Query psy15598
Match_columns 258
No_of_seqs 161 out of 1180
Neff 5.1
Searched_HMMs 46136
Date Fri Aug 16 16:40:50 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy15598.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/15598hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3517|consensus 100.0 1.6E-45 3.4E-50 331.4 12.7 194 28-224 1-207 (334)
2 PF00292 PAX: 'Paired box' dom 100.0 6.5E-35 1.4E-39 240.0 12.9 125 31-155 1-125 (125)
3 cd00131 PAX Paired Box domain 100.0 3.7E-31 7.9E-36 218.0 15.7 125 33-157 3-127 (128)
4 smart00351 PAX Paired Box doma 100.0 3.6E-29 7.8E-34 205.0 14.8 124 32-155 2-125 (125)
5 KOG3862|consensus 100.0 6.1E-29 1.3E-33 226.0 13.1 179 30-221 8-186 (327)
6 COG3415 Transposase and inacti 99.7 1.4E-16 3E-21 133.6 12.6 115 44-164 1-117 (138)
7 KOG0849|consensus 99.7 1.2E-17 2.7E-22 158.3 5.1 131 33-163 1-132 (354)
8 PF13551 HTH_29: Winged helix- 99.7 2.8E-16 6E-21 122.4 11.8 100 53-158 1-112 (112)
9 PF01710 HTH_Tnp_IS630: Transp 99.7 4.7E-16 1E-20 126.2 11.0 103 47-166 2-104 (119)
10 PF13565 HTH_32: Homeodomain-l 99.2 5.9E-11 1.3E-15 87.9 8.1 71 79-154 1-77 (77)
11 PF13011 LZ_Tnp_IS481: leucine 99.0 2.4E-09 5.1E-14 83.3 9.9 80 35-119 1-84 (85)
12 PF13384 HTH_23: Homeodomain-l 99.0 4.7E-10 1E-14 77.1 3.5 44 49-92 3-46 (50)
13 PF13518 HTH_28: Helix-turn-he 98.9 3.4E-09 7.3E-14 72.7 5.1 41 52-92 1-41 (52)
14 PF13936 HTH_38: Helix-turn-he 98.5 8.3E-08 1.8E-12 65.5 3.5 42 45-86 2-43 (44)
15 PRK09413 IS2 repressor TnpA; R 98.4 1.6E-06 3.4E-11 70.6 9.5 49 45-93 10-59 (121)
16 PF02796 HTH_7: Helix-turn-hel 98.4 1.7E-07 3.8E-12 64.0 3.0 41 46-86 4-44 (45)
17 PF01527 HTH_Tnp_1: Transposas 98.4 5.1E-07 1.1E-11 66.5 5.3 46 43-88 2-48 (76)
18 PF04218 CENP-B_N: CENP-B N-te 98.1 3.6E-06 7.8E-11 59.7 4.6 43 45-87 4-46 (53)
19 PF06056 Terminase_5: Putative 98.1 6.5E-06 1.4E-10 59.6 4.7 40 51-90 1-40 (58)
20 COG2826 Tra8 Transposase and i 98.0 4.9E-05 1.1E-09 71.4 9.8 109 46-163 6-123 (318)
21 COG2963 Transposase and inacti 97.9 6.9E-05 1.5E-09 59.8 8.9 49 45-93 5-55 (116)
22 cd00569 HTH_Hin_like Helix-tur 97.9 2.9E-05 6.2E-10 46.8 5.3 39 46-84 4-42 (42)
23 cd01104 HTH_MlrA-CarA Helix-Tu 97.7 0.00027 5.8E-09 50.9 8.0 66 64-133 1-67 (68)
24 PRK09409 IS2 transposase TnpB; 97.7 0.00021 4.6E-09 66.5 9.3 92 58-160 6-102 (301)
25 smart00421 HTH_LUXR helix_turn 97.6 0.00022 4.9E-09 48.1 6.3 42 47-89 3-44 (58)
26 PHA02517 putative transposase 97.5 0.00037 8.1E-09 62.9 7.3 76 73-160 1-77 (277)
27 PF13542 HTH_Tnp_ISL3: Helix-t 97.4 0.00036 7.7E-09 48.0 5.4 44 44-87 8-51 (52)
28 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 97.4 0.00038 8.2E-09 49.3 5.2 42 45-86 2-43 (50)
29 TIGR02531 yecD_yerC TrpR-relat 97.4 0.00031 6.6E-09 55.0 5.1 36 50-85 37-72 (88)
30 cd06171 Sigma70_r4 Sigma70, re 97.4 0.00069 1.5E-08 44.7 5.9 42 48-89 11-52 (55)
31 PF08281 Sigma70_r4_2: Sigma-7 97.3 0.00062 1.3E-08 47.1 5.2 43 47-89 10-52 (54)
32 PF04545 Sigma70_r4: Sigma-70, 97.3 0.00092 2E-08 45.9 5.8 42 47-88 4-45 (50)
33 cd04763 HTH_MlrA-like Helix-Tu 97.2 0.003 6.5E-08 45.8 8.2 66 64-133 1-67 (68)
34 PF01022 HTH_5: Bacterial regu 97.2 0.00051 1.1E-08 46.9 3.9 43 51-93 2-45 (47)
35 PF13412 HTH_24: Winged helix- 97.1 0.0016 3.4E-08 44.2 5.8 43 51-93 3-47 (48)
36 cd06170 LuxR_C_like C-terminal 97.1 0.0018 4E-08 43.9 6.0 39 50-89 3-41 (57)
37 cd01105 HTH_GlnR-like Helix-Tu 97.1 0.0069 1.5E-07 46.7 9.8 71 63-137 1-72 (88)
38 PRK00118 putative DNA-binding 97.1 0.0015 3.2E-08 52.7 6.1 45 45-89 15-59 (104)
39 PF13411 MerR_1: MerR HTH fami 97.0 0.001 2.2E-08 47.9 4.4 66 64-134 1-67 (69)
40 cd04762 HTH_MerR-trunc Helix-T 97.0 0.0018 4E-08 42.5 5.0 44 64-112 1-44 (49)
41 PF01498 HTH_Tnp_Tc3_2: Transp 97.0 0.00061 1.3E-08 50.0 2.8 45 112-161 2-46 (72)
42 PRK10141 DNA-binding transcrip 97.0 0.0015 3.3E-08 53.5 5.3 75 46-120 11-87 (117)
43 PF04552 Sigma54_DBD: Sigma-54 96.9 0.00096 2.1E-08 57.5 3.9 88 63-155 49-148 (160)
44 PF13613 HTH_Tnp_4: Helix-turn 96.9 0.0027 5.9E-08 44.6 5.4 43 47-89 2-45 (53)
45 PF14493 HTH_40: Helix-turn-he 96.9 0.013 2.8E-07 45.3 9.6 84 54-151 4-87 (91)
46 cd04764 HTH_MlrA-like_sg1 Heli 96.9 0.0068 1.5E-07 43.7 7.7 65 64-133 1-66 (67)
47 PHA02535 P terminase ATPase su 96.8 0.0033 7.1E-08 64.0 7.5 42 47-88 2-43 (581)
48 PRK04217 hypothetical protein; 96.8 0.0046 1E-07 50.3 6.8 45 44-88 39-83 (110)
49 cd04765 HTH_MlrA-like_sg2 Heli 96.8 0.018 4E-07 45.5 10.1 69 64-136 1-71 (99)
50 smart00422 HTH_MERR helix_turn 96.8 0.011 2.4E-07 42.4 8.1 50 64-118 1-51 (70)
51 PF02796 HTH_7: Helix-turn-hel 96.7 0.0012 2.7E-08 44.9 2.7 43 102-156 2-44 (45)
52 PF10668 Phage_terminase: Phag 96.7 0.003 6.5E-08 46.3 4.6 44 44-88 1-47 (60)
53 PRK13413 mpi multiple promoter 96.7 0.0027 5.9E-08 55.2 5.1 36 52-87 161-196 (200)
54 cd00090 HTH_ARSR Arsenical Res 96.6 0.0053 1.2E-07 42.9 5.5 49 47-95 3-52 (78)
55 cd04773 HTH_TioE_rpt2 Second H 96.6 0.025 5.3E-07 45.2 9.8 68 64-135 1-69 (108)
56 PF09607 BrkDBD: Brinker DNA-b 96.6 0.0038 8.2E-08 45.6 4.4 43 45-87 3-49 (58)
57 PF12840 HTH_20: Helix-turn-he 96.6 0.0026 5.6E-08 45.5 3.5 48 48-95 7-56 (61)
58 PF12759 HTH_Tnp_IS1: InsA C-t 96.6 0.0031 6.8E-08 44.0 3.7 39 48-86 6-44 (46)
59 PF07037 DUF1323: Putative tra 96.5 0.005 1.1E-07 50.9 5.2 54 64-118 1-56 (122)
60 TIGR02395 rpoN_sigma RNA polym 96.5 0.0086 1.9E-07 58.8 7.8 85 64-153 319-416 (429)
61 PF13309 HTH_22: HTH domain 96.5 0.0039 8.5E-08 45.7 4.1 42 44-85 17-64 (64)
62 PRK15418 transcriptional regul 96.5 0.0051 1.1E-07 57.9 5.8 43 52-94 17-60 (318)
63 cd04774 HTH_YfmP Helix-Turn-He 96.5 0.025 5.5E-07 44.4 8.8 66 64-134 1-68 (96)
64 PF05225 HTH_psq: helix-turn-h 96.5 0.0086 1.9E-07 41.1 5.4 36 51-86 3-39 (45)
65 PF00325 Crp: Bacterial regula 96.5 0.0046 1E-07 39.9 3.7 29 64-92 3-31 (32)
66 TIGR01321 TrpR trp operon repr 96.4 0.0048 1E-07 49.0 4.6 37 51-87 42-79 (94)
67 cd04761 HTH_MerR-SF Helix-Turn 96.4 0.0073 1.6E-07 40.4 4.9 47 64-115 1-47 (49)
68 TIGR03879 near_KaiC_dom probab 96.4 0.0066 1.4E-07 46.1 5.1 44 48-91 16-60 (73)
69 COG1725 Predicted transcriptio 96.4 0.017 3.7E-07 48.1 7.6 107 42-158 6-120 (125)
70 cd01109 HTH_YyaN Helix-Turn-He 96.3 0.063 1.4E-06 42.9 10.5 68 64-135 1-69 (113)
71 cd04770 HTH_HMRTR Helix-Turn-H 96.3 0.066 1.4E-06 43.1 10.7 68 64-135 1-69 (123)
72 smart00550 Zalpha Z-DNA-bindin 96.3 0.012 2.6E-07 43.3 5.8 45 50-94 5-53 (68)
73 cd01106 HTH_TipAL-Mta Helix-Tu 96.3 0.027 5.9E-07 44.3 8.1 67 64-134 1-68 (103)
74 PRK05932 RNA polymerase factor 96.3 0.014 3E-07 57.8 7.6 83 64-153 344-440 (455)
75 PHA02591 hypothetical protein; 96.3 0.009 2E-07 46.2 4.9 50 33-85 30-81 (83)
76 TIGR00721 tfx DNA-binding prot 96.2 0.011 2.5E-07 49.8 6.0 42 47-89 6-47 (137)
77 PRK06759 RNA polymerase factor 96.2 0.013 2.8E-07 47.7 6.1 42 47-88 106-147 (154)
78 PF02954 HTH_8: Bacterial regu 96.1 0.014 3.1E-07 39.1 5.0 37 51-87 5-42 (42)
79 PF09339 HTH_IclR: IclR helix- 96.1 0.0074 1.6E-07 41.9 3.7 41 54-94 6-49 (52)
80 cd00592 HTH_MerR-like Helix-Tu 96.1 0.093 2E-06 40.6 10.2 66 64-134 1-67 (100)
81 cd04782 HTH_BltR Helix-Turn-He 96.1 0.047 1E-06 42.7 8.5 67 64-134 1-68 (97)
82 cd01279 HTH_HspR-like Helix-Tu 96.1 0.027 5.9E-07 44.3 7.1 66 64-134 2-69 (98)
83 cd04767 HTH_HspR-like_MBC Heli 96.1 0.03 6.4E-07 46.3 7.6 65 64-134 2-68 (120)
84 PF01371 Trp_repressor: Trp re 96.1 0.014 3.1E-07 45.7 5.4 39 50-88 35-74 (87)
85 PRK09642 RNA polymerase sigma 96.1 0.016 3.6E-07 47.6 6.1 42 47-88 106-147 (160)
86 smart00345 HTH_GNTR helix_turn 96.0 0.0095 2.1E-07 40.8 3.8 47 50-96 3-53 (60)
87 cd04783 HTH_MerR1 Helix-Turn-H 96.0 0.092 2E-06 42.7 10.2 67 64-135 1-69 (126)
88 PRK12469 RNA polymerase factor 96.0 0.02 4.4E-07 57.2 7.5 83 64-153 370-466 (481)
89 TIGR01529 argR_whole arginine 96.0 0.013 2.8E-07 49.6 5.3 49 111-164 4-52 (146)
90 cd01108 HTH_CueR Helix-Turn-He 96.0 0.089 1.9E-06 43.0 10.1 67 64-134 1-68 (127)
91 PRK11050 manganese transport r 96.0 0.044 9.6E-07 46.2 8.5 43 54-96 40-84 (152)
92 PF06163 DUF977: Bacterial pro 96.0 0.024 5.2E-07 47.4 6.6 52 44-95 1-58 (127)
93 PRK09652 RNA polymerase sigma 96.0 0.019 4.1E-07 47.4 6.0 42 47-88 128-169 (182)
94 PRK09639 RNA polymerase sigma 95.9 0.019 4.2E-07 47.3 6.0 41 47-88 112-152 (166)
95 cd04768 HTH_BmrR-like Helix-Tu 95.9 0.049 1.1E-06 42.5 8.0 67 64-134 1-68 (96)
96 TIGR02937 sigma70-ECF RNA poly 95.9 0.02 4.3E-07 44.9 5.8 42 47-88 110-151 (158)
97 PRK12537 RNA polymerase sigma 95.9 0.019 4.1E-07 48.6 6.0 43 47-89 133-175 (182)
98 PF08822 DUF1804: Protein of u 95.9 0.021 4.6E-07 49.7 6.3 45 48-92 3-48 (165)
99 PRK09047 RNA polymerase factor 95.9 0.021 4.6E-07 46.7 6.1 43 46-88 105-147 (161)
100 TIGR02044 CueR Cu(I)-responsiv 95.9 0.13 2.7E-06 42.1 10.6 67 64-134 1-68 (127)
101 PF12728 HTH_17: Helix-turn-he 95.9 0.01 2.3E-07 40.6 3.5 23 64-86 2-24 (51)
102 TIGR02989 Sig-70_gvs1 RNA poly 95.9 0.022 4.7E-07 46.5 6.1 43 46-88 110-152 (159)
103 PRK11924 RNA polymerase sigma 95.9 0.02 4.3E-07 47.1 5.8 42 47-88 125-166 (179)
104 COG1508 RpoN DNA-directed RNA 95.9 0.033 7.1E-07 55.2 8.2 84 64-153 331-428 (444)
105 cd04788 HTH_NolA-AlbR Helix-Tu 95.9 0.055 1.2E-06 42.2 8.0 67 64-134 1-68 (96)
106 PHA00675 hypothetical protein 95.9 0.019 4.1E-07 44.2 5.1 40 48-87 23-63 (78)
107 cd04766 HTH_HspR Helix-Turn-He 95.9 0.04 8.6E-07 42.4 7.0 66 64-134 2-69 (91)
108 TIGR02985 Sig70_bacteroi1 RNA 95.9 0.024 5.3E-07 45.7 6.2 42 47-88 113-154 (161)
109 cd04780 HTH_MerR-like_sg5 Heli 95.9 0.12 2.5E-06 40.6 9.7 68 64-135 1-70 (95)
110 TIGR01764 excise DNA binding d 95.9 0.0098 2.1E-07 39.3 3.2 23 64-86 2-24 (49)
111 cd04787 HTH_HMRTR_unk Helix-Tu 95.9 0.11 2.4E-06 42.8 10.1 67 64-134 1-68 (133)
112 PF00356 LacI: Bacterial regul 95.9 0.031 6.7E-07 38.6 5.7 40 65-120 1-40 (46)
113 PF00196 GerE: Bacterial regul 95.8 0.017 3.7E-07 40.7 4.6 40 48-88 4-43 (58)
114 TIGR02844 spore_III_D sporulat 95.8 0.042 9.1E-07 42.4 6.9 57 48-119 3-60 (80)
115 TIGR02999 Sig-70_X6 RNA polyme 95.8 0.026 5.5E-07 47.4 6.2 43 47-89 134-176 (183)
116 cd04772 HTH_TioE_rpt1 First He 95.8 0.15 3.3E-06 40.1 10.1 67 65-135 2-68 (99)
117 PF01316 Arg_repressor: Argini 95.8 0.023 4.9E-07 42.8 5.1 51 110-165 6-56 (70)
118 PHA00738 putative HTH transcri 95.8 0.016 3.5E-07 47.2 4.6 51 49-99 10-62 (108)
119 cd01110 HTH_SoxR Helix-Turn-He 95.7 0.052 1.1E-06 45.3 7.8 66 64-134 2-68 (139)
120 PRK12514 RNA polymerase sigma 95.7 0.027 5.8E-07 47.3 6.1 42 47-88 129-170 (179)
121 PRK13919 putative RNA polymera 95.7 0.028 6E-07 47.4 6.1 43 47-89 135-177 (186)
122 PRK12528 RNA polymerase sigma 95.7 0.031 6.7E-07 46.1 6.2 43 47-89 113-155 (161)
123 cd04789 HTH_Cfa Helix-Turn-Hel 95.7 0.068 1.5E-06 42.2 7.9 66 64-134 2-68 (102)
124 cd01282 HTH_MerR-like_sg3 Heli 95.7 0.073 1.6E-06 42.7 8.1 67 64-135 1-68 (112)
125 smart00420 HTH_DEOR helix_turn 95.6 0.035 7.5E-07 37.0 5.3 39 56-94 5-45 (53)
126 COG1595 RpoE DNA-directed RNA 95.6 0.025 5.5E-07 47.9 5.6 44 46-89 126-169 (182)
127 TIGR02043 ZntR Zn(II)-responsi 95.6 0.071 1.5E-06 43.9 8.0 67 64-134 2-69 (131)
128 TIGR02983 SigE-fam_strep RNA p 95.6 0.029 6.4E-07 46.1 5.8 42 48-89 111-152 (162)
129 TIGR02952 Sig70_famx2 RNA poly 95.6 0.034 7.3E-07 45.8 6.1 43 47-89 122-164 (170)
130 PF07900 DUF1670: Protein of u 95.6 0.13 2.9E-06 46.6 10.2 95 52-160 88-190 (220)
131 smart00346 HTH_ICLR helix_turn 95.6 0.11 2.3E-06 38.9 8.3 67 53-121 7-76 (91)
132 cd01111 HTH_MerD Helix-Turn-He 95.6 0.078 1.7E-06 42.5 7.9 68 64-135 1-69 (107)
133 PRK01381 Trp operon repressor; 95.6 0.012 2.5E-07 47.3 3.0 54 51-120 42-96 (99)
134 cd04784 HTH_CadR-PbrR Helix-Tu 95.5 0.2 4.4E-06 40.7 10.4 67 64-134 1-68 (127)
135 PF08279 HTH_11: HTH domain; 95.5 0.03 6.5E-07 38.7 4.7 38 54-91 3-43 (55)
136 cd04775 HTH_Cfa-like Helix-Tur 95.5 0.081 1.8E-06 41.7 7.8 66 64-134 2-68 (102)
137 PRK03975 tfx putative transcri 95.5 0.043 9.3E-07 46.5 6.5 43 45-88 4-46 (141)
138 PRK09514 zntR zinc-responsive 95.5 0.073 1.6E-06 44.5 7.9 67 64-134 2-69 (140)
139 PRK10219 DNA-binding transcrip 95.5 0.15 3.2E-06 39.8 9.1 78 62-160 20-98 (107)
140 TIGR02960 SigX5 RNA polymerase 95.5 0.095 2.1E-06 48.2 9.3 89 47-135 142-231 (324)
141 PRK08241 RNA polymerase factor 95.5 0.1 2.3E-06 48.4 9.7 89 47-135 153-241 (339)
142 TIGR02047 CadR-PbrR Cd(II)/Pb( 95.5 0.24 5.2E-06 40.6 10.7 67 64-134 1-68 (127)
143 PRK07037 extracytoplasmic-func 95.5 0.041 8.8E-07 45.3 6.2 43 47-89 109-151 (163)
144 cd04786 HTH_MerR-like_sg7 Heli 95.5 0.19 4.2E-06 41.6 10.2 88 64-160 1-89 (131)
145 PRK12519 RNA polymerase sigma 95.5 0.029 6.2E-07 47.7 5.4 42 47-88 141-182 (194)
146 cd04785 HTH_CadR-PbrR-like Hel 95.4 0.25 5.5E-06 40.3 10.7 67 64-134 1-68 (126)
147 PRK12547 RNA polymerase sigma 95.4 0.04 8.8E-07 45.8 6.1 43 47-89 112-154 (164)
148 PRK09644 RNA polymerase sigma 95.4 0.037 8E-07 45.9 5.8 44 46-89 107-150 (165)
149 PRK12525 RNA polymerase sigma 95.4 0.044 9.5E-07 45.8 6.2 42 47-88 118-159 (168)
150 PF01978 TrmB: Sugar-specific 95.4 0.03 6.5E-07 40.5 4.5 35 61-95 20-54 (68)
151 PRK12530 RNA polymerase sigma 95.4 0.041 8.9E-07 47.1 6.1 42 47-88 134-175 (189)
152 PRK12529 RNA polymerase sigma 95.4 0.04 8.6E-07 46.7 5.9 42 47-88 127-168 (178)
153 PF01325 Fe_dep_repress: Iron 95.4 0.042 9E-07 39.8 5.1 44 55-98 12-57 (60)
154 cd07377 WHTH_GntR Winged helix 95.4 0.056 1.2E-06 37.6 5.7 30 65-94 27-56 (66)
155 PRK09645 RNA polymerase sigma 95.3 0.047 1E-06 45.5 6.1 42 47-88 118-159 (173)
156 PRK15043 transcriptional regul 95.3 0.075 1.6E-06 48.8 7.9 68 64-135 4-72 (243)
157 TIGR02957 SigX4 RNA polymerase 95.3 0.13 2.8E-06 47.1 9.5 84 47-135 108-191 (281)
158 PRK09648 RNA polymerase sigma 95.3 0.046 1E-06 46.3 6.1 43 47-89 139-181 (189)
159 PRK10046 dpiA two-component re 95.3 0.038 8.2E-07 48.1 5.7 47 48-94 159-208 (225)
160 TIGR03209 P21_Cbot clostridium 95.3 0.023 4.9E-07 46.1 4.0 36 47-82 107-142 (142)
161 PRK12516 RNA polymerase sigma 95.3 0.046 1E-06 46.9 6.1 42 47-88 116-157 (187)
162 PF12116 SpoIIID: Stage III sp 95.3 0.027 5.9E-07 43.7 4.1 34 52-85 4-41 (82)
163 cd01107 HTH_BmrR Helix-Turn-He 95.2 0.13 2.8E-06 40.9 8.1 67 64-134 1-69 (108)
164 PRK09649 RNA polymerase sigma 95.2 0.045 9.8E-07 46.7 5.9 43 47-89 130-172 (185)
165 PRK12532 RNA polymerase sigma 95.2 0.045 9.8E-07 46.7 5.8 42 47-88 136-177 (195)
166 PRK12523 RNA polymerase sigma 95.2 0.053 1.2E-06 45.4 6.2 42 47-88 119-160 (172)
167 PRK09415 RNA polymerase factor 95.2 0.044 9.6E-07 46.3 5.7 43 47-89 127-169 (179)
168 PRK12522 RNA polymerase sigma 95.2 0.049 1.1E-06 45.6 5.9 43 47-89 119-161 (173)
169 TIGR02959 SigZ RNA polymerase 95.2 0.056 1.2E-06 45.4 6.2 42 47-88 100-141 (170)
170 PRK12536 RNA polymerase sigma 95.2 0.054 1.2E-06 45.8 6.1 42 47-88 129-170 (181)
171 TIGR02054 MerD mercuric resist 95.1 0.13 2.8E-06 42.3 8.0 68 63-134 3-71 (120)
172 PRK12520 RNA polymerase sigma 95.1 0.054 1.2E-06 46.1 6.1 42 47-88 131-172 (191)
173 cd04769 HTH_MerR2 Helix-Turn-H 95.1 0.27 5.8E-06 39.5 9.8 67 64-135 1-68 (116)
174 PRK05602 RNA polymerase sigma 95.1 0.05 1.1E-06 46.0 5.8 43 47-89 128-170 (186)
175 TIGR02954 Sig70_famx3 RNA poly 95.1 0.053 1.1E-06 45.1 5.9 43 47-89 119-161 (169)
176 PF07638 Sigma70_ECF: ECF sigm 95.1 0.056 1.2E-06 46.5 6.1 35 54-88 141-176 (185)
177 PF12802 MarR_2: MarR family; 95.1 0.042 9.2E-07 38.4 4.4 31 64-94 22-52 (62)
178 PRK09646 RNA polymerase sigma 95.1 0.057 1.2E-06 46.2 6.1 43 47-89 142-184 (194)
179 PF04297 UPF0122: Putative hel 95.1 0.033 7.2E-07 44.8 4.3 38 51-88 20-58 (101)
180 PRK12512 RNA polymerase sigma 95.1 0.06 1.3E-06 45.4 6.0 42 47-88 131-172 (184)
181 PRK12511 RNA polymerase sigma 95.0 0.058 1.2E-06 46.2 6.0 43 47-89 111-153 (182)
182 PRK13749 transcriptional regul 95.0 0.16 3.4E-06 41.9 8.3 69 63-135 3-72 (121)
183 TIGR02947 SigH_actino RNA poly 95.0 0.027 5.9E-07 48.0 3.9 42 47-88 131-172 (193)
184 PRK06811 RNA polymerase factor 95.0 0.061 1.3E-06 45.8 6.1 43 47-89 131-173 (189)
185 TIGR03001 Sig-70_gmx1 RNA poly 95.0 0.054 1.2E-06 49.0 6.1 42 47-88 161-202 (244)
186 PRK12539 RNA polymerase sigma 95.0 0.058 1.2E-06 45.7 5.9 42 47-88 131-172 (184)
187 PF04967 HTH_10: HTH DNA bindi 95.0 0.087 1.9E-06 37.6 5.8 40 49-88 2-48 (53)
188 smart00342 HTH_ARAC helix_turn 95.0 0.16 3.4E-06 36.3 7.4 77 64-160 2-78 (84)
189 TIGR00122 birA_repr_reg BirA b 95.0 0.063 1.4E-06 39.0 5.3 38 55-92 4-42 (69)
190 PRK08301 sporulation sigma fac 95.0 0.048 1E-06 48.2 5.5 42 47-88 178-223 (234)
191 PRK11511 DNA-binding transcrip 95.0 0.24 5.2E-06 40.3 9.3 86 54-160 12-102 (127)
192 PRK13182 racA polar chromosome 95.0 0.088 1.9E-06 46.1 7.0 63 64-131 1-64 (175)
193 COG2390 DeoR Transcriptional r 95.0 0.047 1E-06 51.9 5.7 42 53-94 15-57 (321)
194 PHA00542 putative Cro-like pro 95.0 0.048 1E-06 41.6 4.7 32 55-86 22-54 (82)
195 PRK12534 RNA polymerase sigma 95.0 0.065 1.4E-06 45.3 6.0 43 47-89 137-179 (187)
196 PRK09637 RNA polymerase sigma 94.9 0.063 1.4E-06 45.8 5.9 43 47-89 106-148 (181)
197 PRK09647 RNA polymerase sigma 94.9 0.066 1.4E-06 46.8 6.2 42 47-88 138-179 (203)
198 PRK12524 RNA polymerase sigma 94.9 0.067 1.5E-06 45.9 6.1 42 47-88 136-177 (196)
199 PRK12526 RNA polymerase sigma 94.9 0.067 1.5E-06 46.5 6.1 43 47-89 153-195 (206)
200 PRK12540 RNA polymerase sigma 94.9 0.067 1.5E-06 45.7 6.0 43 47-89 111-153 (182)
201 TIGR02980 SigBFG RNA polymeras 94.9 0.068 1.5E-06 46.9 6.2 42 47-88 178-219 (227)
202 PRK12543 RNA polymerase sigma 94.9 0.071 1.5E-06 45.0 6.1 42 47-88 117-158 (179)
203 PRK12517 RNA polymerase sigma 94.9 0.069 1.5E-06 45.8 6.0 43 47-89 128-170 (188)
204 TIGR02051 MerR Hg(II)-responsi 94.9 0.14 3.1E-06 41.7 7.6 66 65-134 1-67 (124)
205 PRK06986 fliA flagellar biosyn 94.9 0.06 1.3E-06 47.8 5.8 42 47-88 184-225 (236)
206 COG0789 SoxR Predicted transcr 94.9 0.19 4.1E-06 39.9 8.2 68 64-135 1-69 (124)
207 smart00418 HTH_ARSR helix_turn 94.9 0.072 1.6E-06 36.2 5.0 35 61-95 8-42 (66)
208 PRK12542 RNA polymerase sigma 94.9 0.072 1.6E-06 45.1 6.0 42 47-88 122-163 (185)
209 PRK12527 RNA polymerase sigma 94.9 0.08 1.7E-06 43.5 6.2 42 47-88 105-146 (159)
210 PRK12533 RNA polymerase sigma 94.9 0.061 1.3E-06 47.7 5.8 43 47-89 134-176 (216)
211 TIGR02948 SigW_bacill RNA poly 94.8 0.063 1.4E-06 44.9 5.6 43 47-89 136-178 (187)
212 TIGR01950 SoxR redox-sensitive 94.8 0.3 6.4E-06 41.1 9.6 66 64-134 2-68 (142)
213 PRK12545 RNA polymerase sigma 94.8 0.073 1.6E-06 46.1 6.1 42 47-88 139-180 (201)
214 PRK10227 DNA-binding transcrip 94.8 0.18 4E-06 41.9 8.2 67 64-134 1-68 (135)
215 PRK09636 RNA polymerase sigma 94.8 0.21 4.6E-06 45.8 9.4 44 47-90 115-158 (293)
216 TIGR02984 Sig-70_plancto1 RNA 94.8 0.08 1.7E-06 44.3 6.1 42 47-88 140-181 (189)
217 PRK06704 RNA polymerase factor 94.8 0.062 1.3E-06 48.5 5.7 75 47-123 116-190 (228)
218 PRK08583 RNA polymerase sigma 94.8 0.072 1.6E-06 47.9 6.1 42 47-88 205-246 (257)
219 PRK06930 positive control sigm 94.7 0.081 1.8E-06 45.7 6.1 42 47-88 114-155 (170)
220 PF12298 Bot1p: Eukaryotic mit 94.7 0.15 3.2E-06 44.6 7.7 52 42-93 11-63 (172)
221 PF02001 DUF134: Protein of un 94.7 0.08 1.7E-06 43.0 5.7 42 47-88 41-82 (106)
222 PF08220 HTH_DeoR: DeoR-like h 94.7 0.066 1.4E-06 38.1 4.6 41 53-93 2-44 (57)
223 TIGR02479 FliA_WhiG RNA polyme 94.7 0.078 1.7E-06 46.6 6.1 43 47-89 175-217 (224)
224 COG1438 ArgR Arginine represso 94.7 0.073 1.6E-06 45.7 5.6 52 109-165 6-57 (150)
225 PRK09863 putative frv operon r 94.6 0.29 6.2E-06 49.3 10.7 95 53-159 6-118 (584)
226 PRK12531 RNA polymerase sigma 94.6 0.09 2E-06 45.0 6.1 42 47-88 141-182 (194)
227 PF13730 HTH_36: Helix-turn-he 94.6 0.054 1.2E-06 37.4 3.9 28 65-92 27-54 (55)
228 PRK12541 RNA polymerase sigma 94.6 0.087 1.9E-06 43.4 5.8 43 47-89 112-154 (161)
229 cd04777 HTH_MerR-like_sg1 Heli 94.6 0.24 5.2E-06 39.1 8.1 65 64-134 1-66 (107)
230 PRK11923 algU RNA polymerase s 94.6 0.085 1.8E-06 44.8 5.8 42 47-88 138-179 (193)
231 PRK09640 RNA polymerase sigma 94.6 0.032 6.8E-07 47.5 3.2 42 47-88 134-175 (188)
232 TIGR02943 Sig70_famx1 RNA poly 94.6 0.093 2E-06 44.9 6.1 42 47-88 131-172 (188)
233 PRK11414 colanic acid/biofilm 94.6 0.22 4.7E-06 43.6 8.5 65 45-109 9-80 (221)
234 PF04703 FaeA: FaeA-like prote 94.6 0.053 1.2E-06 39.9 3.9 43 53-95 2-47 (62)
235 PRK03341 arginine repressor; P 94.6 0.1 2.3E-06 45.3 6.4 53 108-165 14-66 (168)
236 PRK12515 RNA polymerase sigma 94.5 0.099 2.2E-06 44.4 6.2 42 47-88 131-172 (189)
237 PRK15002 redox-sensitivie tran 94.5 0.41 8.9E-06 40.9 9.9 66 64-134 12-78 (154)
238 smart00419 HTH_CRP helix_turn_ 94.5 0.058 1.3E-06 35.6 3.8 32 63-94 8-39 (48)
239 PRK15201 fimbriae regulatory p 94.5 0.11 2.3E-06 46.3 6.3 45 44-89 130-174 (198)
240 PRK11179 DNA-binding transcrip 94.5 0.13 2.9E-06 43.1 6.7 42 52-93 10-53 (153)
241 PRK09638 RNA polymerase sigma 94.5 0.043 9.3E-07 45.7 3.7 43 47-89 126-168 (176)
242 TIGR02939 RpoE_Sigma70 RNA pol 94.5 0.077 1.7E-06 44.5 5.3 43 47-89 138-180 (190)
243 PRK12544 RNA polymerase sigma 94.5 0.098 2.1E-06 45.8 6.2 43 46-88 147-189 (206)
244 PRK09635 sigI RNA polymerase s 94.5 0.23 5E-06 46.1 8.9 106 47-157 118-228 (290)
245 TIGR02702 SufR_cyano iron-sulf 94.5 0.09 2E-06 46.0 5.9 43 52-94 2-46 (203)
246 cd04779 HTH_MerR-like_sg4 Heli 94.5 0.2 4.3E-06 41.9 7.6 67 64-135 1-68 (134)
247 PF01381 HTH_3: Helix-turn-hel 94.5 0.051 1.1E-06 37.2 3.5 26 61-86 7-32 (55)
248 PHA01976 helix-turn-helix prot 94.4 0.064 1.4E-06 38.3 4.1 33 53-85 4-37 (67)
249 PF00392 GntR: Bacterial regul 94.4 0.071 1.5E-06 38.2 4.3 34 65-98 26-59 (64)
250 PRK05066 arginine repressor; P 94.4 0.11 2.4E-06 44.6 6.1 52 109-165 9-61 (156)
251 PRK10840 transcriptional regul 94.4 0.097 2.1E-06 44.8 5.8 41 47-88 150-190 (216)
252 PF08765 Mor: Mor transcriptio 94.4 0.045 9.6E-07 43.8 3.4 48 43-90 52-99 (108)
253 PRK12513 RNA polymerase sigma 94.4 0.045 9.8E-07 46.6 3.7 42 47-88 139-180 (194)
254 TIGR02950 SigM_subfam RNA poly 94.4 0.038 8.2E-07 44.8 3.1 41 48-88 106-146 (154)
255 cd04781 HTH_MerR-like_sg6 Heli 94.4 0.26 5.7E-06 39.8 8.0 68 64-136 1-69 (120)
256 PRK12546 RNA polymerase sigma 94.4 0.098 2.1E-06 45.1 5.8 43 47-89 113-155 (188)
257 PRK09651 RNA polymerase sigma 94.4 0.087 1.9E-06 44.2 5.3 42 47-88 119-160 (172)
258 TIGR02859 spore_sigH RNA polym 94.3 0.087 1.9E-06 44.6 5.4 41 49-89 151-191 (198)
259 PRK12538 RNA polymerase sigma 94.3 0.087 1.9E-06 47.2 5.6 42 47-88 171-212 (233)
260 PRK15411 rcsA colanic acid cap 94.3 0.069 1.5E-06 46.8 4.8 40 48-88 138-177 (207)
261 cd04790 HTH_Cfa-like_unk Helix 94.3 0.28 6E-06 42.4 8.5 67 64-134 2-69 (172)
262 PRK06474 hypothetical protein; 94.3 0.073 1.6E-06 46.2 4.9 50 45-94 5-58 (178)
263 TIGR03338 phnR_burk phosphonat 94.3 0.21 4.6E-06 43.1 7.7 59 51-109 19-80 (212)
264 PRK11169 leucine-responsive tr 94.3 0.1 2.2E-06 44.3 5.6 42 52-93 15-58 (164)
265 PRK12535 RNA polymerase sigma 94.2 0.11 2.3E-06 45.1 5.8 43 47-89 133-175 (196)
266 PRK04280 arginine repressor; P 94.2 0.12 2.6E-06 43.9 5.9 51 110-165 5-55 (148)
267 TIGR02835 spore_sigmaE RNA pol 94.2 0.11 2.4E-06 46.2 5.9 42 47-88 178-223 (234)
268 PRK09641 RNA polymerase sigma 94.2 0.12 2.6E-06 43.2 5.8 42 47-88 136-177 (187)
269 cd04776 HTH_GnyR Helix-Turn-He 94.2 0.29 6.4E-06 39.7 7.8 66 64-135 1-67 (118)
270 COG3355 Predicted transcriptio 94.2 0.14 3.1E-06 42.8 6.0 33 61-93 40-72 (126)
271 PF05344 DUF746: Domain of Unk 94.1 0.097 2.1E-06 39.1 4.5 35 55-89 5-39 (65)
272 cd00092 HTH_CRP helix_turn_hel 94.1 0.081 1.8E-06 37.3 4.0 33 63-95 25-57 (67)
273 PF07750 GcrA: GcrA cell cycle 94.1 0.07 1.5E-06 46.0 4.3 39 49-87 4-43 (162)
274 PF11198 DUF2857: Protein of u 94.1 1.2 2.6E-05 38.9 12.0 93 53-158 77-178 (180)
275 COG2964 Uncharacterized protei 94.1 0.1 2.2E-06 47.4 5.3 41 51-91 174-219 (220)
276 PF05930 Phage_AlpA: Prophage 94.0 0.032 6.9E-07 38.8 1.6 23 64-86 4-26 (51)
277 COG3677 Transposase and inacti 94.0 0.093 2E-06 43.7 4.6 46 48-93 74-119 (129)
278 TIGR03070 couple_hipB transcri 93.9 0.13 2.9E-06 34.8 4.7 30 56-85 7-37 (58)
279 COG2512 Predicted membrane-ass 93.9 0.1 2.2E-06 48.2 5.2 57 44-100 189-247 (258)
280 PRK05803 sporulation sigma fac 93.9 0.12 2.6E-06 45.8 5.5 42 47-88 175-220 (233)
281 COG1710 Uncharacterized protei 93.8 0.14 3.1E-06 42.7 5.4 44 45-88 91-134 (139)
282 PF13565 HTH_32: Homeodomain-l 93.8 0.19 4.1E-06 36.8 5.6 41 44-84 26-77 (77)
283 TIGR02297 HpaA 4-hydroxyphenyl 93.8 0.55 1.2E-05 42.1 9.7 86 54-160 189-279 (287)
284 PRK04984 fatty acid metabolism 93.8 0.16 3.5E-06 44.8 6.2 57 44-100 4-68 (239)
285 COG1321 TroR Mn-dependent tran 93.8 0.92 2E-05 38.8 10.5 101 52-160 11-123 (154)
286 PF13545 HTH_Crp_2: Crp-like h 93.8 0.096 2.1E-06 38.0 4.0 31 64-94 29-59 (76)
287 TIGR02885 spore_sigF RNA polym 93.8 0.17 3.6E-06 44.6 6.2 42 47-88 183-224 (231)
288 PRK07408 RNA polymerase sigma 93.7 0.16 3.4E-06 46.0 6.1 42 47-88 203-244 (256)
289 PRK09954 putative kinase; Prov 93.7 0.12 2.7E-06 48.4 5.4 43 51-93 3-47 (362)
290 TIGR02941 Sigma_B RNA polymera 93.6 0.16 3.5E-06 45.6 5.9 42 47-88 205-246 (255)
291 PRK13509 transcriptional repre 93.6 0.15 3.2E-06 46.4 5.7 44 50-93 4-49 (251)
292 PRK11303 DNA-binding transcrip 93.6 0.13 2.8E-06 46.5 5.2 44 64-120 1-44 (328)
293 PRK07670 RNA polymerase sigma 93.6 0.17 3.8E-06 45.4 6.0 41 48-88 202-242 (251)
294 PRK08295 RNA polymerase factor 93.5 0.18 4E-06 43.0 5.9 41 47-88 155-195 (208)
295 PRK05572 sporulation sigma fac 93.5 0.16 3.5E-06 45.6 5.8 42 47-88 202-243 (252)
296 PF01047 MarR: MarR family; I 93.5 0.2 4.4E-06 34.8 5.1 34 61-94 15-48 (59)
297 PRK01905 DNA-binding protein F 93.5 0.2 4.3E-06 37.8 5.3 36 52-87 38-74 (77)
298 smart00344 HTH_ASNC helix_turn 93.5 0.25 5.5E-06 38.3 6.2 41 54-94 6-48 (108)
299 PRK00441 argR arginine repress 93.5 0.21 4.6E-06 42.5 6.1 51 110-165 5-55 (149)
300 PRK05911 RNA polymerase sigma 93.4 0.19 4.2E-06 45.5 6.1 42 47-88 205-246 (257)
301 COG0735 Fur Fe2+/Zn2+ uptake r 93.4 0.27 5.9E-06 41.3 6.5 54 104-163 17-71 (145)
302 PRK11608 pspF phage shock prot 93.3 0.14 3E-06 48.2 5.2 37 51-87 286-323 (326)
303 smart00354 HTH_LACI helix_turn 93.3 0.2 4.4E-06 36.7 5.1 41 65-121 2-42 (70)
304 PRK09191 two-component respons 93.3 0.21 4.6E-06 43.5 5.9 44 47-90 88-131 (261)
305 PF13936 HTH_38: Helix-turn-he 93.3 0.078 1.7E-06 35.9 2.5 41 104-156 3-43 (44)
306 TIGR02325 C_P_lyase_phnF phosp 93.2 0.18 4E-06 44.2 5.5 52 49-100 10-69 (238)
307 PRK13503 transcriptional activ 93.2 0.77 1.7E-05 40.8 9.5 78 62-160 186-264 (278)
308 TIGR02337 HpaR homoprotocatech 93.2 0.56 1.2E-05 37.2 7.8 64 55-118 32-100 (118)
309 PRK09483 response regulator; P 93.1 0.19 4E-06 42.0 5.2 40 48-88 149-188 (217)
310 PRK12518 RNA polymerase sigma 93.1 0.096 2.1E-06 43.6 3.4 42 47-88 120-161 (175)
311 cd07153 Fur_like Ferric uptake 93.1 0.23 5.1E-06 39.0 5.4 43 52-94 2-52 (116)
312 PRK10430 DNA-binding transcrip 93.1 0.29 6.3E-06 42.8 6.5 46 48-93 159-208 (239)
313 cd07153 Fur_like Ferric uptake 93.1 0.29 6.2E-06 38.5 5.9 48 111-163 3-51 (116)
314 PRK06288 RNA polymerase sigma 93.1 0.24 5.2E-06 45.0 6.2 42 47-88 212-253 (268)
315 PF13443 HTH_26: Cro/C1-type H 93.1 0.11 2.4E-06 36.6 3.2 27 60-86 7-33 (63)
316 PRK10906 DNA-binding transcrip 93.1 0.17 3.7E-06 46.1 5.2 44 50-93 4-49 (252)
317 PRK09643 RNA polymerase sigma 93.0 0.26 5.7E-06 42.2 6.0 42 47-88 134-175 (192)
318 PRK14999 histidine utilization 93.0 0.21 4.6E-06 44.4 5.7 54 47-100 12-73 (241)
319 smart00347 HTH_MARR helix_turn 93.0 0.77 1.7E-05 34.1 7.9 41 54-94 13-55 (101)
320 PRK13752 putative transcriptio 93.0 0.54 1.2E-05 39.6 7.7 67 64-134 8-75 (144)
321 PHA02943 hypothetical protein; 92.9 1.1 2.5E-05 38.8 9.7 56 44-99 1-60 (165)
322 PRK12427 flagellar biosynthesi 92.9 0.26 5.6E-06 44.1 6.1 43 47-89 183-225 (231)
323 PRK11014 transcriptional repre 92.9 0.22 4.9E-06 41.1 5.3 50 48-97 7-59 (141)
324 COG2345 Predicted transcriptio 92.9 0.25 5.3E-06 44.8 6.0 50 45-94 5-56 (218)
325 PRK10703 DNA-binding transcrip 92.9 0.17 3.8E-06 45.9 5.1 41 64-120 2-42 (341)
326 COG1654 BirA Biotin operon rep 92.9 0.34 7.4E-06 37.3 5.8 37 64-100 20-57 (79)
327 PF07374 DUF1492: Protein of u 92.9 0.33 7.1E-06 38.3 5.9 38 51-88 59-96 (100)
328 TIGR02607 antidote_HigA addict 92.9 0.29 6.3E-06 35.8 5.3 26 60-85 15-40 (78)
329 PRK07122 RNA polymerase sigma 92.9 0.23 5E-06 45.4 5.8 42 47-88 215-256 (264)
330 TIGR02846 spore_sigmaK RNA pol 92.8 0.24 5.3E-06 43.8 5.8 42 47-88 174-219 (227)
331 PRK08215 sporulation sigma fac 92.8 0.24 5.1E-06 44.7 5.8 42 47-88 209-250 (258)
332 PF10654 DUF2481: Protein of u 92.8 0.15 3.3E-06 42.1 4.1 36 54-89 71-106 (126)
333 PRK09480 slmA division inhibit 92.8 0.23 5.1E-06 41.5 5.4 45 42-86 1-53 (194)
334 COG1522 Lrp Transcriptional re 92.8 0.24 5.2E-06 40.6 5.3 43 51-93 8-52 (154)
335 PRK11475 DNA-binding transcrip 92.8 0.19 4.1E-06 44.4 5.0 41 47-88 134-174 (207)
336 COG2771 CsgD DNA-binding HTH d 92.8 0.28 6.2E-06 34.0 4.9 34 55-88 11-44 (65)
337 TIGR02404 trehalos_R_Bsub treh 92.8 0.27 5.9E-06 43.3 6.0 36 65-100 26-61 (233)
338 PF13412 HTH_24: Winged helix- 92.8 0.29 6.3E-06 33.0 4.8 42 109-160 3-44 (48)
339 COG2197 CitB Response regulato 92.7 0.21 4.6E-06 44.0 5.2 35 54-88 154-188 (211)
340 PRK11534 DNA-binding transcrip 92.7 0.51 1.1E-05 41.2 7.6 58 52-109 16-76 (224)
341 COG5484 Uncharacterized conser 92.7 0.14 3E-06 47.6 4.1 38 51-88 7-44 (279)
342 COG3398 Uncharacterized protei 92.7 0.89 1.9E-05 41.6 9.1 104 48-161 98-216 (240)
343 smart00529 HTH_DTXR Helix-turn 92.7 1.1 2.4E-05 33.9 8.4 32 66-97 2-33 (96)
344 PRK10100 DNA-binding transcrip 92.6 0.2 4.4E-06 44.5 4.9 40 48-88 156-195 (216)
345 COG1802 GntR Transcriptional r 92.6 0.33 7.2E-06 42.8 6.3 65 50-114 23-90 (230)
346 PRK00430 fis global DNA-bindin 92.6 0.3 6.5E-06 38.6 5.3 38 51-88 55-93 (95)
347 PF08535 KorB: KorB domain; I 92.6 0.23 5E-06 38.3 4.6 84 61-156 1-85 (93)
348 PF13022 HTH_Tnp_1_2: Helix-tu 92.5 0.45 9.7E-06 40.6 6.6 77 64-165 35-113 (142)
349 PF13592 HTH_33: Winged helix- 92.5 0.22 4.7E-06 35.7 4.1 41 121-166 2-43 (60)
350 PRK09492 treR trehalose repres 92.5 0.2 4.3E-06 45.0 4.8 23 64-86 5-27 (315)
351 PRK10572 DNA-binding transcrip 92.5 0.9 1.9E-05 41.0 9.1 78 62-160 198-276 (290)
352 PF07141 Phage_term_sma: Putat 92.5 0.26 5.5E-06 42.0 5.1 51 37-87 4-55 (174)
353 PRK11402 DNA-binding transcrip 92.4 0.3 6.5E-06 43.4 5.8 54 47-100 9-70 (241)
354 cd04778 HTH_MerR-like_sg2 Heli 92.4 0.66 1.4E-05 41.8 8.0 67 64-135 2-69 (219)
355 TIGR01610 phage_O_Nterm phage 92.4 0.45 9.8E-06 37.1 6.1 33 62-94 46-78 (95)
356 PRK13719 conjugal transfer tra 92.3 0.25 5.5E-06 44.7 5.2 41 47-88 143-183 (217)
357 COG2188 PhnF Transcriptional r 92.3 0.3 6.5E-06 43.8 5.7 57 44-100 4-68 (236)
358 PRK09764 DNA-binding transcrip 92.3 0.31 6.8E-06 43.3 5.8 53 48-100 6-66 (240)
359 COG2207 AraC AraC-type DNA-bin 92.3 2.2 4.8E-05 32.5 9.9 89 51-160 24-113 (127)
360 TIGR01636 phage_rinA phage tra 92.3 0.38 8.3E-06 39.8 5.9 42 48-89 83-126 (134)
361 TIGR02018 his_ut_repres histid 92.3 0.3 6.5E-06 43.1 5.6 36 65-100 27-62 (230)
362 PRK11512 DNA-binding transcrip 92.3 0.85 1.8E-05 37.5 7.9 55 62-116 53-110 (144)
363 PRK10079 phosphonate metabolis 92.2 0.18 4E-06 44.8 4.2 53 48-100 17-72 (241)
364 PRK09726 antitoxin HipB; Provi 92.2 0.32 6.8E-06 37.2 5.0 35 51-85 12-47 (88)
365 PF13404 HTH_AsnC-type: AsnC-t 92.2 0.43 9.4E-06 32.2 5.1 40 108-157 2-41 (42)
366 PRK10014 DNA-binding transcrip 92.1 0.25 5.4E-06 44.9 5.0 22 64-85 7-28 (342)
367 PRK10072 putative transcriptio 92.1 0.26 5.6E-06 39.2 4.4 27 60-86 43-69 (96)
368 PF03444 HrcA_DNA-bdg: Winged 92.1 0.85 1.9E-05 35.2 7.1 53 51-103 8-65 (78)
369 PF01475 FUR: Ferric uptake re 92.1 0.21 4.5E-06 39.8 4.0 48 110-162 9-57 (120)
370 PRK11922 RNA polymerase sigma 92.1 0.21 4.5E-06 44.3 4.3 41 48-88 150-190 (231)
371 TIGR02405 trehalos_R_Ecol treh 92.1 0.23 5E-06 44.8 4.7 23 64-86 2-24 (311)
372 PRK15369 two component system 92.0 0.42 9E-06 38.7 5.7 41 48-89 150-190 (211)
373 PRK10411 DNA-binding transcrip 91.9 0.33 7.1E-06 43.9 5.5 44 51-94 4-49 (240)
374 PF13404 HTH_AsnC-type: AsnC-t 91.9 0.54 1.2E-05 31.7 5.2 34 54-87 6-41 (42)
375 TIGR02394 rpoS_proteo RNA poly 91.9 0.32 6.9E-06 44.6 5.5 42 47-88 222-267 (285)
376 PRK11523 DNA-binding transcrip 91.9 0.42 9.1E-06 42.7 6.1 58 43-100 4-69 (253)
377 PRK10339 DNA-binding transcrip 91.8 0.25 5.3E-06 44.9 4.6 42 64-120 2-44 (327)
378 TIGR02850 spore_sigG RNA polym 91.8 0.4 8.7E-06 43.2 5.9 42 47-88 206-247 (254)
379 PF00126 HTH_1: Bacterial regu 91.8 0.36 7.8E-06 34.2 4.5 36 55-90 5-40 (60)
380 PRK09526 lacI lac repressor; R 91.7 0.27 5.8E-06 44.6 4.8 23 64-86 6-28 (342)
381 PRK10651 transcriptional regul 91.7 0.36 7.9E-06 39.7 5.1 40 48-88 156-195 (216)
382 TIGR02392 rpoH_proteo alternat 91.7 0.32 7E-06 44.3 5.2 42 47-88 218-261 (270)
383 COG2522 Predicted transcriptio 91.6 0.25 5.5E-06 40.9 4.0 39 50-88 8-47 (119)
384 PRK10434 srlR DNA-bindng trans 91.6 0.34 7.5E-06 44.1 5.3 44 50-93 4-49 (256)
385 PRK11361 acetoacetate metaboli 91.6 0.32 6.8E-06 46.7 5.3 38 50-87 416-454 (457)
386 TIGR02393 RpoD_Cterm RNA polym 91.6 0.34 7.4E-06 43.1 5.1 42 47-88 176-221 (238)
387 TIGR03020 EpsA transcriptional 91.6 0.34 7.4E-06 44.4 5.2 42 47-89 190-231 (247)
388 PRK09791 putative DNA-binding 91.5 0.75 1.6E-05 41.3 7.4 55 54-111 10-66 (302)
389 PRK09393 ftrA transcriptional 91.5 1.2 2.7E-05 41.1 9.0 86 54-160 221-311 (322)
390 PRK10225 DNA-binding transcrip 91.5 0.48 1E-05 42.4 6.0 49 52-100 18-70 (257)
391 TIGR01889 Staph_reg_Sar staphy 91.5 1.2 2.7E-05 35.1 7.7 57 62-118 42-101 (109)
392 PF13601 HTH_34: Winged helix 91.4 0.48 1E-05 36.0 5.1 67 52-118 1-73 (80)
393 PRK13502 transcriptional activ 91.4 1.5 3.2E-05 39.3 9.1 88 52-160 177-269 (282)
394 PRK10727 DNA-binding transcrip 91.4 0.33 7.1E-06 44.4 4.9 40 65-120 3-42 (343)
395 PRK13501 transcriptional activ 91.3 1.8 4E-05 39.1 9.7 78 62-160 191-269 (290)
396 TIGR02431 pcaR_pcaU beta-ketoa 91.3 0.35 7.5E-06 43.3 5.0 41 54-94 12-55 (248)
397 PRK10401 DNA-binding transcrip 91.3 0.35 7.6E-06 44.3 5.1 41 64-120 2-42 (346)
398 TIGR03697 NtcA_cyano global ni 91.2 0.27 5.9E-06 41.1 4.0 32 64-95 144-175 (193)
399 COG1191 FliA DNA-directed RNA 91.2 0.45 9.8E-06 43.8 5.7 42 47-88 196-237 (247)
400 PRK15320 transcriptional activ 91.2 0.43 9.4E-06 43.3 5.4 43 47-90 164-206 (251)
401 PF12844 HTH_19: Helix-turn-he 91.2 0.37 8E-06 34.0 4.1 31 56-86 4-35 (64)
402 PRK10371 DNA-binding transcrip 91.1 1.7 3.6E-05 40.2 9.4 78 62-160 206-284 (302)
403 PRK03837 transcriptional regul 91.1 0.31 6.7E-06 42.9 4.4 36 65-100 39-74 (241)
404 PF05263 DUF722: Protein of un 91.0 0.48 1E-05 39.7 5.2 42 48-90 82-126 (130)
405 PRK12682 transcriptional regul 91.0 0.69 1.5E-05 41.9 6.7 36 55-90 7-43 (309)
406 PRK09462 fur ferric uptake reg 91.0 0.77 1.7E-05 38.2 6.4 52 106-163 15-68 (148)
407 TIGR02417 fruct_sucro_rep D-fr 91.0 0.39 8.4E-06 43.4 5.0 43 65-120 1-43 (327)
408 PRK09464 pdhR transcriptional 90.9 0.29 6.2E-06 43.7 4.0 50 51-100 18-71 (254)
409 COG2186 FadR Transcriptional r 90.8 0.77 1.7E-05 41.4 6.7 56 45-100 8-71 (241)
410 PRK09706 transcriptional repre 90.8 0.47 1E-05 38.8 4.9 36 52-87 6-42 (135)
411 PRK15481 transcriptional regul 90.8 0.54 1.2E-05 45.0 6.1 36 65-100 31-66 (431)
412 TIGR02915 PEP_resp_reg putativ 90.8 0.41 8.9E-06 45.9 5.2 38 51-88 405-443 (445)
413 PF13551 HTH_29: Winged helix- 90.8 0.83 1.8E-05 35.0 6.0 40 48-87 58-111 (112)
414 PRK14987 gluconate operon tran 90.7 0.33 7.1E-06 44.1 4.3 41 64-120 6-46 (331)
415 PRK00215 LexA repressor; Valid 90.7 0.71 1.5E-05 40.1 6.2 33 64-96 24-57 (205)
416 PRK11639 zinc uptake transcrip 90.6 0.64 1.4E-05 40.0 5.8 53 106-164 24-77 (169)
417 PRK03573 transcriptional regul 90.6 1 2.2E-05 36.8 6.7 55 63-117 46-103 (144)
418 COG1476 Predicted transcriptio 90.5 0.48 1E-05 35.7 4.2 32 54-85 4-36 (68)
419 PRK10163 DNA-binding transcrip 90.5 0.55 1.2E-05 42.9 5.5 44 51-94 25-71 (271)
420 TIGR03541 reg_near_HchA LuxR f 90.5 0.63 1.4E-05 41.5 5.8 41 47-88 171-211 (232)
421 TIGR02997 Sig70-cyanoRpoD RNA 90.4 0.54 1.2E-05 43.5 5.5 42 47-88 249-294 (298)
422 cd00093 HTH_XRE Helix-turn-hel 90.4 0.48 1E-05 30.3 3.8 25 61-85 10-34 (58)
423 PRK15090 DNA-binding transcrip 90.4 0.57 1.2E-05 42.2 5.5 41 54-94 17-59 (257)
424 PRK09990 DNA-binding transcrip 90.3 0.94 2E-05 40.3 6.8 36 65-100 33-68 (251)
425 cd06571 Bac_DnaA_C C-terminal 90.3 1.1 2.3E-05 34.5 6.2 43 47-89 27-71 (90)
426 smart00530 HTH_XRE Helix-turn- 90.2 0.47 1E-05 30.1 3.6 25 61-85 8-32 (56)
427 PRK09978 DNA-binding transcrip 90.2 2.9 6.3E-05 39.0 10.1 90 49-160 140-234 (274)
428 PF13560 HTH_31: Helix-turn-he 90.2 0.61 1.3E-05 33.2 4.5 24 62-85 13-36 (64)
429 PF13463 HTH_27: Winged helix 90.1 0.54 1.2E-05 33.2 4.1 32 62-93 17-48 (68)
430 PRK12423 LexA repressor; Provi 90.0 0.93 2E-05 39.8 6.4 48 48-96 4-59 (202)
431 TIGR02944 suf_reg_Xantho FeS a 90.0 1.1 2.4E-05 36.2 6.4 33 63-95 25-57 (130)
432 PRK03902 manganese transport t 90.0 1.4 3E-05 36.3 7.1 44 51-94 8-53 (142)
433 PF13744 HTH_37: Helix-turn-he 90.0 0.5 1.1E-05 35.6 4.1 30 56-85 23-53 (80)
434 PRK10820 DNA-binding transcrip 89.9 0.48 1E-05 47.4 5.1 37 52-88 475-511 (520)
435 PF02082 Rrf2: Transcriptional 89.9 0.23 5E-06 37.4 2.2 31 64-94 26-56 (83)
436 PRK15115 response regulator Gl 89.9 0.55 1.2E-05 45.0 5.2 37 52-88 399-436 (444)
437 TIGR02787 codY_Gpos GTP-sensin 89.8 0.65 1.4E-05 43.0 5.4 44 54-97 186-232 (251)
438 TIGR02812 fadR_gamma fatty aci 89.8 0.81 1.8E-05 40.3 5.9 51 50-100 13-67 (235)
439 PRK13918 CRP/FNR family transc 89.8 0.53 1.1E-05 39.8 4.5 31 64-94 150-180 (202)
440 PRK09834 DNA-binding transcrip 89.8 0.77 1.7E-05 41.6 5.8 45 50-94 10-57 (263)
441 TIGR01481 ccpA catabolite cont 89.8 0.68 1.5E-05 41.8 5.5 23 64-86 2-24 (329)
442 PRK11569 transcriptional repre 89.8 0.71 1.5E-05 42.2 5.6 42 53-94 30-74 (274)
443 COG1349 GlpR Transcriptional r 89.7 0.6 1.3E-05 42.5 5.1 45 49-93 3-49 (253)
444 PF12793 SgrR_N: Sugar transpo 89.7 3.2 7E-05 33.8 8.8 40 64-103 20-61 (115)
445 TIGR00637 ModE_repress ModE mo 89.6 2.1 4.5E-05 33.8 7.5 63 53-115 6-72 (99)
446 cd01392 HTH_LacI Helix-turn-he 89.6 0.2 4.2E-06 33.9 1.4 37 68-120 2-38 (52)
447 PRK10403 transcriptional regul 89.6 0.74 1.6E-05 37.6 5.1 40 48-88 154-193 (215)
448 PRK10421 DNA-binding transcrip 89.5 0.75 1.6E-05 41.1 5.5 50 51-100 10-63 (253)
449 TIGR00738 rrf2_super rrf2 fami 89.5 1.6 3.4E-05 35.1 6.9 32 63-94 25-56 (132)
450 TIGR02974 phageshock_pspF psp 89.5 0.59 1.3E-05 44.1 5.0 36 52-87 293-329 (329)
451 PRK10360 DNA-binding transcrip 89.5 0.81 1.7E-05 37.5 5.3 41 48-89 138-178 (196)
452 cd00569 HTH_Hin_like Helix-tur 89.4 1.3 2.8E-05 25.7 4.9 41 102-154 2-42 (42)
453 PRK10188 DNA-binding transcrip 89.4 0.7 1.5E-05 41.7 5.2 41 47-88 179-219 (240)
454 COG1846 MarR Transcriptional r 89.4 2.1 4.6E-05 32.5 7.3 71 48-118 20-94 (126)
455 PRK07500 rpoH2 RNA polymerase 89.4 0.81 1.8E-05 42.4 5.8 41 48-88 228-270 (289)
456 PRK11753 DNA-binding transcrip 89.4 0.44 9.5E-06 40.5 3.7 31 64-94 169-199 (211)
457 PRK11388 DNA-binding transcrip 89.3 0.48 1E-05 48.2 4.6 41 48-88 588-629 (638)
458 COG3413 Predicted DNA binding 89.2 1.1 2.3E-05 39.6 6.2 42 47-88 155-203 (215)
459 PRK11013 DNA-binding transcrip 89.2 1.7 3.6E-05 39.4 7.6 57 54-113 9-67 (309)
460 smart00550 Zalpha Z-DNA-bindin 89.1 1.1 2.3E-05 33.0 5.2 45 108-162 5-51 (68)
461 COG2973 TrpR Trp operon repres 89.0 1.2 2.6E-05 35.9 5.7 31 52-82 48-79 (103)
462 PRK15185 transcriptional regul 89.0 2.4 5.3E-05 40.3 8.7 87 52-160 207-298 (309)
463 PRK15424 propionate catabolism 88.9 0.73 1.6E-05 46.8 5.4 39 50-88 496-535 (538)
464 COG1342 Predicted DNA-binding 88.8 1.1 2.3E-05 36.1 5.2 42 47-88 33-74 (99)
465 TIGR01884 cas_HTH CRISPR locus 88.8 0.98 2.1E-05 39.5 5.6 42 53-94 145-188 (203)
466 PRK05657 RNA polymerase sigma 88.8 0.84 1.8E-05 43.1 5.6 42 47-88 262-307 (325)
467 PRK10423 transcriptional repre 88.8 0.74 1.6E-05 41.4 5.0 19 67-85 2-20 (327)
468 PF14549 P22_Cro: DNA-binding 88.7 0.43 9.3E-06 34.8 2.8 19 65-83 11-29 (60)
469 PRK11161 fumarate/nitrate redu 88.7 0.54 1.2E-05 40.9 3.9 33 64-96 185-217 (235)
470 PRK11169 leucine-responsive tr 88.7 0.69 1.5E-05 39.2 4.4 47 106-162 11-57 (164)
471 PF04645 DUF603: Protein of un 88.6 0.71 1.5E-05 40.6 4.4 37 56-92 11-48 (181)
472 COG3311 AlpA Predicted transcr 88.6 1 2.2E-05 34.1 4.7 23 65-87 15-37 (70)
473 smart00352 POU Found in Pit-Oc 88.4 1.3 2.8E-05 34.0 5.2 34 52-85 12-52 (75)
474 PRK13870 transcriptional regul 88.4 0.88 1.9E-05 40.9 5.2 41 47-88 173-213 (234)
475 TIGR00498 lexA SOS regulatory 88.4 0.87 1.9E-05 39.3 5.0 45 51-95 6-58 (199)
476 PRK10870 transcriptional repre 88.4 1.6 3.5E-05 37.5 6.6 56 63-118 71-129 (176)
477 PRK13777 transcriptional regul 88.3 2.7 5.9E-05 37.0 8.1 57 62-118 58-117 (185)
478 PRK13500 transcriptional activ 88.3 3.6 7.7E-05 38.0 9.2 88 52-160 207-299 (312)
479 PF12833 HTH_18: Helix-turn-he 88.2 1.3 2.8E-05 32.4 5.1 72 69-160 1-73 (81)
480 PRK13890 conjugal transfer pro 88.1 0.9 1.9E-05 37.1 4.6 36 50-85 4-40 (120)
481 PF01726 LexA_DNA_bind: LexA D 88.1 2.2 4.7E-05 31.4 6.2 33 62-94 22-57 (65)
482 PRK10923 glnG nitrogen regulat 88.1 0.88 1.9E-05 44.0 5.3 38 50-87 428-466 (469)
483 PRK04424 fatty acid biosynthes 88.0 0.79 1.7E-05 39.9 4.5 45 49-93 5-51 (185)
484 COG1609 PurR Transcriptional r 87.9 0.89 1.9E-05 42.6 5.1 40 65-120 2-41 (333)
485 TIGR01818 ntrC nitrogen regula 87.9 0.84 1.8E-05 43.9 5.0 38 50-87 425-463 (463)
486 PF00376 MerR: MerR family reg 87.9 0.56 1.2E-05 31.0 2.6 25 65-93 1-25 (38)
487 PRK11886 bifunctional biotin-- 87.8 1.1 2.3E-05 41.9 5.5 39 54-92 7-47 (319)
488 PRK15121 right oriC-binding tr 87.8 4 8.7E-05 37.2 9.2 86 54-160 8-98 (289)
489 COG4565 CitB Response regulato 87.8 1.9 4E-05 39.4 6.7 49 46-94 153-204 (224)
490 PF09862 DUF2089: Protein of u 87.8 7.3 0.00016 32.0 9.6 80 47-133 33-112 (113)
491 PRK10402 DNA-binding transcrip 87.8 1.1 2.4E-05 39.2 5.3 32 64-95 170-201 (226)
492 COG2739 Uncharacterized protei 87.7 1.1 2.4E-05 36.3 4.8 36 53-88 22-58 (105)
493 PRK15186 AraC family transcrip 87.6 2.8 6E-05 39.2 8.1 84 56-160 190-273 (291)
494 COG5352 Uncharacterized protei 87.6 0.69 1.5E-05 39.7 3.7 42 51-92 5-48 (169)
495 PRK11139 DNA-binding transcrip 87.6 2.8 6.1E-05 37.5 7.9 57 53-112 10-68 (297)
496 TIGR02424 TF_pcaQ pca operon t 87.5 2.1 4.5E-05 38.2 7.0 58 54-114 8-67 (300)
497 COG1961 PinR Site-specific rec 87.5 0.89 1.9E-05 40.0 4.5 47 46-92 159-206 (222)
498 PRK14165 winged helix-turn-hel 87.4 1 2.2E-05 40.7 5.0 55 63-117 21-75 (217)
499 PRK09802 DNA-binding transcrip 87.4 1.1 2.4E-05 41.1 5.3 45 50-94 16-62 (269)
500 COG1414 IclR Transcriptional r 87.4 1.3 2.9E-05 40.1 5.8 44 54-97 7-53 (246)
No 1
>KOG3517|consensus
Probab=100.00 E-value=1.6e-45 Score=331.36 Aligned_cols=194 Identities=70% Similarity=1.093 Sum_probs=179.4
Q ss_pred CCCCcchhhccCCcccCCCCCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCC
Q psy15598 28 SGQQYGEVNQLGGVFVNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTT 107 (258)
Q Consensus 28 ~~~~~~~~nq~~~~~~~gR~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT 107 (258)
|+++|||||||||||||||++++++|.|||+|.+.|...|+|+|+|.||..||+||+.||.|+|++.|+.++|++||++|
T Consensus 1 ~~~~~GEVNQLGGVFVNGRPLPna~RlrIVELarlGiRPCDISRQLrvSHGCVSKILaRy~EtGsIlPGaIGGSkPRVTT 80 (334)
T KOG3517|consen 1 MEPSYGEVNQLGGVFVNGRPLPNAIRLRIVELARLGIRPCDISRQLRVSHGCVSKILARYNETGSILPGAIGGSKPRVTT 80 (334)
T ss_pred CCccccchhhccceeEcCccCcchhhhhHHHHHHcCCCccchhhhhhhccchHHHHHHHhccCCcccccccCCCCCccCC
Confidence 68899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCCCCCCCCCCC---------CCCCCCCCC
Q psy15598 108 PKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSSIVQHHHHP---------HIYNSIYPS 178 (258)
Q Consensus 108 ~e~~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~~~~~~~~~~---------~~~~~~~~~ 178 (258)
+.++++|+.+++.+|.+++|||+|+|+++|+|++++++|+|+|+|+||++.+.+-+++.|+. +.||.+|.
T Consensus 81 P~VV~~IR~~Kq~DPGIFAWEIRDRLlsdgiCDk~NvPSVSSISRILRNKiGsLaqqg~y~t~kqp~~qpslpyN~~~~- 159 (334)
T KOG3517|consen 81 PKVVKYIRSLKQRDPGIFAWEIRDRLLSDGICDKYNVPSVSSISRILRNKIGSLAQQGTYGTVKQPSGQPSLPYNGGYS- 159 (334)
T ss_pred hhHHHHHHHhhccCCceeeehhhhhhhhcccccccCCcchHHHHHHHHhhhcccccCCCcccccCCCCCCCccCCCCcc-
Confidence 99999999999999999999999999999999999999999999999999999999998874 78999875
Q ss_pred CCCCCCCCCCccCCCCCCCCCCCCC----CCCCCCCCCcchhhhhhccCC
Q psy15598 179 YPYPSNTSPTVSCTKVPIGSLTPPP----RPQVCWPSSHSVTDILSAAAG 224 (258)
Q Consensus 179 ~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~ 224 (258)
|+++.+... ...+++.++++|.. ..+.+||++|||++|||+++=
T Consensus 160 ~~~ss~~~~--~~a~~~~~~g~p~~~~h~~~~qswpsahSv~~ilgir~~ 207 (334)
T KOG3517|consen 160 YPSSSSQNI--NLAKIGDPPGVPQQPGHVQQHQSWPSAHSVHHILGIRAY 207 (334)
T ss_pred CCCCCccch--hhhhcCCCCCCCCCccccccccccccccchhhhhHHHHH
Confidence 666554443 37788888887764 678999999999999997653
No 2
>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=100.00 E-value=6.5e-35 Score=240.02 Aligned_cols=125 Identities=76% Similarity=1.261 Sum_probs=100.0
Q ss_pred CcchhhccCCcccCCCCCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHH
Q psy15598 31 QYGEVNQLGGVFVNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKV 110 (258)
Q Consensus 31 ~~~~~nq~~~~~~~gR~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~ 110 (258)
++++||||||+|+|||+|+.++|.+||+|+++|++.++||++|.||++||+||++||+|||++.|+..+|++|++.++++
T Consensus 1 g~~~~NqlGg~~~nGrPLp~~~R~rIvela~~G~rp~~Isr~l~Vs~gcVsKIl~Ry~eTGsi~Pg~iGGskprv~tp~v 80 (125)
T PF00292_consen 1 GQGRVNQLGGVFINGRPLPNELRQRIVELAKEGVRPCDISRQLRVSHGCVSKILSRYRETGSIRPGPIGGSKPRVATPEV 80 (125)
T ss_dssp S-EEE-TTS-EEETTSSS-HHHHHHHHHHHHTT--HHHHHHHHT--HHHHHHHHHHHHHHS-SS----S----SSS-HCH
T ss_pred CCccccccCceeeCCccCcHHHHHHHHHHhhhcCCHHHHHHHHccchhHHHHHHHHHHHhcccCcccccCCCCCCCChHH
Confidence 35889999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHH
Q psy15598 111 VSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILR 155 (258)
Q Consensus 111 ~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLr 155 (258)
+.+|.+++.+||.+++|||+++|.++|+|..+++||.|+|+|+||
T Consensus 81 ~~~I~~~k~enP~ifawEiR~~L~~~gvc~~~~~PsvssInRilr 125 (125)
T PF00292_consen 81 VEKIEQYKRENPTIFAWEIRDRLIADGVCDRSNVPSVSSINRILR 125 (125)
T ss_dssp HHHHHHHHHH-TTS-HHHHHHHHHHTTSS-TTTS--HHHHHHHHH
T ss_pred HHHHHHHHhcCCCcchHHHHHHHHHcCCCCCCCCCCHHHHHHhhC
Confidence 999999999999999999999999999999999999999999997
No 3
>cd00131 PAX Paired Box domain
Probab=99.97 E-value=3.7e-31 Score=217.98 Aligned_cols=125 Identities=82% Similarity=1.295 Sum_probs=118.9
Q ss_pred chhhccCCcccCCCCCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHH
Q psy15598 33 GEVNQLGGVFVNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVS 112 (258)
Q Consensus 33 ~~~nq~~~~~~~gR~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~ 112 (258)
+++||+||+|+|+++||.|+|.+||+++++|++.++||++|+||++||++|+++|+++|++.|++++|.+|++++++.+.
T Consensus 3 ~~~~~~~~~~~m~~~lS~d~R~rIv~~~~~G~s~~~iA~~~~Vs~~tV~r~i~r~~e~G~v~pk~~gg~rpr~~~~~~~~ 82 (128)
T cd00131 3 GGVNQLGGVFVNGRPLPDSIRQRIVELAQSGIRPCDISRQLRVSHGCVSKILNRYYETGSIRPGAIGGSKPRVATPEVVK 82 (128)
T ss_pred ccccCCCccccCCCcCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCCCCCCCCCCcCCHHHHH
Confidence 57999999999999999999999999999999999999999999999999999999999999999888678988998889
Q ss_pred HHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhc
Q psy15598 113 YIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNK 157 (258)
Q Consensus 113 ~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~ 157 (258)
+|+++++++|++|++||++.|.+.|++++.+.||.|||+|+|+++
T Consensus 83 ~i~~~v~~~p~~Tl~El~~~L~~~gv~~~~~~~s~stI~R~L~~~ 127 (128)
T cd00131 83 KIEIYKQENPGMFAWEIRDRLLQEGVCDKSNVPSVSSINRILRNK 127 (128)
T ss_pred HHHHHHHHCCCCCHHHHHHHHHHcCCcccCCCCCHHHHHHHHHhc
Confidence 999999999999999999999888998888889999999999975
No 4
>smart00351 PAX Paired Box domain.
Probab=99.96 E-value=3.6e-29 Score=204.97 Aligned_cols=124 Identities=81% Similarity=1.256 Sum_probs=118.5
Q ss_pred cchhhccCCcccCCCCCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHH
Q psy15598 32 YGEVNQLGGVFVNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVV 111 (258)
Q Consensus 32 ~~~~nq~~~~~~~gR~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~ 111 (258)
..++||+||.|+|+++||.|+|.+||.++++|++.++||++||||++||++|+++|+++|.+.|++++|.+|+++++++.
T Consensus 2 ~~~~~~~~~~~~~~~~~s~~~R~riv~~~~~G~s~~~iA~~~gvs~~tV~kwi~r~~~~G~~~pk~~gg~rp~~~~~~~~ 81 (125)
T smart00351 2 HGGVNQLGGVFVNGRPLPDEERQRIVELAQNGVRPCDISRQLCVSHGCVSKILGRYYETGSIRPGAIGGSKPKVATPKVV 81 (125)
T ss_pred CCccccCCCeecCCCCCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCcCCCCCCCCccCHHHH
Confidence 46799999999999999999999999999999999999999999999999999999999999999888778999999999
Q ss_pred HHHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHH
Q psy15598 112 SYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILR 155 (258)
Q Consensus 112 ~~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLr 155 (258)
.+|+++++++|+++++||++.|.+.|+++..+.||.|||+|+|+
T Consensus 82 ~~I~~~~~~~p~~t~~el~~~L~~~gv~~~~~~Ps~sti~~~l~ 125 (125)
T smart00351 82 KKIADYKQENPGIFAWEIRDRLLSEGVCDKDNVPSVSSINRILR 125 (125)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHHHcCCCcCCCCCChhhHHHhhC
Confidence 99999999999999999999999999998899999999999985
No 5
>KOG3862|consensus
Probab=99.96 E-value=6.1e-29 Score=225.98 Aligned_cols=179 Identities=58% Similarity=0.879 Sum_probs=156.5
Q ss_pred CCcchhhccCCcccCCCCCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHH
Q psy15598 30 QQYGEVNQLGGVFVNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPK 109 (258)
Q Consensus 30 ~~~~~~nq~~~~~~~gR~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e 109 (258)
-++++||||||||||||+++..+|.+|++|+++|...++|+++|.||..||++++-||.|+|+++++..+|++|++.++.
T Consensus 8 ~ghgGvNQLGGvFVNGRPlpd~Vr~rIv~La~~gvrpcdisrQl~vShGcvSkil~r~yEtgS~~pg~iggsk~KvAtp~ 87 (327)
T KOG3862|consen 8 SGHGGVNQLGGVFVNGRPLPDVVRQRIVELAQNGVRPCDISRQLRVSHGCVSKILGRYYETGSIRPGVIGGSKPKVATPK 87 (327)
T ss_pred CCccchhhccceeecCccCchHHHHHHHHHHHcCCcchhHHHHHhhccCCchhHHHHHHHhcCcccCCCCCCccccccch
Confidence 37899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCc
Q psy15598 110 VVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSSIVQHHHHPHIYNSIYPSYPYPSNTSPTV 189 (258)
Q Consensus 110 ~~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 189 (258)
+++.|..++++||.+++||||++|.++++|..++++|++.|+|++|++...+.....+... ......
T Consensus 88 Vvk~i~~~k~~n~~mfaweiR~~l~~~~ic~~d~vpsVssinri~r~~~~~~~~~~~~s~v-------------sk~l~~ 154 (327)
T KOG3862|consen 88 VVKKIALYKRQNPTMFAWEIRDRLLAEPICDNDTVPSVSSINRIIRTKVQQKQLGITHSCV-------------TKVLAR 154 (327)
T ss_pred HHHHHHHHhhcCcchhhhhhhhhhhcccccCCCCCchHHHHHHHHHHhhhhcccCCccchh-------------hccccC
Confidence 9999999999999999999999999999999999999999999999988876554443310 112223
Q ss_pred cCCCCCCCCCCCCCCCCCCCCCCcchhhhhhc
Q psy15598 190 SCTKVPIGSLTPPPRPQVCWPSSHSVTDILSA 221 (258)
Q Consensus 190 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 221 (258)
+++.+++....|+.+....-+.++||+.||++
T Consensus 155 ~h~a~~s~~~~P~~~~~~~s~~~~Si~~~~~~ 186 (327)
T KOG3862|consen 155 GHTAVPSSASPPPSSVQSDSVGSYSINGLLGI 186 (327)
T ss_pred cccccccCCCCCCCCcccCCCCceeecccccc
Confidence 35556666656666777777778999999884
No 6
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=99.71 E-value=1.4e-16 Score=133.63 Aligned_cols=115 Identities=23% Similarity=0.275 Sum_probs=101.0
Q ss_pred CCCCCCHHHHHHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHhCC
Q psy15598 44 NGRPLPNSVRMRIVELA-QLGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQKDP 122 (258)
Q Consensus 44 ~gR~~S~dlR~RIV~L~-~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~nP 122 (258)
|.++++.++|.+++.++ .+|+|+++||++||||.+||++|++||+++|.+.+...+++||+++++++...|++.+++..
T Consensus 1 ~~k~~s~~~R~~~~~~~~~~G~S~re~Ak~~gvs~sTvy~wv~r~~e~G~~l~~~~~~GrP~kl~~~q~~~l~e~~~~k~ 80 (138)
T COG3415 1 MAKPFSNDLRERVVDAVVGEGLSCREAAKRFGVSISTVYRWVRRYRETGLDLPPKPRKGRPRKLSEEQLEILLERLREKD 80 (138)
T ss_pred CCchhhHHHHHHHHHHHHHcCccHHHHHHHhCccHHHHHHHHHHhccccccccCccCCCCCcccCHHHHHHHHHHHhccc
Confidence 56889999999999998 58999999999999999999999999999998755444444999999999999999988764
Q ss_pred CCCHHHHHHHHH-hcCCCCCCCCCCHHHHHHHHHhccCCCCCC
Q psy15598 123 GIFAWEIRDRLL-SDGVCDKFNVPSVSSISRILRNKIGSSIVQ 164 (258)
Q Consensus 123 ~ita~EIr~~L~-~~Gv~v~~~~pS~STI~RiLrr~~~~~~~~ 164 (258)
+++.+++..|. +.|+.. +.++|+++|++.+..--++
T Consensus 81 -wTl~~~~~~l~~e~gv~y-----~~~~v~~~l~~~GlsykK~ 117 (138)
T COG3415 81 -WTLKELVEELGLEFGVWY-----HASAVRRLLHELGLSYKKP 117 (138)
T ss_pred -chHHHHHHHHhhhcCeEE-----eHHHHHHHHHHcCCCcCCC
Confidence 99999999987 689986 9999999999998875544
No 7
>KOG0849|consensus
Probab=99.69 E-value=1.2e-17 Score=158.32 Aligned_cols=131 Identities=64% Similarity=1.082 Sum_probs=125.4
Q ss_pred chhhccCCcccCCCCCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCC-CCCHHHH
Q psy15598 33 GEVNQLGGVFVNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPR-VTTPKVV 111 (258)
Q Consensus 33 ~~~nq~~~~~~~gR~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPr-klT~e~~ 111 (258)
+++||+||+|+++++++.+.|..|+++...|.+.+.|+++|.||+.||.++++||.++|++.|+..+|++|+ +.+++++
T Consensus 1 ~~~n~~~~~f~~~~~~~~~~r~~~~~~a~~~~~~~~~~~~l~vs~~~~~~il~r~~~~~~i~p~~i~~~~~~~~~t~~~~ 80 (354)
T KOG0849|consen 1 GRVNQLGGVFINGRPLPNHTRQKIVEMAHKGIRPCVISRQLKVSHGCVSKILNRYYRTGSIRPGGIGGSKPRIVATPEVE 80 (354)
T ss_pred CCcccCCcccccCCCCCCchhhccccccccccCcccchhhhhhhhHHHHhhhcccccccccccccccccccCCCCCchhH
Confidence 479999999999999999999999999999999999999999999999999999999999999999988888 7779999
Q ss_pred HHHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCCCCC
Q psy15598 112 SYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSSIV 163 (258)
Q Consensus 112 ~~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~~~~ 163 (258)
.+|..++.++|.+++|||++.|...++|+.++.+|.++|+|.|++....+.+
T Consensus 81 ~~i~~~k~~~P~~~~~~ir~~l~~~~~~~~~t~Ps~ssi~r~~r~~~~~~d~ 132 (354)
T KOG0849|consen 81 AKIEQYKRENPAMFAWEIRDQLLHEGLCTQATLPSVSSINRVLRNGALGKDQ 132 (354)
T ss_pred HHHHHHHhcCCcccchhhhhcccCcccccCCCCCChhhhhHHhhcccccccc
Confidence 9999999999999999999999999999999999999999999988888776
No 8
>PF13551 HTH_29: Winged helix-turn helix
Probab=99.69 E-value=2.8e-16 Score=122.40 Aligned_cols=100 Identities=32% Similarity=0.449 Sum_probs=86.6
Q ss_pred HHHHHHHHHcCCC-HHHHHHHhCCCHHHHHHHHHHhhhhC--Cccc-CCCCCCCCCC-CCHHHHHHHHHHHHhCC-----
Q psy15598 53 RMRIVELAQLGIR-PCDISRQLRVSHGCVSKILARYHETG--SILP-GAIGGSKPRV-TTPKVVSYIKELKQKDP----- 122 (258)
Q Consensus 53 R~RIV~L~~~G~S-~~eIAr~LGVSrsTVsRwikRyrEtG--sl~p-k~rgG~RPrk-lT~e~~~~I~~lv~~nP----- 122 (258)
|.+||.++.+|++ ..+||+.||||++||++|+++|+++| .+.+ ++++| +|+. +++++.+.|++++.++|
T Consensus 1 R~~~l~l~~~g~~~~~~ia~~lg~s~~Tv~r~~~~~~~~G~~~l~~~~~~~g-~~~~~l~~~~~~~l~~~~~~~p~~g~~ 79 (112)
T PF13551_consen 1 RAQILLLLAEGVSTIAEIARRLGISRRTVYRWLKRYREGGIEGLLPRKPRGG-RPRKRLSEEQRAQLIELLRENPPEGRS 79 (112)
T ss_pred CHHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHcccHHHHHhccccCC-CCCCCCCHHHHHHHHHHHHHCCCCCCC
Confidence 6789999999995 99999999999999999999999999 4556 45555 6766 89999999999999988
Q ss_pred CCCHHHHHHHH-H-hcCCCCCCCCCCHHHHHHHHHhcc
Q psy15598 123 GIFAWEIRDRL-L-SDGVCDKFNVPSVSSISRILRNKI 158 (258)
Q Consensus 123 ~ita~EIr~~L-~-~~Gv~v~~~~pS~STI~RiLrr~~ 158 (258)
.++..+|++.| . ..|+.+ |.+||+|+|+++|
T Consensus 80 ~~t~~~l~~~l~~~~~~~~~-----s~~ti~r~L~~~G 112 (112)
T PF13551_consen 80 RWTLEELAEWLIEEEFGIDV-----SPSTIRRILKRAG 112 (112)
T ss_pred cccHHHHHHHHHHhccCccC-----CHHHHHHHHHHCc
Confidence 57899999987 4 357765 9999999999875
No 9
>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=99.67 E-value=4.7e-16 Score=126.22 Aligned_cols=103 Identities=24% Similarity=0.291 Sum_probs=89.7
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCH
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFA 126 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~nP~ita 126 (258)
.||.|+|.+||..++.|.+.++||+.|+||++||++|++ ..++|++.++++++ + ++. .+.|.+++.++|++++
T Consensus 2 aYS~DlR~rVl~~~~~g~s~~eaa~~F~VS~~Tv~~W~k-~~~~G~~~~k~r~~-~--Kid---~~~L~~~v~~~pd~tl 74 (119)
T PF01710_consen 2 AYSLDLRQRVLAYIEKGKSIREAAKRFGVSRNTVYRWLK-RKETGDLEPKPRGR-K--KID---RDELKALVEENPDATL 74 (119)
T ss_pred CCCHHHHHHHHHHHHccchHHHHHHHhCcHHHHHHHHHH-hccccccccccccc-c--ccc---HHHHHHHHHHCCCcCH
Confidence 489999999999999999999999999999999999999 66799998887665 2 553 4568899999999999
Q ss_pred HHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCCCCCCCC
Q psy15598 127 WEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSSIVQHH 166 (258)
Q Consensus 127 ~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~~~~~~~ 166 (258)
.||+..| | ||.+||+++|++.+..+-+...
T Consensus 75 ~Ela~~l---~-------Vs~~ti~~~Lkrlg~t~KK~~~ 104 (119)
T PF01710_consen 75 RELAERL---G-------VSPSTIWRALKRLGITRKKKTL 104 (119)
T ss_pred HHHHHHc---C-------CCHHHHHHHHHHcCchhccCcc
Confidence 9998776 3 3999999999999998766553
No 10
>PF13565 HTH_32: Homeodomain-like domain
Probab=99.21 E-value=5.9e-11 Score=87.90 Aligned_cols=71 Identities=31% Similarity=0.362 Sum_probs=59.5
Q ss_pred HHHHHHHHhhhhC-----CcccCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHh-cCCCCCCCCCCHHHHHH
Q psy15598 79 CVSKILARYHETG-----SILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLS-DGVCDKFNVPSVSSISR 152 (258)
Q Consensus 79 TVsRwikRyrEtG-----sl~pk~rgG~RPrklT~e~~~~I~~lv~~nP~ita~EIr~~L~~-~Gv~v~~~~pS~STI~R 152 (258)
||++|+++|++.| +..+++++| +|++ ++++++.|++++.++|.++..+|++.|.+ .|+.+ .||.+||+|
T Consensus 1 Tv~rw~~ry~~~G~~gL~~~~~~~~~G-rp~~-~~e~~~~i~~~~~~~p~wt~~~i~~~L~~~~g~~~---~~S~~tv~R 75 (77)
T PF13565_consen 1 TVYRWLKRYREEGLEGLKDRKRRPRPG-RPRK-DPEQRERIIALIEEHPRWTPREIAEYLEEEFGISV---RVSRSTVYR 75 (77)
T ss_pred CHHHHHHHHHhhCchhhhcccccCCCC-CCCC-cHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCC---CccHhHHHH
Confidence 8999999999999 333445566 7777 88888999999999999999999999985 57642 369999999
Q ss_pred HH
Q psy15598 153 IL 154 (258)
Q Consensus 153 iL 154 (258)
+|
T Consensus 76 ~L 77 (77)
T PF13565_consen 76 IL 77 (77)
T ss_pred hC
Confidence 87
No 11
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=99.03 E-value=2.4e-09 Score=83.32 Aligned_cols=80 Identities=30% Similarity=0.390 Sum_probs=63.7
Q ss_pred hhccCCcccCCCCCCHHHHHHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCC--cccCC-CCCCCCCCCCHHH
Q psy15598 35 VNQLGGVFVNGRPLPNSVRMRIVELA-QLGIRPCDISRQLRVSHGCVSKILARYHETGS--ILPGA-IGGSKPRVTTPKV 110 (258)
Q Consensus 35 ~nq~~~~~~~gR~~S~dlR~RIV~L~-~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGs--l~pk~-rgG~RPrklT~e~ 110 (258)
||.+ .|.+ |+..-|.++|.++ ++|.+.+++|+.||||+.|++||++||++.|. +.++. ++.+.|..+.++.
T Consensus 1 Mn~H----~nA~-Lt~~gR~~lv~~vv~~g~~~a~aA~~~gVS~~Ta~kW~~Ryra~G~~GL~DRSSRP~~sP~~t~~~~ 75 (85)
T PF13011_consen 1 MNSH----KNAR-LTPRGRLRLVRRVVEQGWPVAHAAAEFGVSRRTAYKWLARYRAEGEAGLQDRSSRPHRSPRRTPPEV 75 (85)
T ss_pred CCCC----CCCC-CCHHHHHHHHHHHHHcCCcHHHHHHHhCCCHHHHHHHHHHHHHcCcccccccCCCCCCCCccCCHHH
Confidence 4666 4444 9999999999987 67999999999999999999999999999985 33333 2334567788888
Q ss_pred HHHHHHHHH
Q psy15598 111 VSYIKELKQ 119 (258)
Q Consensus 111 ~~~I~~lv~ 119 (258)
++.|+++.+
T Consensus 76 ~~~I~~lRr 84 (85)
T PF13011_consen 76 ERRIIELRR 84 (85)
T ss_pred HHHHHHHhc
Confidence 888887753
No 12
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=98.97 E-value=4.7e-10 Score=77.06 Aligned_cols=44 Identities=30% Similarity=0.462 Sum_probs=26.7
Q ss_pred CHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCC
Q psy15598 49 PNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETGS 92 (258)
Q Consensus 49 S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGs 92 (258)
+.+.|..||.++.+|++.++||+.||||++||++|+++|++.|.
T Consensus 3 ~~~~R~~ii~l~~~G~s~~~ia~~lgvs~~Tv~~w~kr~~~~G~ 46 (50)
T PF13384_consen 3 SEERRAQIIRLLREGWSIREIAKRLGVSRSTVYRWIKRYREEGL 46 (50)
T ss_dssp -------HHHHHHHT--HHHHHHHHTS-HHHHHHHHT-------
T ss_pred chhHHHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHHHcccccc
Confidence 56789999999999999999999999999999999999998883
No 13
>PF13518 HTH_28: Helix-turn-helix domain
Probab=98.88 E-value=3.4e-09 Score=72.71 Aligned_cols=41 Identities=34% Similarity=0.516 Sum_probs=38.6
Q ss_pred HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCC
Q psy15598 52 VRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETGS 92 (258)
Q Consensus 52 lR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGs 92 (258)
+|.+||+++.+|.|..+||++||||++||++|+++|++.|.
T Consensus 1 ~r~~iv~~~~~g~s~~~~a~~~gis~~tv~~w~~~y~~~G~ 41 (52)
T PF13518_consen 1 FRLQIVELYLEGESVREIAREFGISRSTVYRWIKRYREGGI 41 (52)
T ss_pred CHHHHHHHHHcCCCHHHHHHHHCCCHhHHHHHHHHHHhcCH
Confidence 37889999999999999999999999999999999999884
No 14
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=98.53 E-value=8.3e-08 Score=65.49 Aligned_cols=42 Identities=29% Similarity=0.333 Sum_probs=26.3
Q ss_pred CCCCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHH
Q psy15598 45 GRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILAR 86 (258)
Q Consensus 45 gR~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikR 86 (258)
.+.++.+.|..|..++++|+|.++||+.||+|++||+++++|
T Consensus 2 ~~~Lt~~eR~~I~~l~~~G~s~~~IA~~lg~s~sTV~relkR 43 (44)
T PF13936_consen 2 YKHLTPEERNQIEALLEQGMSIREIAKRLGRSRSTVSRELKR 43 (44)
T ss_dssp ----------HHHHHHCS---HHHHHHHTT--HHHHHHHHHH
T ss_pred ccchhhhHHHHHHHHHHcCCCHHHHHHHHCcCcHHHHHHHhc
Confidence 457899999999999999999999999999999999999987
No 15
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=98.44 E-value=1.6e-06 Score=70.58 Aligned_cols=49 Identities=18% Similarity=0.198 Sum_probs=44.1
Q ss_pred CCCCCHHHHHHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCc
Q psy15598 45 GRPLPNSVRMRIVELA-QLGIRPCDISRQLRVSHGCVSKILARYHETGSI 93 (258)
Q Consensus 45 gR~~S~dlR~RIV~L~-~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl 93 (258)
.+.||.+++..||..+ +.|.++++||+.||||.+||++|+++|++.|..
T Consensus 10 rr~ys~EfK~~aV~~~~~~g~sv~evA~e~gIs~~tl~~W~r~y~~~~~~ 59 (121)
T PRK09413 10 RRRRTTQEKIAIVQQSFEPGMTVSLVARQHGVAASQLFLWRKQYQEGSLT 59 (121)
T ss_pred CCCCCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHhhcccc
Confidence 4779999999999975 579999999999999999999999999987653
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=98.42 E-value=1.7e-07 Score=63.98 Aligned_cols=41 Identities=27% Similarity=0.327 Sum_probs=33.8
Q ss_pred CCCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHH
Q psy15598 46 RPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILAR 86 (258)
Q Consensus 46 R~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikR 86 (258)
+.++.+....|++|+.+|++..+||++||||++||||+++.
T Consensus 4 ~~~~~~~~~~i~~l~~~G~si~~IA~~~gvsr~TvyR~l~~ 44 (45)
T PF02796_consen 4 PKLSKEQIEEIKELYAEGMSIAEIAKQFGVSRSTVYRYLNK 44 (45)
T ss_dssp SSSSHCCHHHHHHHHHTT--HHHHHHHTTS-HHHHHHHHCC
T ss_pred CCCCHHHHHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 34777778999999999999999999999999999999863
No 17
>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=98.40 E-value=5.1e-07 Score=66.45 Aligned_cols=46 Identities=13% Similarity=0.224 Sum_probs=38.2
Q ss_pred cCCCCCCHHHHHHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 43 VNGRPLPNSVRMRIVELA-QLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 43 ~~gR~~S~dlR~RIV~L~-~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
...+.||.++|.+||..+ ..|.++.+||+.+||+.+|+++|++.|.
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLESGESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp -SS----HHHHHHHHHHHHHHHCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHCCCceEeeecccccccccccHHHHHHh
Confidence 455789999999999998 7899999999999999999999999998
No 18
>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=98.14 E-value=3.6e-06 Score=59.65 Aligned_cols=43 Identities=28% Similarity=0.365 Sum_probs=35.3
Q ss_pred CCCCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHh
Q psy15598 45 GRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARY 87 (258)
Q Consensus 45 gR~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRy 87 (258)
-+.|+.+.+..||.++++|.+.++||+.|||+++||+.|++.-
T Consensus 4 R~~LTl~eK~~iI~~~e~g~s~~~ia~~fgv~~sTv~~I~K~k 46 (53)
T PF04218_consen 4 RKSLTLEEKLEIIKRLEEGESKRDIAREFGVSRSTVSTILKNK 46 (53)
T ss_dssp SSS--HHHHHHHHHHHHCTT-HHHHHHHHT--CCHHHHHHHCH
T ss_pred CccCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHhH
Confidence 3569999999999999999999999999999999999999874
No 19
>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=98.06 E-value=6.5e-06 Score=59.65 Aligned_cols=40 Identities=23% Similarity=0.205 Sum_probs=36.9
Q ss_pred HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhh
Q psy15598 51 SVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHET 90 (258)
Q Consensus 51 dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEt 90 (258)
|.|.++..|+-+|+++++||+.|||+++||+.|.+++.-.
T Consensus 1 e~k~~A~~LY~~G~~~~eIA~~Lg~~~~TV~~W~~r~~W~ 40 (58)
T PF06056_consen 1 EVKEQARSLYLQGWSIKEIAEELGVPRSTVYSWKDRYKWD 40 (58)
T ss_pred CHHHHHHHHHHcCCCHHHHHHHHCCChHHHHHHHHhhCcc
Confidence 4688999999999999999999999999999999999744
No 20
>COG2826 Tra8 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]
Probab=97.96 E-value=4.9e-05 Score=71.40 Aligned_cols=109 Identities=18% Similarity=0.115 Sum_probs=85.7
Q ss_pred CCCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCC---------cccCCCCCCCCCCCCHHHHHHHHH
Q psy15598 46 RPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETGS---------ILPGAIGGSKPRVTTPKVVSYIKE 116 (258)
Q Consensus 46 R~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGs---------l~pk~rgG~RPrklT~e~~~~I~~ 116 (258)
..++.+.|.+|-.+.+.|+|.++||++||..++||+|=++|-...+. +.-..++..++-.++++..+.|.+
T Consensus 6 ~hLT~~eR~~I~~l~~~~~S~reIA~~LgRh~sTIsRElkRn~~~~~Y~a~~A~~~~~~~rrr~~~k~~~~~eL~~~V~e 85 (318)
T COG2826 6 KHLTLFERYEIERLLKAKMSIREIAKQLNRHHSTISRELKRNRTRDIYSAVKAQERYRMLRRRRIRKLKLNPELRELVLE 85 (318)
T ss_pred hhCCHHHHHHHHHHHHcCCCHHHHHHHhCCCcchhhHHHhcCCccceeeHHHHHHHHHHhhcccCCcccCCHHHHHHHHH
Confidence 37999999999999999999999999999999999999888543331 111111212456688999999999
Q ss_pred HHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCCCCC
Q psy15598 117 LKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSSIV 163 (258)
Q Consensus 117 lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~~~~ 163 (258)
.+++ .++..+|...|.... +|.+||+|+|.-...+...
T Consensus 86 ~L~~--~wSPEQI~g~l~~~~-------i~~eTIYr~ly~~~~~a~~ 123 (318)
T COG2826 86 KLKS--KWSPEQIIGRLKKSK-------ISFETIYRWLYQGKSEALR 123 (318)
T ss_pred HHHh--hCCHHHHHHHHHhcc-------cCHHHHHHHHhhccchhhh
Confidence 9887 789999999998653 4899999999876666555
No 21
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=97.93 E-value=6.9e-05 Score=59.83 Aligned_cols=49 Identities=14% Similarity=0.222 Sum_probs=44.5
Q ss_pred CCCCCHHHHHHHHHHHH-cCCCHHHHHHHhCC-CHHHHHHHHHHhhhhCCc
Q psy15598 45 GRPLPNSVRMRIVELAQ-LGIRPCDISRQLRV-SHGCVSKILARYHETGSI 93 (258)
Q Consensus 45 gR~~S~dlR~RIV~L~~-~G~S~~eIAr~LGV-SrsTVsRwikRyrEtGsl 93 (258)
-+.||.++|.+||.++. .|.++++||+.||| +.+++++|++.|.+.+..
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~sv~~vAr~~gv~~~~~l~~W~~~~~~~~~~ 55 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGDTVSEVAREFGIVSATQLYKWRIQLQKGGGL 55 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCccHHHHHHHhCCCChHHHHHHHHHHHHcccc
Confidence 46799999999999986 68999999999995 999999999999987754
No 22
>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=97.93 E-value=2.9e-05 Score=46.79 Aligned_cols=39 Identities=23% Similarity=0.231 Sum_probs=35.2
Q ss_pred CCCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Q psy15598 46 RPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKIL 84 (258)
Q Consensus 46 R~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwi 84 (258)
+.++.+.+..|++++.+|.+..+||+.|+||++||++|+
T Consensus 4 ~~~~~~~~~~i~~~~~~~~s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 4 PKLTPEQIEEARRLLAAGESVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred CcCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHhC
Confidence 347788888999999999999999999999999999985
No 23
>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=97.70 E-value=0.00027 Score=50.88 Aligned_cols=66 Identities=17% Similarity=0.185 Sum_probs=45.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHH
Q psy15598 64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRL 133 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L 133 (258)
++..++|+.+||+.+|+++|.+++ |.+.+....+ ..+..++++...|..++. .+-.++..+|++.|
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---GLPAPQRTDG-GHRLYSEADVARLRLIRRLTSEGVRISQAAALA 67 (68)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHhC---CCCCCCcCCC-CCeecCHHHHHHHHHHHHHHHCCCCHHHHHHHh
Confidence 478899999999999999999765 4444333232 346777777666655543 22477888887655
No 24
>PRK09409 IS2 transposase TnpB; Reviewed
Probab=97.69 E-value=0.00021 Score=66.48 Aligned_cols=92 Identities=22% Similarity=0.200 Sum_probs=69.4
Q ss_pred HHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHhc-
Q psy15598 58 ELAQLGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSD- 136 (258)
Q Consensus 58 ~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~nP~ita~EIr~~L~~~- 136 (258)
.+...++++..+++.||||++|.|+|++++..- ..... .+..-..+....|.++..+++......|...|...
T Consensus 6 ~~~~~~~~v~~lC~~l~VsRs~yY~~~~r~~~~---~~~~~---~~~~~~~~l~~~I~~i~~~~~~yG~Rri~~~L~~~g 79 (301)
T PRK09409 6 ALIARGWGVSLVSRCLRVSRAQLHVILRRTDDW---MDGRR---SRHTDDTDVLLRIHHVIGELPTYGYRRVWALLRRQA 79 (301)
T ss_pred HHHhcCCcHHHHHHhcCcChHHhhhhccccccc---ccccc---ccCcchHHHHHHHHHHHHhCccCCHHHHHHHHHhhh
Confidence 456788999999999999999999999986421 11111 11222345677788887788889999999999865
Q ss_pred ---CC-CCCCCCCCHHHHHHHHHhccCC
Q psy15598 137 ---GV-CDKFNVPSVSSISRILRNKIGS 160 (258)
Q Consensus 137 ---Gv-~v~~~~pS~STI~RiLrr~~~~ 160 (258)
|+ . ++..+|.|+|++.+..
T Consensus 80 ~~~g~~~-----v~~k~V~RlMr~~Gl~ 102 (301)
T PRK09409 80 ELDGMPA-----INAKRVYRIMRQNALL 102 (301)
T ss_pred cccCccc-----cCHHHHHHHHHHcCCc
Confidence 54 3 4999999999998876
No 25
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=97.62 E-value=0.00022 Score=48.14 Aligned_cols=42 Identities=21% Similarity=0.294 Sum_probs=36.2
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE 89 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE 89 (258)
.++.+.+. |+.++..|++..+||+.|+||++||++++++..+
T Consensus 3 ~l~~~e~~-i~~~~~~g~s~~eia~~l~is~~tv~~~~~~~~~ 44 (58)
T smart00421 3 SLTPRERE-VLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMR 44 (58)
T ss_pred CCCHHHHH-HHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 36776665 7788889999999999999999999999998753
No 26
>PHA02517 putative transposase OrfB; Reviewed
Probab=97.45 E-value=0.00037 Score=62.88 Aligned_cols=76 Identities=11% Similarity=0.102 Sum_probs=57.0
Q ss_pred hCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHh-CCCCCHHHHHHHHHhcCCCCCCCCCCHHHHH
Q psy15598 73 LRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQK-DPGIFAWEIRDRLLSDGVCDKFNVPSVSSIS 151 (258)
Q Consensus 73 LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~-nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~ 151 (258)
||||++|.|+|+++... |..+.+ + ....++..+.|+++..+ ++....+.|...|.+.|+.+ |.+||+
T Consensus 1 l~vsrs~yY~~~~~~~~-----p~~~~~-~-~~~~~~l~~~I~~i~~~~~~~~G~r~I~~~L~~~g~~v-----s~~tV~ 68 (277)
T PHA02517 1 LGIAPSTYYRCQQQRHH-----PDKRRA-R-AQHDDWLKSEILRVYDENHQVYGVRKVWRQLNREGIRV-----ARCTVG 68 (277)
T ss_pred CCCChHHHHHHHhccCC-----cchhhh-h-hhhhHHHHHHHHHHHHHhCCCCCHHHHHHHHHhcCccc-----CHHHHH
Confidence 68999999999987531 111111 1 12345567788888765 57889999999999889875 999999
Q ss_pred HHHHhccCC
Q psy15598 152 RILRNKIGS 160 (258)
Q Consensus 152 RiLrr~~~~ 160 (258)
|+|++.+..
T Consensus 69 Rim~~~gl~ 77 (277)
T PHA02517 69 RLMKELGLA 77 (277)
T ss_pred HHHHHcCCc
Confidence 999998874
No 27
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=97.44 E-value=0.00036 Score=47.99 Aligned_cols=44 Identities=25% Similarity=0.326 Sum_probs=40.6
Q ss_pred CCCCCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHh
Q psy15598 44 NGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARY 87 (258)
Q Consensus 44 ~gR~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRy 87 (258)
.+..++..++..|+.++.+..+.++||+.+|||.+||.+++++|
T Consensus 8 ~~~r~T~~~~~~i~~~~~~~~s~~~vA~~~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 8 RYCRITKRLEQYILKLLRESRSFKDVARELGVSWSTVRRIFDRY 51 (52)
T ss_pred cCCcHHHHHHHHHHHHHhhcCCHHHHHHHHCCCHHHHHHHHHhh
Confidence 45568999999999999888999999999999999999999987
No 28
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=97.40 E-value=0.00038 Score=49.29 Aligned_cols=42 Identities=29% Similarity=0.523 Sum_probs=32.4
Q ss_pred CCCCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHH
Q psy15598 45 GRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILAR 86 (258)
Q Consensus 45 gR~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikR 86 (258)
|+.++..++.+|..+.+.|++..+||++++-|+.+|.++++.
T Consensus 2 G~~Lt~~Eqaqid~m~qlG~s~~~isr~i~RSr~~Ir~yl~d 43 (50)
T PF11427_consen 2 GKTLTDAEQAQIDVMHQLGMSLREISRRIGRSRTCIRRYLKD 43 (50)
T ss_dssp S----HHHHHHHHHHHHTT--HHHHHHHHT--HHHHHHHHHS
T ss_pred CCcCCHHHHHHHHHHHHhchhHHHHHHHhCccHHHHHHHhcC
Confidence 678999999999999999999999999999999999999875
No 29
>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=97.39 E-value=0.00031 Score=55.02 Aligned_cols=36 Identities=17% Similarity=0.288 Sum_probs=32.0
Q ss_pred HHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598 50 NSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILA 85 (258)
Q Consensus 50 ~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwik 85 (258)
...|..|+.+..+|++.++||+.||||++||+||.+
T Consensus 37 Ls~R~~I~~ll~~G~S~~eIA~~LgISrsTIyRi~R 72 (88)
T TIGR02531 37 LAQRLQVAKMLKQGKTYSDIEAETGASTATISRVKR 72 (88)
T ss_pred hhHHHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 356788889999999999999999999999999664
No 30
>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=97.35 E-value=0.00069 Score=44.71 Aligned_cols=42 Identities=26% Similarity=0.250 Sum_probs=36.0
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598 48 LPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE 89 (258)
Q Consensus 48 ~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE 89 (258)
++.+.|..+...+.+|++..+||+.+|+|.+||++|+.+.++
T Consensus 11 l~~~~~~~~~~~~~~~~~~~~ia~~~~~s~~~i~~~~~~~~~ 52 (55)
T cd06171 11 LPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALK 52 (55)
T ss_pred CCHHHHHHHHHHHhcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 667777666666679999999999999999999999999764
No 31
>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=97.28 E-value=0.00062 Score=47.13 Aligned_cols=43 Identities=23% Similarity=0.273 Sum_probs=32.0
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE 89 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE 89 (258)
.++...|.-+...+-+|++..+||+.+|+|.+||.+++.|-++
T Consensus 10 ~L~~~~r~i~~l~~~~g~s~~eIa~~l~~s~~~v~~~l~ra~~ 52 (54)
T PF08281_consen 10 QLPERQREIFLLRYFQGMSYAEIAEILGISESTVKRRLRRARK 52 (54)
T ss_dssp CS-HHHHHHHHHHHTS---HHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHCcCHHHHHHHHCcCHHHHHHHHHHHHh
Confidence 3567777766666779999999999999999999999998753
No 32
>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=97.26 E-value=0.00092 Score=45.86 Aligned_cols=42 Identities=29% Similarity=0.279 Sum_probs=35.3
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.++.+.|.-|...+.+|++..+||+.||+|++||+++.++-.
T Consensus 4 ~L~~~er~vi~~~y~~~~t~~eIa~~lg~s~~~V~~~~~~al 45 (50)
T PF04545_consen 4 QLPPREREVIRLRYFEGLTLEEIAERLGISRSTVRRILKRAL 45 (50)
T ss_dssp TS-HHHHHHHHHHHTST-SHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcCCCCHHHHHHHHCCcHHHHHHHHHHHH
Confidence 467888887777788999999999999999999999998864
No 33
>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=97.19 E-value=0.003 Score=45.84 Aligned_cols=66 Identities=15% Similarity=0.213 Sum_probs=43.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHH
Q psy15598 64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRL 133 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L 133 (258)
++..++|+.+|||.+|++.|.+.+ |.+.+....+ ..+..+.++...|..... .+-.+++.+|+..|
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---GLLKPQRSDG-GHRLFNDADIDRILEIKRWIDNGVQVSKVKKLL 67 (68)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHhc---CCCCCCcCCC-CCcccCHHHHHHHHHHHHHHHcCCCHHHHHHHh
Confidence 467899999999999999886553 5555544333 346788776665544422 22466777776544
No 34
>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=97.19 E-value=0.00051 Score=46.94 Aligned_cols=43 Identities=28% Similarity=0.519 Sum_probs=38.2
Q ss_pred HHHHHHHHHHHcC-CCHHHHHHHhCCCHHHHHHHHHHhhhhCCc
Q psy15598 51 SVRMRIVELAQLG-IRPCDISRQLRVSHGCVSKILARYHETGSI 93 (258)
Q Consensus 51 dlR~RIV~L~~~G-~S~~eIAr~LGVSrsTVsRwikRyrEtGsl 93 (258)
+.|.+|+.+..+| ++.++||+.|++|++||++-++..++.|-+
T Consensus 2 ~~R~~Il~~L~~~~~~~~el~~~l~~s~~~vs~hL~~L~~~glV 45 (47)
T PF01022_consen 2 PTRLRILKLLSEGPLTVSELAEELGLSQSTVSHHLKKLREAGLV 45 (47)
T ss_dssp HHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred HHHHHHHHHHHhCCCchhhHHHhccccchHHHHHHHHHHHCcCe
Confidence 5799999998765 799999999999999999999999998865
No 35
>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=97.12 E-value=0.0016 Score=44.23 Aligned_cols=43 Identities=21% Similarity=0.381 Sum_probs=35.1
Q ss_pred HHHHHHHHHHH-c-CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCc
Q psy15598 51 SVRMRIVELAQ-L-GIRPCDISRQLRVSHGCVSKILARYHETGSI 93 (258)
Q Consensus 51 dlR~RIV~L~~-~-G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl 93 (258)
+.+.+|+.... + +.+.++||+.+|+|.+||++.+++..+.|-+
T Consensus 3 ~~~~~Il~~l~~~~~~t~~ela~~~~is~~tv~~~l~~L~~~g~I 47 (48)
T PF13412_consen 3 ETQRKILNYLRENPRITQKELAEKLGISRSTVNRYLKKLEEKGLI 47 (48)
T ss_dssp HHHHHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHHHCcCc
Confidence 45677888765 3 5999999999999999999999999998865
No 36
>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=97.11 E-value=0.0018 Score=43.88 Aligned_cols=39 Identities=21% Similarity=0.187 Sum_probs=32.8
Q ss_pred HHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598 50 NSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE 89 (258)
Q Consensus 50 ~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE 89 (258)
...+. |+.++..|++..+||+.|++|.+||++++++.++
T Consensus 3 ~~e~~-i~~~~~~~~s~~eia~~l~~s~~tv~~~~~~~~~ 41 (57)
T cd06170 3 PRERE-VLRLLAEGKTNKEIADILGISEKTVKTHLRNIMR 41 (57)
T ss_pred HHHHH-HHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 33444 7777789999999999999999999999998753
No 37
>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=97.09 E-value=0.0069 Score=46.67 Aligned_cols=71 Identities=18% Similarity=0.072 Sum_probs=50.7
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHhcC
Q psy15598 63 GIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLLSDG 137 (258)
Q Consensus 63 G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~~~G 137 (258)
+++..++|+.+|||.+|++.|-+ .|.+.|....+...+..++++...|..... .+-.+++.+|++.|....
T Consensus 1 ~~ti~evA~~~gvs~~tLR~ye~----~Gll~p~r~~~~g~R~Ys~~dv~~l~~I~~Lr~~G~sl~~i~~~l~~~~ 72 (88)
T cd01105 1 VIGIGEVSKLTGVSPRQLRYWEE----KGLIKSIRSDGGGQRKYSLADVDRLLVIKELLDEGFTLAAAVEKLRRRR 72 (88)
T ss_pred CcCHHHHHHHHCcCHHHHHHHHH----CCCCCCCccCCCCceecCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHcc
Confidence 46889999999999999998843 476666544322346788777766555533 335789999999887544
No 38
>PRK00118 putative DNA-binding protein; Validated
Probab=97.08 E-value=0.0015 Score=52.69 Aligned_cols=45 Identities=18% Similarity=0.130 Sum_probs=39.0
Q ss_pred CCCCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598 45 GRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE 89 (258)
Q Consensus 45 gR~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE 89 (258)
+..++...|.-++..+.+|+|.++||+.+|||++||++++.|-+.
T Consensus 15 ~~~L~ekqRevl~L~y~eg~S~~EIAe~lGIS~~TV~r~L~RArk 59 (104)
T PRK00118 15 GSLLTEKQRNYMELYYLDDYSLGEIAEEFNVSRQAVYDNIKRTEK 59 (104)
T ss_pred hccCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 345788888877777889999999999999999999999998653
No 39
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=97.04 E-value=0.001 Score=47.93 Aligned_cols=66 Identities=18% Similarity=0.156 Sum_probs=43.8
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHH
Q psy15598 64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLL 134 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~ 134 (258)
++..++|+.+|||.+||+.|.+++. +.+....+ ..+..++++...|..+.. .+-.++..+|++.|.
T Consensus 1 yti~eva~~~gvs~~tlr~y~~~gl----l~~~~~~~-g~r~y~~~dv~~l~~i~~l~~~G~sl~~I~~~l~ 67 (69)
T PF13411_consen 1 YTIKEVAKLLGVSPSTLRYYEREGL----LPPPRDEN-GYRYYSEEDVERLREIKELRKQGMSLEEIKKLLK 67 (69)
T ss_dssp EEHHHHHHHTTTTHHHHHHHHHTTS----STTBESTT-SSEEE-HHHHHHHHHHHHHHHTTTHHHHHHHHH-
T ss_pred CcHHHHHHHHCcCHHHHHHHHHhcC----cccccccC-ceeeccHHHHHHHHHHHHHHHCcCCHHHHHHHHc
Confidence 3678999999999999999977654 54444333 347788887776655533 124666777766664
No 40
>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=96.99 E-value=0.0018 Score=42.52 Aligned_cols=44 Identities=14% Similarity=0.143 Sum_probs=29.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHH
Q psy15598 64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVS 112 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~ 112 (258)
++..++|+.||||++||++|+++ |.+.+....+ +....+.++..
T Consensus 1 ~s~~e~a~~lgvs~~tl~~~~~~----g~~~~~~~~~-~~~~~~~~ei~ 44 (49)
T cd04762 1 LTTKEAAELLGVSPSTLRRWVKE----GKLKAIRTPG-GHRRFPEEDLE 44 (49)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHc----CCCCceeCCC-CceecCHHHHH
Confidence 47789999999999999999986 4443332233 33445544433
No 41
>PF01498 HTH_Tnp_Tc3_2: Transposase; InterPro: IPR002492 Transposase proteins are necessary for efficient DNA transposition. This family includes the amino-terminal region of Tc1, Tc1A, Tc1B and Tc2B transposases of Caenorhabditis elegans. The region encompasses the specific DNA binding and second DNA recognition domains as well as an amino-terminal region of the catalytic domain of Tc3 as described in []. Tc3 is a member of the Tc1/mariner family of transposable elements. This entry also includes histone-lysine N-methyltransferase SETMAR, which is a SET domain and mariner transposase fusion gene-containing protein. This histone methyltransferase has sequence-specific DNA-binding activity and recognises the 19-mer core of the 5'-terminal inverted repeats (TIRs) of the Hsmar1 element. This protein has DNA nicking activity, and has in vivo end joining activity and may mediate genomic integration of foreign DNA [, , , ]. 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, 0015074 DNA integration; PDB: 3K9K_B 3F2K_B 3K9J_B 1U78_A.
Probab=96.97 E-value=0.00061 Score=49.96 Aligned_cols=45 Identities=31% Similarity=0.336 Sum_probs=21.8
Q ss_pred HHHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCCC
Q psy15598 112 SYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSS 161 (258)
Q Consensus 112 ~~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~~ 161 (258)
+.|+.++..+|.+++.+|...|...|+.+ |.+||.|+|++.+...
T Consensus 2 r~I~~~v~~~p~~s~~~i~~~l~~~~~~v-----S~~TI~r~L~~~g~~~ 46 (72)
T PF01498_consen 2 RRIVRMVRRNPRISAREIAQELQEAGISV-----SKSTIRRRLREAGLKK 46 (72)
T ss_dssp --------------HHHHHHHT---T--S------HHHHHHHHHHT-EEE
T ss_pred cHHHHHHHHCCCCCHHHHHHHHHHccCCc-----CHHHHHHHHHHcCccc
Confidence 57888999999999999999998668876 9999999999987654
No 42
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=96.96 E-value=0.0015 Score=53.54 Aligned_cols=75 Identities=23% Similarity=0.327 Sum_probs=56.5
Q ss_pred CCCCHHHHHHHHHHHH--cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHh
Q psy15598 46 RPLPNSVRMRIVELAQ--LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQK 120 (258)
Q Consensus 46 R~~S~dlR~RIV~L~~--~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~ 120 (258)
+.+++..|.+|+.+.. .++++.+|++.|+++++||++-++..++.|-|...+.|..+--.+.+....++..++..
T Consensus 11 kaLadptRl~IL~~L~~~~~~~v~ela~~l~lsqstvS~HL~~L~~AGLV~~~r~Gr~~~Y~l~~~~~~~~~~~~~~ 87 (117)
T PRK10141 11 KILSDETRLGIVLLLRESGELCVCDLCTALDQSQPKISRHLALLRESGLLLDRKQGKWVHYRLSPHIPAWAAKIIEQ 87 (117)
T ss_pred HHhCCHHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEEEcCEEEEEECchHHHHHHHHHHH
Confidence 4578899999999885 35899999999999999999999999999988665554322233445555555554443
No 43
>PF04552 Sigma54_DBD: Sigma-54, DNA binding domain; InterPro: IPR007634 This DNA-binding domain is based on peptide fragmentation data. This domain is proximal to DNA in the promoter/holoenzyme complex. Furthermore, this region contains a putative helix-turn-helix motif. At the C terminus, there is a highly conserved region known as the RpoN box and is the signature of the sigma-54 proteins [].; PDB: 2AHQ_A 2O9L_A 2O8K_A.
Probab=96.92 E-value=0.00096 Score=57.47 Aligned_cols=88 Identities=19% Similarity=0.289 Sum_probs=28.9
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHH-HhhhhC--Cc-----ccCCCCCCCCC-CCCHHHHHHHHHHHHh-CC--CCCHHHHH
Q psy15598 63 GIRPCDISRQLRVSHGCVSKILA-RYHETG--SI-----LPGAIGGSKPR-VTTPKVVSYIKELKQK-DP--GIFAWEIR 130 (258)
Q Consensus 63 G~S~~eIAr~LGVSrsTVsRwik-RyrEtG--sl-----~pk~rgG~RPr-klT~e~~~~I~~lv~~-nP--~ita~EIr 130 (258)
-++.++||..||++.|||+|.++ +|.++. .+ -.......... ...+.+...|.+++.+ ++ -++=.+|.
T Consensus 49 PLt~~~iA~~lgl~~STVSRav~~Ky~~t~~Gi~plk~fF~~~~~~~~~~~~S~~~ik~~i~~lI~~Ed~~~PlSD~~i~ 128 (160)
T PF04552_consen 49 PLTMKDIADELGLHESTVSRAVKNKYIQTPRGIFPLKDFFSRSVSSGSGEEFSSEAIKARIKELIEEEDKKKPLSDQEIA 128 (160)
T ss_dssp ------------------------------------S-----SS--SS-SS---TTH-HHHHHHHTTS-TTS---HHHHH
T ss_pred CCCHHHHHHHhCCCHhHHHHHHcCceeecCCeeeeHHHhccccccCCCCcccHHHHHHHHHHHHHHhcCCCCCCCHHHHH
Confidence 46889999999999999999765 566554 21 12211110111 1224467788888875 33 46788999
Q ss_pred HHHHhcCCCCCCCCCCHHHHHHHHH
Q psy15598 131 DRLLSDGVCDKFNVPSVSSISRILR 155 (258)
Q Consensus 131 ~~L~~~Gv~v~~~~pS~STI~RiLr 155 (258)
+.|.+.|+.+ |++||...=.
T Consensus 129 ~~L~~~gi~i-----sRRTVaKYR~ 148 (160)
T PF04552_consen 129 ELLKEEGIKI-----SRRTVAKYRE 148 (160)
T ss_dssp HHHTTTTS--------HHHHHHHHH
T ss_pred HHHHHcCCCc-----cHHHHHHHHH
Confidence 9999999986 9999976543
No 44
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=96.89 E-value=0.0027 Score=44.58 Aligned_cols=43 Identities=16% Similarity=0.266 Sum_probs=36.4
Q ss_pred CCCHHHHHHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598 47 PLPNSVRMRIVELA-QLGIRPCDISRQLRVSHGCVSKILARYHE 89 (258)
Q Consensus 47 ~~S~dlR~RIV~L~-~~G~S~~eIAr~LGVSrsTVsRwikRyrE 89 (258)
.++.+.|.-++..+ +.|.+..++|..||||++||+||++.+.+
T Consensus 2 kLs~~d~lll~L~~LR~~~~~~~La~~FgIs~stvsri~~~~~~ 45 (53)
T PF13613_consen 2 KLSLEDQLLLTLMYLRLNLTFQDLAYRFGISQSTVSRIFHEWIP 45 (53)
T ss_pred CCCHHHHHHHHHHHHHcCCcHhHHhhheeecHHHHHHHHHHHHH
Confidence 46677776666664 68999999999999999999999999864
No 45
>PF14493 HTH_40: Helix-turn-helix domain
Probab=96.88 E-value=0.013 Score=45.26 Aligned_cols=84 Identities=19% Similarity=0.086 Sum_probs=65.1
Q ss_pred HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHH
Q psy15598 54 MRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFAWEIRDRL 133 (258)
Q Consensus 54 ~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~nP~ita~EIr~~L 133 (258)
..-+.++++|+|..+||+.-+++.+||..-+.++...|...+- ...++.+..+.|...+++.....++.|.+.|
T Consensus 4 ~~T~~l~~~G~si~eIA~~R~L~~sTI~~HL~~~~~~g~~~~~------~~~l~~e~~~~I~~~~~~~~~~~lk~i~e~l 77 (91)
T PF14493_consen 4 QITYELFQKGLSIEEIAKIRGLKESTIYGHLAELIESGEPLDI------EELLSEEEIKQIEDAIEKLGSEKLKPIKEAL 77 (91)
T ss_pred HHHHHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHHHhCCCCCH------HHhCCHHHHHHHHHHHHHcCcccHHHHHHHC
Confidence 4457788999999999999999999999999999998862111 1447778888898888887777787777766
Q ss_pred HhcCCCCCCCCCCHHHHH
Q psy15598 134 LSDGVCDKFNVPSVSSIS 151 (258)
Q Consensus 134 ~~~Gv~v~~~~pS~STI~ 151 (258)
. -. +|...|+
T Consensus 78 ~---~~-----~sy~~iR 87 (91)
T PF14493_consen 78 P---GD-----YSYFEIR 87 (91)
T ss_pred C---CC-----CCHHHHH
Confidence 3 22 3666664
No 46
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=96.88 E-value=0.0068 Score=43.75 Aligned_cols=65 Identities=17% Similarity=0.222 Sum_probs=42.9
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHH
Q psy15598 64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRL 133 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L 133 (258)
++..++|+.+|||.+|++.|.+++. -..++..+ ..+..+.++...|...+. .+-..++.+|+..|
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 YTIKEVSEIIGVKPHTLRYYEKEFN---LYIPRTEN--GRRYYTDEDIELLKKIKTLLEKGLSIKEIKEIL 66 (67)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHhcC---CCCCCCCC--CceeeCHHHHHHHHHHHHHHHCCCCHHHHHHHh
Confidence 4688999999999999999977643 11222222 346788777666655533 22467777776654
No 47
>PHA02535 P terminase ATPase subunit; Provisional
Probab=96.83 E-value=0.0033 Score=63.97 Aligned_cols=42 Identities=17% Similarity=0.109 Sum_probs=40.0
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.|+.|+|..++.++.+|.++++||++|||+.+||++|.++++
T Consensus 2 ~yt~EfK~~Av~Ly~~G~sv~eIA~~LGv~~~Tl~~W~kr~~ 43 (581)
T PHA02535 2 AYDDDVRRAAKFLYWQGWTVAEIAEELGLKSRTIYSWKERDG 43 (581)
T ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCChhHHHHHhcccc
Confidence 489999999999998899999999999999999999999986
No 48
>PRK04217 hypothetical protein; Provisional
Probab=96.80 E-value=0.0046 Score=50.34 Aligned_cols=45 Identities=13% Similarity=0.089 Sum_probs=36.5
Q ss_pred CCCCCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 44 NGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 44 ~gR~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
....++.+.|..+..+..+|++..+||+.||||++||++.+++-+
T Consensus 39 p~~~Lt~eereai~l~~~eGlS~~EIAk~LGIS~sTV~r~L~RAr 83 (110)
T PRK04217 39 PPIFMTYEEFEALRLVDYEGLTQEEAGKRMGVSRGTVWRALTSAR 83 (110)
T ss_pred CcccCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 345588888844444445999999999999999999999999864
No 49
>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=96.79 E-value=0.018 Score=45.45 Aligned_cols=69 Identities=16% Similarity=0.176 Sum_probs=51.4
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH--hCCCCCHHHHHHHHHhc
Q psy15598 64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ--KDPGIFAWEIRDRLLSD 136 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~--~nP~ita~EIr~~L~~~ 136 (258)
++..++|+.+|||.+|++.|.+.+ |.+.+....+ ..+..++++...|..++. ++-.+++.+|++.|...
T Consensus 1 yti~EvA~~~gVs~~tLR~ye~~~---gli~p~r~~~-g~R~Yt~~di~~l~~I~~llr~~G~~l~~i~~~l~~~ 71 (99)
T cd04765 1 FSIGEVAEILGLPPHVLRYWETEF---PQLKPVKRAG-GRRYYRPKDVELLLLIKHLLYEKGYTIEGAKQALKED 71 (99)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHc---CCCCCcCCCC-CCeeeCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHhc
Confidence 467899999999999999996663 4444433333 457788888887777653 45688999999988753
No 50
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=96.78 E-value=0.011 Score=42.38 Aligned_cols=50 Identities=14% Similarity=0.136 Sum_probs=35.8
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccC-CCCCCCCCCCCHHHHHHHHHHH
Q psy15598 64 IRPCDISRQLRVSHGCVSKILARYHETGSILPG-AIGGSKPRVTTPKVVSYIKELK 118 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk-~rgG~RPrklT~e~~~~I~~lv 118 (258)
++..++|+.+|||.+|+++|.+ .|.+.+. ...+ ..+..+.++...|....
T Consensus 1 ~s~~eva~~~gvs~~tlr~~~~----~gli~~~~~~~~-g~r~y~~~dl~~l~~i~ 51 (70)
T smart00422 1 YTIGEVAKLAGVSVRTLRYYER----IGLLPPPIRTEG-GYRLYSDEDLERLRFIK 51 (70)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCccCCC-CCEecCHHHHHHHHHHH
Confidence 4789999999999999999965 6777654 2222 34667777766655543
No 51
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=96.75 E-value=0.0012 Score=44.85 Aligned_cols=43 Identities=28% Similarity=0.363 Sum_probs=33.3
Q ss_pred CCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHh
Q psy15598 102 KPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRN 156 (258)
Q Consensus 102 RPrklT~e~~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr 156 (258)
||++++++..+.|.++..+. .+..+|++.+ | +|++||+|+|+.
T Consensus 2 Rp~~~~~~~~~~i~~l~~~G--~si~~IA~~~---g-------vsr~TvyR~l~~ 44 (45)
T PF02796_consen 2 RPPKLSKEQIEEIKELYAEG--MSIAEIAKQF---G-------VSRSTVYRYLNK 44 (45)
T ss_dssp SSSSSSHCCHHHHHHHHHTT----HHHHHHHT---T-------S-HHHHHHHHCC
T ss_pred cCCCCCHHHHHHHHHHHHCC--CCHHHHHHHH---C-------cCHHHHHHHHhc
Confidence 88999998888999988774 7888887766 3 499999999964
No 52
>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=96.71 E-value=0.003 Score=46.33 Aligned_cols=44 Identities=25% Similarity=0.237 Sum_probs=34.5
Q ss_pred CCCCCCHHHHHHHHHHHHc---CCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 44 NGRPLPNSVRMRIVELAQL---GIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 44 ~gR~~S~dlR~RIV~L~~~---G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
|+|.-|. .|.+..+++.+ .+...+||++||||.+||++|-.+.+
T Consensus 1 M~r~Rsp-~rdkA~e~y~~~~g~i~lkdIA~~Lgvs~~tIr~WK~~dk 47 (60)
T PF10668_consen 1 MARKRSP-NRDKAFEIYKESNGKIKLKDIAEKLGVSESTIRKWKSRDK 47 (60)
T ss_pred CCCCCCc-CHHHHHHHHHHhCCCccHHHHHHHHCCCHHHHHHHhhhcc
Confidence 3444333 67788888763 48999999999999999999998753
No 53
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=96.69 E-value=0.0027 Score=55.20 Aligned_cols=36 Identities=25% Similarity=0.368 Sum_probs=32.1
Q ss_pred HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHh
Q psy15598 52 VRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARY 87 (258)
Q Consensus 52 lR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRy 87 (258)
.+.+|..++.+|+|.++||+.||||++||+|+++.+
T Consensus 161 ~~~~i~~~~~~g~s~~~iak~lgis~~Tv~r~~k~~ 196 (200)
T PRK13413 161 KEEKIKKLLDKGTSKSEIARKLGVSRTTLARFLKTR 196 (200)
T ss_pred hHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHhc
Confidence 346788888899999999999999999999999864
No 54
>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=96.64 E-value=0.0053 Score=42.92 Aligned_cols=49 Identities=24% Similarity=0.413 Sum_probs=40.5
Q ss_pred CCCHHHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCccc
Q psy15598 47 PLPNSVRMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILARYHETGSILP 95 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~p 95 (258)
.++.+.+..|+..+. .+.+..+|++.++++++||++.+++..+.|-+..
T Consensus 3 ~~~~~~~~~il~~l~~~~~~~~ei~~~~~i~~~~i~~~l~~L~~~g~i~~ 52 (78)
T cd00090 3 ALSDPTRLRILRLLLEGPLTVSELAERLGLSQSTVSRHLKKLEEAGLVES 52 (78)
T ss_pred cccChHHHHHHHHHHHCCcCHHHHHHHHCcCHhHHHHHHHHHHHCCCeEE
Confidence 455566777888754 4499999999999999999999999999997643
No 55
>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=96.62 E-value=0.025 Score=45.19 Aligned_cols=68 Identities=15% Similarity=0.141 Sum_probs=49.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHh
Q psy15598 64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLLS 135 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~~ 135 (258)
++..++|+.+|||.+|++.|.+ .|.+.|..+.++.-+..++++...|..... ..-.+++.+|++.|..
T Consensus 1 ~~i~eva~~~gvs~~tlR~ye~----~Gll~p~~~~~~g~R~Y~~~dl~~l~~I~~lr~~G~~l~~I~~~l~~ 69 (108)
T cd04773 1 MTIGELAHLLGVPPSTLRHWEK----EGLLSPDREPETGYRVYDPSDVRDARLIHLLRRGGYLLEQIATVVEQ 69 (108)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCcCCCCCceeeCHHHHHHHHHHHHHHHCCCCHHHHHHHHHH
Confidence 5789999999999999988844 577766544322457788877776655543 2236889999888864
No 56
>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=96.59 E-value=0.0038 Score=45.56 Aligned_cols=43 Identities=21% Similarity=0.236 Sum_probs=31.4
Q ss_pred CCCCCHHHHHHHHHHHH-cCC---CHHHHHHHhCCCHHHHHHHHHHh
Q psy15598 45 GRPLPNSVRMRIVELAQ-LGI---RPCDISRQLRVSHGCVSKILARY 87 (258)
Q Consensus 45 gR~~S~dlR~RIV~L~~-~G~---S~~eIAr~LGVSrsTVsRwikRy 87 (258)
-+.|+..++.++|+.++ .+. ..+++|+.|+|++.+|.+|++.-
T Consensus 3 rrsy~~~FKL~Vv~~a~~~~nc~~~~RAaarkf~V~r~~Vr~W~kqe 49 (58)
T PF09607_consen 3 RRSYTAEFKLKVVEYAEKDNNCKGNQRAAARKFNVSRRQVRKWRKQE 49 (58)
T ss_dssp -----HHHHHHHHHHHHH-TTTTT-HHHHHHHTTS-HHHHHHHHTTH
T ss_pred ccccChHHHHHHHHHHHHccchhhhHHHHHHHhCccHHHHHHHHHHH
Confidence 36799999999999985 454 45999999999999999999764
No 57
>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=96.57 E-value=0.0026 Score=45.46 Aligned_cols=48 Identities=27% Similarity=0.398 Sum_probs=41.8
Q ss_pred CCHHHHHHHHHHH-H-cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCccc
Q psy15598 48 LPNSVRMRIVELA-Q-LGIRPCDISRQLRVSHGCVSKILARYHETGSILP 95 (258)
Q Consensus 48 ~S~dlR~RIV~L~-~-~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~p 95 (258)
+++..|.+|+.+. . .+++..+||+.||++.+||++-++..++-|-|+.
T Consensus 7 L~~p~R~~Il~~L~~~~~~t~~ela~~l~~~~~t~s~hL~~L~~aGli~~ 56 (61)
T PF12840_consen 7 LSDPTRLRILRLLASNGPMTVSELAEELGISQSTVSYHLKKLEEAGLIEV 56 (61)
T ss_dssp HTSHHHHHHHHHHHHCSTBEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred hCCHHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEE
Confidence 5678999999998 4 5799999999999999999999999999997743
No 58
>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=96.56 E-value=0.0031 Score=43.95 Aligned_cols=39 Identities=28% Similarity=0.318 Sum_probs=35.4
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHH
Q psy15598 48 LPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILAR 86 (258)
Q Consensus 48 ~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikR 86 (258)
+...++++||++..+|..++++||.|+||..||-|-+|.
T Consensus 6 ~kpgikeqIvema~nG~GiRdtaRvL~I~~nTVlrtLK~ 44 (46)
T PF12759_consen 6 RKPGIKEQIVEMAFNGSGIRDTARVLKISINTVLRTLKN 44 (46)
T ss_pred cCccHHHHHHHHHhcCCcchhhHhHhcchHHHHHHHHhc
Confidence 456788999999999999999999999999999988774
No 59
>PF07037 DUF1323: Putative transcription regulator (DUF1323); InterPro: IPR010749 This family consists of several hypothetical Enterobacterial proteins of around 120 residues in length. The function of this family is unknown.
Probab=96.51 E-value=0.005 Score=50.93 Aligned_cols=54 Identities=17% Similarity=0.348 Sum_probs=37.4
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCC--CCHHHHHHHHHHH
Q psy15598 64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRV--TTPKVVSYIKELK 118 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrk--lT~e~~~~I~~lv 118 (258)
|+..|+|..+|+|+.||.||+++..=.-.-.|+-.|| |-+. +++.+.++|...-
T Consensus 1 MT~eELA~~tG~srQTINrWvRkegW~T~p~pGVkGG-rARLIhId~~V~efi~s~~ 56 (122)
T PF07037_consen 1 MTPEELAELTGYSRQTINRWVRKEGWKTEPKPGVKGG-RARLIHIDEQVREFIRSIP 56 (122)
T ss_pred CCHHHHHHHhCccHHHHHHHHHhcCceeccCCccccc-cceeeeecHHHHHHHHhhH
Confidence 6789999999999999999999863111223433455 4443 5577777777664
No 60
>TIGR02395 rpoN_sigma RNA polymerase sigma-54 factor. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called sigma-54, or RpoN (unrelated to sigma 70-type factors such as RpoD/SigA). RpoN is responsible for enhancer-dependent transcription, and its presence characteristically is associated with varied panels of activators, most of which are enhancer-binding proteins (but see Brahmachary, et al., PubMed:15231786). RpoN may be responsible for transcription of nitrogen fixation genes, flagellins, pilins, etc., and synonyms for the gene symbol rpoN, such as ntrA, reflect these observations
Probab=96.50 E-value=0.0086 Score=58.79 Aligned_cols=85 Identities=15% Similarity=0.281 Sum_probs=61.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH-hhhhC--Cc-----ccCCCCC-C-CCCCCCHHHHHHHHHHHHhC-C--CCCHHHHH
Q psy15598 64 IRPCDISRQLRVSHGCVSKILAR-YHETG--SI-----LPGAIGG-S-KPRVTTPKVVSYIKELKQKD-P--GIFAWEIR 130 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikR-yrEtG--sl-----~pk~rgG-~-RPrklT~e~~~~I~~lv~~n-P--~ita~EIr 130 (258)
++.++||..+||+.|||+|.++. |.++. .+ -.....+ . .....+..+...|.+++... + -++=.+|.
T Consensus 319 LtlkdiA~~lglheSTVSRav~~Kyi~tp~Gi~~lk~FFs~~~~~~~~g~~~S~~~Ik~~I~~lI~~E~~~~PlSD~~I~ 398 (429)
T TIGR02395 319 LTLREVAEELGLHESTISRAINNKYLQTPRGVFELKYFFSRGVQTDSGEGEVSSTAIKALIKELIAAEDKRKPLSDQKIA 398 (429)
T ss_pred CcHHHHHHHhCCCccchhhhhcCceEecCCceEEHHHhcCCccCCCCCCCccCHHHHHHHHHHHHHhcCCCCCCCHHHHH
Confidence 58899999999999999999874 55554 22 1111110 0 01244567888999998743 3 26788999
Q ss_pred HHHHhcCCCCCCCCCCHHHHHHH
Q psy15598 131 DRLLSDGVCDKFNVPSVSSISRI 153 (258)
Q Consensus 131 ~~L~~~Gv~v~~~~pS~STI~Ri 153 (258)
+.|++.|+.+ |++||...
T Consensus 399 ~~L~~~Gi~I-----aRRTVaKY 416 (429)
T TIGR02395 399 ELLKEKGIKI-----ARRTVAKY 416 (429)
T ss_pred HHHHhcCCCe-----ehHHHHHH
Confidence 9999999986 99999776
No 61
>PF13309 HTH_22: HTH domain
Probab=96.50 E-value=0.0039 Score=45.72 Aligned_cols=42 Identities=21% Similarity=0.217 Sum_probs=35.3
Q ss_pred CCCCCCHHHHHHHHHHHH-cCC-----CHHHHHHHhCCCHHHHHHHHH
Q psy15598 44 NGRPLPNSVRMRIVELAQ-LGI-----RPCDISRQLRVSHGCVSKILA 85 (258)
Q Consensus 44 ~gR~~S~dlR~RIV~L~~-~G~-----S~~eIAr~LGVSrsTVsRwik 85 (258)
....++.+.|..||.... .|. +...+|+.||||+.|||++++
T Consensus 17 ~~~~l~~~~k~~iV~~L~~~G~F~lKgav~~vA~~L~iS~~TVY~YLr 64 (64)
T PF13309_consen 17 PPSRLSKEEKKEIVRQLYEKGIFLLKGAVEYVAEKLGISRATVYRYLR 64 (64)
T ss_pred ChhhCCHHHHHHHHHHHHHCCCcccCcHHHHHHHHHCCCHHHHHHHcC
Confidence 445688899999998875 685 888999999999999999874
No 62
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=96.48 E-value=0.0051 Score=57.94 Aligned_cols=43 Identities=23% Similarity=0.332 Sum_probs=37.4
Q ss_pred HHHHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598 52 VRMRIVELA-QLGIRPCDISRQLRVSHGCVSKILARYHETGSIL 94 (258)
Q Consensus 52 lR~RIV~L~-~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~ 94 (258)
+-.+|-.++ .+|++..|||++|||||.+|+|.+++-++.|-++
T Consensus 17 l~~~vA~lYY~~g~tQ~eIA~~lgiSR~~VsRlL~~Ar~~GiV~ 60 (318)
T PRK15418 17 LVARIAWFYYHDGLTQSEIGERLGLTRLKVSRLLEKGRQSGIIR 60 (318)
T ss_pred HHHHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHcCcEE
Confidence 455666665 5899999999999999999999999999999763
No 63
>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=96.48 E-value=0.025 Score=44.38 Aligned_cols=66 Identities=12% Similarity=0.224 Sum_probs=49.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hC-CCCCHHHHHHHHH
Q psy15598 64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KD-PGIFAWEIRDRLL 134 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~n-P~ita~EIr~~L~ 134 (258)
++..++|+.+|||.+|++.|.+ .|.+.|....+ ..+..++.+...|..++. .+ -.++..+|+..|.
T Consensus 1 ~~I~e~a~~~gvs~~tLR~ye~----~Gll~p~r~~~-g~R~Y~~~dv~~l~~I~~L~~~~G~~l~ei~~~l~ 68 (96)
T cd04774 1 YKVDEVAKRLGLTKRTLKYYEE----IGLVSPERSEG-RYRLYSEEDLKRLERILRLREVLGFSLQEVTHFLE 68 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCcCCC-CCEEECHHHHHHHHHHHHHHHHcCCCHHHHHHHHh
Confidence 4678999999999999999954 47776654433 567888887777766544 22 4789999988876
No 64
>PF05225 HTH_psq: helix-turn-helix, Psq domain; InterPro: IPR007889 This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster []. In pipsqueak this domain binds to GAGA sequence []. The pipsqueak family, which includes proteins from fungi, sea urchins, nematodes, insects, and vertebrates appear to be proteins essential for sequence-specific targeting of a polycomb group protein complex [].; GO: 0003677 DNA binding; PDB: 2COB_A.
Probab=96.47 E-value=0.0086 Score=41.09 Aligned_cols=36 Identities=11% Similarity=0.158 Sum_probs=26.2
Q ss_pred HHHHHHHHHHHcC-CCHHHHHHHhCCCHHHHHHHHHH
Q psy15598 51 SVRMRIVELAQLG-IRPCDISRQLRVSHGCVSKILAR 86 (258)
Q Consensus 51 dlR~RIV~L~~~G-~S~~eIAr~LGVSrsTVsRwikR 86 (258)
+.=...|+.+.+| +|.+++|+.|||+++|+++.++.
T Consensus 3 e~l~~Ai~~v~~g~~S~r~AA~~ygVp~sTL~~r~~g 39 (45)
T PF05225_consen 3 EDLQKAIEAVKNGKMSIRKAAKKYGVPRSTLRRRLRG 39 (45)
T ss_dssp HHHHHHHHHHHTTSS-HHHHHHHHT--HHHHHHHHHH
T ss_pred HHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHcC
Confidence 3345566777777 99999999999999999977665
No 65
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=96.45 E-value=0.0046 Score=39.94 Aligned_cols=29 Identities=28% Similarity=0.418 Sum_probs=24.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHhhhhCC
Q psy15598 64 IRPCDISRQLRVSHGCVSKILARYHETGS 92 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGs 92 (258)
++..|||..+|+++-||+|.++++++.|.
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 67899999999999999999999998875
No 66
>TIGR01321 TrpR trp operon repressor, proteobacterial. This model represents TrpR, the repressor of the trp operon. It is found so far only in the gamma subdivision of the proteobacteria and in Chlamydia trachomatis. All members belong to species capable of tryptophan biosynthesis.
Probab=96.45 E-value=0.0048 Score=49.04 Aligned_cols=37 Identities=22% Similarity=0.240 Sum_probs=30.6
Q ss_pred HHHHHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHHHHh
Q psy15598 51 SVRMRIVELA-QLGIRPCDISRQLRVSHGCVSKILARY 87 (258)
Q Consensus 51 dlR~RIV~L~-~~G~S~~eIAr~LGVSrsTVsRwikRy 87 (258)
..|.+|+... +.|+|.++||+.+|||++||.|+-+-.
T Consensus 42 ~~R~~i~~~Ll~~~~tQrEIa~~lGiS~atIsR~sn~l 79 (94)
T TIGR01321 42 GDRIRIVNELLNGNMSQREIASKLGVSIATITRGSNNL 79 (94)
T ss_pred HHHHHHHHHHHhCCCCHHHHHHHhCCChhhhhHHHhhc
Confidence 4677777644 568999999999999999999987654
No 67
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=96.44 E-value=0.0073 Score=40.44 Aligned_cols=47 Identities=13% Similarity=0.135 Sum_probs=33.1
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHH
Q psy15598 64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIK 115 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~ 115 (258)
++..++|+.+||+.+||++|.++ |.+.+....| ..+..++++...|.
T Consensus 1 ~~~~e~a~~~gv~~~tlr~~~~~----g~l~~~~~~~-~~~~y~~~~v~~l~ 47 (49)
T cd04761 1 YTIGELAKLTGVSPSTLRYYERI----GLLSPARTEG-GYRLYSDADLERLR 47 (49)
T ss_pred CcHHHHHHHHCcCHHHHHHHHHC----CCCCCCcCCC-CCEEeCHHHHHHhh
Confidence 47889999999999999999655 4444333333 44667777666654
No 68
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=96.44 E-value=0.0066 Score=46.15 Aligned_cols=44 Identities=14% Similarity=0.154 Sum_probs=34.9
Q ss_pred CCHHHHHHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHHHHhhhhC
Q psy15598 48 LPNSVRMRIVELA-QLGIRPCDISRQLRVSHGCVSKILARYHETG 91 (258)
Q Consensus 48 ~S~dlR~RIV~L~-~~G~S~~eIAr~LGVSrsTVsRwikRyrEtG 91 (258)
++...|...+... .+|+|.++||+.+|||.+||..|+++-...|
T Consensus 16 l~~~~r~af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~~~~~~ 60 (73)
T TIGR03879 16 VDSLAEAAAALAREEAGKTASEIAEELGRTEQTVRNHLKGETKAG 60 (73)
T ss_pred CCHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhcCcccc
Confidence 5666666555544 4899999999999999999999999854444
No 69
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=96.38 E-value=0.017 Score=48.13 Aligned_cols=107 Identities=17% Similarity=0.210 Sum_probs=69.7
Q ss_pred ccCCCCCCHHHHHHHHHHHHcCC--------CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHH
Q psy15598 42 FVNGRPLPNSVRMRIVELAQLGI--------RPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSY 113 (258)
Q Consensus 42 ~~~gR~~S~dlR~RIV~L~~~G~--------S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~ 113 (258)
|-+.+|+...+..+|......|. |+++.|..++|+..||.|-++...+.|-+....+.| ...++...+.
T Consensus 6 f~s~~PIY~QI~~qIk~~I~~g~l~pGdkLPSvRelA~~~~VNpnTv~raY~eLE~eG~i~t~rg~G---~fV~~~~~~~ 82 (125)
T COG1725 6 FDSSKPIYEQIANQIKEQIASGELKPGDKLPSVRELAKDLGVNPNTVQRAYQELEREGIVETKRGKG---TFVTEDAKEI 82 (125)
T ss_pred cCCCCCHHHHHHHHHHHHHHhCCcCCCCCCCcHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCee---EEEcCCchhh
Confidence 45778888888888888876553 999999999999999999999999999886654333 4444332222
Q ss_pred HHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhcc
Q psy15598 114 IKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKI 158 (258)
Q Consensus 114 I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~ 158 (258)
+.+....--...+.++.+.++..|+ |...|..+|+...
T Consensus 83 ~~~~~~~~~~~~l~~~I~~~~~~G~-------s~eei~~~~~~~~ 120 (125)
T COG1725 83 LDQLKRELAEEELEEFIEEAKALGL-------SLEEILELLKEIY 120 (125)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCC-------CHHHHHHHHHHHH
Confidence 2222211101122233344444554 7778877777544
No 70
>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB. Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=96.32 E-value=0.063 Score=42.86 Aligned_cols=68 Identities=12% Similarity=0.112 Sum_probs=48.4
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHh
Q psy15598 64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLLS 135 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~~ 135 (258)
++..++|+.+|||.+|++.|-+ .|.+.+..+.....+..++++...|..... ..-.+++.||++.|..
T Consensus 1 ~~i~e~a~~~gvs~~tlr~ye~----~gll~~~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~ 69 (113)
T cd01109 1 YTIKEVAEKTGLSADTLRYYEK----EGLLPPVKRDENGIRDFTEEDLEWLEFIKCLRNTGMSIKDIKEYAEL 69 (113)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCCcCCCCCccCCHHHHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 4788999999999999987754 577644333322457788877776655433 2357899999988863
No 71
>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=96.31 E-value=0.066 Score=43.14 Aligned_cols=68 Identities=16% Similarity=0.227 Sum_probs=49.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHh
Q psy15598 64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLLS 135 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~~ 135 (258)
+++.++|+.+|||.+|++- |.+.|.+.|..+..+.-|..++++...|..... .+-.+++.||++.+..
T Consensus 1 ~~I~eva~~~gvs~~tLRy----Ye~~GLl~p~~r~~~gyR~Y~~~~i~~l~~I~~lr~~G~sl~eI~~~l~~ 69 (123)
T cd04770 1 MKIGELAKAAGVSPDTIRY----YERIGLLPPPQRSENGYRLYGEADLARLRFIRRAQALGFSLAEIRELLSL 69 (123)
T ss_pred CCHHHHHHHHCcCHHHHHH----HHHCCCCCCCCCCCCCCccCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHh
Confidence 5789999999999999954 666788875444333567888877776655533 4457899999988863
No 72
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=96.30 E-value=0.012 Score=43.35 Aligned_cols=45 Identities=16% Similarity=0.333 Sum_probs=39.7
Q ss_pred HHHHHHHHHHHHc--C--CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598 50 NSVRMRIVELAQL--G--IRPCDISRQLRVSHGCVSKILARYHETGSIL 94 (258)
Q Consensus 50 ~dlR~RIV~L~~~--G--~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~ 94 (258)
...+.+|+.++.. + ++..+||+.|||++++|++.+.+..+.|.|.
T Consensus 5 ~~~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~ 53 (68)
T smart00550 5 DSLEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKKGKVC 53 (68)
T ss_pred hHHHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 4577888888753 4 8999999999999999999999999999874
No 73
>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=96.29 E-value=0.027 Score=44.25 Aligned_cols=67 Identities=16% Similarity=0.141 Sum_probs=46.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHH
Q psy15598 64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLL 134 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~ 134 (258)
++..++|+.+|||.+|++.|.+ .|.+.+..+.+..-+..++++...|..+.. ..-.++..+|+..+.
T Consensus 1 ~ti~eva~~~gvs~~tlR~ye~----~Gll~~~~~~~~g~R~y~~~di~~l~~i~~lr~~g~~l~~i~~~~~ 68 (103)
T cd01106 1 YTVGEVAKLTGVSVRTLHYYDE----IGLLKPSRRTENGYRLYTEEDLERLQQILFLKELGFSLKEIKELLK 68 (103)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCccCCCCceeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 4788999999999999997765 576655433222346788877766544422 234788999888775
No 74
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=96.26 E-value=0.014 Score=57.81 Aligned_cols=83 Identities=19% Similarity=0.309 Sum_probs=60.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH-hhhhC--Cc-----ccCC---CCCCCCCCCCHHHHHHHHHHHHh-CC--CCCHHHH
Q psy15598 64 IRPCDISRQLRVSHGCVSKILAR-YHETG--SI-----LPGA---IGGSKPRVTTPKVVSYIKELKQK-DP--GIFAWEI 129 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikR-yrEtG--sl-----~pk~---rgG~RPrklT~e~~~~I~~lv~~-nP--~ita~EI 129 (258)
++.++||..+|++.|||+|.++. |.++. .+ -... ..| ....+..+...|.+++.. ++ -++=.+|
T Consensus 344 LtlkdvAe~lglheSTVSRav~~Kyv~tp~Gi~~lk~FFs~~~~~~~g--~~~S~~~Ik~~Ik~lI~~Ed~~~PlSD~~I 421 (455)
T PRK05932 344 LVLKDIAEELGMHESTISRATTNKYMATPRGIFELKYFFSSAVSTDGG--GEASSTAIRALIKKLIAAENPKKPLSDSKI 421 (455)
T ss_pred ccHHHHHHHhCCCccchhhhhcCceeecCCceEEHHHhcccccCCCCC--ccccHHHHHHHHHHHHHhcCCCCCCCHHHH
Confidence 48899999999999999999874 55543 21 1111 111 123446778899999884 33 3678899
Q ss_pred HHHHHhcCCCCCCCCCCHHHHHHH
Q psy15598 130 RDRLLSDGVCDKFNVPSVSSISRI 153 (258)
Q Consensus 130 r~~L~~~Gv~v~~~~pS~STI~Ri 153 (258)
.+.|++.|+.+ |++||...
T Consensus 422 ~~~L~~~Gi~I-----aRRTVaKY 440 (455)
T PRK05932 422 AELLKEQGIDV-----ARRTVAKY 440 (455)
T ss_pred HHHHHHcCCCe-----ehHHHHHH
Confidence 99999999986 99999776
No 75
>PHA02591 hypothetical protein; Provisional
Probab=96.25 E-value=0.009 Score=46.16 Aligned_cols=50 Identities=30% Similarity=0.296 Sum_probs=39.2
Q ss_pred chhhccCCc--ccCCCCCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598 33 GEVNQLGGV--FVNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILA 85 (258)
Q Consensus 33 ~~~nq~~~~--~~~gR~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwik 85 (258)
-.+=|.||+ |+- --+|++.-.-+|.+.|+|..+||+.|||+..+|+++++
T Consensus 30 ~k~vqv~~~ryfi~---~~dd~~~vA~eL~eqGlSqeqIA~~LGVsqetVrKYL~ 81 (83)
T PHA02591 30 QKVVQVGQTRYFVE---SEDDLISVTHELARKGFTVEKIASLLGVSVRKVRRYLE 81 (83)
T ss_pred HHhheeCCEEEEEe---ccchHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHh
Confidence 345566663 222 23578888888899999999999999999999999875
No 76
>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=96.23 E-value=0.011 Score=49.76 Aligned_cols=42 Identities=26% Similarity=0.430 Sum_probs=34.8
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE 89 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE 89 (258)
.++. ...+|+.+..+|++..+||+.||+|++||+++.++.++
T Consensus 6 ~Lte-~qr~VL~Lr~~GlTq~EIAe~LgiS~stV~~~e~ra~k 47 (137)
T TIGR00721 6 FLTE-RQIKVLELREKGLSQKEIAKELKTTRANVSAIEKRAME 47 (137)
T ss_pred CCCH-HHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHhHHH
Confidence 3444 44467777789999999999999999999999999764
No 77
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=96.21 E-value=0.013 Score=47.70 Aligned_cols=42 Identities=17% Similarity=0.037 Sum_probs=37.0
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.++...|.-|+..+-+|++..+||+.||||.+||+.++.|-+
T Consensus 106 ~L~~~~r~ii~l~~~~~~s~~EIA~~l~is~~tV~~~~~ra~ 147 (154)
T PRK06759 106 VLDEKEKYIIFERFFVGKTMGEIALETEMTYYQVRWIYRQAL 147 (154)
T ss_pred hCCHHHHHHHHHHHhcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 477777777777778999999999999999999999999865
No 78
>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=96.15 E-value=0.014 Score=39.10 Aligned_cols=37 Identities=19% Similarity=0.208 Sum_probs=29.1
Q ss_pred HHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHHh
Q psy15598 51 SVRMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILARY 87 (258)
Q Consensus 51 dlR~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwikRy 87 (258)
-.|.-|...++ .+....++|+.||||++|+++-+++|
T Consensus 5 ~E~~~i~~aL~~~~gn~~~aA~~Lgisr~tL~~klkk~ 42 (42)
T PF02954_consen 5 FEKQLIRQALERCGGNVSKAARLLGISRRTLYRKLKKY 42 (42)
T ss_dssp HHHHHHHHHHHHTTT-HHHHHHHHTS-HHHHHHHHHHC
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHhC
Confidence 35666666665 57899999999999999999999886
No 79
>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=96.14 E-value=0.0074 Score=41.87 Aligned_cols=41 Identities=24% Similarity=0.371 Sum_probs=33.6
Q ss_pred HHHHHHHH---cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598 54 MRIVELAQ---LGIRPCDISRQLRVSHGCVSKILARYHETGSIL 94 (258)
Q Consensus 54 ~RIV~L~~---~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~ 94 (258)
.+|++++. .+++..+||+.+|++++||+|+++...+.|-+.
T Consensus 6 l~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~~~g~v~ 49 (52)
T PF09339_consen 6 LRILEALAESGGPLTLSEIARALGLPKSTVHRLLQTLVEEGYVE 49 (52)
T ss_dssp HHHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCcCee
Confidence 45666664 357899999999999999999999999998763
No 80
>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=96.10 E-value=0.093 Score=40.56 Aligned_cols=66 Identities=17% Similarity=0.204 Sum_probs=47.8
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHH
Q psy15598 64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLL 134 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~ 134 (258)
++..++|+.+||+.+||..|.+ .|.+.+....+ ..+..+.++...+...+. ....++..+|...+.
T Consensus 1 ~~~~eva~~~gi~~~tlr~~~~----~Gll~~~~~~~-g~r~y~~~dv~~l~~i~~l~~~g~~~~~i~~~l~ 67 (100)
T cd00592 1 YTIGEVAKLLGVSVRTLRYYEE----KGLLPPERSEN-GYRLYSEEDLERLRLIRRLRELGLSLKEIRELLD 67 (100)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH----CCCcCCCcCCC-CCcccCHHHHHHHHHHHHHHHcCCCHHHHHHHHh
Confidence 4788999999999999999965 46665544333 456788877766665543 225788888887776
No 81
>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=96.10 E-value=0.047 Score=42.71 Aligned_cols=67 Identities=18% Similarity=0.140 Sum_probs=47.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHH
Q psy15598 64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLL 134 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~ 134 (258)
++..++|+.+|||.+|++.|-+ .|.+.|..++.+.-|..++++...|..... ..-.+++.+|++.+.
T Consensus 1 ~~i~eva~~~gvs~~tlR~ye~----~Gll~p~~~~~~gyR~Y~~~~~~~l~~I~~lr~~G~~l~eI~~~l~ 68 (97)
T cd04782 1 FTTGEFAKLCGISKQTLFHYDK----IGLFKPEIVKENGYRYYTLEQFEQLDIILLLKELGISLKEIKDYLD 68 (97)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCccCCCCCccCCHHHHHHHHHHHHHHHcCCCHHHHHHHHh
Confidence 4678999999999999987744 688877544322457788777665554433 334788999988775
No 82
>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=96.09 E-value=0.027 Score=44.25 Aligned_cols=66 Identities=12% Similarity=0.145 Sum_probs=48.8
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH--hCCCCCHHHHHHHHH
Q psy15598 64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ--KDPGIFAWEIRDRLL 134 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~--~nP~ita~EIr~~L~ 134 (258)
++..++|+.+|||.+|++.|. +.|.+.|....+ ..+..+..+...|...+. .+-.+++.+|+..|.
T Consensus 2 ~~i~eva~~~gVs~~tLR~ye----~~Gli~p~r~~~-g~R~Ys~~dv~~l~~I~~L~~~~G~~l~~i~~~l~ 69 (98)
T cd01279 2 YPISVAAELLGIHPQTLRVYD----RLGLVSPARTNG-GGRRYSNNDLELLRQVQRLSQDEGFNLAGIKRIIE 69 (98)
T ss_pred cCHHHHHHHHCcCHHHHHHHH----HCCCCCCCcCCC-CCeeECHHHHHHHHHHHHHHHHCCCCHHHHHHHHH
Confidence 478899999999999999884 367776643333 457788887777776644 335888988887775
No 83
>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=96.08 E-value=0.03 Score=46.27 Aligned_cols=65 Identities=12% Similarity=0.139 Sum_probs=46.1
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH--hCCCCCHHHHHHHHH
Q psy15598 64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ--KDPGIFAWEIRDRLL 134 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~--~nP~ita~EIr~~L~ 134 (258)
++..++|+.+|||.+|++.|.++ |.+.+...+ ..|..++++...|..++. .+-.+++.+|+..|.
T Consensus 2 ysI~eVA~~~GVs~~TLR~wE~~----GLl~p~r~~--G~R~Ys~~dv~rL~~I~~L~~e~G~~l~eI~~~L~ 68 (120)
T cd04767 2 YPIGVVAELLNIHPETLRIWERH----GLIKPARRN--GQRLYSNNDLKRLRFIKKLINEKGLNIAGVKQILS 68 (120)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC----CCCCCcCCC--CcEEECHHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 57899999999999999977764 777665443 457788887776655543 224666666666554
No 84
>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=96.07 E-value=0.014 Score=45.67 Aligned_cols=39 Identities=15% Similarity=0.200 Sum_probs=34.9
Q ss_pred HHHHHHHHH-HHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 50 NSVRMRIVE-LAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 50 ~dlR~RIV~-L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
...|.+|+. +..+|++.++||+.+|||..||.|.-+-.+
T Consensus 35 l~~R~~va~~lL~~g~syreIa~~tgvS~aTItRvsr~Lk 74 (87)
T PF01371_consen 35 LAQRWQVAKELLDEGKSYREIAEETGVSIATITRVSRCLK 74 (87)
T ss_dssp HHHHHHHHHHHHHTTSSHHHHHHHHTSTHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 357899998 899999999999999999999999877665
No 85
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=96.06 E-value=0.016 Score=47.61 Aligned_cols=42 Identities=19% Similarity=0.099 Sum_probs=36.4
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.++...|.-++..+.+|+|..+||+.||||.+||...+.|.+
T Consensus 106 ~Lp~~~r~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Rar 147 (160)
T PRK09642 106 ELPENYRDVVLAHYLEEKSYQEIALQEKIEVKTVEMKLYRAR 147 (160)
T ss_pred hCCHHHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 377777877777778999999999999999999998888865
No 86
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=96.03 E-value=0.0095 Score=40.81 Aligned_cols=47 Identities=26% Similarity=0.333 Sum_probs=36.7
Q ss_pred HHHHHHHHHH-HHcC--C-CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccC
Q psy15598 50 NSVRMRIVEL-AQLG--I-RPCDISRQLRVSHGCVSKILARYHETGSILPG 96 (258)
Q Consensus 50 ~dlR~RIV~L-~~~G--~-S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk 96 (258)
..++..|+.. +..| + +..++|+.|+||++||++.+++..+.|-+...
T Consensus 3 ~~l~~~i~~~~~~~~~~l~s~~~la~~~~vs~~tv~~~l~~L~~~g~i~~~ 53 (60)
T smart00345 3 ERLREDIVSGELRPGDKLPSERELAAQLGVSRTTVREALSRLEAEGLVQRR 53 (60)
T ss_pred HHHHHHHHcCCCCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence 3456666654 2333 4 89999999999999999999999999987533
No 87
>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=96.02 E-value=0.092 Score=42.75 Aligned_cols=67 Identities=18% Similarity=0.235 Sum_probs=47.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc-cCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHh
Q psy15598 64 IRPCDISRQLRVSHGCVSKILARYHETGSIL-PGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLLS 135 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~-pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~~ 135 (258)
+++.++|+.+|||.+||+ -|.+.|.+. +....+ .-|..++++...|..... .+-.+++.||++.|..
T Consensus 1 m~I~e~a~~~gvs~~tlR----~Ye~~GLl~~~~r~~~-gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~ 69 (126)
T cd04783 1 LTIGELAKAAGVNVETIR----YYQRRGLLPEPPRPEG-GYRRYPEETVTRLRFIKRAQELGFTLDEIAELLEL 69 (126)
T ss_pred CCHHHHHHHHCcCHHHHH----HHHHCCCCCCCCcCCC-CCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHhc
Confidence 578899999999999994 446678886 333333 457788877666544432 3347889999888753
No 88
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=96.01 E-value=0.02 Score=57.16 Aligned_cols=83 Identities=20% Similarity=0.339 Sum_probs=60.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH-hhhhC--Ccc-----c---CCCCCCCCCCCCHHHHHHHHHHHHh-CCC--CCHHHH
Q psy15598 64 IRPCDISRQLRVSHGCVSKILAR-YHETG--SIL-----P---GAIGGSKPRVTTPKVVSYIKELKQK-DPG--IFAWEI 129 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikR-yrEtG--sl~-----p---k~rgG~RPrklT~e~~~~I~~lv~~-nP~--ita~EI 129 (258)
++.++||..+|++.|||+|.++. |.++. .+. . ...+| ....+..++..|++++.. ++. ++=.+|
T Consensus 370 LtlkdVAe~lglHeSTVSRa~~~KY~~tp~GifeLK~FFs~~v~~~~g--~~~Ss~~Ik~~Ik~lI~~Ed~~kPLSD~~I 447 (481)
T PRK12469 370 LVLRDVAEELGLHESTISRATGNKYMATPRGTFEFKHFFPRKLEAAGG--GECSAAAVRALIKEMIAAEQAGDPLSDVAL 447 (481)
T ss_pred CcHHHHHHHhCCCcchhhHHhcCceeecCCceEeHHHhhccccCCCCC--ccccHHHHHHHHHHHHHhcCCCCCCCHHHH
Confidence 48899999999999999999864 55544 221 1 11111 123456788899999884 443 678899
Q ss_pred HHHHHhcCCCCCCCCCCHHHHHHH
Q psy15598 130 RDRLLSDGVCDKFNVPSVSSISRI 153 (258)
Q Consensus 130 r~~L~~~Gv~v~~~~pS~STI~Ri 153 (258)
.+.|++.|+.+ |++||...
T Consensus 448 ~~~L~~~GI~I-----ARRTVAKY 466 (481)
T PRK12469 448 AEMLAGRGVLI-----ARRTVAKY 466 (481)
T ss_pred HHHHHhcCCCe-----echhHHHH
Confidence 99999999986 99999765
No 89
>TIGR01529 argR_whole arginine repressor. This model includes most members of the arginine-responsive transcriptional regulator family ArgR. This hexameric protein binds DNA at its amino end to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbor-joining tree, some of these paralogous sequences show long branches and differ significantly in an otherwise well-conserved C-terminal region motif GT[VIL][AC]GDDT. These paralogs are excluded from the seed and score in the gray zone of this model, between trusted and noise cutoffs.
Probab=96.00 E-value=0.013 Score=49.55 Aligned_cols=49 Identities=20% Similarity=0.162 Sum_probs=43.4
Q ss_pred HHHHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCCCCCC
Q psy15598 111 VSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSSIVQ 164 (258)
Q Consensus 111 ~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~~~~~ 164 (258)
...|.+++++++..++.||.+.|.+.|+.+ |.+||+|.|++.+..|...
T Consensus 4 ~~~i~~Li~~~~i~tqeeL~~~L~~~G~~v-----sqaTIsRdL~elglvk~~~ 52 (146)
T TIGR01529 4 QERIKEIITEEKISTQEELVALLKAEGIEV-----TQATVSRDLRELGAVKVRD 52 (146)
T ss_pred HHHHHHHHHcCCCCCHHHHHHHHHHhCCCc-----CHHHHHHHHHHcCCEEEEC
Confidence 456888889999999999999999999986 9999999999999987554
No 90
>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=96.00 E-value=0.089 Score=43.01 Aligned_cols=67 Identities=18% Similarity=0.208 Sum_probs=47.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHH
Q psy15598 64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLL 134 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~ 134 (258)
+++.++|+.+|||..|++-|-+ .|.+.|..+..+.-|..++++...|..... .+-.+++.||+..+.
T Consensus 1 m~I~e~a~~~gvs~~tlRyYe~----~GLl~~~~r~~~g~R~Y~~~~~~~l~~I~~lr~~G~sL~eI~~~l~ 68 (127)
T cd01108 1 MNIGEAAKLTGLSAKMIRYYEE----IGLIPPPSRSDNGYRVYNQRDIEELRFIRRARDLGFSLEEIRELLA 68 (127)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCCcCCCCceecCHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 5789999999999999875544 577764333222457788877766655543 345789999998775
No 91
>PRK11050 manganese transport regulator MntR; Provisional
Probab=96.00 E-value=0.044 Score=46.22 Aligned_cols=43 Identities=30% Similarity=0.327 Sum_probs=35.0
Q ss_pred HHHHHHHH--cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccC
Q psy15598 54 MRIVELAQ--LGIRPCDISRQLRVSHGCVSKILARYHETGSILPG 96 (258)
Q Consensus 54 ~RIV~L~~--~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk 96 (258)
..|..++. .+.+.++||+.|+||+++|++++++..+.|.+...
T Consensus 40 ~~I~~~l~~~~~~t~~eLA~~l~is~stVsr~l~~Le~~GlI~r~ 84 (152)
T PRK11050 40 ELIADLIAEVGEARQVDIAARLGVSQPTVAKMLKRLARDGLVEMR 84 (152)
T ss_pred HHHHHHHHhcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence 34444443 46899999999999999999999999999977543
No 92
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=95.97 E-value=0.024 Score=47.36 Aligned_cols=52 Identities=23% Similarity=0.305 Sum_probs=44.7
Q ss_pred CCCCCCHHH----HHHHHHHHH-cC-CCHHHHHHHhCCCHHHHHHHHHHhhhhCCccc
Q psy15598 44 NGRPLPNSV----RMRIVELAQ-LG-IRPCDISRQLRVSHGCVSKILARYHETGSILP 95 (258)
Q Consensus 44 ~gR~~S~dl----R~RIV~L~~-~G-~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~p 95 (258)
|+++++.+. ..+||++++ .| ++..+++..+|+++.||.+.++...++|.|..
T Consensus 1 Ma~~~T~eer~eLk~rIvElVRe~GRiTi~ql~~~TGasR~Tvk~~lreLVa~G~l~~ 58 (127)
T PF06163_consen 1 MARVFTPEEREELKARIVELVREHGRITIKQLVAKTGASRNTVKRYLRELVARGDLYR 58 (127)
T ss_pred CCCcCCHHHHHHHHHHHHHHHHHcCCccHHHHHHHHCCCHHHHHHHHHHHHHcCCeEe
Confidence 677888764 577888876 56 89999999999999999999999999999843
No 93
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=95.97 E-value=0.019 Score=47.41 Aligned_cols=42 Identities=21% Similarity=0.261 Sum_probs=35.7
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.++...|.-++..+-.|++.++||+.||||.+||+.++.|-+
T Consensus 128 ~L~~~~r~vl~l~~~~~~s~~eIA~~lgis~~tV~~~l~ra~ 169 (182)
T PRK09652 128 SLPEELRTAITLREIEGLSYEEIAEIMGCPIGTVRSRIFRAR 169 (182)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 477777776666667999999999999999999999998865
No 94
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=95.94 E-value=0.019 Score=47.27 Aligned_cols=41 Identities=20% Similarity=0.206 Sum_probs=37.0
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.++...|.-++..+ +|++..+||+.||||.+||++.+.|-+
T Consensus 112 ~L~~~~r~il~l~~-~g~s~~eIA~~lgis~~tV~~~i~ra~ 152 (166)
T PRK09639 112 KMTERDRTVLLLRF-SGYSYKEIAEALGIKESSVGTTLARAK 152 (166)
T ss_pred cCCHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 48888888777878 999999999999999999999998875
No 95
>cd04768 HTH_BmrR-like Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators. Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=95.94 E-value=0.049 Score=42.49 Aligned_cols=67 Identities=15% Similarity=0.104 Sum_probs=48.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHH
Q psy15598 64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLL 134 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~ 134 (258)
++..++|+.+|||.+|++-|-+ .|.+.|..+..+.-|..+.++...|..... .+-.+++.+|++.+.
T Consensus 1 ~ti~eva~~~gvs~~tLRyye~----~Gll~p~~~~~~gyR~Y~~~~l~~l~~I~~lr~~G~~l~~I~~~l~ 68 (96)
T cd04768 1 LTIGEFAKLAGVSIRTLRHYDD----IGLFKPAKIAENGYRYYSYAQLYQLQFILFLRELGFSLAEIKELLD 68 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCccCCCCeeeCCHHHHHHHHHHHHHHHcCCCHHHHHHHHh
Confidence 4688999999999999977765 487877554322457788877666655533 334789999988775
No 96
>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=95.94 E-value=0.02 Score=44.86 Aligned_cols=42 Identities=29% Similarity=0.300 Sum_probs=35.1
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.++...|.-|...+-.|++..+||+.||||++||++++++-+
T Consensus 110 ~L~~~~~~ii~~~~~~g~s~~eIA~~l~~s~~~v~~~~~~~~ 151 (158)
T TIGR02937 110 KLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRAR 151 (158)
T ss_pred hCCHHHHHHHhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 467777765555557899999999999999999999999875
No 97
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=95.93 E-value=0.019 Score=48.59 Aligned_cols=43 Identities=21% Similarity=0.220 Sum_probs=36.0
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE 89 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE 89 (258)
.++.+.|.-|+..+-+|++..+||+.||||.+||+.++.|-++
T Consensus 133 ~L~~~~r~i~~l~~~~~~s~~eIA~~lgis~~tV~~~l~ra~~ 175 (182)
T PRK12537 133 QLEPARRNCILHAYVDGCSHAEIAQRLGAPLGTVKAWIKRSLK 175 (182)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHHHCCChhhHHHHHHHHHH
Confidence 4677777656666679999999999999999999999998763
No 98
>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=95.93 E-value=0.021 Score=49.67 Aligned_cols=45 Identities=11% Similarity=0.030 Sum_probs=42.4
Q ss_pred CCHHHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCC
Q psy15598 48 LPNSVRMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILARYHETGS 92 (258)
Q Consensus 48 ~S~dlR~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwikRyrEtGs 92 (258)
++.+.|.++-.++- ++++...||..+|||.+|++||.++-++.|+
T Consensus 3 h~~e~R~~~R~~YV~~~~sLe~aA~~~gVs~~TarrWK~~Ak~~GD 48 (165)
T PF08822_consen 3 HPQETRDAVRRAYVFDRLSLEQAAAKCGVSYATARRWKREAKAKGD 48 (165)
T ss_pred CcHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHHHHHHcCC
Confidence 67899999999986 8899999999999999999999999999996
No 99
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=95.92 E-value=0.021 Score=46.71 Aligned_cols=43 Identities=16% Similarity=0.160 Sum_probs=36.7
Q ss_pred CCCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 46 RPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 46 R~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
..++...|.-++..+-+|++.++||+.||||.+||+..+.|-+
T Consensus 105 ~~Lp~~~r~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~ra~ 147 (161)
T PRK09047 105 QKLPARQREAFLLRYWEDMDVAETAAAMGCSEGSVKTHCSRAT 147 (161)
T ss_pred HhCCHHHHHHHHHHHHhcCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 3477777776666678999999999999999999999988865
No 100
>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=95.92 E-value=0.13 Score=42.08 Aligned_cols=67 Identities=15% Similarity=0.159 Sum_probs=48.2
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHH
Q psy15598 64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLL 134 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~ 134 (258)
|++.++|+.+|||..|++-| .+.|.+.|..+..+.-|..++++...|..... ..-.+++.||++.|.
T Consensus 1 m~I~e~a~~~gvs~~tlRyY----e~~GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~ 68 (127)
T TIGR02044 1 MNIGQVAKLTGLSSKMIRYY----EEKGLIPPPLRSEGGYRTYTQQHLDELRLISRARQVGFSLEECKELLN 68 (127)
T ss_pred CCHHHHHHHHCcCHHHHHHH----HHCCCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHCCCCHHHHHHHHH
Confidence 57899999999999998644 45677766444322457888887776655533 345789999998875
No 101
>PF12728 HTH_17: Helix-turn-helix domain
Probab=95.90 E-value=0.01 Score=40.58 Aligned_cols=23 Identities=13% Similarity=0.215 Sum_probs=21.1
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q psy15598 64 IRPCDISRQLRVSHGCVSKILAR 86 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikR 86 (258)
++..|+|+.||||++||++|+++
T Consensus 2 lt~~e~a~~l~is~~tv~~~~~~ 24 (51)
T PF12728_consen 2 LTVKEAAELLGISRSTVYRWIRQ 24 (51)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHc
Confidence 57899999999999999999975
No 102
>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=95.89 E-value=0.022 Score=46.52 Aligned_cols=43 Identities=26% Similarity=0.271 Sum_probs=37.1
Q ss_pred CCCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 46 RPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 46 R~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
..+|.+.|.-++..+-+|++.++||+.||||.+||+..+.|-+
T Consensus 110 ~~L~~~~r~v~~l~~~~g~~~~eIA~~l~is~~tv~~~l~Rar 152 (159)
T TIGR02989 110 EKLPERQRELLQLRYQRGVSLTALAEQLGRTVNAVYKALSRLR 152 (159)
T ss_pred HHCCHHHHHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 3577788776666677999999999999999999999999876
No 103
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=95.89 E-value=0.02 Score=47.14 Aligned_cols=42 Identities=26% Similarity=0.233 Sum_probs=36.3
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.++...|.-++..+.+|++..+||+.||+|.+||++++.|.+
T Consensus 125 ~L~~~~r~i~~l~~~~~~~~~eIA~~lgis~~tv~~~~~ra~ 166 (179)
T PRK11924 125 ALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRAR 166 (179)
T ss_pred hCCHHHHHHhhHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 377777776666667999999999999999999999999875
No 104
>COG1508 RpoN DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription]
Probab=95.89 E-value=0.033 Score=55.16 Aligned_cols=84 Identities=15% Similarity=0.238 Sum_probs=61.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH-hhhhC--Ccc--------cCCCCCCCCCCCCHHHHHHHHHHHH-hCC--CCCHHHH
Q psy15598 64 IRPCDISRQLRVSHGCVSKILAR-YHETG--SIL--------PGAIGGSKPRVTTPKVVSYIKELKQ-KDP--GIFAWEI 129 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikR-yrEtG--sl~--------pk~rgG~RPrklT~e~~~~I~~lv~-~nP--~ita~EI 129 (258)
+..++||..+|++.|||+|.++. |..+. .++ -...+| .-.-.++.++..|++++. +++ -++=.+|
T Consensus 331 L~LrdvA~~i~~HESTISRai~nKy~~tprG~feLK~FFs~~i~s~~g-g~~~S~~~Ik~~Ik~lI~~E~~~~pLSD~kI 409 (444)
T COG1508 331 LVLRDVADEIGMHESTISRAITNKYLATPRGLFELKYFFSSSLASSEG-GEASSTEAIKALIKKLIEAEDKKKPLSDSKI 409 (444)
T ss_pred ccHHHHHHHhCccHHHHHHHHhcccccCCcceeeHHHHHHHhccCCCC-CccccHHHHHHHHHHHHhhccCCCCCCHHHH
Confidence 68899999999999999998864 55544 321 111112 112234588999999987 455 4678889
Q ss_pred HHHHHhcCCCCCCCCCCHHHHHHH
Q psy15598 130 RDRLLSDGVCDKFNVPSVSSISRI 153 (258)
Q Consensus 130 r~~L~~~Gv~v~~~~pS~STI~Ri 153 (258)
.+.|++.|+.+ +++||...
T Consensus 410 a~lLkekGi~i-----ARRTVAKY 428 (444)
T COG1508 410 AELLKEKGIDV-----ARRTVAKY 428 (444)
T ss_pred HHHHHHcCCch-----hHHhHHHH
Confidence 99999999986 99999654
No 105
>cd04788 HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR. Helix-turn-helix (HTH) transcription regulators NolA and AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp. NC92, NolA is required for efficient nodulation of host plants. In Xanthomonas albilineans, AlbR regulates the expression of the pathotoxin, albicidin. These proteins are putatively comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=95.89 E-value=0.055 Score=42.22 Aligned_cols=67 Identities=13% Similarity=0.128 Sum_probs=47.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHH
Q psy15598 64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLL 134 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~ 134 (258)
|+..++|+.+|||.+|++.|-+ .|.+.|..+..+.-+..++++...|..... .+-.+++.||+..+.
T Consensus 1 m~i~eva~~~gvs~~tlR~ye~----~Gll~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~~l~eI~~~l~ 68 (96)
T cd04788 1 WKIGELARRTGLSVRTLHHYDH----IGLLSPSQRTEGGHRLYDRADIRRLHQIIALRRLGFSLREIGRALD 68 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCccCCCCceeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHh
Confidence 5788999999999999987764 677766443222457788877665554433 234788999988775
No 106
>PHA00675 hypothetical protein
Probab=95.88 E-value=0.019 Score=44.19 Aligned_cols=40 Identities=25% Similarity=0.297 Sum_probs=34.9
Q ss_pred CCHHHHHHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHHHHh
Q psy15598 48 LPNSVRMRIVELA-QLGIRPCDISRQLRVSHGCVSKILARY 87 (258)
Q Consensus 48 ~S~dlR~RIV~L~-~~G~S~~eIAr~LGVSrsTVsRwikRy 87 (258)
|....=.+|..+. .+|.|..+||+.||||++||+.|.+..
T Consensus 23 Lt~~qV~~IR~l~~r~G~s~~~IA~~fGVsrstV~~I~~gk 63 (78)
T PHA00675 23 LTDAEVERIRELHEVEGMSYAVLAEKFEQSKGAIAKICRYE 63 (78)
T ss_pred cCHHHHHHHHHHHHhcCccHHHHHHHhCCCHHHHHHHHccc
Confidence 7776667788888 799999999999999999999998654
No 107
>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=95.86 E-value=0.04 Score=42.44 Aligned_cols=66 Identities=9% Similarity=0.106 Sum_probs=48.4
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH--hCCCCCHHHHHHHHH
Q psy15598 64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ--KDPGIFAWEIRDRLL 134 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~--~nP~ita~EIr~~L~ 134 (258)
++..++|+.+|||.+||+.|.+ .|-+.|....+ ..+..++.+...+...+. .+-.++..+|+..|.
T Consensus 2 ~~i~e~A~~~gvs~~tLr~ye~----~Gli~p~r~~~-g~R~y~~~dv~~l~~i~~L~~d~g~~l~~i~~~l~ 69 (91)
T cd04766 2 YVISVAAELSGMHPQTLRLYER----LGLLSPSRTDG-GTRRYSERDIERLRRIQRLTQELGVNLAGVKRILE 69 (91)
T ss_pred cCHHHHHHHHCcCHHHHHHHHH----CCCcCCCcCCC-CCeeECHHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 4788999999999999999854 58887754433 457788887777766654 335778887766653
No 108
>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=95.86 E-value=0.024 Score=45.67 Aligned_cols=42 Identities=19% Similarity=0.169 Sum_probs=35.1
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.++...|.-+...+-+|++..+||+.||||.+||+.++.|-+
T Consensus 113 ~L~~~~r~il~l~~~~~~~~~eIA~~lgis~~tv~~~~~ra~ 154 (161)
T TIGR02985 113 KLPEQCRKIFILSRFEGKSYKEIAEELGISVKTVEYHISKAL 154 (161)
T ss_pred HCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 467666665555577999999999999999999999999865
No 109
>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=95.86 E-value=0.12 Score=40.60 Aligned_cols=68 Identities=16% Similarity=0.202 Sum_probs=49.8
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHh--CCCCCHHHHHHHHHh
Q psy15598 64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQK--DPGIFAWEIRDRLLS 135 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~--nP~ita~EIr~~L~~ 135 (258)
++..++|+.+|||.+||+.|.+ .|.+.|..+.+..-+..++++...|.....- +-.++..+|+..|..
T Consensus 1 m~I~eva~~~gvs~~tlR~Ye~----~GLl~p~~r~~~g~r~Y~~~dv~~l~~I~~L~~~~G~~l~~I~~~l~~ 70 (95)
T cd04780 1 MRMSELSKRSGVSVATIKYYLR----EGLLPEGRRLAPNQAEYSEAHVERLRLIRALQQEGGLPISQIKEVLDA 70 (95)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCcCCCCCCeecCHHHHHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 5788999999999999877766 5777664333323467888888877766442 247889999887765
No 110
>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=95.85 E-value=0.0098 Score=39.26 Aligned_cols=23 Identities=17% Similarity=0.258 Sum_probs=20.9
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q psy15598 64 IRPCDISRQLRVSHGCVSKILAR 86 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikR 86 (258)
++..++|+.||||++||++|++.
T Consensus 2 lt~~e~a~~lgis~~ti~~~~~~ 24 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTVYRLIHE 24 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHc
Confidence 57899999999999999999864
No 111
>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=95.85 E-value=0.11 Score=42.80 Aligned_cols=67 Identities=15% Similarity=0.150 Sum_probs=48.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHH
Q psy15598 64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLL 134 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~ 134 (258)
|++.++|+.+|||.+|++-| .+.|.+.|....++.-|..++++...|..... .+-.+++.||++.|.
T Consensus 1 m~IgE~A~~~gvs~~TLRyY----E~~GLl~p~r~~~~gyR~Y~~~~~~~l~~I~~lr~~G~sL~eI~~~l~ 68 (133)
T cd04787 1 MKVKELANAAGVTPDTVRFY----TRIGLLRPTRDPVNGYRLYSEKDLSRLRFILSARQLGFSLKDIKEILS 68 (133)
T ss_pred CCHHHHHHHHCcCHHHHHHH----HHCCCCCCCcCCCCCeeeCCHHHHHHHHHHHHHHHcCCCHHHHHHHHh
Confidence 57889999999999998444 56788877654322457788877666555432 335789999998886
No 112
>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=95.85 E-value=0.031 Score=38.65 Aligned_cols=40 Identities=25% Similarity=0.235 Sum_probs=31.9
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHh
Q psy15598 65 RPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQK 120 (258)
Q Consensus 65 S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~ 120 (258)
+.++||+..|||.+||+|.++.- ...+++.+++|.+..++
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 56899999999999999988642 23678888888877654
No 113
>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=95.85 E-value=0.017 Score=40.68 Aligned_cols=40 Identities=20% Similarity=0.259 Sum_probs=32.3
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 48 LPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 48 ~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
+|...+ +|+.++..|++..+||+.++||.+||+..+++-.
T Consensus 4 LT~~E~-~vl~~l~~G~~~~eIA~~l~is~~tV~~~~~~i~ 43 (58)
T PF00196_consen 4 LTEREL-EVLRLLAQGMSNKEIAEELGISEKTVKSHRRRIM 43 (58)
T ss_dssp S-HHHH-HHHHHHHTTS-HHHHHHHHTSHHHHHHHHHHHHH
T ss_pred cCHHHH-HHHHHHHhcCCcchhHHhcCcchhhHHHHHHHHH
Confidence 344333 5888899999999999999999999999988865
No 114
>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID. Members of this protein are the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if and only if the species is capable of endospore formation as occurs in the model species Bacillus subtilis. SpoIIID is a DNA binding protein that, in B. subtilis, downregulates many genes but also turns on ten genes.
Probab=95.81 E-value=0.042 Score=42.38 Aligned_cols=57 Identities=14% Similarity=0.128 Sum_probs=43.4
Q ss_pred CCHHHHHHHHHHHHcC-CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH
Q psy15598 48 LPNSVRMRIVELAQLG-IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ 119 (258)
Q Consensus 48 ~S~dlR~RIV~L~~~G-~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~ 119 (258)
|=.+-+.+|++++..| .+..+||+.+|||++||++.++. .+..++++.++.|.+...
T Consensus 3 ~~~~R~~~I~e~l~~~~~ti~dvA~~~gvS~~TVsr~L~~---------------~~~~Vs~~Tr~rV~~aa~ 60 (80)
T TIGR02844 3 YIEERVLEIGKYIVETKATVRETAKVFGVSKSTVHKDVTE---------------RLPEINPELAEEVKEVLD 60 (80)
T ss_pred cHHHHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHhcC---------------CCCCCCHHHHHHHHHHHc
Confidence 3355678888887656 69999999999999999996521 112367888888888887
No 115
>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=95.79 E-value=0.026 Score=47.40 Aligned_cols=43 Identities=14% Similarity=-0.026 Sum_probs=37.0
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE 89 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE 89 (258)
.++...|.-++..+-+|+|..+||+.||||.+||...+.|-+.
T Consensus 134 ~Lp~~~r~v~~l~~~~g~s~~EIA~~lgis~~tVk~~l~Rar~ 176 (183)
T TIGR02999 134 QVDPRQAEVVELRFFAGLTVEEIAELLGVSVRTVERDWRFARA 176 (183)
T ss_pred cCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 3788888766666779999999999999999999999988653
No 116
>cd04772 HTH_TioE_rpt1 First Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD contains the N-terminal or first repeat (rpt1) of these tandem MerR-like domain proteins.
Probab=95.77 E-value=0.15 Score=40.09 Aligned_cols=67 Identities=19% Similarity=0.235 Sum_probs=46.4
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHh
Q psy15598 65 RPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLS 135 (258)
Q Consensus 65 S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~nP~ita~EIr~~L~~ 135 (258)
+..++|+.+|||.+|++.| .+.|.+.+..+....-+..++++...|..+..-...+++.++++.+..
T Consensus 2 ~i~e~A~~~gvs~~tlR~Y----e~~Gll~~~~r~~~g~R~Y~~~~v~~l~~I~~l~~g~~l~~i~~~~~~ 68 (99)
T cd04772 2 RTVDLARAIGLSPQTVRNY----ESLGLIPPAERTANGYRIYTDKHIAALRAYRALLPGYGYRVAQRIMRA 68 (99)
T ss_pred CHHHHHHHHCcCHHHHHHH----HHcCCCCCCCcCCCCCeecCHHHHHHHHHHHHHhhCCCHHHHHHHHHH
Confidence 5789999999999999866 447877653332223577888877776655443247778887765553
No 117
>PF01316 Arg_repressor: Arginine repressor, DNA binding domain; InterPro: IPR020900 The arginine dihydrolase (AD) pathway is found in many prokaryotes and some primitive eukaryotes, an example of the latter being Giardia lamblia (Giardia intestinalis) []. The three-enzyme anaerobic pathway breaks down L-arginine to form 1 mol of ATP, carbon dioxide and ammonia. In simpler bacteria, the first enzyme, arginine deiminase, can account for up to 10% of total cell protein []. Most prokaryotic arginine deiminase pathways are under the control of a repressor gene, termed ArgR []. This is a negative regulator, and will only release the arginine deiminase operon for expression in the presence of arginine []. The crystal structure of apo-ArgR from Bacillus stearothermophilus has been determined to 2.5A by means of X-ray crystallography []. The protein exists as a hexamer of identical subunits, and is shown to have six DNA-binding domains, clustered around a central oligomeric core when bound to arginine. It predominantly interacts with A.T residues in ARG boxes. This hexameric protein binds DNA at its N terminus to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbour-joining tree, some of these paralogous sequences show long branches and differ significantly from the well-conserved C-terminal region. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0006525 arginine metabolic process; PDB: 1AOY_A 3V4G_A 3LAJ_D 3FHZ_A 3LAP_B 3ERE_D 2P5L_C 1F9N_D 2P5K_A 1B4A_A ....
Probab=95.77 E-value=0.023 Score=42.80 Aligned_cols=51 Identities=22% Similarity=0.139 Sum_probs=39.4
Q ss_pred HHHHHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCCCCCCC
Q psy15598 110 VVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSSIVQH 165 (258)
Q Consensus 110 ~~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~~~~~~ 165 (258)
-...|.+++.++.-.+..||.+.|.+.|+.+ +.+||+|-|+..+..|....
T Consensus 6 R~~~I~~li~~~~i~sQ~eL~~~L~~~Gi~v-----TQaTiSRDLkeL~~vKv~~~ 56 (70)
T PF01316_consen 6 RQELIKELISEHEISSQEELVELLEEEGIEV-----TQATISRDLKELGAVKVPDG 56 (70)
T ss_dssp HHHHHHHHHHHS---SHHHHHHHHHHTT-T-------HHHHHHHHHHHT-EEEECT
T ss_pred HHHHHHHHHHHCCcCCHHHHHHHHHHcCCCc-----chhHHHHHHHHcCcEEeeCC
Confidence 3678999999999889999999999999986 99999999999999987643
No 118
>PHA00738 putative HTH transcription regulator
Probab=95.75 E-value=0.016 Score=47.16 Aligned_cols=51 Identities=27% Similarity=0.202 Sum_probs=44.1
Q ss_pred CHHHHHHHHHHHHc--CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCC
Q psy15598 49 PNSVRMRIVELAQL--GIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIG 99 (258)
Q Consensus 49 S~dlR~RIV~L~~~--G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rg 99 (258)
-+..|.+||.++.. ++++++|+..|++|++||++-++--++-|-|...+.|
T Consensus 10 ~dptRr~IL~lL~~~e~~~V~eLae~l~lSQptVS~HLKvLreAGLV~srK~G 62 (108)
T PHA00738 10 AKILRRKILELIAENYILSASLISHTLLLSYTTVLRHLKILNEQGYIELYKEG 62 (108)
T ss_pred CCHHHHHHHHHHHHcCCccHHHHHHhhCCCHHHHHHHHHHHHHCCceEEEEEC
Confidence 34689999998765 3899999999999999999999999999988766554
No 119
>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=95.73 E-value=0.052 Score=45.34 Aligned_cols=66 Identities=18% Similarity=0.184 Sum_probs=49.2
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHH
Q psy15598 64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLL 134 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~ 134 (258)
+++.++|+.+|||.+|++-|-+. |.+.|....+ .-|..++++...|..+.. .+-.+++.||++.|.
T Consensus 2 ~~I~EvA~~~Gvs~~tLRyYE~~----GLl~p~r~~~-g~R~Y~~~dl~~l~~I~~lr~~G~sl~eI~~~l~ 68 (139)
T cd01110 2 LSVGEVAKRSGVAVSALHFYEQK----GLIASWRNAG-NQRRYPRDVLRRIAFIKVAQRLGLSLAEIAEALA 68 (139)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHC----CCCCCCcCCC-CCeEECHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 68899999999999999776654 7776643333 457788887776665544 345789999998875
No 120
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=95.72 E-value=0.027 Score=47.30 Aligned_cols=42 Identities=12% Similarity=0.078 Sum_probs=36.9
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.++.+.|.-++..+-+|+|..+||+.||||.+||+..+.|.+
T Consensus 129 ~L~~~~r~i~~l~~~~g~s~~eIA~~lgis~~tV~~~l~Rar 170 (179)
T PRK12514 129 ELEKDRAAAVRRAYLEGLSYKELAERHDVPLNTMRTWLRRSL 170 (179)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHHHCCChHHHHHHHHHHH
Confidence 377788877777778999999999999999999999998865
No 121
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=95.71 E-value=0.028 Score=47.40 Aligned_cols=43 Identities=19% Similarity=0.119 Sum_probs=36.7
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE 89 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE 89 (258)
.++...|.-++..+-+|++..+||+.+|||.+||+.++.|.++
T Consensus 135 ~L~~~~r~vl~l~~~~~~s~~eIA~~lgis~~~V~~~l~ra~~ 177 (186)
T PRK13919 135 ALSPEERRVIEVLYYQGYTHREAAQLLGLPLGTLKTRARRALS 177 (186)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4777777666666789999999999999999999999988763
No 122
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=95.69 E-value=0.031 Score=46.13 Aligned_cols=43 Identities=21% Similarity=0.233 Sum_probs=35.7
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE 89 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE 89 (258)
.++.+.|.-++..+-+|++..+||+.||||.+||...+.|-++
T Consensus 113 ~L~~~~r~v~~L~~~~g~s~~EIA~~l~is~~tV~~~l~ra~~ 155 (161)
T PRK12528 113 GLPPLVKRAFLLAQVDGLGYGEIATELGISLATVKRYLNKAAM 155 (161)
T ss_pred HCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4666777655555679999999999999999999999998764
No 123
>cd04789 HTH_Cfa Helix-Turn-Helix DNA binding domain of the Cfa transcription regulator. Putative helix-turn-helix (HTH) MerR-like transcription regulator; the N-terminal domain of Cfa, a cyclopropane fatty acid synthase and other related methyltransferases. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=95.68 E-value=0.068 Score=42.21 Aligned_cols=66 Identities=12% Similarity=0.037 Sum_probs=46.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHH
Q psy15598 64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLL 134 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~ 134 (258)
++..++|+.+|||.+|++.|-+ .|.+.|....+ .-+..++++...|..... .+-.+++.+|+..+.
T Consensus 2 ~~i~eva~~~gvs~~tlR~ye~----~Gll~~~r~~~-g~R~Y~~~~l~~l~~I~~l~~~G~~l~ei~~~l~ 68 (102)
T cd04789 2 YTISELAEKAGISRSTLLYYEK----LGLITGTRNAN-GYRLYPDSDLQRLLLIQQLQAGGLSLKECLACLQ 68 (102)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCcCCC-CCeeCCHHHHHHHHHHHHHHHCCCCHHHHHHHHc
Confidence 5789999999999999985544 58877643332 457788877766654422 334788888887663
No 124
>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=95.65 E-value=0.073 Score=42.66 Aligned_cols=67 Identities=18% Similarity=0.229 Sum_probs=49.4
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHh
Q psy15598 64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLLS 135 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~~ 135 (258)
+++.++|+.+|||.+|++-|-+ .|-+.|....+ .-|..++++...|..... ..-.+++.||++.+..
T Consensus 1 m~i~eva~~~gvs~~tlR~Ye~----~GLl~p~r~~~-g~R~Y~~~~~~~l~~I~~lr~~G~sl~eI~~~l~~ 68 (112)
T cd01282 1 MRIGELAARTGVSVRSLRYYEE----QGLLVPERSAN-GYRDYDEAAVDRVRQIRRLLAAGLTLEEIREFLPC 68 (112)
T ss_pred CCHHHHHHHHCCCHHHHHHHHH----CCCCCCCcCCC-CCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 5788999999999999987755 48887644333 457888887776665544 3347899999987763
No 125
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=95.64 E-value=0.035 Score=36.98 Aligned_cols=39 Identities=23% Similarity=0.285 Sum_probs=32.9
Q ss_pred HHHHHH--cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598 56 IVELAQ--LGIRPCDISRQLRVSHGCVSKILARYHETGSIL 94 (258)
Q Consensus 56 IV~L~~--~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~ 94 (258)
|+.... .+++..+||+.|++|++||++.+++..+.|-+.
T Consensus 5 il~~l~~~~~~s~~~l~~~l~~s~~tv~~~l~~L~~~g~i~ 45 (53)
T smart00420 5 ILELLAQQGKVSVEELAELLGVSEMTIRRDLNKLEEQGLLT 45 (53)
T ss_pred HHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 444432 468999999999999999999999999998775
No 126
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=95.63 E-value=0.025 Score=47.92 Aligned_cols=44 Identities=25% Similarity=0.239 Sum_probs=39.6
Q ss_pred CCCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598 46 RPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE 89 (258)
Q Consensus 46 R~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE 89 (258)
..++.+.|.-++...-+|+|..+||+.+|||.+||..++.|-++
T Consensus 126 ~~Lp~~~R~~~~l~~~~gls~~EIA~~l~i~~~tVks~l~ra~~ 169 (182)
T COG1595 126 ARLPPRQREAFLLRYLEGLSYEEIAEILGISVGTVKSRLHRARK 169 (182)
T ss_pred HhCCHHHhHHhhhHhhcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 35888999888888889999999999999999999999998764
No 127
>TIGR02043 ZntR Zn(II)-responsive transcriptional regulator. This model represents the zinc and cadmium (II) responsive transcriptional activator of the gamma proteobacterial zinc efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-Cys-X(8-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=95.61 E-value=0.071 Score=43.93 Aligned_cols=67 Identities=18% Similarity=0.164 Sum_probs=49.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHH
Q psy15598 64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLL 134 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~ 134 (258)
+++.++|+.+|||..|++.|-+ .|.+.|..+....-|..++++...|..+.. .+-.+++.||++.+.
T Consensus 2 ~~I~e~a~~~gvs~~tlR~Ye~----~GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sl~eI~~~l~ 69 (131)
T TIGR02043 2 FQIGELAKLCGVTSDTLRFYEK----NGLIKPAGRTDSGYRLYTDEDQKRLRFILKAKELGFTLDEIKELLS 69 (131)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCCcCCCCceecCHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 5789999999999999877664 477776544322457788877666655533 345889999998886
No 128
>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=95.61 E-value=0.029 Score=46.10 Aligned_cols=42 Identities=24% Similarity=0.269 Sum_probs=35.3
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598 48 LPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE 89 (258)
Q Consensus 48 ~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE 89 (258)
++...|.-++..+-+|++..+||..||||.+||+.++.|-++
T Consensus 111 L~~~~r~i~~l~~~~g~s~~eIA~~lgis~~tV~~~l~ra~~ 152 (162)
T TIGR02983 111 LPARQRAVVVLRYYEDLSEAQVAEALGISVGTVKSRLSRALA 152 (162)
T ss_pred CCHHHHHHhhhHHHhcCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 566666666566679999999999999999999999998764
No 129
>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=95.60 E-value=0.034 Score=45.80 Aligned_cols=43 Identities=16% Similarity=0.108 Sum_probs=36.4
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE 89 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE 89 (258)
.++...|.-++..+-+|++..+||+.||||.+||...+.|-++
T Consensus 122 ~L~~~~r~vl~l~~~~g~s~~eIA~~l~is~~tv~~~l~ra~~ 164 (170)
T TIGR02952 122 ILTPKQQHVIALRFGQNLPIAEVARILGKTEGAVKILQFRAIK 164 (170)
T ss_pred hCCHHHHHHHHHHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 5777777666666779999999999999999999999988763
No 130
>PF07900 DUF1670: Protein of unknown function (DUF1670); InterPro: IPR012872 The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=95.57 E-value=0.13 Score=46.60 Aligned_cols=95 Identities=23% Similarity=0.222 Sum_probs=64.7
Q ss_pred HHHHHHHHH----HcC--CCHHHHHHHhCCCHHHHHHHHHHhhhh-CCcccCCCCC-CCCCCCCHHHHHHHHHHHHhCCC
Q psy15598 52 VRMRIVELA----QLG--IRPCDISRQLRVSHGCVSKILARYHET-GSILPGAIGG-SKPRVTTPKVVSYIKELKQKDPG 123 (258)
Q Consensus 52 lR~RIV~L~----~~G--~S~~eIAr~LGVSrsTVsRwikRyrEt-Gsl~pk~rgG-~RPrklT~e~~~~I~~lv~~nP~ 123 (258)
...+|+.+. ++| ++..++|..|+||.+||++-++.|++. |.+.|...-- ...+.+ .+...|.++..+ .
T Consensus 88 r~~rIvRl~~EAy~QgglLT~~Dla~LL~~S~~TI~~~i~~yq~e~g~vvPtrG~i~DiGp~~--tHK~~ii~~~l~--g 163 (220)
T PF07900_consen 88 RKHRIVRLTNEAYDQGGLLTQEDLAMLLGISPRTISKDIKEYQKEHGVVVPTRGTIHDIGPGV--THKKIIIRLYLK--G 163 (220)
T ss_pred HHHHHHHHHHHHHHcCCcccHHHHHHHHCCCHHHHHHHHHHHHHHcCceeccCCcccccCCcc--hHHHHHHHHHHc--C
Confidence 345666654 344 699999999999999999999999987 8876653210 111222 355666666555 3
Q ss_pred CCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCC
Q psy15598 124 IFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGS 160 (258)
Q Consensus 124 ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~ 160 (258)
....||+++.. =|..+|-|.++.....
T Consensus 164 ~~~~eiar~t~----------HS~~av~rYi~~F~rV 190 (220)
T PF07900_consen 164 KPTPEIARRTN----------HSPEAVDRYIKDFKRV 190 (220)
T ss_pred CCHHHHHHHhc----------cCHHHHHHHHHhhHHh
Confidence 56677877664 2888888888765443
No 131
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=95.57 E-value=0.11 Score=38.93 Aligned_cols=67 Identities=15% Similarity=0.232 Sum_probs=46.6
Q ss_pred HHHHHHHHH---cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHhC
Q psy15598 53 RMRIVELAQ---LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQKD 121 (258)
Q Consensus 53 R~RIV~L~~---~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~n 121 (258)
-.+|++++. .+++..+||+.+|++++||++.++...+.|-+.....+| .-.++......-..+....
T Consensus 7 ~~~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~~~g~l~~~~~~~--~y~l~~~~~~~~~~~~~~~ 76 (91)
T smart00346 7 GLAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQELGYVEQDGQNG--RYRLGPKVLELGQSYLSSL 76 (91)
T ss_pred HHHHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeeecCCCC--ceeecHHHHHHHHHHHhcC
Confidence 355666654 358999999999999999999999999999875432222 2345555555555554443
No 132
>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=95.56 E-value=0.078 Score=42.46 Aligned_cols=68 Identities=15% Similarity=0.048 Sum_probs=49.9
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHh
Q psy15598 64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLLS 135 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~~ 135 (258)
+++.++|+.+|||..|++.|-+ .|.+.|..+..+.-+..++++...|..... ..-.+++.+|++.|..
T Consensus 1 y~Ige~A~~~gvs~~tlR~ye~----~GLl~p~~r~~~g~R~Y~~~~l~~l~~I~~lr~~G~~l~~I~~~l~~ 69 (107)
T cd01111 1 YSISQLALDAGVSVHIVRDYLL----RGLLHPVARTEGGYGLFDDCALQRLRFVRAAFEAGIGLDELARLCRA 69 (107)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 4678999999999999876655 488876544322467788888777766544 3458889999888863
No 133
>PRK01381 Trp operon repressor; Provisional
Probab=95.56 E-value=0.012 Score=47.32 Aligned_cols=54 Identities=20% Similarity=0.326 Sum_probs=40.0
Q ss_pred HHHHHHHHHHHcC-CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHh
Q psy15598 51 SVRMRIVELAQLG-IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQK 120 (258)
Q Consensus 51 dlR~RIV~L~~~G-~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~ 120 (258)
..|.+|+.+...| +|.++||+.+|||.+||.|--+-.+ ..+++.+++|..++..
T Consensus 42 ~~R~~I~~~L~~g~~sQREIa~~lGvSiaTITRgsn~Lk----------------~~~~~~k~~l~~~l~~ 96 (99)
T PRK01381 42 GTRVRIVEELLRGELSQREIKQELGVGIATITRGSNSLK----------------TAPPEFKEWLEQQLLK 96 (99)
T ss_pred HHHHHHHHHHHcCCcCHHHHHHHhCCceeeehhhHHHhc----------------cCCHHHHHHHHHHhcc
Confidence 4677888877665 9999999999999999988665543 1235667777666543
No 134
>cd04784 HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators. Helix-turn-helix (HTH) CadR and PbrR transcription regulators including Pseudomonas aeruginosa CadR and Ralstonia metallidurans PbrR that regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which form a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=95.55 E-value=0.2 Score=40.73 Aligned_cols=67 Identities=12% Similarity=0.136 Sum_probs=47.2
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHH
Q psy15598 64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLL 134 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~ 134 (258)
+++.++|+.+|||..|++-| .+.|.+.|..+..+.-|..++++...|..... ..-.+++.||++.|.
T Consensus 1 m~IgevA~~~gvs~~tLRyY----e~~GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~ 68 (127)
T cd04784 1 MKIGELAKKTGCSVETIRYY----EKEGLLPAPARSANNYRLYDEEHLERLLFIRRCRSLDMSLDEIRTLLQ 68 (127)
T ss_pred CCHHHHHHHHCcCHHHHHHH----HHCCCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 57889999999999998554 44677765444322458888887765544422 233789999998875
No 135
>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=95.54 E-value=0.03 Score=38.73 Aligned_cols=38 Identities=21% Similarity=0.330 Sum_probs=31.4
Q ss_pred HHHHHHH-H-c-CCCHHHHHHHhCCCHHHHHHHHHHhhhhC
Q psy15598 54 MRIVELA-Q-L-GIRPCDISRQLRVSHGCVSKILARYHETG 91 (258)
Q Consensus 54 ~RIV~L~-~-~-G~S~~eIAr~LGVSrsTVsRwikRyrEtG 91 (258)
.+|+.+. + . .++..++|+.|+||++||++-++.-++.|
T Consensus 3 ~~il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i~~L~~~~ 43 (55)
T PF08279_consen 3 KQILKLLLESKEPITAKELAEELGVSRRTIRRDIKELREWG 43 (55)
T ss_dssp HHHHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence 4566665 3 2 38999999999999999999999999988
No 136
>cd04775 HTH_Cfa-like Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulators; the HTH domain of Cfa, a cyclopropane fatty acid synthase, and other related methyltransferases, as well as, the N-terminal domain of a conserved, uncharacterized ~172 a.a. protein. Based on sequence similarity of the N-terminal domain, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimil
Probab=95.53 E-value=0.081 Score=41.72 Aligned_cols=66 Identities=18% Similarity=0.132 Sum_probs=45.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHH
Q psy15598 64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLL 134 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~ 134 (258)
++..++|+.+|||.+|++.|-+ .|-+.+....+ .-+..++++...|...+. .+-.++..+|+..+.
T Consensus 2 ~~i~eva~~~gvs~~tLR~ye~----~Gll~~~r~~~-g~R~Y~~~dl~~l~~I~~l~~~G~~l~ei~~~~~ 68 (102)
T cd04775 2 YTIGQMSRKFGVSRSTLLYYES----IGLIPSARSEA-NYRLYSEADLSRLEKIVFLQAGGLPLEEIAGCLA 68 (102)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCCCCC-CCeeeCHHHHHHHHHHHHHHHCCCCHHHHHHHHc
Confidence 5789999999999999965554 57774433223 447778777666555533 334788999987664
No 137
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=95.52 E-value=0.043 Score=46.52 Aligned_cols=43 Identities=23% Similarity=0.242 Sum_probs=35.0
Q ss_pred CCCCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 45 GRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 45 gR~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
...++...| +|+.+..+|++..+||+.||+|++||++|.++-+
T Consensus 4 ~~~Lt~rqr-eVL~lr~~GlTq~EIAe~LGiS~~tVs~ie~ra~ 46 (141)
T PRK03975 4 ESFLTERQI-EVLRLRERGLTQQEIADILGTSRANVSSIEKRAR 46 (141)
T ss_pred ccCCCHHHH-HHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 334555554 5667778999999999999999999999999865
No 138
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=95.51 E-value=0.073 Score=44.46 Aligned_cols=67 Identities=18% Similarity=0.183 Sum_probs=49.1
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHH
Q psy15598 64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLL 134 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~ 134 (258)
+++.++|+.+|||..||+.|-+ .|.+.|..+..+.-|..++++...|..+.. ..-.+++.||++.|.
T Consensus 2 ~~I~e~a~~~gvs~~tlR~Ye~----~GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~ 69 (140)
T PRK09514 2 YRIGELAKLAEVTPDTLRFYEK----QGLMDPEVRTEGGYRLYTEQDLQRLRFIRRAKQLGFTLEEIRELLS 69 (140)
T ss_pred CcHHHHHHHHCcCHHHHHHHHH----CCCCCCcccCCCCCeeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 5789999999999999987744 577776544332457888887776655533 344789999998875
No 139
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=95.50 E-value=0.15 Score=39.77 Aligned_cols=78 Identities=10% Similarity=0.066 Sum_probs=52.4
Q ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHH-HHHHHHHHHHhCCCCCHHHHHHHHHhcCCCC
Q psy15598 62 LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPK-VVSYIKELKQKDPGIFAWEIRDRLLSDGVCD 140 (258)
Q Consensus 62 ~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e-~~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v 140 (258)
+..+..+||+.+++|.+++.|..+++- |. .|...... -.+...+++ .+.+.+..+|+..+ |..
T Consensus 20 ~~~~~~~lA~~~~~S~~~l~r~f~~~~--g~---------s~~~~i~~~Rl~~a~~~L-~~~~~~i~~iA~~~---Gf~- 83 (107)
T PRK10219 20 QPLNIDVVAKKSGYSKWYLQRMFRTVT--HQ---------TLGDYIRQRRLLLAAVEL-RTTERPIFDIAMDL---GYV- 83 (107)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHH--Cc---------CHHHHHHHHHHHHHHHHH-HccCCCHHHHHHHH---CCC-
Confidence 468999999999999999999999973 21 22222111 122233333 34567777776665 665
Q ss_pred CCCCCCHHHHHHHHHhccCC
Q psy15598 141 KFNVPSVSSISRILRNKIGS 160 (258)
Q Consensus 141 ~~~~pS~STI~RiLrr~~~~ 160 (258)
+.+...|.+++.-+.
T Consensus 84 -----~~s~f~~~Fk~~~G~ 98 (107)
T PRK10219 84 -----SQQTFSRVFRRQFDR 98 (107)
T ss_pred -----CHHHHHHHHHHHHCc
Confidence 889999999876543
No 140
>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=95.50 E-value=0.095 Score=48.17 Aligned_cols=89 Identities=18% Similarity=0.119 Sum_probs=55.1
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCc-ccCCCCCCCCCCCCHHHHHHHHHHHHhCCCCC
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETGSI-LPGAIGGSKPRVTTPKVVSYIKELKQKDPGIF 125 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl-~pk~rgG~RPrklT~e~~~~I~~lv~~nP~it 125 (258)
.++...|.-++..+-+|++..+||+.||||.+||+..+.|-++.=.- ....++...+.....+..+.|.+++..--.--
T Consensus 142 ~Lp~~~R~v~~L~~~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~~~~~~~~~~~~~~~~v~~~~~a~~~gD 221 (324)
T TIGR02960 142 YLPPRQRAVLLLRDVLGWRAAETAELLGTSTASVNSALQRARATLDEVGPSARDDQLAQPPSPEEQDLLERYIAAFESYD 221 (324)
T ss_pred hCCHHHhhHhhhHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhcccccccccCCCCCHHHHHHHHHHHHHHHcCC
Confidence 47777777666667799999999999999999999999887753211 11111111123344555555555554322334
Q ss_pred HHHHHHHHHh
Q psy15598 126 AWEIRDRLLS 135 (258)
Q Consensus 126 a~EIr~~L~~ 135 (258)
...|.+.|.+
T Consensus 222 ~~~l~~Lla~ 231 (324)
T TIGR02960 222 LDALTALLHE 231 (324)
T ss_pred HHHHHHHhcC
Confidence 5556665544
No 141
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=95.49 E-value=0.1 Score=48.44 Aligned_cols=89 Identities=15% Similarity=0.083 Sum_probs=54.3
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCH
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFA 126 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~nP~ita 126 (258)
.++.+.|.-++..+-+|++..+||+.||+|.+||...+.|-++.=.-......+..+.....+..+.+.+++..--.--.
T Consensus 153 ~Lp~~~R~v~~L~~~~g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~~~~~~~~~~~~~~~~~~~~v~~~~~A~~~gD~ 232 (339)
T PRK08241 153 HLPPRQRAVLILRDVLGWSAAEVAELLDTSVAAVNSALQRARATLAERGPSAADTLREPDDPEERALLARYVAAFEAYDV 232 (339)
T ss_pred hCCHHHhhhhhhHHhhCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhhcCCCcccccCCCCChHHHHHHHHHHHHHhcCCH
Confidence 46777777666666799999999999999999999999887754211000001112334445555555565553222234
Q ss_pred HHHHHHHHh
Q psy15598 127 WEIRDRLLS 135 (258)
Q Consensus 127 ~EIr~~L~~ 135 (258)
..+.+.|.+
T Consensus 233 ~~l~~lla~ 241 (339)
T PRK08241 233 DALVALLTE 241 (339)
T ss_pred HHHHHHhcC
Confidence 455555543
No 142
>TIGR02047 CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional regulator. This model represents the cadmium(II) and/or lead(II) responsive transcriptional activator of the proteobacterial metal efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(6-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=95.48 E-value=0.24 Score=40.59 Aligned_cols=67 Identities=19% Similarity=0.166 Sum_probs=46.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHH
Q psy15598 64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLL 134 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~ 134 (258)
|++.++|+.+|||..|++.|-+ .|.+.+..+..+.-|..++++...|..... ..-.+++.||++.|.
T Consensus 1 m~I~e~a~~~gvs~~tlR~Ye~----~GLl~~~~r~~~gyR~Y~~~~l~~l~~I~~lr~lG~sL~eI~~~l~ 68 (127)
T TIGR02047 1 MKIGELAQKTGVSVETIRFYEK----QGLLPPPARTDNNYRVYTVGHVERLAFIRNCRTLDMSLAEIRQLLR 68 (127)
T ss_pred CcHHHHHHHHCcCHHHHHHHHH----CCCCCCCCcCCCCCCcCCHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 5788999999999999876644 577754333222457788877665554433 234789999988775
No 143
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=95.47 E-value=0.041 Score=45.29 Aligned_cols=43 Identities=26% Similarity=0.224 Sum_probs=34.8
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE 89 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE 89 (258)
.++...|.-++..+-+|++.++||+.||||.+||+..+.|-++
T Consensus 109 ~L~~~~r~v~~l~~~~~~s~~EIA~~lgis~~tV~~~l~ra~~ 151 (163)
T PRK07037 109 ELPARTRYAFEMYRLHGETQKDIARELGVSPTLVNFMIRDALV 151 (163)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4666666655555679999999999999999999999887653
No 144
>cd04786 HTH_MerR-like_sg7 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 7) with a conserved cysteine present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic su
Probab=95.46 E-value=0.19 Score=41.62 Aligned_cols=88 Identities=14% Similarity=0.141 Sum_probs=55.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHhcCCCCCC
Q psy15598 64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLLSDGVCDKF 142 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~~~Gv~v~~ 142 (258)
|++.++|+.+|||.+|++-|- +.|.+.|..+....-|..++++...|.-... ..-.+++.||++.|......
T Consensus 1 m~Ige~a~~~gvs~~tLRyYE----~~GLl~p~~r~~~gyR~Y~~~~v~~l~~I~~lr~~GfsL~eI~~ll~~~~~~--- 73 (131)
T cd04786 1 MKIGELAKRSGMAASRIRFYE----AEGLLSSVERSANGYRDYPPETVWVLEIISSAQQAGFSLDEIRQLLPADASN--- 73 (131)
T ss_pred CCHHHHHHHHCcCHHHHHHHH----HCCCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcccCC---
Confidence 578899999999999986554 4677766444332457788776665544433 23478999999888632111
Q ss_pred CCCCHHHHHHHHHhccCC
Q psy15598 143 NVPSVSSISRILRNKIGS 160 (258)
Q Consensus 143 ~~pS~STI~RiLrr~~~~ 160 (258)
.+...+...|.++..+
T Consensus 74 --~~~~~~~~~l~~k~~~ 89 (131)
T cd04786 74 --WQHDELLAALERKVAD 89 (131)
T ss_pred --CCHHHHHHHHHHHHHH
Confidence 1334555555544433
No 145
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=95.46 E-value=0.029 Score=47.73 Aligned_cols=42 Identities=21% Similarity=0.249 Sum_probs=35.1
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.++.+.|.-++..+-+|++.++||+.||+|.+||..++.|.+
T Consensus 141 ~L~~~~~~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Ra~ 182 (194)
T PRK12519 141 QLPESQRQVLELAYYEGLSQSEIAKRLGIPLGTVKARARQGL 182 (194)
T ss_pred hCCHHHhhhhhhhhhcCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 467776665555567999999999999999999999998865
No 146
>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=95.44 E-value=0.25 Score=40.28 Aligned_cols=67 Identities=18% Similarity=0.186 Sum_probs=47.4
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHH
Q psy15598 64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLL 134 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~ 134 (258)
+++.++|+.+|||.+|++-| .+.|.+.+..+..+.-|..++++...|..... ..-.+++.||++.+.
T Consensus 1 ~~I~e~a~~~gvs~~tlR~Y----e~~Gll~~~~r~~~g~R~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~ 68 (126)
T cd04785 1 LSIGELARRTGVNVETIRYY----ESIGLLPEPARTAGGYRLYGAAHVERLRFIRRARDLGFSLEEIRALLA 68 (126)
T ss_pred CCHHHHHHHHCcCHHHHHHH----HHCCCCCCCCcCCCCccccCHHHHHHHHHHHHHHHCCCCHHHHHHHHh
Confidence 57889999999999998754 44677765433222457788887776655543 334788999988775
No 147
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=95.44 E-value=0.04 Score=45.83 Aligned_cols=43 Identities=16% Similarity=0.176 Sum_probs=36.1
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE 89 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE 89 (258)
.++...|.-++..+-+|++..+||+.||||.+||...+.|-+.
T Consensus 112 ~L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~tV~~~l~Rar~ 154 (164)
T PRK12547 112 LLSADQREAIILIGASGFSYEDAAAICGCAVGTIKSRVSRARN 154 (164)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 3666777666666679999999999999999999999998763
No 148
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=95.43 E-value=0.037 Score=45.92 Aligned_cols=44 Identities=14% Similarity=0.030 Sum_probs=37.5
Q ss_pred CCCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598 46 RPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE 89 (258)
Q Consensus 46 R~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE 89 (258)
..++.+.|.-++..+-+|++..+||+.||+|.+||+.++.|-++
T Consensus 107 ~~L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~tv~~~l~Rar~ 150 (165)
T PRK09644 107 HTLPVIEAQAILLCDVHELTYEEAASVLDLKLNTYKSHLFRGRK 150 (165)
T ss_pred HhCCHHHHHHHHhHHHhcCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 45778788766666779999999999999999999999998763
No 149
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=95.40 E-value=0.044 Score=45.80 Aligned_cols=42 Identities=17% Similarity=0.205 Sum_probs=36.3
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.++...|.-++..+-+|++..+||+.||+|.+||...+.|-.
T Consensus 118 ~L~~~~r~v~~L~~~eg~s~~EIA~~l~is~~tV~~~l~ra~ 159 (168)
T PRK12525 118 GLSGKARAAFLMSQLEGLTYVEIGERLGVSLSRIHQYMVEAF 159 (168)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 477887776666678999999999999999999999998865
No 150
>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=95.39 E-value=0.03 Score=40.53 Aligned_cols=35 Identities=20% Similarity=0.235 Sum_probs=31.7
Q ss_pred HcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCccc
Q psy15598 61 QLGIRPCDISRQLRVSHGCVSKILARYHETGSILP 95 (258)
Q Consensus 61 ~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~p 95 (258)
..+++..+||+.+|+++++|++.+++..+.|-+..
T Consensus 20 ~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~GlV~~ 54 (68)
T PF01978_consen 20 NGPATAEEIAEELGISRSTVYRALKSLEEKGLVER 54 (68)
T ss_dssp HCHEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE
T ss_pred cCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence 45689999999999999999999999999998753
No 151
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=95.38 E-value=0.041 Score=47.11 Aligned_cols=42 Identities=17% Similarity=0.177 Sum_probs=35.7
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.++...|.-++..+-+|++..+||+.||+|.+||..++.|-+
T Consensus 134 ~Lp~~~R~v~~L~~~~g~s~~EIA~~lgis~~tVk~~l~RAr 175 (189)
T PRK12530 134 HLPAQQARVFMMREYLELSSEQICQECDISTSNLHVLLYRAR 175 (189)
T ss_pred hCCHHHHHHHhHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 467777766666667999999999999999999999998865
No 152
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=95.36 E-value=0.04 Score=46.67 Aligned_cols=42 Identities=19% Similarity=0.241 Sum_probs=35.8
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.++.+.|.-|+...-+|++..+||+.||||.+||...+.|-.
T Consensus 127 ~Lp~~~R~v~~L~~~~g~s~~EIA~~lgis~~tVk~~l~rAl 168 (178)
T PRK12529 127 TLRPRVKQAFLMATLDGMKQKDIAQALDIALPTVKKYIHQAY 168 (178)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 477777766666677999999999999999999999988754
No 153
>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=95.36 E-value=0.042 Score=39.79 Aligned_cols=44 Identities=32% Similarity=0.386 Sum_probs=34.4
Q ss_pred HHHHHHHc--CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCC
Q psy15598 55 RIVELAQL--GIRPCDISRQLRVSHGCVSKILARYHETGSILPGAI 98 (258)
Q Consensus 55 RIV~L~~~--G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~r 98 (258)
.|..+.++ ..+..+||+.|+||++||..-+++..+.|-+.-.+.
T Consensus 12 ~Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~~GlV~~~~y 57 (60)
T PF01325_consen 12 AIYELSEEGGPVRTKDIAERLGVSPPTVTEMLKRLAEKGLVEYEPY 57 (60)
T ss_dssp HHHHHHHCTSSBBHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT
T ss_pred HHHHHHcCCCCccHHHHHHHHCCChHHHHHHHHHHHHCCCEEecCC
Confidence 44555543 479999999999999999999999999998754443
No 154
>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=95.35 E-value=0.056 Score=37.61 Aligned_cols=30 Identities=20% Similarity=0.289 Sum_probs=28.0
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598 65 RPCDISRQLRVSHGCVSKILARYHETGSIL 94 (258)
Q Consensus 65 S~~eIAr~LGVSrsTVsRwikRyrEtGsl~ 94 (258)
+.++||+.|+||+.||++.+++..+.|-+.
T Consensus 27 ~~~~la~~~~is~~~v~~~l~~L~~~G~i~ 56 (66)
T cd07377 27 SERELAEELGVSRTTVREALRELEAEGLVE 56 (66)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 489999999999999999999999999874
No 155
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=95.32 E-value=0.047 Score=45.49 Aligned_cols=42 Identities=21% Similarity=0.199 Sum_probs=34.9
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.++...|.-++..+-+|++..+||+.||+|.+||...+.|-+
T Consensus 118 ~L~~~~r~vl~L~~~~g~s~~EIA~~lgis~~tV~~~l~ra~ 159 (173)
T PRK09645 118 QLSPEHRAVLVRSYYRGWSTAQIAADLGIPEGTVKSRLHYAL 159 (173)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 477777775555567999999999999999999988887765
No 156
>PRK15043 transcriptional regulator MirA; Provisional
Probab=95.31 E-value=0.075 Score=48.80 Aligned_cols=68 Identities=18% Similarity=0.248 Sum_probs=50.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHh
Q psy15598 64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLLS 135 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~~ 135 (258)
+++.++|+.+|||..|++.|.+|| |.+.|....+ ..|..++++.+.|..++. .+-.++..+|+..|..
T Consensus 4 ytIgeVA~~~GVs~~TLR~wErr~---GLL~P~Rt~~-G~R~Ys~~dv~rL~~I~~l~~~G~~i~eIk~ll~~ 72 (243)
T PRK15043 4 YTIGEVALLCDINPVTLRAWQRRY---GLLKPQRTDG-GHRLFNDADIDRIREIKRWIDNGVQVSKVKMLLSN 72 (243)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHhc---CCCCCccCCC-CCEEECHHHHHHHHHHHHHHHcCCCHHHHHHHHhc
Confidence 688999999999999999998775 6776654444 457788887777665543 2336788888877753
No 157
>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=95.31 E-value=0.13 Score=47.09 Aligned_cols=84 Identities=10% Similarity=-0.018 Sum_probs=56.2
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCH
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFA 126 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~nP~ita 126 (258)
.++...|.-++...-.|++..|||+.||+|.+||+..+.|-+..=. .. .. +.....+++.+.+.+++..--.--.
T Consensus 108 ~L~~~~R~v~~L~~~~g~s~~EIA~~lg~s~~tVr~~l~RAr~~Lr--~~-~~--~~~~~~~~~~~~~~~f~~a~~~gD~ 182 (281)
T TIGR02957 108 RLSPLERAVFVLREVFDYPYEEIASIVGKSEANCRQLVSRARRHLD--AR-RP--RFEVSREESRQLLERFVEAAQTGDL 182 (281)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH--hh-CC--CCCCChHHHHHHHHHHHHHHHhCCH
Confidence 4777888776666779999999999999999999999999875411 11 00 1223345555666666554333445
Q ss_pred HHHHHHHHh
Q psy15598 127 WEIRDRLLS 135 (258)
Q Consensus 127 ~EIr~~L~~ 135 (258)
..+...|.+
T Consensus 183 ~~l~~lL~~ 191 (281)
T TIGR02957 183 DGLLELLAE 191 (281)
T ss_pred HHHHHHHhh
Confidence 666666654
No 158
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=95.31 E-value=0.046 Score=46.33 Aligned_cols=43 Identities=16% Similarity=0.226 Sum_probs=36.2
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE 89 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE 89 (258)
.++...|.-|+..+-+|++..+||+.||||.+||...+.|-++
T Consensus 139 ~L~~~~r~i~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~ 181 (189)
T PRK09648 139 TLPEKQREILILRVVVGLSAEETAEAVGSTPGAVRVAQHRALA 181 (189)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4677777666666779999999999999999999999988653
No 159
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=95.31 E-value=0.038 Score=48.06 Aligned_cols=47 Identities=11% Similarity=0.076 Sum_probs=38.6
Q ss_pred CCHHHHHHHHHHHHc---CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598 48 LPNSVRMRIVELAQL---GIRPCDISRQLRVSHGCVSKILARYHETGSIL 94 (258)
Q Consensus 48 ~S~dlR~RIV~L~~~---G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~ 94 (258)
++.....+|+.++.+ |.+.++||+.|+||..||.+.+..-.+.|.+.
T Consensus 159 ~~~Lt~r~Vl~~~~~g~~g~s~~eIa~~l~iS~~Tv~~~~~~~~~~~~~~ 208 (225)
T PRK10046 159 IDPLTLNAVRKLFKEPGVQHTAETVAQALTISRTTARRYLEYCASRHLII 208 (225)
T ss_pred CCHHHHHHHHHHHHcCCCCcCHHHHHHHhCccHHHHHHHHHHHHhCCeEE
Confidence 333333388888877 48999999999999999999999999999653
No 160
>TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR. Similarly, tetanus toxin production of Clostridium tetani is regulated by TetR which is a very close relative of BotR. Both BotR and TetR are members of the TIGR02937 subfamily of sigma-70 RNA polymerase sigma factors. Functional complementation experiments have been done for botR and tetR in highly transformable strain of Clostridium perfringens host cells to assess functional interchangeability of sigma factors and it has been confirmed that they are interchangeable in vivo.
Probab=95.29 E-value=0.023 Score=46.06 Aligned_cols=36 Identities=28% Similarity=0.311 Sum_probs=30.4
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHH
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSK 82 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsR 82 (258)
.++.+.|.-|+..+-+|+|..+||+.||+|.+||++
T Consensus 107 ~Lp~~~r~v~~l~~~~~~s~~EIA~~l~is~~tV~~ 142 (142)
T TIGR03209 107 ILPNKQKKIIYMKFFEDMKEIDIAKKLHISRQSVYK 142 (142)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHhhcC
Confidence 467777766666677999999999999999999974
No 161
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=95.27 E-value=0.046 Score=46.94 Aligned_cols=42 Identities=17% Similarity=0.237 Sum_probs=35.8
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.++...|.-++...-+|++..+||+.||||.+||...+.|-+
T Consensus 116 ~Lp~~~r~i~~L~~~~g~s~~EIA~~Lgis~~tVk~~l~Rar 157 (187)
T PRK12516 116 QLPDDQREAIILVGASGFAYEEAAEICGCAVGTIKSRVNRAR 157 (187)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 467777766666677999999999999999999999988865
No 162
>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=95.26 E-value=0.027 Score=43.66 Aligned_cols=34 Identities=21% Similarity=0.296 Sum_probs=23.3
Q ss_pred HHHHHHHHH----HcCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598 52 VRMRIVELA----QLGIRPCDISRQLRVSHGCVSKILA 85 (258)
Q Consensus 52 lR~RIV~L~----~~G~S~~eIAr~LGVSrsTVsRwik 85 (258)
++.|+|+.. +...+++++|+.||||+|||++=+.
T Consensus 4 IeeR~i~i~~yIi~~~aTVR~~Ak~FGvSKSTVHkDvt 41 (82)
T PF12116_consen 4 IEERVIEIANYIIETKATVRQAAKVFGVSKSTVHKDVT 41 (82)
T ss_dssp HHHHHHHHHHHHHHH---HHHHHHHHTS-HHHHHHHHT
T ss_pred HHHHHHHHHHHHHHcccHHHHHHHHHCCcHHHHHHHHH
Confidence 455566543 4689999999999999999998664
No 163
>cd01107 HTH_BmrR Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=95.24 E-value=0.13 Score=40.90 Aligned_cols=67 Identities=15% Similarity=0.156 Sum_probs=48.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCC-CCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHH
Q psy15598 64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGG-SKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLL 134 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG-~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~ 134 (258)
++..++|+.+|||.+|++-|.+ .|-+.|..+.+ +..|..++.+...|..... .+-.+++.+|...+.
T Consensus 1 ~~i~eva~~~gis~~tlR~ye~----~GLi~p~~~~~~ngyR~Y~~~~i~~l~~I~~lr~~G~sl~~i~~l~~ 69 (108)
T cd01107 1 FTIGEFAKLSNLSIKALRYYDK----IGLLKPAYVDPDTGYRYYSAEQLERLNRIKYLRDLGFPLEEIKEILD 69 (108)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH----cCCCCCCcCCCCCCccccCHHHHHHHHHHHHHHHcCCCHHHHHHHHh
Confidence 4688999999999999977765 48787754321 2467888887777665543 234788889987665
No 164
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=95.23 E-value=0.045 Score=46.67 Aligned_cols=43 Identities=19% Similarity=0.233 Sum_probs=37.0
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE 89 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE 89 (258)
.++.+.|.-++..+-+|++..+||+.||+|.+||...+.|-+.
T Consensus 130 ~Lp~~~r~v~~L~~~~g~s~~EIA~~lgis~~tVk~~l~Rar~ 172 (185)
T PRK09649 130 DLTTDQREALLLTQLLGLSYADAAAVCGCPVGTIRSRVARARD 172 (185)
T ss_pred hCCHHHhHHhhhHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4777777766666779999999999999999999999988764
No 165
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=95.22 E-value=0.045 Score=46.73 Aligned_cols=42 Identities=19% Similarity=0.219 Sum_probs=35.5
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.++...|.-++..+-+|++..+||+.||||.+||+..+.|-+
T Consensus 136 ~L~~~~r~i~~L~~~~g~s~~EIA~~lgis~~tVk~~l~Rar 177 (195)
T PRK12532 136 NLPENTARVFTLKEILGFSSDEIQQMCGISTSNYHTIMHRAR 177 (195)
T ss_pred hCCHHHHHHhhhHHHhCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 467777766666677999999999999999999999988865
No 166
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=95.22 E-value=0.053 Score=45.37 Aligned_cols=42 Identities=24% Similarity=0.218 Sum_probs=35.0
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.++.+.|.-++..+-+|++..+||+.||||.+||...+.|-.
T Consensus 119 ~Lp~~~r~v~~L~~~~g~s~~EIA~~lgis~~tV~~~l~ra~ 160 (172)
T PRK12523 119 KLSSKARAAFLYNRLDGMGHAEIAERLGVSVSRVRQYLAQGL 160 (172)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 466777765555567999999999999999999999998865
No 167
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=95.21 E-value=0.044 Score=46.34 Aligned_cols=43 Identities=21% Similarity=0.151 Sum_probs=36.9
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE 89 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE 89 (258)
.++...|.-++..+-+|++..+||+.||||.+||...+.|.++
T Consensus 127 ~L~~~~r~v~~l~~~~g~s~~EIA~~l~is~~tv~~~l~Ra~~ 169 (179)
T PRK09415 127 SLPIKYREVIYLFYYEELSIKEIAEVTGVNENTVKTRLKKAKE 169 (179)
T ss_pred hCCHHHhhHhHhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4777777666666779999999999999999999999999764
No 168
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=95.20 E-value=0.049 Score=45.55 Aligned_cols=43 Identities=16% Similarity=0.063 Sum_probs=36.0
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE 89 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE 89 (258)
.++...|.-++..+-+|++..+||+.||||.+||+..+.|-+.
T Consensus 119 ~L~~~~r~i~~l~~~~~~s~~EIA~~lgis~~tV~~~l~Ra~~ 161 (173)
T PRK12522 119 LLNEKYKTVLVLYYYEQYSYKEMSEILNIPIGTVKYRLNYAKK 161 (173)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 4677777656655679999999999999999999999998753
No 169
>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=95.17 E-value=0.056 Score=45.39 Aligned_cols=42 Identities=21% Similarity=0.229 Sum_probs=36.0
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.++.+.|.-++..+-+|++..+||+.||+|.+||+..+.|-+
T Consensus 100 ~L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~tV~~~l~Rar 141 (170)
T TIGR02959 100 ELPDEYREAIRLTELEGLSQQEIAEKLGLSLSGAKSRVQRGR 141 (170)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 577877766666678999999999999999999999988765
No 170
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=95.16 E-value=0.054 Score=45.79 Aligned_cols=42 Identities=21% Similarity=0.283 Sum_probs=35.0
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.++...|.-++..+-+|++.++||+.||||.+||...+.|-+
T Consensus 129 ~L~~~~r~v~~l~~~~g~s~~EIA~~l~is~~tV~~~l~rar 170 (181)
T PRK12536 129 QLPDRQRLPIVHVKLEGLSVAETAQLTGLSESAVKVGIHRGL 170 (181)
T ss_pred HCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 466666665555667999999999999999999999998865
No 171
>TIGR02054 MerD mercuric resistence transcriptional repressor protein MerD. This model represents a transcriptional repressor protein of the MerR family (pfam00376) whose expression is regulated by the mercury-sensitive transcriptional activator, MerR. MerD has been shown to repress the transcription of the mer operon.
Probab=95.15 E-value=0.13 Score=42.34 Aligned_cols=68 Identities=15% Similarity=0.068 Sum_probs=50.7
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHH
Q psy15598 63 GIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLL 134 (258)
Q Consensus 63 G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~ 134 (258)
.+++.++|+.+|||..||+-|-+ .|.+.|..+..+.-|..++++...|.-... ..-.+++.+|+..|.
T Consensus 3 ~~tI~elA~~~gvs~~tlR~Ye~----~GLL~p~~r~~~gyR~Y~~~~l~rL~~I~~lr~~G~~L~eI~~ll~ 71 (120)
T TIGR02054 3 AYTISRLAEDAGVSVHVVRDYLL----RGLLHPVRRTTSGYGIFDDASLQRLRFVRAAFEAGIGLGELARLCR 71 (120)
T ss_pred CCcHHHHHHHHCcCHHHHHHHHH----CCCCCCCccCCCCCeeCCHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 47899999999999999865544 588877655333567888887777666644 445788999988775
No 172
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=95.14 E-value=0.054 Score=46.09 Aligned_cols=42 Identities=17% Similarity=0.187 Sum_probs=35.9
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.++.+.|.-++..+-+|+|..+||..||+|.+||...+.|-+
T Consensus 131 ~Lp~~~r~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Rar 172 (191)
T PRK12520 131 RLPPRTGRVFMMREWLELETEEICQELQITATNAWVLLYRAR 172 (191)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 377777776666667999999999999999999999988865
No 173
>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=95.14 E-value=0.27 Score=39.54 Aligned_cols=67 Identities=16% Similarity=0.207 Sum_probs=48.8
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHh
Q psy15598 64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLLS 135 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~~ 135 (258)
++..++|+.+|||..|++-|- +.|.+.|..+.+ .-+..++.+...|..... .+=.++..||+..+..
T Consensus 1 ~~ige~a~~~gvs~~tLryYe----~~GLi~p~~~~~-~yR~Y~~~d~~~l~~I~~lr~~G~sl~eI~~~l~~ 68 (116)
T cd04769 1 MYIGELAQQTGVTIKAIRLYE----EKGLLPSPKRSG-NYRVYDAQHVECLRFIKEARQLGFTLAELKAIFAG 68 (116)
T ss_pred CCHHHHHHHHCcCHHHHHHHH----HCCCCCCCCCCC-CceeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHhc
Confidence 578899999999999986554 458887755554 457788877776554432 2247889999888764
No 174
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=95.13 E-value=0.05 Score=46.04 Aligned_cols=43 Identities=23% Similarity=0.298 Sum_probs=36.5
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE 89 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE 89 (258)
.++...|.-++..+-+|++..+||+.||+|.+||+..+.|-+.
T Consensus 128 ~L~~~~r~i~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Rar~ 170 (186)
T PRK05602 128 ALPERQREAIVLQYYQGLSNIEAAAVMDISVDALESLLARGRR 170 (186)
T ss_pred hCCHHHHHHhhHHHhcCCCHHHHHHHhCcCHHHHHHHHHHHHH
Confidence 4677777766666779999999999999999999999988653
No 175
>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=95.13 E-value=0.053 Score=45.07 Aligned_cols=43 Identities=16% Similarity=0.166 Sum_probs=36.1
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE 89 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE 89 (258)
.++.+.|.-++..+-+|++..+||+.||||.+||+..+.|-+.
T Consensus 119 ~L~~~~r~i~~l~~~~g~s~~eiA~~lgis~~tv~~~l~Ra~~ 161 (169)
T TIGR02954 119 TLNDKYQTAIILRYYHDLTIKEIAEVMNKPEGTVKTYLHRALK 161 (169)
T ss_pred hCCHHHhHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4777777655566679999999999999999999999998763
No 176
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=95.09 E-value=0.056 Score=46.50 Aligned_cols=35 Identities=31% Similarity=0.405 Sum_probs=29.9
Q ss_pred HHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 54 MRIVELA-QLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 54 ~RIV~L~-~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.++|.+. -.|+|..|||+.||||.+||+|.++..+
T Consensus 141 ~~~v~l~~~~Gls~~EIA~~lgiS~~tV~r~l~~aR 176 (185)
T PF07638_consen 141 RRVVELRFFEGLSVEEIAERLGISERTVRRRLRRAR 176 (185)
T ss_pred HHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 4556554 5999999999999999999999988765
No 177
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=95.08 E-value=0.042 Score=38.39 Aligned_cols=31 Identities=23% Similarity=0.482 Sum_probs=28.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598 64 IRPCDISRQLRVSHGCVSKILARYHETGSIL 94 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~ 94 (258)
++..+||+.++++++||++.+++..+.|-|.
T Consensus 22 ~t~~~la~~l~~~~~~vs~~v~~L~~~Glv~ 52 (62)
T PF12802_consen 22 LTQSELAERLGISKSTVSRIVKRLEKKGLVE 52 (62)
T ss_dssp EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred cCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 7999999999999999999999999999774
No 178
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=95.08 E-value=0.057 Score=46.23 Aligned_cols=43 Identities=16% Similarity=0.145 Sum_probs=36.0
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE 89 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE 89 (258)
.++...|.-++..+-+|++..+||+.||||.+||..++.|-+.
T Consensus 142 ~L~~~~r~vl~l~~~~~~s~~EIA~~Lgis~~tVk~~l~ra~~ 184 (194)
T PRK09646 142 ALTDTQRESVTLAYYGGLTYREVAERLAVPLGTVKTRMRDGLI 184 (194)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHHhCCChHhHHHHHHHHHH
Confidence 4777777655555679999999999999999999999988753
No 179
>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=95.07 E-value=0.033 Score=44.80 Aligned_cols=38 Identities=21% Similarity=0.292 Sum_probs=28.0
Q ss_pred HHHHHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 51 SVRMRIVELA-QLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 51 dlR~RIV~L~-~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
+...+++.++ .+.+|.++||..+||||..|+.+++|-.
T Consensus 20 ~kQ~~~l~lyy~eDlSlsEIAe~~~iSRqaV~d~ikr~~ 58 (101)
T PF04297_consen 20 EKQREILELYYEEDLSLSEIAEELGISRQAVYDSIKRAE 58 (101)
T ss_dssp HHHHHHHHHHCTS---HHHHHHHCTS-HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHccCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 3444666665 5789999999999999999999999965
No 180
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=95.05 E-value=0.06 Score=45.36 Aligned_cols=42 Identities=24% Similarity=0.258 Sum_probs=35.8
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.++...|.-++..+-+|++..+||+.||+|.+||...+.|-+
T Consensus 131 ~L~~~~r~v~~l~~~~g~s~~eIA~~l~is~~tV~~~l~ra~ 172 (184)
T PRK12512 131 TLPPRQRDVVQSISVEGASIKETAAKLSMSEGAVRVALHRGL 172 (184)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 477777766666667999999999999999999999998865
No 181
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=95.05 E-value=0.058 Score=46.23 Aligned_cols=43 Identities=19% Similarity=0.241 Sum_probs=37.0
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE 89 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE 89 (258)
.++...|.-++..+-+|++..+||+.||||.+||...+.|-+.
T Consensus 111 ~Lp~~~R~v~~L~~~eg~s~~EIA~~lgis~~tV~~~l~Rar~ 153 (182)
T PRK12511 111 DLPEEQRAALHLVAIEGLSYQEAAAVLGIPIGTLMSRIGRARA 153 (182)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHHHHHH
Confidence 5788888777666779999999999999999999999877653
No 182
>PRK13749 transcriptional regulator MerD; Provisional
Probab=95.04 E-value=0.16 Score=41.93 Aligned_cols=69 Identities=13% Similarity=0.024 Sum_probs=52.4
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHh
Q psy15598 63 GIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLLS 135 (258)
Q Consensus 63 G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~~ 135 (258)
.+++.++|+.+|||..||+- |.+.|-+.|..+..+.-|..++++...|..+.. +.-.+++.||++.|..
T Consensus 3 ~~tIgelA~~~gvS~~tiR~----YE~~GLl~p~~r~~~gyR~Y~~~~l~rL~~I~~~r~~G~sL~eI~~ll~l 72 (121)
T PRK13749 3 AYTVSRLALDAGVSVHIVRD----YLLRGLLRPVACTTGGYGLFDDAALQRLCFVRAAFEAGIGLDALARLCRA 72 (121)
T ss_pred CCcHHHHHHHHCCCHHHHHH----HHHCCCCCCCCcCCCCCccCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhh
Confidence 37899999999999999854 455688766545323568889988888766655 4568999999988864
No 183
>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=95.03 E-value=0.027 Score=48.00 Aligned_cols=42 Identities=21% Similarity=0.203 Sum_probs=35.9
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.++...|.-++..+-+|++..+||+.||||.+||...+.|-+
T Consensus 131 ~Lp~~~r~i~~L~~~~g~s~~EIA~~lgis~~tVk~~l~Rar 172 (193)
T TIGR02947 131 GLPEEFRQAVYLADVEGFAYKEIAEIMGTPIGTVMSRLHRGR 172 (193)
T ss_pred hCCHHHhhheeehhhcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 467777776666677999999999999999999999988865
No 184
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=95.03 E-value=0.061 Score=45.85 Aligned_cols=43 Identities=19% Similarity=0.248 Sum_probs=36.2
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE 89 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE 89 (258)
.++.+.|.-++..+-+|++..+||+.||+|.+||+..+.|-+.
T Consensus 131 ~L~~~~r~i~~l~~~~g~s~~EIAe~lgis~~~V~~~l~Ra~~ 173 (189)
T PRK06811 131 DLEKLDREIFIRRYLLGEKIEEIAKKLGLTRSAIDNRLSRGRK 173 (189)
T ss_pred hCCHHHHHHHHHHHHccCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 5777777655555679999999999999999999999988764
No 185
>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=95.03 E-value=0.054 Score=49.01 Aligned_cols=42 Identities=19% Similarity=0.120 Sum_probs=37.0
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.++...|.-|+..+-+|+|.++||..||||.+||...+.|-+
T Consensus 161 ~Lp~~~R~v~~L~~~eg~S~~EIA~~Lgis~~TVk~rl~RAr 202 (244)
T TIGR03001 161 ALSERERHLLRLHFVDGLSMDRIGAMYQVHRSTVSRWVAQAR 202 (244)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 477778877777778999999999999999999999999875
No 186
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=95.02 E-value=0.058 Score=45.74 Aligned_cols=42 Identities=19% Similarity=0.269 Sum_probs=36.3
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.++...|.-++..+-+|++..+||+.||||.+||+..+.|-+
T Consensus 131 ~L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~tV~~~l~ra~ 172 (184)
T PRK12539 131 RLPEKMRLAIQAVKLEGLSVAEAATRSGMSESAVKVSVHRGL 172 (184)
T ss_pred hCCHHHHHHHHHHHHcCCcHHHHHHHHCcCHHHHHHHHHHHH
Confidence 477777776666677999999999999999999999998865
No 187
>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=95.02 E-value=0.087 Score=37.63 Aligned_cols=40 Identities=23% Similarity=0.277 Sum_probs=32.0
Q ss_pred CHHHHHHHHHHHHcCC-------CHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 49 PNSVRMRIVELAQLGI-------RPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 49 S~dlR~RIV~L~~~G~-------S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
+...|.-+..+++.|. +..++|+.||||++|++.-+++-.
T Consensus 2 T~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~~LRrae 48 (53)
T PF04967_consen 2 TDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVSEHLRRAE 48 (53)
T ss_pred CHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 4555666666677663 889999999999999999998864
No 188
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=95.01 E-value=0.16 Score=36.26 Aligned_cols=77 Identities=19% Similarity=0.296 Sum_probs=53.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHhcCCCCCCC
Q psy15598 64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFN 143 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~ 143 (258)
.+..+||+.+|+|.+++++.+++.. |. .++ ..+.......+.+++..+ .++..+|+..+ |+.
T Consensus 2 ~~~~~la~~~~~s~~~l~~~f~~~~--~~-s~~-------~~~~~~r~~~a~~~l~~~-~~~~~~ia~~~---g~~---- 63 (84)
T smart00342 2 LTLEDLAEALGMSPRHLQRLFKKET--GT-TPK-------QYLRDRRLERARRLLRDT-DLSVTEIALRV---GFS---- 63 (84)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHh--Cc-CHH-------HHHHHHHHHHHHHHHHcC-CCCHHHHHHHh---CCC----
Confidence 5789999999999999999999763 11 000 112223345566666665 78888887766 553
Q ss_pred CCCHHHHHHHHHhccCC
Q psy15598 144 VPSVSSISRILRNKIGS 160 (258)
Q Consensus 144 ~pS~STI~RiLrr~~~~ 160 (258)
|.+...|.+++.-+.
T Consensus 64 --s~~~f~r~Fk~~~g~ 78 (84)
T smart00342 64 --SQSYFSRAFKKLFGV 78 (84)
T ss_pred --ChHHHHHHHHHHHCc
Confidence 889999999876543
No 189
>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=95.01 E-value=0.063 Score=39.03 Aligned_cols=38 Identities=21% Similarity=0.258 Sum_probs=32.7
Q ss_pred HHHHHHHcC-CCHHHHHHHhCCCHHHHHHHHHHhhhhCC
Q psy15598 55 RIVELAQLG-IRPCDISRQLRVSHGCVSKILARYHETGS 92 (258)
Q Consensus 55 RIV~L~~~G-~S~~eIAr~LGVSrsTVsRwikRyrEtGs 92 (258)
+|+.+..++ .+..+||+.||||++||++-+++.++.|-
T Consensus 4 ~il~~L~~~~~~~~eLa~~l~vS~~tv~~~l~~L~~~g~ 42 (69)
T TIGR00122 4 RLLALLADNPFSGEKLGEALGMSRTAVNKHIQTLREWGV 42 (69)
T ss_pred HHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCC
Confidence 466666554 68999999999999999999999999886
No 190
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=95.01 E-value=0.048 Score=48.15 Aligned_cols=42 Identities=12% Similarity=0.089 Sum_probs=34.0
Q ss_pred CCCHHHHHHHHHHH----HcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELA----QLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~----~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.++...|.-++..+ .+|+|..+||+.||||.+||.+++.|-+
T Consensus 178 ~Lp~~~R~v~~L~y~l~~~eg~s~~EIA~~lgis~~tVk~~~~rA~ 223 (234)
T PRK08301 178 KLSDREKQIMELRFGLNGGEEKTQKEVADMLGISQSYISRLEKRII 223 (234)
T ss_pred hCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 46777666555555 4899999999999999999999988764
No 191
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=95.01 E-value=0.24 Score=40.29 Aligned_cols=86 Identities=12% Similarity=0.118 Sum_probs=55.5
Q ss_pred HHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHH-HHHHHHHHhCCCCCHHH
Q psy15598 54 MRIVELAQ----LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVV-SYIKELKQKDPGIFAWE 128 (258)
Q Consensus 54 ~RIV~L~~----~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~-~~I~~lv~~nP~ita~E 128 (258)
.+|+..+. +..+..++|+.+|+|++++.|+.+++- |. .|.....+.+ .....++. +.+.+..+
T Consensus 12 ~~~~~~I~~~~~~~~sl~~lA~~~g~S~~~l~r~Fk~~~--G~---------s~~~~l~~~Rl~~A~~~L~-~t~~~i~e 79 (127)
T PRK11511 12 HSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKKET--GH---------SLGQYIRSRKMTEIAQKLK-ESNEPILY 79 (127)
T ss_pred HHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHHH--Cc---------CHHHHHHHHHHHHHHHHHH-cCCCCHHH
Confidence 34444443 458999999999999999999999974 21 1221111111 12223333 45677777
Q ss_pred HHHHHHhcCCCCCCCCCCHHHHHHHHHhccCC
Q psy15598 129 IRDRLLSDGVCDKFNVPSVSSISRILRNKIGS 160 (258)
Q Consensus 129 Ir~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~ 160 (258)
|+..+ |.. +.+...|.+++.-+.
T Consensus 80 IA~~~---Gf~------s~s~F~r~Fkk~~G~ 102 (127)
T PRK11511 80 LAERY---GFE------SQQTLTRTFKNYFDV 102 (127)
T ss_pred HHHHh---CCC------CHHHHHHHHHHHHCc
Confidence 76655 665 889999999877664
No 192
>PRK13182 racA polar chromosome segregation protein; Reviewed
Probab=94.99 E-value=0.088 Score=46.06 Aligned_cols=63 Identities=11% Similarity=0.094 Sum_probs=45.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHH
Q psy15598 64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRD 131 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~ 131 (258)
++..++|+.+|||..||++|.+++. +......+ ..+..++++...|..++. .+-+++..+|+.
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 MKTPFVAKKLGVSPKTVQRWVKQLN----LPCEKNEY-GHYIFTEEDLQLLEYVKSQIEEGQNMQDTQK 64 (175)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCC----CCCCcCCC-CCEEECHHHHHHHHHHHHHHHcCCCHHHHHH
Confidence 4789999999999999999999753 32222222 347788887777766653 445788888865
No 193
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=94.98 E-value=0.047 Score=51.92 Aligned_cols=42 Identities=29% Similarity=0.397 Sum_probs=35.8
Q ss_pred HHHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598 53 RMRIVELA-QLGIRPCDISRQLRVSHGCVSKILARYHETGSIL 94 (258)
Q Consensus 53 R~RIV~L~-~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~ 94 (258)
-.++-.++ .+|++..+||++|||||.+|+|.+++-++.|-|+
T Consensus 15 ~~~~A~lYY~~gltQ~eIA~~LgiSR~~v~rlL~~Ar~~GiV~ 57 (321)
T COG2390 15 LARAAWLYYVEGLTQSEIAERLGISRATVSRLLAKAREEGIVK 57 (321)
T ss_pred HHHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCeEE
Confidence 34444454 5899999999999999999999999999999764
No 194
>PHA00542 putative Cro-like protein
Probab=94.96 E-value=0.048 Score=41.60 Aligned_cols=32 Identities=19% Similarity=0.230 Sum_probs=26.4
Q ss_pred HHHHH-HHcCCCHHHHHHHhCCCHHHHHHHHHH
Q psy15598 55 RIVEL-AQLGIRPCDISRQLRVSHGCVSKILAR 86 (258)
Q Consensus 55 RIV~L-~~~G~S~~eIAr~LGVSrsTVsRwikR 86 (258)
+++.+ ...|++..++|+.+|||++||++|.+.
T Consensus 22 ~l~~~l~~~glTq~elA~~lgIs~~tIsr~e~g 54 (82)
T PHA00542 22 ELVCALIRAGWSQEQIADATDVSQPTICRIYSG 54 (82)
T ss_pred HHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHcC
Confidence 34444 457999999999999999999999754
No 195
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=94.95 E-value=0.065 Score=45.28 Aligned_cols=43 Identities=16% Similarity=0.052 Sum_probs=36.2
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE 89 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE 89 (258)
.++...|.-++..+-+|++..+||+.||||.+||+..+.|-+.
T Consensus 137 ~L~~~~r~i~~l~~~~g~s~~eIA~~lgis~~~v~~~l~Rar~ 179 (187)
T PRK12534 137 ELEPPRSELIRTAFFEGITYEELAARTDTPIGTVKSWIRRGLA 179 (187)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHHhCCChhHHHHHHHHHHH
Confidence 4666777666666679999999999999999999999998763
No 196
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=94.95 E-value=0.063 Score=45.80 Aligned_cols=43 Identities=16% Similarity=0.151 Sum_probs=36.4
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE 89 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE 89 (258)
.++.+.|.-++...-+|++..+||+.||||.+||++.+.|-+.
T Consensus 106 ~L~~~~r~i~~l~~~~g~~~~EIA~~lgis~~tV~~~l~Rar~ 148 (181)
T PRK09637 106 ALPEKYAEALRLTELEGLSQKEIAEKLGLSLSGAKSRVQRGRV 148 (181)
T ss_pred hCCHHHHHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 5777777766666779999999999999999999999887653
No 197
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=94.93 E-value=0.066 Score=46.79 Aligned_cols=42 Identities=26% Similarity=0.297 Sum_probs=36.2
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.++...|.-++..+-+|++..+||+.||||.+||+..+.|-+
T Consensus 138 ~L~~~~r~v~~L~~~~g~s~~EIA~~Lgis~~tV~~~l~RAr 179 (203)
T PRK09647 138 SLPPEFRAAVVLCDIEGLSYEEIAATLGVKLGTVRSRIHRGR 179 (203)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 477777766666677999999999999999999999999975
No 198
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=94.92 E-value=0.067 Score=45.87 Aligned_cols=42 Identities=21% Similarity=0.283 Sum_probs=35.8
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.++...|.-++..+-+|++..+||+.||||.+||..++.|-+
T Consensus 136 ~L~~~~r~i~~L~~~~g~s~~eIA~~lgis~~tV~~~l~Ra~ 177 (196)
T PRK12524 136 ALPERQRQAVVLRHIEGLSNPEIAEVMEIGVEAVESLTARGK 177 (196)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 467777766666667999999999999999999999999865
No 199
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=94.92 E-value=0.067 Score=46.47 Aligned_cols=43 Identities=19% Similarity=0.193 Sum_probs=36.1
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE 89 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE 89 (258)
.|+...|.-|+..+-+|++..+||+.||||.+||..++.|-++
T Consensus 153 ~L~~~~r~vl~l~~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~ 195 (206)
T PRK12526 153 KLPEAQQTVVKGVYFQELSQEQLAQQLNVPLGTVKSRLRLALA 195 (206)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4777777666666779999999999999999999999888653
No 200
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=94.89 E-value=0.067 Score=45.74 Aligned_cols=43 Identities=16% Similarity=0.220 Sum_probs=36.7
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE 89 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE 89 (258)
.++...|.-++..+-+|++..+||+.||||.+||...+.|-++
T Consensus 111 ~Lp~~~R~v~~L~~~~g~s~~EIA~~Lgis~~tV~~~l~RAr~ 153 (182)
T PRK12540 111 KLPQDQREALILVGASGFSYEDAAAICGCAVGTIKSRVNRARS 153 (182)
T ss_pred hCCHHHHHHhhHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4677777777776789999999999999999999999888754
No 201
>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=94.89 E-value=0.068 Score=46.89 Aligned_cols=42 Identities=24% Similarity=0.243 Sum_probs=36.7
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.++...|.-++..+.+|++.++||+.||||.+||++++++-.
T Consensus 178 ~L~~~~r~vl~l~y~~~~s~~eIA~~lgis~~~v~~~~~ra~ 219 (227)
T TIGR02980 178 ALPERERRILLLRFFEDKTQSEIAERLGISQMHVSRLLRRAL 219 (227)
T ss_pred cCCHHHHHHHHHHHhcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 477778877777677999999999999999999999998865
No 202
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=94.89 E-value=0.071 Score=44.97 Aligned_cols=42 Identities=19% Similarity=0.198 Sum_probs=35.4
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.++...|.-++..+-+|++..+||+.||||.+||...+.|-+
T Consensus 117 ~Lp~~~r~i~~l~~~e~~s~~EIA~~lgis~~tV~~~l~ra~ 158 (179)
T PRK12543 117 KLPYKLRQVIILRYLHDYSQEEIAQLLQIPIGTVKSRIHAAL 158 (179)
T ss_pred hCCHHHHHHHHHHHHccCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 377777766666667999999999999999999999888864
No 203
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=94.88 E-value=0.069 Score=45.83 Aligned_cols=43 Identities=19% Similarity=0.142 Sum_probs=36.9
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE 89 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE 89 (258)
.++...|.-++..+-+|++..+||..||||.+||+..+.|.+.
T Consensus 128 ~Lp~~~r~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Rar~ 170 (188)
T PRK12517 128 KLDPEYREPLLLQVIGGFSGEEIAEILDLNKNTVMTRLFRARN 170 (188)
T ss_pred hCCHHHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 5777777766666679999999999999999999999998763
No 204
>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=94.88 E-value=0.14 Score=41.70 Aligned_cols=66 Identities=14% Similarity=0.082 Sum_probs=46.0
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHH
Q psy15598 65 RPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLL 134 (258)
Q Consensus 65 S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~ 134 (258)
++.++|+.+|||..|++.| .+.|.+.+..+..+.-+..++++...|..+.. ..-.+++.||++.|.
T Consensus 1 ~I~e~a~~~gvs~~tlR~Y----e~~GLl~~~~r~~~g~R~Y~~~~l~~l~~I~~l~~~G~sl~eI~~~l~ 67 (124)
T TIGR02051 1 TIGELAKAAGVNVETIRYY----ERKGLLPEPDRPEGGYRRYPEETVKRLRFIKRAQELGFSLEEIGGLLG 67 (124)
T ss_pred CHHHHHHHHCcCHHHHHHH----HHCCCCCCCccCCCCCEeECHHHHHHHHHHHHHHHCCCCHHHHHHHHh
Confidence 4679999999999999655 55677764333222457777777766655432 344789999998885
No 205
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=94.88 E-value=0.06 Score=47.77 Aligned_cols=42 Identities=24% Similarity=0.213 Sum_probs=35.7
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.++...|.-++..+.+|+|..+||+.||||.+||+++++|-+
T Consensus 184 ~L~~~~r~vl~l~~~~g~s~~EIA~~lgis~~tV~~~~~ra~ 225 (236)
T PRK06986 184 SLPEREQLVLSLYYQEELNLKEIGAVLGVSESRVSQIHSQAI 225 (236)
T ss_pred hCCHHHHHHHHhHhccCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 367777766666677999999999999999999999988865
No 206
>COG0789 SoxR Predicted transcriptional regulators [Transcription]
Probab=94.87 E-value=0.19 Score=39.90 Aligned_cols=68 Identities=18% Similarity=0.182 Sum_probs=48.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHh
Q psy15598 64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLLS 135 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~~ 135 (258)
+++.++|+.+|||..|++-| .+.|.+.|..+..+.-|..++++...+..+.. .+-.+++.+|++.|..
T Consensus 1 ~~I~eva~~~gvs~~tLRyY----E~~GLl~p~~~~~~gyR~Ys~~dl~~l~~I~~~r~~G~~L~~I~~~l~~ 69 (124)
T COG0789 1 YTIGEVAKLTGVSVRTLRFY----ERKGLLSPERRDEGGYRYYTPEDLELLQIIKTLRELGFSLAEIKELLDL 69 (124)
T ss_pred CcHHHHHHHhCCCHHHHHHH----HHcCCCCCcccCCCCceecCHHHHHHHHHHHHHHHcCCCHHHHHHHHhc
Confidence 47889999999999998654 45677766655422457888887665554433 2458899999988864
No 207
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=94.86 E-value=0.072 Score=36.16 Aligned_cols=35 Identities=23% Similarity=0.385 Sum_probs=31.4
Q ss_pred HcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCccc
Q psy15598 61 QLGIRPCDISRQLRVSHGCVSKILARYHETGSILP 95 (258)
Q Consensus 61 ~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~p 95 (258)
.+..+..+|++.|++|++||++.+++..+.|-+..
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~~g~i~~ 42 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLREAGLVES 42 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHHCCCeee
Confidence 45689999999999999999999999999997753
No 208
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=94.86 E-value=0.072 Score=45.11 Aligned_cols=42 Identities=19% Similarity=0.137 Sum_probs=35.6
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.++...|.-++..+-+|++..+||+.||+|.+||...+.|-+
T Consensus 122 ~L~~~~r~i~~l~~~~g~s~~EIA~~lgis~~tVk~~l~Rar 163 (185)
T PRK12542 122 ELNESNRQVFKYKVFYNLTYQEISSVMGITEANVRKQFERAR 163 (185)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 477777766666677999999999999999999999988865
No 209
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=94.85 E-value=0.08 Score=43.55 Aligned_cols=42 Identities=21% Similarity=0.249 Sum_probs=34.9
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.++.+.|.-++..+-+|++..+||+.||+|.+||+..+.|-+
T Consensus 105 ~L~~~~r~v~~l~~~~~~s~~eIA~~lgis~~tv~~~l~ra~ 146 (159)
T PRK12527 105 ELPPACRDSFLLRKLEGLSHQQIAEHLGISRSLVEKHIVNAM 146 (159)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 377777765555567999999999999999999999988764
No 210
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=94.85 E-value=0.061 Score=47.73 Aligned_cols=43 Identities=26% Similarity=0.186 Sum_probs=35.5
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE 89 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE 89 (258)
.++...|.-++..+-+|++..+||+.||||.+||+..+.|-+.
T Consensus 134 ~Lp~~~R~v~~L~y~eg~s~~EIAe~LgiS~~tVk~~L~RAr~ 176 (216)
T PRK12533 134 KLPVEYREVLVLRELEDMSYREIAAIADVPVGTVMSRLARARR 176 (216)
T ss_pred cCCHHHHhHhhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4666777666665679999999999999999999999887653
No 211
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=94.84 E-value=0.063 Score=44.95 Aligned_cols=43 Identities=30% Similarity=0.285 Sum_probs=35.7
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE 89 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE 89 (258)
.++...|.-+...+-+|++..+||+.||+|.++|+..+.|-+.
T Consensus 136 ~L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~~v~~~l~Rar~ 178 (187)
T TIGR02948 136 ALPPKYRMVIVLKYMEDLSLKEISEILDLPVGTVKTRIHRGRE 178 (187)
T ss_pred hCCHHHhHHhhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4666666655555679999999999999999999999998753
No 212
>TIGR01950 SoxR redox-sensitive transcriptional activator SoxR. SoxR is a MerR-family homodimeric transcription factor with a 2Fe-2S cluster in each monomer. The motif CIGCGCxxxxxC is conserved. Oxidation of the iron-sulfur cluster activates SoxR. The physiological role in E. coli is response to oxidative stress. It is activated by superoxide, singlet oxygen, nitric oxide (NO), and hydrogen peroxide. In E. coli, SoxR increases expression of transcription factor SoxS; different downstream targets may exist in other species.
Probab=94.84 E-value=0.3 Score=41.11 Aligned_cols=66 Identities=17% Similarity=0.167 Sum_probs=47.4
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHH
Q psy15598 64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLL 134 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~ 134 (258)
+++.++|+.+|||..|++-|-+ .|.+.+....+ .-|..++++...|..+.. .+-.+++.+|++.+.
T Consensus 2 ~~IgevA~~~Gvs~~tLRyYE~----~GLl~~~r~~~-g~R~Y~~~di~~l~~I~~lr~~G~sL~eI~~~l~ 68 (142)
T TIGR01950 2 LTVGELAKRSGVAVSALHFYES----KGLITSIRNSG-NQRRYKRDVLRRVAVIKAAQRVGIPLATIGEALA 68 (142)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH----CCCCCCccCCC-CCEEECHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 6789999999999999866554 48887644333 347788777665555433 234788999998885
No 213
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=94.81 E-value=0.073 Score=46.07 Aligned_cols=42 Identities=21% Similarity=0.235 Sum_probs=35.6
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.++...|.-++..+-+|++..+||..||+|.+||...+.|-+
T Consensus 139 ~Lp~~~r~v~~L~~~eg~s~~EIA~~lgis~~tVk~~l~RAr 180 (201)
T PRK12545 139 HLPEQIGRVFMMREFLDFEIDDICTELTLTANHCSVLLYRAR 180 (201)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 477777777776677999999999999999999998887754
No 214
>PRK10227 DNA-binding transcriptional regulator CueR; Provisional
Probab=94.81 E-value=0.18 Score=41.95 Aligned_cols=67 Identities=16% Similarity=0.212 Sum_probs=49.1
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHH
Q psy15598 64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLL 134 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~ 134 (258)
|++.++|+.+|||..||+- |.+.|.+.|..+..+.-|..++++...|..... ..-.+++.||++.+.
T Consensus 1 m~Ige~a~~~gvs~~tlRy----YE~~GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sl~eI~~~l~ 68 (135)
T PRK10227 1 MNISDVAKITGLTSKAIRF----YEEKGLVTPPMRSENGYRTYTQQHLNELTLLRQARQVGFNLEESGELVN 68 (135)
T ss_pred CCHHHHHHHHCcCHHHHHH----HHHCCCCCCcccCCCCcccCCHHHHHHHHHHHHHHHCCCCHHHHHHHHH
Confidence 5788999999999999854 455677766544322458888888777766544 345889999988775
No 215
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=94.81 E-value=0.21 Score=45.77 Aligned_cols=44 Identities=16% Similarity=0.160 Sum_probs=38.1
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHET 90 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEt 90 (258)
.++...|.-++...-+|++.+|||+.||+|.+||+..+.|-+..
T Consensus 115 ~L~~~~R~v~~L~~~~g~s~~EIA~~lg~s~~tVk~~l~RAr~~ 158 (293)
T PRK09636 115 RLSPLERAAFLLHDVFGVPFDEIASTLGRSPAACRQLASRARKH 158 (293)
T ss_pred hCCHHHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 47888887666666799999999999999999999999998754
No 216
>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=94.80 E-value=0.08 Score=44.30 Aligned_cols=42 Identities=24% Similarity=0.301 Sum_probs=36.5
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.++...|.-|+..+-+|++..+||..||||.+||++-+.|.+
T Consensus 140 ~L~~~~r~vi~l~~~~g~s~~eIA~~lgis~~~v~~~l~Ra~ 181 (189)
T TIGR02984 140 KLPEDYREVILLRHLEGLSFAEVAERMDRSEGAVSMLWVRGL 181 (189)
T ss_pred cCCHHHHHHHHHHHhcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 578887777766677999999999999999999999988865
No 217
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=94.79 E-value=0.062 Score=48.49 Aligned_cols=75 Identities=16% Similarity=0.133 Sum_probs=49.7
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHhCCC
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQKDPG 123 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~nP~ 123 (258)
.++...|.-++...-+|+|.+|||+.+|+|.+||...+.|-++.=...- ..++ .+.-.....+..+..+.++||.
T Consensus 116 ~Lp~~~R~v~lL~~~eg~S~~EIAe~LgiS~~tVksrL~Rark~Lr~~l-~~~~-~~~~~~~~~~~~~~~~~~~~~~ 190 (228)
T PRK06704 116 SLNVQQSAILLLKDVFQYSIADIAKVCSVSEGAVKASLFRSRNRLKTVS-EEGI-EIVEFTDDMEVVVTSIREERPE 190 (228)
T ss_pred hCCHHHhhHhhhHHhhCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH-HhcC-CCCCccccHHHHHHHHHhcCHH
Confidence 4677777666666678999999999999999999999888764321000 0122 1222234456677777777774
No 218
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=94.78 E-value=0.072 Score=47.86 Aligned_cols=42 Identities=14% Similarity=0.065 Sum_probs=35.0
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.++...|.-|+..+-+|++..+||+.||||.+||++++++-.
T Consensus 205 ~L~~~~r~vl~l~~~~g~s~~eIA~~l~is~~tV~~~~~ra~ 246 (257)
T PRK08583 205 VLSDREKSIIQCTFIENLSQKETGERLGISQMHVSRLQRQAI 246 (257)
T ss_pred hCCHHHHHHHHHHHhCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 366677765555567999999999999999999999998765
No 219
>PRK06930 positive control sigma-like factor; Validated
Probab=94.74 E-value=0.081 Score=45.74 Aligned_cols=42 Identities=14% Similarity=0.218 Sum_probs=36.1
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.++...|.-++..+.+|++..+||+.||||.+||..++.|-+
T Consensus 114 ~L~~rer~V~~L~~~eg~s~~EIA~~lgiS~~tVk~~l~Ra~ 155 (170)
T PRK06930 114 VLTEREKEVYLMHRGYGLSYSEIADYLNIKKSTVQSMIERAE 155 (170)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 477777766666678999999999999999999999998865
No 220
>PF12298 Bot1p: Eukaryotic mitochondrial regulator protein ; InterPro: IPR021036 This entry represents Ribosomal protein S35, which localises to the mitochondria in live cells and co-fractionates with purified mitochondrial ribosomes. This group of proteins have a novel function in the control of cell respiration by acting on the mitochondrial protein synthesis machinery and a role in mitochondrial integrity. Observations also indicate that in Schizosaccharomyces pombe (Fission yeast), alterations of mitochondrial function are linked to changes in cell cycle and cell morphology control mechanisms [].
Probab=94.74 E-value=0.15 Score=44.62 Aligned_cols=52 Identities=17% Similarity=0.126 Sum_probs=46.4
Q ss_pred ccCCCCCCHHHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCc
Q psy15598 42 FVNGRPLPNSVRMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILARYHETGSI 93 (258)
Q Consensus 42 ~~~gR~~S~dlR~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl 93 (258)
|+....+|.++|..|+..+. +|++.++||..|||+...|.-+++-+.-.+..
T Consensus 11 f~~~~~lse~~r~~Iy~~~~~~~~sv~~vS~~ygi~~~RV~AIvrLkeiE~~~ 63 (172)
T PF12298_consen 11 FRSNPVLSEELREQIYEDVMQDGKSVREVSQKYGIKIQRVEAIVRLKEIEKRW 63 (172)
T ss_pred CCCCCcCCHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 66777899999999999985 78999999999999999999999998766554
No 221
>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function.
Probab=94.74 E-value=0.08 Score=42.97 Aligned_cols=42 Identities=17% Similarity=0.130 Sum_probs=36.6
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.++.|.-..|-..-.+|++..+.|++.|||++|+++++...+
T Consensus 41 ~L~~dElEAiRL~D~egl~QeeaA~~MgVSR~T~~ril~~AR 82 (106)
T PF02001_consen 41 VLTVDELEAIRLVDYEGLSQEEAAERMGVSRPTFQRILESAR 82 (106)
T ss_pred EeeHHHHHHHHHHHHcCCCHHHHHHHcCCcHHHHHHHHHHHH
Confidence 577888777766667999999999999999999999998865
No 222
>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=94.71 E-value=0.066 Score=38.10 Aligned_cols=41 Identities=22% Similarity=0.396 Sum_probs=35.5
Q ss_pred HHHHHHHHH-cC-CCHHHHHHHhCCCHHHHHHHHHHhhhhCCc
Q psy15598 53 RMRIVELAQ-LG-IRPCDISRQLRVSHGCVSKILARYHETGSI 93 (258)
Q Consensus 53 R~RIV~L~~-~G-~S~~eIAr~LGVSrsTVsRwikRyrEtGsl 93 (258)
+.+|+++++ .| .+..++|+.|+||..||+|=++...+.|.+
T Consensus 2 ~~~Il~~l~~~~~~s~~ela~~~~VS~~TiRRDl~~L~~~g~i 44 (57)
T PF08220_consen 2 QQQILELLKEKGKVSVKELAEEFGVSEMTIRRDLNKLEKQGLI 44 (57)
T ss_pred HHHHHHHHHHcCCEEHHHHHHHHCcCHHHHHHHHHHHHHCCCE
Confidence 456777775 34 799999999999999999999999999875
No 223
>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=94.71 E-value=0.078 Score=46.60 Aligned_cols=43 Identities=14% Similarity=0.120 Sum_probs=37.3
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE 89 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE 89 (258)
.++...|.-++..+-+|+|..+||+.+|||.+||++++++-.+
T Consensus 175 ~L~~~~r~il~l~y~~~~s~~eIA~~lgis~~tV~~~~~ra~~ 217 (224)
T TIGR02479 175 SLSEREQLVLSLYYYEELNLKEIGEVLGLTESRVSQIHSQALK 217 (224)
T ss_pred hCCHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 4778888777777789999999999999999999999888653
No 224
>COG1438 ArgR Arginine repressor [Transcription]
Probab=94.70 E-value=0.073 Score=45.66 Aligned_cols=52 Identities=17% Similarity=0.154 Sum_probs=47.0
Q ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCCCCCCC
Q psy15598 109 KVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSSIVQH 165 (258)
Q Consensus 109 e~~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~~~~~~ 165 (258)
+..+.|++++.++.--+..||.+.|++.|+++ +.+||+|-|+..+..|....
T Consensus 6 ~R~~~Ik~iI~~~~i~TQ~Elv~~L~~~Gi~v-----TQaTvSRDlkelglvKv~~~ 57 (150)
T COG1438 6 ERLELIKEIITEEKISTQEELVELLQEEGIEV-----TQATVSRDLKELGLVKVRNE 57 (150)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHHHcCCeE-----ehHHHHHHHHHcCCEEecCC
Confidence 45788999999999899999999999999986 99999999999999988743
No 225
>PRK09863 putative frv operon regulatory protein; Provisional
Probab=94.64 E-value=0.29 Score=49.31 Aligned_cols=95 Identities=15% Similarity=0.087 Sum_probs=61.6
Q ss_pred HHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHHhhh----hCC-cccCCCCCCCC-----C-------CCCHHHHHHH
Q psy15598 53 RMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILARYHE----TGS-ILPGAIGGSKP-----R-------VTTPKVVSYI 114 (258)
Q Consensus 53 R~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwikRyrE----tGs-l~pk~rgG~RP-----r-------klT~e~~~~I 114 (258)
..+|+.+.. +..+..++|+.||||.+||++-++.-.+ .|. +..+. +|-+= . ...++....+
T Consensus 6 ~~~iL~~L~~~~~t~~~LA~~l~VS~RTIr~dI~~in~~l~~~~~~~i~~~-~Gy~l~~~~~~~~~~~~~~~~~e~~~il 84 (584)
T PRK09863 6 ELKIVDLLEQQDRSGGELAQQLGVSRRTIVRDIAYINFTLNGKAIGSISGS-AKYHLEILNRRSLFQLLQKSDNEDRLLL 84 (584)
T ss_pred HHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhcchhheecC-CceEEEeCCHHHHHHHHhcCCHHHHHHH
Confidence 455666654 5689999999999999999999986643 332 11221 23110 0 0122333344
Q ss_pred HHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccC
Q psy15598 115 KELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIG 159 (258)
Q Consensus 115 ~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~ 159 (258)
..++. +...+..++++.|. ||.+||.+-|++...
T Consensus 85 ~~Ll~-~~~~~~~~La~~l~----------vS~sTi~~dl~~v~~ 118 (584)
T PRK09863 85 LRLLL-NTFTPMAQLASALN----------LSRTWVAERLPRLNQ 118 (584)
T ss_pred HHHHH-cCCccHHHHHHHhC----------CCHHHHHHHHHHHHH
Confidence 44554 55678888888884 599999999987665
No 226
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=94.63 E-value=0.09 Score=45.00 Aligned_cols=42 Identities=14% Similarity=0.137 Sum_probs=34.9
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.++.+.|.-++..+-+|++..+||..||||.+||..-+.|-+
T Consensus 141 ~Lp~~~r~v~~l~~~eg~s~~EIA~~lgis~~tVk~rl~ra~ 182 (194)
T PRK12531 141 RLPKAQRDVLQAVYLEELPHQQVAEMFDIPLGTVKSRLRLAV 182 (194)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHHHHH
Confidence 467777765555577999999999999999999998887765
No 227
>PF13730 HTH_36: Helix-turn-helix domain
Probab=94.62 E-value=0.054 Score=37.42 Aligned_cols=28 Identities=21% Similarity=0.343 Sum_probs=26.3
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHhhhhCC
Q psy15598 65 RPCDISRQLRVSHGCVSKILARYHETGS 92 (258)
Q Consensus 65 S~~eIAr~LGVSrsTVsRwikRyrEtGs 92 (258)
|.+.||+.+|+|++||.++++.-++.|-
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 8899999999999999999999998774
No 228
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=94.61 E-value=0.087 Score=43.42 Aligned_cols=43 Identities=21% Similarity=0.125 Sum_probs=36.5
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE 89 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE 89 (258)
.++...|.-++..+-+|++..+||+.||+|.+||+..+.|-+.
T Consensus 112 ~L~~~~r~v~~l~~~~~~s~~eIA~~lgis~~tv~~~l~Rar~ 154 (161)
T PRK12541 112 SLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRK 154 (161)
T ss_pred HCCHHHHHHhhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4777777766666679999999999999999999999998763
No 229
>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=94.60 E-value=0.24 Score=39.10 Aligned_cols=65 Identities=17% Similarity=0.270 Sum_probs=45.8
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHH
Q psy15598 64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLL 134 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~ 134 (258)
+++.++|+.+|||..|++ -|.+.|-+.|...+| -+..+++....|..... ++-.+++.||++.+.
T Consensus 1 m~Ige~a~~~gvs~~tlR----yYe~~GLl~p~~~~g--~r~Y~~~~~~~l~~I~~lr~~G~sL~eI~~~l~ 66 (107)
T cd04777 1 MKIGKFAKKNNITIDTVR----HYIDLGLLIPEKKGG--QYFFDEKCQDDLEFILELKGLGFSLIEIQKIFS 66 (107)
T ss_pred CCHHHHHHHHCcCHHHHH----HHHHCCCcCCccCCC--ccccCHHHHHHHHHHHHHHHCCCCHHHHHHHHH
Confidence 578899999999999974 455678887754344 24577766655544433 334789999998885
No 230
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=94.59 E-value=0.085 Score=44.79 Aligned_cols=42 Identities=21% Similarity=0.270 Sum_probs=35.0
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.++...|.-++..+-+|++..+||+.||||.+||+..+.|-+
T Consensus 138 ~L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~tv~~~l~Rar 179 (193)
T PRK11923 138 QLPEDLRTALTLREFDGLSYEDIASVMQCPVGTVRSRIFRAR 179 (193)
T ss_pred hCCHHHhHHHhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 366666665666577999999999999999999999988865
No 231
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=94.58 E-value=0.032 Score=47.50 Aligned_cols=42 Identities=10% Similarity=-0.050 Sum_probs=34.2
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.++...|.-++..+-+|++..+||+.||||.+||..++.|-+
T Consensus 134 ~L~~~~r~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Ra~ 175 (188)
T PRK09640 134 HVNPIDREILVLRFVAELEFQEIADIMHMGLSATKMRYKRAL 175 (188)
T ss_pred hcChhheeeeeeHHhcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 356665554444567999999999999999999999999875
No 232
>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=94.57 E-value=0.093 Score=44.93 Aligned_cols=42 Identities=21% Similarity=0.297 Sum_probs=35.0
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.++...|.-++..+-+|++.++||+.||+|.+||...+.|-+
T Consensus 131 ~L~~~~r~v~~l~~~~g~s~~EIA~~lgis~~tvk~rl~Rar 172 (188)
T TIGR02943 131 HLPEQTARVFMMREVLGFESDEICQELEISTSNCHVLLYRAR 172 (188)
T ss_pred hCCHHHHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 466777766666667999999999999999999999888864
No 233
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=94.57 E-value=0.22 Score=43.61 Aligned_cols=65 Identities=14% Similarity=0.106 Sum_probs=44.2
Q ss_pred CCCCCHHHHHHHHHHHHc-----C--CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHH
Q psy15598 45 GRPLPNSVRMRIVELAQL-----G--IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPK 109 (258)
Q Consensus 45 gR~~S~dlR~RIV~L~~~-----G--~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e 109 (258)
...++..+-..|.+.+.. | ++..++|++|||||++|+.-+++-...|-|...+..|-.-..++..
T Consensus 9 ~~~~~e~v~~~l~~~I~~g~l~pG~~L~e~~La~~lgVSRtpVREAL~~L~~eGLV~~~~~~g~~v~~~~~~ 80 (221)
T PRK11414 9 HISLTLQVENDLKHQLSIGALKPGARLITKNLAEQLGMSITPVREALLRLVSVNALSVAPAQAFTVPEVSKR 80 (221)
T ss_pred CCCHHHHHHHHHHHHHHhCCCCCCCccCHHHHHHHHCCCchhHHHHHHHHHHCCCEEecCCCceeecCCCHH
Confidence 334444444444444333 3 4788999999999999999999999999887666555333334443
No 234
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=94.56 E-value=0.053 Score=39.89 Aligned_cols=43 Identities=16% Similarity=0.219 Sum_probs=34.5
Q ss_pred HHHHHHHHH---cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCccc
Q psy15598 53 RMRIVELAQ---LGIRPCDISRQLRVSHGCVSKILARYHETGSILP 95 (258)
Q Consensus 53 R~RIV~L~~---~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~p 95 (258)
+++|++.++ .+++.+|||+.+|+|+.+|++|+..-...|.|+.
T Consensus 2 ke~Il~~i~~~~~p~~T~eiA~~~gls~~~aR~yL~~Le~eG~V~~ 47 (62)
T PF04703_consen 2 KEKILEYIKEQNGPLKTREIADALGLSIYQARYYLEKLEKEGKVER 47 (62)
T ss_dssp HHCHHHHHHHHTS-EEHHHHHHHHTS-HHHHHHHHHHHHHCTSEEE
T ss_pred cHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEE
Confidence 345666554 4689999999999999999999999999998853
No 235
>PRK03341 arginine repressor; Provisional
Probab=94.55 E-value=0.1 Score=45.33 Aligned_cols=53 Identities=13% Similarity=0.058 Sum_probs=46.9
Q ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCCCCCCC
Q psy15598 108 PKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSSIVQH 165 (258)
Q Consensus 108 ~e~~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~~~~~~ 165 (258)
.+-.+.|+++++++.-.+..||.+.|.+.|+.+ |.+||+|-|+.++..|....
T Consensus 14 ~~R~~~I~~li~~~~i~tQ~eL~~~L~~~Gi~v-----TQaTiSRDl~eL~~~Kv~~~ 66 (168)
T PRK03341 14 AARQARIVAILSRQSVRSQAELAALLADEGIEV-----TQATLSRDLDELGAVKLRGA 66 (168)
T ss_pred HHHHHHHHHHHHHCCCccHHHHHHHHHHcCCcc-----cHHHHHHHHHHhcCEeeecC
Confidence 455778999999999999999999999999986 99999999999999986543
No 236
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=94.55 E-value=0.099 Score=44.39 Aligned_cols=42 Identities=10% Similarity=-0.027 Sum_probs=35.8
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.++.+.|.-++..+-+|++..+||+.||||.+||++.+.|-+
T Consensus 131 ~L~~~~r~vl~l~~~~~~s~~eIA~~lgis~~tV~~~l~Rar 172 (189)
T PRK12515 131 KLSPAHREIIDLVYYHEKSVEEVGEIVGIPESTVKTRMFYAR 172 (189)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 577787766666677999999999999999999999888765
No 237
>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional
Probab=94.54 E-value=0.41 Score=40.93 Aligned_cols=66 Identities=18% Similarity=0.233 Sum_probs=48.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHH
Q psy15598 64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLL 134 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~ 134 (258)
+++.++|+.+|||..||+.| .+.|.+.+....+ .-|..++.+.+.|.-... ++-.+++.||++.|.
T Consensus 12 ~~IgevAk~~gvs~~TlRyY----E~~GLi~~~r~~~-g~R~Y~~~~i~~L~~I~~lr~lG~sL~eIk~ll~ 78 (154)
T PRK15002 12 LTPGEVAKRSGVAVSALHFY----ESKGLITSIRNSG-NQRRYKRDVLRYVAIIKIAQRIGIPLATIGEAFG 78 (154)
T ss_pred ccHHHHHHHHCcCHHHHHHH----HHCCCCCCccCCC-CCEEECHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 79999999999999998654 5568777644333 347788777666654422 344789999998886
No 238
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=94.54 E-value=0.058 Score=35.57 Aligned_cols=32 Identities=25% Similarity=0.353 Sum_probs=29.6
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598 63 GIRPCDISRQLRVSHGCVSKILARYHETGSIL 94 (258)
Q Consensus 63 G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~ 94 (258)
.++..+||+.+++|++||++.+++..+.|-+.
T Consensus 8 ~~s~~~la~~l~~s~~tv~~~l~~L~~~g~l~ 39 (48)
T smart00419 8 PLTRQEIAELLGLTRETVSRTLKRLEKEGLIS 39 (48)
T ss_pred ccCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 46889999999999999999999999999874
No 239
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=94.52 E-value=0.11 Score=46.27 Aligned_cols=45 Identities=13% Similarity=0.176 Sum_probs=38.4
Q ss_pred CCCCCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598 44 NGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE 89 (258)
Q Consensus 44 ~gR~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE 89 (258)
-.+.+|...+ +|+.++.+|++.++||+.|+||.+||...+++-.+
T Consensus 130 ~~~~LSpREr-EVLrLLAqGkTnKEIAe~L~IS~rTVkth~srImk 174 (198)
T PRK15201 130 TTRHFSVTER-HLLKLIASGYHLSETAALLSLSEEQTKSLRRSIMR 174 (198)
T ss_pred CCCCCCHHHH-HHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 4556777666 68888999999999999999999999999988763
No 240
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=94.50 E-value=0.13 Score=43.05 Aligned_cols=42 Identities=19% Similarity=0.292 Sum_probs=35.5
Q ss_pred HHHHHHHHHH-cC-CCHHHHHHHhCCCHHHHHHHHHHhhhhCCc
Q psy15598 52 VRMRIVELAQ-LG-IRPCDISRQLRVSHGCVSKILARYHETGSI 93 (258)
Q Consensus 52 lR~RIV~L~~-~G-~S~~eIAr~LGVSrsTVsRwikRyrEtGsl 93 (258)
+=.+|+.+++ +| .|.++||+++|+|++||.+=+++.++.|.+
T Consensus 10 ~D~~Il~~Lq~d~R~s~~eiA~~lglS~~tV~~Ri~rL~~~GvI 53 (153)
T PRK11179 10 LDRGILEALMENARTPYAELAKQFGVSPGTIHVRVEKMKQAGII 53 (153)
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCe
Confidence 4445666664 55 799999999999999999999999999965
No 241
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=94.50 E-value=0.043 Score=45.74 Aligned_cols=43 Identities=16% Similarity=0.197 Sum_probs=36.2
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE 89 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE 89 (258)
.++...|.-++..+-.|++..+||+.||+|.+||+..+.|-++
T Consensus 126 ~L~~~~r~v~~l~~~~g~s~~eIA~~l~is~~~V~~~l~ra~~ 168 (176)
T PRK09638 126 KLDPEFRAPVILKHYYGYTYEEIAKMLNIPEGTVKSRVHHGIK 168 (176)
T ss_pred cCCHHHhheeeehhhcCCCHHHHHHHHCCChhHHHHHHHHHHH
Confidence 3777777666666678999999999999999999999988764
No 242
>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=94.50 E-value=0.077 Score=44.54 Aligned_cols=43 Identities=28% Similarity=0.342 Sum_probs=34.6
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE 89 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE 89 (258)
.++...|.-++..+-+|++..+||+.||+|.+||+.++.|-++
T Consensus 138 ~L~~~~r~v~~l~~~~~~s~~EIA~~lgis~~tv~~~l~rar~ 180 (190)
T TIGR02939 138 ALPEDLRTAITLRELEGLSYEDIARIMDCPVGTVRSRIFRARE 180 (190)
T ss_pred cCCHHHhhhhhhhhhcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 3566666555555579999999999999999999999988753
No 243
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=94.49 E-value=0.098 Score=45.80 Aligned_cols=43 Identities=14% Similarity=0.168 Sum_probs=37.1
Q ss_pred CCCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 46 RPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 46 R~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
..++.+.|.-++..+-+|++..+||+.||||.+||...+.|-+
T Consensus 147 ~~L~~~~r~v~~L~~~~g~s~~EIAe~lgis~~tV~~~l~RAr 189 (206)
T PRK12544 147 DGLPAKYARVFMMREFIELETNEICHAVDLSVSNLNVLLYRAR 189 (206)
T ss_pred HhCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 3577888877777777999999999999999999999988865
No 244
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=94.49 E-value=0.23 Score=46.05 Aligned_cols=106 Identities=11% Similarity=0.032 Sum_probs=65.9
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCH
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFA 126 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~nP~ita 126 (258)
.++...|.-++...-.|++..+||+.||+|.+||+..+.|-++. +... .. +.....+++.+.+.+++..--.--.
T Consensus 118 ~L~p~~R~vf~L~~~~g~s~~EIA~~Lgis~~tVr~~l~RAr~~--Lr~~-~~--~~~~~~~~~~~~~~~f~~a~~~gd~ 192 (290)
T PRK09635 118 RLGPAERVVFVLHEIFGLPYQQIATTIGSQASTCRQLAHRARRK--INES-RI--AASVEPAQHRVVTRAFIEACSNGDL 192 (290)
T ss_pred hCCHHHHHHhhHHHHhCCCHHHHHHHHCcCHHHHHHHHHHHHHH--HHhh-CC--CCCCChHHHHHHHHHHHHHHHhCCH
Confidence 57778777776666799999999999999999999999988754 1111 00 1122334555666666654334445
Q ss_pred HHHHHHHHhc--CCCC---CCCCCCHHHHHHHHHhc
Q psy15598 127 WEIRDRLLSD--GVCD---KFNVPSVSSISRILRNK 157 (258)
Q Consensus 127 ~EIr~~L~~~--Gv~v---~~~~pS~STI~RiLrr~ 157 (258)
..|.+.|.++ |-.. ..-......|.++|...
T Consensus 193 ~~l~~ll~~d~~~~~~~~~~~~~~G~~~v~~~~~~~ 228 (290)
T PRK09635 193 DTLLEVLDPGVAGEIDARKGVVVVGADRVGPTILRH 228 (290)
T ss_pred HHHHHHhhhhhcCCCcCCCCccccCHHHHHHHHHHh
Confidence 6666666431 1111 00113677788887653
No 245
>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=94.48 E-value=0.09 Score=46.00 Aligned_cols=43 Identities=16% Similarity=0.171 Sum_probs=38.0
Q ss_pred HHHHHHHHHH--cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598 52 VRMRIVELAQ--LGIRPCDISRQLRVSHGCVSKILARYHETGSIL 94 (258)
Q Consensus 52 lR~RIV~L~~--~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~ 94 (258)
.|.+|+.++. .+++..+||+.|||+.+||++.+++..+.|-|.
T Consensus 2 tr~~IL~~L~~~~~~t~~eLA~~lgis~~tV~~~L~~Le~~GlV~ 46 (203)
T TIGR02702 2 TKEDILSYLLKQGQATAAALAEALAISPQAVRRHLKDLETEGLIE 46 (203)
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeE
Confidence 5778888764 469999999999999999999999999999874
No 246
>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=94.47 E-value=0.2 Score=41.89 Aligned_cols=67 Identities=16% Similarity=0.187 Sum_probs=48.1
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHh
Q psy15598 64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLLS 135 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~~ 135 (258)
++..++|+.+|||.+|++.|- +.|.+.|....+ .-+..++++...|..... .+-.+++.+|++.+..
T Consensus 1 y~I~e~a~~~gvs~~TLR~Ye----~~GLl~p~r~~~-g~R~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~ 68 (134)
T cd04779 1 YRIGQLAHLAGVSKRTIDYYT----NLGLLTPERSDS-NYRYYDETALDRLQLIEHLKGQRLSLAEIKDQLEE 68 (134)
T ss_pred CCHHHHHHHHCcCHHHHHHHH----HCCCCCCccCCC-CCeeECHHHHHHHHHHHHHHHCCCCHHHHHHHHHh
Confidence 467899999999999998875 458887655433 346677776665554433 3347889999988864
No 247
>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=94.47 E-value=0.051 Score=37.24 Aligned_cols=26 Identities=19% Similarity=0.399 Sum_probs=22.0
Q ss_pred HcCCCHHHHHHHhCCCHHHHHHHHHH
Q psy15598 61 QLGIRPCDISRQLRVSHGCVSKILAR 86 (258)
Q Consensus 61 ~~G~S~~eIAr~LGVSrsTVsRwikR 86 (258)
+.|++..++|+.+|||++||++|.+-
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 57999999999999999999999764
No 248
>PHA01976 helix-turn-helix protein
Probab=94.44 E-value=0.064 Score=38.29 Aligned_cols=33 Identities=15% Similarity=0.254 Sum_probs=27.1
Q ss_pred HHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598 53 RMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILA 85 (258)
Q Consensus 53 R~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwik 85 (258)
-.+|..+.+ .|++..++|+.+|||+++|++|.+
T Consensus 4 ~~rl~~~R~~~glt~~~lA~~~gvs~~~v~~~e~ 37 (67)
T PHA01976 4 AIQLIKARNARAWSAPELSRRAGVRHSLIYDFEA 37 (67)
T ss_pred HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 345555554 799999999999999999999864
No 249
>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=94.44 E-value=0.071 Score=38.24 Aligned_cols=34 Identities=21% Similarity=0.206 Sum_probs=28.5
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCC
Q psy15598 65 RPCDISRQLRVSHGCVSKILARYHETGSILPGAI 98 (258)
Q Consensus 65 S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~r 98 (258)
+..++|++|+||+.||++-+++..+.|-+.-.++
T Consensus 26 s~~~la~~~~vsr~tvr~al~~L~~~g~i~~~~~ 59 (64)
T PF00392_consen 26 SERELAERYGVSRTTVREALRRLEAEGLIERRPG 59 (64)
T ss_dssp -HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT
T ss_pred CHHHHHHHhccCCcHHHHHHHHHHHCCcEEEECC
Confidence 8899999999999999999999999998754443
No 250
>PRK05066 arginine repressor; Provisional
Probab=94.42 E-value=0.11 Score=44.64 Aligned_cols=52 Identities=21% Similarity=0.094 Sum_probs=46.3
Q ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHHhcCCC-CCCCCCCHHHHHHHHHhccCCCCCCC
Q psy15598 109 KVVSYIKELKQKDPGIFAWEIRDRLLSDGVC-DKFNVPSVSSISRILRNKIGSSIVQH 165 (258)
Q Consensus 109 e~~~~I~~lv~~nP~ita~EIr~~L~~~Gv~-v~~~~pS~STI~RiLrr~~~~~~~~~ 165 (258)
+....|++++++++--+..||.+.|++.|+. + +.+||+|-|+..+..|....
T Consensus 9 ~r~~~I~~iI~~~~I~tQeeL~~~L~~~Gi~~v-----TQATiSRDikeL~lvKv~~~ 61 (156)
T PRK05066 9 ELVKAFKALLKEEKFGSQGEIVTALQEQGFDNI-----NQSKVSRMLTKFGAVRTRNA 61 (156)
T ss_pred HHHHHHHHHHhhCCCCCHHHHHHHHHHCCCCee-----cHHHHHHHHHHcCCEEeeCC
Confidence 3467899999999999999999999999998 6 99999999999999986543
No 251
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=94.39 E-value=0.097 Score=44.84 Aligned_cols=41 Identities=17% Similarity=0.149 Sum_probs=35.8
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.+|.-.+ +|+.++.+|+|.++||+.|+||.+||...+++-.
T Consensus 150 ~Lt~rE~-evl~~~~~G~s~~eIA~~l~iS~~TV~~h~~~i~ 190 (216)
T PRK10840 150 RLSPKES-EVLRLFAEGFLVTEIAKKLNRSIKTISSQKKSAM 190 (216)
T ss_pred cCCHHHH-HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 4777665 7888899999999999999999999998888765
No 252
>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=94.39 E-value=0.045 Score=43.76 Aligned_cols=48 Identities=17% Similarity=0.236 Sum_probs=32.1
Q ss_pred cCCCCCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhh
Q psy15598 43 VNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHET 90 (258)
Q Consensus 43 ~~gR~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEt 90 (258)
+++..+....|.+-|..--+|++..++|+.+|+|..+|++++++.+..
T Consensus 52 P~~~~~~~~~R~~~I~~~f~G~n~~eLA~kyglS~r~I~~Ii~~~~~~ 99 (108)
T PF08765_consen 52 PKCDRLLRALRNREIRREFNGMNVRELARKYGLSERQIYRIIKRVRRR 99 (108)
T ss_dssp --SHHHHHHHHHHHHHHH--SS-HHHHHHHHT--HHHHHHHHHHHHH-
T ss_pred eCccHHHHHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 355555567776555544459999999999999999999999998743
No 253
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=94.38 E-value=0.045 Score=46.58 Aligned_cols=42 Identities=17% Similarity=0.096 Sum_probs=34.5
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.++...|.-++..+-+|++..+||+.||||.+||+..+.|-+
T Consensus 139 ~L~~~~r~i~~l~~~~g~s~~EIA~~lgis~~tV~~~l~ra~ 180 (194)
T PRK12513 139 TLPDEQREVFLLREHGDLELEEIAELTGVPEETVKSRLRYAL 180 (194)
T ss_pred hCCHhHhhheeeehccCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 467777765555567999999999999999999998888765
No 254
>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=94.37 E-value=0.038 Score=44.85 Aligned_cols=41 Identities=22% Similarity=0.173 Sum_probs=34.3
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 48 LPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 48 ~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
++...|.-++..+-+|++..+||+.||||.+||+..+.|.+
T Consensus 106 L~~~~r~i~~l~~~~g~s~~eIA~~lgis~~tv~~~l~Ra~ 146 (154)
T TIGR02950 106 LPENYRTVLILREFKEFSYKEIAELLNLSLAKVKSNLFRAR 146 (154)
T ss_pred CCHhheeeeeehhhccCcHHHHHHHHCCCHHHHHHHHHHHH
Confidence 66666665555556899999999999999999999999875
No 255
>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=94.37 E-value=0.26 Score=39.78 Aligned_cols=68 Identities=19% Similarity=0.209 Sum_probs=48.9
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHhc
Q psy15598 64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLLSD 136 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~~~ 136 (258)
+++.++|+.+|||..|++-|-+ .|.+.|..+.+ .-|..++++...|..... ..-++++.+|++.+...
T Consensus 1 m~IgevA~~~gvs~~tlRyYe~----~GLl~p~~~~~-gyR~Y~~~~l~~l~~I~~lr~~G~~L~eI~~~l~~~ 69 (120)
T cd04781 1 LDIAEVARQSGLPASTLRYYEE----KGLIASIGRRG-LRRQYDPQVLDRLALIALGRAAGFSLDEIQAMLSHD 69 (120)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCcCCC-CceecCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcc
Confidence 5788999999999999876655 47776654444 557888887776654422 23478899998877643
No 256
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=94.35 E-value=0.098 Score=45.11 Aligned_cols=43 Identities=19% Similarity=0.235 Sum_probs=37.0
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE 89 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE 89 (258)
.++...|.-++..+-+|++..+||+.||||.+||...+.|-+.
T Consensus 113 ~Lp~~~r~v~~L~~~~g~s~~EIA~~LgiS~~tVk~~l~Rar~ 155 (188)
T PRK12546 113 QLPDEQREALILVGASGFSYEEAAEMCGVAVGTVKSRANRARA 155 (188)
T ss_pred hCCHHHhHHhhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4677777777776789999999999999999999999988753
No 257
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=94.35 E-value=0.087 Score=44.25 Aligned_cols=42 Identities=24% Similarity=0.238 Sum_probs=34.7
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.++.+.|.-++..+-+|++..+||+.||+|.+||...+.|-+
T Consensus 119 ~L~~~~r~i~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Ra~ 160 (172)
T PRK09651 119 GLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKAT 160 (172)
T ss_pred hCCHHHhHHhhhhhccCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 467777655555556999999999999999999999998865
No 258
>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=94.35 E-value=0.087 Score=44.61 Aligned_cols=41 Identities=12% Similarity=0.133 Sum_probs=33.7
Q ss_pred CHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598 49 PNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE 89 (258)
Q Consensus 49 S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE 89 (258)
..+.+..|+.++-+|++..+||+.||+|.+||+..+.|-+.
T Consensus 151 l~~~~~~i~~~~~~~~s~~eIA~~l~~s~~tV~~~l~r~r~ 191 (198)
T TIGR02859 151 LSDLEWKVLQSYLDGKSYQEIACDLNRHVKSIDNALQRVKR 191 (198)
T ss_pred cCHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 44556666767779999999999999999999998888653
No 259
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=94.34 E-value=0.087 Score=47.19 Aligned_cols=42 Identities=17% Similarity=0.282 Sum_probs=34.9
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.++...|.-++..+-+|++..+||+.||||.+||...+.|-+
T Consensus 171 ~Lp~~~R~v~~L~~~eg~s~~EIA~~Lgis~~tVk~~l~RAr 212 (233)
T PRK12538 171 RLPEQQRIAVILSYHENMSNGEIAEVMDTTVAAVESLLKRGR 212 (233)
T ss_pred hCCHHHHHHhhhHHhcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 366667765555567999999999999999999999998865
No 260
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=94.33 E-value=0.069 Score=46.82 Aligned_cols=40 Identities=18% Similarity=0.200 Sum_probs=35.5
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 48 LPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 48 ~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
+|.-.+ +|+.++.+|++.++||++|+||.+||...+++-.
T Consensus 138 LT~RE~-eVL~lla~G~snkeIA~~L~iS~~TVk~h~~~I~ 177 (207)
T PRK15411 138 LSRTES-SMLRMWMAGQGTIQISDQMNIKAKTVSSHKGNIK 177 (207)
T ss_pred CCHHHH-HHHHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHH
Confidence 666555 7899999999999999999999999999988865
No 261
>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=94.32 E-value=0.28 Score=42.41 Aligned_cols=67 Identities=18% Similarity=0.245 Sum_probs=47.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHH
Q psy15598 64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLL 134 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~ 134 (258)
+++.++|+.+|||++||+.|-+ .|.+.|..+..+.-|..++++...|..+.. .+-.+++.+|+..|.
T Consensus 2 ~~I~evA~~~gvs~~tLRyYe~----~GLl~p~~r~~~gyR~Y~~~dl~rL~~I~~lr~~G~sL~eI~~ll~ 69 (172)
T cd04790 2 LTISQLARQFGLSRSTLLYYER----IGLLSPSARSESNYRLYGERDLERLEQICAYRSAGVSLEDIRSLLQ 69 (172)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCccCCCCCccCCHHHHHHHHHHHHHHHcCCCHHHHHHHHh
Confidence 5789999999999999876644 588877544322457788876666544433 334788889888775
No 262
>PRK06474 hypothetical protein; Provisional
Probab=94.31 E-value=0.073 Score=46.23 Aligned_cols=50 Identities=20% Similarity=0.355 Sum_probs=43.6
Q ss_pred CCCCCHHHHHHHHHHHHc-C--CCHHHHHHHh-CCCHHHHHHHHHHhhhhCCcc
Q psy15598 45 GRPLPNSVRMRIVELAQL-G--IRPCDISRQL-RVSHGCVSKILARYHETGSIL 94 (258)
Q Consensus 45 gR~~S~dlR~RIV~L~~~-G--~S~~eIAr~L-GVSrsTVsRwikRyrEtGsl~ 94 (258)
..-++...|.+|+..+.. + ++..+|++.+ +|+.+||||-++...+.|-|.
T Consensus 5 ~~~La~p~R~~Il~~L~~~~~~~ta~el~~~l~~is~aTvYrhL~~L~e~GLI~ 58 (178)
T PRK06474 5 AEILMHPVRMKICQVLMRNKEGLTPLELVKILKDVPQATLYRHLQTMVDSGILH 58 (178)
T ss_pred HHhhCCHHHHHHHHHHHhCCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHCCCEE
Confidence 445888999999998753 3 8999999999 799999999999999999764
No 263
>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=94.26 E-value=0.21 Score=43.11 Aligned_cols=59 Identities=22% Similarity=0.239 Sum_probs=42.1
Q ss_pred HHHHHHHHH-HHcC--CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHH
Q psy15598 51 SVRMRIVEL-AQLG--IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPK 109 (258)
Q Consensus 51 dlR~RIV~L-~~~G--~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e 109 (258)
.+|.+|+.. +.-| ++-.++|++||||+++|+.-+++....|-|...++.|-.=..++.+
T Consensus 19 ~l~~~I~~g~l~pG~~L~e~~La~~lgVSRtpVReAL~~L~~eGlv~~~~~~G~~V~~~~~~ 80 (212)
T TIGR03338 19 EIERAILSGELPPGAKLNESDIAARLGVSRGPVREAFRALEEAGLVRNEKNRGVFVREISLA 80 (212)
T ss_pred HHHHHHHcCCCCCCCEecHHHHHHHhCCChHHHHHHHHHHHHCCCEEEecCCCeEEecCCHH
Confidence 345555553 2334 4778999999999999999999999999987666555332334444
No 264
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=94.25 E-value=0.1 Score=44.28 Aligned_cols=42 Identities=21% Similarity=0.279 Sum_probs=36.0
Q ss_pred HHHHHHHHHH-cC-CCHHHHHHHhCCCHHHHHHHHHHhhhhCCc
Q psy15598 52 VRMRIVELAQ-LG-IRPCDISRQLRVSHGCVSKILARYHETGSI 93 (258)
Q Consensus 52 lR~RIV~L~~-~G-~S~~eIAr~LGVSrsTVsRwikRyrEtGsl 93 (258)
+=.+|+.+++ +| .+.++||+.+|+|++||++=++|..+.|.+
T Consensus 15 ~D~~IL~~Lq~d~R~s~~eiA~~lglS~~tv~~Ri~rL~~~GvI 58 (164)
T PRK11169 15 IDRNILNELQKDGRISNVELSKRVGLSPTPCLERVRRLERQGFI 58 (164)
T ss_pred HHHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCe
Confidence 4556777664 44 899999999999999999999999999965
No 265
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=94.24 E-value=0.11 Score=45.10 Aligned_cols=43 Identities=21% Similarity=0.254 Sum_probs=36.5
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE 89 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE 89 (258)
.++...|.-|+..+-+|++..+||+.||||.+||...+.|-+.
T Consensus 133 ~Lp~~~r~v~~l~~~~g~s~~EIAe~lgis~~tV~~~l~Rar~ 175 (196)
T PRK12535 133 ALPPERREALILTQVLGYTYEEAAKIADVRVGTIRSRVARARA 175 (196)
T ss_pred cCCHHHHHHhhhHHHhCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 4677777766667779999999999999999999999887653
No 266
>PRK04280 arginine repressor; Provisional
Probab=94.21 E-value=0.12 Score=43.92 Aligned_cols=51 Identities=18% Similarity=0.104 Sum_probs=45.6
Q ss_pred HHHHHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCCCCCCC
Q psy15598 110 VVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSSIVQH 165 (258)
Q Consensus 110 ~~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~~~~~~ 165 (258)
-.+.|++++++++--+..||.+.|++.|+.+ +..||+|-|+..+..|....
T Consensus 5 R~~~I~~iI~~~~I~tQeeL~~~L~~~Gi~v-----TQATiSRDikeL~lvKv~~~ 55 (148)
T PRK04280 5 RHIKIREIITNNEIETQDELVDRLREEGFNV-----TQATVSRDIKELHLVKVPLP 55 (148)
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHHHHcCCCe-----ehHHHHHHHHHcCCEEeecC
Confidence 3568999999999999999999999999986 99999999999999986543
No 267
>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=94.18 E-value=0.11 Score=46.19 Aligned_cols=42 Identities=12% Similarity=0.090 Sum_probs=34.0
Q ss_pred CCCHHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELAQ----LGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~----~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.++...|.-|+..+. +|+|..+||+.+|||.+||.+++.|-+
T Consensus 178 ~Lp~~~R~ii~L~~~l~~~eg~s~~EIA~~Lgis~~tV~~~l~ra~ 223 (234)
T TIGR02835 178 KLNDREKKIMELRFGLVGGTEKTQKEVADMLGISQSYISRLEKRIL 223 (234)
T ss_pred hCCHHHHHHHHHHHccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 367777766665552 799999999999999999999987754
No 268
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=94.16 E-value=0.12 Score=43.22 Aligned_cols=42 Identities=26% Similarity=0.228 Sum_probs=34.9
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.++...|.-++..+-+|++..+||+.||||.+||+..+.|-+
T Consensus 136 ~L~~~~r~il~l~~~~~~s~~eIA~~lgis~~~v~~~l~Rar 177 (187)
T PRK09641 136 QLPEKYRTVIVLKYIEDLSLKEISEILDLPVGTVKTRIHRGR 177 (187)
T ss_pred hCCHHHHHHhhhHHhhCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 466666666655566999999999999999999999998875
No 269
>cd04776 HTH_GnyR Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR. Putative helix-turn-helix (HTH) regulatory protein, GnyR, and other related proteins. GnyR belongs to the gnyRDBHAL cluster, which is involved in acyclic isoprenoid degradation in Pseudomonas aeruginosa. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=94.15 E-value=0.29 Score=39.68 Aligned_cols=66 Identities=21% Similarity=0.246 Sum_probs=48.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHh
Q psy15598 64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLLS 135 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~~ 135 (258)
+++.++|+.+|||..|++-|- +.|.+.|...+ .-|..++++...|..... .+-.+++.+|++.+..
T Consensus 1 ~~Igeva~~~gvs~~tlRyYe----~~GLl~p~r~~--gyR~Y~~~~l~~l~~I~~lr~~G~~L~~I~~~l~~ 67 (118)
T cd04776 1 YTISELAREFDVTPRTLRFYE----DKGLLSPERRG--QTRVYSRRDRARLKLILRGKRLGFSLEEIRELLDL 67 (118)
T ss_pred CCHHHHHHHHCcCHHHHHHHH----HCCCCCCcCCC--CccccCHHHHHHHHHHHHHHHCCCCHHHHHHHHHh
Confidence 467899999999999986554 45888775443 458888887777665433 3358899999888863
No 270
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=94.15 E-value=0.14 Score=42.76 Aligned_cols=33 Identities=18% Similarity=0.192 Sum_probs=30.5
Q ss_pred HcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCc
Q psy15598 61 QLGIRPCDISRQLRVSHGCVSKILARYHETGSI 93 (258)
Q Consensus 61 ~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl 93 (258)
+.+++..+||..|+++++||+|-+++..+.|-+
T Consensus 40 ~~~~tvdelae~lnr~rStv~rsl~~L~~~GlV 72 (126)
T COG3355 40 NGPLTVDELAEILNRSRSTVYRSLQNLLEAGLV 72 (126)
T ss_pred cCCcCHHHHHHHHCccHHHHHHHHHHHHHcCCe
Confidence 346899999999999999999999999999976
No 271
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=94.14 E-value=0.097 Score=39.06 Aligned_cols=35 Identities=14% Similarity=0.275 Sum_probs=31.2
Q ss_pred HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598 55 RIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE 89 (258)
Q Consensus 55 RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE 89 (258)
.+|.+.-.-+++.++|++||++..+|.+|+..|++
T Consensus 5 ~fIrlLs~~~s~~~Aa~~lG~~~~~v~~wv~~fR~ 39 (65)
T PF05344_consen 5 AFIRLLSQQISVAQAADRLGTDPGTVRRWVRMFRQ 39 (65)
T ss_pred HHHHHhcccccHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 46667767899999999999999999999999985
No 272
>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=94.13 E-value=0.081 Score=37.27 Aligned_cols=33 Identities=24% Similarity=0.307 Sum_probs=30.3
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCccc
Q psy15598 63 GIRPCDISRQLRVSHGCVSKILARYHETGSILP 95 (258)
Q Consensus 63 G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~p 95 (258)
.++..+||+.+|+|++||++.+++..+.|-+..
T Consensus 25 ~~s~~ela~~~g~s~~tv~r~l~~L~~~g~i~~ 57 (67)
T cd00092 25 PLTRQEIADYLGLTRETVSRTLKELEEEGLISR 57 (67)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence 479999999999999999999999999998753
No 273
>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=94.10 E-value=0.07 Score=46.04 Aligned_cols=39 Identities=28% Similarity=0.299 Sum_probs=33.5
Q ss_pred CHHHHHHHHHHHHcCCCHHHHHHHhC-CCHHHHHHHHHHh
Q psy15598 49 PNSVRMRIVELAQLGIRPCDISRQLR-VSHGCVSKILARY 87 (258)
Q Consensus 49 S~dlR~RIV~L~~~G~S~~eIAr~LG-VSrsTVsRwikRy 87 (258)
+++.-.++-+|+.+|+|.++||++|| ||++.|--.+.|.
T Consensus 4 tde~~~~L~~lw~~G~SasqIA~~lg~vsRnAViGk~hRl 43 (162)
T PF07750_consen 4 TDERVERLRKLWAEGLSASQIARQLGGVSRNAVIGKAHRL 43 (162)
T ss_pred CHHHHHHHHHHHHcCCCHHHHHHHhCCcchhhhhhhhhcc
Confidence 45666778888999999999999999 9999998777774
No 274
>PF11198 DUF2857: Protein of unknown function (DUF2857); InterPro: IPR021364 This is a bacterial family of uncharacterised proteins.
Probab=94.08 E-value=1.2 Score=38.93 Aligned_cols=93 Identities=19% Similarity=0.145 Sum_probs=62.8
Q ss_pred HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHh---CCCC----C
Q psy15598 53 RMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQK---DPGI----F 125 (258)
Q Consensus 53 R~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~---nP~i----t 125 (258)
+++|-.+...|-|..-+.+-||+|.+-|..+.+-- |. + .+.| ||+.++++++..|-...++ .+.. .
T Consensus 77 ~~~idr~L~lGAS~~mm~~~FGls~~ev~~rR~ll---gi--~-~~~G-R~~~~~ee~~~~iW~~W~~~~~~~~~~~~~~ 149 (180)
T PF11198_consen 77 QQLIDRALRLGASIEMMQRLFGLSSAEVAARRRLL---GI--P-VRKG-RPPALSEEEEAAIWRRWQQLMKKRGVDNLDS 149 (180)
T ss_pred HHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHh---CC--C-CCCC-CCCCcCHHHHHHHHHHHHHHHhhcCCCCccc
Confidence 45555667889999999999999999998887664 21 1 2345 8999999888888777653 2222 2
Q ss_pred --HHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhcc
Q psy15598 126 --AWEIRDRLLSDGVCDKFNVPSVSSISRILRNKI 158 (258)
Q Consensus 126 --a~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~ 158 (258)
.-|+.-.+. .-.. +|.++|+..++...
T Consensus 150 ~~~Le~~m~~A-e~~~-----isL~~iW~~i~~w~ 178 (180)
T PF11198_consen 150 PDALELMMLLA-EETN-----ISLTVIWSLIQEWE 178 (180)
T ss_pred hHHHHHHHHHH-HHhC-----CCHHHHHHHHHHHH
Confidence 223222232 2222 38999999998753
No 275
>COG2964 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=94.05 E-value=0.1 Score=47.41 Aligned_cols=41 Identities=22% Similarity=0.294 Sum_probs=31.7
Q ss_pred HHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHHhhhhC
Q psy15598 51 SVRMRIVELAQLGI-----RPCDISRQLRVSHGCVSKILARYHETG 91 (258)
Q Consensus 51 dlR~RIV~L~~~G~-----S~~eIAr~LGVSrsTVsRwikRyrEtG 91 (258)
.-|+-|..|++.|. ....+|+.|+||+.|||+++++++..|
T Consensus 174 ~~reiV~~L~EkGiF~lK~Ai~~VA~~L~iSr~TVY~YL~~~k~~~ 219 (220)
T COG2964 174 KNREIVKALYEKGIFNLKDAINIVADRLGISRHTVYRYLRKFKAGG 219 (220)
T ss_pred HHHHHHHHHHhcCccchhhHHHHHHHHhCCChHHHHHHHHHhhcCC
Confidence 34444445567785 567799999999999999999998655
No 276
>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=93.96 E-value=0.032 Score=38.80 Aligned_cols=23 Identities=17% Similarity=0.374 Sum_probs=19.1
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q psy15598 64 IRPCDISRQLRVSHGCVSKILAR 86 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikR 86 (258)
++..++++.+|||++|+++|+++
T Consensus 4 l~~~ev~~~~g~s~~ti~~~~k~ 26 (51)
T PF05930_consen 4 LRIKEVAELLGVSRSTIYRLIKD 26 (51)
T ss_dssp E-HHHHHHHHSS-HHHHHHHHHH
T ss_pred ccHHHHHHHHCCCHHHHHHHHhc
Confidence 36789999999999999999994
No 277
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=93.96 E-value=0.093 Score=43.70 Aligned_cols=46 Identities=24% Similarity=0.293 Sum_probs=41.3
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCc
Q psy15598 48 LPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETGSI 93 (258)
Q Consensus 48 ~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl 93 (258)
...+.+..++.++..|.+..++|+.++|+.++|.+|++++.+....
T Consensus 74 ~~~~~~~~~~~~~~~~~~i~~~a~~l~i~~~~~~r~~~r~~~~~~~ 119 (129)
T COG3677 74 ALYKIKLQAVTLYMLGLGIRDIARTLGISINTVNRWSKRFGSRVEG 119 (129)
T ss_pred cchHHHHHHHHHHHcCCCcccHHHHhcccHHHHHHHHHhhcchhhc
Confidence 4578899999999999999999999999999999999999866543
No 278
>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=93.92 E-value=0.13 Score=34.82 Aligned_cols=30 Identities=13% Similarity=0.220 Sum_probs=24.9
Q ss_pred HHHHH-HcCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598 56 IVELA-QLGIRPCDISRQLRVSHGCVSKILA 85 (258)
Q Consensus 56 IV~L~-~~G~S~~eIAr~LGVSrsTVsRwik 85 (258)
|-.+. +.|++..++|+.+|||++||++|.+
T Consensus 7 l~~~r~~~gltq~~lA~~~gvs~~~vs~~e~ 37 (58)
T TIGR03070 7 VRARRKALGLTQADLADLAGVGLRFIRDVEN 37 (58)
T ss_pred HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHC
Confidence 33343 4699999999999999999999974
No 279
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=93.89 E-value=0.1 Score=48.22 Aligned_cols=57 Identities=26% Similarity=0.328 Sum_probs=46.4
Q ss_pred CCCCCCHHHHHHHHHHHHc-C-CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCC
Q psy15598 44 NGRPLPNSVRMRIVELAQL-G-IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGG 100 (258)
Q Consensus 44 ~gR~~S~dlR~RIV~L~~~-G-~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG 100 (258)
+-..++.|.+.-|..+.+. | ...+|+.+.+|.|++||+|.+++-.+.|-++--+.|+
T Consensus 189 ~~~~L~~~e~~il~~i~~~GGri~Q~eL~r~lglsktTvsR~L~~LEk~GlIe~~K~G~ 247 (258)
T COG2512 189 NEYDLNEDEKEILDLIRERGGRITQAELRRALGLSKTTVSRILRRLEKRGLIEKEKKGR 247 (258)
T ss_pred ccCCCCHHHHHHHHHHHHhCCEEeHHHHHHhhCCChHHHHHHHHHHHhCCceEEEEeCC
Confidence 4456888888766666654 4 7999999999999999999999999999886555543
No 280
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=93.87 E-value=0.12 Score=45.80 Aligned_cols=42 Identities=21% Similarity=0.114 Sum_probs=34.7
Q ss_pred CCCHHHHHHHHHHH----HcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELA----QLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~----~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.++...|.-++..+ .+|+|.++||..+|||.+||++++.|-+
T Consensus 175 ~Lp~~~R~i~~l~y~~~~~e~~S~~EIA~~lgis~~tV~~~~~rA~ 220 (233)
T PRK05803 175 ILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRAL 220 (233)
T ss_pred hCCHHHHHHHHHHhCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 57777776666655 4899999999999999999999987754
No 281
>COG1710 Uncharacterized protein conserved in archaea [Function unknown]
Probab=93.85 E-value=0.14 Score=42.69 Aligned_cols=44 Identities=25% Similarity=0.366 Sum_probs=40.1
Q ss_pred CCCCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 45 GRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 45 gR~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.+.|+...+.+|-+++++|++.++||+.|||...||+=.+++.+
T Consensus 91 prkyd~~t~~~i~emlr~gk~preIsk~lGIpirTvyY~l~k~k 134 (139)
T COG1710 91 PRKYDRNTLLRIREMLRNGKTPREISKDLGIPIRTVYYLLKKLK 134 (139)
T ss_pred CcccchhHHHHHHHHHHcCCCHHHHHHhhCCchhhhHHHHHHHh
Confidence 45689999999999999999999999999999999999888764
No 282
>PF13565 HTH_32: Homeodomain-like domain
Probab=93.84 E-value=0.19 Score=36.76 Aligned_cols=41 Identities=37% Similarity=0.486 Sum_probs=32.2
Q ss_pred CCCCC-CHHHHHHHHHHHHc--CCCHHHHHHHh----C--C--CHHHHHHHH
Q psy15598 44 NGRPL-PNSVRMRIVELAQL--GIRPCDISRQL----R--V--SHGCVSKIL 84 (258)
Q Consensus 44 ~gR~~-S~dlR~RIV~L~~~--G~S~~eIAr~L----G--V--SrsTVsRwi 84 (258)
.|++. +.+.+..|++++.+ .++..+|+..| | + |.+||+||+
T Consensus 26 ~Grp~~~~e~~~~i~~~~~~~p~wt~~~i~~~L~~~~g~~~~~S~~tv~R~L 77 (77)
T PF13565_consen 26 PGRPRKDPEQRERIIALIEEHPRWTPREIAEYLEEEFGISVRVSRSTVYRIL 77 (77)
T ss_pred CCCCCCcHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCCCccHhHHHHhC
Confidence 44443 58888999999875 48999988887 3 4 999999985
No 283
>TIGR02297 HpaA 4-hydroxyphenylacetate catabolism regulatory protein HpaA. This putative transcriptional regulator, which contains both the substrate-binding, dimerization domain (pfam02311) and the helix-turn-helix DNA-binding domain (pfam00165) of the AraC famil, is located proximal to genes of the 4-hydroxyphenylacetate catabolism pathway.
Probab=93.83 E-value=0.55 Score=42.05 Aligned_cols=86 Identities=17% Similarity=0.190 Sum_probs=57.5
Q ss_pred HHHHHHH----HcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCC-CCHHHHHHHHHHHHhCCCCCHHH
Q psy15598 54 MRIVELA----QLGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRV-TTPKVVSYIKELKQKDPGIFAWE 128 (258)
Q Consensus 54 ~RIV~L~----~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrk-lT~e~~~~I~~lv~~nP~ita~E 128 (258)
.+++..+ .+..+..++|+.+++|++++.|..+++. |. .|.. ++....+...+++ .+.+.+..|
T Consensus 189 ~~~~~~I~~~~~~~~sl~~lA~~~~~S~~~l~r~Fk~~~--G~---------t~~~yi~~~Rl~~A~~lL-~~t~~sI~e 256 (287)
T TIGR02297 189 NRFNFLIEENYKQHLRLPEYADRLGISESRLNDICRRFS--AL---------SPKRLIIERVMQEARRLL-LFTQHSINQ 256 (287)
T ss_pred HHHHHHHHHhhccCCCHHHHHHHHCCCHHHHHHHHHHHh--CC---------CHHHHHHHHHHHHHHHHH-HcCCCCHHH
Confidence 4555444 3568999999999999999999999974 21 1111 1111122222333 356788888
Q ss_pred HHHHHHhcCCCCCCCCCCHHHHHHHHHhccCC
Q psy15598 129 IRDRLLSDGVCDKFNVPSVSSISRILRNKIGS 160 (258)
Q Consensus 129 Ir~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~ 160 (258)
|+..+ |.. |.+.-.|++|+.-+.
T Consensus 257 IA~~~---GF~------s~s~Fsr~FKk~~G~ 279 (287)
T TIGR02297 257 IAYDL---GYK------DPAYFARFFQKETGL 279 (287)
T ss_pred HHHHh---CCC------CHHHHHHHHHHHHCc
Confidence 87766 675 899999999987654
No 284
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=93.82 E-value=0.16 Score=44.81 Aligned_cols=57 Identities=12% Similarity=0.101 Sum_probs=42.3
Q ss_pred CCCCCCHHHHHHHHHHHHcC-------C-CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCC
Q psy15598 44 NGRPLPNSVRMRIVELAQLG-------I-RPCDISRQLRVSHGCVSKILARYHETGSILPGAIGG 100 (258)
Q Consensus 44 ~gR~~S~dlR~RIV~L~~~G-------~-S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG 100 (258)
..+..+......|.+.+..| + +-.++|++|||||+||+.-+++....|-|.-.++.|
T Consensus 4 ~~~~~~~~~~~~l~~~I~~g~l~pG~~LPsE~eLae~~gVSRt~VReAL~~L~~eGlv~~~~g~G 68 (239)
T PRK04984 4 KAQSPAGFAEEYIIESIWNNRFPPGSILPAERELSELIGVTRTTLREVLQRLARDGWLTIQHGKP 68 (239)
T ss_pred cccCHHHHHHHHHHHHHHcCCCCCCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCCCe
Confidence 34445555555555555443 4 688999999999999999999999999887655545
No 285
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=93.79 E-value=0.92 Score=38.75 Aligned_cols=101 Identities=26% Similarity=0.165 Sum_probs=62.6
Q ss_pred HHHHHHHHHH-cC-CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHhC--------
Q psy15598 52 VRMRIVELAQ-LG-IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQKD-------- 121 (258)
Q Consensus 52 lR~RIV~L~~-~G-~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~n-------- 121 (258)
--..|..+.+ .| ....+||+.|+||.+||..-+++-.+.|-+.-.+.+| -.+|+.=.+....+++.+
T Consensus 11 YL~~Iy~l~~~~~~~~~~diA~~L~Vsp~sVt~ml~rL~~~GlV~~~~y~g---i~LT~~G~~~a~~~~r~hrlle~fL~ 87 (154)
T COG1321 11 YLETIYELLEEKGFARTKDIAERLKVSPPSVTEMLKRLERLGLVEYEPYGG---VTLTEKGREKAKELLRKHRLLERFLV 87 (154)
T ss_pred HHHHHHHHHhccCcccHHHHHHHhCCCcHHHHHHHHHHHHCCCeEEecCCC---eEEChhhHHHHHHHHHHHHHHHHHHH
Confidence 3344444554 45 6889999999999999999999999999886555554 556654333322222221
Q ss_pred --CCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCC
Q psy15598 122 --PGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGS 160 (258)
Q Consensus 122 --P~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~ 160 (258)
=.+...+..+.....-.. +|..++.|+.+..+..
T Consensus 88 ~~lg~~~~~~~~ea~~leh~-----~s~~~~~rl~~~l~~~ 123 (154)
T COG1321 88 DVLGLDWEEAHEEAEGLEHA-----LSDETAERLDELLGFP 123 (154)
T ss_pred HHhCCCHHHHHHHHHHHhhc-----CCHHHHHHHHHHhCCC
Confidence 233333333222222222 4888998888877753
No 286
>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=93.78 E-value=0.096 Score=38.05 Aligned_cols=31 Identities=35% Similarity=0.470 Sum_probs=29.2
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598 64 IRPCDISRQLRVSHGCVSKILARYHETGSIL 94 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~ 94 (258)
++..+||..+|+|+.||.|.++++++.|-+.
T Consensus 29 lt~~~iA~~~g~sr~tv~r~l~~l~~~g~I~ 59 (76)
T PF13545_consen 29 LTQEEIADMLGVSRETVSRILKRLKDEGIIE 59 (76)
T ss_dssp SSHHHHHHHHTSCHHHHHHHHHHHHHTTSEE
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 5899999999999999999999999999875
No 287
>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=93.77 E-value=0.17 Score=44.63 Aligned_cols=42 Identities=17% Similarity=0.091 Sum_probs=34.2
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.++...|.-+...+.+|++..+||+.||||..+|+++.++-.
T Consensus 183 ~L~~~e~~i~~~~~~~~~t~~eIA~~lgis~~~V~~~~~~al 224 (231)
T TIGR02885 183 KLDERERQIIMLRYFKDKTQTEVANMLGISQVQVSRLEKKVL 224 (231)
T ss_pred cCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 456666655555566899999999999999999999998864
No 288
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=93.74 E-value=0.16 Score=46.03 Aligned_cols=42 Identities=14% Similarity=0.080 Sum_probs=35.1
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.++...|.-|+..+-+|++..+||+.||||.++|++++++-.
T Consensus 203 ~L~~~~r~vl~l~y~~~~s~~eIA~~lgvs~~~V~~~~~ra~ 244 (256)
T PRK07408 203 QLEERTREVLEFVFLHDLTQKEAAERLGISPVTVSRRVKKGL 244 (256)
T ss_pred cCCHHHHHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 366666666666667999999999999999999999998865
No 289
>PRK09954 putative kinase; Provisional
Probab=93.66 E-value=0.12 Score=48.42 Aligned_cols=43 Identities=19% Similarity=0.291 Sum_probs=36.6
Q ss_pred HHHHHHHHHHHcC--CCHHHHHHHhCCCHHHHHHHHHHhhhhCCc
Q psy15598 51 SVRMRIVELAQLG--IRPCDISRQLRVSHGCVSKILARYHETGSI 93 (258)
Q Consensus 51 dlR~RIV~L~~~G--~S~~eIAr~LGVSrsTVsRwikRyrEtGsl 93 (258)
+...+|+.++++. .+..+||+.|+||++||++.+++.++.|.+
T Consensus 3 ~~~~~il~~l~~~~~~s~~~la~~l~~s~~~v~~~i~~L~~~g~i 47 (362)
T PRK09954 3 NREKEILAILRRNPLIQQNEIADILQISRSRVAAHIMDLMRKGRI 47 (362)
T ss_pred hHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCc
Confidence 4556788887643 799999999999999999999999998853
No 290
>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=93.63 E-value=0.16 Score=45.56 Aligned_cols=42 Identities=14% Similarity=0.073 Sum_probs=34.2
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.++...|.-|...+.+|++..+||+.||||.+||.+++.+-.
T Consensus 205 ~L~~~~r~ii~l~~~~g~s~~eIA~~lgis~~~V~~~~~ra~ 246 (255)
T TIGR02941 205 ILSEREKSIIHCTFEENLSQKETGERLGISQMHVSRLQRQAI 246 (255)
T ss_pred cCCHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 366666665555557899999999999999999999988764
No 291
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=93.62 E-value=0.15 Score=46.36 Aligned_cols=44 Identities=18% Similarity=0.339 Sum_probs=38.2
Q ss_pred HHHHHHHHHHHH-cC-CCHHHHHHHhCCCHHHHHHHHHHhhhhCCc
Q psy15598 50 NSVRMRIVELAQ-LG-IRPCDISRQLRVSHGCVSKILARYHETGSI 93 (258)
Q Consensus 50 ~dlR~RIV~L~~-~G-~S~~eIAr~LGVSrsTVsRwikRyrEtGsl 93 (258)
.+.+.+|+++++ .| ++..++|+.||||..||+|.++...+.|.+
T Consensus 4 ~~R~~~Il~~l~~~~~~~~~ela~~l~vS~~TirRdL~~Le~~g~i 49 (251)
T PRK13509 4 AQRHQILLELLAQLGFVTVEKVIERLGISPATARRDINKLDESGKL 49 (251)
T ss_pred HHHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCE
Confidence 466778888876 34 799999999999999999999999988876
No 292
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=93.57 E-value=0.13 Score=46.45 Aligned_cols=44 Identities=16% Similarity=0.165 Sum_probs=32.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHh
Q psy15598 64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQK 120 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~ 120 (258)
++.++||+..|||++||+|.++.-. + + ...+++.+++|.+..++
T Consensus 1 ~ti~dIA~~aGVS~~TVSrvLn~~~-----------~-~-~~Vs~~tr~rV~~~a~e 44 (328)
T PRK11303 1 MKLDEIARLAGVSRTTASYVINGKA-----------K-Q-YRVSDKTVEKVMAVVRE 44 (328)
T ss_pred CCHHHHHHHhCCCHHHHHHHHcCCC-----------C-C-CCcCHHHHHHHHHHHHH
Confidence 4789999999999999999996310 0 0 12567777777777654
No 293
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=93.55 E-value=0.17 Score=45.37 Aligned_cols=41 Identities=17% Similarity=0.208 Sum_probs=35.2
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 48 LPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 48 ~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
++...|.-|...+.+|++..+||+.||||.+||...+.|-+
T Consensus 202 L~~~~r~vl~l~~~~~~s~~EIA~~lgis~~tV~~~~~ra~ 242 (251)
T PRK07670 202 LSEKEQLVISLFYKEELTLTEIGQVLNLSTSRISQIHSKAL 242 (251)
T ss_pred CCHHHHHHHHHHHhcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 67777766666677999999999999999999999988865
No 294
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=93.55 E-value=0.18 Score=43.04 Aligned_cols=41 Identities=15% Similarity=0.063 Sum_probs=34.8
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.++...|.-++. +-+|++..+||..||||.+||...+.|-+
T Consensus 155 ~L~~~~r~vl~l-~~e~~s~~EIA~~lgis~~tV~~~l~rar 195 (208)
T PRK08295 155 LLSELEKEVLEL-YLDGKSYQEIAEELNRHVKSIDNALQRVK 195 (208)
T ss_pred hCCHHHHHHHHH-HHccCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 467777776666 77999999999999999999998888765
No 295
>PRK05572 sporulation sigma factor SigF; Validated
Probab=93.55 E-value=0.16 Score=45.64 Aligned_cols=42 Identities=14% Similarity=0.140 Sum_probs=34.6
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.++...|.-+...+.+|++..+||+.||||.++|+++.++-.
T Consensus 202 ~L~~~~~~v~~l~~~~~~s~~eIA~~lgis~~~V~~~~~ral 243 (252)
T PRK05572 202 ELDERERLIVYLRYFKDKTQSEVAKRLGISQVQVSRLEKKIL 243 (252)
T ss_pred cCCHHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 366666655555566899999999999999999999998864
No 296
>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=93.52 E-value=0.2 Score=34.75 Aligned_cols=34 Identities=26% Similarity=0.491 Sum_probs=30.2
Q ss_pred HcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598 61 QLGIRPCDISRQLRVSHGCVSKILARYHETGSIL 94 (258)
Q Consensus 61 ~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~ 94 (258)
..|++..+||+.+++++++|.+++++-.+.|-++
T Consensus 15 ~~~~~~~~la~~~~~~~~~~t~~i~~L~~~g~I~ 48 (59)
T PF01047_consen 15 NGGITQSELAEKLGISRSTVTRIIKRLEKKGLIE 48 (59)
T ss_dssp HSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred cCCCCHHHHHHHHCCChhHHHHHHHHHHHCCCEE
Confidence 3679999999999999999999999999999764
No 297
>PRK01905 DNA-binding protein Fis; Provisional
Probab=93.50 E-value=0.2 Score=37.79 Aligned_cols=36 Identities=11% Similarity=0.071 Sum_probs=30.3
Q ss_pred HHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHHh
Q psy15598 52 VRMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILARY 87 (258)
Q Consensus 52 lR~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwikRy 87 (258)
.+..|+.+++ .|-...++|+.||||++|+++.+++|
T Consensus 38 E~~~i~~aL~~~~gn~s~aAr~LGIsrstL~rklkk~ 74 (77)
T PRK01905 38 EKPLLEVVMEQAGGNQSLAAEYLGINRNTLRKKLQQH 74 (77)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHh
Confidence 4555666665 57789999999999999999999997
No 298
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=93.50 E-value=0.25 Score=38.31 Aligned_cols=41 Identities=24% Similarity=0.323 Sum_probs=35.0
Q ss_pred HHHHHHHH-c-CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598 54 MRIVELAQ-L-GIRPCDISRQLRVSHGCVSKILARYHETGSIL 94 (258)
Q Consensus 54 ~RIV~L~~-~-G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~ 94 (258)
.+|+.+.. + ..+.++||+.+|+|++||++.+++..+.|-+.
T Consensus 6 ~~il~~L~~~~~~~~~~la~~l~~s~~tv~~~l~~L~~~g~i~ 48 (108)
T smart00344 6 RKILEELQKDARISLAELAKKVGLSPSTVHNRVKRLEEEGVIK 48 (108)
T ss_pred HHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCee
Confidence 46777664 3 48999999999999999999999999999763
No 299
>PRK00441 argR arginine repressor; Provisional
Probab=93.49 E-value=0.21 Score=42.48 Aligned_cols=51 Identities=14% Similarity=0.053 Sum_probs=45.3
Q ss_pred HHHHHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCCCCCCC
Q psy15598 110 VVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSSIVQH 165 (258)
Q Consensus 110 ~~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~~~~~~ 165 (258)
-...|.++++++...+..||.+.|++.|+.+ |.+||+|-|+..+..|....
T Consensus 5 R~~~I~~ll~~~~~~~q~eL~~~L~~~G~~v-----SqaTisRDl~~L~lvKv~~~ 55 (149)
T PRK00441 5 RHAKILEIINSKEIETQEELAEELKKMGFDV-----TQATVSRDIKELKLIKVLSN 55 (149)
T ss_pred HHHHHHHHHHHcCCCcHHHHHHHHHhcCCCc-----CHHHHHHHHHHcCcEEeECC
Confidence 4668889999999999999999999999986 99999999999999986543
No 300
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=93.43 E-value=0.19 Score=45.55 Aligned_cols=42 Identities=21% Similarity=0.131 Sum_probs=35.5
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.++...|.-|...+.+|++..+||+.||||.++|++++.+-.
T Consensus 205 ~L~~~er~vi~l~y~e~~t~~EIA~~lgis~~~V~~~~~ral 246 (257)
T PRK05911 205 ALEEKERKVMALYYYEELVLKEIGKILGVSESRVSQIHSKAL 246 (257)
T ss_pred cCCHHHHHHHHHHHhcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 477777765555667999999999999999999999998865
No 301
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=93.40 E-value=0.27 Score=41.34 Aligned_cols=54 Identities=22% Similarity=0.186 Sum_probs=40.2
Q ss_pred CCCCHHHHHHHHHHHHhC-CCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCCCCC
Q psy15598 104 RVTTPKVVSYIKELKQKD-PGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSSIV 163 (258)
Q Consensus 104 rklT~e~~~~I~~lv~~n-P~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~~~~ 163 (258)
-++|+. +..|.+++.+. -..++.+|.+.|.+.+..+ |.+||+|.|+-+...+.-
T Consensus 17 lr~T~q-R~~vl~~L~~~~~~~sAeei~~~l~~~~p~i-----slaTVYr~L~~l~e~Glv 71 (145)
T COG0735 17 LRLTPQ-RLAVLELLLEADGHLSAEELYEELREEGPGI-----SLATVYRTLKLLEEAGLV 71 (145)
T ss_pred CCcCHH-HHHHHHHHHhcCCCCCHHHHHHHHHHhCCCC-----CHhHHHHHHHHHHHCCCE
Confidence 446665 44555555544 3499999999999888775 999999999987766543
No 302
>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional
Probab=93.32 E-value=0.14 Score=48.16 Aligned_cols=37 Identities=8% Similarity=0.012 Sum_probs=32.2
Q ss_pred HHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHHh
Q psy15598 51 SVRMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILARY 87 (258)
Q Consensus 51 dlR~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwikRy 87 (258)
..|..|+.+++ .+....++|+.||||++|+||++++|
T Consensus 286 ~Er~~I~~aL~~~~gn~~~aA~~LGIsR~tLyrklk~~ 323 (326)
T PRK11608 286 QEKELLQRSLQQAKFNQKRAAELLGLTYHQLRALLKKH 323 (326)
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHHc
Confidence 35777777776 58889999999999999999999998
No 303
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=93.32 E-value=0.2 Score=36.71 Aligned_cols=41 Identities=20% Similarity=0.197 Sum_probs=31.0
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHhC
Q psy15598 65 RPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQKD 121 (258)
Q Consensus 65 S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~n 121 (258)
+.++||+.+|||++||+++++. ++. .+++....|.+..++-
T Consensus 2 t~~~iA~~~gvS~~TVSr~ln~---------------~~~-v~~~t~~~i~~~~~~~ 42 (70)
T smart00354 2 TIKDVARLAGVSKATVSRVLNG---------------NGR-VSEETREKVLAAMEEL 42 (70)
T ss_pred CHHHHHHHHCCCHHHHHHHHCC---------------CCC-CCHHHHHHHHHHHHHh
Confidence 5789999999999999998731 222 4677777777776654
No 304
>PRK09191 two-component response regulator; Provisional
Probab=93.27 E-value=0.21 Score=43.54 Aligned_cols=44 Identities=16% Similarity=0.073 Sum_probs=36.9
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHET 90 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEt 90 (258)
.++.+.|.-++...-+|++..+||+.+|+|.+||...+.|.++.
T Consensus 88 ~L~~~~r~v~~l~~~~~~s~~eIA~~l~~s~~tV~~~l~ra~~~ 131 (261)
T PRK09191 88 GLTPLPRQAFLLTALEGFSVEEAAEILGVDPAEAEALLDDARAE 131 (261)
T ss_pred hCCHHHhHHHHHHHHhcCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 46777776666666799999999999999999999999888753
No 305
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=93.27 E-value=0.078 Score=35.92 Aligned_cols=41 Identities=34% Similarity=0.402 Sum_probs=22.9
Q ss_pred CCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHh
Q psy15598 104 RVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRN 156 (258)
Q Consensus 104 rklT~e~~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr 156 (258)
+.|+.+++..|..+..+ ..+..+|++.|. .|.+||+|.|++
T Consensus 3 ~~Lt~~eR~~I~~l~~~--G~s~~~IA~~lg----------~s~sTV~relkR 43 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQ--GMSIREIAKRLG----------RSRSTVSRELKR 43 (44)
T ss_dssp ---------HHHHHHCS-----HHHHHHHTT------------HHHHHHHHHH
T ss_pred cchhhhHHHHHHHHHHc--CCCHHHHHHHHC----------cCcHHHHHHHhc
Confidence 34788888888888654 588999988873 399999999987
No 306
>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=93.23 E-value=0.18 Score=44.22 Aligned_cols=52 Identities=15% Similarity=0.170 Sum_probs=40.3
Q ss_pred CHHHHHHHHHHHHcCC--------CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCC
Q psy15598 49 PNSVRMRIVELAQLGI--------RPCDISRQLRVSHGCVSKILARYHETGSILPGAIGG 100 (258)
Q Consensus 49 S~dlR~RIV~L~~~G~--------S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG 100 (258)
-..+...|.+...+|. |-.++|++|||||.||++-+..-.+.|.|..+...|
T Consensus 10 y~~i~~~l~~~I~~g~~~~G~~LPsE~eLa~~~~VSR~TvR~Al~~L~~eGli~r~~G~G 69 (238)
T TIGR02325 10 WRQIADKIEQEIAAGHLRAGDYLPAEMQLAERFGVNRHTVRRAIAALVERGLLRAEQGRG 69 (238)
T ss_pred HHHHHHHHHHHHHcCCCCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCCE
Confidence 3455555656555442 889999999999999999999999999986655444
No 307
>PRK13503 transcriptional activator RhaS; Provisional
Probab=93.20 E-value=0.77 Score=40.83 Aligned_cols=78 Identities=14% Similarity=0.135 Sum_probs=52.6
Q ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCC-HHHHHHHHHHHHhCCCCCHHHHHHHHHhcCCCC
Q psy15598 62 LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTT-PKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCD 140 (258)
Q Consensus 62 ~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT-~e~~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v 140 (258)
+..+..++|+.+++|+++++|..++.- |. .|.... ......-.+++ .+.+++..||+..+ |..
T Consensus 186 ~~~tl~~lA~~~~lS~~~l~r~Fk~~~--G~---------S~~~yi~~~Rl~~A~~LL-~~~~~sI~eIA~~~---GF~- 249 (278)
T PRK13503 186 EEVNWEALADQFSLSLRTLHRQLKQQT--GL---------TPQRYLNRLRLLKARHLL-RHSDASVTDIAYRC---GFG- 249 (278)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHh--Cc---------CHHHHHHHHHHHHHHHHH-HcCCCCHHHHHHHh---CCC-
Confidence 468999999999999999999999863 21 111111 11111112222 45678888888777 665
Q ss_pred CCCCCCHHHHHHHHHhccCC
Q psy15598 141 KFNVPSVSSISRILRNKIGS 160 (258)
Q Consensus 141 ~~~~pS~STI~RiLrr~~~~ 160 (258)
+.+...|+.|+.-+.
T Consensus 250 -----~~s~F~r~FKk~~G~ 264 (278)
T PRK13503 250 -----DSNHFSTLFRREFSW 264 (278)
T ss_pred -----CHHHHHHHHHHHHCc
Confidence 888999999886654
No 308
>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=93.17 E-value=0.56 Score=37.16 Aligned_cols=64 Identities=19% Similarity=0.211 Sum_probs=44.5
Q ss_pred HHHHHH-H-cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCC-C--CCCCCHHHHHHHHHHH
Q psy15598 55 RIVELA-Q-LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGS-K--PRVTTPKVVSYIKELK 118 (258)
Q Consensus 55 RIV~L~-~-~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~-R--PrklT~e~~~~I~~lv 118 (258)
.|+..+ . .+++..+||+.++++++||++.+++..+.|-|.-...... | --.+|++-.+.+.+..
T Consensus 32 ~iL~~l~~~~~~t~~ela~~~~~~~~tvs~~l~~Le~~GlI~r~~~~~D~R~~~v~LT~~G~~~~~~~~ 100 (118)
T TIGR02337 32 RILRILAEQGSMEFTQLANQACILRPSLTGILARLERDGLVTRLKASNDQRRVYISLTPKGQALYASLS 100 (118)
T ss_pred HHHHHHHHcCCcCHHHHHHHhCCCchhHHHHHHHHHHCCCEEeccCCCCCCeeEEEECHhHHHHHHHhh
Confidence 344444 3 5689999999999999999999999999997743222111 2 2346777666655553
No 309
>PRK09483 response regulator; Provisional
Probab=93.14 E-value=0.19 Score=41.99 Aligned_cols=40 Identities=25% Similarity=0.254 Sum_probs=34.0
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 48 LPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 48 ~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
++...+ +|+.++..|++.++||+.|++|.+||...+++-.
T Consensus 149 Lt~rE~-~vl~~~~~G~~~~~Ia~~l~is~~TV~~~~~~i~ 188 (217)
T PRK09483 149 LSEREL-QIMLMITKGQKVNEISEQLNLSPKTVNSYRYRMF 188 (217)
T ss_pred cCHHHH-HHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 665555 4667788999999999999999999999988875
No 310
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=93.13 E-value=0.096 Score=43.56 Aligned_cols=42 Identities=19% Similarity=0.123 Sum_probs=34.1
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.++...|.-++..+-+|++..+||..||+|.+||...+.|-+
T Consensus 120 ~L~~~~r~vl~l~~~~g~s~~eIA~~lg~s~~tv~~~l~Rar 161 (175)
T PRK12518 120 TLSLEHRAVLVLHDLEDLPQKEIAEILNIPVGTVKSRLFYAR 161 (175)
T ss_pred hCCHHHeeeeeehHhcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 366666654444467999999999999999999999998865
No 311
>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=93.10 E-value=0.23 Score=39.01 Aligned_cols=43 Identities=23% Similarity=0.302 Sum_probs=36.7
Q ss_pred HHHHHHHHHHc---CCCHHHHHHHh-----CCCHHHHHHHHHHhhhhCCcc
Q psy15598 52 VRMRIVELAQL---GIRPCDISRQL-----RVSHGCVSKILARYHETGSIL 94 (258)
Q Consensus 52 lR~RIV~L~~~---G~S~~eIAr~L-----GVSrsTVsRwikRyrEtGsl~ 94 (258)
.|..|++.+.+ .+|..+|.+.+ +||++||||.++.+.+.|.+.
T Consensus 2 qR~~Il~~l~~~~~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~Gli~ 52 (116)
T cd07153 2 QRLAILEVLLESDGHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVR 52 (116)
T ss_pred HHHHHHHHHHhCCCCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCEE
Confidence 47788887642 38999999999 699999999999999999764
No 312
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=93.09 E-value=0.29 Score=42.84 Aligned_cols=46 Identities=9% Similarity=0.100 Sum_probs=38.0
Q ss_pred CCHHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCc
Q psy15598 48 LPNSVRMRIVELAQ----LGIRPCDISRQLRVSHGCVSKILARYHETGSI 93 (258)
Q Consensus 48 ~S~dlR~RIV~L~~----~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl 93 (258)
++...+..++.+.. .|++.++||+.|++|..||.+.+++-...|.+
T Consensus 159 Lt~re~~~l~~~i~~~~~~g~s~~eIA~~l~iS~~Tv~~~~~~~~~~~~~ 208 (239)
T PRK10430 159 LTPQTLRTLCQWIDAHQDYEFSTDELANAVNISRVSCRKYLIWLVNCHIL 208 (239)
T ss_pred CCHHHHHHHHHHHHhCCCCCcCHHHHHHHhCchHHHHHHHHHHHHhCCEE
Confidence 55555555555554 79999999999999999999999999888865
No 313
>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=93.08 E-value=0.29 Score=38.50 Aligned_cols=48 Identities=25% Similarity=0.188 Sum_probs=37.4
Q ss_pred HHHHHHHHHhC-CCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCCCCC
Q psy15598 111 VSYIKELKQKD-PGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSSIV 163 (258)
Q Consensus 111 ~~~I~~lv~~n-P~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~~~~ 163 (258)
+..|.+.+.+. ..+++.||.+.|.+.+..+ |.+||+|.|+.+....+-
T Consensus 3 R~~Il~~l~~~~~~~sa~ei~~~l~~~~~~i-----~~~TVYR~L~~L~~~Gli 51 (116)
T cd07153 3 RLAILEVLLESDGHLTAEEIYERLRKKGPSI-----SLATVYRTLELLEEAGLV 51 (116)
T ss_pred HHHHHHHHHhCCCCCCHHHHHHHHHhcCCCC-----CHHHHHHHHHHHHhCCCE
Confidence 45566666654 4689999999999877664 999999999987777653
No 314
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=93.08 E-value=0.24 Score=44.98 Aligned_cols=42 Identities=14% Similarity=0.203 Sum_probs=35.3
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.++...|.-+...+-+|++..+||+.||||.+||++.+.|..
T Consensus 212 ~L~~~~r~vl~l~~~~~~s~~eIA~~lgis~~tV~~~~~ra~ 253 (268)
T PRK06288 212 TLPEREKKVLILYYYEDLTLKEIGKVLGVTESRISQLHTKAV 253 (268)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 477777776666678999999999999999999998877654
No 315
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=93.07 E-value=0.11 Score=36.58 Aligned_cols=27 Identities=33% Similarity=0.507 Sum_probs=20.6
Q ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHHH
Q psy15598 60 AQLGIRPCDISRQLRVSHGCVSKILAR 86 (258)
Q Consensus 60 ~~~G~S~~eIAr~LGVSrsTVsRwikR 86 (258)
.+.|++..++|+..|||++||++|++.
T Consensus 7 ~~~~it~~~La~~~gis~~tl~~~~~~ 33 (63)
T PF13443_consen 7 AERGITQKDLARKTGISRSTLSRILNG 33 (63)
T ss_dssp HHTT--HHHHHHHHT--HHHHHHHHTT
T ss_pred HHcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 457999999999999999999999873
No 316
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=93.05 E-value=0.17 Score=46.08 Aligned_cols=44 Identities=20% Similarity=0.308 Sum_probs=39.0
Q ss_pred HHHHHHHHHHHH-cC-CCHHHHHHHhCCCHHHHHHHHHHhhhhCCc
Q psy15598 50 NSVRMRIVELAQ-LG-IRPCDISRQLRVSHGCVSKILARYHETGSI 93 (258)
Q Consensus 50 ~dlR~RIV~L~~-~G-~S~~eIAr~LGVSrsTVsRwikRyrEtGsl 93 (258)
.+.|.+|+++++ .| .+..++|+.|+||..||+|.++...+.|.+
T Consensus 4 ~~R~~~Il~~l~~~~~~~~~ela~~l~vS~~TiRRdL~~Le~~g~l 49 (252)
T PRK10906 4 TQRHDAIIELVKQQGYVSTEELVEHFSVSPQTIRRDLNDLAEQNKI 49 (252)
T ss_pred HHHHHHHHHHHHHcCCEeHHHHHHHhCCCHHHHHHHHHHHHHCCCE
Confidence 467788898886 45 799999999999999999999999999976
No 317
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=93.02 E-value=0.26 Score=42.23 Aligned_cols=42 Identities=31% Similarity=0.368 Sum_probs=33.5
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.++...|.-++..+-+|++..+||..||||.+||..-+.|-+
T Consensus 134 ~Lp~~~r~i~~l~~~~g~s~~EIA~~lg~s~~tV~~rl~rar 175 (192)
T PRK09643 134 RLPVEQRAALVAVDMQGYSVADAARMLGVAEGTVKSRCARGR 175 (192)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 477777655544567999999999999999999988876654
No 318
>PRK14999 histidine utilization repressor; Provisional
Probab=93.00 E-value=0.21 Score=44.37 Aligned_cols=54 Identities=17% Similarity=0.196 Sum_probs=40.8
Q ss_pred CCCHHHHHHHHHHHHc-----C--C-CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCC
Q psy15598 47 PLPNSVRMRIVELAQL-----G--I-RPCDISRQLRVSHGCVSKILARYHETGSILPGAIGG 100 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~-----G--~-S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG 100 (258)
++-..+...|.+...+ | + +-+++|++||||+.||++-+..-.+.|.|.-+...|
T Consensus 12 ply~qi~~~i~~~I~~g~~~~G~~LPsE~eLa~~~gVSR~TVR~Al~~L~~eGli~r~~GkG 73 (241)
T PRK14999 12 PFYETVKQDICKKIAGGVWQPHDRIPSEAELVAQYGFSRMTINRALRELTDEGWLVRLQGVG 73 (241)
T ss_pred cHHHHHHHHHHHHHHcCCCCCCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCcE
Confidence 3444555555555554 4 2 889999999999999999999999999886555444
No 319
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=93.00 E-value=0.77 Score=34.06 Aligned_cols=41 Identities=20% Similarity=0.393 Sum_probs=34.3
Q ss_pred HHHHHHH-H-cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598 54 MRIVELA-Q-LGIRPCDISRQLRVSHGCVSKILARYHETGSIL 94 (258)
Q Consensus 54 ~RIV~L~-~-~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~ 94 (258)
..|+.++ . .+++..+||+.+++|+++|++.+++..+.|-+.
T Consensus 13 ~~il~~l~~~~~~~~~~la~~~~~s~~~i~~~l~~L~~~g~v~ 55 (101)
T smart00347 13 FLVLRILYEEGPLSVSELAKRLGVSPSTVTRVLDRLEKKGLIR 55 (101)
T ss_pred HHHHHHHHHcCCcCHHHHHHHHCCCchhHHHHHHHHHHCCCeE
Confidence 3455554 3 358999999999999999999999999999874
No 320
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=92.95 E-value=0.54 Score=39.63 Aligned_cols=67 Identities=13% Similarity=0.011 Sum_probs=47.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHH
Q psy15598 64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLL 134 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~ 134 (258)
+++.++|+.+|||..|++-|- +.|.+.+..+..+.-|..++++...|..... ..-.+++.||++.|.
T Consensus 8 ~~IgevAk~~Gvs~~TLRyYE----~~GLl~p~~r~~~gyR~Y~~~~l~rl~~I~~lr~~G~sL~eI~~ll~ 75 (144)
T PRK13752 8 LTIGVFAKAAGVNVETIRFYQ----RKGLLPEPDKPYGSIRRYGEADVTRVRFVKSAQRLGFSLDEIAELLR 75 (144)
T ss_pred ccHHHHHHHHCcCHHHHHHHH----HCCCCCCCccCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHh
Confidence 789999999999999986554 4577765433322457888887776655533 334788999988775
No 321
>PHA02943 hypothetical protein; Provisional
Probab=92.95 E-value=1.1 Score=38.82 Aligned_cols=56 Identities=25% Similarity=0.378 Sum_probs=42.8
Q ss_pred CCCCCCHHHH---HHHHHHHHcC-CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCC
Q psy15598 44 NGRPLPNSVR---MRIVELAQLG-IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIG 99 (258)
Q Consensus 44 ~gR~~S~dlR---~RIV~L~~~G-~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rg 99 (258)
|++..|+... ..|+++.+.| .+.++||+.||+|.+-|+-++.-...+|-+.--.+|
T Consensus 1 MPr~~sd~v~~R~~eILE~Lk~G~~TtseIAkaLGlS~~qa~~~LyvLErEG~VkrV~~G 60 (165)
T PHA02943 1 MPRGMSDTVHTRMIKTLRLLADGCKTTSRIANKLGVSHSMARNALYQLAKEGMVLKVEIG 60 (165)
T ss_pred CCcchhHHHHHHHHHHHHHHhcCCccHHHHHHHHCCCHHHHHHHHHHHHHcCceEEEeec
Confidence 4555666544 4556666677 679999999999999999999999999987543343
No 322
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=92.95 E-value=0.26 Score=44.10 Aligned_cols=43 Identities=9% Similarity=0.108 Sum_probs=36.1
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE 89 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE 89 (258)
.++...|.-|...+.+|++..+||+.||||.++|+++.++..+
T Consensus 183 ~L~~~er~vi~l~~~~~~t~~EIA~~lgis~~~V~q~~~~~~~ 225 (231)
T PRK12427 183 QLDEREQLILHLYYQHEMSLKEIALVLDLTEARICQLNKKIAQ 225 (231)
T ss_pred cCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4667777666666778999999999999999999999988763
No 323
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=92.94 E-value=0.22 Score=41.11 Aligned_cols=50 Identities=16% Similarity=0.177 Sum_probs=39.1
Q ss_pred CCHHHHHHHHHHHH-cC--CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCC
Q psy15598 48 LPNSVRMRIVELAQ-LG--IRPCDISRQLRVSHGCVSKILARYHETGSILPGA 97 (258)
Q Consensus 48 ~S~dlR~RIV~L~~-~G--~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~ 97 (258)
....+|..|..... .| .+.++||+.+|||+..|.+.+++.+..|-+...+
T Consensus 7 ~~YAl~~~i~la~~~~g~~~s~~~ia~~~~is~~~vrk~l~~L~~~Glv~s~~ 59 (141)
T PRK11014 7 TDYGLRALIYMASLPEGRMTSISEVTEVYGVSRNHMVKIINQLSRAGYVTAVR 59 (141)
T ss_pred HhHHHHHHHHHhcCCCCCccCHHHHHHHHCcCHHHHHHHHHHHHhCCEEEEec
Confidence 34456666666543 44 5889999999999999999999999999875444
No 324
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=92.94 E-value=0.25 Score=44.83 Aligned_cols=50 Identities=22% Similarity=0.236 Sum_probs=42.9
Q ss_pred CCCCCHHHHHHHHHHHH--cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598 45 GRPLPNSVRMRIVELAQ--LGIRPCDISRQLRVSHGCVSKILARYHETGSIL 94 (258)
Q Consensus 45 gR~~S~dlR~RIV~L~~--~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~ 94 (258)
.-..+...|.+|+.+.+ .+++..+||++||||..+|++-+....+.|.+.
T Consensus 5 ~~~~~~~tr~~il~lL~~~g~~sa~elA~~Lgis~~avR~HL~~Le~~Glv~ 56 (218)
T COG2345 5 LADPSGSTRERILELLKKSGPVSADELAEELGISPMAVRRHLDDLEAEGLVE 56 (218)
T ss_pred ccCCCccHHHHHHHHHhccCCccHHHHHHHhCCCHHHHHHHHHHHHhCccee
Confidence 33456678999999886 359999999999999999999999999999653
No 325
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=92.93 E-value=0.17 Score=45.95 Aligned_cols=41 Identities=12% Similarity=0.140 Sum_probs=30.4
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHh
Q psy15598 64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQK 120 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~ 120 (258)
.+.++||++.|||++||+|.++.. + .++++.+++|.+..++
T Consensus 2 ~Ti~dIA~~agVS~~TVSrvLn~~---------------~-~vs~~tr~~V~~~a~e 42 (341)
T PRK10703 2 ATIKDVAKRAGVSTTTVSHVINKT---------------R-FVAEETRNAVWAAIKE 42 (341)
T ss_pred CCHHHHHHHhCCCHHHHHHHHcCC---------------C-CCCHHHHHHHHHHHHH
Confidence 378999999999999999999531 1 1456666666666554
No 326
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=92.89 E-value=0.34 Score=37.31 Aligned_cols=37 Identities=22% Similarity=0.242 Sum_probs=31.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHhhhhCC-cccCCCCC
Q psy15598 64 IRPCDISRQLRVSHGCVSKILARYHETGS-ILPGAIGG 100 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGs-l~pk~rgG 100 (258)
.|-.+||+.||+||.+|.+-+++-++.|- |+.....|
T Consensus 20 ~SGe~La~~LgiSRtaVwK~Iq~Lr~~G~~I~s~~~kG 57 (79)
T COG1654 20 VSGEKLAEELGISRTAVWKHIQQLREEGVDIESVRGKG 57 (79)
T ss_pred ccHHHHHHHHCccHHHHHHHHHHHHHhCCceEecCCCc
Confidence 79999999999999999999999999994 44333334
No 327
>PF07374 DUF1492: Protein of unknown function (DUF1492); InterPro: IPR010861 This entry is represented by Streptococcus phage 7201, Orf19. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several hypothetical, highly conserved Streptococcal and related phage proteins. The function of this family is unknown.
Probab=92.87 E-value=0.33 Score=38.28 Aligned_cols=38 Identities=13% Similarity=0.033 Sum_probs=30.5
Q ss_pred HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 51 SVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 51 dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
+.|.-+...+-++++..+||..|++|++|++||.++..
T Consensus 59 ~~r~iL~~~Yi~~~~~~~I~~~l~~S~~t~yr~~~~Al 96 (100)
T PF07374_consen 59 DERLILRMRYINKLTWEQIAEELNISRRTYYRIHKKAL 96 (100)
T ss_pred hHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 34444444456899999999999999999999998864
No 328
>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=92.86 E-value=0.29 Score=35.76 Aligned_cols=26 Identities=27% Similarity=0.457 Sum_probs=23.5
Q ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598 60 AQLGIRPCDISRQLRVSHGCVSKILA 85 (258)
Q Consensus 60 ~~~G~S~~eIAr~LGVSrsTVsRwik 85 (258)
-+.|++..++|+.+|||++||++|.+
T Consensus 15 ~~~~~t~~~lA~~~gis~~tis~~~~ 40 (78)
T TIGR02607 15 EPLGLSIRALAKALGVSRSTLSRIVN 40 (78)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 45799999999999999999999864
No 329
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=92.85 E-value=0.23 Score=45.36 Aligned_cols=42 Identities=24% Similarity=0.280 Sum_probs=34.0
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.++...|.-|...+.+|++..+||+.||||.++|++++++-.
T Consensus 215 ~L~~rer~vl~l~y~~~~t~~EIA~~lgis~~~V~~~~~ral 256 (264)
T PRK07122 215 ALPERERTVLVLRFFESMTQTQIAERVGISQMHVSRLLAKTL 256 (264)
T ss_pred cCCHHHHHHHHHHhcCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 356666655555566899999999999999999999988765
No 330
>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=92.85 E-value=0.24 Score=43.77 Aligned_cols=42 Identities=24% Similarity=0.116 Sum_probs=33.4
Q ss_pred CCCHHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELAQ----LGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~----~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.++...|.-++..+- +|+|..+||+.+|+|.+||.+++.|-+
T Consensus 174 ~L~~~~r~il~l~y~~~~~e~~S~~EIAe~lgis~~tV~~~~~rAl 219 (227)
T TIGR02846 174 VLDGREREVIEMRYGLGDGRRKTQREIAKILGISRSYVSRIEKRAL 219 (227)
T ss_pred hCCHHHHHHHHHHHcCCCCCCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 467777755554443 899999999999999999999988754
No 331
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=92.84 E-value=0.24 Score=44.70 Aligned_cols=42 Identities=12% Similarity=0.134 Sum_probs=33.8
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.++...|.-|...+.+|++..+||+.||||.++|+++.++-.
T Consensus 209 ~L~~~er~vi~~~~~~~~t~~eIA~~lgis~~~V~~~~~~al 250 (258)
T PRK08215 209 KLNDREKLILNLRFFQGKTQMEVAEEIGISQAQVSRLEKAAL 250 (258)
T ss_pred cCCHHHHHHHHHHHhcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 466666655555456899999999999999999999988754
No 332
>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=92.84 E-value=0.15 Score=42.07 Aligned_cols=36 Identities=17% Similarity=0.282 Sum_probs=31.0
Q ss_pred HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598 54 MRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE 89 (258)
Q Consensus 54 ~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE 89 (258)
...|++.+.|++..+||..|+||++||.....+.+.
T Consensus 71 ~Efi~LR~AGlt~~aIAd~F~iS~s~~~nft~~n~~ 106 (126)
T PF10654_consen 71 REFIELRHAGLTCYAIADYFKISKSTVFNFTQNNKK 106 (126)
T ss_pred HHHHHHHhcCCChHHHHHHHhHHHHHHHHHHHHhHH
Confidence 345677789999999999999999999999877654
No 333
>PRK09480 slmA division inhibitor protein; Provisional
Probab=92.83 E-value=0.23 Score=41.46 Aligned_cols=45 Identities=16% Similarity=0.245 Sum_probs=37.4
Q ss_pred ccCCCCCCHHHHHHHHHHH-----Hc---CCCHHHHHHHhCCCHHHHHHHHHH
Q psy15598 42 FVNGRPLPNSVRMRIVELA-----QL---GIRPCDISRQLRVSHGCVSKILAR 86 (258)
Q Consensus 42 ~~~gR~~S~dlR~RIV~L~-----~~---G~S~~eIAr~LGVSrsTVsRwikR 86 (258)
|.|.++-+.+.|.+|++.. +. +.|.++||++.|||++|+|++.+.
T Consensus 1 ~~~~~~~~~~~r~~Il~aa~~l~~~~~G~~~ti~~Ia~~agvs~gt~Y~~F~~ 53 (194)
T PRK09480 1 MAMKRPKKGERREQILQALAQMLESPPGERITTAKLAARVGVSEAALYRHFPS 53 (194)
T ss_pred CCCcCCCchhHHHHHHHHHHHHHHhcCCCccCHHHHHHHhCCCHhHHHHHCCC
Confidence 5688888889999998863 23 479999999999999999987655
No 334
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=92.83 E-value=0.24 Score=40.58 Aligned_cols=43 Identities=26% Similarity=0.394 Sum_probs=35.6
Q ss_pred HHHHHHHHHHH-c-CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCc
Q psy15598 51 SVRMRIVELAQ-L-GIRPCDISRQLRVSHGCVSKILARYHETGSI 93 (258)
Q Consensus 51 dlR~RIV~L~~-~-G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl 93 (258)
++-.+|+...+ + ..+.++||+.+|+|.+||.+-+++..+.|-+
T Consensus 8 ~~D~~IL~~L~~d~r~~~~eia~~lglS~~~v~~Ri~~L~~~GiI 52 (154)
T COG1522 8 DIDRRILRLLQEDARISNAELAERVGLSPSTVLRRIKRLEEEGVI 52 (154)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCce
Confidence 34446777665 3 3799999999999999999999999999954
No 335
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=92.79 E-value=0.19 Score=44.42 Aligned_cols=41 Identities=17% Similarity=0.115 Sum_probs=35.3
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.+|.-.+ +|+.++.+|++.++||++|+||.+||...+++-.
T Consensus 134 ~LT~RE~-eVL~ll~~G~snkeIA~~L~iS~~TV~~h~~~I~ 174 (207)
T PRK11475 134 MLSPTER-EILRFMSRGYSMPQIAEQLERNIKTIRAHKFNVM 174 (207)
T ss_pred CCCHHHH-HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 3665555 7888999999999999999999999998888865
No 336
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=92.77 E-value=0.28 Score=34.03 Aligned_cols=34 Identities=26% Similarity=0.293 Sum_probs=29.5
Q ss_pred HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 55 RIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 55 RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.++.+..+|.+..+||..+++|..||..-+++-.
T Consensus 11 ~v~~l~~~G~s~~eia~~l~is~~tV~~h~~~i~ 44 (65)
T COG2771 11 EILRLVAQGKSNKEIARILGISEETVKTHLRNIY 44 (65)
T ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 4555778999999999999999999998888764
No 337
>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=92.76 E-value=0.27 Score=43.31 Aligned_cols=36 Identities=25% Similarity=0.177 Sum_probs=31.9
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCC
Q psy15598 65 RPCDISRQLRVSHGCVSKILARYHETGSILPGAIGG 100 (258)
Q Consensus 65 S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG 100 (258)
|-.++|++|||||.||++-++.-.+.|.|.-+...|
T Consensus 26 sE~eLa~~~gVSR~TVR~Al~~L~~eGli~r~~G~G 61 (233)
T TIGR02404 26 SEHELMDQYGASRETVRKALNLLTEAGYIQKIQGKG 61 (233)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCCce
Confidence 789999999999999999999999999986555444
No 338
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=92.75 E-value=0.29 Score=32.96 Aligned_cols=42 Identities=21% Similarity=0.238 Sum_probs=32.7
Q ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCC
Q psy15598 109 KVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGS 160 (258)
Q Consensus 109 e~~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~ 160 (258)
+.+..|..++.++|.++..||++.+. +|.+||++.|++....
T Consensus 3 ~~~~~Il~~l~~~~~~t~~ela~~~~----------is~~tv~~~l~~L~~~ 44 (48)
T PF13412_consen 3 ETQRKILNYLRENPRITQKELAEKLG----------ISRSTVNRYLKKLEEK 44 (48)
T ss_dssp HHHHHHHHHHHHCTTS-HHHHHHHHT----------S-HHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHhC----------CCHHHHHHHHHHHHHC
Confidence 34677888889999999999998883 4999999999986543
No 339
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=92.75 E-value=0.21 Score=44.04 Aligned_cols=35 Identities=17% Similarity=0.314 Sum_probs=30.9
Q ss_pred HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 54 MRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 54 ~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
..|+.++.+|++.++||++|++|.+||...+.+-.
T Consensus 154 ~eVL~lla~G~snkeIA~~L~iS~~TVk~h~~~i~ 188 (211)
T COG2197 154 LEVLRLLAEGLSNKEIAEELNLSEKTVKTHVSNIL 188 (211)
T ss_pred HHHHHHHHCCCCHHHHHHHHCCCHhHHHHHHHHHH
Confidence 35668889999999999999999999998888765
No 340
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=92.74 E-value=0.51 Score=41.24 Aligned_cols=58 Identities=10% Similarity=0.105 Sum_probs=41.4
Q ss_pred HHHHHHHHH-HcC--CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHH
Q psy15598 52 VRMRIVELA-QLG--IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPK 109 (258)
Q Consensus 52 lR~RIV~L~-~~G--~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e 109 (258)
+|.+|+... .-| ++..++|++||||+++|+--+++....|-|...++.|-.=+.++.+
T Consensus 16 i~~~I~~g~l~pG~~L~e~eLae~lgVSRtpVREAL~~L~~eGlv~~~~~~G~~V~~~~~~ 76 (224)
T PRK11534 16 LKNDIIRGNFQPDEKLRMSLLTSRYALGVGPLREALSQLVAERLVTVVNQKGYRVASMSEQ 76 (224)
T ss_pred HHHHHHhCCCCCCCcCCHHHHHHHHCCChHHHHHHHHHHHHCCCEEEeCCCceEeCCCCHH
Confidence 455555542 234 5789999999999999999999999999887666555332334444
No 341
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=92.73 E-value=0.14 Score=47.62 Aligned_cols=38 Identities=21% Similarity=0.156 Sum_probs=32.6
Q ss_pred HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 51 SVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 51 dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
+-|..+-.++-+||...+||..||||..||..|.+|+.
T Consensus 7 ~~r~~Akk~yl~gmk~~dIAeklGvspntiksWKrr~g 44 (279)
T COG5484 7 DKRIIAKKDYLKGMKLKDIAEKLGVSPNTIKSWKRRDG 44 (279)
T ss_pred chHHHHHHHHHhhccHHHHHHHhCCChHHHHHHHHhcC
Confidence 44556666788999999999999999999999999863
No 342
>COG3398 Uncharacterized protein conserved in archaea [Function unknown]
Probab=92.67 E-value=0.89 Score=41.65 Aligned_cols=104 Identities=18% Similarity=0.133 Sum_probs=78.4
Q ss_pred CCHHHHHHHHHHHH--cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCC---CCCC----------CHHHHH
Q psy15598 48 LPNSVRMRIVELAQ--LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSK---PRVT----------TPKVVS 112 (258)
Q Consensus 48 ~S~dlR~RIV~L~~--~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~R---Prkl----------T~e~~~ 112 (258)
+-++.|.+|..... -|++.+|+++-+++.|+|.+=-++-.+..+.++.++-+|.. |.-. ..+.-+
T Consensus 98 ~~ns~R~~Iy~~i~~nPG~~lsEl~~nl~i~R~TlRyhlriLe~~~li~a~~~~g~~~yfpa~~t~~~~e~~~Lkn~~~k 177 (240)
T COG3398 98 FLNSKRDGIYNYIKPNPGFSLSELRANLYINRSTLRYHLRILESNPLIEAGRVGGALRYFPADMTYGEAEVLSLKNETSK 177 (240)
T ss_pred HhhhhHHHHHHHhccCCCccHHHHHHhcCCChHHHHHHHHHHHhCcchhhhccCCceEEccCCCCcccchHHHhhchhHH
Confidence 44578999999986 48999999999999999999888888888887766666521 2111 122336
Q ss_pred HHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCCC
Q psy15598 113 YIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSS 161 (258)
Q Consensus 113 ~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~~ 161 (258)
.|...+++++..+..+|+.++. +|..||.=.|++.-...
T Consensus 178 ~I~~eiq~~~~~t~~~ia~~l~----------ls~aTV~~~lk~l~~~G 216 (240)
T COG3398 178 AIIYEIQENKCNTNLLIAYELN----------LSVATVAYHLKKLEELG 216 (240)
T ss_pred HHHHHHhcCCcchHHHHHHHcC----------ccHHHHHHHHHHHHHcC
Confidence 6777788888999988877763 48899988887665443
No 343
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=92.66 E-value=1.1 Score=33.91 Aligned_cols=32 Identities=22% Similarity=0.362 Sum_probs=28.2
Q ss_pred HHHHHHHhCCCHHHHHHHHHHhhhhCCcccCC
Q psy15598 66 PCDISRQLRVSHGCVSKILARYHETGSILPGA 97 (258)
Q Consensus 66 ~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~ 97 (258)
..++|+.|+|+++||++.+++..+.|-+.-.+
T Consensus 2 ~~ela~~l~is~stvs~~l~~L~~~glI~r~~ 33 (96)
T smart00529 2 TSEIAERLNVSPPTVTQMLKKLEKDGLVEYEP 33 (96)
T ss_pred HHHHHHHhCCChHHHHHHHHHHHHCCCEEEcC
Confidence 57999999999999999999999999775443
No 344
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=92.63 E-value=0.2 Score=44.48 Aligned_cols=40 Identities=23% Similarity=0.300 Sum_probs=34.5
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 48 LPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 48 ~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
++. ...+|+.+..+|++.++||+.|+||.+||..++.+-.
T Consensus 156 Lt~-rE~~Vl~l~~~G~s~~eIA~~L~iS~~TVk~~~~~i~ 195 (216)
T PRK10100 156 LTH-REKEILNKLRIGASNNEIARSLFISENTVKTHLYNLF 195 (216)
T ss_pred CCH-HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 665 3346888888899999999999999999999998875
No 345
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=92.61 E-value=0.33 Score=42.77 Aligned_cols=65 Identities=18% Similarity=0.158 Sum_probs=48.7
Q ss_pred HHHHHHHHHHH-HcC--CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHH
Q psy15598 50 NSVRMRIVELA-QLG--IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYI 114 (258)
Q Consensus 50 ~dlR~RIV~L~-~~G--~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I 114 (258)
..+|.+|+..- .-| ++..+||++||||+..|+.-+.+....|-|.-.+++|-.=..++.+..+.|
T Consensus 23 ~~Lr~~Il~g~l~pG~~l~e~~La~~~gvSrtPVReAL~rL~~eGlv~~~p~rG~~V~~~~~~~~~ei 90 (230)
T COG1802 23 EELREAILSGELAPGERLSEEELAEELGVSRTPVREALRRLEAEGLVEIEPNRGAFVAPLSLAEAREI 90 (230)
T ss_pred HHHHHHHHhCCCCCCCCccHHHHHHHhCCCCccHHHHHHHHHHCCCeEecCCCCCeeCCCCHHHHHHH
Confidence 46777777764 345 688999999999999999999999999988766666633344554444433
No 346
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=92.57 E-value=0.3 Score=38.57 Aligned_cols=38 Identities=16% Similarity=0.110 Sum_probs=30.6
Q ss_pred HHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 51 SVRMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 51 dlR~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
..|..|..+++ .+....++|+.||||++|+++.+++|.
T Consensus 55 ~Er~~i~~aL~~~~gn~s~AAr~LGIsRsTL~rKLkr~g 93 (95)
T PRK00430 55 VEAPLLDMVMQYTRGNQTRAALMLGINRGTLRKKLKKYG 93 (95)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhC
Confidence 34555556655 577899999999999999999999973
No 347
>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=92.56 E-value=0.23 Score=38.35 Aligned_cols=84 Identities=19% Similarity=0.258 Sum_probs=40.5
Q ss_pred HcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHh-cCCC
Q psy15598 61 QLGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLS-DGVC 139 (258)
Q Consensus 61 ~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~nP~ita~EIr~~L~~-~Gv~ 139 (258)
+.|++..+||+.||.|++.|++.+.-..-...|...-..| ..........|....+.+| .++...+.. ..-.
T Consensus 1 ~~G~tq~eIA~~lGks~s~Vs~~l~Ll~lP~~i~~~v~~g---~~~~~~a~~~L~~~~~~~~----~~~~~~v~~~~~~~ 73 (93)
T PF08535_consen 1 EFGWTQEEIAKRLGKSRSWVSNHLALLDLPEEIKELVRSG---RISDIRALYELRKLAEKNP----EEVEALVAKAKEEG 73 (93)
T ss_dssp HTT--HHHHHHHTT--HHHHHHHHGGGS--HHHHHHHHTT---S---HHHHHHHHHHHHH-H----HHHHHHH-HSTTS-
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHcCCHHHHHHHHcC---CCchHHHHHHHHHHHHhCH----HHHHHHHHHhcccc
Confidence 4699999999999999999999988653222221111122 2223333444445554543 344444422 2222
Q ss_pred CCCCCCCHHHHHHHHHh
Q psy15598 140 DKFNVPSVSSISRILRN 156 (258)
Q Consensus 140 v~~~~pS~STI~RiLrr 156 (258)
++..++.++.+.
T Consensus 74 -----~t~~~~~~~~~~ 85 (93)
T PF08535_consen 74 -----LTRAAVKALRRE 85 (93)
T ss_dssp ------SHHHHHHHHHH
T ss_pred -----ccHHHHHHHHHH
Confidence 377888555443
No 348
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=92.54 E-value=0.45 Score=40.57 Aligned_cols=77 Identities=18% Similarity=0.208 Sum_probs=40.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHh--cCCCCC
Q psy15598 64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLS--DGVCDK 141 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~nP~ita~EIr~~L~~--~Gv~v~ 141 (258)
.|..+||+.+||+++|+|+|.+.=+. ..++..++..+.=.-...++...|.. .|-.
T Consensus 35 ~T~~eiAee~Gis~~tLYrWr~~~~~--------------------Fiey~n~la~~~~~~~~~eVy~~L~~~i~~~~-- 92 (142)
T PF13022_consen 35 RTQAEIAEEVGISRSTLYRWRQQNKA--------------------FIEYKNELADRFLSSHREEVYTQLMKKIRGGQ-- 92 (142)
T ss_dssp S-HHHHHHHHTS-HHHHHHHHHH-HH--------------------HHHHHHHHHHHHHHTTHHHHHHHHHHHHHSSS--
T ss_pred chHHHHHHHhCCCHHHHHHHHhcCHH--------------------HHHHHHHHHHHHHHHhHHHHHHHHHHHHhCCC--
Confidence 67999999999999999999965221 11111222111111133344444432 1222
Q ss_pred CCCCCHHHHHHHHHhccCCCCCCC
Q psy15598 142 FNVPSVSSISRILRNKIGSSIVQH 165 (258)
Q Consensus 142 ~~~pS~STI~RiLrr~~~~~~~~~ 165 (258)
+|+..|.-+|++.|.-.+++.
T Consensus 93 ---~svKaieLflk~~GLLtDrq~ 113 (142)
T PF13022_consen 93 ---PSVKAIELFLKRHGLLTDRQE 113 (142)
T ss_dssp -----HHHHHHHHHHTT--EEEEE
T ss_pred ---ccHHHHHHHHHHcCcccceee
Confidence 488888888888887665543
No 349
>PF13592 HTH_33: Winged helix-turn helix
Probab=92.52 E-value=0.22 Score=35.73 Aligned_cols=41 Identities=22% Similarity=-0.024 Sum_probs=34.1
Q ss_pred CCCCCHHHHHHHHH-hcCCCCCCCCCCHHHHHHHHHhccCCCCCCCC
Q psy15598 121 DPGIFAWEIRDRLL-SDGVCDKFNVPSVSSISRILRNKIGSSIVQHH 166 (258)
Q Consensus 121 nP~ita~EIr~~L~-~~Gv~v~~~~pS~STI~RiLrr~~~~~~~~~~ 166 (258)
+..+++.+|++.+. +.|+.. |.++|++.|++++...-++..
T Consensus 2 ~~~wt~~~i~~~I~~~fgv~y-----s~~~v~~lL~r~G~s~~kp~~ 43 (60)
T PF13592_consen 2 GGRWTLKEIAAYIEEEFGVKY-----SPSGVYRLLKRLGFSYQKPRP 43 (60)
T ss_pred CCcccHHHHHHHHHHHHCCEE-----cHHHHHHHHHHcCCccccCCC
Confidence 45678999999998 589986 999999999999988665543
No 350
>PRK09492 treR trehalose repressor; Provisional
Probab=92.51 E-value=0.2 Score=44.97 Aligned_cols=23 Identities=30% Similarity=0.388 Sum_probs=21.1
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q psy15598 64 IRPCDISRQLRVSHGCVSKILAR 86 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikR 86 (258)
++.++||+.+|||++||+|.++.
T Consensus 5 ~ti~dIA~~agVS~~TVSrvLn~ 27 (315)
T PRK09492 5 LTIKDIARLSGVGKSTVSRVLNN 27 (315)
T ss_pred CcHHHHHHHhCCCHHHHhHHhCC
Confidence 58899999999999999999964
No 351
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=92.49 E-value=0.9 Score=40.99 Aligned_cols=78 Identities=13% Similarity=0.113 Sum_probs=52.7
Q ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCC-CCHHHHHHHHHHHHhCCCCCHHHHHHHHHhcCCCC
Q psy15598 62 LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRV-TTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCD 140 (258)
Q Consensus 62 ~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrk-lT~e~~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v 140 (258)
+..+..++|+.+++|++++.|..++.- |. .|.. +...-...-..++ ....++..||+..+ |..
T Consensus 198 ~~isl~~lA~~~~lS~~~l~r~Fk~~~--G~---------tp~~~l~~~Rl~~A~~lL-~~t~~sI~eIA~~~---GF~- 261 (290)
T PRK10572 198 SEFDIESVAQHVCLSPSRLAHLFRQQL--GI---------SVLRWREDQRISRAKLLL-QTTRMPIATIGRNV---GYD- 261 (290)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHH--Cc---------CHHHHHHHHHHHHHHHHH-HcCCCCHHHHHHHh---CCC-
Confidence 568999999999999999999999973 21 1111 1111112222223 34678888887766 665
Q ss_pred CCCCCCHHHHHHHHHhccCC
Q psy15598 141 KFNVPSVSSISRILRNKIGS 160 (258)
Q Consensus 141 ~~~~pS~STI~RiLrr~~~~ 160 (258)
+.+...|+.|+.-+.
T Consensus 262 -----d~s~Fsr~FKk~~G~ 276 (290)
T PRK10572 262 -----DQLYFSRVFKKCTGA 276 (290)
T ss_pred -----CHHHHHHHHHHHHCc
Confidence 788999999887654
No 352
>PF07141 Phage_term_sma: Putative bacteriophage terminase small subunit; InterPro: IPR010789 This entry is represented by Bacteriophage 712, Gp1; it is a family of uncharacterised viral proteins. This family consists of several putative Lactococcus bacteriophage terminase small subunit proteins. The exact function of this family is unknown.
Probab=92.49 E-value=0.26 Score=42.03 Aligned_cols=51 Identities=14% Similarity=0.148 Sum_probs=43.0
Q ss_pred ccCCc-ccCCCCCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHh
Q psy15598 37 QLGGV-FVNGRPLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARY 87 (258)
Q Consensus 37 q~~~~-~~~gR~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRy 87 (258)
|.||. -+-++-|...+=.+||.++++|.+.++|+..|.||+.|.+.|...-
T Consensus 4 qnggrptilpkmYtE~Lve~II~~IE~dt~~sEIc~~L~isrKtFyeWrdtk 55 (174)
T PF07141_consen 4 QNGGRPTILPKMYTEPLVEQIIDKIESDTNDSEICTSLHISRKTFYEWRDTK 55 (174)
T ss_pred cCCCCCcccHHhhhhHHHHHHHHHHHcCCcHHHHHHHHhccHHHHHHHHhhh
Confidence 45663 2355668888889999999999999999999999999999998754
No 353
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=92.43 E-value=0.3 Score=43.37 Aligned_cols=54 Identities=20% Similarity=0.268 Sum_probs=41.3
Q ss_pred CCCHHHHHHHHHHHHcCC--------CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCC
Q psy15598 47 PLPNSVRMRIVELAQLGI--------RPCDISRQLRVSHGCVSKILARYHETGSILPGAIGG 100 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~--------S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG 100 (258)
++-..+...|.+...+|. |-.++|++|||||.||++-++.-.+.|.|.-....|
T Consensus 9 p~y~qI~~~i~~~I~~G~~~~g~kLPsE~eLa~~~~VSR~TvR~Al~~L~~eGli~r~~G~G 70 (241)
T PRK11402 9 LLYATVRQRLLDDIAQGVYQAGQQIPTENELCTQYNVSRITIRKAISDLVADGVLIRWQGKG 70 (241)
T ss_pred cHHHHHHHHHHHHHHcCCCCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCce
Confidence 344455666666665542 789999999999999999999999999986554444
No 354
>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=92.42 E-value=0.66 Score=41.79 Aligned_cols=67 Identities=16% Similarity=0.180 Sum_probs=49.2
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHh
Q psy15598 64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQ-KDPGIFAWEIRDRLLS 135 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~-~nP~ita~EIr~~L~~ 135 (258)
+++.++|+..|||.+||+-|-+ .|-+.|..+.+ +-+..++++.+.|..+.. ..-..++.+|++.|..
T Consensus 2 y~i~elA~~~Gvs~~tIR~Ye~----~GLL~p~r~~~-~~r~Y~~~~v~rL~~I~~l~~~G~~L~~I~~~l~~ 69 (219)
T cd04778 2 YRIDDLARAAGTTVRNVRAYQD----RGLLPPPRRRG-RVAIYNDSHLARLRLINQLLERGYTLAHIAELLAA 69 (219)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH----CCCCCCcccCC-CCcccCHHHHHHHHHHHHHHHCCCCHHHHHHHHHh
Confidence 5789999999999999866554 47776654443 456889888887766655 3346778888887764
No 355
>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain. This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.
Probab=92.38 E-value=0.45 Score=37.09 Aligned_cols=33 Identities=15% Similarity=0.090 Sum_probs=30.9
Q ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598 62 LGIRPCDISRQLRVSHGCVSKILARYHETGSIL 94 (258)
Q Consensus 62 ~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~ 94 (258)
..++..+||+.+|+|+.||+|.+++..+.|-|.
T Consensus 46 ~~is~~eLa~~~g~sr~tVsr~L~~Le~~GlI~ 78 (95)
T TIGR01610 46 DRVTATVIAELTGLSRTHVSDAIKSLARRRIIF 78 (95)
T ss_pred CccCHHHHHHHHCcCHHHHHHHHHHHHHCCCee
Confidence 468999999999999999999999999999885
No 356
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=92.35 E-value=0.25 Score=44.73 Aligned_cols=41 Identities=12% Similarity=0.159 Sum_probs=34.7
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.+|... ..|+.++.+|++.++||+.|+||.+||.+.+++-.
T Consensus 143 ~LS~RE-~eVL~Lia~G~SnkEIA~~L~IS~~TVk~hvs~I~ 183 (217)
T PRK13719 143 KVTKYQ-NDVFILYSFGFSHEYIAQLLNITVGSSKNKISEIL 183 (217)
T ss_pred CCCHHH-HHHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 344444 36888889999999999999999999999998876
No 357
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=92.33 E-value=0.3 Score=43.77 Aligned_cols=57 Identities=25% Similarity=0.258 Sum_probs=44.8
Q ss_pred CCCCCCHHHHHHHHHHHHcCC--------CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCC
Q psy15598 44 NGRPLPNSVRMRIVELAQLGI--------RPCDISRQLRVSHGCVSKILARYHETGSILPGAIGG 100 (258)
Q Consensus 44 ~gR~~S~dlR~RIV~L~~~G~--------S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG 100 (258)
++.++-..++..|.+...+|. +-.++|++|||||-||+|-++.-.+.|-|......|
T Consensus 4 ~~~plY~qI~~~i~~~I~~G~~~~G~~LPsE~eLa~~f~VSR~TvRkAL~~L~~eGli~r~~G~G 68 (236)
T COG2188 4 SAMPLYQQIAEDIRQRIESGELPPGDKLPSERELAEQFGVSRMTVRKALDELVEEGLIVRRQGKG 68 (236)
T ss_pred ccCccHHHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHCCcHHHHHHHHHHHHHCCcEEEEecCe
Confidence 344556667777777776653 789999999999999999999999999886554444
No 358
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=92.30 E-value=0.31 Score=43.34 Aligned_cols=53 Identities=21% Similarity=0.140 Sum_probs=39.9
Q ss_pred CCHHHHHHHHHHHHc-----CC---CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCC
Q psy15598 48 LPNSVRMRIVELAQL-----GI---RPCDISRQLRVSHGCVSKILARYHETGSILPGAIGG 100 (258)
Q Consensus 48 ~S~dlR~RIV~L~~~-----G~---S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG 100 (258)
+-..+...|.....+ |. |-.++|++||||+.||++-+....+.|.|.-+.+.|
T Consensus 6 ly~qi~~~L~~~I~~g~~~~G~~LPsE~eL~~~~~VSR~TvR~Al~~L~~eGli~r~~G~G 66 (240)
T PRK09764 6 LYRQIADRIREQIARGELKPGDALPTESALQTEFGVSRVTVRQALRQLVEQQILESIQGSG 66 (240)
T ss_pred HHHHHHHHHHHHHHcCCCCCCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCce
Confidence 334555555555544 42 779999999999999999999999999886555444
No 359
>COG2207 AraC AraC-type DNA-binding domain-containing proteins [Transcription]
Probab=92.30 E-value=2.2 Score=32.53 Aligned_cols=89 Identities=21% Similarity=0.227 Sum_probs=53.5
Q ss_pred HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCC-CCHHHHHHHHHHHHhCCCCCHHHH
Q psy15598 51 SVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRV-TTPKVVSYIKELKQKDPGIFAWEI 129 (258)
Q Consensus 51 dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrk-lT~e~~~~I~~lv~~nP~ita~EI 129 (258)
.....|......+.+..++|+.+|+|++++.+..++.. |. .+.. +.......-.. +..+...+..+|
T Consensus 24 ~~~~~i~~~~~~~~~l~~la~~~g~S~~~l~r~f~~~~--g~---------s~~~~~~~~Rl~~A~~-lL~~~~~~i~~i 91 (127)
T COG2207 24 RALDYIEENLAEPLTLEDLARRLGMSRRTLSRLFKKET--GT---------SPSQYLRQLRLEEARR-LLRSTDLSITEI 91 (127)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHCCCHHHHHHHHHHHH--CC---------CHHHHHHHHHHHHHHH-HHHcCCCCHHHH
Confidence 33344444334568999999999999999999988763 21 1111 11111122222 224445567777
Q ss_pred HHHHHhcCCCCCCCCCCHHHHHHHHHhccCC
Q psy15598 130 RDRLLSDGVCDKFNVPSVSSISRILRNKIGS 160 (258)
Q Consensus 130 r~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~ 160 (258)
+..+ |.. +.+...|..++.-+.
T Consensus 92 A~~~---Gf~------~~s~F~~~Fk~~~g~ 113 (127)
T COG2207 92 ALRL---GYS------SPSHFSRAFKRLFGV 113 (127)
T ss_pred HHHh---CcC------CHHHHHHHHHHHhCC
Confidence 6655 665 777788888876554
No 360
>TIGR01636 phage_rinA phage transcriptional activator, RinA family. This model represents a family of phage proteins, including RinA, a transcriptional activator in staphylococcal phage phi 11. This family shows similarity to ArpU, a phage-related putative autolysin regulator, and to some sporulation-specific sigma factors.
Probab=92.30 E-value=0.38 Score=39.79 Aligned_cols=42 Identities=19% Similarity=0.154 Sum_probs=33.0
Q ss_pred CCHHHHHHHHHHHHcCC--CHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598 48 LPNSVRMRIVELAQLGI--RPCDISRQLRVSHGCVSKILARYHE 89 (258)
Q Consensus 48 ~S~dlR~RIV~L~~~G~--S~~eIAr~LGVSrsTVsRwikRyrE 89 (258)
++.+.|.-|...+-.+. +..+||..|++|++||+++.+++..
T Consensus 83 Ld~~er~II~~rY~~~~~~t~~~Ia~~l~iS~~t~~r~r~~~l~ 126 (134)
T TIGR01636 83 ADEQTRVIIQELYMKKRPLTLVGLAQQLFISKSTAYRLRNHIIE 126 (134)
T ss_pred CCHHHHHHHHHHHccCCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 56666655555555554 9999999999999999999988753
No 361
>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=92.27 E-value=0.3 Score=43.07 Aligned_cols=36 Identities=17% Similarity=0.156 Sum_probs=31.9
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCC
Q psy15598 65 RPCDISRQLRVSHGCVSKILARYHETGSILPGAIGG 100 (258)
Q Consensus 65 S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG 100 (258)
|-+++|++||||+.||++-+..-.+.|.+.-....|
T Consensus 27 sE~eLa~~~~VSR~TVR~Al~~L~~eGli~r~~G~G 62 (230)
T TIGR02018 27 SEHELVAQYGCSRMTVNRALRELTDAGLLERRQGVG 62 (230)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCCE
Confidence 889999999999999999999999999886555444
No 362
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=92.27 E-value=0.85 Score=37.47 Aligned_cols=55 Identities=16% Similarity=0.167 Sum_probs=40.0
Q ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCC--CCC-CCCCCCHHHHHHHHH
Q psy15598 62 LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAI--GGS-KPRVTTPKVVSYIKE 116 (258)
Q Consensus 62 ~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~r--gG~-RPrklT~e~~~~I~~ 116 (258)
.|.+.++||+.++++++||.+.+++..+.|-|.-... .++ +--.+|++-.+.+.+
T Consensus 53 ~~~t~~eLa~~l~i~~~tvsr~l~~Le~~GlI~R~~~~~DrR~~~l~LT~~G~~~~~~ 110 (144)
T PRK11512 53 ACITPVELKKVLSVDLGALTRMLDRLVCKGWVERLPNPNDKRGVLVKLTTSGAAICEQ 110 (144)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeccCcccCCeeEeEEChhHHHHHHH
Confidence 5689999999999999999999999999998743322 221 122466665555444
No 363
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=92.25 E-value=0.18 Score=44.80 Aligned_cols=53 Identities=9% Similarity=0.140 Sum_probs=40.3
Q ss_pred CCHHHHHHHHHHHHcCC---CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCC
Q psy15598 48 LPNSVRMRIVELAQLGI---RPCDISRQLRVSHGCVSKILARYHETGSILPGAIGG 100 (258)
Q Consensus 48 ~S~dlR~RIV~L~~~G~---S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG 100 (258)
+..++|.+|...+..|. |-.++|++|||||.||++-++.-.+.|.|.-+...|
T Consensus 17 i~~~L~~~I~~~~~~G~~LPsE~eLa~~~~VSR~TVR~Al~~L~~eGli~r~~G~G 72 (241)
T PRK10079 17 IAAKLEQELRQHYRCGDYLPAEQQLAARYEVNRHTLRRAIDQLVEKGWVQRRQGVG 72 (241)
T ss_pred HHHHHHHHHhcccCCCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCCE
Confidence 44566666643233452 789999999999999999999999999987555444
No 364
>PRK09726 antitoxin HipB; Provisional
Probab=92.25 E-value=0.32 Score=37.22 Aligned_cols=35 Identities=9% Similarity=0.221 Sum_probs=28.3
Q ss_pred HHHHHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598 51 SVRMRIVELA-QLGIRPCDISRQLRVSHGCVSKILA 85 (258)
Q Consensus 51 dlR~RIV~L~-~~G~S~~eIAr~LGVSrsTVsRwik 85 (258)
.+..+|-.+. +.|++..++|+.+|||++||++|.+
T Consensus 12 ~l~~~lk~~R~~~gltq~elA~~~gvs~~tis~~e~ 47 (88)
T PRK09726 12 QLANAMKLVRQQNGWTQSELAKKIGIKQATISNFEN 47 (88)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHC
Confidence 3445555554 4699999999999999999999976
No 365
>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=92.24 E-value=0.43 Score=32.19 Aligned_cols=40 Identities=25% Similarity=0.147 Sum_probs=31.0
Q ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhc
Q psy15598 108 PKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNK 157 (258)
Q Consensus 108 ~e~~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~ 157 (258)
++.+..|...+++++..+..+|.+.+. +|.+||.+.+++.
T Consensus 2 D~~D~~Il~~Lq~d~r~s~~~la~~lg----------lS~~~v~~Ri~rL 41 (42)
T PF13404_consen 2 DELDRKILRLLQEDGRRSYAELAEELG----------LSESTVRRRIRRL 41 (42)
T ss_dssp -HHHHHHHHHHHH-TTS-HHHHHHHHT----------S-HHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHcCCccHHHHHHHHC----------cCHHHHHHHHHHh
Confidence 456788999999999999999998883 4999999999864
No 366
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=92.14 E-value=0.25 Score=44.87 Aligned_cols=22 Identities=32% Similarity=0.296 Sum_probs=20.8
Q ss_pred CCHHHHHHHhCCCHHHHHHHHH
Q psy15598 64 IRPCDISRQLRVSHGCVSKILA 85 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwik 85 (258)
.+.++||+.+|||++||+|.++
T Consensus 7 ~Ti~dIA~~agVS~~TVSr~Ln 28 (342)
T PRK10014 7 ITIHDVALAAGVSVSTVSLVLS 28 (342)
T ss_pred CcHHHHHHHhCCCHHHHHHHHC
Confidence 6899999999999999999986
No 367
>PRK10072 putative transcriptional regulator; Provisional
Probab=92.11 E-value=0.26 Score=39.16 Aligned_cols=27 Identities=30% Similarity=0.319 Sum_probs=24.3
Q ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHHH
Q psy15598 60 AQLGIRPCDISRQLRVSHGCVSKILAR 86 (258)
Q Consensus 60 ~~~G~S~~eIAr~LGVSrsTVsRwikR 86 (258)
.+.|++..++|+.+|||.+||++|.+.
T Consensus 43 ~~~glTQ~elA~~lGvS~~TVs~WE~G 69 (96)
T PRK10072 43 KGTGLKIDDFARVLGVSVAMVKEWESR 69 (96)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 357999999999999999999999764
No 368
>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=92.11 E-value=0.85 Score=35.19 Aligned_cols=53 Identities=26% Similarity=0.377 Sum_probs=41.3
Q ss_pred HHHHHHHHHHH-cC--CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc--cCCCCCCCC
Q psy15598 51 SVRMRIVELAQ-LG--IRPCDISRQLRVSHGCVSKILARYHETGSIL--PGAIGGSKP 103 (258)
Q Consensus 51 dlR~RIV~L~~-~G--~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~--pk~rgG~RP 103 (258)
++-..||+++. .| +.-++||+.|++|..||++-....++-|-++ |.+.+|+.|
T Consensus 8 ~IL~alV~~Y~~~~~PVgSk~ia~~l~~s~aTIRN~M~~Le~lGlve~~p~~s~GriP 65 (78)
T PF03444_consen 8 EILKALVELYIETGEPVGSKTIAEELGRSPATIRNEMADLEELGLVESQPHPSGGRIP 65 (78)
T ss_pred HHHHHHHHHHHhcCCCcCHHHHHHHHCCChHHHHHHHHHHHHCCCccCCCCCCCCCCc
Confidence 34456777764 34 5779999999999999999999999999885 555666434
No 369
>PF01475 FUR: Ferric uptake regulator family; InterPro: IPR002481 The Ferric uptake regulator (FUR) family includes metal ion uptake regulator proteins. These are responsible for controlling the intracellular concentration of iron in many bacteria. Although iron is essential for most organisms, high concentrations can be toxic because of the formation of hydroxyl radicals []. FURs can also control zinc homeostasis [] and is the subject of research on the pathogenesis of mycobacteria.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1MZB_A 2RGV_B 2FE3_B 3F8N_B 3EYY_B 2W57_A 2FU4_A 2O03_A 3MWM_B 2XIG_B ....
Probab=92.08 E-value=0.21 Score=39.84 Aligned_cols=48 Identities=27% Similarity=0.234 Sum_probs=36.2
Q ss_pred HHHHHHHHHHhCC-CCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCCCC
Q psy15598 110 VVSYIKELKQKDP-GIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSSI 162 (258)
Q Consensus 110 ~~~~I~~lv~~nP-~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~~~ 162 (258)
.+..|.+++.+.+ ..++.||.+.|.+.+..+ |.+||+|.|..+.....
T Consensus 9 ~R~~Il~~l~~~~~~~ta~ei~~~l~~~~~~i-----s~~TVYR~L~~L~e~Gl 57 (120)
T PF01475_consen 9 QRLAILELLKESPEHLTAEEIYDKLRKKGPRI-----SLATVYRTLDLLEEAGL 57 (120)
T ss_dssp HHHHHHHHHHHHSSSEEHHHHHHHHHHTTTT-------HHHHHHHHHHHHHTTS
T ss_pred HHHHHHHHHHcCCCCCCHHHHHHHhhhccCCc-----CHHHHHHHHHHHHHCCe
Confidence 3556666666544 788999999999888775 99999999998776654
No 370
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=92.07 E-value=0.21 Score=44.27 Aligned_cols=41 Identities=20% Similarity=0.209 Sum_probs=33.2
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 48 LPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 48 ~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
++...|.-+...+-+|++..+||+.||||.+||+..+.|.+
T Consensus 150 L~~~~r~i~~l~~~~g~s~~EIAe~lgis~~tVk~~l~Rar 190 (231)
T PRK11922 150 LPDAFRAVFVLRVVEELSVEETAQALGLPEETVKTRLHRAR 190 (231)
T ss_pred CCHHHhhhheeehhcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 66666655444466899999999999999999999988764
No 371
>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=92.06 E-value=0.23 Score=44.81 Aligned_cols=23 Identities=30% Similarity=0.401 Sum_probs=20.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q psy15598 64 IRPCDISRQLRVSHGCVSKILAR 86 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikR 86 (258)
++.++||+.+|||++||+|.++.
T Consensus 2 ~ti~dIA~~agVS~sTVSr~Ln~ 24 (311)
T TIGR02405 2 LTIKDIARLAGVGKSTVSRVLNN 24 (311)
T ss_pred CcHHHHHHHhCCCHHHHHHHhCC
Confidence 47899999999999999999953
No 372
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=91.98 E-value=0.42 Score=38.68 Aligned_cols=41 Identities=24% Similarity=0.235 Sum_probs=34.3
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598 48 LPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE 89 (258)
Q Consensus 48 ~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE 89 (258)
++.. ..+|+.++.+|++.++||+.+++|..||..++++-+.
T Consensus 150 lt~~-e~~vl~l~~~g~~~~~Ia~~l~~s~~tv~~~~~~~~~ 190 (211)
T PRK15369 150 LTPR-ERQILKLITEGYTNRDIAEQLSISIKTVETHRLNMMR 190 (211)
T ss_pred CCHH-HHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 5544 3467777889999999999999999999999998763
No 373
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=91.91 E-value=0.33 Score=43.92 Aligned_cols=44 Identities=25% Similarity=0.351 Sum_probs=36.6
Q ss_pred HHHHHHHHHHH-c-CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598 51 SVRMRIVELAQ-L-GIRPCDISRQLRVSHGCVSKILARYHETGSIL 94 (258)
Q Consensus 51 dlR~RIV~L~~-~-G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~ 94 (258)
+.+.+|++.++ . ..+..++|+.|+||..||+|.++...+.|.+.
T Consensus 4 ~R~~~Il~~l~~~~~~~~~eLa~~l~VS~~TiRRdL~~L~~~~~l~ 49 (240)
T PRK10411 4 ARQQAIVDLLLNHTSLTTEALAEQLNVSKETIRRDLNELQTQGKIL 49 (240)
T ss_pred HHHHHHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 44566777765 3 47999999999999999999999999888764
No 374
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=91.91 E-value=0.54 Score=31.71 Aligned_cols=34 Identities=24% Similarity=0.359 Sum_probs=25.4
Q ss_pred HHHHHHHH-cC-CCHHHHHHHhCCCHHHHHHHHHHh
Q psy15598 54 MRIVELAQ-LG-IRPCDISRQLRVSHGCVSKILARY 87 (258)
Q Consensus 54 ~RIV~L~~-~G-~S~~eIAr~LGVSrsTVsRwikRy 87 (258)
.+|+.+.+ +| .+..+||+.+|+|.+||.+=+++.
T Consensus 6 ~~Il~~Lq~d~r~s~~~la~~lglS~~~v~~Ri~rL 41 (42)
T PF13404_consen 6 RKILRLLQEDGRRSYAELAEELGLSESTVRRRIRRL 41 (42)
T ss_dssp HHHHHHHHH-TTS-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred HHHHHHHHHcCCccHHHHHHHHCcCHHHHHHHHHHh
Confidence 46777765 44 799999999999999999877764
No 375
>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=91.91 E-value=0.32 Score=44.61 Aligned_cols=42 Identities=10% Similarity=0.019 Sum_probs=33.3
Q ss_pred CCCHHHHHHHHHHH----HcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELA----QLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~----~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.++...|.-|+..+ .+|+|..+||..||||.+||..++.+-+
T Consensus 222 ~Lp~~~R~Vl~l~ygL~~~e~~s~~EIA~~Lgis~~tVk~~l~rAl 267 (285)
T TIGR02394 222 ELNERQREVLARRFGLLGYEPATLEEVAAEVGLTRERVRQIQVEAL 267 (285)
T ss_pred cCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHH
Confidence 35666665444443 5899999999999999999999998865
No 376
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=91.89 E-value=0.42 Score=42.73 Aligned_cols=58 Identities=17% Similarity=0.149 Sum_probs=42.0
Q ss_pred cCCCCCCHHHHHHHHHHHHc-----C--C-CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCC
Q psy15598 43 VNGRPLPNSVRMRIVELAQL-----G--I-RPCDISRQLRVSHGCVSKILARYHETGSILPGAIGG 100 (258)
Q Consensus 43 ~~gR~~S~dlR~RIV~L~~~-----G--~-S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG 100 (258)
...++++..+-..|...+.. | + +-+++|++||||+++|+--+++....|-|...++.|
T Consensus 4 ~~~~~~~~~v~~~l~~~I~~g~l~pG~~LpsE~eLae~~gVSRtpVREAL~~L~~eGlV~~~~~~G 69 (253)
T PRK11523 4 TEPRRLYQQLAAELKERIEQGVYLVGDKLPAERFIADEKNVSRTVVREAIIMLEVEGYVEVRKGSG 69 (253)
T ss_pred CCCCcHHHHHHHHHHHHHHcCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCCe
Confidence 34445555554444444433 4 3 468999999999999999999999999886665555
No 377
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=91.83 E-value=0.25 Score=44.88 Aligned_cols=42 Identities=26% Similarity=0.252 Sum_probs=31.8
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCC-CCCHHHHHHHHHHHHh
Q psy15598 64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPR-VTTPKVVSYIKELKQK 120 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPr-klT~e~~~~I~~lv~~ 120 (258)
.+.++||+..|||++||+|.++.. +. ..+++.+++|.+..++
T Consensus 2 ~ti~dIA~~agVS~~TVSrvln~~---------------~~~~vs~~tr~rV~~~a~~ 44 (327)
T PRK10339 2 ATLKDIAIEAGVSLATVSRVLNDD---------------PTLNVKEETKHRILEIAEK 44 (327)
T ss_pred CCHHHHHHHhCCCHHhhhhhhcCC---------------CCCCcCHHHHHHHHHHHHH
Confidence 378999999999999999998542 11 2567777777777664
No 378
>TIGR02850 spore_sigG RNA polymerase sigma-G factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigG. It is also desginated stage III sporulation protein G (SpoIIIG). This protein is rather closely related to sigma-F (SpoIIAC), another sporulation sigma factor.
Probab=91.77 E-value=0.4 Score=43.16 Aligned_cols=42 Identities=14% Similarity=0.130 Sum_probs=34.0
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.++...|.-|...+.+|++.++||+.||||..+|+++.++-.
T Consensus 206 ~L~~rer~vi~~~~~~~~t~~eIA~~lgis~~~V~~~~~ral 247 (254)
T TIGR02850 206 RLNEREKMILNMRFFEGKTQMEVAEEIGISQAQVSRLEKAAL 247 (254)
T ss_pred cCCHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 466666655555556899999999999999999999988864
No 379
>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=91.76 E-value=0.36 Score=34.22 Aligned_cols=36 Identities=17% Similarity=0.147 Sum_probs=29.4
Q ss_pred HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhh
Q psy15598 55 RIVELAQLGIRPCDISRQLRVSHGCVSKILARYHET 90 (258)
Q Consensus 55 RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEt 90 (258)
+++..+.+-.+...+|+.++||.++|++.+++.++.
T Consensus 5 ~~f~~v~~~gs~~~AA~~l~is~~~vs~~i~~LE~~ 40 (60)
T PF00126_consen 5 RYFLAVAETGSISAAAEELGISQSAVSRQIKQLEEE 40 (60)
T ss_dssp HHHHHHHHHSSHHHHHHHCTSSHHHHHHHHHHHHHH
T ss_pred HHHHHHHHhCCHHHHHHHhhccchHHHHHHHHHHHH
Confidence 455555444499999999999999999999999863
No 380
>PRK09526 lacI lac repressor; Reviewed
Probab=91.73 E-value=0.27 Score=44.64 Aligned_cols=23 Identities=30% Similarity=0.411 Sum_probs=21.0
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q psy15598 64 IRPCDISRQLRVSHGCVSKILAR 86 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikR 86 (258)
.+.++||+..|||++||+|.++.
T Consensus 6 ~ti~dIA~~aGVS~~TVSrvLn~ 28 (342)
T PRK09526 6 VTLYDVARYAGVSYQTVSRVLNQ 28 (342)
T ss_pred CcHHHHHHHhCCCHHHHHHHhcC
Confidence 58899999999999999999964
No 381
>PRK10651 transcriptional regulator NarL; Provisional
Probab=91.70 E-value=0.36 Score=39.65 Aligned_cols=40 Identities=23% Similarity=0.294 Sum_probs=35.2
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 48 LPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 48 ~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
++...+ +|+.++.+|++.++||+.|+||..||...+++-+
T Consensus 156 Lt~rE~-~vl~~l~~g~~~~~ia~~l~is~~tV~~~~~~l~ 195 (216)
T PRK10651 156 LTPRER-DILKLIAQGLPNKMIARRLDITESTVKVHVKHML 195 (216)
T ss_pred CCHHHH-HHHHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHH
Confidence 666554 7888889999999999999999999999999876
No 382
>TIGR02392 rpoH_proteo alternative sigma factor RpoH. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors.
Probab=91.66 E-value=0.32 Score=44.31 Aligned_cols=42 Identities=14% Similarity=0.029 Sum_probs=32.4
Q ss_pred CCCHHHHHHHHHHH--HcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELA--QLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~--~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.++...|.-|...+ .+|+|.++||+.||||..+|+++.++-.
T Consensus 218 ~L~~rer~vl~l~y~~~~~~t~~eIA~~lgvS~~~V~q~~~~Al 261 (270)
T TIGR02392 218 SLDARSRRIIEARWLDDDKLTLQELAAEYGVSAERIRQIEKNAM 261 (270)
T ss_pred cCCHHHHHHHHHHhcCCCCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 36666665454445 2489999999999999999998887754
No 383
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=91.64 E-value=0.25 Score=40.87 Aligned_cols=39 Identities=21% Similarity=0.371 Sum_probs=31.8
Q ss_pred HHHHHHHHH-HHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 50 NSVRMRIVE-LAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 50 ~dlR~RIV~-L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
..+|..+.. |.++|+|..+||+.||||++.|+++++-.+
T Consensus 8 PaiRa~lA~~L~eeG~Sq~~iA~LLGltqaAVS~Yls~kr 47 (119)
T COG2522 8 PAIRALLAKELIEEGLSQYRIAKLLGLTQAAVSQYLSGKR 47 (119)
T ss_pred HHHHHHHHHHHHHcCCcHHHHHHHhCCCHHHHHHHHccCC
Confidence 356666554 456899999999999999999999988753
No 384
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=91.61 E-value=0.34 Score=44.07 Aligned_cols=44 Identities=16% Similarity=0.246 Sum_probs=38.9
Q ss_pred HHHHHHHHHHHH-cC-CCHHHHHHHhCCCHHHHHHHHHHhhhhCCc
Q psy15598 50 NSVRMRIVELAQ-LG-IRPCDISRQLRVSHGCVSKILARYHETGSI 93 (258)
Q Consensus 50 ~dlR~RIV~L~~-~G-~S~~eIAr~LGVSrsTVsRwikRyrEtGsl 93 (258)
.+-|.+|+++++ .| ++..++|+.|+||+.||+|=++...+.|.+
T Consensus 4 ~eR~~~Il~~L~~~~~v~v~eLa~~l~VS~~TIRRDL~~Le~~g~l 49 (256)
T PRK10434 4 RQRQAAILEYLQKQGKTSVEELAQYFDTTGTTIRKDLVILEHAGTV 49 (256)
T ss_pred HHHHHHHHHHHHHcCCEEHHHHHHHHCCCHHHHHHHHHHHHHCCCE
Confidence 467788888886 45 799999999999999999999999989866
No 385
>PRK11361 acetoacetate metabolism regulatory protein AtoC; Provisional
Probab=91.60 E-value=0.32 Score=46.66 Aligned_cols=38 Identities=16% Similarity=0.117 Sum_probs=32.7
Q ss_pred HHHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHHh
Q psy15598 50 NSVRMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILARY 87 (258)
Q Consensus 50 ~dlR~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwikRy 87 (258)
...|..|..+++ .|....++|+.||||++|+||.+++|
T Consensus 416 ~~E~~~i~~al~~~~gn~~~aA~~LGisr~tL~rkl~~~ 454 (457)
T PRK11361 416 RVEKRIIMEVLEQQEGNRTRTALMLGISRRALMYKLQEY 454 (457)
T ss_pred HHHHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHh
Confidence 346777777775 47899999999999999999999998
No 386
>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain. This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc.
Probab=91.56 E-value=0.34 Score=43.15 Aligned_cols=42 Identities=10% Similarity=0.057 Sum_probs=34.6
Q ss_pred CCCHHHHHHHHHHH----HcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELA----QLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~----~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.++...|.-|...+ .+|++..+||+.||||..+|+++.++-.
T Consensus 176 ~L~~~er~vl~l~ygl~~~~~~t~~EIA~~lgis~~~V~q~~~~al 221 (238)
T TIGR02393 176 TLTERERKVLRMRYGLLDGRPHTLEEVGKEFNVTRERIRQIESKAL 221 (238)
T ss_pred hCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHH
Confidence 46777776555555 4789999999999999999999988865
No 387
>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=91.56 E-value=0.34 Score=44.37 Aligned_cols=42 Identities=17% Similarity=0.133 Sum_probs=35.3
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE 89 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE 89 (258)
.+|...+ .|+.+..+|++..+||+.|+||..||...+++-.+
T Consensus 190 ~LT~RE~-evl~l~a~G~s~~eIA~~L~IS~~TVk~hl~~i~~ 231 (247)
T TIGR03020 190 LITAREA-EILAWVRDGKTNEEIAAILGISSLTVKNHLQHIFK 231 (247)
T ss_pred CCCHHHH-HHHHHHHCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 5776555 56667789999999999999999999999998763
No 388
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=91.54 E-value=0.75 Score=41.32 Aligned_cols=55 Identities=16% Similarity=0.053 Sum_probs=37.0
Q ss_pred HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh-hCC-cccCCCCCCCCCCCCHHHH
Q psy15598 54 MRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE-TGS-ILPGAIGGSKPRVTTPKVV 111 (258)
Q Consensus 54 ~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE-tGs-l~pk~rgG~RPrklT~e~~ 111 (258)
.+++..+.+-.+.+.+|+.|+||.++|++-+++.++ -|. +-.+ .+ |.-.+|++=+
T Consensus 10 L~~f~~v~~~gs~s~AA~~L~isQ~avS~~i~~LE~~lG~~LF~R--~~-r~~~lT~~G~ 66 (302)
T PRK09791 10 IRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQLFFR--RS-KGVTLTDAGE 66 (302)
T ss_pred HHHHHHHHHcCCHHHHHHHhCCChHHHHHHHHHHHHHhCCeEEEE--cC-CCceECccHH
Confidence 445555444449999999999999999999999986 443 2222 22 4455555433
No 389
>PRK09393 ftrA transcriptional activator FtrA; Provisional
Probab=91.48 E-value=1.2 Score=41.05 Aligned_cols=86 Identities=12% Similarity=0.145 Sum_probs=56.3
Q ss_pred HHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHH-HHHHHHHHHHhCCCCCHHH
Q psy15598 54 MRIVELAQ----LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPK-VVSYIKELKQKDPGIFAWE 128 (258)
Q Consensus 54 ~RIV~L~~----~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e-~~~~I~~lv~~nP~ita~E 128 (258)
.++++.+. +..+..++|+.+|+|.+++.|..+++- |. .|...-.+ -.....+++ .+.+.+..+
T Consensus 221 ~~~~~~i~~~~~~~~sl~~lA~~~~~S~~~l~r~fk~~~--g~---------s~~~~~~~~Rl~~A~~lL-~~~~~~i~~ 288 (322)
T PRK09393 221 GPLIDWMRAHLAEPHTVASLAARAAMSPRTFLRRFEAAT--GM---------TPAEWLLRERLARARDLL-ESSALSIDQ 288 (322)
T ss_pred HHHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHH--Cc---------CHHHHHHHHHHHHHHHHH-HcCCCCHHH
Confidence 34455443 357999999999999999999999974 21 22222111 122222333 345788888
Q ss_pred HHHHHHhcCCCCCCCCCCHHHHHHHHHhccCC
Q psy15598 129 IRDRLLSDGVCDKFNVPSVSSISRILRNKIGS 160 (258)
Q Consensus 129 Ir~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~ 160 (258)
|+..+ |.. +.+...|.+|+.-+.
T Consensus 289 IA~~~---Gf~------~~s~F~r~Fk~~~G~ 311 (322)
T PRK09393 289 IAERA---GFG------SEESLRHHFRRRAAT 311 (322)
T ss_pred HHHHh---CCC------CHHHHHHHHHHHHCc
Confidence 87665 665 889999999876543
No 390
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=91.47 E-value=0.48 Score=42.38 Aligned_cols=49 Identities=20% Similarity=0.232 Sum_probs=37.9
Q ss_pred HHHHHHHH-HHcC--C-CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCC
Q psy15598 52 VRMRIVEL-AQLG--I-RPCDISRQLRVSHGCVSKILARYHETGSILPGAIGG 100 (258)
Q Consensus 52 lR~RIV~L-~~~G--~-S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG 100 (258)
+|.+|+.. +.-| + +-.++|++||||+++|+.-+++....|-|...++.|
T Consensus 18 l~~~I~~g~l~pG~~LpsE~eLa~~~gVSRtpVREAL~~L~~eGlV~~~~~~G 70 (257)
T PRK10225 18 IRDLIIKTPYNPGERLPPEREIAEMLDVTRTVVREALIMLEIKGLVEVRRGAG 70 (257)
T ss_pred HHHHHHhCCCCCCCcCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCCE
Confidence 45555554 2334 4 578999999999999999999999999887666555
No 391
>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=91.46 E-value=1.2 Score=35.08 Aligned_cols=57 Identities=12% Similarity=0.173 Sum_probs=40.8
Q ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCC---CCCHHHHHHHHHHH
Q psy15598 62 LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPR---VTTPKVVSYIKELK 118 (258)
Q Consensus 62 ~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPr---klT~e~~~~I~~lv 118 (258)
.+.+..+||+.++++++||++.+++..+.|-|.-.+....+.. .+|++-...+.++.
T Consensus 42 ~~~t~~eL~~~l~~~~stvs~~i~~Le~kg~I~r~~~~~D~R~~~i~lT~~G~~~~~~~~ 101 (109)
T TIGR01889 42 GKLTLKEIIKEILIKQSALVKIIKKLSKKGYLSKERSEDDERKVIISINKEQRSKIESLI 101 (109)
T ss_pred CcCcHHHHHHHHCCCHHHHHHHHHHHHHCCCEeccCCcccCCeEEEEECHHHHHHHHHHH
Confidence 3599999999999999999999999999997742222221222 26666666555554
No 392
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=91.39 E-value=0.48 Score=35.99 Aligned_cols=67 Identities=24% Similarity=0.319 Sum_probs=46.6
Q ss_pred HHHHHHHHHH--cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCC-CCCCCCC---CCCHHHHHHHHHHH
Q psy15598 52 VRMRIVELAQ--LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGA-IGGSKPR---VTTPKVVSYIKELK 118 (258)
Q Consensus 52 lR~RIV~L~~--~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~-rgG~RPr---klT~e~~~~I~~lv 118 (258)
+|..|+.+.. +.++.++|.+.+|++.+++++-++.-.+.|-|.-.+ ..+++|+ .+|++=++.+.+++
T Consensus 1 vRl~Il~~L~~~~~~~f~~L~~~l~lt~g~Ls~hL~~Le~~GyV~~~k~~~~~~p~t~~~lT~~Gr~~~~~~~ 73 (80)
T PF13601_consen 1 VRLAILALLYANEEATFSELKEELGLTDGNLSKHLKKLEEAGYVEVEKEFEGRRPRTWYSLTDKGREAFERYV 73 (80)
T ss_dssp HHHHHHHHHHHHSEEEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEEEE-SSS--EEEEEE-HHHHHHHHHHH
T ss_pred CHHHHHHHHhhcCCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEEEeccCCCCeEEEEECHHHHHHHHHHH
Confidence 4777877754 568999999999999999999999999999875333 2333665 47777666666654
No 393
>PRK13502 transcriptional activator RhaR; Provisional
Probab=91.38 E-value=1.5 Score=39.34 Aligned_cols=88 Identities=10% Similarity=0.073 Sum_probs=58.5
Q ss_pred HHHHHHHHH----HcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCC-CCCHHHHHHHHHHHHhCCCCCH
Q psy15598 52 VRMRIVELA----QLGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPR-VTTPKVVSYIKELKQKDPGIFA 126 (258)
Q Consensus 52 lR~RIV~L~----~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPr-klT~e~~~~I~~lv~~nP~ita 126 (258)
.-.+++.++ .+..+..++|+.+|+|.+.++|..+++- |. .+. -+...-...-++++ .+.+.+.
T Consensus 177 ~~~~~~~~I~~~~~~~~~~~~lA~~~~iS~~~L~r~fk~~~--G~---------t~~~yi~~~Rl~~A~~lL-~~t~~sI 244 (282)
T PRK13502 177 LLDKLITALANSLECPFALDAFCQQEQCSERVLRQQFRAQT--GM---------TINQYLRQVRICHAQYLL-QHSPLMI 244 (282)
T ss_pred HHHHHHHHHHhcccCCCCHHHHHHHHCcCHHHHHHHHHHHH--Cc---------CHHHHHHHHHHHHHHHHH-HcCCCCH
Confidence 335666664 3467999999999999999999999973 21 111 11111122223333 3457788
Q ss_pred HHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCC
Q psy15598 127 WEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGS 160 (258)
Q Consensus 127 ~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~ 160 (258)
.||+..+ |.. +.+...|+.|+.-+.
T Consensus 245 ~eIA~~~---GF~------d~s~F~r~FKk~~G~ 269 (282)
T PRK13502 245 SEISMQC---GFE------DSNYFSVVFTRETGM 269 (282)
T ss_pred HHHHHHc---CCC------CHHHHHHHHHHHHCc
Confidence 8887766 775 889999999987654
No 394
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=91.36 E-value=0.33 Score=44.39 Aligned_cols=40 Identities=18% Similarity=0.247 Sum_probs=30.5
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHh
Q psy15598 65 RPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQK 120 (258)
Q Consensus 65 S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~ 120 (258)
+.++||+..|||.+||+|.++. +++ .+++.+++|.+..++
T Consensus 3 ti~dIA~~aGVS~~TVSrvLn~---------------~~~-Vs~~tr~rV~~~a~e 42 (343)
T PRK10727 3 TIKDVARLAGVSVATVSRVINN---------------SPK-ASEASRLAVHSAMES 42 (343)
T ss_pred CHHHHHHHhCCCHHHHHHHhCC---------------CCC-CCHHHHHHHHHHHHH
Confidence 7899999999999999999953 112 566777777766654
No 395
>PRK13501 transcriptional activator RhaR; Provisional
Probab=91.33 E-value=1.8 Score=39.13 Aligned_cols=78 Identities=12% Similarity=0.092 Sum_probs=53.3
Q ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCC-CCHHHHHHHHHHHHhCCCCCHHHHHHHHHhcCCCC
Q psy15598 62 LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRV-TTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCD 140 (258)
Q Consensus 62 ~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrk-lT~e~~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v 140 (258)
+-.+..++|+.+++|+++++|..+++- |. .+.. +.......-.++ ..+.+.+..||+..+ |..
T Consensus 191 e~~sl~~lA~~~~lS~~~l~r~Fk~~~--G~---------T~~qyi~~~Ri~~A~~L-L~~t~~sI~eIA~~~---GF~- 254 (290)
T PRK13501 191 AYFDMADFCHKNQLVERSLKQLFRQQT--GM---------SISHYLRQIRLCHAKCL-LRGSEHRISDIAARC---GFE- 254 (290)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHH--Cc---------CHHHHHHHHHHHHHHHH-HHcCCCCHHHHHHHh---CCC-
Confidence 568999999999999999999999863 21 1111 111111122222 255678888887777 665
Q ss_pred CCCCCCHHHHHHHHHhccCC
Q psy15598 141 KFNVPSVSSISRILRNKIGS 160 (258)
Q Consensus 141 ~~~~pS~STI~RiLrr~~~~ 160 (258)
+.+.-.|+.|+..+.
T Consensus 255 -----~~s~F~r~FKk~~G~ 269 (290)
T PRK13501 255 -----DSNYFSAVFTREAGM 269 (290)
T ss_pred -----CHHHHHHHHHHHHCc
Confidence 888999999887664
No 396
>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=91.32 E-value=0.35 Score=43.27 Aligned_cols=41 Identities=12% Similarity=0.235 Sum_probs=35.9
Q ss_pred HHHHHHHH---cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598 54 MRIVELAQ---LGIRPCDISRQLRVSHGCVSKILARYHETGSIL 94 (258)
Q Consensus 54 ~RIV~L~~---~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~ 94 (258)
.+|++++. .+++.+|||+.+|++++||+|+++-..+.|-+.
T Consensus 12 l~IL~~l~~~~~~~~l~eia~~lglpksT~~RlL~tL~~~G~l~ 55 (248)
T TIGR02431 12 LAVIEAFGAERPRLTLTDVAEATGLTRAAARRFLLTLVELGYVT 55 (248)
T ss_pred HHHHHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 46777764 368999999999999999999999999999875
No 397
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=91.28 E-value=0.35 Score=44.25 Aligned_cols=41 Identities=22% Similarity=0.262 Sum_probs=29.7
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHh
Q psy15598 64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQK 120 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~ 120 (258)
.+.++||+..|||++||+|.++.. + ..+++.+++|.+..++
T Consensus 2 ~ti~dIA~~aGVS~~TVSrvLn~~---------------~-~Vs~~tr~kV~~~a~e 42 (346)
T PRK10401 2 ITIRDVARQAGVSVATVSRVLNNS---------------A-LVSADTREAVMKAVSE 42 (346)
T ss_pred CCHHHHHHHhCCCHHHHHHHHCCC---------------C-CCCHHHHHHHHHHHHH
Confidence 478999999999999999999641 1 1455666666666544
No 398
>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=91.23 E-value=0.27 Score=41.14 Aligned_cols=32 Identities=9% Similarity=0.164 Sum_probs=29.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHhhhhCCccc
Q psy15598 64 IRPCDISRQLRVSHGCVSKILARYHETGSILP 95 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~p 95 (258)
++..+||..+|+++.||+|.++++++.|-+.-
T Consensus 144 ~t~~~iA~~lG~tretvsR~l~~l~~~g~I~~ 175 (193)
T TIGR03697 144 LSHQAIAEAIGSTRVTITRLLGDLRKKKLISI 175 (193)
T ss_pred CCHHHHHHHhCCcHHHHHHHHHHHHHCCCEEe
Confidence 58999999999999999999999999998743
No 399
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=91.23 E-value=0.45 Score=43.79 Aligned_cols=42 Identities=21% Similarity=0.309 Sum_probs=34.2
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.++.-.|.-+...+.++++.++||+.||||.+.|+++.++..
T Consensus 196 ~L~EREk~Vl~l~y~eelt~kEI~~~LgISes~VSql~kkai 237 (247)
T COG1191 196 PLPEREKLVLVLRYKEELTQKEIAEVLGISESRVSRLHKKAI 237 (247)
T ss_pred ccCHHHHHHHHHHHHhccCHHHHHHHhCccHHHHHHHHHHHH
Confidence 455555555555567899999999999999999999999875
No 400
>PRK15320 transcriptional activator SprB; Provisional
Probab=91.20 E-value=0.43 Score=43.35 Aligned_cols=43 Identities=9% Similarity=0.104 Sum_probs=35.9
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHET 90 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEt 90 (258)
.+|.-.+ .|+.+..+|++.++||+.|++|.+||++..+|-.+.
T Consensus 164 ~LSdREI-EVL~LLAkG~SNKEIAekL~LS~KTVSTYKnRLLeK 206 (251)
T PRK15320 164 GVTQAKY-ALLILLSSGHPAIELAKKFGLGTKTVSIYRKKVMYR 206 (251)
T ss_pred CCCHHHH-HHHHHHHcCCCHHHHHHHhccchhhHHHHHHHHHHH
Confidence 3554443 677788899999999999999999999999998754
No 401
>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=91.18 E-value=0.37 Score=33.98 Aligned_cols=31 Identities=29% Similarity=0.448 Sum_probs=22.5
Q ss_pred HHHHH-HcCCCHHHHHHHhCCCHHHHHHHHHH
Q psy15598 56 IVELA-QLGIRPCDISRQLRVSHGCVSKILAR 86 (258)
Q Consensus 56 IV~L~-~~G~S~~eIAr~LGVSrsTVsRwikR 86 (258)
|-.+. +.|++..++|+.+|++++++++|.+-
T Consensus 4 lk~~r~~~~lt~~~~a~~~~i~~~~i~~~e~g 35 (64)
T PF12844_consen 4 LKELREEKGLTQKDLAEKLGISRSTISKIENG 35 (64)
T ss_dssp HHHHHHHCT--HHHHHHHHTS-HHHHHHHHTT
T ss_pred HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCC
Confidence 44444 36999999999999999999999754
No 402
>PRK10371 DNA-binding transcriptional regulator MelR; Provisional
Probab=91.15 E-value=1.7 Score=40.23 Aligned_cols=78 Identities=13% Similarity=0.163 Sum_probs=51.6
Q ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHH-HHHHHHHHHhCCCCCHHHHHHHHHhcCCCC
Q psy15598 62 LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKV-VSYIKELKQKDPGIFAWEIRDRLLSDGVCD 140 (258)
Q Consensus 62 ~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~-~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v 140 (258)
+..+..+||+.+|+|++++.|..++. +|. .+....... .....+++ .+++.+..||+..+ |..
T Consensus 206 ~~~tl~~lA~~~~~S~~~l~r~Fk~~--~G~---------t~~~~l~~~Rl~~A~~lL-~~~~~si~eIA~~~---Gf~- 269 (302)
T PRK10371 206 QALTINDVAEHVKLNANYAMGIFQRV--MQL---------TMKQYITAMRINHVRALL-SDTDKSILDIALTA---GFR- 269 (302)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHH--hCC---------CHHHHHHHHHHHHHHHHH-hcCCCCHHHHHHHc---CCC-
Confidence 46899999999999999999999996 332 111111111 12222222 34577887876655 665
Q ss_pred CCCCCCHHHHHHHHHhccCC
Q psy15598 141 KFNVPSVSSISRILRNKIGS 160 (258)
Q Consensus 141 ~~~~pS~STI~RiLrr~~~~ 160 (258)
+.+...|..++.-+.
T Consensus 270 -----~~s~F~r~Fk~~~G~ 284 (302)
T PRK10371 270 -----SSSRFYSTFGKYVGM 284 (302)
T ss_pred -----CHHHHHHHHHHHHCc
Confidence 888999999877553
No 403
>PRK03837 transcriptional regulator NanR; Provisional
Probab=91.10 E-value=0.31 Score=42.86 Aligned_cols=36 Identities=11% Similarity=0.066 Sum_probs=31.9
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCC
Q psy15598 65 RPCDISRQLRVSHGCVSKILARYHETGSILPGAIGG 100 (258)
Q Consensus 65 S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG 100 (258)
+..++|++||||+++|+.-+++....|-|...++.|
T Consensus 39 ~E~~Lae~~gVSRt~VREAL~~L~~eGlv~~~~~~G 74 (241)
T PRK03837 39 SERELMAFFGVGRPAVREALQALKRKGLVQISHGER 74 (241)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCCc
Confidence 789999999999999999999999999886655444
No 404
>PF05263 DUF722: Protein of unknown function (DUF722); InterPro: IPR007927 This entry is represented by Bacteriophage bIL285, Orf38. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=91.04 E-value=0.48 Score=39.74 Aligned_cols=42 Identities=19% Similarity=0.271 Sum_probs=33.0
Q ss_pred CCHHHHHHHHHHH-H--cCCCHHHHHHHhCCCHHHHHHHHHHhhhh
Q psy15598 48 LPNSVRMRIVELA-Q--LGIRPCDISRQLRVSHGCVSKILARYHET 90 (258)
Q Consensus 48 ~S~dlR~RIV~L~-~--~G~S~~eIAr~LGVSrsTVsRwikRyrEt 90 (258)
+..+. .+||.+. . .|++--+||..|+||.+|+++|...|+++
T Consensus 82 l~de~-k~Ii~lry~~r~~~TW~~IA~~l~i~erta~r~~~~fK~~ 126 (130)
T PF05263_consen 82 LIDEE-KRIIKLRYDRRSRRTWYQIAQKLHISERTARRWRDRFKND 126 (130)
T ss_pred hCHHH-HHHHHHHHcccccchHHHHHHHhCccHHHHHHHHHHHHHH
Confidence 44443 4555654 3 46999999999999999999999999864
No 405
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=91.03 E-value=0.69 Score=41.87 Aligned_cols=36 Identities=25% Similarity=0.333 Sum_probs=30.9
Q ss_pred HHH-HHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhh
Q psy15598 55 RIV-ELAQLGIRPCDISRQLRVSHGCVSKILARYHET 90 (258)
Q Consensus 55 RIV-~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEt 90 (258)
+++ .+++.|.+.+++|+.|+||.++|++.+++.++.
T Consensus 7 ~~F~~v~~~~~s~s~AA~~L~isq~avSr~I~~LE~~ 43 (309)
T PRK12682 7 RFVREAVRRNLNLTEAAKALHTSQPGVSKAIIELEEE 43 (309)
T ss_pred HHHHHHHHccCCHHHHHHHhcCccHHHHHHHHHHHHH
Confidence 444 456678999999999999999999999999864
No 406
>PRK09462 fur ferric uptake regulator; Provisional
Probab=90.99 E-value=0.77 Score=38.23 Aligned_cols=52 Identities=23% Similarity=0.191 Sum_probs=39.5
Q ss_pred CCHHHHHHHHHHHHhC--CCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCCCCC
Q psy15598 106 TTPKVVSYIKELKQKD--PGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSSIV 163 (258)
Q Consensus 106 lT~e~~~~I~~lv~~n--P~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~~~~ 163 (258)
+|+. +..|.+.+.+. -.+++.||.+.|.+.+..+ |.+||+|.|..+....+-
T Consensus 15 ~T~q-R~~Il~~l~~~~~~h~sa~eI~~~l~~~~~~i-----~~aTVYR~L~~L~e~Gli 68 (148)
T PRK09462 15 VTLP-RLKILEVLQEPDNHHVSAEDLYKRLIDMGEEI-----GLATVYRVLNQFDDAGIV 68 (148)
T ss_pred CCHH-HHHHHHHHHhCCCCCCCHHHHHHHHHhhCCCC-----CHHHHHHHHHHHHHCCCE
Confidence 5554 55666666543 3789999999999888765 999999999987766553
No 407
>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=90.98 E-value=0.39 Score=43.42 Aligned_cols=43 Identities=16% Similarity=0.156 Sum_probs=31.2
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHh
Q psy15598 65 RPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQK 120 (258)
Q Consensus 65 S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~ 120 (258)
+.++||+..|||.+||+|.++.-. .....+++.+++|.+..++
T Consensus 1 ti~dIA~~aGVS~~TVSrvLn~~~-------------~~~~vs~~tr~rV~~~a~~ 43 (327)
T TIGR02417 1 TLSDIAKLAGVSKTTASYVINGKA-------------KEYRISQETVERVMAVVRE 43 (327)
T ss_pred CHHHHHHHhCCCHHHHHHHHcCCC-------------CCCccCHHHHHHHHHHHHH
Confidence 468999999999999999996310 0013567777777777665
No 408
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=90.93 E-value=0.29 Score=43.68 Aligned_cols=50 Identities=22% Similarity=0.379 Sum_probs=39.2
Q ss_pred HHHHHHHHH-HHcC--C-CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCC
Q psy15598 51 SVRMRIVEL-AQLG--I-RPCDISRQLRVSHGCVSKILARYHETGSILPGAIGG 100 (258)
Q Consensus 51 dlR~RIV~L-~~~G--~-S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG 100 (258)
.+|..|+.. +.-| + +-.++|++||||+++|+--+++....|-|...+++|
T Consensus 18 ~l~~~I~~g~l~pG~~LpsE~eLa~~lgVSRtpVREAL~~L~~eGlv~~~~~~G 71 (254)
T PRK09464 18 QLEFLILEGTLRPGEKLPPERELAKQFDVSRPSLREAIQRLEAKGLLLRRQGGG 71 (254)
T ss_pred HHHHHHHcCCCCCCCcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCce
Confidence 455666554 2345 3 678999999999999999999999999887666555
No 409
>COG2186 FadR Transcriptional regulators [Transcription]
Probab=90.84 E-value=0.77 Score=41.43 Aligned_cols=56 Identities=23% Similarity=0.261 Sum_probs=47.0
Q ss_pred CCCCCHHHHHHHHHHHHcCC--------CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCC
Q psy15598 45 GRPLPNSVRMRIVELAQLGI--------RPCDISRQLRVSHGCVSKILARYHETGSILPGAIGG 100 (258)
Q Consensus 45 gR~~S~dlR~RIV~L~~~G~--------S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG 100 (258)
.+.++.++=.+|.+++.+|. +-+++|++|||||++|+--++.....|.|+.+...|
T Consensus 8 ~~~l~~~v~~~i~~~I~~g~~~~G~~LP~EreLae~fgVSR~~vREAl~~L~a~Glve~r~G~G 71 (241)
T COG2186 8 RRRLADEVAEQIGALIVSGELPPGDRLPSERELAERFGVSRTVVREALKRLEAKGLVEIRQGSG 71 (241)
T ss_pred CCChHHHHHHHHHHHHHcCCCCCCCCCCCHHHHHHHHCCCcHHHHHHHHHHHHCCCeeecCCCc
Confidence 34477888788888877653 689999999999999999999999999998877655
No 410
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=90.84 E-value=0.47 Score=38.85 Aligned_cols=36 Identities=19% Similarity=0.224 Sum_probs=29.3
Q ss_pred HHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHHh
Q psy15598 52 VRMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILARY 87 (258)
Q Consensus 52 lR~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwikRy 87 (258)
+-.+|..+.+ .|++..++|+.+|||++||++|.+.-
T Consensus 6 ~g~rlk~~R~~~gltq~~lA~~~gvs~~~is~~E~g~ 42 (135)
T PRK09706 6 LGQRIRYRRKQLKLSQRSLAKAVKVSHVSISQWERDE 42 (135)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCC
Confidence 4455666654 69999999999999999999997653
No 411
>PRK15481 transcriptional regulatory protein PtsJ; Provisional
Probab=90.81 E-value=0.54 Score=45.00 Aligned_cols=36 Identities=17% Similarity=0.221 Sum_probs=31.1
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCC
Q psy15598 65 RPCDISRQLRVSHGCVSKILARYHETGSILPGAIGG 100 (258)
Q Consensus 65 S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG 100 (258)
+.+++|++|+||++||.+-+.+-.+.|-+...++.|
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 789999999999999999999999999775554444
No 412
>TIGR02915 PEP_resp_reg putative PEP-CTERM system response regulator. Members of this protein family share full-length homology with (but do not include) the acetoacetate metabolism regulatory protein AtoC. These proteins have a Fis family DNA binding sequence (pfam02954), a response regulator receiver domain (pfam00072), and sigma-54 interaction domain (pfam00158).
Probab=90.79 E-value=0.41 Score=45.88 Aligned_cols=38 Identities=5% Similarity=0.060 Sum_probs=31.7
Q ss_pred HHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 51 SVRMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 51 dlR~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
..|..|...++ .+....++|+.|||||+|+||-+++|.
T Consensus 405 ~E~~~i~~al~~~~gn~~~aA~~Lgisr~tl~rkl~~~~ 443 (445)
T TIGR02915 405 AEREAVRKAIARVDGNIARAAELLGITRPTLYDLMKKHG 443 (445)
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHHhC
Confidence 35666777665 578899999999999999999999983
No 413
>PF13551 HTH_29: Winged helix-turn helix
Probab=90.78 E-value=0.83 Score=34.97 Aligned_cols=40 Identities=28% Similarity=0.400 Sum_probs=34.1
Q ss_pred CCHHHHHHHHHHHHc----C---CCHHHHHHHh-------CCCHHHHHHHHHHh
Q psy15598 48 LPNSVRMRIVELAQL----G---IRPCDISRQL-------RVSHGCVSKILARY 87 (258)
Q Consensus 48 ~S~dlR~RIV~L~~~----G---~S~~eIAr~L-------GVSrsTVsRwikRy 87 (258)
++.+.+..|++++.+ | ++..+|+..| .+|.+||++|+++.
T Consensus 58 l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~~~ 111 (112)
T PF13551_consen 58 LSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRILKRA 111 (112)
T ss_pred CCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHHHHHHHHHHC
Confidence 899999999999875 2 6788998865 69999999999873
No 414
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=90.71 E-value=0.33 Score=44.07 Aligned_cols=41 Identities=15% Similarity=0.090 Sum_probs=29.9
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHh
Q psy15598 64 IRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQK 120 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~ 120 (258)
.+.++||+..|||++||+|.++.. + ..+++.+++|.+..++
T Consensus 6 ~ti~dIA~~agVS~~TVSrvLn~~---------------~-~vs~~tr~rV~~~a~e 46 (331)
T PRK14987 6 PVLQDVADRVGVTKMTVSRFLRNP---------------E-QVSVALRGKIAAALDE 46 (331)
T ss_pred CcHHHHHHHhCCCHHHhhhhhCCC---------------C-CCCHHHHHHHHHHHHH
Confidence 588999999999999999998531 1 2455666666655544
No 415
>PRK00215 LexA repressor; Validated
Probab=90.71 E-value=0.71 Score=40.11 Aligned_cols=33 Identities=21% Similarity=0.195 Sum_probs=29.9
Q ss_pred CCHHHHHHHhCC-CHHHHHHHHHHhhhhCCcccC
Q psy15598 64 IRPCDISRQLRV-SHGCVSKILARYHETGSILPG 96 (258)
Q Consensus 64 ~S~~eIAr~LGV-SrsTVsRwikRyrEtGsl~pk 96 (258)
.+.++||+.+|+ +++||++++++..+.|-+...
T Consensus 24 ~s~~ela~~~~~~~~~tv~~~l~~L~~~g~i~~~ 57 (205)
T PRK00215 24 PSRREIADALGLRSPSAVHEHLKALERKGFIRRD 57 (205)
T ss_pred CCHHHHHHHhCCCChHHHHHHHHHHHHCCCEEeC
Confidence 589999999999 999999999999999987543
No 416
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=90.63 E-value=0.64 Score=39.95 Aligned_cols=53 Identities=21% Similarity=0.231 Sum_probs=39.2
Q ss_pred CCHHHHHHHHHHHHhCC-CCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCCCCCC
Q psy15598 106 TTPKVVSYIKELKQKDP-GIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSSIVQ 164 (258)
Q Consensus 106 lT~e~~~~I~~lv~~nP-~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~~~~~ 164 (258)
.|+. +..|.+++.... .+++.+|.+.|.+.+..+ |.+||+|.|..+....+-.
T Consensus 24 ~T~q-R~~IL~~l~~~~~hlSa~eI~~~L~~~~~~i-----s~aTVYRtL~~L~e~Glv~ 77 (169)
T PRK11639 24 LTPQ-RLEVLRLMSLQPGAISAYDLLDLLREAEPQA-----KPPTVYRALDFLLEQGFVH 77 (169)
T ss_pred CCHH-HHHHHHHHHhcCCCCCHHHHHHHHHhhCCCC-----CcchHHHHHHHHHHCCCEE
Confidence 4444 455556655443 689999999999888765 9999999999877665533
No 417
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=90.57 E-value=1 Score=36.76 Aligned_cols=55 Identities=15% Similarity=0.215 Sum_probs=39.9
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCC-C--CCCCCHHHHHHHHHH
Q psy15598 63 GIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGS-K--PRVTTPKVVSYIKEL 117 (258)
Q Consensus 63 G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~-R--PrklT~e~~~~I~~l 117 (258)
|.+.++||+.++++++||.+.+++..+.|-|.-.+.... | --.+|++=++.+.++
T Consensus 46 ~~t~~eLa~~l~~~~~tvt~~v~~Le~~GlV~r~~~~~DrR~~~l~LT~~G~~~~~~~ 103 (144)
T PRK03573 46 EQSQIQLAKAIGIEQPSLVRTLDQLEEKGLISRQTCASDRRAKRIKLTEKAEPLISEV 103 (144)
T ss_pred CCCHHHHHHHhCCChhhHHHHHHHHHHCCCEeeecCCCCcCeeeeEEChHHHHHHHHH
Confidence 589999999999999999999999999998743322111 2 234666655555444
No 418
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=90.50 E-value=0.48 Score=35.67 Aligned_cols=32 Identities=22% Similarity=0.368 Sum_probs=26.4
Q ss_pred HHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598 54 MRIVELA-QLGIRPCDISRQLRVSHGCVSKILA 85 (258)
Q Consensus 54 ~RIV~L~-~~G~S~~eIAr~LGVSrsTVsRwik 85 (258)
.++..+. +.|++..+.|+.+|||+.||..|-+
T Consensus 4 nk~k~~R~~~~ltQ~elA~~vgVsRQTi~~iEk 36 (68)
T COG1476 4 NKLKELRAELGLTQEELAKLVGVSRQTIIAIEK 36 (68)
T ss_pred hHHHHHHHHhCcCHHHHHHHcCcCHHHHHHHHc
Confidence 4566665 4799999999999999999988744
No 419
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=90.46 E-value=0.55 Score=42.88 Aligned_cols=44 Identities=14% Similarity=0.147 Sum_probs=37.3
Q ss_pred HHHHHHHHHHH---cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598 51 SVRMRIVELAQ---LGIRPCDISRQLRVSHGCVSKILARYHETGSIL 94 (258)
Q Consensus 51 dlR~RIV~L~~---~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~ 94 (258)
+.=.+|++++. .+++.+|||+.+|++++||+|+++-..+.|-+.
T Consensus 25 ~r~l~IL~~~~~~~~~~tl~eIa~~lglpkStv~RlL~tL~~~G~l~ 71 (271)
T PRK10163 25 ERGIAILQYLEKSGGSSSVSDISLNLDLPLSTTFRLLKVLQAADFVY 71 (271)
T ss_pred HHHHHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 33456777774 358999999999999999999999999999874
No 420
>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=90.45 E-value=0.63 Score=41.54 Aligned_cols=41 Identities=27% Similarity=0.348 Sum_probs=34.3
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.++...| .|+.+..+|++..+||+.|+||.+||...+++-+
T Consensus 171 ~Lt~re~-evl~~~a~G~t~~eIa~~l~is~~Tv~~~l~~~~ 211 (232)
T TIGR03541 171 VLSERER-EVLAWTALGRRQADIAAILGISERTVENHLRSAR 211 (232)
T ss_pred cCCHHHH-HHHHHHHCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 4666555 4566678999999999999999999999999875
No 421
>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family. This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393).
Probab=90.44 E-value=0.54 Score=43.51 Aligned_cols=42 Identities=21% Similarity=0.139 Sum_probs=34.4
Q ss_pred CCCHHHHHHHHHHH----HcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELA----QLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~----~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.++...|.-|...+ .+++|..+||+.||||+.+|+.+.++-.
T Consensus 249 ~L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVrq~~~rAl 294 (298)
T TIGR02997 249 ELTPRERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKAL 294 (298)
T ss_pred cCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 37777776555555 4789999999999999999999998865
No 422
>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=90.43 E-value=0.48 Score=30.28 Aligned_cols=25 Identities=24% Similarity=0.429 Sum_probs=22.6
Q ss_pred HcCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598 61 QLGIRPCDISRQLRVSHGCVSKILA 85 (258)
Q Consensus 61 ~~G~S~~eIAr~LGVSrsTVsRwik 85 (258)
..|++..++|+.++++..+|++|.+
T Consensus 10 ~~~~s~~~~a~~~~~~~~~v~~~~~ 34 (58)
T cd00093 10 EKGLTQEELAEKLGVSRSTISRIEN 34 (58)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHc
Confidence 4699999999999999999999854
No 423
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=90.41 E-value=0.57 Score=42.19 Aligned_cols=41 Identities=17% Similarity=0.255 Sum_probs=35.6
Q ss_pred HHHHHHHH--cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598 54 MRIVELAQ--LGIRPCDISRQLRVSHGCVSKILARYHETGSIL 94 (258)
Q Consensus 54 ~RIV~L~~--~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~ 94 (258)
.+|++++. .+++.++||+.+|++++||+|+++...+.|-+.
T Consensus 17 l~IL~~l~~~~~l~l~eia~~lgl~kstv~Rll~tL~~~G~l~ 59 (257)
T PRK15090 17 FGILQALGEEREIGITELSQRVMMSKSTVYRFLQTMKTLGYVA 59 (257)
T ss_pred HHHHHHhhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 56777664 358999999999999999999999999999874
No 424
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=90.33 E-value=0.94 Score=40.28 Aligned_cols=36 Identities=17% Similarity=0.154 Sum_probs=32.1
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCC
Q psy15598 65 RPCDISRQLRVSHGCVSKILARYHETGSILPGAIGG 100 (258)
Q Consensus 65 S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG 100 (258)
+-.++|++|||||++|+--+++....|-|...++.|
T Consensus 33 sE~eLa~~~gVSRtpVREAL~~L~~eGlV~~~~~~G 68 (251)
T PRK09990 33 SERRLCEKLGFSRSALREGLTVLRGRGIIETAQGRG 68 (251)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCCCe
Confidence 678999999999999999999999999887666555
No 425
>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=90.26 E-value=1.1 Score=34.53 Aligned_cols=43 Identities=14% Similarity=0.222 Sum_probs=32.8
Q ss_pred CCCHHHHHHHHHHHH-cCCCHHHHHHHhC-CCHHHHHHHHHHhhh
Q psy15598 47 PLPNSVRMRIVELAQ-LGIRPCDISRQLR-VSHGCVSKILARYHE 89 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~-~G~S~~eIAr~LG-VSrsTVsRwikRyrE 89 (258)
.++..-...+..+.+ -|+|..+|++.|| .+++||..-+++.++
T Consensus 27 ~~~~aR~ia~yl~~~~~~~s~~~Ig~~fg~r~hStV~~a~~ri~~ 71 (90)
T cd06571 27 EIALARQIAMYLARELTGLSLPEIGRAFGGRDHSTVLHAVRKIEE 71 (90)
T ss_pred CcchHHHHHHHHHHHHhCCCHHHHHHHhCCCCHhHHHHHHHHHHH
Confidence 455544444444444 4999999999999 999999999999864
No 426
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=90.24 E-value=0.47 Score=30.09 Aligned_cols=25 Identities=24% Similarity=0.412 Sum_probs=22.5
Q ss_pred HcCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598 61 QLGIRPCDISRQLRVSHGCVSKILA 85 (258)
Q Consensus 61 ~~G~S~~eIAr~LGVSrsTVsRwik 85 (258)
..+++..++|+.+||+..+|++|.+
T Consensus 8 ~~~~s~~~la~~~~i~~~~i~~~~~ 32 (56)
T smart00530 8 EKGLTQEELAEKLGVSRSTLSRIEN 32 (56)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHC
Confidence 4689999999999999999998864
No 427
>PRK09978 DNA-binding transcriptional regulator GadX; Provisional
Probab=90.22 E-value=2.9 Score=39.01 Aligned_cols=90 Identities=18% Similarity=0.118 Sum_probs=58.9
Q ss_pred CHHHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHH-HHHHHHHHHHhCCC
Q psy15598 49 PNSVRMRIVELAQ----LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPK-VVSYIKELKQKDPG 123 (258)
Q Consensus 49 S~dlR~RIV~L~~----~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e-~~~~I~~lv~~nP~ 123 (258)
..+...+++..++ +.++..++|+.+|+|++++.|..++. |. .+.....+ -...-.+++ .+.+
T Consensus 140 ~~~~~~~v~~yI~~~~~~~lsl~~lA~~~g~S~~~L~R~Fk~~---G~---------S~~~yl~~~Rl~~A~~LL-~~t~ 206 (274)
T PRK09978 140 QPNMRTRVCTVINNNIAHEWTLARIASELLMSPSLLKKKLREE---ET---------SYSQLLTECRMQRALQLI-VIHG 206 (274)
T ss_pred CHHHHHHHHHHHHhcccCCCCHHHHHHHHCcCHHHHHHHHHhc---CC---------CHHHHHHHHHHHHHHHHH-HcCC
Confidence 3455567777764 35799999999999999999988752 32 11111111 122222233 3456
Q ss_pred CCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCC
Q psy15598 124 IFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGS 160 (258)
Q Consensus 124 ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~ 160 (258)
.+..+|+..+ |.. +.+...|.+++.-+.
T Consensus 207 ~sI~eIA~~~---GF~------s~S~Fsr~FKk~~G~ 234 (274)
T PRK09978 207 FSIKRVAVSC---GYH------SVSYFIYVFRNYYGM 234 (274)
T ss_pred CCHHHHHHHh---CCC------CHHHHHHHHHHHHCc
Confidence 7888887666 675 889999999987665
No 428
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=90.16 E-value=0.61 Score=33.18 Aligned_cols=24 Identities=29% Similarity=0.458 Sum_probs=19.9
Q ss_pred cCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598 62 LGIRPCDISRQLRVSHGCVSKILA 85 (258)
Q Consensus 62 ~G~S~~eIAr~LGVSrsTVsRwik 85 (258)
.|+|..++|+.+|+|.++|++|.+
T Consensus 13 ~gls~~~lA~~~g~s~s~v~~iE~ 36 (64)
T PF13560_consen 13 AGLSQAQLADRLGVSQSTVSRIER 36 (64)
T ss_dssp HTS-HHHHHHHHTS-HHHHHHHHT
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHC
Confidence 599999999999999999988854
No 429
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=90.13 E-value=0.54 Score=33.22 Aligned_cols=32 Identities=25% Similarity=0.466 Sum_probs=27.5
Q ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCc
Q psy15598 62 LGIRPCDISRQLRVSHGCVSKILARYHETGSI 93 (258)
Q Consensus 62 ~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl 93 (258)
..++..+||+.+++++++|++.+++..+-|-|
T Consensus 17 ~~~t~~~l~~~~~~~~~~vs~~i~~L~~~glv 48 (68)
T PF13463_consen 17 GPMTQSDLAERLGISKSTVSRIIKKLEEKGLV 48 (68)
T ss_dssp S-BEHHHHHHHTT--HHHHHHHHHHHHHTTSE
T ss_pred CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCE
Confidence 45899999999999999999999999999987
No 430
>PRK12423 LexA repressor; Provisional
Probab=90.03 E-value=0.93 Score=39.76 Aligned_cols=48 Identities=21% Similarity=0.248 Sum_probs=37.2
Q ss_pred CCHHHHHHHHHHHH-----cCC--CHHHHHHHhC-CCHHHHHHHHHHhhhhCCcccC
Q psy15598 48 LPNSVRMRIVELAQ-----LGI--RPCDISRQLR-VSHGCVSKILARYHETGSILPG 96 (258)
Q Consensus 48 ~S~dlR~RIV~L~~-----~G~--S~~eIAr~LG-VSrsTVsRwikRyrEtGsl~pk 96 (258)
++ ..|.+|++.+. .|. |.++||+.|| +|+++|++.+++..+.|.+...
T Consensus 4 lt-~~q~~il~~l~~~i~~~g~~Ps~~eia~~~g~~s~~~v~~~l~~L~~~G~l~~~ 59 (202)
T PRK12423 4 LT-PKRAAILAFIRERIAQAGQPPSLAEIAQAFGFASRSVARKHVQALAEAGLIEVV 59 (202)
T ss_pred CC-HHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCCCEEec
Confidence 44 44556666543 344 9999999999 5999999999999999987543
No 431
>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=90.00 E-value=1.1 Score=36.20 Aligned_cols=33 Identities=24% Similarity=0.296 Sum_probs=30.3
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCccc
Q psy15598 63 GIRPCDISRQLRVSHGCVSKILARYHETGSILP 95 (258)
Q Consensus 63 G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~p 95 (258)
.++..+||+.+++|+++|++.+++.++.|-+..
T Consensus 25 ~~s~~eia~~l~is~~~v~~~l~~L~~~Gli~~ 57 (130)
T TIGR02944 25 PYSAAEIAEQTGLNAPTVSKILKQLSLAGIVTS 57 (130)
T ss_pred CccHHHHHHHHCcCHHHHHHHHHHHHHCCcEEe
Confidence 379999999999999999999999999998743
No 432
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=89.97 E-value=1.4 Score=36.30 Aligned_cols=44 Identities=20% Similarity=0.255 Sum_probs=35.2
Q ss_pred HHHHHHHHHHH-c-CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598 51 SVRMRIVELAQ-L-GIRPCDISRQLRVSHGCVSKILARYHETGSIL 94 (258)
Q Consensus 51 dlR~RIV~L~~-~-G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~ 94 (258)
+.-..|..+.. . ..+.++||+.|+||.+||++.+++..+.|-|.
T Consensus 8 dyL~~I~~l~~~~~~~~~~ela~~l~vs~~svs~~l~~L~~~Gli~ 53 (142)
T PRK03902 8 DYIEQIYLLIEEKGYARVSDIAEALSVHPSSVTKMVQKLDKDEYLI 53 (142)
T ss_pred HHHHHHHHHHhcCCCcCHHHHHHHhCCChhHHHHHHHHHHHCCCEE
Confidence 34444555554 2 47899999999999999999999999999875
No 433
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=89.97 E-value=0.5 Score=35.58 Aligned_cols=30 Identities=27% Similarity=0.448 Sum_probs=22.3
Q ss_pred HHHHHH-cCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598 56 IVELAQ-LGIRPCDISRQLRVSHGCVSKILA 85 (258)
Q Consensus 56 IV~L~~-~G~S~~eIAr~LGVSrsTVsRwik 85 (258)
|.++.+ .|++.+++|+.+||++++|+++.+
T Consensus 23 i~~~~~~~~ltQ~e~A~~lgisq~~vS~l~~ 53 (80)
T PF13744_consen 23 IRELREERGLTQAELAERLGISQPRVSRLEN 53 (80)
T ss_dssp HHHHHHCCT--HHHHHHHHTS-HHHHHHHHT
T ss_pred HHHHHHHcCCCHHHHHHHHCCChhHHHHHHc
Confidence 444444 599999999999999999999875
No 434
>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional
Probab=89.94 E-value=0.48 Score=47.41 Aligned_cols=37 Identities=22% Similarity=0.269 Sum_probs=31.3
Q ss_pred HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 52 VRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 52 lR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.|..|.+++..+.+.+++|+.||||++|++|-+++|.
T Consensus 475 E~~~i~~~l~~~~~~~~aA~~LGisr~tL~rkl~~~g 511 (520)
T PRK10820 475 ERSVLTRLYRNYPSTRKLAKRLGVSHTAIANKLREYG 511 (520)
T ss_pred HHHHHHHHHHHCCCHHHHHHHhCCCHHHHHHHHHHcC
Confidence 5666666666666899999999999999999999984
No 435
>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=89.93 E-value=0.23 Score=37.44 Aligned_cols=31 Identities=26% Similarity=0.439 Sum_probs=28.6
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598 64 IRPCDISRQLRVSHGCVSKILARYHETGSIL 94 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~ 94 (258)
++..+||+.++++...|.+++++.++.|-+.
T Consensus 26 ~s~~eiA~~~~i~~~~l~kil~~L~~~Gli~ 56 (83)
T PF02082_consen 26 VSSKEIAERLGISPSYLRKILQKLKKAGLIE 56 (83)
T ss_dssp BEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHhhCCeeE
Confidence 7999999999999999999999999999875
No 436
>PRK15115 response regulator GlrR; Provisional
Probab=89.88 E-value=0.55 Score=45.00 Aligned_cols=37 Identities=16% Similarity=0.005 Sum_probs=32.0
Q ss_pred HHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 52 VRMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 52 lR~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.|..|..+++ .+....++|+.|||||+|+||-+++|.
T Consensus 399 E~~~i~~al~~~~gn~~~aA~~Lgisr~tL~rkl~~~~ 436 (444)
T PRK15115 399 ELNYLRKLLQITKGNVTHAARMAGRNRTEFYKLLSRHE 436 (444)
T ss_pred HHHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHHhC
Confidence 6777777765 478899999999999999999999984
No 437
>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=89.83 E-value=0.65 Score=42.96 Aligned_cols=44 Identities=16% Similarity=0.278 Sum_probs=36.7
Q ss_pred HHHHHHHHc--C-CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCC
Q psy15598 54 MRIVELAQL--G-IRPCDISRQLRVSHGCVSKILARYHETGSILPGA 97 (258)
Q Consensus 54 ~RIV~L~~~--G-~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~ 97 (258)
.+|+...+. | .+..++|+++|||+++|++-+++..+.|.++.++
T Consensus 186 ~~IL~~L~~~egrlse~eLAerlGVSRs~ireAlrkLE~aGvIe~r~ 232 (251)
T TIGR02787 186 EHIFEELDGNEGLLVASKIADRVGITRSVIVNALRKLESAGVIESRS 232 (251)
T ss_pred HHHHHHhccccccccHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecc
Confidence 455555543 4 6999999999999999999999999999987665
No 438
>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=89.80 E-value=0.81 Score=40.28 Aligned_cols=51 Identities=14% Similarity=0.130 Sum_probs=40.2
Q ss_pred HHHHHHHHHHH-HcC--C-CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCC
Q psy15598 50 NSVRMRIVELA-QLG--I-RPCDISRQLRVSHGCVSKILARYHETGSILPGAIGG 100 (258)
Q Consensus 50 ~dlR~RIV~L~-~~G--~-S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG 100 (258)
..+|.+|+... .-| + +-.++|++|||||++|+--+++-...|-|...++.|
T Consensus 13 ~~l~~~I~~g~l~pG~~LpsE~~La~~lgVSRtpVREAL~~Le~eGlV~~~~~~G 67 (235)
T TIGR02812 13 EYIVESIWNNRFPPGSILPAERELSELIGVTRTTLREVLQRLARDGWLTIQHGKP 67 (235)
T ss_pred HHHHHHHHcCCCCCCCcCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeCCCc
Confidence 34666666653 345 5 688999999999999999999999999887665555
No 439
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=89.79 E-value=0.53 Score=39.85 Aligned_cols=31 Identities=13% Similarity=0.218 Sum_probs=29.1
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598 64 IRPCDISRQLRVSHGCVSKILARYHETGSIL 94 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~ 94 (258)
++..+||..+|+++.||+|.++++++.|.+.
T Consensus 150 ~t~~~iA~~lG~tretvsR~l~~l~~~g~I~ 180 (202)
T PRK13918 150 ATHDELAAAVGSVRETVTKVIGELSREGYIR 180 (202)
T ss_pred CCHHHHHHHhCccHHHHHHHHHHHHHCCCEE
Confidence 4789999999999999999999999999885
No 440
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=89.78 E-value=0.77 Score=41.62 Aligned_cols=45 Identities=13% Similarity=0.136 Sum_probs=37.5
Q ss_pred HHHHHHHHHHHH---cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598 50 NSVRMRIVELAQ---LGIRPCDISRQLRVSHGCVSKILARYHETGSIL 94 (258)
Q Consensus 50 ~dlR~RIV~L~~---~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~ 94 (258)
.+.-.+|++++. .+++.++||+.+|++++||+|+++...+.|-+.
T Consensus 10 l~ral~iL~~l~~~~~~ls~~eia~~lgl~kstv~RlL~tL~~~g~v~ 57 (263)
T PRK09834 10 LSRGLMVLRALNRLDGGATVGLLAELTGLHRTTVRRLLETLQEEGYVR 57 (263)
T ss_pred HHHHHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 344466777763 248999999999999999999999999999875
No 441
>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=89.78 E-value=0.68 Score=41.79 Aligned_cols=23 Identities=26% Similarity=0.423 Sum_probs=20.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Q psy15598 64 IRPCDISRQLRVSHGCVSKILAR 86 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikR 86 (258)
.+.++||+..|||.+||+|.++.
T Consensus 2 ~ti~dIA~~agvS~~TVSrvLn~ 24 (329)
T TIGR01481 2 VTIYDVAREAGVSMATVSRVVNG 24 (329)
T ss_pred CcHHHHHHHhCCCHHHHHHHhCC
Confidence 47889999999999999999853
No 442
>PRK11569 transcriptional repressor IclR; Provisional
Probab=89.77 E-value=0.71 Score=42.16 Aligned_cols=42 Identities=10% Similarity=0.285 Sum_probs=36.2
Q ss_pred HHHHHHHHH---cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598 53 RMRIVELAQ---LGIRPCDISRQLRVSHGCVSKILARYHETGSIL 94 (258)
Q Consensus 53 R~RIV~L~~---~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~ 94 (258)
=.+|++++. .+++.+|||+.+|++++||+|+++-..+.|-+.
T Consensus 30 al~IL~~l~~~~~~~~lseia~~lglpksTv~RlL~tL~~~G~l~ 74 (274)
T PRK11569 30 GLKLLEWIAESNGSVALTELAQQAGLPNSTTHRLLTTMQQQGFVR 74 (274)
T ss_pred HHHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 356777764 358999999999999999999999999999875
No 443
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=89.75 E-value=0.6 Score=42.55 Aligned_cols=45 Identities=20% Similarity=0.318 Sum_probs=39.9
Q ss_pred CHHHHHHHHHHHH-cC-CCHHHHHHHhCCCHHHHHHHHHHhhhhCCc
Q psy15598 49 PNSVRMRIVELAQ-LG-IRPCDISRQLRVSHGCVSKILARYHETGSI 93 (258)
Q Consensus 49 S~dlR~RIV~L~~-~G-~S~~eIAr~LGVSrsTVsRwikRyrEtGsl 93 (258)
..+-+.+|+++++ +| ++..++|+.|+||..||+|=++...+.|.+
T Consensus 3 ~~eR~~~Il~~l~~~g~v~v~eLa~~~~VS~~TIRRDL~~Le~~g~l 49 (253)
T COG1349 3 KEERHQKILELLKEKGKVSVEELAELFGVSEMTIRRDLNELEEQGLL 49 (253)
T ss_pred hHHHHHHHHHHHHHcCcEEHHHHHHHhCCCHHHHHHhHHHHHHCCcE
Confidence 4567788999986 46 799999999999999999999999999976
No 444
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=89.66 E-value=3.2 Score=33.79 Aligned_cols=40 Identities=23% Similarity=0.348 Sum_probs=33.9
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHhhhhCCc--ccCCCCCCCC
Q psy15598 64 IRPCDISRQLRVSHGCVSKILARYHETGSI--LPGAIGGSKP 103 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl--~pk~rgG~RP 103 (258)
.+..++|..|.+|+.-|..+++++.+.|=| .|+..+|.+.
T Consensus 20 vtl~elA~~l~cS~Rn~r~lLkkm~~~gWi~W~pg~GRG~~S 61 (115)
T PF12793_consen 20 VTLDELAELLFCSRRNARTLLKKMQEEGWITWQPGRGRGNRS 61 (115)
T ss_pred eeHHHHHHHhCCCHHHHHHHHHHHHHCCCeeeeCCCCCCCCC
Confidence 589999999999999999999999999965 5776555343
No 445
>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=89.63 E-value=2.1 Score=33.84 Aligned_cols=63 Identities=14% Similarity=0.146 Sum_probs=45.1
Q ss_pred HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh-hCC-cccCCCCC--CCCCCCCHHHHHHHH
Q psy15598 53 RMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE-TGS-ILPGAIGG--SKPRVTTPKVVSYIK 115 (258)
Q Consensus 53 R~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE-tGs-l~pk~rgG--~RPrklT~e~~~~I~ 115 (258)
..+++..+.+--|.+.+|+.||||.+||++-+++.++ -|. +-.+..+| ++...+|+.-+..+.
T Consensus 6 ~l~~~~av~~~gSis~AA~~L~iS~stvs~~I~~LE~~lg~~Lf~R~~~g~~~~g~~lT~~G~~l~~ 72 (99)
T TIGR00637 6 RVALLKAIARMGSISQAAKDAGISYKSAWDYIRAMNNLSGEPLVERATGGKGGGGAVLTEYGQRLIQ 72 (99)
T ss_pred HHHHHHHHHHhCCHHHHHHHHCCCHHHHHHHHHHHHHHhCCCeEEecCCCCCCCCeeECHHHHHHHH
Confidence 4557777777889999999999999999999999986 343 22332221 255778877666553
No 446
>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=89.63 E-value=0.2 Score=33.94 Aligned_cols=37 Identities=27% Similarity=0.357 Sum_probs=26.7
Q ss_pred HHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHh
Q psy15598 68 DISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQK 120 (258)
Q Consensus 68 eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~ 120 (258)
+||+.+|||++||++|++. ++ ..++.....|.+..++
T Consensus 2 ~lA~~~gvs~~tvs~~l~g---------------~~-~vs~~~~~~i~~~~~~ 38 (52)
T cd01392 2 DIARAAGVSVATVSRVLNG---------------KP-RVSEETRERVLAAAEE 38 (52)
T ss_pred cHHHHHCcCHHHHHHHHcC---------------CC-CCCHHHHHHHHHHHHH
Confidence 7999999999999999853 11 2455666666666554
No 447
>PRK10403 transcriptional regulator NarP; Provisional
Probab=89.55 E-value=0.74 Score=37.64 Aligned_cols=40 Identities=15% Similarity=0.155 Sum_probs=33.9
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 48 LPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 48 ~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
++.... .|+.++..|.+.++||+.+++|.+||...+++-+
T Consensus 154 Lt~~e~-~vl~~~~~g~s~~~ia~~l~~s~~tv~~~~~~i~ 193 (215)
T PRK10403 154 LTEREL-DVLHELAQGLSNKQIASVLNISEQTVKVHIRNLL 193 (215)
T ss_pred CCHHHH-HHHHHHHCCCCHHHHHHHcCCCHHHHHHHHHHHH
Confidence 565444 5777888999999999999999999999988875
No 448
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=89.53 E-value=0.75 Score=41.10 Aligned_cols=50 Identities=30% Similarity=0.392 Sum_probs=38.3
Q ss_pred HHHHHHHHH-HHcC--C-CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCC
Q psy15598 51 SVRMRIVEL-AQLG--I-RPCDISRQLRVSHGCVSKILARYHETGSILPGAIGG 100 (258)
Q Consensus 51 dlR~RIV~L-~~~G--~-S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG 100 (258)
.+|..|+.. +.-| + +-.++|++||||+++|+.-+++-...|-|.-.++.|
T Consensus 10 ~L~~~I~~g~l~pG~~LpsE~eLae~~gVSRtpVREAL~~Le~~GlV~~~~~~G 63 (253)
T PRK10421 10 RVRALIEEKNLEAGMKLPAERQLAMQLGVSRNSLREALAKLVSEGVLLSRRGGG 63 (253)
T ss_pred HHHHHHHcCCCCCCCcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEeCCCe
Confidence 345555554 2335 4 578999999999999999999999999887665555
No 449
>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=89.47 E-value=1.6 Score=35.06 Aligned_cols=32 Identities=19% Similarity=0.297 Sum_probs=29.8
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598 63 GIRPCDISRQLRVSHGCVSKILARYHETGSIL 94 (258)
Q Consensus 63 G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~ 94 (258)
..+..+||+.+++++++|+++++...+.|-+.
T Consensus 25 ~~s~~eia~~~~i~~~~v~~il~~L~~~gli~ 56 (132)
T TIGR00738 25 PVSVKEIAERQGISRSYLEKILRTLRRAGLVE 56 (132)
T ss_pred cCcHHHHHHHHCcCHHHHHHHHHHHHHCCcEE
Confidence 47999999999999999999999999999774
No 450
>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=89.46 E-value=0.59 Score=44.12 Aligned_cols=36 Identities=6% Similarity=-0.037 Sum_probs=29.7
Q ss_pred HHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHHh
Q psy15598 52 VRMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILARY 87 (258)
Q Consensus 52 lR~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwikRy 87 (258)
.|..|...++ .|...+++|+.||||++|+|+.+++|
T Consensus 293 E~~~I~~aL~~~~gn~~~aA~~LGisr~tL~rklkk~ 329 (329)
T TIGR02974 293 EIELLQQALAEAQFNQRKAAELLGLTYHQLRGLLRKH 329 (329)
T ss_pred HHHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHhC
Confidence 4555555555 58899999999999999999999986
No 451
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=89.45 E-value=0.81 Score=37.49 Aligned_cols=41 Identities=24% Similarity=0.245 Sum_probs=33.5
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh
Q psy15598 48 LPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE 89 (258)
Q Consensus 48 ~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE 89 (258)
++...+ .|+.++.+|++.++||+.|++|.+||...+++.++
T Consensus 138 Lt~~E~-~il~~l~~g~~~~~Ia~~l~~s~~tv~~~~~~l~~ 178 (196)
T PRK10360 138 LTKRER-QVAEKLAQGMAVKEIAAELGLSPKTVHVHRANLME 178 (196)
T ss_pred CCHHHH-HHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 444333 56777778999999999999999999999998763
No 452
>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=89.45 E-value=1.3 Score=25.67 Aligned_cols=41 Identities=34% Similarity=0.416 Sum_probs=28.8
Q ss_pred CCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHH
Q psy15598 102 KPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRIL 154 (258)
Q Consensus 102 RPrklT~e~~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiL 154 (258)
|++.++++....|.+...+ ..+..++.+.+ | +|.+||++++
T Consensus 2 r~~~~~~~~~~~i~~~~~~--~~s~~~ia~~~---~-------is~~tv~~~~ 42 (42)
T cd00569 2 RPPKLTPEQIEEARRLLAA--GESVAEIARRL---G-------VSRSTLYRYL 42 (42)
T ss_pred CCCcCCHHHHHHHHHHHHc--CCCHHHHHHHH---C-------CCHHHHHHhC
Confidence 5667777777777777653 44777787666 3 3899998864
No 453
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=89.40 E-value=0.7 Score=41.67 Aligned_cols=41 Identities=15% Similarity=0.198 Sum_probs=34.4
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.+|...+ .|+.+..+|++..+||..|+||..||..-+++-+
T Consensus 179 ~LT~rE~-evl~~~a~G~t~~eIa~~l~is~~TV~~h~~~~~ 219 (240)
T PRK10188 179 NFSKREK-EILKWTAEGKTSAEIAMILSISENTVNFHQKNMQ 219 (240)
T ss_pred CCCHHHH-HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 4665554 5777778999999999999999999999988876
No 454
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=89.39 E-value=2.1 Score=32.53 Aligned_cols=71 Identities=17% Similarity=0.163 Sum_probs=44.8
Q ss_pred CCHHHHHHHHHHHHcCCCH-HHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCC-C--CCCCCHHHHHHHHHHH
Q psy15598 48 LPNSVRMRIVELAQLGIRP-CDISRQLRVSHGCVSKILARYHETGSILPGAIGGS-K--PRVTTPKVVSYIKELK 118 (258)
Q Consensus 48 ~S~dlR~RIV~L~~~G~S~-~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~-R--PrklT~e~~~~I~~lv 118 (258)
++...-.-+..+...+-.. .+||+.++|++++|.+.+++..+.|-|.-...... | --.+|++-.+.+.+..
T Consensus 20 lt~~q~~~L~~l~~~~~~~~~~la~~l~i~~~~vt~~l~~Le~~glv~r~~~~~DrR~~~l~lT~~G~~~~~~~~ 94 (126)
T COG1846 20 LTPPQYQVLLALYEAGGITVKELAERLGLDRSTVTRLLKRLEDKGLIERLRDPEDRRAVLVRLTEKGRELLEQLL 94 (126)
T ss_pred CCHHHHHHHHHHHHhCCCcHHHHHHHHCCCHHHHHHHHHHHHHCCCeeecCCccccceeeEEECccHHHHHHHhc
Confidence 3433333333344444444 99999999999999999999999997743322211 2 2246666666655554
No 455
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=89.38 E-value=0.81 Score=42.37 Aligned_cols=41 Identities=24% Similarity=0.107 Sum_probs=31.7
Q ss_pred CCHHHHHHHHHHHH--cCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 48 LPNSVRMRIVELAQ--LGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 48 ~S~dlR~RIV~L~~--~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
++...|.-|...+- +|+|..+||+.||||+.+|+++.++..
T Consensus 228 L~~rer~vl~lr~~~~~~~t~~EIa~~lgvs~~~V~q~~~~Al 270 (289)
T PRK07500 228 LNERELRIIRERRLREDGATLEALGEELGISKERVRQIEARAL 270 (289)
T ss_pred CCHHHHHHHHHHhcCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 55555544444333 799999999999999999999998865
No 456
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=89.37 E-value=0.44 Score=40.52 Aligned_cols=31 Identities=26% Similarity=0.359 Sum_probs=28.5
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598 64 IRPCDISRQLRVSHGCVSKILARYHETGSIL 94 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~ 94 (258)
.+..+||..+|+++.||+|.++++++.|.+.
T Consensus 169 ~t~~~lA~~lG~tr~tvsR~l~~l~~~gii~ 199 (211)
T PRK11753 169 ITRQEIGRIVGCSREMVGRVLKMLEDQGLIS 199 (211)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHCCCEE
Confidence 4679999999999999999999999999774
No 457
>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional
Probab=89.29 E-value=0.48 Score=48.15 Aligned_cols=41 Identities=17% Similarity=0.185 Sum_probs=34.7
Q ss_pred CCHHHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 48 LPNSVRMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 48 ~S~dlR~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
+....|..|+..++ .|-..+++|+.|||||+|+||-+++|.
T Consensus 588 l~~~E~~~i~~al~~~~gn~~~aA~~LGisR~TLyrklk~~~ 629 (638)
T PRK11388 588 LAELEKEAIINAAQVCGGRIQEMAALLGIGRTTLWRKMKQHG 629 (638)
T ss_pred HHHHHHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHcC
Confidence 44557777888776 577899999999999999999999985
No 458
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=89.19 E-value=1.1 Score=39.56 Aligned_cols=42 Identities=19% Similarity=0.226 Sum_probs=37.0
Q ss_pred CCCHHHHHHHHHHHHcCC-------CHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELAQLGI-------RPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~-------S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.|+...+.-+..+++.|. +.+++|++||||++|+...++|-.
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ehLRrAe 203 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEHLRRAE 203 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 688888888888888774 889999999999999999998865
No 459
>PRK11013 DNA-binding transcriptional regulator LysR; Provisional
Probab=89.16 E-value=1.7 Score=39.43 Aligned_cols=57 Identities=19% Similarity=0.179 Sum_probs=39.2
Q ss_pred HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhh-CC-cccCCCCCCCCCCCCHHHHHH
Q psy15598 54 MRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHET-GS-ILPGAIGGSKPRVTTPKVVSY 113 (258)
Q Consensus 54 ~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEt-Gs-l~pk~rgG~RPrklT~e~~~~ 113 (258)
.+++..+.+-.|.+.+|+.|+||.++|++.+++.++. |. +-.+ .+ +.-.+|+.-+.+
T Consensus 9 L~~f~av~~~gS~s~AAe~L~isqsavS~~Ik~LE~~lg~~Lf~R--~~-~~v~LT~~G~~l 67 (309)
T PRK11013 9 IEIFHAVMTAGSLTEAARLLHTSQPTVSRELARFEKVIGLKLFER--VR-GRLHPTVQGLRL 67 (309)
T ss_pred HHHHHHHHHhCcHHHHHHHHCCCcHHHHHHHHHHHHHhCceeeee--cC-CCcccCHHHHHH
Confidence 4455555555599999999999999999999999863 42 2222 23 446677654333
No 460
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=89.15 E-value=1.1 Score=32.96 Aligned_cols=45 Identities=16% Similarity=0.161 Sum_probs=36.1
Q ss_pred HHHHHHHHHHHHhCCC--CCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCCCC
Q psy15598 108 PKVVSYIKELKQKDPG--IFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSSI 162 (258)
Q Consensus 108 ~e~~~~I~~lv~~nP~--ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~~~ 162 (258)
++.++.|..++.+++. +++.||++.| | ++.++|+|+|..+..+..
T Consensus 5 ~~~~~~IL~~L~~~g~~~~ta~eLa~~l---g-------l~~~~v~r~L~~L~~~G~ 51 (68)
T smart00550 5 DSLEEKILEFLENSGDETSTALQLAKNL---G-------LPKKEVNRVLYSLEKKGK 51 (68)
T ss_pred hHHHHHHHHHHHHCCCCCcCHHHHHHHH---C-------CCHHHHHHHHHHHHHCCC
Confidence 4567888888888766 9999998888 3 488999999987766644
No 461
>COG2973 TrpR Trp operon repressor [Transcription]
Probab=88.98 E-value=1.2 Score=35.89 Aligned_cols=31 Identities=29% Similarity=0.411 Sum_probs=25.4
Q ss_pred HHHHHHHHHHc-CCCHHHHHHHhCCCHHHHHH
Q psy15598 52 VRMRIVELAQL-GIRPCDISRQLRVSHGCVSK 82 (258)
Q Consensus 52 lR~RIV~L~~~-G~S~~eIAr~LGVSrsTVsR 82 (258)
.|.+||...-+ .+|.++|+..||||..||-|
T Consensus 48 ~Rv~Iv~eLL~ge~sQREi~~~LgvsiAtITR 79 (103)
T COG2973 48 TRVRIVEELLRGELSQREIAQKLGVSIATITR 79 (103)
T ss_pred HHHHHHHHHHhccccHHHHHHHhCcchhhhcc
Confidence 56777776654 58999999999999999854
No 462
>PRK15185 transcriptional regulator HilD; Provisional
Probab=88.95 E-value=2.4 Score=40.30 Aligned_cols=87 Identities=11% Similarity=0.101 Sum_probs=55.3
Q ss_pred HHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCC-CCHHHHHHHHHHHHhCCCCCH
Q psy15598 52 VRMRIVELAQ----LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRV-TTPKVVSYIKELKQKDPGIFA 126 (258)
Q Consensus 52 lR~RIV~L~~----~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrk-lT~e~~~~I~~lv~~nP~ita 126 (258)
...+|...++ +.++..++|+.+++|++++.|..+. .|. .+.. +...-.....+++ .+.+.+.
T Consensus 207 ~~erV~~~I~~n~~~~~SledLA~~lgmS~~tL~R~FK~---~G~---------S~~~yl~~~Ri~~A~~LL-~~t~~sI 273 (309)
T PRK15185 207 LKERVYNIISSSPSRQWKLTDVADHIFMSTSTLKRKLAE---EGT---------SFSDIYLSARMNQAAKLL-RIGNHNV 273 (309)
T ss_pred HHHHHHHHHHhCccCCCCHHHHHHHHCcCHHHHHHHHHH---cCC---------CHHHHHHHHHHHHHHHHH-HcCCCCH
Confidence 4445555543 4579999999999999999998874 342 1111 1111111112223 3457788
Q ss_pred HHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCC
Q psy15598 127 WEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGS 160 (258)
Q Consensus 127 ~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~ 160 (258)
.+|+..+ |.. |.+...|.+++..+.
T Consensus 274 seIA~~~---GFs------s~S~FsR~FKk~~G~ 298 (309)
T PRK15185 274 NAVALKC---GYD------STSYFIQCFKKYFKT 298 (309)
T ss_pred HHHHHHh---CCC------CHHHHHHHHHHHHCc
Confidence 8887766 665 889999999887654
No 463
>PRK15424 propionate catabolism operon regulatory protein PrpR; Provisional
Probab=88.86 E-value=0.73 Score=46.75 Aligned_cols=39 Identities=8% Similarity=0.015 Sum_probs=32.9
Q ss_pred HHHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 50 NSVRMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 50 ~dlR~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
...|..|...++ .|-...++|+.|||||+|+||.+++|.
T Consensus 496 ~~Er~~I~~~L~~~~Gn~~~aA~~LGIsRtTL~RkLk~~g 535 (538)
T PRK15424 496 RLLAATLQQALERFNGDKTAAANYLGISRTTLWRRLKAEA 535 (538)
T ss_pred HHHHHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHHhC
Confidence 346777777765 577899999999999999999999985
No 464
>COG1342 Predicted DNA-binding proteins [General function prediction only]
Probab=88.83 E-value=1.1 Score=36.07 Aligned_cols=42 Identities=10% Similarity=0.056 Sum_probs=32.9
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.++.|.-..|-..-.+|++..++|.+.|||++|+++.++..+
T Consensus 33 ~lt~eElEAlRLvD~~~l~QeeAA~rMgISr~Tfwr~l~sAR 74 (99)
T COG1342 33 ILTIEELEALRLVDYEGLTQEEAALRMGISRQTFWRLLTSAR 74 (99)
T ss_pred eecHHHHHHHHHHhHhhccHHHHHHHhcccHHHHHHHHHHHH
Confidence 355665544433345899999999999999999999998875
No 465
>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=88.82 E-value=0.98 Score=39.49 Aligned_cols=42 Identities=17% Similarity=0.293 Sum_probs=35.7
Q ss_pred HHHHHHHHHc--CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598 53 RMRIVELAQL--GIRPCDISRQLRVSHGCVSKILARYHETGSIL 94 (258)
Q Consensus 53 R~RIV~L~~~--G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~ 94 (258)
..+|+....+ +.+.++||+.+++|++||++.+++..+.|-+.
T Consensus 145 ~~~IL~~l~~~g~~s~~eia~~l~is~stv~r~L~~Le~~GlI~ 188 (203)
T TIGR01884 145 ELKVLEVLKAEGEKSVKNIAKKLGKSLSTISRHLRELEKKGLVE 188 (203)
T ss_pred HHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 4566666653 57999999999999999999999999999874
No 466
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=88.82 E-value=0.84 Score=43.11 Aligned_cols=42 Identities=14% Similarity=0.114 Sum_probs=33.7
Q ss_pred CCCHHHHHHHHHHH----HcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELA----QLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~----~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.++...|.-|...+ .+|++..+||+.||||++||..++.|-+
T Consensus 262 ~L~~~~R~vl~lrygL~~~e~~s~~EIA~~Lgis~~tV~~~~~rAl 307 (325)
T PRK05657 262 ELNDKQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQIQVEAL 307 (325)
T ss_pred cCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 46666776555432 4799999999999999999999988865
No 467
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=88.81 E-value=0.74 Score=41.40 Aligned_cols=19 Identities=32% Similarity=0.422 Sum_probs=17.7
Q ss_pred HHHHHHhCCCHHHHHHHHH
Q psy15598 67 CDISRQLRVSHGCVSKILA 85 (258)
Q Consensus 67 ~eIAr~LGVSrsTVsRwik 85 (258)
++||+..|||++||+|.++
T Consensus 2 ~dIA~~agVS~~TVSrvLn 20 (327)
T PRK10423 2 KDVARLAGVSTSTVSHVIN 20 (327)
T ss_pred hhHHHHhCCcHHHHHHHhC
Confidence 6899999999999999996
No 468
>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B.
Probab=88.74 E-value=0.43 Score=34.85 Aligned_cols=19 Identities=26% Similarity=0.319 Sum_probs=17.3
Q ss_pred CHHHHHHHhCCCHHHHHHH
Q psy15598 65 RPCDISRQLRVSHGCVSKI 83 (258)
Q Consensus 65 S~~eIAr~LGVSrsTVsRw 83 (258)
+.+++|+.||||+++|+.|
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 7789999999999999999
No 469
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=88.70 E-value=0.54 Score=40.94 Aligned_cols=33 Identities=21% Similarity=0.435 Sum_probs=29.9
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccC
Q psy15598 64 IRPCDISRQLRVSHGCVSKILARYHETGSILPG 96 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk 96 (258)
++..+||..||+++.||+|.++++++.|.++-.
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 578999999999999999999999999988533
No 470
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=88.65 E-value=0.69 Score=39.21 Aligned_cols=47 Identities=19% Similarity=0.071 Sum_probs=40.4
Q ss_pred CCHHHHHHHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCCCC
Q psy15598 106 TTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGSSI 162 (258)
Q Consensus 106 lT~e~~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~~~ 162 (258)
..++.+..|++.+++|+.++..||++.|. +|.+||+++++++..+..
T Consensus 11 ~lD~~D~~IL~~Lq~d~R~s~~eiA~~lg----------lS~~tv~~Ri~rL~~~Gv 57 (164)
T PRK11169 11 DLDRIDRNILNELQKDGRISNVELSKRVG----------LSPTPCLERVRRLERQGF 57 (164)
T ss_pred hHHHHHHHHHHHhccCCCCCHHHHHHHHC----------cCHHHHHHHHHHHHHCCC
Confidence 34678899999999999999999999883 499999999999877765
No 471
>PF04645 DUF603: Protein of unknown function, DUF603; InterPro: IPR006739 This family includes several uncharacterised proteins from Borrelia species.
Probab=88.58 E-value=0.71 Score=40.62 Aligned_cols=37 Identities=19% Similarity=0.292 Sum_probs=32.7
Q ss_pred HHHHHHcC-CCHHHHHHHhCCCHHHHHHHHHHhhhhCC
Q psy15598 56 IVELAQLG-IRPCDISRQLRVSHGCVSKILARYHETGS 92 (258)
Q Consensus 56 IV~L~~~G-~S~~eIAr~LGVSrsTVsRwikRyrEtGs 92 (258)
-|.++.+| ++..+||+.||||+..|.+..++|...++
T Consensus 11 Yi~yF~eg~L~d~~Ia~~lgvs~~nV~kmR~Kwes~~~ 48 (181)
T PF04645_consen 11 YIFYFKEGRLSDAEIAKELGVSRVNVWKMRQKWESSED 48 (181)
T ss_pred HHHHHhcCCccHHHHHHHHCchHHHHHHHHHHHHhcCC
Confidence 46677888 89999999999999999999999987654
No 472
>COG3311 AlpA Predicted transcriptional regulator [Transcription]
Probab=88.57 E-value=1 Score=34.11 Aligned_cols=23 Identities=9% Similarity=0.192 Sum_probs=20.4
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHh
Q psy15598 65 RPCDISRQLRVSHGCVSKILARY 87 (258)
Q Consensus 65 S~~eIAr~LGVSrsTVsRwikRy 87 (258)
...|++..+|+|++||||+++.-
T Consensus 15 rl~ev~~~~GlSrstiYr~i~~~ 37 (70)
T COG3311 15 RLPEVAQLTGLSRSTIYRLIKDG 37 (70)
T ss_pred hHHHHHHHHCccHHHHHHHHccC
Confidence 56789999999999999999874
No 473
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=88.44 E-value=1.3 Score=34.01 Aligned_cols=34 Identities=18% Similarity=0.261 Sum_probs=27.4
Q ss_pred HHHHHHHHH-HcCCCHHHHHHHhC------CCHHHHHHHHH
Q psy15598 52 VRMRIVELA-QLGIRPCDISRQLR------VSHGCVSKILA 85 (258)
Q Consensus 52 lR~RIV~L~-~~G~S~~eIAr~LG------VSrsTVsRwik 85 (258)
+..++..+. +.|++..++|+.+| +|.+||+||-+
T Consensus 12 ~~~~lk~~R~~lGLTQ~dvA~~lg~~~g~i~SQstISR~Es 52 (75)
T smart00352 12 FAKTFKQRRIKLGFTQADVGLALGALYGPDFSQTTICRFEA 52 (75)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHhcccccCcCCHHHHHHHHh
Confidence 445555554 47999999999999 59999999866
No 474
>PRK13870 transcriptional regulator TraR; Provisional
Probab=88.40 E-value=0.88 Score=40.93 Aligned_cols=41 Identities=15% Similarity=-0.006 Sum_probs=33.9
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
.+|.-.+ .++....+|++..|||..||||.+||..-+++-+
T Consensus 173 ~LT~RE~-E~L~W~A~GKT~~EIa~ILgISe~TV~~Hl~na~ 213 (234)
T PRK13870 173 WLDPKEA-TYLRWIAVGKTMEEIADVEGVKYNSVRVKLREAM 213 (234)
T ss_pred CCCHHHH-HHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 4555444 4666677999999999999999999999998876
No 475
>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=88.39 E-value=0.87 Score=39.35 Aligned_cols=45 Identities=16% Similarity=0.244 Sum_probs=35.0
Q ss_pred HHHHHHHHHHH-----cC--CCHHHHHHHhCCC-HHHHHHHHHHhhhhCCccc
Q psy15598 51 SVRMRIVELAQ-----LG--IRPCDISRQLRVS-HGCVSKILARYHETGSILP 95 (258)
Q Consensus 51 dlR~RIV~L~~-----~G--~S~~eIAr~LGVS-rsTVsRwikRyrEtGsl~p 95 (258)
+...+|+..+. .| .+.++||+.||++ ++||++.+++..+.|-+..
T Consensus 6 ~~q~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~~L~~~g~i~~ 58 (199)
T TIGR00498 6 ARQQEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLKALERKGYIER 58 (199)
T ss_pred HHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHHHHHHCCCEec
Confidence 34445555543 23 5788999999998 9999999999999998753
No 476
>PRK10870 transcriptional repressor MprA; Provisional
Probab=88.36 E-value=1.6 Score=37.52 Aligned_cols=56 Identities=20% Similarity=0.251 Sum_probs=40.9
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCC---CCCCCHHHHHHHHHHH
Q psy15598 63 GIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSK---PRVTTPKVVSYIKELK 118 (258)
Q Consensus 63 G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~R---PrklT~e~~~~I~~lv 118 (258)
+.+..+||+.++++++||.+.+++..+.|-|+-.+.+..+ --.+|++=.+.+.+..
T Consensus 71 ~it~~eLa~~l~l~~~tvsr~v~rLe~kGlV~R~~~~~DrR~~~v~LT~~G~~~~~~i~ 129 (176)
T PRK10870 71 SIQPSELSCALGSSRTNATRIADELEKRGWIERRESDNDRRCLHLQLTEKGHEFLREVL 129 (176)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHHHHHH
Confidence 4788999999999999999999999999987533322212 2237777666665553
No 477
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=88.35 E-value=2.7 Score=36.96 Aligned_cols=57 Identities=12% Similarity=0.007 Sum_probs=41.7
Q ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCC-C--CCCCCHHHHHHHHHHH
Q psy15598 62 LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGS-K--PRVTTPKVVSYIKELK 118 (258)
Q Consensus 62 ~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~-R--PrklT~e~~~~I~~lv 118 (258)
.|.+.++||+.++++++||.+.+++..+.|-|.-.+.... | --.+|++-++.+.++.
T Consensus 58 ~~itq~eLa~~l~l~~sTvtr~l~rLE~kGlI~R~~~~~DrR~~~I~LTekG~~l~~~l~ 117 (185)
T PRK13777 58 KGASISEIAKFGVMHVSTAFNFSKKLEERGYLTFSKKEDDKRNTYIELTEKGEELLLETM 117 (185)
T ss_pred CCcCHHHHHHHHCCCHhhHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHHHHHH
Confidence 5899999999999999999999999999998752222211 2 2236776666555553
No 478
>PRK13500 transcriptional activator RhaR; Provisional
Probab=88.26 E-value=3.6 Score=38.04 Aligned_cols=88 Identities=9% Similarity=0.067 Sum_probs=58.1
Q ss_pred HHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCC-CCHHHHHHHHHHHHhCCCCCH
Q psy15598 52 VRMRIVELAQ----LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRV-TTPKVVSYIKELKQKDPGIFA 126 (258)
Q Consensus 52 lR~RIV~L~~----~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrk-lT~e~~~~I~~lv~~nP~ita 126 (258)
.-.+++..++ +..+..++|+.+++|.+++.|+.|++- |. .|.. +.........+++ .+.+.+.
T Consensus 207 ~l~~i~~yI~~~~~e~isl~~lA~~~~iS~~~L~r~FK~~t--G~---------T~~~yi~~~RL~~A~~LL-~~t~~sI 274 (312)
T PRK13500 207 LLDKLITRLAASLKSPFALDKFCDEASCSERVLRQQFRQQT--GM---------TINQYLRQVRVCHAQYLL-QHSRLLI 274 (312)
T ss_pred HHHHHHHHHHHcccCCCCHHHHHHHHCcCHHHHHHHHHHHH--Cc---------CHHHHHHHHHHHHHHHHH-HcCCCCH
Confidence 3455666654 357999999999999999999999973 22 1111 1111122222222 3457788
Q ss_pred HHHHHHHHhcCCCCCCCCCCHHHHHHHHHhccCC
Q psy15598 127 WEIRDRLLSDGVCDKFNVPSVSSISRILRNKIGS 160 (258)
Q Consensus 127 ~EIr~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~ 160 (258)
.||+..+ |.. +.+...|+.|+.-+.
T Consensus 275 ~eIA~~~---GF~------d~s~Fsr~FKk~~G~ 299 (312)
T PRK13500 275 SDISTEC---GFE------DSNYFSVVFTRETGM 299 (312)
T ss_pred HHHHHHh---CCC------CHHHHHHHHHHHHCc
Confidence 8887766 665 788999999887654
No 479
>PF12833 HTH_18: Helix-turn-helix domain; PDB: 2K9S_A 3LSG_C 3OIO_A 1D5Y_B 3GBG_A 3OOU_A 1BL0_A 1XS9_A 3MN2_B 3MKL_B ....
Probab=88.15 E-value=1.3 Score=32.44 Aligned_cols=72 Identities=22% Similarity=0.293 Sum_probs=44.9
Q ss_pred HHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCC-CCHHHHHHHHHHHHhCCCCCHHHHHHHHHhcCCCCCCCCCCH
Q psy15598 69 ISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRV-TTPKVVSYIKELKQKDPGIFAWEIRDRLLSDGVCDKFNVPSV 147 (258)
Q Consensus 69 IAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrk-lT~e~~~~I~~lv~~nP~ita~EIr~~L~~~Gv~v~~~~pS~ 147 (258)
+|+.||||.+++.++.++.. |. .+.. +...-...+.+++.++++.+..||+..+ |.. +.
T Consensus 1 lA~~~~~s~~~l~~~f~~~~--g~---------s~~~~~~~~R~~~a~~~L~~~~~~~i~~ia~~~---Gf~------~~ 60 (81)
T PF12833_consen 1 LADELGMSERYLSRIFKKET--GM---------SFKQYLRELRLQRAKELLRQNTDLSIAEIAEEC---GFS------SQ 60 (81)
T ss_dssp HHHHCTS-HHHHHHHHHHHH--SS----------HHHHHHHHHHHHHHHHHHHHTT--HHHHHHHT---T-S------SH
T ss_pred ChHHhCcCHHHHHHHHHHHH--Cc---------CHHHHHHHHHHHHHHHHHHHhhcccHHHHHHHc---CCC------CH
Confidence 68999999999999999974 21 1111 2222234444555455788888886655 665 88
Q ss_pred HHHHHHHHhccCC
Q psy15598 148 SSISRILRNKIGS 160 (258)
Q Consensus 148 STI~RiLrr~~~~ 160 (258)
+...|.+++.-+.
T Consensus 61 ~~f~~~fk~~~g~ 73 (81)
T PF12833_consen 61 SHFSRAFKRYFGM 73 (81)
T ss_dssp HHHHHHHHHHHSS
T ss_pred HHHHHHHHHHHCc
Confidence 8888888876543
No 480
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=88.15 E-value=0.9 Score=37.10 Aligned_cols=36 Identities=14% Similarity=0.137 Sum_probs=28.3
Q ss_pred HHHHHHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHHH
Q psy15598 50 NSVRMRIVELA-QLGIRPCDISRQLRVSHGCVSKILA 85 (258)
Q Consensus 50 ~dlR~RIV~L~-~~G~S~~eIAr~LGVSrsTVsRwik 85 (258)
.-+=.+|..+. +.|++..++|+.+|||++|+++|.+
T Consensus 4 ~i~~~~l~~ll~~~Glsq~eLA~~~Gis~~~is~iE~ 40 (120)
T PRK13890 4 YIFFTNVLRLLDERHMTKKELSERSGVSISFLSDLTT 40 (120)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHc
Confidence 33344555655 4799999999999999999998874
No 481
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=88.12 E-value=2.2 Score=31.40 Aligned_cols=33 Identities=21% Similarity=0.261 Sum_probs=28.9
Q ss_pred cCC--CHHHHHHHhCCC-HHHHHHHHHHhhhhCCcc
Q psy15598 62 LGI--RPCDISRQLRVS-HGCVSKILARYHETGSIL 94 (258)
Q Consensus 62 ~G~--S~~eIAr~LGVS-rsTVsRwikRyrEtGsl~ 94 (258)
.|. |.+|||+.||++ .+||++.++.-.+-|.|.
T Consensus 22 ~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le~kG~I~ 57 (65)
T PF01726_consen 22 NGYPPTVREIAEALGLKSTSTVQRHLKALERKGYIR 57 (65)
T ss_dssp HSS---HHHHHHHHTSSSHHHHHHHHHHHHHTTSEE
T ss_pred cCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCcCcc
Confidence 575 779999999996 999999999999999874
No 482
>PRK10923 glnG nitrogen regulation protein NR(I); Provisional
Probab=88.10 E-value=0.88 Score=44.00 Aligned_cols=38 Identities=11% Similarity=0.061 Sum_probs=31.8
Q ss_pred HHHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHHh
Q psy15598 50 NSVRMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILARY 87 (258)
Q Consensus 50 ~dlR~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwikRy 87 (258)
.-.|..|...++ .|....++|+.|||||+|+||-+++|
T Consensus 428 ~~E~~~i~~aL~~~~gn~~~aA~~Lgisr~tL~rkl~~~ 466 (469)
T PRK10923 428 ELERTLLTTALRHTQGHKQEAARLLGWGRNTLTRKLKEL 466 (469)
T ss_pred HHHHHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHHh
Confidence 336666776665 48889999999999999999999988
No 483
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=88.03 E-value=0.79 Score=39.95 Aligned_cols=45 Identities=11% Similarity=0.001 Sum_probs=37.2
Q ss_pred CHHHHHHHHHHHH-cC-CCHHHHHHHhCCCHHHHHHHHHHhhhhCCc
Q psy15598 49 PNSVRMRIVELAQ-LG-IRPCDISRQLRVSHGCVSKILARYHETGSI 93 (258)
Q Consensus 49 S~dlR~RIV~L~~-~G-~S~~eIAr~LGVSrsTVsRwikRyrEtGsl 93 (258)
..+-+.+|++++. .| .+..++|+.|+||..||+|=+....+.|.+
T Consensus 5 ~~~R~~~Il~~l~~~~~~~~~~La~~~~vS~~TiRRDl~~L~~~g~~ 51 (185)
T PRK04424 5 KKERQKALQELIEENPFITDEELAEKFGVSIQTIRLDRMELGIPELR 51 (185)
T ss_pred HHHHHHHHHHHHHHCCCEEHHHHHHHHCcCHHHHHHHHHHHhcchHH
Confidence 3566677887775 45 699999999999999999999998877754
No 484
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=87.94 E-value=0.89 Score=42.62 Aligned_cols=40 Identities=18% Similarity=0.217 Sum_probs=32.1
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHh
Q psy15598 65 RPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQK 120 (258)
Q Consensus 65 S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~ 120 (258)
+.++||+..|||++||+|.++.- + ..+++.+++|.+.+++
T Consensus 2 TikDVA~~AGVS~sTVSrvln~~---------------~-~Vs~eTr~kV~~a~~e 41 (333)
T COG1609 2 TIKDVAKLAGVSKATVSRVLNGS---------------P-YVSEETREKVLAAIKE 41 (333)
T ss_pred CHHHHHHHhCCCHHHHHHHHcCC---------------C-CCCHHHHHHHHHHHHH
Confidence 67899999999999999988752 1 3667778888877664
No 485
>TIGR01818 ntrC nitrogen regulation protein NR(I). This model represents NtrC, a DNA-binding response regulator that is phosphorylated by NtrB and interacts with sigma-54. NtrC usually controls the expression of glutamine synthase, GlnA, and may be called GlnL, GlnG, etc.
Probab=87.92 E-value=0.84 Score=43.90 Aligned_cols=38 Identities=11% Similarity=-0.012 Sum_probs=31.2
Q ss_pred HHHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHHh
Q psy15598 50 NSVRMRIVELAQ-LGIRPCDISRQLRVSHGCVSKILARY 87 (258)
Q Consensus 50 ~dlR~RIV~L~~-~G~S~~eIAr~LGVSrsTVsRwikRy 87 (258)
.-.|..|....+ .|....++|+.|||||+|+||-++++
T Consensus 425 ~~E~~~i~~al~~~~gn~~~aA~~Lgisr~tL~rkl~~~ 463 (463)
T TIGR01818 425 EFERPLLEAALQHTRGHKQEAAALLGWGRNTLTRKLKEL 463 (463)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHhC
Confidence 335666777665 58899999999999999999999864
No 486
>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=87.86 E-value=0.56 Score=31.02 Aligned_cols=25 Identities=16% Similarity=0.166 Sum_probs=19.1
Q ss_pred CHHHHHHHhCCCHHHHHHHHHHhhhhCCc
Q psy15598 65 RPCDISRQLRVSHGCVSKILARYHETGSI 93 (258)
Q Consensus 65 S~~eIAr~LGVSrsTVsRwikRyrEtGsl 93 (258)
++.++|+.+|||.+||+.|-+. |.+
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 4679999999999999777554 655
No 487
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=87.84 E-value=1.1 Score=41.87 Aligned_cols=39 Identities=15% Similarity=0.171 Sum_probs=33.5
Q ss_pred HHHHHHHHc--CCCHHHHHHHhCCCHHHHHHHHHHhhhhCC
Q psy15598 54 MRIVELAQL--GIRPCDISRQLRVSHGCVSKILARYHETGS 92 (258)
Q Consensus 54 ~RIV~L~~~--G~S~~eIAr~LGVSrsTVsRwikRyrEtGs 92 (258)
.+|+.+..+ ..+..+||++||||++||++-+++.++.|-
T Consensus 7 ~~il~~L~~~~~~s~~~LA~~lgvsr~tV~~~l~~L~~~G~ 47 (319)
T PRK11886 7 LQLLSLLADGDFHSGEQLGEELGISRAAIWKHIQTLEEWGL 47 (319)
T ss_pred HHHHHHHHcCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCC
Confidence 356666654 479999999999999999999999999997
No 488
>PRK15121 right oriC-binding transcriptional activator; Provisional
Probab=87.80 E-value=4 Score=37.24 Aligned_cols=86 Identities=7% Similarity=0.014 Sum_probs=52.7
Q ss_pred HHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHH-HHHHHHHHHhCCCCCHHH
Q psy15598 54 MRIVELAQ----LGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKV-VSYIKELKQKDPGIFAWE 128 (258)
Q Consensus 54 ~RIV~L~~----~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~-~~~I~~lv~~nP~ita~E 128 (258)
.++++.++ +..+..++|+.+|+|+.++.|..++.. |. .+....... ......++ ...+.+..+
T Consensus 8 ~~~~~~i~~~~~~~~~l~~lA~~~~~S~~~l~r~F~~~~--g~---------s~~~yi~~~Rl~~A~~~L-~~~~~~i~~ 75 (289)
T PRK15121 8 RDLLIWLEGHLDQPLSLDNVAAKAGYSKWHLQRMFKDVT--GH---------AIGAYIRARRLSKAAVAL-RLTSRPILD 75 (289)
T ss_pred HHHHHHHHhcccCCCCHHHHHHHHCcCHHHHHHHHHHHH--Cc---------CHHHHHHHHHHHHHHHHH-HcCCCCHHH
Confidence 34444443 468999999999999999999999873 21 111111111 11111222 234677777
Q ss_pred HHHHHHhcCCCCCCCCCCHHHHHHHHHhccCC
Q psy15598 129 IRDRLLSDGVCDKFNVPSVSSISRILRNKIGS 160 (258)
Q Consensus 129 Ir~~L~~~Gv~v~~~~pS~STI~RiLrr~~~~ 160 (258)
|+..+ |.. |.++..|.+++.-+.
T Consensus 76 iA~~~---Gf~------s~~~f~r~Fk~~~g~ 98 (289)
T PRK15121 76 IALQY---RFD------SQQTFTRAFKKQFAQ 98 (289)
T ss_pred HHHHH---CCC------CHHHHHHHHHHHHCc
Confidence 76655 664 788888888776554
No 489
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=87.77 E-value=1.9 Score=39.38 Aligned_cols=49 Identities=12% Similarity=0.169 Sum_probs=41.0
Q ss_pred CCCCHHHHHHHHHHHH---cCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598 46 RPLPNSVRMRIVELAQ---LGIRPCDISRQLRVSHGCVSKILARYHETGSIL 94 (258)
Q Consensus 46 R~~S~dlR~RIV~L~~---~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~ 94 (258)
+=++...-++|.+.++ .+.|..++|+.+|+||.|++|++.-....|-++
T Consensus 153 kGi~~~Tl~~i~~~~~~~~~~~Taeela~~~giSRvTaRRYLeyl~~~~~l~ 204 (224)
T COG4565 153 KGLDELTLQKVREALKEPDQELTAEELAQALGISRVTARRYLEYLVSNGILE 204 (224)
T ss_pred CCcCHHHHHHHHHHHhCcCCccCHHHHHHHhCccHHHHHHHHHHHHhcCeee
Confidence 3456667777888876 578999999999999999999999988888653
No 490
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=87.76 E-value=7.3 Score=32.04 Aligned_cols=80 Identities=15% Similarity=-0.022 Sum_probs=54.5
Q ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCH
Q psy15598 47 PLPNSVRMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFA 126 (258)
Q Consensus 47 ~~S~dlR~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~nP~ita 126 (258)
.++.+...=|...+...=+.+++++.||||..||+.=+.+-.+.=.+.+ -+..-....+..|.+.+++ -.+++
T Consensus 33 ~L~~E~~~Fi~~Fi~~rGnlKe~e~~lgiSYPTvR~rLd~ii~~lg~~~------~~~~~~~~~~~~IL~~L~~-GeIs~ 105 (113)
T PF09862_consen 33 RLSPEQLEFIKLFIKNRGNLKEMEKELGISYPTVRNRLDKIIEKLGYEE------DEEEEEEDERKEILDKLEK-GEISV 105 (113)
T ss_pred cCCHHHHHHHHHHHHhcCCHHHHHHHHCCCcHHHHHHHHHHHHHhCCCC------CcccccchhHHHHHHHHHc-CCCCH
Confidence 4777777766667778889999999999999999988877654311100 1122233446677777664 47888
Q ss_pred HHHHHHH
Q psy15598 127 WEIRDRL 133 (258)
Q Consensus 127 ~EIr~~L 133 (258)
.|-.+.|
T Consensus 106 eeA~~~L 112 (113)
T PF09862_consen 106 EEALEIL 112 (113)
T ss_pred HHHHHHh
Confidence 7776655
No 491
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=87.76 E-value=1.1 Score=39.22 Aligned_cols=32 Identities=19% Similarity=0.214 Sum_probs=29.3
Q ss_pred CCHHHHHHHhCCCHHHHHHHHHHhhhhCCccc
Q psy15598 64 IRPCDISRQLRVSHGCVSKILARYHETGSILP 95 (258)
Q Consensus 64 ~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~p 95 (258)
.+..+||..+|+|+.||+|.++++++.|.+..
T Consensus 170 ~t~~~lA~~lG~sretvsR~L~~L~~~G~I~~ 201 (226)
T PRK10402 170 EKHTQAAEYLGVSYRHLLYVLAQFIQDGYLKK 201 (226)
T ss_pred chHHHHHHHHCCcHHHHHHHHHHHHHCCCEEe
Confidence 47799999999999999999999999998743
No 492
>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=87.75 E-value=1.1 Score=36.27 Aligned_cols=36 Identities=17% Similarity=0.226 Sum_probs=29.7
Q ss_pred HHHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHHHHhh
Q psy15598 53 RMRIVELA-QLGIRPCDISRQLRVSHGCVSKILARYH 88 (258)
Q Consensus 53 R~RIV~L~-~~G~S~~eIAr~LGVSrsTVsRwikRyr 88 (258)
....+.++ .+-.|..+||..|+|||+.|+.-++|-.
T Consensus 22 Q~~Y~~lyy~dDlSl~EIAee~~VSRqAIyDnIKr~~ 58 (105)
T COG2739 22 QKNYLELYYLDDLSLSEIAEEFNVSRQAIYDNIKRTE 58 (105)
T ss_pred HHHHHHHHHHhhccHHHHHHHhCccHHHHHHHHHHHH
Confidence 34455554 5789999999999999999999999864
No 493
>PRK15186 AraC family transcriptional regulator; Provisional
Probab=87.62 E-value=2.8 Score=39.21 Aligned_cols=84 Identities=15% Similarity=0.089 Sum_probs=52.7
Q ss_pred HHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHh
Q psy15598 56 IVELAQLGIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKELKQKDPGIFAWEIRDRLLS 135 (258)
Q Consensus 56 IV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~lv~~nP~ita~EIr~~L~~ 135 (258)
|.....+.++..++|+.+|+|++|++|..++. .++.. ..+...-...-..++ .+...+..+|+..+
T Consensus 190 I~~~~~~~~sl~~lA~~~gmS~stl~R~Fk~~--g~s~~---------~~~~~~Rl~~A~~lL-~~~~~sI~~IA~~~-- 255 (291)
T PRK15186 190 IISDISRKWALKDISDSLYMSCSTLKRKLKQE--NTSFS---------EVYLNARMNKATKLL-RNSEYNITRVAYMC-- 255 (291)
T ss_pred HHhCccCCCCHHHHHHHHCcCHHHHHHHHHHc--CCCHH---------HHHHHHHHHHHHHHH-HcCCCCHHHHHHHh--
Confidence 33334467999999999999999999998862 22211 111111111122223 33456777776666
Q ss_pred cCCCCCCCCCCHHHHHHHHHhccCC
Q psy15598 136 DGVCDKFNVPSVSSISRILRNKIGS 160 (258)
Q Consensus 136 ~Gv~v~~~~pS~STI~RiLrr~~~~ 160 (258)
|.. |.+...|.+|+.-+.
T Consensus 256 -GY~------s~S~Fsr~FK~~~G~ 273 (291)
T PRK15186 256 -GYD------SASYFTCVFKKHFKT 273 (291)
T ss_pred -CCC------CHHHHHHHHHHHHCc
Confidence 665 889999999887654
No 494
>COG5352 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=87.55 E-value=0.69 Score=39.70 Aligned_cols=42 Identities=26% Similarity=0.327 Sum_probs=31.3
Q ss_pred HHHHH-HHHHHHcCCCHHHHHHHhC-CCHHHHHHHHHHhhhhCC
Q psy15598 51 SVRMR-IVELAQLGIRPCDISRQLR-VSHGCVSKILARYHETGS 92 (258)
Q Consensus 51 dlR~R-IV~L~~~G~S~~eIAr~LG-VSrsTVsRwikRyrEtGs 92 (258)
|.|.. +-+|+.+|+|.++||++|| ||++.|---+.|..=.|.
T Consensus 5 dERve~LkKLWseGLSASQIAaQLGGVsRnAVIGKVHRL~lsgR 48 (169)
T COG5352 5 DERVETLKKLWSEGLSASQIAAQLGGVSRNAVIGKVHRLGLSGR 48 (169)
T ss_pred HHHHHHHHHHHHcccCHHHHHHHhcCcchhhhheeeeecccccc
Confidence 44544 4456789999999999998 999999766666654444
No 495
>PRK11139 DNA-binding transcriptional activator GcvA; Provisional
Probab=87.55 E-value=2.8 Score=37.50 Aligned_cols=57 Identities=16% Similarity=0.163 Sum_probs=40.2
Q ss_pred HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhhh-CC-cccCCCCCCCCCCCCHHHHH
Q psy15598 53 RMRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHET-GS-ILPGAIGGSKPRVTTPKVVS 112 (258)
Q Consensus 53 R~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrEt-Gs-l~pk~rgG~RPrklT~e~~~ 112 (258)
..+++..+.+--+.+.+|+.|+||.++|++-+++.++. |. +-. |.| +.-.+|+.=+.
T Consensus 10 ~l~~f~~v~~~gs~s~AA~~L~isq~avS~~i~~LE~~lg~~Lf~--R~~-r~l~lT~~G~~ 68 (297)
T PRK11139 10 ALRAFEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGLKLFR--RRN-RSLLLTEEGQR 68 (297)
T ss_pred HHHHHHHHHHhCCHHHHHHHhCCChHHHHHHHHHHHHHhCchheE--ecC-CceeECHhHHH
Confidence 44566666666799999999999999999999999864 32 222 223 45666655333
No 496
>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=87.52 E-value=2.1 Score=38.24 Aligned_cols=58 Identities=14% Similarity=0.095 Sum_probs=39.4
Q ss_pred HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhhh-hCC-cccCCCCCCCCCCCCHHHHHHH
Q psy15598 54 MRIVELAQLGIRPCDISRQLRVSHGCVSKILARYHE-TGS-ILPGAIGGSKPRVTTPKVVSYI 114 (258)
Q Consensus 54 ~RIV~L~~~G~S~~eIAr~LGVSrsTVsRwikRyrE-tGs-l~pk~rgG~RPrklT~e~~~~I 114 (258)
.+++..+.+-.|.+.+|+.|+||.++|++.+++.++ -|. +-.+ .+ +.-.+|+.-+.++
T Consensus 8 l~~f~~v~~~gS~s~AA~~L~isq~avS~~I~~LE~~lg~~LF~R--~~-~~~~lT~~G~~l~ 67 (300)
T TIGR02424 8 LQCFVEVARQGSVKRAAEALHITQPAVSKTLRELEEILGTPLFER--DR-RGIRLTRYGELFL 67 (300)
T ss_pred HHHHHHHHHhCCHHHHHHHhCCChHHHHHHHHHHHHHhCCeEEEE--cC-CCccccHhHHHHH
Confidence 345555555569999999999999999999999986 443 2233 22 4456666544333
No 497
>COG1961 PinR Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]
Probab=87.46 E-value=0.89 Score=39.98 Aligned_cols=47 Identities=23% Similarity=0.309 Sum_probs=41.6
Q ss_pred CCCCHHHHHHHHHHHHcC-CCHHHHHHHhCCCHHHHHHHHHHhhhhCC
Q psy15598 46 RPLPNSVRMRIVELAQLG-IRPCDISRQLRVSHGCVSKILARYHETGS 92 (258)
Q Consensus 46 R~~S~dlR~RIV~L~~~G-~S~~eIAr~LGVSrsTVsRwikRyrEtGs 92 (258)
+....+.+..|+.+...| .+.++||+.+++++.||++|++.....+.
T Consensus 159 ~~~~~~~~~~v~~l~~~~~~~~~~~a~~~~i~~~t~~r~~~~~~~~~~ 206 (222)
T COG1961 159 RKKAEEQAAAVRRLLADGLGSYSEIARALGISRSTVYRILNKLKKRGG 206 (222)
T ss_pred ccccchhHHHHHHHHHhccchHHHHHHHcCccHHHHHHhhhhhhcccc
Confidence 567778888999999999 79999999999999999999999875554
No 498
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=87.45 E-value=1 Score=40.70 Aligned_cols=55 Identities=15% Similarity=0.167 Sum_probs=38.9
Q ss_pred CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCCCCCCCCCCCCHHHHHHHHHH
Q psy15598 63 GIRPCDISRQLRVSHGCVSKILARYHETGSILPGAIGGSKPRVTTPKVVSYIKEL 117 (258)
Q Consensus 63 G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~rgG~RPrklT~e~~~~I~~l 117 (258)
+.|.++||+.|++|++||++++++..+.|-+.....+...--.+|++-+..+.+.
T Consensus 21 ~IS~~eLA~~L~iS~~Tvsr~Lk~LEe~GlI~R~~~~r~~~v~LTekG~~ll~~~ 75 (217)
T PRK14165 21 KISSSEFANHTGTSSKTAARILKQLEDEGYITRTIVPRGQLITITEKGLDVLYNE 75 (217)
T ss_pred CcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEEcCCceEEEECHHHHHHHHHH
Confidence 4789999999999999999999999999987432211112334666555554333
No 499
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=87.42 E-value=1.1 Score=41.12 Aligned_cols=45 Identities=20% Similarity=0.213 Sum_probs=37.4
Q ss_pred HHHHHHHHHHHHc--CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcc
Q psy15598 50 NSVRMRIVELAQL--GIRPCDISRQLRVSHGCVSKILARYHETGSIL 94 (258)
Q Consensus 50 ~dlR~RIV~L~~~--G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~ 94 (258)
.+.+.+|+++++. -++..++|+.|+||..||+|=+..-.+.|.+.
T Consensus 16 ~eR~~~Il~~L~~~~~vtv~eLa~~l~VS~~TIRRDL~~Le~~G~l~ 62 (269)
T PRK09802 16 SERREQIIQRLRQQGSVQVNDLSALYGVSTVTIRNDLAFLEKQGIAV 62 (269)
T ss_pred HHHHHHHHHHHHHcCCEeHHHHHHHHCCCHHHHHHHHHHHHhCCCeE
Confidence 3556777777753 37999999999999999999999998888764
No 500
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=87.42 E-value=1.3 Score=40.05 Aligned_cols=44 Identities=18% Similarity=0.367 Sum_probs=36.1
Q ss_pred HHHHHHHH-c--CCCHHHHHHHhCCCHHHHHHHHHHhhhhCCcccCC
Q psy15598 54 MRIVELAQ-L--GIRPCDISRQLRVSHGCVSKILARYHETGSILPGA 97 (258)
Q Consensus 54 ~RIV~L~~-~--G~S~~eIAr~LGVSrsTVsRwikRyrEtGsl~pk~ 97 (258)
.+|++++. . +++..+||+.+|++++||+|.+....+.|-++-..
T Consensus 7 l~iL~~l~~~~~~l~l~ela~~~glpksT~~RlL~tL~~~G~v~~d~ 53 (246)
T COG1414 7 LAILDLLAEGPGGLSLAELAERLGLPKSTVHRLLQTLVELGYVEQDP 53 (246)
T ss_pred HHHHHHHHhCCCCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEcC
Confidence 45666664 2 35799999999999999999999999999875443
Done!