISPSYLEKILSKLRKAGLVKSVRG 60 (150)
T ss_pred ccHHHHHHHhCcCHHHHHHHHHHHHHcCCEEeecC
Confidence 67899999999999999999999999999976654
No 240
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=95.98 E-value=0.0073 Score=37.97 Aligned_cols=25 Identities=16% Similarity=0.235 Sum_probs=22.7
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILN 27 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~ 27 (77)
..|++..++|..+|||++||++|.+
T Consensus 16 ~~gltq~~lA~~~gvs~~~is~~E~ 40 (135)
T PRK09706 16 QLKLSQRSLAKAVKVSHVSISQWER 40 (135)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 4689999999999999999999954
No 241
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=95.94 E-value=0.014 Score=37.87 Aligned_cols=29 Identities=28% Similarity=0.322 Sum_probs=26.6
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHHh
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQET 32 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~t 32 (77)
.|+|..+||..+|||.+||..++.+-+..
T Consensus 142 ~gls~~EIA~~l~i~~~tVks~l~ra~~~ 170 (182)
T COG1595 142 EGLSYEEIAEILGISVGTVKSRLHRARKK 170 (182)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 69999999999999999999999987653
No 242
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=95.93 E-value=0.014 Score=38.14 Aligned_cols=29 Identities=10% Similarity=0.130 Sum_probs=26.3
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHHh
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQET 32 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~t 32 (77)
.|+|..+||..||+|.+||...+.|-+..
T Consensus 145 ~g~s~~EIA~~lgis~~tVk~~l~Rar~~ 173 (185)
T PRK09649 145 LGLSYADAAAVCGCPVGTIRSRVARARDA 173 (185)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 78999999999999999999999887653
No 243
>PRK09744 DNA-binding transcriptional regulator DicC; Provisional
Probab=95.93 E-value=0.0071 Score=35.37 Aligned_cols=26 Identities=15% Similarity=0.183 Sum_probs=22.3
Q ss_pred CHHHHHHHhccCHHHHHHHHHHHHHhcCCCccc
Q psy15513 7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGV 39 (77)
Q Consensus 7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~ 39 (77)
|...+|+.||||+++|+.| |++-|..
T Consensus 12 s~~kvA~aLGIs~~AVsQW-------Ge~VPe~ 37 (75)
T PRK09744 12 SKTKLANAAGVRLASVAAW-------GELVPEG 37 (75)
T ss_pred cHHHHHHHHCCCHHHHHHH-------hccCcHH
Confidence 6788999999999999999 6766653
No 244
>PRK09526 lacI lac repressor; Reviewed
Probab=95.92 E-value=0.0084 Score=41.61 Aligned_cols=23 Identities=35% Similarity=0.365 Sum_probs=21.1
Q ss_pred CCHHHHHHHhccCHHHHHHHHHH
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNR 28 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r 28 (77)
++..|||++.|||.+||||.++.
T Consensus 6 ~ti~dIA~~aGVS~~TVSrvLn~ 28 (342)
T PRK09526 6 VTLYDVARYAGVSYQTVSRVLNQ 28 (342)
T ss_pred CcHHHHHHHhCCCHHHHHHHhcC
Confidence 68999999999999999999963
No 245
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=95.91 E-value=0.015 Score=37.07 Aligned_cols=28 Identities=11% Similarity=0.093 Sum_probs=26.2
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
+|+|..+||..||||.+||...+.|-+.
T Consensus 127 ~g~s~~eIA~~lgis~~tV~~~l~Rar~ 154 (164)
T PRK12547 127 SGFSYEDAAAICGCAVGTIKSRVSRARN 154 (164)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 7999999999999999999999998765
No 246
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=95.91 E-value=0.014 Score=38.06 Aligned_cols=28 Identities=18% Similarity=0.175 Sum_probs=25.2
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
.|+|..+||..||||.+||...+.|-+.
T Consensus 121 ~g~~~~EIA~~lgis~~tV~~~l~Rar~ 148 (181)
T PRK09637 121 EGLSQKEIAEKLGLSLSGAKSRVQRGRV 148 (181)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 7999999999999999999988877654
No 247
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=95.91 E-value=0.015 Score=37.92 Aligned_cols=28 Identities=11% Similarity=0.046 Sum_probs=25.7
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
.|+|..+||..||||.+||..++.|-+.
T Consensus 149 ~g~s~~EIA~~lgis~~tV~~~l~Ra~~ 176 (188)
T PRK09640 149 AELEFQEIADIMHMGLSATKMRYKRALD 176 (188)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 7899999999999999999999988664
No 248
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=95.89 E-value=0.014 Score=37.50 Aligned_cols=29 Identities=24% Similarity=0.228 Sum_probs=26.4
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
-.|+|..+||..||+|.++|...+.|.+.
T Consensus 150 ~~g~s~~eIA~~lgis~~~v~~~l~Rar~ 178 (187)
T TIGR02948 150 MEDLSLKEISEILDLPVGTVKTRIHRGRE 178 (187)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 37999999999999999999999988764
No 249
>PF13309 HTH_22: HTH domain
Probab=95.89 E-value=0.0051 Score=34.61 Aligned_cols=21 Identities=19% Similarity=0.260 Sum_probs=18.4
Q ss_pred CHHHHHHHhccCHHHHHHHHH
Q psy15513 7 RPCVISRQLRVSHGCVSKILN 27 (77)
Q Consensus 7 s~~~iA~rf~VS~stv~r~~~ 27 (77)
+...+|+.||||..||+++++
T Consensus 44 av~~vA~~L~iS~~TVY~YLr 64 (64)
T PF13309_consen 44 AVEYVAEKLGISRATVYRYLR 64 (64)
T ss_pred HHHHHHHHHCCCHHHHHHHcC
Confidence 566789999999999999874
No 250
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=95.89 E-value=0.011 Score=40.63 Aligned_cols=63 Identities=21% Similarity=0.177 Sum_probs=42.9
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHhCCCCcH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGENPAMFS 68 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~pd~tl 68 (77)
.|+|..|||+.+|+|.+||...+.|-++.=.-.- ..|+..... ......++.++.++||.+-.
T Consensus 131 eg~S~~EIAe~LgiS~~tVksrL~Rark~Lr~~l-~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~ 193 (228)
T PRK06704 131 FQYSIADIAKVCSVSEGAVKASLFRSRNRLKTVS-EEGIEIVEF-TDDMEVVVTSIREERPELLT 193 (228)
T ss_pred hCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH-HhcCCCCCc-cccHHHHHHHHHhcCHHHHH
Confidence 6899999999999999999999877665322111 123322222 23356678899999996544
No 251
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=95.88 E-value=0.015 Score=38.08 Aligned_cols=28 Identities=14% Similarity=0.134 Sum_probs=25.6
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
.|+|..+||..||+|.+||..++.|-+.
T Consensus 149 ~g~s~~EIA~~lgis~~tVk~~l~RAr~ 176 (189)
T PRK12530 149 LELSSEQICQECDISTSNLHVLLYRARL 176 (189)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 6999999999999999999999888664
No 252
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=95.86 E-value=0.015 Score=38.04 Aligned_cols=28 Identities=14% Similarity=0.177 Sum_probs=25.1
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
.|+|..+||..||||.+||...+.|-+.
T Consensus 126 eg~s~~EIA~~lgis~~tV~~~l~Rar~ 153 (182)
T PRK12511 126 EGLSYQEAAAVLGIPIGTLMSRIGRARA 153 (182)
T ss_pred cCCCHHHHHHHhCcCHHHHHHHHHHHHH
Confidence 7999999999999999999999876554
No 253
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=95.86 E-value=0.01 Score=34.76 Aligned_cols=33 Identities=9% Similarity=0.062 Sum_probs=27.8
Q ss_pred cCCCCHHHHHHHhc------cCHHHHHHHHHHHHHhcCCCcccc
Q psy15513 3 AAGVRPCVISRQLR------VSHGCVSKILNRYQETGSIRPGVI 40 (77)
Q Consensus 3 ~~G~s~~~iA~rf~------VS~stv~r~~~r~r~tG~v~pk~~ 40 (77)
+.|+++.++|+.+| +|++||+||-+ |++.++.+
T Consensus 22 ~lGLTQ~dvA~~lg~~~g~i~SQstISR~Es-----~~ls~~n~ 60 (75)
T smart00352 22 KLGFTQADVGLALGALYGPDFSQTTICRFEA-----LQLSFKNM 60 (75)
T ss_pred HcCCCHHHHHHHhcccccCcCCHHHHHHHHh-----cCccHHHH
Confidence 47999999999999 49999999755 88877643
No 254
>PF10654 DUF2481: Protein of unknown function (DUF2481) ; InterPro: IPR018916 This entry is represented by Bacteriophage A500, Gp59. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=95.85 E-value=0.0092 Score=37.69 Aligned_cols=31 Identities=16% Similarity=0.245 Sum_probs=26.8
Q ss_pred ccCCCCHHHHHHHhccCHHHHHHHHHHHHHh
Q psy15513 2 AAAGVRPCVISRQLRVSHGCVSKILNRYQET 32 (77)
Q Consensus 2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r~t 32 (77)
-.+|.|+-+||..|+||.|+|-.+-++.+.+
T Consensus 77 R~AGlt~~aIAd~F~iS~s~~~nft~~n~~e 107 (126)
T PF10654_consen 77 RHAGLTCYAIADYFKISKSTVFNFTQNNKKE 107 (126)
T ss_pred HhcCCChHHHHHHHhHHHHHHHHHHHHhHHH
Confidence 3589999999999999999999988776543
No 255
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=95.85 E-value=0.016 Score=36.64 Aligned_cols=28 Identities=25% Similarity=0.296 Sum_probs=25.9
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
.|+|..+||..||+|.+||...+.+-++
T Consensus 128 ~g~s~~EIA~~l~is~~tV~~~l~ra~~ 155 (161)
T PRK12528 128 DGLGYGEIATELGISLATVKRYLNKAAM 155 (161)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 7999999999999999999999988764
No 256
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=95.83 E-value=0.016 Score=37.74 Aligned_cols=29 Identities=14% Similarity=0.013 Sum_probs=25.5
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
-.|+|..+||..+|+|.+||...+.|.+.
T Consensus 153 ~~g~s~~EIA~~lgis~~tV~~~l~ra~~ 181 (194)
T PRK12513 153 HGDLELEEIAELTGVPEETVKSRLRYALQ 181 (194)
T ss_pred ccCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 37999999999999999999988877654
No 257
>PHA02535 P terminase ATPase subunit; Provisional
Probab=95.82 E-value=0.0045 Score=47.95 Aligned_cols=28 Identities=14% Similarity=0.079 Sum_probs=26.1
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHH
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQ 30 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r 30 (77)
-+|.|+.+||+.+||+.+||++|.++++
T Consensus 16 ~~G~sv~eIA~~LGv~~~Tl~~W~kr~~ 43 (581)
T PHA02535 16 WQGWTVAEIAEELGLKSRTIYSWKERDG 43 (581)
T ss_pred HcCCCHHHHHHHhCCChhHHHHHhcccc
Confidence 3599999999999999999999999977
No 258
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=95.82 E-value=0.006 Score=38.83 Aligned_cols=37 Identities=19% Similarity=0.083 Sum_probs=31.6
Q ss_pred ccCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513 2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG 38 (77)
Q Consensus 2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk 38 (77)
...|++++++|+.++|+.++|.+|.+++.+...--+.
T Consensus 86 ~~~~~~i~~~a~~l~i~~~~~~r~~~r~~~~~~~~~~ 122 (129)
T COG3677 86 YMLGLGIRDIARTLGISINTVNRWSKRFGSRVEGLRL 122 (129)
T ss_pred HHcCCCcccHHHHhcccHHHHHHHHHhhcchhhccCC
Confidence 4568999999999999999999999999887655443
No 259
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=95.82 E-value=0.016 Score=37.86 Aligned_cols=28 Identities=21% Similarity=0.249 Sum_probs=25.4
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
.|+|..+||..||+|.+||...+.|-+.
T Consensus 151 ~g~s~~EIA~~lgis~~tVk~~l~Rar~ 178 (195)
T PRK12532 151 LGFSSDEIQQMCGISTSNYHTIMHRARE 178 (195)
T ss_pred hCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 7999999999999999999998887554
No 260
>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=95.81 E-value=0.011 Score=30.63 Aligned_cols=24 Identities=17% Similarity=0.250 Sum_probs=19.8
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHH
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRY 29 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~ 29 (77)
.|..++|+.+|||.++|.+=+++.
T Consensus 18 ~s~~~la~~lglS~~~v~~Ri~rL 41 (42)
T PF13404_consen 18 RSYAELAEELGLSESTVRRRIRRL 41 (42)
T ss_dssp S-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred ccHHHHHHHHCcCHHHHHHHHHHh
Confidence 889999999999999999877765
No 261
>PRK15320 transcriptional activator SprB; Provisional
Probab=95.79 E-value=0.014 Score=40.52 Aligned_cols=39 Identities=8% Similarity=0.092 Sum_probs=34.7
Q ss_pred ccCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcccc
Q psy15513 2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI 40 (77)
Q Consensus 2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~ 40 (77)
...|+|..+||.+|++|.+||++...+..+.=.+..-|-
T Consensus 176 LAkG~SNKEIAekL~LS~KTVSTYKnRLLeKLgAkN~~~ 214 (251)
T PRK15320 176 LSSGHPAIELAKKFGLGTKTVSIYRKKVMYRLGMDSSPL 214 (251)
T ss_pred HHcCCCHHHHHHHhccchhhHHHHHHHHHHHcCCCCCch
Confidence 357999999999999999999999999999888876654
No 262
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=95.79 E-value=0.013 Score=34.67 Aligned_cols=37 Identities=16% Similarity=0.263 Sum_probs=33.2
Q ss_pred HHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCC
Q psy15513 9 CVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKP 45 (77)
Q Consensus 9 ~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~ 45 (77)
.++|++++|++++|++++++..+.|-|.-.+...+++
T Consensus 40 ~~la~~l~i~~~~vt~~l~~Le~~glv~r~~~~~DrR 76 (126)
T COG1846 40 KELAERLGLDRSTVTRLLKRLEDKGLIERLRDPEDRR 76 (126)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHCCCeeecCCccccc
Confidence 8999999999999999999999999998877665654
No 263
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=95.78 E-value=0.017 Score=37.89 Aligned_cols=28 Identities=14% Similarity=0.156 Sum_probs=25.4
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
+|+|..+||+.||||.+||...+.+-+.
T Consensus 131 ~g~s~~EIA~~Lgis~~tVk~~l~Rar~ 158 (187)
T PRK12516 131 SGFAYEEAAEICGCAVGTIKSRVNRARQ 158 (187)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 7999999999999999999999877654
No 264
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=95.78 E-value=0.011 Score=40.95 Aligned_cols=38 Identities=24% Similarity=0.406 Sum_probs=32.2
Q ss_pred CC-CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCC
Q psy15513 4 AG-VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGG 42 (77)
Q Consensus 4 ~G-~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg 42 (77)
.| ++..++|+.|+||.+||.|.++...+.|-+.- -+||
T Consensus 17 ~~~~~~~ela~~l~vS~~TirRdL~~Le~~g~i~r-~~gg 55 (251)
T PRK13509 17 LGFVTVEKVIERLGISPATARRDINKLDESGKLKK-VRNG 55 (251)
T ss_pred cCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE-ecCC
Confidence 44 89999999999999999999999999888753 2344
No 265
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=95.78 E-value=0.017 Score=37.87 Aligned_cols=28 Identities=14% Similarity=0.218 Sum_probs=25.9
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
.|+|..+||+.||||.+||..++.|-+.
T Consensus 151 ~g~s~~eIA~~lgis~~tV~~~l~Ra~~ 178 (196)
T PRK12524 151 EGLSNPEIAEVMEIGVEAVESLTARGKR 178 (196)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 7999999999999999999999998664
No 266
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=95.78 E-value=0.018 Score=37.37 Aligned_cols=28 Identities=18% Similarity=0.181 Sum_probs=25.7
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
.|+|..+||..||+|.+||...+.|-+.
T Consensus 137 ~g~s~~EIA~~lgis~~tVk~~l~Rar~ 164 (185)
T PRK12542 137 YNLTYQEISSVMGITEANVRKQFERARK 164 (185)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 7999999999999999999999887665
No 267
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=95.76 E-value=0.018 Score=36.76 Aligned_cols=28 Identities=18% Similarity=0.140 Sum_probs=25.7
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
.|+|..+||..||+|.+||...+.|-+.
T Consensus 135 ~g~s~~eIA~~lg~s~~tv~~~l~Rar~ 162 (175)
T PRK12518 135 EDLPQKEIAEILNIPVGTVKSRLFYARR 162 (175)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 7999999999999999999999988664
No 268
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=95.76 E-value=0.018 Score=37.32 Aligned_cols=28 Identities=18% Similarity=0.138 Sum_probs=26.2
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
.|+|..+||..||+|.+||...+.|.++
T Consensus 142 ~g~s~~EIA~~l~is~~tv~~~l~Ra~~ 169 (179)
T PRK09415 142 EELSIKEIAEVTGVNENTVKTRLKKAKE 169 (179)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 7999999999999999999999998775
No 269
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=95.75 E-value=0.017 Score=36.50 Aligned_cols=34 Identities=18% Similarity=0.194 Sum_probs=30.9
Q ss_pred CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513 5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG 38 (77)
Q Consensus 5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk 38 (77)
..+..+||+.|+||++||++.+++..+.|-|...
T Consensus 22 ~~~~~ela~~l~vs~~svs~~l~~L~~~Gli~~~ 55 (142)
T PRK03902 22 YARVSDIAEALSVHPSSVTKMVQKLDKDEYLIYE 55 (142)
T ss_pred CcCHHHHHHHhCCChhHHHHHHHHHHHCCCEEEe
Confidence 4788999999999999999999999999988643
No 270
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=95.75 E-value=0.012 Score=39.36 Aligned_cols=34 Identities=21% Similarity=0.106 Sum_probs=29.5
Q ss_pred ccCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCC
Q psy15513 2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETGSI 35 (77)
Q Consensus 2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v 35 (77)
..+|+|..+||++++||.+||...+++..+.=.+
T Consensus 149 la~G~snkeIA~~L~iS~~TVk~h~~~I~~KL~v 182 (207)
T PRK15411 149 WMAGQGTIQISDQMNIKAKTVSSHKGNIKRKIKT 182 (207)
T ss_pred HHcCCCHHHHHHHcCCCHHHHHHHHHHHHHHhCC
Confidence 3589999999999999999999999988865444
No 271
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=95.75 E-value=0.019 Score=36.68 Aligned_cols=28 Identities=21% Similarity=0.262 Sum_probs=24.7
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
.|+|..+||..||+|.+||...+.|-+.
T Consensus 133 ~g~s~~EIA~~lgis~~tV~~~l~ra~~ 160 (173)
T PRK09645 133 RGWSTAQIAADLGIPEGTVKSRLHYALR 160 (173)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 6999999999999999999888776553
No 272
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=95.75 E-value=0.018 Score=39.03 Aligned_cols=28 Identities=21% Similarity=0.134 Sum_probs=25.3
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
+|+|..+||..||||.+||...+.|-+.
T Consensus 149 eg~s~~EIAe~LgiS~~tVk~~L~RAr~ 176 (216)
T PRK12533 149 EDMSYREIAAIADVPVGTVMSRLARARR 176 (216)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 7999999999999999999999886654
No 273
>PRK01905 DNA-binding protein Fis; Provisional
Probab=95.74 E-value=0.012 Score=34.06 Aligned_cols=27 Identities=19% Similarity=0.257 Sum_probs=23.8
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHH
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRY 29 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~ 29 (77)
..|-...++|+++|||++|+++.+++|
T Consensus 48 ~~~gn~s~aAr~LGIsrstL~rklkk~ 74 (77)
T PRK01905 48 QAGGNQSLAAEYLGINRNTLRKKLQQH 74 (77)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHHh
Confidence 346678899999999999999999986
No 274
>PF07900 DUF1670: Protein of unknown function (DUF1670); InterPro: IPR012872 The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=95.74 E-value=0.11 Score=35.98 Aligned_cols=65 Identities=20% Similarity=0.091 Sum_probs=45.0
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHh-cCCCccccCC-CCCCCCCHHHHHHHHHHHHhCCCCcHHHHHHH
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQET-GSIRPGVIGG-SKPRVATPDVERRIEEYKGENPAMFSWEIRDR 74 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~t-G~v~pk~~gg-~~~~~~~~~~~~~i~~~v~~~pd~tl~El~~~ 74 (77)
.+..|+|..|++|..||++.++.|++. |.+-|...-- +-.+..+ |-.+|.++.-+. .+..|++.+
T Consensus 106 LT~~Dla~LL~~S~~TI~~~i~~yq~e~g~vvPtrG~i~DiGp~~t--HK~~ii~~~l~g--~~~~eiar~ 172 (220)
T PF07900_consen 106 LTQEDLAMLLGISPRTISKDIKEYQKEHGVVVPTRGTIHDIGPGVT--HKKIIIRLYLKG--KPTPEIARR 172 (220)
T ss_pred ccHHHHHHHHCCCHHHHHHHHHHHHHHcCceeccCCcccccCCcch--HHHHHHHHHHcC--CCHHHHHHH
Confidence 788999999999999999999999987 9998875210 1222233 555566554442 455565543
No 275
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=95.71 E-value=0.018 Score=36.57 Aligned_cols=28 Identities=11% Similarity=-0.052 Sum_probs=26.0
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
.|+|..+||..||+|.+||..++.|.++
T Consensus 123 ~g~s~~eIA~~lgis~~tv~~~l~Rar~ 150 (165)
T PRK09644 123 HELTYEEAASVLDLKLNTYKSHLFRGRK 150 (165)
T ss_pred hcCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 7899999999999999999999988765
No 276
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=95.71 E-value=0.019 Score=38.34 Aligned_cols=29 Identities=24% Similarity=0.280 Sum_probs=26.6
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHHh
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQET 32 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~t 32 (77)
.|+|..+||..||||.+||..++.|-+..
T Consensus 153 ~g~s~~EIA~~Lgis~~tV~~~l~RArk~ 181 (203)
T PRK09647 153 EGLSYEEIAATLGVKLGTVRSRIHRGRQQ 181 (203)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 79999999999999999999999987653
No 277
>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=95.71 E-value=0.027 Score=30.78 Aligned_cols=28 Identities=21% Similarity=0.268 Sum_probs=23.9
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
.+.+..++|+.||||.+|++.-+++-..
T Consensus 22 R~~tl~elA~~lgis~st~~~~LRrae~ 49 (53)
T PF04967_consen 22 RRITLEELAEELGISKSTVSEHLRRAER 49 (53)
T ss_pred CcCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 4578899999999999999999887543
No 278
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=95.70 E-value=0.019 Score=39.36 Aligned_cols=28 Identities=14% Similarity=0.144 Sum_probs=25.5
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
.|+|..+||..||||.+||++++.+-+.
T Consensus 220 ~g~s~~eIA~~l~is~~tV~~~~~ra~~ 247 (257)
T PRK08583 220 ENLSQKETGERLGISQMHVSRLQRQAIK 247 (257)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 7999999999999999999999987654
No 279
>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=95.68 E-value=0.076 Score=32.14 Aligned_cols=48 Identities=15% Similarity=0.073 Sum_probs=33.3
Q ss_pred CHHHHHHHhccCHHHHHHHHHHHHHh-cCCCcccc-CC--CCCCCCCHHHHH
Q psy15513 7 RPCVISRQLRVSHGCVSKILNRYQET-GSIRPGVI-GG--SKPRVATPDVER 54 (77)
Q Consensus 7 s~~~iA~rf~VS~stv~r~~~r~r~t-G~v~pk~~-gg--~~~~~~~~~~~~ 54 (77)
|...+|++++||+++|++-+++..+. |..--... || ++...+|++-..
T Consensus 18 Sis~AA~~L~iS~stvs~~I~~LE~~lg~~Lf~R~~~g~~~~g~~lT~~G~~ 69 (99)
T TIGR00637 18 SISQAAKDAGISYKSAWDYIRAMNNLSGEPLVERATGGKGGGGAVLTEYGQR 69 (99)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHhCCCeEEecCCCCCCCCeeECHHHHH
Confidence 88999999999999999999999854 44322222 21 344567775444
No 280
>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=95.67 E-value=0.021 Score=37.98 Aligned_cols=32 Identities=9% Similarity=-0.021 Sum_probs=29.7
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCC
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSI 35 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v 35 (77)
+++|-..+|..+|||.+|+.||-+.-++.|+=
T Consensus 18 ~~~sLe~aA~~~gVs~~TarrWK~~Ak~~GDD 49 (165)
T PF08822_consen 18 DRLSLEQAAAKCGVSYATARRWKREAKAKGDD 49 (165)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHcCCc
Confidence 57889999999999999999999999999975
No 281
>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=95.67 E-value=0.022 Score=36.67 Aligned_cols=28 Identities=18% Similarity=0.216 Sum_probs=24.8
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
.|++..+||..||+|.+||...+.|-+.
T Consensus 115 ~g~s~~eIA~~lgis~~tV~~~l~Rar~ 142 (170)
T TIGR02959 115 EGLSQQEIAEKLGLSLSGAKSRVQRGRK 142 (170)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 7999999999999999999988776553
No 282
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=95.64 E-value=0.01 Score=41.47 Aligned_cols=23 Identities=35% Similarity=0.403 Sum_probs=20.7
Q ss_pred CCHHHHHHHhccCHHHHHHHHHH
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNR 28 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r 28 (77)
++..+||+..|||.+||+|.++.
T Consensus 2 ~ti~dIA~~aGVS~~TVSrvLn~ 24 (346)
T PRK10401 2 ITIRDVARQAGVSVATVSRVLNN 24 (346)
T ss_pred CCHHHHHHHhCCCHHHHHHHHCC
Confidence 47899999999999999999963
No 283
>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building and bidirectional best hits, to represent a conserved family. This family is found in a limited number of bacterial lineages. This family includes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis MC2, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM10152.
Probab=95.64 E-value=0.08 Score=36.91 Aligned_cols=66 Identities=12% Similarity=0.048 Sum_probs=42.0
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCC-CccccCCCCCCCCCHHHHHHHHHHHHhCCCCcHHHHHHHh
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSI-RPGVIGGSKPRVATPDVERRIEEYKGENPAMFSWEIRDRL 75 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v-~pk~~gg~~~~~~~~~~~~~i~~~v~~~pd~tl~El~~~L 75 (77)
.|+|..+||+.||+|.++|...+.|-+..=.- .|. .....+++.+.+.++++.--.--+..|.+.|
T Consensus 123 ~g~s~~EIA~~lg~s~~tVr~~l~RAr~~Lr~~~~~------~~~~~~~~~~~~~~f~~a~~~gD~~~l~~lL 189 (281)
T TIGR02957 123 FDYPYEEIASIVGKSEANCRQLVSRARRHLDARRPR------FEVSREESRQLLERFVEAAQTGDLDGLLELL 189 (281)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCCC------CCCChHHHHHHHHHHHHHHHhCCHHHHHHHH
Confidence 68999999999999999999999988864321 111 1123344555566665554333344444433
No 284
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=95.63 E-value=0.023 Score=36.40 Aligned_cols=28 Identities=18% Similarity=0.186 Sum_probs=25.7
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
+|+|..+||..||+|.+||...+.+-+.
T Consensus 133 eg~s~~EIA~~l~is~~tV~~~l~ra~~ 160 (168)
T PRK12525 133 EGLTYVEIGERLGVSLSRIHQYMVEAFK 160 (168)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 7999999999999999999999987654
No 285
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=95.63 E-value=0.022 Score=36.53 Aligned_cols=29 Identities=21% Similarity=0.120 Sum_probs=26.4
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHHh
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQET 32 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~t 32 (77)
+|+|..+||..+|||.+||...+.|-+..
T Consensus 134 ~~~s~~EIA~~lgis~~tV~~~l~Ra~~~ 162 (173)
T PRK12522 134 EQYSYKEMSEILNIPIGTVKYRLNYAKKQ 162 (173)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 79999999999999999999999887653
No 286
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=95.61 E-value=0.022 Score=37.00 Aligned_cols=28 Identities=21% Similarity=0.232 Sum_probs=25.8
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
.|+|..+||..||||.++|...+.|-+.
T Consensus 153 ~g~s~~eIA~~lgis~~tv~~~l~Rar~ 180 (193)
T PRK11923 153 DGLSYEDIASVMQCPVGTVRSRIFRARE 180 (193)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 7999999999999999999999888764
No 287
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=95.60 E-value=0.022 Score=37.15 Aligned_cols=29 Identities=17% Similarity=0.303 Sum_probs=26.5
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHHh
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQET 32 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~t 32 (77)
+|+|..+||+.||+|.++|...+.|-+..
T Consensus 146 ~g~s~~EIAe~lgis~~~V~~~l~Ra~~~ 174 (189)
T PRK06811 146 LGEKIEEIAKKLGLTRSAIDNRLSRGRKK 174 (189)
T ss_pred ccCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 79999999999999999999999887753
No 288
>COG2452 Predicted site-specific integrase-resolvase [DNA replication, recombination, and repair]
Probab=95.60 E-value=0.021 Score=38.79 Aligned_cols=51 Identities=20% Similarity=0.230 Sum_probs=36.3
Q ss_pred CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHH
Q psy15513 5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYK 60 (77)
Q Consensus 5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v 60 (77)
.|.+.++|.++|||..|+++|.+- |.+.+-...+++.....+ ....+...+
T Consensus 1 ~m~~~e~~~~lgis~~Tl~rw~r~----G~i~~~~~~~gr~~~~ee-~v~~~~~~~ 51 (193)
T COG2452 1 LLRPKEACQLLGISYSTLLRWIRE----GKIRVVTTEGGKYRIPEE-EIKKYLGKR 51 (193)
T ss_pred CCCHHHHHHHhCcCHHHHHHHHHc----CcccceEecCceEeccHh-HHHHHhchh
Confidence 478999999999999999999875 888665555455443333 345555543
No 289
>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=95.58 E-value=0.016 Score=35.90 Aligned_cols=28 Identities=18% Similarity=0.176 Sum_probs=24.3
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
..++..|+|++||||.+||.+.++++-=
T Consensus 70 pd~tl~Ela~~l~Vs~~ti~~~Lkrlg~ 97 (119)
T PF01710_consen 70 PDATLRELAERLGVSPSTIWRALKRLGI 97 (119)
T ss_pred CCcCHHHHHHHcCCCHHHHHHHHHHcCc
Confidence 3578899999999999999999998643
No 290
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=95.57 E-value=0.011 Score=40.40 Aligned_cols=31 Identities=10% Similarity=0.063 Sum_probs=27.0
Q ss_pred ccCCCCHHHHHHHhccCHHHHHHHHHHHHHhc
Q psy15513 2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETG 33 (77)
Q Consensus 2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG 33 (77)
++.| |...+|++++||+++|+|.+++..+.=
T Consensus 13 ~~~g-s~s~AA~~L~isQ~avSr~i~~LE~~l 43 (296)
T PRK09906 13 AEEL-NFTKAAEKLHTAQPSLSQQIKDLENCV 43 (296)
T ss_pred HhhC-CHHHHHHHhCCCCcHHHHHHHHHHHHh
Confidence 3556 899999999999999999999998643
No 291
>PRK11013 DNA-binding transcriptional regulator LysR; Provisional
Probab=95.57 E-value=0.012 Score=40.73 Aligned_cols=47 Identities=23% Similarity=0.146 Sum_probs=33.0
Q ss_pred ccCCCCHHHHHHHhccCHHHHHHHHHHHHHh-cCCCccccCCCCCCCCCHH
Q psy15513 2 AAAGVRPCVISRQLRVSHGCVSKILNRYQET-GSIRPGVIGGSKPRVATPD 51 (77)
Q Consensus 2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r~t-G~v~pk~~gg~~~~~~~~~ 51 (77)
++.| |...+|++++||+++|++.++++.+. |.---.. .+ +.=.+|++
T Consensus 16 ~~~g-S~s~AAe~L~isqsavS~~Ik~LE~~lg~~Lf~R-~~-~~v~LT~~ 63 (309)
T PRK11013 16 MTAG-SLTEAARLLHTSQPTVSRELARFEKVIGLKLFER-VR-GRLHPTVQ 63 (309)
T ss_pred HHhC-cHHHHHHHHCCCcHHHHHHHHHHHHHhCceeeee-cC-CCcccCHH
Confidence 3455 89999999999999999999999954 4433332 22 33345554
No 292
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=95.57 E-value=0.013 Score=40.54 Aligned_cols=36 Identities=19% Similarity=0.126 Sum_probs=29.6
Q ss_pred ccCCCCHHHHHHHhccCHHHHHHHHHHHHHh-cCCCc
Q psy15513 2 AAAGVRPCVISRQLRVSHGCVSKILNRYQET-GSIRP 37 (77)
Q Consensus 2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r~t-G~v~p 37 (77)
++.|.|...+|++++||+++|++.+++..+. |.---
T Consensus 13 ~~~~~s~s~AA~~L~isq~avSr~I~~LE~~lg~~LF 49 (309)
T PRK12682 13 VRRNLNLTEAAKALHTSQPGVSKAIIELEEELGIEIF 49 (309)
T ss_pred HHccCCHHHHHHHhcCccHHHHHHHHHHHHHhCCeeE
Confidence 4567799999999999999999999999854 44333
No 293
>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=95.56 E-value=0.013 Score=31.95 Aligned_cols=25 Identities=28% Similarity=0.401 Sum_probs=19.9
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILN 27 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~ 27 (77)
+.|+|..++|..+|||.+++++|.+
T Consensus 10 ~~~lt~~~~a~~~~i~~~~i~~~e~ 34 (64)
T PF12844_consen 10 EKGLTQKDLAEKLGISRSTISKIEN 34 (64)
T ss_dssp HCT--HHHHHHHHTS-HHHHHHHHT
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHC
Confidence 4689999999999999999999964
No 294
>TIGR03339 phn_lysR aminoethylphosphonate catabolism associated LysR family transcriptional regulator. This group of sequences represents a number of related clades with numerous examples of members adjacent to operons for the degradation of 2-aminoethylphosphonate (AEP) in Pseudomonas, Ralstonia, Bordetella and Burkholderia species. These are transcriptional regulators of the LysR family which contain a helix-turn-helix (HTH) domain (pfam00126) and a periplasmic substrate-binding protein-like domain (pfam03466).
Probab=95.55 E-value=0.013 Score=39.28 Aligned_cols=33 Identities=18% Similarity=0.240 Sum_probs=27.7
Q ss_pred ccCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCC
Q psy15513 2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETGSI 35 (77)
Q Consensus 2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v 35 (77)
++.| |...+|++++||+++|++.+++..+.=.+
T Consensus 9 ~~~g-s~~~AA~~L~isqsavS~~i~~LE~~lg~ 41 (279)
T TIGR03339 9 ARCG-SFTRAAERLGLSQPTVTDQVRKLEERYGV 41 (279)
T ss_pred HhcC-CHHHHHHHhcCCchHHHHHHHHHHHHhCC
Confidence 3456 88999999999999999999999854433
No 295
>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=95.55 E-value=0.023 Score=38.07 Aligned_cols=28 Identities=25% Similarity=0.304 Sum_probs=25.8
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
.|+|..+||+.||||.++|++++++-+.
T Consensus 193 ~~~s~~eIA~~lgis~~~v~~~~~ra~~ 220 (227)
T TIGR02980 193 EDKTQSEIAERLGISQMHVSRLLRRALK 220 (227)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 6899999999999999999999988654
No 296
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=95.55 E-value=0.016 Score=36.48 Aligned_cols=30 Identities=20% Similarity=0.387 Sum_probs=28.5
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCC
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSI 35 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v 35 (77)
.|..++|+++|+|.++|.+-+++..+.|=+
T Consensus 23 ~~~~eia~~lglS~~~v~~Ri~~L~~~GiI 52 (154)
T COG1522 23 ISNAELAERVGLSPSTVLRRIKRLEEEGVI 52 (154)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCce
Confidence 899999999999999999999999999955
No 297
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=95.54 E-value=0.025 Score=36.63 Aligned_cols=28 Identities=18% Similarity=0.248 Sum_probs=25.2
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
+|+|..+||..||||.+||...+.+-..
T Consensus 142 ~g~s~~EIA~~lgis~~tVk~~l~rAl~ 169 (178)
T PRK12529 142 DGMKQKDIAQALDIALPTVKKYIHQAYV 169 (178)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 7999999999999999999999887543
No 298
>PRK06930 positive control sigma-like factor; Validated
Probab=95.54 E-value=0.023 Score=37.45 Aligned_cols=29 Identities=17% Similarity=0.323 Sum_probs=26.3
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
-.|+|..+||..||||.+||..++.+.+.
T Consensus 128 ~eg~s~~EIA~~lgiS~~tVk~~l~Ra~~ 156 (170)
T PRK06930 128 GYGLSYSEIADYLNIKKSTVQSMIERAEK 156 (170)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 47999999999999999999999988664
No 299
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=95.54 E-value=0.025 Score=30.37 Aligned_cols=34 Identities=24% Similarity=0.197 Sum_probs=28.8
Q ss_pred ccCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCC
Q psy15513 2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETGSI 35 (77)
Q Consensus 2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v 35 (77)
...|.|..+||..+++|..||...+.+....-.+
T Consensus 16 ~~~G~s~~eia~~l~is~~tV~~h~~~i~~Kl~~ 49 (65)
T COG2771 16 VAQGKSNKEIARILGISEETVKTHLRNIYRKLGV 49 (65)
T ss_pred HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCC
Confidence 4579999999999999999999999988654433
No 300
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=95.53 E-value=0.025 Score=36.30 Aligned_cols=28 Identities=25% Similarity=0.242 Sum_probs=25.4
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
+|+|..+||..||||.+||...+.+-+.
T Consensus 134 ~g~s~~EIA~~lgis~~tV~~~l~ra~~ 161 (172)
T PRK12523 134 DGMGHAEIAERLGVSVSRVRQYLAQGLR 161 (172)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 7999999999999999999999887554
No 301
>COG1342 Predicted DNA-binding proteins [General function prediction only]
Probab=95.53 E-value=0.022 Score=34.87 Aligned_cols=29 Identities=10% Similarity=0.187 Sum_probs=26.4
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHHh
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQET 32 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~t 32 (77)
.|+++.++|.+.|||++|+.+.++.-|..
T Consensus 48 ~~l~QeeAA~rMgISr~Tfwr~l~sAR~K 76 (99)
T COG1342 48 EGLTQEEAALRMGISRQTFWRLLTSARKK 76 (99)
T ss_pred hhccHHHHHHHhcccHHHHHHHHHHHHHH
Confidence 68999999999999999999999987753
No 302
>PRK09483 response regulator; Provisional
Probab=95.52 E-value=0.019 Score=36.91 Aligned_cols=33 Identities=27% Similarity=0.206 Sum_probs=29.1
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCC
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSI 35 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v 35 (77)
..|++..+||.+|+||.+||...+++.+..=.+
T Consensus 161 ~~G~~~~~Ia~~l~is~~TV~~~~~~i~~Kl~v 193 (217)
T PRK09483 161 TKGQKVNEISEQLNLSPKTVNSYRYRMFSKLNI 193 (217)
T ss_pred HCCCCHHHHHHHhCCCHHHHHHHHHHHHHHcCC
Confidence 479999999999999999999999998875444
No 303
>PF08765 Mor: Mor transcription activator family; InterPro: IPR014875 Mor (Middle operon regulator) is a sequence specific DNA binding protein. It mediates transcription activation through its interactions with the C-terminal domains of the alpha and sigma subunits of bacterial RNA polymerase. The N-terminal region of Mor is the dimerisation region, and the C-terminal contains a helix-turn-helix motif which binds DNA []. ; PDB: 1RR7_A.
Probab=95.51 E-value=0.024 Score=34.67 Aligned_cols=29 Identities=17% Similarity=0.337 Sum_probs=22.9
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHHh
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQET 32 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~t 32 (77)
+|++..++|++||+|...|++++++.+..
T Consensus 71 ~G~n~~eLA~kyglS~r~I~~Ii~~~~~~ 99 (108)
T PF08765_consen 71 NGMNVRELARKYGLSERQIYRIIKRVRRR 99 (108)
T ss_dssp -SS-HHHHHHHHT--HHHHHHHHHHHHH-
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 49999999999999999999999998763
No 304
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=95.51 E-value=0.025 Score=38.33 Aligned_cols=29 Identities=24% Similarity=0.143 Sum_probs=26.0
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
-.|+|..+||+.+|||.+||.+++.+-+.
T Consensus 198 ~~g~s~~EIA~~lgis~~tV~~~~~ra~~ 226 (236)
T PRK06986 198 QEELNLKEIGAVLGVSESRVSQIHSQAIK 226 (236)
T ss_pred ccCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 47999999999999999999999887654
No 305
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=95.50 E-value=0.011 Score=37.00 Aligned_cols=26 Identities=15% Similarity=0.093 Sum_probs=23.5
Q ss_pred ccCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513 2 AAAGVRPCVISRQLRVSHGCVSKILN 27 (77)
Q Consensus 2 ~~~G~s~~~iA~rf~VS~stv~r~~~ 27 (77)
.+.|+|..++|++.|||.+++++|.+
T Consensus 15 ~~~Glsq~eLA~~~Gis~~~is~iE~ 40 (120)
T PRK13890 15 DERHMTKKELSERSGVSISFLSDLTT 40 (120)
T ss_pred HHcCCCHHHHHHHHCcCHHHHHHHHc
Confidence 35799999999999999999999874
No 306
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=95.49 E-value=0.026 Score=36.54 Aligned_cols=28 Identities=14% Similarity=0.239 Sum_probs=25.7
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
.|+|..+||..||+|.+||...+.|-+.
T Consensus 143 ~g~s~~EIA~~lgis~~tV~~~l~Rar~ 170 (186)
T PRK05602 143 QGLSNIEAAAVMDISVDALESLLARGRR 170 (186)
T ss_pred cCCCHHHHHHHhCcCHHHHHHHHHHHHH
Confidence 6999999999999999999999888764
No 307
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in multiple copies in the order Myxococcales. This model supercedes TIGR02233, which has now been retired.
Probab=95.49 E-value=0.025 Score=39.06 Aligned_cols=28 Identities=21% Similarity=0.248 Sum_probs=25.9
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
+|+|..+||..||||.+||...+.|-+.
T Consensus 176 eg~S~~EIA~~Lgis~~TVk~rl~RAr~ 203 (244)
T TIGR03001 176 DGLSMDRIGAMYQVHRSTVSRWVAQARE 203 (244)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 7999999999999999999999888765
No 308
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=95.48 E-value=0.025 Score=36.85 Aligned_cols=28 Identities=14% Similarity=0.140 Sum_probs=25.4
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
.|+|..+||..+|+|.+||...+.|-+.
T Consensus 146 ~g~s~~EIA~~lgis~~tV~~~l~Rar~ 173 (191)
T PRK12520 146 LELETEEICQELQITATNAWVLLYRARM 173 (191)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 6899999999999999999999887654
No 309
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=95.48 E-value=0.028 Score=35.50 Aligned_cols=28 Identities=21% Similarity=0.071 Sum_probs=26.0
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
.|+|..+||..||+|.+||...+.|-+.
T Consensus 127 ~~~s~~eIA~~lgis~~tv~~~l~Rar~ 154 (161)
T PRK12541 127 YGFSYKEIAEMTGLSLAKVKIELHRGRK 154 (161)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 7999999999999999999999988765
No 310
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=95.48 E-value=0.027 Score=36.20 Aligned_cols=28 Identities=25% Similarity=0.245 Sum_probs=25.7
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
.|+|..+||..||||.++|...+.|.+.
T Consensus 151 ~~~s~~eIA~~lgis~~~v~~~l~Rar~ 178 (187)
T PRK09641 151 EDLSLKEISEILDLPVGTVKTRIHRGRE 178 (187)
T ss_pred hCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 6899999999999999999999988764
No 311
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=95.47 E-value=0.064 Score=35.85 Aligned_cols=45 Identities=13% Similarity=0.027 Sum_probs=36.8
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCH
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATP 50 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~ 50 (77)
.+..++|++||||.++|.--+++....|=|...|..|-.....+.
T Consensus 35 L~e~~La~~lgVSRtpVREAL~~L~~eGLV~~~~~~g~~v~~~~~ 79 (221)
T PRK11414 35 LITKNLAEQLGMSITPVREALLRLVSVNALSVAPAQAFTVPEVSK 79 (221)
T ss_pred cCHHHHHHHHCCCchhHHHHHHHHHHCCCEEecCCCceeecCCCH
Confidence 577889999999999999999999999999887766544333443
No 312
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=95.47 E-value=0.027 Score=38.90 Aligned_cols=36 Identities=19% Similarity=0.351 Sum_probs=32.5
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccc
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV 39 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~ 39 (77)
.+++..+||+++|+++|||+|+++.+.+.|=+.-.+
T Consensus 25 ~~ls~~eia~~lgl~kstv~RlL~tL~~~g~v~~~~ 60 (263)
T PRK09834 25 GGATVGLLAELTGLHRTTVRRLLETLQEEGYVRRSA 60 (263)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEec
Confidence 358999999999999999999999999999997544
No 313
>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=95.47 E-value=0.016 Score=37.77 Aligned_cols=25 Identities=20% Similarity=0.250 Sum_probs=22.9
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILN 27 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~ 27 (77)
..|+|..++|.++|||+++|++|-+
T Consensus 36 ~lGmTq~eLAerlGVS~~tIs~iE~ 60 (150)
T TIGR02612 36 ALGMSGAQLAGRLGVTPQRVEALEK 60 (150)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 3699999999999999999999974
No 314
>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=95.46 E-value=0.025 Score=38.37 Aligned_cols=27 Identities=15% Similarity=0.206 Sum_probs=24.5
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQ 30 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r 30 (77)
.|+|..+||+.+|||.+||.+++.+-+
T Consensus 197 eg~s~~EIA~~Lgis~~tV~~~l~ra~ 223 (234)
T TIGR02835 197 TEKTQKEVADMLGISQSYISRLEKRIL 223 (234)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 689999999999999999999987644
No 315
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=95.45 E-value=0.02 Score=39.41 Aligned_cols=38 Identities=26% Similarity=0.352 Sum_probs=32.5
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCC
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGG 42 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg 42 (77)
..++..++|+.|+||.+||.|.++...+.|.+.-. .||
T Consensus 17 ~~~~~~eLa~~l~VS~~TiRRdL~~L~~~~~l~r~-~Gg 54 (240)
T PRK10411 17 TSLTTEALAEQLNVSKETIRRDLNELQTQGKILRN-HGR 54 (240)
T ss_pred CCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEe-cCe
Confidence 34899999999999999999999999998888643 444
No 316
>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=95.43 E-value=0.015 Score=29.55 Aligned_cols=25 Identities=16% Similarity=0.117 Sum_probs=19.8
Q ss_pred CHHHHHHHhccCHHHHHHHHHHHHHhcCC
Q psy15513 7 RPCVISRQLRVSHGCVSKILNRYQETGSI 35 (77)
Q Consensus 7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v 35 (77)
++.++|+.+|||+.|+..|-+. |-+
T Consensus 1 ti~e~A~~~gvs~~tlR~ye~~----Gll 25 (38)
T PF00376_consen 1 TIGEVAKLLGVSPRTLRYYERE----GLL 25 (38)
T ss_dssp EHHHHHHHHTS-HHHHHHHHHT----TSS
T ss_pred CHHHHHHHHCCCHHHHHHHHHC----CCC
Confidence 4679999999999999887554 877
No 317
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=95.41 E-value=0.028 Score=36.89 Aligned_cols=28 Identities=21% Similarity=0.198 Sum_probs=25.9
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
+|+|..+||..+|+|.+||...+.|.+.
T Consensus 143 ~g~s~~EIA~~lgis~~tV~~~l~Rar~ 170 (188)
T PRK12517 143 GGFSGEEIAEILDLNKNTVMTRLFRARN 170 (188)
T ss_pred hCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 7999999999999999999999988765
No 318
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=95.39 E-value=0.029 Score=36.17 Aligned_cols=28 Identities=25% Similarity=0.248 Sum_probs=25.5
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
.|+|..+||..||+|.+||...+.+-+.
T Consensus 146 ~g~s~~eIA~~l~is~~tV~~~l~ra~~ 173 (184)
T PRK12512 146 EGASIKETAAKLSMSEGAVRVALHRGLA 173 (184)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 6999999999999999999999887654
No 319
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=95.39 E-value=0.025 Score=38.45 Aligned_cols=35 Identities=11% Similarity=0.087 Sum_probs=30.9
Q ss_pred ccCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCC
Q psy15513 2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIR 36 (77)
Q Consensus 2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~ 36 (77)
...|++..+||..|+||.+||...+++..+.-.+.
T Consensus 145 LAqGkTnKEIAe~L~IS~rTVkth~srImkKLgV~ 179 (198)
T PRK15201 145 IASGYHLSETAALLSLSEEQTKSLRRSIMRKLHVK 179 (198)
T ss_pred HHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Confidence 35799999999999999999999999998876553
No 320
>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=95.38 E-value=0.031 Score=35.96 Aligned_cols=29 Identities=24% Similarity=0.244 Sum_probs=26.4
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
-.|+|..+||..||+|.+||..++.|-+.
T Consensus 152 ~~~~s~~EIA~~lgis~~tv~~~l~rar~ 180 (190)
T TIGR02939 152 LEGLSYEDIARIMDCPVGTVRSRIFRARE 180 (190)
T ss_pred hcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 37999999999999999999999988765
No 321
>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=95.37 E-value=0.026 Score=36.29 Aligned_cols=33 Identities=9% Similarity=0.166 Sum_probs=30.5
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPG 38 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk 38 (77)
++..+||..+|+|+.||+|.++++++.|-+.-.
T Consensus 144 ~t~~~iA~~lG~tretvsR~l~~l~~~g~I~~~ 176 (193)
T TIGR03697 144 LSHQAIAEAIGSTRVTITRLLGDLRKKKLISIH 176 (193)
T ss_pred CCHHHHHHHhCCcHHHHHHHHHHHHHCCCEEec
Confidence 689999999999999999999999999988654
No 322
>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=95.37 E-value=0.029 Score=38.31 Aligned_cols=34 Identities=9% Similarity=0.153 Sum_probs=32.0
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCc
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP 37 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~p 37 (77)
.+++..|||+++|+++|||+|+++-+.+.|=+..
T Consensus 23 ~~~~l~eia~~lglpksT~~RlL~tL~~~G~l~~ 56 (248)
T TIGR02431 23 PRLTLTDVAEATGLTRAAARRFLLTLVELGYVTS 56 (248)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEe
Confidence 5699999999999999999999999999999974
No 323
>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=95.36 E-value=0.033 Score=32.91 Aligned_cols=28 Identities=21% Similarity=0.315 Sum_probs=25.7
Q ss_pred CCCCHHHHHHHhc-cCHHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLR-VSHGCVSKILNRYQE 31 (77)
Q Consensus 4 ~G~s~~~iA~rf~-VS~stv~r~~~r~r~ 31 (77)
.|+|-.+|++.|| .++|||+.-+++..+
T Consensus 43 ~~~s~~~Ig~~fg~r~hStV~~a~~ri~~ 71 (90)
T cd06571 43 TGLSLPEIGRAFGGRDHSTVLHAVRKIEE 71 (90)
T ss_pred hCCCHHHHHHHhCCCCHhHHHHHHHHHHH
Confidence 4899999999999 999999999998765
No 324
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=95.35 E-value=0.031 Score=36.13 Aligned_cols=28 Identities=14% Similarity=0.154 Sum_probs=25.1
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
+|+|..+||..||||.+||...+.|-+.
T Consensus 132 e~~s~~EIA~~lgis~~tV~~~l~ra~~ 159 (179)
T PRK12543 132 HDYSQEEIAQLLQIPIGTVKSRIHAALK 159 (179)
T ss_pred ccCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 7999999999999999999998877653
No 325
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=95.35 E-value=0.03 Score=36.65 Aligned_cols=28 Identities=18% Similarity=0.177 Sum_probs=25.8
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
.|+|..+||+.+|||.++|..++.|-+.
T Consensus 157 ~~~s~~EIA~~Lgis~~tVk~~l~ra~~ 184 (194)
T PRK09646 157 GGLTYREVAERLAVPLGTVKTRMRDGLI 184 (194)
T ss_pred cCCCHHHHHHHhCCChHhHHHHHHHHHH
Confidence 7899999999999999999999988664
No 326
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=95.33 E-value=0.032 Score=36.46 Aligned_cols=30 Identities=17% Similarity=0.139 Sum_probs=26.3
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHHh
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQET 32 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~t 32 (77)
-.|+|..+||..||+|.+||...+.|-++.
T Consensus 125 ~~g~s~~EIA~~Lgis~~tV~~~l~RAr~~ 154 (182)
T PRK12540 125 ASGFSYEDAAAICGCAVGTIKSRVNRARSK 154 (182)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 379999999999999999999998876653
No 327
>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=95.32 E-value=0.03 Score=37.41 Aligned_cols=36 Identities=17% Similarity=0.175 Sum_probs=32.6
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccc
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV 39 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~ 39 (77)
.+++..++|+.|++|++||++.+++..+.|-+...+
T Consensus 156 g~~s~~eia~~l~is~stv~r~L~~Le~~GlI~r~~ 191 (203)
T TIGR01884 156 GEKSVKNIAKKLGKSLSTISRHLRELEKKGLVEQKG 191 (203)
T ss_pred CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEc
Confidence 357999999999999999999999999999997654
No 328
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=95.31 E-value=0.03 Score=37.15 Aligned_cols=28 Identities=21% Similarity=0.190 Sum_probs=25.4
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
+|+|..+||..||||.+||..++.+-+.
T Consensus 168 ~g~s~~EIA~~lgis~~tV~~~l~Ra~~ 195 (206)
T PRK12526 168 QELSQEQLAQQLNVPLGTVKSRLRLALA 195 (206)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 6999999999999999999999887654
No 329
>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=95.31 E-value=0.032 Score=36.53 Aligned_cols=28 Identities=21% Similarity=0.254 Sum_probs=25.5
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
+|+|..+||..||+|.+||...+.|-+.
T Consensus 146 ~g~s~~EIA~~lgis~~tvk~rl~Rar~ 173 (188)
T TIGR02943 146 LGFESDEICQELEISTSNCHVLLYRARL 173 (188)
T ss_pred hCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 7999999999999999999999887654
No 330
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=95.30 E-value=0.017 Score=40.99 Aligned_cols=27 Identities=22% Similarity=0.218 Sum_probs=25.0
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQ 30 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r 30 (77)
.||+..+||..+|||++||..|-+|+-
T Consensus 18 ~gmk~~dIAeklGvspntiksWKrr~g 44 (279)
T COG5484 18 KGMKLKDIAEKLGVSPNTIKSWKRRDG 44 (279)
T ss_pred hhccHHHHHHHhCCChHHHHHHHHhcC
Confidence 689999999999999999999998864
No 331
>PRK09954 putative kinase; Provisional
Probab=95.30 E-value=0.023 Score=40.59 Aligned_cols=30 Identities=20% Similarity=0.283 Sum_probs=28.9
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCC
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSI 35 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v 35 (77)
+|..++|+.|+||++||.+.+++.++.|-+
T Consensus 18 ~s~~~la~~l~~s~~~v~~~i~~L~~~g~i 47 (362)
T PRK09954 18 IQQNEIADILQISRSRVAAHIMDLMRKGRI 47 (362)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCCc
Confidence 899999999999999999999999999987
No 332
>PF04645 DUF603: Protein of unknown function, DUF603; InterPro: IPR006739 This family includes several uncharacterised proteins from Borrelia species.
Probab=95.29 E-value=0.022 Score=38.16 Aligned_cols=35 Identities=20% Similarity=0.280 Sum_probs=30.7
Q ss_pred CccCC-CCHHHHHHHhccCHHHHHHHHHHHHHhcCC
Q psy15513 1 MAAAG-VRPCVISRQLRVSHGCVSKILNRYQETGSI 35 (77)
Q Consensus 1 l~~~G-~s~~~iA~rf~VS~stv~r~~~r~r~tG~v 35 (77)
+|..| .+-.+||..+|||.+.|.|.-++|...++-
T Consensus 14 yF~eg~L~d~~Ia~~lgvs~~nV~kmR~Kwes~~~s 49 (181)
T PF04645_consen 14 YFKEGRLSDAEIAKELGVSRVNVWKMRQKWESSEDS 49 (181)
T ss_pred HHhcCCccHHHHHHHHCchHHHHHHHHHHHHhcCCc
Confidence 36788 999999999999999999999998876554
No 333
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=95.29 E-value=0.033 Score=35.11 Aligned_cols=28 Identities=21% Similarity=0.254 Sum_probs=25.3
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
+|+|..+||..||+|.+||...+.|-+.
T Consensus 120 ~~~s~~eIA~~lgis~~tv~~~l~ra~~ 147 (159)
T PRK12527 120 EGLSHQQIAEHLGISRSLVEKHIVNAMK 147 (159)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 7999999999999999999999887553
No 334
>PRK05572 sporulation sigma factor SigF; Validated
Probab=95.28 E-value=0.032 Score=38.24 Aligned_cols=29 Identities=14% Similarity=0.190 Sum_probs=25.7
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
-.|+|..+||+.||||+++|+++.++-..
T Consensus 216 ~~~~s~~eIA~~lgis~~~V~~~~~ral~ 244 (252)
T PRK05572 216 FKDKTQSEVAKRLGISQVQVSRLEKKILK 244 (252)
T ss_pred hCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 37899999999999999999999887553
No 335
>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=95.26 E-value=0.033 Score=34.28 Aligned_cols=29 Identities=17% Similarity=0.259 Sum_probs=22.4
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
.+.+|..+||..+|||...|+.+++|-..
T Consensus 31 ~eDlSlsEIAe~~~iSRqaV~d~ikr~~~ 59 (101)
T PF04297_consen 31 EEDLSLSEIAEELGISRQAVYDSIKRAEK 59 (101)
T ss_dssp TS---HHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred ccCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 46789999999999999999999999653
No 336
>TIGR02859 spore_sigH RNA polymerase sigma-H factor. Members of this protein family are RNA polymerase sigma-H factor for sporulation in endospore-forming bacteria. This protein is also called Sigma-30 and SigH. Although rather close homologs are detected in Listeria, Listeria does not form spores and the role of the related sigma factor in that genus is in doubt.
Probab=95.25 E-value=0.035 Score=36.01 Aligned_cols=28 Identities=18% Similarity=0.165 Sum_probs=25.7
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
+|+|..+||..||+|.+||...+.|.++
T Consensus 164 ~~~s~~eIA~~l~~s~~tV~~~l~r~r~ 191 (198)
T TIGR02859 164 DGKSYQEIACDLNRHVKSIDNALQRVKR 191 (198)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 6999999999999999999998888765
No 337
>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=95.24 E-value=0.035 Score=37.26 Aligned_cols=29 Identities=17% Similarity=0.109 Sum_probs=26.0
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
-.|+|..+||..+|||.++|.+++.+-++
T Consensus 189 ~~~~s~~eIA~~lgis~~tV~~~~~ra~~ 217 (224)
T TIGR02479 189 YEELNLKEIGEVLGLTESRVSQIHSQALK 217 (224)
T ss_pred hCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 37999999999999999999999887654
No 338
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=95.23 E-value=0.022 Score=34.46 Aligned_cols=26 Identities=19% Similarity=0.293 Sum_probs=23.2
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRY 29 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~ 29 (77)
.|-...++|+.+|||++|+++.+++|
T Consensus 67 ~~gn~s~AAr~LGIsRsTL~rKLkr~ 92 (95)
T PRK00430 67 TRGNQTRAALMLGINRGTLRKKLKKY 92 (95)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHh
Confidence 45678899999999999999999986
No 339
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=95.23 E-value=0.035 Score=36.00 Aligned_cols=28 Identities=14% Similarity=0.144 Sum_probs=25.7
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
.|+|..+||..||||.+||...+.|-+.
T Consensus 146 ~g~s~~eIA~~lgis~~tV~~~l~ra~~ 173 (184)
T PRK12539 146 EGLSVAEAATRSGMSESAVKVSVHRGLK 173 (184)
T ss_pred cCCcHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 7999999999999999999999987654
No 340
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=95.22 E-value=0.037 Score=38.51 Aligned_cols=35 Identities=14% Similarity=0.107 Sum_probs=32.1
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG 38 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk 38 (77)
.+++..|||+++|+++|||+|+++-+.+.|-+.--
T Consensus 39 ~~~tl~eIa~~lglpkStv~RlL~tL~~~G~l~~~ 73 (271)
T PRK10163 39 GSSSVSDISLNLDLPLSTTFRLLKVLQAADFVYQD 73 (271)
T ss_pred CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEc
Confidence 46899999999999999999999999999999543
No 341
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=95.22 E-value=0.036 Score=36.29 Aligned_cols=28 Identities=18% Similarity=0.205 Sum_probs=25.4
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
+|+|..+||..+|||.+||...+.|.+.
T Consensus 169 e~~s~~EIA~~lgis~~tV~~~l~rar~ 196 (208)
T PRK08295 169 DGKSYQEIAEELNRHVKSIDNALQRVKR 196 (208)
T ss_pred ccCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 6899999999999999999998887664
No 342
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=95.21 E-value=0.035 Score=37.58 Aligned_cols=27 Identities=26% Similarity=0.251 Sum_probs=24.6
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQ 30 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r 30 (77)
+|+|..+||..+|||.+||++++.+-+
T Consensus 194 e~~S~~EIA~~lgis~~tV~~~~~rA~ 220 (233)
T PRK05803 194 KEKTQREIAKALGISRSYVSRIEKRAL 220 (233)
T ss_pred CCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 789999999999999999999987654
No 343
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=95.20 E-value=0.038 Score=35.51 Aligned_cols=28 Identities=29% Similarity=0.345 Sum_probs=25.5
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
.|+|..+||+.+|||.+||...+.|-+.
T Consensus 134 ~g~s~~EIA~~lgis~~tV~~~l~Ra~~ 161 (172)
T PRK09651 134 DGLTYSEIAHKLGVSVSSVKKYVAKATE 161 (172)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 7899999999999999999999987654
No 344
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=95.18 E-value=0.074 Score=36.19 Aligned_cols=37 Identities=19% Similarity=0.309 Sum_probs=33.3
Q ss_pred CHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCC
Q psy15513 7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGS 43 (77)
Q Consensus 7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~ 43 (77)
+-.++|++||||.++|.--+++....|=|..+|.+|-
T Consensus 36 sE~eLa~~lgVSRtpVREAL~~L~~eGlv~~~~~~G~ 72 (254)
T PRK09464 36 PERELAKQFDVSRPSLREAIQRLEAKGLLLRRQGGGT 72 (254)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCcee
Confidence 6789999999999999999999999999988876553
No 345
>TIGR02325 C_P_lyase_phnF phosphonates metabolism transcriptional regulator PhnF. All members of the seed alignment for this family are predicted helix-turn-helix transcriptional regulatory proteins of the broader gntR and are found associated with genes for the import and degradation of phosphonates and/or related compounds (e.g. phosphonites) with a direct C-P bond.
Probab=95.17 E-value=0.028 Score=37.75 Aligned_cols=34 Identities=15% Similarity=0.205 Sum_probs=31.1
Q ss_pred CHHHHHHHhccCHHHHHHHHHHHHHhcCCCcccc
Q psy15513 7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI 40 (77)
Q Consensus 7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~ 40 (77)
|-+++|++||||..||.+-+....+.|-+..++.
T Consensus 34 sE~eLa~~~~VSR~TvR~Al~~L~~eGli~r~~G 67 (238)
T TIGR02325 34 AEMQLAERFGVNRHTVRRAIAALVERGLLRAEQG 67 (238)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 6689999999999999999999999999987753
No 346
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=95.16 E-value=0.036 Score=36.67 Aligned_cols=27 Identities=19% Similarity=0.145 Sum_probs=24.1
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQ 30 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r 30 (77)
.|+|..+||..||+|.+||...+.|-+
T Consensus 154 eg~s~~EIA~~lgis~~tVk~~l~RAr 180 (201)
T PRK12545 154 LDFEIDDICTELTLTANHCSVLLYRAR 180 (201)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 799999999999999999998777644
No 347
>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=95.15 E-value=0.039 Score=35.41 Aligned_cols=28 Identities=21% Similarity=0.269 Sum_probs=25.6
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
.|+|..+||..+|||.+||.+-+.|.+.
T Consensus 155 ~g~s~~eIA~~lgis~~~v~~~l~Ra~~ 182 (189)
T TIGR02984 155 EGLSFAEVAERMDRSEGAVSMLWVRGLA 182 (189)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 7999999999999999999999888664
No 348
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=95.14 E-value=0.037 Score=37.82 Aligned_cols=28 Identities=14% Similarity=0.230 Sum_probs=25.6
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
.|+|..+||..||||.+||...+.|-+.
T Consensus 186 eg~s~~EIA~~Lgis~~tVk~~l~RAr~ 213 (233)
T PRK12538 186 ENMSNGEIAEVMDTTVAAVESLLKRGRQ 213 (233)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 7999999999999999999999888664
No 349
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=95.13 E-value=0.041 Score=35.70 Aligned_cols=28 Identities=14% Similarity=0.156 Sum_probs=25.6
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
.|+|..+||..+|||.+||...+.|-+.
T Consensus 154 ~g~s~~EIA~~lgis~~tV~~~l~Ra~~ 181 (189)
T PRK09648 154 VGLSAEETAEAVGSTPGAVRVAQHRALA 181 (189)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 6899999999999999999999988654
No 350
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=95.13 E-value=0.039 Score=36.92 Aligned_cols=28 Identities=14% Similarity=0.135 Sum_probs=25.6
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
.|+|..+||..||+|.+||...+.|-+.
T Consensus 163 ~g~s~~EIAe~lgis~~tV~~~l~RAr~ 190 (206)
T PRK12544 163 IELETNEICHAVDLSVSNLNVLLYRARL 190 (206)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 6999999999999999999999887664
No 351
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=95.10 E-value=0.042 Score=35.74 Aligned_cols=28 Identities=4% Similarity=-0.045 Sum_probs=24.9
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
.|+|..+||+.||||.+||...+.|-+.
T Consensus 146 ~~~s~~eIA~~lgis~~tV~~~l~Rar~ 173 (189)
T PRK12515 146 HEKSVEEVGEIVGIPESTVKTRMFYARK 173 (189)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 7899999999999999999988777654
No 352
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=95.10 E-value=0.023 Score=37.32 Aligned_cols=25 Identities=16% Similarity=0.227 Sum_probs=23.1
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILN 27 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~ 27 (77)
+.|++..++|+++|||++|+++|.+
T Consensus 18 ~~glt~~elA~~~gis~~~is~~E~ 42 (185)
T PRK09943 18 QQGLSQRRAAELSGLTHSAISTIEQ 42 (185)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHc
Confidence 4799999999999999999999974
No 353
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=95.10 E-value=0.03 Score=36.77 Aligned_cols=33 Identities=18% Similarity=0.090 Sum_probs=28.7
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCC
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSI 35 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v 35 (77)
..|+|..+||++++||.+||...+++..+.=.+
T Consensus 163 ~~G~s~~eIA~~l~iS~~TV~~h~~~i~~Kl~v 195 (216)
T PRK10840 163 AEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGV 195 (216)
T ss_pred HCCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCC
Confidence 479999999999999999999999888765444
No 354
>TIGR02424 TF_pcaQ pca operon transcription factor PcaQ. Members of this family are LysR-family transcription factors associated with operons for catabolism of protocatechuate. Members occur only in Proteobacteria.
Probab=95.10 E-value=0.023 Score=38.87 Aligned_cols=33 Identities=24% Similarity=0.302 Sum_probs=27.5
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHHh-cCCC
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQET-GSIR 36 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~t-G~v~ 36 (77)
+.| |...+|+.++||+++|++.+++..+. |.--
T Consensus 16 ~~g-S~s~AA~~L~isq~avS~~I~~LE~~lg~~L 49 (300)
T TIGR02424 16 RQG-SVKRAAEALHITQPAVSKTLRELEEILGTPL 49 (300)
T ss_pred HhC-CHHHHHHHhCCChHHHHHHHHHHHHHhCCeE
Confidence 455 88999999999999999999999854 4433
No 355
>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=95.08 E-value=0.028 Score=37.17 Aligned_cols=27 Identities=7% Similarity=0.192 Sum_probs=24.5
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQ 30 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r 30 (77)
.|++..+||+.||+|.++|++.++-..
T Consensus 119 ~g~s~~~iA~~lg~s~~~V~r~l~l~~ 145 (187)
T TIGR00180 119 FSMTQEDLAKKIGKSRAHITNLLRLLK 145 (187)
T ss_pred hCCCHHHHHHHHCcCHHHHHHHHHHHc
Confidence 589999999999999999999998743
No 356
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=95.07 E-value=0.042 Score=36.18 Aligned_cols=30 Identities=23% Similarity=0.173 Sum_probs=26.7
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHHh
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQET 32 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~t 32 (77)
-.|+|..+||..||||.+||...+.|-+..
T Consensus 127 ~~g~s~~EIA~~LgiS~~tVk~~l~Rar~~ 156 (188)
T PRK12546 127 ASGFSYEEAAEMCGVAVGTVKSRANRARAR 156 (188)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 379999999999999999999999887653
No 357
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=95.05 E-value=0.034 Score=36.31 Aligned_cols=32 Identities=22% Similarity=0.340 Sum_probs=29.1
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCc
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRP 37 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~p 37 (77)
++..++|..+|+|+.||+|.++++++.|-+.-
T Consensus 169 ~t~~~lA~~lG~tr~tvsR~l~~l~~~gii~~ 200 (211)
T PRK11753 169 ITRQEIGRIVGCSREMVGRVLKMLEDQGLISA 200 (211)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEe
Confidence 56789999999999999999999999997753
No 358
>PRK13348 chromosome replication initiation inhibitor protein; Provisional
Probab=95.05 E-value=0.024 Score=38.72 Aligned_cols=54 Identities=24% Similarity=0.287 Sum_probs=36.2
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHHh-cCCCccccCCCCCCCCCHHHHHHHHHHHH
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQET-GSIRPGVIGGSKPRVATPDVERRIEEYKG 61 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~t-G~v~pk~~gg~~~~~~~~~~~~~i~~~v~ 61 (77)
+.| |...+|++++||+++|++.+++..+. |..--.+ + ++-..|++ ...+.+.++
T Consensus 15 ~~g-s~t~AA~~L~iSQ~avS~~i~~LE~~lg~~Lf~R-~--r~i~lT~~-G~~l~~~a~ 69 (294)
T PRK13348 15 ETG-SFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-G--RPCRPTPA-GQRLLRHLR 69 (294)
T ss_pred HcC-CHHHHHHHhCCCchHHHHHHHHHHHHhCceeeec-C--CCCccChh-HHHHHHHHH
Confidence 455 88999999999999999999999854 4433332 3 23445554 344444443
No 359
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=95.04 E-value=0.038 Score=34.54 Aligned_cols=35 Identities=17% Similarity=0.081 Sum_probs=30.9
Q ss_pred ccCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCC
Q psy15513 2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIR 36 (77)
Q Consensus 2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~ 36 (77)
..+|++..+||+.+++|..||..++++.+..-.+.
T Consensus 161 ~~~g~~~~~Ia~~l~~s~~tv~~~~~~~~~kl~~~ 195 (211)
T PRK15369 161 ITEGYTNRDIAEQLSISIKTVETHRLNMMRKLDVH 195 (211)
T ss_pred HHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Confidence 35799999999999999999999999988876653
No 360
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=95.02 E-value=0.042 Score=35.98 Aligned_cols=28 Identities=14% Similarity=0.137 Sum_probs=25.2
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
+|+|..+||..||||.+||...+.+.+.
T Consensus 156 eg~s~~EIA~~lgis~~tVk~rl~ra~~ 183 (194)
T PRK12531 156 EELPHQQVAEMFDIPLGTVKSRLRLAVE 183 (194)
T ss_pred cCCCHHHHHHHhCcCHHHHHHHHHHHHH
Confidence 7999999999999999999988877654
No 361
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=95.02 E-value=0.032 Score=38.57 Aligned_cols=35 Identities=14% Similarity=0.136 Sum_probs=30.3
Q ss_pred ccCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCC
Q psy15513 2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIR 36 (77)
Q Consensus 2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~ 36 (77)
...|++..+||++|+||.+||.+.+++..+.=.+.
T Consensus 155 ia~G~SnkEIA~~L~IS~~TVk~hvs~I~~KLgv~ 189 (217)
T PRK13719 155 YSFGFSHEYIAQLLNITVGSSKNKISEILKFFGIS 189 (217)
T ss_pred HHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Confidence 35799999999999999999999999988765543
No 362
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=95.01 E-value=0.043 Score=36.32 Aligned_cols=28 Identities=14% Similarity=0.110 Sum_probs=25.1
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
.|+|..+||..||||.+||...+.|-+.
T Consensus 148 ~g~s~~EIAe~lgis~~tV~~~l~Rar~ 175 (196)
T PRK12535 148 LGYTYEEAAKIADVRVGTIRSRVARARA 175 (196)
T ss_pred hCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 7899999999999999999999876554
No 363
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=94.99 E-value=0.11 Score=34.79 Aligned_cols=45 Identities=9% Similarity=0.115 Sum_probs=37.1
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCH
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATP 50 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~ 50 (77)
.+..++|++||||.+.|.--+++....|=|...|..|-.-+..+.
T Consensus 31 L~e~eLae~lgVSRtpVREAL~~L~~eGlv~~~~~~G~~V~~~~~ 75 (224)
T PRK11534 31 LRMSLLTSRYALGVGPLREALSQLVAERLVTVVNQKGYRVASMSE 75 (224)
T ss_pred CCHHHHHHHHCCChHHHHHHHHHHHHCCCEEEeCCCceEeCCCCH
Confidence 577899999999999999999999999999877766554444443
No 364
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=94.99 E-value=0.025 Score=38.95 Aligned_cols=33 Identities=12% Similarity=0.077 Sum_probs=27.9
Q ss_pred ccCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCC
Q psy15513 2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETGSI 35 (77)
Q Consensus 2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v 35 (77)
++.| |...+|++++||+++|++-+++..+.=.+
T Consensus 13 ~~~g-S~s~AA~~L~itQpavS~~i~~LE~~lg~ 45 (305)
T PRK11151 13 AEHR-HFRRAADSCHVSQPTLSGQIRKLEDELGV 45 (305)
T ss_pred HHhC-CHHHHHHHhCCCchHHHHHHHHHHHHhCc
Confidence 3556 89999999999999999999999865433
No 365
>TIGR00498 lexA SOS regulatory protein LexA. LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.
Probab=94.97 E-value=0.042 Score=36.34 Aligned_cols=34 Identities=15% Similarity=0.152 Sum_probs=30.7
Q ss_pred CCHHHHHHHhccC-HHHHHHHHHHHHHhcCCCccc
Q psy15513 6 VRPCVISRQLRVS-HGCVSKILNRYQETGSIRPGV 39 (77)
Q Consensus 6 ~s~~~iA~rf~VS-~stv~r~~~r~r~tG~v~pk~ 39 (77)
.+.+++|+.|++| .+||++.+++..+.|-+....
T Consensus 26 ~~~~ela~~~~~~s~~tv~~~l~~L~~~g~i~~~~ 60 (199)
T TIGR00498 26 PSIREIARAVGLRSPSAAEEHLKALERKGYIERDP 60 (199)
T ss_pred CcHHHHHHHhCCCChHHHHHHHHHHHHCCCEecCC
Confidence 5677999999998 999999999999999997653
No 366
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=94.96 E-value=0.16 Score=35.83 Aligned_cols=66 Identities=9% Similarity=-0.010 Sum_probs=43.2
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCC-CccccCCCCCCCCCHHHHHHHHHHHHhCCCCcHHHHHHHh
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSI-RPGVIGGSKPRVATPDVERRIEEYKGENPAMFSWEIRDRL 75 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v-~pk~~gg~~~~~~~~~~~~~i~~~v~~~pd~tl~El~~~L 75 (77)
.|+|..+||+.+|+|.++|...+.|-++.=.- .|+ .....+++.+.+.++++...+--+..|.+.|
T Consensus 133 ~g~s~~EIA~~Lgis~~tVr~~l~RAr~~Lr~~~~~------~~~~~~~~~~~~~~f~~a~~~gd~~~l~~ll 199 (290)
T PRK09635 133 FGLPYQQIATTIGSQASTCRQLAHRARRKINESRIA------ASVEPAQHRVVTRAFIEACSNGDLDTLLEVL 199 (290)
T ss_pred hCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHhhCCC------CCCChHHHHHHHHHHHHHHHhCCHHHHHHHh
Confidence 68999999999999999999999988764321 121 1122234556666666655444455555444
No 367
>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=94.95 E-value=0.046 Score=36.78 Aligned_cols=28 Identities=14% Similarity=0.154 Sum_probs=25.2
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
.|++..+||..||||+++|+++.++-..
T Consensus 198 ~~~t~~eIA~~lgis~~~V~~~~~~al~ 225 (231)
T TIGR02885 198 KDKTQTEVANMLGISQVQVSRLEKKVLK 225 (231)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 6899999999999999999999887543
No 368
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=94.95 E-value=0.018 Score=39.88 Aligned_cols=23 Identities=30% Similarity=0.244 Sum_probs=20.6
Q ss_pred CCHHHHHHHhccCHHHHHHHHHH
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNR 28 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r 28 (77)
++..+||+..|||++||||-++.
T Consensus 2 ~ti~dIA~~agVS~~TVSrvln~ 24 (327)
T PRK10339 2 ATLKDIAIEAGVSLATVSRVLND 24 (327)
T ss_pred CCHHHHHHHhCCCHHhhhhhhcC
Confidence 36889999999999999999953
No 369
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=94.95 E-value=0.023 Score=39.55 Aligned_cols=34 Identities=18% Similarity=0.133 Sum_probs=28.5
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHHh-cCCC
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQET-GSIR 36 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~t-G~v~ 36 (77)
+.|-|...+|++++||+++|++.++++.+. |.--
T Consensus 14 ~~g~S~s~AA~~L~isQpavS~~ik~LE~~lg~~L 48 (313)
T PRK12684 14 RQNFNLTEAAKALYTSQPGVSKAIIELEDELGVEI 48 (313)
T ss_pred HcCCCHHHHHHHhcCCChHHHHHHHHHHHHhCCee
Confidence 456799999999999999999999999854 4443
No 370
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=94.94 E-value=0.051 Score=37.52 Aligned_cols=38 Identities=16% Similarity=0.302 Sum_probs=33.7
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccC
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIG 41 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~g 41 (77)
.|++..+||+++|+++|||+|++.-..+.|=+...+.+
T Consensus 18 ~~l~l~ela~~~glpksT~~RlL~tL~~~G~v~~d~~~ 55 (246)
T COG1414 18 GGLSLAELAERLGLPKSTVHRLLQTLVELGYVEQDPED 55 (246)
T ss_pred CCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEcCCC
Confidence 34789999999999999999999999999999877543
No 371
>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional
Probab=94.94 E-value=0.021 Score=40.77 Aligned_cols=27 Identities=11% Similarity=0.066 Sum_probs=24.2
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHH
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRY 29 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~ 29 (77)
+.|....++|++||||.+|.+|++++|
T Consensus 297 ~~~gn~~~aA~~LGIsR~tLyrklk~~ 323 (326)
T PRK11608 297 QAKFNQKRAAELLGLTYHQLRALLKKH 323 (326)
T ss_pred HhCCCHHHHHHHhCCCHHHHHHHHHHc
Confidence 356688999999999999999999987
No 372
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=94.92 E-value=0.039 Score=35.85 Aligned_cols=31 Identities=16% Similarity=0.255 Sum_probs=29.5
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCC
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIR 36 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~ 36 (77)
++..+||..+|+|+.||+|.++++++.|-+.
T Consensus 150 ~t~~~iA~~lG~tretvsR~l~~l~~~g~I~ 180 (202)
T PRK13918 150 ATHDELAAAVGSVRETVTKVIGELSREGYIR 180 (202)
T ss_pred CCHHHHHHHhCccHHHHHHHHHHHHHCCCEE
Confidence 5788999999999999999999999999997
No 373
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=94.92 E-value=0.054 Score=37.40 Aligned_cols=43 Identities=19% Similarity=0.273 Sum_probs=34.7
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccc--cCCCCC
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV--IGGSKP 45 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~--~gg~~~ 45 (77)
..++|.-++|++||||..+|.+=+......|-|.... .|-+||
T Consensus 23 ~g~~sa~elA~~Lgis~~avR~HL~~Le~~Glv~~~~~~~g~GRP 67 (218)
T COG2345 23 SGPVSADELAEELGISPMAVRRHLDDLEAEGLVEVERQQGGRGRP 67 (218)
T ss_pred cCCccHHHHHHHhCCCHHHHHHHHHHHHhCcceeeeeccCCCCCC
Confidence 3569999999999999999999999999999664333 333455
No 374
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=94.91 E-value=0.052 Score=37.28 Aligned_cols=35 Identities=14% Similarity=0.229 Sum_probs=32.1
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG 38 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk 38 (77)
.+++..+||+++|+++|||+|+++-+.+.|=+...
T Consensus 27 ~~l~l~eia~~lgl~kstv~Rll~tL~~~G~l~~~ 61 (257)
T PRK15090 27 REIGITELSQRVMMSKSTVYRFLQTMKTLGYVAQE 61 (257)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEc
Confidence 35899999999999999999999999999998654
No 375
>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=94.90 E-value=0.012 Score=33.03 Aligned_cols=22 Identities=18% Similarity=0.235 Sum_probs=17.0
Q ss_pred CHHHHHHHhccCHHHHH-HHHHH
Q psy15513 7 RPCVISRQLRVSHGCVS-KILNR 28 (77)
Q Consensus 7 s~~~iA~rf~VS~stv~-r~~~r 28 (77)
+..+.|+.+|||++|++ .|.+|
T Consensus 14 ~~~~lA~~lgis~st~s~~~~~r 36 (66)
T PF07022_consen 14 SDKELAERLGISKSTLSNNWKKR 36 (66)
T ss_dssp SCHHHHCCTT--HHHHH-HHHHS
T ss_pred CHHHHHHHhCcCHHHhhHHHHhC
Confidence 55699999999999999 78764
No 376
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=94.88 E-value=0.031 Score=38.16 Aligned_cols=32 Identities=13% Similarity=0.095 Sum_probs=27.0
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHH-hcCC
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQE-TGSI 35 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~-tG~v 35 (77)
+.| |...+|++++||+++|++.+++..+ -|.-
T Consensus 14 ~~g-s~s~AA~~L~isqpavS~~I~~LE~~lG~~ 46 (275)
T PRK03601 14 RTR-HFGRAAESLYLTQSAVSFRIRQLENQLGVN 46 (275)
T ss_pred HcC-CHHHHHHHhCCChHHHHHHHHHHHHHhCCc
Confidence 445 8889999999999999999999986 4443
No 377
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=94.87 E-value=0.048 Score=36.86 Aligned_cols=27 Identities=15% Similarity=0.133 Sum_probs=24.2
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQ 30 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r 30 (77)
.|+|..+||..||||.+||...+.|.+
T Consensus 164 ~g~s~~EIAe~lgis~~tVk~~l~Rar 190 (231)
T PRK11922 164 EELSVEETAQALGLPEETVKTRLHRAR 190 (231)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 799999999999999999998877654
No 378
>PRK11569 transcriptional repressor IclR; Provisional
Probab=94.86 E-value=0.054 Score=37.70 Aligned_cols=35 Identities=17% Similarity=0.288 Sum_probs=32.3
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG 38 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk 38 (77)
.+++..+||+++|+++|||+|++.-+.+.|=+...
T Consensus 42 ~~~~lseia~~lglpksTv~RlL~tL~~~G~l~~~ 76 (274)
T PRK11569 42 GSVALTELAQQAGLPNSTTHRLLTTMQQQGFVRQV 76 (274)
T ss_pred CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEc
Confidence 46899999999999999999999999999999744
No 379
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=94.85 E-value=0.043 Score=36.75 Aligned_cols=33 Identities=9% Similarity=0.011 Sum_probs=31.1
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCC
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSI 35 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v 35 (77)
..|+|..+||+.|++|..||.+.+.+....|-+
T Consensus 176 ~~g~s~~eIA~~l~iS~~Tv~~~~~~~~~~~~~ 208 (239)
T PRK10430 176 DYEFSTDELANAVNISRVSCRKYLIWLVNCHIL 208 (239)
T ss_pred CCCcCHHHHHHHhCchHHHHHHHHHHHHhCCEE
Confidence 379999999999999999999999999999987
No 380
>PRK11482 putative DNA-binding transcriptional regulator; Provisional
Probab=94.85 E-value=0.031 Score=39.14 Aligned_cols=46 Identities=9% Similarity=-0.026 Sum_probs=32.7
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHH-hcCCCccccCCCCCCCCCHH
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQE-TGSIRPGVIGGSKPRVATPD 51 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~-tG~v~pk~~gg~~~~~~~~~ 51 (77)
+.| |...+|++++||+++|++.+++..+ -|.---...+ +.-.+|++
T Consensus 42 e~g-s~s~AA~~L~isQpavS~~I~~LE~~lG~~LF~R~~--r~v~lT~~ 88 (317)
T PRK11482 42 VHK-GIVNAAKILNLTPSAISQSIQKLRVIFPDPLFIRKG--QGVTPTAY 88 (317)
T ss_pred HcC-CHHHHHHHhCCChHHHHHHHHHHHHHhCCcceEecC--CCccCCHH
Confidence 445 8899999999999999999999985 4544333222 33345553
No 381
>smart00497 IENR1 Intron encoded nuclease repeat motif. Repeat of unknown function, but possibly DNA-binding via helix-turn-helix motif (Ponting, unpublished).
Probab=94.84 E-value=0.042 Score=28.81 Aligned_cols=23 Identities=30% Similarity=0.343 Sum_probs=20.5
Q ss_pred CCHHHHHHHhccCHHHHHHHHHH
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNR 28 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r 28 (77)
-|..++|+.||+++++|++.++-
T Consensus 18 ~S~~eAa~~lg~~~~~I~~~~~~ 40 (53)
T smart00497 18 SSIREAAKYLGISHSSISKYLNT 40 (53)
T ss_pred cCHHHHHHHhCCCHHHHHHHHhC
Confidence 37899999999999999988774
No 382
>TIGR03418 chol_sulf_TF putative choline sulfate-utilization transcription factor. Members of this protein family are transcription factors of the LysR family. Their genes typically are divergently transcribed from choline-sulfatase genes. That enzyme makes choline, a precursor to the osmoprotectant glycine-betaine, available by hydrolysis of choline sulfate.
Probab=94.81 E-value=0.033 Score=37.91 Aligned_cols=33 Identities=21% Similarity=0.205 Sum_probs=27.5
Q ss_pred ccCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCC
Q psy15513 2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETGSI 35 (77)
Q Consensus 2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v 35 (77)
++.| |...+|++|+||+++|++-+++..+.=.+
T Consensus 13 ~~~g-s~s~AA~~L~itqpavS~~Ik~LE~~lg~ 45 (291)
T TIGR03418 13 ARLA-SFTAAARELGSTQPAVSQQVKRLEEELGT 45 (291)
T ss_pred HHhC-CHHHHHHHhCCCHHHHHHHHHHHHHHhCc
Confidence 3456 88999999999999999999999854433
No 383
>PF07453 NUMOD1: NUMOD1 domain; InterPro: IPR010896 This helix-turn-helix-containing DNA-binding domain is found associated in homing nucleases [].
Probab=94.81 E-value=0.029 Score=27.90 Aligned_cols=20 Identities=30% Similarity=0.260 Sum_probs=17.9
Q ss_pred CCHHHHHHHhccCHHHHHHH
Q psy15513 6 VRPCVISRQLRVSHGCVSKI 25 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~ 25 (77)
-|.+++|+-|+++++++++.
T Consensus 17 ~Si~eAa~~l~i~~~~I~~~ 36 (37)
T PF07453_consen 17 DSIREAARYLGISHSTISKY 36 (37)
T ss_pred cCHHHHHHHhCCCHHHHHHh
Confidence 37899999999999999875
No 384
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=94.81 E-value=0.2 Score=34.94 Aligned_cols=29 Identities=21% Similarity=0.170 Sum_probs=26.7
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHHh
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQET 32 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~t 32 (77)
.|+|..|||+.+|+|.++|...+.|-+..
T Consensus 130 ~g~s~~EIA~~lg~s~~tVk~~l~RAr~~ 158 (293)
T PRK09636 130 FGVPFDEIASTLGRSPAACRQLASRARKH 158 (293)
T ss_pred hCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 68999999999999999999999887754
No 385
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=94.81 E-value=0.04 Score=37.63 Aligned_cols=37 Identities=19% Similarity=0.122 Sum_probs=33.3
Q ss_pred CHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCC
Q psy15513 7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGS 43 (77)
Q Consensus 7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~ 43 (77)
+-+++|++||||.++|.--+++....|=|...+..|-
T Consensus 35 sE~eLa~~~gVSRtpVREAL~~L~~eGlV~~~~~~G~ 71 (257)
T PRK10225 35 PEREIAEMLDVTRTVVREALIMLEIKGLVEVRRGAGI 71 (257)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCCEE
Confidence 5789999999999999999999999999988876554
No 386
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=94.79 E-value=0.041 Score=36.70 Aligned_cols=33 Identities=21% Similarity=0.370 Sum_probs=30.6
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPG 38 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk 38 (77)
++..++|..+|+|+.||+|.++++++.|-+.-.
T Consensus 185 lt~~~iA~~lG~sr~tvsR~l~~l~~~g~I~~~ 217 (235)
T PRK11161 185 MTRGDIGNYLGLTVETISRLLGRFQKSGMLAVK 217 (235)
T ss_pred ccHHHHHHHhCCcHHHHHHHHHHHHHCCCEEec
Confidence 678899999999999999999999999998854
No 387
>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=94.78 E-value=0.055 Score=36.52 Aligned_cols=28 Identities=25% Similarity=0.194 Sum_probs=25.0
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
+|+|..+||+.+|+|.+||.+++.+-+.
T Consensus 193 e~~S~~EIAe~lgis~~tV~~~~~rAl~ 220 (227)
T TIGR02846 193 RRKTQREIAKILGISRSYVSRIEKRALM 220 (227)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 7899999999999999999999877543
No 388
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=94.76 E-value=0.04 Score=32.46 Aligned_cols=37 Identities=19% Similarity=0.287 Sum_probs=33.2
Q ss_pred ccCC-CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513 2 AAAG-VRPCVISRQLRVSHGCVSKILNRYQETGSIRPG 38 (77)
Q Consensus 2 ~~~G-~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk 38 (77)
+..| ++..++|++|+.|.+.|.-.+.++...|.|+--
T Consensus 12 ~~~gr~s~~~Ls~~~~~p~~~VeaMLe~l~~kGkverv 49 (78)
T PRK15431 12 ALRGRMEAAQISQTLNTPQPMINAMLQQLESMGKAVRI 49 (78)
T ss_pred HHcCcccHHHHHHHHCcCHHHHHHHHHHHHHCCCeEee
Confidence 3456 899999999999999999999999999999644
No 389
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=94.74 E-value=0.055 Score=37.35 Aligned_cols=28 Identities=14% Similarity=0.120 Sum_probs=25.5
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
.|+|..+||..||||.++|++++.+-+.
T Consensus 218 ~~~s~~eIA~~lgvs~~~V~~~~~ra~~ 245 (256)
T PRK07408 218 HDLTQKEAAERLGISPVTVSRRVKKGLD 245 (256)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 6899999999999999999999887654
No 390
>PRK11233 nitrogen assimilation transcriptional regulator; Provisional
Probab=94.73 E-value=0.031 Score=38.62 Aligned_cols=30 Identities=10% Similarity=0.118 Sum_probs=26.2
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHHhc
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQETG 33 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG 33 (77)
+.| |...+|++|+||+++|++-++++.+.=
T Consensus 14 ~~~-S~s~AA~~L~isQ~avS~~I~~LE~~l 43 (305)
T PRK11233 14 DIG-SLTQAAEVLHIAQPALSQQVATLEGEL 43 (305)
T ss_pred HcC-CHHHHHHHhCCCchHHHHHHHHHHHHh
Confidence 455 899999999999999999999998543
No 391
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=94.72 E-value=0.032 Score=38.83 Aligned_cols=31 Identities=16% Similarity=0.149 Sum_probs=27.3
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHHhc
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQETG 33 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG 33 (77)
+.|.|...+|++++||+++|++-+++..+.=
T Consensus 14 ~~~~S~s~AA~~L~isQpavS~~I~~LE~~l 44 (309)
T PRK12683 14 RQNFNLTEVANALYTSQSGVSKQIKDLEDEL 44 (309)
T ss_pred HccCCHHHHHHHhcCCcHHHHHHHHHHHHHh
Confidence 4567999999999999999999999998543
No 392
>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.
Probab=94.72 E-value=0.067 Score=32.29 Aligned_cols=38 Identities=24% Similarity=0.302 Sum_probs=32.7
Q ss_pred CCCCHHHHHHHh-----ccCHHHHHHHHHHHHHhcCCCccccC
Q psy15513 4 AGVRPCVISRQL-----RVSHGCVSKILNRYQETGSIRPGVIG 41 (77)
Q Consensus 4 ~G~s~~~iA~rf-----~VS~stv~r~~~r~r~tG~v~pk~~g 41 (77)
..+|..+|...+ .||.+||||-++.+.+-|-+..-..+
T Consensus 15 ~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~Gli~~~~~~ 57 (116)
T cd07153 15 GHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVREIELG 57 (116)
T ss_pred CCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCEEEEEeC
Confidence 348999999888 79999999999999999998765543
No 393
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=94.72 E-value=0.024 Score=39.39 Aligned_cols=39 Identities=26% Similarity=0.306 Sum_probs=33.7
Q ss_pred cCC-CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCC
Q psy15513 3 AAG-VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGG 42 (77)
Q Consensus 3 ~~G-~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg 42 (77)
+.| ++..++|++|+||..||.|=+....+.|-+.-- +||
T Consensus 16 ~~g~v~v~eLa~~~~VS~~TIRRDL~~Le~~g~l~R~-hGG 55 (253)
T COG1349 16 EKGKVSVEELAELFGVSEMTIRRDLNELEEQGLLLRV-HGG 55 (253)
T ss_pred HcCcEEHHHHHHHhCCCHHHHHHhHHHHHHCCcEEEE-eCC
Confidence 455 889999999999999999999999999988743 455
No 394
>PF14502 HTH_41: Helix-turn-helix domain
Probab=94.70 E-value=0.062 Score=28.94 Aligned_cols=36 Identities=25% Similarity=0.330 Sum_probs=31.1
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccC
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIG 41 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~g 41 (77)
.+..+.++.|+||.+||++-++-..+.|-+.=.++|
T Consensus 7 ~tI~e~~~~~~vs~GtiQ~Alk~Le~~gaI~Le~rG 42 (48)
T PF14502_consen 7 PTISEYSEKFGVSRGTIQNALKFLEENGAIKLESRG 42 (48)
T ss_pred CCHHHHHHHhCcchhHHHHHHHHHHHCCcEEeeecC
Confidence 357789999999999999999999999988665554
No 395
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=94.70 E-value=0.047 Score=36.97 Aligned_cols=34 Identities=21% Similarity=0.220 Sum_probs=29.7
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCC
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIR 36 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~ 36 (77)
..|+|..+||+.|++|.+||..++.+....-.+.
T Consensus 168 ~~G~s~~eIA~~L~iS~~TVk~~~~~i~~Kl~v~ 201 (216)
T PRK10100 168 RIGASNNEIARSLFISENTVKTHLYNLFKKIAVK 201 (216)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Confidence 3599999999999999999999999987765553
No 396
>TIGR02018 his_ut_repres histidine utilization repressor, proteobacterial. This model represents a proteobacterial histidine utilization repressor. It is usually found clustered with the enzymes HutUHIG so that it can regulate its own expression as well. A number of species have several paralogs and may fine-tune the regulation according to levels of degradation intermediates such as urocanate. This family belongs to the larger GntR family of transcriptional regulators.
Probab=94.68 E-value=0.044 Score=36.92 Aligned_cols=34 Identities=15% Similarity=0.118 Sum_probs=31.0
Q ss_pred CHHHHHHHhccCHHHHHHHHHHHHHhcCCCcccc
Q psy15513 7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI 40 (77)
Q Consensus 7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~ 40 (77)
|-+++|+.||||..||.+-+....+.|-+..++.
T Consensus 27 sE~eLa~~~~VSR~TVR~Al~~L~~eGli~r~~G 60 (230)
T TIGR02018 27 SEHELVAQYGCSRMTVNRALRELTDAGLLERRQG 60 (230)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 6789999999999999999999999999987753
No 397
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=94.67 E-value=0.05 Score=36.66 Aligned_cols=36 Identities=14% Similarity=0.122 Sum_probs=32.4
Q ss_pred CHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCC
Q psy15513 7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGG 42 (77)
Q Consensus 7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg 42 (77)
|-+++|++||||.+||..=+++....|=|...+..|
T Consensus 33 sE~eLae~~gVSRt~VReAL~~L~~eGlv~~~~g~G 68 (239)
T PRK04984 33 AERELSELIGVTRTTLREVLQRLARDGWLTIQHGKP 68 (239)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCCCe
Confidence 678999999999999999999999999998776544
No 398
>COG2964 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=94.67 E-value=0.036 Score=38.39 Aligned_cols=25 Identities=20% Similarity=0.485 Sum_probs=21.8
Q ss_pred HHHHHHhccCHHHHHHHHHHHHHhc
Q psy15513 9 CVISRQLRVSHGCVSKILNRYQETG 33 (77)
Q Consensus 9 ~~iA~rf~VS~stv~r~~~r~r~tG 33 (77)
-.+|.+|++|+.|||+++++++..|
T Consensus 195 ~~VA~~L~iSr~TVY~YL~~~k~~~ 219 (220)
T COG2964 195 NIVADRLGISRHTVYRYLRKFKAGG 219 (220)
T ss_pred HHHHHHhCCChHHHHHHHHHhhcCC
Confidence 3579999999999999999987655
No 399
>PRK06424 transcription factor; Provisional
Probab=94.66 E-value=0.037 Score=35.91 Aligned_cols=25 Identities=4% Similarity=0.089 Sum_probs=22.9
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILN 27 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~ 27 (77)
+.|+|+.++|+++|||+++|++|-+
T Consensus 95 ~~GLSQ~eLA~~iGvs~stIskiE~ 119 (144)
T PRK06424 95 RLSMSQADLAAKIFERKNVIASIER 119 (144)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHC
Confidence 4799999999999999999999954
No 400
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=94.66 E-value=0.048 Score=36.73 Aligned_cols=32 Identities=25% Similarity=0.268 Sum_probs=29.5
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCc
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRP 37 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~p 37 (77)
++..+||..+|+|+.||+|.++++++.|-+.-
T Consensus 180 lt~~~IA~~lGisretlsR~L~~L~~~GlI~~ 211 (230)
T PRK09391 180 MSRRDIADYLGLTIETVSRALSQLQDRGLIGL 211 (230)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEe
Confidence 57889999999999999999999999998863
No 401
>TIGR02404 trehalos_R_Bsub trehalose operon repressor, B. subtilis-type. This family consists of repressors of the GntR 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 Gram-positive lineages and does not include the TreR from E. coli.
Probab=94.65 E-value=0.048 Score=36.72 Aligned_cols=34 Identities=26% Similarity=0.149 Sum_probs=30.8
Q ss_pred CHHHHHHHhccCHHHHHHHHHHHHHhcCCCcccc
Q psy15513 7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI 40 (77)
Q Consensus 7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~ 40 (77)
|-+++|++||||..||.+-++...+.|-|..++.
T Consensus 26 sE~eLa~~~gVSR~TVR~Al~~L~~eGli~r~~G 59 (233)
T TIGR02404 26 SEHELMDQYGASRETVRKALNLLTEAGYIQKIQG 59 (233)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCC
Confidence 5688999999999999999999999999987653
No 402
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=94.63 E-value=0.037 Score=38.02 Aligned_cols=36 Identities=22% Similarity=0.134 Sum_probs=29.1
Q ss_pred ccCCCCHHHHHHHhccCHHHHHHHHHHHHH-hcCCCcc
Q psy15513 2 AAAGVRPCVISRQLRVSHGCVSKILNRYQE-TGSIRPG 38 (77)
Q Consensus 2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r~-tG~v~pk 38 (77)
++.| |...+|+.++||+++|++-++++.+ .|..--.
T Consensus 17 ~~~g-s~s~AA~~L~isQ~avS~~i~~LE~~lG~~LF~ 53 (302)
T PRK09791 17 ARQG-SIRGASRMLNMSQPALTKSIQELEEGLAAQLFF 53 (302)
T ss_pred HHcC-CHHHHHHHhCCChHHHHHHHHHHHHHhCCeEEE
Confidence 3456 8899999999999999999999984 4554433
No 403
>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=94.62 E-value=0.063 Score=36.75 Aligned_cols=29 Identities=14% Similarity=0.127 Sum_probs=25.7
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
-.|+|..+||..+|||.++|.+++.+-++
T Consensus 219 ~~g~s~~eIA~~lgis~~~V~~~~~ra~~ 247 (255)
T TIGR02941 219 EENLSQKETGERLGISQMHVSRLQRQAIS 247 (255)
T ss_pred cCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 47999999999999999999999877553
No 404
>PRK10216 DNA-binding transcriptional regulator YidZ; Provisional
Probab=94.61 E-value=0.038 Score=38.47 Aligned_cols=32 Identities=16% Similarity=0.185 Sum_probs=27.2
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHH-hcCC
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQE-TGSI 35 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~-tG~v 35 (77)
+.| |...+|++|+||+++||+-+++..+ -|.-
T Consensus 21 e~g-s~t~AA~~L~iSQpavS~~I~~LE~~lg~~ 53 (319)
T PRK10216 21 QER-SVTKAAKRMNVTPSAVSKSLAKLRAWFDDP 53 (319)
T ss_pred HhC-CHHHHHHHhCCCHHHHHHHHHHHHHHhCCc
Confidence 455 8899999999999999999999986 4443
No 405
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=94.61 E-value=0.072 Score=36.19 Aligned_cols=38 Identities=18% Similarity=0.145 Sum_probs=33.7
Q ss_pred CHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCC
Q psy15513 7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSK 44 (77)
Q Consensus 7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~ 44 (77)
+-+++|++||||.++|.--+++....|=|...|..|-.
T Consensus 33 sE~eLa~~~gVSRtpVREAL~~L~~eGlV~~~~~~G~~ 70 (251)
T PRK09990 33 SERRLCEKLGFSRSALREGLTVLRGRGIIETAQGRGSF 70 (251)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCCCeeE
Confidence 67899999999999999999999999999888765543
No 406
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=94.58 E-value=0.051 Score=36.61 Aligned_cols=36 Identities=19% Similarity=0.220 Sum_probs=30.5
Q ss_pred ccCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCc
Q psy15513 2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP 37 (77)
Q Consensus 2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~p 37 (77)
...|+|-.+||.+|++|.+||+..+.+....=.+..
T Consensus 160 la~G~snkeIA~~L~iS~~TVk~h~~~i~~KL~v~~ 195 (211)
T COG2197 160 LAEGLSNKEIAEELNLSEKTVKTHVSNILRKLGVRN 195 (211)
T ss_pred HHCCCCHHHHHHHHCCCHhHHHHHHHHHHHHcCCCC
Confidence 458999999999999999999999988876555543
No 407
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=94.57 E-value=0.14 Score=34.49 Aligned_cols=50 Identities=18% Similarity=0.145 Sum_probs=41.3
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHH
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERR 55 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~ 55 (77)
.+..++|.+||||...|..-+.+....|=|.-.|+.|-.-...+......
T Consensus 40 l~e~~La~~~gvSrtPVReAL~rL~~eGlv~~~p~rG~~V~~~~~~~~~e 89 (230)
T COG1802 40 LSEEELAEELGVSRTPVREALRRLEAEGLVEIEPNRGAFVAPLSLAEARE 89 (230)
T ss_pred ccHHHHHHHhCCCCccHHHHHHHHHHCCCeEecCCCCCeeCCCCHHHHHH
Confidence 67889999999999999999999999999998888776655555444443
No 408
>PRK13698 plasmid-partitioning protein; Provisional
Probab=94.55 E-value=0.054 Score=39.39 Aligned_cols=60 Identities=7% Similarity=0.037 Sum_probs=42.8
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHhCCC
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGENPA 65 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~pd 65 (77)
+.|++..++|+++|+|+++|++.++-..=-..+... ...|..++..|...|..+...+++
T Consensus 174 ~~~~tQeeLA~~lG~SRs~Vsn~Lrla~LP~~vi~~---~~~p~~Ls~gharaL~~ll~~~~~ 233 (323)
T PRK13698 174 EFAGNISALADAENISRKIITRCINTAKLPKSVVAL---FAHPGELSARSGEALQKAFTDKEE 233 (323)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHHHHHHcCCHHHHHH---hhccCCCChhHHHHHHHHhhhCHH
Confidence 347899999999999999999999886543333221 234455666678888888766653
No 409
>PHA02517 putative transposase OrfB; Reviewed
Probab=94.53 E-value=0.094 Score=36.06 Aligned_cols=55 Identities=9% Similarity=0.029 Sum_probs=36.2
Q ss_pred hccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHh-CCCCcHHHHHHHhh
Q psy15513 15 LRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGE-NPAMFSWEIRDRLV 76 (77)
Q Consensus 15 f~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~-~pd~tl~El~~~L~ 76 (77)
||||.||.++|+++... |. +...+....++..+.|.++..+ +|......|.+.|.
T Consensus 1 l~vsrs~yY~~~~~~~~-----p~--~~~~~~~~~~~l~~~I~~i~~~~~~~~G~r~I~~~L~ 56 (277)
T PHA02517 1 LGIAPSTYYRCQQQRHH-----PD--KRRARAQHDDWLKSEILRVYDENHQVYGVRKVWRQLN 56 (277)
T ss_pred CCCChHHHHHHHhccCC-----cc--hhhhhhhhhHHHHHHHHHHHHHhCCCCCHHHHHHHHH
Confidence 79999999999987321 21 1111112345567788888766 57778888887764
No 410
>PRK14999 histidine utilization repressor; Provisional
Probab=94.53 E-value=0.051 Score=36.90 Aligned_cols=33 Identities=12% Similarity=0.105 Sum_probs=30.5
Q ss_pred CHHHHHHHhccCHHHHHHHHHHHHHhcCCCccc
Q psy15513 7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGV 39 (77)
Q Consensus 7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~ 39 (77)
|-+++|++||||..||.+-+....+.|-|.-++
T Consensus 38 sE~eLa~~~gVSR~TVR~Al~~L~~eGli~r~~ 70 (241)
T PRK14999 38 SEAELVAQYGFSRMTINRALRELTDEGWLVRLQ 70 (241)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence 678999999999999999999999999997665
No 411
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=94.52 E-value=0.05 Score=36.66 Aligned_cols=34 Identities=12% Similarity=-0.012 Sum_probs=29.5
Q ss_pred ccCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCC
Q psy15513 2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETGSI 35 (77)
Q Consensus 2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v 35 (77)
.-.|++..+||..|+||..||.....+..+.=.+
T Consensus 146 l~~G~snkeIA~~L~iS~~TV~~h~~~I~~KLgv 179 (207)
T PRK11475 146 MSRGYSMPQIAEQLERNIKTIRAHKFNVMSKLGV 179 (207)
T ss_pred HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCC
Confidence 3479999999999999999999999998775544
No 412
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=94.51 E-value=0.068 Score=36.74 Aligned_cols=27 Identities=15% Similarity=0.235 Sum_probs=24.5
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQ 30 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r 30 (77)
+|+|..+||..||||.++|+++.++-.
T Consensus 224 ~~~t~~eIA~~lgis~~~V~~~~~~al 250 (258)
T PRK08215 224 QGKTQMEVAEEIGISQAQVSRLEKAAL 250 (258)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 689999999999999999999987644
No 413
>PRK06474 hypothetical protein; Provisional
Probab=94.51 E-value=0.051 Score=36.04 Aligned_cols=33 Identities=15% Similarity=0.280 Sum_probs=30.7
Q ss_pred CCHHHHHHHh-ccCHHHHHHHHHHHHHhcCCCcc
Q psy15513 6 VRPCVISRQL-RVSHGCVSKILNRYQETGSIRPG 38 (77)
Q Consensus 6 ~s~~~iA~rf-~VS~stv~r~~~r~r~tG~v~pk 38 (77)
+++.+++..+ +||++|||+-++.+.+.|-|..-
T Consensus 27 ~ta~el~~~l~~is~aTvYrhL~~L~e~GLI~~~ 60 (178)
T PRK06474 27 LTPLELVKILKDVPQATLYRHLQTMVDSGILHVV 60 (178)
T ss_pred CCHHHHHHHhcCCCHHHHHHHHHHHHHCCCEEEe
Confidence 8999999999 79999999999999999998643
No 414
>TIGR02812 fadR_gamma fatty acid metabolism transcriptional regulator FadR. Members of this family are FadR, a transcriptional regulator of fatty acid metabolism, including both biosynthesis and beta-oxidation. It is found exclusively in a subset of Gammaproteobacteria, with strictly one copy per genome. It has an N-terminal DNA-binding domain and a less well conserved C-terminal long chain acyl-CoA-binding domain. FadR from this family heterologously expressed in Escherichia coli show differences in regulatory response and fatty acid binding profiles. The family is nevertheless designated equivalog, as all member proteins have at least nominally the same function.
Probab=94.48 E-value=0.17 Score=34.00 Aligned_cols=38 Identities=13% Similarity=0.144 Sum_probs=33.8
Q ss_pred C-CHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCC
Q psy15513 6 V-RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGS 43 (77)
Q Consensus 6 ~-s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~ 43 (77)
. |-+++|++||||.++|.--+++....|=|...|..|-
T Consensus 30 LpsE~~La~~lgVSRtpVREAL~~Le~eGlV~~~~~~G~ 68 (235)
T TIGR02812 30 LPAERELSELIGVTRTTLREVLQRLARDGWLTIQHGKPT 68 (235)
T ss_pred CcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeCCCcc
Confidence 5 6789999999999999999999999999988875543
No 415
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=94.47 E-value=0.037 Score=38.22 Aligned_cols=32 Identities=19% Similarity=0.170 Sum_probs=27.2
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCC
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSI 35 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v 35 (77)
+.| |...+|++++||+++|++.+++..+.=.+
T Consensus 18 e~g-s~s~AA~~L~isqpavS~~i~~LE~~lg~ 49 (305)
T CHL00180 18 TEG-SFKKAAESLYISQPAVSLQIKNLEKQLNI 49 (305)
T ss_pred HcC-CHHHHHHHhcCCChHHHHHHHHHHHHhCC
Confidence 455 88999999999999999999999865444
No 416
>PRK12681 cysB transcriptional regulator CysB; Reviewed
Probab=94.47 E-value=0.13 Score=36.18 Aligned_cols=33 Identities=15% Similarity=0.133 Sum_probs=27.9
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCC
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSI 35 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v 35 (77)
+.|-|...+|++++||+++|++-+++..+.=.+
T Consensus 14 e~g~S~s~AA~~L~iSQpavS~~I~~LE~~lG~ 46 (324)
T PRK12681 14 NHNLNVSATAEGLYTSQPGISKQVRMLEDELGI 46 (324)
T ss_pred HccCCHHHHHHHhcCCcHHHHHHHHHHHHHhCC
Confidence 455699999999999999999999999855444
No 417
>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=94.46 E-value=0.066 Score=37.40 Aligned_cols=29 Identities=7% Similarity=-0.014 Sum_probs=26.3
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
-.|+|..+||..||||.+||..++.+-++
T Consensus 240 ~e~~s~~EIA~~Lgis~~tVk~~l~rAlk 268 (285)
T TIGR02394 240 YEPATLEEVAAEVGLTRERVRQIQVEALK 268 (285)
T ss_pred CCCccHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 47999999999999999999999988664
No 418
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=94.42 E-value=0.077 Score=34.79 Aligned_cols=28 Identities=25% Similarity=0.246 Sum_probs=24.5
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
.|+|..+||..||||.+||..-+.|-+.
T Consensus 149 ~g~s~~EIA~~lg~s~~tV~~rl~rar~ 176 (192)
T PRK09643 149 QGYSVADAARMLGVAEGTVKSRCARGRA 176 (192)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 7899999999999999999888766543
No 419
>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=94.41 E-value=0.07 Score=29.13 Aligned_cols=24 Identities=17% Similarity=0.108 Sum_probs=20.7
Q ss_pred CCCHHHHHHHhccCHHHHHHHHHH
Q psy15513 5 GVRPCVISRQLRVSHGCVSKILNR 28 (77)
Q Consensus 5 G~s~~~iA~rf~VS~stv~r~~~r 28 (77)
.++..++|+.||||..+..|..++
T Consensus 15 hlp~~eAA~~Lgv~~T~LKr~CR~ 38 (52)
T PF02042_consen 15 HLPIKEAAKELGVSVTTLKRRCRR 38 (52)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHH
Confidence 478899999999999999887654
No 420
>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=94.41 E-value=0.054 Score=37.60 Aligned_cols=27 Identities=11% Similarity=0.038 Sum_probs=23.7
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQ 30 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r 30 (77)
.|+|..+||+.||||..+|+++.++-.
T Consensus 235 ~~~t~~eIA~~lgvS~~~V~q~~~~Al 261 (270)
T TIGR02392 235 DKLTLQELAAEYGVSAERIRQIEKNAM 261 (270)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 589999999999999999997776643
No 421
>PRK03837 transcriptional regulator NanR; Provisional
Probab=94.39 E-value=0.067 Score=35.97 Aligned_cols=37 Identities=11% Similarity=0.066 Sum_probs=33.0
Q ss_pred CHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCC
Q psy15513 7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGS 43 (77)
Q Consensus 7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~ 43 (77)
+-+++|.+||||.++|..-+++....|=|...+..|-
T Consensus 39 ~E~~Lae~~gVSRt~VREAL~~L~~eGlv~~~~~~G~ 75 (241)
T PRK03837 39 SERELMAFFGVGRPAVREALQALKRKGLVQISHGERA 75 (241)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCCce
Confidence 6789999999999999999999999999988765443
No 422
>PRK12680 transcriptional regulator CysB-like protein; Reviewed
Probab=94.39 E-value=0.044 Score=38.68 Aligned_cols=33 Identities=12% Similarity=0.182 Sum_probs=27.5
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCC
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSI 35 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v 35 (77)
+.+.|...+|++++||+++|++.+++..+.=.+
T Consensus 14 e~~gS~s~AA~~L~isQpavS~~I~~LE~~lG~ 46 (327)
T PRK12680 14 DAELNITLAAARVHATQPGLSKQLKQLEDELGF 46 (327)
T ss_pred HccCCHHHHHHHhcCCchHHHHHHHHHHHHhCC
Confidence 334589999999999999999999999855333
No 423
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=94.39 E-value=0.06 Score=36.74 Aligned_cols=37 Identities=22% Similarity=0.277 Sum_probs=33.0
Q ss_pred CHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCC
Q psy15513 7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGS 43 (77)
Q Consensus 7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~ 43 (77)
+-+++|++||||.++|.--+++....|=|...|.+|-
T Consensus 28 sE~eLae~~gVSRtpVREAL~~Le~~GlV~~~~~~G~ 64 (253)
T PRK10421 28 AERQLAMQLGVSRNSLREALAKLVSEGVLLSRRGGGT 64 (253)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEeCCCeE
Confidence 4689999999999999999999999999988876553
No 424
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=94.37 E-value=0.057 Score=36.66 Aligned_cols=34 Identities=9% Similarity=0.153 Sum_probs=30.4
Q ss_pred CHHHHHHHhccCHHHHHHHHHHHHHhcCCCcccc
Q psy15513 7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI 40 (77)
Q Consensus 7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~ 40 (77)
|-.++|+.||||..||.+-+....+.|-+..++.
T Consensus 37 sE~eLa~~~~VSR~TVR~Al~~L~~eGli~r~~G 70 (241)
T PRK10079 37 AEQQLAARYEVNRHTLRRAIDQLVEKGWVQRRQG 70 (241)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 4578999999999999999999999999986653
No 425
>PRK11361 acetoacetate metabolism regulatory protein AtoC; Provisional
Probab=94.32 E-value=0.041 Score=40.08 Aligned_cols=27 Identities=15% Similarity=0.091 Sum_probs=24.2
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHH
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRY 29 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~ 29 (77)
+.|....++|++||||.+|.+|.+++|
T Consensus 428 ~~~gn~~~aA~~LGisr~tL~rkl~~~ 454 (457)
T PRK11361 428 QQEGNRTRTALMLGISRRALMYKLQEY 454 (457)
T ss_pred HhCCCHHHHHHHHCCCHHHHHHHHHHh
Confidence 456688999999999999999999987
No 426
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=94.29 E-value=0.065 Score=33.82 Aligned_cols=31 Identities=23% Similarity=0.101 Sum_probs=27.9
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHHhc
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQETG 33 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG 33 (77)
-.|++..+||+++++|.+||...+++.++.=
T Consensus 150 ~~g~~~~~Ia~~l~~s~~tv~~~~~~l~~Kl 180 (196)
T PRK10360 150 AQGMAVKEIAAELGLSPKTVHVHRANLMEKL 180 (196)
T ss_pred HCCCCHHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence 4689999999999999999999999988753
No 427
>PRK09801 transcriptional activator TtdR; Provisional
Probab=94.27 E-value=0.053 Score=37.84 Aligned_cols=32 Identities=16% Similarity=0.131 Sum_probs=26.6
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCC
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSI 35 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v 35 (77)
+.| |...+|+.|+||+++|++-+++..+.=.+
T Consensus 19 ~~g-s~t~AA~~L~iSQpavS~~I~~LE~~LG~ 50 (310)
T PRK09801 19 HSG-SFSAAAATLGQTPAFVTKRIQILENTLAT 50 (310)
T ss_pred HcC-CHHHHHHHhCcCHHHHHHHHHHHHHHhCC
Confidence 344 78899999999999999999999854333
No 428
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=94.25 E-value=0.066 Score=36.53 Aligned_cols=37 Identities=16% Similarity=0.116 Sum_probs=32.7
Q ss_pred CHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCC
Q psy15513 7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGS 43 (77)
Q Consensus 7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~ 43 (77)
+-+++|++||||.++|.--+++....|=|...|..|-
T Consensus 34 sE~eLae~~gVSRtpVREAL~~L~~eGlV~~~~~~G~ 70 (253)
T PRK11523 34 AERFIADEKNVSRTVVREAIIMLEVEGYVEVRKGSGI 70 (253)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCCee
Confidence 3689999999999999999999999999987776554
No 429
>PRK10403 transcriptional regulator NarP; Provisional
Probab=94.25 E-value=0.061 Score=33.93 Aligned_cols=32 Identities=19% Similarity=0.163 Sum_probs=28.4
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcC
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGS 34 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~ 34 (77)
..|++..+||+.+++|.+||...+++.++.=.
T Consensus 166 ~~g~s~~~ia~~l~~s~~tv~~~~~~i~~kl~ 197 (215)
T PRK10403 166 AQGLSNKQIASVLNISEQTVKVHIRNLLRKLN 197 (215)
T ss_pred HCCCCHHHHHHHcCCCHHHHHHHHHHHHHHcC
Confidence 46899999999999999999999999887543
No 430
>PRK10094 DNA-binding transcriptional activator AllS; Provisional
Probab=94.24 E-value=0.052 Score=37.77 Aligned_cols=30 Identities=13% Similarity=0.135 Sum_probs=25.9
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHHhc
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQETG 33 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG 33 (77)
+.| |..++|++++||+++|++.+++..+.=
T Consensus 15 e~g-s~s~AA~~L~iSQpavS~~I~~LE~~l 44 (308)
T PRK10094 15 ETG-SFSKAAERLCKTTATISYRIKLLEENT 44 (308)
T ss_pred HhC-CHHHHHHHhcCCHHHHHHHHHHHHHHh
Confidence 445 889999999999999999999998543
No 431
>PRK10341 DNA-binding transcriptional activator TdcA; Provisional
Probab=94.24 E-value=0.051 Score=37.67 Aligned_cols=29 Identities=21% Similarity=0.283 Sum_probs=25.7
Q ss_pred CHHHHHHHhccCHHHHHHHHHHHHHhcCC
Q psy15513 7 RPCVISRQLRVSHGCVSKILNRYQETGSI 35 (77)
Q Consensus 7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v 35 (77)
|...+|++|+||+++|++-+++..+.=.+
T Consensus 23 s~s~AA~~L~iSQpavS~~I~~LE~~lg~ 51 (312)
T PRK10341 23 SIGSAAKELGLTQPAVSKIINDIEDYFGV 51 (312)
T ss_pred CHHHHHHHhCCChHHHHHHHHHHHHHhCC
Confidence 88999999999999999999999865444
No 432
>PRK15481 transcriptional regulatory protein PtsJ; Provisional
Probab=94.23 E-value=0.068 Score=38.92 Aligned_cols=36 Identities=17% Similarity=0.188 Sum_probs=32.5
Q ss_pred CHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCC
Q psy15513 7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGG 42 (77)
Q Consensus 7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg 42 (77)
|.+++|+.|+||.+||.+-+.+..+.|-+..++..|
T Consensus 31 s~r~la~~~~vsr~tv~~a~~~L~~~g~i~~~~~~G 66 (431)
T PRK15481 31 PVRELASELGVNRNTVAAAYKRLVTAGLAQSQGRNG 66 (431)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCCCc
Confidence 679999999999999999999999999998776544
No 433
>TIGR02787 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY. This model represents the full length of CodY, a pleiotropic repressor in Bacillus subtilis and other Firmicutes (low-GC Gram-positive bacteria) that responds to intracellular levels of GTP and branched chain amino acids. The C-terminal helix-turn-helix DNA-binding region is modeled by pfam08222 in Pfam.
Probab=94.21 E-value=0.096 Score=36.91 Aligned_cols=36 Identities=14% Similarity=0.377 Sum_probs=33.6
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccC
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIG 41 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~g 41 (77)
.+..++|.+||||+++|..=++++.+.|-+..++-|
T Consensus 199 lse~eLAerlGVSRs~ireAlrkLE~aGvIe~r~LG 234 (251)
T TIGR02787 199 LVASKIADRVGITRSVIVNALRKLESAGVIESRSLG 234 (251)
T ss_pred ccHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeccCC
Confidence 899999999999999999999999999999988734
No 434
>PRK12679 cbl transcriptional regulator Cbl; Reviewed
Probab=94.20 E-value=0.048 Score=37.99 Aligned_cols=34 Identities=18% Similarity=0.181 Sum_probs=28.4
Q ss_pred ccCCCCHHHHHHHhccCHHHHHHHHHHHHHh-cCC
Q psy15513 2 AAAGVRPCVISRQLRVSHGCVSKILNRYQET-GSI 35 (77)
Q Consensus 2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r~t-G~v 35 (77)
++.|-|...+|++++||+++|++-+++..+. |..
T Consensus 13 ~~~~~s~s~AA~~L~iSQ~avSr~I~~LE~~lg~~ 47 (316)
T PRK12679 13 ARQDYNLTEVANMLFTSQSGVSRHIRELEDELGIE 47 (316)
T ss_pred HHcCCCHHHHHHHhcCCchHHHHHHHHHHHHhCCE
Confidence 3456699999999999999999999999854 443
No 435
>TIGR03541 reg_near_HchA LuxR family transcriptional regulatory, chaperone HchA-associated. Members of this protein family belong to the LuxR transcriptional regulator family, and contain both autoinducer binding (pfam03472) and transcriptional regulator (pfam00196) domains. Members, however, occur only in a few members of the Gammaproteobacteria that have the chaperone/aminopeptidase HchA, and are always encoded by the adjacent gene.
Probab=94.20 E-value=0.064 Score=36.53 Aligned_cols=32 Identities=25% Similarity=0.210 Sum_probs=28.2
Q ss_pred ccCCCCHHHHHHHhccCHHHHHHHHHHHHHhc
Q psy15513 2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETG 33 (77)
Q Consensus 2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG 33 (77)
...|++..+||..|+||.+||...+++.+..=
T Consensus 183 ~a~G~t~~eIa~~l~is~~Tv~~~l~~~~~kl 214 (232)
T TIGR03541 183 TALGRRQADIAAILGISERTVENHLRSARRKL 214 (232)
T ss_pred HHCCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 35799999999999999999999999987543
No 436
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=94.18 E-value=0.04 Score=38.22 Aligned_cols=39 Identities=15% Similarity=0.230 Sum_probs=33.0
Q ss_pred cCC-CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCC
Q psy15513 3 AAG-VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGG 42 (77)
Q Consensus 3 ~~G-~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg 42 (77)
+.| ++..++|+.|+||..||.|=++...+.|-+.-. +||
T Consensus 16 ~~~~v~v~eLa~~l~VS~~TIRRDL~~Le~~g~l~r~-~Gg 55 (256)
T PRK10434 16 KQGKTSVEELAQYFDTTGTTIRKDLVILEHAGTVIRT-YGG 55 (256)
T ss_pred HcCCEEHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEE-ECC
Confidence 345 889999999999999999999999999987643 454
No 437
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=94.17 E-value=0.089 Score=36.61 Aligned_cols=29 Identities=17% Similarity=0.241 Sum_probs=25.7
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
-.|++..+||..||||.++|.+++++-..
T Consensus 229 ~~~~t~~EIA~~lgis~~~V~~~~~ral~ 257 (264)
T PRK07122 229 FESMTQTQIAERVGISQMHVSRLLAKTLA 257 (264)
T ss_pred cCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 36999999999999999999999887654
No 438
>PRK14997 LysR family transcriptional regulator; Provisional
Probab=94.16 E-value=0.058 Score=36.95 Aligned_cols=46 Identities=15% Similarity=0.096 Sum_probs=32.2
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHHh-cCCCccccCCCCCCCCCHH
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQET-GSIRPGVIGGSKPRVATPD 51 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~t-G~v~pk~~gg~~~~~~~~~ 51 (77)
+.| |...+|++++||+++|++-+++..+. |..--.+. +++-.+|++
T Consensus 15 ~~g-s~s~AA~~L~isQpavS~~I~~LE~~lG~~LF~R~--~r~~~lT~~ 61 (301)
T PRK14997 15 EEG-GFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRT--TRQFNVTEV 61 (301)
T ss_pred HcC-CHHHHHHHhCCCHHHHHHHHHHHHHHhCCEeeeec--cCcceEcHh
Confidence 344 78899999999999999999999854 43333322 233445554
No 439
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=94.14 E-value=0.09 Score=36.35 Aligned_cols=28 Identities=25% Similarity=0.128 Sum_probs=25.3
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
.|++..+||..||||.++|.+++.+-+.
T Consensus 220 e~~t~~EIA~~lgis~~~V~~~~~ral~ 247 (257)
T PRK05911 220 EELVLKEIGKILGVSESRVSQIHSKALL 247 (257)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 6899999999999999999999887654
No 440
>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=94.09 E-value=0.07 Score=35.17 Aligned_cols=36 Identities=22% Similarity=0.258 Sum_probs=31.0
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccC
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIG 41 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~g 41 (77)
++..++|..+++|.+||+|.++.+.+.+=+...+.|
T Consensus 76 ~t~~~ia~~l~iS~~Tv~r~ik~L~e~~iI~k~~~G 111 (165)
T PF05732_consen 76 ATQKEIAEKLGISKPTVSRAIKELEEKNIIKKIRNG 111 (165)
T ss_pred eeHHHHHHHhCCCHHHHHHHHHHHHhCCcEEEccCC
Confidence 478899999999999999999999999877655433
No 441
>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=94.08 E-value=0.087 Score=27.31 Aligned_cols=23 Identities=26% Similarity=0.294 Sum_probs=20.5
Q ss_pred CCCCHHHHHHHhccCHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKIL 26 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~ 26 (77)
.++|.++||++.|||++++++..
T Consensus 15 ~~~s~~~Ia~~~gvs~~~~y~~f 37 (47)
T PF00440_consen 15 EAVSIRDIARRAGVSKGSFYRYF 37 (47)
T ss_dssp TTSSHHHHHHHHTSCHHHHHHHC
T ss_pred HhCCHHHHHHHHccchhhHHHHc
Confidence 46899999999999999999764
No 442
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=94.06 E-value=0.051 Score=36.82 Aligned_cols=30 Identities=23% Similarity=0.204 Sum_probs=26.1
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHHhc
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQETG 33 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG 33 (77)
+.| |...+|++++||+++|++.+++..+.=
T Consensus 16 e~~-s~t~AA~~L~isqpavS~~I~~LE~~l 45 (290)
T PRK10837 16 KSG-STTQASVMLALSQSAVSAALTDLEGQL 45 (290)
T ss_pred HcC-CHHHHHHHhCCCccHHHHHHHHHHHHh
Confidence 445 889999999999999999999998543
No 443
>PRK10651 transcriptional regulator NarL; Provisional
Probab=94.05 E-value=0.087 Score=33.33 Aligned_cols=33 Identities=18% Similarity=0.297 Sum_probs=29.4
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCC
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSI 35 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v 35 (77)
..|++..+||+.++||..||...+++.+..=.+
T Consensus 168 ~~g~~~~~ia~~l~is~~tV~~~~~~l~~Kl~~ 200 (216)
T PRK10651 168 AQGLPNKMIARRLDITESTVKVHVKHMLKKMKL 200 (216)
T ss_pred HcCCCHHHHHHHcCCCHHHHHHHHHHHHHHcCC
Confidence 478999999999999999999999999876544
No 444
>PF03428 RP-C: Replication protein C N-terminal domain; InterPro: IPR005090 Proteins in this group have homology with the RepC protein of Agrobacterium Ri and Ti plasmids []. They may be involved in plasmid replication and stabilisation functions.
Probab=94.03 E-value=0.12 Score=34.59 Aligned_cols=40 Identities=20% Similarity=0.187 Sum_probs=34.5
Q ss_pred CCHHHHHHHh-ccCHHHHHHHHHHHHHhcCCCccccCCCCC
Q psy15513 6 VRPCVISRQL-RVSHGCVSKILNRYQETGSIRPGVIGGSKP 45 (77)
Q Consensus 6 ~s~~~iA~rf-~VS~stv~r~~~r~r~tG~v~pk~~gg~~~ 45 (77)
.|..++|.++ |+|.+|+.+.+.+..+.|=+..+..+.+++
T Consensus 71 pSN~~La~r~~G~s~~tlrR~l~~LveaGLI~rrDS~NgkR 111 (177)
T PF03428_consen 71 PSNAQLAERLNGMSERTLRRHLARLVEAGLIVRRDSPNGKR 111 (177)
T ss_pred cCHHHHHHHHcCCCHHHHHHHHHHHHHCCCeeeccCCCCCc
Confidence 4778999999 999999999999999999998876544444
No 445
>TIGR03020 EpsA transcriptional regulator EpsA. Proteins in this family include a C-terminal LuxR transcriptional regulator domain (pfam00196). These proteins are positioned proximal to either EpsH-containing exopolysaccharide biosynthesis operons of the Methylobacillus type, or the associated PEP-CTERM-containing genes.
Probab=94.03 E-value=0.062 Score=37.50 Aligned_cols=34 Identities=21% Similarity=0.131 Sum_probs=29.7
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCC
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIR 36 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~ 36 (77)
..|+|..+||+.|+||.+||...+++.++.=.+.
T Consensus 203 a~G~s~~eIA~~L~IS~~TVk~hl~~i~~KL~v~ 236 (247)
T TIGR03020 203 RDGKTNEEIAAILGISSLTVKNHLQHIFKKLDVR 236 (247)
T ss_pred HCCCCHHHHHHHHCcCHHHHHHHHHHHHHHhCCC
Confidence 4799999999999999999999999988755443
No 446
>PRK11557 putative DNA-binding transcriptional regulator; Provisional
Probab=94.00 E-value=0.063 Score=37.02 Aligned_cols=25 Identities=16% Similarity=0.222 Sum_probs=22.8
Q ss_pred CCCHHHHHHHhccCHHHHHHHHHHH
Q psy15513 5 GVRPCVISRQLRVSHGCVSKILNRY 29 (77)
Q Consensus 5 G~s~~~iA~rf~VS~stv~r~~~r~ 29 (77)
.+|..++|++.+||.+||.|..++.
T Consensus 30 ~~si~elA~~~~vS~aTv~Rf~kkl 54 (278)
T PRK11557 30 HLSSQQLANEAGVSQSSVVKFAQKL 54 (278)
T ss_pred hcCHHHHHHHhCCCHHHHHHHHHHc
Confidence 4899999999999999999998864
No 447
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=94.00 E-value=0.1 Score=35.74 Aligned_cols=29 Identities=17% Similarity=0.130 Sum_probs=25.8
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
-+|+|..+||..||||.++|..++.+-+.
T Consensus 215 ~~~~s~~EIA~~lgis~~tV~~~~~ra~~ 243 (251)
T PRK07670 215 KEELTLTEIGQVLNLSTSRISQIHSKALF 243 (251)
T ss_pred hcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 37899999999999999999999887654
No 448
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=93.94 E-value=0.086 Score=33.56 Aligned_cols=34 Identities=12% Similarity=0.194 Sum_probs=31.4
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccc
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV 39 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~ 39 (77)
=|.|+.|..++|+++||+|-.+...+.|=|..+.
T Consensus 36 PSvRelA~~~~VNpnTv~raY~eLE~eG~i~t~r 69 (125)
T COG1725 36 PSVRELAKDLGVNPNTVQRAYQELEREGIVETKR 69 (125)
T ss_pred CcHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEec
Confidence 3889999999999999999999999999998764
No 449
>PRK09191 two-component response regulator; Provisional
Probab=93.91 E-value=0.1 Score=34.85 Aligned_cols=30 Identities=13% Similarity=0.060 Sum_probs=26.9
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHHHhc
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQETG 33 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r~tG 33 (77)
+|+|..+||..+|+|.+||...+.+.++.=
T Consensus 103 ~~~s~~eIA~~l~~s~~tV~~~l~ra~~~l 132 (261)
T PRK09191 103 EGFSVEEAAEILGVDPAEAEALLDDARAEI 132 (261)
T ss_pred hcCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 689999999999999999999998877643
No 450
>COG2186 FadR Transcriptional regulators [Transcription]
Probab=93.89 E-value=0.093 Score=36.10 Aligned_cols=36 Identities=19% Similarity=0.255 Sum_probs=32.3
Q ss_pred CHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCC
Q psy15513 7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGG 42 (77)
Q Consensus 7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg 42 (77)
+-+++|.+||||.++|.=-++.....|-|.+++..|
T Consensus 36 ~EreLae~fgVSR~~vREAl~~L~a~Glve~r~G~G 71 (241)
T COG2186 36 SERELAERFGVSRTVVREALKRLEAKGLVEIRQGSG 71 (241)
T ss_pred CHHHHHHHHCCCcHHHHHHHHHHHHCCCeeecCCCc
Confidence 368899999999999999999999999999987544
No 451
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=93.88 E-value=0.068 Score=34.94 Aligned_cols=30 Identities=17% Similarity=0.321 Sum_probs=25.2
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCc
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP 37 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~p 37 (77)
+.|+|..++|.++|||++++++|- .|...|
T Consensus 80 ~~glSqeeLA~~lgvs~s~IsriE-----~G~~~P 109 (154)
T TIGR00270 80 KRGWSQEQLAKKIQEKESLIKKIE-----NAEIEP 109 (154)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHH-----CCCCCC
Confidence 479999999999999999999984 465544
No 452
>PRK15482 transcriptional regulator MurR; Provisional
Probab=93.84 E-value=0.074 Score=36.95 Aligned_cols=25 Identities=20% Similarity=0.369 Sum_probs=22.6
Q ss_pred CCCHHHHHHHhccCHHHHHHHHHHH
Q psy15513 5 GVRPCVISRQLRVSHGCVSKILNRY 29 (77)
Q Consensus 5 G~s~~~iA~rf~VS~stv~r~~~r~ 29 (77)
.+|..++|++.+||.+||.|..++.
T Consensus 34 ~~si~elA~~~~vS~aTv~Rf~kkL 58 (285)
T PRK15482 34 SVSSRKMAKQLGISQSSIVKFAQKL 58 (285)
T ss_pred hcCHHHHHHHhCCCHHHHHHHHHHh
Confidence 4799999999999999999998764
No 453
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=93.81 E-value=0.11 Score=35.86 Aligned_cols=28 Identities=14% Similarity=0.143 Sum_probs=24.2
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHH
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQ 30 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r 30 (77)
-.|+|..+||..||||.++|.+++.+-+
T Consensus 226 ~~~~s~~eIA~~lgis~~tV~~~~~ra~ 253 (268)
T PRK06288 226 YEDLTLKEIGKVLGVTESRISQLHTKAV 253 (268)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 3789999999999999999997776544
No 454
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=93.77 E-value=0.08 Score=35.44 Aligned_cols=33 Identities=15% Similarity=0.220 Sum_probs=30.3
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPG 38 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk 38 (77)
.+..++|..+|+|+-||+|.++++++.|-+...
T Consensus 170 ~t~~~lA~~lG~sretvsR~L~~L~~~G~I~~~ 202 (226)
T PRK10402 170 EKHTQAAEYLGVSYRHLLYVLAQFIQDGYLKKS 202 (226)
T ss_pred chHHHHHHHHCCcHHHHHHHHHHHHHCCCEEee
Confidence 467899999999999999999999999988764
No 455
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=93.77 E-value=0.095 Score=35.59 Aligned_cols=34 Identities=15% Similarity=0.095 Sum_probs=30.7
Q ss_pred CHHHHHHHhccCHHHHHHHHHHHHHhcCCCcccc
Q psy15513 7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI 40 (77)
Q Consensus 7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~ 40 (77)
|-+++|+.||||..||.+-+......|-|.-++.
T Consensus 31 sE~eL~~~~~VSR~TvR~Al~~L~~eGli~r~~G 64 (240)
T PRK09764 31 TESALQTEFGVSRVTVRQALRQLVEQQILESIQG 64 (240)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 5689999999999999999999999999986653
No 456
>COG1339 Transcriptional regulator of a riboflavin/FAD biosynthetic operon [Transcription / Coenzyme metabolism]
Probab=93.75 E-value=0.13 Score=35.30 Aligned_cols=34 Identities=21% Similarity=0.330 Sum_probs=30.9
Q ss_pred CCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513 5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG 38 (77)
Q Consensus 5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk 38 (77)
+.+..++|+++++|.-|++||++...+.|.+.-.
T Consensus 19 ~~t~~ela~~l~~S~qta~R~l~~le~~~~I~R~ 52 (214)
T COG1339 19 KVTSSELAKRLGVSSQTAARKLKELEDEGYITRT 52 (214)
T ss_pred cccHHHHHHHhCcCcHHHHHHHHhhccCCcEEEE
Confidence 3789999999999999999999999999998644
No 457
>PRK10082 cell density-dependent motility repressor; Provisional
Probab=93.74 E-value=0.083 Score=36.41 Aligned_cols=46 Identities=11% Similarity=0.029 Sum_probs=32.2
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHHh-cCCCccccCCCCCCCCCHH
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQET-GSIRPGVIGGSKPRVATPD 51 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~t-G~v~pk~~gg~~~~~~~~~ 51 (77)
+.| |..++|+.++||+++|++-++++.+. |..--.+ . +++-.+|++
T Consensus 24 e~g-S~t~AA~~L~iSQpavS~~I~~LE~~lG~~Lf~R-~-~r~~~lT~~ 70 (303)
T PRK10082 24 KCR-NFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNR-Q-VTPLQLSEQ 70 (303)
T ss_pred hcC-CHHHHHHHhCCChHHHHHHHHHHHHHcCCEEEEe-c-CCCCccCHH
Confidence 445 88999999999999999999999854 4333322 2 233445554
No 458
>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=93.73 E-value=0.078 Score=34.89 Aligned_cols=71 Identities=20% Similarity=0.224 Sum_probs=17.3
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHH-HhcC-CCccc------cCCCCCC-CCCHHHHHHHHHHHHhC---CCCcHHHHHH
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQ-ETGS-IRPGV------IGGSKPR-VATPDVERRIEEYKGEN---PAMFSWEIRD 73 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r-~tG~-v~pk~------~gg~~~~-~~~~~~~~~i~~~v~~~---pd~tl~El~~ 73 (77)
++..+||..+||+.|||+|.++-.+ +|.. +-|-+ .+.+... .........|.++|++. ..++=.+|++
T Consensus 50 Lt~~~iA~~lgl~~STVSRav~~Ky~~t~~Gi~plk~fF~~~~~~~~~~~~S~~~ik~~i~~lI~~Ed~~~PlSD~~i~~ 129 (160)
T PF04552_consen 50 LTMKDIADELGLHESTVSRAVKNKYIQTPRGIFPLKDFFSRSVSSGSGEEFSSEAIKARIKELIEEEDKKKPLSDQEIAE 129 (160)
T ss_dssp -----------------------------------S-----SS--SS-SS---TTH-HHHHHHHTTS-TTS---HHHHHH
T ss_pred CCHHHHHHHhCCCHhHHHHHHcCceeecCCeeeeHHHhccccccCCCCcccHHHHHHHHHHHHHHhcCCCCCCCHHHHHH
Confidence 5678999999999999999876543 4432 22222 1111111 12233556789999873 3477788888
Q ss_pred Hhh
Q psy15513 74 RLV 76 (77)
Q Consensus 74 ~L~ 76 (77)
.|.
T Consensus 130 ~L~ 132 (160)
T PF04552_consen 130 LLK 132 (160)
T ss_dssp HHT
T ss_pred HHH
Confidence 774
No 459
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=93.66 E-value=0.12 Score=35.22 Aligned_cols=29 Identities=7% Similarity=0.100 Sum_probs=26.0
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
..|+|..+||..+|||.+.|+++.++..+
T Consensus 197 ~~~~t~~EIA~~lgis~~~V~q~~~~~~~ 225 (231)
T PRK12427 197 QHEMSLKEIALVLDLTEARICQLNKKIAQ 225 (231)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 36899999999999999999999888764
No 460
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=93.66 E-value=0.1 Score=35.39 Aligned_cols=33 Identities=15% Similarity=0.096 Sum_probs=30.1
Q ss_pred CHHHHHHHhccCHHHHHHHHHHHHHhcCCCccc
Q psy15513 7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGV 39 (77)
Q Consensus 7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~ 39 (77)
|-+++|+.||||..||.+-++...+.|-|..++
T Consensus 35 sE~eLa~~~~VSR~TvR~Al~~L~~eGli~r~~ 67 (241)
T PRK11402 35 TENELCTQYNVSRITIRKAISDLVADGVLIRWQ 67 (241)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence 557899999999999999999999999998664
No 461
>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=93.64 E-value=0.052 Score=38.97 Aligned_cols=27 Identities=11% Similarity=0.066 Sum_probs=23.9
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHH
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRY 29 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~ 29 (77)
..|....++|+++|||.+|.++.+++|
T Consensus 303 ~~~gn~~~aA~~LGisr~tL~rklkk~ 329 (329)
T TIGR02974 303 EAQFNQRKAAELLGLTYHQLRGLLRKH 329 (329)
T ss_pred HhCCCHHHHHHHhCCCHHHHHHHHHhC
Confidence 456788999999999999999999875
No 462
>PRK09775 putative DNA-binding transcriptional regulator; Provisional
Probab=93.63 E-value=0.087 Score=39.60 Aligned_cols=38 Identities=13% Similarity=0.131 Sum_probs=32.6
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCC
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGG 42 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg 42 (77)
+.-.+..++|.+|+||++||++-++.. .|.|...+.|.
T Consensus 11 ~g~~~~~eL~~~l~~sq~~~s~~L~~L--~~~V~~~~~gr 48 (442)
T PRK09775 11 QGPLSAAELAARLGVSQATLSRLLAAL--GDQVVRFGKAR 48 (442)
T ss_pred cCCCCHHHHHHHhCCCHHHHHHHHHHh--hcceeEeccCc
Confidence 344899999999999999999999999 78887776654
No 463
>PRK09508 leuO leucine transcriptional activator; Reviewed
Probab=93.61 E-value=0.082 Score=36.69 Aligned_cols=32 Identities=16% Similarity=0.122 Sum_probs=26.5
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHHh-cCC
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQET-GSI 35 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~t-G~v 35 (77)
+.| |...+|+.|+||+++|++=+++..+. |.-
T Consensus 35 e~g-s~s~AA~~L~isQpavS~~I~~LE~~lg~~ 67 (314)
T PRK09508 35 QEQ-NITRAAHNLGMSQPAVSNAVARLKVMFNDE 67 (314)
T ss_pred hcC-CHHHHHHHhCCCHHHHHHHHHHHHHhhCCC
Confidence 445 78899999999999999999999854 443
No 464
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=93.60 E-value=0.091 Score=34.18 Aligned_cols=25 Identities=8% Similarity=0.147 Sum_probs=19.9
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHH
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQ 30 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r 30 (77)
.+..+||+-.|||.+|.++|.++-+
T Consensus 35 ~T~~eiAee~Gis~~tLYrWr~~~~ 59 (142)
T PF13022_consen 35 RTQAEIAEEVGISRSTLYRWRQQNK 59 (142)
T ss_dssp S-HHHHHHHHTS-HHHHHHHHHH-H
T ss_pred chHHHHHHHhCCCHHHHHHHHhcCH
Confidence 6788999999999999999997644
No 465
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=93.58 E-value=0.084 Score=37.01 Aligned_cols=28 Identities=18% Similarity=0.181 Sum_probs=25.0
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHH
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQ 30 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r 30 (77)
..+++..+||+.+|||.|.|+++.++.-
T Consensus 210 ~eelt~kEI~~~LgISes~VSql~kkai 237 (247)
T COG1191 210 KEELTQKEIAEVLGISESRVSRLHKKAI 237 (247)
T ss_pred HhccCHHHHHHHhCccHHHHHHHHHHHH
Confidence 4678999999999999999999998764
No 466
>PHA02943 hypothetical protein; Provisional
Probab=93.58 E-value=0.2 Score=33.18 Aligned_cols=42 Identities=26% Similarity=0.331 Sum_probs=36.3
Q ss_pred cCC-CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCC
Q psy15513 3 AAG-VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSK 44 (77)
Q Consensus 3 ~~G-~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~ 44 (77)
+.| .+..+||+++|+|.+-|.-.+......|-|..-+.|...
T Consensus 21 k~G~~TtseIAkaLGlS~~qa~~~LyvLErEG~VkrV~~G~~t 63 (165)
T PHA02943 21 ADGCKTTSRIANKLGVSHSMARNALYQLAKEGMVLKVEIGRAA 63 (165)
T ss_pred hcCCccHHHHHHHHCCCHHHHHHHHHHHHHcCceEEEeecceE
Confidence 456 779999999999999999999999999999887766433
No 467
>PRK10632 transcriptional regulator; Provisional
Probab=93.52 E-value=0.09 Score=36.47 Aligned_cols=28 Identities=18% Similarity=0.232 Sum_probs=25.0
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhc
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETG 33 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG 33 (77)
-|...+|++++||+++|++=+++..+.=
T Consensus 17 gS~t~AA~~L~isQpavS~~I~~LE~~l 44 (309)
T PRK10632 17 GSFTAAARQLQMSVSSISQTVSKLEDEL 44 (309)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence 3889999999999999999999998643
No 468
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=93.52 E-value=0.15 Score=32.24 Aligned_cols=32 Identities=22% Similarity=0.124 Sum_probs=28.4
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcC
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGS 34 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~ 34 (77)
..|+|..+||+.+++|..||..++.+.+..=.
T Consensus 162 ~~g~s~~eIa~~l~~s~~tv~~~~~~~~~kl~ 193 (210)
T PRK09935 162 VSGLSNKEIADQLLLSNKTVSAHKSNIYGKLG 193 (210)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence 36899999999999999999999999886543
No 469
>PRK10086 DNA-binding transcriptional regulator DsdC; Provisional
Probab=93.47 E-value=0.088 Score=36.56 Aligned_cols=26 Identities=19% Similarity=0.309 Sum_probs=24.0
Q ss_pred CHHHHHHHhccCHHHHHHHHHHHHHh
Q psy15513 7 RPCVISRQLRVSHGCVSKILNRYQET 32 (77)
Q Consensus 7 s~~~iA~rf~VS~stv~r~~~r~r~t 32 (77)
|...+|+.++||+++|++=+++..+.
T Consensus 30 s~s~AA~~L~iSQpavS~~I~~LE~~ 55 (311)
T PRK10086 30 SFALAADELSLTPSAVSHRINQLEEE 55 (311)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 88899999999999999999998854
No 470
>PRK04140 hypothetical protein; Provisional
Probab=93.46 E-value=0.077 Score=38.43 Aligned_cols=25 Identities=28% Similarity=0.304 Sum_probs=22.9
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHH
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILN 27 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~ 27 (77)
+.|+|..++|+.+|||++||++|.+
T Consensus 137 ~~GlSq~eLA~~lGVSr~tIskyE~ 161 (317)
T PRK04140 137 ELGLSLGELASELGVSRRTISKYEN 161 (317)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 4799999999999999999999964
No 471
>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional
Probab=93.46 E-value=0.064 Score=40.69 Aligned_cols=24 Identities=25% Similarity=0.452 Sum_probs=22.2
Q ss_pred CHHHHHHHhccCHHHHHHHHHHHH
Q psy15513 7 RPCVISRQLRVSHGCVSKILNRYQ 30 (77)
Q Consensus 7 s~~~iA~rf~VS~stv~r~~~r~r 30 (77)
+.+++|++||||++|++|-++.|-
T Consensus 488 ~~~~aA~~LGisr~tL~rkl~~~g 511 (520)
T PRK10820 488 STRKLAKRLGVSHTAIANKLREYG 511 (520)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHcC
Confidence 788999999999999999999874
No 472
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=93.44 E-value=0.074 Score=37.95 Aligned_cols=41 Identities=20% Similarity=0.216 Sum_probs=29.6
Q ss_pred CHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHhC
Q psy15513 7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGEN 63 (77)
Q Consensus 7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~ 63 (77)
+..+||+..|||++||||-++.. + ...++.++.|++.+++-
T Consensus 2 TikDVA~~AGVS~sTVSrvln~~---------------~-~Vs~eTr~kV~~a~~el 42 (333)
T COG1609 2 TIKDVAKLAGVSKATVSRVLNGS---------------P-YVSEETREKVLAAIKEL 42 (333)
T ss_pred CHHHHHHHhCCCHHHHHHHHcCC---------------C-CCCHHHHHHHHHHHHHH
Confidence 57899999999999999998641 1 23344566677666653
No 473
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=93.42 E-value=0.093 Score=36.74 Aligned_cols=36 Identities=22% Similarity=0.175 Sum_probs=31.6
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCC
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGG 42 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg 42 (77)
++..++|+.|+||..||.|=+....+.|-+.- -+||
T Consensus 32 vtv~eLa~~l~VS~~TIRRDL~~Le~~G~l~r-~~GG 67 (269)
T PRK09802 32 VQVNDLSALYGVSTVTIRNDLAFLEKQGIAVR-AYGG 67 (269)
T ss_pred EeHHHHHHHHCCCHHHHHHHHHHHHhCCCeEE-EeCC
Confidence 78999999999999999999999999998873 3455
No 474
>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=93.41 E-value=0.14 Score=35.12 Aligned_cols=27 Identities=15% Similarity=0.238 Sum_probs=24.6
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQ 30 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r 30 (77)
+|++..+||..||||.++|+++.++..
T Consensus 221 ~~~t~~eIA~~lgis~~~V~~~~~ral 247 (254)
T TIGR02850 221 EGKTQMEVAEEIGISQAQVSRLEKAAL 247 (254)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 689999999999999999999987754
No 475
>TIGR02915 PEP_resp_reg putative PEP-CTERM system response regulator. Members of this protein family share full-length homology with (but do not include) the acetoacetate metabolism regulatory protein AtoC. These proteins have a Fis family DNA binding sequence (pfam02954), a response regulator receiver domain (pfam00072), and sigma-54 interaction domain (pfam00158).
Probab=93.41 E-value=0.071 Score=38.87 Aligned_cols=27 Identities=4% Similarity=0.064 Sum_probs=23.8
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHH
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRY 29 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~ 29 (77)
+.|....++|+.||||.+|.+|-+++|
T Consensus 416 ~~~gn~~~aA~~Lgisr~tl~rkl~~~ 442 (445)
T TIGR02915 416 RVDGNIARAAELLGITRPTLYDLMKKH 442 (445)
T ss_pred HhCCCHHHHHHHhCCCHHHHHHHHHHh
Confidence 445678889999999999999999987
No 476
>COG1737 RpiR Transcriptional regulators [Transcription]
Probab=93.41 E-value=0.067 Score=37.49 Aligned_cols=25 Identities=12% Similarity=0.170 Sum_probs=22.3
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHH
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQ 30 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r 30 (77)
+|..++|++.|||++||.|..+++-
T Consensus 37 ~si~elA~~a~VS~aTv~Rf~~kLG 61 (281)
T COG1737 37 LSIAELAERAGVSPATVVRFARKLG 61 (281)
T ss_pred HHHHHHHHHhCCCHHHHHHHHHHcC
Confidence 6789999999999999999988753
No 477
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=93.38 E-value=0.14 Score=36.36 Aligned_cols=31 Identities=16% Similarity=0.092 Sum_probs=28.8
Q ss_pred CCCHHHHHHHhccCHHHHHHHHHHHHHhcCC
Q psy15513 5 GVRPCVISRQLRVSHGCVSKILNRYQETGSI 35 (77)
Q Consensus 5 G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v 35 (77)
.++..++|++|+||.+||.+-++..++.|-+
T Consensus 18 ~~s~~~LA~~lgvsr~tV~~~l~~L~~~G~~ 48 (319)
T PRK11886 18 FHSGEQLGEELGISRAAIWKHIQTLEEWGLD 48 (319)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHHHCCCc
Confidence 4788899999999999999999999999983
No 478
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=93.36 E-value=0.2 Score=25.27 Aligned_cols=27 Identities=15% Similarity=0.121 Sum_probs=20.4
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHH
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRY 29 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~ 29 (77)
....+..++|..+|+|.+...|..+++
T Consensus 6 ~~~~~l~~iA~~~g~S~~~f~r~Fk~~ 32 (42)
T PF00165_consen 6 QQKLTLEDIAEQAGFSPSYFSRLFKKE 32 (42)
T ss_dssp -SS--HHHHHHHHTS-HHHHHHHHHHH
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 356899999999999999999988764
No 479
>PRK11302 DNA-binding transcriptional regulator HexR; Provisional
Probab=93.33 E-value=0.097 Score=36.00 Aligned_cols=25 Identities=12% Similarity=0.142 Sum_probs=22.5
Q ss_pred CCCHHHHHHHhccCHHHHHHHHHHH
Q psy15513 5 GVRPCVISRQLRVSHGCVSKILNRY 29 (77)
Q Consensus 5 G~s~~~iA~rf~VS~stv~r~~~r~ 29 (77)
-+|..++|+..+||.+||.|..++.
T Consensus 34 ~~si~~lA~~~~vS~aTv~Rf~kkl 58 (284)
T PRK11302 34 HSSIATLAKMANVSEPTVNRFCRSL 58 (284)
T ss_pred hcCHHHHHHHhCCCHHHHHHHHHHc
Confidence 3789999999999999999998763
No 480
>PRK11062 nhaR transcriptional activator NhaR; Provisional
Probab=93.32 E-value=0.099 Score=35.99 Aligned_cols=32 Identities=9% Similarity=0.043 Sum_probs=26.5
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCC
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSI 35 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v 35 (77)
+.| |...+|++|+||+++|++=+++..+.=.+
T Consensus 17 e~g-s~s~AA~~L~isqpavS~~I~~LE~~lg~ 48 (296)
T PRK11062 17 KEG-SVVGAAEALFLTPQTITGQIKALEERLQG 48 (296)
T ss_pred hcC-CHHHHHHHhCCChHHHHHHHHHHHHHcCc
Confidence 344 88999999999999999999999854333
No 481
>PF12964 DUF3853: Protein of unknown function (DUF3853); InterPro: IPR024363 This entry represents a family of uncharacterised proteins that were found by clustering human gut metagenomic sequences [].
Probab=93.32 E-value=0.064 Score=32.76 Aligned_cols=27 Identities=19% Similarity=0.274 Sum_probs=21.6
Q ss_pred HHHHHHHhccCHHHHHHHHHHHHHhcCCCcc
Q psy15513 8 PCVISRQLRVSHGCVSKILNRYQETGSIRPG 38 (77)
Q Consensus 8 ~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk 38 (77)
...+|+-||+|.+||+||-+ +|-+.+.
T Consensus 48 ~~GlAklfgcSv~Ta~RiK~----sG~id~A 74 (96)
T PF12964_consen 48 LKGLAKLFGCSVPTANRIKK----SGKIDPA 74 (96)
T ss_pred HHHHHHHhCCCchhHHHHHh----cCCccHH
Confidence 45699999999999999854 4777654
No 482
>COG1710 Uncharacterized protein conserved in archaea [Function unknown]
Probab=93.27 E-value=0.088 Score=33.65 Aligned_cols=31 Identities=26% Similarity=0.382 Sum_probs=27.1
Q ss_pred CccCCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 1 MAAAGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 1 l~~~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
|+.+|+.+++||+-+||...||+-+++....
T Consensus 105 mlr~gk~preIsk~lGIpirTvyY~l~k~k~ 135 (139)
T COG1710 105 MLRNGKTPREISKDLGIPIRTVYYLLKKLKK 135 (139)
T ss_pred HHHcCCCHHHHHHhhCCchhhhHHHHHHHhh
Confidence 4678999999999999999999999886543
No 483
>PRK11074 putative DNA-binding transcriptional regulator; Provisional
Probab=93.25 E-value=0.1 Score=35.92 Aligned_cols=36 Identities=17% Similarity=0.101 Sum_probs=28.7
Q ss_pred ccCCCCHHHHHHHhccCHHHHHHHHHHHHH-hcCCCcc
Q psy15513 2 AAAGVRPCVISRQLRVSHGCVSKILNRYQE-TGSIRPG 38 (77)
Q Consensus 2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r~-tG~v~pk 38 (77)
++.| |...+|++|+||+++|++-+++..+ -|.---.
T Consensus 14 ~e~~-s~s~AA~~L~isQpavS~~I~~LE~~lg~~LF~ 50 (300)
T PRK11074 14 ARTG-SFSAAAQELHRVPSAVSYTVRQLEEWLAVPLFE 50 (300)
T ss_pred HHhC-CHHHHHHHhCCCHHHHHHHHHHHHHHhCCeeEE
Confidence 3455 8899999999999999999999984 4544433
No 484
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=93.17 E-value=0.16 Score=35.75 Aligned_cols=29 Identities=24% Similarity=0.258 Sum_probs=25.8
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
.+|+|..+||+.||||.++|..+..+-..
T Consensus 243 ~~~~t~~EIa~~lgvs~~~V~q~~~~Al~ 271 (289)
T PRK07500 243 EDGATLEALGEELGISKERVRQIEARALE 271 (289)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 37899999999999999999999887654
No 485
>PRK15092 DNA-binding transcriptional repressor LrhA; Provisional
Probab=93.15 E-value=0.11 Score=36.46 Aligned_cols=43 Identities=14% Similarity=0.173 Sum_probs=31.3
Q ss_pred CHHHHHHHhccCHHHHHHHHHHHHHh-cCCCccccCCCCCCCCCHH
Q psy15513 7 RPCVISRQLRVSHGCVSKILNRYQET-GSIRPGVIGGSKPRVATPD 51 (77)
Q Consensus 7 s~~~iA~rf~VS~stv~r~~~r~r~t-G~v~pk~~gg~~~~~~~~~ 51 (77)
|...+|++++||+++|++-+++..+. |.---.+ .+ ++-.+|++
T Consensus 27 s~s~AA~~L~iSQpavS~~I~~LE~~lG~~LF~R-~~-~~~~LT~~ 70 (310)
T PRK15092 27 TFAAAAAAVCRTQSAVSQQMQRLEQLVGKELFAR-HG-RNKLLTEH 70 (310)
T ss_pred CHHHHHHHhCCChHHHHHHHHHHHHHhCcceEEE-CC-CCceECHh
Confidence 78899999999999999999999854 4433332 22 33456664
No 486
>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=93.15 E-value=0.17 Score=34.39 Aligned_cols=29 Identities=7% Similarity=0.087 Sum_probs=25.4
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
..|+|..+||..||||.++|.++.++-..
T Consensus 194 ~~~~t~~EIA~~lgis~~~V~q~~~~al~ 222 (238)
T TIGR02393 194 GRPHTLEEVGKEFNVTRERIRQIESKALR 222 (238)
T ss_pred CCCccHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 36899999999999999999999877554
No 487
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=93.09 E-value=0.17 Score=35.58 Aligned_cols=27 Identities=15% Similarity=0.007 Sum_probs=24.5
Q ss_pred CCCCHHHHHHHhccCHHHHHHHHHHHH
Q psy15513 4 AGVRPCVISRQLRVSHGCVSKILNRYQ 30 (77)
Q Consensus 4 ~G~s~~~iA~rf~VS~stv~r~~~r~r 30 (77)
.|+|..+||+.||||.++|+.+.++..
T Consensus 247 ~~~Tl~EIA~~lgvS~~rVrqi~~~Al 273 (284)
T PRK06596 247 DKSTLQELAAEYGVSAERVRQIEKNAM 273 (284)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 589999999999999999999988754
No 488
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=93.09 E-value=0.17 Score=36.41 Aligned_cols=29 Identities=10% Similarity=0.062 Sum_probs=25.7
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
-.|+|..+||..+|||.+||..++.+-+.
T Consensus 280 ~e~~s~~EIA~~Lgis~~tV~~~~~rAl~ 308 (325)
T PRK05657 280 YEAATLEDVAREIGLTRERVRQIQVEALR 308 (325)
T ss_pred CCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 47899999999999999999999877554
No 489
>PRK13870 transcriptional regulator TraR; Provisional
Probab=93.05 E-value=0.18 Score=34.60 Aligned_cols=34 Identities=21% Similarity=0.063 Sum_probs=29.5
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCC
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIR 36 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~ 36 (77)
.+|.+..|||..+|||.+||..-++.-++.=.+.
T Consensus 186 A~GKT~~EIa~ILgISe~TV~~Hl~na~~KLga~ 219 (234)
T PRK13870 186 AVGKTMEEIADVEGVKYNSVRVKLREAMKRFDVR 219 (234)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCCC
Confidence 4799999999999999999999999988754443
No 490
>PRK03635 chromosome replication initiation inhibitor protein; Validated
Probab=93.05 E-value=0.14 Score=35.07 Aligned_cols=55 Identities=16% Similarity=0.209 Sum_probs=37.2
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHHh-cCCCccccCCCCCCCCCHHHHHHHHHHHHh
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQET-GSIRPGVIGGSKPRVATPDVERRIEEYKGE 62 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~t-G~v~pk~~gg~~~~~~~~~~~~~i~~~v~~ 62 (77)
+.| |...+|++++||+++|++-+++..+. |..--.+ + +.-..|++ .+.+...+++
T Consensus 15 e~g-s~s~AA~~L~isq~avS~~I~~LE~~lg~~LF~R-~--~~~~lT~~-G~~l~~~a~~ 70 (294)
T PRK03635 15 REG-SFERAAQKLHITQSAVSQRIKALEERVGQVLLVR-T--QPCRPTEA-GQRLLRHARQ 70 (294)
T ss_pred HcC-CHHHHHHHhCCChHHHHHHHHHHHHHhCceeeec-C--CCCccCHH-HHHHHHHHHH
Confidence 344 88999999999999999999999855 4443333 2 34456664 4444444433
No 491
>PRK15424 propionate catabolism operon regulatory protein PrpR; Provisional
Probab=93.04 E-value=0.087 Score=40.48 Aligned_cols=28 Identities=11% Similarity=-0.007 Sum_probs=24.5
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHH
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQ 30 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r 30 (77)
+.|....++|++||||.+|.+|++++|-
T Consensus 508 ~~~Gn~~~aA~~LGIsRtTL~RkLk~~g 535 (538)
T PRK15424 508 RFNGDKTAAANYLGISRTTLWRRLKAEA 535 (538)
T ss_pred HhCCCHHHHHHHhCCCHHHHHHHHHHhC
Confidence 4566788999999999999999999874
No 492
>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=92.98 E-value=0.12 Score=31.28 Aligned_cols=24 Identities=13% Similarity=0.217 Sum_probs=20.0
Q ss_pred CHHHHHHHhccCHHHHHHHHHHHH
Q psy15513 7 RPCVISRQLRVSHGCVSKILNRYQ 30 (77)
Q Consensus 7 s~~~iA~rf~VS~stv~r~~~r~r 30 (77)
....+|+..||+.|+|+||-.-+.
T Consensus 25 gq~~vA~~~Gv~eStISR~k~~~~ 48 (91)
T PF05269_consen 25 GQKKVAEAMGVDESTISRWKNDFI 48 (91)
T ss_dssp HHHHHHHHHTSSTTTHHHHHHHHH
T ss_pred hhHHHHHHhCCCHHHHHHHHhhHH
Confidence 467899999999999999965443
No 493
>TIGR03298 argP transcriptional regulator, ArgP family. ArgP used to be known as IciA. ArgP is a positive regulator of argK. It is a negative autoregulator in presence of arginine. It competes with DnaA for oriC iteron (13-mer) binding. It activates dnaA and nrd transcription. It has been demonstrated to be part of the pho regulon (PubMed:10589831). ArgP mutants convey canavanine (an L-arginine structural homolog) sensitivity (PubMed: 15150242).
Probab=92.90 E-value=0.12 Score=35.20 Aligned_cols=55 Identities=18% Similarity=0.088 Sum_probs=36.8
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCC-CccccCCCCCCCCCHHHHHHHHHHHHh
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSI-RPGVIGGSKPRVATPDVERRIEEYKGE 62 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v-~pk~~gg~~~~~~~~~~~~~i~~~v~~ 62 (77)
+.| |...+|++++||+++|++-+++..+.=.+ --- ++ ++-.+|++ .+.+.+.++.
T Consensus 14 ~~~-s~t~AA~~L~isQpavS~~I~~LE~~lg~~Lf~-R~--r~~~lT~~-G~~l~~~~~~ 69 (292)
T TIGR03298 14 EEG-SFERAAAALSVTPSAVSQRIKALEERLGQPLLV-RT--QPCRATEA-GQRLLRHARQ 69 (292)
T ss_pred HcC-CHHHHHHHhCCCHHHHHHHHHHHHHHhCchhee-cC--CCCcCCHh-HHHHHHHHHH
Confidence 344 88999999999999999999999865433 222 22 34456664 3444444433
No 494
>PF08222 HTH_CodY: CodY helix-turn-helix domain; InterPro: IPR013198 This family consists of the C-terminal helix-turn-helix domain found in several bacterial GTP-sensing transcriptional pleiotropic repressor CodY proteins. CodY has been found to repress the dipeptide transport operon (dpp) of Bacillus subtilis in nutrient-rich conditions []. The CodY protein also has a repressor effect on many genes in Lactococcus lactis during growth in milk [].; PDB: 2B0L_C.
Probab=92.87 E-value=0.2 Score=28.11 Aligned_cols=36 Identities=14% Similarity=0.377 Sum_probs=30.2
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccC
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIG 41 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~g 41 (77)
.-...||.++||+.|.+.+-++.+..-|-++.+..|
T Consensus 5 lvas~iAd~~GiTRSvIVNALRKleSaGvIesrSlG 40 (61)
T PF08222_consen 5 LVASKIADRVGITRSVIVNALRKLESAGVIESRSLG 40 (61)
T ss_dssp E-HHHHHHHHT--HHHHHHHHHHHHHTTSEEEEETT
T ss_pred ehHHHHHHHhCccHHHHHHHHHHHHhcCceeecccC
Confidence 456789999999999999999999999999988765
No 495
>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=92.85 E-value=0.08 Score=30.63 Aligned_cols=29 Identities=10% Similarity=0.132 Sum_probs=23.3
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHH
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQE 31 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~ 31 (77)
+...+..++|..+.||.+|+.+.+++.++
T Consensus 28 ~~~~s~~~la~~~~iS~sti~~~i~~l~~ 56 (87)
T PF05043_consen 28 NEYVSIEDLAEELFISRSTIYRDIKKLNK 56 (87)
T ss_dssp -SEEEHHHHHHHHT--HHHHHHHHHHHHH
T ss_pred CCCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 45678899999999999999999998875
No 496
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=92.81 E-value=0.15 Score=34.80 Aligned_cols=33 Identities=27% Similarity=0.231 Sum_probs=29.9
Q ss_pred CHHHHHHHhccCHHHHHHHHHHHHHhcCCCccc
Q psy15513 7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGV 39 (77)
Q Consensus 7 s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~ 39 (77)
|-+++|++|+||..||.|-++...+.|-+....
T Consensus 33 sE~eLa~~f~VSR~TvRkAL~~L~~eGli~r~~ 65 (236)
T COG2188 33 SERELAEQFGVSRMTVRKALDELVEEGLIVRRQ 65 (236)
T ss_pred CHHHHHHHHCCcHHHHHHHHHHHHHCCcEEEEe
Confidence 457899999999999999999999999987764
No 497
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=92.78 E-value=0.13 Score=35.30 Aligned_cols=35 Identities=20% Similarity=0.133 Sum_probs=30.1
Q ss_pred ccCCCCHHHHHHHhccCHHHHHHHHHHHHHhcCCC
Q psy15513 2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIR 36 (77)
Q Consensus 2 ~~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~ 36 (77)
...|++..+||..|+||..||..-++..++.=.+.
T Consensus 191 ~a~G~t~~eIa~~l~is~~TV~~h~~~~~~KL~~~ 225 (240)
T PRK10188 191 TAEGKTSAEIAMILSISENTVNFHQKNMQKKFNAP 225 (240)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Confidence 35799999999999999999999999988765443
No 498
>PRK09986 DNA-binding transcriptional activator XapR; Provisional
Probab=92.78 E-value=0.095 Score=35.57 Aligned_cols=30 Identities=10% Similarity=-0.004 Sum_probs=26.2
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHHhc
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQETG 33 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~tG 33 (77)
+.| |...+|+.++||+++|++-++++.+.=
T Consensus 20 ~~g-s~t~AA~~L~itq~avS~~i~~LE~~l 49 (294)
T PRK09986 20 EEL-HFGRAAARLNISQPPLSIHIKELEDQL 49 (294)
T ss_pred Hhc-CHHHHHHHhCCCCCHHHHHHHHHHHHh
Confidence 455 889999999999999999999998543
No 499
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=92.78 E-value=0.17 Score=33.80 Aligned_cols=54 Identities=13% Similarity=0.244 Sum_probs=39.4
Q ss_pred CCHHHHHHHhccCHHHHHHHHHHHHHhcCCCccccCCCCCCCCCHHHHHHHHHHHHhCCCC
Q psy15513 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVERRIEEYKGENPAM 66 (77)
Q Consensus 6 ~s~~~iA~rf~VS~stv~r~~~r~r~tG~v~pk~~gg~~~~~~~~~~~~~i~~~v~~~pd~ 66 (77)
++..+||..+|++..||+|.++.+++.| +. . ++++-.+. +.+.+.++...+|-+
T Consensus 174 ~t~~~iA~~lG~tretvsR~l~~L~~~g-l~-~--~~~~i~I~---d~~~L~~~~~~~~~~ 227 (236)
T PRK09392 174 YEKRVLASYLGMTPENLSRAFAALASHG-VH-V--DGSAVTIT---DPAGLARFAKPSPLI 227 (236)
T ss_pred CCHHHHHHHhCCChhHHHHHHHHHHhCC-eE-e--eCCEEEEc---CHHHHHHhhccCCCC
Confidence 4578999999999999999999999999 63 2 22222333 355577777777654
No 500
>PRK09863 putative frv operon regulatory protein; Provisional
Probab=92.72 E-value=0.59 Score=35.71 Aligned_cols=72 Identities=10% Similarity=-0.029 Sum_probs=45.9
Q ss_pred cCCCCHHHHHHHhccCHHHHHHHHHHHHH----hcC-CCccccCCCCCCC------------CCHHHHHHHHHHHHhCCC
Q psy15513 3 AAGVRPCVISRQLRVSHGCVSKILNRYQE----TGS-IRPGVIGGSKPRV------------ATPDVERRIEEYKGENPA 65 (77)
Q Consensus 3 ~~G~s~~~iA~rf~VS~stv~r~~~r~r~----tG~-v~pk~~gg~~~~~------------~~~~~~~~i~~~v~~~pd 65 (77)
+..++..++|+.||||..||.+-++...+ .|- +..+. +|.+-.. ..++....+..++. +..
T Consensus 15 ~~~~t~~~LA~~l~VS~RTIr~dI~~in~~l~~~~~~~i~~~-~Gy~l~~~~~~~~~~~~~~~~~e~~~il~~Ll~-~~~ 92 (584)
T PRK09863 15 QQDRSGGELAQQLGVSRRTIVRDIAYINFTLNGKAIGSISGS-AKYHLEILNRRSLFQLLQKSDNEDRLLLLRLLL-NTF 92 (584)
T ss_pred cCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhcchhheecC-CceEEEeCCHHHHHHHHhcCCHHHHHHHHHHHH-cCC
Confidence 45689999999999999999999997754 232 12221 2333111 12222334445665 556
Q ss_pred CcHHHHHHHhh
Q psy15513 66 MFSWEIRDRLV 76 (77)
Q Consensus 66 ~tl~El~~~L~ 76 (77)
+++.+|++.|-
T Consensus 93 ~~~~~La~~l~ 103 (584)
T PRK09863 93 TPMAQLASALN 103 (584)
T ss_pred ccHHHHHHHhC
Confidence 89999999874
Done!