Query psy1904
Match_columns 163
No_of_seqs 196 out of 1518
Neff 9.1
Searched_HMMs 46136
Date Fri Aug 16 19:14:01 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1904.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1904hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0849|consensus 100.0 1.1E-29 2.3E-34 199.8 8.7 158 1-158 27-236 (354)
2 PF00292 PAX: 'Paired box' dom 99.9 6E-27 1.3E-31 157.0 5.5 90 1-90 29-118 (125)
3 KOG3517|consensus 99.9 3.1E-25 6.6E-30 162.2 4.5 91 1-91 32-122 (334)
4 KOG0484|consensus 99.9 1.1E-23 2.3E-28 134.5 0.2 65 93-157 12-76 (125)
5 KOG0488|consensus 99.9 3.7E-23 8E-28 159.7 2.2 66 95-160 169-234 (309)
6 KOG0489|consensus 99.9 3.8E-23 8.3E-28 157.0 0.6 62 97-158 158-219 (261)
7 KOG0842|consensus 99.9 2.9E-22 6.2E-27 152.7 3.9 63 95-157 150-212 (307)
8 KOG0850|consensus 99.8 1.7E-22 3.7E-27 146.3 1.7 69 94-162 118-186 (245)
9 KOG0485|consensus 99.8 5.2E-22 1.1E-26 142.5 1.2 65 94-158 100-164 (268)
10 KOG0493|consensus 99.8 7.8E-22 1.7E-26 145.1 2.0 97 62-158 209-306 (342)
11 KOG0843|consensus 99.8 1.4E-21 3E-26 136.6 2.7 60 97-156 101-160 (197)
12 KOG0487|consensus 99.8 2.1E-21 4.7E-26 148.0 3.0 66 92-157 229-294 (308)
13 KOG0494|consensus 99.8 7.9E-21 1.7E-25 139.7 3.7 68 96-163 138-206 (332)
14 KOG0492|consensus 99.8 7.8E-21 1.7E-25 135.6 2.5 64 93-156 139-202 (246)
15 KOG3862|consensus 99.8 3.2E-20 6.9E-25 137.3 4.6 85 1-85 37-121 (327)
16 KOG2251|consensus 99.8 3.3E-20 7.2E-25 133.8 3.5 64 93-156 32-95 (228)
17 PF00046 Homeobox: Homeobox do 99.7 6.4E-19 1.4E-23 104.3 0.7 57 99-155 1-57 (57)
18 KOG0844|consensus 99.7 1.1E-18 2.3E-23 131.3 1.1 64 96-159 179-242 (408)
19 TIGR01565 homeo_ZF_HD homeobox 99.7 9.5E-18 2.1E-22 98.2 4.6 52 99-150 2-57 (58)
20 KOG0848|consensus 99.7 1.5E-18 3.3E-23 128.2 1.1 61 96-156 197-257 (317)
21 KOG0491|consensus 99.7 1.1E-18 2.3E-23 120.5 -2.1 62 97-158 99-160 (194)
22 cd00131 PAX Paired Box domain 99.7 4.1E-16 8.8E-21 106.7 7.5 77 2-78 30-106 (128)
23 smart00389 HOX Homeodomain. DN 99.6 1.7E-16 3.6E-21 93.4 3.3 55 100-154 2-56 (56)
24 KOG0486|consensus 99.6 1.3E-16 2.8E-21 120.6 3.3 62 96-157 110-171 (351)
25 smart00351 PAX Paired Box doma 99.6 2.1E-15 4.6E-20 102.8 7.9 77 2-78 30-106 (125)
26 KOG3802|consensus 99.6 8.4E-16 1.8E-20 119.9 5.0 62 97-158 293-354 (398)
27 cd00086 homeodomain Homeodomai 99.6 5.1E-16 1.1E-20 92.2 2.8 57 100-156 2-58 (59)
28 KOG0483|consensus 99.6 9.9E-16 2.1E-20 110.9 3.2 55 101-155 53-107 (198)
29 COG5576 Homeodomain-containing 99.5 3.5E-15 7.5E-20 104.7 3.4 59 98-156 51-109 (156)
30 KOG0847|consensus 99.5 2.6E-15 5.7E-20 108.4 1.1 62 96-157 165-226 (288)
31 KOG4577|consensus 99.5 1.6E-14 3.5E-19 108.1 2.7 61 97-157 166-226 (383)
32 KOG0490|consensus 99.5 2E-14 4.4E-19 107.6 2.7 63 95-157 57-119 (235)
33 KOG1168|consensus 99.2 4.7E-12 1E-16 95.1 2.1 64 97-160 308-371 (385)
34 KOG2252|consensus 99.2 2.4E-11 5.1E-16 98.5 6.2 132 3-153 341-475 (558)
35 COG3415 Transposase and inacti 99.0 9.6E-10 2.1E-14 75.6 6.7 76 4-80 20-95 (138)
36 KOG0775|consensus 98.9 1E-09 2.2E-14 82.1 3.4 55 100-154 169-232 (304)
37 PF01710 HTH_Tnp_IS630: Transp 98.8 5.3E-09 1.1E-13 70.7 4.9 66 3-75 16-81 (119)
38 KOG0774|consensus 98.7 1.3E-08 2.9E-13 75.7 3.6 60 98-157 188-250 (334)
39 PF05920 Homeobox_KN: Homeobox 98.6 4.4E-09 9.5E-14 57.1 -0.2 35 118-152 6-40 (40)
40 PF13551 HTH_29: Winged helix- 98.6 1.1E-07 2.3E-12 63.1 6.3 64 1-64 7-74 (112)
41 PF13384 HTH_23: Homeodomain-l 98.3 1.3E-07 2.9E-12 53.9 0.7 31 3-33 15-45 (50)
42 KOG0490|consensus 98.3 4.4E-07 9.5E-12 67.9 2.6 62 95-156 150-211 (235)
43 PF13011 LZ_Tnp_IS481: leucine 98.1 8.5E-06 1.9E-10 51.3 5.9 57 3-59 23-82 (85)
44 PF02796 HTH_7: Helix-turn-hel 97.9 3E-06 6.5E-11 47.2 0.7 27 1-27 17-43 (45)
45 PF13518 HTH_28: Helix-turn-he 97.9 1E-05 2.2E-10 46.2 2.2 32 3-34 10-41 (52)
46 PF13936 HTH_38: Helix-turn-he 97.8 1.4E-05 3E-10 44.3 2.3 26 3-28 18-43 (44)
47 KOG1146|consensus 97.6 3.3E-05 7.2E-10 69.0 1.9 60 97-156 902-961 (1406)
48 PF13565 HTH_32: Homeodomain-l 97.4 0.0006 1.3E-08 42.1 5.8 57 21-79 1-62 (77)
49 PRK09413 IS2 repressor TnpA; R 97.4 0.00054 1.2E-08 46.3 5.7 35 3-37 27-61 (121)
50 PF06056 Terminase_5: Putative 97.3 0.00015 3.2E-09 42.6 1.9 27 3-29 11-37 (58)
51 PF04218 CENP-B_N: CENP-B N-te 97.3 9.5E-05 2.1E-09 42.6 1.0 28 2-29 19-46 (53)
52 PHA02591 hypothetical protein; 97.0 0.00038 8.1E-09 42.7 1.7 27 1-27 55-81 (83)
53 PF01325 Fe_dep_repress: Iron 96.9 0.0011 2.4E-08 39.1 2.8 32 4-35 21-52 (60)
54 PF00325 Crp: Bacterial regula 96.8 0.0014 3.1E-08 33.5 2.7 28 6-33 3-30 (32)
55 PF00356 LacI: Bacterial regul 96.8 0.0062 1.3E-07 33.9 5.2 19 8-26 2-20 (46)
56 KOG0773|consensus 96.8 0.0011 2.3E-08 52.7 2.8 60 98-157 239-301 (342)
57 PRK15418 transcriptional regul 96.7 0.0012 2.7E-08 51.9 2.9 37 3-39 27-63 (318)
58 PF01022 HTH_5: Bacterial regu 96.7 0.0011 2.4E-08 37.1 1.7 33 2-34 12-44 (47)
59 PF13412 HTH_24: Winged helix- 96.6 0.0026 5.6E-08 35.6 3.1 31 4-34 16-46 (48)
60 PF09339 HTH_IclR: IclR helix- 96.6 0.0019 4.1E-08 36.9 2.4 32 4-35 17-48 (52)
61 cd01104 HTH_MlrA-CarA Helix-Tu 96.5 0.015 3.2E-07 34.8 5.9 31 6-39 1-31 (68)
62 PF11569 Homez: Homeodomain le 96.4 0.00076 1.6E-08 39.0 -0.1 42 110-151 10-51 (56)
63 cd04762 HTH_MerR-trunc Helix-T 96.4 0.0086 1.9E-07 32.9 4.2 30 6-39 1-30 (49)
64 PF13744 HTH_37: Helix-turn-he 96.3 0.0022 4.7E-08 40.1 1.6 25 3-27 29-53 (80)
65 COG2522 Predicted transcriptio 96.3 0.002 4.4E-08 43.2 1.4 29 1-29 18-46 (119)
66 PF07037 DUF1323: Putative tra 96.2 0.015 3.3E-07 38.8 5.1 53 6-58 1-54 (122)
67 PF13443 HTH_26: Cro/C1-type H 96.1 0.0027 5.8E-08 37.5 1.2 26 1-26 6-31 (63)
68 smart00421 HTH_LUXR helix_turn 96.1 0.0067 1.5E-07 34.5 2.9 27 3-29 16-42 (58)
69 PF01381 HTH_3: Helix-turn-hel 96.1 0.0048 1E-07 35.3 2.2 24 3-26 7-30 (55)
70 PF01527 HTH_Tnp_1: Transposas 96.1 0.0045 9.7E-08 37.9 2.1 28 3-30 21-48 (76)
71 PF12759 HTH_Tnp_IS1: InsA C-t 96.0 0.0039 8.5E-08 34.4 1.5 28 1-28 17-44 (46)
72 TIGR03879 near_KaiC_dom probab 95.9 0.0077 1.7E-07 36.9 2.5 28 4-31 31-58 (73)
73 TIGR02531 yecD_yerC TrpR-relat 95.9 0.007 1.5E-07 38.6 2.4 24 3-26 48-71 (88)
74 PHA00542 putative Cro-like pro 95.9 0.0048 1E-07 38.8 1.6 24 3-26 29-52 (82)
75 PHA01976 helix-turn-helix prot 95.9 0.0094 2E-07 35.6 2.8 24 3-26 13-36 (67)
76 PRK10072 putative transcriptio 95.8 0.0096 2.1E-07 38.6 2.9 24 3-26 44-67 (96)
77 PF04545 Sigma70_r4: Sigma-70, 95.8 0.011 2.3E-07 33.3 2.8 26 4-29 19-44 (50)
78 COG2390 DeoR Transcriptional r 95.8 0.0081 1.7E-07 47.3 2.9 38 3-40 24-61 (321)
79 PF12728 HTH_17: Helix-turn-he 95.8 0.012 2.5E-07 33.3 2.9 46 6-56 2-47 (51)
80 smart00419 HTH_CRP helix_turn_ 95.8 0.012 2.6E-07 32.5 2.8 32 6-37 9-40 (48)
81 COG2944 Predicted transcriptio 95.8 0.011 2.5E-07 38.6 3.0 30 4-38 56-85 (104)
82 PF13613 HTH_Tnp_4: Helix-turn 95.7 0.0089 1.9E-07 34.3 2.2 26 4-29 18-43 (53)
83 cd00569 HTH_Hin_like Helix-tur 95.7 0.0088 1.9E-07 30.5 2.1 24 3-26 19-42 (42)
84 TIGR01321 TrpR trp operon repr 95.7 0.0054 1.2E-07 39.4 1.3 25 3-27 53-77 (94)
85 PF12802 MarR_2: MarR family; 95.7 0.0092 2E-07 34.9 2.3 31 6-36 22-52 (62)
86 cd06171 Sigma70_r4 Sigma70, re 95.7 0.014 2.9E-07 32.6 2.9 28 3-30 24-51 (55)
87 TIGR03070 couple_hipB transcri 95.6 0.0097 2.1E-07 34.1 2.1 24 3-26 13-36 (58)
88 smart00550 Zalpha Z-DNA-bindin 95.6 0.014 3E-07 35.3 2.8 33 5-37 22-54 (68)
89 PF08279 HTH_11: HTH domain; 95.5 0.012 2.6E-07 33.7 2.2 29 5-33 15-43 (55)
90 PRK04217 hypothetical protein; 95.4 0.016 3.5E-07 38.5 2.9 27 3-29 56-82 (110)
91 PF13560 HTH_31: Helix-turn-he 95.4 0.016 3.6E-07 34.3 2.7 24 3-26 12-35 (64)
92 cd00092 HTH_CRP helix_turn_hel 95.4 0.023 4.9E-07 33.7 3.2 34 4-37 24-57 (67)
93 smart00354 HTH_LACI helix_turn 95.4 0.013 2.9E-07 35.5 2.2 20 7-26 2-21 (70)
94 smart00420 HTH_DEOR helix_turn 95.3 0.023 5.1E-07 31.7 3.1 34 4-37 13-46 (53)
95 PF10668 Phage_terminase: Phag 95.3 0.011 2.5E-07 34.7 1.7 24 5-28 22-45 (60)
96 PF08281 Sigma70_r4_2: Sigma-7 95.3 0.016 3.5E-07 33.0 2.3 27 4-30 25-51 (54)
97 cd01392 HTH_LacI Helix-turn-he 95.3 0.012 2.7E-07 33.2 1.7 17 10-26 2-18 (52)
98 PF02954 HTH_8: Bacterial regu 95.3 0.012 2.5E-07 32.1 1.5 27 3-29 16-42 (42)
99 TIGR02607 antidote_HigA addict 95.2 0.014 3E-07 35.9 1.9 25 2-26 15-39 (78)
100 PF01047 MarR: MarR family; I 95.1 0.017 3.6E-07 33.5 1.9 32 4-35 16-47 (59)
101 PRK00118 putative DNA-binding 95.1 0.025 5.4E-07 37.2 2.9 27 3-29 31-57 (104)
102 PF13542 HTH_Tnp_ISL3: Helix-t 95.0 0.019 4E-07 32.5 2.0 25 5-29 27-51 (52)
103 cd04761 HTH_MerR-SF Helix-Turn 95.0 0.055 1.2E-06 29.9 3.9 31 6-40 1-31 (49)
104 PF04218 CENP-B_N: CENP-B N-te 95.0 0.026 5.5E-07 32.4 2.5 46 99-149 1-46 (53)
105 PHA02535 P terminase ATPase su 95.0 0.047 1E-06 46.2 5.0 26 4-29 17-42 (581)
106 PF03444 HrcA_DNA-bdg: Winged 95.0 0.056 1.2E-06 33.5 4.1 41 6-46 24-66 (78)
107 TIGR01764 excise DNA binding d 95.0 0.026 5.7E-07 31.0 2.5 32 6-41 2-33 (49)
108 PRK11050 manganese transport r 94.9 0.03 6.5E-07 39.3 3.2 35 4-38 50-84 (152)
109 smart00345 HTH_GNTR helix_turn 94.9 0.024 5.2E-07 32.6 2.3 30 7-36 22-51 (60)
110 PHA00738 putative HTH transcri 94.9 0.02 4.4E-07 37.6 2.1 38 5-42 26-63 (108)
111 PRK10141 DNA-binding transcrip 94.8 0.024 5.1E-07 38.1 2.4 54 5-58 30-83 (117)
112 PF08535 KorB: KorB domain; I 94.8 0.023 5E-07 36.5 2.2 26 4-29 2-27 (93)
113 PF04703 FaeA: FaeA-like prote 94.8 0.019 4.2E-07 34.1 1.7 36 4-39 14-49 (62)
114 cd04763 HTH_MlrA-like Helix-Tu 94.8 0.18 4E-06 30.1 6.1 31 6-39 1-31 (68)
115 smart00352 POU Found in Pit-Oc 94.8 0.025 5.5E-07 34.7 2.2 24 3-26 22-51 (75)
116 smart00418 HTH_ARSR helix_turn 94.8 0.036 7.7E-07 32.1 2.8 35 3-37 8-42 (66)
117 TIGR01610 phage_O_Nterm phage 94.7 0.038 8.2E-07 35.7 3.1 35 3-37 45-79 (95)
118 PF13730 HTH_36: Helix-turn-he 94.7 0.037 8.1E-07 31.6 2.7 28 7-34 27-54 (55)
119 PF01978 TrmB: Sugar-specific 94.6 0.012 2.6E-07 35.4 0.5 34 4-37 21-54 (68)
120 PF05930 Phage_AlpA: Prophage 94.6 0.018 4E-07 32.6 1.3 37 6-46 4-41 (51)
121 cd06170 LuxR_C_like C-terminal 94.6 0.045 9.8E-07 31.0 2.9 26 4-29 14-39 (57)
122 TIGR02844 spore_III_D sporulat 94.5 0.021 4.6E-07 35.7 1.5 21 6-26 20-40 (80)
123 smart00346 HTH_ICLR helix_turn 94.5 0.056 1.2E-06 34.1 3.5 35 4-38 19-53 (91)
124 TIGR02944 suf_reg_Xantho FeS a 94.5 0.062 1.3E-06 36.5 3.9 40 5-44 25-66 (130)
125 PRK11512 DNA-binding transcrip 94.5 0.043 9.4E-07 38.0 3.1 40 4-43 53-92 (144)
126 KOG3623|consensus 94.5 0.022 4.8E-07 48.9 1.9 51 105-156 564-614 (1007)
127 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 94.4 0.024 5.1E-07 32.1 1.4 27 2-28 17-43 (50)
128 PF04967 HTH_10: HTH DNA bindi 94.4 0.049 1.1E-06 31.2 2.7 26 4-29 22-47 (53)
129 PF02001 DUF134: Protein of un 94.4 0.041 8.9E-07 36.2 2.6 26 4-29 56-81 (106)
130 PRK09726 antitoxin HipB; Provi 94.3 0.035 7.6E-07 35.2 2.2 24 3-26 23-46 (88)
131 COG3311 AlpA Predicted transcr 94.3 0.14 3E-06 31.1 4.6 51 6-59 14-64 (70)
132 TIGR00721 tfx DNA-binding prot 94.3 0.048 1E-06 37.7 2.9 27 3-29 19-45 (137)
133 PRK03975 tfx putative transcri 94.3 0.049 1.1E-06 37.8 2.9 27 3-29 19-45 (141)
134 PHA00675 hypothetical protein 94.2 0.042 9.2E-07 33.8 2.2 26 3-28 37-62 (78)
135 COG2963 Transposase and inacti 94.2 0.069 1.5E-06 35.5 3.5 36 4-39 23-59 (116)
136 smart00529 HTH_DTXR Helix-turn 94.1 0.05 1.1E-06 34.7 2.7 32 7-38 1-32 (96)
137 PF12840 HTH_20: Helix-turn-he 94.1 0.034 7.4E-07 32.6 1.7 34 3-36 22-55 (61)
138 PRK11169 leucine-responsive tr 94.1 0.055 1.2E-06 38.4 3.0 35 2-36 24-59 (164)
139 cd04764 HTH_MlrA-like_sg1 Heli 94.1 0.3 6.4E-06 29.0 5.9 23 6-28 1-23 (67)
140 TIGR00122 birA_repr_reg BirA b 94.1 0.058 1.3E-06 32.4 2.7 33 3-35 11-43 (69)
141 smart00530 HTH_XRE Helix-turn- 94.0 0.037 8E-07 30.4 1.6 25 2-26 7-31 (56)
142 PF05344 DUF746: Domain of Unk 93.9 0.073 1.6E-06 31.7 2.8 41 6-46 14-61 (65)
143 PF08220 HTH_DeoR: DeoR-like h 93.9 0.035 7.7E-07 32.3 1.4 31 6-36 15-45 (57)
144 PRK11179 DNA-binding transcrip 93.9 0.043 9.4E-07 38.5 2.2 34 3-36 20-54 (153)
145 PF13463 HTH_27: Winged helix 93.8 0.053 1.2E-06 32.2 2.2 33 3-35 16-48 (68)
146 PF00196 GerE: Bacterial regul 93.8 0.069 1.5E-06 30.9 2.6 27 3-29 16-42 (58)
147 PF02082 Rrf2: Transcriptional 93.8 0.044 9.6E-07 34.3 1.8 38 6-43 26-65 (83)
148 PF05225 HTH_psq: helix-turn-h 93.7 0.072 1.6E-06 29.4 2.4 25 4-28 14-39 (45)
149 PRK11303 DNA-binding transcrip 93.7 0.046 1E-06 42.5 2.2 23 6-28 1-23 (328)
150 PF14493 HTH_40: Helix-turn-he 93.7 0.14 3.1E-06 32.6 4.1 68 1-74 9-76 (91)
151 PRK09706 transcriptional repre 93.6 0.081 1.7E-06 36.3 3.1 24 3-26 16-39 (135)
152 PF13545 HTH_Crp_2: Crp-like h 93.6 0.087 1.9E-06 32.0 2.9 31 6-36 29-59 (76)
153 PRK09492 treR trehalose repres 93.5 0.054 1.2E-06 41.9 2.3 23 6-28 5-27 (315)
154 smart00422 HTH_MERR helix_turn 93.5 0.4 8.7E-06 28.5 5.7 29 6-38 1-29 (70)
155 PRK13890 conjugal transfer pro 93.5 0.045 9.7E-07 36.9 1.6 25 2-26 15-39 (120)
156 cd00090 HTH_ARSR Arsenical Res 93.5 0.069 1.5E-06 31.8 2.3 35 4-38 19-53 (78)
157 TIGR02405 trehalos_R_Ecol treh 93.4 0.052 1.1E-06 42.0 2.1 23 6-28 2-24 (311)
158 cd04765 HTH_MlrA-like_sg2 Heli 93.4 0.54 1.2E-05 30.5 6.6 67 6-77 1-70 (99)
159 TIGR03830 CxxCG_CxxCG_HTH puta 93.4 0.088 1.9E-06 35.4 2.9 24 3-26 76-99 (127)
160 PRK01381 Trp operon repressor; 93.3 0.029 6.2E-07 36.4 0.4 21 5-25 55-75 (99)
161 PF07900 DUF1670: Protein of u 93.3 0.16 3.5E-06 37.7 4.3 109 4-144 103-216 (220)
162 PF01371 Trp_repressor: Trp re 93.3 0.049 1.1E-06 34.6 1.4 26 3-28 47-72 (87)
163 PRK11014 transcriptional repre 93.3 0.092 2E-06 36.3 2.9 39 6-44 26-66 (141)
164 PF13411 MerR_1: MerR HTH fami 93.2 0.18 3.8E-06 30.1 3.8 46 7-57 2-47 (69)
165 PF14549 P22_Cro: DNA-binding 93.2 0.075 1.6E-06 31.3 2.0 19 7-25 11-29 (60)
166 PRK03573 transcriptional regul 93.2 0.091 2E-06 36.2 2.9 40 4-43 45-84 (144)
167 TIGR02337 HpaR homoprotocatech 93.2 0.1 2.2E-06 34.7 3.0 36 4-39 41-76 (118)
168 PRK06424 transcription factor; 93.1 0.096 2.1E-06 36.5 2.8 24 3-26 95-118 (144)
169 PF14502 HTH_41: Helix-turn-he 93.1 0.097 2.1E-06 29.3 2.3 31 7-37 8-38 (48)
170 cd07377 WHTH_GntR Winged helix 93.1 0.11 2.4E-06 30.3 2.7 30 7-36 27-56 (66)
171 PF09012 FeoC: FeoC like trans 93.0 0.048 1E-06 32.9 1.0 35 3-37 11-46 (69)
172 PRK09526 lacI lac repressor; R 93.0 0.081 1.8E-06 41.3 2.6 23 6-28 6-28 (342)
173 PF02376 CUT: CUT domain; Int 93.0 0.026 5.6E-07 35.9 -0.2 28 2-29 23-51 (87)
174 COG3620 Predicted transcriptio 92.9 0.1 2.2E-06 37.0 2.6 30 4-38 17-46 (187)
175 cd00093 HTH_XRE Helix-turn-hel 92.9 0.071 1.5E-06 29.4 1.6 24 3-26 10-33 (58)
176 cd01106 HTH_TipAL-Mta Helix-Tu 92.8 0.46 9.9E-06 30.9 5.6 66 6-75 1-67 (103)
177 PF12844 HTH_19: Helix-turn-he 92.7 0.096 2.1E-06 30.8 2.1 24 3-26 10-33 (64)
178 PRK14987 gluconate operon tran 92.6 0.068 1.5E-06 41.7 1.7 23 6-28 6-28 (331)
179 PRK10014 DNA-binding transcrip 92.6 0.08 1.7E-06 41.4 2.1 23 6-28 7-29 (342)
180 TIGR02612 mob_myst_A mobile my 92.6 0.1 2.2E-06 36.7 2.3 24 3-26 36-59 (150)
181 COG1476 Predicted transcriptio 92.5 0.12 2.5E-06 31.3 2.2 24 3-26 12-35 (68)
182 smart00344 HTH_ASNC helix_turn 92.5 0.097 2.1E-06 34.2 2.1 32 5-36 17-48 (108)
183 PRK08359 transcription factor; 92.5 0.13 2.8E-06 37.1 2.8 24 3-26 96-119 (176)
184 cd01105 HTH_GlnR-like Helix-Tu 92.1 0.7 1.5E-05 29.2 5.7 68 5-76 1-69 (88)
185 PF13309 HTH_22: HTH domain 92.0 0.1 2.2E-06 31.1 1.6 20 8-27 45-64 (64)
186 PRK10401 DNA-binding transcrip 92.0 0.11 2.3E-06 40.9 2.2 23 6-28 2-24 (346)
187 cd04773 HTH_TioE_rpt2 Second H 92.0 0.67 1.5E-05 30.5 5.6 67 6-76 1-68 (108)
188 PRK10703 DNA-binding transcrip 92.0 0.11 2.4E-06 40.7 2.2 22 7-28 3-24 (341)
189 TIGR01889 Staph_reg_Sar staphy 91.9 0.63 1.4E-05 30.6 5.5 41 4-44 42-82 (109)
190 COG1321 TroR Mn-dependent tran 91.9 0.15 3.3E-06 35.9 2.6 38 6-43 25-62 (154)
191 TIGR01481 ccpA catabolite cont 91.9 0.11 2.4E-06 40.4 2.1 23 6-28 2-24 (329)
192 PRK10423 transcriptional repre 91.7 0.1 2.3E-06 40.4 1.8 19 9-27 2-20 (327)
193 PRK14165 winged helix-turn-hel 91.7 0.18 3.8E-06 37.6 2.9 34 5-38 21-54 (217)
194 TIGR00270 conserved hypothetic 91.7 0.19 4E-06 35.5 2.9 24 3-26 80-103 (154)
195 PF00392 GntR: Bacterial regul 91.6 0.21 4.5E-06 29.5 2.7 30 7-36 26-55 (64)
196 TIGR00180 parB_part ParB-like 91.5 0.12 2.7E-06 37.4 1.9 25 4-28 119-143 (187)
197 PF12116 SpoIIID: Stage III sp 91.4 0.15 3.1E-06 31.7 1.8 21 6-26 20-40 (82)
198 PRK10727 DNA-binding transcrip 91.3 0.13 2.9E-06 40.2 2.1 21 7-27 3-23 (343)
199 PRK10339 DNA-binding transcrip 91.2 0.12 2.6E-06 40.2 1.7 24 6-29 2-25 (327)
200 cd04774 HTH_YfmP Helix-Turn-He 91.2 0.98 2.1E-05 29.1 5.7 64 6-75 1-67 (96)
201 PRK10870 transcriptional repre 91.1 0.66 1.4E-05 33.3 5.3 54 5-58 71-127 (176)
202 TIGR02431 pcaR_pcaU beta-ketoa 91.1 0.25 5.4E-06 37.3 3.2 34 4-37 23-56 (248)
203 PRK03902 manganese transport t 90.9 0.27 5.8E-06 33.9 3.0 32 5-36 22-53 (142)
204 PF01418 HTH_6: Helix-turn-hel 90.9 0.17 3.7E-06 31.2 1.8 25 5-29 34-58 (77)
205 COG2826 Tra8 Transposase and i 90.9 0.12 2.5E-06 40.2 1.2 31 3-33 21-51 (318)
206 PF13404 HTH_AsnC-type: AsnC-t 90.8 0.18 4E-06 27.4 1.6 24 6-29 18-41 (42)
207 TIGR02417 fruct_sucro_rep D-fr 90.8 0.16 3.6E-06 39.4 2.0 21 8-28 2-22 (327)
208 PF09607 BrkDBD: Brinker DNA-b 90.7 0.2 4.2E-06 29.2 1.8 19 11-29 31-49 (58)
209 cd04782 HTH_BltR Helix-Turn-He 90.7 1.3 2.8E-05 28.5 5.9 64 6-75 1-67 (97)
210 COG1522 Lrp Transcriptional re 90.7 0.19 4.2E-06 34.8 2.2 30 6-35 23-52 (154)
211 COG1342 Predicted DNA-binding 90.6 0.25 5.3E-06 31.8 2.3 27 4-30 48-74 (99)
212 PRK01905 DNA-binding protein F 90.3 0.22 4.7E-06 30.8 1.9 26 4-29 49-74 (77)
213 PRK00215 LexA repressor; Valid 90.3 0.29 6.4E-06 35.8 2.9 34 6-39 24-58 (205)
214 PRK11920 rirA iron-responsive 90.2 0.38 8.3E-06 33.8 3.3 39 6-44 25-65 (153)
215 PRK09943 DNA-binding transcrip 90.2 0.23 5E-06 35.8 2.3 24 3-26 18-41 (185)
216 PF00126 HTH_1: Bacterial regu 90.2 0.3 6.5E-06 28.5 2.3 25 7-31 15-39 (60)
217 smart00347 HTH_MARR helix_turn 90.2 0.5 1.1E-05 29.8 3.6 36 4-39 23-58 (101)
218 cd04788 HTH_NolA-AlbR Helix-Tu 90.1 1.4 3E-05 28.3 5.6 64 6-75 1-67 (96)
219 PRK09637 RNA polymerase sigma 90.0 0.32 6.9E-06 34.9 2.8 26 4-29 121-146 (181)
220 PRK15431 ferrous iron transpor 90.0 0.27 5.9E-06 30.5 2.1 36 1-36 11-47 (78)
221 PF01710 HTH_Tnp_IS630: Transp 89.9 0.29 6.3E-06 32.8 2.4 26 4-29 70-95 (119)
222 PRK10163 DNA-binding transcrip 89.9 0.36 7.7E-06 37.1 3.2 33 4-36 39-71 (271)
223 PRK10857 DNA-binding transcrip 89.9 0.38 8.2E-06 34.3 3.1 41 6-46 26-68 (164)
224 PF08765 Mor: Mor transcriptio 89.8 0.34 7.3E-06 32.0 2.6 28 4-31 71-98 (108)
225 cd04766 HTH_HspR Helix-Turn-He 89.8 1.3 2.8E-05 28.1 5.3 48 6-58 2-49 (91)
226 cd01109 HTH_YyaN Helix-Turn-He 89.8 1.6 3.5E-05 28.8 6.0 67 6-76 1-68 (113)
227 PF00376 MerR: MerR family reg 89.8 0.29 6.2E-06 26.0 1.8 25 7-35 1-25 (38)
228 COG3093 VapI Plasmid maintenan 89.7 0.44 9.6E-06 31.2 3.0 49 4-68 22-70 (104)
229 PRK13182 racA polar chromosome 89.6 1.3 2.7E-05 32.0 5.6 62 6-73 1-64 (175)
230 cd06571 Bac_DnaA_C C-terminal 89.6 0.39 8.6E-06 30.5 2.8 27 4-30 43-70 (90)
231 TIGR02010 IscR iron-sulfur clu 89.6 0.41 8.9E-06 32.8 3.0 41 6-46 26-68 (135)
232 PRK15320 transcriptional activ 89.5 0.37 8E-06 35.5 2.7 29 4-32 178-206 (251)
233 PRK11569 transcriptional repre 89.5 0.4 8.6E-06 36.9 3.2 34 4-37 42-75 (274)
234 cd00592 HTH_MerR-like Helix-Tu 89.4 1.9 4E-05 27.7 5.9 64 6-74 1-65 (100)
235 COG1959 Predicted transcriptio 89.4 0.47 1E-05 33.2 3.2 40 6-45 26-67 (150)
236 PRK09834 DNA-binding transcrip 89.3 0.42 9.2E-06 36.5 3.2 32 5-36 26-57 (263)
237 PRK00430 fis global DNA-bindin 89.3 0.28 6.1E-06 31.7 1.9 26 4-29 67-92 (95)
238 TIGR00738 rrf2_super rrf2 fami 89.2 0.75 1.6E-05 31.1 4.1 41 5-45 25-67 (132)
239 COG3355 Predicted transcriptio 89.2 0.43 9.3E-06 32.5 2.7 33 3-35 40-72 (126)
240 PRK13509 transcriptional repre 89.1 0.26 5.5E-06 37.5 1.9 33 4-36 17-50 (251)
241 cd04789 HTH_Cfa Helix-Turn-Hel 89.0 2 4.3E-05 27.9 5.8 63 6-74 2-66 (102)
242 COG5606 Uncharacterized conser 89.0 0.17 3.7E-06 31.9 0.7 24 3-26 39-62 (91)
243 PF07453 NUMOD1: NUMOD1 domain 89.0 0.33 7.1E-06 25.4 1.7 20 7-26 18-37 (37)
244 PF01726 LexA_DNA_bind: LexA D 89.0 0.51 1.1E-05 28.2 2.7 33 4-36 22-57 (65)
245 PRK09744 DNA-binding transcrip 89.0 0.39 8.4E-06 29.4 2.2 18 8-25 13-30 (75)
246 TIGR02702 SufR_cyano iron-sulf 88.9 0.48 1.1E-05 34.7 3.1 33 4-36 14-46 (203)
247 PRK12511 RNA polymerase sigma 88.8 0.44 9.6E-06 34.3 2.9 26 4-29 126-151 (182)
248 cd04767 HTH_HspR-like_MBC Heli 88.7 1.5 3.3E-05 29.5 5.2 64 6-75 2-67 (120)
249 PRK15090 DNA-binding transcrip 88.6 0.51 1.1E-05 35.9 3.2 34 4-37 27-60 (257)
250 PF07022 Phage_CI_repr: Bacter 88.6 0.22 4.8E-06 29.7 1.0 21 7-27 14-35 (66)
251 PRK10906 DNA-binding transcrip 88.6 0.25 5.5E-06 37.6 1.5 40 3-43 16-56 (252)
252 PRK12516 RNA polymerase sigma 88.6 0.47 1E-05 34.2 2.9 26 4-29 131-156 (187)
253 PF07750 GcrA: GcrA cell cycle 88.5 0.36 7.8E-06 34.3 2.2 28 2-29 15-43 (162)
254 PRK13777 transcriptional regul 88.4 0.55 1.2E-05 34.1 3.1 35 4-38 58-92 (185)
255 cd04772 HTH_TioE_rpt1 First He 88.3 3 6.6E-05 26.9 6.3 61 7-71 2-62 (99)
256 cd01279 HTH_HspR-like Helix-Tu 88.3 2.3 5E-05 27.4 5.7 63 6-74 2-67 (98)
257 TIGR03697 NtcA_cyano global ni 88.2 0.5 1.1E-05 33.8 2.8 33 6-38 144-176 (193)
258 PRK12533 RNA polymerase sigma 88.2 0.5 1.1E-05 35.1 2.9 27 3-29 148-174 (216)
259 PRK06474 hypothetical protein; 88.2 0.44 9.4E-06 34.4 2.4 32 6-37 27-59 (178)
260 PRK13918 CRP/FNR family transc 88.1 0.49 1.1E-05 34.1 2.8 31 6-36 150-180 (202)
261 cd04780 HTH_MerR-like_sg5 Heli 88.1 2.4 5.1E-05 27.3 5.6 66 6-75 1-68 (95)
262 cd04775 HTH_Cfa-like Helix-Tur 88.0 2.4 5.1E-05 27.6 5.7 64 6-74 2-66 (102)
263 smart00497 IENR1 Intron encode 88.0 0.51 1.1E-05 26.4 2.2 22 7-28 19-40 (53)
264 PRK10411 DNA-binding transcrip 87.8 0.3 6.5E-06 36.9 1.5 32 5-36 18-49 (240)
265 COG1414 IclR Transcriptional r 87.7 0.6 1.3E-05 35.4 3.0 35 5-39 19-53 (246)
266 TIGR00498 lexA SOS regulatory 87.6 0.54 1.2E-05 34.2 2.7 35 4-38 22-59 (199)
267 PRK15043 transcriptional regul 87.6 2 4.4E-05 32.6 5.8 67 5-76 3-71 (243)
268 COG1609 PurR Transcriptional r 87.5 0.41 8.8E-06 37.9 2.1 21 7-27 2-22 (333)
269 PF04297 UPF0122: Putative hel 87.5 0.51 1.1E-05 30.8 2.2 26 4-29 32-57 (101)
270 TIGR02959 SigZ RNA polymerase 87.2 0.66 1.4E-05 32.8 2.9 26 4-29 115-140 (170)
271 PRK04140 hypothetical protein; 87.2 0.6 1.3E-05 36.8 2.9 24 3-26 137-160 (317)
272 COG2524 Predicted transcriptio 87.0 0.88 1.9E-05 34.8 3.5 43 6-48 26-70 (294)
273 COG2452 Predicted site-specifi 86.9 0.86 1.9E-05 33.1 3.3 48 5-56 1-48 (193)
274 PRK11161 fumarate/nitrate redu 86.8 0.63 1.4E-05 34.5 2.7 33 6-38 185-217 (235)
275 cd04783 HTH_MerR1 Helix-Turn-H 86.7 2.6 5.6E-05 28.4 5.5 65 6-76 1-68 (126)
276 PRK12540 RNA polymerase sigma 86.6 0.72 1.6E-05 33.1 2.9 27 3-29 125-151 (182)
277 COG3677 Transposase and inacti 86.5 0.6 1.3E-05 31.9 2.2 37 2-38 86-122 (129)
278 PRK09391 fixK transcriptional 86.5 0.69 1.5E-05 34.4 2.8 31 6-36 180-210 (230)
279 cd01282 HTH_MerR-like_sg3 Heli 86.4 3.4 7.4E-05 27.3 5.9 65 6-75 1-66 (112)
280 COG2771 CsgD DNA-binding HTH d 86.2 1 2.2E-05 26.0 2.9 27 3-29 17-43 (65)
281 cd01110 HTH_SoxR Helix-Turn-He 86.2 3.2 6.9E-05 28.6 5.8 66 6-76 2-68 (139)
282 TIGR03001 Sig-70_gmx1 RNA poly 86.0 0.79 1.7E-05 34.7 2.9 26 4-29 176-201 (244)
283 cd04779 HTH_MerR-like_sg4 Heli 86.0 3.1 6.6E-05 28.6 5.6 65 6-76 1-67 (134)
284 PF00165 HTH_AraC: Bacterial r 85.9 1 2.3E-05 24.0 2.6 26 4-29 7-32 (42)
285 cd07153 Fur_like Ferric uptake 85.9 1.1 2.4E-05 29.5 3.2 37 4-40 15-56 (116)
286 cd04770 HTH_HMRTR Helix-Turn-H 85.8 3.8 8.2E-05 27.4 5.9 67 6-76 1-68 (123)
287 PRK08241 RNA polymerase factor 85.7 2.4 5.1E-05 33.5 5.6 27 4-30 168-194 (339)
288 PF04645 DUF603: Protein of un 85.6 0.75 1.6E-05 32.8 2.4 33 3-35 16-49 (181)
289 cd04768 HTH_BmrR-like Helix-Tu 85.5 3.7 8.1E-05 26.3 5.5 30 6-39 1-30 (96)
290 cd01111 HTH_MerD Helix-Turn-He 85.4 5 0.00011 26.3 6.2 64 6-75 1-67 (107)
291 TIGR02043 ZntR Zn(II)-responsi 85.3 3.6 7.7E-05 28.0 5.7 65 6-76 2-69 (131)
292 PF03297 Ribosomal_S25: S25 ri 85.3 0.67 1.4E-05 30.5 1.9 33 6-38 60-92 (105)
293 TIGR02044 CueR Cu(I)-responsiv 85.3 3.9 8.5E-05 27.6 5.8 65 6-76 1-68 (127)
294 PF00440 TetR_N: Bacterial reg 85.2 0.96 2.1E-05 24.8 2.3 23 4-26 15-37 (47)
295 COG3888 Predicted transcriptio 85.1 0.79 1.7E-05 35.1 2.4 45 4-48 19-63 (321)
296 PRK12423 LexA repressor; Provi 85.0 0.74 1.6E-05 33.8 2.3 34 4-37 22-58 (202)
297 PRK09334 30S ribosomal protein 85.0 0.69 1.5E-05 29.3 1.8 33 6-38 42-74 (86)
298 TIGR00637 ModE_repress ModE mo 85.0 0.97 2.1E-05 29.3 2.6 28 7-34 18-46 (99)
299 PF08822 DUF1804: Protein of u 84.8 1.2 2.6E-05 31.7 3.1 31 4-34 18-48 (165)
300 PRK10434 srlR DNA-bindng trans 84.8 0.53 1.2E-05 35.9 1.5 35 3-37 16-51 (256)
301 PHA02943 hypothetical protein; 84.7 0.98 2.1E-05 31.7 2.6 41 3-43 21-62 (165)
302 COG1356 tfx Transcriptional re 84.7 0.9 2E-05 30.8 2.3 29 1-29 19-47 (143)
303 PRK11922 RNA polymerase sigma 84.6 1 2.2E-05 33.6 2.9 26 4-29 164-189 (231)
304 COG5484 Uncharacterized conser 84.5 0.74 1.6E-05 35.0 2.1 26 4-29 18-43 (279)
305 COG1846 MarR Transcriptional r 84.4 0.82 1.8E-05 29.8 2.1 32 9-40 40-71 (126)
306 PRK10402 DNA-binding transcrip 84.3 0.91 2E-05 33.6 2.5 33 6-38 170-202 (226)
307 TIGR03338 phnR_burk phosphonat 84.3 2 4.3E-05 31.4 4.3 38 6-43 35-72 (212)
308 cd01108 HTH_CueR Helix-Turn-He 84.2 4.4 9.6E-05 27.4 5.7 65 6-76 1-68 (127)
309 PRK11013 DNA-binding transcrip 84.1 0.67 1.4E-05 35.9 1.8 26 3-29 17-42 (309)
310 TIGR02054 MerD mercuric resist 84.0 6.6 0.00014 26.4 6.4 65 5-75 3-70 (120)
311 PF09048 Cro: Cro; InterPro: 83.9 1.1 2.4E-05 26.1 2.2 21 8-28 15-35 (59)
312 cd04769 HTH_MerR2 Helix-Turn-H 83.9 4.4 9.4E-05 26.9 5.5 65 6-75 1-66 (116)
313 PRK09954 putative kinase; Prov 83.9 1 2.2E-05 35.9 2.8 30 6-35 18-47 (362)
314 PRK12546 RNA polymerase sigma 83.8 1.2 2.5E-05 32.2 2.9 27 3-29 127-153 (188)
315 PRK09906 DNA-binding transcrip 83.5 0.69 1.5E-05 35.4 1.7 26 3-29 14-39 (296)
316 cd01107 HTH_BmrR Helix-Turn-He 83.5 5.5 0.00012 26.0 5.8 65 6-74 1-67 (108)
317 PRK09514 zntR zinc-responsive 83.5 4.3 9.4E-05 28.0 5.5 65 6-76 2-69 (140)
318 cd04784 HTH_CadR-PbrR Helix-Tu 83.5 5 0.00011 27.0 5.7 67 6-76 1-68 (127)
319 PF04967 HTH_10: HTH DNA bindi 83.4 1.2 2.6E-05 25.5 2.2 38 105-142 1-40 (53)
320 COG1813 Predicted transcriptio 83.4 1.1 2.4E-05 31.8 2.5 31 3-38 90-120 (165)
321 PRK12682 transcriptional regul 83.3 0.78 1.7E-05 35.5 1.9 28 2-29 13-40 (309)
322 PRK15201 fimbriae regulatory p 83.3 0.96 2.1E-05 32.7 2.1 29 3-31 146-174 (198)
323 TIGR02047 CadR-PbrR Cd(II)/Pb( 83.2 5.8 0.00013 26.8 5.9 65 6-76 1-68 (127)
324 PRK06704 RNA polymerase factor 83.2 1.2 2.7E-05 33.4 2.8 60 4-66 131-191 (228)
325 TIGR02960 SigX5 RNA polymerase 83.2 1.1 2.4E-05 35.0 2.7 26 4-29 157-182 (324)
326 cd04786 HTH_MerR-like_sg7 Heli 83.1 5.7 0.00012 27.1 5.9 65 6-76 1-68 (131)
327 TIGR03339 phn_lysR aminoethylp 83.1 0.85 1.8E-05 34.3 2.0 23 7-29 13-35 (279)
328 PRK10227 DNA-binding transcrip 83.0 7 0.00015 26.8 6.3 65 6-76 1-68 (135)
329 PF06322 Phage_NinH: Phage Nin 83.0 1 2.2E-05 26.5 1.8 19 8-26 19-37 (64)
330 COG1349 GlpR Transcriptional r 83.0 0.64 1.4E-05 35.4 1.3 36 2-37 15-51 (253)
331 PRK08154 anaerobic benzoate ca 82.9 1.2 2.7E-05 34.8 2.9 24 3-26 39-62 (309)
332 cd04785 HTH_CadR-PbrR-like Hel 82.8 5.9 0.00013 26.7 5.9 65 6-76 1-68 (126)
333 PRK15411 rcsA colanic acid cap 82.8 0.92 2E-05 33.3 2.0 27 3-29 150-176 (207)
334 TIGR02787 codY_Gpos GTP-sensin 82.7 1.6 3.6E-05 33.0 3.3 36 6-41 199-234 (251)
335 TIGR00373 conserved hypothetic 82.4 1.4 3.1E-05 31.1 2.7 32 5-36 28-59 (158)
336 PRK11233 nitrogen assimilation 82.3 0.86 1.9E-05 35.2 1.8 23 7-29 17-39 (305)
337 TIGR02684 dnstrm_HI1420 probab 82.0 1.2 2.5E-05 28.4 2.0 21 4-26 44-64 (89)
338 COG3655 Predicted transcriptio 81.8 0.68 1.5E-05 28.3 0.8 26 1-26 11-36 (73)
339 PRK11151 DNA-binding transcrip 81.6 0.94 2E-05 34.9 1.8 27 3-30 14-40 (305)
340 PF05732 RepL: Firmicute plasm 81.6 1.2 2.7E-05 31.7 2.2 34 6-39 76-109 (165)
341 cd04776 HTH_GnyR Helix-Turn-He 81.3 6.5 0.00014 26.2 5.6 65 6-76 1-66 (118)
342 PRK13832 plasmid partitioning 81.3 1.1 2.5E-05 37.4 2.2 28 1-28 114-141 (520)
343 PF12964 DUF3853: Protein of u 81.1 1 2.2E-05 29.0 1.4 28 8-39 48-75 (96)
344 COG2345 Predicted transcriptio 80.9 2 4.4E-05 32.0 3.2 43 4-46 24-68 (218)
345 PRK09791 putative DNA-binding 80.9 1.1 2.4E-05 34.4 1.9 26 3-29 18-43 (302)
346 cd04787 HTH_HMRTR_unk Helix-Tu 80.8 6.5 0.00014 26.8 5.5 67 6-76 1-68 (133)
347 PRK12684 transcriptional regul 80.7 1.1 2.4E-05 34.8 1.9 28 2-29 13-40 (313)
348 PRK09636 RNA polymerase sigma 80.5 1.7 3.6E-05 33.7 2.8 26 4-29 130-155 (293)
349 PF02042 RWP-RK: RWP-RK domain 80.4 2.2 4.9E-05 24.3 2.6 25 5-29 15-39 (52)
350 PF05269 Phage_CII: Bacterioph 80.3 1.7 3.7E-05 27.8 2.3 21 7-27 25-45 (91)
351 TIGR02957 SigX4 RNA polymerase 80.3 1.8 3.8E-05 33.4 2.9 27 4-30 123-149 (281)
352 PRK09392 ftrB transcriptional 80.2 1.7 3.8E-05 32.2 2.7 29 6-35 174-202 (236)
353 cd04777 HTH_MerR-like_sg1 Heli 80.1 2.9 6.3E-05 27.3 3.5 65 6-76 1-66 (107)
354 PRK15002 redox-sensitivie tran 80.1 6.3 0.00014 27.8 5.4 65 6-76 12-78 (154)
355 PRK10840 transcriptional regul 80.0 1.9 4.2E-05 31.3 2.9 26 4-29 164-189 (216)
356 cd04790 HTH_Cfa-like_unk Helix 80.0 7.7 0.00017 27.7 5.9 64 6-75 2-68 (172)
357 COG0789 SoxR Predicted transcr 79.9 7.8 0.00017 25.6 5.6 67 6-76 1-68 (124)
358 PRK13749 transcriptional regul 79.7 14 0.00031 24.9 6.8 66 5-76 3-71 (121)
359 PRK10430 DNA-binding transcrip 79.6 1.9 4.2E-05 32.0 2.8 32 4-35 177-208 (239)
360 PRK13719 conjugal transfer tra 79.1 2.2 4.8E-05 31.8 2.9 27 3-29 156-182 (217)
361 PRK11414 colanic acid/biofilm 79.1 5.1 0.00011 29.5 4.9 37 6-42 35-71 (221)
362 PRK04424 fatty acid biosynthes 78.9 1.2 2.5E-05 32.3 1.4 32 4-35 19-51 (185)
363 TIGR03418 chol_sulf_TF putativ 78.8 1.4 3E-05 33.6 1.9 23 7-29 17-39 (291)
364 TIGR01950 SoxR redox-sensitive 78.8 7.6 0.00016 26.9 5.4 66 6-76 2-68 (142)
365 PRK09483 response regulator; P 78.7 2.2 4.9E-05 30.5 2.9 27 3-29 161-187 (217)
366 PRK09775 putative DNA-binding 78.3 1.8 3.8E-05 35.9 2.4 28 2-29 10-37 (442)
367 PRK11886 bifunctional biotin-- 78.3 2.4 5.2E-05 33.3 3.1 31 4-34 17-47 (319)
368 PRK12683 transcriptional regul 78.2 1.5 3.2E-05 34.0 1.9 28 2-29 13-40 (309)
369 PRK09191 two-component respons 78.1 2.1 4.6E-05 31.9 2.7 28 4-31 103-130 (261)
370 PRK12679 cbl transcriptional r 78.0 1.5 3.3E-05 34.0 1.9 28 2-29 13-40 (316)
371 PF05043 Mga: Mga helix-turn-h 77.9 1.5 3.2E-05 27.4 1.5 28 4-31 29-56 (87)
372 PHA02701 ORF020 dsRNA-binding 77.8 1.9 4.1E-05 31.2 2.1 33 6-38 20-52 (183)
373 PF12793 SgrR_N: Sugar transpo 77.6 6.9 0.00015 26.1 4.7 42 6-47 20-63 (115)
374 PF04552 Sigma54_DBD: Sigma-54 77.5 0.73 1.6E-05 32.7 0.0 22 6-27 50-71 (160)
375 PRK09635 sigI RNA polymerase s 77.3 2.4 5.2E-05 33.0 2.8 27 4-30 133-159 (290)
376 COG1709 Predicted transcriptio 77.2 1.2 2.6E-05 33.1 1.0 22 5-26 40-61 (241)
377 PRK10216 DNA-binding transcrip 77.2 1.7 3.6E-05 33.8 1.9 23 7-29 24-46 (319)
378 PF03428 RP-C: Replication pro 76.9 3.5 7.5E-05 29.8 3.3 38 6-43 71-109 (177)
379 TIGR02051 MerR Hg(II)-responsi 76.7 9.6 0.00021 25.6 5.3 64 7-76 1-67 (124)
380 PF01527 HTH_Tnp_1: Transposas 76.2 0.89 1.9E-05 27.4 0.1 45 100-148 2-46 (76)
381 smart00342 HTH_ARAC helix_turn 76.0 3.1 6.7E-05 24.9 2.6 24 6-29 2-25 (84)
382 PRK03341 arginine repressor; P 75.7 2.6 5.6E-05 30.2 2.4 24 6-29 30-58 (168)
383 PF13693 HTH_35: Winged helix- 75.7 1.4 3.1E-05 27.3 0.9 24 3-26 13-36 (78)
384 PRK10856 cytoskeletal protein 75.6 3 6.5E-05 33.2 3.0 24 3-26 25-48 (331)
385 PRK11534 DNA-binding transcrip 75.3 6.5 0.00014 29.0 4.6 33 6-38 31-63 (224)
386 PRK13348 chromosome replicatio 75.2 2 4.3E-05 32.8 1.9 23 7-29 18-40 (294)
387 PRK00441 argR arginine repress 75.0 2.2 4.9E-05 29.8 1.9 24 6-29 19-47 (149)
388 TIGR03454 partition_RepB plasm 74.9 2.1 4.5E-05 34.0 1.9 27 3-29 175-201 (325)
389 TIGR02293 TAS_TIGR02293 putati 74.8 2.9 6.3E-05 28.6 2.4 23 4-26 35-57 (133)
390 PRK13698 plasmid-partitioning 74.7 2.8 6.1E-05 33.2 2.5 26 4-29 175-200 (323)
391 PRK09802 DNA-binding transcrip 74.7 2 4.3E-05 33.0 1.7 31 6-36 32-62 (269)
392 PRK12680 transcriptional regul 74.7 2.2 4.7E-05 33.5 2.0 27 4-30 15-41 (327)
393 PF08667 BetR: BetR domain; I 74.6 2 4.3E-05 30.1 1.5 19 8-26 25-43 (147)
394 PRK10837 putative DNA-binding 74.4 2 4.4E-05 32.6 1.7 23 7-29 19-41 (290)
395 PF13022 HTH_Tnp_1_2: Helix-tu 74.3 3 6.6E-05 28.9 2.3 23 6-28 35-57 (142)
396 PF03333 PapB: Adhesin biosynt 74.3 3.5 7.7E-05 26.4 2.5 29 3-31 51-79 (91)
397 PRK11482 putative DNA-binding 74.1 2.3 4.9E-05 33.2 2.0 23 7-29 45-67 (317)
398 TIGR02325 C_P_lyase_phnF phosp 74.1 3.1 6.7E-05 31.0 2.6 33 7-39 34-66 (238)
399 PRK12681 cysB transcriptional 74.0 2.2 4.8E-05 33.4 1.9 27 3-29 14-40 (324)
400 PRK06266 transcription initiat 73.7 3 6.6E-05 30.1 2.4 34 4-37 34-68 (178)
401 COG2186 FadR Transcriptional r 73.4 3.5 7.7E-05 31.1 2.8 37 8-44 37-73 (241)
402 PHA03103 double-strand RNA-bin 73.0 4.1 8.9E-05 29.6 2.9 34 4-37 26-59 (183)
403 TIGR02424 TF_pcaQ pca operon t 73.0 3.2 6.9E-05 31.7 2.5 23 7-29 19-41 (300)
404 TIGR03298 argP transcriptional 73.0 2.5 5.5E-05 32.2 1.9 24 7-30 17-40 (292)
405 TIGR02404 trehalos_R_Bsub treh 72.8 3.5 7.5E-05 30.7 2.6 32 7-38 26-57 (233)
406 COG1654 BirA Biotin operon rep 72.7 4.7 0.0001 25.1 2.7 32 6-37 20-51 (79)
407 cd04781 HTH_MerR-like_sg6 Heli 72.6 15 0.00033 24.4 5.5 64 6-75 1-66 (120)
408 PF06970 RepA_N: Replication i 72.4 3.2 7E-05 25.6 1.9 23 6-28 53-75 (76)
409 PRK14999 histidine utilization 72.1 3.7 8E-05 30.8 2.6 30 7-36 38-67 (241)
410 PRK11475 DNA-binding transcrip 71.7 4.5 9.8E-05 29.8 2.9 27 3-29 147-173 (207)
411 PRK10225 DNA-binding transcrip 71.7 3 6.5E-05 31.5 2.0 37 7-43 35-71 (257)
412 PRK10681 DNA-binding transcrip 71.6 2.4 5.3E-05 32.2 1.6 31 3-33 18-49 (252)
413 TIGR02018 his_ut_repres histid 71.4 3.8 8.2E-05 30.4 2.5 33 7-39 27-59 (230)
414 PF08222 HTH_CodY: CodY helix- 71.3 3 6.5E-05 24.2 1.5 36 6-41 5-40 (61)
415 KOG1146|consensus 71.3 1.7 3.6E-05 40.3 0.6 63 99-161 445-507 (1406)
416 PRK09464 pdhR transcriptional 71.0 3.4 7.3E-05 31.2 2.2 36 7-42 36-71 (254)
417 PRK11402 DNA-binding transcrip 70.7 4 8.7E-05 30.5 2.5 31 8-38 36-66 (241)
418 PF14947 HTH_45: Winged helix- 70.6 2.6 5.7E-05 25.8 1.3 53 2-58 16-68 (77)
419 COG5625 Predicted transcriptio 70.5 3.9 8.5E-05 26.6 2.0 33 4-36 35-67 (113)
420 COG2973 TrpR Trp operon repres 70.5 2.4 5.3E-05 27.4 1.1 19 6-24 61-79 (103)
421 PRK10094 DNA-binding transcrip 70.4 4 8.7E-05 31.6 2.6 23 7-29 18-40 (308)
422 PF07374 DUF1492: Protein of u 70.3 5.4 0.00012 25.8 2.7 26 4-29 70-95 (100)
423 PF07471 Phage_Nu1: Phage DNA 69.9 2.2 4.7E-05 30.4 0.9 20 7-26 4-23 (164)
424 PF13592 HTH_33: Winged helix- 69.9 4.2 9.2E-05 23.6 2.0 20 10-29 13-34 (60)
425 PRK13752 putative transcriptio 69.7 19 0.0004 25.0 5.5 64 6-75 8-74 (144)
426 PRK10421 DNA-binding transcrip 69.6 3.7 8.1E-05 31.0 2.2 36 8-43 29-64 (253)
427 PF06163 DUF977: Bacterial pro 69.5 5.7 0.00012 27.0 2.7 34 4-37 24-58 (127)
428 COG5352 Uncharacterized protei 69.4 2.7 5.8E-05 29.0 1.2 36 3-38 16-52 (169)
429 PRK10079 phosphonate metabolis 69.3 4.5 9.7E-05 30.3 2.5 31 8-38 38-68 (241)
430 TIGR03613 RutR pyrimidine util 69.3 4 8.6E-05 29.3 2.2 23 4-26 27-49 (202)
431 PF07506 RepB: RepB plasmid pa 69.2 3.5 7.6E-05 29.8 1.9 26 2-27 18-43 (185)
432 CHL00180 rbcR LysR transcripti 69.1 4.1 8.9E-05 31.4 2.4 23 7-29 21-43 (305)
433 PF10654 DUF2481: Protein of u 68.9 4.1 8.9E-05 27.1 1.9 29 1-29 76-104 (126)
434 TIGR02812 fadR_gamma fatty aci 68.7 5 0.00011 29.8 2.7 33 7-39 32-64 (235)
435 PRK11074 putative DNA-binding 68.6 3.5 7.7E-05 31.6 1.9 23 7-29 18-40 (300)
436 COG1339 Transcriptional regula 68.6 5 0.00011 29.5 2.5 31 6-36 20-50 (214)
437 PRK09990 DNA-binding transcrip 68.6 6.1 0.00013 29.7 3.2 32 7-38 33-64 (251)
438 PRK11242 DNA-binding transcrip 68.6 4.2 9.1E-05 30.9 2.3 25 7-31 17-41 (296)
439 COG1802 GntR Transcriptional r 68.6 13 0.00029 27.5 4.9 39 6-44 40-78 (230)
440 PRK15482 transcriptional regul 68.5 4.4 9.6E-05 31.2 2.4 25 5-29 34-58 (285)
441 PRK15421 DNA-binding transcrip 68.2 3.8 8.2E-05 32.0 2.0 26 3-29 15-40 (317)
442 PRK05638 threonine synthase; V 68.1 4.4 9.5E-05 33.5 2.4 36 2-37 381-418 (442)
443 PF08784 RPA_C: Replication pr 68.0 3.9 8.3E-05 26.4 1.7 35 3-37 63-97 (102)
444 PRK04984 fatty acid metabolism 67.7 4.9 0.00011 29.9 2.5 31 7-37 33-63 (239)
445 PRK03601 transcriptional regul 67.5 4.9 0.00011 30.5 2.5 25 7-31 17-41 (275)
446 COG1510 Predicted transcriptio 67.4 6.6 0.00014 28.2 2.8 40 4-43 40-79 (177)
447 PRK11557 putative DNA-binding 67.3 4.8 0.0001 30.8 2.4 25 5-29 30-54 (278)
448 PRK11302 DNA-binding transcrip 66.4 5.1 0.00011 30.6 2.4 24 6-29 35-58 (284)
449 PRK11337 DNA-binding transcrip 66.4 5 0.00011 30.9 2.3 25 5-29 46-70 (292)
450 PF08299 Bac_DnaA_C: Bacterial 66.2 5.9 0.00013 23.8 2.1 25 4-28 44-69 (70)
451 PRK03837 transcriptional regul 66.1 5.6 0.00012 29.6 2.5 31 7-37 39-69 (241)
452 PRK09462 fur ferric uptake reg 66.1 8.3 0.00018 26.7 3.2 35 4-38 32-71 (148)
453 PF09397 Ftsk_gamma: Ftsk gamm 66.0 5.8 0.00013 23.7 2.0 36 4-39 19-54 (65)
454 PRK11139 DNA-binding transcrip 65.8 5.7 0.00012 30.4 2.5 23 7-29 22-44 (297)
455 PRK09986 DNA-binding transcrip 65.7 5.1 0.00011 30.4 2.2 23 7-29 23-45 (294)
456 PRK09764 DNA-binding transcrip 65.6 6 0.00013 29.6 2.6 30 7-36 31-60 (240)
457 PRK10082 cell density-dependen 65.6 5.7 0.00012 30.6 2.5 23 7-29 27-49 (303)
458 PRK05602 RNA polymerase sigma 65.5 1.5 3.3E-05 31.3 -0.6 36 127-162 146-181 (186)
459 TIGR01529 argR_whole arginine 65.4 7.6 0.00016 27.0 2.9 25 5-29 16-45 (146)
460 PRK11523 DNA-binding transcrip 65.4 5.4 0.00012 30.1 2.3 31 8-38 35-67 (253)
461 KOG3862|consensus 65.2 0.69 1.5E-05 35.4 -2.5 24 103-126 224-247 (327)
462 COG0640 ArsR Predicted transcr 65.2 8.5 0.00018 23.7 2.9 39 5-43 39-77 (110)
463 PRK10341 DNA-binding transcrip 65.1 5.8 0.00013 30.7 2.5 23 7-29 23-45 (312)
464 PF13601 HTH_34: Winged helix 65.1 4.4 9.6E-05 25.1 1.5 43 4-46 13-56 (80)
465 PRK10086 DNA-binding transcrip 64.6 6.2 0.00013 30.5 2.6 23 7-29 30-52 (311)
466 COG1737 RpiR Transcriptional r 64.2 4.5 9.8E-05 31.2 1.7 24 6-29 37-60 (281)
467 PRK00118 putative DNA-binding 64.1 1.2 2.6E-05 29.2 -1.2 52 105-161 18-69 (104)
468 PHA01083 hypothetical protein 64.0 5.1 0.00011 28.0 1.7 21 6-26 17-37 (149)
469 TIGR03734 PRTRC_parB PRTRC sys 63.8 5.4 0.00012 34.0 2.2 26 3-28 106-132 (554)
470 PRK14997 LysR family transcrip 63.5 6.6 0.00014 30.0 2.5 23 7-29 18-40 (301)
471 PF11972 HTH_13: HTH DNA bindi 63.4 9.3 0.0002 21.9 2.4 24 6-29 14-37 (54)
472 PRK10219 DNA-binding transcrip 62.8 10 0.00022 24.5 3.0 26 4-29 20-45 (107)
473 PF10078 DUF2316: Uncharacteri 62.7 8.2 0.00018 24.6 2.4 25 3-27 21-45 (89)
474 PRK09801 transcriptional activ 62.6 7 0.00015 30.3 2.5 23 7-29 22-44 (310)
475 PRK03635 chromosome replicatio 62.5 6.7 0.00014 30.0 2.4 23 7-29 18-40 (294)
476 PRK10632 transcriptional regul 62.5 6.9 0.00015 30.2 2.5 24 6-29 17-40 (309)
477 TIGR02036 dsdC D-serine deamin 62.3 7.3 0.00016 30.0 2.6 23 7-29 24-46 (302)
478 COG4901 Ribosomal protein S25 62.3 8.5 0.00018 25.1 2.4 33 6-38 60-92 (107)
479 COG1309 AcrR Transcriptional r 62.1 5.9 0.00013 27.0 1.9 24 3-26 30-53 (201)
480 PRK09508 leuO leucine transcri 61.8 7.2 0.00016 30.2 2.5 23 7-29 38-60 (314)
481 PRK11062 nhaR transcriptional 61.8 7.3 0.00016 29.9 2.5 23 7-29 20-42 (296)
482 PRK11511 DNA-binding transcrip 61.6 8.9 0.00019 25.8 2.6 25 5-29 25-49 (127)
483 COG2188 PhnF Transcriptional r 61.6 7.7 0.00017 29.1 2.5 31 8-38 34-64 (236)
484 PF07278 DUF1441: Protein of u 61.5 28 0.0006 24.5 5.0 47 6-60 2-48 (152)
485 PRK13866 plasmid partitioning 61.4 5.8 0.00013 31.6 1.9 28 2-29 176-203 (336)
486 TIGR03433 padR_acidobact trans 61.3 24 0.00052 22.6 4.5 32 6-37 18-57 (100)
487 COG1725 Predicted transcriptio 61.3 9.4 0.0002 26.0 2.6 32 7-38 37-68 (125)
488 PF02002 TFIIE_alpha: TFIIE al 61.2 3.1 6.6E-05 27.0 0.2 32 5-36 27-58 (105)
489 PRK15092 DNA-binding transcrip 60.8 8 0.00017 30.1 2.6 23 7-29 27-49 (310)
490 PF06530 Phage_antitermQ: Phag 60.4 10 0.00022 25.6 2.7 26 4-29 77-102 (125)
491 smart00531 TFIIE Transcription 60.2 8.6 0.00019 26.7 2.4 26 6-31 16-41 (147)
492 PRK00082 hrcA heat-inducible t 60.2 14 0.00031 29.5 3.9 41 6-46 26-69 (339)
493 PRK04172 pheS phenylalanyl-tRN 59.9 10 0.00022 31.8 3.2 33 4-36 19-51 (489)
494 PRK09975 DNA-binding transcrip 59.8 7.3 0.00016 28.2 2.1 23 4-26 30-52 (213)
495 PF04760 IF2_N: Translation in 59.5 6.4 0.00014 22.2 1.4 22 5-26 3-24 (54)
496 smart00843 Ftsk_gamma This dom 59.0 26 0.00057 20.8 3.9 35 5-39 19-53 (63)
497 PF01498 HTH_Tnp_Tc3_2: Transp 58.9 9.2 0.0002 22.7 2.1 25 5-29 13-42 (72)
498 COG1318 Predicted transcriptio 58.6 9.1 0.0002 27.5 2.2 27 3-29 59-85 (182)
499 TIGR03337 phnR transcriptional 58.5 10 0.00022 28.0 2.7 31 7-37 27-57 (231)
500 PRK14996 TetR family transcrip 58.1 7.1 0.00015 27.9 1.7 23 4-26 27-49 (192)
No 1
>KOG0849|consensus
Probab=99.96 E-value=1.1e-29 Score=199.78 Aligned_cols=158 Identities=56% Similarity=0.911 Sum_probs=139.5
Q ss_pred CccCCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCC-cCChHHHHHHHHHHHhCCCCCchhhhhhhhhhc
Q psy1904 1 MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR-VATPDVEKRIEEYKKTNPNITSWEVRDKLIKVS 79 (163)
Q Consensus 1 ~~~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~-~~~~~~~~~i~~~~~~~p~~~~~e~~~~l~~~~ 79 (163)
||..|++||+|++.|.||++||++||++|.++|++.|+.+||.+|+ +.++.++..|.+++.++|++++|++++.+..+.
T Consensus 27 ~a~~~~~~~~~~~~l~vs~~~~~~il~r~~~~~~i~p~~i~~~~~~~~~t~~~~~~i~~~k~~~P~~~~~~ir~~l~~~~ 106 (354)
T KOG0849|consen 27 MAHKGIRPCVISRQLKVSHGCVSKILNRYYRTGSIRPGGIGGSKPRIVATPEVEAKIEQYKRENPAMFAWEIRDQLLHEG 106 (354)
T ss_pred ccccccCcccchhhhhhhhHHHHhhhcccccccccccccccccccCCCCCchhHHHHHHHHhcCCcccchhhhhcccCcc
Confidence 6789999999999999999999999999999999999999999999 889999999999999999999999999999873
Q ss_pred cCC----------------------C-----------------------------CCCCCCCccccccccccccCcCCHH
Q psy1904 80 RLD----------------------D-----------------------------SDTESEPGIVLKRKQRRSRTTFTSA 108 (163)
Q Consensus 80 ~~~----------------------~-----------------------------~~~~~~~~~~~~~~~rr~Rt~~t~~ 108 (163)
.++ . .+.+..+.....++.+|.||+|+..
T Consensus 107 ~~~~~t~Ps~ssi~r~~r~~~~~~d~~~~~~~~~~~~~~~~~~~~gs~~~~s~~~~~~~~~p~~~~~~~~rr~rtsft~~ 186 (354)
T KOG0849|consen 107 LCTQATLPSVSSINRVLRNGALGKDQGLPSQQVTKEKSPSISGALGSQAGASLLSADDEEPPGYALQRGGRRNRTSFSPS 186 (354)
T ss_pred cccCCCCCChhhhhHHhhccccccccccccccccccccCCcccccCCccccccccCCccccccccccccccccccccccc
Confidence 331 1 0001112223346678889999999
Q ss_pred HHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCCC
Q psy1904 109 QLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCLP 158 (163)
Q Consensus 109 q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~~ 158 (163)
|+..|+..|+.++||++..|+.||.++++++..|.|||+|+|++++|+..
T Consensus 187 Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~ 236 (354)
T KOG0849|consen 187 QLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHR 236 (354)
T ss_pred hHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhccc
Confidence 99999999999999999999999999999999999999999999999874
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=99.93 E-value=6e-27 Score=156.96 Aligned_cols=90 Identities=67% Similarity=1.094 Sum_probs=67.0
Q ss_pred CccCCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHHHHHhCCCCCchhhhhhhhhhcc
Q psy1904 1 MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPNITSWEVRDKLIKVSR 80 (163)
Q Consensus 1 ~~~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~~~~~~p~~~~~e~~~~l~~~~~ 80 (163)
||++|++|||||++|.||++||+|||++|+|||++.||.+||++|++.++.+++.|.+++.++|.+++||+++.|..+.-
T Consensus 29 la~~G~rp~~Isr~l~Vs~gcVsKIl~Ry~eTGsi~Pg~iGGskprv~tp~v~~~I~~~k~enP~ifawEiR~~L~~~gv 108 (125)
T PF00292_consen 29 LAKEGVRPCDISRQLRVSHGCVSKILSRYRETGSIRPGPIGGSKPRVATPEVVEKIEQYKRENPTIFAWEIRDRLIADGV 108 (125)
T ss_dssp HHHTT--HHHHHHHHT--HHHHHHHHHHHHHHS-SS----S----SSS-HCHHHHHHHHHHH-TTS-HHHHHHHHHHTTS
T ss_pred HhhhcCCHHHHHHHHccchhHHHHHHHHHHHhcccCcccccCCCCCCCChHHHHHHHHHHhcCCCcchHHHHHHHHHcCC
Confidence 67899999999999999999999999999999999999999999999999999999999999999999999999999988
Q ss_pred CCCCCCCCCC
Q psy1904 81 LDDSDTESEP 90 (163)
Q Consensus 81 ~~~~~~~~~~ 90 (163)
++.++.++.+
T Consensus 109 c~~~~~Psvs 118 (125)
T PF00292_consen 109 CDRSNVPSVS 118 (125)
T ss_dssp S-TTTS--HH
T ss_pred CCCCCCCCHH
Confidence 8877665543
No 3
>KOG3517|consensus
Probab=99.91 E-value=3.1e-25 Score=162.17 Aligned_cols=91 Identities=58% Similarity=0.955 Sum_probs=85.1
Q ss_pred CccCCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHHHHHhCCCCCchhhhhhhhhhcc
Q psy1904 1 MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPNITSWEVRDKLIKVSR 80 (163)
Q Consensus 1 ~~~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~~~~~~p~~~~~e~~~~l~~~~~ 80 (163)
||+-|++||||+|+|.||++||||||.||.|||++-||.+||++|++.++.+++.|.++++.+|++++||++|+|..+.-
T Consensus 32 LarlGiRPCDISRQLrvSHGCVSKILaRy~EtGsIlPGaIGGSkPRVTTP~VV~~IR~~Kq~DPGIFAWEIRDRLlsdgi 111 (334)
T KOG3517|consen 32 LARLGIRPCDISRQLRVSHGCVSKILARYNETGSILPGAIGGSKPRVTTPKVVKYIRSLKQRDPGIFAWEIRDRLLSDGI 111 (334)
T ss_pred HHHcCCCccchhhhhhhccchHHHHHHHhccCCcccccccCCCCCccCChhHHHHHHHhhccCCceeeehhhhhhhhccc
Confidence 68899999999999999999999999999999999999999999999999999999999999999999999999999988
Q ss_pred CCCCCCCCCCc
Q psy1904 81 LDDSDTESEPG 91 (163)
Q Consensus 81 ~~~~~~~~~~~ 91 (163)
||..+.++.++
T Consensus 112 CDk~NvPSVSS 122 (334)
T KOG3517|consen 112 CDKYNVPSVSS 122 (334)
T ss_pred ccccCCcchHH
Confidence 87666555443
No 4
>KOG0484|consensus
Probab=99.87 E-value=1.1e-23 Score=134.49 Aligned_cols=65 Identities=54% Similarity=0.716 Sum_probs=61.3
Q ss_pred ccccccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCC
Q psy1904 93 VLKRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCL 157 (163)
Q Consensus 93 ~~~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~ 157 (163)
..++|+||.||.||..||.+||+.|.+.+||++.+|++||..++|++..|+|||||||+|.++|.
T Consensus 12 ~ekrKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQE 76 (125)
T KOG0484|consen 12 TEKRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQE 76 (125)
T ss_pred hHHHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHH
Confidence 34678899999999999999999999999999999999999999999999999999999998864
No 5
>KOG0488|consensus
Probab=99.87 E-value=3.7e-23 Score=159.74 Aligned_cols=66 Identities=30% Similarity=0.446 Sum_probs=62.7
Q ss_pred ccccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCCCCC
Q psy1904 95 KRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCLPSV 160 (163)
Q Consensus 95 ~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~~~~ 160 (163)
++|.|+.||+||..|+..||+.|++.+|++..+|.+||..|||+..|||+||||||+||||+...+
T Consensus 169 pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~g 234 (309)
T KOG0488|consen 169 PKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAEG 234 (309)
T ss_pred CcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHhh
Confidence 477888999999999999999999999999999999999999999999999999999999988763
No 6
>KOG0489|consensus
Probab=99.86 E-value=3.8e-23 Score=157.04 Aligned_cols=62 Identities=29% Similarity=0.326 Sum_probs=58.8
Q ss_pred ccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCCC
Q psy1904 97 KQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCLP 158 (163)
Q Consensus 97 ~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~~ 158 (163)
+.||.||.||..|+.+||+.|+.|+|+++..|.+||..|.|+|+|||||||||||||||.-.
T Consensus 158 ~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k 219 (261)
T KOG0489|consen 158 KSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENK 219 (261)
T ss_pred CCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhc
Confidence 46899999999999999999999999999999999999999999999999999999997543
No 7
>KOG0842|consensus
Probab=99.85 E-value=2.9e-22 Score=152.72 Aligned_cols=63 Identities=32% Similarity=0.409 Sum_probs=59.6
Q ss_pred ccccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCC
Q psy1904 95 KRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCL 157 (163)
Q Consensus 95 ~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~ 157 (163)
.+++||.|..||..|+.+||+.|.+++|++.++|++||..|.||++||||||||||.|.||+-
T Consensus 150 ~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~ 212 (307)
T KOG0842|consen 150 KRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQ 212 (307)
T ss_pred cccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhh
Confidence 556778899999999999999999999999999999999999999999999999999999864
No 8
>KOG0850|consensus
Probab=99.85 E-value=1.7e-22 Score=146.28 Aligned_cols=69 Identities=29% Similarity=0.443 Sum_probs=64.1
Q ss_pred cccccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCCCCCCC
Q psy1904 94 LKRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCLPSVSG 162 (163)
Q Consensus 94 ~~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~~~~~~ 162 (163)
+.+|.|+.||.|+..||..|.+.|++++|+-.++|.+||..|||+.+||||||||||.|.||.+..+++
T Consensus 118 k~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k~g~~ 186 (245)
T KOG0850|consen 118 KGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKKQGSG 186 (245)
T ss_pred CcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHhcCCC
Confidence 346778899999999999999999999999999999999999999999999999999999998886553
No 9
>KOG0485|consensus
Probab=99.83 E-value=5.2e-22 Score=142.50 Aligned_cols=65 Identities=25% Similarity=0.347 Sum_probs=60.8
Q ss_pred cccccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCCC
Q psy1904 94 LKRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCLP 158 (163)
Q Consensus 94 ~~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~~ 158 (163)
...++|+.||+|+..|+..||..|+...|++..+|.-||.+|.|+|+||||||||||.||||+..
T Consensus 100 g~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~a 164 (268)
T KOG0485|consen 100 GDDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYA 164 (268)
T ss_pred cccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHh
Confidence 34467789999999999999999999999999999999999999999999999999999999764
No 10
>KOG0493|consensus
Probab=99.83 E-value=7.8e-22 Score=145.13 Aligned_cols=97 Identities=19% Similarity=0.355 Sum_probs=72.9
Q ss_pred hCCCCC-chhhhhhhhhhccCCCCCCCCCCccccccccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcc
Q psy1904 62 TNPNIT-SWEVRDKLIKVSRLDDSDTESEPGIVLKRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTET 140 (163)
Q Consensus 62 ~~p~~~-~~e~~~~l~~~~~~~~~~~~~~~~~~~~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~ 140 (163)
+.|.|+ +|.+|.++.+......-.-..-......+--+|+||.||.+||..|+..|+.|.|++...|.+||.+|+|.|.
T Consensus 209 ~~p~mwPAWVycTRYSDRPSsGPR~Rk~kkkk~~~~eeKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEs 288 (342)
T KOG0493|consen 209 AQPSMWPAWVYCTRYSDRPSSGPRHRKPKKKKSSSKEEKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNES 288 (342)
T ss_pred cCccccceeeeeecccCCCCCCcccccccccCCccchhcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHH
Confidence 345565 7999998876433221110000000011224688999999999999999999999999999999999999999
Q ss_pred cccccccccccccccCCC
Q psy1904 141 RVQQFVLGTAGFLLSCLP 158 (163)
Q Consensus 141 ~v~~WFqnrR~k~kr~~~ 158 (163)
||||||||+|+|.||.--
T Consensus 289 QIKIWFQNKRAKiKKsTg 306 (342)
T KOG0493|consen 289 QIKIWFQNKRAKIKKSTG 306 (342)
T ss_pred HhhHHhhhhhhhhhhccC
Confidence 999999999999998543
No 11
>KOG0843|consensus
Probab=99.83 E-value=1.4e-21 Score=136.64 Aligned_cols=60 Identities=28% Similarity=0.385 Sum_probs=57.8
Q ss_pred ccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccC
Q psy1904 97 KQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSC 156 (163)
Q Consensus 97 ~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~ 156 (163)
+.+|.||+||.+||..||..|+.++|....+|+.||..|+|++.||||||||||.|.||.
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~ 160 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRM 160 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHH
Confidence 678999999999999999999999999999999999999999999999999999999873
No 12
>KOG0487|consensus
Probab=99.83 E-value=2.1e-21 Score=148.00 Aligned_cols=66 Identities=24% Similarity=0.236 Sum_probs=61.8
Q ss_pred cccccccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCC
Q psy1904 92 IVLKRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCL 157 (163)
Q Consensus 92 ~~~~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~ 157 (163)
....+..|++|..+|+.|+.+||+.|..|.|++...|.+|+..|+|+++||||||||||+|.||..
T Consensus 229 ~~~~~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~ 294 (308)
T KOG0487|consen 229 ASSARRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVN 294 (308)
T ss_pred cccccccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhh
Confidence 344567889999999999999999999999999999999999999999999999999999999875
No 13
>KOG0494|consensus
Probab=99.81 E-value=7.9e-21 Score=139.72 Aligned_cols=68 Identities=44% Similarity=0.658 Sum_probs=63.2
Q ss_pred cccccc-cCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCCCCCCCC
Q psy1904 96 RKQRRS-RTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCLPSVSGR 163 (163)
Q Consensus 96 ~~~rr~-Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~~~~~~~ 163 (163)
+++||. ||.||..|+++||+.|++.+||+...|+.||..+.|.|.+|+|||||||+||+|-...|||+
T Consensus 138 k~kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~wg~s 206 (332)
T KOG0494|consen 138 KKKRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRWGGS 206 (332)
T ss_pred ccccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhcCcc
Confidence 334454 99999999999999999999999999999999999999999999999999999999999874
No 14
>KOG0492|consensus
Probab=99.81 E-value=7.8e-21 Score=135.59 Aligned_cols=64 Identities=27% Similarity=0.403 Sum_probs=59.6
Q ss_pred ccccccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccC
Q psy1904 93 VLKRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSC 156 (163)
Q Consensus 93 ~~~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~ 156 (163)
.+++.+|++||.||.+||..||+.|.+.+|+++.+|.+++..|.||++||||||||||+|.||.
T Consensus 139 rKhk~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRl 202 (246)
T KOG0492|consen 139 RKHKPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRL 202 (246)
T ss_pred cccCCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHH
Confidence 3445678899999999999999999999999999999999999999999999999999999873
No 15
>KOG3862|consensus
Probab=99.80 E-value=3.2e-20 Score=137.27 Aligned_cols=85 Identities=66% Similarity=1.109 Sum_probs=80.6
Q ss_pred CccCCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHHHHHhCCCCCchhhhhhhhhhcc
Q psy1904 1 MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPNITSWEVRDKLIKVSR 80 (163)
Q Consensus 1 ~~~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~~~~~~p~~~~~e~~~~l~~~~~ 80 (163)
||+.|++|||||++|.|||||||+||.+|.|||+++||.+||++|.+.++-+++.|..+++++|.|++||+++.+..+.-
T Consensus 37 La~~gvrpcdisrQl~vShGcvSkil~r~yEtgS~~pg~iggsk~KvAtp~Vvk~i~~~k~~n~~mfaweiR~~l~~~~i 116 (327)
T KOG3862|consen 37 LAQNGVRPCDISRQLRVSHGCVSKILGRYYETGSIRPGVIGGSKPKVATPKVVKKIALYKRQNPTMFAWEIRDRLLAEPI 116 (327)
T ss_pred HHHcCCcchhHHHHHhhccCCchhHHHHHHHhcCcccCCCCCCccccccchHHHHHHHHhhcCcchhhhhhhhhhhcccc
Confidence 78999999999999999999999999999999999999999999999999999999999999999999999999999866
Q ss_pred CCCCC
Q psy1904 81 LDDSD 85 (163)
Q Consensus 81 ~~~~~ 85 (163)
++.+.
T Consensus 117 c~~d~ 121 (327)
T KOG3862|consen 117 CDNDT 121 (327)
T ss_pred cCCCC
Confidence 65444
No 16
>KOG2251|consensus
Probab=99.79 E-value=3.3e-20 Score=133.82 Aligned_cols=64 Identities=44% Similarity=0.589 Sum_probs=60.9
Q ss_pred ccccccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccC
Q psy1904 93 VLKRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSC 156 (163)
Q Consensus 93 ~~~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~ 156 (163)
..+++.||.||.|+..|+++||..|.+.+||++..|++||.+|+|.+.+|+|||.|||+|++++
T Consensus 32 ~~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~q 95 (228)
T KOG2251|consen 32 SGPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQ 95 (228)
T ss_pred ccchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHh
Confidence 4467899999999999999999999999999999999999999999999999999999999864
No 17
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=99.73 E-value=6.4e-19 Score=104.25 Aligned_cols=57 Identities=37% Similarity=0.536 Sum_probs=54.7
Q ss_pred ccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCccccccccccccccccc
Q psy1904 99 RRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLS 155 (163)
Q Consensus 99 rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr 155 (163)
|+.|+.||.+|+..|+..|..++||+..++..||..+||+..+|++||+|+|.++|+
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHHhCc
Confidence 478899999999999999999999999999999999999999999999999999875
No 18
>KOG0844|consensus
Probab=99.72 E-value=1.1e-18 Score=131.28 Aligned_cols=64 Identities=28% Similarity=0.306 Sum_probs=60.3
Q ss_pred cccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCCCC
Q psy1904 96 RKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCLPS 159 (163)
Q Consensus 96 ~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~~~ 159 (163)
..-||.||.||.+|+..||+.|-+..|.+++.|.+||..|+|+|..|||||||||+|.|||.-.
T Consensus 179 dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRla 242 (408)
T KOG0844|consen 179 DQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLA 242 (408)
T ss_pred HHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhh
Confidence 4578999999999999999999999999999999999999999999999999999999998543
No 19
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class. This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam model pfam00046. It is found in both C4 and C3 plants.
Probab=99.71 E-value=9.5e-18 Score=98.23 Aligned_cols=52 Identities=17% Similarity=0.291 Sum_probs=50.4
Q ss_pred ccccCcCCHHHHHHHHHhccCCCC----CCHHHHHHHHHHhCCCcccccccccccc
Q psy1904 99 RRSRTTFTSAQLEELEKSFQRSHY----PDIYTREALANKFGMTETRVQQFVLGTA 150 (163)
Q Consensus 99 rr~Rt~~t~~q~~~Le~~F~~~~~----p~~~~r~~la~~l~l~~~~v~~WFqnrR 150 (163)
+|.||.||.+|+..|+..|+.+.| |+..++.+||..+||++.+|+|||||.+
T Consensus 2 kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 2 KRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 688999999999999999999999 9999999999999999999999999965
No 20
>KOG0848|consensus
Probab=99.71 E-value=1.5e-18 Score=128.23 Aligned_cols=61 Identities=28% Similarity=0.383 Sum_probs=56.7
Q ss_pred cccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccC
Q psy1904 96 RKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSC 156 (163)
Q Consensus 96 ~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~ 156 (163)
+.+-+.|.+||..|..+||+.|..++|.++..+.+||.-|+|+|+||||||||||+|++|.
T Consensus 197 RTkDKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~ 257 (317)
T KOG0848|consen 197 RTKDKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKD 257 (317)
T ss_pred ecccceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHH
Confidence 3444679999999999999999999999999999999999999999999999999999764
No 21
>KOG0491|consensus
Probab=99.69 E-value=1.1e-18 Score=120.52 Aligned_cols=62 Identities=31% Similarity=0.452 Sum_probs=58.7
Q ss_pred ccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCCC
Q psy1904 97 KQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCLP 158 (163)
Q Consensus 97 ~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~~ 158 (163)
+.++.||+|+..|+..|++.|+...|++..++.+||..|+|++.|||.||||||+|.||++.
T Consensus 99 ~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r 160 (194)
T KOG0491|consen 99 RRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQR 160 (194)
T ss_pred HhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHh
Confidence 45678999999999999999999999999999999999999999999999999999998765
No 22
>cd00131 PAX Paired Box domain
Probab=99.65 E-value=4.1e-16 Score=106.70 Aligned_cols=77 Identities=73% Similarity=1.236 Sum_probs=70.6
Q ss_pred ccCCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHHHHHhCCCCCchhhhhhhhhh
Q psy1904 2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPNITSWEVRDKLIKV 78 (163)
Q Consensus 2 ~~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~~~~~~p~~~~~e~~~~l~~~ 78 (163)
+.+|+++++||++|+||.+||++|+++|+++|++.|++.||.+|+..++..+..+..+.+++|+.+++|+++.|.++
T Consensus 30 ~~~G~s~~~iA~~~~Vs~~tV~r~i~r~~e~G~v~pk~~gg~rpr~~~~~~~~~i~~~v~~~p~~Tl~El~~~L~~~ 106 (128)
T cd00131 30 AQSGIRPCDISRQLRVSHGCVSKILNRYYETGSIRPGAIGGSKPRVATPEVVKKIEIYKQENPGMFAWEIRDRLLQE 106 (128)
T ss_pred HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCCCCCCCCCCcCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHc
Confidence 46899999999999999999999999999999999999988888888888888888889999999999999998754
No 23
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.63 E-value=1.7e-16 Score=93.42 Aligned_cols=55 Identities=44% Similarity=0.643 Sum_probs=52.2
Q ss_pred cccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccc
Q psy1904 100 RSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLL 154 (163)
Q Consensus 100 r~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~k 154 (163)
+.|+.|+..|+..|+..|..++||+..++..||..+||+..+|++||+|+|++.+
T Consensus 2 k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 2 RKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence 5678899999999999999999999999999999999999999999999999864
No 24
>KOG0486|consensus
Probab=99.63 E-value=1.3e-16 Score=120.56 Aligned_cols=62 Identities=45% Similarity=0.580 Sum_probs=59.0
Q ss_pred cccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCC
Q psy1904 96 RKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCL 157 (163)
Q Consensus 96 ~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~ 157 (163)
.|+||.||.||.+|+.+||..|++|.||+...|++||.-++|+|..|+|||.|||+||+|..
T Consensus 110 ~KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrE 171 (351)
T KOG0486|consen 110 SKQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRE 171 (351)
T ss_pred hhhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhh
Confidence 37889999999999999999999999999999999999999999999999999999998754
No 25
>smart00351 PAX Paired Box domain.
Probab=99.62 E-value=2.1e-15 Score=102.83 Aligned_cols=77 Identities=70% Similarity=1.177 Sum_probs=71.3
Q ss_pred ccCCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHHHHHhCCCCCchhhhhhhhhh
Q psy1904 2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPNITSWEVRDKLIKV 78 (163)
Q Consensus 2 ~~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~~~~~~p~~~~~e~~~~l~~~ 78 (163)
..+|.+..+||++||||.+||++|+++|+++|++.|.+.||.+|...++.....|..+.+++|+++++++++.|.+.
T Consensus 30 ~~~G~s~~~iA~~~gvs~~tV~kwi~r~~~~G~~~pk~~gg~rp~~~~~~~~~~I~~~~~~~p~~t~~el~~~L~~~ 106 (125)
T smart00351 30 AQNGVRPCDISRQLCVSHGCVSKILGRYYETGSIRPGAIGGSKPKVATPKVVKKIADYKQENPGIFAWEIRDRLLSE 106 (125)
T ss_pred HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCcCCCCCCCCccCHHHHHHHHHHHHHCCCCCHHHHHHHHHHc
Confidence 35899999999999999999999999999999999999998888888888888888899999999999999999854
No 26
>KOG3802|consensus
Probab=99.60 E-value=8.4e-16 Score=119.89 Aligned_cols=62 Identities=18% Similarity=0.231 Sum_probs=59.6
Q ss_pred ccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCCC
Q psy1904 97 KQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCLP 158 (163)
Q Consensus 97 ~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~~ 158 (163)
++|++||.|.......||.+|.+|+.|+..+..+||.+|+|....|+|||+|||.|.||--+
T Consensus 293 RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 293 RKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred cccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence 67889999999999999999999999999999999999999999999999999999999766
No 27
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=99.60 E-value=5.1e-16 Score=92.18 Aligned_cols=57 Identities=42% Similarity=0.630 Sum_probs=53.9
Q ss_pred cccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccC
Q psy1904 100 RSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSC 156 (163)
Q Consensus 100 r~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~ 156 (163)
+.|+.|+..|+..|+..|..++||+..++..||..+||++.+|++||+|+|.+.++.
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence 467899999999999999999999999999999999999999999999999998764
No 28
>KOG0483|consensus
Probab=99.58 E-value=9.9e-16 Score=110.95 Aligned_cols=55 Identities=22% Similarity=0.302 Sum_probs=52.0
Q ss_pred ccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCccccccccccccccccc
Q psy1904 101 SRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLS 155 (163)
Q Consensus 101 ~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr 155 (163)
++-.|+.+|+..||..|+.+.|+....+..||..|||.++||.|||||||||||.
T Consensus 53 kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~ 107 (198)
T KOG0483|consen 53 KKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKT 107 (198)
T ss_pred ccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccc
Confidence 3457899999999999999999999999999999999999999999999999985
No 29
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.54 E-value=3.5e-15 Score=104.68 Aligned_cols=59 Identities=25% Similarity=0.264 Sum_probs=54.1
Q ss_pred cccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccC
Q psy1904 98 QRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSC 156 (163)
Q Consensus 98 ~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~ 156 (163)
.+++|+.-|.+|+.+|++.|+.++||+..+|..|+..++|++..|+|||||+|++.|+.
T Consensus 51 ~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~ 109 (156)
T COG5576 51 PKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKK 109 (156)
T ss_pred CcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHh
Confidence 34556667999999999999999999999999999999999999999999999998753
No 30
>KOG0847|consensus
Probab=99.52 E-value=2.6e-15 Score=108.36 Aligned_cols=62 Identities=27% Similarity=0.390 Sum_probs=57.0
Q ss_pred cccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCC
Q psy1904 96 RKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCL 157 (163)
Q Consensus 96 ~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~ 157 (163)
.+++..|.+|+-.|+..||..|+..+|+-..++.+||..+|+++.||+|||||||.||+|..
T Consensus 165 G~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkh 226 (288)
T KOG0847|consen 165 GQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKH 226 (288)
T ss_pred ccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhh
Confidence 34556788999999999999999999999999999999999999999999999999998743
No 31
>KOG4577|consensus
Probab=99.48 E-value=1.6e-14 Score=108.14 Aligned_cols=61 Identities=28% Similarity=0.334 Sum_probs=57.7
Q ss_pred ccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCC
Q psy1904 97 KQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCL 157 (163)
Q Consensus 97 ~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~ 157 (163)
..+|+||++|..||+-|+.+|...+.|.+..|+.|+..+||..+.|+|||||||+|.||.-
T Consensus 166 ~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLK 226 (383)
T KOG4577|consen 166 SNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLK 226 (383)
T ss_pred ccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhh
Confidence 3579999999999999999999999999999999999999999999999999999998743
No 32
>KOG0490|consensus
Probab=99.47 E-value=2e-14 Score=107.62 Aligned_cols=63 Identities=33% Similarity=0.356 Sum_probs=59.8
Q ss_pred ccccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCC
Q psy1904 95 KRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCL 157 (163)
Q Consensus 95 ~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~ 157 (163)
..++++.||.|+..|+.+|++.|+..+||+...++.||..+++++..|+|||||+|+||+++.
T Consensus 57 ~~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~ 119 (235)
T KOG0490|consen 57 KFSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEE 119 (235)
T ss_pred hccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhh
Confidence 456789999999999999999999999999999999999999999999999999999998765
No 33
>KOG1168|consensus
Probab=99.21 E-value=4.7e-12 Score=95.12 Aligned_cols=64 Identities=19% Similarity=0.211 Sum_probs=58.8
Q ss_pred ccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCCCCC
Q psy1904 97 KQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCLPSV 160 (163)
Q Consensus 97 ~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~~~~ 160 (163)
.++|+||.+-.-....||..|...+.|+......||.+|+|....|+|||+|.|.|.||.-.|.
T Consensus 308 ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~~Sa 371 (385)
T KOG1168|consen 308 EKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKRSA 371 (385)
T ss_pred ccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhhhhh
Confidence 3568899999999999999999999999999999999999999999999999999999865544
No 34
>KOG2252|consensus
Probab=99.21 E-value=2.4e-11 Score=98.48 Aligned_cols=132 Identities=17% Similarity=0.275 Sum_probs=89.5
Q ss_pred cCCCChhhhHH-HhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHHHHHhCCCCCc--hhhhhhhhhhc
Q psy1904 3 AAGVRPCVISR-QLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPNITS--WEVRDKLIKVS 79 (163)
Q Consensus 3 ~~g~~~~~ia~-~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~~~~~~p~~~~--~e~~~~l~~~~ 79 (163)
..+|.++..|+ +|+.|+||+|.||...+....+.-| . .....+..++ + .|.+.. +.++..-. .
T Consensus 341 ~~sIpQaiFAervLcRSQGTLSDLLrnPKPW~klKsG----R---etFrRM~~WL----~-eP~~~r~m~~L~~~a~--k 406 (558)
T KOG2252|consen 341 RYSIPQAIFAERVLCRSQGTLSDLLRNPKPWSKLKSG----R---ETFRRMANWL----E-EPEFQRLMSALRKKAC--K 406 (558)
T ss_pred hcCCcHHHHHHHHhhcccchHHHHhhCCCchhhhccc----c---HHHHHHHHHh----c-CHHHHHHHHHHHHHHh--h
Confidence 35789999998 8999999999999776555555543 1 1112222222 1 222111 11211111 1
Q ss_pred cCCCCCCCCCCccccccccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCccccccccccccccc
Q psy1904 80 RLDDSDTESEPGIVLKRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFL 153 (163)
Q Consensus 80 ~~~~~~~~~~~~~~~~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~ 153 (163)
+.+. ++.....-..+++|.+||..|..-|...|+.+++|+..+.+.|+.+|+|....|.+||-|-|.+.
T Consensus 407 Rke~-----ep~~d~~~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 407 RKEQ-----EPTDDKMLQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred hccc-----CCCccccccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 1111 11111222456779999999999999999999999999999999999999999999999988773
No 35
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=99.02 E-value=9.6e-10 Score=75.61 Aligned_cols=76 Identities=21% Similarity=0.176 Sum_probs=62.6
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHHHHHhCCCCCchhhhhhhhhhcc
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPNITSWEVRDKLIKVSR 80 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~~~~~~p~~~~~e~~~~l~~~~~ 80 (163)
.|+|..+||++||||.+||++|+++++++|...|...++++|+..+....+.+.+..++.. ++.-+++..+..+..
T Consensus 20 ~G~S~re~Ak~~gvs~sTvy~wv~r~~e~G~~l~~~~~~GrP~kl~~~q~~~l~e~~~~k~-wTl~~~~~~l~~e~g 95 (138)
T COG3415 20 EGLSCREAAKRFGVSISTVYRWVRRYRETGLDLPPKPRKGRPRKLSEEQLEILLERLREKD-WTLKELVEELGLEFG 95 (138)
T ss_pred cCccHHHHHHHhCccHHHHHHHHHHhccccccccCccCCCCCcccCHHHHHHHHHHHhccc-chHHHHHHHHhhhcC
Confidence 7999999999999999999999999999999988888889999888888887766665544 666666666554433
No 36
>KOG0775|consensus
Probab=98.90 E-value=1e-09 Score=82.07 Aligned_cols=55 Identities=20% Similarity=0.246 Sum_probs=48.6
Q ss_pred cccCcCCHHH---------HHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccc
Q psy1904 100 RSRTTFTSAQ---------LEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLL 154 (163)
Q Consensus 100 r~Rt~~t~~q---------~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~k 154 (163)
-+||.+..++ ...|...|..++||+..++.+||+.+||+..||-+||.|||.+.+
T Consensus 169 lPrTIWDGEet~yCFKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDR 232 (304)
T KOG0775|consen 169 LPRTIWDGEETVYCFKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDR 232 (304)
T ss_pred CCCccccCceeeeehhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhh
Confidence 3566655544 568999999999999999999999999999999999999999986
No 37
>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=98.84 E-value=5.3e-09 Score=70.73 Aligned_cols=66 Identities=23% Similarity=0.375 Sum_probs=55.4
Q ss_pred cCCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHHHHHhCCCCCchhhhhhh
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPNITSWEVRDKL 75 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~~~~~~p~~~~~e~~~~l 75 (163)
..|.+++++|++|+||.+||.+|++ ..++|++.|.+.|+. .. ..+.+.++.+++|+++..|+...+
T Consensus 16 ~~g~s~~eaa~~F~VS~~Tv~~W~k-~~~~G~~~~k~r~~~--Ki----d~~~L~~~v~~~pd~tl~Ela~~l 81 (119)
T PF01710_consen 16 EKGKSIREAAKRFGVSRNTVYRWLK-RKETGDLEPKPRGRK--KI----DRDELKALVEENPDATLRELAERL 81 (119)
T ss_pred HccchHHHHHHHhCcHHHHHHHHHH-hcccccccccccccc--cc----cHHHHHHHHHHCCCcCHHHHHHHc
Confidence 3688999999999999999999999 778999999886654 21 244577889999999999988765
No 38
>KOG0774|consensus
Probab=98.70 E-value=1.3e-08 Score=75.70 Aligned_cols=60 Identities=23% Similarity=0.323 Sum_probs=55.5
Q ss_pred cccccCcCCHHHHHHHHHhc---cCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCC
Q psy1904 98 QRRSRTTFTSAQLEELEKSF---QRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCL 157 (163)
Q Consensus 98 ~rr~Rt~~t~~q~~~Le~~F---~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~ 157 (163)
.+|+|..|+..-.++|...| -.|+||+...+++||.+++++..||-.||.|.|-++||.+
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~ 250 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNM 250 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhh
Confidence 46788899999999999998 4679999999999999999999999999999999999865
No 39
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=98.64 E-value=4.4e-09 Score=57.14 Aligned_cols=35 Identities=17% Similarity=0.403 Sum_probs=29.2
Q ss_pred cCCCCCCHHHHHHHHHHhCCCcccccccccccccc
Q psy1904 118 QRSHYPDIYTREALANKFGMTETRVQQFVLGTAGF 152 (163)
Q Consensus 118 ~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k 152 (163)
..++||+..++..||..+||+..||..||-|.|.+
T Consensus 6 ~~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 6 LHNPYPSKEEKEELAKQTGLSRKQISNWFINARRR 40 (40)
T ss_dssp TTSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence 35799999999999999999999999999998864
No 40
>PF13551 HTH_29: Winged helix-turn helix
Probab=98.64 E-value=1.1e-07 Score=63.12 Aligned_cols=64 Identities=31% Similarity=0.519 Sum_probs=51.4
Q ss_pred CccCCCC-hhhhHHHhhcchhhHHHHHhhhhhcc--CCCCCCCCCCCCCc-CChHHHHHHHHHHHhCC
Q psy1904 1 MAAAGVR-PCVISRQLRVSHGCVSKILNRYQETG--SIRPGVIGGSKPRV-ATPDVEKRIEEYKKTNP 64 (163)
Q Consensus 1 ~~~~g~~-~~~ia~~~~vs~~~vs~~l~~~~~tG--~~~Pg~~Gg~~p~~-~~~~~~~~i~~~~~~~p 64 (163)
|..+|.+ +.+||+.||||..||++|+++|.+.| .+.+...++.+|.. .++.+.+.+.++..++|
T Consensus 7 l~~~g~~~~~~ia~~lg~s~~Tv~r~~~~~~~~G~~~l~~~~~~~g~~~~~l~~~~~~~l~~~~~~~p 74 (112)
T PF13551_consen 7 LLAEGVSTIAEIARRLGISRRTVYRWLKRYREGGIEGLLPRKPRGGRPRKRLSEEQRAQLIELLRENP 74 (112)
T ss_pred HHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHcccHHHHHhccccCCCCCCCCCHHHHHHHHHHHHHCC
Confidence 3468996 99999999999999999999999999 56662223344444 68888888888888887
No 41
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=98.34 E-value=1.3e-07 Score=53.89 Aligned_cols=31 Identities=32% Similarity=0.485 Sum_probs=20.8
Q ss_pred cCCCChhhhHHHhhcchhhHHHHHhhhhhcc
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKILNRYQETG 33 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG 33 (163)
.+|.+..+||+.||||.+||++|+++|++.|
T Consensus 15 ~~G~s~~~ia~~lgvs~~Tv~~w~kr~~~~G 45 (50)
T PF13384_consen 15 REGWSIREIAKRLGVSRSTVYRWIKRYREEG 45 (50)
T ss_dssp HHT--HHHHHHHHTS-HHHHHHHHT------
T ss_pred HCCCCHHHHHHHHCcCHHHHHHHHHHccccc
Confidence 3599999999999999999999999999887
No 42
>KOG0490|consensus
Probab=98.29 E-value=4.4e-07 Score=67.85 Aligned_cols=62 Identities=39% Similarity=0.516 Sum_probs=57.7
Q ss_pred ccccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccC
Q psy1904 95 KRKQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSC 156 (163)
Q Consensus 95 ~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~ 156 (163)
..+.++.|+.|+..|+..+...|..+++|+...+..|+..+++++..|++||+|+|++.++.
T Consensus 150 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~ 211 (235)
T KOG0490|consen 150 NKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKH 211 (235)
T ss_pred ccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhh
Confidence 34677889999999999999999999999999999999999999999999999999998763
No 43
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=98.15 E-value=8.5e-06 Score=51.30 Aligned_cols=57 Identities=28% Similarity=0.339 Sum_probs=40.2
Q ss_pred cCCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCC---CCCCCCcCChHHHHHHHHH
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI---GGSKPRVATPDVEKRIEEY 59 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~---Gg~~p~~~~~~~~~~i~~~ 59 (163)
++|++..++|+.||||..|++||+.+|++.|.-..-.- ....|.-..+..+..|..+
T Consensus 23 ~~g~~~a~aA~~~gVS~~Ta~kW~~Ryra~G~~GL~DRSSRP~~sP~~t~~~~~~~I~~l 82 (85)
T PF13011_consen 23 EQGWPVAHAAAEFGVSRRTAYKWLARYRAEGEAGLQDRSSRPHRSPRRTPPEVERRIIEL 82 (85)
T ss_pred HcCCcHHHHHHHhCCCHHHHHHHHHHHHHcCcccccccCCCCCCCCccCCHHHHHHHHHH
Confidence 47899999999999999999999999999886543221 1123333345555555444
No 44
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=97.93 E-value=3e-06 Score=47.24 Aligned_cols=27 Identities=33% Similarity=0.444 Sum_probs=21.5
Q ss_pred CccCCCChhhhHHHhhcchhhHHHHHh
Q psy1904 1 MAAAGVRPCVISRQLRVSHGCVSKILN 27 (163)
Q Consensus 1 ~~~~g~~~~~ia~~~~vs~~~vs~~l~ 27 (163)
|..+|++..+||+.||||.+||+++|.
T Consensus 17 l~~~G~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 17 LYAEGMSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp HHHTT--HHHHHHHTTS-HHHHHHHHC
T ss_pred HHHCCCCHHHHHHHHCcCHHHHHHHHh
Confidence 346899999999999999999999985
No 45
>PF13518 HTH_28: Helix-turn-helix domain
Probab=97.86 E-value=1e-05 Score=46.17 Aligned_cols=32 Identities=28% Similarity=0.449 Sum_probs=29.5
Q ss_pred cCCCChhhhHHHhhcchhhHHHHHhhhhhccC
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGS 34 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~ 34 (163)
.+|.+..+||+.||||.++|++|+++|.+.|.
T Consensus 10 ~~g~s~~~~a~~~gis~~tv~~w~~~y~~~G~ 41 (52)
T PF13518_consen 10 LEGESVREIAREFGISRSTVYRWIKRYREGGI 41 (52)
T ss_pred HcCCCHHHHHHHHCCCHhHHHHHHHHHHhcCH
Confidence 36889999999999999999999999999884
No 46
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=97.84 E-value=1.4e-05 Score=44.35 Aligned_cols=26 Identities=31% Similarity=0.376 Sum_probs=19.6
Q ss_pred cCCCChhhhHHHhhcchhhHHHHHhh
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKILNR 28 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l~~ 28 (163)
++|++..+||+.||+|++||++.|++
T Consensus 18 ~~G~s~~~IA~~lg~s~sTV~relkR 43 (44)
T PF13936_consen 18 EQGMSIREIAKRLGRSRSTVSRELKR 43 (44)
T ss_dssp CS---HHHHHHHTT--HHHHHHHHHH
T ss_pred HcCCCHHHHHHHHCcCcHHHHHHHhc
Confidence 58999999999999999999999976
No 47
>KOG1146|consensus
Probab=97.57 E-value=3.3e-05 Score=68.97 Aligned_cols=60 Identities=17% Similarity=0.250 Sum_probs=56.2
Q ss_pred ccccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccC
Q psy1904 97 KQRRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSC 156 (163)
Q Consensus 97 ~~rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~ 156 (163)
.+++.||.++..||..+...|....||...+.+.|-..+++..+.|.+||||-|.|.++.
T Consensus 902 ~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~ 961 (1406)
T KOG1146|consen 902 GRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKA 961 (1406)
T ss_pred hhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhh
Confidence 356789999999999999999999999999999999999999999999999999998874
No 48
>PF13565 HTH_32: Homeodomain-like domain
Probab=97.42 E-value=0.0006 Score=42.07 Aligned_cols=57 Identities=26% Similarity=0.359 Sum_probs=44.0
Q ss_pred hHHHHHhhhhhcc-----CCCCCCCCCCCCCcCChHHHHHHHHHHHhCCCCCchhhhhhhhhhc
Q psy1904 21 CVSKILNRYQETG-----SIRPGVIGGSKPRVATPDVEKRIEEYKKTNPNITSWEVRDKLIKVS 79 (163)
Q Consensus 21 ~vs~~l~~~~~tG-----~~~Pg~~Gg~~p~~~~~~~~~~i~~~~~~~p~~~~~e~~~~l~~~~ 79 (163)
||++|+++|++.| +..+++..|.. +. ++...+.|.++..++|.++..++...+...-
T Consensus 1 Tv~rw~~ry~~~G~~gL~~~~~~~~~Grp-~~-~~e~~~~i~~~~~~~p~wt~~~i~~~L~~~~ 62 (77)
T PF13565_consen 1 TVYRWLKRYREEGLEGLKDRKRRPRPGRP-RK-DPEQRERIIALIEEHPRWTPREIAEYLEEEF 62 (77)
T ss_pred CHHHHHHHHHhhCchhhhcccccCCCCCC-CC-cHHHHHHHHHHHHhCCCCCHHHHHHHHHHHh
Confidence 7999999999999 65444444433 44 6777788889999999999988888877643
No 49
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=97.39 E-value=0.00054 Score=46.32 Aligned_cols=35 Identities=20% Similarity=0.214 Sum_probs=30.5
Q ss_pred cCCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP 37 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P 37 (163)
..|.+..+||+.||||.+++++|.++|++.|....
T Consensus 27 ~~g~sv~evA~e~gIs~~tl~~W~r~y~~~~~~~~ 61 (121)
T PRK09413 27 EPGMTVSLVARQHGVAASQLFLWRKQYQEGSLTAV 61 (121)
T ss_pred cCCCCHHHHHHHHCcCHHHHHHHHHHHhhcccccc
Confidence 46899999999999999999999999987665443
No 50
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=97.31 E-value=0.00015 Score=42.61 Aligned_cols=27 Identities=26% Similarity=0.273 Sum_probs=25.4
Q ss_pred cCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
..|+++.+||+.|||+.+||+.|.+++
T Consensus 11 ~~G~~~~eIA~~Lg~~~~TV~~W~~r~ 37 (58)
T PF06056_consen 11 LQGWSIKEIAEELGVPRSTVYSWKDRY 37 (58)
T ss_pred HcCCCHHHHHHHHCCChHHHHHHHHhh
Confidence 479999999999999999999999887
No 51
>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=97.31 E-value=9.5e-05 Score=42.62 Aligned_cols=28 Identities=32% Similarity=0.345 Sum_probs=22.0
Q ss_pred ccCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904 2 AAAGVRPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 2 ~~~g~~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
.+.|.+.++||+.|||+.+||+.|++.-
T Consensus 19 ~e~g~s~~~ia~~fgv~~sTv~~I~K~k 46 (53)
T PF04218_consen 19 LEEGESKRDIAREFGVSRSTVSTILKNK 46 (53)
T ss_dssp HHCTT-HHHHHHHHT--CCHHHHHHHCH
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHHhH
Confidence 3578999999999999999999999753
No 52
>PHA02591 hypothetical protein; Provisional
Probab=97.03 E-value=0.00038 Score=42.70 Aligned_cols=27 Identities=30% Similarity=0.254 Sum_probs=24.9
Q ss_pred CccCCCChhhhHHHhhcchhhHHHHHh
Q psy1904 1 MAAAGVRPCVISRQLRVSHGCVSKILN 27 (163)
Q Consensus 1 ~~~~g~~~~~ia~~~~vs~~~vs~~l~ 27 (163)
|+..|+++.+||+.|||++.+|+++|.
T Consensus 55 L~eqGlSqeqIA~~LGVsqetVrKYL~ 81 (83)
T PHA02591 55 LARKGFTVEKIASLLGVSVRKVRRYLE 81 (83)
T ss_pred HHHcCCCHHHHHHHhCCCHHHHHHHHh
Confidence 567899999999999999999999984
No 53
>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=96.86 E-value=0.0011 Score=39.14 Aligned_cols=32 Identities=34% Similarity=0.449 Sum_probs=27.8
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhhhhccCC
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSI 35 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~ 35 (163)
..++..+||+.|+||++||+..++++.+.|=+
T Consensus 21 ~~v~~~~iA~~L~vs~~tvt~ml~~L~~~GlV 52 (60)
T PF01325_consen 21 GPVRTKDIAERLGVSPPTVTEMLKRLAEKGLV 52 (60)
T ss_dssp SSBBHHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred CCccHHHHHHHHCCChHHHHHHHHHHHHCCCE
Confidence 45899999999999999999999999887755
No 54
>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=96.84 E-value=0.0014 Score=33.53 Aligned_cols=28 Identities=25% Similarity=0.387 Sum_probs=23.5
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhcc
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETG 33 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG 33 (163)
++..|||..+|++.-||||+|+++++.|
T Consensus 3 mtr~diA~~lG~t~ETVSR~l~~l~~~g 30 (32)
T PF00325_consen 3 MTRQDIADYLGLTRETVSRILKKLERQG 30 (32)
T ss_dssp --HHHHHHHHTS-HHHHHHHHHHHHHTT
T ss_pred cCHHHHHHHhCCcHHHHHHHHHHHHHcC
Confidence 5678999999999999999999998876
No 55
>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=96.78 E-value=0.0062 Score=33.94 Aligned_cols=19 Identities=37% Similarity=0.396 Sum_probs=17.8
Q ss_pred hhhhHHHhhcchhhHHHHH
Q psy1904 8 PCVISRQLRVSHGCVSKIL 26 (163)
Q Consensus 8 ~~~ia~~~~vs~~~vs~~l 26 (163)
..|||+..|||.+|||+.|
T Consensus 2 i~dIA~~agvS~~TVSr~l 20 (46)
T PF00356_consen 2 IKDIAREAGVSKSTVSRVL 20 (46)
T ss_dssp HHHHHHHHTSSHHHHHHHH
T ss_pred HHHHHHHHCcCHHHHHHHH
Confidence 4699999999999999999
No 56
>KOG0773|consensus
Probab=96.77 E-value=0.0011 Score=52.70 Aligned_cols=60 Identities=17% Similarity=0.268 Sum_probs=48.4
Q ss_pred cccccCcCCHHHHHHHHHh-cc--CCCCCCHHHHHHHHHHhCCCcccccccccccccccccCC
Q psy1904 98 QRRSRTTFTSAQLEELEKS-FQ--RSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCL 157 (163)
Q Consensus 98 ~rr~Rt~~t~~q~~~Le~~-F~--~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~ 157 (163)
..|.+..+......+|+.. |+ ..+||+..++..||.++||+..||.+||-|.|.+..+.+
T Consensus 239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p~ 301 (342)
T KOG0773|consen 239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKPM 301 (342)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCCch
Confidence 3445557888888888766 22 357999999999999999999999999999998876543
No 57
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=96.73 E-value=0.0012 Score=51.87 Aligned_cols=37 Identities=24% Similarity=0.400 Sum_probs=33.7
Q ss_pred cCCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCC
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV 39 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~ 39 (163)
.+|+.+.|||++||||..+|+|+|+.-++.|-+.-..
T Consensus 27 ~~g~tQ~eIA~~lgiSR~~VsRlL~~Ar~~GiV~I~I 63 (318)
T PRK15418 27 HDGLTQSEIGERLGLTRLKVSRLLEKGRQSGIIRVQI 63 (318)
T ss_pred hcCCCHHHHHHHhCCCHHHHHHHHHHHHHcCcEEEEE
Confidence 3799999999999999999999999999999886554
No 58
>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=96.69 E-value=0.0011 Score=37.07 Aligned_cols=33 Identities=21% Similarity=0.343 Sum_probs=27.3
Q ss_pred ccCCCChhhhHHHhhcchhhHHHHHhhhhhccC
Q psy1904 2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETGS 34 (163)
Q Consensus 2 ~~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~ 34 (163)
++.-...||||+.|++|+++|++-|+..++.|=
T Consensus 12 ~~~~~~~~el~~~l~~s~~~vs~hL~~L~~~gl 44 (47)
T PF01022_consen 12 SEGPLTVSELAEELGLSQSTVSHHLKKLREAGL 44 (47)
T ss_dssp TTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTS
T ss_pred HhCCCchhhHHHhccccchHHHHHHHHHHHCcC
Confidence 343478999999999999999999999988774
No 59
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=96.64 E-value=0.0026 Score=35.57 Aligned_cols=31 Identities=19% Similarity=0.384 Sum_probs=25.9
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhhhhccC
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGS 34 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~ 34 (163)
.+++..|||+.+|+|.++|++.++...+.|-
T Consensus 16 ~~~t~~ela~~~~is~~tv~~~l~~L~~~g~ 46 (48)
T PF13412_consen 16 PRITQKELAEKLGISRSTVNRYLKKLEEKGL 46 (48)
T ss_dssp TTS-HHHHHHHHTS-HHHHHHHHHHHHHTTS
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHCcC
Confidence 4599999999999999999999999877663
No 60
>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=96.61 E-value=0.0019 Score=36.87 Aligned_cols=32 Identities=22% Similarity=0.363 Sum_probs=27.5
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhhhhccCC
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSI 35 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~ 35 (163)
.+++..|||+.+|++.++|+++|..+.+.|=+
T Consensus 17 ~~~t~~eia~~~gl~~stv~r~L~tL~~~g~v 48 (52)
T PF09339_consen 17 GPLTLSEIARALGLPKSTVHRLLQTLVEEGYV 48 (52)
T ss_dssp SCEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHHCcCe
Confidence 45789999999999999999999999887754
No 61
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=96.48 E-value=0.015 Score=34.79 Aligned_cols=31 Identities=23% Similarity=0.202 Sum_probs=24.5
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCC
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV 39 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~ 39 (163)
+++.|+|+.+|||.+++.+|.++. |.+.|..
T Consensus 1 ~s~~eva~~~gvs~~tlr~w~~~~---g~~~~~r 31 (68)
T cd01104 1 YTIGAVARLTGVSPDTLRAWERRY---GLPAPQR 31 (68)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHhC---CCCCCCc
Confidence 367899999999999999997554 6555543
No 62
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=96.43 E-value=0.00076 Score=38.99 Aligned_cols=42 Identities=14% Similarity=0.201 Sum_probs=30.8
Q ss_pred HHHHHHhccCCCCCCHHHHHHHHHHhCCCccccccccccccc
Q psy1904 110 LEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAG 151 (163)
Q Consensus 110 ~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~ 151 (163)
...|+..|...+++.......|..+.+|+..||+.||-.+..
T Consensus 10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~ 51 (56)
T PF11569_consen 10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERMQ 51 (56)
T ss_dssp -HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS-
T ss_pred hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhcc
Confidence 456999999999999999999999999999999999976543
No 63
>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=96.38 E-value=0.0086 Score=32.93 Aligned_cols=30 Identities=13% Similarity=0.169 Sum_probs=23.7
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCC
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV 39 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~ 39 (163)
++..|+|+.||||.+||.+|.+. |.+.+..
T Consensus 1 ~s~~e~a~~lgvs~~tl~~~~~~----g~~~~~~ 30 (49)
T cd04762 1 LTTKEAAELLGVSPSTLRRWVKE----GKLKAIR 30 (49)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHc----CCCCcee
Confidence 35789999999999999999854 6665443
No 64
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=96.32 E-value=0.0022 Score=40.13 Aligned_cols=25 Identities=24% Similarity=0.396 Sum_probs=20.4
Q ss_pred cCCCChhhhHHHhhcchhhHHHHHh
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKILN 27 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l~ 27 (163)
..|+++.|+|+.+||+++.||++++
T Consensus 29 ~~~ltQ~e~A~~lgisq~~vS~l~~ 53 (80)
T PF13744_consen 29 ERGLTQAELAERLGISQPRVSRLEN 53 (80)
T ss_dssp CCT--HHHHHHHHTS-HHHHHHHHT
T ss_pred HcCCCHHHHHHHHCCChhHHHHHHc
Confidence 5799999999999999999999984
No 65
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=96.29 E-value=0.002 Score=43.23 Aligned_cols=29 Identities=21% Similarity=0.351 Sum_probs=25.4
Q ss_pred CccCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904 1 MAAAGVRPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 1 ~~~~g~~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
|..+|+++-+||..||||++-||++|+..
T Consensus 18 L~eeG~Sq~~iA~LLGltqaAVS~Yls~k 46 (119)
T COG2522 18 LIEEGLSQYRIAKLLGLTQAAVSQYLSGK 46 (119)
T ss_pred HHHcCCcHHHHHHHhCCCHHHHHHHHccC
Confidence 34579999999999999999999999543
No 66
>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=96.21 E-value=0.015 Score=38.78 Aligned_cols=53 Identities=17% Similarity=0.210 Sum_probs=40.3
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCC-CCcCChHHHHHHHH
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSK-PRVATPDVEKRIEE 58 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~-p~~~~~~~~~~i~~ 58 (163)
|.|.|+|..+|+|.=||.||.+..-=.....||+-||.. --..+..+.+.+..
T Consensus 1 MT~eELA~~tG~srQTINrWvRkegW~T~p~pGVkGGrARLIhId~~V~efi~s 54 (122)
T PF07037_consen 1 MTPEELAELTGYSRQTINRWVRKEGWKTEPKPGVKGGRARLIHIDEQVREFIRS 54 (122)
T ss_pred CCHHHHHHHhCccHHHHHHHHHhcCceeccCCccccccceeeeecHHHHHHHHh
Confidence 578999999999999999999888667777899877753 22444555555544
No 67
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=96.12 E-value=0.0027 Score=37.53 Aligned_cols=26 Identities=31% Similarity=0.488 Sum_probs=20.4
Q ss_pred CccCCCChhhhHHHhhcchhhHHHHH
Q psy1904 1 MAAAGVRPCVISRQLRVSHGCVSKIL 26 (163)
Q Consensus 1 ~~~~g~~~~~ia~~~~vs~~~vs~~l 26 (163)
|++.|+++.++|+..|||.++|++|+
T Consensus 6 m~~~~it~~~La~~~gis~~tl~~~~ 31 (63)
T PF13443_consen 6 MAERGITQKDLARKTGISRSTLSRIL 31 (63)
T ss_dssp HHHTT--HHHHHHHHT--HHHHHHHH
T ss_pred HHHcCCCHHHHHHHHCcCHHHHHHHH
Confidence 46789999999999999999999998
No 68
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=96.11 E-value=0.0067 Score=34.49 Aligned_cols=27 Identities=26% Similarity=0.310 Sum_probs=24.8
Q ss_pred cCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
..|++..+||+.|+||.++|++++.+.
T Consensus 16 ~~g~s~~eia~~l~is~~tv~~~~~~~ 42 (58)
T smart00421 16 AEGLTNKEIAERLGISEKTVKTHLSNI 42 (58)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 478999999999999999999999875
No 69
>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=96.09 E-value=0.0048 Score=35.31 Aligned_cols=24 Identities=21% Similarity=0.372 Sum_probs=20.8
Q ss_pred cCCCChhhhHHHhhcchhhHHHHH
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKIL 26 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l 26 (163)
+.|+++.|+|+.+|||.++|++|+
T Consensus 7 ~~gls~~~la~~~gis~~~i~~~~ 30 (55)
T PF01381_consen 7 EKGLSQKELAEKLGISRSTISRIE 30 (55)
T ss_dssp HTTS-HHHHHHHHTS-HHHHHHHH
T ss_pred HcCCCHHHHHHHhCCCcchhHHHh
Confidence 479999999999999999999997
No 70
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=96.07 E-value=0.0045 Score=37.94 Aligned_cols=28 Identities=14% Similarity=0.287 Sum_probs=25.0
Q ss_pred cCCCChhhhHHHhhcchhhHHHHHhhhh
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKILNRYQ 30 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~~ 30 (163)
..|.+..+||+.+||+.+++++|++.|.
T Consensus 21 ~~g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 21 ESGESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp HHHCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred HCCCceEeeecccccccccccHHHHHHh
Confidence 3678999999999999999999999997
No 71
>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=96.04 E-value=0.0039 Score=34.45 Aligned_cols=28 Identities=29% Similarity=0.274 Sum_probs=25.2
Q ss_pred CccCCCChhhhHHHhhcchhhHHHHHhh
Q psy1904 1 MAAAGVRPCVISRQLRVSHGCVSKILNR 28 (163)
Q Consensus 1 ~~~~g~~~~~ia~~~~vs~~~vs~~l~~ 28 (163)
||..|...+|+|+.|+||..||.+-|+.
T Consensus 17 ma~nG~GiRdtaRvL~I~~nTVlrtLK~ 44 (46)
T PF12759_consen 17 MAFNGSGIRDTARVLKISINTVLRTLKN 44 (46)
T ss_pred HHhcCCcchhhHhHhcchHHHHHHHHhc
Confidence 5778999999999999999999998864
No 72
>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=95.92 E-value=0.0077 Score=36.94 Aligned_cols=28 Identities=21% Similarity=0.220 Sum_probs=25.0
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhhhh
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~ 31 (163)
+|++..|||+.+|||.++|..++.....
T Consensus 31 eGlS~kEIAe~LGIS~~TVk~~l~~~~~ 58 (73)
T TIGR03879 31 AGKTASEIAEELGRTEQTVRNHLKGETK 58 (73)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHhcCcc
Confidence 7999999999999999999999976433
No 73
>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD. This model represents a protein subfamily found mostly in the Firmicutes (Bacillus and allies). This family is similar in sequence to the trp operon repressor TrpR described by TIGR01321, and represents a distinct clade within the broader family described by pfam01371. At least one species, Xylella fastidiosa, in the Proteobacteria, has a member of both this family and TIGR01321. Several genomes with a member of this family do not synthesize tryptophan, and members of this family should not be considered trp operon repressors without new evidence.
Probab=95.90 E-value=0.007 Score=38.59 Aligned_cols=24 Identities=17% Similarity=0.171 Sum_probs=22.2
Q ss_pred cCCCChhhhHHHhhcchhhHHHHH
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKIL 26 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l 26 (163)
..|.+..+||+.||||.+||+++.
T Consensus 48 ~~G~S~~eIA~~LgISrsTIyRi~ 71 (88)
T TIGR02531 48 KQGKTYSDIEAETGASTATISRVK 71 (88)
T ss_pred HCCCCHHHHHHHHCcCHHHHHHHH
Confidence 478999999999999999999976
No 74
>PHA00542 putative Cro-like protein
Probab=95.89 E-value=0.0048 Score=38.79 Aligned_cols=24 Identities=25% Similarity=0.259 Sum_probs=22.7
Q ss_pred cCCCChhhhHHHhhcchhhHHHHH
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKIL 26 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l 26 (163)
..|+++.++|+.+|||+++|++|+
T Consensus 29 ~~glTq~elA~~lgIs~~tIsr~e 52 (82)
T PHA00542 29 RAGWSQEQIADATDVSQPTICRIY 52 (82)
T ss_pred HCCCCHHHHHHHHCcCHHHHHHHH
Confidence 468999999999999999999997
No 75
>PHA01976 helix-turn-helix protein
Probab=95.87 E-value=0.0094 Score=35.57 Aligned_cols=24 Identities=21% Similarity=0.166 Sum_probs=22.5
Q ss_pred cCCCChhhhHHHhhcchhhHHHHH
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKIL 26 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l 26 (163)
..|+++.++|+.+|||+++|++|.
T Consensus 13 ~~glt~~~lA~~~gvs~~~v~~~e 36 (67)
T PHA01976 13 ARAWSAPELSRRAGVRHSLIYDFE 36 (67)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHH
Confidence 478999999999999999999996
No 76
>PRK10072 putative transcriptional regulator; Provisional
Probab=95.83 E-value=0.0096 Score=38.59 Aligned_cols=24 Identities=25% Similarity=0.212 Sum_probs=22.5
Q ss_pred cCCCChhhhHHHhhcchhhHHHHH
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKIL 26 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l 26 (163)
+.|+++.++|+.+|||.++|++|.
T Consensus 44 ~~glTQ~elA~~lGvS~~TVs~WE 67 (96)
T PRK10072 44 GTGLKIDDFARVLGVSVAMVKEWE 67 (96)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHH
Confidence 469999999999999999999997
No 77
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=95.82 E-value=0.011 Score=33.31 Aligned_cols=26 Identities=31% Similarity=0.437 Sum_probs=22.7
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
.|.+..|||+.||||.++|++++.+-
T Consensus 19 ~~~t~~eIa~~lg~s~~~V~~~~~~a 44 (50)
T PF04545_consen 19 EGLTLEEIAERLGISRSTVRRILKRA 44 (50)
T ss_dssp ST-SHHHHHHHHTSCHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHCCcHHHHHHHHHHH
Confidence 68899999999999999999998664
No 78
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=95.81 E-value=0.0081 Score=47.33 Aligned_cols=38 Identities=24% Similarity=0.450 Sum_probs=34.2
Q ss_pred cCCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCC
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI 40 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~ 40 (163)
.+|+.+.|||++||||..+|+++|+.-++.|-+.-...
T Consensus 24 ~~gltQ~eIA~~LgiSR~~v~rlL~~Ar~~GiV~I~i~ 61 (321)
T COG2390 24 VEGLTQSEIAERLGISRATVSRLLAKAREEGIVKISIN 61 (321)
T ss_pred hcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCeEEEEeC
Confidence 47999999999999999999999999999998875543
No 79
>PF12728 HTH_17: Helix-turn-helix domain
Probab=95.81 E-value=0.012 Score=33.27 Aligned_cols=46 Identities=22% Similarity=0.341 Sum_probs=30.4
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHH
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRI 56 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i 56 (163)
+++.|+|+.||||.++|.+|++. |.+.+-..|+. -.....++++.+
T Consensus 2 lt~~e~a~~l~is~~tv~~~~~~----g~i~~~~~g~~-~~~~~~~l~~~~ 47 (51)
T PF12728_consen 2 LTVKEAAELLGISRSTVYRWIRQ----GKIPPFKIGRK-WRIPKSDLDRWL 47 (51)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHc----CCCCeEEeCCE-EEEeHHHHHHHH
Confidence 46789999999999999999844 66654433432 333334444443
No 80
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=95.78 E-value=0.012 Score=32.45 Aligned_cols=32 Identities=25% Similarity=0.348 Sum_probs=28.9
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRP 37 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P 37 (163)
++..|||+.+++|.++|++.|+.+.+.|-+..
T Consensus 9 ~s~~~la~~l~~s~~tv~~~l~~L~~~g~l~~ 40 (48)
T smart00419 9 LTRQEIAELLGLTRETVSRTLKRLEKEGLISR 40 (48)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence 67889999999999999999999999887753
No 81
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=95.77 E-value=0.011 Score=38.61 Aligned_cols=30 Identities=37% Similarity=0.466 Sum_probs=24.9
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCC
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG 38 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg 38 (163)
-|+++.+.|+.||||.+||++| |.|-..|.
T Consensus 56 ~~lSQ~vFA~~L~vs~~Tv~~W-----EqGr~kPs 85 (104)
T COG2944 56 LGLSQPVFARYLGVSVSTVRKW-----EQGRKKPS 85 (104)
T ss_pred hCCCHHHHHHHHCCCHHHHHHH-----HcCCcCCC
Confidence 5799999999999999999999 45555443
No 82
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=95.74 E-value=0.0089 Score=34.26 Aligned_cols=26 Identities=15% Similarity=0.293 Sum_probs=23.1
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
.|..-.++|.+||||++||++|...+
T Consensus 18 ~~~~~~~La~~FgIs~stvsri~~~~ 43 (53)
T PF13613_consen 18 LNLTFQDLAYRFGISQSTVSRIFHEW 43 (53)
T ss_pred cCCcHhHHhhheeecHHHHHHHHHHH
Confidence 46778899999999999999998766
No 83
>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=95.72 E-value=0.0088 Score=30.47 Aligned_cols=24 Identities=38% Similarity=0.451 Sum_probs=21.6
Q ss_pred cCCCChhhhHHHhhcchhhHHHHH
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKIL 26 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l 26 (163)
..|.+..+||+.|+||.++|++|+
T Consensus 19 ~~~~s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 19 AAGESVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHhC
Confidence 367899999999999999999985
No 84
>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=95.71 E-value=0.0054 Score=39.43 Aligned_cols=25 Identities=20% Similarity=0.202 Sum_probs=22.3
Q ss_pred cCCCChhhhHHHhhcchhhHHHHHh
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKILN 27 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l~ 27 (163)
..|+++.+||+.+|||.++|+|+-+
T Consensus 53 ~~~~tQrEIa~~lGiS~atIsR~sn 77 (94)
T TIGR01321 53 NGNMSQREIASKLGVSIATITRGSN 77 (94)
T ss_pred hCCCCHHHHHHHhCCChhhhhHHHh
Confidence 3579999999999999999999853
No 85
>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=95.70 E-value=0.0092 Score=34.94 Aligned_cols=31 Identities=23% Similarity=0.483 Sum_probs=27.3
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIR 36 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~ 36 (163)
+++.|||+.+++++++|++++++..+-|=+.
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 8999999999999999999999998887663
No 86
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=95.69 E-value=0.014 Score=32.56 Aligned_cols=28 Identities=25% Similarity=0.258 Sum_probs=25.3
Q ss_pred cCCCChhhhHHHhhcchhhHHHHHhhhh
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKILNRYQ 30 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~~ 30 (163)
..|+++.+||..+|+|.++|++++.+.+
T Consensus 24 ~~~~~~~~ia~~~~~s~~~i~~~~~~~~ 51 (55)
T cd06171 24 GEGLSYEEIAEILGISRSTVRQRLHRAL 51 (55)
T ss_pred hcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 3789999999999999999999997764
No 87
>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=95.62 E-value=0.0097 Score=34.08 Aligned_cols=24 Identities=13% Similarity=0.147 Sum_probs=22.5
Q ss_pred cCCCChhhhHHHhhcchhhHHHHH
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKIL 26 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l 26 (163)
..|+++.++|+.+|||+++|++|.
T Consensus 13 ~~gltq~~lA~~~gvs~~~vs~~e 36 (58)
T TIGR03070 13 ALGLTQADLADLAGVGLRFIRDVE 36 (58)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHH
Confidence 468999999999999999999997
No 88
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=95.59 E-value=0.014 Score=35.31 Aligned_cols=33 Identities=12% Similarity=0.269 Sum_probs=30.5
Q ss_pred CCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904 5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRP 37 (163)
Q Consensus 5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P 37 (163)
|+++.|||+.|||+..+|.+.|..+.+.|-+.-
T Consensus 22 ~~ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~~ 54 (68)
T smart00550 22 TSTALQLAKNLGLPKKEVNRVLYSLEKKGKVCK 54 (68)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence 599999999999999999999999999988854
No 89
>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=95.49 E-value=0.012 Score=33.69 Aligned_cols=29 Identities=17% Similarity=0.284 Sum_probs=26.2
Q ss_pred CCChhhhHHHhhcchhhHHHHHhhhhhcc
Q psy1904 5 GVRPCVISRQLRVSHGCVSKILNRYQETG 33 (163)
Q Consensus 5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG 33 (163)
.++..+||+.|+||..||.+.++..++.|
T Consensus 15 ~it~~eLa~~l~vS~rTi~~~i~~L~~~~ 43 (55)
T PF08279_consen 15 PITAKELAEELGVSRRTIRRDIKELREWG 43 (55)
T ss_dssp SBEHHHHHHHCTS-HHHHHHHHHHHHHTT
T ss_pred CcCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence 48999999999999999999999998888
No 90
>PRK04217 hypothetical protein; Provisional
Probab=95.44 E-value=0.016 Score=38.48 Aligned_cols=27 Identities=22% Similarity=0.284 Sum_probs=24.3
Q ss_pred cCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
.+|++..+||++||||.+||+++|.+.
T Consensus 56 ~eGlS~~EIAk~LGIS~sTV~r~L~RA 82 (110)
T PRK04217 56 YEGLTQEEAGKRMGVSRGTVWRALTSA 82 (110)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 378999999999999999999999654
No 91
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=95.42 E-value=0.016 Score=34.31 Aligned_cols=24 Identities=33% Similarity=0.461 Sum_probs=20.3
Q ss_pred cCCCChhhhHHHhhcchhhHHHHH
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKIL 26 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l 26 (163)
..|++..++|+++|||.++|++|.
T Consensus 12 ~~gls~~~lA~~~g~s~s~v~~iE 35 (64)
T PF13560_consen 12 RAGLSQAQLADRLGVSQSTVSRIE 35 (64)
T ss_dssp CHTS-HHHHHHHHTS-HHHHHHHH
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHH
Confidence 368999999999999999999996
No 92
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=95.38 E-value=0.023 Score=33.67 Aligned_cols=34 Identities=24% Similarity=0.274 Sum_probs=30.3
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP 37 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P 37 (163)
..++..|||+.+|+|.++|+++|+.+.+.|-+..
T Consensus 24 ~~~s~~ela~~~g~s~~tv~r~l~~L~~~g~i~~ 57 (67)
T cd00092 24 LPLTRQEIADYLGLTRETVSRTLKELEEEGLISR 57 (67)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence 3489999999999999999999999988887753
No 93
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=95.36 E-value=0.013 Score=35.48 Aligned_cols=20 Identities=30% Similarity=0.305 Sum_probs=18.7
Q ss_pred ChhhhHHHhhcchhhHHHHH
Q psy1904 7 RPCVISRQLRVSHGCVSKIL 26 (163)
Q Consensus 7 ~~~~ia~~~~vs~~~vs~~l 26 (163)
...|||+.+|||.+|||++|
T Consensus 2 t~~~iA~~~gvS~~TVSr~l 21 (70)
T smart00354 2 TIKDVARLAGVSKATVSRVL 21 (70)
T ss_pred CHHHHHHHHCCCHHHHHHHH
Confidence 56799999999999999998
No 94
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=95.35 E-value=0.023 Score=31.73 Aligned_cols=34 Identities=24% Similarity=0.270 Sum_probs=30.0
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP 37 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P 37 (163)
.+++..+||+.|+||.++|++.|+.+.+-|-+..
T Consensus 13 ~~~s~~~l~~~l~~s~~tv~~~l~~L~~~g~i~~ 46 (53)
T smart00420 13 GKVSVEELAELLGVSEMTIRRDLNKLEEQGLLTR 46 (53)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence 4689999999999999999999999988776653
No 95
>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=95.33 E-value=0.011 Score=34.73 Aligned_cols=24 Identities=25% Similarity=0.285 Sum_probs=21.5
Q ss_pred CCChhhhHHHhhcchhhHHHHHhh
Q psy1904 5 GVRPCVISRQLRVSHGCVSKILNR 28 (163)
Q Consensus 5 g~~~~~ia~~~~vs~~~vs~~l~~ 28 (163)
++.--|||+.||||.+||++|-.+
T Consensus 22 ~i~lkdIA~~Lgvs~~tIr~WK~~ 45 (60)
T PF10668_consen 22 KIKLKDIAEKLGVSESTIRKWKSR 45 (60)
T ss_pred CccHHHHHHHHCCCHHHHHHHhhh
Confidence 388999999999999999999654
No 96
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=95.29 E-value=0.016 Score=33.01 Aligned_cols=27 Identities=26% Similarity=0.342 Sum_probs=20.9
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhhh
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRYQ 30 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~ 30 (163)
.|++..|||+.+|+|.++|..++.+-+
T Consensus 25 ~g~s~~eIa~~l~~s~~~v~~~l~ra~ 51 (54)
T PF08281_consen 25 QGMSYAEIAEILGISESTVKRRLRRAR 51 (54)
T ss_dssp S---HHHHHHHCTS-HHHHHHHHHHHH
T ss_pred HCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 789999999999999999999997754
No 97
>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=95.26 E-value=0.012 Score=33.16 Aligned_cols=17 Identities=41% Similarity=0.462 Sum_probs=16.4
Q ss_pred hhHHHhhcchhhHHHHH
Q psy1904 10 VISRQLRVSHGCVSKIL 26 (163)
Q Consensus 10 ~ia~~~~vs~~~vs~~l 26 (163)
+||+++|||.+||++|+
T Consensus 2 ~lA~~~gvs~~tvs~~l 18 (52)
T cd01392 2 DIARAAGVSVATVSRVL 18 (52)
T ss_pred cHHHHHCcCHHHHHHHH
Confidence 79999999999999998
No 98
>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=95.26 E-value=0.012 Score=32.06 Aligned_cols=27 Identities=22% Similarity=0.331 Sum_probs=21.8
Q ss_pred cCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
..|-...++|+.||||..++++.+++|
T Consensus 16 ~~~gn~~~aA~~Lgisr~tL~~klkk~ 42 (42)
T PF02954_consen 16 RCGGNVSKAARLLGISRRTLYRKLKKY 42 (42)
T ss_dssp HTTT-HHHHHHHHTS-HHHHHHHHHHC
T ss_pred HhCCCHHHHHHHHCCCHHHHHHHHHhC
Confidence 456778899999999999999998775
No 99
>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=95.21 E-value=0.014 Score=35.92 Aligned_cols=25 Identities=24% Similarity=0.409 Sum_probs=23.2
Q ss_pred ccCCCChhhhHHHhhcchhhHHHHH
Q psy1904 2 AAAGVRPCVISRQLRVSHGCVSKIL 26 (163)
Q Consensus 2 ~~~g~~~~~ia~~~~vs~~~vs~~l 26 (163)
...|+++.++|+.+|||.++|++|+
T Consensus 15 ~~~~~t~~~lA~~~gis~~tis~~~ 39 (78)
T TIGR02607 15 EPLGLSIRALAKALGVSRSTLSRIV 39 (78)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHH
Confidence 4579999999999999999999997
No 100
>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=95.07 E-value=0.017 Score=33.53 Aligned_cols=32 Identities=25% Similarity=0.563 Sum_probs=27.7
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhhhhccCC
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSI 35 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~ 35 (163)
.|+++.+||+.++++.++|++++++..+-|=+
T Consensus 16 ~~~~~~~la~~~~~~~~~~t~~i~~L~~~g~I 47 (59)
T PF01047_consen 16 GGITQSELAEKLGISRSTVTRIIKRLEKKGLI 47 (59)
T ss_dssp SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred CCCCHHHHHHHHCCChhHHHHHHHHHHHCCCE
Confidence 56899999999999999999999998777755
No 101
>PRK00118 putative DNA-binding protein; Validated
Probab=95.07 E-value=0.025 Score=37.19 Aligned_cols=27 Identities=19% Similarity=0.149 Sum_probs=24.5
Q ss_pred cCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
..|++..+||+.+|||.+||++++.+.
T Consensus 31 ~eg~S~~EIAe~lGIS~~TV~r~L~RA 57 (104)
T PRK00118 31 LDDYSLGEIAEEFNVSRQAVYDNIKRT 57 (104)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 368999999999999999999999764
No 102
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=95.03 E-value=0.019 Score=32.49 Aligned_cols=25 Identities=32% Similarity=0.449 Sum_probs=22.4
Q ss_pred CCChhhhHHHhhcchhhHHHHHhhh
Q psy1904 5 GVRPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 5 g~~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
..+..+||+.+|||..||.+|+.++
T Consensus 27 ~~s~~~vA~~~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 27 SRSFKDVARELGVSWSTVRRIFDRY 51 (52)
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHhh
Confidence 3688999999999999999999775
No 103
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=95.01 E-value=0.055 Score=29.90 Aligned_cols=31 Identities=13% Similarity=0.085 Sum_probs=24.3
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCC
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI 40 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~ 40 (163)
++..|+|+.+||+..||..|. +.|-+.|...
T Consensus 1 ~~~~e~a~~~gv~~~tlr~~~----~~g~l~~~~~ 31 (49)
T cd04761 1 YTIGELAKLTGVSPSTLRYYE----RIGLLSPART 31 (49)
T ss_pred CcHHHHHHHHCcCHHHHHHHH----HCCCCCCCcC
Confidence 467899999999999999986 4476665433
No 104
>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=95.00 E-value=0.026 Score=32.40 Aligned_cols=46 Identities=20% Similarity=0.427 Sum_probs=35.7
Q ss_pred ccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCccccccccccc
Q psy1904 99 RRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGT 149 (163)
Q Consensus 99 rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnr 149 (163)
+++|..+|-++-..+-..++... ...+||..+|++..+|..|..|+
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~k 46 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKNK 46 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHHHHCH
T ss_pred CCCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHhH
Confidence 46788999999888888888886 57789999999999999999885
No 105
>PHA02535 P terminase ATPase subunit; Provisional
Probab=95.00 E-value=0.047 Score=46.22 Aligned_cols=26 Identities=15% Similarity=0.143 Sum_probs=24.4
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
+|.++.+||+.|||+.+||++|.+++
T Consensus 17 ~G~sv~eIA~~LGv~~~Tl~~W~kr~ 42 (581)
T PHA02535 17 QGWTVAEIAEELGLKSRTIYSWKERD 42 (581)
T ss_pred cCCCHHHHHHHhCCChhHHHHHhccc
Confidence 59999999999999999999998776
No 106
>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=94.97 E-value=0.056 Score=33.50 Aligned_cols=41 Identities=24% Similarity=0.370 Sum_probs=36.8
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCC--CCCCCCCCCC
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIR--PGVIGGSKPR 46 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~--Pg~~Gg~~p~ 46 (163)
+.-..||+.+++|.+||...+..+.+.|-+. |++.||..|.
T Consensus 24 VgSk~ia~~l~~s~aTIRN~M~~Le~lGlve~~p~~s~GriPT 66 (78)
T PF03444_consen 24 VGSKTIAEELGRSPATIRNEMADLEELGLVESQPHPSGGRIPT 66 (78)
T ss_pred cCHHHHHHHHCCChHHHHHHHHHHHHCCCccCCCCCCCCCCcC
Confidence 6778999999999999999999999999993 8888888775
No 107
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=94.96 E-value=0.026 Score=31.03 Aligned_cols=32 Identities=19% Similarity=0.276 Sum_probs=24.3
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCC
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIG 41 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~G 41 (163)
++..|+|+.||||.++|.+|++ .|.+.+-..|
T Consensus 2 lt~~e~a~~lgis~~ti~~~~~----~g~i~~~~~g 33 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTVYRLIH----EGELPAYRVG 33 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHHH----cCCCCeEEeC
Confidence 4678999999999999999984 3655443344
No 108
>PRK11050 manganese transport regulator MntR; Provisional
Probab=94.90 E-value=0.03 Score=39.34 Aligned_cols=35 Identities=29% Similarity=0.378 Sum_probs=31.4
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCC
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG 38 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg 38 (163)
.++++.+||+.|+||+++|+++++++.+.|-+...
T Consensus 50 ~~~t~~eLA~~l~is~stVsr~l~~Le~~GlI~r~ 84 (152)
T PRK11050 50 GEARQVDIAARLGVSQPTVAKMLKRLARDGLVEMR 84 (152)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence 56999999999999999999999999999877543
No 109
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=94.88 E-value=0.024 Score=32.56 Aligned_cols=30 Identities=27% Similarity=0.365 Sum_probs=27.8
Q ss_pred ChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904 7 RPCVISRQLRVSHGCVSKILNRYQETGSIR 36 (163)
Q Consensus 7 ~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~ 36 (163)
+..+||+.|+||.++|.+.+++..+.|-+.
T Consensus 22 s~~~la~~~~vs~~tv~~~l~~L~~~g~i~ 51 (60)
T smart00345 22 SERELAAQLGVSRTTVREALSRLEAEGLVQ 51 (60)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 788999999999999999999999988774
No 110
>PHA00738 putative HTH transcription regulator
Probab=94.87 E-value=0.02 Score=37.62 Aligned_cols=38 Identities=26% Similarity=0.183 Sum_probs=33.8
Q ss_pred CCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCC
Q psy1904 5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGG 42 (163)
Q Consensus 5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg 42 (163)
++..|+|+..|++|+++||+=|+-.++.|-+.-...|-
T Consensus 26 ~~~V~eLae~l~lSQptVS~HLKvLreAGLV~srK~Gr 63 (108)
T PHA00738 26 ILSASLISHTLLLSYTTVLRHLKILNEQGYIELYKEGR 63 (108)
T ss_pred CccHHHHHHhhCCCHHHHHHHHHHHHHCCceEEEEECC
Confidence 48899999999999999999999999999987766553
No 111
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=94.83 E-value=0.024 Score=38.13 Aligned_cols=54 Identities=17% Similarity=0.174 Sum_probs=41.3
Q ss_pred CCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHH
Q psy1904 5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEE 58 (163)
Q Consensus 5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~ 58 (163)
++..+|||+.|++++++||+=|+-.++.|=+.....|...-....+...+++..
T Consensus 30 ~~~v~ela~~l~lsqstvS~HL~~L~~AGLV~~~r~Gr~~~Y~l~~~~~~~~~~ 83 (117)
T PRK10141 30 ELCVCDLCTALDQSQPKISRHLALLRESGLLLDRKQGKWVHYRLSPHIPAWAAK 83 (117)
T ss_pred CcCHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEEEcCEEEEEECchHHHHHHH
Confidence 488999999999999999999999999999987766654333333444444444
No 112
>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=94.82 E-value=0.023 Score=36.46 Aligned_cols=26 Identities=27% Similarity=0.193 Sum_probs=19.9
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
.|+++.|||+++|.|.+.|++.|.-.
T Consensus 2 ~G~tq~eIA~~lGks~s~Vs~~l~Ll 27 (93)
T PF08535_consen 2 FGWTQEEIAKRLGKSRSWVSNHLALL 27 (93)
T ss_dssp TT--HHHHHHHTT--HHHHHHHHGGG
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 59999999999999999999999654
No 113
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=94.81 E-value=0.019 Score=34.07 Aligned_cols=36 Identities=14% Similarity=0.167 Sum_probs=30.3
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCC
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV 39 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~ 39 (163)
.+++..|||..+|||..+|.++|......|-+..-+
T Consensus 14 ~p~~T~eiA~~~gls~~~aR~yL~~Le~eG~V~~~~ 49 (62)
T PF04703_consen 14 GPLKTREIADALGLSIYQARYYLEKLEKEGKVERSP 49 (62)
T ss_dssp S-EEHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEES
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEec
Confidence 458889999999999999999999999999886433
No 114
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=94.81 E-value=0.18 Score=30.07 Aligned_cols=31 Identities=6% Similarity=0.088 Sum_probs=23.8
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCC
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV 39 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~ 39 (163)
++..|+|+.+|||..++..|.+.. |-+.|..
T Consensus 1 ~~i~e~A~~~gVs~~tlr~ye~~~---gl~~~~r 31 (68)
T cd04763 1 YTIGEVALLTGIKPHVLRAWEREF---GLLKPQR 31 (68)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHhc---CCCCCCc
Confidence 367899999999999999885333 6666644
No 115
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=94.77 E-value=0.025 Score=34.75 Aligned_cols=24 Identities=13% Similarity=0.174 Sum_probs=21.6
Q ss_pred cCCCChhhhHHHhh------cchhhHHHHH
Q psy1904 3 AAGVRPCVISRQLR------VSHGCVSKIL 26 (163)
Q Consensus 3 ~~g~~~~~ia~~~~------vs~~~vs~~l 26 (163)
..|+++.|+|+.+| +|+++|++|.
T Consensus 22 ~lGLTQ~dvA~~lg~~~g~i~SQstISR~E 51 (75)
T smart00352 22 KLGFTQADVGLALGALYGPDFSQTTICRFE 51 (75)
T ss_pred HcCCCHHHHHHHhcccccCcCCHHHHHHHH
Confidence 36999999999999 4999999984
No 116
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=94.76 E-value=0.036 Score=32.07 Aligned_cols=35 Identities=23% Similarity=0.413 Sum_probs=30.6
Q ss_pred cCCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP 37 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P 37 (163)
...++..+|++.|+||.++|++.|++..+-|-+.-
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~~g~i~~ 42 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLREAGLVES 42 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHHCCCeee
Confidence 34588999999999999999999999988887753
No 117
>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=94.74 E-value=0.038 Score=35.66 Aligned_cols=35 Identities=20% Similarity=0.140 Sum_probs=31.6
Q ss_pred cCCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP 37 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P 37 (163)
..++++.|||..+|+|..+|++.|+.+.+.|=+..
T Consensus 45 ~~~is~~eLa~~~g~sr~tVsr~L~~Le~~GlI~r 79 (95)
T TIGR01610 45 QDRVTATVIAELTGLSRTHVSDAIKSLARRRIIFR 79 (95)
T ss_pred CCccCHHHHHHHHCcCHHHHHHHHHHHHHCCCeee
Confidence 35689999999999999999999999999998863
No 118
>PF13730 HTH_36: Helix-turn-helix domain
Probab=94.69 E-value=0.037 Score=31.60 Aligned_cols=28 Identities=21% Similarity=0.373 Sum_probs=25.7
Q ss_pred ChhhhHHHhhcchhhHHHHHhhhhhccC
Q psy1904 7 RPCVISRQLRVSHGCVSKILNRYQETGS 34 (163)
Q Consensus 7 ~~~~ia~~~~vs~~~vs~~l~~~~~tG~ 34 (163)
+...||+.+|+|..||++.++...+.|-
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 7789999999999999999999988773
No 119
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=94.64 E-value=0.012 Score=35.39 Aligned_cols=34 Identities=21% Similarity=0.303 Sum_probs=30.0
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP 37 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P 37 (163)
.+++..|||+.+|++.++|++.|+...+.|-+.-
T Consensus 21 ~~~t~~eIa~~l~i~~~~v~~~L~~L~~~GlV~~ 54 (68)
T PF01978_consen 21 GPATAEEIAEELGISRSTVYRALKSLEEKGLVER 54 (68)
T ss_dssp CHEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence 4488999999999999999999999988887743
No 120
>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=94.64 E-value=0.018 Score=32.64 Aligned_cols=37 Identities=24% Similarity=0.475 Sum_probs=22.7
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCC-CCCCCCCCCCC
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSI-RPGVIGGSKPR 46 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~-~Pg~~Gg~~p~ 46 (163)
++..|+++.+|||.+|++++.+. |.+ .|-.+|+....
T Consensus 4 l~~~ev~~~~g~s~~ti~~~~k~----g~FP~pvklg~r~~~ 41 (51)
T PF05930_consen 4 LRIKEVAELLGVSRSTIYRLIKD----GKFPKPVKLGGRAVR 41 (51)
T ss_dssp E-HHHHHHHHSS-HHHHHHHHHH----HH---SEESSS----
T ss_pred ccHHHHHHHHCCCHHHHHHHHhc----ccCCCCEEECCCccc
Confidence 46789999999999999999863 444 44445654433
No 121
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=94.58 E-value=0.045 Score=30.97 Aligned_cols=26 Identities=23% Similarity=0.187 Sum_probs=24.2
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
.|++..+||+.|+||.++|.+++.+.
T Consensus 14 ~~~s~~eia~~l~~s~~tv~~~~~~~ 39 (57)
T cd06170 14 EGKTNKEIADILGISEKTVKTHLRNI 39 (57)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 68999999999999999999999775
No 122
>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=94.54 E-value=0.021 Score=35.67 Aligned_cols=21 Identities=19% Similarity=0.116 Sum_probs=19.9
Q ss_pred CChhhhHHHhhcchhhHHHHH
Q psy1904 6 VRPCVISRQLRVSHGCVSKIL 26 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l 26 (163)
+...|||+.||||.+||++.|
T Consensus 20 ~ti~dvA~~~gvS~~TVsr~L 40 (80)
T TIGR02844 20 ATVRETAKVFGVSKSTVHKDV 40 (80)
T ss_pred CCHHHHHHHhCCCHHHHHHHh
Confidence 788999999999999999988
No 123
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=94.53 E-value=0.056 Score=34.07 Aligned_cols=35 Identities=23% Similarity=0.424 Sum_probs=31.6
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCC
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG 38 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg 38 (163)
.+++..|||+.++|+.++|+++|....+.|-+...
T Consensus 19 ~~~t~~~ia~~l~i~~~tv~r~l~~L~~~g~l~~~ 53 (91)
T smart00346 19 GGLTLAELAERLGLSKSTAHRLLNTLQELGYVEQD 53 (91)
T ss_pred CCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeeec
Confidence 35999999999999999999999999999988654
No 124
>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=94.50 E-value=0.062 Score=36.52 Aligned_cols=40 Identities=30% Similarity=0.381 Sum_probs=33.3
Q ss_pred CCChhhhHHHhhcchhhHHHHHhhhhhccCCCC--CCCCCCC
Q psy1904 5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRP--GVIGGSK 44 (163)
Q Consensus 5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P--g~~Gg~~ 44 (163)
.++..+||+.++||.++|+++|....+.|-+.- |..||-.
T Consensus 25 ~~s~~eia~~l~is~~~v~~~l~~L~~~Gli~~~~g~~ggy~ 66 (130)
T TIGR02944 25 PYSAAEIAEQTGLNAPTVSKILKQLSLAGIVTSKRGVEGGYT 66 (130)
T ss_pred CccHHHHHHHHCcCHHHHHHHHHHHHHCCcEEecCCCCCChh
Confidence 389999999999999999999999999998853 3444443
No 125
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=94.50 E-value=0.043 Score=37.96 Aligned_cols=40 Identities=20% Similarity=0.311 Sum_probs=34.2
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCC
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGS 43 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~ 43 (163)
.|+++.+||+.++|+.++|++++++..+.|=+.-.....+
T Consensus 53 ~~~t~~eLa~~l~i~~~tvsr~l~~Le~~GlI~R~~~~~D 92 (144)
T PRK11512 53 ACITPVELKKVLSVDLGALTRMLDRLVCKGWVERLPNPND 92 (144)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeccCccc
Confidence 5699999999999999999999999999998865544333
No 126
>KOG3623|consensus
Probab=94.49 E-value=0.022 Score=48.91 Aligned_cols=51 Identities=14% Similarity=0.166 Sum_probs=45.3
Q ss_pred CCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccC
Q psy1904 105 FTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSC 156 (163)
Q Consensus 105 ~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~ 156 (163)
|+.. +..|...|..|..|+..+...+|.+.||+..-|+.||++++++..+.
T Consensus 564 ~~~p-~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv 614 (1007)
T KOG3623|consen 564 FNHP-TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSV 614 (1007)
T ss_pred cCCc-HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhh
Confidence 4443 78889999999999999999999999999999999999999987653
No 127
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=94.42 E-value=0.024 Score=32.14 Aligned_cols=27 Identities=26% Similarity=0.423 Sum_probs=20.3
Q ss_pred ccCCCChhhhHHHhhcchhhHHHHHhh
Q psy1904 2 AAAGVRPCVISRQLRVSHGCVSKILNR 28 (163)
Q Consensus 2 ~~~g~~~~~ia~~~~vs~~~vs~~l~~ 28 (163)
-+.|++-.+||++++-|..||.++|+-
T Consensus 17 ~qlG~s~~~isr~i~RSr~~Ir~yl~d 43 (50)
T PF11427_consen 17 HQLGMSLREISRRIGRSRTCIRRYLKD 43 (50)
T ss_dssp HHTT--HHHHHHHHT--HHHHHHHHHS
T ss_pred HHhchhHHHHHHHhCccHHHHHHHhcC
Confidence 357999999999999999999999853
No 128
>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=94.41 E-value=0.049 Score=31.25 Aligned_cols=26 Identities=23% Similarity=0.262 Sum_probs=22.9
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
.+++..|||+.||||.++|+.-|.+-
T Consensus 22 R~~tl~elA~~lgis~st~~~~LRra 47 (53)
T PF04967_consen 22 RRITLEELAEELGISKSTVSEHLRRA 47 (53)
T ss_pred CcCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 46788999999999999999998764
No 129
>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function.
Probab=94.40 E-value=0.041 Score=36.25 Aligned_cols=26 Identities=19% Similarity=0.267 Sum_probs=24.3
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
+|+++.+.|++.|||.+|+.++|..-
T Consensus 56 egl~QeeaA~~MgVSR~T~~ril~~A 81 (106)
T PF02001_consen 56 EGLSQEEAAERMGVSRPTFQRILESA 81 (106)
T ss_pred cCCCHHHHHHHcCCcHHHHHHHHHHH
Confidence 79999999999999999999999765
No 130
>PRK09726 antitoxin HipB; Provisional
Probab=94.32 E-value=0.035 Score=35.21 Aligned_cols=24 Identities=8% Similarity=0.278 Sum_probs=22.6
Q ss_pred cCCCChhhhHHHhhcchhhHHHHH
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKIL 26 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l 26 (163)
..|+++.++|+.+|||+++|++|+
T Consensus 23 ~~gltq~elA~~~gvs~~tis~~e 46 (88)
T PRK09726 23 QNGWTQSELAKKIGIKQATISNFE 46 (88)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHH
Confidence 469999999999999999999997
No 131
>COG3311 AlpA Predicted transcriptional regulator [Transcription]
Probab=94.30 E-value=0.14 Score=31.14 Aligned_cols=51 Identities=12% Similarity=0.213 Sum_probs=37.2
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHHH
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEY 59 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~~ 59 (163)
++--|++..+|+|.+||+++++.- .-..|-.+|+........++++++...
T Consensus 14 lrl~ev~~~~GlSrstiYr~i~~~---~FPkpvklG~r~v~W~~SEI~~Wi~~~ 64 (70)
T COG3311 14 LRLPEVAQLTGLSRSTIYRLIKDG---TFPKPVKLGGRSVAWPESEIDEWIASR 64 (70)
T ss_pred hhHHHHHHHHCccHHHHHHHHccC---CCCCCeecCcccccccHHHHHHHHHHH
Confidence 566789999999999999998553 333566678766666667777766443
No 132
>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=94.28 E-value=0.048 Score=37.68 Aligned_cols=27 Identities=26% Similarity=0.367 Sum_probs=24.3
Q ss_pred cCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
..|+++.+||++||+|.++|+.++++.
T Consensus 19 ~~GlTq~EIAe~LgiS~stV~~~e~ra 45 (137)
T TIGR00721 19 EKGLSQKEIAKELKTTRANVSAIEKRA 45 (137)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHHhH
Confidence 379999999999999999999888664
No 133
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=94.26 E-value=0.049 Score=37.82 Aligned_cols=27 Identities=30% Similarity=0.257 Sum_probs=24.5
Q ss_pred cCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
..|++..+||+.||+|.++|+.++++.
T Consensus 19 ~~GlTq~EIAe~LGiS~~tVs~ie~ra 45 (141)
T PRK03975 19 ERGLTQQEIADILGTSRANVSSIEKRA 45 (141)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 379999999999999999999998664
No 134
>PHA00675 hypothetical protein
Probab=94.20 E-value=0.042 Score=33.76 Aligned_cols=26 Identities=23% Similarity=0.436 Sum_probs=22.7
Q ss_pred cCCCChhhhHHHhhcchhhHHHHHhh
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKILNR 28 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l~~ 28 (163)
.+|.+..+||+.||||.++|+.|...
T Consensus 37 r~G~s~~~IA~~fGVsrstV~~I~~g 62 (78)
T PHA00675 37 VEGMSYAVLAEKFEQSKGAIAKICRY 62 (78)
T ss_pred hcCccHHHHHHHhCCCHHHHHHHHcc
Confidence 36889999999999999999998643
No 135
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=94.20 E-value=0.069 Score=35.53 Aligned_cols=36 Identities=17% Similarity=0.151 Sum_probs=31.0
Q ss_pred CCCChhhhHHHhhc-chhhHHHHHhhhhhccCCCCCC
Q psy1904 4 AGVRPCVISRQLRV-SHGCVSKILNRYQETGSIRPGV 39 (163)
Q Consensus 4 ~g~~~~~ia~~~~v-s~~~vs~~l~~~~~tG~~~Pg~ 39 (163)
.|.+.++||+.||| +.+.+++|+.++.+.+...+..
T Consensus 23 ~g~sv~~vAr~~gv~~~~~l~~W~~~~~~~~~~~~~~ 59 (116)
T COG2963 23 GGDTVSEVAREFGIVSATQLYKWRIQLQKGGGLAFSG 59 (116)
T ss_pred cCccHHHHHHHhCCCChHHHHHHHHHHHHcccccccC
Confidence 57889999999995 9999999999998887666543
No 136
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=94.14 E-value=0.05 Score=34.73 Aligned_cols=32 Identities=25% Similarity=0.419 Sum_probs=27.8
Q ss_pred ChhhhHHHhhcchhhHHHHHhhhhhccCCCCC
Q psy1904 7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPG 38 (163)
Q Consensus 7 ~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg 38 (163)
++.+||+.|+|+.++|++.+.+..+.|=+.-.
T Consensus 1 ~~~ela~~l~is~stvs~~l~~L~~~glI~r~ 32 (96)
T smart00529 1 RTSEIAERLNVSPPTVTQMLKKLEKDGLVEYE 32 (96)
T ss_pred CHHHHHHHhCCChHHHHHHHHHHHHCCCEEEc
Confidence 46799999999999999999999888877543
No 137
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=94.13 E-value=0.034 Score=32.64 Aligned_cols=34 Identities=24% Similarity=0.348 Sum_probs=28.9
Q ss_pred cCCCChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIR 36 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~ 36 (163)
..+++..+||+.|+++.++|+.=|+...+.|=+.
T Consensus 22 ~~~~t~~ela~~l~~~~~t~s~hL~~L~~aGli~ 55 (61)
T PF12840_consen 22 NGPMTVSELAEELGISQSTVSYHLKKLEEAGLIE 55 (61)
T ss_dssp CSTBEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeE
Confidence 4679999999999999999999999998877553
No 138
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=94.11 E-value=0.055 Score=38.44 Aligned_cols=35 Identities=17% Similarity=0.282 Sum_probs=31.2
Q ss_pred ccCC-CChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904 2 AAAG-VRPCVISRQLRVSHGCVSKILNRYQETGSIR 36 (163)
Q Consensus 2 ~~~g-~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~ 36 (163)
.+.| ++..+||+++|+|.++|.+=+++..+.|-+.
T Consensus 24 q~d~R~s~~eiA~~lglS~~tv~~Ri~rL~~~GvI~ 59 (164)
T PRK11169 24 QKDGRISNVELSKRVGLSPTPCLERVRRLERQGFIQ 59 (164)
T ss_pred ccCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeE
Confidence 3455 8999999999999999999999999999874
No 139
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=94.09 E-value=0.3 Score=29.03 Aligned_cols=23 Identities=9% Similarity=-0.074 Sum_probs=19.9
Q ss_pred CChhhhHHHhhcchhhHHHHHhh
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNR 28 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~ 28 (163)
+++.|+|+.+|||.+|+..|-+.
T Consensus 1 ~~i~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 1 YTIKEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHh
Confidence 46789999999999999998644
No 140
>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=94.05 E-value=0.058 Score=32.43 Aligned_cols=33 Identities=18% Similarity=0.140 Sum_probs=28.4
Q ss_pred cCCCChhhhHHHhhcchhhHHHHHhhhhhccCC
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSI 35 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~ 35 (163)
+.-++..+||..|+||.++|++-++...+.|-.
T Consensus 11 ~~~~~~~eLa~~l~vS~~tv~~~l~~L~~~g~~ 43 (69)
T TIGR00122 11 DNPFSGEKLGEALGMSRTAVNKHIQTLREWGVD 43 (69)
T ss_pred cCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCe
Confidence 334678899999999999999999999887764
No 141
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=93.97 E-value=0.037 Score=30.37 Aligned_cols=25 Identities=24% Similarity=0.341 Sum_probs=22.8
Q ss_pred ccCCCChhhhHHHhhcchhhHHHHH
Q psy1904 2 AAAGVRPCVISRQLRVSHGCVSKIL 26 (163)
Q Consensus 2 ~~~g~~~~~ia~~~~vs~~~vs~~l 26 (163)
...|++..++|+.+||+.++|++|+
T Consensus 7 ~~~~~s~~~la~~~~i~~~~i~~~~ 31 (56)
T smart00530 7 EEKGLTQEELAEKLGVSRSTLSRIE 31 (56)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHH
Confidence 3578999999999999999999997
No 142
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=93.91 E-value=0.073 Score=31.73 Aligned_cols=41 Identities=17% Similarity=0.314 Sum_probs=30.9
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhh-------hccCCCCCCCCCCCCC
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQ-------ETGSIRPGVIGGSKPR 46 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~-------~tG~~~Pg~~Gg~~p~ 46 (163)
++-.|+|+++|+.+++|.+|+..++ .+|.+.+.+--|.+|.
T Consensus 14 ~s~~~Aa~~lG~~~~~v~~wv~~fR~wll~LDPSG~~E~RVRLg~r~a 61 (65)
T PF05344_consen 14 ISVAQAADRLGTDPGTVRRWVRMFRQWLLQLDPSGHWEARVRLGVRPA 61 (65)
T ss_pred ccHHHHHHHHCcCHHHHHHHHHHHHHHHHHcCCCCChHHHhhcCCCCC
Confidence 5678999999999999999998875 4566665554445544
No 143
>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=93.90 E-value=0.035 Score=32.25 Aligned_cols=31 Identities=23% Similarity=0.347 Sum_probs=28.2
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIR 36 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~ 36 (163)
++..|+|..|+||..||.+=|....+.|-+.
T Consensus 15 ~s~~ela~~~~VS~~TiRRDl~~L~~~g~i~ 45 (57)
T PF08220_consen 15 VSVKELAEEFGVSEMTIRRDLNKLEKQGLIK 45 (57)
T ss_pred EEHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 7889999999999999999999998888753
No 144
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=93.90 E-value=0.043 Score=38.48 Aligned_cols=34 Identities=18% Similarity=0.316 Sum_probs=30.8
Q ss_pred cCC-CChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904 3 AAG-VRPCVISRQLRVSHGCVSKILNRYQETGSIR 36 (163)
Q Consensus 3 ~~g-~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~ 36 (163)
++| ++..+||+.+|+|.++|.+=+++..+.|-+.
T Consensus 20 ~d~R~s~~eiA~~lglS~~tV~~Ri~rL~~~GvI~ 54 (153)
T PRK11179 20 ENARTPYAELAKQFGVSPGTIHVRVEKMKQAGIIT 54 (153)
T ss_pred HcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCee
Confidence 445 8999999999999999999999999999875
No 145
>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=93.81 E-value=0.053 Score=32.19 Aligned_cols=33 Identities=21% Similarity=0.437 Sum_probs=27.3
Q ss_pred cCCCChhhhHHHhhcchhhHHHHHhhhhhccCC
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSI 35 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~ 35 (163)
+..+++.+||+.++++.++|++++++..+-|=+
T Consensus 16 ~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~glv 48 (68)
T PF13463_consen 16 DGPMTQSDLAERLGISKSTVSRIIKKLEEKGLV 48 (68)
T ss_dssp TS-BEHHHHHHHTT--HHHHHHHHHHHHHTTSE
T ss_pred CCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCE
Confidence 456899999999999999999999999888876
No 146
>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=93.79 E-value=0.069 Score=30.92 Aligned_cols=27 Identities=26% Similarity=0.278 Sum_probs=23.3
Q ss_pred cCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
-.|.+..+||+.++||..||...+...
T Consensus 16 ~~G~~~~eIA~~l~is~~tV~~~~~~i 42 (58)
T PF00196_consen 16 AQGMSNKEIAEELGISEKTVKSHRRRI 42 (58)
T ss_dssp HTTS-HHHHHHHHTSHHHHHHHHHHHH
T ss_pred HhcCCcchhHHhcCcchhhHHHHHHHH
Confidence 379999999999999999999988665
No 147
>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=93.76 E-value=0.044 Score=34.30 Aligned_cols=38 Identities=32% Similarity=0.456 Sum_probs=32.3
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCC--CCCCCCC
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIR--PGVIGGS 43 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~--Pg~~Gg~ 43 (163)
++..+||++++++...|.+++....+.|=+. .|..||-
T Consensus 26 ~s~~eiA~~~~i~~~~l~kil~~L~~~Gli~s~~G~~GGy 65 (83)
T PF02082_consen 26 VSSKEIAERLGISPSYLRKILQKLKKAGLIESSRGRGGGY 65 (83)
T ss_dssp BEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETSTTSEE
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHhhCCeeEecCCCCCce
Confidence 7889999999999999999999999999885 5555654
No 148
>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=93.68 E-value=0.072 Score=29.43 Aligned_cols=25 Identities=12% Similarity=0.191 Sum_probs=19.3
Q ss_pred CC-CChhhhHHHhhcchhhHHHHHhh
Q psy1904 4 AG-VRPCVISRQLRVSHGCVSKILNR 28 (163)
Q Consensus 4 ~g-~~~~~ia~~~~vs~~~vs~~l~~ 28 (163)
.| ++...+|+.|||..+|+++.++.
T Consensus 14 ~g~~S~r~AA~~ygVp~sTL~~r~~g 39 (45)
T PF05225_consen 14 NGKMSIRKAAKKYGVPRSTLRRRLRG 39 (45)
T ss_dssp TTSS-HHHHHHHHT--HHHHHHHHHH
T ss_pred hCCCCHHHHHHHHCcCHHHHHHHHcC
Confidence 45 99999999999999999988754
No 149
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=93.66 E-value=0.046 Score=42.46 Aligned_cols=23 Identities=26% Similarity=0.239 Sum_probs=20.5
Q ss_pred CChhhhHHHhhcchhhHHHHHhh
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNR 28 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~ 28 (163)
|...|||+..|||.+|||+.|+.
T Consensus 1 ~ti~dIA~~aGVS~~TVSrvLn~ 23 (328)
T PRK11303 1 MKLDEIARLAGVSRTTASYVING 23 (328)
T ss_pred CCHHHHHHHhCCCHHHHHHHHcC
Confidence 46789999999999999999954
No 150
>PF14493 HTH_40: Helix-turn-helix domain
Probab=93.66 E-value=0.14 Score=32.59 Aligned_cols=68 Identities=12% Similarity=0.068 Sum_probs=46.3
Q ss_pred CccCCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHHHHHhCCCCCchhhhhh
Q psy1904 1 MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPNITSWEVRDK 74 (163)
Q Consensus 1 ~~~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~~~~~~p~~~~~e~~~~ 74 (163)
|.+.|+++.+||+.-+++.+||..-|-.+...|..-+-. ...+....+.|.+..+..+.....++.+.
T Consensus 9 l~~~G~si~eIA~~R~L~~sTI~~HL~~~~~~g~~~~~~------~~l~~e~~~~I~~~~~~~~~~~lk~i~e~ 76 (91)
T PF14493_consen 9 LFQKGLSIEEIAKIRGLKESTIYGHLAELIESGEPLDIE------ELLSEEEIKQIEDAIEKLGSEKLKPIKEA 76 (91)
T ss_pred HHHcCCCHHHHHHHcCCCHHHHHHHHHHHHHhCCCCCHH------HhCCHHHHHHHHHHHHHcCcccHHHHHHH
Confidence 356899999999999999999999999998888732211 22344455556565555554444444443
No 151
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=93.65 E-value=0.081 Score=36.27 Aligned_cols=24 Identities=17% Similarity=0.241 Sum_probs=22.4
Q ss_pred cCCCChhhhHHHhhcchhhHHHHH
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKIL 26 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l 26 (163)
..|+++.++|+.+|||.++|++|.
T Consensus 16 ~~gltq~~lA~~~gvs~~~is~~E 39 (135)
T PRK09706 16 QLKLSQRSLAKAVKVSHVSISQWE 39 (135)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHH
Confidence 368999999999999999999996
No 152
>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=93.61 E-value=0.087 Score=32.03 Aligned_cols=31 Identities=35% Similarity=0.467 Sum_probs=28.7
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIR 36 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~ 36 (163)
++..+||..+|+|..+|++.|+.+++.|-+.
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 6789999999999999999999999988775
No 153
>PRK09492 treR trehalose repressor; Provisional
Probab=93.53 E-value=0.054 Score=41.87 Aligned_cols=23 Identities=30% Similarity=0.323 Sum_probs=21.0
Q ss_pred CChhhhHHHhhcchhhHHHHHhh
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNR 28 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~ 28 (163)
+...|||+.+|||.+|||+.|+.
T Consensus 5 ~ti~dIA~~agVS~~TVSrvLn~ 27 (315)
T PRK09492 5 LTIKDIARLSGVGKSTVSRVLNN 27 (315)
T ss_pred CcHHHHHHHhCCCHHHHhHHhCC
Confidence 57889999999999999999964
No 154
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=93.49 E-value=0.4 Score=28.48 Aligned_cols=29 Identities=14% Similarity=0.067 Sum_probs=24.6
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCCCC
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPG 38 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg 38 (163)
+++.|+|+.+|||..++..|. +.|-+.|.
T Consensus 1 ~s~~eva~~~gvs~~tlr~~~----~~gli~~~ 29 (70)
T smart00422 1 YTIGEVAKLAGVSVRTLRYYE----RIGLLPPP 29 (70)
T ss_pred CCHHHHHHHHCcCHHHHHHHH----HCCCCCCC
Confidence 468899999999999999986 46888775
No 155
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=93.47 E-value=0.045 Score=36.94 Aligned_cols=25 Identities=16% Similarity=0.090 Sum_probs=23.2
Q ss_pred ccCCCChhhhHHHhhcchhhHHHHH
Q psy1904 2 AAAGVRPCVISRQLRVSHGCVSKIL 26 (163)
Q Consensus 2 ~~~g~~~~~ia~~~~vs~~~vs~~l 26 (163)
...|+++.|+|++.|||.+++++|.
T Consensus 15 ~~~Glsq~eLA~~~Gis~~~is~iE 39 (120)
T PRK13890 15 DERHMTKKELSERSGVSISFLSDLT 39 (120)
T ss_pred HHcCCCHHHHHHHHCcCHHHHHHHH
Confidence 4579999999999999999999997
No 156
>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=93.45 E-value=0.069 Score=31.79 Aligned_cols=35 Identities=20% Similarity=0.360 Sum_probs=30.9
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCC
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG 38 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg 38 (163)
.+++..+||+.|+++.++|+++|+...+.|-+...
T Consensus 19 ~~~~~~ei~~~~~i~~~~i~~~l~~L~~~g~i~~~ 53 (78)
T cd00090 19 GPLTVSELAERLGLSQSTVSRHLKKLEEAGLVESR 53 (78)
T ss_pred CCcCHHHHHHHHCcCHhHHHHHHHHHHHCCCeEEE
Confidence 34889999999999999999999999888877654
No 157
>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=93.43 E-value=0.052 Score=42.03 Aligned_cols=23 Identities=30% Similarity=0.336 Sum_probs=20.4
Q ss_pred CChhhhHHHhhcchhhHHHHHhh
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNR 28 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~ 28 (163)
++..|||+.+|||.+|||+.|+.
T Consensus 2 ~ti~dIA~~agVS~sTVSr~Ln~ 24 (311)
T TIGR02405 2 LTIKDIARLAGVGKSTVSRVLNN 24 (311)
T ss_pred CcHHHHHHHhCCCHHHHHHHhCC
Confidence 46789999999999999999953
No 158
>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=93.39 E-value=0.54 Score=30.49 Aligned_cols=67 Identities=13% Similarity=0.070 Sum_probs=42.7
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCC-CCCCCCcCChHHHHHHHHHHH--hCCCCCchhhhhhhhh
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI-GGSKPRVATPDVEKRIEEYKK--TNPNITSWEVRDKLIK 77 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~-Gg~~p~~~~~~~~~~i~~~~~--~~p~~~~~e~~~~l~~ 77 (163)
+++.|+|+.+|||.+|+..|-+. .|-+.|... ||. +.-+......+..+.. ..-+++..+++.-+..
T Consensus 1 yti~EvA~~~gVs~~tLR~ye~~---~gli~p~r~~~g~--R~Yt~~di~~l~~I~~llr~~G~~l~~i~~~l~~ 70 (99)
T cd04765 1 FSIGEVAEILGLPPHVLRYWETE---FPQLKPVKRAGGR--RYYRPKDVELLLLIKHLLYEKGYTIEGAKQALKE 70 (99)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHH---cCCCCCcCCCCCC--eeeCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHh
Confidence 36789999999999999998543 365666433 332 3334555555555443 3456777777766553
No 159
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=93.38 E-value=0.088 Score=35.43 Aligned_cols=24 Identities=13% Similarity=0.029 Sum_probs=22.5
Q ss_pred cCCCChhhhHHHhhcchhhHHHHH
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKIL 26 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l 26 (163)
+.|+++.++|+.+|+|+++|++|.
T Consensus 76 ~~gltq~~lA~~lg~~~~tis~~e 99 (127)
T TIGR03830 76 KLGLSQREAAELLGGGVNAFSRYE 99 (127)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHH
Confidence 468999999999999999999996
No 160
>PRK01381 Trp operon repressor; Provisional
Probab=93.30 E-value=0.029 Score=36.40 Aligned_cols=21 Identities=14% Similarity=0.180 Sum_probs=19.6
Q ss_pred CCChhhhHHHhhcchhhHHHH
Q psy1904 5 GVRPCVISRQLRVSHGCVSKI 25 (163)
Q Consensus 5 g~~~~~ia~~~~vs~~~vs~~ 25 (163)
++++.+||+.+|||.+||+|-
T Consensus 55 ~~sQREIa~~lGvSiaTITRg 75 (99)
T PRK01381 55 ELSQREIKQELGVGIATITRG 75 (99)
T ss_pred CcCHHHHHHHhCCceeeehhh
Confidence 499999999999999999984
No 161
>PF07900 DUF1670: Protein of unknown function (DUF1670); InterPro: IPR012872 The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=93.27 E-value=0.16 Score=37.67 Aligned_cols=109 Identities=24% Similarity=0.258 Sum_probs=64.7
Q ss_pred CC-CChhhhHHHhhcchhhHHHHHhhhhhc-cCCCCCCCCCCCCCcCChHHHHHHHHH-HHhCCCCCchhhhhhhhhhcc
Q psy1904 4 AG-VRPCVISRQLRVSHGCVSKILNRYQET-GSIRPGVIGGSKPRVATPDVEKRIEEY-KKTNPNITSWEVRDKLIKVSR 80 (163)
Q Consensus 4 ~g-~~~~~ia~~~~vs~~~vs~~l~~~~~t-G~~~Pg~~Gg~~p~~~~~~~~~~i~~~-~~~~p~~~~~e~~~~l~~~~~ 80 (163)
.| ....|+|-.|++|..||++.++.|++. |-+-|.. |....-..+-.+-..+... .+..+ ..+
T Consensus 103 gglLT~~Dla~LL~~S~~TI~~~i~~yq~e~g~vvPtr-G~i~DiGp~~tHK~~ii~~~l~g~~---~~e---------- 168 (220)
T PF07900_consen 103 GGLLTQEDLAMLLGISPRTISKDIKEYQKEHGVVVPTR-GTIHDIGPGVTHKKIIIRLYLKGKP---TPE---------- 168 (220)
T ss_pred CCcccHHHHHHHHCCCHHHHHHHHHHHHHHcCceeccC-CcccccCCcchHHHHHHHHHHcCCC---HHH----------
Confidence 44 788999999999999999999999655 9999864 2211111111111111111 11100 000
Q ss_pred CCCCCCCCCCccccccccccccCcCCHHHHHHHHHhccCCCCC--CHHHHHHHHHHhCCCcccccc
Q psy1904 81 LDDSDTESEPGIVLKRKQRRSRTTFTSAQLEELEKSFQRSHYP--DIYTREALANKFGMTETRVQQ 144 (163)
Q Consensus 81 ~~~~~~~~~~~~~~~~~~rr~Rt~~t~~q~~~Le~~F~~~~~p--~~~~r~~la~~l~l~~~~v~~ 144 (163)
=..+|.+|.+.+..--+.|.+-.+. ....-+++|..+|+++.-|+-
T Consensus 169 ------------------iar~t~HS~~av~rYi~~F~rV~~l~~~~~~~~eia~~tg~S~~Lv~e 216 (220)
T PF07900_consen 169 ------------------IARRTNHSPEAVDRYIKDFKRVLMLYEKGMSPEEIAFITGMSERLVKE 216 (220)
T ss_pred ------------------HHHHhccCHHHHHHHHHhhHHhHHHHHcCCCHHHHHHHHCCCHHHHHH
Confidence 1224666777776666677666554 233456788889988876653
No 162
>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=93.27 E-value=0.049 Score=34.59 Aligned_cols=26 Identities=15% Similarity=0.155 Sum_probs=22.8
Q ss_pred cCCCChhhhHHHhhcchhhHHHHHhh
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKILNR 28 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l~~ 28 (163)
..|++..+||+.+|||-+||+|.-+-
T Consensus 47 ~~g~syreIa~~tgvS~aTItRvsr~ 72 (87)
T PF01371_consen 47 DEGKSYREIAEETGVSIATITRVSRC 72 (87)
T ss_dssp HTTSSHHHHHHHHTSTHHHHHHHHHH
T ss_pred HCCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 47999999999999999999996543
No 163
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=93.26 E-value=0.092 Score=36.29 Aligned_cols=39 Identities=23% Similarity=0.355 Sum_probs=33.1
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCC--CCCCCCCCC
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSI--RPGVIGGSK 44 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~--~Pg~~Gg~~ 44 (163)
++..+||+.++||..+|.++|......|=+ .+|..||-.
T Consensus 26 ~s~~~ia~~~~is~~~vrk~l~~L~~~Glv~s~~G~~GG~~ 66 (141)
T PRK11014 26 TSISEVTEVYGVSRNHMVKIINQLSRAGYVTAVRGKNGGIR 66 (141)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHHHHhCCEEEEecCCCCCee
Confidence 677999999999999999999999999987 556556543
No 164
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=93.21 E-value=0.18 Score=30.07 Aligned_cols=46 Identities=15% Similarity=0.113 Sum_probs=31.0
Q ss_pred ChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHH
Q psy1904 7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIE 57 (163)
Q Consensus 7 ~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~ 57 (163)
+..|+|+.+|||..+|..|.+ .|-+.|....+.. +.=+......+.
T Consensus 2 ti~eva~~~gvs~~tlr~y~~----~gll~~~~~~~g~-r~y~~~dv~~l~ 47 (69)
T PF13411_consen 2 TIKEVAKLLGVSPSTLRYYER----EGLLPPPRDENGY-RYYSEEDVERLR 47 (69)
T ss_dssp EHHHHHHHTTTTHHHHHHHHH----TTSSTTBESTTSS-EEE-HHHHHHHH
T ss_pred cHHHHHHHHCcCHHHHHHHHH----hcCcccccccCce-eeccHHHHHHHH
Confidence 568999999999999999974 4668777633332 444444544443
No 165
>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B.
Probab=93.21 E-value=0.075 Score=31.32 Aligned_cols=19 Identities=26% Similarity=0.281 Sum_probs=16.6
Q ss_pred ChhhhHHHhhcchhhHHHH
Q psy1904 7 RPCVISRQLRVSHGCVSKI 25 (163)
Q Consensus 7 ~~~~ia~~~~vs~~~vs~~ 25 (163)
+...+|+.||||+++|+.|
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 5678999999999999999
No 166
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=93.20 E-value=0.091 Score=36.22 Aligned_cols=40 Identities=10% Similarity=0.243 Sum_probs=33.9
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCC
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGS 43 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~ 43 (163)
.|+++.|||+.++++.++|++++++..+-|=+.-.....+
T Consensus 45 ~~~t~~eLa~~l~~~~~tvt~~v~~Le~~GlV~r~~~~~D 84 (144)
T PRK03573 45 PEQSQIQLAKAIGIEQPSLVRTLDQLEEKGLISRQTCASD 84 (144)
T ss_pred CCCCHHHHHHHhCCChhhHHHHHHHHHHCCCEeeecCCCC
Confidence 3689999999999999999999999999998865544333
No 167
>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=93.15 E-value=0.1 Score=34.72 Aligned_cols=36 Identities=14% Similarity=0.167 Sum_probs=31.9
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCC
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV 39 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~ 39 (163)
.++++.+||+.++++.++|++.+++..+.|=+.--.
T Consensus 41 ~~~t~~ela~~~~~~~~tvs~~l~~Le~~GlI~r~~ 76 (118)
T TIGR02337 41 GSMEFTQLANQACILRPSLTGILARLERDGLVTRLK 76 (118)
T ss_pred CCcCHHHHHHHhCCCchhHHHHHHHHHHCCCEEecc
Confidence 568999999999999999999999999998886443
No 168
>PRK06424 transcription factor; Provisional
Probab=93.13 E-value=0.096 Score=36.51 Aligned_cols=24 Identities=4% Similarity=0.088 Sum_probs=22.7
Q ss_pred cCCCChhhhHHHhhcchhhHHHHH
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKIL 26 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l 26 (163)
..|+++.++|+++||+.++|++|.
T Consensus 95 ~~GLSQ~eLA~~iGvs~stIskiE 118 (144)
T PRK06424 95 RLSMSQADLAAKIFERKNVIASIE 118 (144)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHH
Confidence 479999999999999999999996
No 169
>PF14502 HTH_41: Helix-turn-helix domain
Probab=93.11 E-value=0.097 Score=29.27 Aligned_cols=31 Identities=26% Similarity=0.376 Sum_probs=27.4
Q ss_pred ChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904 7 RPCVISRQLRVSHGCVSKILNRYQETGSIRP 37 (163)
Q Consensus 7 ~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P 37 (163)
...|.++.|+||.|||+.-|+-..+.|.+.-
T Consensus 8 tI~e~~~~~~vs~GtiQ~Alk~Le~~gaI~L 38 (48)
T PF14502_consen 8 TISEYSEKFGVSRGTIQNALKFLEENGAIKL 38 (48)
T ss_pred CHHHHHHHhCcchhHHHHHHHHHHHCCcEEe
Confidence 5678999999999999999999988887753
No 170
>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=93.10 E-value=0.11 Score=30.35 Aligned_cols=30 Identities=20% Similarity=0.298 Sum_probs=27.2
Q ss_pred ChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904 7 RPCVISRQLRVSHGCVSKILNRYQETGSIR 36 (163)
Q Consensus 7 ~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~ 36 (163)
+..+||..|+||..+|++.|+++.+.|-+.
T Consensus 27 ~~~~la~~~~is~~~v~~~l~~L~~~G~i~ 56 (66)
T cd07377 27 SERELAEELGVSRTTVREALRELEAEGLVE 56 (66)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 378999999999999999999999988764
No 171
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=92.98 E-value=0.048 Score=32.90 Aligned_cols=35 Identities=26% Similarity=0.422 Sum_probs=28.6
Q ss_pred cCC-CChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904 3 AAG-VRPCVISRQLRVSHGCVSKILNRYQETGSIRP 37 (163)
Q Consensus 3 ~~g-~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P 37 (163)
+.| ++..|||+.|+++...|.-.|..+..-|-+.-
T Consensus 11 ~~~~~S~~eLa~~~~~s~~~ve~mL~~l~~kG~I~~ 46 (69)
T PF09012_consen 11 ERGRVSLAELAREFGISPEAVEAMLEQLIRKGYIRK 46 (69)
T ss_dssp HS-SEEHHHHHHHTT--HHHHHHHHHHHHCCTSCEE
T ss_pred HcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEE
Confidence 445 88999999999999999999999999998853
No 172
>PRK09526 lacI lac repressor; Reviewed
Probab=92.98 E-value=0.081 Score=41.34 Aligned_cols=23 Identities=35% Similarity=0.365 Sum_probs=21.0
Q ss_pred CChhhhHHHhhcchhhHHHHHhh
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNR 28 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~ 28 (163)
+...|||+..|||.+|||+.|+.
T Consensus 6 ~ti~dIA~~aGVS~~TVSrvLn~ 28 (342)
T PRK09526 6 VTLYDVARYAGVSYQTVSRVLNQ 28 (342)
T ss_pred CcHHHHHHHhCCCHHHHHHHhcC
Confidence 67899999999999999999954
No 173
>PF02376 CUT: CUT domain; InterPro: IPR003350 A class, also called ONECUT, of homeodomain proteins. The CUT domain is a DNA-binding motif which can bind independently or in cooperation with the homeodomain (IPR001356 from INTERPRO), often found downstream of the CUT domain. Proteins display two modes of DNA binding, which hinge on the homeodomain and on the linker that separates it from the cut domain, and two modes of transcriptional stimulation, which hinge on the homeodomain [].; GO: 0003677 DNA binding; PDB: 1WH6_A 2D5V_A 2CSF_A 1X2L_A 2O49_A 2O4A_A 1YSE_A 1S7E_A 1WIZ_A 1WH8_A.
Probab=92.97 E-value=0.026 Score=35.92 Aligned_cols=28 Identities=21% Similarity=0.350 Sum_probs=21.4
Q ss_pred ccCCCChhhhHH-HhhcchhhHHHHHhhh
Q psy1904 2 AAAGVRPCVISR-QLRVSHGCVSKILNRY 29 (163)
Q Consensus 2 ~~~g~~~~~ia~-~~~vs~~~vs~~l~~~ 29 (163)
...++++...|+ +||.|+|+++.+|...
T Consensus 23 ~~~~IsQ~~Fa~~vL~rsqgtlsdlL~~P 51 (87)
T PF02376_consen 23 KRNNISQRVFAKKVLNRSQGTLSDLLRKP 51 (87)
T ss_dssp HHTT--HHHHHHHTTSS-HHHHHHHHHSC
T ss_pred HHcCCCHHHHHHHHhccChhHHHHHhCCC
Confidence 457899999999 8999999999999643
No 174
>COG3620 Predicted transcriptional regulator with C-terminal CBS domains [Transcription]
Probab=92.89 E-value=0.1 Score=36.99 Aligned_cols=30 Identities=23% Similarity=0.501 Sum_probs=25.6
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCC
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG 38 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg 38 (163)
-|+++.|+|++-||||+.+-|| |.|.+.|.
T Consensus 17 LGitQ~dLA~~aGVSQ~~IArl-----E~G~vdPr 46 (187)
T COG3620 17 LGITQKDLARRAGVSQPYIARL-----EAGKVDPR 46 (187)
T ss_pred cCCCHHHHHHHcCccHHHHHHH-----hcCCCCcc
Confidence 4899999999999999999998 56666664
No 175
>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=92.86 E-value=0.071 Score=29.38 Aligned_cols=24 Identities=25% Similarity=0.374 Sum_probs=22.3
Q ss_pred cCCCChhhhHHHhhcchhhHHHHH
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKIL 26 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l 26 (163)
..|++..++|+.++++.++|++|+
T Consensus 10 ~~~~s~~~~a~~~~~~~~~v~~~~ 33 (58)
T cd00093 10 EKGLTQEELAEKLGVSRSTISRIE 33 (58)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHH
Confidence 468999999999999999999997
No 176
>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=92.79 E-value=0.46 Score=30.92 Aligned_cols=66 Identities=15% Similarity=0.121 Sum_probs=37.8
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHHHHH-hCCCCCchhhhhhh
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPNITSWEVRDKL 75 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~~~~-~~p~~~~~e~~~~l 75 (163)
+++.|+|+.+|||..|+..|. ..|-+.|...++..-+.-+......+..+.. ..-+++..++..-+
T Consensus 1 ~ti~eva~~~gvs~~tlR~ye----~~Gll~~~~~~~~g~R~y~~~di~~l~~i~~lr~~g~~l~~i~~~~ 67 (103)
T cd01106 1 YTVGEVAKLTGVSVRTLHYYD----EIGLLKPSRRTENGYRLYTEEDLERLQQILFLKELGFSLKEIKELL 67 (103)
T ss_pred CCHHHHHHHHCcCHHHHHHHH----HCCCCCCCccCCCCceeeCHHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence 467899999999999999875 4588877432221223334444444422211 11356655555443
No 177
>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=92.68 E-value=0.096 Score=30.77 Aligned_cols=24 Identities=25% Similarity=0.365 Sum_probs=19.5
Q ss_pred cCCCChhhhHHHhhcchhhHHHHH
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKIL 26 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l 26 (163)
..|+++.++|+.+||+.+++++|.
T Consensus 10 ~~~lt~~~~a~~~~i~~~~i~~~e 33 (64)
T PF12844_consen 10 EKGLTQKDLAEKLGISRSTISKIE 33 (64)
T ss_dssp HCT--HHHHHHHHTS-HHHHHHHH
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHH
Confidence 368999999999999999999997
No 178
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=92.65 E-value=0.068 Score=41.68 Aligned_cols=23 Identities=17% Similarity=0.150 Sum_probs=20.8
Q ss_pred CChhhhHHHhhcchhhHHHHHhh
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNR 28 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~ 28 (163)
+...|||+..|||.+|||+.|+.
T Consensus 6 ~ti~dIA~~agVS~~TVSrvLn~ 28 (331)
T PRK14987 6 PVLQDVADRVGVTKMTVSRFLRN 28 (331)
T ss_pred CcHHHHHHHhCCCHHHhhhhhCC
Confidence 57889999999999999999943
No 179
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=92.61 E-value=0.08 Score=41.39 Aligned_cols=23 Identities=22% Similarity=0.143 Sum_probs=21.6
Q ss_pred CChhhhHHHhhcchhhHHHHHhh
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNR 28 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~ 28 (163)
++..|||+.+|||.+|||+.|+.
T Consensus 7 ~Ti~dIA~~agVS~~TVSr~Ln~ 29 (342)
T PRK10014 7 ITIHDVALAAGVSVSTVSLVLSG 29 (342)
T ss_pred CcHHHHHHHhCCCHHHHHHHHCC
Confidence 78899999999999999999975
No 180
>TIGR02612 mob_myst_A mobile mystery protein A. Members of this protein family are found in mobization-related contexts more often than not, including within a CRISPR-associated gene region in Geobacter sulfurreducens PCA, and on plasmids in Agrobacterium tumefaciens and Coxiella burnetii, always together with mobile mystery protein B, a member of the Fic protein family (pfam02661). This protein is encoded by the upstream member of the gene pair and belongs to a family of helix-turn-helix DNA binding proteins (pfam01381).
Probab=92.59 E-value=0.1 Score=36.68 Aligned_cols=24 Identities=21% Similarity=0.249 Sum_probs=22.4
Q ss_pred cCCCChhhhHHHhhcchhhHHHHH
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKIL 26 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l 26 (163)
..|+++.++|+++|||+++|++|.
T Consensus 36 ~lGmTq~eLAerlGVS~~tIs~iE 59 (150)
T TIGR02612 36 ALGMSGAQLAGRLGVTPQRVEALE 59 (150)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHH
Confidence 369999999999999999999996
No 181
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=92.53 E-value=0.12 Score=31.26 Aligned_cols=24 Identities=17% Similarity=0.203 Sum_probs=22.1
Q ss_pred cCCCChhhhHHHhhcchhhHHHHH
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKIL 26 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l 26 (163)
..|+++.++|+.+|||.-||..|-
T Consensus 12 ~~~ltQ~elA~~vgVsRQTi~~iE 35 (68)
T COG1476 12 ELGLTQEELAKLVGVSRQTIIAIE 35 (68)
T ss_pred HhCcCHHHHHHHcCcCHHHHHHHH
Confidence 478999999999999999999984
No 182
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=92.52 E-value=0.097 Score=34.18 Aligned_cols=32 Identities=19% Similarity=0.379 Sum_probs=29.3
Q ss_pred CCChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904 5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIR 36 (163)
Q Consensus 5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~ 36 (163)
.++..+||+.+|+|.++|.+.+++..+.|-+.
T Consensus 17 ~~~~~~la~~l~~s~~tv~~~l~~L~~~g~i~ 48 (108)
T smart00344 17 RISLAELAKKVGLSPSTVHNRVKRLEEEGVIK 48 (108)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCee
Confidence 48899999999999999999999998888775
No 183
>PRK08359 transcription factor; Validated
Probab=92.46 E-value=0.13 Score=37.08 Aligned_cols=24 Identities=17% Similarity=0.214 Sum_probs=22.2
Q ss_pred cCCCChhhhHHHhhcchhhHHHHH
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKIL 26 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l 26 (163)
..|+++.++|..+||+.++|++|-
T Consensus 96 ~kglSQeeLA~~lgvs~stI~~iE 119 (176)
T PRK08359 96 KSGLSYEELSHEVGLSVNDLRRIA 119 (176)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHH
Confidence 479999999999999999999984
No 184
>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=92.14 E-value=0.7 Score=29.22 Aligned_cols=68 Identities=19% Similarity=0.058 Sum_probs=39.3
Q ss_pred CCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHHHHH-hCCCCCchhhhhhhh
Q psy1904 5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPNITSWEVRDKLI 76 (163)
Q Consensus 5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~~~~-~~p~~~~~e~~~~l~ 76 (163)
++++.|+|+.+|||..++..|- +.|-+.|....+..-+.=+......+..... ..-+++..+++.-+.
T Consensus 1 ~~ti~evA~~~gvs~~tLR~ye----~~Gll~p~r~~~~g~R~Ys~~dv~~l~~I~~Lr~~G~sl~~i~~~l~ 69 (88)
T cd01105 1 VIGIGEVSKLTGVSPRQLRYWE----EKGLIKSIRSDGGGQRKYSLADVDRLLVIKELLDEGFTLAAAVEKLR 69 (88)
T ss_pred CcCHHHHHHHHCcCHHHHHHHH----HCCCCCCCccCCCCceecCHHHHHHHHHHHHHHHCCCCHHHHHHHHH
Confidence 4688999999999999999884 4587777543221122223334333322211 124566655555544
No 185
>PF13309 HTH_22: HTH domain
Probab=92.03 E-value=0.1 Score=31.13 Aligned_cols=20 Identities=20% Similarity=0.283 Sum_probs=17.4
Q ss_pred hhhhHHHhhcchhhHHHHHh
Q psy1904 8 PCVISRQLRVSHGCVSKILN 27 (163)
Q Consensus 8 ~~~ia~~~~vs~~~vs~~l~ 27 (163)
...+|+.||||..||++.|+
T Consensus 45 v~~vA~~L~iS~~TVY~YLr 64 (64)
T PF13309_consen 45 VEYVAEKLGISRATVYRYLR 64 (64)
T ss_pred HHHHHHHHCCCHHHHHHHcC
Confidence 35789999999999999874
No 186
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=92.03 E-value=0.11 Score=40.88 Aligned_cols=23 Identities=35% Similarity=0.403 Sum_probs=20.3
Q ss_pred CChhhhHHHhhcchhhHHHHHhh
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNR 28 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~ 28 (163)
++..|||+..|||.+|||+.|+.
T Consensus 2 ~ti~dIA~~aGVS~~TVSrvLn~ 24 (346)
T PRK10401 2 ITIRDVARQAGVSVATVSRVLNN 24 (346)
T ss_pred CCHHHHHHHhCCCHHHHHHHHCC
Confidence 46789999999999999999954
No 187
>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=91.98 E-value=0.67 Score=30.51 Aligned_cols=67 Identities=10% Similarity=0.024 Sum_probs=40.0
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHHHHHh-CCCCCchhhhhhhh
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKT-NPNITSWEVRDKLI 76 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~~~~~-~p~~~~~e~~~~l~ 76 (163)
+++.|+|+.+|||..|+..|- +.|-+.|....+..-+.-++.....+..+..- .-++...++..-+.
T Consensus 1 ~~i~eva~~~gvs~~tlR~ye----~~Gll~p~~~~~~g~R~Y~~~dl~~l~~I~~lr~~G~~l~~I~~~l~ 68 (108)
T cd04773 1 MTIGELAHLLGVPPSTLRHWE----KEGLLSPDREPETGYRVYDPSDVRDARLIHLLRRGGYLLEQIATVVE 68 (108)
T ss_pred CCHHHHHHHHCcCHHHHHHHH----HCCCCCCCcCCCCCceeeCHHHHHHHHHHHHHHHCCCCHHHHHHHHH
Confidence 578899999999999999885 55888875532222233344444444333222 22456656655443
No 188
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=91.98 E-value=0.11 Score=40.66 Aligned_cols=22 Identities=23% Similarity=0.305 Sum_probs=20.0
Q ss_pred ChhhhHHHhhcchhhHHHHHhh
Q psy1904 7 RPCVISRQLRVSHGCVSKILNR 28 (163)
Q Consensus 7 ~~~~ia~~~~vs~~~vs~~l~~ 28 (163)
...|||+..|||.+|||+.|+.
T Consensus 3 Ti~dIA~~agVS~~TVSrvLn~ 24 (341)
T PRK10703 3 TIKDVAKRAGVSTTTVSHVINK 24 (341)
T ss_pred CHHHHHHHhCCCHHHHHHHHcC
Confidence 5789999999999999999964
No 189
>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=91.93 E-value=0.63 Score=30.57 Aligned_cols=41 Identities=10% Similarity=0.208 Sum_probs=34.2
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCC
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSK 44 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~ 44 (163)
.++++.+||..++++.++|++.+++..+-|=+.=.....++
T Consensus 42 ~~~t~~eL~~~l~~~~stvs~~i~~Le~kg~I~r~~~~~D~ 82 (109)
T TIGR01889 42 GKLTLKEIIKEILIKQSALVKIIKKLSKKGYLSKERSEDDE 82 (109)
T ss_pred CcCcHHHHHHHHCCCHHHHHHHHHHHHHCCCEeccCCcccC
Confidence 35999999999999999999999999999988654444443
No 190
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=91.90 E-value=0.15 Score=35.94 Aligned_cols=38 Identities=29% Similarity=0.427 Sum_probs=32.5
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCC
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGS 43 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~ 43 (163)
++..|||+.|+|+.+||+..+++..+-|=+.--+-+|-
T Consensus 25 ~~~~diA~~L~Vsp~sVt~ml~rL~~~GlV~~~~y~gi 62 (154)
T COG1321 25 ARTKDIAERLKVSPPSVTEMLKRLERLGLVEYEPYGGV 62 (154)
T ss_pred ccHHHHHHHhCCCcHHHHHHHHHHHHCCCeEEecCCCe
Confidence 88899999999999999999999999998865444443
No 191
>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=91.86 E-value=0.11 Score=40.36 Aligned_cols=23 Identities=30% Similarity=0.377 Sum_probs=20.2
Q ss_pred CChhhhHHHhhcchhhHHHHHhh
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNR 28 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~ 28 (163)
+...|||+..|||.+|||+.|+.
T Consensus 2 ~ti~dIA~~agvS~~TVSrvLn~ 24 (329)
T TIGR01481 2 VTIYDVAREAGVSMATVSRVVNG 24 (329)
T ss_pred CcHHHHHHHhCCCHHHHHHHhCC
Confidence 35679999999999999999954
No 192
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=91.75 E-value=0.1 Score=40.43 Aligned_cols=19 Identities=32% Similarity=0.361 Sum_probs=17.7
Q ss_pred hhhHHHhhcchhhHHHHHh
Q psy1904 9 CVISRQLRVSHGCVSKILN 27 (163)
Q Consensus 9 ~~ia~~~~vs~~~vs~~l~ 27 (163)
.|||+..|||.+|||+.|+
T Consensus 2 ~dIA~~agVS~~TVSrvLn 20 (327)
T PRK10423 2 KDVARLAGVSTSTVSHVIN 20 (327)
T ss_pred hhHHHHhCCcHHHHHHHhC
Confidence 5899999999999999995
No 193
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=91.74 E-value=0.18 Score=37.65 Aligned_cols=34 Identities=15% Similarity=0.267 Sum_probs=30.9
Q ss_pred CCChhhhHHHhhcchhhHHHHHhhhhhccCCCCC
Q psy1904 5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG 38 (163)
Q Consensus 5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg 38 (163)
+++..+||+.+++|+++|+++|++..+.|=+.-.
T Consensus 21 ~IS~~eLA~~L~iS~~Tvsr~Lk~LEe~GlI~R~ 54 (217)
T PRK14165 21 KISSSEFANHTGTSSKTAARILKQLEDEGYITRT 54 (217)
T ss_pred CcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence 5889999999999999999999999999888544
No 194
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=91.72 E-value=0.19 Score=35.49 Aligned_cols=24 Identities=13% Similarity=0.218 Sum_probs=22.4
Q ss_pred cCCCChhhhHHHhhcchhhHHHHH
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKIL 26 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l 26 (163)
..|+++.++|..+||++++|++|.
T Consensus 80 ~~glSqeeLA~~lgvs~s~IsriE 103 (154)
T TIGR00270 80 KRGWSQEQLAKKIQEKESLIKKIE 103 (154)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHH
Confidence 479999999999999999999995
No 195
>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=91.62 E-value=0.21 Score=29.49 Aligned_cols=30 Identities=23% Similarity=0.309 Sum_probs=25.4
Q ss_pred ChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904 7 RPCVISRQLRVSHGCVSKILNRYQETGSIR 36 (163)
Q Consensus 7 ~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~ 36 (163)
+..+||++|+||..+|.+-|....+.|-+.
T Consensus 26 s~~~la~~~~vsr~tvr~al~~L~~~g~i~ 55 (64)
T PF00392_consen 26 SERELAERYGVSRTTVREALRRLEAEGLIE 55 (64)
T ss_dssp -HHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred CHHHHHHHhccCCcHHHHHHHHHHHCCcEE
Confidence 678999999999999999999998888764
No 196
>TIGR00180 parB_part ParB-like partition proteins. This model represents the most well-conserved core of a set of chromosomal and plasmid partition proteins related to ParB, including Spo0J, RepB, and SopB. Spo0J has been shown to bind a specific DNA sequence that, when introduced into a plasmid, can serve as partition site. Study of RepB, which has nicking-closing activity, suggests that it forms a transient protein-DNA covalent intermediate during the strand transfer reaction.
Probab=91.52 E-value=0.12 Score=37.44 Aligned_cols=25 Identities=8% Similarity=0.187 Sum_probs=23.1
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhh
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNR 28 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~ 28 (163)
.|+++.+||+.||+|.++|++.|.-
T Consensus 119 ~g~s~~~iA~~lg~s~~~V~r~l~l 143 (187)
T TIGR00180 119 FSMTQEDLAKKIGKSRAHITNLLRL 143 (187)
T ss_pred hCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 5899999999999999999999855
No 197
>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=91.37 E-value=0.15 Score=31.71 Aligned_cols=21 Identities=19% Similarity=0.120 Sum_probs=16.3
Q ss_pred CChhhhHHHhhcchhhHHHHH
Q psy1904 6 VRPCVISRQLRVSHGCVSKIL 26 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l 26 (163)
....++|+.||||.|||.+=+
T Consensus 20 aTVR~~Ak~FGvSKSTVHkDv 40 (82)
T PF12116_consen 20 ATVRQAAKVFGVSKSTVHKDV 40 (82)
T ss_dssp --HHHHHHHHTS-HHHHHHHH
T ss_pred cHHHHHHHHHCCcHHHHHHHH
Confidence 456789999999999999976
No 198
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=91.34 E-value=0.13 Score=40.25 Aligned_cols=21 Identities=29% Similarity=0.290 Sum_probs=19.4
Q ss_pred ChhhhHHHhhcchhhHHHHHh
Q psy1904 7 RPCVISRQLRVSHGCVSKILN 27 (163)
Q Consensus 7 ~~~~ia~~~~vs~~~vs~~l~ 27 (163)
...|||+..|||.+|||+.|+
T Consensus 3 ti~dIA~~aGVS~~TVSrvLn 23 (343)
T PRK10727 3 TIKDVARLAGVSVATVSRVIN 23 (343)
T ss_pred CHHHHHHHhCCCHHHHHHHhC
Confidence 578999999999999999994
No 199
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=91.21 E-value=0.12 Score=40.23 Aligned_cols=24 Identities=29% Similarity=0.195 Sum_probs=20.8
Q ss_pred CChhhhHHHhhcchhhHHHHHhhh
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
+...|||+..|||.+|||+.|+..
T Consensus 2 ~ti~dIA~~agVS~~TVSrvln~~ 25 (327)
T PRK10339 2 ATLKDIAIEAGVSLATVSRVLNDD 25 (327)
T ss_pred CCHHHHHHHhCCCHHhhhhhhcCC
Confidence 357899999999999999999643
No 200
>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=91.19 E-value=0.98 Score=29.09 Aligned_cols=64 Identities=19% Similarity=0.238 Sum_probs=38.5
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHH---HHHhCCCCCchhhhhhh
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEE---YKKTNPNITSWEVRDKL 75 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~---~~~~~p~~~~~e~~~~l 75 (163)
+++.++|+++|||.+|+..|. +.|-+.|....+. .+.=+......+.. +.++ -+++..++..-+
T Consensus 1 ~~I~e~a~~~gvs~~tLR~ye----~~Gll~p~r~~~g-~R~Y~~~dv~~l~~I~~L~~~-~G~~l~ei~~~l 67 (96)
T cd04774 1 YKVDEVAKRLGLTKRTLKYYE----EIGLVSPERSEGR-YRLYSEEDLKRLERILRLREV-LGFSLQEVTHFL 67 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHH----HCCCCCCCcCCCC-CEEECHHHHHHHHHHHHHHHH-cCCCHHHHHHHH
Confidence 467899999999999999986 4588877554322 22233334444433 3321 356665555443
No 201
>PRK10870 transcriptional repressor MprA; Provisional
Probab=91.13 E-value=0.66 Score=33.31 Aligned_cols=54 Identities=17% Similarity=0.200 Sum_probs=39.7
Q ss_pred CCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCC---cCChHHHHHHHH
Q psy1904 5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR---VATPDVEKRIEE 58 (163)
Q Consensus 5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~---~~~~~~~~~i~~ 58 (163)
++.+.|||+.++++.++|++++++..+-|=+.-.....++-. ..++.-.+.+..
T Consensus 71 ~it~~eLa~~l~l~~~tvsr~v~rLe~kGlV~R~~~~~DrR~~~v~LT~~G~~~~~~ 127 (176)
T PRK10870 71 SIQPSELSCALGSSRTNATRIADELEKRGWIERRESDNDRRCLHLQLTEKGHEFLRE 127 (176)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHHHH
Confidence 488999999999999999999999999998866554444323 234444444433
No 202
>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=91.12 E-value=0.25 Score=37.35 Aligned_cols=34 Identities=9% Similarity=0.153 Sum_probs=31.3
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP 37 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P 37 (163)
.+++..|||+.+|++.+||+++|.-+.+.|=+..
T Consensus 23 ~~~~l~eia~~lglpksT~~RlL~tL~~~G~l~~ 56 (248)
T TIGR02431 23 PRLTLTDVAEATGLTRAAARRFLLTLVELGYVTS 56 (248)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEe
Confidence 5699999999999999999999999999998864
No 203
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=90.93 E-value=0.27 Score=33.93 Aligned_cols=32 Identities=19% Similarity=0.246 Sum_probs=29.3
Q ss_pred CCChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904 5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIR 36 (163)
Q Consensus 5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~ 36 (163)
.++..+||+.|+||.++|++.|++..+.|-+.
T Consensus 22 ~~~~~ela~~l~vs~~svs~~l~~L~~~Gli~ 53 (142)
T PRK03902 22 YARVSDIAEALSVHPSSVTKMVQKLDKDEYLI 53 (142)
T ss_pred CcCHHHHHHHhCCChhHHHHHHHHHHHCCCEE
Confidence 38889999999999999999999999988775
No 204
>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []. Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.
Probab=90.93 E-value=0.17 Score=31.17 Aligned_cols=25 Identities=8% Similarity=0.103 Sum_probs=20.1
Q ss_pred CCChhhhHHHhhcchhhHHHHHhhh
Q psy1904 5 GVRPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 5 g~~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
.++..|||+..+||.+||.|..+..
T Consensus 34 ~~si~elA~~~~vS~sti~Rf~kkL 58 (77)
T PF01418_consen 34 FMSISELAEKAGVSPSTIVRFCKKL 58 (77)
T ss_dssp T--HHHHHHHCTS-HHHHHHHHHHC
T ss_pred HccHHHHHHHcCCCHHHHHHHHHHh
Confidence 4688999999999999999998775
No 205
>COG2826 Tra8 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]
Probab=90.87 E-value=0.12 Score=40.20 Aligned_cols=31 Identities=26% Similarity=0.311 Sum_probs=26.9
Q ss_pred cCCCChhhhHHHhhcchhhHHHHHhhhhhcc
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKILNRYQETG 33 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG 33 (163)
++|+|..+||++||..++||++=|++-.-.+
T Consensus 21 ~~~~S~reIA~~LgRh~sTIsRElkRn~~~~ 51 (318)
T COG2826 21 KAKMSIREIAKQLNRHHSTISRELKRNRTRD 51 (318)
T ss_pred HcCCCHHHHHHHhCCCcchhhHHHhcCCccc
Confidence 5799999999999999999999998864433
No 206
>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=90.78 E-value=0.18 Score=27.35 Aligned_cols=24 Identities=17% Similarity=0.250 Sum_probs=19.0
Q ss_pred CChhhhHHHhhcchhhHHHHHhhh
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
++..+||+.+|||.++|.+=+++.
T Consensus 18 ~s~~~la~~lglS~~~v~~Ri~rL 41 (42)
T PF13404_consen 18 RSYAELAEELGLSESTVRRRIRRL 41 (42)
T ss_dssp S-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred ccHHHHHHHHCcCHHHHHHHHHHh
Confidence 788999999999999998866553
No 207
>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=90.76 E-value=0.16 Score=39.40 Aligned_cols=21 Identities=24% Similarity=0.199 Sum_probs=18.9
Q ss_pred hhhhHHHhhcchhhHHHHHhh
Q psy1904 8 PCVISRQLRVSHGCVSKILNR 28 (163)
Q Consensus 8 ~~~ia~~~~vs~~~vs~~l~~ 28 (163)
..|||+..|||.+|||+.|+.
T Consensus 2 i~dIA~~aGVS~~TVSrvLn~ 22 (327)
T TIGR02417 2 LSDIAKLAGVSKTTASYVING 22 (327)
T ss_pred HHHHHHHhCCCHHHHHHHHcC
Confidence 579999999999999999954
No 208
>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=90.69 E-value=0.2 Score=29.23 Aligned_cols=19 Identities=26% Similarity=0.240 Sum_probs=16.3
Q ss_pred hHHHhhcchhhHHHHHhhh
Q psy1904 11 ISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 11 ia~~~~vs~~~vs~~l~~~ 29 (163)
.|+.|+|+..+|.+|+++-
T Consensus 31 aarkf~V~r~~Vr~W~kqe 49 (58)
T PF09607_consen 31 AARKFNVSRRQVRKWRKQE 49 (58)
T ss_dssp HHHHTTS-HHHHHHHHTTH
T ss_pred HHHHhCccHHHHHHHHHHH
Confidence 8999999999999999654
No 209
>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=90.68 E-value=1.3 Score=28.52 Aligned_cols=64 Identities=14% Similarity=0.187 Sum_probs=37.9
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCC--CCCCCCcCChHHHHHHHHHHH-hCCCCCchhhhhhh
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI--GGSKPRVATPDVEKRIEEYKK-TNPNITSWEVRDKL 75 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~--Gg~~p~~~~~~~~~~i~~~~~-~~p~~~~~e~~~~l 75 (163)
+++.|+|+.+|||..|+.-|- +.|-+.|... +|.+ .=+......+..... ..-+++..++..-+
T Consensus 1 ~~i~eva~~~gvs~~tlR~ye----~~Gll~p~~~~~~gyR--~Y~~~~~~~l~~I~~lr~~G~~l~eI~~~l 67 (97)
T cd04782 1 FTTGEFAKLCGISKQTLFHYD----KIGLFKPEIVKENGYR--YYTLEQFEQLDIILLLKELGISLKEIKDYL 67 (97)
T ss_pred CCHHHHHHHHCcCHHHHHHHH----HCCCCCCCccCCCCCc--cCCHHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence 467899999999999988874 5699988532 3332 233333333322211 12256666666543
No 210
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=90.66 E-value=0.19 Score=34.81 Aligned_cols=30 Identities=20% Similarity=0.387 Sum_probs=28.1
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCC
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSI 35 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~ 35 (163)
++..+||+.+|+|.++|.+.+++..+.|-+
T Consensus 23 ~~~~eia~~lglS~~~v~~Ri~~L~~~GiI 52 (154)
T COG1522 23 ISNAELAERVGLSPSTVLRRIKRLEEEGVI 52 (154)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCce
Confidence 889999999999999999999999988855
No 211
>COG1342 Predicted DNA-binding proteins [General function prediction only]
Probab=90.63 E-value=0.25 Score=31.77 Aligned_cols=27 Identities=11% Similarity=0.185 Sum_probs=24.5
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhhh
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRYQ 30 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~ 30 (163)
.|+++-|.|.+.|||.+|+.++|+.-+
T Consensus 48 ~~l~QeeAA~rMgISr~Tfwr~l~sAR 74 (99)
T COG1342 48 EGLTQEEAALRMGISRQTFWRLLTSAR 74 (99)
T ss_pred hhccHHHHHHHhcccHHHHHHHHHHHH
Confidence 689999999999999999999997653
No 212
>PRK01905 DNA-binding protein Fis; Provisional
Probab=90.33 E-value=0.22 Score=30.79 Aligned_cols=26 Identities=19% Similarity=0.270 Sum_probs=22.8
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
.|-...++|++||||.+++++.++++
T Consensus 49 ~~gn~s~aAr~LGIsrstL~rklkk~ 74 (77)
T PRK01905 49 AGGNQSLAAEYLGINRNTLRKKLQQH 74 (77)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHh
Confidence 45667889999999999999999886
No 213
>PRK00215 LexA repressor; Validated
Probab=90.27 E-value=0.29 Score=35.83 Aligned_cols=34 Identities=24% Similarity=0.226 Sum_probs=30.1
Q ss_pred CChhhhHHHhhc-chhhHHHHHhhhhhccCCCCCC
Q psy1904 6 VRPCVISRQLRV-SHGCVSKILNRYQETGSIRPGV 39 (163)
Q Consensus 6 ~~~~~ia~~~~v-s~~~vs~~l~~~~~tG~~~Pg~ 39 (163)
++..|||+.||+ +.+||+++|++..+.|-+....
T Consensus 24 ~s~~ela~~~~~~~~~tv~~~l~~L~~~g~i~~~~ 58 (205)
T PRK00215 24 PSRREIADALGLRSPSAVHEHLKALERKGFIRRDP 58 (205)
T ss_pred CCHHHHHHHhCCCChHHHHHHHHHHHHCCCEEeCC
Confidence 467799999999 9999999999999999886554
No 214
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=90.24 E-value=0.38 Score=33.79 Aligned_cols=39 Identities=33% Similarity=0.340 Sum_probs=33.4
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCC--CCCCCCCCC
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSI--RPGVIGGSK 44 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~--~Pg~~Gg~~ 44 (163)
++..+||++++||..++.||+...+..|=+ ..|+.||-.
T Consensus 25 ~s~~eIA~~~~is~~~L~kIl~~L~~aGlv~S~rG~~GGy~ 65 (153)
T PRK11920 25 SRIPEIARAYGVSELFLFKILQPLVEAGLVETVRGRNGGVR 65 (153)
T ss_pred CcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeecCCCCCee
Confidence 688999999999999999999999999977 446666653
No 215
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=90.19 E-value=0.23 Score=35.82 Aligned_cols=24 Identities=17% Similarity=0.227 Sum_probs=22.6
Q ss_pred cCCCChhhhHHHhhcchhhHHHHH
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKIL 26 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l 26 (163)
+.|+++.++|+.+|||+++|++|.
T Consensus 18 ~~glt~~elA~~~gis~~~is~~E 41 (185)
T PRK09943 18 QQGLSQRRAAELSGLTHSAISTIE 41 (185)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHH
Confidence 479999999999999999999997
No 216
>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=90.19 E-value=0.3 Score=28.45 Aligned_cols=25 Identities=20% Similarity=0.361 Sum_probs=22.0
Q ss_pred ChhhhHHHhhcchhhHHHHHhhhhh
Q psy1904 7 RPCVISRQLRVSHGCVSKILNRYQE 31 (163)
Q Consensus 7 ~~~~ia~~~~vs~~~vs~~l~~~~~ 31 (163)
+....|+.++||+++|++.++...+
T Consensus 15 s~~~AA~~l~is~~~vs~~i~~LE~ 39 (60)
T PF00126_consen 15 SISAAAEELGISQSAVSRQIKQLEE 39 (60)
T ss_dssp SHHHHHHHCTSSHHHHHHHHHHHHH
T ss_pred CHHHHHHHhhccchHHHHHHHHHHH
Confidence 6778999999999999999988843
No 217
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=90.16 E-value=0.5 Score=29.80 Aligned_cols=36 Identities=25% Similarity=0.400 Sum_probs=31.8
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCC
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV 39 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~ 39 (163)
.++.+.+||+.+++|.++|++.++...+.|-+.-..
T Consensus 23 ~~~~~~~la~~~~~s~~~i~~~l~~L~~~g~v~~~~ 58 (101)
T smart00347 23 GPLSVSELAKRLGVSPSTVTRVLDRLEKKGLIRRLP 58 (101)
T ss_pred CCcCHHHHHHHHCCCchhHHHHHHHHHHCCCeEecC
Confidence 358999999999999999999999999999886443
No 218
>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=90.08 E-value=1.4 Score=28.31 Aligned_cols=64 Identities=14% Similarity=0.178 Sum_probs=39.0
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCC--CCCCCCCcCChHHHHHHHHHHH-hCCCCCchhhhhhh
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV--IGGSKPRVATPDVEKRIEEYKK-TNPNITSWEVRDKL 75 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~--~Gg~~p~~~~~~~~~~i~~~~~-~~p~~~~~e~~~~l 75 (163)
+++.|+|+.+|||..|+.-|- +.|-+.|.. .+|.+ .=+......+..... ..-+++..++..-+
T Consensus 1 m~i~eva~~~gvs~~tlR~ye----~~Gll~p~~r~~~gyR--~Y~~~~l~~l~~I~~lr~~G~~l~eI~~~l 67 (96)
T cd04788 1 WKIGELARRTGLSVRTLHHYD----HIGLLSPSQRTEGGHR--LYDRADIRRLHQIIALRRLGFSLREIGRAL 67 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHH----HCCCCCCCccCCCCce--eeCHHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence 578899999999999998875 568888843 23333 233444433322221 12256666666544
No 219
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=90.00 E-value=0.32 Score=34.92 Aligned_cols=26 Identities=19% Similarity=0.193 Sum_probs=23.6
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
.|++..|||..||||.++|...+.+-
T Consensus 121 ~g~~~~EIA~~lgis~~tV~~~l~Ra 146 (181)
T PRK09637 121 EGLSQKEIAEKLGLSLSGAKSRVQRG 146 (181)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 79999999999999999999988554
No 220
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=89.99 E-value=0.27 Score=30.47 Aligned_cols=36 Identities=19% Similarity=0.371 Sum_probs=31.9
Q ss_pred CccCC-CChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904 1 MAAAG-VRPCVISRQLRVSHGCVSKILNRYQETGSIR 36 (163)
Q Consensus 1 ~~~~g-~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~ 36 (163)
|+..| ++..+||+.|+.+...|.-.|.++..-|.+.
T Consensus 11 l~~~gr~s~~~Ls~~~~~p~~~VeaMLe~l~~kGkve 47 (78)
T PRK15431 11 LALRGRMEAAQISQTLNTPQPMINAMLQQLESMGKAV 47 (78)
T ss_pred HHHcCcccHHHHHHHHCcCHHHHHHHHHHHHHCCCeE
Confidence 45667 8999999999999999999999998888774
No 221
>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=89.92 E-value=0.29 Score=32.83 Aligned_cols=26 Identities=19% Similarity=0.236 Sum_probs=23.4
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
.++...|||+.||||.++|++.|+++
T Consensus 70 pd~tl~Ela~~l~Vs~~ti~~~Lkrl 95 (119)
T PF01710_consen 70 PDATLRELAERLGVSPSTIWRALKRL 95 (119)
T ss_pred CCcCHHHHHHHcCCCHHHHHHHHHHc
Confidence 45777899999999999999999887
No 222
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=89.92 E-value=0.36 Score=37.11 Aligned_cols=33 Identities=15% Similarity=0.114 Sum_probs=30.3
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIR 36 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~ 36 (163)
.+++..|||+.+|++.+||+++|+.+.+.|=+.
T Consensus 39 ~~~tl~eIa~~lglpkStv~RlL~tL~~~G~l~ 71 (271)
T PRK10163 39 GSSSVSDISLNLDLPLSTTFRLLKVLQAADFVY 71 (271)
T ss_pred CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 468999999999999999999999999999883
No 223
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=89.90 E-value=0.38 Score=34.26 Aligned_cols=41 Identities=22% Similarity=0.297 Sum_probs=35.4
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCC--CCCCCCCCCC
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIR--PGVIGGSKPR 46 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~--Pg~~Gg~~p~ 46 (163)
++..+||+.++|+...+.++|....+.|=+. .|..||-.+.
T Consensus 26 vs~~eIA~~~~ip~~~l~kIl~~L~~aGLv~s~rG~~GGy~La 68 (164)
T PRK10857 26 VPLADISERQGISLSYLEQLFSRLRKNGLVSSVRGPGGGYLLG 68 (164)
T ss_pred CcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeCCCCCCCeecc
Confidence 8999999999999999999999999999886 4656665544
No 224
>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=89.82 E-value=0.34 Score=31.96 Aligned_cols=28 Identities=18% Similarity=0.351 Sum_probs=21.9
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhhhh
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~ 31 (163)
.|....++|+.+|+|...|.+|+++.+.
T Consensus 71 ~G~n~~eLA~kyglS~r~I~~Ii~~~~~ 98 (108)
T PF08765_consen 71 NGMNVRELARKYGLSERQIYRIIKRVRR 98 (108)
T ss_dssp -SS-HHHHHHHHT--HHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4889999999999999999999988743
No 225
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=89.79 E-value=1.3 Score=28.05 Aligned_cols=48 Identities=13% Similarity=0.089 Sum_probs=32.3
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHH
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEE 58 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~ 58 (163)
+++.++|+.+|||..|+..|. +.|-+.|....+. .+.-++.....+..
T Consensus 2 ~~i~e~A~~~gvs~~tLr~ye----~~Gli~p~r~~~g-~R~y~~~dv~~l~~ 49 (91)
T cd04766 2 YVISVAAELSGMHPQTLRLYE----RLGLLSPSRTDGG-TRRYSERDIERLRR 49 (91)
T ss_pred cCHHHHHHHHCcCHHHHHHHH----HCCCcCCCcCCCC-CeeECHHHHHHHHH
Confidence 467899999999999999986 4588888543222 23334444444433
No 226
>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=89.79 E-value=1.6 Score=28.81 Aligned_cols=67 Identities=12% Similarity=0.035 Sum_probs=40.1
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHHHHH-hCCCCCchhhhhhhh
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPNITSWEVRDKLI 76 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~~~~-~~p~~~~~e~~~~l~ 76 (163)
+++.|+|+.+|||..|+..|- +.|-+.|..-.....+.-+......+..+.. ..-+++..++..-+.
T Consensus 1 ~~i~e~a~~~gvs~~tlr~ye----~~gll~~~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~ 68 (113)
T cd01109 1 YTIKEVAEKTGLSADTLRYYE----KEGLLPPVKRDENGIRDFTEEDLEWLEFIKCLRNTGMSIKDIKEYAE 68 (113)
T ss_pred CCHHHHHHHHCcCHHHHHHHH----HCCCCCCCCcCCCCCccCCHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 468899999999999998874 5588855332212223344444444432221 123677777776554
No 227
>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=89.76 E-value=0.29 Score=25.95 Aligned_cols=25 Identities=16% Similarity=0.112 Sum_probs=19.4
Q ss_pred ChhhhHHHhhcchhhHHHHHhhhhhccCC
Q psy1904 7 RPCVISRQLRVSHGCVSKILNRYQETGSI 35 (163)
Q Consensus 7 ~~~~ia~~~~vs~~~vs~~l~~~~~tG~~ 35 (163)
++.|+|+.+|||..|+..|- +.|-+
T Consensus 1 ti~e~A~~~gvs~~tlR~ye----~~Gll 25 (38)
T PF00376_consen 1 TIGEVAKLLGVSPRTLRYYE----REGLL 25 (38)
T ss_dssp EHHHHHHHHTS-HHHHHHHH----HTTSS
T ss_pred CHHHHHHHHCCCHHHHHHHH----HCCCC
Confidence 36799999999999998885 44766
No 228
>COG3093 VapI Plasmid maintenance system antidote protein [General function prediction only]
Probab=89.68 E-value=0.44 Score=31.19 Aligned_cols=49 Identities=22% Similarity=0.391 Sum_probs=37.7
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHHHHHhCCCCCc
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPNITS 68 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~~~~~~p~~~~ 68 (163)
.|+++.++|+.+||+..+|+.|+ .|. +..+.+..-.+....+..|.++.
T Consensus 22 ~glt~~~lA~~lgV~r~~is~li--------------ng~--~~iT~dmAlrL~k~fGtspefWl 70 (104)
T COG3093 22 LGLTQTELAEALGVTRNTISELI--------------NGR--RAITADMALRLAKVFGTSPEFWL 70 (104)
T ss_pred ccCCHHHHHHHhCCCHHHHHHHH--------------cCC--cCCCHHHHHHHHHHhCCCHHHHH
Confidence 48999999999999999999998 222 34566777777777777776653
No 229
>PRK13182 racA polar chromosome segregation protein; Reviewed
Probab=89.64 E-value=1.3 Score=31.99 Aligned_cols=62 Identities=13% Similarity=0.106 Sum_probs=38.3
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCC-CCCCCCcCChHHHHHHHHHHH-hCCCCCchhhhh
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI-GGSKPRVATPDVEKRIEEYKK-TNPNITSWEVRD 73 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~-Gg~~p~~~~~~~~~~i~~~~~-~~p~~~~~e~~~ 73 (163)
+++.++|+.+|||..||.+|-++ |.+.+... +|. +.-+.....++..+.. .+-++...++..
T Consensus 1 mti~evA~~lGVS~~TLRrw~k~----g~L~~~R~~~G~--R~y~~~dl~~L~~I~~l~~~Gm~i~~i~~ 64 (175)
T PRK13182 1 MKTPFVAKKLGVSPKTVQRWVKQ----LNLPCEKNEYGH--YIFTEEDLQLLEYVKSQIEEGQNMQDTQK 64 (175)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHc----CCCCCCcCCCCC--EEECHHHHHHHHHHHHHHHcCCCHHHHHH
Confidence 46789999999999999999754 55544332 333 2334445556654442 233566655544
No 230
>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=89.61 E-value=0.39 Score=30.49 Aligned_cols=27 Identities=19% Similarity=0.282 Sum_probs=24.1
Q ss_pred CCCChhhhHHHhh-cchhhHHHHHhhhh
Q psy1904 4 AGVRPCVISRQLR-VSHGCVSKILNRYQ 30 (163)
Q Consensus 4 ~g~~~~~ia~~~~-vs~~~vs~~l~~~~ 30 (163)
-|++-.+|++.|| .+++||+.-+++..
T Consensus 43 ~~~s~~~Ig~~fg~r~hStV~~a~~ri~ 70 (90)
T cd06571 43 TGLSLPEIGRAFGGRDHSTVLHAVRKIE 70 (90)
T ss_pred hCCCHHHHHHHhCCCCHhHHHHHHHHHH
Confidence 4899999999999 99999999887763
No 231
>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR. This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system.
Probab=89.60 E-value=0.41 Score=32.76 Aligned_cols=41 Identities=20% Similarity=0.331 Sum_probs=34.4
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCC--CCCCCCCCCC
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIR--PGVIGGSKPR 46 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~--Pg~~Gg~~p~ 46 (163)
++..+||+.++|+...+.++|....+.|=+. .|..||-.+.
T Consensus 26 ~s~~~ia~~~~ip~~~l~kil~~L~~~glv~s~~G~~Ggy~l~ 68 (135)
T TIGR02010 26 VTLADISERQGISLSYLEQLFAKLRKAGLVKSVRGPGGGYQLG 68 (135)
T ss_pred CcHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEeCCCCCEecc
Confidence 7899999999999999999999999999875 3555654443
No 232
>PRK15320 transcriptional activator SprB; Provisional
Probab=89.46 E-value=0.37 Score=35.49 Aligned_cols=29 Identities=10% Similarity=0.124 Sum_probs=26.1
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhhhhc
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRYQET 32 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~t 32 (163)
.|.+..|||..|++|.+||++.+.+..+-
T Consensus 178 kG~SNKEIAekL~LS~KTVSTYKnRLLeK 206 (251)
T PRK15320 178 SGHPAIELAKKFGLGTKTVSIYRKKVMYR 206 (251)
T ss_pred cCCCHHHHHHHhccchhhHHHHHHHHHHH
Confidence 79999999999999999999999887443
No 233
>PRK11569 transcriptional repressor IclR; Provisional
Probab=89.46 E-value=0.4 Score=36.88 Aligned_cols=34 Identities=18% Similarity=0.329 Sum_probs=30.9
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP 37 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P 37 (163)
.+++..|||+.+|++.+||+++|..+.+.|=+.-
T Consensus 42 ~~~~lseia~~lglpksTv~RlL~tL~~~G~l~~ 75 (274)
T PRK11569 42 GSVALTELAQQAGLPNSTTHRLLTTMQQQGFVRQ 75 (274)
T ss_pred CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence 4589999999999999999999999999998853
No 234
>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=89.39 E-value=1.9 Score=27.67 Aligned_cols=64 Identities=14% Similarity=0.151 Sum_probs=36.8
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHHHHHh-CCCCCchhhhhh
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKT-NPNITSWEVRDK 74 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~~~~~-~p~~~~~e~~~~ 74 (163)
++..|+|+.+||+..+|..|.+ .|-+.|...++.. +.-+......+.....- ..++...++..-
T Consensus 1 ~~~~eva~~~gi~~~tlr~~~~----~Gll~~~~~~~g~-r~y~~~dv~~l~~i~~l~~~g~~~~~i~~~ 65 (100)
T cd00592 1 YTIGEVAKLLGVSVRTLRYYEE----KGLLPPERSENGY-RLYSEEDLERLRLIRRLRELGLSLKEIREL 65 (100)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH----CCCcCCCcCCCCC-cccCHHHHHHHHHHHHHHHcCCCHHHHHHH
Confidence 4678999999999999999863 4777665543322 22333333333322211 145555554443
No 235
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=89.35 E-value=0.47 Score=33.23 Aligned_cols=40 Identities=25% Similarity=0.398 Sum_probs=34.3
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCC--CCCCCCCCCC
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSI--RPGVIGGSKP 45 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~--~Pg~~Gg~~p 45 (163)
++..+||++.+||...+.+++...+.-|=+ .+|+.||-.-
T Consensus 26 ~s~~~IA~~~~is~~~L~kil~~L~kaGlV~S~rG~~GGy~L 67 (150)
T COG1959 26 VSSAEIAERQGISPSYLEKILSKLRKAGLVKSVRGKGGGYRL 67 (150)
T ss_pred ccHHHHHHHhCcCHHHHHHHHHHHHHcCCEEeecCCCCCccC
Confidence 668999999999999999999999999988 4566676643
No 236
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=89.34 E-value=0.42 Score=36.47 Aligned_cols=32 Identities=22% Similarity=0.393 Sum_probs=29.7
Q ss_pred CCChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904 5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIR 36 (163)
Q Consensus 5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~ 36 (163)
+++..|||+.+|++.+||+++|..+.+.|=+.
T Consensus 26 ~ls~~eia~~lgl~kstv~RlL~tL~~~g~v~ 57 (263)
T PRK09834 26 GATVGLLAELTGLHRTTVRRLLETLQEEGYVR 57 (263)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 48999999999999999999999998888774
No 237
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=89.28 E-value=0.28 Score=31.66 Aligned_cols=26 Identities=19% Similarity=0.293 Sum_probs=22.9
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
.|-....+|++||||.+|+.+.|+++
T Consensus 67 ~~gn~s~AAr~LGIsRsTL~rKLkr~ 92 (95)
T PRK00430 67 TRGNQTRAALMLGINRGTLRKKLKKY 92 (95)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHh
Confidence 45667889999999999999999886
No 238
>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=89.19 E-value=0.75 Score=31.07 Aligned_cols=41 Identities=24% Similarity=0.328 Sum_probs=33.8
Q ss_pred CCChhhhHHHhhcchhhHHHHHhhhhhccCCC--CCCCCCCCC
Q psy1904 5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIR--PGVIGGSKP 45 (163)
Q Consensus 5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~--Pg~~Gg~~p 45 (163)
.++..+||+.++++.++|.++|......|=+. .|..||-.+
T Consensus 25 ~~s~~eia~~~~i~~~~v~~il~~L~~~gli~~~~g~~ggy~l 67 (132)
T TIGR00738 25 PVSVKEIAERQGISRSYLEKILRTLRRAGLVESVRGPGGGYRL 67 (132)
T ss_pred cCcHHHHHHHHCcCHHHHHHHHHHHHHCCcEEeccCCCCCccC
Confidence 48999999999999999999999999988775 344455444
No 239
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=89.16 E-value=0.43 Score=32.45 Aligned_cols=33 Identities=18% Similarity=0.187 Sum_probs=29.1
Q ss_pred cCCCChhhhHHHhhcchhhHHHHHhhhhhccCC
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSI 35 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~ 35 (163)
+.++.--+||++++++.|||+|-|+..-+.|-+
T Consensus 40 ~~~~tvdelae~lnr~rStv~rsl~~L~~~GlV 72 (126)
T COG3355 40 NGPLTVDELAEILNRSRSTVYRSLQNLLEAGLV 72 (126)
T ss_pred cCCcCHHHHHHHHCccHHHHHHHHHHHHHcCCe
Confidence 345888999999999999999999999888766
No 240
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=89.13 E-value=0.26 Score=37.53 Aligned_cols=33 Identities=21% Similarity=0.393 Sum_probs=29.8
Q ss_pred CC-CChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904 4 AG-VRPCVISRQLRVSHGCVSKILNRYQETGSIR 36 (163)
Q Consensus 4 ~g-~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~ 36 (163)
.| ++..|+|+.|+||..||.|.|+...+.|-+.
T Consensus 17 ~~~~~~~ela~~l~vS~~TirRdL~~Le~~g~i~ 50 (251)
T PRK13509 17 LGFVTVEKVIERLGISPATARRDINKLDESGKLK 50 (251)
T ss_pred cCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 44 8999999999999999999999998888774
No 241
>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=89.05 E-value=2 Score=27.93 Aligned_cols=63 Identities=10% Similarity=0.009 Sum_probs=37.9
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCC-CCCCCCcCChHHHHHHHHHHH-hCCCCCchhhhhh
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI-GGSKPRVATPDVEKRIEEYKK-TNPNITSWEVRDK 74 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~-Gg~~p~~~~~~~~~~i~~~~~-~~p~~~~~e~~~~ 74 (163)
+++.|+|+.+|||..|+.-|- +.|-+.|... +|.+ .=+....+.+.-+.. ..-+++..++..-
T Consensus 2 ~~i~eva~~~gvs~~tlR~ye----~~Gll~~~r~~~g~R--~Y~~~~l~~l~~I~~l~~~G~~l~ei~~~ 66 (102)
T cd04789 2 YTISELAEKAGISRSTLLYYE----KLGLITGTRNANGYR--LYPDSDLQRLLLIQQLQAGGLSLKECLAC 66 (102)
T ss_pred CCHHHHHHHHCcCHHHHHHHH----HCCCCCCCcCCCCCe--eCCHHHHHHHHHHHHHHHCCCCHHHHHHH
Confidence 578899999999999998765 5588887543 3332 223334444432211 2235666665553
No 242
>COG5606 Uncharacterized conserved small protein [Function unknown]
Probab=89.03 E-value=0.17 Score=31.88 Aligned_cols=24 Identities=25% Similarity=0.279 Sum_probs=22.1
Q ss_pred cCCCChhhhHHHhhcchhhHHHHH
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKIL 26 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l 26 (163)
+.++++.+||..|||+++.||.+.
T Consensus 39 q~~l~Q~qiae~lgV~qprvS~l~ 62 (91)
T COG5606 39 QAALSQAQIAELLGVTQPRVSDLA 62 (91)
T ss_pred HHHHHHHHHHHHhCCCCchHHHHH
Confidence 568899999999999999999986
No 243
>PF07453 NUMOD1: NUMOD1 domain; InterPro: IPR010896 This helix-turn-helix-containing DNA-binding domain is found associated in homing nucleases [].
Probab=88.99 E-value=0.33 Score=25.35 Aligned_cols=20 Identities=35% Similarity=0.375 Sum_probs=17.6
Q ss_pred ChhhhHHHhhcchhhHHHHH
Q psy1904 7 RPCVISRQLRVSHGCVSKIL 26 (163)
Q Consensus 7 ~~~~ia~~~~vs~~~vs~~l 26 (163)
+..++|+-||+++++|++.|
T Consensus 18 Si~eAa~~l~i~~~~I~~~l 37 (37)
T PF07453_consen 18 SIREAARYLGISHSTISKYL 37 (37)
T ss_pred CHHHHHHHhCCCHHHHHHhC
Confidence 57899999999999998864
No 244
>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=88.97 E-value=0.51 Score=28.18 Aligned_cols=33 Identities=27% Similarity=0.420 Sum_probs=27.1
Q ss_pred CCCCh--hhhHHHhhcc-hhhHHHHHhhhhhccCCC
Q psy1904 4 AGVRP--CVISRQLRVS-HGCVSKILNRYQETGSIR 36 (163)
Q Consensus 4 ~g~~~--~~ia~~~~vs-~~~vs~~l~~~~~tG~~~ 36 (163)
.|.+| .|||+.||++ .++|...|+...+-|-+.
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 46555 6999999996 999999999999888774
No 245
>PRK09744 DNA-binding transcriptional regulator DicC; Provisional
Probab=88.97 E-value=0.39 Score=29.36 Aligned_cols=18 Identities=11% Similarity=0.062 Sum_probs=16.4
Q ss_pred hhhhHHHhhcchhhHHHH
Q psy1904 8 PCVISRQLRVSHGCVSKI 25 (163)
Q Consensus 8 ~~~ia~~~~vs~~~vs~~ 25 (163)
...+|+.||||++.||.|
T Consensus 13 ~~kvA~aLGIs~~AVsQW 30 (75)
T PRK09744 13 KTKLANAAGVRLASVAAW 30 (75)
T ss_pred HHHHHHHHCCCHHHHHHH
Confidence 457899999999999999
No 246
>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=88.87 E-value=0.48 Score=34.74 Aligned_cols=33 Identities=18% Similarity=0.306 Sum_probs=30.4
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIR 36 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~ 36 (163)
.+++..+||+.|+|+.++|++.|+.+.+.|-+.
T Consensus 14 ~~~t~~eLA~~lgis~~tV~~~L~~Le~~GlV~ 46 (203)
T TIGR02702 14 GQATAAALAEALAISPQAVRRHLKDLETEGLIE 46 (203)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeE
Confidence 459999999999999999999999998888884
No 247
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=88.82 E-value=0.44 Score=34.26 Aligned_cols=26 Identities=15% Similarity=0.171 Sum_probs=23.8
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
+|++..|||+.||||.++|...+.+-
T Consensus 126 eg~s~~EIA~~lgis~~tV~~~l~Ra 151 (182)
T PRK12511 126 EGLSYQEAAAVLGIPIGTLMSRIGRA 151 (182)
T ss_pred cCCCHHHHHHHhCcCHHHHHHHHHHH
Confidence 79999999999999999999998654
No 248
>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=88.72 E-value=1.5 Score=29.55 Aligned_cols=64 Identities=20% Similarity=0.227 Sum_probs=41.4
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHHHHH--hCCCCCchhhhhhh
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK--TNPNITSWEVRDKL 75 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~~~~--~~p~~~~~e~~~~l 75 (163)
+++.++|+.+|||..|+..|- +.|-+.|...+|. +.-+......+.-+.. .+.+++..+++.-+
T Consensus 2 ysI~eVA~~~GVs~~TLR~wE----~~GLl~p~r~~G~--R~Ys~~dv~rL~~I~~L~~e~G~~l~eI~~~L 67 (120)
T cd04767 2 YPIGVVAELLNIHPETLRIWE----RHGLIKPARRNGQ--RLYSNNDLKRLRFIKKLINEKGLNIAGVKQIL 67 (120)
T ss_pred CCHHHHHHHHCcCHHHHHHHH----HCCCCCCcCCCCc--EEECHHHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence 578899999999999999875 3488888655444 3334444444433322 22567776666543
No 249
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=88.62 E-value=0.51 Score=35.87 Aligned_cols=34 Identities=15% Similarity=0.244 Sum_probs=30.7
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP 37 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P 37 (163)
.+++..|||+.+|++.+||+++|+.+.+.|=+.-
T Consensus 27 ~~l~l~eia~~lgl~kstv~Rll~tL~~~G~l~~ 60 (257)
T PRK15090 27 REIGITELSQRVMMSKSTVYRFLQTMKTLGYVAQ 60 (257)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence 3588999999999999999999999999998854
No 250
>PF07022 Phage_CI_repr: Bacteriophage CI repressor helix-turn-helix domain; InterPro: IPR010744 This family consists of several phage CI repressor proteins and related bacterial sequences. The CI repressor is known to function as a transcriptional switch, determining whether transcription is lytic or lysogenic [].; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2FJR_B.
Probab=88.62 E-value=0.22 Score=29.73 Aligned_cols=21 Identities=14% Similarity=0.172 Sum_probs=16.0
Q ss_pred ChhhhHHHhhcchhhHH-HHHh
Q psy1904 7 RPCVISRQLRVSHGCVS-KILN 27 (163)
Q Consensus 7 ~~~~ia~~~~vs~~~vs-~~l~ 27 (163)
+..|+|+.||||+++|+ .|.+
T Consensus 14 ~~~~lA~~lgis~st~s~~~~~ 35 (66)
T PF07022_consen 14 SDKELAERLGISKSTLSNNWKK 35 (66)
T ss_dssp SCHHHHCCTT--HHHHH-HHHH
T ss_pred CHHHHHHHhCcCHHHhhHHHHh
Confidence 45699999999999999 7764
No 251
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=88.59 E-value=0.25 Score=37.61 Aligned_cols=40 Identities=25% Similarity=0.309 Sum_probs=32.6
Q ss_pred cCC-CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCC
Q psy1904 3 AAG-VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGS 43 (163)
Q Consensus 3 ~~g-~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~ 43 (163)
+.| ++..|||+.|+||..||.|-|....+.|-+. ...||-
T Consensus 16 ~~~~~~~~ela~~l~vS~~TiRRdL~~Le~~g~l~-r~~GGa 56 (252)
T PRK10906 16 QQGYVSTEELVEHFSVSPQTIRRDLNDLAEQNKIL-RHHGGA 56 (252)
T ss_pred HcCCEeHHHHHHHhCCCHHHHHHHHHHHHHCCCEE-EecCCE
Confidence 345 8899999999999999999999998888874 334443
No 252
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=88.57 E-value=0.47 Score=34.25 Aligned_cols=26 Identities=15% Similarity=0.126 Sum_probs=24.0
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
+|++..|||+.||||.++|...|.+-
T Consensus 131 ~g~s~~EIA~~Lgis~~tVk~~l~Ra 156 (187)
T PRK12516 131 SGFAYEEAAEICGCAVGTIKSRVNRA 156 (187)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 79999999999999999999998664
No 253
>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=88.48 E-value=0.36 Score=34.32 Aligned_cols=28 Identities=36% Similarity=0.377 Sum_probs=24.8
Q ss_pred ccCCCChhhhHHHhh-cchhhHHHHHhhh
Q psy1904 2 AAAGVRPCVISRQLR-VSHGCVSKILNRY 29 (163)
Q Consensus 2 ~~~g~~~~~ia~~~~-vs~~~vs~~l~~~ 29 (163)
-.+|++..+||++|| ||.+.|.=.+.++
T Consensus 15 w~~G~SasqIA~~lg~vsRnAViGk~hRl 43 (162)
T PF07750_consen 15 WAEGLSASQIARQLGGVSRNAVIGKAHRL 43 (162)
T ss_pred HHcCCCHHHHHHHhCCcchhhhhhhhhcc
Confidence 358999999999999 9999998887766
No 254
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=88.38 E-value=0.55 Score=34.14 Aligned_cols=35 Identities=11% Similarity=0.091 Sum_probs=31.8
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCC
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG 38 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg 38 (163)
.|+++.+||+.+++..+||++++++..+-|=+.=.
T Consensus 58 ~~itq~eLa~~l~l~~sTvtr~l~rLE~kGlI~R~ 92 (185)
T PRK13777 58 KGASISEIAKFGVMHVSTAFNFSKKLEERGYLTFS 92 (185)
T ss_pred CCcCHHHHHHHHCCCHhhHHHHHHHHHHCCCEEec
Confidence 67999999999999999999999999999988633
No 255
>cd04772 HTH_TioE_rpt1 First Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD contains the N-terminal or first repeat (rpt1) of these tandem MerR-like domain proteins.
Probab=88.32 E-value=3 Score=26.89 Aligned_cols=61 Identities=18% Similarity=0.180 Sum_probs=35.8
Q ss_pred ChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHHHHHhCCCCCchhh
Q psy1904 7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPNITSWEV 71 (163)
Q Consensus 7 ~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~~~~~~p~~~~~e~ 71 (163)
++.|+|+.+|||..|+..|. +.|-+.|..-....-+.=+......+.-+..-..++...++
T Consensus 2 ~i~e~A~~~gvs~~tlR~Ye----~~Gll~~~~r~~~g~R~Y~~~~v~~l~~I~~l~~g~~l~~i 62 (99)
T cd04772 2 RTVDLARAIGLSPQTVRNYE----SLGLIPPAERTANGYRIYTDKHIAALRAYRALLPGYGYRVA 62 (99)
T ss_pred CHHHHHHHHCcCHHHHHHHH----HcCCCCCCCcCCCCCeecCHHHHHHHHHHHHHhhCCCHHHH
Confidence 57899999999999998874 56888774322112233344555555333322234444443
No 256
>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=88.26 E-value=2.3 Score=27.41 Aligned_cols=63 Identities=11% Similarity=0.146 Sum_probs=37.5
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCC-CCCCCCcCChHHHHHHHHHHH--hCCCCCchhhhhh
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI-GGSKPRVATPDVEKRIEEYKK--TNPNITSWEVRDK 74 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~-Gg~~p~~~~~~~~~~i~~~~~--~~p~~~~~e~~~~ 74 (163)
+++.++|+.+|||.+++..|. +.|-+.|... +|. +.-+......+..... ..-+++..++..-
T Consensus 2 ~~i~eva~~~gVs~~tLR~ye----~~Gli~p~r~~~g~--R~Ys~~dv~~l~~I~~L~~~~G~~l~~i~~~ 67 (98)
T cd01279 2 YPISVAAELLGIHPQTLRVYD----RLGLVSPARTNGGG--RRYSNNDLELLRQVQRLSQDEGFNLAGIKRI 67 (98)
T ss_pred cCHHHHHHHHCcCHHHHHHHH----HCCCCCCCcCCCCC--eeECHHHHHHHHHHHHHHHHCCCCHHHHHHH
Confidence 467899999999999999885 4587777432 333 2234444444433322 2235555544443
No 257
>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=88.19 E-value=0.5 Score=33.77 Aligned_cols=33 Identities=9% Similarity=0.166 Sum_probs=29.8
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCCCC
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPG 38 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg 38 (163)
++..|||..+|+|.-+|+++|+++++.|-+.-.
T Consensus 144 ~t~~~iA~~lG~tretvsR~l~~l~~~g~I~~~ 176 (193)
T TIGR03697 144 LSHQAIAEAIGSTRVTITRLLGDLRKKKLISIH 176 (193)
T ss_pred CCHHHHHHHhCCcHHHHHHHHHHHHHCCCEEec
Confidence 578999999999999999999999999887644
No 258
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=88.17 E-value=0.5 Score=35.07 Aligned_cols=27 Identities=22% Similarity=0.101 Sum_probs=24.0
Q ss_pred cCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
.+|++..|||+.||||.++|...|.+-
T Consensus 148 ~eg~s~~EIAe~LgiS~~tVk~~L~RA 174 (216)
T PRK12533 148 LEDMSYREIAAIADVPVGTVMSRLARA 174 (216)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 379999999999999999999988654
No 259
>PRK06474 hypothetical protein; Provisional
Probab=88.16 E-value=0.44 Score=34.39 Aligned_cols=32 Identities=16% Similarity=0.323 Sum_probs=29.9
Q ss_pred CChhhhHHHh-hcchhhHHHHHhhhhhccCCCC
Q psy1904 6 VRPCVISRQL-RVSHGCVSKILNRYQETGSIRP 37 (163)
Q Consensus 6 ~~~~~ia~~~-~vs~~~vs~~l~~~~~tG~~~P 37 (163)
+++++|+..+ +|+.+||++-|+.+.+.|-+..
T Consensus 27 ~ta~el~~~l~~is~aTvYrhL~~L~e~GLI~~ 59 (178)
T PRK06474 27 LTPLELVKILKDVPQATLYRHLQTMVDSGILHV 59 (178)
T ss_pred CCHHHHHHHhcCCCHHHHHHHHHHHHHCCCEEE
Confidence 8999999999 7999999999999999998864
No 260
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=88.13 E-value=0.49 Score=34.14 Aligned_cols=31 Identities=16% Similarity=0.255 Sum_probs=29.1
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIR 36 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~ 36 (163)
++..+||..+|++..+|+++|+++++.|-+.
T Consensus 150 ~t~~~iA~~lG~tretvsR~l~~l~~~g~I~ 180 (202)
T PRK13918 150 ATHDELAAAVGSVRETVTKVIGELSREGYIR 180 (202)
T ss_pred CCHHHHHHHhCccHHHHHHHHHHHHHCCCEE
Confidence 5688999999999999999999999999987
No 261
>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=88.10 E-value=2.4 Score=27.26 Aligned_cols=66 Identities=14% Similarity=0.156 Sum_probs=39.9
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHHHHHh--CCCCCchhhhhhh
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKT--NPNITSWEVRDKL 75 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~~~~~--~p~~~~~e~~~~l 75 (163)
++..|+|+.+|||..++.-|. +.|-+.|....+..-+.-+......+.....- .-++...++..-+
T Consensus 1 m~I~eva~~~gvs~~tlR~Ye----~~GLl~p~~r~~~g~r~Y~~~dv~~l~~I~~L~~~~G~~l~~I~~~l 68 (95)
T cd04780 1 MRMSELSKRSGVSVATIKYYL----REGLLPEGRRLAPNQAEYSEAHVERLRLIRALQQEGGLPISQIKEVL 68 (95)
T ss_pred CCHHHHHHHHCcCHHHHHHHH----HCCCCCCCcCCCCCCeecCHHHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence 567899999999999998886 45888874322122233455555555443322 1245555555443
No 262
>cd04775 HTH_Cfa-like Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulators; the HTH domain of Cfa, a cyclopropane fatty acid synthase, and other related methyltransferases, as well as, the N-terminal domain of a conserved, uncharacterized ~172 a.a. protein. Based on sequence similarity of the N-terminal domain, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimil
Probab=88.04 E-value=2.4 Score=27.55 Aligned_cols=64 Identities=16% Similarity=0.059 Sum_probs=37.4
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHHHHH-hCCCCCchhhhhh
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPNITSWEVRDK 74 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~~~~-~~p~~~~~e~~~~ 74 (163)
+++.|+|+.+|||..|+.-|- +.|-+.|....+ .-+.=+......+..... ..-+++..+++.-
T Consensus 2 ~~i~eva~~~gvs~~tLR~ye----~~Gll~~~r~~~-g~R~Y~~~dl~~l~~I~~l~~~G~~l~ei~~~ 66 (102)
T cd04775 2 YTIGQMSRKFGVSRSTLLYYE----SIGLIPSARSEA-NYRLYSEADLSRLEKIVFLQAGGLPLEEIAGC 66 (102)
T ss_pred CCHHHHHHHHCcCHHHHHHHH----HCCCCCCCCCCC-CCeeeCHHHHHHHHHHHHHHHCCCCHHHHHHH
Confidence 478899999999999996664 458885543322 122233334433332221 2236777666654
No 263
>smart00497 IENR1 Intron encoded nuclease repeat motif. Repeat of unknown function, but possibly DNA-binding via helix-turn-helix motif (Ponting, unpublished).
Probab=87.96 E-value=0.51 Score=26.44 Aligned_cols=22 Identities=32% Similarity=0.374 Sum_probs=19.6
Q ss_pred ChhhhHHHhhcchhhHHHHHhh
Q psy1904 7 RPCVISRQLRVSHGCVSKILNR 28 (163)
Q Consensus 7 ~~~~ia~~~~vs~~~vs~~l~~ 28 (163)
+..++|+.||+++++|++.++.
T Consensus 19 S~~eAa~~lg~~~~~I~~~~~~ 40 (53)
T smart00497 19 SIREAAKYLGISHSSISKYLNT 40 (53)
T ss_pred CHHHHHHHhCCCHHHHHHHHhC
Confidence 6789999999999999999854
No 264
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=87.78 E-value=0.3 Score=36.93 Aligned_cols=32 Identities=28% Similarity=0.381 Sum_probs=28.9
Q ss_pred CCChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904 5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIR 36 (163)
Q Consensus 5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~ 36 (163)
.++..|||+.|+||..||.|.|+...+.|.+.
T Consensus 18 ~~~~~eLa~~l~VS~~TiRRdL~~L~~~~~l~ 49 (240)
T PRK10411 18 SLTTEALAEQLNVSKETIRRDLNELQTQGKIL 49 (240)
T ss_pred CCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 48999999999999999999999998877764
No 265
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=87.68 E-value=0.6 Score=35.42 Aligned_cols=35 Identities=17% Similarity=0.347 Sum_probs=31.4
Q ss_pred CCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCC
Q psy1904 5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV 39 (163)
Q Consensus 5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~ 39 (163)
|++..|||+++|++.+||+++|....+.|=+.--.
T Consensus 19 ~l~l~ela~~~glpksT~~RlL~tL~~~G~v~~d~ 53 (246)
T COG1414 19 GLSLAELAERLGLPKSTVHRLLQTLVELGYVEQDP 53 (246)
T ss_pred CCCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEcC
Confidence 46799999999999999999999999999887654
No 266
>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=87.62 E-value=0.54 Score=34.25 Aligned_cols=35 Identities=20% Similarity=0.352 Sum_probs=29.3
Q ss_pred CCCChh--hhHHHhhcc-hhhHHHHHhhhhhccCCCCC
Q psy1904 4 AGVRPC--VISRQLRVS-HGCVSKILNRYQETGSIRPG 38 (163)
Q Consensus 4 ~g~~~~--~ia~~~~vs-~~~vs~~l~~~~~tG~~~Pg 38 (163)
.|..|. |||+.||++ .+||++.|++..+.|-+...
T Consensus 22 ~~~~~~~~ela~~~~~~s~~tv~~~l~~L~~~g~i~~~ 59 (199)
T TIGR00498 22 TGYPPSIREIARAVGLRSPSAAEEHLKALERKGYIERD 59 (199)
T ss_pred cCCCCcHHHHHHHhCCCChHHHHHHHHHHHHCCCEecC
Confidence 344454 999999998 99999999999999887654
No 267
>PRK15043 transcriptional regulator MirA; Provisional
Probab=87.62 E-value=2 Score=32.59 Aligned_cols=67 Identities=18% Similarity=0.196 Sum_probs=42.5
Q ss_pred CCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCC-CCCCCCcCChHHHHHHHHHHHh-CCCCCchhhhhhhh
Q psy1904 5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI-GGSKPRVATPDVEKRIEEYKKT-NPNITSWEVRDKLI 76 (163)
Q Consensus 5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~-Gg~~p~~~~~~~~~~i~~~~~~-~p~~~~~e~~~~l~ 76 (163)
-+++.++|+.+|||..|+..|-+++ |-+.|... ||.+ .=+....+.+..+..- .-++...+++.-+.
T Consensus 3 ~ytIgeVA~~~GVs~~TLR~wErr~---GLL~P~Rt~~G~R--~Ys~~dv~rL~~I~~l~~~G~~i~eIk~ll~ 71 (243)
T PRK15043 3 LYTIGEVALLCDINPVTLRAWQRRY---GLLKPQRTDGGHR--LFNDADIDRIREIKRWIDNGVQVSKVKMLLS 71 (243)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHhc---CCCCCccCCCCCE--EECHHHHHHHHHHHHHHHcCCCHHHHHHHHh
Confidence 3688999999999999999987655 88888654 4333 3344444444332221 23566656555443
No 268
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=87.53 E-value=0.41 Score=37.89 Aligned_cols=21 Identities=29% Similarity=0.319 Sum_probs=19.0
Q ss_pred ChhhhHHHhhcchhhHHHHHh
Q psy1904 7 RPCVISRQLRVSHGCVSKILN 27 (163)
Q Consensus 7 ~~~~ia~~~~vs~~~vs~~l~ 27 (163)
..-|||+..|||.+|||+.|+
T Consensus 2 TikDVA~~AGVS~sTVSrvln 22 (333)
T COG1609 2 TIKDVAKLAGVSKATVSRVLN 22 (333)
T ss_pred CHHHHHHHhCCCHHHHHHHHc
Confidence 467999999999999999994
No 269
>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=87.47 E-value=0.51 Score=30.83 Aligned_cols=26 Identities=19% Similarity=0.252 Sum_probs=20.2
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
+..|-.+||..+|||...|+.++++-
T Consensus 32 eDlSlsEIAe~~~iSRqaV~d~ikr~ 57 (101)
T PF04297_consen 32 EDLSLSEIAEELGISRQAVYDSIKRA 57 (101)
T ss_dssp S---HHHHHHHCTS-HHHHHHHHHHH
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 56889999999999999999999774
No 270
>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=87.22 E-value=0.66 Score=32.81 Aligned_cols=26 Identities=19% Similarity=0.198 Sum_probs=23.9
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
.|.+..|||+.||+|.++|...|.+-
T Consensus 115 ~g~s~~eIA~~lgis~~tV~~~l~Ra 140 (170)
T TIGR02959 115 EGLSQQEIAEKLGLSLSGAKSRVQRG 140 (170)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 78999999999999999999998664
No 271
>PRK04140 hypothetical protein; Provisional
Probab=87.20 E-value=0.6 Score=36.85 Aligned_cols=24 Identities=25% Similarity=0.264 Sum_probs=22.6
Q ss_pred cCCCChhhhHHHhhcchhhHHHHH
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKIL 26 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l 26 (163)
..|+++.++|+.+|||.++|++|+
T Consensus 137 ~~GlSq~eLA~~lGVSr~tIskyE 160 (317)
T PRK04140 137 ELGLSLGELASELGVSRRTISKYE 160 (317)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHH
Confidence 479999999999999999999997
No 272
>COG2524 Predicted transcriptional regulator, contains C-terminal CBS domains [Transcription]
Probab=87.04 E-value=0.88 Score=34.82 Aligned_cols=43 Identities=26% Similarity=0.416 Sum_probs=38.6
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCC--CCCCCCCCCCCcC
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSI--RPGVIGGSKPRVA 48 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~--~Pg~~Gg~~p~~~ 48 (163)
++=.|||..++...|||...++.++..|-+ .||+.||..|...
T Consensus 26 IKgeeIA~~l~rnpGTVRNqmq~LkaLgLVegvpGPkGGY~PT~k 70 (294)
T COG2524 26 IKGEEIAEVLNRNPGTVRNQMQSLKALGLVEGVPGPKGGYKPTSK 70 (294)
T ss_pred cchHHHHHHHccCcchHHHHHHHHHhcCccccccCCCCCccccHH
Confidence 677899999999999999999999999988 7899999988744
No 273
>COG2452 Predicted site-specific integrase-resolvase [DNA replication, recombination, and repair]
Probab=86.88 E-value=0.86 Score=33.07 Aligned_cols=48 Identities=23% Similarity=0.339 Sum_probs=34.7
Q ss_pred CCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHH
Q psy1904 5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRI 56 (163)
Q Consensus 5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i 56 (163)
.+.|.+.|+++|||..|+.+|. .-|-+.+-..-+.+-+...++....+
T Consensus 1 ~m~~~e~~~~lgis~~Tl~rw~----r~G~i~~~~~~~gr~~~~ee~v~~~~ 48 (193)
T COG2452 1 LLRPKEACQLLGISYSTLLRWI----REGKIRVVTTEGGKYRIPEEEIKKYL 48 (193)
T ss_pred CCCHHHHHHHhCcCHHHHHHHH----HcCcccceEecCceEeccHhHHHHHh
Confidence 3689999999999999999997 44888776655555555444444433
No 274
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=86.83 E-value=0.63 Score=34.51 Aligned_cols=33 Identities=21% Similarity=0.370 Sum_probs=29.7
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCCCC
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPG 38 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg 38 (163)
++..+||..+|+|..+|+|+|+++++.|-+.-.
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 567899999999999999999999999988744
No 275
>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=86.66 E-value=2.6 Score=28.43 Aligned_cols=65 Identities=17% Similarity=0.144 Sum_probs=38.8
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCCC-CCC-CCCCCCcCChHHHHHHHHHHH-hCCCCCchhhhhhhh
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRP-GVI-GGSKPRVATPDVEKRIEEYKK-TNPNITSWEVRDKLI 76 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P-g~~-Gg~~p~~~~~~~~~~i~~~~~-~~p~~~~~e~~~~l~ 76 (163)
+++.|+|+++|||..|+.-| .+.|-+.| ... +|. +.-+......+.-+.. ..-+++..++..-+.
T Consensus 1 m~I~e~a~~~gvs~~tlR~Y----e~~GLl~~~~r~~~gy--R~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~ 68 (126)
T cd04783 1 LTIGELAKAAGVNVETIRYY----QRRGLLPEPPRPEGGY--RRYPEETVTRLRFIKRAQELGFTLDEIAELLE 68 (126)
T ss_pred CCHHHHHHHHCcCHHHHHHH----HHCCCCCCCCcCCCCC--eecCHHHHHHHHHHHHHHHcCCCHHHHHHHHh
Confidence 57889999999999999544 56788874 332 332 3334444444322221 123566766665543
No 276
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=86.64 E-value=0.72 Score=33.10 Aligned_cols=27 Identities=19% Similarity=0.132 Sum_probs=24.4
Q ss_pred cCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
.+|++..|||+.||+|.++|...|.+-
T Consensus 125 ~~g~s~~EIA~~Lgis~~tV~~~l~RA 151 (182)
T PRK12540 125 ASGFSYEDAAAICGCAVGTIKSRVNRA 151 (182)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 379999999999999999999998664
No 277
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=86.52 E-value=0.6 Score=31.91 Aligned_cols=37 Identities=19% Similarity=0.083 Sum_probs=30.4
Q ss_pred ccCCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCC
Q psy1904 2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG 38 (163)
Q Consensus 2 ~~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg 38 (163)
+..|.++.++|+.++|+.++|.+|..+..+.....++
T Consensus 86 ~~~~~~i~~~a~~l~i~~~~~~r~~~r~~~~~~~~~~ 122 (129)
T COG3677 86 YMLGLGIRDIARTLGISINTVNRWSKRFGSRVEGLRL 122 (129)
T ss_pred HHcCCCcccHHHHhcccHHHHHHHHHhhcchhhccCC
Confidence 4567999999999999999999999888665555444
No 278
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=86.50 E-value=0.69 Score=34.43 Aligned_cols=31 Identities=26% Similarity=0.302 Sum_probs=28.4
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIR 36 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~ 36 (163)
++..|||..+|++..+|+|+|+.+++.|-+.
T Consensus 180 lt~~~IA~~lGisretlsR~L~~L~~~GlI~ 210 (230)
T PRK09391 180 MSRRDIADYLGLTIETVSRALSQLQDRGLIG 210 (230)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCcEE
Confidence 4568999999999999999999999999875
No 279
>cd01282 HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 3). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=86.44 E-value=3.4 Score=27.28 Aligned_cols=65 Identities=18% Similarity=0.187 Sum_probs=39.7
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHHHHHh-CCCCCchhhhhhh
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKT-NPNITSWEVRDKL 75 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~~~~~-~p~~~~~e~~~~l 75 (163)
+++.|+|+.+|||..|+.-|- +.|-+.|....+. -+.=+..+...+..+..- .-++...++..-+
T Consensus 1 m~i~eva~~~gvs~~tlR~Ye----~~GLl~p~r~~~g-~R~Y~~~~~~~l~~I~~lr~~G~sl~eI~~~l 66 (112)
T cd01282 1 MRIGELAARTGVSVRSLRYYE----EQGLLVPERSANG-YRDYDEAAVDRVRQIRRLLAAGLTLEEIREFL 66 (112)
T ss_pred CCHHHHHHHHCCCHHHHHHHH----HCCCCCCCcCCCC-CeecCHHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence 578899999999999988875 4588888543222 233334444444332221 2356666666544
No 280
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=86.20 E-value=1 Score=26.03 Aligned_cols=27 Identities=30% Similarity=0.272 Sum_probs=24.2
Q ss_pred cCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
-.|.+..+||..+++|..||...+...
T Consensus 17 ~~G~s~~eia~~l~is~~tV~~h~~~i 43 (65)
T COG2771 17 AQGKSNKEIARILGISEETVKTHLRNI 43 (65)
T ss_pred HCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 368999999999999999999988665
No 281
>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=86.20 E-value=3.2 Score=28.63 Aligned_cols=66 Identities=18% Similarity=0.156 Sum_probs=42.1
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHHHHH-hCCCCCchhhhhhhh
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPNITSWEVRDKLI 76 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~~~~-~~p~~~~~e~~~~l~ 76 (163)
+++.|+|+.+|||..|+.-|- +.|-+.|....+. -+.=+......+..+.. ..-+++..++..-+.
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 LSVGEVAKRSGVAVSALHFYE----QKGLIASWRNAGN-QRRYPRDVLRRIAFIKVAQRLGLSLAEIAEALA 68 (139)
T ss_pred CCHHHHHHHHCcCHHHHHHHH----HCCCCCCCcCCCC-CeEECHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 678999999999999988875 4488877544322 23334455555533322 234677777776543
No 282
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in multiple copies in the order Myxococcales. This model supercedes TIGR02233, which has now been retired.
Probab=85.98 E-value=0.79 Score=34.71 Aligned_cols=26 Identities=19% Similarity=0.202 Sum_probs=23.6
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
+|++..|||.+||||.+||...|.+-
T Consensus 176 eg~S~~EIA~~Lgis~~TVk~rl~RA 201 (244)
T TIGR03001 176 DGLSMDRIGAMYQVHRSTVSRWVAQA 201 (244)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 78999999999999999999988554
No 283
>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=85.96 E-value=3.1 Score=28.60 Aligned_cols=65 Identities=14% Similarity=0.163 Sum_probs=40.6
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCC-CCCCCCcCChHHHHHHHHHHH-hCCCCCchhhhhhhh
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI-GGSKPRVATPDVEKRIEEYKK-TNPNITSWEVRDKLI 76 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~-Gg~~p~~~~~~~~~~i~~~~~-~~p~~~~~e~~~~l~ 76 (163)
+++.++|+.+|||..|+..|- +.|-+.|... +|.+ .=+......+..+.. ..-+++..++.+-+.
T Consensus 1 y~I~e~a~~~gvs~~TLR~Ye----~~GLl~p~r~~~g~R--~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~ 67 (134)
T cd04779 1 YRIGQLAHLAGVSKRTIDYYT----NLGLLTPERSDSNYR--YYDETALDRLQLIEHLKGQRLSLAEIKDQLE 67 (134)
T ss_pred CCHHHHHHHHCcCHHHHHHHH----HCCCCCCccCCCCCe--eECHHHHHHHHHHHHHHHCCCCHHHHHHHHH
Confidence 467899999999999998885 5699988664 3332 223334333322221 133577777776543
No 284
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=85.93 E-value=1 Score=23.98 Aligned_cols=26 Identities=15% Similarity=0.128 Sum_probs=20.6
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
..++..|||..+|+|.+..+++.++.
T Consensus 7 ~~~~l~~iA~~~g~S~~~f~r~Fk~~ 32 (42)
T PF00165_consen 7 QKLTLEDIAEQAGFSPSYFSRLFKKE 32 (42)
T ss_dssp SS--HHHHHHHHTS-HHHHHHHHHHH
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 56889999999999999999998775
No 285
>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=85.86 E-value=1.1 Score=29.52 Aligned_cols=37 Identities=22% Similarity=0.251 Sum_probs=31.5
Q ss_pred CCCChhhhHHHh-----hcchhhHHHHHhhhhhccCCCCCCC
Q psy1904 4 AGVRPCVISRQL-----RVSHGCVSKILNRYQETGSIRPGVI 40 (163)
Q Consensus 4 ~g~~~~~ia~~~-----~vs~~~vs~~l~~~~~tG~~~Pg~~ 40 (163)
..+++.||...+ +||.+||++.|+.+.+-|-+.--..
T Consensus 15 ~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~Gli~~~~~ 56 (116)
T cd07153 15 GHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVREIEL 56 (116)
T ss_pred CCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCEEEEEe
Confidence 348999999988 6999999999999999998875443
No 286
>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=85.84 E-value=3.8 Score=27.37 Aligned_cols=67 Identities=15% Similarity=0.175 Sum_probs=39.5
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHHHHH-hCCCCCchhhhhhhh
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPNITSWEVRDKLI 76 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~~~~-~~p~~~~~e~~~~l~ 76 (163)
+++.|+|+++|||..|+.- |.+.|-+.|..-....-+.=+......+..+.. ..-+++..++..-+.
T Consensus 1 ~~I~eva~~~gvs~~tLRy----Ye~~GLl~p~~r~~~gyR~Y~~~~i~~l~~I~~lr~~G~sl~eI~~~l~ 68 (123)
T cd04770 1 MKIGELAKAAGVSPDTIRY----YERIGLLPPPQRSENGYRLYGEADLARLRFIRRAQALGFSLAEIRELLS 68 (123)
T ss_pred CCHHHHHHHHCcCHHHHHH----HHHCCCCCCCCCCCCCCccCCHHHHHHHHHHHHHHHCCCCHHHHHHHHH
Confidence 4788999999999999854 456799986432212223334444444432211 233677777766543
No 287
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=85.69 E-value=2.4 Score=33.46 Aligned_cols=27 Identities=22% Similarity=0.270 Sum_probs=24.4
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhhh
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRYQ 30 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~ 30 (163)
.|++..|||+.||+|.++|...|.+-+
T Consensus 168 ~g~s~~EIA~~lgis~~tVk~~l~RAr 194 (339)
T PRK08241 168 LGWSAAEVAELLDTSVAAVNSALQRAR 194 (339)
T ss_pred hCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 799999999999999999999886653
No 288
>PF04645 DUF603: Protein of unknown function, DUF603; InterPro: IPR006739 This family includes several uncharacterised proteins from Borrelia species.
Probab=85.59 E-value=0.75 Score=32.76 Aligned_cols=33 Identities=21% Similarity=0.322 Sum_probs=28.4
Q ss_pred cCC-CChhhhHHHhhcchhhHHHHHhhhhhccCC
Q psy1904 3 AAG-VRPCVISRQLRVSHGCVSKILNRYQETGSI 35 (163)
Q Consensus 3 ~~g-~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~ 35 (163)
..| .+-.|||..||||.+.|.+.-++|....+-
T Consensus 16 ~eg~L~d~~Ia~~lgvs~~nV~kmR~Kwes~~~s 49 (181)
T PF04645_consen 16 KEGRLSDAEIAKELGVSRVNVWKMRQKWESSEDS 49 (181)
T ss_pred hcCCccHHHHHHHHCchHHHHHHHHHHHHhcCCc
Confidence 467 889999999999999999999998655544
No 289
>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=85.54 E-value=3.7 Score=26.27 Aligned_cols=30 Identities=13% Similarity=0.138 Sum_probs=24.6
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCC
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV 39 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~ 39 (163)
+++.|+|+.+|||..|+.-|- +.|-+.|..
T Consensus 1 ~ti~eva~~~gvs~~tLRyye----~~Gll~p~~ 30 (96)
T cd04768 1 LTIGEFAKLAGVSIRTLRHYD----DIGLFKPAK 30 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHH----HCCCCCCCc
Confidence 367899999999999988875 458888854
No 290
>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=85.44 E-value=5 Score=26.32 Aligned_cols=64 Identities=17% Similarity=0.094 Sum_probs=39.8
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCC-C-CCCCCCcCChHHHHHHHHHHH-hCCCCCchhhhhhh
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV-I-GGSKPRVATPDVEKRIEEYKK-TNPNITSWEVRDKL 75 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~-~-Gg~~p~~~~~~~~~~i~~~~~-~~p~~~~~e~~~~l 75 (163)
.++.|+|+.+|||..|+.-|- ..|-+.|.. . +|. +.=+......+.-+.. ..-++...++..-+
T Consensus 1 y~Ige~A~~~gvs~~tlR~ye----~~GLl~p~~r~~~g~--R~Y~~~~l~~l~~I~~lr~~G~~l~~I~~~l 67 (107)
T cd01111 1 YSISQLALDAGVSVHIVRDYL----LRGLLHPVARTEGGY--GLFDDCALQRLRFVRAAFEAGIGLDELARLC 67 (107)
T ss_pred CCHHHHHHHHCcCHHHHHHHH----HCCCCCCCCcCCCCC--eecCHHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence 367899999999999998875 459998853 2 333 3334444444433332 23356666665544
No 291
>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=85.35 E-value=3.6 Score=28.03 Aligned_cols=65 Identities=18% Similarity=0.189 Sum_probs=40.6
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCC--CCCCCCCcCChHHHHHHHHHHH-hCCCCCchhhhhhhh
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV--IGGSKPRVATPDVEKRIEEYKK-TNPNITSWEVRDKLI 76 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~--~Gg~~p~~~~~~~~~~i~~~~~-~~p~~~~~e~~~~l~ 76 (163)
+++.|+|+++|||..|+.-|- +.|-+.|.. .+|.+ .=+......+..+.. ..-+++..++..-+.
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 FQIGELAKLCGVTSDTLRFYE----KNGLIKPAGRTDSGYR--LYTDEDQKRLRFILKAKELGFTLDEIKELLS 69 (131)
T ss_pred CCHHHHHHHHCcCHHHHHHHH----HCCCCCCCCcCCCCce--ecCHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 578999999999999988875 558888853 23333 223344444432221 234677777766543
No 292
>PF03297 Ribosomal_S25: S25 ribosomal protein; InterPro: IPR004977 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S25 ribosomal protein is a component of the 40S ribosomal subunit.; PDB: 2XZM_8 2XZN_8 3O30_Q 3U5G_Z 3IZB_V 3U5C_Z 3O2Z_Q 3IZ6_V.
Probab=85.31 E-value=0.67 Score=30.51 Aligned_cols=33 Identities=27% Similarity=0.542 Sum_probs=30.8
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCCCC
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPG 38 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg 38 (163)
|.|..||.+|+|+-|.+.++|+.+.+.|.+.+-
T Consensus 60 ITp~~lserlkI~~SlAr~~Lr~L~~kG~Ik~V 92 (105)
T PF03297_consen 60 ITPSVLSERLKINGSLARKALRELESKGLIKPV 92 (105)
T ss_dssp ECHHHHHHHHCCSCHHHHHHHHHHHHCCSSEEE
T ss_pred eeHHHHHHhHhhHHHHHHHHHHHHHHCCCEEEE
Confidence 678999999999999999999999999999875
No 293
>TIGR02044 CueR Cu(I)-responsive transcriptional regulator. This model represents the copper-, silver- and gold- (I) responsive transcriptional activator of the gamma proteobacterial copper efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X7-Cys. This family also lacks a conserved cysteine at the N-terminal end of the dimerization helix which is required for the binding of divalent metals such as zinc; here it is replaced by a serine residue.
Probab=85.25 E-value=3.9 Score=27.60 Aligned_cols=65 Identities=15% Similarity=0.162 Sum_probs=40.0
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCC--CCCCCCCcCChHHHHHHHHHHH-hCCCCCchhhhhhhh
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV--IGGSKPRVATPDVEKRIEEYKK-TNPNITSWEVRDKLI 76 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~--~Gg~~p~~~~~~~~~~i~~~~~-~~p~~~~~e~~~~l~ 76 (163)
|++.|+|+++|||..|+.-|- +.|-+.|.. .+|.+ .=+......+..+.. ..-+++..++..-+.
T Consensus 1 m~I~e~a~~~gvs~~tlRyYe----~~GLl~p~~r~~~gyR--~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~ 68 (127)
T TIGR02044 1 MNIGQVAKLTGLSSKMIRYYE----EKGLIPPPLRSEGGYR--TYTQQHLDELRLISRARQVGFSLEECKELLN 68 (127)
T ss_pred CCHHHHHHHHCcCHHHHHHHH----HCCCCCCCCcCCCCCe--ecCHHHHHHHHHHHHHHHCCCCHHHHHHHHH
Confidence 578899999999999987664 669888743 24433 233444444432221 234677777765443
No 294
>PF00440 TetR_N: Bacterial regulatory proteins, tetR family; InterPro: IPR001647 This entry represents a DNA-binding domain with a helix-turn-helix (HTH) structure that is found in several bacterial and archaeal transcriptional regulators, such as TetR, the tetracycline resistance repressor. Numerous other transcriptional regulatory proteins also contain HTH-type DNA-binding domains, and can be grouped into subfamiles based on sequence similarity. The domain represented by this entry is found in a subfamily of proteins that includes the transcriptional regulators TetR, TetC, AcrR, BetI, Bm3R1, EnvR, QacR, MtrR, TcmR, Ttk, YbiH, and YhgD [, , ]. Many of these proteins function as repressors that control the level of susceptibility to hydrophobic antibiotics and detergents. They all have similar molecular weights, ranging from 21 to 25 kDa. The helix-turn-helix motif is located in the initial third of the protein. The 3D structure of the homodimeric TetR protein complexed with 7-chloro-tetracycline-magnesium has been determined to 2.1 A resolution []. TetR folds into ten alpha-helices with connecting turns and loops. The three N-terminal alpha-helices of the repressor form the DNA-binding domain: this structural motif encompasses an HTH fold with an inverse orientation compared with that of other DNA-binding proteins.; GO: 0003677 DNA binding; PDB: 3NPI_B 3IUV_A 3CCY_A 2JK3_A 2FX0_A 2JJ7_A 2WV1_B 3BTI_D 3BR6_E 3BR5_A ....
Probab=85.16 E-value=0.96 Score=24.82 Aligned_cols=23 Identities=26% Similarity=0.294 Sum_probs=20.6
Q ss_pred CCCChhhhHHHhhcchhhHHHHH
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKIL 26 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l 26 (163)
++++..+||++.|||.+++++..
T Consensus 15 ~~~s~~~Ia~~~gvs~~~~y~~f 37 (47)
T PF00440_consen 15 EAVSIRDIARRAGVSKGSFYRYF 37 (47)
T ss_dssp TTSSHHHHHHHHTSCHHHHHHHC
T ss_pred HhCCHHHHHHHHccchhhHHHHc
Confidence 56899999999999999999864
No 295
>COG3888 Predicted transcriptional regulator [Transcription]
Probab=85.07 E-value=0.79 Score=35.15 Aligned_cols=45 Identities=22% Similarity=0.383 Sum_probs=39.1
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcC
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVA 48 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~ 48 (163)
.|+.+.||.+..|.|.+|||..|..+.+.|-+.=...+|..-++.
T Consensus 19 ~GI~Q~eIeel~GlSKStvSEaLs~LE~~giv~RrkvsGKs~rVw 63 (321)
T COG3888 19 EGIDQTEIEELMGLSKSTVSEALSELEKQGIVKRRKVSGKSKRVW 63 (321)
T ss_pred CCccHHHHHHHhCcchhHHHHHHHHHHhcCeeeeeeecCcceEEe
Confidence 689999999999999999999999999999998777777654443
No 296
>PRK12423 LexA repressor; Provisional
Probab=85.04 E-value=0.74 Score=33.79 Aligned_cols=34 Identities=24% Similarity=0.278 Sum_probs=29.3
Q ss_pred CCC--ChhhhHHHhh-cchhhHHHHHhhhhhccCCCC
Q psy1904 4 AGV--RPCVISRQLR-VSHGCVSKILNRYQETGSIRP 37 (163)
Q Consensus 4 ~g~--~~~~ia~~~~-vs~~~vs~~l~~~~~tG~~~P 37 (163)
.|+ +..|||+.|| +|.++|++.|+.+.+.|-+.-
T Consensus 22 ~g~~Ps~~eia~~~g~~s~~~v~~~l~~L~~~G~l~~ 58 (202)
T PRK12423 22 AGQPPSLAEIAQAFGFASRSVARKHVQALAEAGLIEV 58 (202)
T ss_pred cCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCCCEEe
Confidence 455 7889999999 599999999999999888754
No 297
>PRK09334 30S ribosomal protein S25e; Provisional
Probab=85.03 E-value=0.69 Score=29.27 Aligned_cols=33 Identities=15% Similarity=0.304 Sum_probs=30.7
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCCCC
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPG 38 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg 38 (163)
|.|..||.+|+|+-|-+.++|+.+.+.|.+.+-
T Consensus 42 ITps~lserlkI~~SlAr~~Lr~L~~kG~Ik~V 74 (86)
T PRK09334 42 VTPYTLASKYGIKISVAKKVLRELEKRGVLVLY 74 (86)
T ss_pred EcHHHHHHHhcchHHHHHHHHHHHHHCCCEEEE
Confidence 679999999999999999999999999998775
No 298
>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=84.96 E-value=0.97 Score=29.34 Aligned_cols=28 Identities=7% Similarity=0.058 Sum_probs=23.1
Q ss_pred ChhhhHHHhhcchhhHHHHHhhhh-hccC
Q psy1904 7 RPCVISRQLRVSHGCVSKILNRYQ-ETGS 34 (163)
Q Consensus 7 ~~~~ia~~~~vs~~~vs~~l~~~~-~tG~ 34 (163)
+....|+.|+||+++|++-++... ..|.
T Consensus 18 Sis~AA~~L~iS~stvs~~I~~LE~~lg~ 46 (99)
T TIGR00637 18 SISQAAKDAGISYKSAWDYIRAMNNLSGE 46 (99)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHhCC
Confidence 567889999999999999998883 3444
No 299
>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=84.84 E-value=1.2 Score=31.74 Aligned_cols=31 Identities=10% Similarity=0.019 Sum_probs=27.4
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhhhhccC
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGS 34 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~ 34 (163)
++++...+|..+|||.+|+.+|-..-++.|+
T Consensus 18 ~~~sLe~aA~~~gVs~~TarrWK~~Ak~~GD 48 (165)
T PF08822_consen 18 DRLSLEQAAAKCGVSYATARRWKREAKAKGD 48 (165)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHHcCC
Confidence 5788899999999999999999888777775
No 300
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=84.79 E-value=0.53 Score=35.90 Aligned_cols=35 Identities=11% Similarity=0.148 Sum_probs=30.5
Q ss_pred cCC-CChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904 3 AAG-VRPCVISRQLRVSHGCVSKILNRYQETGSIRP 37 (163)
Q Consensus 3 ~~g-~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P 37 (163)
+.| ++..|+|+.|+||..||.|=|....+.|-+.=
T Consensus 16 ~~~~v~v~eLa~~l~VS~~TIRRDL~~Le~~g~l~r 51 (256)
T PRK10434 16 KQGKTSVEELAQYFDTTGTTIRKDLVILEHAGTVIR 51 (256)
T ss_pred HcCCEEHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence 345 88999999999999999999999988887643
No 301
>PHA02943 hypothetical protein; Provisional
Probab=84.71 E-value=0.98 Score=31.71 Aligned_cols=41 Identities=27% Similarity=0.342 Sum_probs=34.0
Q ss_pred cCC-CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCC
Q psy1904 3 AAG-VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGS 43 (163)
Q Consensus 3 ~~g-~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~ 43 (163)
+.| .+..+||+.||+|++-|.-+|.-...-|-+.--..|..
T Consensus 21 k~G~~TtseIAkaLGlS~~qa~~~LyvLErEG~VkrV~~G~~ 62 (165)
T PHA02943 21 ADGCKTTSRIANKLGVSHSMARNALYQLAKEGMVLKVEIGRA 62 (165)
T ss_pred hcCCccHHHHHHHHCCCHHHHHHHHHHHHHcCceEEEeecce
Confidence 456 66889999999999999999999988898876555644
No 302
>COG1356 tfx Transcriptional regulator [DNA replication, recombination and repair]
Probab=84.66 E-value=0.9 Score=30.79 Aligned_cols=29 Identities=28% Similarity=0.382 Sum_probs=25.2
Q ss_pred CccCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904 1 MAAAGVRPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 1 ~~~~g~~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
|-..|.++.+||++||-+.+.||-|-++.
T Consensus 19 lRekG~tQ~eIA~~L~TTraNvSaIEkrA 47 (143)
T COG1356 19 LREKGLTQSEIARILKTTRANVSAIEKRA 47 (143)
T ss_pred hhhccccHHHHHHHHccchhhHHHHHHHH
Confidence 34579999999999999999999987664
No 303
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=84.64 E-value=1 Score=33.63 Aligned_cols=26 Identities=15% Similarity=0.119 Sum_probs=23.4
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
.|.+..+||+.||||.++|...+.+.
T Consensus 164 ~g~s~~EIAe~lgis~~tVk~~l~Ra 189 (231)
T PRK11922 164 EELSVEETAQALGLPEETVKTRLHRA 189 (231)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 78999999999999999999988554
No 304
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=84.53 E-value=0.74 Score=34.96 Aligned_cols=26 Identities=23% Similarity=0.239 Sum_probs=24.0
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
.||+-.|||..||||..||.+|-.++
T Consensus 18 ~gmk~~dIAeklGvspntiksWKrr~ 43 (279)
T COG5484 18 KGMKLKDIAEKLGVSPNTIKSWKRRD 43 (279)
T ss_pred hhccHHHHHHHhCCChHHHHHHHHhc
Confidence 68999999999999999999998765
No 305
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=84.41 E-value=0.82 Score=29.85 Aligned_cols=32 Identities=19% Similarity=0.305 Sum_probs=28.5
Q ss_pred hhhHHHhhcchhhHHHHHhhhhhccCCCCCCC
Q psy1904 9 CVISRQLRVSHGCVSKILNRYQETGSIRPGVI 40 (163)
Q Consensus 9 ~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~ 40 (163)
.+||+.++|+.++|++++++..+-|-+.-...
T Consensus 40 ~~la~~l~i~~~~vt~~l~~Le~~glv~r~~~ 71 (126)
T COG1846 40 KELAERLGLDRSTVTRLLKRLEDKGLIERLRD 71 (126)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHCCCeeecCC
Confidence 89999999999999999999999998865443
No 306
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=84.28 E-value=0.91 Score=33.64 Aligned_cols=33 Identities=15% Similarity=0.220 Sum_probs=29.9
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCCCC
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPG 38 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg 38 (163)
.+..|||..+|+|.-+|+|.|+++.+.|-+...
T Consensus 170 ~t~~~lA~~lG~sretvsR~L~~L~~~G~I~~~ 202 (226)
T PRK10402 170 EKHTQAAEYLGVSYRHLLYVLAQFIQDGYLKKS 202 (226)
T ss_pred chHHHHHHHHCCcHHHHHHHHHHHHHCCCEEee
Confidence 467999999999999999999999999988754
No 307
>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=84.26 E-value=2 Score=31.40 Aligned_cols=38 Identities=26% Similarity=0.347 Sum_probs=31.4
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCC
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGS 43 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~ 43 (163)
++-.++|+.||||.++|..-|.+....|=+.-.+..|.
T Consensus 35 L~e~~La~~lgVSRtpVReAL~~L~~eGlv~~~~~~G~ 72 (212)
T TIGR03338 35 LNESDIAARLGVSRGPVREAFRALEEAGLVRNEKNRGV 72 (212)
T ss_pred ecHHHHHHHhCCChHHHHHHHHHHHHCCCEEEecCCCe
Confidence 45678999999999999999999999999855443444
No 308
>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=84.21 E-value=4.4 Score=27.35 Aligned_cols=65 Identities=15% Similarity=0.110 Sum_probs=39.8
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCCCC-C-CCCCCCCcCChHHHHHHHHHH-HhCCCCCchhhhhhhh
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPG-V-IGGSKPRVATPDVEKRIEEYK-KTNPNITSWEVRDKLI 76 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg-~-~Gg~~p~~~~~~~~~~i~~~~-~~~p~~~~~e~~~~l~ 76 (163)
+++.|+|+.+|||..|+.-|- +.|-+.|. . .+|.+ .=+......+..+. -..-+++..+++.-+.
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 MNIGEAAKLTGLSAKMIRYYE----EIGLIPPPSRSDNGYR--VYNQRDIEELRFIRRARDLGFSLEEIRELLA 68 (127)
T ss_pred CCHHHHHHHHCcCHHHHHHHH----HCCCCCCCCcCCCCce--ecCHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 578899999999999988764 55888753 3 23333 23344444443222 1234677777776443
No 309
>PRK11013 DNA-binding transcriptional regulator LysR; Provisional
Probab=84.13 E-value=0.67 Score=35.89 Aligned_cols=26 Identities=35% Similarity=0.425 Sum_probs=22.8
Q ss_pred cCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
+.| +....|+.|+||+++||+.++++
T Consensus 17 ~~g-S~s~AAe~L~isqsavS~~Ik~L 42 (309)
T PRK11013 17 TAG-SLTEAARLLHTSQPTVSRELARF 42 (309)
T ss_pred HhC-cHHHHHHHHCCCcHHHHHHHHHH
Confidence 444 77889999999999999999888
No 310
>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=83.96 E-value=6.6 Score=26.41 Aligned_cols=65 Identities=15% Similarity=0.082 Sum_probs=41.9
Q ss_pred CCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCC--CCCCCCcCChHHHHHHHHHHH-hCCCCCchhhhhhh
Q psy1904 5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI--GGSKPRVATPDVEKRIEEYKK-TNPNITSWEVRDKL 75 (163)
Q Consensus 5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~--Gg~~p~~~~~~~~~~i~~~~~-~~p~~~~~e~~~~l 75 (163)
.+++.|+|+.+|||..||.-|- +.|-+.|..- +|.+ .=++.+...+.-+.. ..-++...+++.-+
T Consensus 3 ~~tI~elA~~~gvs~~tlR~Ye----~~GLL~p~~r~~~gyR--~Y~~~~l~rL~~I~~lr~~G~~L~eI~~ll 70 (120)
T TIGR02054 3 AYTISRLAEDAGVSVHVVRDYL----LRGLLHPVRRTTSGYG--IFDDASLQRLRFVRAAFEAGIGLGELARLC 70 (120)
T ss_pred CCcHHHHHHHHCcCHHHHHHHH----HCCCCCCCccCCCCCe--eCCHHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence 5789999999999999988775 5588888643 4433 334555555533332 23456666666543
No 311
>PF09048 Cro: Cro; InterPro: IPR000655 Bacteriophage lambda encodes two repressors: the Cro repressor that acts to turn off early gene transcription during the lytic cycle, and the lambda or cI repressor that is required to maintain lysogenic growth. Together the Cro and cI repressors form a helix-turn-helix (HTH) superfamily. The lambda Cro repressor binds to DNA as a highly flexible dimer. The crystal structure of the lambda Cro repressor [] reveals a HTH DNA-binding protein with an alpha/beta fold that differs from other Cro family members, possibly by an evolutionary fold change []. Most Cro proteins, such as Enterobacteria phage P22 Cro and Bacteriophage 434 Cro, have an all-alpha structure that is thought to be ancestral to lambda Cro, where the fourth and fifth helices are replaced by a beta-sheet, possibly as a result of secondary structure switching rather than by nonhomologous replacement []. This entry represents the lambda-type Cro repressor with an alpha/beta topology.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 5CRO_A 2ECS_A 2OVG_A 6CRO_A 1D1L_A 2ORC_A 1D1M_B 3ORC_A 1ORC_A 2A63_A ....
Probab=83.95 E-value=1.1 Score=26.13 Aligned_cols=21 Identities=29% Similarity=0.395 Sum_probs=17.8
Q ss_pred hhhhHHHhhcchhhHHHHHhh
Q psy1904 8 PCVISRQLRVSHGCVSKILNR 28 (163)
Q Consensus 8 ~~~ia~~~~vs~~~vs~~l~~ 28 (163)
+.+.|+.|||+++.|||-|+.
T Consensus 15 Q~kaA~~lGV~Q~AIsKAlr~ 35 (59)
T PF09048_consen 15 QAKAARALGVTQSAISKALRA 35 (59)
T ss_dssp HHHHHHHHTS-HHHHHHHHHC
T ss_pred hHHHHHHcCCcHHHHHHHHHc
Confidence 678999999999999999854
No 312
>cd04769 HTH_MerR2 Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MerR2 and related proteins. MerR2 in Bacillus cereus RC607 regulates resistance to organomercurials. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=83.89 E-value=4.4 Score=26.90 Aligned_cols=65 Identities=15% Similarity=0.091 Sum_probs=39.4
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHHHHH-hCCCCCchhhhhhh
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPNITSWEVRDKL 75 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~~~~-~~p~~~~~e~~~~l 75 (163)
++..++|+.+|||..|+.-|- +.|-+.|....+ .-+.-+......+..+.. ..-+++..++..-+
T Consensus 1 ~~ige~a~~~gvs~~tLryYe----~~GLi~p~~~~~-~yR~Y~~~d~~~l~~I~~lr~~G~sl~eI~~~l 66 (116)
T cd04769 1 MYIGELAQQTGVTIKAIRLYE----EKGLLPSPKRSG-NYRVYDAQHVECLRFIKEARQLGFTLAELKAIF 66 (116)
T ss_pred CCHHHHHHHHCcCHHHHHHHH----HCCCCCCCCCCC-CceeeCHHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence 467899999999999987764 669998854333 223334444444322211 12356666666543
No 313
>PRK09954 putative kinase; Provisional
Probab=83.89 E-value=1 Score=35.86 Aligned_cols=30 Identities=20% Similarity=0.283 Sum_probs=27.9
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCC
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSI 35 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~ 35 (163)
++..+||+.|+||.++|.+.+++..+.|-+
T Consensus 18 ~s~~~la~~l~~s~~~v~~~i~~L~~~g~i 47 (362)
T PRK09954 18 IQQNEIADILQISRSRVAAHIMDLMRKGRI 47 (362)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCCc
Confidence 899999999999999999999999887765
No 314
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=83.78 E-value=1.2 Score=32.23 Aligned_cols=27 Identities=26% Similarity=0.176 Sum_probs=24.3
Q ss_pred cCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
..|.+..|||+.||||.++|...|.+-
T Consensus 127 ~~g~s~~EIA~~LgiS~~tVk~~l~Ra 153 (188)
T PRK12546 127 ASGFSYEEAAEMCGVAVGTVKSRANRA 153 (188)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 379999999999999999999998664
No 315
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=83.54 E-value=0.69 Score=35.37 Aligned_cols=26 Identities=8% Similarity=0.059 Sum_probs=22.6
Q ss_pred cCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
+.| +...+|+.|+||+++||+.++..
T Consensus 14 ~~g-s~s~AA~~L~isQ~avSr~i~~L 39 (296)
T PRK09906 14 EEL-NFTKAAEKLHTAQPSLSQQIKDL 39 (296)
T ss_pred hhC-CHHHHHHHhCCCCcHHHHHHHHH
Confidence 444 67889999999999999999887
No 316
>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=83.53 E-value=5.5 Score=26.04 Aligned_cols=65 Identities=11% Similarity=0.120 Sum_probs=38.1
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCC-CCCCCCcCChHHHHHHHHHHHh-CCCCCchhhhhh
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI-GGSKPRVATPDVEKRIEEYKKT-NPNITSWEVRDK 74 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~-Gg~~p~~~~~~~~~~i~~~~~~-~p~~~~~e~~~~ 74 (163)
+++.|+|+.+|||.+|+.-|. +.|-+.|... +....+.=+......+..+..- .-++...++..-
T Consensus 1 ~~i~eva~~~gis~~tlR~ye----~~GLi~p~~~~~~ngyR~Y~~~~i~~l~~I~~lr~~G~sl~~i~~l 67 (108)
T cd01107 1 FTIGEFAKLSNLSIKALRYYD----KIGLLKPAYVDPDTGYRYYSAEQLERLNRIKYLRDLGFPLEEIKEI 67 (108)
T ss_pred CCHHHHHHHHCcCHHHHHHHH----HcCCCCCCcCCCCCCccccCHHHHHHHHHHHHHHHcCCCHHHHHHH
Confidence 467899999999999998875 4588888442 2122233344444444332221 124555555543
No 317
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=83.47 E-value=4.3 Score=27.98 Aligned_cols=65 Identities=22% Similarity=0.248 Sum_probs=40.7
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCC--CCCCCCCcCChHHHHHHHHHHH-hCCCCCchhhhhhhh
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV--IGGSKPRVATPDVEKRIEEYKK-TNPNITSWEVRDKLI 76 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~--~Gg~~p~~~~~~~~~~i~~~~~-~~p~~~~~e~~~~l~ 76 (163)
+++.|+|+.+|||..|+.-|- +.|-+.|.. .+|. +.=+......+..+.. ..-+++..++..-+.
T Consensus 2 ~~I~e~a~~~gvs~~tlR~Ye----~~GLl~p~~r~~~gy--R~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~ 69 (140)
T PRK09514 2 YRIGELAKLAEVTPDTLRFYE----KQGLMDPEVRTEGGY--RLYTEQDLQRLRFIRRAKQLGFTLEEIRELLS 69 (140)
T ss_pred CcHHHHHHHHCcCHHHHHHHH----HCCCCCCcccCCCCC--eeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 578899999999999998875 558888853 2333 3334444444433221 233677777776543
No 318
>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=83.47 E-value=5 Score=27.01 Aligned_cols=67 Identities=10% Similarity=0.103 Sum_probs=39.5
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHHHHH-hCCCCCchhhhhhhh
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPNITSWEVRDKLI 76 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~~~~-~~p~~~~~e~~~~l~ 76 (163)
+++.|+|+++|||..|+.-|- +.|-+.|..-....-+.=+......+..+.. ..-+++..++..-+.
T Consensus 1 m~IgevA~~~gvs~~tLRyYe----~~GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~ 68 (127)
T cd04784 1 MKIGELAKKTGCSVETIRYYE----KEGLLPAPARSANNYRLYDEEHLERLLFIRRCRSLDMSLDEIRTLLQ 68 (127)
T ss_pred CCHHHHHHHHCcCHHHHHHHH----HCCCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 578899999999999987764 6688876432112223334444443322211 122577777776543
No 319
>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=83.44 E-value=1.2 Score=25.47 Aligned_cols=38 Identities=29% Similarity=0.481 Sum_probs=30.7
Q ss_pred CCHHHHHHHHHhccCCCC--CCHHHHHHHHHHhCCCcccc
Q psy1904 105 FTSAQLEELEKSFQRSHY--PDIYTREALANKFGMTETRV 142 (163)
Q Consensus 105 ~t~~q~~~Le~~F~~~~~--p~~~~r~~la~~l~l~~~~v 142 (163)
+|+.|.+.|..+|+..-| |-.....+||..+|++...+
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~ 40 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTV 40 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHH
Confidence 578899999999887754 55567789999999987654
No 320
>COG1813 Predicted transcription factor, homolog of eukaryotic MBF1 [Transcription]
Probab=83.44 E-value=1.1 Score=31.83 Aligned_cols=31 Identities=19% Similarity=0.388 Sum_probs=26.1
Q ss_pred cCCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCC
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG 38 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg 38 (163)
+.|+|+.|+|+.++++.+.|.+| |.|.+.|.
T Consensus 90 ~~G~SqedLA~ki~ek~svI~~i-----E~g~~~P~ 120 (165)
T COG1813 90 KRGLSQEDLAAKLKEKVSVIRRI-----ERGEATPN 120 (165)
T ss_pred HcCCCHHHHHHHhcccHHHHHHH-----HhcccCcc
Confidence 57999999999999999999998 55655554
No 321
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=83.35 E-value=0.78 Score=35.46 Aligned_cols=28 Identities=18% Similarity=0.148 Sum_probs=24.8
Q ss_pred ccCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904 2 AAAGVRPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 2 ~~~g~~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
++.|-+-..+|+.|+||+++||+-++..
T Consensus 13 ~~~~~s~s~AA~~L~isq~avSr~I~~L 40 (309)
T PRK12682 13 VRRNLNLTEAAKALHTSQPGVSKAIIEL 40 (309)
T ss_pred HHccCCHHHHHHHhcCccHHHHHHHHHH
Confidence 4466788899999999999999999888
No 322
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=83.32 E-value=0.96 Score=32.73 Aligned_cols=29 Identities=14% Similarity=0.099 Sum_probs=25.4
Q ss_pred cCCCChhhhHHHhhcchhhHHHHHhhhhh
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKILNRYQE 31 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~~~ 31 (163)
-+|.+-.|||+.|+||.+||...+.+..+
T Consensus 146 AqGkTnKEIAe~L~IS~rTVkth~srImk 174 (198)
T PRK15201 146 ASGYHLSETAALLSLSEEQTKSLRRSIMR 174 (198)
T ss_pred HCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 37999999999999999999999877633
No 323
>TIGR02047 CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional regulator. This model represents the cadmium(II) and/or lead(II) responsive transcriptional activator of the proteobacterial metal efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(6-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=83.22 E-value=5.8 Score=26.82 Aligned_cols=65 Identities=15% Similarity=0.147 Sum_probs=39.7
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCC--CCCCCCCcCChHHHHHHHHHHH-hCCCCCchhhhhhhh
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV--IGGSKPRVATPDVEKRIEEYKK-TNPNITSWEVRDKLI 76 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~--~Gg~~p~~~~~~~~~~i~~~~~-~~p~~~~~e~~~~l~ 76 (163)
+++.++|+.+|||..|+.-|- +.|-+.|.. .+|.+ .=+......+..+.. ..-+++..++..-+.
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 MKIGELAQKTGVSVETIRFYE----KQGLLPPPARTDNNYR--VYTVGHVERLAFIRNCRTLDMSLAEIRQLLR 68 (127)
T ss_pred CcHHHHHHHHCcCHHHHHHHH----HCCCCCCCCcCCCCCC--cCCHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 578899999999999988774 568887643 23333 233444433432221 233677777766543
No 324
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=83.22 E-value=1.2 Score=33.39 Aligned_cols=60 Identities=20% Similarity=0.222 Sum_probs=37.1
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhhhhc-cCCCCCCCCCCCCCcCChHHHHHHHHHHHhCCCC
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRYQET-GSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPNI 66 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~t-G~~~Pg~~Gg~~p~~~~~~~~~~i~~~~~~~p~~ 66 (163)
.|++-.|||+.+|+|.++|...|.+-++. ...-+. |+..+. ...+..-.+....+++|..
T Consensus 131 eg~S~~EIAe~LgiS~~tVksrL~Rark~Lr~~l~~--~~~~~~-~~~~~~~~~~~~~~~~~~~ 191 (228)
T PRK06704 131 FQYSIADIAKVCSVSEGAVKASLFRSRNRLKTVSEE--GIEIVE-FTDDMEVVVTSIREERPEL 191 (228)
T ss_pred hCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHh--cCCCCC-ccccHHHHHHHHHhcCHHH
Confidence 68999999999999999999987554221 111111 111111 1344555666777788743
No 325
>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=83.21 E-value=1.1 Score=35.00 Aligned_cols=26 Identities=27% Similarity=0.284 Sum_probs=23.9
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
.|++..|||+.||||.++|...|.+-
T Consensus 157 ~g~s~~EIA~~lgis~~tV~~~l~Ra 182 (324)
T TIGR02960 157 LGWRAAETAELLGTSTASVNSALQRA 182 (324)
T ss_pred hCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 68999999999999999999998665
No 326
>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=83.14 E-value=5.7 Score=27.08 Aligned_cols=65 Identities=12% Similarity=0.094 Sum_probs=39.9
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCC--CCCCCCcCChHHHHHHHHHHH-hCCCCCchhhhhhhh
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI--GGSKPRVATPDVEKRIEEYKK-TNPNITSWEVRDKLI 76 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~--Gg~~p~~~~~~~~~~i~~~~~-~~p~~~~~e~~~~l~ 76 (163)
|++.|+|+++|||..|+.-|- +.|-+.|..- +|. +.=+......+.-+.. ..-+++..++..-+.
T Consensus 1 m~Ige~a~~~gvs~~tLRyYE----~~GLl~p~~r~~~gy--R~Y~~~~v~~l~~I~~lr~~GfsL~eI~~ll~ 68 (131)
T cd04786 1 MKIGELAKRSGMAASRIRFYE----AEGLLSSVERSANGY--RDYPPETVWVLEIISSAQQAGFSLDEIRQLLP 68 (131)
T ss_pred CCHHHHHHHHCcCHHHHHHHH----HCCCCCCCCcCCCCC--eecCHHHHHHHHHHHHHHHcCCCHHHHHHHHh
Confidence 578899999999999987764 5688877432 333 2223444444432222 223577777776553
No 327
>TIGR03339 phn_lysR aminoethylphosphonate catabolism associated LysR family transcriptional regulator. This group of sequences represents a number of related clades with numerous examples of members adjacent to operons for the degradation of 2-aminoethylphosphonate (AEP) in Pseudomonas, Ralstonia, Bordetella and Burkholderia species. These are transcriptional regulators of the LysR family which contain a helix-turn-helix (HTH) domain (pfam00126) and a periplasmic substrate-binding protein-like domain (pfam03466).
Probab=83.09 E-value=0.85 Score=34.34 Aligned_cols=23 Identities=13% Similarity=0.148 Sum_probs=21.1
Q ss_pred ChhhhHHHhhcchhhHHHHHhhh
Q psy1904 7 RPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 7 ~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
+-..+|+.|+||+++||+.+++.
T Consensus 13 s~~~AA~~L~isqsavS~~i~~L 35 (279)
T TIGR03339 13 SFTRAAERLGLSQPTVTDQVRKL 35 (279)
T ss_pred CHHHHHHHhcCCchHHHHHHHHH
Confidence 67789999999999999999887
No 328
>PRK10227 DNA-binding transcriptional regulator CueR; Provisional
Probab=83.02 E-value=7 Score=26.80 Aligned_cols=65 Identities=11% Similarity=0.132 Sum_probs=41.4
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCC--CCCCCCcCChHHHHHHHHHHH-hCCCCCchhhhhhhh
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI--GGSKPRVATPDVEKRIEEYKK-TNPNITSWEVRDKLI 76 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~--Gg~~p~~~~~~~~~~i~~~~~-~~p~~~~~e~~~~l~ 76 (163)
|++.|+|+++|||..|+.-| .+.|-+.|..- +|. +.=+......+..+.. ..-++...++.+-+.
T Consensus 1 m~Ige~a~~~gvs~~tlRyY----E~~GLl~p~~r~~~gy--R~Y~~~~l~~l~~I~~lr~~G~sl~eI~~~l~ 68 (135)
T PRK10227 1 MNISDVAKITGLTSKAIRFY----EEKGLVTPPMRSENGY--RTYTQQHLNELTLLRQARQVGFNLEESGELVN 68 (135)
T ss_pred CCHHHHHHHHCcCHHHHHHH----HHCCCCCCcccCCCCc--ccCCHHHHHHHHHHHHHHHCCCCHHHHHHHHH
Confidence 57889999999999998776 46688877532 333 3334455555543332 233677777766543
No 329
>PF06322 Phage_NinH: Phage NinH protein; InterPro: IPR010454 This entry is represented by Bacteriophage 933W, NinH. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=82.97 E-value=1 Score=26.48 Aligned_cols=19 Identities=21% Similarity=0.281 Sum_probs=17.8
Q ss_pred hhhhHHHhhcchhhHHHHH
Q psy1904 8 PCVISRQLRVSHGCVSKIL 26 (163)
Q Consensus 8 ~~~ia~~~~vs~~~vs~~l 26 (163)
..|+|++|+++.+||.|++
T Consensus 19 qtEvaR~l~c~R~TVrKY~ 37 (64)
T PF06322_consen 19 QTEVARRLGCNRATVRKYS 37 (64)
T ss_pred HHHHHHHhcccHHHHHHHh
Confidence 5799999999999999998
No 330
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=82.96 E-value=0.64 Score=35.42 Aligned_cols=36 Identities=22% Similarity=0.256 Sum_probs=31.7
Q ss_pred ccCC-CChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904 2 AAAG-VRPCVISRQLRVSHGCVSKILNRYQETGSIRP 37 (163)
Q Consensus 2 ~~~g-~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P 37 (163)
.+.| ++..|+|+.|+||..||.|=|....+.|-+.=
T Consensus 15 ~~~g~v~v~eLa~~~~VS~~TIRRDL~~Le~~g~l~R 51 (253)
T COG1349 15 KEKGKVSVEELAELFGVSEMTIRRDLNELEEQGLLLR 51 (253)
T ss_pred HHcCcEEHHHHHHHhCCCHHHHHHhHHHHHHCCcEEE
Confidence 3466 88999999999999999999999999998853
No 331
>PRK08154 anaerobic benzoate catabolism transcriptional regulator; Reviewed
Probab=82.93 E-value=1.2 Score=34.82 Aligned_cols=24 Identities=17% Similarity=0.245 Sum_probs=22.4
Q ss_pred cCCCChhhhHHHhhcchhhHHHHH
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKIL 26 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l 26 (163)
+.|+++.++|+.+|||.++|++|.
T Consensus 39 ~~gltq~~lA~~~gvs~~~i~~~E 62 (309)
T PRK08154 39 RRGMSRKVLAQASGVSERYLAQLE 62 (309)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHH
Confidence 479999999999999999999995
No 332
>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=82.84 E-value=5.9 Score=26.69 Aligned_cols=65 Identities=15% Similarity=0.173 Sum_probs=39.6
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCC--CCCCCCCcCChHHHHHHHHHHH-hCCCCCchhhhhhhh
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV--IGGSKPRVATPDVEKRIEEYKK-TNPNITSWEVRDKLI 76 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~--~Gg~~p~~~~~~~~~~i~~~~~-~~p~~~~~e~~~~l~ 76 (163)
+++.++|+.+|||..|+.-|- +.|-+.|.. .+|. +.=+......+..+.. ..-+++..++..-+.
T Consensus 1 ~~I~e~a~~~gvs~~tlR~Ye----~~Gll~~~~r~~~g~--R~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~ 68 (126)
T cd04785 1 LSIGELARRTGVNVETIRYYE----SIGLLPEPARTAGGY--RLYGAAHVERLRFIRRARDLGFSLEEIRALLA 68 (126)
T ss_pred CCHHHHHHHHCcCHHHHHHHH----HCCCCCCCCcCCCCc--cccCHHHHHHHHHHHHHHHCCCCHHHHHHHHh
Confidence 468899999999999988764 568887643 2333 3334444444433222 233567766665443
No 333
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=82.76 E-value=0.92 Score=33.34 Aligned_cols=27 Identities=26% Similarity=0.214 Sum_probs=24.5
Q ss_pred cCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
-+|.+-.|||+.|+||..||...+++.
T Consensus 150 a~G~snkeIA~~L~iS~~TVk~h~~~I 176 (207)
T PRK15411 150 MAGQGTIQISDQMNIKAKTVSSHKGNI 176 (207)
T ss_pred HcCCCHHHHHHHcCCCHHHHHHHHHHH
Confidence 479999999999999999999988765
No 334
>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=82.74 E-value=1.6 Score=33.01 Aligned_cols=36 Identities=14% Similarity=0.377 Sum_probs=32.5
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCC
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIG 41 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~G 41 (163)
++..+||+++|||.+.|..-++++.+.|-+...+.|
T Consensus 199 lse~eLAerlGVSRs~ireAlrkLE~aGvIe~r~LG 234 (251)
T TIGR02787 199 LVASKIADRVGITRSVIVNALRKLESAGVIESRSLG 234 (251)
T ss_pred ccHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeccCC
Confidence 899999999999999999999999999999766533
No 335
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=82.40 E-value=1.4 Score=31.13 Aligned_cols=32 Identities=22% Similarity=0.143 Sum_probs=29.5
Q ss_pred CCChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904 5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIR 36 (163)
Q Consensus 5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~ 36 (163)
-++..|||+.|||+...|.++|..+.+-|=+.
T Consensus 28 ~~tdEeLa~~Lgi~~~~VRk~L~~L~e~~Lv~ 59 (158)
T TIGR00373 28 EFTDEEISLELGIKLNEVRKALYALYDAGLAD 59 (158)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCce
Confidence 38899999999999999999999999999884
No 336
>PRK11233 nitrogen assimilation transcriptional regulator; Provisional
Probab=82.27 E-value=0.86 Score=35.20 Aligned_cols=23 Identities=9% Similarity=0.125 Sum_probs=20.8
Q ss_pred ChhhhHHHhhcchhhHHHHHhhh
Q psy1904 7 RPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 7 ~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
+-..+|+.|+||+++||+-+++.
T Consensus 17 S~s~AA~~L~isQ~avS~~I~~L 39 (305)
T PRK11233 17 SLTQAAEVLHIAQPALSQQVATL 39 (305)
T ss_pred CHHHHHHHhCCCchHHHHHHHHH
Confidence 67889999999999999999776
No 337
>TIGR02684 dnstrm_HI1420 probable addiction module antidote protein. gene pairs, when found on the bacterial chromosome, are located often with prophage regions, but also both in integrated plasmid regions and in housekeeping gene regions. Analysis suggests that the gene pair may serve as an addiction module.
Probab=81.96 E-value=1.2 Score=28.44 Aligned_cols=21 Identities=24% Similarity=0.381 Sum_probs=18.7
Q ss_pred CCCChhhhHHHhhcchhhHHHHH
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKIL 26 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l 26 (163)
.|++ ++|++.|||.+++++|.
T Consensus 44 ~glS--qLAe~~GIs~stLs~iE 64 (89)
T TIGR02684 44 RGMT--QLARKTGLSRESLYKAL 64 (89)
T ss_pred CChH--HHHHHHCCCHHHHHHHH
Confidence 4776 59999999999999997
No 338
>COG3655 Predicted transcriptional regulator [Transcription]
Probab=81.78 E-value=0.68 Score=28.34 Aligned_cols=26 Identities=15% Similarity=0.224 Sum_probs=23.4
Q ss_pred CccCCCChhhhHHHhhcchhhHHHHH
Q psy1904 1 MAAAGVRPCVISRQLRVSHGCVSKIL 26 (163)
Q Consensus 1 ~~~~g~~~~~ia~~~~vs~~~vs~~l 26 (163)
|++.+++--|+|++.|||.++++++.
T Consensus 11 l~~r~~~~~eLa~~igis~~~ls~l~ 36 (73)
T COG3655 11 LADRKISLKELAEAIGISEANLSKLK 36 (73)
T ss_pred HHHHhhhHHHHHHHHcccHHHHHHHH
Confidence 46778999999999999999999984
No 339
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=81.60 E-value=0.94 Score=34.87 Aligned_cols=27 Identities=11% Similarity=0.043 Sum_probs=23.2
Q ss_pred cCCCChhhhHHHhhcchhhHHHHHhhhh
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKILNRYQ 30 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~~ 30 (163)
+.| +....|++|+||+++||+-++..+
T Consensus 14 ~~g-S~s~AA~~L~itQpavS~~i~~LE 40 (305)
T PRK11151 14 EHR-HFRRAADSCHVSQPTLSGQIRKLE 40 (305)
T ss_pred HhC-CHHHHHHHhCCCchHHHHHHHHHH
Confidence 445 778899999999999999998773
No 340
>PF05732 RepL: Firmicute plasmid replication protein (RepL); InterPro: IPR008813 This entry consists of proteins thought to be involved in plasmid replication. ; GO: 0006260 DNA replication, 0006276 plasmid maintenance
Probab=81.56 E-value=1.2 Score=31.68 Aligned_cols=34 Identities=21% Similarity=0.236 Sum_probs=29.8
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCC
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV 39 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~ 39 (163)
++..+||..+++|..||++.++.+.+.+-+.-..
T Consensus 76 ~t~~~ia~~l~iS~~Tv~r~ik~L~e~~iI~k~~ 109 (165)
T PF05732_consen 76 ATQKEIAEKLGISKPTVSRAIKELEEKNIIKKIR 109 (165)
T ss_pred eeHHHHHHHhCCCHHHHHHHHHHHHhCCcEEEcc
Confidence 4678999999999999999999999998886553
No 341
>cd04776 HTH_GnyR Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR. Putative helix-turn-helix (HTH) regulatory protein, GnyR, and other related proteins. GnyR belongs to the gnyRDBHAL cluster, which is involved in acyclic isoprenoid degradation in Pseudomonas aeruginosa. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=81.32 E-value=6.5 Score=26.25 Aligned_cols=65 Identities=17% Similarity=0.200 Sum_probs=42.1
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHHHHH-hCCCCCchhhhhhhh
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPNITSWEVRDKLI 76 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~~~~-~~p~~~~~e~~~~l~ 76 (163)
+++.|+|+.+|||..|+.-|- +.|-+.|...+|. +.=++.....+..... ..-+++..++..-+.
T Consensus 1 ~~Igeva~~~gvs~~tlRyYe----~~GLl~p~r~~gy--R~Y~~~~l~~l~~I~~lr~~G~~L~~I~~~l~ 66 (118)
T cd04776 1 YTISELAREFDVTPRTLRFYE----DKGLLSPERRGQT--RVYSRRDRARLKLILRGKRLGFSLEEIRELLD 66 (118)
T ss_pred CCHHHHHHHHCcCHHHHHHHH----HCCCCCCcCCCCc--cccCHHHHHHHHHHHHHHHCCCCHHHHHHHHH
Confidence 467899999999999987764 5699998766543 3334445544432221 234677777666544
No 342
>PRK13832 plasmid partitioning protein; Provisional
Probab=81.27 E-value=1.1 Score=37.45 Aligned_cols=28 Identities=18% Similarity=0.110 Sum_probs=24.1
Q ss_pred CccCCCChhhhHHHhhcchhhHHHHHhh
Q psy1904 1 MAAAGVRPCVISRQLRVSHGCVSKILNR 28 (163)
Q Consensus 1 ~~~~g~~~~~ia~~~~vs~~~vs~~l~~ 28 (163)
|...|+++.+||++||+|.++|++++..
T Consensus 114 Lie~G~T~EeIA~~lG~S~~~V~rlllL 141 (520)
T PRK13832 114 LVALGWTEEAIAVALALPVRQIRKLRLL 141 (520)
T ss_pred HHhcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 3468999999999999999999996643
No 343
>PF12964 DUF3853: Protein of unknown function (DUF3853); InterPro: IPR024363 This entry represents a family of uncharacterised proteins that were found by clustering human gut metagenomic sequences [].
Probab=81.14 E-value=1 Score=29.03 Aligned_cols=28 Identities=18% Similarity=0.306 Sum_probs=21.6
Q ss_pred hhhhHHHhhcchhhHHHHHhhhhhccCCCCCC
Q psy1904 8 PCVISRQLRVSHGCVSKILNRYQETGSIRPGV 39 (163)
Q Consensus 8 ~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~ 39 (163)
...||+.||+|.+||.||- ..|-+.+..
T Consensus 48 ~~GlAklfgcSv~Ta~RiK----~sG~id~AI 75 (96)
T PF12964_consen 48 LKGLAKLFGCSVPTANRIK----KSGKIDPAI 75 (96)
T ss_pred HHHHHHHhCCCchhHHHHH----hcCCccHHH
Confidence 3579999999999999985 446665543
No 344
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=80.87 E-value=2 Score=32.01 Aligned_cols=43 Identities=19% Similarity=0.262 Sum_probs=33.4
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC--CCCCCCCCC
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP--GVIGGSKPR 46 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P--g~~Gg~~p~ 46 (163)
.+++.-|||++||||.-.|.+=|..+...|-+.- ...|-.+|.
T Consensus 24 g~~sa~elA~~Lgis~~avR~HL~~Le~~Glv~~~~~~~g~GRP~ 68 (218)
T COG2345 24 GPVSADELAEELGISPMAVRRHLDDLEAEGLVEVERQQGGRGRPA 68 (218)
T ss_pred CCccHHHHHHHhCCCHHHHHHHHHHHHhCcceeeeeccCCCCCCc
Confidence 3499999999999999999999999998885522 223444555
No 345
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=80.86 E-value=1.1 Score=34.43 Aligned_cols=26 Identities=23% Similarity=0.250 Sum_probs=22.7
Q ss_pred cCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
+.| +-..+|+.|+||+++||+-++.+
T Consensus 18 ~~g-s~s~AA~~L~isQ~avS~~i~~L 43 (302)
T PRK09791 18 RQG-SIRGASRMLNMSQPALTKSIQEL 43 (302)
T ss_pred HcC-CHHHHHHHhCCChHHHHHHHHHH
Confidence 445 67789999999999999999888
No 346
>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=80.78 E-value=6.5 Score=26.75 Aligned_cols=67 Identities=12% Similarity=0.076 Sum_probs=40.2
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHHHHH-hCCCCCchhhhhhhh
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPNITSWEVRDKLI 76 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~~~~-~~p~~~~~e~~~~l~ 76 (163)
|++.|+|+.+|||..|+.-| .+.|=+.|.......-+.=+......+..+.. ..-+++..++..-+.
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 57889999999999998544 56698988654211123333444444422211 234677777776543
No 347
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=80.69 E-value=1.1 Score=34.83 Aligned_cols=28 Identities=18% Similarity=0.105 Sum_probs=24.6
Q ss_pred ccCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904 2 AAAGVRPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 2 ~~~g~~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
++.|-+-...|+.|+||+++||+.++.+
T Consensus 13 ~~~g~S~s~AA~~L~isQpavS~~ik~L 40 (313)
T PRK12684 13 VRQNFNLTEAAKALYTSQPGVSKAIIEL 40 (313)
T ss_pred HHcCCCHHHHHHHhcCCChHHHHHHHHH
Confidence 3456688899999999999999999888
No 348
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=80.52 E-value=1.7 Score=33.68 Aligned_cols=26 Identities=23% Similarity=0.158 Sum_probs=24.1
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
.|++..|||+.||+|.++|...|.+-
T Consensus 130 ~g~s~~EIA~~lg~s~~tVk~~l~RA 155 (293)
T PRK09636 130 FGVPFDEIASTLGRSPAACRQLASRA 155 (293)
T ss_pred hCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 68999999999999999999998765
No 349
>PF02042 RWP-RK: RWP-RK domain; InterPro: IPR003035 This domain is named RWP-RK after a conserved motif at the C terminus of the domain. The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development [].
Probab=80.39 E-value=2.2 Score=24.29 Aligned_cols=25 Identities=16% Similarity=0.104 Sum_probs=20.7
Q ss_pred CCChhhhHHHhhcchhhHHHHHhhh
Q psy1904 5 GVRPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 5 g~~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
.++..|+|+.||||..++.++-.++
T Consensus 15 hlp~~eAA~~Lgv~~T~LKr~CR~~ 39 (52)
T PF02042_consen 15 HLPIKEAAKELGVSVTTLKRRCRRL 39 (52)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHc
Confidence 4788899999999999888876543
No 350
>PF05269 Phage_CII: Bacteriophage CII protein; InterPro: IPR007933 The CII protein is a transcription activator, conserved in bacteriophage lambda and related phages, that plays a key role in the decision between lytic or lysogenic phage development. CII is regulated at multiple levels including transcription, translation initiation, mRNA stability, and proteolysis []. Conditions that stabilise cII favour lysogenic development. The lambda CII protein activates three specific promoters, binding to direct repeat sequences rather than the more usual inverted repeats. Structurally, CII is a homotetramer where each monomer is composed of four alpha helices and a disordered C terminus [, ]. The alpha helical region is responsible for DNA binding and multimerisation. The homotetramer has an unusual spatial arrangement that allows recognition of the direct repeat sequences.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1ZS4_C 1ZPQ_C 1XWR_A.
Probab=80.31 E-value=1.7 Score=27.82 Aligned_cols=21 Identities=14% Similarity=0.202 Sum_probs=18.3
Q ss_pred ChhhhHHHhhcchhhHHHHHh
Q psy1904 7 RPCVISRQLRVSHGCVSKILN 27 (163)
Q Consensus 7 ~~~~ia~~~~vs~~~vs~~l~ 27 (163)
.+..+|+..||+.|+||||..
T Consensus 25 gq~~vA~~~Gv~eStISR~k~ 45 (91)
T PF05269_consen 25 GQKKVAEAMGVDESTISRWKN 45 (91)
T ss_dssp HHHHHHHHHTSSTTTHHHHHH
T ss_pred hhHHHHHHhCCCHHHHHHHHh
Confidence 467899999999999999963
No 351
>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=80.25 E-value=1.8 Score=33.41 Aligned_cols=27 Identities=11% Similarity=0.027 Sum_probs=24.5
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhhh
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRYQ 30 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~ 30 (163)
.|++..|||+.||+|.++|...+.+-+
T Consensus 123 ~g~s~~EIA~~lg~s~~tVr~~l~RAr 149 (281)
T TIGR02957 123 FDYPYEEIASIVGKSEANCRQLVSRAR 149 (281)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 689999999999999999999987763
No 352
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=80.21 E-value=1.7 Score=32.18 Aligned_cols=29 Identities=14% Similarity=0.240 Sum_probs=26.2
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCC
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSI 35 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~ 35 (163)
++..|||..+|++.-+|+++|+.+++.| +
T Consensus 174 ~t~~~iA~~lG~tretvsR~l~~L~~~g-l 202 (236)
T PRK09392 174 YEKRVLASYLGMTPENLSRAFAALASHG-V 202 (236)
T ss_pred CCHHHHHHHhCCChhHHHHHHHHHHhCC-e
Confidence 3457899999999999999999999999 5
No 353
>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=80.12 E-value=2.9 Score=27.26 Aligned_cols=65 Identities=11% Similarity=0.131 Sum_probs=39.7
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHHHHH-hCCCCCchhhhhhhh
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPNITSWEVRDKLI 76 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~~~~-~~p~~~~~e~~~~l~ 76 (163)
+++.++|+++|||..|+.-+ .+.|=+.|...+|.+-. +......+.-+.. ..=+++..++.+-+.
T Consensus 1 m~Ige~a~~~gvs~~tlRyY----e~~GLl~p~~~~g~r~Y--~~~~~~~l~~I~~lr~~G~sL~eI~~~l~ 66 (107)
T cd04777 1 MKIGKFAKKNNITIDTVRHY----IDLGLLIPEKKGGQYFF--DEKCQDDLEFILELKGLGFSLIEIQKIFS 66 (107)
T ss_pred CCHHHHHHHHCcCHHHHHHH----HHCCCcCCccCCCcccc--CHHHHHHHHHHHHHHHCCCCHHHHHHHHH
Confidence 57889999999999987665 56798888654444322 2233333322211 122677777776543
No 354
>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional
Probab=80.10 E-value=6.3 Score=27.75 Aligned_cols=65 Identities=15% Similarity=0.108 Sum_probs=41.7
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCC-CCCCCCcCChHHHHHHHHHHH-hCCCCCchhhhhhhh
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI-GGSKPRVATPDVEKRIEEYKK-TNPNITSWEVRDKLI 76 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~-Gg~~p~~~~~~~~~~i~~~~~-~~p~~~~~e~~~~l~ 76 (163)
+++.|+|+++|||..|+.-|- +.|-+.|... +|. +.=+......+.-+.. ..-+++..+++.-+.
T Consensus 12 ~~IgevAk~~gvs~~TlRyYE----~~GLi~~~r~~~g~--R~Y~~~~i~~L~~I~~lr~lG~sL~eIk~ll~ 78 (154)
T PRK15002 12 LTPGEVAKRSGVAVSALHFYE----SKGLITSIRNSGNQ--RRYKRDVLRYVAIIKIAQRIGIPLATIGEAFG 78 (154)
T ss_pred ccHHHHHHHHCcCHHHHHHHH----HCCCCCCccCCCCC--EEECHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 788999999999999987764 6698888543 333 3334444544433221 233577777766544
No 355
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=80.03 E-value=1.9 Score=31.35 Aligned_cols=26 Identities=19% Similarity=0.132 Sum_probs=23.9
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
.|.+-.+||+.|+||.+||...+.+.
T Consensus 164 ~G~s~~eIA~~l~iS~~TV~~h~~~i 189 (216)
T PRK10840 164 EGFLVTEIAKKLNRSIKTISSQKKSA 189 (216)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 79999999999999999999988665
No 356
>cd04790 HTH_Cfa-like_unk Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulator; conserved, Cfa-like, unknown proteins (~172 a.a.). The N-terminal domain of these proteins appears to be related to the HTH domain of Cfa, a cyclopropane fatty acid synthase. These Cfa-like proteins have a unique C-terminal domain with conserved histidines (motif HXXFX7HXXF). Based on sequence similarity of the N-terminal domains, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domain
Probab=80.02 E-value=7.7 Score=27.75 Aligned_cols=64 Identities=14% Similarity=0.173 Sum_probs=38.1
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCC--CCCCCCCcCChHHHHHHHHHHH-hCCCCCchhhhhhh
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV--IGGSKPRVATPDVEKRIEEYKK-TNPNITSWEVRDKL 75 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~--~Gg~~p~~~~~~~~~~i~~~~~-~~p~~~~~e~~~~l 75 (163)
+++.|+|+.+|||..|+.-|- +.|-+.|.. .+|.+- =+......+..+.. ..-++...++..-+
T Consensus 2 ~~I~evA~~~gvs~~tLRyYe----~~GLl~p~~r~~~gyR~--Y~~~dl~rL~~I~~lr~~G~sL~eI~~ll 68 (172)
T cd04790 2 LTISQLARQFGLSRSTLLYYE----RIGLLSPSARSESNYRL--YGERDLERLEQICAYRSAGVSLEDIRSLL 68 (172)
T ss_pred CCHHHHHHHHCcCHHHHHHHH----HCCCCCCCccCCCCCcc--CCHHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence 478899999999999988875 569888853 233332 23333333322221 12355666655544
No 357
>COG0789 SoxR Predicted transcriptional regulators [Transcription]
Probab=79.89 E-value=7.8 Score=25.64 Aligned_cols=67 Identities=15% Similarity=0.095 Sum_probs=41.3
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHHHHHh-CCCCCchhhhhhhh
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKT-NPNITSWEVRDKLI 76 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~~~~~-~p~~~~~e~~~~l~ 76 (163)
+++.++|+.+|||..|+.-| .+.|-+.|.......-+.=+..+...+..+..- .-+++..++.+-+.
T Consensus 1 ~~I~eva~~~gvs~~tLRyY----E~~GLl~p~~~~~~gyR~Ys~~dl~~l~~I~~~r~~G~~L~~I~~~l~ 68 (124)
T COG0789 1 YTIGEVAKLTGVSVRTLRFY----ERKGLLSPERRDEGGYRYYTPEDLELLQIIKTLRELGFSLAEIKELLD 68 (124)
T ss_pred CcHHHHHHHhCCCHHHHHHH----HHcCCCCCcccCCCCceecCHHHHHHHHHHHHHHHcCCCHHHHHHHHh
Confidence 46789999999999987766 567999887543222233344444444333222 33667766666554
No 358
>PRK13749 transcriptional regulator MerD; Provisional
Probab=79.74 E-value=14 Score=24.89 Aligned_cols=66 Identities=17% Similarity=0.081 Sum_probs=43.4
Q ss_pred CCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCC--CCCCCCcCChHHHHHHHHHHH-hCCCCCchhhhhhhh
Q psy1904 5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI--GGSKPRVATPDVEKRIEEYKK-TNPNITSWEVRDKLI 76 (163)
Q Consensus 5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~--Gg~~p~~~~~~~~~~i~~~~~-~~p~~~~~e~~~~l~ 76 (163)
.+++.|+|+.+|||..||.-+- +.|=+.|-.- +|.+ .=+......+.-+.. ..-+++..+++.-+.
T Consensus 3 ~~tIgelA~~~gvS~~tiR~YE----~~GLl~p~~r~~~gyR--~Y~~~~l~rL~~I~~~r~~G~sL~eI~~ll~ 71 (121)
T PRK13749 3 AYTVSRLALDAGVSVHIVRDYL----LRGLLRPVACTTGGYG--LFDDAALQRLCFVRAAFEAGIGLDALARLCR 71 (121)
T ss_pred CCcHHHHHHHHCCCHHHHHHHH----HCCCCCCCCcCCCCCc--cCCHHHHHHHHHHHHHHHcCCCHHHHHHHHh
Confidence 4789999999999999987764 5588877533 4433 335555555544433 344677777766554
No 359
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=79.62 E-value=1.9 Score=32.01 Aligned_cols=32 Identities=9% Similarity=0.014 Sum_probs=29.5
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhhhhccCC
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSI 35 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~ 35 (163)
.|++-.+||+.|++|..||.+.+......|-+
T Consensus 177 ~g~s~~eIA~~l~iS~~Tv~~~~~~~~~~~~~ 208 (239)
T PRK10430 177 YEFSTDELANAVNISRVSCRKYLIWLVNCHIL 208 (239)
T ss_pred CCcCHHHHHHHhCchHHHHHHHHHHHHhCCEE
Confidence 78999999999999999999999998777776
No 360
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=79.11 E-value=2.2 Score=31.78 Aligned_cols=27 Identities=15% Similarity=0.247 Sum_probs=24.4
Q ss_pred cCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
-.|.+-.|||+.|+||.+||...+.+.
T Consensus 156 a~G~SnkEIA~~L~IS~~TVk~hvs~I 182 (217)
T PRK13719 156 SFGFSHEYIAQLLNITVGSSKNKISEI 182 (217)
T ss_pred HCCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 369999999999999999999988776
No 361
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=79.11 E-value=5.1 Score=29.51 Aligned_cols=37 Identities=16% Similarity=0.089 Sum_probs=30.8
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCC
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGG 42 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg 42 (163)
++..+||+.||||.++|..-|.+....|=+.-.+..|
T Consensus 35 L~e~~La~~lgVSRtpVREAL~~L~~eGLV~~~~~~g 71 (221)
T PRK11414 35 LITKNLAEQLGMSITPVREALLRLVSVNALSVAPAQA 71 (221)
T ss_pred cCHHHHHHHHCCCchhHHHHHHHHHHCCCEEecCCCc
Confidence 5678999999999999999999999999885443333
No 362
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=78.85 E-value=1.2 Score=32.35 Aligned_cols=32 Identities=6% Similarity=-0.120 Sum_probs=26.3
Q ss_pred CC-CChhhhHHHhhcchhhHHHHHhhhhhccCC
Q psy1904 4 AG-VRPCVISRQLRVSHGCVSKILNRYQETGSI 35 (163)
Q Consensus 4 ~g-~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~ 35 (163)
.| ++..|+|+.|+||..||.|=|..+.+.|.+
T Consensus 19 ~~~~~~~~La~~~~vS~~TiRRDl~~L~~~g~~ 51 (185)
T PRK04424 19 NPFITDEELAEKFGVSIQTIRLDRMELGIPELR 51 (185)
T ss_pred CCCEEHHHHHHHHCcCHHHHHHHHHHHhcchHH
Confidence 44 778999999999999999999887555443
No 363
>TIGR03418 chol_sulf_TF putative choline sulfate-utilization transcription factor. Members of this protein family are transcription factors of the LysR family. Their genes typically are divergently transcribed from choline-sulfatase genes. That enzyme makes choline, a precursor to the osmoprotectant glycine-betaine, available by hydrolysis of choline sulfate.
Probab=78.82 E-value=1.4 Score=33.61 Aligned_cols=23 Identities=22% Similarity=0.268 Sum_probs=20.9
Q ss_pred ChhhhHHHhhcchhhHHHHHhhh
Q psy1904 7 RPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 7 ~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
+-..+|+.|+||+++||+-++..
T Consensus 17 s~s~AA~~L~itqpavS~~Ik~L 39 (291)
T TIGR03418 17 SFTAAARELGSTQPAVSQQVKRL 39 (291)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHH
Confidence 66789999999999999999877
No 364
>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=78.77 E-value=7.6 Score=26.90 Aligned_cols=66 Identities=17% Similarity=0.150 Sum_probs=40.5
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHHHHHh-CCCCCchhhhhhhh
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKT-NPNITSWEVRDKLI 76 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~~~~~-~p~~~~~e~~~~l~ 76 (163)
+++.|+|+.+|||..|+.-|- +.|-+.|....+.. +.=+......+..+..- .-+++..++..-+.
T Consensus 2 ~~IgevA~~~Gvs~~tLRyYE----~~GLl~~~r~~~g~-R~Y~~~di~~l~~I~~lr~~G~sL~eI~~~l~ 68 (142)
T TIGR01950 2 LTVGELAKRSGVAVSALHFYE----SKGLITSIRNSGNQ-RRYKRDVLRRVAVIKAAQRVGIPLATIGEALA 68 (142)
T ss_pred CCHHHHHHHHCcCHHHHHHHH----HCCCCCCccCCCCC-EEECHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 578999999999999987765 55888885433322 33334444444332221 22577777666543
No 365
>PRK09483 response regulator; Provisional
Probab=78.68 E-value=2.2 Score=30.54 Aligned_cols=27 Identities=30% Similarity=0.273 Sum_probs=24.4
Q ss_pred cCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
..|.+-.+||+.|+||..||...+++.
T Consensus 161 ~~G~~~~~Ia~~l~is~~TV~~~~~~i 187 (217)
T PRK09483 161 TKGQKVNEISEQLNLSPKTVNSYRYRM 187 (217)
T ss_pred HCCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 368999999999999999999998776
No 366
>PRK09775 putative DNA-binding transcriptional regulator; Provisional
Probab=78.35 E-value=1.8 Score=35.85 Aligned_cols=28 Identities=18% Similarity=0.301 Sum_probs=24.0
Q ss_pred ccCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904 2 AAAGVRPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 2 ~~~g~~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
.+.-.+..|||.+|+||+++||+-|...
T Consensus 10 ~~g~~~~~eL~~~l~~sq~~~s~~L~~L 37 (442)
T PRK09775 10 LQGPLSAAELAARLGVSQATLSRLLAAL 37 (442)
T ss_pred hcCCCCHHHHHHHhCCCHHHHHHHHHHh
Confidence 4445899999999999999999999654
No 367
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=78.30 E-value=2.4 Score=33.29 Aligned_cols=31 Identities=16% Similarity=0.129 Sum_probs=28.1
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhhhhccC
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGS 34 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~ 34 (163)
..++..+||+.|+||.++|.+-++...+.|-
T Consensus 17 ~~~s~~~LA~~lgvsr~tV~~~l~~L~~~G~ 47 (319)
T PRK11886 17 DFHSGEQLGEELGISRAAIWKHIQTLEEWGL 47 (319)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCC
Confidence 3478889999999999999999999998887
No 368
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=78.15 E-value=1.5 Score=34.04 Aligned_cols=28 Identities=18% Similarity=0.167 Sum_probs=24.5
Q ss_pred ccCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904 2 AAAGVRPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 2 ~~~g~~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
++.|-+-..+|++|+||+++||+-+++.
T Consensus 13 ~~~~~S~s~AA~~L~isQpavS~~I~~L 40 (309)
T PRK12683 13 VRQNFNLTEVANALYTSQSGVSKQIKDL 40 (309)
T ss_pred HHccCCHHHHHHHhcCCcHHHHHHHHHH
Confidence 3456788899999999999999999888
No 369
>PRK09191 two-component response regulator; Provisional
Probab=78.12 E-value=2.1 Score=31.91 Aligned_cols=28 Identities=14% Similarity=0.119 Sum_probs=24.9
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhhhh
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~ 31 (163)
+|++..|||+.+|+|.++|...+.+.++
T Consensus 103 ~~~s~~eIA~~l~~s~~tV~~~l~ra~~ 130 (261)
T PRK09191 103 EGFSVEEAAEILGVDPAEAEALLDDARA 130 (261)
T ss_pred hcCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 6899999999999999999999876643
No 370
>PRK12679 cbl transcriptional regulator Cbl; Reviewed
Probab=78.04 E-value=1.5 Score=34.04 Aligned_cols=28 Identities=18% Similarity=0.144 Sum_probs=24.4
Q ss_pred ccCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904 2 AAAGVRPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 2 ~~~g~~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
++.|-+-..+|++|+||+++||+-+++.
T Consensus 13 ~~~~~s~s~AA~~L~iSQ~avSr~I~~L 40 (316)
T PRK12679 13 ARQDYNLTEVANMLFTSQSGVSRHIREL 40 (316)
T ss_pred HHcCCCHHHHHHHhcCCchHHHHHHHHH
Confidence 3456678899999999999999999888
No 371
>PF05043 Mga: Mga helix-turn-helix domain; InterPro: IPR007737 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions []. The family also contains VirR like proteins which match only at the C terminus of the alignment.; PDB: 3SQN_A.
Probab=77.91 E-value=1.5 Score=27.40 Aligned_cols=28 Identities=11% Similarity=0.140 Sum_probs=22.0
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhhhh
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRYQE 31 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~ 31 (163)
..++..++|..+.||.+|+.+.++..++
T Consensus 29 ~~~s~~~la~~~~iS~sti~~~i~~l~~ 56 (87)
T PF05043_consen 29 EYVSIEDLAEELFISRSTIYRDIKKLNK 56 (87)
T ss_dssp SEEEHHHHHHHHT--HHHHHHHHHHHHH
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4577889999999999999999987743
No 372
>PHA02701 ORF020 dsRNA-binding PKR inhibitor; Provisional
Probab=77.78 E-value=1.9 Score=31.21 Aligned_cols=33 Identities=18% Similarity=0.244 Sum_probs=30.0
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCCCC
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPG 38 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg 38 (163)
+.+-+||+.||++.+.|-|-|.++.+.|.+..-
T Consensus 20 ~~a~~i~k~l~i~k~~vNr~LY~L~~~~~v~~~ 52 (183)
T PHA02701 20 LPAKRIAKELGISKHEANRCLYRLLESDAVSCE 52 (183)
T ss_pred CcHHHHHHHhCccHHHHHHHHHHHhhcCcEecC
Confidence 888999999999999999999999999988543
No 373
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=77.57 E-value=6.9 Score=26.11 Aligned_cols=42 Identities=26% Similarity=0.358 Sum_probs=35.9
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCC--CCCCCCCCCCCc
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSI--RPGVIGGSKPRV 47 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~--~Pg~~Gg~~p~~ 47 (163)
++..|||..|..|.--|+.+|+++.+.|=+ .|+..=|.++..
T Consensus 20 vtl~elA~~l~cS~Rn~r~lLkkm~~~gWi~W~pg~GRG~~S~L 63 (115)
T PF12793_consen 20 VTLDELAELLFCSRRNARTLLKKMQEEGWITWQPGRGRGNRSQL 63 (115)
T ss_pred eeHHHHHHHhCCCHHHHHHHHHHHHHCCCeeeeCCCCCCCCCee
Confidence 678899999999999999999999999977 788765555553
No 374
>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=77.55 E-value=0.73 Score=32.70 Aligned_cols=22 Identities=18% Similarity=0.229 Sum_probs=0.0
Q ss_pred CChhhhHHHhhcchhhHHHHHh
Q psy1904 6 VRPCVISRQLRVSHGCVSKILN 27 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~ 27 (163)
+...|||..+||+.||||+.++
T Consensus 50 Lt~~~iA~~lgl~~STVSRav~ 71 (160)
T PF04552_consen 50 LTMKDIADELGLHESTVSRAVK 71 (160)
T ss_dssp ----------------------
T ss_pred CCHHHHHHHhCCCHhHHHHHHc
Confidence 4567999999999999999874
No 375
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=77.28 E-value=2.4 Score=32.96 Aligned_cols=27 Identities=11% Similarity=0.142 Sum_probs=24.5
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhhh
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRYQ 30 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~ 30 (163)
.|++..|||+.||+|.++|..++.+-+
T Consensus 133 ~g~s~~EIA~~Lgis~~tVr~~l~RAr 159 (290)
T PRK09635 133 FGLPYQQIATTIGSQASTCRQLAHRAR 159 (290)
T ss_pred hCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 689999999999999999999997663
No 376
>COG1709 Predicted transcriptional regulator [Transcription]
Probab=77.25 E-value=1.2 Score=33.14 Aligned_cols=22 Identities=27% Similarity=0.327 Sum_probs=20.3
Q ss_pred CCChhhhHHHhhcchhhHHHHH
Q psy1904 5 GVRPCVISRQLRVSHGCVSKIL 26 (163)
Q Consensus 5 g~~~~~ia~~~~vs~~~vs~~l 26 (163)
++++.+||+.||||+|.+|.+-
T Consensus 40 ~vSQ~elA~~l~vSpSVISDYE 61 (241)
T COG1709 40 NVSQTELARELGVSPSVISDYE 61 (241)
T ss_pred CccHHHHHHHhCCCcceeehhh
Confidence 6899999999999999999974
No 377
>PRK10216 DNA-binding transcriptional regulator YidZ; Provisional
Probab=77.18 E-value=1.7 Score=33.81 Aligned_cols=23 Identities=22% Similarity=0.313 Sum_probs=20.7
Q ss_pred ChhhhHHHhhcchhhHHHHHhhh
Q psy1904 7 RPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 7 ~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
+....|+.|+||+++||+-+++.
T Consensus 24 s~t~AA~~L~iSQpavS~~I~~L 46 (319)
T PRK10216 24 SVTKAAKRMNVTPSAVSKSLAKL 46 (319)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHH
Confidence 66788999999999999999777
No 378
>PF03428 RP-C: Replication protein C N-terminal domain; InterPro: IPR005090 Proteins in this group have homology with the RepC protein of Agrobacterium Ri and Ti plasmids []. They may be involved in plasmid replication and stabilisation functions.
Probab=76.94 E-value=3.5 Score=29.79 Aligned_cols=38 Identities=18% Similarity=0.177 Sum_probs=32.7
Q ss_pred CChhhhHHHh-hcchhhHHHHHhhhhhccCCCCCCCCCC
Q psy1904 6 VRPCVISRQL-RVSHGCVSKILNRYQETGSIRPGVIGGS 43 (163)
Q Consensus 6 ~~~~~ia~~~-~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~ 43 (163)
.|.+++|.++ |+|.+||.+.|....+.|-+.....++.
T Consensus 71 pSN~~La~r~~G~s~~tlrR~l~~LveaGLI~rrDS~Ng 109 (177)
T PF03428_consen 71 PSNAQLAERLNGMSERTLRRHLARLVEAGLIVRRDSPNG 109 (177)
T ss_pred cCHHHHHHHHcCCCHHHHHHHHHHHHHCCCeeeccCCCC
Confidence 4678999999 9999999999999999999988654444
No 379
>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=76.74 E-value=9.6 Score=25.61 Aligned_cols=64 Identities=14% Similarity=0.108 Sum_probs=38.6
Q ss_pred ChhhhHHHhhcchhhHHHHHhhhhhccCCCCCC--CCCCCCCcCChHHHHHHHHHHH-hCCCCCchhhhhhhh
Q psy1904 7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGV--IGGSKPRVATPDVEKRIEEYKK-TNPNITSWEVRDKLI 76 (163)
Q Consensus 7 ~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~--~Gg~~p~~~~~~~~~~i~~~~~-~~p~~~~~e~~~~l~ 76 (163)
++.++|+++|||..|+.-| .+.|-+.|.. .+|.+ .-+......+.-+.. ..-+++..++..-+.
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----ERKGLLPEPDRPEGGYR--RYPEETVKRLRFIKRAQELGFSLEEIGGLLG 67 (124)
T ss_pred CHHHHHHHHCcCHHHHHHH----HHCCCCCCCccCCCCCE--eECHHHHHHHHHHHHHHHCCCCHHHHHHHHh
Confidence 3679999999999999655 4568887543 23333 234444444433221 233677777776543
No 380
>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=76.15 E-value=0.89 Score=27.45 Aligned_cols=45 Identities=9% Similarity=0.206 Sum_probs=28.6
Q ss_pred cccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccc
Q psy1904 100 RSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLG 148 (163)
Q Consensus 100 r~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqn 148 (163)
+.|..||+++...+-..+. .......++|..+|++..++..|-.-
T Consensus 2 ~~r~~ys~e~K~~~v~~~~----~~g~sv~~va~~~gi~~~~l~~W~~~ 46 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYL----ESGESVSEVAREYGISPSTLYNWRKQ 46 (76)
T ss_dssp -SS----HHHHHHHHHHHH----HHHCHHHHHHHHHTS-HHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHH----HCCCceEeeecccccccccccHHHHH
Confidence 3567889988777766651 12246778999999999999999643
No 381
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=76.04 E-value=3.1 Score=24.88 Aligned_cols=24 Identities=8% Similarity=0.158 Sum_probs=21.4
Q ss_pred CChhhhHHHhhcchhhHHHHHhhh
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
++..+||+.+|+|.+.+.+++++.
T Consensus 2 ~~~~~la~~~~~s~~~l~~~f~~~ 25 (84)
T smart00342 2 LTLEDLAEALGMSPRHLQRLFKKE 25 (84)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHH
Confidence 567899999999999999999765
No 382
>PRK03341 arginine repressor; Provisional
Probab=75.74 E-value=2.6 Score=30.17 Aligned_cols=24 Identities=17% Similarity=0.250 Sum_probs=22.0
Q ss_pred CChhhhHHHh-----hcchhhHHHHHhhh
Q psy1904 6 VRPCVISRQL-----RVSHGCVSKILNRY 29 (163)
Q Consensus 6 ~~~~~ia~~~-----~vs~~~vs~~l~~~ 29 (163)
.++.|+++.| .||++||||.|+..
T Consensus 30 ~tQ~eL~~~L~~~Gi~vTQaTiSRDl~eL 58 (168)
T PRK03341 30 RSQAELAALLADEGIEVTQATLSRDLDEL 58 (168)
T ss_pred ccHHHHHHHHHHcCCcccHHHHHHHHHHh
Confidence 6789999999 99999999999776
No 383
>PF13693 HTH_35: Winged helix-turn-helix DNA-binding; PDB: 1NEQ_A 1NER_A.
Probab=75.68 E-value=1.4 Score=27.33 Aligned_cols=24 Identities=21% Similarity=0.310 Sum_probs=19.6
Q ss_pred cCCCChhhhHHHhhcchhhHHHHH
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKIL 26 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l 26 (163)
+.|++-.+||+.+|++.+|+...|
T Consensus 13 krG~sL~~lsr~~Gl~~~tl~nal 36 (78)
T PF13693_consen 13 KRGTSLAALSREAGLSSSTLRNAL 36 (78)
T ss_dssp TTS--HHHHHHHHSS-HHHHHHTT
T ss_pred HcCCCHHHHHHHcCCCHHHHHHHH
Confidence 589999999999999999999987
No 384
>PRK10856 cytoskeletal protein RodZ; Provisional
Probab=75.59 E-value=3 Score=33.17 Aligned_cols=24 Identities=17% Similarity=0.237 Sum_probs=22.3
Q ss_pred cCCCChhhhHHHhhcchhhHHHHH
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKIL 26 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l 26 (163)
+.|+++.++|++++|+.++|+.|.
T Consensus 25 ~~GlSq~~vA~~l~l~~~~I~~iE 48 (331)
T PRK10856 25 QLGLTQQAVAERLCLKVSTVRDIE 48 (331)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHH
Confidence 369999999999999999999995
No 385
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=75.35 E-value=6.5 Score=28.99 Aligned_cols=33 Identities=9% Similarity=0.166 Sum_probs=29.1
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCCCC
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPG 38 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg 38 (163)
++..++|+.||||.+.|..-|.+...-|=+.-.
T Consensus 31 L~e~eLae~lgVSRtpVREAL~~L~~eGlv~~~ 63 (224)
T PRK11534 31 LRMSLLTSRYALGVGPLREALSQLVAERLVTVV 63 (224)
T ss_pred CCHHHHHHHHCCChHHHHHHHHHHHHCCCEEEe
Confidence 667899999999999999999999999977433
No 386
>PRK13348 chromosome replication initiation inhibitor protein; Provisional
Probab=75.23 E-value=2 Score=32.83 Aligned_cols=23 Identities=22% Similarity=0.212 Sum_probs=20.9
Q ss_pred ChhhhHHHhhcchhhHHHHHhhh
Q psy1904 7 RPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 7 ~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
+-...|+.|+||+++||+-+++.
T Consensus 18 s~t~AA~~L~iSQ~avS~~i~~L 40 (294)
T PRK13348 18 SFERAARRLHVTPSAVSQRIKAL 40 (294)
T ss_pred CHHHHHHHhCCCchHHHHHHHHH
Confidence 56778999999999999999888
No 387
>PRK00441 argR arginine repressor; Provisional
Probab=75.00 E-value=2.2 Score=29.85 Aligned_cols=24 Identities=17% Similarity=0.239 Sum_probs=21.6
Q ss_pred CChhhhHHHh-----hcchhhHHHHHhhh
Q psy1904 6 VRPCVISRQL-----RVSHGCVSKILNRY 29 (163)
Q Consensus 6 ~~~~~ia~~~-----~vs~~~vs~~l~~~ 29 (163)
.++.|+++.| +||++||+|-|+..
T Consensus 19 ~~q~eL~~~L~~~G~~vSqaTisRDl~~L 47 (149)
T PRK00441 19 ETQEELAEELKKMGFDVTQATVSRDIKEL 47 (149)
T ss_pred CcHHHHHHHHHhcCCCcCHHHHHHHHHHc
Confidence 6789999997 99999999999766
No 388
>TIGR03454 partition_RepB plasmid partitioning protein RepB. Members of this family are the RepB protein involved in replicon partitioning. RepB is found, in general, as part of a repABC operon in plasmids and small chromosomes, separate from the main chromosome, in various bacteria. This model describes a rather narrow clade of proteins; it should be noted that additional homologs scoring below the trusted cutoff have very similar functions, although they may be named differently.
Probab=74.90 E-value=2.1 Score=33.99 Aligned_cols=27 Identities=19% Similarity=0.201 Sum_probs=24.2
Q ss_pred cCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
..|++..+||+.||++.++||++|.-.
T Consensus 175 ~~G~~~~~ia~~Lg~~ks~vSr~lsl~ 201 (325)
T TIGR03454 175 DRGFDRDTIMAALSVDKTELSRMISVA 201 (325)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 478999999999999999999999654
No 389
>TIGR02293 TAS_TIGR02293 putative toxin-antitoxin system antitoxin component, TIGR02293 family. Proteins in this family are found almost exclusively in the Proteobacteria, but also in Gloeobacter violaceus PCC 7421, a cyanobacterium. This family was proposed by Makarova, et al. (2009) to be the antitoxin component of a new class of type 2 toxin-antitoxin system, or addiction module.
Probab=74.78 E-value=2.9 Score=28.58 Aligned_cols=23 Identities=4% Similarity=0.076 Sum_probs=20.7
Q ss_pred CCCChhhhHHHhhcchhhHHHHH
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKIL 26 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l 26 (163)
-|++..+++..+|||.+|++++.
T Consensus 35 l~ls~~el~~~lgis~~Tl~R~~ 57 (133)
T TIGR02293 35 LAIGKAEIFKATGIPKATLQRRK 57 (133)
T ss_pred HCCCHHHHHHHHCCCHHHHHHHh
Confidence 47889999999999999999986
No 390
>PRK13698 plasmid-partitioning protein; Provisional
Probab=74.73 E-value=2.8 Score=33.18 Aligned_cols=26 Identities=8% Similarity=0.102 Sum_probs=23.3
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
.|..+.+||+++|+|.+.|++.|+-.
T Consensus 175 ~~~tQeeLA~~lG~SRs~Vsn~Lrla 200 (323)
T PRK13698 175 FAGNISALADAENISRKIITRCINTA 200 (323)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 47899999999999999999998654
No 391
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=74.70 E-value=2 Score=33.04 Aligned_cols=31 Identities=19% Similarity=0.078 Sum_probs=28.6
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIR 36 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~ 36 (163)
++..|+|+.|+||..||.|=|....+.|-+.
T Consensus 32 vtv~eLa~~l~VS~~TIRRDL~~Le~~G~l~ 62 (269)
T PRK09802 32 VQVNDLSALYGVSTVTIRNDLAFLEKQGIAV 62 (269)
T ss_pred EeHHHHHHHHCCCHHHHHHHHHHHHhCCCeE
Confidence 7889999999999999999999998888875
No 392
>PRK12680 transcriptional regulator CysB-like protein; Reviewed
Probab=74.66 E-value=2.2 Score=33.51 Aligned_cols=27 Identities=15% Similarity=0.230 Sum_probs=23.5
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhhh
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRYQ 30 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~ 30 (163)
.+-+-..+|+.|+||+++||+-+++.+
T Consensus 15 ~~gS~s~AA~~L~isQpavS~~I~~LE 41 (327)
T PRK12680 15 AELNITLAAARVHATQPGLSKQLKQLE 41 (327)
T ss_pred ccCCHHHHHHHhcCCchHHHHHHHHHH
Confidence 355778899999999999999998883
No 393
>PF08667 BetR: BetR domain; InterPro: IPR013975 CheY-like phosphoacceptor (or receiver [REC]) domain is a common module in a variety of response regulators of the bacterial signal transduction systems. BetR is one of the many response regulators and is encoded mainly in Burkholderia spp. It is a N-terminal helix-turn-helix domain (HTH) and has been shown to be related to the XRE-type HTH domain (IPR001387 from INTERPRO), it has been suggested that BetR would have dimerization, protein-protein interaction, and activation/relief-of-inhibition properties [].
Probab=74.61 E-value=2 Score=30.06 Aligned_cols=19 Identities=16% Similarity=0.170 Sum_probs=17.3
Q ss_pred hhhhHHHhhcchhhHHHHH
Q psy1904 8 PCVISRQLRVSHGCVSKIL 26 (163)
Q Consensus 8 ~~~ia~~~~vs~~~vs~~l 26 (163)
..+||+.|+||.+++++.|
T Consensus 25 ~s~LA~iL~Is~ssa~RKL 43 (147)
T PF08667_consen 25 ASELADILGISYSSAYRKL 43 (147)
T ss_pred HHHHHHHHCCCHHHHHHHh
Confidence 3679999999999999988
No 394
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=74.43 E-value=2 Score=32.57 Aligned_cols=23 Identities=26% Similarity=0.210 Sum_probs=20.7
Q ss_pred ChhhhHHHhhcchhhHHHHHhhh
Q psy1904 7 RPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 7 ~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
+-...|+.|+||+++||+-++..
T Consensus 19 s~t~AA~~L~isqpavS~~I~~L 41 (290)
T PRK10837 19 STTQASVMLALSQSAVSAALTDL 41 (290)
T ss_pred CHHHHHHHhCCCccHHHHHHHHH
Confidence 66788999999999999999777
No 395
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=74.26 E-value=3 Score=28.85 Aligned_cols=23 Identities=9% Similarity=0.159 Sum_probs=18.9
Q ss_pred CChhhhHHHhhcchhhHHHHHhh
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNR 28 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~ 28 (163)
.+..+||+-+||+.+|+++|...
T Consensus 35 ~T~~eiAee~Gis~~tLYrWr~~ 57 (142)
T PF13022_consen 35 RTQAEIAEEVGISRSTLYRWRQQ 57 (142)
T ss_dssp S-HHHHHHHHTS-HHHHHHHHHH
T ss_pred chHHHHHHHhCCCHHHHHHHHhc
Confidence 56789999999999999999854
No 396
>PF03333 PapB: Adhesin biosynthesis transcription regulatory protein; InterPro: IPR004356 P pili, or fimbriae, are ~68A in diameter and 1 micron in length, the bulk of which is a fibre composed of the main structural protein PapA []. At its tip, the pilus is terminated by a fibrillum consisting of repeating units of the PapE protein. This, in turn, is topped by the adhesins, PapF and PapG, both of which are needed for receptor binding. The tip fibrillum is anchored to the main PapA fibre by the PapK pilus-adaptor protein. PapH, an outer membrane protein, then anchors the entire rod in the bacterial envelope []. A cytoplasmic chaperone (PapD) assists in assembling the monomers of the macromolecule in the membrane. All of the functional pap genes are arranged in a cluster (operon) on the Escherichia coli genome. It is believed that selective pressure exerted by the host's urinal and intestinal tract isoreceptors forced the spread of this operon to other strains via lateral transfer []. PapB, encoded within the cluster, acts as a transcriptional regulator of the functional pap genes and is located in the bacterial cytoplasm []. Its mechanism involves differential binding to separate sites in the cluster, suggesting that this protein is both an activator and repressor of pilus-adhesion transcription. The protein shares similarity with other E. coli fimbrial- adhesion transcription regulators, such as AfaA, DaaA and FanB. ; GO: 0006355 regulation of transcription, DNA-dependent; PDB: 3M8J_A.
Probab=74.25 E-value=3.5 Score=26.37 Aligned_cols=29 Identities=21% Similarity=0.276 Sum_probs=21.1
Q ss_pred cCCCChhhhHHHhhcchhhHHHHHhhhhh
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKILNRYQE 31 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~~~ 31 (163)
..|.+.-+++.+.||++|..+.-|++...
T Consensus 51 V~G~srkeac~~~gV~~syfs~~L~rL~~ 79 (91)
T PF03333_consen 51 VDGLSRKEACERHGVNQSYFSRALNRLNR 79 (91)
T ss_dssp TT---HHHHHHHTT--HHHHHHHHHHHHH
T ss_pred HcCCcHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 37999999999999999999999988754
No 397
>PRK11482 putative DNA-binding transcriptional regulator; Provisional
Probab=74.14 E-value=2.3 Score=33.20 Aligned_cols=23 Identities=9% Similarity=0.203 Sum_probs=20.7
Q ss_pred ChhhhHHHhhcchhhHHHHHhhh
Q psy1904 7 RPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 7 ~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
+-...|++|+||+++||+-+++.
T Consensus 45 s~s~AA~~L~isQpavS~~I~~L 67 (317)
T PRK11482 45 GIVNAAKILNLTPSAISQSIQKL 67 (317)
T ss_pred CHHHHHHHhCCChHHHHHHHHHH
Confidence 56788999999999999999777
No 398
>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=74.12 E-value=3.1 Score=30.95 Aligned_cols=33 Identities=15% Similarity=0.256 Sum_probs=28.5
Q ss_pred ChhhhHHHhhcchhhHHHHHhhhhhccCCCCCC
Q psy1904 7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGV 39 (163)
Q Consensus 7 ~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~ 39 (163)
+-.++|+.||||..||.+-|..+...|=+.-..
T Consensus 34 sE~eLa~~~~VSR~TvR~Al~~L~~eGli~r~~ 66 (238)
T TIGR02325 34 AEMQLAERFGVNRHTVRRAIAALVERGLLRAEQ 66 (238)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence 446899999999999999999999988885543
No 399
>PRK12681 cysB transcriptional regulator CysB; Reviewed
Probab=74.01 E-value=2.2 Score=33.41 Aligned_cols=27 Identities=15% Similarity=0.110 Sum_probs=23.8
Q ss_pred cCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
+.|-+...+|+.|+||+++||+-+++.
T Consensus 14 e~g~S~s~AA~~L~iSQpavS~~I~~L 40 (324)
T PRK12681 14 NHNLNVSATAEGLYTSQPGISKQVRML 40 (324)
T ss_pred HccCCHHHHHHHhcCCcHHHHHHHHHH
Confidence 345678899999999999999999888
No 400
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=73.68 E-value=3 Score=30.08 Aligned_cols=34 Identities=24% Similarity=0.207 Sum_probs=30.5
Q ss_pred CC-CChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904 4 AG-VRPCVISRQLRVSHGCVSKILNRYQETGSIRP 37 (163)
Q Consensus 4 ~g-~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P 37 (163)
+| ++..|||..|||+...|.++|..+.+-|-+.-
T Consensus 34 ~g~~tdeeLA~~Lgi~~~~VRk~L~~L~e~gLv~~ 68 (178)
T PRK06266 34 KGEVTDEEIAEQTGIKLNTVRKILYKLYDARLADY 68 (178)
T ss_pred cCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEE
Confidence 45 88899999999999999999999999888763
No 401
>COG2186 FadR Transcriptional regulators [Transcription]
Probab=73.38 E-value=3.5 Score=31.09 Aligned_cols=37 Identities=19% Similarity=0.234 Sum_probs=31.7
Q ss_pred hhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCC
Q psy1904 8 PCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSK 44 (163)
Q Consensus 8 ~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~ 44 (163)
-.++|++||||.++|..-|+.+..-|=+.+....|..
T Consensus 37 EreLae~fgVSR~~vREAl~~L~a~Glve~r~G~Gt~ 73 (241)
T COG2186 37 ERELAERFGVSRTVVREALKRLEAKGLVEIRQGSGTF 73 (241)
T ss_pred HHHHHHHHCCCcHHHHHHHHHHHHCCCeeecCCCceE
Confidence 3689999999999999999999999999887655553
No 402
>PHA03103 double-strand RNA-binding protein; Provisional
Probab=73.00 E-value=4.1 Score=29.56 Aligned_cols=34 Identities=29% Similarity=0.421 Sum_probs=30.9
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP 37 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P 37 (163)
.++.+-+||+.||++.+.|-|.|..+.+.|.+..
T Consensus 26 ~~~~a~~i~~~l~~~k~~vNr~LY~l~~~~~v~~ 59 (183)
T PHA03103 26 EGITAIEISRKLNIEKSEVNKQLYKLQREGMVYM 59 (183)
T ss_pred CCccHHHHHHHhCCCHHHHHHHHHHHHhcCceec
Confidence 5689999999999999999999999999998843
No 403
>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=72.99 E-value=3.2 Score=31.74 Aligned_cols=23 Identities=22% Similarity=0.232 Sum_probs=21.3
Q ss_pred ChhhhHHHhhcchhhHHHHHhhh
Q psy1904 7 RPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 7 ~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
+...+|+.|+||+++||+-+++.
T Consensus 19 S~s~AA~~L~isq~avS~~I~~L 41 (300)
T TIGR02424 19 SVKRAAEALHITQPAVSKTLREL 41 (300)
T ss_pred CHHHHHHHhCCChHHHHHHHHHH
Confidence 67789999999999999999888
No 404
>TIGR03298 argP transcriptional regulator, ArgP family. ArgP used to be known as IciA. ArgP is a positive regulator of argK. It is a negative autoregulator in presence of arginine. It competes with DnaA for oriC iteron (13-mer) binding. It activates dnaA and nrd transcription. It has been demonstrated to be part of the pho regulon (PubMed:10589831). ArgP mutants convey canavanine (an L-arginine structural homolog) sensitivity (PubMed: 15150242).
Probab=72.97 E-value=2.5 Score=32.21 Aligned_cols=24 Identities=17% Similarity=0.119 Sum_probs=21.4
Q ss_pred ChhhhHHHhhcchhhHHHHHhhhh
Q psy1904 7 RPCVISRQLRVSHGCVSKILNRYQ 30 (163)
Q Consensus 7 ~~~~ia~~~~vs~~~vs~~l~~~~ 30 (163)
+-...|+.|+||+++||+-+++.+
T Consensus 17 s~t~AA~~L~isQpavS~~I~~LE 40 (292)
T TIGR03298 17 SFERAAAALSVTPSAVSQRIKALE 40 (292)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHH
Confidence 667899999999999999998883
No 405
>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=72.83 E-value=3.5 Score=30.70 Aligned_cols=32 Identities=28% Similarity=0.221 Sum_probs=27.7
Q ss_pred ChhhhHHHhhcchhhHHHHHhhhhhccCCCCC
Q psy1904 7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPG 38 (163)
Q Consensus 7 ~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg 38 (163)
+-.++|+.||||..||.+-|....+.|-+.-.
T Consensus 26 sE~eLa~~~gVSR~TVR~Al~~L~~eGli~r~ 57 (233)
T TIGR02404 26 SEHELMDQYGASRETVRKALNLLTEAGYIQKI 57 (233)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence 45789999999999999999999888888543
No 406
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=72.75 E-value=4.7 Score=25.09 Aligned_cols=32 Identities=22% Similarity=0.223 Sum_probs=28.3
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRP 37 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P 37 (163)
+|--+||+.||+|...|-|-.+..++.|----
T Consensus 20 ~SGe~La~~LgiSRtaVwK~Iq~Lr~~G~~I~ 51 (79)
T COG1654 20 VSGEKLAEELGISRTAVWKHIQQLREEGVDIE 51 (79)
T ss_pred ccHHHHHHHHCccHHHHHHHHHHHHHhCCceE
Confidence 77789999999999999999999999886533
No 407
>cd04781 HTH_MerR-like_sg6 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 6) with at least two conserved cysteines present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, an
Probab=72.60 E-value=15 Score=24.40 Aligned_cols=64 Identities=19% Similarity=0.128 Sum_probs=38.8
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCC-CCCCCCcCChHHHHHHHHHHHh-CCCCCchhhhhhh
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI-GGSKPRVATPDVEKRIEEYKKT-NPNITSWEVRDKL 75 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~-Gg~~p~~~~~~~~~~i~~~~~~-~p~~~~~e~~~~l 75 (163)
+++.|+|+.+|||..|+.-|- +.|-+.|... +|. +.=+......+.....- .-+++..++..-+
T Consensus 1 m~IgevA~~~gvs~~tlRyYe----~~GLl~p~~~~~gy--R~Y~~~~l~~l~~I~~lr~~G~~L~eI~~~l 66 (120)
T cd04781 1 LDIAEVARQSGLPASTLRYYE----EKGLIASIGRRGLR--RQYDPQVLDRLALIALGRAAGFSLDEIQAML 66 (120)
T ss_pred CCHHHHHHHHCcCHHHHHHHH----HCCCCCCCcCCCCc--eecCHHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence 467899999999999987765 4588887433 333 33344444444322111 2256666666544
No 408
>PF06970 RepA_N: Replication initiator protein A (RepA) N-terminus; InterPro: IPR010724 This entry represents the N terminus (approximately 80 residues) of replication initiator protein A (RepA), a DNA replication initiator in plasmids []. Most proteins in this entry are bacterial, but archaeal and eukaryotic members are also included.
Probab=72.38 E-value=3.2 Score=25.57 Aligned_cols=23 Identities=17% Similarity=0.042 Sum_probs=20.1
Q ss_pred CChhhhHHHhhcchhhHHHHHhh
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNR 28 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~ 28 (163)
.+..++++.|++|..||.++++.
T Consensus 53 ~s~eel~~~L~~s~~tv~~~~ke 75 (76)
T PF06970_consen 53 FSIEELMELLNCSKSTVIKAKKE 75 (76)
T ss_pred eeHHHHHHHHCCCHHHHHHHHHc
Confidence 36789999999999999999864
No 409
>PRK14999 histidine utilization repressor; Provisional
Probab=72.08 E-value=3.7 Score=30.77 Aligned_cols=30 Identities=13% Similarity=0.191 Sum_probs=27.2
Q ss_pred ChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904 7 RPCVISRQLRVSHGCVSKILNRYQETGSIR 36 (163)
Q Consensus 7 ~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~ 36 (163)
+-.++|+.||||..||.+-|..+...|-+.
T Consensus 38 sE~eLa~~~gVSR~TVR~Al~~L~~eGli~ 67 (241)
T PRK14999 38 SEAELVAQYGFSRMTINRALRELTDEGWLV 67 (241)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 557899999999999999999998888884
No 410
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=71.66 E-value=4.5 Score=29.79 Aligned_cols=27 Identities=15% Similarity=0.012 Sum_probs=24.1
Q ss_pred cCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
-.|.+--+||+.|+||..||...+.+.
T Consensus 147 ~~G~snkeIA~~L~iS~~TV~~h~~~I 173 (207)
T PRK11475 147 SRGYSMPQIAEQLERNIKTIRAHKFNV 173 (207)
T ss_pred HCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 369999999999999999999888665
No 411
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=71.65 E-value=3 Score=31.54 Aligned_cols=37 Identities=19% Similarity=0.122 Sum_probs=30.3
Q ss_pred ChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCC
Q psy1904 7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGS 43 (163)
Q Consensus 7 ~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~ 43 (163)
+-.++|+.||||.++|..-|.+...-|=+...+..|.
T Consensus 35 sE~eLa~~~gVSRtpVREAL~~L~~eGlV~~~~~~G~ 71 (257)
T PRK10225 35 PEREIAEMLDVTRTVVREALIMLEIKGLVEVRRGAGI 71 (257)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCCEE
Confidence 3568999999999999999999999999854443333
No 412
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=71.64 E-value=2.4 Score=32.17 Aligned_cols=31 Identities=16% Similarity=0.023 Sum_probs=26.6
Q ss_pred cCC-CChhhhHHHhhcchhhHHHHHhhhhhcc
Q psy1904 3 AAG-VRPCVISRQLRVSHGCVSKILNRYQETG 33 (163)
Q Consensus 3 ~~g-~~~~~ia~~~~vs~~~vs~~l~~~~~tG 33 (163)
+.| ++..|+|+.|+||..||.|=|....+.+
T Consensus 18 ~~~~v~v~eLa~~~~VS~~TIRRDL~~Le~~~ 49 (252)
T PRK10681 18 RSDKLHLKDAAALLGVSEMTIRRDLNAHSAPV 49 (252)
T ss_pred HcCCCcHHHHHHHhCCCHHHHHHHHHHhhcCe
Confidence 445 8999999999999999999999876544
No 413
>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=71.43 E-value=3.8 Score=30.44 Aligned_cols=33 Identities=15% Similarity=0.167 Sum_probs=28.1
Q ss_pred ChhhhHHHhhcchhhHHHHHhhhhhccCCCCCC
Q psy1904 7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGV 39 (163)
Q Consensus 7 ~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~ 39 (163)
+-.++|+.||||..||.+-|....+-|-+.-..
T Consensus 27 sE~eLa~~~~VSR~TVR~Al~~L~~eGli~r~~ 59 (230)
T TIGR02018 27 SEHELVAQYGCSRMTVNRALRELTDAGLLERRQ 59 (230)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence 456899999999999999999998888885433
No 414
>PF08222 HTH_CodY: CodY helix-turn-helix domain; InterPro: IPR013198 This family consists of the C-terminal helix-turn-helix domain found in several bacterial GTP-sensing transcriptional pleiotropic repressor CodY proteins. CodY has been found to repress the dipeptide transport operon (dpp) of Bacillus subtilis in nutrient-rich conditions []. The CodY protein also has a repressor effect on many genes in Lactococcus lactis during growth in milk [].; PDB: 2B0L_C.
Probab=71.33 E-value=3 Score=24.23 Aligned_cols=36 Identities=14% Similarity=0.377 Sum_probs=27.2
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCC
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIG 41 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~G 41 (163)
+-.+.||.++||+.+.|..-|+.+...|-+.....|
T Consensus 5 lvas~iAd~~GiTRSvIVNALRKleSaGvIesrSlG 40 (61)
T PF08222_consen 5 LVASKIADRVGITRSVIVNALRKLESAGVIESRSLG 40 (61)
T ss_dssp E-HHHHHHHHT--HHHHHHHHHHHHHTTSEEEEETT
T ss_pred ehHHHHHHHhCccHHHHHHHHHHHHhcCceeecccC
Confidence 456889999999999999999999888877654433
No 415
>KOG1146|consensus
Probab=71.29 E-value=1.7 Score=40.30 Aligned_cols=63 Identities=13% Similarity=-0.000 Sum_probs=55.0
Q ss_pred ccccCcCCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCCCCCC
Q psy1904 99 RRSRTTFTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCLPSVS 161 (163)
Q Consensus 99 rr~Rt~~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~~~~~ 161 (163)
+-.++.++..|...|...|....||.-.+.+.++..|++..+.+..||++++.++..+.+..|
T Consensus 445 ~~~s~r~~~~~t~~L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~~a 507 (1406)
T KOG1146|consen 445 LLESKRSLEGQTVVLHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPRLA 507 (1406)
T ss_pred hhhhhcccccceeeeecccccccCCccchhhhhHHHhhhcccccccccchhHhHhcccccccc
Confidence 345788888999999999999999999999999999999999999999998888877766544
No 416
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=70.99 E-value=3.4 Score=31.15 Aligned_cols=36 Identities=19% Similarity=0.303 Sum_probs=29.6
Q ss_pred ChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCC
Q psy1904 7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGG 42 (163)
Q Consensus 7 ~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg 42 (163)
+-.++|+.||||.++|..-|.+....|=+.-.+..|
T Consensus 36 sE~eLa~~lgVSRtpVREAL~~L~~eGlv~~~~~~G 71 (254)
T PRK09464 36 PERELAKQFDVSRPSLREAIQRLEAKGLLLRRQGGG 71 (254)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCce
Confidence 457899999999999999999999999874433333
No 417
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=70.67 E-value=4 Score=30.55 Aligned_cols=31 Identities=16% Similarity=0.120 Sum_probs=27.2
Q ss_pred hhhhHHHhhcchhhHHHHHhhhhhccCCCCC
Q psy1904 8 PCVISRQLRVSHGCVSKILNRYQETGSIRPG 38 (163)
Q Consensus 8 ~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg 38 (163)
-.++|+.||||..||.+-|..+.+.|=+.-.
T Consensus 36 E~eLa~~~~VSR~TvR~Al~~L~~eGli~r~ 66 (241)
T PRK11402 36 ENELCTQYNVSRITIRKAISDLVADGVLIRW 66 (241)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence 3689999999999999999999888888543
No 418
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=70.63 E-value=2.6 Score=25.84 Aligned_cols=53 Identities=19% Similarity=0.229 Sum_probs=34.0
Q ss_pred ccCCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHH
Q psy1904 2 AAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEE 58 (163)
Q Consensus 2 ~~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~ 58 (163)
+..|.++.+|+...+++..++.++|....+.|-+.- +..-...|+.-.+.+..
T Consensus 16 ~~~~~~~t~i~~~~~L~~~~~~~yL~~L~~~gLI~~----~~~~Y~lTekG~~~l~~ 68 (77)
T PF14947_consen 16 SKGGAKKTEIMYKANLNYSTLKKYLKELEEKGLIKK----KDGKYRLTEKGKEFLEE 68 (77)
T ss_dssp -TT-B-HHHHHTTST--HHHHHHHHHHHHHTTSEEE----ETTEEEE-HHHHHHHHH
T ss_pred HcCCCCHHHHHHHhCcCHHHHHHHHHHHHHCcCeeC----CCCEEEECccHHHHHHH
Confidence 356789999999999999999999999999998832 22223445544444433
No 419
>COG5625 Predicted transcription regulator containing HTH domain [Transcription]
Probab=70.54 E-value=3.9 Score=26.62 Aligned_cols=33 Identities=24% Similarity=0.307 Sum_probs=27.0
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIR 36 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~ 36 (163)
.||+..+|++.|+||.-||.--+.-+...|-++
T Consensus 35 ~~mri~ei~rEl~is~rtvr~~v~~l~rrGll~ 67 (113)
T COG5625 35 RGMRIREIQRELGISERTVRAAVAVLLRRGLLA 67 (113)
T ss_pred CCchHHHHHHHHhHHHHHHHHHHHHHHHhhHHH
Confidence 579999999999999999987776666556554
No 420
>COG2973 TrpR Trp operon repressor [Transcription]
Probab=70.52 E-value=2.4 Score=27.36 Aligned_cols=19 Identities=21% Similarity=0.337 Sum_probs=17.8
Q ss_pred CChhhhHHHhhcchhhHHH
Q psy1904 6 VRPCVISRQLRVSHGCVSK 24 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~ 24 (163)
+++.||+..||||.++|-|
T Consensus 61 ~sQREi~~~LgvsiAtITR 79 (103)
T COG2973 61 LSQREIAQKLGVSIATITR 79 (103)
T ss_pred ccHHHHHHHhCcchhhhcc
Confidence 8999999999999999876
No 421
>PRK10094 DNA-binding transcriptional activator AllS; Provisional
Probab=70.43 E-value=4 Score=31.61 Aligned_cols=23 Identities=9% Similarity=0.004 Sum_probs=20.8
Q ss_pred ChhhhHHHhhcchhhHHHHHhhh
Q psy1904 7 RPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 7 ~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
+-..+|++|+||+++||+-+++.
T Consensus 18 s~s~AA~~L~iSQpavS~~I~~L 40 (308)
T PRK10094 18 SFSKAAERLCKTTATISYRIKLL 40 (308)
T ss_pred CHHHHHHHhcCCHHHHHHHHHHH
Confidence 66789999999999999999776
No 422
>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=70.25 E-value=5.4 Score=25.80 Aligned_cols=26 Identities=15% Similarity=0.126 Sum_probs=22.3
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
.+++.-+||..|++|.++++++.++.
T Consensus 70 ~~~~~~~I~~~l~~S~~t~yr~~~~A 95 (100)
T PF07374_consen 70 NKLTWEQIAEELNISRRTYYRIHKKA 95 (100)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 46777899999999999999998653
No 423
>PF07471 Phage_Nu1: Phage DNA packaging protein Nu1; InterPro: IPR010906 This entry is represented by the Bacteriophage lambda, Nu1, terminase small subunit. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Terminase, the DNA packaging enzyme of bacteriophage lambda, is a heteromultimer composed of subunits Nu1 and A. The smaller Nu1 terminase subunit has a low-affinity ATPase stimulated by non-specific DNA [].; PDB: 1J9I_A.
Probab=69.90 E-value=2.2 Score=30.43 Aligned_cols=20 Identities=15% Similarity=0.107 Sum_probs=15.9
Q ss_pred ChhhhHHHhhcchhhHHHHH
Q psy1904 7 RPCVISRQLRVSHGCVSKIL 26 (163)
Q Consensus 7 ~~~~ia~~~~vs~~~vs~~l 26 (163)
...++|++||||..||.+|.
T Consensus 4 nk~~lA~i~gvS~~ti~~W~ 23 (164)
T PF07471_consen 4 NKKELAEIFGVSERTIDKWQ 23 (164)
T ss_dssp EHHHHHHHTT--HHHHHHHT
T ss_pred CHHHHHHHHCCCHHHHHHHH
Confidence 35689999999999999996
No 424
>PF13592 HTH_33: Winged helix-turn helix
Probab=69.90 E-value=4.2 Score=23.59 Aligned_cols=20 Identities=30% Similarity=0.428 Sum_probs=16.0
Q ss_pred hhHHHhhc--chhhHHHHHhhh
Q psy1904 10 VISRQLRV--SHGCVSKILNRY 29 (163)
Q Consensus 10 ~ia~~~~v--s~~~vs~~l~~~ 29 (163)
-|.+.||| |.++|++||++.
T Consensus 13 ~I~~~fgv~ys~~~v~~lL~r~ 34 (60)
T PF13592_consen 13 YIEEEFGVKYSPSGVYRLLKRL 34 (60)
T ss_pred HHHHHHCCEEcHHHHHHHHHHc
Confidence 36678886 788999999876
No 425
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=69.70 E-value=19 Score=25.02 Aligned_cols=64 Identities=14% Similarity=0.059 Sum_probs=39.8
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCC--CCCCCCcCChHHHHHHHHHHH-hCCCCCchhhhhhh
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI--GGSKPRVATPDVEKRIEEYKK-TNPNITSWEVRDKL 75 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~--Gg~~p~~~~~~~~~~i~~~~~-~~p~~~~~e~~~~l 75 (163)
+++.++|+++|||..|+.-|- +.|=+.|... +|. +.=+......+.-+.. ..-+++..++++-+
T Consensus 8 ~~IgevAk~~Gvs~~TLRyYE----~~GLl~p~~r~~~gy--R~Y~~~~l~rl~~I~~lr~~G~sL~eI~~ll 74 (144)
T PRK13752 8 LTIGVFAKAAGVNVETIRFYQ----RKGLLPEPDKPYGSI--RRYGEADVTRVRFVKSAQRLGFSLDEIAELL 74 (144)
T ss_pred ccHHHHHHHHCcCHHHHHHHH----HCCCCCCCccCCCCC--eecCHHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence 789999999999999987764 5588876432 343 3334444444432222 13357777777644
No 426
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=69.55 E-value=3.7 Score=30.96 Aligned_cols=36 Identities=22% Similarity=0.291 Sum_probs=29.5
Q ss_pred hhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCC
Q psy1904 8 PCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGS 43 (163)
Q Consensus 8 ~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~ 43 (163)
-.++|++||||.++|..-|++....|=+.-.+..|.
T Consensus 29 E~eLae~~gVSRtpVREAL~~Le~~GlV~~~~~~G~ 64 (253)
T PRK10421 29 ERQLAMQLGVSRNSLREALAKLVSEGVLLSRRGGGT 64 (253)
T ss_pred HHHHHHHhCCCHHHHHHHHHHHHHCCCEEEeCCCeE
Confidence 578999999999999999999999998854333333
No 427
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=69.47 E-value=5.7 Score=26.96 Aligned_cols=34 Identities=15% Similarity=0.205 Sum_probs=31.0
Q ss_pred CC-CChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904 4 AG-VRPCVISRQLRVSHGCVSKILNRYQETGSIRP 37 (163)
Q Consensus 4 ~g-~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P 37 (163)
+| +...|++..+|+|..+|.+.+...-++|.+--
T Consensus 24 ~GRiTi~ql~~~TGasR~Tvk~~lreLVa~G~l~~ 58 (127)
T PF06163_consen 24 HGRITIKQLVAKTGASRNTVKRYLRELVARGDLYR 58 (127)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHHcCCeEe
Confidence 45 88899999999999999999999999999954
No 428
>COG5352 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=69.42 E-value=2.7 Score=29.05 Aligned_cols=36 Identities=28% Similarity=0.409 Sum_probs=26.1
Q ss_pred cCCCChhhhHHHhh-cchhhHHHHHhhhhhccCCCCC
Q psy1904 3 AAGVRPCVISRQLR-VSHGCVSKILNRYQETGSIRPG 38 (163)
Q Consensus 3 ~~g~~~~~ia~~~~-vs~~~vs~~l~~~~~tG~~~Pg 38 (163)
.+|.+.++||++|| ||.+.|.=..-++.-+|--.|+
T Consensus 16 seGLSASQIAaQLGGVsRnAVIGKVHRL~lsgR~~~~ 52 (169)
T COG5352 16 SEGLSASQIAAQLGGVSRNAVIGKVHRLGLSGRAKPT 52 (169)
T ss_pred HcccCHHHHHHHhcCcchhhhheeeeeccccccCCcC
Confidence 37999999999986 9988887666555444444443
No 429
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=69.27 E-value=4.5 Score=30.32 Aligned_cols=31 Identities=10% Similarity=0.238 Sum_probs=26.9
Q ss_pred hhhhHHHhhcchhhHHHHHhhhhhccCCCCC
Q psy1904 8 PCVISRQLRVSHGCVSKILNRYQETGSIRPG 38 (163)
Q Consensus 8 ~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg 38 (163)
-.++|+.||||..||.+-|..+...|-+.-.
T Consensus 38 E~eLa~~~~VSR~TVR~Al~~L~~eGli~r~ 68 (241)
T PRK10079 38 EQQLAARYEVNRHTLRRAIDQLVEKGWVQRR 68 (241)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence 4689999999999999999999888888543
No 430
>TIGR03613 RutR pyrimidine utilization regulatory protein R. This protein is observed in operons extremely similar to that characterized in E. coli K-12 responsible for the import and catabolism of pyrimidines, primarily uracil. This protein is a member of the TetR family of transcriptional regulators defined by the N-teminal model pfam00440 and the C-terminal model pfam08362 (YcdC-like protein, C-terminal region).
Probab=69.26 E-value=4 Score=29.33 Aligned_cols=23 Identities=17% Similarity=0.042 Sum_probs=20.7
Q ss_pred CCCChhhhHHHhhcchhhHHHHH
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKIL 26 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l 26 (163)
+|++..+||+..|||+++++..-
T Consensus 27 ~~~s~~~IA~~agvs~~~lY~hF 49 (202)
T TIGR03613 27 HGTSLEQIAELAGVSKTNLLYYF 49 (202)
T ss_pred ccCCHHHHHHHhCCCHHHHHHHc
Confidence 56899999999999999999874
No 431
>PF07506 RepB: RepB plasmid partitioning protein; InterPro: IPR011111 This family includes proteins with sequence similarity to the RepB partitioning protein of the large Ti (tumour-inducing) plasmids of Agrobacterium tumefaciens [, ].
Probab=69.18 E-value=3.5 Score=29.79 Aligned_cols=26 Identities=19% Similarity=0.330 Sum_probs=23.3
Q ss_pred ccCCCChhhhHHHhhcchhhHHHHHh
Q psy1904 2 AAAGVRPCVISRQLRVSHGCVSKILN 27 (163)
Q Consensus 2 ~~~g~~~~~ia~~~~vs~~~vs~~l~ 27 (163)
-..|++..+|+..|+|+.+.|++.|.
T Consensus 18 ~~~G~~~~~I~~aL~id~~~ls~~~~ 43 (185)
T PF07506_consen 18 EERGFSREEIAAALGIDKSYLSRMLS 43 (185)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 35799999999999999999988875
No 432
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=69.08 E-value=4.1 Score=31.36 Aligned_cols=23 Identities=17% Similarity=0.082 Sum_probs=20.9
Q ss_pred ChhhhHHHhhcchhhHHHHHhhh
Q psy1904 7 RPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 7 ~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
+...+|+.|+||+++||+.++..
T Consensus 21 s~s~AA~~L~isqpavS~~i~~L 43 (305)
T CHL00180 21 SFKKAAESLYISQPAVSLQIKNL 43 (305)
T ss_pred CHHHHHHHhcCCChHHHHHHHHH
Confidence 56788999999999999999877
No 433
>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=68.86 E-value=4.1 Score=27.09 Aligned_cols=29 Identities=17% Similarity=0.264 Sum_probs=24.3
Q ss_pred CccCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904 1 MAAAGVRPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 1 ~~~~g~~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
|-++|++-..||.-|+||.|+|-..-...
T Consensus 76 LR~AGlt~~aIAd~F~iS~s~~~nft~~n 104 (126)
T PF10654_consen 76 LRHAGLTCYAIADYFKISKSTVFNFTQNN 104 (126)
T ss_pred HHhcCCChHHHHHHHhHHHHHHHHHHHHh
Confidence 34689999999999999999998876443
No 434
>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=68.68 E-value=5 Score=29.85 Aligned_cols=33 Identities=15% Similarity=0.205 Sum_probs=29.1
Q ss_pred ChhhhHHHhhcchhhHHHHHhhhhhccCCCCCC
Q psy1904 7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGV 39 (163)
Q Consensus 7 ~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~ 39 (163)
+-.++|+.||||.++|..-|.+....|-+...+
T Consensus 32 sE~~La~~lgVSRtpVREAL~~Le~eGlV~~~~ 64 (235)
T TIGR02812 32 AERELSELIGVTRTTLREVLQRLARDGWLTIQH 64 (235)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeC
Confidence 567899999999999999999999999885443
No 435
>PRK11074 putative DNA-binding transcriptional regulator; Provisional
Probab=68.63 E-value=3.5 Score=31.64 Aligned_cols=23 Identities=13% Similarity=0.112 Sum_probs=20.8
Q ss_pred ChhhhHHHhhcchhhHHHHHhhh
Q psy1904 7 RPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 7 ~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
+-...|+.|+||+++||+-++..
T Consensus 18 s~s~AA~~L~isQpavS~~I~~L 40 (300)
T PRK11074 18 SFSAAAQELHRVPSAVSYTVRQL 40 (300)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHH
Confidence 56778999999999999999888
No 436
>COG1339 Transcriptional regulator of a riboflavin/FAD biosynthetic operon [Transcription / Coenzyme metabolism]
Probab=68.60 E-value=5 Score=29.48 Aligned_cols=31 Identities=23% Similarity=0.395 Sum_probs=28.3
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIR 36 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~ 36 (163)
++-.++|+.+++|.-|++|||+...+.|-+.
T Consensus 20 ~t~~ela~~l~~S~qta~R~l~~le~~~~I~ 50 (214)
T COG1339 20 VTSSELAKRLGVSSQTAARKLKELEDEGYIT 50 (214)
T ss_pred ccHHHHHHHhCcCcHHHHHHHHhhccCCcEE
Confidence 7788999999999999999999998888775
No 437
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=68.60 E-value=6.1 Score=29.67 Aligned_cols=32 Identities=16% Similarity=0.187 Sum_probs=28.1
Q ss_pred ChhhhHHHhhcchhhHHHHHhhhhhccCCCCC
Q psy1904 7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPG 38 (163)
Q Consensus 7 ~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg 38 (163)
+-.+||+.||||.++|..-|.+....|=+.-.
T Consensus 33 sE~eLa~~~gVSRtpVREAL~~L~~eGlV~~~ 64 (251)
T PRK09990 33 SERRLCEKLGFSRSALREGLTVLRGRGIIETA 64 (251)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence 45799999999999999999999999987443
No 438
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=68.60 E-value=4.2 Score=30.94 Aligned_cols=25 Identities=20% Similarity=0.232 Sum_probs=21.6
Q ss_pred ChhhhHHHhhcchhhHHHHHhhhhh
Q psy1904 7 RPCVISRQLRVSHGCVSKILNRYQE 31 (163)
Q Consensus 7 ~~~~ia~~~~vs~~~vs~~l~~~~~ 31 (163)
+-..+|+.|+||+++||+-+++.++
T Consensus 17 s~s~AA~~L~isqsavS~~i~~LE~ 41 (296)
T PRK11242 17 NFTRAAEALHVSQPTLSQQIRQLEE 41 (296)
T ss_pred CHHHHHHHcCCCchHHHHHHHHHHH
Confidence 5677899999999999999988733
No 439
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=68.56 E-value=13 Score=27.49 Aligned_cols=39 Identities=21% Similarity=0.214 Sum_probs=32.7
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCC
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSK 44 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~ 44 (163)
++..+||++||||..-|..-|.+...-|-+.--+..|-.
T Consensus 40 l~e~~La~~~gvSrtPVReAL~rL~~eGlv~~~p~rG~~ 78 (230)
T COG1802 40 LSEEELAEELGVSRTPVREALRRLEAEGLVEIEPNRGAF 78 (230)
T ss_pred ccHHHHHHHhCCCCccHHHHHHHHHHCCCeEecCCCCCe
Confidence 677899999999999999999999999988655544443
No 440
>PRK15482 transcriptional regulator MurR; Provisional
Probab=68.53 E-value=4.4 Score=31.16 Aligned_cols=25 Identities=20% Similarity=0.369 Sum_probs=22.1
Q ss_pred CCChhhhHHHhhcchhhHHHHHhhh
Q psy1904 5 GVRPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 5 g~~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
-++..+||+..+||.+||.|.-++.
T Consensus 34 ~~si~elA~~~~vS~aTv~Rf~kkL 58 (285)
T PRK15482 34 SVSSRKMAKQLGISQSSIVKFAQKL 58 (285)
T ss_pred hcCHHHHHHHhCCCHHHHHHHHHHh
Confidence 3788999999999999999988665
No 441
>PRK15421 DNA-binding transcriptional regulator MetR; Provisional
Probab=68.21 E-value=3.8 Score=31.97 Aligned_cols=26 Identities=12% Similarity=0.215 Sum_probs=21.9
Q ss_pred cCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
+.| +...+|+.|+||+++||+-++.+
T Consensus 15 ~~g-s~s~AA~~L~iSqpaVS~~Ik~L 40 (317)
T PRK15421 15 NCG-SLAAAAATLHQTQSALSHQFSDL 40 (317)
T ss_pred HcC-CHHHHHHHhCCCHHHHHHHHHHH
Confidence 344 67789999999999999998776
No 442
>PRK05638 threonine synthase; Validated
Probab=68.09 E-value=4.4 Score=33.45 Aligned_cols=36 Identities=17% Similarity=0.169 Sum_probs=30.8
Q ss_pred ccCCCChhhhHHHhh--cchhhHHHHHhhhhhccCCCC
Q psy1904 2 AAAGVRPCVISRQLR--VSHGCVSKILNRYQETGSIRP 37 (163)
Q Consensus 2 ~~~g~~~~~ia~~~~--vs~~~vs~~l~~~~~tG~~~P 37 (163)
++.-+..+||++.|+ +|.++|++.|+...+.|=+.-
T Consensus 381 ~~~~~~~~el~~~l~~~~s~~~v~~hL~~Le~~GLV~~ 418 (442)
T PRK05638 381 SEREMYGYEIWKALGKPLKYQAVYQHIKELEELGLIEE 418 (442)
T ss_pred hhCCccHHHHHHHHcccCCcchHHHHHHHHHHCCCEEE
Confidence 344578899999998 999999999999999987753
No 443
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=68.03 E-value=3.9 Score=26.38 Aligned_cols=35 Identities=31% Similarity=0.346 Sum_probs=29.8
Q ss_pred cCCCChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP 37 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P 37 (163)
.+|+...+|+++|+++...|...+..+...|.+-.
T Consensus 63 ~~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs 97 (102)
T PF08784_consen 63 EEGVHVDEIAQQLGMSENEVRKALDFLSNEGHIYS 97 (102)
T ss_dssp TTTEEHHHHHHHSTS-HHHHHHHHHHHHHTTSEEE
T ss_pred CCcccHHHHHHHhCcCHHHHHHHHHHHHhCCeEec
Confidence 57999999999999999999999998888776643
No 444
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=67.71 E-value=4.9 Score=29.94 Aligned_cols=31 Identities=16% Similarity=0.250 Sum_probs=27.8
Q ss_pred ChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904 7 RPCVISRQLRVSHGCVSKILNRYQETGSIRP 37 (163)
Q Consensus 7 ~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P 37 (163)
+-.++|+.||||.++|..-|.+....|=+.-
T Consensus 33 sE~eLae~~gVSRt~VReAL~~L~~eGlv~~ 63 (239)
T PRK04984 33 AERELSELIGVTRTTLREVLQRLARDGWLTI 63 (239)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence 4578999999999999999999999998853
No 445
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=67.55 E-value=4.9 Score=30.48 Aligned_cols=25 Identities=12% Similarity=0.114 Sum_probs=21.2
Q ss_pred ChhhhHHHhhcchhhHHHHHhhhhh
Q psy1904 7 RPCVISRQLRVSHGCVSKILNRYQE 31 (163)
Q Consensus 7 ~~~~ia~~~~vs~~~vs~~l~~~~~ 31 (163)
+-..+|+.|+||+++||+-++..++
T Consensus 17 s~s~AA~~L~isqpavS~~I~~LE~ 41 (275)
T PRK03601 17 HFGRAAESLYLTQSAVSFRIRQLEN 41 (275)
T ss_pred CHHHHHHHhCCChHHHHHHHHHHHH
Confidence 4567899999999999999988743
No 446
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=67.37 E-value=6.6 Score=28.20 Aligned_cols=40 Identities=20% Similarity=0.137 Sum_probs=31.4
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCC
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGS 43 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~ 43 (163)
.=+...||++.+|+|.+.||--++.....+-+.-...-|.
T Consensus 40 ~Pmtl~Ei~E~lg~Sks~vS~~lkkL~~~~lV~~~~~~G~ 79 (177)
T COG1510 40 KPLTLDEIAEALGMSKSNVSMGLKKLQDWNLVKKVFEKGD 79 (177)
T ss_pred CCccHHHHHHHHCCCcchHHHHHHHHHhcchHHhhhccCc
Confidence 3478899999999999999999998877776654443334
No 447
>PRK11557 putative DNA-binding transcriptional regulator; Provisional
Probab=67.32 E-value=4.8 Score=30.78 Aligned_cols=25 Identities=16% Similarity=0.222 Sum_probs=22.4
Q ss_pred CCChhhhHHHhhcchhhHHHHHhhh
Q psy1904 5 GVRPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 5 g~~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
.++..+||+..+||.+||.|..++.
T Consensus 30 ~~si~elA~~~~vS~aTv~Rf~kkl 54 (278)
T PRK11557 30 HLSSQQLANEAGVSQSSVVKFAQKL 54 (278)
T ss_pred hcCHHHHHHHhCCCHHHHHHHHHHc
Confidence 4788999999999999999998665
No 448
>PRK11302 DNA-binding transcriptional regulator HexR; Provisional
Probab=66.42 E-value=5.1 Score=30.64 Aligned_cols=24 Identities=13% Similarity=0.167 Sum_probs=21.7
Q ss_pred CChhhhHHHhhcchhhHHHHHhhh
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
++..+||+..+||.+||.|..++.
T Consensus 35 ~si~~lA~~~~vS~aTv~Rf~kkl 58 (284)
T PRK11302 35 SSIATLAKMANVSEPTVNRFCRSL 58 (284)
T ss_pred cCHHHHHHHhCCCHHHHHHHHHHc
Confidence 688999999999999999998665
No 449
>PRK11337 DNA-binding transcriptional repressor RpiR; Provisional
Probab=66.41 E-value=5 Score=30.92 Aligned_cols=25 Identities=20% Similarity=0.227 Sum_probs=22.1
Q ss_pred CCChhhhHHHhhcchhhHHHHHhhh
Q psy1904 5 GVRPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 5 g~~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
.++..+||+..+||.+||.|..++.
T Consensus 46 ~~si~~lA~~~~vS~aTi~Rf~kkL 70 (292)
T PRK11337 46 ATALKDIAEALAVSEAMIVKVAKKL 70 (292)
T ss_pred hcCHHHHHHHhCCChHHHHHHHHHc
Confidence 3688999999999999999998665
No 450
>PF08299 Bac_DnaA_C: Bacterial dnaA protein helix-turn-helix; InterPro: IPR013159 This entry represents the C-terminal domain of bacterial DnaA proteins [, , ] that play an important role in initiating and regulating chromosomal replication. DnaA is an ATP- and DNA-binding protein. It binds specifically to 9 bp nucleotide repeats known as dnaA boxes which are found in the chromosome origin of replication (oriC). DnaA is a protein of about 50 kDa that contains two conserved regions: the first is located in the N-terminal half and corresponds to the ATP-binding domain, the second is located in the C-terminal half and could be involved in DNA-binding. The protein may also bind the RNA polymerase beta subunit, the dnaB and dnaZ proteins, and the groE gene products (chaperonins) [].; GO: 0005524 ATP binding, 0043565 sequence-specific DNA binding, 0006270 DNA-dependent DNA replication initiation, 0006275 regulation of DNA replication; PDB: 2HCB_B 3R8F_C 1L8Q_A 3PVP_B 3PVV_A 1J1V_A.
Probab=66.16 E-value=5.9 Score=23.83 Aligned_cols=25 Identities=20% Similarity=0.331 Sum_probs=19.0
Q ss_pred CCCChhhhHHHhh-cchhhHHHHHhh
Q psy1904 4 AGVRPCVISRQLR-VSHGCVSKILNR 28 (163)
Q Consensus 4 ~g~~~~~ia~~~~-vs~~~vs~~l~~ 28 (163)
-|++-.+|++.|| .+|+||..-+++
T Consensus 44 ~~~sl~~Ig~~fg~rdHstV~~a~~k 69 (70)
T PF08299_consen 44 TGLSLSEIGRYFGGRDHSTVIHAIRK 69 (70)
T ss_dssp S---HHHHHHHCTSSTHHHHHHHHHH
T ss_pred hCCCHHHHHHHhCCCCHHHHHHHHHh
Confidence 3788899999999 999999887654
No 451
>PRK03837 transcriptional regulator NanR; Provisional
Probab=66.11 E-value=5.6 Score=29.59 Aligned_cols=31 Identities=13% Similarity=0.152 Sum_probs=28.1
Q ss_pred ChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904 7 RPCVISRQLRVSHGCVSKILNRYQETGSIRP 37 (163)
Q Consensus 7 ~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P 37 (163)
+-.+||++||||.++|..-|..+...|=+.-
T Consensus 39 ~E~~Lae~~gVSRt~VREAL~~L~~eGlv~~ 69 (241)
T PRK03837 39 SERELMAFFGVGRPAVREALQALKRKGLVQI 69 (241)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHCCCEEE
Confidence 5679999999999999999999999998854
No 452
>PRK09462 fur ferric uptake regulator; Provisional
Probab=66.09 E-value=8.3 Score=26.68 Aligned_cols=35 Identities=17% Similarity=0.361 Sum_probs=29.5
Q ss_pred CCCChhhhHHHh-----hcchhhHHHHHhhhhhccCCCCC
Q psy1904 4 AGVRPCVISRQL-----RVSHGCVSKILNRYQETGSIRPG 38 (163)
Q Consensus 4 ~g~~~~~ia~~~-----~vs~~~vs~~l~~~~~tG~~~Pg 38 (163)
..+++.||-+.| +||.+||+|.|..+.+.|-+..-
T Consensus 32 ~h~sa~eI~~~l~~~~~~i~~aTVYR~L~~L~e~Gli~~~ 71 (148)
T PRK09462 32 HHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAGIVTRH 71 (148)
T ss_pred CCCCHHHHHHHHHhhCCCCCHHHHHHHHHHHHHCCCEEEE
Confidence 358899998877 48999999999999999988653
No 453
>PF09397 Ftsk_gamma: Ftsk gamma domain; InterPro: IPR018541 This domain directs oriented DNA translocation and forms a winged helix structure []. Mutated proteins with substitutions in the FtsK gamma DNA-recognition helix are impaired in DNA binding []. ; PDB: 2VE9_B 2VE8_E 2J5O_A 2J5P_A.
Probab=65.99 E-value=5.8 Score=23.69 Aligned_cols=36 Identities=17% Similarity=0.438 Sum_probs=28.5
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCC
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV 39 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~ 39 (163)
..+|.+-|-++|+|....+.+|+.+..+.|-+.|..
T Consensus 19 ~~~S~S~lQR~~rIGynrAariid~LE~~GiVs~~~ 54 (65)
T PF09397_consen 19 GKASISLLQRKFRIGYNRAARIIDQLEEEGIVSPAN 54 (65)
T ss_dssp TCECHHHHHHHHT--HHHHHHHHHHHHHCTSBE---
T ss_pred CCccHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCCC
Confidence 347888999999999999999999999999998874
No 454
>PRK11139 DNA-binding transcriptional activator GcvA; Provisional
Probab=65.83 E-value=5.7 Score=30.38 Aligned_cols=23 Identities=17% Similarity=0.163 Sum_probs=20.2
Q ss_pred ChhhhHHHhhcchhhHHHHHhhh
Q psy1904 7 RPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 7 ~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
+-..+|+.|+||+++||+-+++.
T Consensus 22 s~s~AA~~L~isq~avS~~i~~L 44 (297)
T PRK11139 22 SFTRAAEELFVTQAAVSHQIKAL 44 (297)
T ss_pred CHHHHHHHhCCChHHHHHHHHHH
Confidence 45678999999999999999877
No 455
>PRK09986 DNA-binding transcriptional activator XapR; Provisional
Probab=65.71 E-value=5.1 Score=30.45 Aligned_cols=23 Identities=13% Similarity=0.057 Sum_probs=20.9
Q ss_pred ChhhhHHHhhcchhhHHHHHhhh
Q psy1904 7 RPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 7 ~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
+...+|+.|+||+++||+-++++
T Consensus 23 s~t~AA~~L~itq~avS~~i~~L 45 (294)
T PRK09986 23 HFGRAAARLNISQPPLSIHIKEL 45 (294)
T ss_pred CHHHHHHHhCCCCCHHHHHHHHH
Confidence 66788999999999999999887
No 456
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=65.62 E-value=6 Score=29.61 Aligned_cols=30 Identities=17% Similarity=0.220 Sum_probs=27.0
Q ss_pred ChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904 7 RPCVISRQLRVSHGCVSKILNRYQETGSIR 36 (163)
Q Consensus 7 ~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~ 36 (163)
+-.++|+.||||..||.+-|..+...|-+.
T Consensus 31 sE~eL~~~~~VSR~TvR~Al~~L~~eGli~ 60 (240)
T PRK09764 31 TESALQTEFGVSRVTVRQALRQLVEQQILE 60 (240)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 347999999999999999999998888884
No 457
>PRK10082 cell density-dependent motility repressor; Provisional
Probab=65.57 E-value=5.7 Score=30.55 Aligned_cols=23 Identities=13% Similarity=0.039 Sum_probs=20.7
Q ss_pred ChhhhHHHhhcchhhHHHHHhhh
Q psy1904 7 RPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 7 ~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
+...+|+.|+||+++||+-++++
T Consensus 27 S~t~AA~~L~iSQpavS~~I~~L 49 (303)
T PRK10082 27 NFSQAAVSRNVSQPAFSRRIRAL 49 (303)
T ss_pred CHHHHHHHhCCChHHHHHHHHHH
Confidence 45678999999999999999888
No 458
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=65.54 E-value=1.5 Score=31.25 Aligned_cols=36 Identities=11% Similarity=0.149 Sum_probs=31.7
Q ss_pred HHHHHHHHhCCCcccccccccccccccccCCCCCCC
Q psy1904 127 TREALANKFGMTETRVQQFVLGTAGFLLSCLPSVSG 162 (163)
Q Consensus 127 ~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~~~~~~ 162 (163)
.-.++|..+|++...|+.+...-|.+.++++...||
T Consensus 146 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~~ 181 (186)
T PRK05602 146 SNIEAAAVMDISVDALESLLARGRRALRAQLADLPG 181 (186)
T ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHHhccc
Confidence 456899999999999999999989998888887775
No 459
>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=65.39 E-value=7.6 Score=27.04 Aligned_cols=25 Identities=20% Similarity=0.146 Sum_probs=20.9
Q ss_pred CCChhhhHHHhh-----cchhhHHHHHhhh
Q psy1904 5 GVRPCVISRQLR-----VSHGCVSKILNRY 29 (163)
Q Consensus 5 g~~~~~ia~~~~-----vs~~~vs~~l~~~ 29 (163)
-.++.||.+.|. ||++||||.|+..
T Consensus 16 i~tqeeL~~~L~~~G~~vsqaTIsRdL~el 45 (146)
T TIGR01529 16 ISTQEELVALLKAEGIEVTQATVSRDLREL 45 (146)
T ss_pred CCCHHHHHHHHHHhCCCcCHHHHHHHHHHc
Confidence 367889998887 9999999988665
No 460
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=65.38 E-value=5.4 Score=30.06 Aligned_cols=31 Identities=23% Similarity=0.295 Sum_probs=27.8
Q ss_pred hhhhHHHhhcchhhHHHHHhhhhhccCC--CCC
Q psy1904 8 PCVISRQLRVSHGCVSKILNRYQETGSI--RPG 38 (163)
Q Consensus 8 ~~~ia~~~~vs~~~vs~~l~~~~~tG~~--~Pg 38 (163)
-.+||+.||||.++|..-|+.....|=+ .||
T Consensus 35 E~eLae~~gVSRtpVREAL~~L~~eGlV~~~~~ 67 (253)
T PRK11523 35 ERFIADEKNVSRTVVREAIIMLEVEGYVEVRKG 67 (253)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 4789999999999999999999999987 454
No 461
>KOG3862|consensus
Probab=65.24 E-value=0.69 Score=35.44 Aligned_cols=24 Identities=50% Similarity=1.000 Sum_probs=21.4
Q ss_pred CcCCHHHHHHHHHhccCCCCCCHH
Q psy1904 103 TTFTSAQLEELEKSFQRSHYPDIY 126 (163)
Q Consensus 103 t~~t~~q~~~Le~~F~~~~~p~~~ 126 (163)
..|+..+++.|+..|+..+|+...
T Consensus 224 d~ft~~~~~~ld~~~~r~~y~~~~ 247 (327)
T KOG3862|consen 224 DAFTQQHLEPLDRSFERPHYPLVY 247 (327)
T ss_pred ccccccccccccceeecccccccc
Confidence 578999999999999999998764
No 462
>COG0640 ArsR Predicted transcriptional regulators [Transcription]
Probab=65.17 E-value=8.5 Score=23.67 Aligned_cols=39 Identities=21% Similarity=0.201 Sum_probs=32.7
Q ss_pred CCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCC
Q psy1904 5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGS 43 (163)
Q Consensus 5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~ 43 (163)
....|+|+..+++++++|+.-|....+.|-+.-...|+.
T Consensus 39 ~~~~~~l~~~~~~~~~~v~~hL~~L~~~glv~~~~~~~~ 77 (110)
T COG0640 39 ELTVGELAEALGLSQSTVSHHLKVLREAGLVELRREGRL 77 (110)
T ss_pred CccHHHHHHHHCCChhHHHHHHHHHHHCCCeEEEecccE
Confidence 467899999999999999999999999998876444433
No 463
>PRK10341 DNA-binding transcriptional activator TdcA; Provisional
Probab=65.08 E-value=5.8 Score=30.68 Aligned_cols=23 Identities=26% Similarity=0.345 Sum_probs=20.4
Q ss_pred ChhhhHHHhhcchhhHHHHHhhh
Q psy1904 7 RPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 7 ~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
+-..+|+.|+||+++||+-+++.
T Consensus 23 s~s~AA~~L~iSQpavS~~I~~L 45 (312)
T PRK10341 23 SIGSAAKELGLTQPAVSKIINDI 45 (312)
T ss_pred CHHHHHHHhCCChHHHHHHHHHH
Confidence 45678999999999999999887
No 464
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=65.07 E-value=4.4 Score=25.08 Aligned_cols=43 Identities=23% Similarity=0.419 Sum_probs=30.8
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCC-CCCCCCC
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV-IGGSKPR 46 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~-~Gg~~p~ 46 (163)
..+...+|.+.++++.|++++-|+...+-|=+.-.. ..+.+|+
T Consensus 13 ~~~~f~~L~~~l~lt~g~Ls~hL~~Le~~GyV~~~k~~~~~~p~ 56 (80)
T PF13601_consen 13 EEATFSELKEELGLTDGNLSKHLKKLEEAGYVEVEKEFEGRRPR 56 (80)
T ss_dssp SEEEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEEEE-SSS--E
T ss_pred CCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEEEeccCCCCe
Confidence 447788999999999999999999999999885433 3345565
No 465
>PRK10086 DNA-binding transcriptional regulator DsdC; Provisional
Probab=64.57 E-value=6.2 Score=30.53 Aligned_cols=23 Identities=17% Similarity=0.274 Sum_probs=20.4
Q ss_pred ChhhhHHHhhcchhhHHHHHhhh
Q psy1904 7 RPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 7 ~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
+...+|+.|+||+++||+-++..
T Consensus 30 s~s~AA~~L~iSQpavS~~I~~L 52 (311)
T PRK10086 30 SFALAADELSLTPSAVSHRINQL 52 (311)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHH
Confidence 45678999999999999999777
No 466
>COG1737 RpiR Transcriptional regulators [Transcription]
Probab=64.19 E-value=4.5 Score=31.22 Aligned_cols=24 Identities=13% Similarity=0.191 Sum_probs=21.2
Q ss_pred CChhhhHHHhhcchhhHHHHHhhh
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
++..|||+..|||.+||.|..++.
T Consensus 37 ~si~elA~~a~VS~aTv~Rf~~kL 60 (281)
T COG1737 37 LSIAELAERAGVSPATVVRFARKL 60 (281)
T ss_pred HHHHHHHHHhCCCHHHHHHHHHHc
Confidence 467899999999999999988665
No 467
>PRK00118 putative DNA-binding protein; Validated
Probab=64.14 E-value=1.2 Score=29.23 Aligned_cols=52 Identities=15% Similarity=0.165 Sum_probs=37.3
Q ss_pred CCHHHHHHHHHhccCCCCCCHHHHHHHHHHhCCCcccccccccccccccccCCCCCC
Q psy1904 105 FTSAQLEELEKSFQRSHYPDIYTREALANKFGMTETRVQQFVLGTAGFLLSCLPSVS 161 (163)
Q Consensus 105 ~t~~q~~~Le~~F~~~~~p~~~~r~~la~~l~l~~~~v~~WFqnrR~k~kr~~~~~~ 161 (163)
+++.|...+.-.|.... ...++|..+|++...|+.|...-|.+.+.++..+|
T Consensus 18 L~ekqRevl~L~y~eg~-----S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~~~~~ 69 (104)
T PRK00118 18 LTEKQRNYMELYYLDDY-----SLGEIAEEFNVSRQAVYDNIKRTEKLLEDYEEKLH 69 (104)
T ss_pred CCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHC
Confidence 34555556655444432 45689999999999999999888877777666555
No 468
>PHA01083 hypothetical protein
Probab=64.03 E-value=5.1 Score=27.97 Aligned_cols=21 Identities=33% Similarity=0.265 Sum_probs=18.3
Q ss_pred CChhhhHHHhhcchhhHHHHH
Q psy1904 6 VRPCVISRQLRVSHGCVSKIL 26 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l 26 (163)
++=-+||+.||||.+.||+|-
T Consensus 17 ~sdkqLA~~LGVs~q~IS~~R 37 (149)
T PHA01083 17 VQYKQIAHDLGVSPQKISKMR 37 (149)
T ss_pred ccHHHHHHHhCCCHHHHHHHH
Confidence 445689999999999999996
No 469
>TIGR03734 PRTRC_parB PRTRC system ParB family protein. A novel genetic system characterized by six major proteins, included a ParB homolog and a ThiF homolog, is designated PRTRC, or ParB-Related,ThiF-Related Cassette. It is often found on plasmids. This protein family the member related to ParB, and is designated PRTRC system ParB family protein.
Probab=63.75 E-value=5.4 Score=34.00 Aligned_cols=26 Identities=15% Similarity=0.031 Sum_probs=22.5
Q ss_pred cCCC-ChhhhHHHhhcchhhHHHHHhh
Q psy1904 3 AAGV-RPCVISRQLRVSHGCVSKILNR 28 (163)
Q Consensus 3 ~~g~-~~~~ia~~~~vs~~~vs~~l~~ 28 (163)
..|. ++.+||++||+|.++|++.|+.
T Consensus 106 ~~g~~t~eeIA~~lG~S~~~V~rrLkL 132 (554)
T TIGR03734 106 GRCKGDREEAARRLGWSPATLDRRLAL 132 (554)
T ss_pred hhcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 3455 8999999999999999999965
No 470
>PRK14997 LysR family transcriptional regulator; Provisional
Probab=63.51 E-value=6.6 Score=30.04 Aligned_cols=23 Identities=13% Similarity=0.127 Sum_probs=20.2
Q ss_pred ChhhhHHHhhcchhhHHHHHhhh
Q psy1904 7 RPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 7 ~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
+-..+|+.|+||+++||+-++..
T Consensus 18 s~s~AA~~L~isQpavS~~I~~L 40 (301)
T PRK14997 18 GFAAAGRALDEPKSKLSRRIAQL 40 (301)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHH
Confidence 45678999999999999999777
No 471
>PF11972 HTH_13: HTH DNA binding domain; InterPro: IPR021068 The proteins in this entry have not been characterised. They contain a C-terminal helix-turn-helix DNA binding domain.
Probab=63.35 E-value=9.3 Score=21.94 Aligned_cols=24 Identities=13% Similarity=0.357 Sum_probs=20.6
Q ss_pred CChhhhHHHhhcchhhHHHHHhhh
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
++.--||+.|+||+..+.+++..+
T Consensus 14 Vsa~mva~~L~vT~~~A~~li~eL 37 (54)
T PF11972_consen 14 VSAPMVAKELGVTPQAAQRLIAEL 37 (54)
T ss_pred ccHHHHHHHhCCCHHHHHHHHHHh
Confidence 567789999999999999998554
No 472
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=62.81 E-value=10 Score=24.46 Aligned_cols=26 Identities=8% Similarity=0.112 Sum_probs=23.3
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
..++..+||+.+++|..++.++.+++
T Consensus 20 ~~~~~~~lA~~~~~S~~~l~r~f~~~ 45 (107)
T PRK10219 20 QPLNIDVVAKKSGYSKWYLQRMFRTV 45 (107)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 34889999999999999999999876
No 473
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=62.74 E-value=8.2 Score=24.59 Aligned_cols=25 Identities=24% Similarity=0.310 Sum_probs=23.0
Q ss_pred cCCCChhhhHHHhhcchhhHHHHHh
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKILN 27 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l~ 27 (163)
..|++..+||..|++|..-|.++|.
T Consensus 21 ~~~ls~~~ia~dL~~s~~~le~vL~ 45 (89)
T PF10078_consen 21 LSGLSLEQIAADLGTSPEHLEQVLN 45 (89)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 4799999999999999999999983
No 474
>PRK09801 transcriptional activator TtdR; Provisional
Probab=62.63 E-value=7 Score=30.30 Aligned_cols=23 Identities=13% Similarity=0.065 Sum_probs=20.3
Q ss_pred ChhhhHHHhhcchhhHHHHHhhh
Q psy1904 7 RPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 7 ~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
+-..+|+.|+||+++||+-+++.
T Consensus 22 s~t~AA~~L~iSQpavS~~I~~L 44 (310)
T PRK09801 22 SFSAAAATLGQTPAFVTKRIQIL 44 (310)
T ss_pred CHHHHHHHhCcCHHHHHHHHHHH
Confidence 45678999999999999999887
No 475
>PRK03635 chromosome replication initiation inhibitor protein; Validated
Probab=62.54 E-value=6.7 Score=30.02 Aligned_cols=23 Identities=13% Similarity=0.195 Sum_probs=21.1
Q ss_pred ChhhhHHHhhcchhhHHHHHhhh
Q psy1904 7 RPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 7 ~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
+....|++|+||+++||+-+++.
T Consensus 18 s~s~AA~~L~isq~avS~~I~~L 40 (294)
T PRK03635 18 SFERAAQKLHITQSAVSQRIKAL 40 (294)
T ss_pred CHHHHHHHhCCChHHHHHHHHHH
Confidence 66788999999999999999888
No 476
>PRK10632 transcriptional regulator; Provisional
Probab=62.54 E-value=6.9 Score=30.24 Aligned_cols=24 Identities=21% Similarity=0.271 Sum_probs=21.2
Q ss_pred CChhhhHHHhhcchhhHHHHHhhh
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
-+...+|++|+||+++||+-++..
T Consensus 17 gS~t~AA~~L~isQpavS~~I~~L 40 (309)
T PRK10632 17 GSFTAAARQLQMSVSSISQTVSKL 40 (309)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHH
Confidence 356788999999999999999877
No 477
>TIGR02036 dsdC D-serine deaminase transcriptional activator. This family, part of the LysR family of transcriptional regulators, activates transcription of the gene for D-serine deaminase, dsdA. Trusted members of this family so far are found adjacent to dsdA and only in Gammaproteobacteria, including E. coli, Vibrio cholerae, and Colwellia psychrerythraea.
Probab=62.35 E-value=7.3 Score=30.00 Aligned_cols=23 Identities=13% Similarity=0.274 Sum_probs=20.0
Q ss_pred ChhhhHHHhhcchhhHHHHHhhh
Q psy1904 7 RPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 7 ~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
+-...|+.|+||+++||+-++..
T Consensus 24 s~s~AA~~L~isQpavS~~I~~L 46 (302)
T TIGR02036 24 SFSLAAEELSLTPSAISHRINQL 46 (302)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHH
Confidence 45678999999999999999777
No 478
>COG4901 Ribosomal protein S25 [Translation, ribosomal structure and biogenesis]
Probab=62.34 E-value=8.5 Score=25.14 Aligned_cols=33 Identities=18% Similarity=0.370 Sum_probs=30.1
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCCCC
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPG 38 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg 38 (163)
++|-.||-++||+-|-..++|+.+.+.|.+.+=
T Consensus 60 VTpy~la~r~gI~~SvAr~vLR~LeeeGvv~lv 92 (107)
T COG4901 60 VTPYVLASRYGINGSVARIVLRHLEEEGVVQLV 92 (107)
T ss_pred ecHHHHHHHhccchHHHHHHHHHHHhCCceeee
Confidence 788999999999999999999999999988764
No 479
>COG1309 AcrR Transcriptional regulator [Transcription]
Probab=62.08 E-value=5.9 Score=26.98 Aligned_cols=24 Identities=21% Similarity=0.192 Sum_probs=21.4
Q ss_pred cCCCChhhhHHHhhcchhhHHHHH
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKIL 26 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l 26 (163)
-++++..+||+..|||.+++++..
T Consensus 30 ~~~~t~~~Ia~~agvs~~~~Y~~f 53 (201)
T COG1309 30 YAATTVDEIAKAAGVSKGTLYRHF 53 (201)
T ss_pred cCCCCHHHHHHHhCCCcchhHHHc
Confidence 357899999999999999999875
No 480
>PRK09508 leuO leucine transcriptional activator; Reviewed
Probab=61.75 E-value=7.2 Score=30.16 Aligned_cols=23 Identities=22% Similarity=0.226 Sum_probs=19.6
Q ss_pred ChhhhHHHhhcchhhHHHHHhhh
Q psy1904 7 RPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 7 ~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
+-..+|+.|+||+++||+-+++.
T Consensus 38 s~s~AA~~L~isQpavS~~I~~L 60 (314)
T PRK09508 38 NITRAAHNLGMSQPAVSNAVARL 60 (314)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHH
Confidence 35678999999999999999666
No 481
>PRK11062 nhaR transcriptional activator NhaR; Provisional
Probab=61.75 E-value=7.3 Score=29.86 Aligned_cols=23 Identities=4% Similarity=0.021 Sum_probs=20.1
Q ss_pred ChhhhHHHhhcchhhHHHHHhhh
Q psy1904 7 RPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 7 ~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
+...+|+.|+||+++||+-++..
T Consensus 20 s~s~AA~~L~isqpavS~~I~~L 42 (296)
T PRK11062 20 SVVGAAEALFLTPQTITGQIKAL 42 (296)
T ss_pred CHHHHHHHhCCChHHHHHHHHHH
Confidence 45678999999999999999776
No 482
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=61.62 E-value=8.9 Score=25.78 Aligned_cols=25 Identities=8% Similarity=0.049 Sum_probs=22.8
Q ss_pred CCChhhhHHHhhcchhhHHHHHhhh
Q psy1904 5 GVRPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 5 g~~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
-++..+||+.+|||..++.++.++.
T Consensus 25 ~~sl~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 25 PLSLEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 4788999999999999999999776
No 483
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=61.55 E-value=7.7 Score=29.11 Aligned_cols=31 Identities=29% Similarity=0.264 Sum_probs=26.7
Q ss_pred hhhhHHHhhcchhhHHHHHhhhhhccCCCCC
Q psy1904 8 PCVISRQLRVSHGCVSKILNRYQETGSIRPG 38 (163)
Q Consensus 8 ~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg 38 (163)
-.++|++|+||.-||.+-|..+.+-|-+.-.
T Consensus 34 E~eLa~~f~VSR~TvRkAL~~L~~eGli~r~ 64 (236)
T COG2188 34 ERELAEQFGVSRMTVRKALDELVEEGLIVRR 64 (236)
T ss_pred HHHHHHHHCCcHHHHHHHHHHHHHCCcEEEE
Confidence 3589999999999999999999888877543
No 484
>PF07278 DUF1441: Protein of unknown function (DUF1441); InterPro: IPR009901 This entry is represented by Bacteriophage VT1-Sakai, H0025. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several hypothetical Enterobacterial proteins of around 160 residues in length. The function of this family is unknown.
Probab=61.47 E-value=28 Score=24.55 Aligned_cols=47 Identities=11% Similarity=0.051 Sum_probs=30.3
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhhccCCCCCCCCCCCCCcCChHHHHHHHHHH
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYK 60 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~~Gg~~p~~~~~~~~~~i~~~~ 60 (163)
+++.+||..||+...||++=|+-. . +.+|+..........+.+..+.
T Consensus 2 ~nI~qlA~~~g~~R~TV~~RL~~~------~--p~~g~~~~~~lY~l~dv~~~l~ 48 (152)
T PF07278_consen 2 WNINQLAEAFGLHRQTVAKRLKGA------N--PAAGSNRGLKLYALRDVLPALF 48 (152)
T ss_pred CCHHHHHHHHcccHHHHHHHHccC------C--CCCCCCCCCCcchHHHHHHHHh
Confidence 578899999999999999988433 3 2234433444445555454433
No 485
>PRK13866 plasmid partitioning protein RepB; Provisional
Probab=61.44 E-value=5.8 Score=31.61 Aligned_cols=28 Identities=18% Similarity=0.202 Sum_probs=24.9
Q ss_pred ccCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904 2 AAAGVRPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 2 ~~~g~~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
...|++..+|+..|+++.+.||++|.-.
T Consensus 176 ~~~g~~~~~i~~aL~~~~s~vS~~l~v~ 203 (336)
T PRK13866 176 EDAGFDRATIIAALSTDKADLSRYITVA 203 (336)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 3579999999999999999999998665
No 486
>TIGR03433 padR_acidobact transcriptional regulator, Acidobacterial, PadR-family. Members of this protein family are putative transcriptional regulators of the PadR family, as found in species of the Acidobacteria. This family of proteins has expanded greatly in this lineage, and where it regularly is found in the vicinity of a putative transporter protein
Probab=61.32 E-value=24 Score=22.64 Aligned_cols=32 Identities=25% Similarity=0.403 Sum_probs=25.5
Q ss_pred CChhhhHHH--------hhcchhhHHHHHhhhhhccCCCC
Q psy1904 6 VRPCVISRQ--------LRVSHGCVSKILNRYQETGSIRP 37 (163)
Q Consensus 6 ~~~~~ia~~--------~~vs~~~vs~~l~~~~~tG~~~P 37 (163)
+..-||++. +.|++++|+.+|.+..+-|-+..
T Consensus 18 ~~GYei~~~l~~~~~~~~~i~~gtlY~~L~rLe~~GlI~~ 57 (100)
T TIGR03433 18 LHGYGIAQRIQQISEDVLQVEEGSLYPALHRLERRGWIAA 57 (100)
T ss_pred CCHHHHHHHHHHHcCCccccCCCcHHHHHHHHHHCCCeEE
Confidence 444555554 47999999999999999998876
No 487
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=61.30 E-value=9.4 Score=25.95 Aligned_cols=32 Identities=13% Similarity=0.245 Sum_probs=28.0
Q ss_pred ChhhhHHHhhcchhhHHHHHhhhhhccCCCCC
Q psy1904 7 RPCVISRQLRVSHGCVSKILNRYQETGSIRPG 38 (163)
Q Consensus 7 ~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg 38 (163)
|-.++|..++|+..||+|-.+-..+-|-+.-.
T Consensus 37 SvRelA~~~~VNpnTv~raY~eLE~eG~i~t~ 68 (125)
T COG1725 37 SVRELAKDLGVNPNTVQRAYQELEREGIVETK 68 (125)
T ss_pred cHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEe
Confidence 56799999999999999999998888888544
No 488
>PF02002 TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024550 The general transcription factor TFIIE has an essential role in eukaryotic transcription initiation, together with RNA polymerase II and other general factors. Human TFIIE consists of two subunits, TFIIE-alpha and TFIIE-beta, and joins the preinitiation complex after RNA polymerase II and TFIIF []. This entry represents a helix-turn-helix (HTH) domain found in eukaryotic TFIIE-alpha []. It is also found in proteins from archaebacteria that are presumed to be TFIIE-alpha subunits [], the transcriptional regulator SarR, and also DNA-directed RNA polymerase III subunit Rpc3.; PDB: 1VD4_A 1Q1H_A.
Probab=61.18 E-value=3.1 Score=27.05 Aligned_cols=32 Identities=22% Similarity=0.283 Sum_probs=24.5
Q ss_pred CCChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904 5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIR 36 (163)
Q Consensus 5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~ 36 (163)
.++-.|||+.+|+....|.++|....+-|-+.
T Consensus 27 ~l~de~la~~~~l~~~~vRkiL~~L~~~~lv~ 58 (105)
T PF02002_consen 27 ELTDEDLAKKLGLKPKEVRKILYKLYEDGLVS 58 (105)
T ss_dssp -B-HHHHHHTT-S-HHHHHHHHHHHHHHSS-E
T ss_pred CcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeE
Confidence 37889999999999999999999998877763
No 489
>PRK15092 DNA-binding transcriptional repressor LrhA; Provisional
Probab=60.77 E-value=8 Score=30.09 Aligned_cols=23 Identities=13% Similarity=0.157 Sum_probs=20.1
Q ss_pred ChhhhHHHhhcchhhHHHHHhhh
Q psy1904 7 RPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 7 ~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
+-..+|+.|+||+++||+-+++.
T Consensus 27 s~s~AA~~L~iSQpavS~~I~~L 49 (310)
T PRK15092 27 TFAAAAAAVCRTQSAVSQQMQRL 49 (310)
T ss_pred CHHHHHHHhCCChHHHHHHHHHH
Confidence 45678999999999999999777
No 490
>PF06530 Phage_antitermQ: Phage antitermination protein Q; InterPro: IPR010534 This entry is represented by Bacteriophage 933W, GpQ. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several phage antitermination protein Q and related bacterial sequences. Phage 993W gene Q encodes a phage-specific positive regulator of late gene expression, thought, by analogy to the corresponding gene of phage lambda, to be a transcription antiterminator. GpQ positively regulates expression of the phage late gene operons. Bacterial host RNA polymerase modified by antitermination proteins transcribes through termination sites that otherwise prevent expression of the regulated genes [, ].; GO: 0003677 DNA binding, 0060567 negative regulation of transcription termination, DNA-dependent
Probab=60.37 E-value=10 Score=25.61 Aligned_cols=26 Identities=35% Similarity=0.419 Sum_probs=23.4
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
.|++-..||+.+++|.++|.+.|+.-
T Consensus 77 ~g~s~r~IA~~~~~s~~~ir~~l~~a 102 (125)
T PF06530_consen 77 YGWSKRQIARKLKCSEGKIRKRLQRA 102 (125)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHh
Confidence 58999999999999999999998653
No 491
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=60.24 E-value=8.6 Score=26.71 Aligned_cols=26 Identities=19% Similarity=0.176 Sum_probs=24.7
Q ss_pred CChhhhHHHhhcchhhHHHHHhhhhh
Q psy1904 6 VRPCVISRQLRVSHGCVSKILNRYQE 31 (163)
Q Consensus 6 ~~~~~ia~~~~vs~~~vs~~l~~~~~ 31 (163)
++--|||+.+|+....|.++|..+.+
T Consensus 16 ~~dedLa~~l~i~~n~vRkiL~~L~e 41 (147)
T smart00531 16 VTEEDLAELLGIKQKQLRKILYLLYD 41 (147)
T ss_pred cCHHHHHHHhCCCHHHHHHHHHHHHh
Confidence 78899999999999999999999988
No 492
>PRK00082 hrcA heat-inducible transcription repressor; Provisional
Probab=60.19 E-value=14 Score=29.46 Aligned_cols=41 Identities=24% Similarity=0.391 Sum_probs=32.7
Q ss_pred CChhhhHHH--hhcchhhHHHHHhhhhhccCCC-CCCCCCCCCC
Q psy1904 6 VRPCVISRQ--LRVSHGCVSKILNRYQETGSIR-PGVIGGSKPR 46 (163)
Q Consensus 6 ~~~~~ia~~--~~vs~~~vs~~l~~~~~tG~~~-Pg~~Gg~~p~ 46 (163)
++-.++|+. |+||.+||.+-+....+.|-+. |-..+|.-|+
T Consensus 26 v~s~~l~~~~~l~~S~aTIR~dm~~Le~~G~l~~~h~sagrIPT 69 (339)
T PRK00082 26 VGSKTLSKRYGLGVSSATIRNDMADLEELGLLEKPHTSSGRIPT 69 (339)
T ss_pred cCHHHHHHHhCCCCChHHHHHHHHHHHhCCCcCCCcCCCCCCcC
Confidence 677899977 9999999999999999999984 4334455444
No 493
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=59.88 E-value=10 Score=31.81 Aligned_cols=33 Identities=12% Similarity=0.192 Sum_probs=29.2
Q ss_pred CCCChhhhHHHhhcchhhHHHHHhhhhhccCCC
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIR 36 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~ 36 (163)
.++++.+||+.+++++++|.+++++...-|=+.
T Consensus 19 ~~~s~~eLA~~l~l~~~tVt~~i~~Le~kGlV~ 51 (489)
T PRK04172 19 KEATLEELAEKLGLPPEAVMRAAEWLEEKGLVK 51 (489)
T ss_pred CCCCHHHHHHHhCcCHHHHHHHHHHHHhCCCEE
Confidence 458999999999999999999999998877654
No 494
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=59.80 E-value=7.3 Score=28.20 Aligned_cols=23 Identities=13% Similarity=0.120 Sum_probs=20.7
Q ss_pred CCCChhhhHHHhhcchhhHHHHH
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKIL 26 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l 26 (163)
++++..+||+..|||.+|+++.-
T Consensus 30 ~~~ti~~Ia~~agvsk~t~Y~~F 52 (213)
T PRK09975 30 SNTTLNDIADAANVTRGAIYWHF 52 (213)
T ss_pred ccCCHHHHHHHcCCCHHHHHHHc
Confidence 56899999999999999999864
No 495
>PF04760 IF2_N: Translation initiation factor IF-2, N-terminal region; InterPro: IPR006847 This region is found in the N-terminal half of translation initiation factor IF-2. It is found in two copies in IF-2 alpha isoforms, and in only one copy in the N-terminally truncated beta and gamma isoforms []. Its function is unknown.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1ND9_A.
Probab=59.51 E-value=6.4 Score=22.18 Aligned_cols=22 Identities=23% Similarity=0.309 Sum_probs=19.1
Q ss_pred CCChhhhHHHhhcchhhHHHHH
Q psy1904 5 GVRPCVISRQLRVSHGCVSKIL 26 (163)
Q Consensus 5 g~~~~~ia~~~~vs~~~vs~~l 26 (163)
.++..|+|+.+||+..-|.+.|
T Consensus 3 ~i~V~elAk~l~v~~~~ii~~l 24 (54)
T PF04760_consen 3 KIRVSELAKELGVPSKEIIKKL 24 (54)
T ss_dssp EE-TTHHHHHHSSSHHHHHHHH
T ss_pred ceEHHHHHHHHCcCHHHHHHHH
Confidence 4678999999999999999988
No 496
>smart00843 Ftsk_gamma This domain directs oriented DNA translocation and forms a winged helix structure. Mutated proteins with substitutions in the FtsK gamma DNA-recognition helix are impaired in DNA binding.
Probab=58.96 E-value=26 Score=20.76 Aligned_cols=35 Identities=17% Similarity=0.471 Sum_probs=31.7
Q ss_pred CCChhhhHHHhhcchhhHHHHHhhhhhccCCCCCC
Q psy1904 5 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV 39 (163)
Q Consensus 5 g~~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~Pg~ 39 (163)
-+|.+-|=|+|+|......+|+.+..+.|-+.|..
T Consensus 19 ~~S~S~lQR~~~IGynrAariid~lE~~GiV~p~~ 53 (63)
T smart00843 19 KASTSLLQRRLRIGYNRAARLIDQLEEEGIVGPAN 53 (63)
T ss_pred CCChHHHHHHHhcchhHHHHHHHHHHHCcCCCCCC
Confidence 37888899999999999999999999999999863
No 497
>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=58.86 E-value=9.2 Score=22.75 Aligned_cols=25 Identities=20% Similarity=0.295 Sum_probs=17.8
Q ss_pred CCChhhhHHHh-----hcchhhHHHHHhhh
Q psy1904 5 GVRPCVISRQL-----RVSHGCVSKILNRY 29 (163)
Q Consensus 5 g~~~~~ia~~~-----~vs~~~vs~~l~~~ 29 (163)
.++..+|+..| .||..||.+.|...
T Consensus 13 ~~s~~~i~~~l~~~~~~vS~~TI~r~L~~~ 42 (72)
T PF01498_consen 13 RISAREIAQELQEAGISVSKSTIRRRLREA 42 (72)
T ss_dssp ---HHHHHHHT---T--S-HHHHHHHHHHT
T ss_pred CCCHHHHHHHHHHccCCcCHHHHHHHHHHc
Confidence 37788999988 89999999999665
No 498
>COG1318 Predicted transcriptional regulators [Transcription]
Probab=58.56 E-value=9.1 Score=27.49 Aligned_cols=27 Identities=22% Similarity=0.213 Sum_probs=24.0
Q ss_pred cCCCChhhhHHHhhcchhhHHHHHhhh
Q psy1904 3 AAGVRPCVISRQLRVSHGCVSKILNRY 29 (163)
Q Consensus 3 ~~g~~~~~ia~~~~vs~~~vs~~l~~~ 29 (163)
..|+...+||+-||++..||.++|+--
T Consensus 59 kag~Ti~EIAeelG~TeqTir~hlkge 85 (182)
T COG1318 59 KAGMTISEIAEELGRTEQTVRNHLKGE 85 (182)
T ss_pred HccCcHHHHHHHhCCCHHHHHHHHhcc
Confidence 478999999999999999999999543
No 499
>TIGR03337 phnR transcriptional regulator protein. 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 Salmonella, Vibrio Aeromonas hydrophila, Hahella chejuensis and Psychromonas ingrahamii.
Probab=58.48 E-value=10 Score=27.95 Aligned_cols=31 Identities=10% Similarity=0.183 Sum_probs=27.0
Q ss_pred ChhhhHHHhhcchhhHHHHHhhhhhccCCCC
Q psy1904 7 RPCVISRQLRVSHGCVSKILNRYQETGSIRP 37 (163)
Q Consensus 7 ~~~~ia~~~~vs~~~vs~~l~~~~~tG~~~P 37 (163)
+..++|+.||||..||.+-|....+.|-+.-
T Consensus 27 sE~eLa~~~~Vsr~Tvr~Al~~L~~eGli~~ 57 (231)
T TIGR03337 27 SERDLGERFNTTRVTIREALQQLEAEGLIYR 57 (231)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCeEEE
Confidence 4678999999999999999999988887743
No 500
>PRK14996 TetR family transcriptional regulator; Provisional
Probab=58.07 E-value=7.1 Score=27.86 Aligned_cols=23 Identities=22% Similarity=0.244 Sum_probs=20.6
Q ss_pred CCCChhhhHHHhhcchhhHHHHH
Q psy1904 4 AGVRPCVISRQLRVSHGCVSKIL 26 (163)
Q Consensus 4 ~g~~~~~ia~~~~vs~~~vs~~l 26 (163)
.|++..+||+..|||.++++..-
T Consensus 27 ~~tSi~~Ia~~aGvsk~~lY~~F 49 (192)
T PRK14996 27 AAMTVRRIASEAQVAAGQVHHHF 49 (192)
T ss_pred hhccHHHHHHHhCCCcHHHHHHc
Confidence 45899999999999999999875
Done!