Query psy672
Match_columns 314
No_of_seqs 181 out of 1625
Neff 8.9
Searched_HMMs 46136
Date Fri Aug 16 16:40:29 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy672.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/672hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF13359 DDE_Tnp_4: DDE superf 100.0 3.1E-39 6.8E-44 266.0 5.1 150 117-266 1-158 (158)
2 KOG4585|consensus 100.0 5.2E-38 1.1E-42 283.2 12.1 293 9-313 7-320 (326)
3 PF04827 Plant_tran: Plant tra 100.0 5.7E-36 1.2E-40 243.4 9.2 185 89-274 2-203 (205)
4 PF13612 DDE_Tnp_1_3: Transpos 99.2 1E-11 2.2E-16 100.7 3.6 128 109-244 2-149 (155)
5 PF13613 HTH_Tnp_4: Helix-turn 99.2 5E-11 1.1E-15 79.0 5.3 50 38-87 2-51 (53)
6 PF13586 DDE_Tnp_1_2: Transpos 98.2 1E-06 2.2E-11 64.9 3.7 76 191-267 1-87 (88)
7 PF01609 DDE_Tnp_1: Transposas 98.1 3.4E-07 7.3E-12 77.8 -2.1 149 113-267 5-213 (213)
8 PF02796 HTH_7: Helix-turn-hel 96.7 0.00072 1.6E-08 42.9 1.4 42 35-77 2-43 (45)
9 PF04545 Sigma70_r4: Sigma-70, 96.4 0.004 8.7E-08 40.3 3.5 45 38-83 4-48 (50)
10 PF13936 HTH_38: Helix-turn-he 96.2 0.002 4.3E-08 40.6 1.1 41 37-78 3-43 (44)
11 PF13340 DUF4096: Putative tra 96.0 0.0093 2E-07 42.2 3.6 62 20-82 4-67 (75)
12 PF13011 LZ_Tnp_IS481: leucine 95.8 0.014 3E-07 42.1 3.8 49 34-82 4-52 (85)
13 PF13384 HTH_23: Homeodomain-l 95.4 0.0052 1.1E-07 39.6 0.6 39 42-81 5-43 (50)
14 PF13518 HTH_28: Helix-turn-he 95.3 0.013 2.8E-07 38.0 2.1 37 44-81 2-38 (52)
15 PF04218 CENP-B_N: CENP-B N-te 95.2 0.01 2.3E-07 39.0 1.3 42 36-78 4-45 (53)
16 smart00351 PAX Paired Box doma 95.1 0.028 6E-07 44.1 3.8 45 36-81 15-59 (125)
17 PF05225 HTH_psq: helix-turn-h 94.7 0.027 5.8E-07 35.6 2.2 37 42-78 2-39 (45)
18 cd06571 Bac_DnaA_C C-terminal 94.6 0.085 1.8E-06 38.7 5.1 53 33-85 22-75 (90)
19 PF12116 SpoIIID: Stage III sp 94.4 0.023 5E-07 40.0 1.5 44 42-85 5-49 (82)
20 cd00131 PAX Paired Box domain 94.4 0.051 1.1E-06 42.8 3.7 46 36-82 15-60 (128)
21 cd00569 HTH_Hin_like Helix-tur 94.2 0.044 9.5E-07 32.0 2.4 41 35-76 2-42 (42)
22 COG3415 Transposase and inacti 94.0 0.047 1E-06 43.4 2.8 45 38-82 4-48 (138)
23 PRK09413 IS2 repressor TnpA; R 93.7 0.076 1.6E-06 41.3 3.5 46 36-81 10-55 (121)
24 PF01527 HTH_Tnp_1: Transposas 93.7 0.038 8.3E-07 38.9 1.6 45 36-80 4-48 (76)
25 PRK00118 putative DNA-binding 93.4 0.11 2.4E-06 39.1 3.7 48 37-85 16-63 (104)
26 smart00421 HTH_LUXR helix_turn 93.1 0.14 3.1E-06 33.3 3.7 45 38-84 3-47 (58)
27 cd06171 Sigma70_r4 Sigma70, re 92.9 0.12 2.6E-06 33.0 3.0 43 39-82 11-53 (55)
28 PRK04217 hypothetical protein; 92.7 0.18 3.8E-06 38.5 4.0 49 37-86 41-89 (110)
29 PRK09639 RNA polymerase sigma 92.2 0.18 3.8E-06 41.1 3.8 48 38-87 112-159 (166)
30 PF13542 HTH_Tnp_ISL3: Helix-t 92.1 0.11 2.4E-06 33.6 2.0 32 48-79 20-51 (52)
31 TIGR03879 near_KaiC_dom probab 92.0 0.14 3.1E-06 35.8 2.5 41 38-78 15-55 (73)
32 PRK12529 RNA polymerase sigma 91.4 0.27 5.8E-06 40.8 4.1 48 38-86 127-174 (178)
33 cd06170 LuxR_C_like C-terminal 91.1 0.3 6.5E-06 31.7 3.4 43 40-84 2-44 (57)
34 PF08281 Sigma70_r4_2: Sigma-7 91.0 0.27 5.9E-06 32.0 3.0 44 38-82 10-53 (54)
35 PRK09652 RNA polymerase sigma 90.9 0.27 5.8E-06 40.4 3.6 49 38-87 128-176 (182)
36 TIGR02531 yecD_yerC TrpR-relat 90.9 0.17 3.7E-06 36.9 2.1 32 46-77 41-72 (88)
37 PRK08301 sporulation sigma fac 90.1 0.34 7.5E-06 42.1 3.7 50 38-87 178-230 (234)
38 PRK05911 RNA polymerase sigma 89.5 0.44 9.4E-06 42.2 4.0 50 38-88 205-254 (257)
39 TIGR02952 Sig70_famx2 RNA poly 89.5 0.46 9.9E-06 38.7 3.9 47 38-85 122-168 (170)
40 TIGR01321 TrpR trp operon repr 89.5 0.28 6.1E-06 36.1 2.2 41 39-79 33-79 (94)
41 PRK12547 RNA polymerase sigma 89.4 0.49 1.1E-05 38.6 3.9 48 38-86 112-159 (164)
42 PF07374 DUF1492: Protein of u 89.4 0.39 8.6E-06 35.9 3.1 43 40-83 57-99 (100)
43 PRK12519 RNA polymerase sigma 89.3 0.33 7E-06 40.8 2.9 48 39-87 142-189 (194)
44 TIGR02985 Sig70_bacteroi1 RNA 89.3 0.49 1.1E-05 37.9 3.9 47 38-85 113-159 (161)
45 PRK12511 RNA polymerase sigma 89.2 0.48 1E-05 39.5 3.8 50 38-88 111-160 (182)
46 PRK06030 hypothetical protein; 89.1 0.88 1.9E-05 35.5 4.9 47 37-83 51-97 (124)
47 PRK12530 RNA polymerase sigma 89.0 0.45 9.7E-06 39.9 3.5 48 38-86 134-181 (189)
48 PHA00542 putative Cro-like pro 89.0 0.3 6.6E-06 35.1 2.1 33 46-78 22-54 (82)
49 PRK07037 extracytoplasmic-func 88.8 0.55 1.2E-05 38.1 3.8 47 39-86 110-156 (163)
50 PRK09415 RNA polymerase factor 88.8 0.48 1E-05 39.3 3.5 49 38-87 127-175 (179)
51 PRK12514 RNA polymerase sigma 88.7 0.56 1.2E-05 38.7 3.8 48 38-86 129-176 (179)
52 PRK12516 RNA polymerase sigma 88.5 0.57 1.2E-05 39.3 3.8 49 38-87 116-164 (187)
53 TIGR00721 tfx DNA-binding prot 88.5 0.55 1.2E-05 37.3 3.4 46 38-85 6-51 (137)
54 TIGR02844 spore_III_D sporulat 88.4 0.34 7.3E-06 34.7 2.0 37 41-77 4-41 (80)
55 PF01710 HTH_Tnp_IS630: Transp 88.3 0.67 1.5E-05 35.9 3.8 69 8-79 26-95 (119)
56 PRK03975 tfx putative transcri 88.2 0.62 1.4E-05 37.2 3.6 47 37-85 5-51 (141)
57 PRK12533 RNA polymerase sigma 88.0 0.6 1.3E-05 40.2 3.7 49 38-87 134-182 (216)
58 PRK15320 transcriptional activ 88.0 0.58 1.3E-05 39.3 3.3 45 38-84 164-208 (251)
59 PRK12524 RNA polymerase sigma 88.0 0.66 1.4E-05 39.1 3.9 48 38-86 136-183 (196)
60 PRK09638 RNA polymerase sigma 88.0 0.3 6.5E-06 40.2 1.7 48 38-86 126-173 (176)
61 TIGR02989 Sig-70_gvs1 RNA poly 87.9 0.63 1.4E-05 37.5 3.6 47 38-85 111-157 (159)
62 COG3293 Transposase and inacti 87.9 0.19 4.2E-06 39.1 0.5 93 145-246 2-101 (124)
63 PF04967 HTH_10: HTH DNA bindi 87.8 0.3 6.6E-06 31.9 1.3 29 56-84 24-52 (53)
64 PRK09641 RNA polymerase sigma 87.8 0.62 1.3E-05 38.6 3.6 48 38-86 136-183 (187)
65 TIGR02937 sigma70-ECF RNA poly 87.8 0.63 1.4E-05 36.6 3.6 47 38-85 110-156 (158)
66 PRK09047 RNA polymerase factor 87.8 0.72 1.6E-05 37.2 3.9 48 38-86 106-153 (161)
67 PRK12531 RNA polymerase sigma 87.8 0.7 1.5E-05 38.8 3.9 47 39-86 142-188 (194)
68 PF13751 DDE_Tnp_1_6: Transpos 87.8 0.22 4.8E-06 38.7 0.8 50 219-269 73-123 (125)
69 PRK05803 sporulation sigma fac 87.8 0.58 1.2E-05 40.7 3.5 49 38-86 175-226 (233)
70 PF12802 MarR_2: MarR family; 87.6 0.59 1.3E-05 31.1 2.8 26 56-81 22-47 (62)
71 PF13412 HTH_24: Winged helix- 87.5 0.56 1.2E-05 29.7 2.4 28 54-81 16-43 (48)
72 PRK12537 RNA polymerase sigma 87.3 0.75 1.6E-05 38.2 3.8 46 39-85 134-179 (182)
73 PRK12515 RNA polymerase sigma 87.3 0.75 1.6E-05 38.4 3.8 48 38-86 131-178 (189)
74 PRK05602 RNA polymerase sigma 87.2 0.7 1.5E-05 38.4 3.6 48 39-87 129-176 (186)
75 PRK11924 RNA polymerase sigma 87.1 0.71 1.5E-05 37.8 3.6 48 38-86 125-172 (179)
76 COG3316 Transposase and inacti 87.1 5.2 0.00011 34.2 8.7 187 38-270 8-200 (215)
77 PRK12512 RNA polymerase sigma 87.1 0.79 1.7E-05 38.0 3.8 48 38-86 131-178 (184)
78 PRK11923 algU RNA polymerase s 87.0 0.69 1.5E-05 38.7 3.4 52 38-90 138-189 (193)
79 PF00196 GerE: Bacterial regul 86.9 0.49 1.1E-05 31.4 2.0 44 39-84 4-47 (58)
80 PHA00675 hypothetical protein 86.9 0.49 1.1E-05 33.2 2.0 40 38-77 22-61 (78)
81 TIGR03001 Sig-70_gmx1 RNA poly 86.8 0.78 1.7E-05 40.3 3.8 47 38-85 161-207 (244)
82 PRK07408 RNA polymerase sigma 86.7 0.84 1.8E-05 40.4 4.0 48 38-86 203-250 (256)
83 TIGR02392 rpoH_proteo alternat 86.6 0.78 1.7E-05 40.9 3.8 48 38-85 218-266 (270)
84 PF13551 HTH_29: Winged helix- 86.5 0.51 1.1E-05 35.5 2.2 36 48-83 4-40 (112)
85 TIGR02983 SigE-fam_strep RNA p 86.5 0.86 1.9E-05 36.9 3.7 47 39-86 111-157 (162)
86 TIGR02835 spore_sigmaE RNA pol 86.4 0.85 1.8E-05 39.7 3.8 49 38-86 178-229 (234)
87 PRK09643 RNA polymerase sigma 86.4 0.85 1.8E-05 38.3 3.7 49 38-87 134-182 (192)
88 PF13730 HTH_36: Helix-turn-he 86.4 0.71 1.5E-05 30.1 2.5 43 39-81 3-51 (55)
89 TIGR02984 Sig-70_plancto1 RNA 86.3 1 2.2E-05 37.4 4.1 48 38-86 140-187 (189)
90 PF01047 MarR: MarR family; I 86.2 0.76 1.7E-05 30.3 2.7 39 43-81 5-43 (59)
91 COG2739 Uncharacterized protei 86.0 1.1 2.4E-05 33.2 3.6 44 42-85 20-63 (105)
92 TIGR02950 SigM_subfam RNA poly 86.0 0.34 7.4E-06 38.8 1.0 47 39-86 106-152 (154)
93 PRK12534 RNA polymerase sigma 86.0 0.98 2.1E-05 37.5 3.9 47 39-86 138-184 (187)
94 PF08279 HTH_11: HTH domain; 86.0 0.78 1.7E-05 29.9 2.6 30 54-83 14-43 (55)
95 TIGR02960 SigX5 RNA polymerase 85.8 1.2 2.5E-05 40.7 4.6 52 38-90 142-193 (324)
96 PRK12546 RNA polymerase sigma 85.8 0.97 2.1E-05 37.9 3.7 49 38-87 113-161 (188)
97 TIGR02939 RpoE_Sigma70 RNA pol 85.6 0.86 1.9E-05 37.9 3.3 49 38-87 138-186 (190)
98 PRK12540 RNA polymerase sigma 85.6 1 2.2E-05 37.5 3.8 49 38-87 111-159 (182)
99 TIGR02954 Sig70_famx3 RNA poly 85.6 1 2.3E-05 36.7 3.7 48 38-86 119-166 (169)
100 PF01022 HTH_5: Bacterial regu 85.6 0.58 1.3E-05 29.6 1.7 38 44-81 4-41 (47)
101 PRK12532 RNA polymerase sigma 85.5 0.94 2E-05 38.0 3.5 48 38-86 136-183 (195)
102 PRK05572 sporulation sigma fac 85.5 1.1 2.3E-05 39.5 4.0 48 38-86 202-249 (252)
103 PRK09645 RNA polymerase sigma 85.5 1.1 2.4E-05 36.7 3.9 47 39-86 119-165 (173)
104 PF13309 HTH_22: HTH domain 85.5 0.66 1.4E-05 31.7 2.1 41 37-77 19-64 (64)
105 PF01325 Fe_dep_repress: Iron 85.4 1.1 2.3E-05 30.2 3.1 41 41-81 5-48 (60)
106 PRK06811 RNA polymerase factor 85.4 0.99 2.1E-05 37.7 3.6 47 38-85 131-177 (189)
107 PF13610 DDE_Tnp_IS240: DDE do 85.2 1.5 3.3E-05 34.8 4.4 131 116-271 5-139 (140)
108 PF00872 Transposase_mut: Tran 85.2 1.4 3E-05 41.5 4.8 130 49-207 108-247 (381)
109 TIGR02948 SigW_bacill RNA poly 85.1 1 2.2E-05 37.3 3.5 48 38-86 136-183 (187)
110 COG2963 Transposase and inacti 85.1 1.1 2.4E-05 34.3 3.5 48 36-83 5-53 (116)
111 PF08299 Bac_DnaA_C: Bacterial 85.0 0.58 1.3E-05 32.5 1.7 45 35-79 25-70 (70)
112 PRK12539 RNA polymerase sigma 84.9 1.2 2.5E-05 37.1 3.8 48 38-86 131-178 (184)
113 PF01710 HTH_Tnp_IS630: Transp 84.8 0.45 9.7E-06 36.9 1.1 30 49-78 12-41 (119)
114 PRK12544 RNA polymerase sigma 84.8 1.2 2.6E-05 38.0 3.8 48 38-86 148-195 (206)
115 PRK12520 RNA polymerase sigma 84.8 1.4 3E-05 36.8 4.2 48 38-86 131-178 (191)
116 PRK06759 RNA polymerase factor 84.7 1.1 2.4E-05 35.8 3.5 46 38-84 106-151 (154)
117 TIGR02980 SigBFG RNA polymeras 84.6 1.3 2.8E-05 38.2 4.1 47 38-85 178-224 (227)
118 PF00356 LacI: Bacterial regul 84.5 0.24 5.1E-06 31.4 -0.5 21 58-78 2-22 (46)
119 PRK06596 RNA polymerase factor 84.4 1 2.2E-05 40.5 3.4 48 38-85 230-278 (284)
120 PRK12523 RNA polymerase sigma 84.1 1.4 3E-05 36.2 3.9 47 38-85 119-165 (172)
121 PRK08583 RNA polymerase sigma 84.0 1.4 3E-05 38.9 4.0 47 38-85 205-251 (257)
122 TIGR02846 spore_sigmaK RNA pol 84.0 1.3 2.7E-05 38.4 3.7 48 38-85 174-224 (227)
123 TIGR02393 RpoD_Cterm RNA polym 83.7 1.1 2.4E-05 39.0 3.3 48 38-85 176-226 (238)
124 TIGR02394 rpoS_proteo RNA poly 83.4 1.2 2.7E-05 39.9 3.6 50 38-87 222-274 (285)
125 PRK07500 rpoH2 RNA polymerase 83.1 1.3 2.9E-05 39.8 3.6 49 38-86 227-276 (289)
126 PRK12525 RNA polymerase sigma 82.9 1.8 3.9E-05 35.3 4.1 47 38-85 118-164 (168)
127 TIGR02885 spore_sigF RNA polym 82.8 1.7 3.7E-05 37.6 4.1 47 38-85 183-229 (231)
128 TIGR02943 Sig70_famx1 RNA poly 82.7 1.6 3.5E-05 36.4 3.8 48 38-86 131-178 (188)
129 PRK08215 sporulation sigma fac 82.6 1.7 3.7E-05 38.4 4.0 47 38-85 209-255 (258)
130 PRK06704 RNA polymerase factor 82.4 1.5 3.2E-05 38.2 3.4 52 38-90 116-167 (228)
131 PF04297 UPF0122: Putative hel 82.2 1.5 3.3E-05 32.8 3.0 44 42-85 20-63 (101)
132 PRK06986 fliA flagellar biosyn 82.2 1.6 3.6E-05 37.9 3.7 48 38-86 184-231 (236)
133 TIGR01636 phage_rinA phage tra 82.1 2.1 4.5E-05 33.9 4.0 48 39-86 83-131 (134)
134 PRK13919 putative RNA polymera 81.6 2 4.4E-05 35.5 4.0 47 39-86 136-182 (186)
135 PRK11512 DNA-binding transcrip 81.6 3 6.4E-05 33.2 4.8 45 37-81 36-80 (144)
136 PRK09648 RNA polymerase sigma 81.5 2.1 4.4E-05 35.7 4.0 47 38-85 139-185 (189)
137 PRK12522 RNA polymerase sigma 81.4 1.6 3.4E-05 35.8 3.2 52 39-91 120-171 (173)
138 PRK08295 RNA polymerase factor 81.3 1.8 4E-05 36.5 3.6 47 38-86 155-201 (208)
139 TIGR02850 spore_sigG RNA polym 81.2 1.7 3.7E-05 38.3 3.6 47 38-85 206-252 (254)
140 TIGR02997 Sig70-cyanoRpoD RNA 81.2 1.4 3E-05 39.9 3.0 45 38-82 249-296 (298)
141 COG1191 FliA DNA-directed RNA 81.0 2.1 4.6E-05 37.6 3.9 48 38-86 196-243 (247)
142 cd00092 HTH_CRP helix_turn_hel 80.8 1.4 3E-05 29.7 2.3 26 56-81 26-51 (67)
143 PF00126 HTH_1: Bacterial regu 80.8 2 4.3E-05 28.7 2.9 40 45-85 4-43 (60)
144 PRK07670 RNA polymerase sigma 80.6 2.2 4.8E-05 37.5 4.0 47 38-85 201-247 (251)
145 smart00346 HTH_ICLR helix_turn 80.6 1.9 4.1E-05 31.1 3.0 40 42-81 4-46 (91)
146 PRK12527 RNA polymerase sigma 80.5 2.3 5E-05 34.2 3.9 48 39-87 106-153 (159)
147 PRK09642 RNA polymerase sigma 80.1 2.4 5.2E-05 34.1 3.8 47 39-86 107-153 (160)
148 PF05344 DUF746: Domain of Unk 80.1 1.8 3.9E-05 29.4 2.5 43 44-86 2-44 (65)
149 PRK06930 positive control sigm 80.1 2.1 4.5E-05 35.4 3.4 48 38-86 114-161 (170)
150 PRK07405 RNA polymerase sigma 80.0 1.9 4.2E-05 39.4 3.5 48 38-85 256-306 (317)
151 PRK13870 transcriptional regul 79.7 1.3 2.7E-05 38.7 2.2 47 37-85 172-218 (234)
152 TIGR02941 Sigma_B RNA polymera 79.7 2.1 4.5E-05 37.7 3.5 47 38-85 205-251 (255)
153 PRK12543 RNA polymerase sigma 79.6 2.3 5.1E-05 35.1 3.7 48 38-86 117-164 (179)
154 PRK09637 RNA polymerase sigma 79.2 2.4 5.1E-05 35.2 3.6 51 38-89 106-156 (181)
155 smart00550 Zalpha Z-DNA-bindin 79.0 1.9 4.2E-05 29.7 2.5 42 40-81 6-48 (68)
156 PRK01381 Trp operon repressor; 78.9 1 2.2E-05 33.5 1.1 40 39-78 33-78 (99)
157 PF01371 Trp_repressor: Trp re 78.8 2.1 4.6E-05 31.1 2.7 38 42-79 36-73 (87)
158 PF09339 HTH_IclR: IclR helix- 78.5 0.73 1.6E-05 29.8 0.2 38 44-81 4-44 (52)
159 PRK15201 fimbriae regulatory p 78.3 1.9 4.1E-05 35.7 2.5 45 38-84 133-177 (198)
160 PRK07122 RNA polymerase sigma 78.1 2.6 5.7E-05 37.4 3.7 47 38-85 215-261 (264)
161 PRK15411 rcsA colanic acid cap 78.1 1.9 4E-05 36.8 2.7 45 38-84 137-181 (207)
162 PRK09636 RNA polymerase sigma 77.7 4.1 8.9E-05 36.7 4.9 50 39-89 116-165 (293)
163 PRK12517 RNA polymerase sigma 77.5 3 6.4E-05 34.9 3.7 48 39-87 129-176 (188)
164 PRK14086 dnaA chromosomal repl 77.5 5.6 0.00012 39.6 6.1 52 34-85 548-599 (617)
165 TIGR02479 FliA_WhiG RNA polyme 77.3 3.3 7.2E-05 35.6 4.1 47 38-85 175-221 (224)
166 PRK00149 dnaA chromosomal repl 77.2 6.4 0.00014 37.8 6.4 53 33-85 380-433 (450)
167 PRK12545 RNA polymerase sigma 77.1 3 6.6E-05 35.2 3.7 49 38-87 139-187 (201)
168 TIGR02957 SigX4 RNA polymerase 77.0 3.9 8.4E-05 36.6 4.5 51 38-89 108-158 (281)
169 PRK12536 RNA polymerase sigma 76.5 3.4 7.4E-05 34.1 3.8 46 39-85 130-175 (181)
170 PRK12535 RNA polymerase sigma 76.5 3.5 7.5E-05 34.8 3.9 51 39-90 134-184 (196)
171 PRK11922 RNA polymerase sigma 76.4 1.6 3.5E-05 37.8 1.9 49 39-88 150-198 (231)
172 PRK15418 transcriptional regul 76.4 1.8 4E-05 39.6 2.3 68 47-116 21-89 (318)
173 PF09862 DUF2089: Protein of u 76.1 3.1 6.7E-05 31.8 3.0 47 38-85 33-79 (113)
174 PRK09649 RNA polymerase sigma 75.3 3.1 6.8E-05 34.6 3.3 47 38-85 130-176 (185)
175 PRK01905 DNA-binding protein F 75.0 6 0.00013 27.9 4.2 29 51-79 46-74 (77)
176 TIGR02959 SigZ RNA polymerase 74.9 4.2 9.1E-05 33.3 3.9 50 38-88 100-149 (170)
177 PF06056 Terminase_5: Putative 74.7 2.6 5.6E-05 28.1 2.1 32 46-79 6-37 (58)
178 smart00342 HTH_ARAC helix_turn 74.6 3.2 6.9E-05 28.8 2.7 67 8-81 9-77 (84)
179 TIGR02859 spore_sigH RNA polym 74.1 3.8 8.3E-05 34.2 3.5 43 42-85 153-195 (198)
180 PF13560 HTH_31: Helix-turn-he 74.0 1.8 3.9E-05 29.2 1.2 28 50-77 9-36 (64)
181 PRK14088 dnaA chromosomal repl 74.0 4.5 9.7E-05 38.8 4.3 52 33-84 365-416 (440)
182 PF07638 Sigma70_ECF: ECF sigm 74.0 4.7 0.0001 33.6 4.0 46 39-85 136-181 (185)
183 PRK07406 RNA polymerase sigma 74.0 3.5 7.7E-05 38.6 3.5 48 38-85 311-361 (373)
184 PRK09646 RNA polymerase sigma 73.9 4.3 9.3E-05 34.0 3.8 48 38-86 142-189 (194)
185 PRK09647 RNA polymerase sigma 73.7 4.3 9.3E-05 34.4 3.7 48 39-87 139-186 (203)
186 PRK12427 flagellar biosynthesi 73.6 4.1 8.9E-05 35.4 3.7 46 38-84 183-228 (231)
187 PRK09640 RNA polymerase sigma 73.0 1.6 3.4E-05 36.4 0.9 48 39-87 135-182 (188)
188 PRK05657 RNA polymerase sigma 73.0 4 8.7E-05 37.5 3.6 49 38-86 262-313 (325)
189 PRK07598 RNA polymerase sigma 72.9 3.8 8.3E-05 38.9 3.5 47 38-84 350-399 (415)
190 TIGR02999 Sig-70_X6 RNA polyme 72.8 4.5 9.7E-05 33.3 3.6 46 39-85 135-180 (183)
191 PHA02591 hypothetical protein; 72.7 2.9 6.3E-05 29.4 1.9 39 40-78 44-82 (83)
192 PF10654 DUF2481: Protein of u 72.7 2.2 4.8E-05 32.3 1.5 35 51-85 75-110 (126)
193 PRK06288 RNA polymerase sigma 72.1 4.7 0.0001 35.8 3.7 47 38-85 212-258 (268)
194 PRK12538 RNA polymerase sigma 72.1 4 8.7E-05 35.5 3.2 48 39-87 172-219 (233)
195 TIGR03697 NtcA_cyano global ni 72.0 3.8 8.2E-05 33.9 3.0 45 38-82 112-170 (193)
196 PF13463 HTH_27: Winged helix 71.9 3 6.5E-05 28.2 2.0 35 48-82 8-45 (68)
197 TIGR01610 phage_O_Nterm phage 71.7 3.3 7.2E-05 30.5 2.3 28 54-81 46-73 (95)
198 PF13545 HTH_Crp_2: Crp-like h 71.7 3.3 7.2E-05 28.7 2.2 25 57-81 30-54 (76)
199 PRK05949 RNA polymerase sigma 71.4 4.4 9.5E-05 37.3 3.5 48 38-85 266-316 (327)
200 PRK12513 RNA polymerase sigma 71.0 2.4 5.2E-05 35.4 1.6 47 39-86 140-186 (194)
201 TIGR02947 SigH_actino RNA poly 71.0 2.4 5.3E-05 35.4 1.6 48 39-87 132-179 (193)
202 PF01978 TrmB: Sugar-specific 70.8 2.7 5.9E-05 28.7 1.5 39 42-81 10-48 (68)
203 PRK03573 transcriptional regul 70.7 3.3 7.1E-05 32.9 2.2 44 38-81 28-72 (144)
204 PRK09635 sigI RNA polymerase s 70.5 6.5 0.00014 35.5 4.3 50 39-89 119-168 (290)
205 PRK12528 RNA polymerase sigma 70.4 4.9 0.00011 32.4 3.2 46 38-84 113-158 (161)
206 PF02001 DUF134: Protein of un 70.4 6.8 0.00015 29.6 3.7 47 38-85 41-87 (106)
207 PF01381 HTH_3: Helix-turn-hel 70.3 1.6 3.4E-05 28.2 0.2 27 52-78 6-32 (55)
208 PF12840 HTH_20: Helix-turn-he 70.0 2.8 6E-05 28.0 1.4 31 52-82 21-51 (61)
209 PRK14087 dnaA chromosomal repl 69.8 9.4 0.0002 36.8 5.5 53 33-85 379-432 (450)
210 PRK09210 RNA polymerase sigma 69.7 4.6 9.9E-05 37.8 3.3 48 38-85 305-355 (367)
211 PF00325 Crp: Bacterial regula 69.7 2 4.4E-05 24.9 0.6 24 57-80 4-27 (32)
212 PRK13719 conjugal transfer tra 69.5 4 8.7E-05 35.0 2.5 46 37-84 142-187 (217)
213 smart00418 HTH_ARSR helix_turn 69.4 3 6.5E-05 27.3 1.5 29 53-81 8-36 (66)
214 smart00345 HTH_GNTR helix_turn 69.2 2.4 5.2E-05 27.6 0.9 25 57-81 22-46 (60)
215 cd00090 HTH_ARSR Arsenical Res 69.1 5.4 0.00012 26.9 2.8 30 52-81 17-46 (78)
216 PRK10188 DNA-binding transcrip 68.3 4.2 9E-05 35.6 2.5 46 37-84 178-223 (240)
217 smart00419 HTH_CRP helix_turn_ 67.9 2.7 5.9E-05 26.0 1.0 27 55-81 8-34 (48)
218 PRK11753 DNA-binding transcrip 67.7 5.7 0.00012 33.4 3.2 44 38-81 138-194 (211)
219 PF04703 FaeA: FaeA-like prote 67.7 3.3 7.2E-05 28.0 1.4 38 43-80 3-40 (62)
220 PRK10840 transcriptional regul 67.2 3.9 8.6E-05 34.6 2.1 45 38-84 150-194 (216)
221 PHA00738 putative HTH transcri 67.1 4.1 8.9E-05 30.8 1.9 29 56-84 27-55 (108)
222 PF05263 DUF722: Protein of un 67.1 5.6 0.00012 31.3 2.7 46 39-84 82-128 (130)
223 TIGR02337 HpaR homoprotocatech 66.6 12 0.00027 28.4 4.7 45 38-82 25-69 (118)
224 PRK13413 mpi multiple promoter 66.5 3.4 7.3E-05 35.0 1.5 30 49-78 166-195 (200)
225 PRK12542 RNA polymerase sigma 66.5 7.4 0.00016 32.2 3.6 50 39-89 123-172 (185)
226 COG0593 DnaA ATPase involved i 66.4 8.3 0.00018 36.5 4.2 53 33-85 343-395 (408)
227 PRK12422 chromosomal replicati 66.3 13 0.00029 35.7 5.7 52 33-84 375-426 (445)
228 COG2771 CsgD DNA-binding HTH d 66.2 5.8 0.00013 26.3 2.4 37 48-84 12-48 (65)
229 PRK12518 RNA polymerase sigma 66.1 3 6.6E-05 34.1 1.2 35 52-86 133-167 (175)
230 TIGR03541 reg_near_HchA LuxR f 66.1 4.7 0.0001 35.0 2.4 47 36-84 169-215 (232)
231 COG2390 DeoR Transcriptional r 65.6 4.1 8.8E-05 37.3 2.0 66 47-114 18-84 (321)
232 PRK10402 DNA-binding transcrip 65.6 5.2 0.00011 34.4 2.6 56 38-93 148-208 (226)
233 PRK09644 RNA polymerase sigma 65.4 6.9 0.00015 31.7 3.2 48 38-86 108-155 (165)
234 PF05043 Mga: Mga helix-turn-h 65.3 5.1 0.00011 28.7 2.1 43 42-85 18-60 (87)
235 smart00344 HTH_ASNC helix_turn 64.9 9 0.00019 28.6 3.5 39 42-81 5-43 (108)
236 PRK11475 DNA-binding transcrip 64.7 4.9 0.00011 34.3 2.2 45 38-84 134-178 (207)
237 COG2197 CitB Response regulato 64.6 4.5 9.8E-05 34.6 2.0 45 38-84 148-192 (211)
238 PRK07921 RNA polymerase sigma 64.5 7.5 0.00016 35.7 3.5 48 38-85 262-312 (324)
239 PRK12526 RNA polymerase sigma 64.3 8.2 0.00018 32.7 3.6 47 39-86 154-200 (206)
240 PRK12541 RNA polymerase sigma 64.3 7.4 0.00016 31.3 3.1 48 38-86 112-159 (161)
241 PRK08241 RNA polymerase factor 64.3 11 0.00023 34.7 4.5 50 39-89 154-203 (339)
242 smart00420 HTH_DEOR helix_turn 64.2 7.9 0.00017 24.2 2.7 27 55-81 14-40 (53)
243 PF00165 HTH_AraC: Bacterial r 63.8 2.5 5.4E-05 25.8 0.2 29 52-80 5-33 (42)
244 PF12964 DUF3853: Protein of u 63.6 3.7 8.1E-05 30.2 1.1 32 59-90 49-82 (96)
245 cd01392 HTH_LacI Helix-turn-he 63.5 3 6.5E-05 26.6 0.5 19 60-78 2-20 (52)
246 cd04762 HTH_MerR-trunc Helix-T 63.4 2.5 5.4E-05 26.1 0.1 21 58-78 3-23 (49)
247 PRK09651 RNA polymerase sigma 63.3 7.5 0.00016 31.8 3.0 48 38-86 119-166 (172)
248 PRK12682 transcriptional regul 63.0 6.4 0.00014 35.4 2.8 46 43-88 4-50 (309)
249 PRK05901 RNA polymerase sigma 62.6 8 0.00017 37.7 3.5 48 38-85 447-497 (509)
250 PRK11161 fumarate/nitrate redu 62.0 8.3 0.00018 33.1 3.2 44 38-81 153-210 (235)
251 PF02209 VHP: Villin headpiece 61.9 1.5 3.4E-05 26.1 -1.0 24 2-26 3-26 (36)
252 PRK10100 DNA-binding transcrip 61.9 6.7 0.00015 33.7 2.6 45 38-84 155-199 (216)
253 COG1595 RpoE DNA-directed RNA 61.7 8.6 0.00019 31.8 3.1 48 39-87 128-175 (182)
254 PF10668 Phage_terminase: Phag 61.6 4.5 9.8E-05 27.2 1.1 30 48-77 13-44 (60)
255 smart00347 HTH_MARR helix_turn 61.4 11 0.00023 27.3 3.3 44 39-82 8-51 (101)
256 TIGR00122 birA_repr_reg BirA b 61.3 5.8 0.00013 27.1 1.7 30 52-81 9-39 (69)
257 PRK09483 response regulator; P 61.3 6.3 0.00014 32.9 2.3 45 38-84 148-192 (217)
258 PF09607 BrkDBD: Brinker DNA-b 61.3 7.6 0.00016 25.8 2.1 42 36-77 3-47 (58)
259 COG5421 Transposase [DNA repli 61.2 13 0.00027 35.7 4.3 56 141-199 154-211 (480)
260 PRK13918 CRP/FNR family transc 61.1 8.7 0.00019 32.1 3.1 43 39-81 119-175 (202)
261 TIGR00637 ModE_repress ModE mo 60.5 7.4 0.00016 29.0 2.3 38 48-85 9-46 (99)
262 PRK09391 fixK transcriptional 60.4 9.3 0.0002 32.9 3.2 45 38-82 152-206 (230)
263 TIGR01889 Staph_reg_Sar staphy 60.4 11 0.00023 28.5 3.2 43 39-81 23-69 (109)
264 COG3413 Predicted DNA binding 60.3 13 0.00028 31.8 4.1 48 38-85 155-208 (215)
265 TIGR01764 excise DNA binding d 60.1 3.3 7.2E-05 25.6 0.3 22 57-78 3-24 (49)
266 TIGR03020 EpsA transcriptional 59.5 11 0.00024 33.1 3.5 46 37-84 189-234 (247)
267 PF13404 HTH_AsnC-type: AsnC-t 59.0 11 0.00024 23.2 2.5 25 54-78 16-40 (42)
268 PF13744 HTH_37: Helix-turn-he 58.8 6.4 0.00014 28.0 1.6 36 42-77 16-53 (80)
269 PRK00215 LexA repressor; Valid 58.7 9.2 0.0002 32.4 2.9 27 56-82 24-51 (205)
270 PF12728 HTH_17: Helix-turn-he 58.0 3.8 8.2E-05 26.1 0.3 21 57-77 3-23 (51)
271 COG2522 Predicted transcriptio 57.9 8.3 0.00018 29.8 2.2 26 52-77 19-44 (119)
272 smart00352 POU Found in Pit-Oc 57.7 5 0.00011 28.2 0.8 28 50-77 19-52 (75)
273 COG3355 Predicted transcriptio 57.6 9.4 0.0002 29.8 2.4 42 42-83 29-70 (126)
274 PHA01976 helix-turn-helix prot 56.8 6.5 0.00014 26.5 1.3 27 51-77 11-37 (67)
275 smart00354 HTH_LACI helix_turn 56.4 3.4 7.3E-05 28.5 -0.2 21 57-77 2-22 (70)
276 smart00153 VHP Villin headpiec 56.4 3.2 6.9E-05 24.8 -0.3 21 2-23 3-23 (36)
277 TIGR03209 P21_Cbot clostridium 56.4 6.6 0.00014 30.9 1.5 35 38-73 107-141 (142)
278 PF00292 PAX: 'Paired box' dom 56.1 15 0.00033 28.6 3.3 47 36-83 15-61 (125)
279 PRK10870 transcriptional repre 55.8 12 0.00026 31.0 3.0 45 37-81 51-97 (176)
280 TIGR03070 couple_hipB transcri 55.6 7.8 0.00017 24.9 1.5 26 52-77 12-37 (58)
281 PRK12683 transcriptional regul 55.4 10 0.00022 34.2 2.8 43 43-85 4-46 (309)
282 PF14493 HTH_40: Helix-turn-he 54.6 15 0.00033 26.7 3.0 39 46-84 4-42 (91)
283 PF08148 DSHCT: DSHCT (NUC185) 53.8 19 0.0004 30.0 3.8 48 42-89 101-148 (180)
284 COG1342 Predicted DNA-binding 53.7 9.2 0.0002 28.2 1.7 46 39-85 34-79 (99)
285 PF13551 HTH_29: Winged helix- 53.7 35 0.00075 25.2 5.1 69 8-78 20-110 (112)
286 PRK12679 cbl transcriptional r 52.9 12 0.00026 33.8 2.8 43 43-85 4-46 (316)
287 PRK11233 nitrogen assimilation 52.8 12 0.00026 33.5 2.8 41 44-85 5-45 (305)
288 PRK11179 DNA-binding transcrip 52.6 19 0.00041 29.0 3.6 44 39-82 7-50 (153)
289 PF08220 HTH_DeoR: DeoR-like h 52.3 14 0.0003 24.3 2.3 26 55-80 14-39 (57)
290 PRK10163 DNA-binding transcrip 52.0 16 0.00034 32.5 3.4 88 38-125 20-130 (271)
291 PRK10141 DNA-binding transcrip 51.9 14 0.0003 28.5 2.5 41 42-82 16-57 (117)
292 PF13556 HTH_30: PucR C-termin 51.5 11 0.00024 24.9 1.8 36 49-84 6-41 (59)
293 PRK10403 transcriptional regul 51.5 27 0.00059 28.6 4.6 45 38-84 153-197 (215)
294 PF13701 DDE_Tnp_1_4: Transpos 51.4 53 0.0012 31.6 7.0 121 67-198 103-229 (448)
295 PF02954 HTH_8: Bacterial regu 50.9 6.4 0.00014 24.1 0.4 26 53-78 16-41 (42)
296 PRK10401 DNA-binding transcrip 50.7 14 0.0003 33.8 2.8 21 57-77 3-23 (346)
297 PRK10651 transcriptional regul 50.6 13 0.00027 30.7 2.4 45 38-84 155-199 (216)
298 smart00760 Bac_DnaA_C Bacteria 50.2 15 0.00033 24.3 2.3 34 33-66 23-56 (60)
299 PF00392 GntR: Bacterial regul 50.1 6.9 0.00015 26.3 0.6 23 59-81 28-50 (64)
300 COG2964 Uncharacterized protei 50.1 27 0.00058 30.0 4.2 65 14-79 145-215 (220)
301 TIGR00180 parB_part ParB-like 49.9 16 0.00035 30.5 2.9 42 36-77 100-142 (187)
302 TIGR02405 trehalos_R_Ecol treh 49.9 5.1 0.00011 36.0 -0.2 21 57-77 3-23 (311)
303 PF05269 Phage_CII: Bacterioph 49.9 5.8 0.00013 29.1 0.1 29 57-85 25-53 (91)
304 PRK10360 DNA-binding transcrip 49.8 13 0.00029 30.3 2.4 45 38-84 137-181 (196)
305 PF07022 Phage_CI_repr: Bacter 49.4 11 0.00024 25.6 1.5 23 56-78 13-36 (66)
306 cd07377 WHTH_GntR Winged helix 49.3 8.5 0.00018 25.4 0.9 25 57-81 27-51 (66)
307 PRK10072 putative transcriptio 49.1 8 0.00017 28.7 0.8 27 51-77 42-68 (96)
308 TIGR02431 pcaR_pcaU beta-ketoa 49.1 15 0.00033 32.0 2.8 44 39-82 5-51 (248)
309 PRK11050 manganese transport r 48.3 16 0.00035 29.4 2.6 29 54-82 50-78 (152)
310 TIGR02702 SufR_cyano iron-sulf 48.1 17 0.00037 30.8 2.8 40 41-81 2-41 (203)
311 PRK09492 treR trehalose repres 47.9 5.4 0.00012 35.8 -0.3 23 56-78 5-27 (315)
312 PF04552 Sigma54_DBD: Sigma-54 47.4 6.2 0.00014 32.2 0.0 22 56-77 50-71 (160)
313 PRK09958 DNA-binding transcrip 47.4 15 0.00033 30.2 2.4 45 38-84 143-187 (204)
314 PRK12684 transcriptional regul 47.2 16 0.00035 32.9 2.7 46 43-88 4-50 (313)
315 PRK09834 DNA-binding transcrip 47.2 17 0.00036 32.2 2.7 44 39-82 7-53 (263)
316 PF13443 HTH_26: Cro/C1-type H 46.2 5.5 0.00012 26.5 -0.4 26 53-78 8-33 (63)
317 PRK09392 ftrB transcriptional 45.8 19 0.00042 30.9 2.9 46 38-83 146-201 (236)
318 TIGR01884 cas_HTH CRISPR locus 45.4 25 0.00054 29.7 3.4 35 47-81 147-183 (203)
319 PF08280 HTH_Mga: M protein tr 45.2 23 0.00049 23.4 2.5 40 44-84 9-48 (59)
320 PRK11569 transcriptional repre 45.2 25 0.00055 31.2 3.6 45 38-82 23-70 (274)
321 COG1654 BirA Biotin operon rep 44.9 22 0.00048 25.3 2.5 37 49-85 11-49 (79)
322 PF00440 TetR_N: Bacterial reg 44.9 6 0.00013 24.8 -0.4 30 54-83 15-44 (47)
323 PRK13777 transcriptional regul 44.7 26 0.00055 29.4 3.3 43 37-79 41-83 (185)
324 PRK09526 lacI lac repressor; R 44.6 6.9 0.00015 35.6 -0.2 23 56-78 6-28 (342)
325 PRK10014 DNA-binding transcrip 44.2 6.9 0.00015 35.5 -0.2 23 56-78 7-29 (342)
326 COG1414 IclR Transcriptional r 44.1 26 0.00057 30.7 3.4 40 43-82 4-46 (246)
327 TIGR03418 chol_sulf_TF putativ 43.8 18 0.0004 31.9 2.5 41 44-85 5-45 (291)
328 PRK05658 RNA polymerase sigma 43.5 21 0.00046 35.9 3.1 48 38-85 556-606 (619)
329 PRK12681 cysB transcriptional 43.3 21 0.00046 32.4 2.8 46 43-88 4-50 (324)
330 COG2512 Predicted membrane-ass 43.0 28 0.00062 30.8 3.4 45 37-81 191-236 (258)
331 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 42.9 22 0.00048 22.9 2.0 41 36-77 2-42 (50)
332 PF08765 Mor: Mor transcriptio 42.4 31 0.00067 26.0 3.2 49 36-84 48-101 (108)
333 PRK10703 DNA-binding transcrip 42.2 8.1 0.00018 35.1 -0.1 22 57-78 3-24 (341)
334 PRK11303 DNA-binding transcrip 42.0 8.3 0.00018 34.8 -0.1 22 57-78 2-23 (328)
335 PRK14987 gluconate operon tran 41.9 6.7 0.00014 35.5 -0.7 23 56-78 6-28 (331)
336 PRK15369 two component system 41.9 21 0.00046 29.0 2.4 44 39-84 150-193 (211)
337 PRK09726 antitoxin HipB; Provi 41.9 20 0.00043 25.9 1.9 26 52-77 22-47 (88)
338 PF02650 HTH_WhiA: WhiA C-term 41.9 40 0.00087 24.4 3.5 43 38-81 37-82 (85)
339 PRK15092 DNA-binding transcrip 41.8 19 0.00042 32.5 2.3 47 39-85 9-55 (310)
340 COG3677 Transposase and inacti 41.7 26 0.00056 27.5 2.7 46 40-85 74-119 (129)
341 PRK10079 phosphonate metabolis 41.1 55 0.0012 28.3 5.0 48 17-81 14-61 (241)
342 PRK04140 hypothetical protein; 41.0 23 0.0005 32.4 2.6 65 10-77 96-161 (317)
343 cd00131 PAX Paired Box domain 40.9 59 0.0013 25.4 4.6 70 8-78 41-126 (128)
344 TIGR02944 suf_reg_Xantho FeS a 40.9 25 0.00054 27.3 2.5 26 56-81 26-51 (130)
345 PRK15090 DNA-binding transcrip 40.8 27 0.00059 30.6 3.1 45 38-82 9-55 (257)
346 PRK10094 DNA-binding transcrip 40.6 25 0.00055 31.6 2.9 41 44-85 6-46 (308)
347 PRK11151 DNA-binding transcrip 40.5 24 0.00052 31.5 2.7 41 44-85 5-45 (305)
348 PRK10423 transcriptional repre 40.1 10 0.00022 34.1 0.2 19 59-77 2-20 (327)
349 TIGR01637 phage_arpU phage tra 39.9 42 0.00092 26.1 3.7 50 38-87 79-129 (132)
350 CHL00180 rbcR LysR transcripti 39.8 26 0.00057 31.3 2.9 40 46-85 10-49 (305)
351 PRK09906 DNA-binding transcrip 39.7 21 0.00046 31.6 2.2 40 46-85 6-45 (296)
352 COG1522 Lrp Transcriptional re 39.5 31 0.00067 27.4 3.0 41 42-83 10-50 (154)
353 PRK09508 leuO leucine transcri 39.2 28 0.00061 31.3 3.0 43 43-85 24-66 (314)
354 PRK12680 transcriptional regul 39.2 26 0.00056 31.9 2.7 46 44-89 5-51 (327)
355 smart00529 HTH_DTXR Helix-turn 39.1 16 0.00034 26.5 1.1 25 58-82 2-26 (96)
356 PRK10339 DNA-binding transcrip 39.1 8.1 0.00018 35.0 -0.6 22 57-78 3-24 (327)
357 TIGR02607 antidote_HigA addict 39.0 14 0.0003 25.7 0.7 27 51-77 14-40 (78)
358 PRK11013 DNA-binding transcrip 38.9 26 0.00056 31.5 2.7 41 44-85 8-48 (309)
359 TIGR03830 CxxCG_CxxCG_HTH puta 38.8 17 0.00037 27.9 1.3 30 49-78 72-101 (127)
360 PRK10341 DNA-binding transcrip 38.4 25 0.00055 31.5 2.6 43 43-85 9-51 (312)
361 PRK08558 adenine phosphoribosy 38.0 23 0.0005 30.9 2.1 39 39-77 7-45 (238)
362 PF06530 Phage_antitermQ: Phag 37.9 35 0.00075 26.5 2.9 42 43-84 66-107 (125)
363 PF13022 HTH_Tnp_1_2: Helix-tu 37.7 27 0.00058 27.8 2.2 36 56-91 35-73 (142)
364 TIGR02417 fruct_sucro_rep D-fr 37.6 11 0.00024 33.9 0.1 21 58-78 2-22 (327)
365 COG1476 Predicted transcriptio 37.5 16 0.00034 25.2 0.8 28 50-77 9-36 (68)
366 PRK15421 DNA-binding transcrip 37.5 32 0.0007 31.1 3.1 42 43-85 5-46 (317)
367 COG1508 RpoN DNA-directed RNA 37.4 14 0.00029 35.3 0.6 22 56-77 331-352 (444)
368 PF05930 Phage_AlpA: Prophage 37.1 12 0.00025 24.0 0.1 20 58-77 6-25 (51)
369 TIGR02684 dnstrm_HI1420 probab 36.9 20 0.00044 26.1 1.3 35 43-77 31-65 (89)
370 COG1846 MarR Transcriptional r 36.7 40 0.00086 25.1 3.1 24 59-82 40-63 (126)
371 cd04761 HTH_MerR-SF Helix-Turn 36.5 11 0.00024 23.4 -0.1 21 58-78 3-23 (49)
372 PF14549 P22_Cro: DNA-binding 36.4 10 0.00023 25.4 -0.2 25 57-82 11-35 (60)
373 PRK09791 putative DNA-binding 36.3 30 0.00065 30.8 2.7 41 45-85 9-49 (302)
374 TIGR00498 lexA SOS regulatory 36.2 32 0.00069 28.9 2.6 41 42-82 8-53 (199)
375 PRK09801 transcriptional activ 36.1 37 0.0008 30.6 3.2 45 40-85 6-50 (310)
376 PF03333 PapB: Adhesin biosynt 35.6 82 0.0018 23.1 4.3 40 41-80 39-78 (91)
377 TIGR02036 dsdC D-serine deamin 35.5 31 0.00067 30.9 2.6 42 44-85 11-52 (302)
378 TIGR01481 ccpA catabolite cont 34.9 12 0.00026 33.8 -0.2 22 57-78 3-24 (329)
379 PRK13509 transcriptional repre 34.9 39 0.00085 29.7 3.1 40 42-81 4-45 (251)
380 PF00665 rve: Integrase core d 34.8 15 0.00032 27.6 0.3 16 225-240 105-120 (120)
381 cd01104 HTH_MlrA-CarA Helix-Tu 34.4 16 0.00034 24.6 0.4 21 58-78 3-23 (68)
382 PRK11169 leucine-responsive tr 34.3 28 0.00061 28.3 1.9 29 54-82 27-55 (164)
383 PRK10727 DNA-binding transcrip 34.3 12 0.00026 34.1 -0.3 22 57-78 3-24 (343)
384 PRK13348 chromosome replicatio 34.1 33 0.00071 30.4 2.5 38 48-85 9-46 (294)
385 PRK10837 putative DNA-binding 34.1 31 0.00066 30.4 2.3 41 45-85 7-47 (290)
386 PF07453 NUMOD1: NUMOD1 domain 34.1 10 0.00022 22.4 -0.5 22 54-75 15-36 (37)
387 PRK10046 dpiA two-component re 34.1 27 0.00059 29.7 1.9 33 47-79 166-201 (225)
388 PRK03601 transcriptional regul 34.0 37 0.0008 29.9 2.8 40 46-85 6-45 (275)
389 PRK11242 DNA-binding transcrip 33.7 31 0.00067 30.5 2.3 37 49-85 9-45 (296)
390 PRK09191 two-component respons 33.5 41 0.00088 29.0 3.0 49 38-87 88-136 (261)
391 PF01726 LexA_DNA_bind: LexA D 33.4 46 0.00099 22.6 2.5 26 55-80 25-51 (65)
392 TIGR02424 TF_pcaQ pca operon t 33.2 35 0.00075 30.3 2.6 39 47-85 9-47 (300)
393 COG1609 PurR Transcriptional r 33.1 15 0.00032 33.8 0.1 22 57-78 2-23 (333)
394 PRK09706 transcriptional repre 32.8 24 0.00051 27.7 1.2 28 51-78 14-41 (135)
395 PF07750 GcrA: GcrA cell cycle 32.5 24 0.00051 28.9 1.2 37 42-78 5-42 (162)
396 PRK10219 DNA-binding transcrip 32.4 43 0.00094 24.8 2.6 27 54-80 20-46 (107)
397 TIGR03339 phn_lysR aminoethylp 31.9 28 0.00061 30.3 1.7 37 49-85 5-41 (279)
398 PRK10632 transcriptional regul 31.9 36 0.00077 30.6 2.4 38 48-85 9-46 (309)
399 PF01418 HTH_6: Helix-turn-hel 31.5 18 0.00038 25.4 0.3 24 55-78 34-57 (77)
400 PRK03902 manganese transport t 31.3 43 0.00093 26.4 2.5 26 56-81 23-48 (142)
401 PRK11482 putative DNA-binding 31.2 42 0.0009 30.4 2.7 43 43-85 31-73 (317)
402 PRK10434 srlR DNA-bindng trans 31.2 49 0.0011 29.1 3.1 42 41-82 3-46 (256)
403 PRK10086 DNA-binding transcrip 30.9 42 0.0009 30.1 2.7 41 45-85 18-58 (311)
404 PRK00430 fis global DNA-bindin 30.9 48 0.001 24.4 2.5 27 52-78 65-91 (95)
405 TIGR02404 trehalos_R_Bsub treh 30.5 24 0.00052 30.4 1.0 46 20-81 4-50 (233)
406 smart00497 IENR1 Intron encode 30.5 20 0.00042 22.8 0.3 24 55-78 17-40 (53)
407 PF01526 DDE_Tnp_Tn3: Tn3 tran 30.5 4.7E+02 0.01 24.7 9.8 121 37-170 25-153 (388)
408 PRK11402 DNA-binding transcrip 30.4 1E+02 0.0022 26.7 4.9 49 16-81 10-59 (241)
409 PRK13832 plasmid partitioning 29.7 53 0.0011 32.0 3.2 43 35-77 98-140 (520)
410 PRK09935 transcriptional regul 29.6 50 0.0011 27.0 2.8 45 38-84 149-193 (210)
411 TIGR03298 argP transcriptional 29.4 47 0.001 29.3 2.7 38 48-85 8-45 (292)
412 COG2944 Predicted transcriptio 29.4 20 0.00043 27.0 0.2 26 51-76 53-78 (104)
413 PRK10906 DNA-binding transcrip 29.4 59 0.0013 28.6 3.3 41 42-82 4-46 (252)
414 PRK10430 DNA-binding transcrip 29.4 54 0.0012 28.1 3.0 32 53-84 176-207 (239)
415 PRK13503 transcriptional activ 29.1 74 0.0016 27.9 3.9 26 55-80 187-212 (278)
416 smart00530 HTH_XRE Helix-turn- 29.1 31 0.00067 20.8 1.1 26 52-77 7-32 (56)
417 PRK10216 DNA-binding transcrip 28.8 45 0.00097 30.1 2.5 41 45-85 12-52 (319)
418 PRK11564 stationary phase indu 28.8 80 0.0017 30.0 4.3 50 37-86 9-61 (426)
419 TIGR02612 mob_myst_A mobile my 28.7 26 0.00056 28.3 0.8 38 39-78 24-61 (150)
420 PRK11139 DNA-binding transcrip 28.4 44 0.00096 29.6 2.4 42 43-85 9-50 (297)
421 cd00093 HTH_XRE Helix-turn-hel 28.0 36 0.00078 20.7 1.3 25 53-77 10-34 (58)
422 PRK10082 cell density-dependen 27.9 50 0.0011 29.4 2.6 41 45-85 15-55 (303)
423 TIGR03454 partition_RepB plasm 27.9 60 0.0013 29.8 3.1 45 35-79 157-201 (325)
424 PRK09390 fixJ response regulat 27.8 63 0.0014 25.9 3.1 34 51-84 152-185 (202)
425 PF06322 Phage_NinH: Phage Nin 27.7 25 0.00054 23.6 0.4 26 53-78 14-39 (64)
426 PRK11074 putative DNA-binding 27.7 49 0.0011 29.4 2.5 39 47-85 8-46 (300)
427 PF05732 RepL: Firmicute plasm 27.6 27 0.00058 28.7 0.7 26 56-81 76-101 (165)
428 PRK11886 bifunctional biotin-- 27.4 50 0.0011 30.0 2.6 37 45-81 6-44 (319)
429 PRK03635 chromosome replicatio 27.4 53 0.0011 29.1 2.7 37 49-85 10-46 (294)
430 PF03050 DDE_Tnp_IS66: Transpo 27.3 73 0.0016 28.1 3.6 73 39-126 4-81 (271)
431 PRK11511 DNA-binding transcrip 27.3 58 0.0013 25.2 2.6 27 54-80 24-50 (127)
432 PF08535 KorB: KorB domain; I 27.1 22 0.00048 25.9 0.1 24 54-77 2-25 (93)
433 PF13601 HTH_34: Winged helix 27.0 44 0.00095 23.7 1.7 32 53-84 12-43 (80)
434 PRK09986 DNA-binding transcrip 27.0 46 0.001 29.3 2.2 41 44-85 11-51 (294)
435 COG2188 PhnF Transcriptional r 26.8 1.2E+02 0.0026 26.3 4.7 51 15-82 7-58 (236)
436 cd07153 Fur_like Ferric uptake 26.6 64 0.0014 24.2 2.7 17 65-81 31-47 (116)
437 PRK11062 nhaR transcriptional 26.5 55 0.0012 29.1 2.6 40 46-85 9-48 (296)
438 TIGR00270 conserved hypothetic 26.3 54 0.0012 26.6 2.3 26 52-77 79-104 (154)
439 PRK10411 DNA-binding transcrip 26.3 60 0.0013 28.3 2.7 27 55-81 18-44 (240)
440 TIGR03734 PRTRC_parB PRTRC sys 26.2 60 0.0013 32.1 2.9 42 36-77 89-131 (554)
441 TIGR02325 C_P_lyase_phnF phosp 26.0 33 0.00071 29.5 1.0 23 59-81 36-58 (238)
442 PF07037 DUF1323: Putative tra 25.9 29 0.00062 26.7 0.5 21 58-78 3-23 (122)
443 COG4941 Predicted RNA polymera 25.6 86 0.0019 29.0 3.6 51 34-85 116-166 (415)
444 TIGR02395 rpoN_sigma RNA polym 25.3 18 0.00039 34.6 -0.8 31 56-96 319-349 (429)
445 PF09012 FeoC: FeoC like trans 25.1 39 0.00084 23.0 1.1 31 49-79 6-38 (69)
446 PF00376 MerR: MerR family reg 24.8 19 0.0004 21.6 -0.5 19 59-77 3-21 (38)
447 PRK14997 LysR family transcrip 24.8 53 0.0011 29.1 2.2 38 48-85 9-46 (301)
448 PRK06474 hypothetical protein; 24.7 67 0.0015 26.6 2.6 27 56-82 27-54 (178)
449 PRK14999 histidine utilization 24.7 36 0.00077 29.5 1.0 23 59-81 40-62 (241)
450 PRK04424 fatty acid biosynthes 24.7 66 0.0014 26.8 2.6 41 41-81 5-47 (185)
451 PF12844 HTH_19: Helix-turn-he 24.6 26 0.00056 23.2 0.1 27 52-78 9-35 (64)
452 PRK13558 bacterio-opsin activa 24.6 93 0.002 31.3 4.1 48 38-85 607-660 (665)
453 TIGR02018 his_ut_repres histid 24.6 36 0.00078 29.2 1.0 46 20-81 5-51 (230)
454 PF13411 MerR_1: MerR HTH fami 24.4 22 0.00048 23.9 -0.3 22 59-80 4-25 (69)
455 TIGR03384 betaine_BetI transcr 24.1 24 0.00052 28.8 -0.2 33 55-87 28-60 (189)
456 PRK14165 winged helix-turn-hel 23.6 74 0.0016 27.4 2.7 27 56-82 22-48 (217)
457 PF05598 DUF772: Transposase d 23.6 1.9E+02 0.0041 19.7 4.5 45 37-81 3-65 (77)
458 PRK09764 DNA-binding transcrip 23.3 40 0.00086 29.2 1.0 22 60-81 34-55 (240)
459 TIGR02698 CopY_TcrY copper tra 22.6 1.4E+02 0.0031 23.2 4.0 39 42-81 6-48 (130)
460 PRK06424 transcription factor; 22.5 49 0.0011 26.5 1.3 27 51-77 93-119 (144)
461 PRK15243 transcriptional regul 22.5 80 0.0017 28.4 2.9 42 43-85 7-48 (297)
462 PRK12469 RNA polymerase factor 22.3 24 0.00052 34.3 -0.6 31 56-96 370-400 (481)
463 PRK13698 plasmid-partitioning 22.1 63 0.0014 29.6 2.1 40 39-78 158-199 (323)
464 PRK13500 transcriptional activ 22.1 1.5E+02 0.0032 26.7 4.6 38 43-80 206-247 (312)
465 PRK09943 DNA-binding transcrip 21.9 41 0.00088 27.9 0.8 27 51-77 16-42 (185)
466 COG5606 Uncharacterized conser 21.8 16 0.00035 26.4 -1.4 63 13-80 2-66 (91)
467 PF09182 PuR_N: Bacterial puri 21.8 1.1E+02 0.0024 21.2 2.8 43 43-85 4-50 (70)
468 PRK05932 RNA polymerase factor 21.7 24 0.00051 34.1 -0.8 31 56-96 344-374 (455)
469 PRK09744 DNA-binding transcrip 21.4 31 0.00066 24.2 -0.1 20 56-75 11-30 (75)
470 PRK09802 DNA-binding transcrip 21.1 93 0.002 27.6 3.0 42 40-81 14-57 (269)
471 TIGR00738 rrf2_super rrf2 fami 20.8 68 0.0015 24.7 1.9 28 55-82 25-52 (132)
472 COG5566 Uncharacterized conser 20.7 47 0.001 25.9 0.8 28 54-81 101-128 (137)
473 PF05584 Sulfolobus_pRN: Sulfo 20.4 1.2E+02 0.0026 21.2 2.7 41 39-81 4-44 (72)
474 PF08822 DUF1804: Protein of u 20.4 92 0.002 25.6 2.5 38 42-79 6-43 (165)
475 PRK00423 tfb transcription ini 20.3 1.5E+02 0.0033 26.9 4.2 31 54-84 275-305 (310)
476 PRK12423 LexA repressor; Provi 20.2 87 0.0019 26.4 2.5 26 56-81 26-52 (202)
477 PRK13890 conjugal transfer pro 20.2 38 0.00081 26.1 0.2 25 53-77 16-40 (120)
478 PRK15183 Vi polysaccharide bio 20.1 74 0.0016 23.9 1.7 53 43-95 86-138 (143)
479 cd04764 HTH_MlrA-like_sg1 Heli 20.0 41 0.0009 22.5 0.4 20 59-78 4-23 (67)
No 1
>PF13359 DDE_Tnp_4: DDE superfamily endonuclease
Probab=100.00 E-value=3.1e-39 Score=265.96 Aligned_cols=150 Identities=46% Similarity=0.708 Sum_probs=138.4
Q ss_pred eeceEEEEecCCC--CCCCcccCCCCceeeeeeeecCCcccEEEeecCCCCCcChhhhhccCcchhhhh-cCCcceEEEe
Q psy672 117 VDCTHVPIQLPSV--ENGENFRNRKGTFSLNVQVIGGPNLEIWDVVSGWPGSVHDSRIFTNSRVCHRFE-RGEVRGILLG 193 (314)
Q Consensus 117 iDgt~i~i~~P~~--~~~~~y~~~k~~~s~~~q~v~d~~g~i~~~~~~~pGs~~D~~i~~~s~~~~~l~-~~~~~~~llg 193 (314)
||||+|++++|.. .+...|+++|+.|++|+|++||++|+|++++.++||++||+.+|++|++...++ ..+.++++||
T Consensus 1 iDgt~v~i~~P~~~~~~~~~y~~~k~~~~~~~q~v~d~~g~i~~v~~~~~Gs~~D~~i~~~s~~~~~l~~~~~~~~~~l~ 80 (158)
T PF13359_consen 1 IDGTHVPIQRPSDKEEQREFYSGKKKNHSLKVQIVCDPDGRIIYVSVGWPGSVHDSTIFRQSGLLDRLEQAFPPGEYLLG 80 (158)
T ss_pred CccEEEEEEeCCccccccccccCCCCcceEeEEEEEeccceeEeeecccccccccccccccccccceeecccccCccccc
Confidence 7999999999943 268899999999999999999999999999999999999999999999888765 2334799999
Q ss_pred CCCCCCcccccccCCC----CCCchhhhhhhhhhhhHHHHHHHHHHHHhhhhhccccccCC-hhhHHHHHHHHHHHhh
Q psy672 194 DSGYAQNTFLYTPLLN----PTTPQEQRYNKAHIKTRNSVERLFGIWKRRFACLRRKLANS-PVTCTHIVTACAVLHN 266 (314)
Q Consensus 194 D~gY~~~~~l~~P~~~----~~~~~~~~fN~~~s~~R~~vE~~fg~lK~rf~~L~~~~~~~-~~~~~~~i~a~~~LhN 266 (314)
|+||++.+++++|+++ +.+++|+.||+.|++.|.+||++||+||+||++|+.+++.+ .+.+..+|.|||+|||
T Consensus 81 D~gy~~~~~~~~P~~~~~~~~l~~~e~~~N~~~s~~R~~vE~~~~~lK~rf~~l~~~~~~~~~~~~~~ii~~~~~LhN 158 (158)
T PF13359_consen 81 DSGYPLSPYLLTPYKKPKGRELTPEEKEFNRRHSSARIIVERAFGRLKSRFRILRGRLRLSRPEKAPQIILACCVLHN 158 (158)
T ss_pred cccccccccccccccccccccccccccchhccccceeeeeHHHHHHHHHhcccCCcccCCCcHhHHHHHHheeEEEEC
Confidence 9999999999999973 34799999999999999999999999999999998889988 9999999999999999
No 2
>KOG4585|consensus
Probab=100.00 E-value=5.2e-38 Score=283.18 Aligned_cols=293 Identities=25% Similarity=0.370 Sum_probs=228.9
Q ss_pred ccccCHHHHHHhhHHhhhhhhcccCC--CCCC-CCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 9 ALRFSKDVVLNIIFPLARNVLETNTM--QGVK-QPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 9 ~frmsr~~f~~~L~~~l~~~~~~~~~--~~~~-~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
.|++++.+|. .|+............ .... +++..++++.|+.++++.+.+.++..||...+|+ .+......
T Consensus 7 ~~~~s~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~i~~~fg~~~~~~-----~~~~~~~~ 80 (326)
T KOG4585|consen 7 EFRKSYTTFD-KICSLVQSLNVVKNSGFMLSSLLPADTLVAVALWRLKTGESLRTVEKKFGLGQSTC-----KFLEEKED 80 (326)
T ss_pred HHHHHHHHHH-HHhhhhhhhhhhcccchhhhccccHHhhhhhhhccccccchHHHHHHHcCCcchhh-----hHHHhhhc
Confidence 6899999999 999886544221111 1111 2288899999999999999999999999999988 55666667
Q ss_pred hccccccCCCc--hhhhHHHhhhcCCCCCceeeeeceEEEEecCCCCCCCcccCCCCceeeeeeeecCCcccEEEeecCC
Q psy672 86 AHVNYVKFPEQ--LAPTKVAFQGIGNFPGVVGCVDCTHVPIQLPSVENGENFRNRKGTFSLNVQVIGGPNLEIWDVVSGW 163 (314)
Q Consensus 86 ~~~~~i~~P~~--~~~~~~~f~~~~~~p~~~g~iDgt~i~i~~P~~~~~~~y~~~k~~~s~~~q~v~d~~g~i~~~~~~~ 163 (314)
+++.++.||.. ...+.+.++. +|+|+|++|+||+++..| ......|.++ .++.|+|+|||.+++|+++.+|+
T Consensus 81 ~~~~~~~~p~~~~~~~i~~~~~~---~~~~~g~~d~~hi~~~~~-~~~~~~~~n~--~~~~Nvlav~n~d~~f~~v~vg~ 154 (326)
T KOG4585|consen 81 LAPHFLKWPSRRILYEIRERFES---LPNCVGAIDTTHIPIRVP-PKSGSVYFNK--EQSKNLLAVCNFDMRFIYVDVGW 154 (326)
T ss_pred ccchhhcCchhhhhhhhcccccc---ccchhccccccccceecC-cccccccccc--ccchhhhheecCCceEEEEEccC
Confidence 89999999987 6667666665 999999999999999988 6667777777 78899999999999999999999
Q ss_pred CCCcChhhhhccCcchhhhhcCCcceEEEeCCCCCC------------cccccccCCCCC-CchhhhhhhhhhhhHHHHH
Q psy672 164 PGSVHDSRIFTNSRVCHRFERGEVRGILLGDSGYAQ------------NTFLYTPLLNPT-TPQEQRYNKAHIKTRNSVE 230 (314)
Q Consensus 164 pGs~~D~~i~~~s~~~~~l~~~~~~~~llgD~gY~~------------~~~l~~P~~~~~-~~~~~~fN~~~s~~R~~vE 230 (314)
||+.||+.|+..+.........+...|.|.|.||+. .+++++|+..+. +..++.||.+|+..|.++|
T Consensus 155 ~Gs~~D~kvl~~~~~~~~~~~~~~~k~yl~d~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~elFN~rh~~~r~v~e 234 (326)
T KOG4585|consen 155 PGSAHDTKVLQDSLLYKRNFPHPPLKYYLVDSGYPLRPGLLGPIGFPLYSLLMFPYGGPQPTNSQELFNKRHSSLRSVAE 234 (326)
T ss_pred CCCccHHHHHHhhcccccccccCCccccccccCcccccccccccccccchhhhcccCCCCCCchHHHHhhhhhhHHHHHH
Confidence 999999999999887765444432245555555554 455556665553 5788899999999999999
Q ss_pred HHHHHHHhhhhhccccccCChhhHHHHHHHHHHHhhhccccCCCCCCCccchh--hhh-ccccccCCCCCCchHHHHHHH
Q psy672 231 RLFGIWKRRFACLRRKLANSPVTCTHIVTACAVLHNIAVQTRQELPAEDEVEE--EVE-EDVVVNDGVGRNGAGAVIRRA 307 (314)
Q Consensus 231 ~~fg~lK~rf~~L~~~~~~~~~~~~~~i~a~~~LhN~~~~~~~~~~~~~~~~~--~~~-~~~~~~~~~~~~~~~~~~R~~ 307 (314)
++||.||+||++|.+.......+...+|.|||+|||++++..+.++++...+. +.+ .........+....+...|++
T Consensus 235 ~~fg~lk~rw~il~~~~~~~~~~~~~iV~a~caLHN~~~~~~~~~~~~~~~e~~~d~~~~~~~~~~~~~~~~~~~~~r~~ 314 (326)
T KOG4585|consen 235 RAFGVLKAKWRILQRREKYDLKKLPKIVTACCALHNIIRDSDEEDPDDPKWEKFDDYGENVAHLRYAPQQRDYMEKIRDN 314 (326)
T ss_pred HHHHHhhhhhHHHhhcccccccchHHHHHHHHHHHHHHHhhcccccccccccccccccccchhcccchhHHHHHHHHHHH
Confidence 99999999999999876677889999999999999999999987766553321 111 111122223457778899999
Q ss_pred HHHhhc
Q psy672 308 FINEHF 313 (314)
Q Consensus 308 ~~~~~f 313 (314)
|+.+.+
T Consensus 315 l~~~l~ 320 (326)
T KOG4585|consen 315 LLSELW 320 (326)
T ss_pred HHHHHH
Confidence 988765
No 3
>PF04827 Plant_tran: Plant transposon protein; InterPro: IPR006912 This entry represents a putative Harbinger transposase-derived nuclease, which is thought to have nuclease activity. However it does not have transposase activity [, ]. ; GO: 0016788 hydrolase activity, acting on ester bonds
Probab=100.00 E-value=5.7e-36 Score=243.44 Aligned_cols=185 Identities=25% Similarity=0.494 Sum_probs=165.2
Q ss_pred ccccCCCc--hhhhHHHhhhcCCCCCceeeeeceEEEEe-cCCCCCCCcccCCCCceeeeeeeecCCcccEEEeecCCCC
Q psy672 89 NYVKFPEQ--LAPTKVAFQGIGNFPGVVGCVDCTHVPIQ-LPSVENGENFRNRKGTFSLNVQVIGGPNLEIWDVVSGWPG 165 (314)
Q Consensus 89 ~~i~~P~~--~~~~~~~f~~~~~~p~~~g~iDgt~i~i~-~P~~~~~~~y~~~k~~~s~~~q~v~d~~g~i~~~~~~~pG 165 (314)
+|++-|+. .+++. .+.+..||||.+|.|||+|+.++ +|....+.+.++++|.+|+.+++|++++++|++++.|.||
T Consensus 2 ~YLr~P~~~d~~rll-~~~e~rGFpGmlGSIDCmHw~WkncP~aw~g~~~~G~~g~pTiiLEaVAs~dlwIWhaffG~~G 80 (205)
T PF04827_consen 2 EYLRRPTNEDLERLL-QIGEARGFPGMLGSIDCMHWEWKNCPTAWKGQYTRGKEGVPTIILEAVASHDLWIWHAFFGMPG 80 (205)
T ss_pred cccCCCChhHHHHHH-HhhhhcCCCccccceeEEEeehhcchHHhhhcccCCCCCCCeehhhhhhccchhhhheeeccCC
Confidence 57777887 55665 44556799999999999999999 7744445555699999999999999999999999999999
Q ss_pred CcChhhhhccCcchhhhhcCCc-------------ceEEEeCCCCCCcccccccCCCCCCchhhhhhhhhhhhHHHHHHH
Q psy672 166 SVHDSRIFTNSRVCHRFERGEV-------------RGILLGDSGYAQNTFLYTPLLNPTTPQEQRYNKAHIKTRNSVERL 232 (314)
Q Consensus 166 s~~D~~i~~~s~~~~~l~~~~~-------------~~~llgD~gY~~~~~l~~P~~~~~~~~~~~fN~~~s~~R~~vE~~ 232 (314)
|.||..|+..|++...+..|.. -.|.|+|..||.+..+++.++.|.+.+++.|.....++|..||+|
T Consensus 81 S~NDiNVL~~Splf~~~~~G~ap~v~f~VNg~~Y~~gYYLaDGiYP~watfvktI~~p~~~k~k~fa~~QE~~RKDVErA 160 (205)
T PF04827_consen 81 SNNDINVLDRSPLFDDLLQGQAPRVQFTVNGHEYNMGYYLADGIYPEWATFVKTISLPQGEKRKLFAKHQESARKDVERA 160 (205)
T ss_pred cccccccccccHHHHHHhcCcCCceEEEecCeecccceeeccCcCcchHhHhhhcchhhchhhHHHHHhCHHHHHHHHHH
Confidence 9999999999999998877731 569999999999999999999999999999999999999999999
Q ss_pred HHHHHhhhhhcccccc-CChhhHHHHHHHHHHHhhhccccCCC
Q psy672 233 FGIWKRRFACLRRKLA-NSPVTCTHIVTACAVLHNIAVQTRQE 274 (314)
Q Consensus 233 fg~lK~rf~~L~~~~~-~~~~~~~~~i~a~~~LhN~~~~~~~~ 274 (314)
||.|++||+|++.+-+ ++.+.+..|+.||++||||+++++.+
T Consensus 161 FGVLQaRfaIi~~p~r~w~~~~l~~Im~aCiILHNMIvEDEr~ 203 (205)
T PF04827_consen 161 FGVLQARFAIIRGPARLWDREDLANIMRACIILHNMIVEDERD 203 (205)
T ss_pred HHHHHHHHHHhcCchhccCHHHHHHHHHHHHHhhheeEecccc
Confidence 9999999999998665 68899999999999999999987643
No 4
>PF13612 DDE_Tnp_1_3: Transposase DDE domain
Probab=99.20 E-value=1e-11 Score=100.75 Aligned_cols=128 Identities=18% Similarity=0.260 Sum_probs=97.0
Q ss_pred CCCCceeeeeceEEEEecCCCCC---------CCcccCCCCceeeeeeeecCCcccEEEeecCCCCCcChhhhhccCcch
Q psy672 109 NFPGVVGCVDCTHVPIQLPSVEN---------GENFRNRKGTFSLNVQVIGGPNLEIWDVVSGWPGSVHDSRIFTNSRVC 179 (314)
Q Consensus 109 ~~p~~~g~iDgt~i~i~~P~~~~---------~~~y~~~k~~~s~~~q~v~d~~g~i~~~~~~~pGs~~D~~i~~~s~~~ 179 (314)
|-+..+.+||.|.||+..+.... ...|+..+-+|++|++++|+.+|.++.+... ||++||..++..- .
T Consensus 2 ~~~~~i~~iDS~Pi~vC~~~R~~r~k~~~~~a~~G~~a~~~fyGfKlHllv~~~G~i~~~~lT-~an~~D~~~~~~l--~ 78 (155)
T PF13612_consen 2 GQCTGIYIIDSFPIPVCHNIRIKRHKVFKGLAYRGYCAMGWFYGFKLHLLVNDSGEIVAFTLT-PANVHDRKVLEEL--S 78 (155)
T ss_pred CCccEEEEEecCChhHhCccchhhhccccCccccceeccceeEeeeeeeEEccCCcEEEEEEc-ccccccccccccc--c
Confidence 34567889999999998663221 1234455567899999999999999999887 9999999887331 1
Q ss_pred hhhhcCCcceEEEeCCCCCCcc----------cccccCCCCCC-chhhhhhhhhhhhHHHHHHHHHHHHhhhhhcc
Q psy672 180 HRFERGEVRGILLGDSGYAQNT----------FLYTPLLNPTT-PQEQRYNKAHIKTRNSVERLFGIWKRRFACLR 244 (314)
Q Consensus 180 ~~l~~~~~~~~llgD~gY~~~~----------~l~~P~~~~~~-~~~~~fN~~~s~~R~~vE~~fg~lK~rf~~L~ 244 (314)
... ...++||+||-... .++||.++... .....+++.+.+.|..||.+|+.||+.|.+=+
T Consensus 79 ----~~~-~g~l~gDkGYis~~L~~~L~~~gI~L~t~~RkNmk~~~~~~~~~~l~~~R~~IETvfs~Lk~~~~ie~ 149 (155)
T PF13612_consen 79 ----ENL-KGKLFGDKGYISKELKDELKEQGIKLITPRRKNMKNKLMPLFDKLLLRKRRIIETVFSQLKNQFNIEH 149 (155)
T ss_pred ----ccc-ccceecchhhhcchHHhhhhhceEEEeccccccccccccchhhhhhhheeeEeehHHHHHHHhhceEe
Confidence 111 34799999996532 47889886653 33456788999999999999999999888765
No 5
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=99.17 E-value=5e-11 Score=79.01 Aligned_cols=50 Identities=22% Similarity=0.141 Sum_probs=47.5
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHhc
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAH 87 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~ 87 (314)
++++++|++++|.||++|.++.++|..||||+|||++++++++++|+...
T Consensus 2 kLs~~d~lll~L~~LR~~~~~~~La~~FgIs~stvsri~~~~~~~L~~~l 51 (53)
T PF13613_consen 2 KLSLEDQLLLTLMYLRLNLTFQDLAYRFGISQSTVSRIFHEWIPLLYQVL 51 (53)
T ss_pred CCCHHHHHHHHHHHHHcCCcHhHHhhheeecHHHHHHHHHHHHHHHHHhc
Confidence 57999999999999999999999999999999999999999999998743
No 6
>PF13586 DDE_Tnp_1_2: Transposase DDE domain
Probab=98.24 E-value=1e-06 Score=64.89 Aligned_cols=76 Identities=20% Similarity=0.259 Sum_probs=55.9
Q ss_pred EEeCCCCCCcc--------cccc---cCCCCCCchhhhhhhhhhhhHHHHHHHHHHHHhhhhhccccccCChhhHHHHHH
Q psy672 191 LLGDSGYAQNT--------FLYT---PLLNPTTPQEQRYNKAHIKTRNSVERLFGIWKRRFACLRRKLANSPVTCTHIVT 259 (314)
Q Consensus 191 llgD~gY~~~~--------~l~~---P~~~~~~~~~~~fN~~~s~~R~~vE~~fg~lK~rf~~L~~~~~~~~~~~~~~i~ 259 (314)
++||+||.... .+.+ +-+++....+..+...+.+.|.+||++|+.||. |+.|...+.........++.
T Consensus 1 v~aDkgYd~~~~r~~l~~~gi~~~i~~~~~~~~~~~~~~d~~~~~~Rw~VEr~f~wlk~-~Rrl~~ryek~~~s~~~~v~ 79 (88)
T PF13586_consen 1 VLADKGYDSRALREYLRERGIRPVIPKRGRRKKRRPRKFDFRLYKRRWVVERTFAWLKR-FRRLATRYEKLASSFLAFVH 79 (88)
T ss_pred CcccCCcCCHHHHHHHHHCCCEEecCCCCCccccccCccchhhhccceehhhhhHHHHH-cCccccccccCHHHHHHHHH
Confidence 57999998631 2222 222222233678889999999999999999999 99999888888887777887
Q ss_pred HHHHHhhh
Q psy672 260 ACAVLHNI 267 (314)
Q Consensus 260 a~~~LhN~ 267 (314)
.+|++-++
T Consensus 80 la~~~i~l 87 (88)
T PF13586_consen 80 LACIVIWL 87 (88)
T ss_pred HHHHHHHh
Confidence 77776554
No 7
>PF01609 DDE_Tnp_1: Transposase DDE domain; InterPro: IPR002559 Autonomous mobile genetic elements such as transposon or insertion sequences (IS) encode an enzyme, transposase, that is required for excising and inserting the mobile element. Transposases have been grouped into various families [, , ]. This family includes the IS4 transposase. 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: 3ECP_A 4DM0_A 1MUS_A 1MUH_A 1MM8_A 1B7E_A.
Probab=98.08 E-value=3.4e-07 Score=77.75 Aligned_cols=149 Identities=19% Similarity=0.250 Sum_probs=85.2
Q ss_pred ceeeeeceEEEEecCCCCCCCcccCCCCceeeeeeeec-CCcccEEEeecCCCCCcChhhhhccCcchhhhhcCCcceEE
Q psy672 113 VVGCVDCTHVPIQLPSVENGENFRNRKGTFSLNVQVIG-GPNLEIWDVVSGWPGSVHDSRIFTNSRVCHRFERGEVRGIL 191 (314)
Q Consensus 113 ~~g~iDgt~i~i~~P~~~~~~~y~~~k~~~s~~~q~v~-d~~g~i~~~~~~~pGs~~D~~i~~~s~~~~~l~~~~~~~~l 191 (314)
.+-+||+|.|+.. +.......+.+++...++++++++ +..|.++.+... +|+.+|...+.+ +.+. ..+..+..+
T Consensus 5 ~~~~iD~T~i~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~d~~~~~~--ll~~-~~~~~~~~v 79 (213)
T PF01609_consen 5 RVVAIDGTTIRTP-HDKSARRYKKGKKRGFGYKLHLAVDDNSGLPLSVKVT-PGNVHDSKALPE--LLER-KPGRKPDLV 79 (213)
T ss_dssp EEEEEETTT--EE-EEEEE-B-SSGGGHSSHGGHHHHHHHHHGGGGGGEEE-EEEGG-HHHHHH--HHTT------EEEE
T ss_pred eEEEEECcEEEee-cchhhhcccCCCCcCCCEeEEEEEeecccceeeeecc-ccccceeecccc--cccc-cccccccce
Confidence 4569999999988 101112334455566778999999 557778888887 999999988776 2222 223448899
Q ss_pred EeCCCCCCcc----------cccccCCCCCC-----------------------------------chhhhhhhh-----
Q psy672 192 LGDSGYAQNT----------FLYTPLLNPTT-----------------------------------PQEQRYNKA----- 221 (314)
Q Consensus 192 lgD~gY~~~~----------~l~~P~~~~~~-----------------------------------~~~~~fN~~----- 221 (314)
++|+||.... ..+.|.+.... ..+......
T Consensus 80 v~D~gy~s~~~~~~l~~~~~~~vi~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 159 (213)
T PF01609_consen 80 VADRGYDSAENLEALKERGIHFVIRLKKNRKKKIQKIENKFWKSFDRRSARKKPKQKSKRVRVVIRKEQKKKGYFLVTNI 159 (213)
T ss_dssp EE-S--BBTTHHHHHHTS---EEEEE--EEEE-TTS-EEEE--EEEEEEEEEEETGGGEEEEEEEEEECS--TTS---EE
T ss_pred eecccccceeccccccccccccccccccccccccccchhhcccccccccccccccccccccccccccccccccccccccc
Confidence 9999998643 11233332110 001111122
Q ss_pred ---------hhhhHHHHHHHHHHHHhhhhhccccccCChhhHHHHHHHHHHHhhh
Q psy672 222 ---------HIKTRNSVERLFGIWKRRFACLRRKLANSPVTCTHIVTACAVLHNI 267 (314)
Q Consensus 222 ---------~s~~R~~vE~~fg~lK~rf~~L~~~~~~~~~~~~~~i~a~~~LhN~ 267 (314)
..+.|..||+.|..||+.|. +......+.+.+...+.++++-.|+
T Consensus 160 ~~~~~~~~~~Y~~Rw~IE~~f~~lK~~~~-l~~~~~~~~~~~~~~~~~~~la~nl 213 (213)
T PF01609_consen 160 TTLPRDTAALYRRRWQIERFFRELKQFLG-LERLRVRSPERIEAHLFLTLLAYNL 213 (213)
T ss_dssp EEEESS--SHHHCGGHHHHHHHHHTTTTT-GGGS--SSHHHHHHHHHHHHHH---
T ss_pred cccccccceeecccchhhHHHHHHHhcCC-CchhcccCHHHHHHHHHHHHhhCcC
Confidence 89999999999999999544 3322334677788888888877775
No 8
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=96.74 E-value=0.00072 Score=42.89 Aligned_cols=42 Identities=21% Similarity=0.274 Sum_probs=31.1
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHH
Q psy672 35 QGVKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVK 77 (314)
Q Consensus 35 ~~~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~ 77 (314)
|++.++.+ ++.-++..+..|.+..++|..||||++||.+++.
T Consensus 2 Rp~~~~~~-~~~~i~~l~~~G~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 2 RPPKLSKE-QIEEIKELYAEGMSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp SSSSSSHC-CHHHHHHHHHTT--HHHHHHHTTS-HHHHHHHHC
T ss_pred cCCCCCHH-HHHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHh
Confidence 34445544 5666777889999999999999999999999875
No 9
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=96.44 E-value=0.004 Score=40.28 Aligned_cols=45 Identities=24% Similarity=0.359 Sum_probs=38.2
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHH
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKAL 83 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l 83 (314)
.+|++++-.+.++| ..+.++.++|..+|+|.+||+++.++.+.-|
T Consensus 4 ~L~~~er~vi~~~y-~~~~t~~eIa~~lg~s~~~V~~~~~~al~kL 48 (50)
T PF04545_consen 4 QLPPREREVIRLRY-FEGLTLEEIAERLGISRSTVRRILKRALKKL 48 (50)
T ss_dssp TS-HHHHHHHHHHH-TST-SHHHHHHHHTSCHHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHh-cCCCCHHHHHHHHCCcHHHHHHHHHHHHHHh
Confidence 57889999998888 7788899999999999999999999887655
No 10
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=96.24 E-value=0.002 Score=40.62 Aligned_cols=41 Identities=20% Similarity=0.111 Sum_probs=23.2
Q ss_pred CCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHH
Q psy672 37 VKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKE 78 (314)
Q Consensus 37 ~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~ 78 (314)
+.++++++..+.- ++..|.+.+.+|..+|+|+|||++.+++
T Consensus 3 ~~Lt~~eR~~I~~-l~~~G~s~~~IA~~lg~s~sTV~relkR 43 (44)
T PF13936_consen 3 KHLTPEERNQIEA-LLEQGMSIREIAKRLGRSRSTVSRELKR 43 (44)
T ss_dssp ---------HHHH-HHCS---HHHHHHHTT--HHHHHHHHHH
T ss_pred cchhhhHHHHHHH-HHHcCCCHHHHHHHHCcCcHHHHHHHhc
Confidence 3567777777664 4689999999999999999999999875
No 11
>PF13340 DUF4096: Putative transposase of IS4/5 family (DUF4096)
Probab=95.95 E-value=0.0093 Score=42.24 Aligned_cols=62 Identities=16% Similarity=0.068 Sum_probs=49.2
Q ss_pred hhHHhhhhhhcccC--CCCCCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHH
Q psy672 20 IIFPLARNVLETNT--MQGVKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKA 82 (314)
Q Consensus 20 ~L~~~l~~~~~~~~--~~~~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~ 82 (314)
...+.|++.+.... +++...+..+-+-..|+.+.+|++++.+...|| +.+||++.+.++...
T Consensus 4 ~~W~~i~p~lp~~~~~~~~~~~~~R~v~~ail~~lrtG~~Wr~LP~~fg-~~~tv~~~f~rW~~~ 67 (75)
T PF13340_consen 4 EEWALIEPLLPPRKPRGGRPRIDLREVLNAILYVLRTGCPWRDLPEDFG-PWSTVYRRFRRWSRS 67 (75)
T ss_pred HHHHHHHhhCCCCCCCCCCCccchHHHHhcccccceecceecccchhcc-CcCcHHHHHHHHHHc
Confidence 44556666665432 334567888889999999999999999999999 888999999988764
No 12
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=95.79 E-value=0.014 Score=42.10 Aligned_cols=49 Identities=18% Similarity=0.188 Sum_probs=44.5
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHH
Q psy672 34 MQGVKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKA 82 (314)
Q Consensus 34 ~~~~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~ 82 (314)
..+..+++..++.++-..+..|.+...++..||||..|+++|+.++-..
T Consensus 4 H~nA~Lt~~gR~~lv~~vv~~g~~~a~aA~~~gVS~~Ta~kW~~Ryra~ 52 (85)
T PF13011_consen 4 HKNARLTPRGRLRLVRRVVEQGWPVAHAAAEFGVSRRTAYKWLARYRAE 52 (85)
T ss_pred CCCCCCCHHHHHHHHHHHHHcCCcHHHHHHHhCCCHHHHHHHHHHHHHc
Confidence 3566799999999999999999999999999999999999999988754
No 13
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=95.43 E-value=0.0052 Score=39.65 Aligned_cols=39 Identities=21% Similarity=0.145 Sum_probs=22.7
Q ss_pred HHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHH
Q psy672 42 MTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSK 81 (314)
Q Consensus 42 ~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~ 81 (314)
+.++.+...+. .|.+..++|..+|||++||++|++++..
T Consensus 5 ~~R~~ii~l~~-~G~s~~~ia~~lgvs~~Tv~~w~kr~~~ 43 (50)
T PF13384_consen 5 ERRAQIIRLLR-EGWSIREIAKRLGVSRSTVYRWIKRYRE 43 (50)
T ss_dssp -----HHHHHH-HT--HHHHHHHHTS-HHHHHHHHT----
T ss_pred hHHHHHHHHHH-CCCCHHHHHHHHCcCHHHHHHHHHHccc
Confidence 34444444444 4999999999999999999999988753
No 14
>PF13518 HTH_28: Helix-turn-helix domain
Probab=95.29 E-value=0.013 Score=37.98 Aligned_cols=37 Identities=24% Similarity=0.317 Sum_probs=31.4
Q ss_pred HHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHH
Q psy672 44 RLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSK 81 (314)
Q Consensus 44 ~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~ 81 (314)
++.+...++ .|.+...+|..||||.+|+.+|+.++-.
T Consensus 2 r~~iv~~~~-~g~s~~~~a~~~gis~~tv~~w~~~y~~ 38 (52)
T PF13518_consen 2 RLQIVELYL-EGESVREIAREFGISRSTVYRWIKRYRE 38 (52)
T ss_pred HHHHHHHHH-cCCCHHHHHHHHCCCHhHHHHHHHHHHh
Confidence 455666667 6779999999999999999999998876
No 15
>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=95.16 E-value=0.01 Score=38.95 Aligned_cols=42 Identities=17% Similarity=0.174 Sum_probs=30.8
Q ss_pred CCCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHH
Q psy672 36 GVKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKE 78 (314)
Q Consensus 36 ~~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~ 78 (314)
+..+++++++-+. ..+-.|.+..++|..|||++||++.++..
T Consensus 4 R~~LTl~eK~~iI-~~~e~g~s~~~ia~~fgv~~sTv~~I~K~ 45 (53)
T PF04218_consen 4 RKSLTLEEKLEII-KRLEEGESKRDIAREFGVSRSTVSTILKN 45 (53)
T ss_dssp SSS--HHHHHHHH-HHHHCTT-HHHHHHHHT--CCHHHHHHHC
T ss_pred CccCCHHHHHHHH-HHHHcCCCHHHHHHHhCCCHHHHHHHHHh
Confidence 4568889998774 45788889999999999999999998864
No 16
>smart00351 PAX Paired Box domain.
Probab=95.08 E-value=0.028 Score=44.07 Aligned_cols=45 Identities=16% Similarity=0.042 Sum_probs=38.8
Q ss_pred CCCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHH
Q psy672 36 GVKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSK 81 (314)
Q Consensus 36 ~~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~ 81 (314)
+..+|.+.+.-+.+.+. .|.+..++|..||||++||++|++++-+
T Consensus 15 ~~~~s~~~R~riv~~~~-~G~s~~~iA~~~gvs~~tV~kwi~r~~~ 59 (125)
T smart00351 15 GRPLPDEERQRIVELAQ-NGVRPCDISRQLCVSHGCVSKILGRYYE 59 (125)
T ss_pred CCCCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 34588888888877765 8999999999999999999999999855
No 17
>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=94.68 E-value=0.027 Score=35.62 Aligned_cols=37 Identities=19% Similarity=0.157 Sum_probs=29.4
Q ss_pred HHHHHHHHHHhhcC-CcccccCCcccccHHHHHHHHHH
Q psy672 42 MTRLLAVIQFYATG-NFQIFTGDSHGVSQPTMCRLVKE 78 (314)
Q Consensus 42 ~~~l~~~L~~L~~g-~~~~~l~~~fgis~stv~~~~~~ 78 (314)
++.+..+|..+.+| .+++.+|..|||+++|+++.++.
T Consensus 2 ee~l~~Ai~~v~~g~~S~r~AA~~ygVp~sTL~~r~~g 39 (45)
T PF05225_consen 2 EEDLQKAIEAVKNGKMSIRKAAKKYGVPRSTLRRRLRG 39 (45)
T ss_dssp HHHHHHHHHHHHTTSS-HHHHHHHHT--HHHHHHHHHH
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHcC
Confidence 57788888888888 99999999999999999987653
No 18
>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=94.57 E-value=0.085 Score=38.72 Aligned_cols=53 Identities=13% Similarity=0.112 Sum_probs=47.3
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCcccccCCccc-ccHHHHHHHHHHHHHHHHH
Q psy672 33 TMQGVKQPPMTRLLAVIQFYATGNFQIFTGDSHG-VSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 33 ~~~~~~~s~~~~l~~~L~~L~~g~~~~~l~~~fg-is~stv~~~~~~v~~~l~~ 85 (314)
..+...++..-++++.|..-..|.++.++|..|| .+.|||+..++++-..+.+
T Consensus 22 ~~R~~~~~~aR~ia~yl~~~~~~~s~~~Ig~~fg~r~hStV~~a~~ri~~~~~~ 75 (90)
T cd06571 22 KSRKKEIALARQIAMYLARELTGLSLPEIGRAFGGRDHSTVLHAVRKIEELLEE 75 (90)
T ss_pred CCCCcCcchHHHHHHHHHHHHhCCCHHHHHHHhCCCCHhHHHHHHHHHHHHHHh
Confidence 3455678899999999999999999999999999 9999999999999988764
No 19
>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=94.36 E-value=0.023 Score=40.03 Aligned_cols=44 Identities=18% Similarity=0.082 Sum_probs=30.6
Q ss_pred HHH-HHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 42 MTR-LLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 42 ~~~-l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
+++ +-++=+.+.+..+.+.+|..||||+|||++=+.+=+..|..
T Consensus 5 eeR~i~i~~yIi~~~aTVR~~Ak~FGvSKSTVHkDvteRL~~in~ 49 (82)
T PF12116_consen 5 EERVIEIANYIIETKATVRQAAKVFGVSKSTVHKDVTERLPKINP 49 (82)
T ss_dssp HHHHHHHHHHHHHH---HHHHHHHHTS-HHHHHHHHTTHHHHH-H
T ss_pred HHHHHHHHHHHHHcccHHHHHHHHHCCcHHHHHHHHHHHHHhcCH
Confidence 344 44677778899999999999999999999887765655553
No 20
>cd00131 PAX Paired Box domain
Probab=94.36 E-value=0.051 Score=42.76 Aligned_cols=46 Identities=15% Similarity=0.081 Sum_probs=39.5
Q ss_pred CCCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHH
Q psy672 36 GVKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKA 82 (314)
Q Consensus 36 ~~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~ 82 (314)
..++|.+.+.-+.+.+ ..|.+...+|.+||||++||.+|++++-+.
T Consensus 15 ~~~lS~d~R~rIv~~~-~~G~s~~~iA~~~~Vs~~tV~r~i~r~~e~ 60 (128)
T cd00131 15 GRPLPDSIRQRIVELA-QSGIRPCDISRQLRVSHGCVSKILNRYYET 60 (128)
T ss_pred CCcCCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHHHHHc
Confidence 3568888888777665 689999999999999999999999988764
No 21
>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=94.18 E-value=0.044 Score=32.03 Aligned_cols=41 Identities=24% Similarity=0.179 Sum_probs=29.6
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHH
Q psy672 35 QGVKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLV 76 (314)
Q Consensus 35 ~~~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~ 76 (314)
+...++.+++..+.. .+..+.+...++..+|+|.+|+++++
T Consensus 2 r~~~~~~~~~~~i~~-~~~~~~s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 2 RPPKLTPEQIEEARR-LLAAGESVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred CCCcCCHHHHHHHHH-HHHcCCCHHHHHHHHCCCHHHHHHhC
Confidence 344456655544444 45677899999999999999999863
No 22
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=93.99 E-value=0.047 Score=43.36 Aligned_cols=45 Identities=20% Similarity=0.071 Sum_probs=40.1
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHH
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKA 82 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~ 82 (314)
..+.+.+.+++..++..|.+.+++|.+||||.+|+.+++++.-+-
T Consensus 4 ~~s~~~R~~~~~~~~~~G~S~re~Ak~~gvs~sTvy~wv~r~~e~ 48 (138)
T COG3415 4 PFSNDLRERVVDAVVGEGLSCREAAKRFGVSISTVYRWVRRYRET 48 (138)
T ss_pred hhhHHHHHHHHHHHHHcCccHHHHHHHhCccHHHHHHHHHHhccc
Confidence 345678888999999999999999999999999999999988763
No 23
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=93.69 E-value=0.076 Score=41.32 Aligned_cols=46 Identities=15% Similarity=0.229 Sum_probs=42.2
Q ss_pred CCCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHH
Q psy672 36 GVKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSK 81 (314)
Q Consensus 36 ~~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~ 81 (314)
+...+.+.++.++...+.+|.+..++|..||||.+|+++|.+++..
T Consensus 10 rr~ys~EfK~~aV~~~~~~g~sv~evA~e~gIs~~tl~~W~r~y~~ 55 (121)
T PRK09413 10 RRRRTTQEKIAIVQQSFEPGMTVSLVARQHGVAASQLFLWRKQYQE 55 (121)
T ss_pred CCCCCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHhh
Confidence 4568999999999999999999999999999999999999998754
No 24
>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=93.68 E-value=0.038 Score=38.89 Aligned_cols=45 Identities=20% Similarity=0.242 Sum_probs=37.9
Q ss_pred CCCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHH
Q psy672 36 GVKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVS 80 (314)
Q Consensus 36 ~~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~ 80 (314)
+...|++.++-++-.++..|.+..+++..+||+.+|+++|.....
T Consensus 4 r~~ys~e~K~~~v~~~~~~g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 4 RRRYSPEFKLQAVREYLESGESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp S----HHHHHHHHHHHHHHHCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHCCCceEeeecccccccccccHHHHHHh
Confidence 456899999999999999999999999999999999999999987
No 25
>PRK00118 putative DNA-binding protein; Validated
Probab=93.37 E-value=0.11 Score=39.12 Aligned_cols=48 Identities=15% Similarity=0.061 Sum_probs=38.7
Q ss_pred CCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 37 VKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 37 ~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
+.+|..++-++.|+ +-.|.++..+|+.+|+|++||.+++.+....+-+
T Consensus 16 ~~L~ekqRevl~L~-y~eg~S~~EIAe~lGIS~~TV~r~L~RArkkLr~ 63 (104)
T PRK00118 16 SLLTEKQRNYMELY-YLDDYSLGEIAEEFNVSRQAVYDNIKRTEKLLED 63 (104)
T ss_pred ccCCHHHHHHHHHH-HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 44667766666444 5569999999999999999999999988877765
No 26
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=93.14 E-value=0.14 Score=33.25 Aligned_cols=45 Identities=18% Similarity=0.245 Sum_probs=35.2
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHH
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALA 84 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~ 84 (314)
.++..++-++ .++..|.+..++|..+|+|.+||.+++.+....|.
T Consensus 3 ~l~~~e~~i~--~~~~~g~s~~eia~~l~is~~tv~~~~~~~~~kl~ 47 (58)
T smart00421 3 SLTPREREVL--RLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLG 47 (58)
T ss_pred CCCHHHHHHH--HHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Confidence 3566555533 33578999999999999999999999998876654
No 27
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=92.93 E-value=0.12 Score=33.02 Aligned_cols=43 Identities=19% Similarity=0.200 Sum_probs=34.0
Q ss_pred CCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHH
Q psy672 39 QPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKA 82 (314)
Q Consensus 39 ~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~ 82 (314)
+++.++-++.+.|+ .|.++.+++..+|+|.+|+.+++++....
T Consensus 11 l~~~~~~~~~~~~~-~~~~~~~ia~~~~~s~~~i~~~~~~~~~~ 53 (55)
T cd06171 11 LPEREREVILLRFG-EGLSYEEIAEILGISRSTVRQRLHRALKK 53 (55)
T ss_pred CCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 55666666655554 77899999999999999999999887543
No 28
>PRK04217 hypothetical protein; Provisional
Probab=92.75 E-value=0.18 Score=38.49 Aligned_cols=49 Identities=22% Similarity=0.068 Sum_probs=38.7
Q ss_pred CCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672 37 VKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA 86 (314)
Q Consensus 37 ~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 86 (314)
..++.+++-++ ..+.-.|.++.++|+.+|||.+||.+++.+....|.+.
T Consensus 41 ~~Lt~eereai-~l~~~eGlS~~EIAk~LGIS~sTV~r~L~RArkkLre~ 89 (110)
T PRK04217 41 IFMTYEEFEAL-RLVDYEGLTQEEAGKRMGVSRGTVWRALTSARKKVAQM 89 (110)
T ss_pred ccCCHHHHHHH-HHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 34677776443 44445888999999999999999999999988888763
No 29
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=92.18 E-value=0.18 Score=41.14 Aligned_cols=48 Identities=13% Similarity=0.220 Sum_probs=43.0
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHhc
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAH 87 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~ 87 (314)
.+|+.++-++.|.+ .|.++.++|..+|+|.+||...+.+....|-..+
T Consensus 112 ~L~~~~r~il~l~~--~g~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l 159 (166)
T PRK09639 112 KMTERDRTVLLLRF--SGYSYKEIAEALGIKESSVGTTLARAKKKFRKIY 159 (166)
T ss_pred cCCHHHHHHHHHHH--cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 48888998888877 9999999999999999999999999998887654
No 30
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=92.12 E-value=0.11 Score=33.57 Aligned_cols=32 Identities=16% Similarity=0.159 Sum_probs=26.2
Q ss_pred HHHHhhcCCcccccCCcccccHHHHHHHHHHH
Q psy672 48 VIQFYATGNFQIFTGDSHGVSQPTMCRLVKEV 79 (314)
Q Consensus 48 ~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v 79 (314)
.+..+....++..+|..+|+|.+||.+++++.
T Consensus 20 i~~~~~~~~s~~~vA~~~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 20 ILKLLRESRSFKDVARELGVSWSTVRRIFDRY 51 (52)
T ss_pred HHHHHhhcCCHHHHHHHHCCCHHHHHHHHHhh
Confidence 34445555799999999999999999999874
No 31
>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=92.04 E-value=0.14 Score=35.85 Aligned_cols=41 Identities=12% Similarity=0.069 Sum_probs=37.2
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHH
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKE 78 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~ 78 (314)
.+|...+.+..|.+.-.|.++.++|+.+|+|.+||..+++.
T Consensus 15 ~l~~~~r~af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 15 WVDSLAEAAAALAREEAGKTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred cCCHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 57788888888888889999999999999999999998875
No 32
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=91.40 E-value=0.27 Score=40.79 Aligned_cols=48 Identities=10% Similarity=0.095 Sum_probs=41.5
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA 86 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 86 (314)
++|++++.++.|.++ .|.++.++|..+|+|.+||...+++....+.+.
T Consensus 127 ~Lp~~~R~v~~L~~~-~g~s~~EIA~~lgis~~tVk~~l~rAl~~~~~~ 174 (178)
T PRK12529 127 TLRPRVKQAFLMATL-DGMKQKDIAQALDIALPTVKKYIHQAYVTCLSL 174 (178)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 478888888888877 889999999999999999999999887777653
No 33
>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=91.14 E-value=0.3 Score=31.68 Aligned_cols=43 Identities=21% Similarity=0.299 Sum_probs=33.1
Q ss_pred CHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHH
Q psy672 40 PPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALA 84 (314)
Q Consensus 40 s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~ 84 (314)
+..++-++.+ +..|.+..++|..+|+|.+|+..++++....+.
T Consensus 2 ~~~e~~i~~~--~~~~~s~~eia~~l~~s~~tv~~~~~~~~~~l~ 44 (57)
T cd06170 2 TPREREVLRL--LAEGKTNKEIADILGISEKTVKTHLRNIMRKLG 44 (57)
T ss_pred CHHHHHHHHH--HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHhC
Confidence 3444443333 468899999999999999999999998876554
No 34
>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=90.99 E-value=0.27 Score=31.98 Aligned_cols=44 Identities=18% Similarity=0.331 Sum_probs=31.4
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHH
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKA 82 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~ 82 (314)
++|+.++-++.|.|+ .|.++.++|+.+|+|.+||...+.+....
T Consensus 10 ~L~~~~r~i~~l~~~-~g~s~~eIa~~l~~s~~~v~~~l~ra~~~ 53 (54)
T PF08281_consen 10 QLPERQREIFLLRYF-QGMSYAEIAEILGISESTVKRRLRRARKK 53 (54)
T ss_dssp CS-HHHHHHHHHHHT-S---HHHHHHHCTS-HHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHH-HCcCHHHHHHHHCcCHHHHHHHHHHHHhh
Confidence 467777777766554 67889999999999999999998887654
No 35
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=90.91 E-value=0.27 Score=40.44 Aligned_cols=49 Identities=14% Similarity=0.022 Sum_probs=41.3
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHhc
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAH 87 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~ 87 (314)
.+|+.++.++.|.++ .|.++.++|..+|+|.+||...+++...-|-+.+
T Consensus 128 ~L~~~~r~vl~l~~~-~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 176 (182)
T PRK09652 128 SLPEELRTAITLREI-EGLSYEEIAEIMGCPIGTVRSRIFRAREALRAKL 176 (182)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 477888887777776 6889999999999999999999998888777644
No 36
>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=90.89 E-value=0.17 Score=36.92 Aligned_cols=32 Identities=22% Similarity=0.276 Sum_probs=27.4
Q ss_pred HHHHHHhhcCCcccccCCcccccHHHHHHHHH
Q psy672 46 LAVIQFYATGNFQIFTGDSHGVSQPTMCRLVK 77 (314)
Q Consensus 46 ~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~ 77 (314)
...+.++..|.+..++|+.+|||++|++++.+
T Consensus 41 ~~I~~ll~~G~S~~eIA~~LgISrsTIyRi~R 72 (88)
T TIGR02531 41 LQVAKMLKQGKTYSDIEAETGASTATISRVKR 72 (88)
T ss_pred HHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 55566789999999999999999999999553
No 37
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=90.08 E-value=0.34 Score=42.06 Aligned_cols=50 Identities=24% Similarity=0.254 Sum_probs=42.8
Q ss_pred CCCHHHHHHHHHHHh---hcCCcccccCCcccccHHHHHHHHHHHHHHHHHhc
Q psy672 38 KQPPMTRLLAVIQFY---ATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAH 87 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L---~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~ 87 (314)
.+|+.++-++.|.|+ -.|.++.++|+.+|||.+||....++....|-+..
T Consensus 178 ~Lp~~~R~v~~L~y~l~~~eg~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~~l 230 (234)
T PRK08301 178 KLSDREKQIMELRFGLNGGEEKTQKEVADMLGISQSYISRLEKRIIKRLKKEI 230 (234)
T ss_pred hCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 477888888888774 58999999999999999999999999988887644
No 38
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=89.54 E-value=0.44 Score=42.21 Aligned_cols=50 Identities=14% Similarity=0.139 Sum_probs=42.9
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHhcc
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAHV 88 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~~ 88 (314)
.+|+.++.++.|+|+ .+.++.++|..+|+|.++|..+.++...-|-....
T Consensus 205 ~L~~~er~vi~l~y~-e~~t~~EIA~~lgis~~~V~~~~~ral~kLr~~l~ 254 (257)
T PRK05911 205 ALEEKERKVMALYYY-EELVLKEIGKILGVSESRVSQIHSKALLKLRATLS 254 (257)
T ss_pred cCCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 478888888888875 68899999999999999999999998888876543
No 39
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.
Probab=89.53 E-value=0.46 Score=38.72 Aligned_cols=47 Identities=15% Similarity=0.046 Sum_probs=40.6
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
++|+.++.++.|.|+ .|.++.++|..+|+|.+||....++....|-+
T Consensus 122 ~L~~~~r~vl~l~~~-~g~s~~eIA~~l~is~~tv~~~l~ra~~~Lr~ 168 (170)
T TIGR02952 122 ILTPKQQHVIALRFG-QNLPIAEVARILGKTEGAVKILQFRAIKKLAR 168 (170)
T ss_pred hCCHHHHHHHHHHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 578888888888766 58999999999999999999999998877754
No 40
>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=89.47 E-value=0.28 Score=36.12 Aligned_cols=41 Identities=17% Similarity=-0.037 Sum_probs=32.9
Q ss_pred CCHHHHHHHHHHH------hhcCCcccccCCcccccHHHHHHHHHHH
Q psy672 39 QPPMTRLLAVIQF------YATGNFQIFTGDSHGVSQPTMCRLVKEV 79 (314)
Q Consensus 39 ~s~~~~l~~~L~~------L~~g~~~~~l~~~fgis~stv~~~~~~v 79 (314)
+++.++-.+.++| +..+.+++.++...|||.+||+|+-+..
T Consensus 33 LTp~E~~~l~~R~~i~~~Ll~~~~tQrEIa~~lGiS~atIsR~sn~l 79 (94)
T TIGR01321 33 LTRSEREDLGDRIRIVNELLNGNMSQREIASKLGVSIATITRGSNNL 79 (94)
T ss_pred CCHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHhCCChhhhhHHHhhc
Confidence 6778887777775 3457899999999999999999876543
No 41
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=89.43 E-value=0.49 Score=38.59 Aligned_cols=48 Identities=13% Similarity=-0.038 Sum_probs=41.1
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA 86 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 86 (314)
++|+.++-++.|.++ .|.++.++|..+|+|.+||...+.+....|-+.
T Consensus 112 ~L~~~~r~v~~l~~~-~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 159 (164)
T PRK12547 112 LLSADQREAIILIGA-SGFSYEDAAAICGCAVGTIKSRVSRARNRLQEL 159 (164)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 467777777777777 888999999999999999999999998888763
No 42
>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=89.42 E-value=0.39 Score=35.93 Aligned_cols=43 Identities=21% Similarity=0.240 Sum_probs=37.1
Q ss_pred CHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHH
Q psy672 40 PPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKAL 83 (314)
Q Consensus 40 s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l 83 (314)
.++++.++.++|+ ++.++.++++.+++|++|++++-++.+..|
T Consensus 57 d~~~r~iL~~~Yi-~~~~~~~I~~~l~~S~~t~yr~~~~Al~~L 99 (100)
T PF07374_consen 57 DPDERLILRMRYI-NKLTWEQIAEELNISRRTYYRIHKKALKEL 99 (100)
T ss_pred ChhHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHhc
Confidence 4788899999888 678899999999999999999988876644
No 43
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=89.31 E-value=0.33 Score=40.75 Aligned_cols=48 Identities=17% Similarity=0.151 Sum_probs=39.4
Q ss_pred CCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHhc
Q psy672 39 QPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAH 87 (314)
Q Consensus 39 ~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~ 87 (314)
+|++++-++.|.++. |.++.++|+.+|+|.+||...+.+....|-+..
T Consensus 142 L~~~~~~v~~l~~~~-g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 189 (194)
T PRK12519 142 LPESQRQVLELAYYE-GLSQSEIAKRLGIPLGTVKARARQGLLKLRELL 189 (194)
T ss_pred CCHHHhhhhhhhhhc-CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 566666666666655 899999999999999999999999888887643
No 44
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
Probab=89.30 E-value=0.49 Score=37.92 Aligned_cols=47 Identities=19% Similarity=0.241 Sum_probs=39.4
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
.+|+.++-++.|.++ .|.++.++|..+|+|.+||....++....|-+
T Consensus 113 ~L~~~~r~il~l~~~-~~~~~~eIA~~lgis~~tv~~~~~ra~~~Lr~ 159 (161)
T TIGR02985 113 KLPEQCRKIFILSRF-EGKSYKEIAEELGISVKTVEYHISKALKELRK 159 (161)
T ss_pred HCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 367788888888666 68899999999999999999999988776653
No 45
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=89.15 E-value=0.48 Score=39.51 Aligned_cols=50 Identities=14% Similarity=0.034 Sum_probs=42.3
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHhcc
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAHV 88 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~~ 88 (314)
++|+..+-++.|.++ .|.++.++|..+|+|.+||...+.+....|-+...
T Consensus 111 ~Lp~~~R~v~~L~~~-eg~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~~~ 160 (182)
T PRK12511 111 DLPEEQRAALHLVAI-EGLSYQEAAAVLGIPIGTLMSRIGRARAALRAFEE 160 (182)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHH
Confidence 477777777777777 58999999999999999999999999988876543
No 46
>PRK06030 hypothetical protein; Provisional
Probab=89.11 E-value=0.88 Score=35.48 Aligned_cols=47 Identities=9% Similarity=0.008 Sum_probs=43.0
Q ss_pred CCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHH
Q psy672 37 VKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKAL 83 (314)
Q Consensus 37 ~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l 83 (314)
..+...-|++|.|.+--++.++..+|..||.+.|||..-++.+-+.+
T Consensus 51 k~i~~aRqIAMYL~r~~~~~sl~~IG~~FGRDHSTV~haikkIe~~~ 97 (124)
T PRK06030 51 REVSRIRQIAMYVAHVSLGWPMNEVALAFGRDRTTVGHACHTVEDLR 97 (124)
T ss_pred cccchHHHHHHHHHHHHcCCCHHHHHHHHCCChhHHHHHHHHHHHHh
Confidence 57889999999999999999999999999999999999999777655
No 47
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=88.99 E-value=0.45 Score=39.89 Aligned_cols=48 Identities=10% Similarity=0.058 Sum_probs=41.3
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA 86 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 86 (314)
++|+..+-++.|.++. |.++.++|..+|+|.+||...+++....|-+.
T Consensus 134 ~Lp~~~R~v~~L~~~~-g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~ 181 (189)
T PRK12530 134 HLPAQQARVFMMREYL-ELSSEQICQECDISTSNLHVLLYRARLQLQAC 181 (189)
T ss_pred hCCHHHHHHHhHHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4677788888887766 89999999999999999999999988888763
No 48
>PHA00542 putative Cro-like protein
Probab=88.97 E-value=0.3 Score=35.11 Aligned_cols=33 Identities=33% Similarity=0.411 Sum_probs=27.5
Q ss_pred HHHHHHhhcCCcccccCCcccccHHHHHHHHHH
Q psy672 46 LAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKE 78 (314)
Q Consensus 46 ~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~ 78 (314)
-+...+...|.+..++|+..|||++|++++.+.
T Consensus 22 ~l~~~l~~~glTq~elA~~lgIs~~tIsr~e~g 54 (82)
T PHA00542 22 ELVCALIRAGWSQEQIADATDVSQPTICRIYSG 54 (82)
T ss_pred HHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHcC
Confidence 334456788999999999999999999998753
No 49
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=88.81 E-value=0.55 Score=38.06 Aligned_cols=47 Identities=17% Similarity=0.123 Sum_probs=37.7
Q ss_pred CCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672 39 QPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA 86 (314)
Q Consensus 39 ~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 86 (314)
+|+.++-++.|.++ .|.++.++|+.+|+|.+||...+.+...-|-+.
T Consensus 110 L~~~~r~v~~l~~~-~~~s~~EIA~~lgis~~tV~~~l~ra~~~lr~~ 156 (163)
T PRK07037 110 LPARTRYAFEMYRL-HGETQKDIARELGVSPTLVNFMIRDALVHCRKC 156 (163)
T ss_pred CCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 56666666666654 488999999999999999999988888877763
No 50
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=88.76 E-value=0.48 Score=39.25 Aligned_cols=49 Identities=16% Similarity=0.156 Sum_probs=41.2
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHhc
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAH 87 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~ 87 (314)
.+|+.++-++.|.++. |.++.++|..+|+|.+||...+.+....|-+..
T Consensus 127 ~L~~~~r~v~~l~~~~-g~s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~~l 175 (179)
T PRK09415 127 SLPIKYREVIYLFYYE-ELSIKEIAEVTGVNENTVKTRLKKAKELLKKGL 175 (179)
T ss_pred hCCHHHhhHhHhHHhc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4777777777777765 889999999999999999999999988887643
No 51
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=88.67 E-value=0.56 Score=38.74 Aligned_cols=48 Identities=13% Similarity=0.027 Sum_probs=40.3
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA 86 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 86 (314)
.+|++.+-.+.|.++ .|.++.++|+.+|+|.+||...+++....|-+.
T Consensus 129 ~L~~~~r~i~~l~~~-~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 176 (179)
T PRK12514 129 ELEKDRAAAVRRAYL-EGLSYKELAERHDVPLNTMRTWLRRSLLKLREC 176 (179)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCChHHHHHHHHHHHHHHHHH
Confidence 367777777777765 788999999999999999999999988887653
No 52
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=88.54 E-value=0.57 Score=39.25 Aligned_cols=49 Identities=14% Similarity=0.059 Sum_probs=41.0
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHhc
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAH 87 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~ 87 (314)
.+|+.++-++.|.++ .|.++.++|+.+|+|.+||...+.+....|-+.+
T Consensus 116 ~Lp~~~r~i~~L~~~-~g~s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l 164 (187)
T PRK12516 116 QLPDDQREAIILVGA-SGFAYEEAAEICGCAVGTIKSRVNRARQRLQEIL 164 (187)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 366777777777666 8999999999999999999999999998888643
No 53
>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=88.51 E-value=0.55 Score=37.29 Aligned_cols=46 Identities=7% Similarity=-0.021 Sum_probs=38.7
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
-++..++-.+.| +..|.++.++|+.+|+|++||+.+.++...-|-.
T Consensus 6 ~Lte~qr~VL~L--r~~GlTq~EIAe~LgiS~stV~~~e~ra~kkLr~ 51 (137)
T TIGR00721 6 FLTERQIKVLEL--REKGLSQKEIAKELKTTRANVSAIEKRAMENIEK 51 (137)
T ss_pred CCCHHHHHHHHH--HHcCCCHHHHHHHHCcCHHHHHHHHHhHHHHHHH
Confidence 467777777777 3799999999999999999999999988877763
No 54
>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=88.43 E-value=0.34 Score=34.67 Aligned_cols=37 Identities=22% Similarity=0.186 Sum_probs=28.3
Q ss_pred HHHHHHHHHHHhhcC-CcccccCCcccccHHHHHHHHH
Q psy672 41 PMTRLLAVIQFYATG-NFQIFTGDSHGVSQPTMCRLVK 77 (314)
Q Consensus 41 ~~~~l~~~L~~L~~g-~~~~~l~~~fgis~stv~~~~~ 77 (314)
+++++...+-+|..| .+..++|+.||+|.+||++.++
T Consensus 4 ~~~R~~~I~e~l~~~~~ti~dvA~~~gvS~~TVsr~L~ 41 (80)
T TIGR02844 4 IEERVLEIGKYIVETKATVRETAKVFGVSKSTVHKDVT 41 (80)
T ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHhc
Confidence 355666666676663 4567899999999999999775
No 55
>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=88.26 E-value=0.67 Score=35.86 Aligned_cols=69 Identities=17% Similarity=0.097 Sum_probs=43.0
Q ss_pred cccccCHHHHHHhhHHhhhhh-hcccCCCCCCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHH
Q psy672 8 EALRFSKDVVLNIIFPLARNV-LETNTMQGVKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEV 79 (314)
Q Consensus 8 ~~frmsr~~f~~~L~~~l~~~-~~~~~~~~~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v 79 (314)
..|.+|+.++. ..+..-+.. +......+..+. ...+..+.--....+..+++..||||.+|+++.+++.
T Consensus 26 ~~F~VS~~Tv~-~W~k~~~~G~~~~k~r~~~Kid--~~~L~~~v~~~pd~tl~Ela~~l~Vs~~ti~~~Lkrl 95 (119)
T PF01710_consen 26 KRFGVSRNTVY-RWLKRKETGDLEPKPRGRKKID--RDELKALVEENPDATLRELAERLGVSPSTIWRALKRL 95 (119)
T ss_pred HHhCcHHHHHH-HHHHhccccccccccccccccc--HHHHHHHHHHCCCcCHHHHHHHcCCCHHHHHHHHHHc
Confidence 57999999999 666643332 222111111443 3333333333455677899999999999999887764
No 56
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=88.15 E-value=0.62 Score=37.16 Aligned_cols=47 Identities=13% Similarity=0.056 Sum_probs=39.3
Q ss_pred CCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 37 VKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 37 ~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
..+++.++-.+.| ...|.++.++|+.+|+|++||+.+.++...-|-+
T Consensus 5 ~~Lt~rqreVL~l--r~~GlTq~EIAe~LGiS~~tVs~ie~ra~kkLr~ 51 (141)
T PRK03975 5 SFLTERQIEVLRL--RERGLTQQEIADILGTSRANVSSIEKRARENIEK 51 (141)
T ss_pred cCCCHHHHHHHHH--HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4577888877777 3699999999999999999999999987776654
No 57
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=88.01 E-value=0.6 Score=40.18 Aligned_cols=49 Identities=16% Similarity=0.018 Sum_probs=41.7
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHhc
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAH 87 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~ 87 (314)
.+|+.++-++.|+|+ .|.++.++|+.+|||.+||...+++....|-+..
T Consensus 134 ~Lp~~~R~v~~L~y~-eg~s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l 182 (216)
T PRK12533 134 KLPVEYREVLVLREL-EDMSYREIAAIADVPVGTVMSRLARARRRLAALL 182 (216)
T ss_pred cCCHHHHhHhhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 467777777777777 6999999999999999999999999888888643
No 58
>PRK15320 transcriptional activator SprB; Provisional
Probab=87.98 E-value=0.58 Score=39.32 Aligned_cols=45 Identities=18% Similarity=0.183 Sum_probs=37.9
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHH
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALA 84 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~ 84 (314)
.+|..+. -.|.+|+.|.+.+++|+.+++|.+||+.+..+...-+.
T Consensus 164 ~LSdREI--EVL~LLAkG~SNKEIAekL~LS~KTVSTYKnRLLeKLg 208 (251)
T PRK15320 164 GVTQAKY--ALLILLSSGHPAIELAKKFGLGTKTVSIYRKKVMYRLG 208 (251)
T ss_pred CCCHHHH--HHHHHHHcCCCHHHHHHHhccchhhHHHHHHHHHHHcC
Confidence 3444443 67888999999999999999999999999999888766
No 59
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=87.96 E-value=0.66 Score=39.05 Aligned_cols=48 Identities=17% Similarity=0.128 Sum_probs=41.2
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA 86 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 86 (314)
.+|+.++-++.|.++ .|.++.++|+.+|+|.+||...+++....|-..
T Consensus 136 ~L~~~~r~i~~L~~~-~g~s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~ 183 (196)
T PRK12524 136 ALPERQRQAVVLRHI-EGLSNPEIAEVMEIGVEAVESLTARGKRALAAL 183 (196)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 467777777777777 789999999999999999999999998888763
No 60
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=87.96 E-value=0.3 Score=40.21 Aligned_cols=48 Identities=19% Similarity=0.146 Sum_probs=41.5
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA 86 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 86 (314)
.+|+.++.++.|.++ .|.++.++|..+|+|.+||...+.+....|-..
T Consensus 126 ~L~~~~r~v~~l~~~-~g~s~~eIA~~l~is~~~V~~~l~ra~~~l~~~ 173 (176)
T PRK09638 126 KLDPEFRAPVILKHY-YGYTYEEIAKMLNIPEGTVKSRVHHGIKQLRKE 173 (176)
T ss_pred cCCHHHhheeeehhh-cCCCHHHHHHHHCCChhHHHHHHHHHHHHHHHH
Confidence 477888888888776 699999999999999999999999988887763
No 61
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=87.91 E-value=0.63 Score=37.46 Aligned_cols=47 Identities=15% Similarity=0.199 Sum_probs=40.7
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
.+|+.++-++.|.++ .|.++.++|..+|+|.+||...+++....|-+
T Consensus 111 ~L~~~~r~v~~l~~~-~g~~~~eIA~~l~is~~tv~~~l~Rar~~Lr~ 157 (159)
T TIGR02989 111 KLPERQRELLQLRYQ-RGVSLTALAEQLGRTVNAVYKALSRLRVRLRD 157 (159)
T ss_pred HCCHHHHHHHHHHHh-cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Confidence 488888888888665 78999999999999999999999988877754
No 62
>COG3293 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=87.86 E-value=0.19 Score=39.08 Aligned_cols=93 Identities=16% Similarity=0.125 Sum_probs=62.0
Q ss_pred eeeeecCCcccEEEeecCCCCCcChhhhhccCcchhhhhcCCcceEEEeCCCCCCcccccccCCCCC-------Cchhhh
Q psy672 145 NVQVIGGPNLEIWDVVSGWPGSVHDSRIFTNSRVCHRFERGEVRGILLGDSGYAQNTFLYTPLLNPT-------TPQEQR 217 (314)
Q Consensus 145 ~~q~v~d~~g~i~~~~~~~pGs~~D~~i~~~s~~~~~l~~~~~~~~llgD~gY~~~~~l~~P~~~~~-------~~~~~~ 217 (314)
+.+.++|..|+++....+ +|..+ ...-. ..+-+ ..-.-+|+|.+|...+|...|-..+. ...+..
T Consensus 2 ~~~~l~D~~~~~i~~~lp-~~~~~-~~~~~-~~~~~-----~~v~~~i~~~~~~g~~wr~~p~~~~~~~~~~~~~~~~~~ 73 (124)
T COG3293 2 KLHALVDAEWRPVEPLLP-PAKYG-GPPGV-TLLRD-----REVLNGIADLLYTGCAWRALPADFPPATTVIPYRRFRRW 73 (124)
T ss_pred CcccccccccceeeccCC-CcccC-CCCCC-ccccc-----HHHHHHHHHHhccchHHHHhHHHhCCCceEeCCCcchhh
Confidence 467899999999999886 54433 21110 00000 01224678899988777665544321 123577
Q ss_pred hhhhhhhhHHHHHHHHHHHHhhhhhcccc
Q psy672 218 YNKAHIKTRNSVERLFGIWKRRFACLRRK 246 (314)
Q Consensus 218 fN~~~s~~R~~vE~~fg~lK~rf~~L~~~ 246 (314)
++..+...|..+|+.|+.+|. |+.+...
T Consensus 74 ~~~g~~~~~~~~~~~f~~~~~-~r~~~~~ 101 (124)
T COG3293 74 FKRGLWKRRNLVERTFGRLKQ-FRRTATR 101 (124)
T ss_pred HHHHHHHHHHHHHHHHHHHhc-ccceecc
Confidence 889999999999999999998 8888754
No 63
>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=87.84 E-value=0.3 Score=31.95 Aligned_cols=29 Identities=14% Similarity=0.165 Sum_probs=24.5
Q ss_pred CcccccCCcccccHHHHHHHHHHHHHHHH
Q psy672 56 NFQIFTGDSHGVSQPTMCRLVKEVSKALA 84 (314)
Q Consensus 56 ~~~~~l~~~fgis~stv~~~~~~v~~~l~ 84 (314)
.+..++|+.+|||++|++..+++...-|.
T Consensus 24 ~tl~elA~~lgis~st~~~~LRrae~kli 52 (53)
T PF04967_consen 24 ITLEELAEELGISKSTVSEHLRRAERKLI 52 (53)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Confidence 45578999999999999999998877654
No 64
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=87.84 E-value=0.62 Score=38.64 Aligned_cols=48 Identities=13% Similarity=0.090 Sum_probs=41.2
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA 86 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 86 (314)
.+|..++-++.|.|+ .|.++.++|+.+|||.+||...+++....|-..
T Consensus 136 ~L~~~~r~il~l~~~-~~~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T PRK09641 136 QLPEKYRTVIVLKYI-EDLSLKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred hCCHHHHHHhhhHHh-hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 467788888878776 799999999999999999999999988877753
No 65
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=87.84 E-value=0.63 Score=36.60 Aligned_cols=47 Identities=26% Similarity=0.285 Sum_probs=38.3
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
.+|+.++-++.+.++ .|.++.++|..+|+|.+||.+...++...|-+
T Consensus 110 ~L~~~~~~ii~~~~~-~g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 110 KLPEREREVLVLRYL-EGLSYKEIAEILGISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred hCCHHHHHHHhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 467777777666555 68999999999999999999999998776653
No 66
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=87.82 E-value=0.72 Score=37.21 Aligned_cols=48 Identities=21% Similarity=0.235 Sum_probs=40.5
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA 86 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 86 (314)
.+|+.++-++.|.++ .|.++.++|..+|+|.+||...+.+....|-..
T Consensus 106 ~Lp~~~r~v~~l~~~-~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~ 153 (161)
T PRK09047 106 KLPARQREAFLLRYW-EDMDVAETAAAMGCSEGSVKTHCSRATHALAKA 153 (161)
T ss_pred hCCHHHHHHHHHHHH-hcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 477777777777665 588899999999999999999999999888763
No 67
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=87.81 E-value=0.7 Score=38.84 Aligned_cols=47 Identities=9% Similarity=0.035 Sum_probs=38.2
Q ss_pred CCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672 39 QPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA 86 (314)
Q Consensus 39 ~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 86 (314)
+|+..+-++.|.++ .|.++.++|..+|||.+||...+++....|-..
T Consensus 142 Lp~~~r~v~~l~~~-eg~s~~EIA~~lgis~~tVk~rl~ra~~~Lr~~ 188 (194)
T PRK12531 142 LPKAQRDVLQAVYL-EELPHQQVAEMFDIPLGTVKSRLRLAVEKLRHS 188 (194)
T ss_pred CCHHHHHHHHHHHH-cCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHH
Confidence 55566666666655 889999999999999999999999888887753
No 68
>PF13751 DDE_Tnp_1_6: Transposase DDE domain
Probab=87.81 E-value=0.22 Score=38.69 Aligned_cols=50 Identities=28% Similarity=0.218 Sum_probs=37.3
Q ss_pred hhhhhhhHH-HHHHHHHHHHhhhhhccccccCChhhHHHHHHHHHHHhhhcc
Q psy672 219 NKAHIKTRN-SVERLFGIWKRRFACLRRKLANSPVTCTHIVTACAVLHNIAV 269 (314)
Q Consensus 219 N~~~s~~R~-~vE~~fg~lK~rf~~L~~~~~~~~~~~~~~i~a~~~LhN~~~ 269 (314)
...+.+.|. .||++||.||. +--|..........+..-+...|+.|||..
T Consensus 73 ~k~~y~~R~~~VE~~fg~~K~-~~g~~r~~~rG~~kv~~~~~l~a~a~Nl~r 123 (125)
T PF13751_consen 73 GKELYKQRSIKVEGVFGTIKR-NHGLRRFRYRGLEKVRIEFLLAAIAYNLKR 123 (125)
T ss_pred hhhhhheeecccccccccchh-ccCCccccccchhhhHHHHHHHHHHHHHHH
Confidence 356777888 99999999999 455543333456788888888888999853
No 69
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=87.76 E-value=0.58 Score=40.69 Aligned_cols=49 Identities=14% Similarity=0.129 Sum_probs=42.2
Q ss_pred CCCHHHHHHHHHHHh---hcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672 38 KQPPMTRLLAVIQFY---ATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA 86 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L---~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 86 (314)
.+|+.++.++.|.|+ -.|.++.++|..+|+|.+||.+..++....|-..
T Consensus 175 ~Lp~~~R~i~~l~y~~~~~e~~S~~EIA~~lgis~~tV~~~~~rA~~kLr~~ 226 (233)
T PRK05803 175 ILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRALKKLFKE 226 (233)
T ss_pred hCCHHHHHHHHHHhCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 588899999999886 4678999999999999999999988887777653
No 70
>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=87.58 E-value=0.59 Score=31.15 Aligned_cols=26 Identities=31% Similarity=0.377 Sum_probs=22.3
Q ss_pred CcccccCCcccccHHHHHHHHHHHHH
Q psy672 56 NFQIFTGDSHGVSQPTMCRLVKEVSK 81 (314)
Q Consensus 56 ~~~~~l~~~fgis~stv~~~~~~v~~ 81 (314)
.+..+|++.++++++|+++.+++...
T Consensus 22 ~t~~~la~~l~~~~~~vs~~v~~L~~ 47 (62)
T PF12802_consen 22 LTQSELAERLGISKSTVSRIVKRLEK 47 (62)
T ss_dssp EEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred cCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 58899999999999999999887765
No 71
>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=87.46 E-value=0.56 Score=29.68 Aligned_cols=28 Identities=21% Similarity=0.253 Sum_probs=22.8
Q ss_pred cCCcccccCCcccccHHHHHHHHHHHHH
Q psy672 54 TGNFQIFTGDSHGVSQPTMCRLVKEVSK 81 (314)
Q Consensus 54 ~g~~~~~l~~~fgis~stv~~~~~~v~~ 81 (314)
.+.+..++|+.+|+|.+||++++++..+
T Consensus 16 ~~~t~~ela~~~~is~~tv~~~l~~L~~ 43 (48)
T PF13412_consen 16 PRITQKELAEKLGISRSTVNRYLKKLEE 43 (48)
T ss_dssp TTS-HHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 4478899999999999999999998764
No 72
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=87.32 E-value=0.75 Score=38.16 Aligned_cols=46 Identities=22% Similarity=0.195 Sum_probs=37.5
Q ss_pred CCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 39 QPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 39 ~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
+|+..+.++.|. +-.|.++.++|+.+|||.+||....++....|-+
T Consensus 134 L~~~~r~i~~l~-~~~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 179 (182)
T PRK12537 134 LEPARRNCILHA-YVDGCSHAEIAQRLGAPLGTVKAWIKRSLKALRE 179 (182)
T ss_pred CCHHHHHHHHHH-HHcCCCHHHHHHHHCCChhhHHHHHHHHHHHHHH
Confidence 555666555554 5788999999999999999999999999888765
No 73
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=87.28 E-value=0.75 Score=38.39 Aligned_cols=48 Identities=21% Similarity=0.241 Sum_probs=41.2
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA 86 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 86 (314)
++|++++-++.|.++ .|.++.++|+.+|+|.+||...+.+....|-..
T Consensus 131 ~L~~~~r~vl~l~~~-~~~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 178 (189)
T PRK12515 131 KLSPAHREIIDLVYY-HEKSVEEVGEIVGIPESTVKTRMFYARKKLAEL 178 (189)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 477777777777776 889999999999999999999999988888764
No 74
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=87.16 E-value=0.7 Score=38.44 Aligned_cols=48 Identities=23% Similarity=0.261 Sum_probs=41.0
Q ss_pred CCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHhc
Q psy672 39 QPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAH 87 (314)
Q Consensus 39 ~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~ 87 (314)
+|+.++-++.|.++. |.++.++|+.+|+|..||...+++....|-+..
T Consensus 129 L~~~~r~i~~l~~~~-g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 176 (186)
T PRK05602 129 LPERQREAIVLQYYQ-GLSNIEAAAVMDISVDALESLLARGRRALRAQL 176 (186)
T ss_pred CCHHHHHHhhHHHhc-CCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHH
Confidence 677777777777764 999999999999999999999999988887643
No 75
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=87.14 E-value=0.71 Score=37.76 Aligned_cols=48 Identities=15% Similarity=0.158 Sum_probs=39.8
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA 86 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 86 (314)
.+|+.++-++.|.++ .|.++.++|..+|+|.+||.+.+++....|-+.
T Consensus 125 ~L~~~~r~i~~l~~~-~~~~~~eIA~~lgis~~tv~~~~~ra~~~lr~~ 172 (179)
T PRK11924 125 ALPVKQREVFLLRYV-EGLSYREIAEILGVPVGTVKSRLRRARQLLREC 172 (179)
T ss_pred hCCHHHHHHhhHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 366777777767666 689999999999999999999999988877653
No 76
>COG3316 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=87.08 E-value=5.2 Score=34.19 Aligned_cols=187 Identities=14% Similarity=0.064 Sum_probs=108.7
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCc-----ccccHHHHHHHHHHHHHHHHHhccccccCCCchhhhHHHhhhcCCCCC
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDS-----HGVSQPTMCRLVKEVSKALAQAHVNYVKFPEQLAPTKVAFQGIGNFPG 112 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~-----fgis~stv~~~~~~v~~~l~~~~~~~i~~P~~~~~~~~~f~~~~~~p~ 112 (314)
.++-.-+...+=+||+.+.+++++.+. ..++.+|+++++.+....+.......-+ . ++
T Consensus 8 ~f~~~vi~~~V~~yl~~~Ls~r~v~e~l~~rgi~v~h~Ti~rwv~k~~~~~~~~~~~r~~----------------~-~~ 70 (215)
T COG3316 8 QFPRNIIAVAVWLYLRYGLSLRDVEEMLAERGIEVDHETIHRWVQKYGPLLARRLKRRKR----------------K-AG 70 (215)
T ss_pred hcchhhHHHHHHHHhhcchhhccHHHHHHHcCcchhHHHHHHHHHHHhHHHHHHhhhhcc----------------c-cc
Confidence 455555555666677778999887664 3567889999999999988874422211 1 11
Q ss_pred ceeeeeceEEEEecCCCCCCCcccCCCCceeeeeeeecCCcccEEEeecCCCCCcChhhhhccCcchhhhhcCCcceEEE
Q psy672 113 VVGCVDCTHVPIQLPSVENGENFRNRKGTFSLNVQVIGGPNLEIWDVVSGWPGSVHDSRIFTNSRVCHRFERGEVRGILL 192 (314)
Q Consensus 113 ~~g~iDgt~i~i~~P~~~~~~~y~~~k~~~s~~~q~v~d~~g~i~~~~~~~pGs~~D~~i~~~s~~~~~l~~~~~~~~ll 192 (314)
-.=.||-|.|+|.-- . + -+-..||.+|..+++...--=+...+..| +...++....+.-++
T Consensus 71 ~~w~vDEt~ikv~gk---w---~---------ylyrAid~~g~~Ld~~L~~rRn~~aAk~F----l~kllk~~g~p~v~v 131 (215)
T COG3316 71 DSWRVDETYIKVNGK---W---H---------YLYRAIDADGLTLDVWLSKRRNALAAKAF----LKKLLKKHGEPRVFV 131 (215)
T ss_pred cceeeeeeEEeeccE---e---e---------ehhhhhccCCCeEEEEEEcccCcHHHHHH----HHHHHHhcCCCceEE
Confidence 111689888887311 0 0 11246788899999888644445555443 333344433367888
Q ss_pred eCCCCCCcccccccCCCCCCchhhhhhhhhhhh-HHHHHHHHHHHHhhhhhccccccCChhhHHHHHHHHHHHhhhccc
Q psy672 193 GDSGYAQNTFLYTPLLNPTTPQEQRYNKAHIKT-RNSVERLFGIWKRRFACLRRKLANSPVTCTHIVTACAVLHNIAVQ 270 (314)
Q Consensus 193 gD~gY~~~~~l~~P~~~~~~~~~~~fN~~~s~~-R~~vE~~fg~lK~rf~~L~~~~~~~~~~~~~~i~a~~~LhN~~~~ 270 (314)
.|++=-....+-.--. .+-++-++. .+.+|+-+..+|.|=+-+. .+. ++..+..++...-.+|++-..
T Consensus 132 tDka~s~~~A~~~l~~--------~~ehr~~~ylnN~iE~dh~~iKrr~~~~~-~f~-~~~sa~~~~~gie~i~~~~~~ 200 (215)
T COG3316 132 TDKAPSYTAALRKLGS--------EVEHRTSKYLNNRIEQDHRPIKRRTRPMK-RFK-SLSSAASTISGIESIHMLYKR 200 (215)
T ss_pred ecCccchHHHHHhcCc--------chheecccccccchhhcchhHHHHhcccc-cCC-ChHHHHHHHHhHHHHHHHHhh
Confidence 8876433211110000 111222222 4778999999998766552 222 344566666666677776544
No 77
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=87.05 E-value=0.79 Score=38.01 Aligned_cols=48 Identities=19% Similarity=0.060 Sum_probs=40.4
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA 86 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 86 (314)
++|+.++-++.|.|+. |.++.++|..+|+|.+||...+++....|-+.
T Consensus 131 ~L~~~~r~v~~l~~~~-g~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~ 178 (184)
T PRK12512 131 TLPPRQRDVVQSISVE-GASIKETAAKLSMSEGAVRVALHRGLAALAAK 178 (184)
T ss_pred hCCHHHHHHHHHHHHc-CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 3677777777776665 89999999999999999999999999888764
No 78
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=87.00 E-value=0.69 Score=38.72 Aligned_cols=52 Identities=12% Similarity=0.008 Sum_probs=42.4
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHhcccc
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAHVNY 90 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~~~~ 90 (314)
.+|++++-++.|.++ .|.++.++|+.+|+|..||...+.+....|-+....+
T Consensus 138 ~L~~~~r~v~~l~~~-~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~~~ 189 (193)
T PRK11923 138 QLPEDLRTALTLREF-DGLSYEDIASVMQCPVGTVRSRIFRAREAIDKALQPL 189 (193)
T ss_pred hCCHHHhHHHhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 366777777777765 7889999999999999999999999988887755443
No 79
>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=86.91 E-value=0.49 Score=31.38 Aligned_cols=44 Identities=18% Similarity=0.175 Sum_probs=34.7
Q ss_pred CCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHH
Q psy672 39 QPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALA 84 (314)
Q Consensus 39 ~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~ 84 (314)
++..+.- +|.+++.|.+..++|...|||.+||..+..++..-+.
T Consensus 4 LT~~E~~--vl~~l~~G~~~~eIA~~l~is~~tV~~~~~~i~~Kl~ 47 (58)
T PF00196_consen 4 LTERELE--VLRLLAQGMSNKEIAEELGISEKTVKSHRRRIMKKLG 47 (58)
T ss_dssp S-HHHHH--HHHHHHTTS-HHHHHHHHTSHHHHHHHHHHHHHHHHT
T ss_pred cCHHHHH--HHHHHHhcCCcchhHHhcCcchhhHHHHHHHHHHHhC
Confidence 4444433 5778999999999999999999999999998877654
No 80
>PHA00675 hypothetical protein
Probab=86.89 E-value=0.49 Score=33.17 Aligned_cols=40 Identities=8% Similarity=-0.031 Sum_probs=28.5
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHH
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVK 77 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~ 77 (314)
.+...+--.+-..+-+.|.++..||..||||++||..|.+
T Consensus 22 KLt~~qV~~IR~l~~r~G~s~~~IA~~fGVsrstV~~I~~ 61 (78)
T PHA00675 22 KLTDAEVERIRELHEVEGMSYAVLAEKFEQSKGAIAKICR 61 (78)
T ss_pred ccCHHHHHHHHHHHHhcCccHHHHHHHhCCCHHHHHHHHc
Confidence 3444333333333337888999999999999999987765
No 81
>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=86.79 E-value=0.78 Score=40.28 Aligned_cols=47 Identities=21% Similarity=0.190 Sum_probs=39.7
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
++|..++-++.|.++ .|.++.++|..+|||.+||...+.+....|-+
T Consensus 161 ~Lp~~~R~v~~L~~~-eg~S~~EIA~~Lgis~~TVk~rl~RAr~~Lr~ 207 (244)
T TIGR03001 161 ALSERERHLLRLHFV-DGLSMDRIGAMYQVHRSTVSRWVAQARERLLE 207 (244)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 356666777777665 78899999999999999999999999998876
No 82
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=86.70 E-value=0.84 Score=40.35 Aligned_cols=48 Identities=23% Similarity=0.162 Sum_probs=41.6
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA 86 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 86 (314)
.+++.++.++.|+|+ .|.++.++|..+|+|.++|++..++...-|-..
T Consensus 203 ~L~~~~r~vl~l~y~-~~~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~ 250 (256)
T PRK07408 203 QLEERTREVLEFVFL-HDLTQKEAAERLGISPVTVSRRVKKGLDQLKKL 250 (256)
T ss_pred cCCHHHHHHHHHHHH-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 477888888888876 588999999999999999999999998887763
No 83
>TIGR02392 rpoH_proteo alternative sigma factor RpoH. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors.
Probab=86.63 E-value=0.78 Score=40.89 Aligned_cols=48 Identities=15% Similarity=0.077 Sum_probs=42.0
Q ss_pred CCCHHHHHHHHHHHhh-cCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 38 KQPPMTRLLAVIQFYA-TGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~-~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
.+|..++..+.|+|+. .+.++.++|..+|||.++|+++.++.+.-|-.
T Consensus 218 ~L~~rer~vl~l~y~~~~~~t~~eIA~~lgvS~~~V~q~~~~Al~kLr~ 266 (270)
T TIGR02392 218 SLDARSRRIIEARWLDDDKLTLQELAAEYGVSAERIRQIEKNAMKKLKA 266 (270)
T ss_pred cCCHHHHHHHHHHhcCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4888999999999974 47899999999999999999999988877764
No 84
>PF13551 HTH_29: Winged helix-turn helix
Probab=86.51 E-value=0.51 Score=35.54 Aligned_cols=36 Identities=19% Similarity=0.211 Sum_probs=31.0
Q ss_pred HHHHhhcCCc-ccccCCcccccHHHHHHHHHHHHHHH
Q psy672 48 VIQFYATGNF-QIFTGDSHGVSQPTMCRLVKEVSKAL 83 (314)
Q Consensus 48 ~L~~L~~g~~-~~~l~~~fgis~stv~~~~~~v~~~l 83 (314)
+|..+..|.+ ...+|..+|+|.+||+++++++...-
T Consensus 4 ~l~l~~~g~~~~~~ia~~lg~s~~Tv~r~~~~~~~~G 40 (112)
T PF13551_consen 4 ILLLLAEGVSTIAEIARRLGISRRTVYRWLKRYREGG 40 (112)
T ss_pred HHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHccc
Confidence 5666888985 99999999999999999999987543
No 85
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=86.47 E-value=0.86 Score=36.86 Aligned_cols=47 Identities=15% Similarity=0.189 Sum_probs=39.6
Q ss_pred CCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672 39 QPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA 86 (314)
Q Consensus 39 ~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 86 (314)
+|+.++.++.|.+ -.|.++.++|+.+|+|.+||...+.+....|-+.
T Consensus 111 L~~~~r~i~~l~~-~~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 157 (162)
T TIGR02983 111 LPARQRAVVVLRY-YEDLSEAQVAEALGISVGTVKSRLSRALARLREL 157 (162)
T ss_pred CCHHHHHHhhhHH-HhcCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 5667777766666 5699999999999999999999999999888764
No 86
>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigE, also called SpoIIGB and sigma-29. As characterized in Bacillus subtilis, this protein is synthesized as a precursor, specifically in the mother cell compartment, and must cleaved by the SpoIIGA protein to be made active.
Probab=86.45 E-value=0.85 Score=39.66 Aligned_cols=49 Identities=27% Similarity=0.277 Sum_probs=43.0
Q ss_pred CCCHHHHHHHHHHHh---hcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672 38 KQPPMTRLLAVIQFY---ATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA 86 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L---~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 86 (314)
.+|+.++.++.|.++ ..|.++.++|+..|+|.+||....++....|-+.
T Consensus 178 ~Lp~~~R~ii~L~~~l~~~eg~s~~EIA~~Lgis~~tV~~~l~ra~~~LR~~ 229 (234)
T TIGR02835 178 KLNDREKKIMELRFGLVGGTEKTQKEVADMLGISQSYISRLEKRILKRLKKE 229 (234)
T ss_pred hCCHHHHHHHHHHHccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 588999999999886 3789999999999999999999998888877653
No 87
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=86.45 E-value=0.85 Score=38.28 Aligned_cols=49 Identities=18% Similarity=0.044 Sum_probs=40.6
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHhc
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAH 87 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~ 87 (314)
.+|+.++.++.|.++ .|.++.++|..+|+|.+||...+.+....|-+..
T Consensus 134 ~Lp~~~r~i~~l~~~-~g~s~~EIA~~lg~s~~tV~~rl~rar~~Lr~~l 182 (192)
T PRK09643 134 RLPVEQRAALVAVDM-QGYSVADAARMLGVAEGTVKSRCARGRARLAELL 182 (192)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 377778877777666 7899999999999999999999988888777643
No 88
>PF13730 HTH_36: Helix-turn-helix domain
Probab=86.40 E-value=0.71 Score=30.10 Aligned_cols=43 Identities=26% Similarity=0.281 Sum_probs=30.7
Q ss_pred CCHH-HHHHHHHHHhhcC-----CcccccCCcccccHHHHHHHHHHHHH
Q psy672 39 QPPM-TRLLAVIQFYATG-----NFQIFTGDSHGVSQPTMCRLVKEVSK 81 (314)
Q Consensus 39 ~s~~-~~l~~~L~~L~~g-----~~~~~l~~~fgis~stv~~~~~~v~~ 81 (314)
+++. ..|.+.|..+++. .+.+.+++..|+|+.||.+++++..+
T Consensus 3 Ls~~~~~v~~~l~~~~~~~~~~~pS~~~la~~~g~s~~Tv~~~i~~L~~ 51 (55)
T PF13730_consen 3 LSPTAKLVYLYLASYANKNGGCFPSQETLAKDLGVSRRTVQRAIKELEE 51 (55)
T ss_pred CCHHHHHHHHHHHHhcCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4443 3455666666522 25678999999999999999987654
No 89
>TIGR02984 Sig-70_plancto1 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are apparently found only in the Planctomycetaceae family including the genuses Gemmata and Pirellula (in which seven sequences are found).
Probab=86.32 E-value=1 Score=37.37 Aligned_cols=48 Identities=17% Similarity=0.057 Sum_probs=40.8
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA 86 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 86 (314)
.+|+.++-++.|.++ .|.++.++|..+|||.+||...+++....|-+.
T Consensus 140 ~L~~~~r~vi~l~~~-~g~s~~eIA~~lgis~~~v~~~l~Ra~~~Lr~~ 187 (189)
T TIGR02984 140 KLPEDYREVILLRHL-EGLSFAEVAERMDRSEGAVSMLWVRGLARLRQI 187 (189)
T ss_pred cCCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 477887777777666 889999999999999999999999988877653
No 90
>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=86.23 E-value=0.76 Score=30.35 Aligned_cols=39 Identities=23% Similarity=0.285 Sum_probs=27.3
Q ss_pred HHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHH
Q psy672 43 TRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSK 81 (314)
Q Consensus 43 ~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~ 81 (314)
+-.++...+=..+.+..++++.++++++++++++++...
T Consensus 5 q~~iL~~l~~~~~~~~~~la~~~~~~~~~~t~~i~~L~~ 43 (59)
T PF01047_consen 5 QFRILRILYENGGITQSELAEKLGISRSTVTRIIKRLEK 43 (59)
T ss_dssp HHHHHHHHHHHSSEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHcCCCCHHHHHHHHCCChhHHHHHHHHHHH
Confidence 333333333345578899999999999999998887654
No 91
>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=86.02 E-value=1.1 Score=33.17 Aligned_cols=44 Identities=14% Similarity=0.098 Sum_probs=35.2
Q ss_pred HHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 42 MTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 42 ~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
..|....=.|+....|...+|+.|+||++.|+..++++...|..
T Consensus 20 ~KQ~~Y~~lyy~dDlSl~EIAee~~VSRqAIyDnIKr~~~~L~~ 63 (105)
T COG2739 20 KKQKNYLELYYLDDLSLSEIAEEFNVSRQAIYDNIKRTEKILED 63 (105)
T ss_pred HHHHHHHHHHHHhhccHHHHHHHhCccHHHHHHHHHHHHHHHHH
Confidence 34444444455667788999999999999999999999998874
No 92
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.
Probab=85.99 E-value=0.34 Score=38.81 Aligned_cols=47 Identities=11% Similarity=0.024 Sum_probs=38.5
Q ss_pred CCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672 39 QPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA 86 (314)
Q Consensus 39 ~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 86 (314)
+|+.++-++.|.++ .|.++.++|..+|+|.+||...+++....|-+.
T Consensus 106 L~~~~r~i~~l~~~-~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~~ 152 (154)
T TIGR02950 106 LPENYRTVLILREF-KEFSYKEIAELLNLSLAKVKSNLFRARKELKKL 152 (154)
T ss_pred CCHhheeeeeehhh-ccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 56666666666656 799999999999999999999999988877653
No 93
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=85.98 E-value=0.98 Score=37.54 Aligned_cols=47 Identities=13% Similarity=-0.012 Sum_probs=37.7
Q ss_pred CCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672 39 QPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA 86 (314)
Q Consensus 39 ~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 86 (314)
+|+.++-++.|.+ -.|.++.++|..+|+|.+||...+++....|-..
T Consensus 138 L~~~~r~i~~l~~-~~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 184 (187)
T PRK12534 138 LEPPRSELIRTAF-FEGITYEELAARTDTPIGTVKSWIRRGLAKLKAC 184 (187)
T ss_pred CCHHHHHHHHHHH-HcCCCHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Confidence 5555555555554 4899999999999999999999999998887764
No 94
>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=85.96 E-value=0.78 Score=29.89 Aligned_cols=30 Identities=23% Similarity=0.094 Sum_probs=24.0
Q ss_pred cCCcccccCCcccccHHHHHHHHHHHHHHH
Q psy672 54 TGNFQIFTGDSHGVSQPTMCRLVKEVSKAL 83 (314)
Q Consensus 54 ~g~~~~~l~~~fgis~stv~~~~~~v~~~l 83 (314)
.+.+..++|+.+|||+.||.+.+...-+.+
T Consensus 14 ~~it~~eLa~~l~vS~rTi~~~i~~L~~~~ 43 (55)
T PF08279_consen 14 EPITAKELAEELGVSRRTIRRDIKELREWG 43 (55)
T ss_dssp TSBEHHHHHHHCTS-HHHHHHHHHHHHHTT
T ss_pred CCcCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence 336778999999999999999998876554
No 95
>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=85.84 E-value=1.2 Score=40.68 Aligned_cols=52 Identities=15% Similarity=0.153 Sum_probs=43.2
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHhcccc
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAHVNY 90 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~~~~ 90 (314)
++|+.++.++.|.++ .|.++.++|+.+|+|.+||...+.+....|-+.....
T Consensus 142 ~Lp~~~R~v~~L~~~-~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~ 193 (324)
T TIGR02960 142 YLPPRQRAVLLLRDV-LGWRAAETAELLGTSTASVNSALQRARATLDEVGPSA 193 (324)
T ss_pred hCCHHHhhHhhhHHH-hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhcccc
Confidence 467777777777665 7889999999999999999999999999998755543
No 96
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=85.75 E-value=0.97 Score=37.90 Aligned_cols=49 Identities=16% Similarity=0.060 Sum_probs=42.9
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHhc
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAH 87 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~ 87 (314)
.+|+.++-++.|.++ .|.++.++|..+|||.+||...+.+....|-+..
T Consensus 113 ~Lp~~~r~v~~L~~~-~g~s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l 161 (188)
T PRK12546 113 QLPDEQREALILVGA-SGFSYEEAAEMCGVAVGTVKSRANRARARLAELL 161 (188)
T ss_pred hCCHHHhHHhhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 477888888888777 8999999999999999999999999999888644
No 97
>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoE. This protein may be called sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.
Probab=85.63 E-value=0.86 Score=37.87 Aligned_cols=49 Identities=12% Similarity=-0.050 Sum_probs=40.2
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHhc
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAH 87 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~ 87 (314)
.+|+.++-++.|.|+ .|.++.++|..+|+|.+||...+++....|-+..
T Consensus 138 ~L~~~~r~v~~l~~~-~~~s~~EIA~~lgis~~tv~~~l~rar~~Lr~~l 186 (190)
T TIGR02939 138 ALPEDLRTAITLREL-EGLSYEDIARIMDCPVGTVRSRIFRAREAIAIRL 186 (190)
T ss_pred cCCHHHhhhhhhhhh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 356666666666655 8899999999999999999999999998888644
No 98
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=85.57 E-value=1 Score=37.48 Aligned_cols=49 Identities=16% Similarity=0.029 Sum_probs=41.1
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHhc
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAH 87 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~ 87 (314)
++|+.++-++.|.++ .|.++.++|..+|+|.+||...+++....|-+.+
T Consensus 111 ~Lp~~~R~v~~L~~~-~g~s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l 159 (182)
T PRK12540 111 KLPQDQREALILVGA-SGFSYEDAAAICGCAVGTIKSRVNRARSKLSALL 159 (182)
T ss_pred hCCHHHHHHhhHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 366677777767665 8899999999999999999999999999988744
No 99
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.
Probab=85.57 E-value=1 Score=36.71 Aligned_cols=48 Identities=8% Similarity=0.051 Sum_probs=38.9
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA 86 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 86 (314)
++|+.++-++.|.++. |.++.++|..+|+|.+||...+.+....|-+.
T Consensus 119 ~L~~~~r~i~~l~~~~-g~s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~~ 166 (169)
T TIGR02954 119 TLNDKYQTAIILRYYH-DLTIKEIAEVMNKPEGTVKTYLHRALKKLKKR 166 (169)
T ss_pred hCCHHHhHHHHHHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3666666666565555 89999999999999999999999998888764
No 100
>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=85.57 E-value=0.58 Score=29.59 Aligned_cols=38 Identities=18% Similarity=0.130 Sum_probs=26.9
Q ss_pred HHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHH
Q psy672 44 RLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSK 81 (314)
Q Consensus 44 ~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~ 81 (314)
++-+.........+..++++.+|+|++|++++++...+
T Consensus 4 R~~Il~~L~~~~~~~~el~~~l~~s~~~vs~hL~~L~~ 41 (47)
T PF01022_consen 4 RLRILKLLSEGPLTVSELAEELGLSQSTVSHHLKKLRE 41 (47)
T ss_dssp HHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHHHhCCCchhhHHHhccccchHHHHHHHHHHH
Confidence 34443333445567789999999999999999887654
No 101
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=85.50 E-value=0.94 Score=38.02 Aligned_cols=48 Identities=15% Similarity=0.119 Sum_probs=40.6
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA 86 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 86 (314)
.+|+.++-++.|.++ .|.++.++|..+|+|.+||...+++....|-+.
T Consensus 136 ~L~~~~r~i~~L~~~-~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 183 (195)
T PRK12532 136 NLPENTARVFTLKEI-LGFSSDEIQQMCGISTSNYHTIMHRARESLRQC 183 (195)
T ss_pred hCCHHHHHHhhhHHH-hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 467777777777666 788899999999999999999999999888864
No 102
>PRK05572 sporulation sigma factor SigF; Validated
Probab=85.49 E-value=1.1 Score=39.48 Aligned_cols=48 Identities=21% Similarity=0.347 Sum_probs=42.0
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA 86 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 86 (314)
.+|+.++.++.|+|+ .|.++.++|..+|+|.++|+++.++...-|-..
T Consensus 202 ~L~~~~~~v~~l~~~-~~~s~~eIA~~lgis~~~V~~~~~ral~kLr~~ 249 (252)
T PRK05572 202 ELDERERLIVYLRYF-KDKTQSEVAKRLGISQVQVSRLEKKILKQMKEK 249 (252)
T ss_pred cCCHHHHHHHHHHHh-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 588888888888775 678999999999999999999999998887753
No 103
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=85.49 E-value=1.1 Score=36.66 Aligned_cols=47 Identities=19% Similarity=0.167 Sum_probs=38.3
Q ss_pred CCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672 39 QPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA 86 (314)
Q Consensus 39 ~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 86 (314)
+|+.++-++.|.+ -.|.++.++|+.+|+|.+||...+++....|-+.
T Consensus 119 L~~~~r~vl~L~~-~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~ 165 (173)
T PRK09645 119 LSPEHRAVLVRSY-YRGWSTAQIAADLGIPEGTVKSRLHYALRALRLA 165 (173)
T ss_pred CCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 5666666665555 4588999999999999999999999988888764
No 104
>PF13309 HTH_22: HTH domain
Probab=85.47 E-value=0.66 Score=31.66 Aligned_cols=41 Identities=22% Similarity=0.391 Sum_probs=32.3
Q ss_pred CCCCHHHHHHHHHHHhhcCCcc-----cccCCcccccHHHHHHHHH
Q psy672 37 VKQPPMTRLLAVIQFYATGNFQ-----IFTGDSHGVSQPTMCRLVK 77 (314)
Q Consensus 37 ~~~s~~~~l~~~L~~L~~g~~~-----~~l~~~fgis~stv~~~~~ 77 (314)
..++.++++-+.-.....|... ..+|+.+|||+.||++|++
T Consensus 19 ~~l~~~~k~~iV~~L~~~G~F~lKgav~~vA~~L~iS~~TVY~YLr 64 (64)
T PF13309_consen 19 SRLSKEEKKEIVRQLYEKGIFLLKGAVEYVAEKLGISRATVYRYLR 64 (64)
T ss_pred hhCCHHHHHHHHHHHHHCCCcccCcHHHHHHHHHCCCHHHHHHHcC
Confidence 4577888888877777777433 5789999999999999863
No 105
>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=85.41 E-value=1.1 Score=30.16 Aligned_cols=41 Identities=20% Similarity=0.188 Sum_probs=31.1
Q ss_pred HHHHHHHHHHHhh---cCCcccccCCcccccHHHHHHHHHHHHH
Q psy672 41 PMTRLLAVIQFYA---TGNFQIFTGDSHGVSQPTMCRLVKEVSK 81 (314)
Q Consensus 41 ~~~~l~~~L~~L~---~g~~~~~l~~~fgis~stv~~~~~~v~~ 81 (314)
..+.-+-+++.|. ...+..++|+.+|+|.+||+..+++...
T Consensus 5 ~~e~YL~~Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~ 48 (60)
T PF01325_consen 5 SEEDYLKAIYELSEEGGPVRTKDIAERLGVSPPTVTEMLKRLAE 48 (60)
T ss_dssp HHHHHHHHHHHHHHCTSSBBHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHcCCCCccHHHHHHHHCCChHHHHHHHHHHHH
Confidence 4556667777777 4456678999999999999999888764
No 106
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=85.36 E-value=0.99 Score=37.72 Aligned_cols=47 Identities=11% Similarity=0.144 Sum_probs=41.0
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
.+|+.++-++.|.++ .|.++.++|+.+|+|.+||...+.+....|-.
T Consensus 131 ~L~~~~r~i~~l~~~-~g~s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~ 177 (189)
T PRK06811 131 DLEKLDREIFIRRYL-LGEKIEEIAKKLGLTRSAIDNRLSRGRKKLQK 177 (189)
T ss_pred hCCHHHHHHHHHHHH-ccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 478888888888776 68999999999999999999999998888765
No 107
>PF13610 DDE_Tnp_IS240: DDE domain
Probab=85.24 E-value=1.5 Score=34.84 Aligned_cols=131 Identities=15% Similarity=0.086 Sum_probs=75.9
Q ss_pred eeeceEEEEecCCCCCCCcccCCCCceeeeeeeecCCcccEEEeecCCCCCcChhhhhccCcchhhhhcC-CcceEEEeC
Q psy672 116 CVDCTHVPIQLPSVENGENFRNRKGTFSLNVQVIGGPNLEIWDVVSGWPGSVHDSRIFTNSRVCHRFERG-EVRGILLGD 194 (314)
Q Consensus 116 ~iDgt~i~i~~P~~~~~~~y~~~k~~~s~~~q~v~d~~g~i~~~~~~~pGs~~D~~i~~~s~~~~~l~~~-~~~~~llgD 194 (314)
.||-|.|+|.- ++ .=+-.++|++|+++++.+.---...++.-| +...+... ..+..++.|
T Consensus 5 ~~DEt~iki~G-----------~~----~yl~~aiD~~~~~l~~~ls~~Rd~~aA~~F----l~~~l~~~~~~p~~ivtD 65 (140)
T PF13610_consen 5 HVDETYIKIKG-----------KW----HYLWRAIDAEGNILDFYLSKRRDTAAAKRF----LKRALKRHRGEPRVIVTD 65 (140)
T ss_pred EEeeEEEEECC-----------EE----EEEEEeecccccchhhhhhhhcccccceee----ccccceeeccccceeecc
Confidence 68888888741 10 112468999999998888633333333222 22233332 235677778
Q ss_pred CC--CCCcccccccC-CCCCCchhhhhhhhhhhhHHHHHHHHHHHHhhhhhccccccCChhhHHHHHHHHHHHhhhcccc
Q psy672 195 SG--YAQNTFLYTPL-LNPTTPQEQRYNKAHIKTRNSVERLFGIWKRRFACLRRKLANSPVTCTHIVTACAVLHNIAVQT 271 (314)
Q Consensus 195 ~g--Y~~~~~l~~P~-~~~~~~~~~~fN~~~s~~R~~vE~~fg~lK~rf~~L~~~~~~~~~~~~~~i~a~~~LhN~~~~~ 271 (314)
++ |+.--.-+.+- ..+. ...-....-.++.||+-+..+|.|.+... ++ .+.+.+..++.+-.+.||+....
T Consensus 66 k~~aY~~A~~~l~~~~~~~~----~v~~~~~k~~nN~iE~~h~~~K~r~r~~~-gF-ks~~~A~~~l~~~~~~~n~~r~~ 139 (140)
T PF13610_consen 66 KLPAYPAAIKELNPEGRLHD----KVEHRQRKYLNNRIERDHRTIKRRTRPMN-GF-KSFRSAQRTLSGFEAYHNFRRPH 139 (140)
T ss_pred cCCccchhhhhccccccccc----ccceeechhhhChhhHhhhhhhhhccccc-Cc-CCHHHHHHHHHHHHHHHHHhCCC
Confidence 65 43211111111 0000 00001112246789999999999887665 34 36788999999999999997643
No 108
>PF00872 Transposase_mut: Transposase, Mutator family; InterPro: IPR001207 Autonomous mobile genetic elements such as transposon or insertion sequences (IS) encode an enzyme, transposase, that is required for excising and inserting the mobile element. Transposases have been grouped into various families [, , ]. The mutator family of transposases consists of a number of elements that include, mutator from maize, IsT2 from Thiobacillus ferrooxidans, Is256 from Staphylococcus aureus, Is1201 from Lactobacillus helveticus, Is1081 from Mycobacterium bovis, IsRm3 from Rhizobium meliloti and others. 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
Probab=85.17 E-value=1.4 Score=41.45 Aligned_cols=130 Identities=15% Similarity=0.091 Sum_probs=73.4
Q ss_pred HHHhhcCCcccccCCc----cc---ccHHHHHHHHHHHHHHHHHhccccccCCCchhhhHHHhhhcCCCCCceeeeeceE
Q psy672 49 IQFYATGNFQIFTGDS----HG---VSQPTMCRLVKEVSKALAQAHVNYVKFPEQLAPTKVAFQGIGNFPGVVGCVDCTH 121 (314)
Q Consensus 49 L~~L~~g~~~~~l~~~----fg---is~stv~~~~~~v~~~l~~~~~~~i~~P~~~~~~~~~f~~~~~~p~~~g~iDgt~ 121 (314)
+..+..|.+.+++... +| +|++||++++.++.+.+.....+-+ .+.|-.+-.|||++
T Consensus 108 ~~ly~~G~Str~i~~~l~~l~g~~~~S~s~vSri~~~~~~~~~~w~~R~L----------------~~~~y~~l~iD~~~ 171 (381)
T PF00872_consen 108 ISLYLKGVSTRDIEEALEELYGEVAVSKSTVSRITKQLDEEVEAWRNRPL----------------ESEPYPYLWIDGTY 171 (381)
T ss_pred hhhhccccccccccchhhhhhcccccCchhhhhhhhhhhhhHHHHhhhcc----------------ccccccceeeeeee
Confidence 3446777777766654 46 8999999999998887775432221 12223455899999
Q ss_pred EEEecCCCCCCCcccCCCCceeeeeeeecCCccc--EEEeecCCCCCcChhhhhccCcchhhhhcCCc-ceEEEeCCCCC
Q psy672 122 VPIQLPSVENGENFRNRKGTFSLNVQVIGGPNLE--IWDVVSGWPGSVHDSRIFTNSRVCHRFERGEV-RGILLGDSGYA 198 (314)
Q Consensus 122 i~i~~P~~~~~~~y~~~k~~~s~~~q~v~d~~g~--i~~~~~~~pGs~~D~~i~~~s~~~~~l~~~~~-~~~llgD~gY~ 198 (314)
+++..- . .-..-++-+-+.+|.+|+ ++.+..+ ++ -+...|.+ -+.+.-++|.. ...+++|.+=.
T Consensus 172 ~kvr~~-~--------~~~~~~~~v~iGi~~dG~r~vLg~~~~-~~--Es~~~W~~-~l~~L~~RGl~~~~lvv~Dg~~g 238 (381)
T PF00872_consen 172 FKVRED-G--------RVVKKAVYVAIGIDEDGRREVLGFWVG-DR--ESAASWRE-FLQDLKERGLKDILLVVSDGHKG 238 (381)
T ss_pred cccccc-c--------ccccchhhhhhhhhcccccceeeeecc-cC--CccCEeee-cchhhhhccccccceeecccccc
Confidence 988632 1 111223445566777775 7777766 22 22223321 12222233332 56778887655
Q ss_pred CcccccccC
Q psy672 199 QNTFLYTPL 207 (314)
Q Consensus 199 ~~~~l~~P~ 207 (314)
+..-+-.-|
T Consensus 239 l~~ai~~~f 247 (381)
T PF00872_consen 239 LKEAIREVF 247 (381)
T ss_pred ccccccccc
Confidence 544444434
No 109
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=85.07 E-value=1 Score=37.32 Aligned_cols=48 Identities=15% Similarity=0.164 Sum_probs=40.6
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA 86 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 86 (314)
.+|+.++-++.|.++ .|.++.++|+.+|+|.+||...+++....|-..
T Consensus 136 ~L~~~~r~v~~l~~~-~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T TIGR02948 136 ALPPKYRMVIVLKYM-EDLSLKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred hCCHHHhHHhhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 477777777777666 689999999999999999999999998887764
No 110
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=85.06 E-value=1.1 Score=34.26 Aligned_cols=48 Identities=19% Similarity=0.196 Sum_probs=42.9
Q ss_pred CCCCCHHHHHHHHHHHhhcCCcccccCCcccc-cHHHHHHHHHHHHHHH
Q psy672 36 GVKQPPMTRLLAVIQFYATGNFQIFTGDSHGV-SQPTMCRLVKEVSKAL 83 (314)
Q Consensus 36 ~~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgi-s~stv~~~~~~v~~~l 83 (314)
+..+|.+.++-++-.++..|.+...+|..||| +.+++++|+.+....-
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~sv~~vAr~~gv~~~~~l~~W~~~~~~~~ 53 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGDTVSEVAREFGIVSATQLYKWRIQLQKGG 53 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCccHHHHHHHhCCCChHHHHHHHHHHHHcc
Confidence 45689999999999999999999999999996 9999999998877643
No 111
>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=85.02 E-value=0.58 Score=32.52 Aligned_cols=45 Identities=13% Similarity=0.085 Sum_probs=33.9
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCcccccCCccc-ccHHHHHHHHHHH
Q psy672 35 QGVKQPPMTRLLAVIQFYATGNFQIFTGDSHG-VSQPTMCRLVKEV 79 (314)
Q Consensus 35 ~~~~~s~~~~l~~~L~~L~~g~~~~~l~~~fg-is~stv~~~~~~v 79 (314)
+...+.-.-++++.|..-.++.++.++|..|| .+.|||...++++
T Consensus 25 R~~~i~~aR~va~yL~r~~~~~sl~~Ig~~fg~rdHstV~~a~~ki 70 (70)
T PF08299_consen 25 RKRKIVEARQVAMYLARELTGLSLSEIGRYFGGRDHSTVIHAIRKI 70 (70)
T ss_dssp --HHHHHHHHHHHHHHHHHS---HHHHHHHCTSSTHHHHHHHHHHH
T ss_pred CChhhcchHHHHHHHHHHHhCCCHHHHHHHhCCCCHHHHHHHHHhC
Confidence 33445667788888888888999999999999 9999999887764
No 112
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=84.85 E-value=1.2 Score=37.09 Aligned_cols=48 Identities=23% Similarity=0.130 Sum_probs=41.6
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA 86 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 86 (314)
.+|+.++-++.|.++ .|.++.++|+.+|+|.+||...+++....|-+.
T Consensus 131 ~L~~~~r~v~~l~~~-~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 178 (184)
T PRK12539 131 RLPEKMRLAIQAVKL-EGLSVAEAATRSGMSESAVKVSVHRGLKALAAL 178 (184)
T ss_pred hCCHHHHHHHHHHHH-cCCcHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 477788877877777 499999999999999999999999999888763
No 113
>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=84.84 E-value=0.45 Score=36.85 Aligned_cols=30 Identities=23% Similarity=0.341 Sum_probs=26.4
Q ss_pred HHHhhcCCcccccCCcccccHHHHHHHHHH
Q psy672 49 IQFYATGNFQIFTGDSHGVSQPTMCRLVKE 78 (314)
Q Consensus 49 L~~L~~g~~~~~l~~~fgis~stv~~~~~~ 78 (314)
|-++..|.+..+++..|+||.+||.+|+.+
T Consensus 12 l~~~~~g~s~~eaa~~F~VS~~Tv~~W~k~ 41 (119)
T PF01710_consen 12 LAYIEKGKSIREAAKRFGVSRNTVYRWLKR 41 (119)
T ss_pred HHHHHccchHHHHHHHhCcHHHHHHHHHHh
Confidence 357778889999999999999999999884
No 114
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=84.78 E-value=1.2 Score=38.00 Aligned_cols=48 Identities=8% Similarity=-0.022 Sum_probs=41.0
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA 86 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 86 (314)
.+|+.++-++.|.++. |.++.++|..+|+|.+||...+++....|-+.
T Consensus 148 ~L~~~~r~v~~L~~~~-g~s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~ 195 (206)
T PRK12544 148 GLPAKYARVFMMREFI-ELETNEICHAVDLSVSNLNVLLYRARLRLREC 195 (206)
T ss_pred hCCHHHHHHHHHHHHc-CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 4777777777777655 88999999999999999999999999988874
No 115
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=84.76 E-value=1.4 Score=36.83 Aligned_cols=48 Identities=10% Similarity=0.059 Sum_probs=40.4
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA 86 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 86 (314)
++|+.++-++.|.++ .|.++.++|+.+|+|.+||...+.+....|-+.
T Consensus 131 ~Lp~~~r~v~~l~~~-~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 178 (191)
T PRK12520 131 RLPPRTGRVFMMREW-LELETEEICQELQITATNAWVLLYRARMRLREC 178 (191)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 477778877777665 468899999999999999999999999888763
No 116
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=84.69 E-value=1.1 Score=35.81 Aligned_cols=46 Identities=4% Similarity=0.029 Sum_probs=37.4
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHH
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALA 84 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~ 84 (314)
.+|+.++-++.|.|+ .|.++.++|..+|+|.+||.....+....|-
T Consensus 106 ~L~~~~r~ii~l~~~-~~~s~~EIA~~l~is~~tV~~~~~ra~~~Lr 151 (154)
T PRK06759 106 VLDEKEKYIIFERFF-VGKTMGEIALETEMTYYQVRWIYRQALEKMR 151 (154)
T ss_pred hCCHHHHHHHHHHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHh
Confidence 467777777766665 5788999999999999999999998777664
No 117
>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily. This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.
Probab=84.64 E-value=1.3 Score=38.20 Aligned_cols=47 Identities=23% Similarity=0.390 Sum_probs=40.4
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
.+|+.++-++.|+|+ .|.++.++|+.+|+|.+||....++....|-.
T Consensus 178 ~L~~~~r~vl~l~y~-~~~s~~eIA~~lgis~~~v~~~~~ra~~~Lr~ 224 (227)
T TIGR02980 178 ALPERERRILLLRFF-EDKTQSEIAERLGISQMHVSRLLRRALKKLRE 224 (227)
T ss_pred cCCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 478888888878765 68899999999999999999999998887764
No 118
>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=84.46 E-value=0.24 Score=31.45 Aligned_cols=21 Identities=24% Similarity=0.273 Sum_probs=18.0
Q ss_pred ccccCCcccccHHHHHHHHHH
Q psy672 58 QIFTGDSHGVSQPTMCRLVKE 78 (314)
Q Consensus 58 ~~~l~~~fgis~stv~~~~~~ 78 (314)
..++|+..|+|.+||+++++.
T Consensus 2 i~dIA~~agvS~~TVSr~ln~ 22 (46)
T PF00356_consen 2 IKDIAREAGVSKSTVSRVLNG 22 (46)
T ss_dssp HHHHHHHHTSSHHHHHHHHTT
T ss_pred HHHHHHHHCcCHHHHHHHHhC
Confidence 467899999999999998864
No 119
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=84.40 E-value=1 Score=40.50 Aligned_cols=48 Identities=15% Similarity=0.071 Sum_probs=42.1
Q ss_pred CCCHHHHHHHHHHHhh-cCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 38 KQPPMTRLLAVIQFYA-TGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~-~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
.++..++..+.++|+. .+.++.++|..+|||+++|+++-++.+.-|-.
T Consensus 230 ~L~~rEr~VL~lry~~~~~~Tl~EIA~~lgvS~~rVrqi~~~Al~kLR~ 278 (284)
T PRK06596 230 GLDERSRDIIEARWLDDDKSTLQELAAEYGVSAERVRQIEKNAMKKLKA 278 (284)
T ss_pred cCCHHHHHHHHHHhcCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4788899999999975 57899999999999999999999988877765
No 120
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=84.12 E-value=1.4 Score=36.16 Aligned_cols=47 Identities=13% Similarity=0.022 Sum_probs=38.9
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
.+|+.++-++.|.++ .|.++.++|+.+|+|.+||...+.+...-+..
T Consensus 119 ~Lp~~~r~v~~L~~~-~g~s~~EIA~~lgis~~tV~~~l~ra~~~~~~ 165 (172)
T PRK12523 119 KLSSKARAAFLYNRL-DGMGHAEIAERLGVSVSRVRQYLAQGLRQCYI 165 (172)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 467777777777665 58999999999999999999999888777664
No 121
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=84.03 E-value=1.4 Score=38.92 Aligned_cols=47 Identities=23% Similarity=0.237 Sum_probs=40.0
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
.+|+.++-++.|.|+ .|.++.++|..+|||.+||....++....|-.
T Consensus 205 ~L~~~~r~vl~l~~~-~g~s~~eIA~~l~is~~tV~~~~~ra~~kLr~ 251 (257)
T PRK08583 205 VLSDREKSIIQCTFI-ENLSQKETGERLGISQMHVSRLQRQAIKKLRE 251 (257)
T ss_pred hCCHHHHHHHHHHHh-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 477777777777664 78899999999999999999999999888765
No 122
>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor. The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homolog sigma-E (sigma-29) (see TIGR02835), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note that in Bacillus subtilis (and apparently also Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K.
Probab=83.98 E-value=1.3 Score=38.41 Aligned_cols=48 Identities=15% Similarity=0.086 Sum_probs=42.0
Q ss_pred CCCHHHHHHHHHHHh---hcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 38 KQPPMTRLLAVIQFY---ATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L---~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
.+|+.++-++.|.|+ ..|.++.++|+.+|+|.+||.+..++....|-.
T Consensus 174 ~L~~~~r~il~l~y~~~~~e~~S~~EIAe~lgis~~tV~~~~~rAl~~Lr~ 224 (227)
T TIGR02846 174 VLDGREREVIEMRYGLGDGRRKTQREIAKILGISRSYVSRIEKRALMKLYK 224 (227)
T ss_pred hCCHHHHHHHHHHHcCCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 578888888888886 488999999999999999999999988887765
No 123
>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain. This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc.
Probab=83.69 E-value=1.1 Score=39.03 Aligned_cols=48 Identities=8% Similarity=0.101 Sum_probs=41.7
Q ss_pred CCCHHHHHHHHHHHh---hcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 38 KQPPMTRLLAVIQFY---ATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L---~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
.+|+.++..+.|+|. ..+.++..+|..+|||.++|.++..+...-|-.
T Consensus 176 ~L~~~er~vl~l~ygl~~~~~~t~~EIA~~lgis~~~V~q~~~~al~kLr~ 226 (238)
T TIGR02393 176 TLTERERKVLRMRYGLLDGRPHTLEEVGKEFNVTRERIRQIESKALRKLRH 226 (238)
T ss_pred hCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHhh
Confidence 478889999999884 467899999999999999999999988877764
No 124
>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393).
Probab=83.43 E-value=1.2 Score=39.91 Aligned_cols=50 Identities=12% Similarity=0.048 Sum_probs=43.7
Q ss_pred CCCHHHHHHHHHHH-h--hcCCcccccCCcccccHHHHHHHHHHHHHHHHHhc
Q psy672 38 KQPPMTRLLAVIQF-Y--ATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAH 87 (314)
Q Consensus 38 ~~s~~~~l~~~L~~-L--~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~ 87 (314)
.+|..++..+.|+| | -.|.++.++|..+|+|.+||....++....|-...
T Consensus 222 ~Lp~~~R~Vl~l~ygL~~~e~~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~~l 274 (285)
T TIGR02394 222 ELNERQREVLARRFGLLGYEPATLEEVAAEVGLTRERVRQIQVEALKKLRRIL 274 (285)
T ss_pred cCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 58888999999988 4 57889999999999999999999999988887643
No 125
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=83.07 E-value=1.3 Score=39.84 Aligned_cols=49 Identities=12% Similarity=0.076 Sum_probs=43.2
Q ss_pred CCCHHHHHHHHHHHh-hcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672 38 KQPPMTRLLAVIQFY-ATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA 86 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L-~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 86 (314)
.+|+.++.++.|+|+ ..+.++.++|..+|||+++|..+.++...-|-..
T Consensus 227 ~L~~rer~vl~lr~~~~~~~t~~EIa~~lgvs~~~V~q~~~~Al~kLr~~ 276 (289)
T PRK07500 227 TLNERELRIIRERRLREDGATLEALGEELGISKERVRQIEARALEKLRRA 276 (289)
T ss_pred cCCHHHHHHHHHHhcCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 488899999999886 3688999999999999999999999998888763
No 126
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=82.87 E-value=1.8 Score=35.32 Aligned_cols=47 Identities=19% Similarity=0.139 Sum_probs=39.2
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
.+|+..+.++.|. +-.|.++.++|+.+|+|.+||...+.+....+..
T Consensus 118 ~L~~~~r~v~~L~-~~eg~s~~EIA~~l~is~~tV~~~l~ra~~~~~~ 164 (168)
T PRK12525 118 GLSGKARAAFLMS-QLEGLTYVEIGERLGVSLSRIHQYMVEAFKCCYQ 164 (168)
T ss_pred hCCHHHHHHHHHH-HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3777777766666 4678899999999999999999999988887765
No 127
>TIGR02885 spore_sigF RNA polymerase sigma-F factor. Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore.
Probab=82.83 E-value=1.7 Score=37.59 Aligned_cols=47 Identities=23% Similarity=0.357 Sum_probs=39.8
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
.+|..++.++.|+|+ .|.+..++|..+|+|.++|+++.++...-|-.
T Consensus 183 ~L~~~e~~i~~~~~~-~~~t~~eIA~~lgis~~~V~~~~~~al~~Lr~ 229 (231)
T TIGR02885 183 KLDERERQIIMLRYF-KDKTQTEVANMLGISQVQVSRLEKKVLKKMKE 229 (231)
T ss_pred cCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 577888888777664 67899999999999999999999998877654
No 128
>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=82.67 E-value=1.6 Score=36.44 Aligned_cols=48 Identities=13% Similarity=0.004 Sum_probs=38.5
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA 86 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 86 (314)
++|+.++-++.|.|+ .|.++.++|+.+|+|.+||...+.+....|-+.
T Consensus 131 ~L~~~~r~v~~l~~~-~g~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~ 178 (188)
T TIGR02943 131 HLPEQTARVFMMREV-LGFESDEICQELEISTSNCHVLLYRARLSLRAC 178 (188)
T ss_pred hCCHHHHHHHHHHHH-hCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 356666665555554 489999999999999999999999998888764
No 129
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=82.61 E-value=1.7 Score=38.39 Aligned_cols=47 Identities=26% Similarity=0.420 Sum_probs=40.0
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
.+++.++.++.+.|+ .|.++.++|..+|+|.++|+++.++...-|-.
T Consensus 209 ~L~~~er~vi~~~~~-~~~t~~eIA~~lgis~~~V~~~~~~al~kLr~ 255 (258)
T PRK08215 209 KLNDREKLILNLRFF-QGKTQMEVAEEIGISQAQVSRLEKAALKHMRK 255 (258)
T ss_pred cCCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 477888888888775 67899999999999999999999998877654
No 130
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=82.35 E-value=1.5 Score=38.17 Aligned_cols=52 Identities=6% Similarity=-0.137 Sum_probs=42.4
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHhcccc
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAHVNY 90 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~~~~ 90 (314)
.+|+.++.++.|.++- |.++.++|+.+|+|.+||...+.+....|-+...+-
T Consensus 116 ~Lp~~~R~v~lL~~~e-g~S~~EIAe~LgiS~~tVksrL~Rark~Lr~~l~~~ 167 (228)
T PRK06704 116 SLNVQQSAILLLKDVF-QYSIADIAKVCSVSEGAVKASLFRSRNRLKTVSEEG 167 (228)
T ss_pred hCCHHHhhHhhhHHhh-CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhc
Confidence 4677777776666544 799999999999999999999999999988765443
No 131
>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=82.21 E-value=1.5 Score=32.77 Aligned_cols=44 Identities=14% Similarity=0.154 Sum_probs=33.4
Q ss_pred HHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 42 MTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 42 ~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
+.|--+.-.|+-...|.+.+|+.+|||+..|+..+++....|..
T Consensus 20 ~kQ~~~l~lyy~eDlSlsEIAe~~~iSRqaV~d~ikr~~~~L~~ 63 (101)
T PF04297_consen 20 EKQREILELYYEEDLSLSEIAEELGISRQAVYDSIKRAEKKLEE 63 (101)
T ss_dssp HHHHHHHHHHCTS---HHHHHHHCTS-HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 44444555778889999999999999999999999999988874
No 132
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=82.17 E-value=1.6 Score=37.86 Aligned_cols=48 Identities=17% Similarity=0.186 Sum_probs=40.4
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA 86 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 86 (314)
.+|+.++-++.|.| -.|.++.++|..+|+|.+||....++....|-..
T Consensus 184 ~L~~~~r~vl~l~~-~~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~ 231 (236)
T PRK06986 184 SLPEREQLVLSLYY-QEELNLKEIGAVLGVSESRVSQIHSQAIKRLRAR 231 (236)
T ss_pred hCCHHHHHHHHhHh-ccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 46777777777766 4788999999999999999999999998888764
No 133
>TIGR01636 phage_rinA phage transcriptional activator, RinA family. This model represents a family of phage proteins, including RinA, a transcriptional activator in staphylococcal phage phi 11. This family shows similarity to ArpU, a phage-related putative autolysin regulator, and to some sporulation-specific sigma factors.
Probab=82.11 E-value=2.1 Score=33.88 Aligned_cols=48 Identities=17% Similarity=0.122 Sum_probs=40.8
Q ss_pred CCHHHHHHHHHHHhhc-CCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672 39 QPPMTRLLAVIQFYAT-GNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA 86 (314)
Q Consensus 39 ~s~~~~l~~~L~~L~~-g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 86 (314)
++.+++-++-+.|+.. ..++..+|..+|+|++|+++.-++++..+...
T Consensus 83 Ld~~er~II~~rY~~~~~~t~~~Ia~~l~iS~~t~~r~r~~~l~kla~~ 131 (134)
T TIGR01636 83 ADEQTRVIIQELYMKKRPLTLVGLAQQLFISKSTAYRLRNHIIEAVAEE 131 (134)
T ss_pred CCHHHHHHHHHHHccCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 6788898999988753 34899999999999999999999988887753
No 134
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=81.62 E-value=2 Score=35.54 Aligned_cols=47 Identities=13% Similarity=0.130 Sum_probs=38.7
Q ss_pred CCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672 39 QPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA 86 (314)
Q Consensus 39 ~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 86 (314)
+|..++-++.|.+ -.|.++.++|+.+|+|.+||....++....|-+.
T Consensus 136 L~~~~r~vl~l~~-~~~~s~~eIA~~lgis~~~V~~~l~ra~~~Lr~~ 182 (186)
T PRK13919 136 LSPEERRVIEVLY-YQGYTHREAAQLLGLPLGTLKTRARRALSRLKEV 182 (186)
T ss_pred CCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 6666676666665 5688899999999999999999999988888753
No 135
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=81.61 E-value=3 Score=33.22 Aligned_cols=45 Identities=7% Similarity=-0.068 Sum_probs=32.7
Q ss_pred CCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHH
Q psy672 37 VKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSK 81 (314)
Q Consensus 37 ~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~ 81 (314)
..+++.+-.++...+-..+.+..++++.++++++|+++.+++...
T Consensus 36 ~glt~~q~~vL~~l~~~~~~t~~eLa~~l~i~~~tvsr~l~~Le~ 80 (144)
T PRK11512 36 LDITAAQFKVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLVC 80 (144)
T ss_pred cCCCHHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 456665554433334455678999999999999999998887654
No 136
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=81.51 E-value=2.1 Score=35.69 Aligned_cols=47 Identities=13% Similarity=0.107 Sum_probs=38.4
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
++|+.++-++.|.|+. |.++.++|..+|+|.+||...+++....|-.
T Consensus 139 ~L~~~~r~i~~l~~~~-g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 185 (189)
T PRK09648 139 TLPEKQREILILRVVV-GLSAEETAEAVGSTPGAVRVAQHRALARLRA 185 (189)
T ss_pred hCCHHHHHHHHHHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4667777666666655 8889999999999999999999988877765
No 137
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=81.39 E-value=1.6 Score=35.82 Aligned_cols=52 Identities=8% Similarity=0.028 Sum_probs=40.8
Q ss_pred CCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHhccccc
Q psy672 39 QPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAHVNYV 91 (314)
Q Consensus 39 ~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~~~~i 91 (314)
+|+..+ -+++.++-.|.++.++|..+|+|.+||...+.+....|-+....+|
T Consensus 120 L~~~~r-~i~~l~~~~~~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~~~~ 171 (173)
T PRK12522 120 LNEKYK-TVLVLYYYEQYSYKEMSEILNIPIGTVKYRLNYAKKQMREHLEGFV 171 (173)
T ss_pred CCHHHH-HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHHh
Confidence 444444 3444556688999999999999999999999999999988666554
No 138
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=81.27 E-value=1.8 Score=36.51 Aligned_cols=47 Identities=6% Similarity=0.089 Sum_probs=39.4
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA 86 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 86 (314)
.+|+.++-++.| ++ .|.++.++|..+|+|.+||...+++....|-+.
T Consensus 155 ~L~~~~r~vl~l-~~-e~~s~~EIA~~lgis~~tV~~~l~rar~~Lr~~ 201 (208)
T PRK08295 155 LLSELEKEVLEL-YL-DGKSYQEIAEELNRHVKSIDNALQRVKRKLEKY 201 (208)
T ss_pred hCCHHHHHHHHH-HH-ccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 466777777777 55 789999999999999999999999988887763
No 139
>TIGR02850 spore_sigG RNA polymerase sigma-G factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigG. It is also desginated stage III sporulation protein G (SpoIIIG). This protein is rather closely related to sigma-F (SpoIIAC), another sporulation sigma factor.
Probab=81.23 E-value=1.7 Score=38.27 Aligned_cols=47 Identities=21% Similarity=0.407 Sum_probs=40.2
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
.+++.++.++.++|+ .|.++.++|..+|+|.++|+++.++.+.-|-.
T Consensus 206 ~L~~rer~vi~~~~~-~~~t~~eIA~~lgis~~~V~~~~~ral~kLr~ 252 (254)
T TIGR02850 206 RLNEREKMILNMRFF-EGKTQMEVAEEIGISQAQVSRLEKAALKHMRK 252 (254)
T ss_pred cCCHHHHHHHHHHHc-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHh
Confidence 578888888888775 67899999999999999999999988876653
No 140
>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family. This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393).
Probab=81.23 E-value=1.4 Score=39.89 Aligned_cols=45 Identities=11% Similarity=0.102 Sum_probs=39.3
Q ss_pred CCCHHHHHHHHHHHh---hcCCcccccCCcccccHHHHHHHHHHHHHH
Q psy672 38 KQPPMTRLLAVIQFY---ATGNFQIFTGDSHGVSQPTMCRLVKEVSKA 82 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L---~~g~~~~~l~~~fgis~stv~~~~~~v~~~ 82 (314)
.+|+.++..+.|+|. ..+.++.++|..+|||+++|..+.++...-
T Consensus 249 ~L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVrq~~~rAl~k 296 (298)
T TIGR02997 249 ELTPRERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKALRK 296 (298)
T ss_pred cCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 488999999999885 578899999999999999999998887654
No 141
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=81.03 E-value=2.1 Score=37.59 Aligned_cols=48 Identities=23% Similarity=0.319 Sum_probs=41.5
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA 86 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 86 (314)
.++-.+|+.+.|+| -.+.++..+|+..|||++.|+++..+.+..|-+.
T Consensus 196 ~L~EREk~Vl~l~y-~eelt~kEI~~~LgISes~VSql~kkai~kLr~~ 243 (247)
T COG1191 196 PLPEREKLVLVLRY-KEELTQKEIAEVLGISESRVSRLHKKAIKKLRKE 243 (247)
T ss_pred ccCHHHHHHHHHHH-HhccCHHHHHHHhCccHHHHHHHHHHHHHHHHHH
Confidence 47778899999988 5678889999999999999999999998887753
No 142
>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=80.84 E-value=1.4 Score=29.72 Aligned_cols=26 Identities=23% Similarity=0.279 Sum_probs=22.3
Q ss_pred CcccccCCcccccHHHHHHHHHHHHH
Q psy672 56 NFQIFTGDSHGVSQPTMCRLVKEVSK 81 (314)
Q Consensus 56 ~~~~~l~~~fgis~stv~~~~~~v~~ 81 (314)
.+..++++.+|+|++|++++++....
T Consensus 26 ~s~~ela~~~g~s~~tv~r~l~~L~~ 51 (67)
T cd00092 26 LTRQEIADYLGLTRETVSRTLKELEE 51 (67)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 46678999999999999999888765
No 143
>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=80.79 E-value=2 Score=28.66 Aligned_cols=40 Identities=23% Similarity=0.312 Sum_probs=30.7
Q ss_pred HHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 45 LLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 45 l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
+-+++....+| ++...|+.+++|++++++.+++.-..+..
T Consensus 4 l~~f~~v~~~g-s~~~AA~~l~is~~~vs~~i~~LE~~lg~ 43 (60)
T PF00126_consen 4 LRYFLAVAETG-SISAAAEELGISQSAVSRQIKQLEEELGV 43 (60)
T ss_dssp HHHHHHHHHHS-SHHHHHHHCTSSHHHHHHHHHHHHHHHTS
T ss_pred HHHHHHHHHhC-CHHHHHHHhhccchHHHHHHHHHHHHhCC
Confidence 33344444444 78899999999999999999998887764
No 144
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=80.62 E-value=2.2 Score=37.46 Aligned_cols=47 Identities=9% Similarity=0.066 Sum_probs=40.3
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
.+|+.++-++.|.|+ .|.++.++|..+|+|.+||...+++....|-.
T Consensus 201 ~L~~~~r~vl~l~~~-~~~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~ 247 (251)
T PRK07670 201 QLSEKEQLVISLFYK-EELTLTEIGQVLNLSTSRISQIHSKALFKLKK 247 (251)
T ss_pred cCCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 477888888887774 88899999999999999999999998887765
No 145
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=80.55 E-value=1.9 Score=31.14 Aligned_cols=40 Identities=28% Similarity=0.330 Sum_probs=31.0
Q ss_pred HHHHHHHHHHhhc---CCcccccCCcccccHHHHHHHHHHHHH
Q psy672 42 MTRLLAVIQFYAT---GNFQIFTGDSHGVSQPTMCRLVKEVSK 81 (314)
Q Consensus 42 ~~~l~~~L~~L~~---g~~~~~l~~~fgis~stv~~~~~~v~~ 81 (314)
..+.+..|.+++. +.+..++++.+|++++|+++++.....
T Consensus 4 ~~r~~~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~~ 46 (91)
T smart00346 4 LERGLAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQE 46 (91)
T ss_pred HHHHHHHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 3455556666654 367789999999999999999988765
No 146
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=80.54 E-value=2.3 Score=34.24 Aligned_cols=48 Identities=15% Similarity=0.103 Sum_probs=38.6
Q ss_pred CCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHhc
Q psy672 39 QPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAH 87 (314)
Q Consensus 39 ~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~ 87 (314)
+|++++-++.| .+-.|.++.++|..+|+|.+||...+.+....|-...
T Consensus 106 L~~~~r~v~~l-~~~~~~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~l 153 (159)
T PRK12527 106 LPPACRDSFLL-RKLEGLSHQQIAEHLGISRSLVEKHIVNAMKHCRVRM 153 (159)
T ss_pred CCHHHHHHHHH-HHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 66666655555 4568889999999999999999999999988887643
No 147
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=80.14 E-value=2.4 Score=34.15 Aligned_cols=47 Identities=11% Similarity=-0.005 Sum_probs=37.2
Q ss_pred CCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672 39 QPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA 86 (314)
Q Consensus 39 ~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 86 (314)
+|+.++-++.|. +-.|.++.++|+.+|+|.+||...+.+....|-+.
T Consensus 107 Lp~~~r~v~~l~-~~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 153 (160)
T PRK09642 107 LPENYRDVVLAH-YLEEKSYQEIALQEKIEVKTVEMKLYRARKWIKKH 153 (160)
T ss_pred CCHHHHHHHHHH-HHhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 555555555444 45788999999999999999999999988888764
No 148
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=80.11 E-value=1.8 Score=29.43 Aligned_cols=43 Identities=21% Similarity=0.157 Sum_probs=38.0
Q ss_pred HHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672 44 RLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA 86 (314)
Q Consensus 44 ~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 86 (314)
++-.+..+|+...+..++|+..|+...++.+++..+-..+.++
T Consensus 2 ~~~~fIrlLs~~~s~~~Aa~~lG~~~~~v~~wv~~fR~wll~L 44 (65)
T PF05344_consen 2 KARAFIRLLSQQISVAQAADRLGTDPGTVRRWVRMFRQWLLQL 44 (65)
T ss_pred cHHHHHHHhcccccHHHHHHHHCcCHHHHHHHHHHHHHHHHHc
Confidence 3445678899999999999999999999999999999999875
No 149
>PRK06930 positive control sigma-like factor; Validated
Probab=80.11 E-value=2.1 Score=35.41 Aligned_cols=48 Identities=10% Similarity=0.104 Sum_probs=39.3
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA 86 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 86 (314)
.+|+.++-++.|. +..|.++.++|..+|+|.+||...+.+....|-..
T Consensus 114 ~L~~rer~V~~L~-~~eg~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~ 161 (170)
T PRK06930 114 VLTEREKEVYLMH-RGYGLSYSEIADYLNIKKSTVQSMIERAEKKIARQ 161 (170)
T ss_pred hCCHHHHHHHHHH-HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 4666666555544 58899999999999999999999999998888763
No 150
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=79.96 E-value=1.9 Score=39.37 Aligned_cols=48 Identities=13% Similarity=0.180 Sum_probs=42.4
Q ss_pred CCCHHHHHHHHHHHh---hcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 38 KQPPMTRLLAVIQFY---ATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L---~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
.+|+.++..+.|+|. ..+.++.++|..+|||+++|..+..+...-|-.
T Consensus 256 ~L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVRqi~~rAl~kLr~ 306 (317)
T PRK07405 256 DLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKLRK 306 (317)
T ss_pred cCCHHHHHHHHHHhhcCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 488999999999986 467899999999999999999999998888775
No 151
>PRK13870 transcriptional regulator TraR; Provisional
Probab=79.75 E-value=1.3 Score=38.70 Aligned_cols=47 Identities=17% Similarity=0.175 Sum_probs=40.1
Q ss_pred CCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 37 VKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 37 ~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
..+++.|+ =+|.|.+.|.+..++|...|||++||..++++...-|..
T Consensus 172 ~~LT~RE~--E~L~W~A~GKT~~EIa~ILgISe~TV~~Hl~na~~KLga 218 (234)
T PRK13870 172 AWLDPKEA--TYLRWIAVGKTMEEIADVEGVKYNSVRVKLREAMKRFDV 218 (234)
T ss_pred CCCCHHHH--HHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCC
Confidence 35666665 468899999999999999999999999999998877663
No 152
>TIGR02941 Sigma_B RNA polymerase sigma-B factor. This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.
Probab=79.65 E-value=2.1 Score=37.73 Aligned_cols=47 Identities=21% Similarity=0.198 Sum_probs=40.2
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
.+|+.++-.+.|.|+ .|.++.++|..+|+|.+||....++....|-.
T Consensus 205 ~L~~~~r~ii~l~~~-~g~s~~eIA~~lgis~~~V~~~~~ra~~~Lr~ 251 (255)
T TIGR02941 205 ILSEREKSIIHCTFE-ENLSQKETGERLGISQMHVSRLQRQAISKLKE 251 (255)
T ss_pred cCCHHHHHHHHHHHc-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 478888887777765 68899999999999999999999988887765
No 153
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=79.58 E-value=2.3 Score=35.07 Aligned_cols=48 Identities=19% Similarity=0.128 Sum_probs=38.5
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA 86 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 86 (314)
.+|+.++-++.|. +-.|.++.++|+.+|+|.+||...+++....|-+.
T Consensus 117 ~Lp~~~r~i~~l~-~~e~~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~ 164 (179)
T PRK12543 117 KLPYKLRQVIILR-YLHDYSQEEIAQLLQIPIGTVKSRIHAALKKLRQK 164 (179)
T ss_pred hCCHHHHHHHHHH-HHccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3677777666664 44677999999999999999999999888877653
No 154
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=79.15 E-value=2.4 Score=35.22 Aligned_cols=51 Identities=14% Similarity=-0.045 Sum_probs=40.0
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHhccc
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAHVN 89 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~~~ 89 (314)
.+|+.++.++.|.+ -.|.++.++|..+|+|.+||...+.+....|-+....
T Consensus 106 ~L~~~~r~i~~l~~-~~g~~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 156 (181)
T PRK09637 106 ALPEKYAEALRLTE-LEGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKELLEG 156 (181)
T ss_pred hCCHHHHHHHHHHH-hcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 36666666655554 5788899999999999999999999998888875433
No 155
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=79.03 E-value=1.9 Score=29.66 Aligned_cols=42 Identities=10% Similarity=0.184 Sum_probs=31.5
Q ss_pred CHHHHHHHHHHHhhc-CCcccccCCcccccHHHHHHHHHHHHH
Q psy672 40 PPMTRLLAVIQFYAT-GNFQIFTGDSHGVSQPTMCRLVKEVSK 81 (314)
Q Consensus 40 s~~~~l~~~L~~L~~-g~~~~~l~~~fgis~stv~~~~~~v~~ 81 (314)
+.+++++.+|..-+. +.+..+|+..+|+++++|++.+.....
T Consensus 6 ~~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~ 48 (68)
T smart00550 6 SLEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEK 48 (68)
T ss_pred HHHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 356677776665544 478899999999999999887766543
No 156
>PRK01381 Trp operon repressor; Provisional
Probab=78.90 E-value=1 Score=33.50 Aligned_cols=40 Identities=18% Similarity=-0.002 Sum_probs=29.9
Q ss_pred CCHHHHHHHHHHH------hhcCCcccccCCcccccHHHHHHHHHH
Q psy672 39 QPPMTRLLAVIQF------YATGNFQIFTGDSHGVSQPTMCRLVKE 78 (314)
Q Consensus 39 ~s~~~~l~~~L~~------L~~g~~~~~l~~~fgis~stv~~~~~~ 78 (314)
+++.++=+++.++ +..+.+++.++...|||.+||+|.-+.
T Consensus 33 lTp~Er~al~~R~~I~~~L~~g~~sQREIa~~lGvSiaTITRgsn~ 78 (99)
T PRK01381 33 LTPDEREALGTRVRIVEELLRGELSQREIKQELGVGIATITRGSNS 78 (99)
T ss_pred CCHHHHHHHHHHHHHHHHHHcCCcCHHHHHHHhCCceeeehhhHHH
Confidence 5667766666554 334589999999999999998876543
No 157
>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=78.76 E-value=2.1 Score=31.10 Aligned_cols=38 Identities=18% Similarity=0.215 Sum_probs=29.9
Q ss_pred HHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHH
Q psy672 42 MTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEV 79 (314)
Q Consensus 42 ~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v 79 (314)
.+++.++=-.|..|.+|+++++..|+|-.|++|.-+..
T Consensus 36 ~~R~~va~~lL~~g~syreIa~~tgvS~aTItRvsr~L 73 (87)
T PF01371_consen 36 AQRWQVAKELLDEGKSYREIAEETGVSIATITRVSRCL 73 (87)
T ss_dssp HHHHHHHHHHHHTTSSHHHHHHHHTSTHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 44455554468899999999999999999999875543
No 158
>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=78.49 E-value=0.73 Score=29.81 Aligned_cols=38 Identities=18% Similarity=0.253 Sum_probs=27.1
Q ss_pred HHHHHHHHhhcC---CcccccCCcccccHHHHHHHHHHHHH
Q psy672 44 RLLAVIQFYATG---NFQIFTGDSHGVSQPTMCRLVKEVSK 81 (314)
Q Consensus 44 ~l~~~L~~L~~g---~~~~~l~~~fgis~stv~~~~~~v~~ 81 (314)
+.+-.|..++.. .+..++++..|++++|+++++.....
T Consensus 4 ral~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~~ 44 (52)
T PF09339_consen 4 RALRILEALAESGGPLTLSEIARALGLPKSTVHRLLQTLVE 44 (52)
T ss_dssp HHHHHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 444455555533 35789999999999999999887654
No 159
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=78.29 E-value=1.9 Score=35.72 Aligned_cols=45 Identities=16% Similarity=0.163 Sum_probs=38.2
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHH
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALA 84 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~ 84 (314)
.+|+.|. -+|.+++.|.+..++|+.+++|.+||..+..++..-|.
T Consensus 133 ~LSpREr--EVLrLLAqGkTnKEIAe~L~IS~rTVkth~srImkKLg 177 (198)
T PRK15201 133 HFSVTER--HLLKLIASGYHLSETAALLSLSEEQTKSLRRSIMRKLH 177 (198)
T ss_pred CCCHHHH--HHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 4777665 45667999999999999999999999999998887665
No 160
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=78.10 E-value=2.6 Score=37.41 Aligned_cols=47 Identities=23% Similarity=0.349 Sum_probs=39.4
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
.+|+.++-++.|+|+ .|.++.++|..+|+|.++|.++.++...-|-.
T Consensus 215 ~L~~rer~vl~l~y~-~~~t~~EIA~~lgis~~~V~~~~~ral~kLr~ 261 (264)
T PRK07122 215 ALPERERTVLVLRFF-ESMTQTQIAERVGISQMHVSRLLAKTLARLRD 261 (264)
T ss_pred cCCHHHHHHHHHHhc-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 367777777777775 68899999999999999999999988877764
No 161
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=78.09 E-value=1.9 Score=36.80 Aligned_cols=45 Identities=9% Similarity=0.206 Sum_probs=38.7
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHH
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALA 84 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~ 84 (314)
.+++.|+ =.|.+++.|.+..++|+..++|.+||..+..++..-|.
T Consensus 137 ~LT~RE~--eVL~lla~G~snkeIA~~L~iS~~TVk~h~~~I~~KL~ 181 (207)
T PRK15411 137 SLSRTES--SMLRMWMAGQGTIQISDQMNIKAKTVSSHKGNIKRKIK 181 (207)
T ss_pred cCCHHHH--HHHHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHHHHhC
Confidence 3666666 45677999999999999999999999999998887766
No 162
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=77.73 E-value=4.1 Score=36.66 Aligned_cols=50 Identities=16% Similarity=0.095 Sum_probs=40.1
Q ss_pred CCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHhccc
Q psy672 39 QPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAHVN 89 (314)
Q Consensus 39 ~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~~~ 89 (314)
+|+.++-++.|.+ -.|.++.++|+.+|+|.+||...+++....|-+..+.
T Consensus 116 L~~~~R~v~~L~~-~~g~s~~EIA~~lg~s~~tVk~~l~RAr~~Lr~~~~~ 165 (293)
T PRK09636 116 LSPLERAAFLLHD-VFGVPFDEIASTLGRSPAACRQLASRARKHVRAARPR 165 (293)
T ss_pred CCHHHHHHHHHHH-HhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCCC
Confidence 6666666555544 4578999999999999999999999999999875544
No 163
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=77.53 E-value=3 Score=34.87 Aligned_cols=48 Identities=13% Similarity=0.004 Sum_probs=38.0
Q ss_pred CCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHhc
Q psy672 39 QPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAH 87 (314)
Q Consensus 39 ~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~ 87 (314)
+|...+-++.| ++-.|.++.++|..+|||.+||...+.+....|.+..
T Consensus 129 Lp~~~r~v~~l-~~~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 176 (188)
T PRK12517 129 LDPEYREPLLL-QVIGGFSGEEIAEILDLNKNTVMTRLFRARNQLKEAL 176 (188)
T ss_pred CCHHHHHHHHH-HHHhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 55555554444 4556889999999999999999999999998888643
No 164
>PRK14086 dnaA chromosomal replication initiation protein; Provisional
Probab=77.49 E-value=5.6 Score=39.65 Aligned_cols=52 Identities=10% Similarity=0.013 Sum_probs=47.2
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 34 MQGVKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 34 ~~~~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
.|...+...-|++|.|.+=-++.++..||..||.+.|||...++++-+.|.+
T Consensus 548 ~R~~~i~~aRqiAMYL~r~lt~~Sl~~IG~~FgRdHSTV~~A~~kI~~~~~~ 599 (617)
T PRK14086 548 SRSRVLVTARQIAMYLCRELTDLSLPKIGQQFGRDHTTVMHADRKIRALMAE 599 (617)
T ss_pred CCCcccchHHHHHHHHHHHHcCCCHHHHHHHhCCChhHHHHHHHHHHHHHHh
Confidence 4556788899999999999999999999999999999999999999987774
No 165
>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family. Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.
Probab=77.31 E-value=3.3 Score=35.59 Aligned_cols=47 Identities=13% Similarity=0.204 Sum_probs=39.4
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
.+|+.++-++.|.|+ .|.++.++|..+|+|.+||.+..++....|-.
T Consensus 175 ~L~~~~r~il~l~y~-~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~ 221 (224)
T TIGR02479 175 SLSEREQLVLSLYYY-EELNLKEIGEVLGLTESRVSQIHSQALKKLRA 221 (224)
T ss_pred hCCHHHHHHHHHHHh-CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 477888887777774 67889999999999999999999888877654
No 166
>PRK00149 dnaA chromosomal replication initiation protein; Reviewed
Probab=77.22 E-value=6.4 Score=37.83 Aligned_cols=53 Identities=13% Similarity=0.075 Sum_probs=47.5
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCcccccCCcc-cccHHHHHHHHHHHHHHHHH
Q psy672 33 TMQGVKQPPMTRLLAVIQFYATGNFQIFTGDSH-GVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 33 ~~~~~~~s~~~~l~~~L~~L~~g~~~~~l~~~f-gis~stv~~~~~~v~~~l~~ 85 (314)
.+|...+...-|++|.|.+--++.++.++|..| |.+.|||...++++-..+.+
T Consensus 380 ~~R~~~~~~aR~iamyl~~~~~~~s~~~Ig~~fg~rdhstV~~a~~~i~~~~~~ 433 (450)
T PRK00149 380 KSRTRNIARPRQIAMYLAKELTDLSLPEIGRAFGGRDHTTVLHAVRKIEKLLEE 433 (450)
T ss_pred CCCCcccChHHHHHHHHHHHhcCCCHHHHHHHcCCCCHhHHHHHHHHHHHHHHh
Confidence 356678889999999999999999999999999 59999999999999987763
No 167
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=77.08 E-value=3 Score=35.20 Aligned_cols=49 Identities=6% Similarity=-0.126 Sum_probs=39.6
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHhc
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAH 87 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~ 87 (314)
.+|+..+-++.|.| -.|.++.++|..+|+|.+||...+.+....|-+.+
T Consensus 139 ~Lp~~~r~v~~L~~-~eg~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l 187 (201)
T PRK12545 139 HLPEQIGRVFMMRE-FLDFEIDDICTELTLTANHCSVLLYRARTRLRTCL 187 (201)
T ss_pred hCCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 36677777666665 46778999999999999999999999888887643
No 168
>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=76.97 E-value=3.9 Score=36.61 Aligned_cols=51 Identities=16% Similarity=0.137 Sum_probs=39.7
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHhccc
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAHVN 89 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~~~ 89 (314)
.+|+.++-++.|. .-.|.++.++|+.+|+|.+||...+++....|-+..+.
T Consensus 108 ~L~~~~R~v~~L~-~~~g~s~~EIA~~lg~s~~tVr~~l~RAr~~Lr~~~~~ 158 (281)
T TIGR02957 108 RLSPLERAVFVLR-EVFDYPYEEIASIVGKSEANCRQLVSRARRHLDARRPR 158 (281)
T ss_pred hCCHHHHHHHHHH-HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCCC
Confidence 3556665555444 44588899999999999999999999999999875443
No 169
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=76.54 E-value=3.4 Score=34.12 Aligned_cols=46 Identities=26% Similarity=0.131 Sum_probs=36.9
Q ss_pred CCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 39 QPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 39 ~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
+|+.++.++.|. +-.|.++.++|+.+|+|.+||...+++....|-+
T Consensus 130 L~~~~r~v~~l~-~~~g~s~~EIA~~l~is~~tV~~~l~rar~~Lr~ 175 (181)
T PRK12536 130 LPDRQRLPIVHV-KLEGLSVAETAQLTGLSESAVKVGIHRGLKALAA 175 (181)
T ss_pred CCHHHHHHHHHH-HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 556566544444 4678899999999999999999999998888776
No 170
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=76.45 E-value=3.5 Score=34.76 Aligned_cols=51 Identities=18% Similarity=0.070 Sum_probs=40.3
Q ss_pred CCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHhcccc
Q psy672 39 QPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAHVNY 90 (314)
Q Consensus 39 ~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~~~~ 90 (314)
+|+..+-++.|.++ .|.++.++|+.+|+|.+||...+++....|-+...++
T Consensus 134 Lp~~~r~v~~l~~~-~g~s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l~~~ 184 (196)
T PRK12535 134 LPPERREALILTQV-LGYTYEEAAKIADVRVGTIRSRVARARADLIAATATG 184 (196)
T ss_pred CCHHHHHHhhhHHH-hCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhccc
Confidence 55556665555544 5677999999999999999999999999998866554
No 171
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=76.40 E-value=1.6 Score=37.78 Aligned_cols=49 Identities=14% Similarity=0.124 Sum_probs=39.6
Q ss_pred CCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHhcc
Q psy672 39 QPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAHV 88 (314)
Q Consensus 39 ~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~~ 88 (314)
+|+.++-++.|.++ .|.++.++|+.+|+|.+||...+.+....|-+...
T Consensus 150 L~~~~r~i~~l~~~-~g~s~~EIAe~lgis~~tVk~~l~Rar~kLr~~l~ 198 (231)
T PRK11922 150 LPDAFRAVFVLRVV-EELSVEETAQALGLPEETVKTRLHRARRLLRESLA 198 (231)
T ss_pred CCHHHhhhheeehh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 66666666666554 48999999999999999999999999888887443
No 172
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=76.36 E-value=1.8 Score=39.56 Aligned_cols=68 Identities=12% Similarity=0.047 Sum_probs=48.9
Q ss_pred HHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHhccccccCCCc-hhhhHHHhhhcCCCCCceee
Q psy672 47 AVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAHVNYVKFPEQ-LAPTKVAFQGIGNFPGVVGC 116 (314)
Q Consensus 47 ~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~~~~i~~P~~-~~~~~~~f~~~~~~p~~~g~ 116 (314)
++=+|+-.|.++.++|+.+|+|+++|+|++.+.-+.=. -+--|.-|.. ...+...+.+..++..|+-+
T Consensus 21 vA~lYY~~g~tQ~eIA~~lgiSR~~VsRlL~~Ar~~Gi--V~I~I~~~~~~~~~Le~~L~~~fgLk~~iVv 89 (318)
T PRK15418 21 IAWFYYHDGLTQSEIGERLGLTRLKVSRLLEKGRQSGI--IRVQINSRFEGCLELENALRQHFSLQHIRVL 89 (318)
T ss_pred HHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHcCc--EEEEEeCCCccHHHHHHHHHHHhCCCEEEEE
Confidence 67788899999999999999999999999988765422 1122333444 44566666666788877533
No 173
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=76.09 E-value=3.1 Score=31.82 Aligned_cols=47 Identities=15% Similarity=0.159 Sum_probs=37.1
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
.++.+++-+ ...++.+.++..+++..+|||=+||..-+++++.+|--
T Consensus 33 ~L~~E~~~F-i~~Fi~~rGnlKe~e~~lgiSYPTvR~rLd~ii~~lg~ 79 (113)
T PF09862_consen 33 RLSPEQLEF-IKLFIKNRGNLKEMEKELGISYPTVRNRLDKIIEKLGY 79 (113)
T ss_pred cCCHHHHHH-HHHHHHhcCCHHHHHHHHCCCcHHHHHHHHHHHHHhCC
Confidence 455555554 45566667788999999999999999999999988864
No 174
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=75.26 E-value=3.1 Score=34.57 Aligned_cols=47 Identities=15% Similarity=0.015 Sum_probs=37.5
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
++|+.++-++.|.++ .|.++.++|+.+|+|.+||...+.+....|-+
T Consensus 130 ~Lp~~~r~v~~L~~~-~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 176 (185)
T PRK09649 130 DLTTDQREALLLTQL-LGLSYADAAAVCGCPVGTIRSRVARARDALLA 176 (185)
T ss_pred hCCHHHhHHhhhHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 356666666655544 57779999999999999999999998888775
No 175
>PRK01905 DNA-binding protein Fis; Provisional
Probab=74.97 E-value=6 Score=27.93 Aligned_cols=29 Identities=14% Similarity=0.278 Sum_probs=23.2
Q ss_pred HhhcCCcccccCCcccccHHHHHHHHHHH
Q psy672 51 FYATGNFQIFTGDSHGVSQPTMCRLVKEV 79 (314)
Q Consensus 51 ~L~~g~~~~~l~~~fgis~stv~~~~~~v 79 (314)
+-.++......|+..|||++|+++..++.
T Consensus 46 L~~~~gn~s~aAr~LGIsrstL~rklkk~ 74 (77)
T PRK01905 46 MEQAGGNQSLAAEYLGINRNTLRKKLQQH 74 (77)
T ss_pred HHHcCCCHHHHHHHHCCCHHHHHHHHHHh
Confidence 34466778889999999999999887753
No 176
>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=74.93 E-value=4.2 Score=33.26 Aligned_cols=50 Identities=18% Similarity=0.029 Sum_probs=40.1
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHhcc
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAHV 88 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~~ 88 (314)
.+|+.++.++.|.+ -.|.++.++|..+|+|.+||...+.+....|-....
T Consensus 100 ~L~~~~r~v~~l~~-~~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 149 (170)
T TIGR02959 100 ELPDEYREAIRLTE-LEGLSQQEIAEKLGLSLSGAKSRVQRGRKKLKELLE 149 (170)
T ss_pred hCCHHHHHHHHHHH-HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 46676666666655 567889999999999999999999999888887543
No 177
>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=74.70 E-value=2.6 Score=28.13 Aligned_cols=32 Identities=13% Similarity=0.071 Sum_probs=25.9
Q ss_pred HHHHHHhhcCCcccccCCcccccHHHHHHHHHHH
Q psy672 46 LAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEV 79 (314)
Q Consensus 46 ~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v 79 (314)
+..|++ .|-+..++|+.+|++.+||+.+..+-
T Consensus 6 A~~LY~--~G~~~~eIA~~Lg~~~~TV~~W~~r~ 37 (58)
T PF06056_consen 6 ARSLYL--QGWSIKEIAEELGVPRSTVYSWKDRY 37 (58)
T ss_pred HHHHHH--cCCCHHHHHHHHCCChHHHHHHHHhh
Confidence 444443 68899999999999999999887753
No 178
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=74.59 E-value=3.2 Score=28.81 Aligned_cols=67 Identities=18% Similarity=0.049 Sum_probs=47.1
Q ss_pred cccccCHHHHHHhhHHhhhhhhcccCCCCCCCCHHHHHHHHHHHhhcC-CcccccCCcccc-cHHHHHHHHHHHHH
Q psy672 8 EALRFSKDVVLNIIFPLARNVLETNTMQGVKQPPMTRLLAVIQFYATG-NFQIFTGDSHGV-SQPTMCRLVKEVSK 81 (314)
Q Consensus 8 ~~frmsr~~f~~~L~~~l~~~~~~~~~~~~~~s~~~~l~~~L~~L~~g-~~~~~l~~~fgi-s~stv~~~~~~v~~ 81 (314)
+.+.++...|. .++........ ...-...++.-++.++..+ .+..++|..+|. |.+..++.|++...
T Consensus 9 ~~~~~s~~~l~-~~f~~~~~~s~------~~~~~~~r~~~a~~~l~~~~~~~~~ia~~~g~~s~~~f~r~Fk~~~g 77 (84)
T smart00342 9 EALGMSPRHLQ-RLFKKETGTTP------KQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFG 77 (84)
T ss_pred HHhCCCHHHHH-HHHHHHhCcCH------HHHHHHHHHHHHHHHHHcCCCCHHHHHHHhCCCChHHHHHHHHHHHC
Confidence 56788888888 77665431100 1112345667777777776 788999999999 99999999987653
No 179
>TIGR02859 spore_sigH RNA polymerase sigma-H factor. Members of this protein family are RNA polymerase sigma-H factor for sporulation in endospore-forming bacteria. This protein is also called Sigma-30 and SigH. Although rather close homologs are detected in Listeria, Listeria does not form spores and the role of the related sigma factor in that genus is in doubt.
Probab=74.06 E-value=3.8 Score=34.19 Aligned_cols=43 Identities=7% Similarity=0.018 Sum_probs=33.1
Q ss_pred HHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 42 MTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 42 ~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
+.+-.+.+.++ .|.++.++|+.+|+|.+||...+++....|-.
T Consensus 153 ~~~~~i~~~~~-~~~s~~eIA~~l~~s~~tV~~~l~r~r~~L~~ 195 (198)
T TIGR02859 153 DLEWKVLQSYL-DGKSYQEIACDLNRHVKSIDNALQRVKRKLEK 195 (198)
T ss_pred HHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 33333344444 89999999999999999999888888777654
No 180
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=74.05 E-value=1.8 Score=29.18 Aligned_cols=28 Identities=32% Similarity=0.266 Sum_probs=21.6
Q ss_pred HHhhcCCcccccCCcccccHHHHHHHHH
Q psy672 50 QFYATGNFQIFTGDSHGVSQPTMCRLVK 77 (314)
Q Consensus 50 ~~L~~g~~~~~l~~~fgis~stv~~~~~ 77 (314)
.+-+.|.+..++|+..|+|.++++++-+
T Consensus 9 ~R~~~gls~~~lA~~~g~s~s~v~~iE~ 36 (64)
T PF13560_consen 9 LRERAGLSQAQLADRLGVSQSTVSRIER 36 (64)
T ss_dssp HHHCHTS-HHHHHHHHTS-HHHHHHHHT
T ss_pred HHHHcCCCHHHHHHHHCcCHHHHHHHHC
Confidence 3445789999999999999999998764
No 181
>PRK14088 dnaA chromosomal replication initiation protein; Provisional
Probab=74.02 E-value=4.5 Score=38.83 Aligned_cols=52 Identities=19% Similarity=0.151 Sum_probs=46.7
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHH
Q psy672 33 TMQGVKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALA 84 (314)
Q Consensus 33 ~~~~~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~ 84 (314)
.+|...+...-|++|.|.+=-++.++.++|..||.+.|||...++++-..+.
T Consensus 365 ~~R~~~i~~aR~iamyl~r~~~~~s~~~Ig~~fgr~hstV~~a~~~i~~~~~ 416 (440)
T PRK14088 365 NSRNVKALLARRIGMYVAKNYLGSSLRTIAEKFNRSHPVVVDSVKKVKDSLL 416 (440)
T ss_pred CCCCccccHHHHHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 3466788899999999999999999999999999999999999999998763
No 182
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=73.99 E-value=4.7 Score=33.63 Aligned_cols=46 Identities=20% Similarity=0.280 Sum_probs=34.3
Q ss_pred CCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 39 QPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 39 ~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
+++++.=.+.|.++ .|.+..++|...|||.+||.+.....-..|..
T Consensus 136 l~~~~~~~v~l~~~-~Gls~~EIA~~lgiS~~tV~r~l~~aR~~l~~ 181 (185)
T PF07638_consen 136 LDPRQRRVVELRFF-EGLSVEEIAERLGISERTVRRRLRRARAWLRR 181 (185)
T ss_pred cCHHHHHHHHHHHH-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 33444444455444 78899999999999999999998887766654
No 183
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=73.99 E-value=3.5 Score=38.58 Aligned_cols=48 Identities=10% Similarity=0.114 Sum_probs=41.4
Q ss_pred CCCHHHHHHHHHHHh---hcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 38 KQPPMTRLLAVIQFY---ATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L---~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
.+++.++..+.|+|+ ..+.++..+|..+|||+.+|..+-.+.+.-|-.
T Consensus 311 ~L~~rEr~IL~lrygl~~~~~~Tl~EIA~~lgiS~eRVRQie~rAL~KLR~ 361 (373)
T PRK07406 311 TLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRH 361 (373)
T ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHhc
Confidence 488999999999886 246799999999999999999999988877764
No 184
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=73.88 E-value=4.3 Score=33.98 Aligned_cols=48 Identities=13% Similarity=0.016 Sum_probs=38.4
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA 86 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 86 (314)
++|+.++-++.|. +-.|.++.++|+.+|+|.+||...+++....|-..
T Consensus 142 ~L~~~~r~vl~l~-~~~~~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~ 189 (194)
T PRK09646 142 ALTDTQRESVTLA-YYGGLTYREVAERLAVPLGTVKTRMRDGLIRLRDC 189 (194)
T ss_pred hCCHHHHHHHHHH-HHcCCCHHHHHHHhCCChHhHHHHHHHHHHHHHHH
Confidence 3666666655554 45679999999999999999999999988888763
No 185
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=73.72 E-value=4.3 Score=34.45 Aligned_cols=48 Identities=21% Similarity=0.111 Sum_probs=37.9
Q ss_pred CCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHhc
Q psy672 39 QPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAH 87 (314)
Q Consensus 39 ~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~ 87 (314)
+|+..+-++.|. .-.|.++.++|+.+|+|.+||...+.+....|-+..
T Consensus 139 L~~~~r~v~~L~-~~~g~s~~EIA~~Lgis~~tV~~~l~RArk~Lr~~l 186 (203)
T PRK09647 139 LPPEFRAAVVLC-DIEGLSYEEIAATLGVKLGTVRSRIHRGRQQLRAAL 186 (203)
T ss_pred CCHHHHHHHHHH-HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 555555444444 467889999999999999999999999988888643
No 186
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=73.60 E-value=4.1 Score=35.38 Aligned_cols=46 Identities=9% Similarity=0.161 Sum_probs=38.4
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHH
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALA 84 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~ 84 (314)
.+++.++-.+.|+| ..|.++.++|..+|||+++|+++-++...-|-
T Consensus 183 ~L~~~er~vi~l~~-~~~~t~~EIA~~lgis~~~V~q~~~~~~~kLr 228 (231)
T PRK12427 183 QLDEREQLILHLYY-QHEMSLKEIALVLDLTEARICQLNKKIAQKIK 228 (231)
T ss_pred cCCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 46778888887777 46889999999999999999999888777654
No 187
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=73.00 E-value=1.6 Score=36.42 Aligned_cols=48 Identities=13% Similarity=0.058 Sum_probs=35.3
Q ss_pred CCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHhc
Q psy672 39 QPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAH 87 (314)
Q Consensus 39 ~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~ 87 (314)
+|+.++=++.|. +-.|.++.++|..+|||.+||...+.+....|-...
T Consensus 135 L~~~~r~v~~l~-~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 182 (188)
T PRK09640 135 VNPIDREILVLR-FVAELEFQEIADIMHMGLSATKMRYKRALDKLREKF 182 (188)
T ss_pred cChhheeeeeeH-HhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 333433333333 347789999999999999999999999888887643
No 188
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=72.97 E-value=4 Score=37.48 Aligned_cols=49 Identities=10% Similarity=0.068 Sum_probs=42.4
Q ss_pred CCCHHHHHHHHHHH-h--hcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672 38 KQPPMTRLLAVIQF-Y--ATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA 86 (314)
Q Consensus 38 ~~s~~~~l~~~L~~-L--~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 86 (314)
.+|+.++.++.+.| | -.|.++..+|..+|||.+||..+.++....|-..
T Consensus 262 ~L~~~~R~vl~lrygL~~~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~ 313 (325)
T PRK05657 262 ELNDKQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQIQVEALRRLREI 313 (325)
T ss_pred cCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 48888888888877 4 3678999999999999999999999999888764
No 189
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=72.90 E-value=3.8 Score=38.86 Aligned_cols=47 Identities=11% Similarity=0.061 Sum_probs=40.6
Q ss_pred CCCHHHHHHHHHHHh---hcCCcccccCCcccccHHHHHHHHHHHHHHHH
Q psy672 38 KQPPMTRLLAVIQFY---ATGNFQIFTGDSHGVSQPTMCRLVKEVSKALA 84 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L---~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~ 84 (314)
.+++.++-.+.|+|. +.+.++.++|..+|+|.++|..+.++....|-
T Consensus 350 ~L~~reR~VI~LRygl~d~~~~Tl~EIA~~LGvS~erVRqie~rAl~KLR 399 (415)
T PRK07598 350 DLTSRERDVIRMRFGLADGHTYSLAEIGRALDLSRERVRQIESKALQKLR 399 (415)
T ss_pred hCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHh
Confidence 488899999999885 35679999999999999999999998877776
No 190
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=72.78 E-value=4.5 Score=33.31 Aligned_cols=46 Identities=20% Similarity=0.081 Sum_probs=37.2
Q ss_pred CCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 39 QPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 39 ~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
+|+.++-++.|. +-.|.++.++|+.+|+|.+||...+++....|-+
T Consensus 135 Lp~~~r~v~~l~-~~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 180 (183)
T TIGR02999 135 VDPRQAEVVELR-FFAGLTVEEIAELLGVSVRTVERDWRFARAWLAD 180 (183)
T ss_pred CCHHHHHHHHHH-HHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 666666655554 4468889999999999999999999998888765
No 191
>PHA02591 hypothetical protein; Provisional
Probab=72.66 E-value=2.9 Score=29.42 Aligned_cols=39 Identities=13% Similarity=0.017 Sum_probs=32.1
Q ss_pred CHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHH
Q psy672 40 PPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKE 78 (314)
Q Consensus 40 s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~ 78 (314)
+-++-+.++=.....|.+...+|...|+++.+|++|.+.
T Consensus 44 ~~dd~~~vA~eL~eqGlSqeqIA~~LGVsqetVrKYL~~ 82 (83)
T PHA02591 44 SEDDLISVTHELARKGFTVEKIASLLGVSVRKVRRYLES 82 (83)
T ss_pred ccchHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHhc
Confidence 345556666666789999999999999999999999864
No 192
>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=72.66 E-value=2.2 Score=32.25 Aligned_cols=35 Identities=14% Similarity=0.090 Sum_probs=27.8
Q ss_pred Hhh-cCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 51 FYA-TGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 51 ~L~-~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
-|+ -|.+...+|+.|+||+||+..++.+.-..-..
T Consensus 75 ~LR~AGlt~~aIAd~F~iS~s~~~nft~~n~~eYyr 110 (126)
T PF10654_consen 75 ELRHAGLTCYAIADYFKISKSTVFNFTQNNKKEYYR 110 (126)
T ss_pred HHHhcCCChHHHHHHHhHHHHHHHHHHHHhHHHHHH
Confidence 344 46889999999999999999998776655443
No 193
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=72.10 E-value=4.7 Score=35.81 Aligned_cols=47 Identities=15% Similarity=0.241 Sum_probs=39.3
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
.+|+.++-++.|+|+ .|.++.++|..+|+|.+||.+..++....|-.
T Consensus 212 ~L~~~~r~vl~l~~~-~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~ 258 (268)
T PRK06288 212 TLPEREKKVLILYYY-EDLTLKEIGKVLGVTESRISQLHTKAVLQLRA 258 (268)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 478888888777764 68899999999999999999888887777665
No 194
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=72.06 E-value=4 Score=35.50 Aligned_cols=48 Identities=13% Similarity=0.139 Sum_probs=38.1
Q ss_pred CCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHhc
Q psy672 39 QPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAH 87 (314)
Q Consensus 39 ~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~ 87 (314)
+|..++-++.|. +-.|.++.++|+.+|+|.+||...+++....|-+..
T Consensus 172 Lp~~~R~v~~L~-~~eg~s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~l 219 (233)
T PRK12538 172 LPEQQRIAVILS-YHENMSNGEIAEVMDTTVAAVESLLKRGRQQLRDLL 219 (233)
T ss_pred CCHHHHHHhhhH-HhcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 555666555544 457889999999999999999999999998887643
No 195
>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=71.98 E-value=3.8 Score=33.93 Aligned_cols=45 Identities=16% Similarity=0.229 Sum_probs=36.5
Q ss_pred CCCHHHHHHHHHHHhhc--------------CCcccccCCcccccHHHHHHHHHHHHHH
Q psy672 38 KQPPMTRLLAVIQFYAT--------------GNFQIFTGDSHGVSQPTMCRLVKEVSKA 82 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~--------------g~~~~~l~~~fgis~stv~~~~~~v~~~ 82 (314)
..+++++|+-+|..|+. ..+..++|...|+++.||+|.++++...
T Consensus 112 ~~~~~~Rla~~L~~l~~~~~~~~~~~~~~~~~~t~~~iA~~lG~tretvsR~l~~l~~~ 170 (193)
T TIGR03697 112 HRDMGSRLVSFLLILCRDFGVPGQRGVTIDLRLSHQAIAEAIGSTRVTITRLLGDLRKK 170 (193)
T ss_pred hCCHHHHHHHHHHHHHHHhCCCCCCeEEecCCCCHHHHHHHhCCcHHHHHHHHHHHHHC
Confidence 35789999999887753 1356789999999999999999988764
No 196
>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=71.91 E-value=3 Score=28.19 Aligned_cols=35 Identities=23% Similarity=0.313 Sum_probs=24.7
Q ss_pred HHHHhh---cCCcccccCCcccccHHHHHHHHHHHHHH
Q psy672 48 VIQFYA---TGNFQIFTGDSHGVSQPTMCRLVKEVSKA 82 (314)
Q Consensus 48 ~L~~L~---~g~~~~~l~~~fgis~stv~~~~~~v~~~ 82 (314)
+|.+++ ...+..++++.++++++++++.+++..+.
T Consensus 8 vL~~l~~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~ 45 (68)
T PF13463_consen 8 VLRALAHSDGPMTQSDLAERLGISKSTVSRIIKKLEEK 45 (68)
T ss_dssp HHHHHT--TS-BEHHHHHHHTT--HHHHHHHHHHHHHT
T ss_pred HHHHHHccCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 355555 34667899999999999999888877654
No 197
>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=71.72 E-value=3.3 Score=30.54 Aligned_cols=28 Identities=11% Similarity=0.220 Sum_probs=23.1
Q ss_pred cCCcccccCCcccccHHHHHHHHHHHHH
Q psy672 54 TGNFQIFTGDSHGVSQPTMCRLVKEVSK 81 (314)
Q Consensus 54 ~g~~~~~l~~~fgis~stv~~~~~~v~~ 81 (314)
...+..++|...|+|++||++.+++...
T Consensus 46 ~~is~~eLa~~~g~sr~tVsr~L~~Le~ 73 (95)
T TIGR01610 46 DRVTATVIAELTGLSRTHVSDAIKSLAR 73 (95)
T ss_pred CccCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4467788999999999999988877654
No 198
>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A ....
Probab=71.65 E-value=3.3 Score=28.70 Aligned_cols=25 Identities=32% Similarity=0.373 Sum_probs=21.3
Q ss_pred cccccCCcccccHHHHHHHHHHHHH
Q psy672 57 FQIFTGDSHGVSQPTMCRLVKEVSK 81 (314)
Q Consensus 57 ~~~~l~~~fgis~stv~~~~~~v~~ 81 (314)
+..++|...|+|+.|+++.++++.+
T Consensus 30 t~~~iA~~~g~sr~tv~r~l~~l~~ 54 (76)
T PF13545_consen 30 TQEEIADMLGVSRETVSRILKRLKD 54 (76)
T ss_dssp SHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4567899999999999999888765
No 199
>PRK05949 RNA polymerase sigma factor; Validated
Probab=71.43 E-value=4.4 Score=37.25 Aligned_cols=48 Identities=15% Similarity=0.164 Sum_probs=41.3
Q ss_pred CCCHHHHHHHHHHHh-h--cCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 38 KQPPMTRLLAVIQFY-A--TGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L-~--~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
.+++.++-.+.|+|. . .+.++.++|+.+|+|+++|..+..+....|-.
T Consensus 266 ~L~~rer~Vi~lr~gl~~~e~~Tl~EIa~~lgiS~erVrq~~~rAl~kLr~ 316 (327)
T PRK05949 266 ELTPQQREVLTLRFGLEDGKELSLAKVGERLNLSRERVRQLEHQALAHLRR 316 (327)
T ss_pred hCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 488899998888874 3 56899999999999999999999998887765
No 200
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=71.00 E-value=2.4 Score=35.43 Aligned_cols=47 Identities=13% Similarity=0.050 Sum_probs=36.1
Q ss_pred CCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672 39 QPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA 86 (314)
Q Consensus 39 ~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 86 (314)
+|+.++-++.|+ +-.|.++.++|..+|+|.+||...+.+....|-+.
T Consensus 140 L~~~~r~i~~l~-~~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~ 186 (194)
T PRK12513 140 LPDEQREVFLLR-EHGDLELEEIAELTGVPEETVKSRLRYALQKLREL 186 (194)
T ss_pred CCHhHhhheeee-hccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 455555544443 35788999999999999999999888888877763
No 201
>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and (with the exception of a paralog in Thermobifida fusca YX) one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor in an apparent operon.
Probab=70.95 E-value=2.4 Score=35.40 Aligned_cols=48 Identities=15% Similarity=0.033 Sum_probs=38.1
Q ss_pred CCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHhc
Q psy672 39 QPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAH 87 (314)
Q Consensus 39 ~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~ 87 (314)
+|+..+-++.|. +-.|.++.++|..+|+|.+||...+.+....|-+..
T Consensus 132 Lp~~~r~i~~L~-~~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 179 (193)
T TIGR02947 132 LPEEFRQAVYLA-DVEGFAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQL 179 (193)
T ss_pred CCHHHhhheeeh-hhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 555556555554 456788999999999999999999999998888644
No 202
>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=70.75 E-value=2.7 Score=28.67 Aligned_cols=39 Identities=13% Similarity=0.164 Sum_probs=28.8
Q ss_pred HHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHH
Q psy672 42 MTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSK 81 (314)
Q Consensus 42 ~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~ 81 (314)
+.++..+|. -..+.+..++++..|+++++|++++++..+
T Consensus 10 E~~vy~~Ll-~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~ 48 (68)
T PF01978_consen 10 EAKVYLALL-KNGPATAEEIAEELGISRSTVYRALKSLEE 48 (68)
T ss_dssp HHHHHHHHH-HHCHEEHHHHHHHHTSSHHHHHHHHHHHHH
T ss_pred HHHHHHHHH-HcCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 444555554 233477889999999999999998887665
No 203
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=70.65 E-value=3.3 Score=32.90 Aligned_cols=44 Identities=18% Similarity=0.264 Sum_probs=31.4
Q ss_pred CCCHHHH-HHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHH
Q psy672 38 KQPPMTR-LLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSK 81 (314)
Q Consensus 38 ~~s~~~~-l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~ 81 (314)
.+++.+- ++..|.....+.+..++++.++++++|+++.+++...
T Consensus 28 glt~~q~~vL~~l~~~~~~~t~~eLa~~l~~~~~tvt~~v~~Le~ 72 (144)
T PRK03573 28 ELTQTHWVTLHNIHQLPPEQSQIQLAKAIGIEQPSLVRTLDQLEE 72 (144)
T ss_pred CCCHHHHHHHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHHHHHH
Confidence 4655553 4444444444568899999999999999988777654
No 204
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=70.49 E-value=6.5 Score=35.46 Aligned_cols=50 Identities=14% Similarity=0.173 Sum_probs=38.6
Q ss_pred CCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHhccc
Q psy672 39 QPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAHVN 89 (314)
Q Consensus 39 ~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~~~ 89 (314)
+|+.++-++.| +.-.|.++.++|+.+|+|.+||...+++....|-...+.
T Consensus 119 L~p~~R~vf~L-~~~~g~s~~EIA~~Lgis~~tVr~~l~RAr~~Lr~~~~~ 168 (290)
T PRK09635 119 LGPAERVVFVL-HEIFGLPYQQIATTIGSQASTCRQLAHRARRKINESRIA 168 (290)
T ss_pred CCHHHHHHhhH-HHHhCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHhhCCC
Confidence 44555544444 445689999999999999999999999999988875443
No 205
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=70.43 E-value=4.9 Score=32.38 Aligned_cols=46 Identities=15% Similarity=0.129 Sum_probs=36.1
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHH
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALA 84 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~ 84 (314)
++|+.++-++.|. +-.|.++.++|..+|+|.+||...+++....|.
T Consensus 113 ~L~~~~r~v~~L~-~~~g~s~~EIA~~l~is~~tV~~~l~ra~~~~~ 158 (161)
T PRK12528 113 GLPPLVKRAFLLA-QVDGLGYGEIATELGISLATVKRYLNKAAMRCY 158 (161)
T ss_pred HCCHHHHHHHHHH-HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 3566666655554 456888999999999999999999998877654
No 206
>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function.
Probab=70.40 E-value=6.8 Score=29.60 Aligned_cols=47 Identities=23% Similarity=0.208 Sum_probs=36.3
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
.+++++-=++-|..+ .|.++.+.|...|||++|+++++.+.-.-|.+
T Consensus 41 ~L~~dElEAiRL~D~-egl~QeeaA~~MgVSR~T~~ril~~ARkKiA~ 87 (106)
T PF02001_consen 41 VLTVDELEAIRLVDY-EGLSQEEAAERMGVSRPTFQRILESARKKIAD 87 (106)
T ss_pred EeeHHHHHHHHHHHH-cCCCHHHHHHHcCCcHHHHHHHHHHHHHHHHH
Confidence 356666666666555 45889999999999999999999877666654
No 207
>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=70.33 E-value=1.6 Score=28.25 Aligned_cols=27 Identities=22% Similarity=0.250 Sum_probs=22.0
Q ss_pred hhcCCcccccCCcccccHHHHHHHHHH
Q psy672 52 YATGNFQIFTGDSHGVSQPTMCRLVKE 78 (314)
Q Consensus 52 L~~g~~~~~l~~~fgis~stv~~~~~~ 78 (314)
-..|.++.++|...|+|++|++++.+.
T Consensus 6 ~~~gls~~~la~~~gis~~~i~~~~~g 32 (55)
T PF01381_consen 6 KEKGLSQKELAEKLGISRSTISRIENG 32 (55)
T ss_dssp HHTTS-HHHHHHHHTS-HHHHHHHHTT
T ss_pred HHcCCCHHHHHHHhCCCcchhHHHhcC
Confidence 467899999999999999999998765
No 208
>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=69.97 E-value=2.8 Score=28.01 Aligned_cols=31 Identities=19% Similarity=0.120 Sum_probs=25.5
Q ss_pred hhcCCcccccCCcccccHHHHHHHHHHHHHH
Q psy672 52 YATGNFQIFTGDSHGVSQPTMCRLVKEVSKA 82 (314)
Q Consensus 52 L~~g~~~~~l~~~fgis~stv~~~~~~v~~~ 82 (314)
-..+.+..++++.+|++.+|+++.++...++
T Consensus 21 ~~~~~t~~ela~~l~~~~~t~s~hL~~L~~a 51 (61)
T PF12840_consen 21 SNGPMTVSELAEELGISQSTVSYHLKKLEEA 51 (61)
T ss_dssp HCSTBEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred cCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 4566888999999999999999999877654
No 209
>PRK14087 dnaA chromosomal replication initiation protein; Provisional
Probab=69.80 E-value=9.4 Score=36.76 Aligned_cols=53 Identities=9% Similarity=0.096 Sum_probs=47.4
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCcccccCCccc-ccHHHHHHHHHHHHHHHHH
Q psy672 33 TMQGVKQPPMTRLLAVIQFYATGNFQIFTGDSHG-VSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 33 ~~~~~~~s~~~~l~~~L~~L~~g~~~~~l~~~fg-is~stv~~~~~~v~~~l~~ 85 (314)
..|...+...-|++|.|.+=-++.++..+|..|| .+.|||..-++++-..+.+
T Consensus 379 ~~R~~~i~~~RqiamyL~r~~t~~sl~~IG~~FggrdHsTV~~a~~ki~~~~~~ 432 (450)
T PRK14087 379 KARSKSIVTARHIAMYLTKEILNHTLAQIGEEFGGRDHTTVINAERKIEKMLKK 432 (450)
T ss_pred CCCCccccHHHHHHHHHHHHHcCCCHHHHHHHhCCCChHHHHHHHHHHHHHHHh
Confidence 3456678999999999999999999999999997 9999999999999888764
No 210
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=69.67 E-value=4.6 Score=37.76 Aligned_cols=48 Identities=10% Similarity=0.102 Sum_probs=39.6
Q ss_pred CCCHHHHHHHHHHHh-h--cCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 38 KQPPMTRLLAVIQFY-A--TGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L-~--~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
.++..++..+.|+|. . .+.++..+|..||||++.|+++-.+.+.-|-.
T Consensus 305 ~L~~rEr~Vl~lrygl~~~~~~tl~EIa~~lgvs~erVrQi~~~Al~kLr~ 355 (367)
T PRK09210 305 TLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRH 355 (367)
T ss_pred hCCHHHHHHHHHHhccCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHhC
Confidence 488899999999885 3 45799999999999999999998777666553
No 211
>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=69.66 E-value=2 Score=24.87 Aligned_cols=24 Identities=21% Similarity=0.342 Sum_probs=19.1
Q ss_pred cccccCCcccccHHHHHHHHHHHH
Q psy672 57 FQIFTGDSHGVSQPTMCRLVKEVS 80 (314)
Q Consensus 57 ~~~~l~~~fgis~stv~~~~~~v~ 80 (314)
+..++|+..|++..||+|.+.++-
T Consensus 4 tr~diA~~lG~t~ETVSR~l~~l~ 27 (32)
T PF00325_consen 4 TRQDIADYLGLTRETVSRILKKLE 27 (32)
T ss_dssp -HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CHHHHHHHhCCcHHHHHHHHHHHH
Confidence 456889999999999999998764
No 212
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=69.47 E-value=4 Score=34.98 Aligned_cols=46 Identities=13% Similarity=0.118 Sum_probs=38.0
Q ss_pred CCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHH
Q psy672 37 VKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALA 84 (314)
Q Consensus 37 ~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~ 84 (314)
..+++.++= .|..++.|.+..++|+.+++|.+||..++.++..-+-
T Consensus 142 ~~LS~RE~e--VL~Lia~G~SnkEIA~~L~IS~~TVk~hvs~I~~KLg 187 (217)
T PRK13719 142 NKVTKYQND--VFILYSFGFSHEYIAQLLNITVGSSKNKISEILKFFG 187 (217)
T ss_pred CCCCHHHHH--HHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 346666654 4566899999999999999999999999999887665
No 213
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=69.42 E-value=3 Score=27.31 Aligned_cols=29 Identities=17% Similarity=0.135 Sum_probs=23.9
Q ss_pred hcCCcccccCCcccccHHHHHHHHHHHHH
Q psy672 53 ATGNFQIFTGDSHGVSQPTMCRLVKEVSK 81 (314)
Q Consensus 53 ~~g~~~~~l~~~fgis~stv~~~~~~v~~ 81 (314)
....+..+++..+|+|.+|+++.+++...
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~ 36 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLRE 36 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 44567788999999999999999887654
No 214
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=69.17 E-value=2.4 Score=27.62 Aligned_cols=25 Identities=16% Similarity=0.117 Sum_probs=20.7
Q ss_pred cccccCCcccccHHHHHHHHHHHHH
Q psy672 57 FQIFTGDSHGVSQPTMCRLVKEVSK 81 (314)
Q Consensus 57 ~~~~l~~~fgis~stv~~~~~~v~~ 81 (314)
+..++++.||+|++|+.+.+.....
T Consensus 22 s~~~la~~~~vs~~tv~~~l~~L~~ 46 (60)
T smart00345 22 SERELAAQLGVSRTTVREALSRLEA 46 (60)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4567888999999999988887665
No 215
>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=69.06 E-value=5.4 Score=26.93 Aligned_cols=30 Identities=20% Similarity=0.166 Sum_probs=23.9
Q ss_pred hhcCCcccccCCcccccHHHHHHHHHHHHH
Q psy672 52 YATGNFQIFTGDSHGVSQPTMCRLVKEVSK 81 (314)
Q Consensus 52 L~~g~~~~~l~~~fgis~stv~~~~~~v~~ 81 (314)
..++.+..++++.+|++.+|+.+.++....
T Consensus 17 ~~~~~~~~ei~~~~~i~~~~i~~~l~~L~~ 46 (78)
T cd00090 17 LEGPLTVSELAERLGLSQSTVSRHLKKLEE 46 (78)
T ss_pred HHCCcCHHHHHHHHCcCHhHHHHHHHHHHH
Confidence 334478889999999999999988877543
No 216
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=68.31 E-value=4.2 Score=35.60 Aligned_cols=46 Identities=13% Similarity=0.115 Sum_probs=38.5
Q ss_pred CCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHH
Q psy672 37 VKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALA 84 (314)
Q Consensus 37 ~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~ 84 (314)
..+++.++= +|.+++.|.+..++|..+|||..||..++.++..-|.
T Consensus 178 ~~LT~rE~e--vl~~~a~G~t~~eIa~~l~is~~TV~~h~~~~~~KL~ 223 (240)
T PRK10188 178 MNFSKREKE--ILKWTAEGKTSAEIAMILSISENTVNFHQKNMQKKFN 223 (240)
T ss_pred CCCCHHHHH--HHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 356766654 5667799999999999999999999999999887765
No 217
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=67.90 E-value=2.7 Score=26.04 Aligned_cols=27 Identities=19% Similarity=0.207 Sum_probs=22.4
Q ss_pred CCcccccCCcccccHHHHHHHHHHHHH
Q psy672 55 GNFQIFTGDSHGVSQPTMCRLVKEVSK 81 (314)
Q Consensus 55 g~~~~~l~~~fgis~stv~~~~~~v~~ 81 (314)
..+..++|+.+|+|++|++++++....
T Consensus 8 ~~s~~~la~~l~~s~~tv~~~l~~L~~ 34 (48)
T smart00419 8 PLTRQEIAELLGLTRETVSRTLKRLEK 34 (48)
T ss_pred ccCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 356678999999999999998887765
No 218
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=67.71 E-value=5.7 Score=33.45 Aligned_cols=44 Identities=16% Similarity=0.067 Sum_probs=34.8
Q ss_pred CCCHHHHHHHHHHHhhcC-------------CcccccCCcccccHHHHHHHHHHHHH
Q psy672 38 KQPPMTRLLAVIQFYATG-------------NFQIFTGDSHGVSQPTMCRLVKEVSK 81 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g-------------~~~~~l~~~fgis~stv~~~~~~v~~ 81 (314)
..++.++++-+|..++.. .+..++|...|+++.|++|+++++.+
T Consensus 138 ~~~~~~Rl~~~L~~l~~~~~~~~~~~~~~~~~t~~~lA~~lG~tr~tvsR~l~~l~~ 194 (211)
T PRK11753 138 FLDVTGRIAQTLLDLAKQPDAMTHPDGMQIKITRQEIGRIVGCSREMVGRVLKMLED 194 (211)
T ss_pred hcChhhHHHHHHHHHHHhcCCcCCCCceecCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 468899999988877641 23367899999999999999887765
No 219
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=67.70 E-value=3.3 Score=28.02 Aligned_cols=38 Identities=13% Similarity=0.033 Sum_probs=28.1
Q ss_pred HHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHH
Q psy672 43 TRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVS 80 (314)
Q Consensus 43 ~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~ 80 (314)
++++-+|....++.+-+++|+.+|+|..++.+|.....
T Consensus 3 e~Il~~i~~~~~p~~T~eiA~~~gls~~~aR~yL~~Le 40 (62)
T PF04703_consen 3 EKILEYIKEQNGPLKTREIADALGLSIYQARYYLEKLE 40 (62)
T ss_dssp HCHHHHHHHHTS-EEHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred HHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 45555666667778889999999999999998876543
No 220
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=67.19 E-value=3.9 Score=34.60 Aligned_cols=45 Identities=18% Similarity=0.203 Sum_probs=38.7
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHH
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALA 84 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~ 84 (314)
.+++.++ -.|..++.|.+..++|+..++|.+||..+..++..-|.
T Consensus 150 ~Lt~rE~--evl~~~~~G~s~~eIA~~l~iS~~TV~~h~~~i~~Kl~ 194 (216)
T PRK10840 150 RLSPKES--EVLRLFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLG 194 (216)
T ss_pred cCCHHHH--HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence 4777775 56778899999999999999999999999988877665
No 221
>PHA00738 putative HTH transcription regulator
Probab=67.07 E-value=4.1 Score=30.78 Aligned_cols=29 Identities=14% Similarity=-0.034 Sum_probs=24.9
Q ss_pred CcccccCCcccccHHHHHHHHHHHHHHHH
Q psy672 56 NFQIFTGDSHGVSQPTMCRLVKEVSKALA 84 (314)
Q Consensus 56 ~~~~~l~~~fgis~stv~~~~~~v~~~l~ 84 (314)
.+-.++++.|++|+++|++.++-.-+|=.
T Consensus 27 ~~V~eLae~l~lSQptVS~HLKvLreAGL 55 (108)
T PHA00738 27 LSASLISHTLLLSYTTVLRHLKILNEQGY 55 (108)
T ss_pred ccHHHHHHhhCCCHHHHHHHHHHHHHCCc
Confidence 67778999999999999999998877633
No 222
>PF05263 DUF722: Protein of unknown function (DUF722); InterPro: IPR007927 This entry is represented by Bacteriophage bIL285, Orf38. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=67.05 E-value=5.6 Score=31.27 Aligned_cols=46 Identities=7% Similarity=-0.010 Sum_probs=37.7
Q ss_pred CCHHHHHHHHHHHhhc-CCcccccCCcccccHHHHHHHHHHHHHHHH
Q psy672 39 QPPMTRLLAVIQFYAT-GNFQIFTGDSHGVSQPTMCRLVKEVSKALA 84 (314)
Q Consensus 39 ~s~~~~l~~~L~~L~~-g~~~~~l~~~fgis~stv~~~~~~v~~~l~ 84 (314)
+..+++-++-|.|.+. +.+|..+|..+++|++|+.++..+|-..+.
T Consensus 82 l~de~k~Ii~lry~~r~~~TW~~IA~~l~i~erta~r~~~~fK~~i~ 128 (130)
T PF05263_consen 82 LIDEEKRIIKLRYDRRSRRTWYQIAQKLHISERTARRWRDRFKNDIY 128 (130)
T ss_pred hCHHHHHHHHHHHcccccchHHHHHHHhCccHHHHHHHHHHHHHHhc
Confidence 4456677777777775 799999999999999999999998876553
No 223
>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=66.62 E-value=12 Score=28.40 Aligned_cols=45 Identities=4% Similarity=-0.020 Sum_probs=30.5
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHH
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKA 82 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~ 82 (314)
.+++.+-.++....-..+.+..++++.+|++++|+++.+++....
T Consensus 25 ~lt~~q~~iL~~l~~~~~~t~~ela~~~~~~~~tvs~~l~~Le~~ 69 (118)
T TIGR02337 25 GLTEQQWRILRILAEQGSMEFTQLANQACILRPSLTGILARLERD 69 (118)
T ss_pred CCCHHHHHHHHHHHHcCCcCHHHHHHHhCCCchhHHHHHHHHHHC
Confidence 355555433322233455778899999999999999887776653
No 224
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=66.48 E-value=3.4 Score=34.97 Aligned_cols=30 Identities=23% Similarity=0.338 Sum_probs=26.1
Q ss_pred HHHhhcCCcccccCCcccccHHHHHHHHHH
Q psy672 49 IQFYATGNFQIFTGDSHGVSQPTMCRLVKE 78 (314)
Q Consensus 49 L~~L~~g~~~~~l~~~fgis~stv~~~~~~ 78 (314)
..++..|.+...+|..+|||++|++++.+.
T Consensus 166 ~~~~~~g~s~~~iak~lgis~~Tv~r~~k~ 195 (200)
T PRK13413 166 KKLLDKGTSKSEIARKLGVSRTTLARFLKT 195 (200)
T ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHHHh
Confidence 345678999999999999999999999863
No 225
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=66.48 E-value=7.4 Score=32.17 Aligned_cols=50 Identities=6% Similarity=-0.043 Sum_probs=38.3
Q ss_pred CCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHhccc
Q psy672 39 QPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAHVN 89 (314)
Q Consensus 39 ~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~~~ 89 (314)
+|+.++-++.|. +-.|.++.++|+.+|+|.+||...+.+....|-.....
T Consensus 123 L~~~~r~i~~l~-~~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~ 172 (185)
T PRK12542 123 LNESNRQVFKYK-VFYNLTYQEISSVMGITEANVRKQFERARKRVQNMIGG 172 (185)
T ss_pred CCHHHHHHHHHH-HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHcc
Confidence 455555544443 45678999999999999999999999999888775433
No 226
>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]
Probab=66.37 E-value=8.3 Score=36.47 Aligned_cols=53 Identities=9% Similarity=0.051 Sum_probs=47.8
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 33 TMQGVKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 33 ~~~~~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
..|...+...-|++|.|.+--+..++..+|+.||-..|||...++.+...+.+
T Consensus 343 ~~R~~~i~~~RqiamyL~r~lt~~Slp~IG~~FgrdHtTV~~a~~kI~~~~~~ 395 (408)
T COG0593 343 KSRTRNIVRPRQIAMYLARELTNLSLPEIGKAFGRDHTTVLHAVRKIEQLIEE 395 (408)
T ss_pred cccccccchHHHHHHHHHHHHccCcHHHHHHHhCCCccHHHHHHHHHHHHHhc
Confidence 45667788999999999999999999999999999999999999999888874
No 227
>PRK12422 chromosomal replication initiation protein; Provisional
Probab=66.30 E-value=13 Score=35.70 Aligned_cols=52 Identities=12% Similarity=0.041 Sum_probs=47.1
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHH
Q psy672 33 TMQGVKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALA 84 (314)
Q Consensus 33 ~~~~~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~ 84 (314)
..|...+...-|++|.|.+=-++.++.++|..||-+.|||..-++++-+.+.
T Consensus 375 ~~R~~~i~~~Rqiamyl~r~~t~~s~~~IG~~fgrdHsTV~~a~~ki~~~~~ 426 (445)
T PRK12422 375 RSQSREYVLPRQVAMYLCRQKLSLSYVKIGDVFSRDHSTVISSIRAISQKLE 426 (445)
T ss_pred CCCCcccccHHHHHHHHHHHhcCCCHHHHHHHhCCChHHHHHHHHHHHHHHH
Confidence 4566788999999999999999999999999999999999999999988774
No 228
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=66.22 E-value=5.8 Score=26.27 Aligned_cols=37 Identities=16% Similarity=0.286 Sum_probs=31.3
Q ss_pred HHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHH
Q psy672 48 VIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALA 84 (314)
Q Consensus 48 ~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~ 84 (314)
.+.+++.|.+..++|..+++|..||..+..++..-+.
T Consensus 12 v~~l~~~G~s~~eia~~l~is~~tV~~h~~~i~~Kl~ 48 (65)
T COG2771 12 ILRLVAQGKSNKEIARILGISEETVKTHLRNIYRKLG 48 (65)
T ss_pred HHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Confidence 4567888999999999999999999999888865544
No 229
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=66.11 E-value=3 Score=34.07 Aligned_cols=35 Identities=9% Similarity=-0.137 Sum_probs=30.5
Q ss_pred hhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672 52 YATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA 86 (314)
Q Consensus 52 L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 86 (314)
+-.|.++.++|..+|+|.+||...+++....|-+.
T Consensus 133 ~~~g~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~ 167 (175)
T PRK12518 133 DLEDLPQKEIAEILNIPVGTVKSRLFYARRQLRKF 167 (175)
T ss_pred HhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 34677799999999999999999999999888864
No 230
>TIGR03541 reg_near_HchA LuxR family transcriptional regulatory, chaperone HchA-associated. Members of this protein family belong to the LuxR transcriptional regulator family, and contain both autoinducer binding (pfam03472) and transcriptional regulator (pfam00196) domains. Members, however, occur only in a few members of the Gammaproteobacteria that have the chaperone/aminopeptidase HchA, and are always encoded by the adjacent gene.
Probab=66.11 E-value=4.7 Score=34.98 Aligned_cols=47 Identities=17% Similarity=0.092 Sum_probs=39.0
Q ss_pred CCCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHH
Q psy672 36 GVKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALA 84 (314)
Q Consensus 36 ~~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~ 84 (314)
...+|+.++=.+.+ .+.|.+..++|..+|+|.+||..++.+...-|.
T Consensus 169 ~~~Lt~re~evl~~--~a~G~t~~eIa~~l~is~~Tv~~~l~~~~~kl~ 215 (232)
T TIGR03541 169 AGVLSEREREVLAW--TALGRRQADIAAILGISERTVENHLRSARRKLG 215 (232)
T ss_pred hccCCHHHHHHHHH--HHCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHC
Confidence 34677777765555 589999999999999999999999999877665
No 231
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=65.63 E-value=4.1 Score=37.32 Aligned_cols=66 Identities=15% Similarity=0.156 Sum_probs=44.4
Q ss_pred HHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHhccccccCCCc-hhhhHHHhhhcCCCCCce
Q psy672 47 AVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAHVNYVKFPEQ-LAPTKVAFQGIGNFPGVV 114 (314)
Q Consensus 47 ~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~~~~i~~P~~-~~~~~~~f~~~~~~p~~~ 114 (314)
++=.||-.|.+++++|+.+|||+.+|+|.+.+.-+-= +-+-.|.-|.. .-.+.....+..+++.|+
T Consensus 18 ~A~lYY~~gltQ~eIA~~LgiSR~~v~rlL~~Ar~~G--iV~I~i~~~~~~~~~Le~~L~~~fgL~~a~ 84 (321)
T COG2390 18 AAWLYYVEGLTQSEIAERLGISRATVSRLLAKAREEG--IVKISINSPVEGCLELEQQLKERFGLKEAI 84 (321)
T ss_pred HHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHCC--eEEEEeCCCCcchHHHHHHHHHhcCCCeEE
Confidence 4556788999999999999999999999988765421 12222333333 333555556666777775
No 232
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=65.61 E-value=5.2 Score=34.38 Aligned_cols=56 Identities=16% Similarity=0.127 Sum_probs=41.6
Q ss_pred CCCHHHHHHHHHHHhhcC----CcccccCCcccccHHHHHHHHHHHHHH-HHHhccccccC
Q psy672 38 KQPPMTRLLAVIQFYATG----NFQIFTGDSHGVSQPTMCRLVKEVSKA-LAQAHVNYVKF 93 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g----~~~~~l~~~fgis~stv~~~~~~v~~~-l~~~~~~~i~~ 93 (314)
..+++++|+.+|..+..+ .+..++|..+|+++.|++|.++++.+. +.......|..
T Consensus 148 ~~~~~~Rla~~L~~~~~~~~~~~t~~~lA~~lG~sretvsR~L~~L~~~G~I~~~~~~i~I 208 (226)
T PRK10402 148 SFPLENRLAAFILLTQEGDLYHEKHTQAAEYLGVSYRHLLYVLAQFIQDGYLKKSKRGYLI 208 (226)
T ss_pred cChHHHHHHHHHHhcccCCcccchHHHHHHHHCCcHHHHHHHHHHHHHCCCEEeeCCEEEE
Confidence 358999999999876543 345789999999999999999998874 34443334443
No 233
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=65.41 E-value=6.9 Score=31.66 Aligned_cols=48 Identities=8% Similarity=-0.114 Sum_probs=38.4
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA 86 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 86 (314)
.+|+.++-++.|. +-.|.++.++|..+|+|.+||...+++....|-+.
T Consensus 108 ~L~~~~r~v~~l~-~~~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~ 155 (165)
T PRK09644 108 TLPVIEAQAILLC-DVHELTYEEAASVLDLKLNTYKSHLFRGRKRLKAL 155 (165)
T ss_pred hCCHHHHHHHHhH-HHhcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3666666655554 45678899999999999999999999999888764
No 234
>PF05043 Mga: Mga helix-turn-helix domain; InterPro: IPR007737 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions []. The family also contains VirR like proteins which match only at the C terminus of the alignment.; PDB: 3SQN_A.
Probab=65.26 E-value=5.1 Score=28.74 Aligned_cols=43 Identities=19% Similarity=0.094 Sum_probs=31.7
Q ss_pred HHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 42 MTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 42 ~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
.-+++..|. ...+.+..++++.+.||+||+.+.++++-+.|..
T Consensus 18 ~~~ll~~ll-~~~~~s~~~la~~~~iS~sti~~~i~~l~~~l~~ 60 (87)
T PF05043_consen 18 NYQLLKLLL-NNEYVSIEDLAEELFISRSTIYRDIKKLNKYLKK 60 (87)
T ss_dssp HHHHHHHHH-H-SEEEHHHHHHHHT--HHHHHHHHHHHHHHHHC
T ss_pred HHHHHHHHH-cCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 344444443 5677888999999999999999999999998874
No 235
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=64.91 E-value=9 Score=28.60 Aligned_cols=39 Identities=18% Similarity=0.119 Sum_probs=29.3
Q ss_pred HHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHH
Q psy672 42 MTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSK 81 (314)
Q Consensus 42 ~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~ 81 (314)
+.+++..|.. ....++.++++.+|+|++|+.+.+++..+
T Consensus 5 D~~il~~L~~-~~~~~~~~la~~l~~s~~tv~~~l~~L~~ 43 (108)
T smart00344 5 DRKILEELQK-DARISLAELAKKVGLSPSTVHNRVKRLEE 43 (108)
T ss_pred HHHHHHHHHH-hCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 3444444443 23578999999999999999998888766
No 236
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=64.70 E-value=4.9 Score=34.26 Aligned_cols=45 Identities=16% Similarity=0.144 Sum_probs=37.2
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHH
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALA 84 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~ 84 (314)
.+++.|+ =.|..++.|.+..++|+..+||..||..+..++..-|.
T Consensus 134 ~LT~RE~--eVL~ll~~G~snkeIA~~L~iS~~TV~~h~~~I~~KLg 178 (207)
T PRK11475 134 MLSPTER--EILRFMSRGYSMPQIAEQLERNIKTIRAHKFNVMSKLG 178 (207)
T ss_pred CCCHHHH--HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence 3666655 45677899999999999999999999999988876654
No 237
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=64.56 E-value=4.5 Score=34.57 Aligned_cols=45 Identities=18% Similarity=0.189 Sum_probs=37.2
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHH
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALA 84 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~ 84 (314)
.++..+. -.|..++.|.+-.++|+..++|.+||..++.+...-|.
T Consensus 148 ~LT~RE~--eVL~lla~G~snkeIA~~L~iS~~TVk~h~~~i~~KL~ 192 (211)
T COG2197 148 LLTPREL--EVLRLLAEGLSNKEIAEELNLSEKTVKTHVSNILRKLG 192 (211)
T ss_pred CCCHHHH--HHHHHHHCCCCHHHHHHHHCCCHhHHHHHHHHHHHHcC
Confidence 3555554 45677999999999999999999999999998877665
No 238
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=64.53 E-value=7.5 Score=35.69 Aligned_cols=48 Identities=15% Similarity=0.138 Sum_probs=40.3
Q ss_pred CCCHHHHHHHHHHHh-h--cCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 38 KQPPMTRLLAVIQFY-A--TGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L-~--~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
.++..++..+.++|. . ...++.++|..||||+..|+++-.+.+.-|-.
T Consensus 262 ~L~eREr~Vl~~rygl~~~~~~Tl~eIa~~lgvS~eRVrQIe~~Al~KLr~ 312 (324)
T PRK07921 262 TLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLRN 312 (324)
T ss_pred hCCHHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 478889999999884 2 34789999999999999999998888877764
No 239
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=64.34 E-value=8.2 Score=32.66 Aligned_cols=47 Identities=13% Similarity=-0.036 Sum_probs=36.7
Q ss_pred CCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672 39 QPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA 86 (314)
Q Consensus 39 ~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 86 (314)
+|+.++.++.|. +-.|.++.++|+.+|+|.+||...+++....|.+.
T Consensus 154 L~~~~r~vl~l~-~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 200 (206)
T PRK12526 154 LPEAQQTVVKGV-YFQELSQEQLAQQLNVPLGTVKSRLRLALAKLKVQ 200 (206)
T ss_pred CCHHHHHHHHHH-HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 455555554444 45688899999999999999999999888887763
No 240
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=64.34 E-value=7.4 Score=31.31 Aligned_cols=48 Identities=13% Similarity=-0.008 Sum_probs=38.3
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA 86 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 86 (314)
.+|+.++.++.|.+ -.|.++.++|..+|+|.+||...+++....|-++
T Consensus 112 ~L~~~~r~v~~l~~-~~~~s~~eIA~~lgis~~tv~~~l~Rar~~L~~~ 159 (161)
T PRK12541 112 SLPLERRNVLLLRD-YYGFSYKEIAEMTGLSLAKVKIELHRGRKETKSI 159 (161)
T ss_pred HCCHHHHHHhhhHH-hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 46677777666654 4677889999999999999999999988877653
No 241
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=64.32 E-value=11 Score=34.68 Aligned_cols=50 Identities=14% Similarity=0.155 Sum_probs=40.2
Q ss_pred CCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHhccc
Q psy672 39 QPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAHVN 89 (314)
Q Consensus 39 ~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~~~ 89 (314)
+|+.++-++.|. +-.|.++.++|+.+|+|.+||...+.+....|-+..+.
T Consensus 154 Lp~~~R~v~~L~-~~~g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~~~~ 203 (339)
T PRK08241 154 LPPRQRAVLILR-DVLGWSAAEVAELLDTSVAAVNSALQRARATLAERGPS 203 (339)
T ss_pred CCHHHhhhhhhH-HhhCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhhcCCC
Confidence 566666666554 45678999999999999999999999999999875443
No 242
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=64.24 E-value=7.9 Score=24.25 Aligned_cols=27 Identities=19% Similarity=0.073 Sum_probs=22.6
Q ss_pred CCcccccCCcccccHHHHHHHHHHHHH
Q psy672 55 GNFQIFTGDSHGVSQPTMCRLVKEVSK 81 (314)
Q Consensus 55 g~~~~~l~~~fgis~stv~~~~~~v~~ 81 (314)
+.+..+++..|++|.+|+++.+..+..
T Consensus 14 ~~s~~~l~~~l~~s~~tv~~~l~~L~~ 40 (53)
T smart00420 14 KVSVEELAELLGVSEMTIRRDLNKLEE 40 (53)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 456678899999999999999887655
No 243
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=63.77 E-value=2.5 Score=25.80 Aligned_cols=29 Identities=17% Similarity=0.099 Sum_probs=21.1
Q ss_pred hhcCCcccccCCcccccHHHHHHHHHHHH
Q psy672 52 YATGNFQIFTGDSHGVSQPTMCRLVKEVS 80 (314)
Q Consensus 52 L~~g~~~~~l~~~fgis~stv~~~~~~v~ 80 (314)
+.+..+..++|..+|+|.+..++.|++..
T Consensus 5 ~~~~~~l~~iA~~~g~S~~~f~r~Fk~~~ 33 (42)
T PF00165_consen 5 LQQKLTLEDIAEQAGFSPSYFSRLFKKET 33 (42)
T ss_dssp T-SS--HHHHHHHHTS-HHHHHHHHHHHT
T ss_pred ccCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 34566778999999999999999998764
No 244
>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=63.56 E-value=3.7 Score=30.19 Aligned_cols=32 Identities=25% Similarity=0.157 Sum_probs=23.4
Q ss_pred cccCCcccccHHHHHHHHHHHH--HHHHHhcccc
Q psy672 59 IFTGDSHGVSQPTMCRLVKEVS--KALAQAHVNY 90 (314)
Q Consensus 59 ~~l~~~fgis~stv~~~~~~v~--~~l~~~~~~~ 90 (314)
.-+|..||+|.+|++|+...-. +||......+
T Consensus 49 ~GlAklfgcSv~Ta~RiK~sG~id~AI~Q~Gr~I 82 (96)
T PF12964_consen 49 KGLAKLFGCSVPTANRIKKSGKIDPAITQIGRKI 82 (96)
T ss_pred HHHHHHhCCCchhHHHHHhcCCccHHHHHcCCEE
Confidence 5689999999999999987422 4555554433
No 245
>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=63.50 E-value=3 Score=26.57 Aligned_cols=19 Identities=26% Similarity=0.333 Sum_probs=16.3
Q ss_pred ccCCcccccHHHHHHHHHH
Q psy672 60 FTGDSHGVSQPTMCRLVKE 78 (314)
Q Consensus 60 ~l~~~fgis~stv~~~~~~ 78 (314)
++|+..|||.+||+++++.
T Consensus 2 ~lA~~~gvs~~tvs~~l~g 20 (52)
T cd01392 2 DIARAAGVSVATVSRVLNG 20 (52)
T ss_pred cHHHHHCcCHHHHHHHHcC
Confidence 5788899999999998764
No 246
>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=63.37 E-value=2.5 Score=26.14 Aligned_cols=21 Identities=38% Similarity=0.374 Sum_probs=17.9
Q ss_pred ccccCCcccccHHHHHHHHHH
Q psy672 58 QIFTGDSHGVSQPTMCRLVKE 78 (314)
Q Consensus 58 ~~~l~~~fgis~stv~~~~~~ 78 (314)
..++|+.+|||.+|+.+++.+
T Consensus 3 ~~e~a~~lgvs~~tl~~~~~~ 23 (49)
T cd04762 3 TKEAAELLGVSPSTLRRWVKE 23 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHc
Confidence 457888999999999998875
No 247
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=63.26 E-value=7.5 Score=31.77 Aligned_cols=48 Identities=15% Similarity=-0.032 Sum_probs=37.1
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA 86 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 86 (314)
.+|++++-++. ..+-.|.++.++|..+|+|.+||...+++....+...
T Consensus 119 ~L~~~~r~i~~-l~~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~~~~~ 166 (172)
T PRK09651 119 GLNGKTREAFL-LSQLDGLTYSEIAHKLGVSVSSVKKYVAKATEHCLLF 166 (172)
T ss_pred hCCHHHhHHhh-hhhccCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 36666665444 4455678899999999999999999999988877653
No 248
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=62.99 E-value=6.4 Score=35.42 Aligned_cols=46 Identities=15% Similarity=0.106 Sum_probs=38.7
Q ss_pred HHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH-hcc
Q psy672 43 TRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ-AHV 88 (314)
Q Consensus 43 ~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~-~~~ 88 (314)
.+|-.++....+|.+++..|+..+||+|+|++.+++.-..+-. ++.
T Consensus 4 ~~L~~F~~v~~~~~s~s~AA~~L~isq~avSr~I~~LE~~lg~~LF~ 50 (309)
T PRK12682 4 QQLRFVREAVRRNLNLTEAAKALHTSQPGVSKAIIELEEELGIEIFI 50 (309)
T ss_pred HHHHHHHHHHHccCCHHHHHHHhcCccHHHHHHHHHHHHHhCCeeEE
Confidence 4566666677788899999999999999999999999998885 443
No 249
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=62.65 E-value=8 Score=37.74 Aligned_cols=48 Identities=10% Similarity=0.076 Sum_probs=41.5
Q ss_pred CCCHHHHHHHHHHHh---hcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 38 KQPPMTRLLAVIQFY---ATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L---~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
.++..++..+.|+|. ..+.++..+|..||||++.|+++-.+.+.-|-.
T Consensus 447 ~L~eREr~VI~lRyGL~~~e~~TL~EIa~~lGVSrERVRQIe~kAL~KLR~ 497 (509)
T PRK05901 447 TLSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESKTLRKLRH 497 (509)
T ss_pred hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 488999999999984 456899999999999999999999888877764
No 250
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=62.03 E-value=8.3 Score=33.12 Aligned_cols=44 Identities=25% Similarity=0.228 Sum_probs=35.7
Q ss_pred CCCHHHHHHHHHHHhhc--------------CCcccccCCcccccHHHHHHHHHHHHH
Q psy672 38 KQPPMTRLLAVIQFYAT--------------GNFQIFTGDSHGVSQPTMCRLVKEVSK 81 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~--------------g~~~~~l~~~fgis~stv~~~~~~v~~ 81 (314)
..+++++++.+|..+.. ..+..++|...|+++.|++|.++++..
T Consensus 153 ~~~~~~Rla~~L~~l~~~~~~~~~~~~~~~~~lt~~~iA~~lG~sr~tvsR~l~~l~~ 210 (235)
T PRK11161 153 KKNAEERLAAFIYNLSRRFAQRGFSPREFRLTMTRGDIGNYLGLTVETISRLLGRFQK 210 (235)
T ss_pred CCCHHHHHHHHHHHHHHHHhhcCCCCceeEccccHHHHHHHhCCcHHHHHHHHHHHHH
Confidence 35789999999998763 135578999999999999999887665
No 251
>PF02209 VHP: Villin headpiece domain; InterPro: IPR003128 Villin is an F-actin bundling protein involved in the maintenance of the microvilli of the absorptive epithelia. The villin-type "headpiece" domain is a modular motif found at the extreme C terminus of larger "core" domains in over 25 cytoskeletal proteins in plants and animals, often in assocation with the Gelsolin repeat. Although the headpiece is classified as an F-actin-binding domain, it has been shown that not all headpiece domains are intrinsically F-actin-binding motifs, surface charge distribution may be an important element for F-actin recognition []. An autonomously folding, 35 residue, thermostable subdomain (HP36) of the full-length 76 amino acid residue villin headpiece, is the smallest known example of a cooperatively folded domain of a naturally occurring protein. The structure of HP36, as determined by NMR spectroscopy, consists of three short helices surrounding a tightly packed hydrophobic core []. ; GO: 0003779 actin binding, 0007010 cytoskeleton organization; PDB: 1ZV6_A 1QZP_A 1UND_A 2PPZ_A 3TJW_B 1YU8_X 2JM0_A 1WY4_A 3MYC_A 1YU5_X ....
Probab=61.88 E-value=1.5 Score=26.12 Aligned_cols=24 Identities=4% Similarity=-0.049 Sum_probs=16.1
Q ss_pred CCCccccccccCHHHHHHhhHHhhh
Q psy672 2 PLWTEQEALRFSKDVVLNIIFPLAR 26 (314)
Q Consensus 2 ~~~~~~~~frmsr~~f~~~L~~~l~ 26 (314)
.+-+|.+.|.|+|+.|. .|=..=+
T Consensus 3 sd~dF~~vFgm~~~eF~-~lP~WKq 26 (36)
T PF02209_consen 3 SDEDFEKVFGMSREEFY-KLPKWKQ 26 (36)
T ss_dssp -HHHHHHHHSS-HHHHH-HS-HHHH
T ss_pred CHHHHHHHHCCCHHHHH-HChHHHH
Confidence 44567799999999999 7654433
No 252
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=61.88 E-value=6.7 Score=33.67 Aligned_cols=45 Identities=13% Similarity=0.007 Sum_probs=36.0
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHH
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALA 84 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~ 84 (314)
.+++.++= .|.+++.|.+..++|+.+++|.+||..++.+...-+.
T Consensus 155 ~Lt~rE~~--Vl~l~~~G~s~~eIA~~L~iS~~TVk~~~~~i~~Kl~ 199 (216)
T PRK10100 155 LLTHREKE--ILNKLRIGASNNEIARSLFISENTVKTHLYNLFKKIA 199 (216)
T ss_pred CCCHHHHH--HHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 36665554 3455677999999999999999999999998877665
No 253
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=61.66 E-value=8.6 Score=31.75 Aligned_cols=48 Identities=19% Similarity=0.203 Sum_probs=38.6
Q ss_pred CCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHhc
Q psy672 39 QPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAH 87 (314)
Q Consensus 39 ~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~ 87 (314)
+|+.++-++.|.++ .|.++.++|+.+|||.+||...+++....|-+..
T Consensus 128 Lp~~~R~~~~l~~~-~gls~~EIA~~l~i~~~tVks~l~ra~~~l~~~l 175 (182)
T COG1595 128 LPPRQREAFLLRYL-EGLSYEEIAEILGISVGTVKSRLHRARKKLREQL 175 (182)
T ss_pred CCHHHhHHhhhHhh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 55666665555544 6788999999999999999999999999888643
No 254
>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=61.59 E-value=4.5 Score=27.15 Aligned_cols=30 Identities=13% Similarity=0.051 Sum_probs=22.9
Q ss_pred HHHHhhcC--CcccccCCcccccHHHHHHHHH
Q psy672 48 VIQFYATG--NFQIFTGDSHGVSQPTMCRLVK 77 (314)
Q Consensus 48 ~L~~L~~g--~~~~~l~~~fgis~stv~~~~~ 77 (314)
+-.|+.++ ....+||+.+|||.+||.++-.
T Consensus 13 ~e~y~~~~g~i~lkdIA~~Lgvs~~tIr~WK~ 44 (60)
T PF10668_consen 13 FEIYKESNGKIKLKDIAEKLGVSESTIRKWKS 44 (60)
T ss_pred HHHHHHhCCCccHHHHHHHHCCCHHHHHHHhh
Confidence 34456554 5778999999999999997654
No 255
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=61.37 E-value=11 Score=27.27 Aligned_cols=44 Identities=20% Similarity=0.166 Sum_probs=30.2
Q ss_pred CCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHH
Q psy672 39 QPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKA 82 (314)
Q Consensus 39 ~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~ 82 (314)
++..+..++.+.....+.+..+++..+++|++++++.+++..+.
T Consensus 8 l~~~~~~il~~l~~~~~~~~~~la~~~~~s~~~i~~~l~~L~~~ 51 (101)
T smart00347 8 LTPTQFLVLRILYEEGPLSVSELAKRLGVSPSTVTRVLDRLEKK 51 (101)
T ss_pred CCHHHHHHHHHHHHcCCcCHHHHHHHHCCCchhHHHHHHHHHHC
Confidence 44343333333333345688899999999999999988887764
No 256
>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=61.33 E-value=5.8 Score=27.11 Aligned_cols=30 Identities=13% Similarity=0.197 Sum_probs=23.5
Q ss_pred hhcC-CcccccCCcccccHHHHHHHHHHHHH
Q psy672 52 YATG-NFQIFTGDSHGVSQPTMCRLVKEVSK 81 (314)
Q Consensus 52 L~~g-~~~~~l~~~fgis~stv~~~~~~v~~ 81 (314)
|+.+ .+..++++.+|+|++||++.+...-.
T Consensus 9 L~~~~~~~~eLa~~l~vS~~tv~~~l~~L~~ 39 (69)
T TIGR00122 9 LADNPFSGEKLGEALGMSRTAVNKHIQTLRE 39 (69)
T ss_pred HHcCCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4433 44678999999999999999888754
No 257
>PRK09483 response regulator; Provisional
Probab=61.30 E-value=6.3 Score=32.87 Aligned_cols=45 Identities=9% Similarity=-0.029 Sum_probs=36.9
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHH
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALA 84 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~ 84 (314)
.++..+.=.+ .+++.|.+..++|..+++|.+||..++++...-|.
T Consensus 148 ~Lt~rE~~vl--~~~~~G~~~~~Ia~~l~is~~TV~~~~~~i~~Kl~ 192 (217)
T PRK09483 148 SLSERELQIM--LMITKGQKVNEISEQLNLSPKTVNSYRYRMFSKLN 192 (217)
T ss_pred ccCHHHHHHH--HHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence 4776666543 56789999999999999999999999988877664
No 258
>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=61.25 E-value=7.6 Score=25.83 Aligned_cols=42 Identities=17% Similarity=-0.005 Sum_probs=28.8
Q ss_pred CCCCCHHHHHHHHHHHhhcCC---cccccCCcccccHHHHHHHHH
Q psy672 36 GVKQPPMTRLLAVIQFYATGN---FQIFTGDSHGVSQPTMCRLVK 77 (314)
Q Consensus 36 ~~~~s~~~~l~~~L~~L~~g~---~~~~l~~~fgis~stv~~~~~ 77 (314)
+...++.-+|-+.-++..++. .++..|..|||++..|.+|..
T Consensus 3 rrsy~~~FKL~Vv~~a~~~~nc~~~~RAaarkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 3 RRSYTAEFKLKVVEYAEKDNNCKGNQRAAARKFNVSRRQVRKWRK 47 (58)
T ss_dssp -----HHHHHHHHHHHHH-TTTTT-HHHHHHHTTS-HHHHHHHHT
T ss_pred ccccChHHHHHHHHHHHHccchhhhHHHHHHHhCccHHHHHHHHH
Confidence 345778888988888888775 558899999999998887765
No 259
>COG5421 Transposase [DNA replication, recombination, and repair]
Probab=61.22 E-value=13 Score=35.73 Aligned_cols=56 Identities=16% Similarity=0.205 Sum_probs=40.2
Q ss_pred ceeeeeeeecCCcccEEEeecCCCCCcChhhhhccCcchhhhhc-CCc-ceEEEeCCCCCC
Q psy672 141 TFSLNVQVIGGPNLEIWDVVSGWPGSVHDSRIFTNSRVCHRFER-GEV-RGILLGDSGYAQ 199 (314)
Q Consensus 141 ~~s~~~q~v~d~~g~i~~~~~~~pGs~~D~~i~~~s~~~~~l~~-~~~-~~~llgD~gY~~ 199 (314)
-.-+++..+++..|-.+.+.+ ++|+.+|...+... .+.+.. +.. +.++++|+|+-.
T Consensus 154 l~QI~vsMi~~~~gIPl~~~v-~~Gni~D~~~~~~t--i~kl~~~l~~~~~~~V~Dkgf~S 211 (480)
T COG5421 154 LPQINVSMIVNQKGIPLFVRV-YSGNISDKNTLIKT--IQKLKSVLVKDEVYLVADKGFNS 211 (480)
T ss_pred cceeEEEEEEcCCCCceEEEc-cCCCccchHHHHHH--HHHHHHhcccceEEEEEcccccc
Confidence 458889999999988887777 59999999877542 222222 211 379999999954
No 260
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=61.09 E-value=8.7 Score=32.05 Aligned_cols=43 Identities=16% Similarity=0.166 Sum_probs=35.2
Q ss_pred CCHHHHHHHHHHHhhc--------C------CcccccCCcccccHHHHHHHHHHHHH
Q psy672 39 QPPMTRLLAVIQFYAT--------G------NFQIFTGDSHGVSQPTMCRLVKEVSK 81 (314)
Q Consensus 39 ~s~~~~l~~~L~~L~~--------g------~~~~~l~~~fgis~stv~~~~~~v~~ 81 (314)
.++.++|+.+|..|+. + .+..++|...|+++.||+|.++++.+
T Consensus 119 ~~~~~Rla~~Ll~l~~~~~~~~~~~~~~~~~~t~~~iA~~lG~tretvsR~l~~l~~ 175 (202)
T PRK13918 119 QRLKNRIAAALLELSDTPLATQEDSGETMIYATHDELAAAVGSVRETVTKVIGELSR 175 (202)
T ss_pred CchHHHHHHHHHHHHHHhCCCCCCCCeEEecCCHHHHHHHhCccHHHHHHHHHHHHH
Confidence 5689999999887764 1 24568899999999999999998876
No 261
>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=60.50 E-value=7.4 Score=28.98 Aligned_cols=38 Identities=8% Similarity=0.103 Sum_probs=31.2
Q ss_pred HHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 48 VIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 48 ~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
+|.-+....++...|+..|||++|+++.+++.-..+-.
T Consensus 9 ~~~av~~~gSis~AA~~L~iS~stvs~~I~~LE~~lg~ 46 (99)
T TIGR00637 9 LLKAIARMGSISQAAKDAGISYKSAWDYIRAMNNLSGE 46 (99)
T ss_pred HHHHHHHhCCHHHHHHHHCCCHHHHHHHHHHHHHHhCC
Confidence 34445556778899999999999999999998888775
No 262
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=60.40 E-value=9.3 Score=32.94 Aligned_cols=45 Identities=18% Similarity=0.231 Sum_probs=36.4
Q ss_pred CCCHHHHHHHHHHHhhc--C--------CcccccCCcccccHHHHHHHHHHHHHH
Q psy672 38 KQPPMTRLLAVIQFYAT--G--------NFQIFTGDSHGVSQPTMCRLVKEVSKA 82 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~--g--------~~~~~l~~~fgis~stv~~~~~~v~~~ 82 (314)
..+++++|+-+|..++. | .+..++|...|+++.|++|.++++.+.
T Consensus 152 ~~~~~~Rla~~Ll~l~~~~g~~~~i~i~lt~~~IA~~lGisretlsR~L~~L~~~ 206 (230)
T PRK09391 152 RKTAMERVAAFLLEMDERLGGAGMMALPMSRRDIADYLGLTIETVSRALSQLQDR 206 (230)
T ss_pred CCCHHHHHHHHHHHHHHHhCCCCEEEecCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 36899999999988753 1 345689999999999999998887653
No 263
>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=60.36 E-value=11 Score=28.49 Aligned_cols=43 Identities=12% Similarity=-0.012 Sum_probs=30.5
Q ss_pred CCHHHH-HHHHHHHhh---cCCcccccCCcccccHHHHHHHHHHHHH
Q psy672 39 QPPMTR-LLAVIQFYA---TGNFQIFTGDSHGVSQPTMCRLVKEVSK 81 (314)
Q Consensus 39 ~s~~~~-l~~~L~~L~---~g~~~~~l~~~fgis~stv~~~~~~v~~ 81 (314)
+++.+- ++..|..+. .+.+..+++..++++++|+++.+++...
T Consensus 23 ls~~q~~vL~~l~~~~~~~~~~t~~eL~~~l~~~~stvs~~i~~Le~ 69 (109)
T TIGR01889 23 LSLEELLILYYLGKLENNEGKLTLKEIIKEILIKQSALVKIIKKLSK 69 (109)
T ss_pred CCHHHHHHHHHHHhhhccCCcCcHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 444443 444444322 3588999999999999999998887665
No 264
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=60.34 E-value=13 Score=31.83 Aligned_cols=48 Identities=8% Similarity=0.044 Sum_probs=35.1
Q ss_pred CCCHHHHHHHHHHH-hhcC-----CcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 38 KQPPMTRLLAVIQF-YATG-----NFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 38 ~~s~~~~l~~~L~~-L~~g-----~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
.++..+.-++.+-| +|.. .+..+||+.||||++|++.++++...-|..
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ehLRrAe~Kl~~ 208 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEHLRRAERKLIE 208 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 57666654444444 3332 455789999999999999999998887775
No 265
>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=60.12 E-value=3.3 Score=25.64 Aligned_cols=22 Identities=32% Similarity=0.339 Sum_probs=17.7
Q ss_pred cccccCCcccccHHHHHHHHHH
Q psy672 57 FQIFTGDSHGVSQPTMCRLVKE 78 (314)
Q Consensus 57 ~~~~l~~~fgis~stv~~~~~~ 78 (314)
+..++++.+|||++|+.+++++
T Consensus 3 t~~e~a~~lgis~~ti~~~~~~ 24 (49)
T TIGR01764 3 TVEEAAEYLGVSKDTVYRLIHE 24 (49)
T ss_pred CHHHHHHHHCCCHHHHHHHHHc
Confidence 4567888999999999888753
No 266
>TIGR03020 EpsA transcriptional regulator EpsA. Proteins in this family include a C-terminal LuxR transcriptional regulator domain (pfam00196). These proteins are positioned proximal to either EpsH-containing exopolysaccharide biosynthesis operons of the Methylobacillus type, or the associated PEP-CTERM-containing genes.
Probab=59.51 E-value=11 Score=33.14 Aligned_cols=46 Identities=13% Similarity=0.012 Sum_probs=38.3
Q ss_pred CCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHH
Q psy672 37 VKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALA 84 (314)
Q Consensus 37 ~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~ 84 (314)
..+|+.++=.+.| ++.|.+..++|+.+|||..||..++.+...-+.
T Consensus 189 ~~LT~RE~evl~l--~a~G~s~~eIA~~L~IS~~TVk~hl~~i~~KL~ 234 (247)
T TIGR03020 189 GLITAREAEILAW--VRDGKTNEEIAAILGISSLTVKNHLQHIFKKLD 234 (247)
T ss_pred cCCCHHHHHHHHH--HHCCCCHHHHHHHHCcCHHHHHHHHHHHHHHhC
Confidence 3578877766665 679999999999999999999999998876554
No 267
>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=58.98 E-value=11 Score=23.18 Aligned_cols=25 Identities=16% Similarity=0.169 Sum_probs=19.3
Q ss_pred cCCcccccCCcccccHHHHHHHHHH
Q psy672 54 TGNFQIFTGDSHGVSQPTMCRLVKE 78 (314)
Q Consensus 54 ~g~~~~~l~~~fgis~stv~~~~~~ 78 (314)
.-.++..+|+..|+|.+||.+-+.+
T Consensus 16 ~r~s~~~la~~lglS~~~v~~Ri~r 40 (42)
T PF13404_consen 16 GRRSYAELAEELGLSESTVRRRIRR 40 (42)
T ss_dssp TTS-HHHHHHHHTS-HHHHHHHHHH
T ss_pred CCccHHHHHHHHCcCHHHHHHHHHH
Confidence 3468889999999999999987765
No 268
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=58.77 E-value=6.4 Score=27.95 Aligned_cols=36 Identities=31% Similarity=0.384 Sum_probs=25.5
Q ss_pred HHHHHHHHHHhh--cCCcccccCCcccccHHHHHHHHH
Q psy672 42 MTRLLAVIQFYA--TGNFQIFTGDSHGVSQPTMCRLVK 77 (314)
Q Consensus 42 ~~~l~~~L~~L~--~g~~~~~l~~~fgis~stv~~~~~ 77 (314)
..+|+..|..+. .|.++.++|+..|+++++++++.+
T Consensus 16 k~~l~~~i~~~~~~~~ltQ~e~A~~lgisq~~vS~l~~ 53 (80)
T PF13744_consen 16 KAQLMAAIRELREERGLTQAELAERLGISQPRVSRLEN 53 (80)
T ss_dssp HHHHHHHHHHHHHCCT--HHHHHHHHTS-HHHHHHHHT
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHCCChhHHHHHHc
Confidence 445555555554 678999999999999999998874
No 269
>PRK00215 LexA repressor; Validated
Probab=58.72 E-value=9.2 Score=32.35 Aligned_cols=27 Identities=15% Similarity=0.185 Sum_probs=23.4
Q ss_pred CcccccCCcccc-cHHHHHHHHHHHHHH
Q psy672 56 NFQIFTGDSHGV-SQPTMCRLVKEVSKA 82 (314)
Q Consensus 56 ~~~~~l~~~fgi-s~stv~~~~~~v~~~ 82 (314)
.+..++++.+|+ +++|+++++......
T Consensus 24 ~s~~ela~~~~~~~~~tv~~~l~~L~~~ 51 (205)
T PRK00215 24 PSRREIADALGLRSPSAVHEHLKALERK 51 (205)
T ss_pred CCHHHHHHHhCCCChHHHHHHHHHHHHC
Confidence 467799999999 999999998887754
No 270
>PF12728 HTH_17: Helix-turn-helix domain
Probab=57.99 E-value=3.8 Score=26.09 Aligned_cols=21 Identities=19% Similarity=0.276 Sum_probs=17.6
Q ss_pred cccccCCcccccHHHHHHHHH
Q psy672 57 FQIFTGDSHGVSQPTMCRLVK 77 (314)
Q Consensus 57 ~~~~l~~~fgis~stv~~~~~ 77 (314)
+..++|+.+|||.+|+.++++
T Consensus 3 t~~e~a~~l~is~~tv~~~~~ 23 (51)
T PF12728_consen 3 TVKEAAELLGISRSTVYRWIR 23 (51)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 456788899999999998875
No 271
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=57.93 E-value=8.3 Score=29.78 Aligned_cols=26 Identities=15% Similarity=0.179 Sum_probs=23.1
Q ss_pred hhcCCcccccCCcccccHHHHHHHHH
Q psy672 52 YATGNFQIFTGDSHGVSQPTMCRLVK 77 (314)
Q Consensus 52 L~~g~~~~~l~~~fgis~stv~~~~~ 77 (314)
-..|.++..+|+..|+|++.|++|++
T Consensus 19 ~eeG~Sq~~iA~LLGltqaAVS~Yls 44 (119)
T COG2522 19 IEEGLSQYRIAKLLGLTQAAVSQYLS 44 (119)
T ss_pred HHcCCcHHHHHHHhCCCHHHHHHHHc
Confidence 33499999999999999999999986
No 272
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=57.73 E-value=5 Score=28.22 Aligned_cols=28 Identities=32% Similarity=0.347 Sum_probs=23.6
Q ss_pred HHhhcCCcccccCCccc------ccHHHHHHHHH
Q psy672 50 QFYATGNFQIFTGDSHG------VSQPTMCRLVK 77 (314)
Q Consensus 50 ~~L~~g~~~~~l~~~fg------is~stv~~~~~ 77 (314)
.+...|.++.++|...| +|++|++++-+
T Consensus 19 ~R~~lGLTQ~dvA~~lg~~~g~i~SQstISR~Es 52 (75)
T smart00352 19 RRIKLGFTQADVGLALGALYGPDFSQTTICRFEA 52 (75)
T ss_pred HHHHcCCCHHHHHHHhcccccCcCCHHHHHHHHh
Confidence 44667899999999999 59999999766
No 273
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=57.57 E-value=9.4 Score=29.81 Aligned_cols=42 Identities=10% Similarity=-0.107 Sum_probs=32.3
Q ss_pred HHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHH
Q psy672 42 MTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKAL 83 (314)
Q Consensus 42 ~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l 83 (314)
+-.+...|.--..+.+-.++|...++++|||++.+++...+-
T Consensus 29 Dv~v~~~LL~~~~~~tvdelae~lnr~rStv~rsl~~L~~~G 70 (126)
T COG3355 29 DVEVYKALLEENGPLTVDELAEILNRSRSTVYRSLQNLLEAG 70 (126)
T ss_pred HHHHHHHHHhhcCCcCHHHHHHHHCccHHHHHHHHHHHHHcC
Confidence 444555544445667889999999999999999999988763
No 274
>PHA01976 helix-turn-helix protein
Probab=56.78 E-value=6.5 Score=26.51 Aligned_cols=27 Identities=11% Similarity=-0.068 Sum_probs=23.2
Q ss_pred HhhcCCcccccCCcccccHHHHHHHHH
Q psy672 51 FYATGNFQIFTGDSHGVSQPTMCRLVK 77 (314)
Q Consensus 51 ~L~~g~~~~~l~~~fgis~stv~~~~~ 77 (314)
+-..|.+..++|+..|+|++++++|-+
T Consensus 11 R~~~glt~~~lA~~~gvs~~~v~~~e~ 37 (67)
T PHA01976 11 RNARAWSAPELSRRAGVRHSLIYDFEA 37 (67)
T ss_pred HHHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 455788899999999999999998765
No 275
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=56.45 E-value=3.4 Score=28.53 Aligned_cols=21 Identities=24% Similarity=0.222 Sum_probs=17.3
Q ss_pred cccccCCcccccHHHHHHHHH
Q psy672 57 FQIFTGDSHGVSQPTMCRLVK 77 (314)
Q Consensus 57 ~~~~l~~~fgis~stv~~~~~ 77 (314)
+..++|+..|+|.+||+++++
T Consensus 2 t~~~iA~~~gvS~~TVSr~ln 22 (70)
T smart00354 2 TIKDVARLAGVSKATVSRVLN 22 (70)
T ss_pred CHHHHHHHHCCCHHHHHHHHC
Confidence 346788899999999999764
No 276
>smart00153 VHP Villin headpiece domain.
Probab=56.44 E-value=3.2 Score=24.77 Aligned_cols=21 Identities=5% Similarity=-0.062 Sum_probs=16.3
Q ss_pred CCCccccccccCHHHHHHhhHH
Q psy672 2 PLWTEQEALRFSKDVVLNIIFP 23 (314)
Q Consensus 2 ~~~~~~~~frmsr~~f~~~L~~ 23 (314)
.+-+|++.|.|||+.|. .|=.
T Consensus 3 sdeeF~~vfgmsr~eF~-~LP~ 23 (36)
T smart00153 3 SDEDFEEVFGMTREEFY-KLPL 23 (36)
T ss_pred CHHHHHHHHCCCHHHHH-hCcH
Confidence 34567789999999999 6543
No 277
>TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR. Similarly, tetanus toxin production of Clostridium tetani is regulated by TetR which is a very close relative of BotR. Both BotR and TetR are members of the TIGR02937 subfamily of sigma-70 RNA polymerase sigma factors. Functional complementation experiments have been done for botR and tetR in highly transformable strain of Clostridium perfringens host cells to assess functional interchangeability of sigma factors and it has been confirmed that they are interchangeable in vivo.
Probab=56.41 E-value=6.6 Score=30.86 Aligned_cols=35 Identities=9% Similarity=0.071 Sum_probs=27.4
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHH
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMC 73 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~ 73 (314)
.+|+..+-++.| +.-.|.++.++|..+|+|.+||.
T Consensus 107 ~Lp~~~r~v~~l-~~~~~~s~~EIA~~l~is~~tV~ 141 (142)
T TIGR03209 107 ILPNKQKKIIYM-KFFEDMKEIDIAKKLHISRQSVY 141 (142)
T ss_pred hCCHHHHHHHHH-HHHcCCCHHHHHHHHCcCHHhhc
Confidence 466666666666 44568899999999999999985
No 278
>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=56.13 E-value=15 Score=28.65 Aligned_cols=47 Identities=15% Similarity=0.036 Sum_probs=31.6
Q ss_pred CCCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHH
Q psy672 36 GVKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKAL 83 (314)
Q Consensus 36 ~~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l 83 (314)
+.++|.+.+.-+.=+ ...|....+++.++.||.++|++++.++-+.-
T Consensus 15 GrPLp~~~R~rIvel-a~~G~rp~~Isr~l~Vs~gcVsKIl~Ry~eTG 61 (125)
T PF00292_consen 15 GRPLPNELRQRIVEL-AKEGVRPCDISRQLRVSHGCVSKILSRYRETG 61 (125)
T ss_dssp TSSS-HHHHHHHHHH-HHTT--HHHHHHHHT--HHHHHHHHHHHHHHS
T ss_pred CccCcHHHHHHHHHH-hhhcCCHHHHHHHHccchhHHHHHHHHHHHhc
Confidence 345777776655422 24799999999999999999999999986553
No 279
>PRK10870 transcriptional repressor MprA; Provisional
Probab=55.76 E-value=12 Score=31.00 Aligned_cols=45 Identities=13% Similarity=0.023 Sum_probs=29.0
Q ss_pred CCCCHHH-HHHHHHHHhhc-CCcccccCCcccccHHHHHHHHHHHHH
Q psy672 37 VKQPPMT-RLLAVIQFYAT-GNFQIFTGDSHGVSQPTMCRLVKEVSK 81 (314)
Q Consensus 37 ~~~s~~~-~l~~~L~~L~~-g~~~~~l~~~fgis~stv~~~~~~v~~ 81 (314)
..+++.+ .++..|+...+ +.+..+|++.++++++|+++.+++...
T Consensus 51 ~gLt~~q~~iL~~L~~~~~~~it~~eLa~~l~l~~~tvsr~v~rLe~ 97 (176)
T PRK10870 51 QGINETLFMALITLESQENHSIQPSELSCALGSSRTNATRIADELEK 97 (176)
T ss_pred CCCCHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3455543 23333332222 356789999999999999988776543
No 280
>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=55.60 E-value=7.8 Score=24.88 Aligned_cols=26 Identities=23% Similarity=0.069 Sum_probs=22.4
Q ss_pred hhcCCcccccCCcccccHHHHHHHHH
Q psy672 52 YATGNFQIFTGDSHGVSQPTMCRLVK 77 (314)
Q Consensus 52 L~~g~~~~~l~~~fgis~stv~~~~~ 77 (314)
-..|.++.++|...|+|+++++++.+
T Consensus 12 ~~~gltq~~lA~~~gvs~~~vs~~e~ 37 (58)
T TIGR03070 12 KALGLTQADLADLAGVGLRFIRDVEN 37 (58)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHC
Confidence 44688889999999999999998864
No 281
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=55.40 E-value=10 Score=34.19 Aligned_cols=43 Identities=12% Similarity=0.067 Sum_probs=37.2
Q ss_pred HHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 43 TRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 43 ~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
.+|-.++....+|.++...|+.+++|++++++.+++.-+.+-.
T Consensus 4 ~~L~~F~~v~~~~~S~s~AA~~L~isQpavS~~I~~LE~~lg~ 46 (309)
T PRK12683 4 QQLRIIREAVRQNFNLTEVANALYTSQSGVSKQIKDLEDELGV 46 (309)
T ss_pred HHHHHHHHHHHccCCHHHHHHHhcCCcHHHHHHHHHHHHHhCC
Confidence 4566666677788899999999999999999999999998875
No 282
>PF14493 HTH_40: Helix-turn-helix domain
Probab=54.61 E-value=15 Score=26.67 Aligned_cols=39 Identities=10% Similarity=0.106 Sum_probs=34.3
Q ss_pred HHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHH
Q psy672 46 LAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALA 84 (314)
Q Consensus 46 ~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~ 84 (314)
..|+..+..|.+..++|..-|++.+||..++-+.+..-.
T Consensus 4 ~~T~~l~~~G~si~eIA~~R~L~~sTI~~HL~~~~~~g~ 42 (91)
T PF14493_consen 4 QITYELFQKGLSIEEIAKIRGLKESTIYGHLAELIESGE 42 (91)
T ss_pred HHHHHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHHHhCC
Confidence 467888899999999999999999999999888877644
No 283
>PF08148 DSHCT: DSHCT (NUC185) domain; InterPro: IPR012961 This C-terminal domain is found in DOB1/SK12/helY-like DEAD box helicases [].; GO: 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides; PDB: 4A4Z_A 2XGJ_B 3L9O_A.
Probab=53.83 E-value=19 Score=29.99 Aligned_cols=48 Identities=15% Similarity=0.130 Sum_probs=38.4
Q ss_pred HHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHhccc
Q psy672 42 MTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAHVN 89 (314)
Q Consensus 42 ~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~~~ 89 (314)
.-.++-..+.++.|.++.++-..-++.++.+.|+++++.+.|-.+..-
T Consensus 101 ~~~l~~~v~~Wa~G~~~~~i~~~t~l~EGdiVR~~rRl~dlLrql~~a 148 (180)
T PF08148_consen 101 DPGLMEVVYAWASGASFAEILEMTDLFEGDIVRWIRRLIDLLRQLANA 148 (180)
T ss_dssp TTTTHHHHHHHHCT--HHHHCCT-SS-HHHHHHHHHHHHHHHHHHHHH
T ss_pred CccHHHHHHHHHCCCCHHHHHhcCCCCchHHHHHHHHHHHHHHHHHHH
Confidence 345777789999999999999999999999999999999999986544
No 284
>COG1342 Predicted DNA-binding proteins [General function prediction only]
Probab=53.72 E-value=9.2 Score=28.15 Aligned_cols=46 Identities=22% Similarity=0.125 Sum_probs=31.8
Q ss_pred CCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 39 QPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 39 ~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
+++++-=++-|.-+ .+.++.+.|.+.|||++|+++.++..-.-+..
T Consensus 34 lt~eElEAlRLvD~-~~l~QeeAA~rMgISr~Tfwr~l~sAR~KvA~ 79 (99)
T COG1342 34 LTIEELEALRLVDY-EGLTQEEAALRMGISRQTFWRLLTSARKKVAD 79 (99)
T ss_pred ecHHHHHHHHHHhH-hhccHHHHHHHhcccHHHHHHHHHHHHHHHHH
Confidence 44555444433333 46788899999999999999998866554443
No 285
>PF13551 HTH_29: Winged helix-turn helix
Probab=53.72 E-value=35 Score=25.22 Aligned_cols=69 Identities=19% Similarity=0.121 Sum_probs=38.5
Q ss_pred cccccCHHHHHHhhHHhhhhh----hcc-c--CCCCCC-CCHHHHHHHHHHHhhcCC-------cccccCC-----c--c
Q psy672 8 EALRFSKDVVLNIIFPLARNV----LET-N--TMQGVK-QPPMTRLLAVIQFYATGN-------FQIFTGD-----S--H 65 (314)
Q Consensus 8 ~~frmsr~~f~~~L~~~l~~~----~~~-~--~~~~~~-~s~~~~l~~~L~~L~~g~-------~~~~l~~-----~--f 65 (314)
+.+.+++.++. ..+...... +.. . .++... +++++.- ..+-++.... +...++. . .
T Consensus 20 ~~lg~s~~Tv~-r~~~~~~~~G~~~l~~~~~~~g~~~~~l~~~~~~-~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~ 97 (112)
T PF13551_consen 20 RRLGISRRTVY-RWLKRYREGGIEGLLPRKPRGGRPRKRLSEEQRA-QLIELLRENPPEGRSRWTLEELAEWLIEEEFGI 97 (112)
T ss_pred HHHCcCHHHHH-HHHHHHHcccHHHHHhccccCCCCCCCCCHHHHH-HHHHHHHHCCCCCCCcccHHHHHHHHHHhccCc
Confidence 57889999999 777665543 222 1 122233 5555544 3333333322 2334443 2 2
Q ss_pred cccHHHHHHHHHH
Q psy672 66 GVSQPTMCRLVKE 78 (314)
Q Consensus 66 gis~stv~~~~~~ 78 (314)
.+|.+|+.+++++
T Consensus 98 ~~s~~ti~r~L~~ 110 (112)
T PF13551_consen 98 DVSPSTIRRILKR 110 (112)
T ss_pred cCCHHHHHHHHHH
Confidence 6789999998875
No 286
>PRK12679 cbl transcriptional regulator Cbl; Reviewed
Probab=52.88 E-value=12 Score=33.82 Aligned_cols=43 Identities=14% Similarity=0.055 Sum_probs=37.0
Q ss_pred HHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 43 TRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 43 ~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
.+|-.++....++.++...|+..++|++++++.+++.-..+-.
T Consensus 4 ~~l~~f~~v~~~~~s~s~AA~~L~iSQ~avSr~I~~LE~~lg~ 46 (316)
T PRK12679 4 QQLKIIREAARQDYNLTEVANMLFTSQSGVSRHIRELEDELGI 46 (316)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHhcCCchHHHHHHHHHHHHhCC
Confidence 4566666666777899999999999999999999999999885
No 287
>PRK11233 nitrogen assimilation transcriptional regulator; Provisional
Probab=52.79 E-value=12 Score=33.55 Aligned_cols=41 Identities=17% Similarity=0.161 Sum_probs=32.3
Q ss_pred HHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 44 RLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 44 ~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
+|-.++ -++...++...|+..|||+++|++.+++.-..+..
T Consensus 5 ~L~~F~-~v~~~~S~s~AA~~L~isQ~avS~~I~~LE~~lg~ 45 (305)
T PRK11233 5 RLKYFV-KIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQ 45 (305)
T ss_pred HHHHHH-HHHHcCCHHHHHHHhCCCchHHHHHHHHHHHHhCC
Confidence 333444 44444589999999999999999999999988874
No 288
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=52.57 E-value=19 Score=28.97 Aligned_cols=44 Identities=16% Similarity=0.052 Sum_probs=30.8
Q ss_pred CCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHH
Q psy672 39 QPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKA 82 (314)
Q Consensus 39 ~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~ 82 (314)
++..++-.+.+..-..-.++..+|+..|+|++||.+-+++..+.
T Consensus 7 lD~~D~~Il~~Lq~d~R~s~~eiA~~lglS~~tV~~Ri~rL~~~ 50 (153)
T PRK11179 7 IDNLDRGILEALMENARTPYAELAKQFGVSPGTIHVRVEKMKQA 50 (153)
T ss_pred cCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 43333333333333344889999999999999999988887764
No 289
>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=52.29 E-value=14 Score=24.34 Aligned_cols=26 Identities=19% Similarity=0.120 Sum_probs=21.0
Q ss_pred CCcccccCCcccccHHHHHHHHHHHH
Q psy672 55 GNFQIFTGDSHGVSQPTMCRLVKEVS 80 (314)
Q Consensus 55 g~~~~~l~~~fgis~stv~~~~~~v~ 80 (314)
..+..++++.||||..|+.+-+....
T Consensus 14 ~~s~~ela~~~~VS~~TiRRDl~~L~ 39 (57)
T PF08220_consen 14 KVSVKELAEEFGVSEMTIRRDLNKLE 39 (57)
T ss_pred CEEHHHHHHHHCcCHHHHHHHHHHHH
Confidence 35667899999999999998877543
No 290
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=52.02 E-value=16 Score=32.50 Aligned_cols=88 Identities=11% Similarity=0.018 Sum_probs=56.8
Q ss_pred CCCHHHHHHHHHHHhhc---CCcccccCCcccccHHHHHHHHHHHHHHHHHh----cccc------ccC-----CC-c--
Q psy672 38 KQPPMTRLLAVIQFYAT---GNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA----HVNY------VKF-----PE-Q-- 96 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~---g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~----~~~~------i~~-----P~-~-- 96 (314)
.++.-++.+-.|..++. +.+..++++..|+++||++++++.....=+-. ...| +.+ .. .
T Consensus 20 ~~~sl~r~l~IL~~~~~~~~~~tl~eIa~~lglpkStv~RlL~tL~~~G~l~~~~~~~~Y~lG~~l~~Lg~~~~~~~~l~ 99 (271)
T PRK10163 20 GAQALERGIAILQYLEKSGGSSSVSDISLNLDLPLSTTFRLLKVLQAADFVYQDSQLGWWHIGLGVFNVGAAYIHNRDVL 99 (271)
T ss_pred cchHHHHHHHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcCCCCeEEecHHHHHHHHHHHhcCCHH
Confidence 46778888888888874 35678999999999999999999887643210 1111 000 00 1
Q ss_pred --hhhhHHHhhhcCCCCCceeeeeceEEEEe
Q psy672 97 --LAPTKVAFQGIGNFPGVVGCVDCTHVPIQ 125 (314)
Q Consensus 97 --~~~~~~~f~~~~~~p~~~g~iDgt~i~i~ 125 (314)
............+-.-.+++.|++++-+-
T Consensus 100 ~~a~p~l~~La~~~getv~l~v~~g~~~v~i 130 (271)
T PRK10163 100 SVAGPFMRRLMLLSGETVNVAIRNGNEAVLI 130 (271)
T ss_pred HHHHHHHHHHHHHHCCeEEEEEEECCEEEEE
Confidence 12233344455567777888888876553
No 291
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=51.89 E-value=14 Score=28.51 Aligned_cols=41 Identities=20% Similarity=0.113 Sum_probs=29.6
Q ss_pred HHHHHHHHHHhhc-CCcccccCCcccccHHHHHHHHHHHHHH
Q psy672 42 MTRLLAVIQFYAT-GNFQIFTGDSHGVSQPTMCRLVKEVSKA 82 (314)
Q Consensus 42 ~~~l~~~L~~L~~-g~~~~~l~~~fgis~stv~~~~~~v~~~ 82 (314)
+.++.+......+ ..+..++++.+|++++|++++++...++
T Consensus 16 ptRl~IL~~L~~~~~~~v~ela~~l~lsqstvS~HL~~L~~A 57 (117)
T PRK10141 16 ETRLGIVLLLRESGELCVCDLCTALDQSQPKISRHLALLRES 57 (117)
T ss_pred HHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 4455444433333 3567789999999999999999888776
No 292
>PF13556 HTH_30: PucR C-terminal helix-turn-helix domain; PDB: 3ONQ_B.
Probab=51.50 E-value=11 Score=24.91 Aligned_cols=36 Identities=11% Similarity=0.102 Sum_probs=29.9
Q ss_pred HHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHH
Q psy672 49 IQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALA 84 (314)
Q Consensus 49 L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~ 84 (314)
-.|+.++++....|+..+|++.|+..-++++.+.+-
T Consensus 6 ~~yl~~~~n~~~tA~~L~iHrNTl~yRl~ki~~l~g 41 (59)
T PF13556_consen 6 RAYLENNGNISKTARALHIHRNTLRYRLKKIEELLG 41 (59)
T ss_dssp HHHHHTTT-HHHHHHHHTS-HHHHHHHHHHHHHHHS
T ss_pred HHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Confidence 357889999999999999999999999998887764
No 293
>PRK10403 transcriptional regulator NarP; Provisional
Probab=51.47 E-value=27 Score=28.58 Aligned_cols=45 Identities=13% Similarity=0.043 Sum_probs=36.5
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHH
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALA 84 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~ 84 (314)
.++..+.- .|.++..|.+..++++..++|..||..++.++..-|.
T Consensus 153 ~Lt~~e~~--vl~~~~~g~s~~~ia~~l~~s~~tv~~~~~~i~~kl~ 197 (215)
T PRK10403 153 VLTERELD--VLHELAQGLSNKQIASVLNISEQTVKVHIRNLLRKLN 197 (215)
T ss_pred cCCHHHHH--HHHHHHCCCCHHHHHHHcCCCHHHHHHHHHHHHHHcC
Confidence 35555554 4667889999999999999999999999999887664
No 294
>PF13701 DDE_Tnp_1_4: Transposase DDE domain group 1
Probab=51.43 E-value=53 Score=31.62 Aligned_cols=121 Identities=22% Similarity=0.218 Sum_probs=63.9
Q ss_pred ccHHHHHHHHHHHHHHHHH-hccccccCCCchhhhHHHhhhcCCCCCceeeeeceEEEEecCCCCCCCcccCCCCceeee
Q psy672 67 VSQPTMCRLVKEVSKALAQ-AHVNYVKFPEQLAPTKVAFQGIGNFPGVVGCVDCTHVPIQLPSVENGENFRNRKGTFSLN 145 (314)
Q Consensus 67 is~stv~~~~~~v~~~l~~-~~~~~i~~P~~~~~~~~~f~~~~~~p~~~g~iDgt~i~i~~P~~~~~~~y~~~k~~~s~~ 145 (314)
.|++|++|..+.+...-.. +...++. .....+.+ .-..++-=||.|..++.- ..++..|.++++.+++.
T Consensus 103 as~~t~sR~e~~~~~~~~~~~~~~~~~------~~~~~~~~--~~~~i~LDiD~T~~~~~G--~Qe~~~~n~y~g~~gY~ 172 (448)
T PF13701_consen 103 ASQPTLSRLENRPDERDLKRLRRALVD------LFLASYKK--PPKEIVLDIDSTVDDVHG--EQEGAVFNTYYGEDGYH 172 (448)
T ss_pred cchhhHHHHHccccHHHHHHHHHHHHH------HHHHHhcc--ccceEEEecccccccchh--hcccccccccCCCcccc
Confidence 5788999888776654332 2222211 11112211 223355558888766542 22334455666666666
Q ss_pred eeeecC-CcccEEEeecCCCCCcChhhhhcc--Ccchhhhhc-CCc-ceEEEeCCCCC
Q psy672 146 VQVIGG-PNLEIWDVVSGWPGSVHDSRIFTN--SRVCHRFER-GEV-RGILLGDSGYA 198 (314)
Q Consensus 146 ~q~v~d-~~g~i~~~~~~~pGs~~D~~i~~~--s~~~~~l~~-~~~-~~~llgD~gY~ 198 (314)
=+++.+ ..|.++.+.. .||+.|-+.=... ..+...+.+ .+. .-.+=||+||.
T Consensus 173 PL~~f~g~~G~~l~a~L-RpGn~~sa~g~~~fL~~~l~~lr~~~~~~~ILvR~DSgF~ 229 (448)
T PF13701_consen 173 PLVAFDGQTGYLLAAEL-RPGNVHSAKGAAEFLKRVLRRLRQRWPDTRILVRGDSGFA 229 (448)
T ss_pred cceeccCCCCceEEEEc-cCCCCChHHHHHHHHHHHHHHHhhhCccceEEEEecCccC
Confidence 555554 4888888765 5999988632211 011222222 222 23466999995
No 295
>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=50.87 E-value=6.4 Score=24.12 Aligned_cols=26 Identities=23% Similarity=0.247 Sum_probs=19.1
Q ss_pred hcCCcccccCCcccccHHHHHHHHHH
Q psy672 53 ATGNFQIFTGDSHGVSQPTMCRLVKE 78 (314)
Q Consensus 53 ~~g~~~~~l~~~fgis~stv~~~~~~ 78 (314)
.++......|...|||++|+++-+.+
T Consensus 16 ~~~gn~~~aA~~Lgisr~tL~~klkk 41 (42)
T PF02954_consen 16 RCGGNVSKAARLLGISRRTLYRKLKK 41 (42)
T ss_dssp HTTT-HHHHHHHHTS-HHHHHHHHHH
T ss_pred HhCCCHHHHHHHHCCCHHHHHHHHHh
Confidence 35566788999999999999976654
No 296
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=50.75 E-value=14 Score=33.76 Aligned_cols=21 Identities=24% Similarity=0.207 Sum_probs=19.1
Q ss_pred cccccCCcccccHHHHHHHHH
Q psy672 57 FQIFTGDSHGVSQPTMCRLVK 77 (314)
Q Consensus 57 ~~~~l~~~fgis~stv~~~~~ 77 (314)
+..++|+..|||.+||+++++
T Consensus 3 ti~dIA~~aGVS~~TVSrvLn 23 (346)
T PRK10401 3 TIRDVARQAGVSVATVSRVLN 23 (346)
T ss_pred CHHHHHHHhCCCHHHHHHHHC
Confidence 567899999999999999997
No 297
>PRK10651 transcriptional regulator NarL; Provisional
Probab=50.58 E-value=13 Score=30.72 Aligned_cols=45 Identities=18% Similarity=0.259 Sum_probs=36.4
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHH
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALA 84 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~ 84 (314)
.+++.+. =.|.++..|.+...++..+++|..||..++.+...-|.
T Consensus 155 ~Lt~rE~--~vl~~l~~g~~~~~ia~~l~is~~tV~~~~~~l~~Kl~ 199 (216)
T PRK10651 155 QLTPRER--DILKLIAQGLPNKMIARRLDITESTVKVHVKHMLKKMK 199 (216)
T ss_pred cCCHHHH--HHHHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHHHHcC
Confidence 3666664 44556889999999999999999999999998876654
No 298
>smart00760 Bac_DnaA_C Bacterial dnaA protein helix-turn-helix domain. Could be involved in DNA-binding.
Probab=50.24 E-value=15 Score=24.32 Aligned_cols=34 Identities=9% Similarity=-0.114 Sum_probs=29.3
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCcccccCCccc
Q psy672 33 TMQGVKQPPMTRLLAVIQFYATGNFQIFTGDSHG 66 (314)
Q Consensus 33 ~~~~~~~s~~~~l~~~L~~L~~g~~~~~l~~~fg 66 (314)
..|...++..-++++.|..--.|.++.++|..||
T Consensus 23 ~~R~~~~~~aR~iamyla~~~~~~sl~~Ig~~fg 56 (60)
T smart00760 23 KSRKREIVLARQIAMYLARELTDLSLPEIGKIFG 56 (60)
T ss_pred CCCCcchhHHHHHHHHHHHHHHCCCHHHHHHHhC
Confidence 3455778889999999999889999999999997
No 299
>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=50.10 E-value=6.9 Score=26.28 Aligned_cols=23 Identities=17% Similarity=0.213 Sum_probs=16.9
Q ss_pred cccCCcccccHHHHHHHHHHHHH
Q psy672 59 IFTGDSHGVSQPTMCRLVKEVSK 81 (314)
Q Consensus 59 ~~l~~~fgis~stv~~~~~~v~~ 81 (314)
.++++.||+|++|+.+.+.....
T Consensus 28 ~~la~~~~vsr~tvr~al~~L~~ 50 (64)
T PF00392_consen 28 RELAERYGVSRTTVREALRRLEA 50 (64)
T ss_dssp HHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHHHhccCCcHHHHHHHHHHH
Confidence 45677999999999887776543
No 300
>COG2964 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=50.07 E-value=27 Score=29.99 Aligned_cols=65 Identities=15% Similarity=0.130 Sum_probs=36.6
Q ss_pred HHHHHHhhHHhhhhhhcccCCCCCCCCH-HHHHHHHHHHhhcCCcc-----cccCCcccccHHHHHHHHHHH
Q psy672 14 KDVVLNIIFPLARNVLETNTMQGVKQPP-MTRLLAVIQFYATGNFQ-----IFTGDSHGVSQPTMCRLVKEV 79 (314)
Q Consensus 14 r~~f~~~L~~~l~~~~~~~~~~~~~~s~-~~~l~~~L~~L~~g~~~-----~~l~~~fgis~stv~~~~~~v 79 (314)
.+.+. .|+..+...+.........++- .+.--+++-.+..|... ..+|+..|||+.||++|+++.
T Consensus 145 ~~~ve-~lv~~~~e~~~~~v~~~~~~~~~~~~reiV~~L~EkGiF~lK~Ai~~VA~~L~iSr~TVY~YL~~~ 215 (220)
T COG2964 145 ASSVE-DLVAQLLEWTIQEVNADRLLSNNAKNREIVKALYEKGIFNLKDAINIVADRLGISRHTVYRYLRKF 215 (220)
T ss_pred hhHHH-HHHHHHHHHHHHhhcccccccchHHHHHHHHHHHhcCccchhhHHHHHHHHhCCChHHHHHHHHHh
Confidence 34455 5555554443322112222222 33333555556666543 457888999999999999865
No 301
>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=49.92 E-value=16 Score=30.46 Aligned_cols=42 Identities=14% Similarity=0.105 Sum_probs=32.6
Q ss_pred CCCCCHHHHHHHHHHHhh-cCCcccccCCcccccHHHHHHHHH
Q psy672 36 GVKQPPMTRLLAVIQFYA-TGNFQIFTGDSHGVSQPTMCRLVK 77 (314)
Q Consensus 36 ~~~~s~~~~l~~~L~~L~-~g~~~~~l~~~fgis~stv~~~~~ 77 (314)
+..+++.++.......+. .|.+...+|+.+|+|+++|+++..
T Consensus 100 r~~lt~~e~a~~~~~l~~~~g~s~~~iA~~lg~s~~~V~r~l~ 142 (187)
T TIGR00180 100 REDLSPIEEAQAYKRLLEKFSMTQEDLAKKIGKSRAHITNLLR 142 (187)
T ss_pred ccCCCHHHHHHHHHHHHHHhCCCHHHHHHHHCcCHHHHHHHHH
Confidence 346777777665555554 578889999999999999998765
No 302
>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=49.91 E-value=5.1 Score=36.04 Aligned_cols=21 Identities=19% Similarity=0.186 Sum_probs=19.0
Q ss_pred cccccCCcccccHHHHHHHHH
Q psy672 57 FQIFTGDSHGVSQPTMCRLVK 77 (314)
Q Consensus 57 ~~~~l~~~fgis~stv~~~~~ 77 (314)
+..++|+..|||++||+++++
T Consensus 3 ti~dIA~~agVS~sTVSr~Ln 23 (311)
T TIGR02405 3 TIKDIARLAGVGKSTVSRVLN 23 (311)
T ss_pred cHHHHHHHhCCCHHHHHHHhC
Confidence 457899999999999999996
No 303
>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=49.87 E-value=5.8 Score=29.08 Aligned_cols=29 Identities=21% Similarity=0.253 Sum_probs=22.2
Q ss_pred cccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 57 FQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 57 ~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
++..+|+..|+++||++|+-..+..-++.
T Consensus 25 gq~~vA~~~Gv~eStISR~k~~~~~~~a~ 53 (91)
T PF05269_consen 25 GQKKVAEAMGVDESTISRWKNDFIEKMAM 53 (91)
T ss_dssp HHHHHHHHHTSSTTTHHHHHHHHHHHHHH
T ss_pred hhHHHHHHhCCCHHHHHHHHhhHHHHHHH
Confidence 34678999999999999988665554443
No 304
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=49.78 E-value=13 Score=30.28 Aligned_cols=45 Identities=18% Similarity=0.068 Sum_probs=35.6
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHH
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALA 84 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~ 84 (314)
.+++.+. -.|.+|+.|.+..++++.+++|.+|+..++.++..-+.
T Consensus 137 ~Lt~~E~--~il~~l~~g~~~~~Ia~~l~~s~~tv~~~~~~l~~Kl~ 181 (196)
T PRK10360 137 PLTKRER--QVAEKLAQGMAVKEIAAELGLSPKTVHVHRANLMEKLG 181 (196)
T ss_pred CCCHHHH--HHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 3555444 34566888999999999999999999999998877654
No 305
>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=49.41 E-value=11 Score=25.59 Aligned_cols=23 Identities=17% Similarity=0.196 Sum_probs=16.8
Q ss_pred CcccccCCcccccHHHHH-HHHHH
Q psy672 56 NFQIFTGDSHGVSQPTMC-RLVKE 78 (314)
Q Consensus 56 ~~~~~l~~~fgis~stv~-~~~~~ 78 (314)
.+..++|+.+|||++|++ .+..+
T Consensus 13 ~~~~~lA~~lgis~st~s~~~~~r 36 (66)
T PF07022_consen 13 KSDKELAERLGISKSTLSNNWKKR 36 (66)
T ss_dssp SSCHHHHCCTT--HHHHH-HHHHS
T ss_pred CCHHHHHHHhCcCHHHhhHHHHhC
Confidence 345689999999999999 67664
No 306
>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=49.32 E-value=8.5 Score=25.43 Aligned_cols=25 Identities=20% Similarity=0.234 Sum_probs=20.4
Q ss_pred cccccCCcccccHHHHHHHHHHHHH
Q psy672 57 FQIFTGDSHGVSQPTMCRLVKEVSK 81 (314)
Q Consensus 57 ~~~~l~~~fgis~stv~~~~~~v~~ 81 (314)
+..+++..||+|++|+++.+.+..+
T Consensus 27 ~~~~la~~~~is~~~v~~~l~~L~~ 51 (66)
T cd07377 27 SERELAEELGVSRTTVREALRELEA 51 (66)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4567888999999999988877665
No 307
>PRK10072 putative transcriptional regulator; Provisional
Probab=49.13 E-value=8 Score=28.68 Aligned_cols=27 Identities=19% Similarity=-0.120 Sum_probs=23.9
Q ss_pred HhhcCCcccccCCcccccHHHHHHHHH
Q psy672 51 FYATGNFQIFTGDSHGVSQPTMCRLVK 77 (314)
Q Consensus 51 ~L~~g~~~~~l~~~fgis~stv~~~~~ 77 (314)
+-..|.++..+|+.+|+|.+||++|.+
T Consensus 42 R~~~glTQ~elA~~lGvS~~TVs~WE~ 68 (96)
T PRK10072 42 RKGTGLKIDDFARVLGVSVAMVKEWES 68 (96)
T ss_pred HHHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 446799999999999999999999875
No 308
>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=49.12 E-value=15 Score=32.04 Aligned_cols=44 Identities=16% Similarity=0.228 Sum_probs=35.4
Q ss_pred CCHHHHHHHHHHHhhc---CCcccccCCcccccHHHHHHHHHHHHHH
Q psy672 39 QPPMTRLLAVIQFYAT---GNFQIFTGDSHGVSQPTMCRLVKEVSKA 82 (314)
Q Consensus 39 ~s~~~~l~~~L~~L~~---g~~~~~l~~~fgis~stv~~~~~~v~~~ 82 (314)
++.-++.+-.|..++. +.+..++++..|+++||+++++......
T Consensus 5 v~sl~ral~IL~~l~~~~~~~~l~eia~~lglpksT~~RlL~tL~~~ 51 (248)
T TIGR02431 5 VASLARGLAVIEAFGAERPRLTLTDVAEATGLTRAAARRFLLTLVEL 51 (248)
T ss_pred HHHHHHHHHHHHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 4456677777877764 3678899999999999999999988764
No 309
>PRK11050 manganese transport regulator MntR; Provisional
Probab=48.26 E-value=16 Score=29.42 Aligned_cols=29 Identities=28% Similarity=0.423 Sum_probs=24.7
Q ss_pred cCCcccccCCcccccHHHHHHHHHHHHHH
Q psy672 54 TGNFQIFTGDSHGVSQPTMCRLVKEVSKA 82 (314)
Q Consensus 54 ~g~~~~~l~~~fgis~stv~~~~~~v~~~ 82 (314)
.+.+..++++.+++|++++++.+.+....
T Consensus 50 ~~~t~~eLA~~l~is~stVsr~l~~Le~~ 78 (152)
T PRK11050 50 GEARQVDIAARLGVSQPTVAKMLKRLARD 78 (152)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 45688899999999999999998887663
No 310
>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=48.14 E-value=17 Score=30.78 Aligned_cols=40 Identities=10% Similarity=0.106 Sum_probs=29.5
Q ss_pred HHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHH
Q psy672 41 PMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSK 81 (314)
Q Consensus 41 ~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~ 81 (314)
...+++..|..- .+.+..++++.+|++.+||++.+.+...
T Consensus 2 tr~~IL~~L~~~-~~~t~~eLA~~lgis~~tV~~~L~~Le~ 41 (203)
T TIGR02702 2 TKEDILSYLLKQ-GQATAAALAEALAISPQAVRRHLKDLET 41 (203)
T ss_pred HHHHHHHHHHHc-CCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 345555555443 4478889999999999999988776554
No 311
>PRK09492 treR trehalose repressor; Provisional
Probab=47.91 E-value=5.4 Score=35.79 Aligned_cols=23 Identities=17% Similarity=0.148 Sum_probs=20.5
Q ss_pred CcccccCCcccccHHHHHHHHHH
Q psy672 56 NFQIFTGDSHGVSQPTMCRLVKE 78 (314)
Q Consensus 56 ~~~~~l~~~fgis~stv~~~~~~ 78 (314)
.+.+++|+..|||.+||+++++.
T Consensus 5 ~ti~dIA~~agVS~~TVSrvLn~ 27 (315)
T PRK09492 5 LTIKDIARLSGVGKSTVSRVLNN 27 (315)
T ss_pred CcHHHHHHHhCCCHHHHhHHhCC
Confidence 46789999999999999999984
No 312
>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=47.39 E-value=6.2 Score=32.23 Aligned_cols=22 Identities=27% Similarity=0.224 Sum_probs=0.0
Q ss_pred CcccccCCcccccHHHHHHHHH
Q psy672 56 NFQIFTGDSHGVSQPTMCRLVK 77 (314)
Q Consensus 56 ~~~~~l~~~fgis~stv~~~~~ 77 (314)
.+..++|+..|+|.|||+|.+.
T Consensus 50 Lt~~~iA~~lgl~~STVSRav~ 71 (160)
T PF04552_consen 50 LTMKDIADELGLHESTVSRAVK 71 (160)
T ss_dssp ----------------------
T ss_pred CCHHHHHHHhCCCHhHHHHHHc
Confidence 5678999999999999999876
No 313
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=47.36 E-value=15 Score=30.15 Aligned_cols=45 Identities=11% Similarity=0.094 Sum_probs=37.1
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHH
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALA 84 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~ 84 (314)
.++..+. -.|..|..|.+..++++.+++|.+||..++.+...-|.
T Consensus 143 ~lt~~E~--~vl~~l~~g~~~~~I~~~l~~s~~tv~~~~~~l~~Kl~ 187 (204)
T PRK09958 143 SLSKQEI--SVMRYILDGKDNNDIAEKMFISNKTVSTYKSRLMEKLE 187 (204)
T ss_pred cCCHHHH--HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence 4666554 46777888999999999999999999999998887664
No 314
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=47.19 E-value=16 Score=32.91 Aligned_cols=46 Identities=15% Similarity=0.061 Sum_probs=37.2
Q ss_pred HHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH-hcc
Q psy672 43 TRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ-AHV 88 (314)
Q Consensus 43 ~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~-~~~ 88 (314)
.+|-+++....+|.++...|+..++|+++|++.+++.-..+.. ++.
T Consensus 4 ~~L~~f~~v~~~g~S~s~AA~~L~isQpavS~~ik~LE~~lg~~Lf~ 50 (313)
T PRK12684 4 HQLRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEDELGVEIFT 50 (313)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHhcCCChHHHHHHHHHHHHhCCeeEE
Confidence 3555555556667799999999999999999999999998885 443
No 315
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=47.18 E-value=17 Score=32.18 Aligned_cols=44 Identities=18% Similarity=0.266 Sum_probs=35.3
Q ss_pred CCHHHHHHHHHHHhhc---CCcccccCCcccccHHHHHHHHHHHHHH
Q psy672 39 QPPMTRLLAVIQFYAT---GNFQIFTGDSHGVSQPTMCRLVKEVSKA 82 (314)
Q Consensus 39 ~s~~~~l~~~L~~L~~---g~~~~~l~~~fgis~stv~~~~~~v~~~ 82 (314)
++.-++.+-.|..|+. +.+..++++.+|+++||++++++.....
T Consensus 7 v~sl~ral~iL~~l~~~~~~ls~~eia~~lgl~kstv~RlL~tL~~~ 53 (263)
T PRK09834 7 VRGLSRGLMVLRALNRLDGGATVGLLAELTGLHRTTVRRLLETLQEE 53 (263)
T ss_pred HHHHHHHHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 4556677777887764 2578899999999999999999988764
No 316
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=46.20 E-value=5.5 Score=26.47 Aligned_cols=26 Identities=23% Similarity=0.318 Sum_probs=18.8
Q ss_pred hcCCcccccCCcccccHHHHHHHHHH
Q psy672 53 ATGNFQIFTGDSHGVSQPTMCRLVKE 78 (314)
Q Consensus 53 ~~g~~~~~l~~~fgis~stv~~~~~~ 78 (314)
..|.+..++++.-|+|++|++++++.
T Consensus 8 ~~~it~~~La~~~gis~~tl~~~~~~ 33 (63)
T PF13443_consen 8 ERGITQKDLARKTGISRSTLSRILNG 33 (63)
T ss_dssp HTT--HHHHHHHHT--HHHHHHHHTT
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 46678889999999999999998874
No 317
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=45.82 E-value=19 Score=30.86 Aligned_cols=46 Identities=9% Similarity=0.045 Sum_probs=35.8
Q ss_pred CCCHHHHHHHHHHHhhcCC--------c--ccccCCcccccHHHHHHHHHHHHHHH
Q psy672 38 KQPPMTRLLAVIQFYATGN--------F--QIFTGDSHGVSQPTMCRLVKEVSKAL 83 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~--------~--~~~l~~~fgis~stv~~~~~~v~~~l 83 (314)
..++.++++-+|..++... + ..++|...|+++.|++|.++++.+.=
T Consensus 146 ~~~~~~Rla~~Ll~~~~~~~~~~~~~i~~t~~~iA~~lG~tretvsR~l~~L~~~g 201 (236)
T PRK09392 146 LRSSAERLANYLLKQSLRQGGADVVTLPYEKRVLASYLGMTPENLSRAFAALASHG 201 (236)
T ss_pred cCCHHHHHHHHHHHhccccCCCcEEEeeCCHHHHHHHhCCChhHHHHHHHHHHhCC
Confidence 4589999999998876421 2 35689999999999999998876543
No 318
>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein. Most but not all examples of this family are associated with CRISPR loci, a combination of DNA repeats and characteristic proteins encoded near the repeat cluster. The C-terminal region of this protein is homologous to DNA-binding helix-turn-helix domains with predicted transcriptional regulatory activity.
Probab=45.42 E-value=25 Score=29.72 Aligned_cols=35 Identities=20% Similarity=0.230 Sum_probs=26.9
Q ss_pred HHHHHhhc--CCcccccCCcccccHHHHHHHHHHHHH
Q psy672 47 AVIQFYAT--GNFQIFTGDSHGVSQPTMCRLVKEVSK 81 (314)
Q Consensus 47 ~~L~~L~~--g~~~~~l~~~fgis~stv~~~~~~v~~ 81 (314)
..|.++.. +.+..++++.+|+|++|+++.+.+..+
T Consensus 147 ~IL~~l~~~g~~s~~eia~~l~is~stv~r~L~~Le~ 183 (203)
T TIGR01884 147 KVLEVLKAEGEKSVKNIAKKLGKSLSTISRHLRELEK 183 (203)
T ss_pred HHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 34555553 458899999999999999988887554
No 319
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [].; PDB: 2WTE_A 3SQN_A.
Probab=45.22 E-value=23 Score=23.44 Aligned_cols=40 Identities=13% Similarity=0.068 Sum_probs=28.5
Q ss_pred HHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHH
Q psy672 44 RLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALA 84 (314)
Q Consensus 44 ~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~ 84 (314)
+|+-.|.- ....+..+++...|+|..|+..++.+.-..+-
T Consensus 9 ~Ll~~L~~-~~~~~~~ela~~l~~S~rti~~~i~~L~~~f~ 48 (59)
T PF08280_consen 9 KLLELLLK-NKWITLKELAKKLNISERTIKNDINELNEFFP 48 (59)
T ss_dssp HHHHHHHH-HTSBBHHHHHHHCTS-HHHHHHHHHHHHTT--
T ss_pred HHHHHHHc-CCCCcHHHHHHHHCCCHHHHHHHHHHHHHHhh
Confidence 44455555 66678899999999999999998887655443
No 320
>PRK11569 transcriptional repressor IclR; Provisional
Probab=45.21 E-value=25 Score=31.24 Aligned_cols=45 Identities=18% Similarity=0.256 Sum_probs=37.2
Q ss_pred CCCHHHHHHHHHHHhhc---CCcccccCCcccccHHHHHHHHHHHHHH
Q psy672 38 KQPPMTRLLAVIQFYAT---GNFQIFTGDSHGVSQPTMCRLVKEVSKA 82 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~---g~~~~~l~~~fgis~stv~~~~~~v~~~ 82 (314)
.++.-++.+-.|.+|+. +.+..++++..|+++||++++++.....
T Consensus 23 ~v~sl~ral~IL~~l~~~~~~~~lseia~~lglpksTv~RlL~tL~~~ 70 (274)
T PRK11569 23 QVQSLTRGLKLLEWIAESNGSVALTELAQQAGLPNSTTHRLLTTMQQQ 70 (274)
T ss_pred CccHHHHHHHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 36677888888888874 3578899999999999999999987764
No 321
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=44.89 E-value=22 Score=25.33 Aligned_cols=37 Identities=11% Similarity=0.187 Sum_probs=27.5
Q ss_pred HHHhhcC--CcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 49 IQFYATG--NFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 49 L~~L~~g--~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
|..+.++ .+-..+|+..|+|+.+|.+.+.+.-+.-+.
T Consensus 11 ll~~~~~~~~SGe~La~~LgiSRtaVwK~Iq~Lr~~G~~ 49 (79)
T COG1654 11 LLLLLTGNFVSGEKLAEELGISRTAVWKHIQQLREEGVD 49 (79)
T ss_pred HHHHcCCCcccHHHHHHHHCccHHHHHHHHHHHHHhCCc
Confidence 3344444 566789999999999999998887765443
No 322
>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=44.88 E-value=6 Score=24.79 Aligned_cols=30 Identities=17% Similarity=0.073 Sum_probs=23.9
Q ss_pred cCCcccccCCcccccHHHHHHHHHHHHHHH
Q psy672 54 TGNFQIFTGDSHGVSQPTMCRLVKEVSKAL 83 (314)
Q Consensus 54 ~g~~~~~l~~~fgis~stv~~~~~~v~~~l 83 (314)
.+.+.+++++..|+|+++++++|..--..+
T Consensus 15 ~~~s~~~Ia~~~gvs~~~~y~~f~~k~~l~ 44 (47)
T PF00440_consen 15 EAVSIRDIARRAGVSKGSFYRYFPSKDDLL 44 (47)
T ss_dssp TTSSHHHHHHHHTSCHHHHHHHCSSHHHHH
T ss_pred HhCCHHHHHHHHccchhhHHHHcCCHHHHH
Confidence 446778999999999999999887554444
No 323
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=44.71 E-value=26 Score=29.40 Aligned_cols=43 Identities=9% Similarity=-0.052 Sum_probs=30.5
Q ss_pred CCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHH
Q psy672 37 VKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEV 79 (314)
Q Consensus 37 ~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v 79 (314)
..+++.+-..+...+-..|.+..++|+..+++++|+++.+.+.
T Consensus 41 ~gLt~~q~~iL~~L~~~~~itq~eLa~~l~l~~sTvtr~l~rL 83 (185)
T PRK13777 41 YDLNINEHHILWIAYHLKGASISEIAKFGVMHVSTAFNFSKKL 83 (185)
T ss_pred CCCCHHHHHHHHHHHhCCCcCHHHHHHHHCCCHhhHHHHHHHH
Confidence 3466665544444444567899999999999999988766644
No 324
>PRK09526 lacI lac repressor; Reviewed
Probab=44.62 E-value=6.9 Score=35.58 Aligned_cols=23 Identities=22% Similarity=0.170 Sum_probs=20.3
Q ss_pred CcccccCCcccccHHHHHHHHHH
Q psy672 56 NFQIFTGDSHGVSQPTMCRLVKE 78 (314)
Q Consensus 56 ~~~~~l~~~fgis~stv~~~~~~ 78 (314)
.+..++|+..|||.+||+++++.
T Consensus 6 ~ti~dIA~~aGVS~~TVSrvLn~ 28 (342)
T PRK09526 6 VTLYDVARYAGVSYQTVSRVLNQ 28 (342)
T ss_pred CcHHHHHHHhCCCHHHHHHHhcC
Confidence 35689999999999999999983
No 325
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=44.18 E-value=6.9 Score=35.54 Aligned_cols=23 Identities=17% Similarity=-0.009 Sum_probs=20.7
Q ss_pred CcccccCCcccccHHHHHHHHHH
Q psy672 56 NFQIFTGDSHGVSQPTMCRLVKE 78 (314)
Q Consensus 56 ~~~~~l~~~fgis~stv~~~~~~ 78 (314)
.+.+++|+.+|||.+||+++++.
T Consensus 7 ~Ti~dIA~~agVS~~TVSr~Ln~ 29 (342)
T PRK10014 7 ITIHDVALAAGVSVSTVSLVLSG 29 (342)
T ss_pred CcHHHHHHHhCCCHHHHHHHHCC
Confidence 46789999999999999999875
No 326
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=44.13 E-value=26 Score=30.67 Aligned_cols=40 Identities=23% Similarity=0.346 Sum_probs=30.5
Q ss_pred HHHHHHHHHhhcC---CcccccCCcccccHHHHHHHHHHHHHH
Q psy672 43 TRLLAVIQFYATG---NFQIFTGDSHGVSQPTMCRLVKEVSKA 82 (314)
Q Consensus 43 ~~l~~~L~~L~~g---~~~~~l~~~fgis~stv~~~~~~v~~~ 82 (314)
++-+-.|.+|+.+ .+..++++..|+++||+++++......
T Consensus 4 ~ral~iL~~l~~~~~~l~l~ela~~~glpksT~~RlL~tL~~~ 46 (246)
T COG1414 4 ERALAILDLLAEGPGGLSLAELAERLGLPKSTVHRLLQTLVEL 46 (246)
T ss_pred HHHHHHHHHHHhCCCCCCHHHHHHHhCcCHHHHHHHHHHHHHC
Confidence 3445556666633 348899999999999999999887764
No 327
>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=43.79 E-value=18 Score=31.93 Aligned_cols=41 Identities=20% Similarity=0.159 Sum_probs=31.9
Q ss_pred HHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 44 RLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 44 ~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
+|-.++. ++...+++..|+.++||+|++++.+++.-+.+-.
T Consensus 5 ~L~~f~~-v~~~gs~s~AA~~L~itqpavS~~Ik~LE~~lg~ 45 (291)
T TIGR03418 5 ALRVFES-AARLASFTAAARELGSTQPAVSQQVKRLEEELGT 45 (291)
T ss_pred HHHHHHH-HHHhCCHHHHHHHhCCCHHHHHHHHHHHHHHhCc
Confidence 3434444 4444589999999999999999999999887763
No 328
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=43.45 E-value=21 Score=35.88 Aligned_cols=48 Identities=13% Similarity=0.153 Sum_probs=39.5
Q ss_pred CCCHHHHHHHHHHHh---hcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 38 KQPPMTRLLAVIQFY---ATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L---~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
.++..++..+.++|. ....++..+|..||||++.|+++-.+.+.-|-.
T Consensus 556 ~L~~rE~~Vl~~r~g~~~~~~~tl~ei~~~lgvs~eRVrQie~~al~kLr~ 606 (619)
T PRK05658 556 SLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 606 (619)
T ss_pred cCCHHHHHHHHHhcCCCCCCCccHHHHHHHhCCCHHHHHHHHHHHHHHHhc
Confidence 478889999999885 356788999999999999999888877766653
No 329
>PRK12681 cysB transcriptional regulator CysB; Reviewed
Probab=43.31 E-value=21 Score=32.45 Aligned_cols=46 Identities=15% Similarity=0.146 Sum_probs=36.8
Q ss_pred HHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH-hcc
Q psy672 43 TRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ-AHV 88 (314)
Q Consensus 43 ~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~-~~~ 88 (314)
.+|-.++....+|.+++..|+..++|++++++.+++.-..+-. ++.
T Consensus 4 ~~L~~f~avae~g~S~s~AA~~L~iSQpavS~~I~~LE~~lG~~LF~ 50 (324)
T PRK12681 4 QQLRYIVEVVNHNLNVSATAEGLYTSQPGISKQVRMLEDELGIQIFA 50 (324)
T ss_pred HHHHHHHHHHHccCCHHHHHHHhcCCcHHHHHHHHHHHHHhCCEeEE
Confidence 3455555556677799999999999999999999999998874 443
No 330
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=42.95 E-value=28 Score=30.79 Aligned_cols=45 Identities=16% Similarity=0.116 Sum_probs=36.2
Q ss_pred CCCCHHHHHHHHHHHhhcC-CcccccCCcccccHHHHHHHHHHHHH
Q psy672 37 VKQPPMTRLLAVIQFYATG-NFQIFTGDSHGVSQPTMCRLVKEVSK 81 (314)
Q Consensus 37 ~~~s~~~~l~~~L~~L~~g-~~~~~l~~~fgis~stv~~~~~~v~~ 81 (314)
..++.+++-.+-+..=..| ..+.++.+..|.|++|++|++++..+
T Consensus 191 ~~L~~~e~~il~~i~~~GGri~Q~eL~r~lglsktTvsR~L~~LEk 236 (258)
T COG2512 191 YDLNEDEKEILDLIRERGGRITQAELRRALGLSKTTVSRILRRLEK 236 (258)
T ss_pred CCCCHHHHHHHHHHHHhCCEEeHHHHHHhhCCChHHHHHHHHHHHh
Confidence 5677777777666665566 68889999999999999999988765
No 331
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=42.93 E-value=22 Score=22.90 Aligned_cols=41 Identities=15% Similarity=0.036 Sum_probs=23.8
Q ss_pred CCCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHH
Q psy672 36 GVKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVK 77 (314)
Q Consensus 36 ~~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~ 77 (314)
+..++..||--+-++ ...|.+..+++.+.|-|+..+.+|++
T Consensus 2 G~~Lt~~Eqaqid~m-~qlG~s~~~isr~i~RSr~~Ir~yl~ 42 (50)
T PF11427_consen 2 GKTLTDAEQAQIDVM-HQLGMSLREISRRIGRSRTCIRRYLK 42 (50)
T ss_dssp S----HHHHHHHHHH-HHTT--HHHHHHHHT--HHHHHHHHH
T ss_pred CCcCCHHHHHHHHHH-HHhchhHHHHHHHhCccHHHHHHHhc
Confidence 455777777655443 45677888899999999988888765
No 332
>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=42.37 E-value=31 Score=25.98 Aligned_cols=49 Identities=20% Similarity=0.225 Sum_probs=26.7
Q ss_pred CCCCCHHHHHHHHHH-----HhhcCCcccccCCcccccHHHHHHHHHHHHHHHH
Q psy672 36 GVKQPPMTRLLAVIQ-----FYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALA 84 (314)
Q Consensus 36 ~~~~s~~~~l~~~L~-----~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~ 84 (314)
.-.+|-...+...+. .--.|.+..+||..||+|..+|.+++++.-....
T Consensus 48 ~iyiP~~~~~~~~~R~~~I~~~f~G~n~~eLA~kyglS~r~I~~Ii~~~~~~~~ 101 (108)
T PF08765_consen 48 QIYIPKCDRLLRALRNREIRREFNGMNVRELARKYGLSERQIYRIIKRVRRRER 101 (108)
T ss_dssp ------SHHHHHHHHHHHHHHH--SS-HHHHHHHHT--HHHHHHHHHHHHH---
T ss_pred eEEeeCccHHHHHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 334555555444433 2235888999999999999999999998765443
No 333
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=42.22 E-value=8.1 Score=35.13 Aligned_cols=22 Identities=18% Similarity=0.203 Sum_probs=19.8
Q ss_pred cccccCCcccccHHHHHHHHHH
Q psy672 57 FQIFTGDSHGVSQPTMCRLVKE 78 (314)
Q Consensus 57 ~~~~l~~~fgis~stv~~~~~~ 78 (314)
+..++|+..|||.+||+++++.
T Consensus 3 Ti~dIA~~agVS~~TVSrvLn~ 24 (341)
T PRK10703 3 TIKDVAKRAGVSTTTVSHVINK 24 (341)
T ss_pred CHHHHHHHhCCCHHHHHHHHcC
Confidence 5678999999999999999984
No 334
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=41.99 E-value=8.3 Score=34.79 Aligned_cols=22 Identities=18% Similarity=0.046 Sum_probs=19.3
Q ss_pred cccccCCcccccHHHHHHHHHH
Q psy672 57 FQIFTGDSHGVSQPTMCRLVKE 78 (314)
Q Consensus 57 ~~~~l~~~fgis~stv~~~~~~ 78 (314)
+..++|+..|||.+|||++++.
T Consensus 2 ti~dIA~~aGVS~~TVSrvLn~ 23 (328)
T PRK11303 2 KLDEIARLAGVSRTTASYVING 23 (328)
T ss_pred CHHHHHHHhCCCHHHHHHHHcC
Confidence 4578999999999999999875
No 335
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=41.93 E-value=6.7 Score=35.54 Aligned_cols=23 Identities=22% Similarity=0.307 Sum_probs=19.8
Q ss_pred CcccccCCcccccHHHHHHHHHH
Q psy672 56 NFQIFTGDSHGVSQPTMCRLVKE 78 (314)
Q Consensus 56 ~~~~~l~~~fgis~stv~~~~~~ 78 (314)
.+..++|+..|||.+||+++++.
T Consensus 6 ~ti~dIA~~agVS~~TVSrvLn~ 28 (331)
T PRK14987 6 PVLQDVADRVGVTKMTVSRFLRN 28 (331)
T ss_pred CcHHHHHHHhCCCHHHhhhhhCC
Confidence 35679999999999999999853
No 336
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=41.87 E-value=21 Score=28.99 Aligned_cols=44 Identities=14% Similarity=0.147 Sum_probs=34.7
Q ss_pred CCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHH
Q psy672 39 QPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALA 84 (314)
Q Consensus 39 ~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~ 84 (314)
+++.+.=+ |.++..|.+..++|+..++|..||..++.+...-+.
T Consensus 150 lt~~e~~v--l~l~~~g~~~~~Ia~~l~~s~~tv~~~~~~~~~kl~ 193 (211)
T PRK15369 150 LTPRERQI--LKLITEGYTNRDIAEQLSISIKTVETHRLNMMRKLD 193 (211)
T ss_pred CCHHHHHH--HHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 55544433 445789999999999999999999999998777665
No 337
>PRK09726 antitoxin HipB; Provisional
Probab=41.86 E-value=20 Score=25.87 Aligned_cols=26 Identities=19% Similarity=0.170 Sum_probs=22.9
Q ss_pred hhcCCcccccCCcccccHHHHHHHHH
Q psy672 52 YATGNFQIFTGDSHGVSQPTMCRLVK 77 (314)
Q Consensus 52 L~~g~~~~~l~~~fgis~stv~~~~~ 77 (314)
-..|.+..++|+..|||++|++++.+
T Consensus 22 ~~~gltq~elA~~~gvs~~tis~~e~ 47 (88)
T PRK09726 22 QQNGWTQSELAKKIGIKQATISNFEN 47 (88)
T ss_pred HHcCCCHHHHHHHHCcCHHHHHHHHC
Confidence 45788899999999999999998876
No 338
>PF02650 HTH_WhiA: WhiA C-terminal HTH domain; InterPro: IPR023054 This domain is found at the C terminus of the sporulation regulator WhiA. It is predicted to form a DNA binding helix-turn-helix structure []. ; PDB: 3HYI_A.
Probab=41.86 E-value=40 Score=24.36 Aligned_cols=43 Identities=14% Similarity=0.033 Sum_probs=28.0
Q ss_pred CCCHHHHHHHHHHHhhcC-CcccccCCcc--cccHHHHHHHHHHHHH
Q psy672 38 KQPPMTRLLAVIQFYATG-NFQIFTGDSH--GVSQPTMCRLVKEVSK 81 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g-~~~~~l~~~f--gis~stv~~~~~~v~~ 81 (314)
.+|...+- ++..++.+. .+..++|+.+ .||+|++..+++++..
T Consensus 37 ~l~~~l~~-~a~lRl~~Pd~SL~EL~~~~~~~iSKSgvnhrlrKl~~ 82 (85)
T PF02650_consen 37 KLPEKLRE-FAELRLENPDASLKELGELLEPPISKSGVNHRLRKLKK 82 (85)
T ss_dssp GS-HHHHH-HHHHHHH-TTS-HHHHHHTT--T--HHHHHHHHHHHHH
T ss_pred cCCHHHHH-HHHHHHHCccccHHHHHHHHcCcCcHHHHHHHHHHHHH
Confidence 45555554 444555554 7899999999 9999999999887754
No 339
>PRK15092 DNA-binding transcriptional repressor LrhA; Provisional
Probab=41.80 E-value=19 Score=32.48 Aligned_cols=47 Identities=11% Similarity=0.003 Sum_probs=39.3
Q ss_pred CCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 39 QPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 39 ~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
+...-+.+-.+.-++...++...|+..+||+++|++.+++.-..+..
T Consensus 9 ~~m~l~~L~~F~~v~e~gs~s~AA~~L~iSQpavS~~I~~LE~~lG~ 55 (310)
T PRK15092 9 INLDLDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGK 55 (310)
T ss_pred hcCCHHHHHHHHHHHHcCCHHHHHHHhCCChHHHHHHHHHHHHHhCc
Confidence 34455666677777888899999999999999999999999998874
No 340
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=41.74 E-value=26 Score=27.49 Aligned_cols=46 Identities=17% Similarity=0.117 Sum_probs=38.1
Q ss_pred CHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 40 PPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 40 s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
+.......+..++.+|.+..++++..||+.+++.++..++...+..
T Consensus 74 ~~~~~~~~~~~~~~~~~~i~~~a~~l~i~~~~~~r~~~r~~~~~~~ 119 (129)
T COG3677 74 ALYKIKLQAVTLYMLGLGIRDIARTLGISINTVNRWSKRFGSRVEG 119 (129)
T ss_pred cchHHHHHHHHHHHcCCCcccHHHHhcccHHHHHHHHHhhcchhhc
Confidence 3355566666777888888999999999999999999999888775
No 341
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=41.12 E-value=55 Score=28.33 Aligned_cols=48 Identities=15% Similarity=0.098 Sum_probs=29.6
Q ss_pred HHHhhHHhhhhhhcccCCCCCCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHH
Q psy672 17 VLNIIFPLARNVLETNTMQGVKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSK 81 (314)
Q Consensus 17 f~~~L~~~l~~~~~~~~~~~~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~ 81 (314)
.. +|.+.|+..+...-..+..+|.|.. |++.||||+.||.+.+.....
T Consensus 14 Y~-qi~~~L~~~I~~~~~~G~~LPsE~e----------------La~~~~VSR~TVR~Al~~L~~ 61 (241)
T PRK10079 14 YQ-EIAAKLEQELRQHYRCGDYLPAEQQ----------------LAARYEVNRHTLRRAIDQLVE 61 (241)
T ss_pred HH-HHHHHHHHHHhcccCCCCcCCCHHH----------------HHHHHCCCHHHHHHHHHHHHH
Confidence 44 5555555544321122345665554 566999999999987776654
No 342
>PRK04140 hypothetical protein; Provisional
Probab=40.98 E-value=23 Score=32.39 Aligned_cols=65 Identities=14% Similarity=-0.051 Sum_probs=44.2
Q ss_pred cccCHHH-HHHhhHHhhhhhhcccCCCCCCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHH
Q psy672 10 LRFSKDV-VLNIIFPLARNVLETNTMQGVKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVK 77 (314)
Q Consensus 10 frmsr~~-f~~~L~~~l~~~~~~~~~~~~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~ 77 (314)
.-++.+| |. .+++-..|.+.. ..++-.+...-..+- -.+-..|.++.++|+..|+|++|+++|-+
T Consensus 96 ~~~~~~tl~~-~~~~g~~p~v~~-~~Gg~~v~i~GerLk-~lRe~~GlSq~eLA~~lGVSr~tIskyE~ 161 (317)
T PRK04140 96 PALSPDTLYD-DFVEGEPPLIYA-APGGFYVKIDGDVLR-EAREELGLSLGELASELGVSRRTISKYEN 161 (317)
T ss_pred eeecHHHHHH-HHhCCCCceEEE-cCCCeeehhhHHHHH-HHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 3467888 55 776666654332 333444444443333 34677899999999999999999998876
No 343
>cd00131 PAX Paired Box domain
Probab=40.93 E-value=59 Score=25.36 Aligned_cols=70 Identities=19% Similarity=0.240 Sum_probs=39.0
Q ss_pred cccccCHHHHHHhhHHhhhhh--hccc--CCCCCC-CCHHH-HHHHHHHHhhcCCcccccCCcc---cc-------cHHH
Q psy672 8 EALRFSKDVVLNIIFPLARNV--LETN--TMQGVK-QPPMT-RLLAVIQFYATGNFQIFTGDSH---GV-------SQPT 71 (314)
Q Consensus 8 ~~frmsr~~f~~~L~~~l~~~--~~~~--~~~~~~-~s~~~-~l~~~L~~L~~g~~~~~l~~~f---gi-------s~st 71 (314)
+.|.+++.+.. .++...+.. +.+. .++++. ....+ ..+..+..-.-..+..++++.+ |+ |.||
T Consensus 41 ~~~~Vs~~tV~-r~i~r~~e~G~v~pk~~gg~rpr~~~~~~~~~i~~~v~~~p~~Tl~El~~~L~~~gv~~~~~~~s~st 119 (128)
T cd00131 41 RQLRVSHGCVS-KILNRYYETGSIRPGAIGGSKPRVATPEVVKKIEIYKQENPGMFAWEIRDRLLQEGVCDKSNVPSVSS 119 (128)
T ss_pred HHHCcCHHHHH-HHHHHHHHcCCcCCCCCCCCCCCcCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCCcccCCCCCHHH
Confidence 67999999999 888776643 2221 222233 33332 3233332222234445554442 55 9999
Q ss_pred HHHHHHH
Q psy672 72 MCRLVKE 78 (314)
Q Consensus 72 v~~~~~~ 78 (314)
++++++.
T Consensus 120 I~R~L~~ 126 (128)
T cd00131 120 INRILRN 126 (128)
T ss_pred HHHHHHh
Confidence 9998764
No 344
>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=40.91 E-value=25 Score=27.27 Aligned_cols=26 Identities=19% Similarity=0.365 Sum_probs=21.8
Q ss_pred CcccccCCcccccHHHHHHHHHHHHH
Q psy672 56 NFQIFTGDSHGVSQPTMCRLVKEVSK 81 (314)
Q Consensus 56 ~~~~~l~~~fgis~stv~~~~~~v~~ 81 (314)
.+..++++.+|+|++++++++.....
T Consensus 26 ~s~~eia~~l~is~~~v~~~l~~L~~ 51 (130)
T TIGR02944 26 YSAAEIAEQTGLNAPTVSKILKQLSL 51 (130)
T ss_pred ccHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 46678999999999999988877665
No 345
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=40.84 E-value=27 Score=30.64 Aligned_cols=45 Identities=9% Similarity=0.093 Sum_probs=36.0
Q ss_pred CCCHHHHHHHHHHHhhcC--CcccccCCcccccHHHHHHHHHHHHHH
Q psy672 38 KQPPMTRLLAVIQFYATG--NFQIFTGDSHGVSQPTMCRLVKEVSKA 82 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g--~~~~~l~~~fgis~stv~~~~~~v~~~ 82 (314)
.++.-++.+-.|..|+.. .+..++++..|+++||++++++.....
T Consensus 9 ~v~sl~r~l~IL~~l~~~~~l~l~eia~~lgl~kstv~Rll~tL~~~ 55 (257)
T PRK15090 9 SVSSVLKVFGILQALGEEREIGITELSQRVMMSKSTVYRFLQTMKTL 55 (257)
T ss_pred ccHHHHHHHHHHHHhhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 466777777778777654 467899999999999999999887754
No 346
>PRK10094 DNA-binding transcriptional activator AllS; Provisional
Probab=40.61 E-value=25 Score=31.59 Aligned_cols=41 Identities=10% Similarity=-0.053 Sum_probs=32.3
Q ss_pred HHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 44 RLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 44 ~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
+|-++ ..+....++...|+..++|++++++.+++.-..+-.
T Consensus 6 ~L~~f-~~v~e~gs~s~AA~~L~iSQpavS~~I~~LE~~lg~ 46 (308)
T PRK10094 6 TLRTF-IAVAETGSFSKAAERLCKTTATISYRIKLLEENTGV 46 (308)
T ss_pred HHHHH-HHHHHhCCHHHHHHHhcCCHHHHHHHHHHHHHHhCC
Confidence 34433 344455588999999999999999999999988774
No 347
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=40.55 E-value=24 Score=31.52 Aligned_cols=41 Identities=22% Similarity=0.246 Sum_probs=32.9
Q ss_pred HHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 44 RLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 44 ~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
+|-+++....+| ++...|+..+||+++|++.+++.-..+..
T Consensus 5 ~L~~f~~v~~~g-S~s~AA~~L~itQpavS~~i~~LE~~lg~ 45 (305)
T PRK11151 5 DLEYLVALAEHR-HFRRAADSCHVSQPTLSGQIRKLEDELGV 45 (305)
T ss_pred HHHHHHHHHHhC-CHHHHHHHhCCCchHHHHHHHHHHHHhCc
Confidence 444445555555 89999999999999999999999988774
No 348
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=40.05 E-value=10 Score=34.15 Aligned_cols=19 Identities=21% Similarity=0.244 Sum_probs=17.4
Q ss_pred cccCCcccccHHHHHHHHH
Q psy672 59 IFTGDSHGVSQPTMCRLVK 77 (314)
Q Consensus 59 ~~l~~~fgis~stv~~~~~ 77 (314)
.++|+..|||.+||+|+++
T Consensus 2 ~dIA~~agVS~~TVSrvLn 20 (327)
T PRK10423 2 KDVARLAGVSTSTVSHVIN 20 (327)
T ss_pred hhHHHHhCCcHHHHHHHhC
Confidence 5789999999999999996
No 349
>TIGR01637 phage_arpU phage transcriptional regulator, ArpU family. This model represents a family of phage proteins, including ArpU, called a putative autolysin regulatory protein. ArpU was described as a regulator of cellular muramidase-2 of Enterococcus hirae but appears to have been cloned from a prophage. This family appears related to the RinA family of bacteriophage transcriptional activators and to some sporulation-specific sigma factors. We propose that this is a phage transcriptional activator family.
Probab=39.92 E-value=42 Score=26.08 Aligned_cols=50 Identities=12% Similarity=0.107 Sum_probs=39.8
Q ss_pred CCCHHHHHHHHHHHhh-cCCcccccCCcccccHHHHHHHHHHHHHHHHHhc
Q psy672 38 KQPPMTRLLAVIQFYA-TGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAH 87 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~-~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~ 87 (314)
.++..++-.+...|+. .+.+...++..+|+|+++.++.-++.+..++..+
T Consensus 79 ~l~~~~r~Il~~~Yl~~~~~~~~~I~~~l~~s~~~~y~~k~~Al~~fA~~l 129 (132)
T TIGR01637 79 QLDEISRQILYDKYLEPDQKYDYQIMMELGYSHRQYYRIKKRALLRFATLY 129 (132)
T ss_pred hCCHHHHHHHHHHHcCccccchHHHHHHhCCcHHHHHHHHHHHHHHHHHHh
Confidence 4677888888888887 3566778999999999999998888777776543
No 350
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=39.78 E-value=26 Score=31.32 Aligned_cols=40 Identities=25% Similarity=0.249 Sum_probs=32.9
Q ss_pred HHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 46 LAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 46 ~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
+-++.-+....++...|+..++|++++++.+++.-+.|..
T Consensus 10 L~~f~~v~e~gs~s~AA~~L~isqpavS~~i~~LE~~lg~ 49 (305)
T CHL00180 10 LRILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNI 49 (305)
T ss_pred HHHHHHHHHcCCHHHHHHHhcCCChHHHHHHHHHHHHhCC
Confidence 4444455556689999999999999999999999998874
No 351
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=39.70 E-value=21 Score=31.64 Aligned_cols=40 Identities=13% Similarity=0.141 Sum_probs=33.3
Q ss_pred HHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 46 LAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 46 ~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
+-++..++...+++..|+..++|+|++++.+++.-+.+-.
T Consensus 6 L~~f~~v~~~gs~s~AA~~L~isQ~avSr~i~~LE~~lg~ 45 (296)
T PRK09906 6 LRYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGV 45 (296)
T ss_pred HHHHHHHHhhCCHHHHHHHhCCCCcHHHHHHHHHHHHhCC
Confidence 4445556666699999999999999999999999988774
No 352
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=39.50 E-value=31 Score=27.39 Aligned_cols=41 Identities=22% Similarity=0.181 Sum_probs=30.1
Q ss_pred HHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHH
Q psy672 42 MTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKAL 83 (314)
Q Consensus 42 ~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l 83 (314)
+.+++-.|..=+. .++..+|+..|+|.+|+++.+++..+.-
T Consensus 10 D~~IL~~L~~d~r-~~~~eia~~lglS~~~v~~Ri~~L~~~G 50 (154)
T COG1522 10 DRRILRLLQEDAR-ISNAELAERVGLSPSTVLRRIKRLEEEG 50 (154)
T ss_pred HHHHHHHHHHhCC-CCHHHHHHHHCCCHHHHHHHHHHHHHCC
Confidence 3444444444333 7889999999999999999988877653
No 353
>PRK09508 leuO leucine transcriptional activator; Reviewed
Probab=39.20 E-value=28 Score=31.29 Aligned_cols=43 Identities=19% Similarity=0.219 Sum_probs=35.6
Q ss_pred HHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 43 TRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 43 ~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
.+.+-++..++...++...|+..+||++||++.+++.-..+..
T Consensus 24 l~~L~~f~avae~gs~s~AA~~L~isQpavS~~I~~LE~~lg~ 66 (314)
T PRK09508 24 LNLLTVFDAVMQEQNITRAAHNLGMSQPAVSNAVARLKVMFND 66 (314)
T ss_pred hHHHHHHHHHHhcCCHHHHHHHhCCCHHHHHHHHHHHHHhhCC
Confidence 3445566666677779999999999999999999999998874
No 354
>PRK12680 transcriptional regulator CysB-like protein; Reviewed
Probab=39.15 E-value=26 Score=31.94 Aligned_cols=46 Identities=13% Similarity=0.169 Sum_probs=34.9
Q ss_pred HHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH-hccc
Q psy672 44 RLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ-AHVN 89 (314)
Q Consensus 44 ~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~-~~~~ 89 (314)
+|-+++....++.+++..|+..+||+++|++.+++.-+.+.. ++.+
T Consensus 5 ~L~~F~~vae~~gS~s~AA~~L~isQpavS~~I~~LE~~lG~~LF~R 51 (327)
T PRK12680 5 QLRYLVAIADAELNITLAAARVHATQPGLSKQLKQLEDELGFLLFVR 51 (327)
T ss_pred HHHHHHHHHHccCCHHHHHHHhcCCchHHHHHHHHHHHHhCCeEEEE
Confidence 333333333346789999999999999999999999998885 4433
No 355
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=39.14 E-value=16 Score=26.52 Aligned_cols=25 Identities=24% Similarity=0.364 Sum_probs=20.6
Q ss_pred ccccCCcccccHHHHHHHHHHHHHH
Q psy672 58 QIFTGDSHGVSQPTMCRLVKEVSKA 82 (314)
Q Consensus 58 ~~~l~~~fgis~stv~~~~~~v~~~ 82 (314)
..++++.+|+|++|+++.+.+....
T Consensus 2 ~~ela~~l~is~stvs~~l~~L~~~ 26 (96)
T smart00529 2 TSEIAERLNVSPPTVTQMLKKLEKD 26 (96)
T ss_pred HHHHHHHhCCChHHHHHHHHHHHHC
Confidence 3568889999999999998887663
No 356
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=39.08 E-value=8.1 Score=34.96 Aligned_cols=22 Identities=23% Similarity=0.184 Sum_probs=19.5
Q ss_pred cccccCCcccccHHHHHHHHHH
Q psy672 57 FQIFTGDSHGVSQPTMCRLVKE 78 (314)
Q Consensus 57 ~~~~l~~~fgis~stv~~~~~~ 78 (314)
+..++|+..|||++||+++++.
T Consensus 3 ti~dIA~~agVS~~TVSrvln~ 24 (327)
T PRK10339 3 TLKDIAIEAGVSLATVSRVLND 24 (327)
T ss_pred CHHHHHHHhCCCHHhhhhhhcC
Confidence 4578999999999999999874
No 357
>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=39.01 E-value=14 Score=25.66 Aligned_cols=27 Identities=26% Similarity=0.281 Sum_probs=23.3
Q ss_pred HhhcCCcccccCCcccccHHHHHHHHH
Q psy672 51 FYATGNFQIFTGDSHGVSQPTMCRLVK 77 (314)
Q Consensus 51 ~L~~g~~~~~l~~~fgis~stv~~~~~ 77 (314)
.-..|.+..++|...|+|++|++++.+
T Consensus 14 ~~~~~~t~~~lA~~~gis~~tis~~~~ 40 (78)
T TIGR02607 14 LEPLGLSIRALAKALGVSRSTLSRIVN 40 (78)
T ss_pred HHHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 455788899999999999999999865
No 358
>PRK11013 DNA-binding transcriptional regulator LysR; Provisional
Probab=38.89 E-value=26 Score=31.45 Aligned_cols=41 Identities=15% Similarity=0.093 Sum_probs=32.3
Q ss_pred HHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 44 RLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 44 ~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
+|-+++....+ .+++..|+..++|+|+|++.+++.-.-+-.
T Consensus 8 ~L~~f~av~~~-gS~s~AAe~L~isqsavS~~Ik~LE~~lg~ 48 (309)
T PRK11013 8 HIEIFHAVMTA-GSLTEAARLLHTSQPTVSRELARFEKVIGL 48 (309)
T ss_pred HHHHHHHHHHh-CcHHHHHHHHCCCcHHHHHHHHHHHHHhCc
Confidence 44444444444 589999999999999999999999988774
No 359
>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=38.83 E-value=17 Score=27.92 Aligned_cols=30 Identities=13% Similarity=-0.064 Sum_probs=25.1
Q ss_pred HHHhhcCCcccccCCcccccHHHHHHHHHH
Q psy672 49 IQFYATGNFQIFTGDSHGVSQPTMCRLVKE 78 (314)
Q Consensus 49 L~~L~~g~~~~~l~~~fgis~stv~~~~~~ 78 (314)
..+-..|.+..++|..+|+|++|+++|-+.
T Consensus 72 ~~r~~~gltq~~lA~~lg~~~~tis~~e~g 101 (127)
T TIGR03830 72 RIRKKLGLSQREAAELLGGGVNAFSRYERG 101 (127)
T ss_pred HHHHHcCCCHHHHHHHhCCCHHHHHHHHCC
Confidence 335567999999999999999999998663
No 360
>PRK10341 DNA-binding transcriptional activator TdcA; Provisional
Probab=38.39 E-value=25 Score=31.54 Aligned_cols=43 Identities=16% Similarity=0.259 Sum_probs=34.5
Q ss_pred HHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 43 TRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 43 ~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
.+.+-++.-++...++...|+..+||++++++.+++.-+.+..
T Consensus 9 ~~~L~~F~av~e~gs~s~AA~~L~iSQpavS~~I~~LE~~lg~ 51 (312)
T PRK10341 9 TQHLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGV 51 (312)
T ss_pred HHHHHHHHHHHHcCCHHHHHHHhCCChHHHHHHHHHHHHHhCC
Confidence 3334445556667788899999999999999999999998874
No 361
>PRK08558 adenine phosphoribosyltransferase; Provisional
Probab=38.00 E-value=23 Score=30.91 Aligned_cols=39 Identities=13% Similarity=0.067 Sum_probs=33.1
Q ss_pred CCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHH
Q psy672 39 QPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVK 77 (314)
Q Consensus 39 ~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~ 77 (314)
+-...++.-.|..|+..-+|++++..+|++.|.++||++
T Consensus 7 ~~~~~~~v~~lr~lk~~~ty~el~~~~g~p~~~l~RYv~ 45 (238)
T PRK08558 7 VRLQLRAVRVLRSLKKTYTYEELSSITGLPESVLNRYVN 45 (238)
T ss_pred HHHHHHHHHHHHHHhcccCHHHHHHHHCCCHHHHHHHHc
Confidence 334566777888899999999999999999999999975
No 362
>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=37.87 E-value=35 Score=26.53 Aligned_cols=42 Identities=10% Similarity=0.082 Sum_probs=32.8
Q ss_pred HHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHH
Q psy672 43 TRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALA 84 (314)
Q Consensus 43 ~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~ 84 (314)
+..-+.+.|+..|.+.+.+|...++|..++.+........|.
T Consensus 66 ~~~~ll~~~Yv~g~s~r~IA~~~~~s~~~ir~~l~~ae~~i~ 107 (125)
T PF06530_consen 66 EEYDLLILYYVYGWSKRQIARKLKCSEGKIRKRLQRAEGFID 107 (125)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHhhhhHh
Confidence 345566667778999999999999999999887776555444
No 363
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=37.73 E-value=27 Score=27.79 Aligned_cols=36 Identities=14% Similarity=0.179 Sum_probs=26.1
Q ss_pred CcccccCCcccccHHHHHHHHH--H-HHHHHHHhccccc
Q psy672 56 NFQIFTGDSHGVSQPTMCRLVK--E-VSKALAQAHVNYV 91 (314)
Q Consensus 56 ~~~~~l~~~fgis~stv~~~~~--~-v~~~l~~~~~~~i 91 (314)
.+...+|...||+++|+++|-+ + |+..+..+..++.
T Consensus 35 ~T~~eiAee~Gis~~tLYrWr~~~~~Fiey~n~la~~~~ 73 (142)
T PF13022_consen 35 RTQAEIAEEVGISRSTLYRWRQQNKAFIEYKNELADRFL 73 (142)
T ss_dssp S-HHHHHHHHTS-HHHHHHHHHH-HHHHHHHHHHHHHHH
T ss_pred chHHHHHHHhCCCHHHHHHHHhcCHHHHHHHHHHHHHHH
Confidence 5678999999999999999985 3 6666665554443
No 364
>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=37.59 E-value=11 Score=33.92 Aligned_cols=21 Identities=19% Similarity=0.135 Sum_probs=18.4
Q ss_pred ccccCCcccccHHHHHHHHHH
Q psy672 58 QIFTGDSHGVSQPTMCRLVKE 78 (314)
Q Consensus 58 ~~~l~~~fgis~stv~~~~~~ 78 (314)
..++|+..|||.+||+++++.
T Consensus 2 i~dIA~~aGVS~~TVSrvLn~ 22 (327)
T TIGR02417 2 LSDIAKLAGVSKTTASYVING 22 (327)
T ss_pred HHHHHHHhCCCHHHHHHHHcC
Confidence 468899999999999999874
No 365
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=37.52 E-value=16 Score=25.24 Aligned_cols=28 Identities=25% Similarity=0.070 Sum_probs=22.8
Q ss_pred HHhhcCCcccccCCcccccHHHHHHHHH
Q psy672 50 QFYATGNFQIFTGDSHGVSQPTMCRLVK 77 (314)
Q Consensus 50 ~~L~~g~~~~~l~~~fgis~stv~~~~~ 77 (314)
++-..|.++.++|...|||+.|+..+=+
T Consensus 9 ~R~~~~ltQ~elA~~vgVsRQTi~~iEk 36 (68)
T COG1476 9 LRAELGLTQEELAKLVGVSRQTIIAIEK 36 (68)
T ss_pred HHHHhCcCHHHHHHHcCcCHHHHHHHHc
Confidence 4455789999999999999999886543
No 366
>PRK15421 DNA-binding transcriptional regulator MetR; Provisional
Probab=37.45 E-value=32 Score=31.09 Aligned_cols=42 Identities=10% Similarity=0.111 Sum_probs=33.4
Q ss_pred HHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 43 TRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 43 ~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
.+|-.++....+| ++...|+..++|+++|++.+++.-..+-.
T Consensus 5 ~~L~~f~av~~~g-s~s~AA~~L~iSqpaVS~~Ik~LE~~lg~ 46 (317)
T PRK15421 5 KHLKTLQALRNCG-SLAAAAATLHQTQSALSHQFSDLEQRLGF 46 (317)
T ss_pred HHHHHHHHHHHcC-CHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 3444555555555 88999999999999999999999988874
No 367
>COG1508 RpoN DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription]
Probab=37.45 E-value=14 Score=35.33 Aligned_cols=22 Identities=18% Similarity=0.209 Sum_probs=19.2
Q ss_pred CcccccCCcccccHHHHHHHHH
Q psy672 56 NFQIFTGDSHGVSQPTMCRLVK 77 (314)
Q Consensus 56 ~~~~~l~~~fgis~stv~~~~~ 77 (314)
.+.+++|+.+|+++|||+|++.
T Consensus 331 L~LrdvA~~i~~HESTISRai~ 352 (444)
T COG1508 331 LVLRDVADEIGMHESTISRAIT 352 (444)
T ss_pred ccHHHHHHHhCccHHHHHHHHh
Confidence 4558999999999999999865
No 368
>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=37.11 E-value=12 Score=24.03 Aligned_cols=20 Identities=35% Similarity=0.416 Sum_probs=15.7
Q ss_pred ccccCCcccccHHHHHHHHH
Q psy672 58 QIFTGDSHGVSQPTMCRLVK 77 (314)
Q Consensus 58 ~~~l~~~fgis~stv~~~~~ 77 (314)
..++++.+|+|++|+++.++
T Consensus 6 ~~ev~~~~g~s~~ti~~~~k 25 (51)
T PF05930_consen 6 IKEVAELLGVSRSTIYRLIK 25 (51)
T ss_dssp HHHHHHHHSS-HHHHHHHHH
T ss_pred HHHHHHHHCCCHHHHHHHHh
Confidence 35677889999999998887
No 369
>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=36.86 E-value=20 Score=26.11 Aligned_cols=35 Identities=9% Similarity=0.164 Sum_probs=26.0
Q ss_pred HHHHHHHHHhhcCCcccccCCcccccHHHHHHHHH
Q psy672 43 TRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVK 77 (314)
Q Consensus 43 ~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~ 77 (314)
..+..+|..++.-..+.++|+.-|||++|++++.+
T Consensus 31 ~~~~~~l~~~r~~~glSqLAe~~GIs~stLs~iE~ 65 (89)
T TIGR02684 31 AYIAHALGYIARARGMTQLARKTGLSRESLYKALS 65 (89)
T ss_pred HHHHHHHHHHHHHCChHHHHHHHCCCHHHHHHHHc
Confidence 34556666666554555799999999999998865
No 370
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=36.68 E-value=40 Score=25.08 Aligned_cols=24 Identities=21% Similarity=0.340 Sum_probs=21.0
Q ss_pred cccCCcccccHHHHHHHHHHHHHH
Q psy672 59 IFTGDSHGVSQPTMCRLVKEVSKA 82 (314)
Q Consensus 59 ~~l~~~fgis~stv~~~~~~v~~~ 82 (314)
.++++..+++++++++.+++....
T Consensus 40 ~~la~~l~i~~~~vt~~l~~Le~~ 63 (126)
T COG1846 40 KELAERLGLDRSTVTRLLKRLEDK 63 (126)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHC
Confidence 899999999999999988877653
No 371
>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=36.49 E-value=11 Score=23.36 Aligned_cols=21 Identities=19% Similarity=-0.016 Sum_probs=16.5
Q ss_pred ccccCCcccccHHHHHHHHHH
Q psy672 58 QIFTGDSHGVSQPTMCRLVKE 78 (314)
Q Consensus 58 ~~~l~~~fgis~stv~~~~~~ 78 (314)
..++|+.+||+.+|+..|..+
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~~ 23 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYERI 23 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 356788899999999888544
No 372
>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B.
Probab=36.42 E-value=10 Score=25.41 Aligned_cols=25 Identities=24% Similarity=0.092 Sum_probs=17.7
Q ss_pred cccccCCcccccHHHHHHHHHHHHHH
Q psy672 57 FQIFTGDSHGVSQPTMCRLVKEVSKA 82 (314)
Q Consensus 57 ~~~~l~~~fgis~stv~~~~~~v~~~ 82 (314)
+...+|+.+|||+++|+.| ...+.+
T Consensus 11 ~~~~lAkalGVs~~aVs~W-~~~IP~ 35 (60)
T PF14549_consen 11 GQSKLAKALGVSPQAVSQW-GERIPA 35 (60)
T ss_dssp SHHHHHHHHTS-HHHHHHH-HTS--H
T ss_pred CHHHHHHHHCCCHHHHHHh-cCccCH
Confidence 5568899999999999999 444443
No 373
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=36.30 E-value=30 Score=30.80 Aligned_cols=41 Identities=17% Similarity=0.148 Sum_probs=32.5
Q ss_pred HHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 45 LLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 45 l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
.+-++..+....++...|+..++|+++|++.+++.-..+-.
T Consensus 9 ~L~~f~~v~~~gs~s~AA~~L~isQ~avS~~i~~LE~~lG~ 49 (302)
T PRK09791 9 QIRAFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAA 49 (302)
T ss_pred HHHHHHHHHHcCCHHHHHHHhCCChHHHHHHHHHHHHHhCC
Confidence 33344444445589999999999999999999999998874
No 374
>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=36.16 E-value=32 Score=28.87 Aligned_cols=41 Identities=12% Similarity=0.071 Sum_probs=28.1
Q ss_pred HHHHHHHHHHh-h-c--CCcccccCCccccc-HHHHHHHHHHHHHH
Q psy672 42 MTRLLAVIQFY-A-T--GNFQIFTGDSHGVS-QPTMCRLVKEVSKA 82 (314)
Q Consensus 42 ~~~l~~~L~~L-~-~--g~~~~~l~~~fgis-~stv~~~~~~v~~~ 82 (314)
+.+++-+|.-. . + ..+.+++|+.+|++ ++||++.+.+..+.
T Consensus 8 q~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~~L~~~ 53 (199)
T TIGR00498 8 QQEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLKALERK 53 (199)
T ss_pred HHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHHHHHHC
Confidence 34455555433 1 2 25667999999998 99999888776653
No 375
>PRK09801 transcriptional activator TtdR; Provisional
Probab=36.08 E-value=37 Score=30.57 Aligned_cols=45 Identities=11% Similarity=0.124 Sum_probs=34.3
Q ss_pred CHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 40 PPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 40 s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
+.-.+|-.++ .++...++...|+.+++|+++|++.+++.-+.|-.
T Consensus 6 ~~~~~L~~F~-~v~~~gs~t~AA~~L~iSQpavS~~I~~LE~~LG~ 50 (310)
T PRK09801 6 PLAKDLQVLV-EIVHSGSFSAAAATLGQTPAFVTKRIQILENTLAT 50 (310)
T ss_pred HHHHHHHHHH-HHHHcCCHHHHHHHhCcCHHHHHHHHHHHHHHhCC
Confidence 3444554444 45555678889999999999999999999988774
No 376
>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=35.64 E-value=82 Score=23.11 Aligned_cols=40 Identities=18% Similarity=0.268 Sum_probs=25.7
Q ss_pred HHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHH
Q psy672 41 PMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVS 80 (314)
Q Consensus 41 ~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~ 80 (314)
.+.-+.+.=-||-.|.+-..+++++||++|-.++.+.+.-
T Consensus 39 S~kiI~AL~dyLV~G~srkeac~~~gV~~syfs~~L~rL~ 78 (91)
T PF03333_consen 39 SEKIIAALRDYLVDGLSRKEACERHGVNQSYFSRALNRLN 78 (91)
T ss_dssp -HHHHHHHHHHHTT---HHHHHHHTT--HHHHHHHHHHHH
T ss_pred cHHHHHHHHHHHHcCCcHHHHHHHhCCCHHHHHHHHHHHH
Confidence 3444445556799999999999999999998887766544
No 377
>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=35.52 E-value=31 Score=30.87 Aligned_cols=42 Identities=5% Similarity=0.126 Sum_probs=33.8
Q ss_pred HHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 44 RLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 44 ~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
..+-++.-++...++...|+.++||++||++.+++.-..|-.
T Consensus 11 ~~L~~F~~va~~gs~s~AA~~L~isQpavS~~I~~LE~~lg~ 52 (302)
T TIGR02036 11 SKMHTFEVAARHQSFSLAAEELSLTPSAISHRINQLEEELGI 52 (302)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHCCCHHHHHHHHHHHHHHhCC
Confidence 334445556667788899999999999999999999988774
No 378
>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=34.89 E-value=12 Score=33.77 Aligned_cols=22 Identities=27% Similarity=0.243 Sum_probs=19.2
Q ss_pred cccccCCcccccHHHHHHHHHH
Q psy672 57 FQIFTGDSHGVSQPTMCRLVKE 78 (314)
Q Consensus 57 ~~~~l~~~fgis~stv~~~~~~ 78 (314)
+..++|+.-|||.+|||++++.
T Consensus 3 ti~dIA~~agvS~~TVSrvLn~ 24 (329)
T TIGR01481 3 TIYDVAREAGVSMATVSRVVNG 24 (329)
T ss_pred cHHHHHHHhCCCHHHHHHHhCC
Confidence 4578999999999999999864
No 379
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=34.88 E-value=39 Score=29.66 Aligned_cols=40 Identities=15% Similarity=0.095 Sum_probs=30.2
Q ss_pred HHHHHHHHHHhhcC--CcccccCCcccccHHHHHHHHHHHHH
Q psy672 42 MTRLLAVIQFYATG--NFQIFTGDSHGVSQPTMCRLVKEVSK 81 (314)
Q Consensus 42 ~~~l~~~L~~L~~g--~~~~~l~~~fgis~stv~~~~~~v~~ 81 (314)
+++....|.+|... .+..++++.||||++|+.|.++...+
T Consensus 4 ~~R~~~Il~~l~~~~~~~~~ela~~l~vS~~TirRdL~~Le~ 45 (251)
T PRK13509 4 AQRHQILLELLAQLGFVTVEKVIERLGISPATARRDINKLDE 45 (251)
T ss_pred HHHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 34555556666644 56678999999999999999998755
No 380
>PF00665 rve: Integrase core domain; InterPro: IPR001584 Integrase comprises three domains capable of folding independently and whose three-dimensional structures are known. However, the manner in which the N-terminal, catalytic, and C-terminal domains interact in the holoenzyme remains obscure. Numerous studies indicate that the enzyme functions as a multimer, minimally a dimer. The integrase proteins from Human immunodeficiency virus 1 (HIV-1) and Avian sarcoma virus (ASV) have been studied most carefully with respect to the structural basis of catalysis. Although the active site of ASV integrase does not undergo significant conformational changes on binding the required metal cofactor, that of HIV-1 does. This active site-mediated conformational change in HIV-1 reorganises the catalytic core and C-terminal domains and appears to promote an interaction that is favourable for catalysis []. Retroviral integrase is synthesised as part of the POL polyprotein that contains; an aspartyl protease, a reverse transcriptase, RNase H and integrase. POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. The presence of retrovirus integrase-related gene sequences in eukaryotes is known. Bacterial transposases involved in the transposition of the insertion sequence also belong to this group. HIV integrase catalyses the incorporation of virally derived DNA into the human genome. This unique step in the virus life cycle provides a variety of points for intervention and hence is an attractive target for the development of new therapeutics for the treatment of AIDS []. Substrate recognition by the retroviral integrase enzyme is critical for retroviral integration. To catalyse this recombination event, integrase must recognise and act on two types of substrates, viral DNA and host DNA, yet the necessary interactions exhibit markedly different degrees of specificity [].; GO: 0015074 DNA integration; PDB: 3AO3_A 3OVN_A 3AO5_A 3AO4_A 3AO1_A 1C6V_D 3HPG_A 3HPH_A 3OYD_A 3OYF_B ....
Probab=34.76 E-value=15 Score=27.57 Aligned_cols=16 Identities=38% Similarity=0.414 Sum_probs=13.2
Q ss_pred hHHHHHHHHHHHHhhh
Q psy672 225 TRNSVERLFGIWKRRF 240 (314)
Q Consensus 225 ~R~~vE~~fg~lK~rf 240 (314)
....||+.++.||.+|
T Consensus 105 ~ng~vEr~~~~l~~~~ 120 (120)
T PF00665_consen 105 QNGFVERFNRTLKRRI 120 (120)
T ss_dssp HHHHHHHHHHHHHHHH
T ss_pred hccHHHHHHHHHHHhC
Confidence 4457999999999876
No 381
>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=34.37 E-value=16 Score=24.59 Aligned_cols=21 Identities=19% Similarity=0.056 Sum_probs=17.7
Q ss_pred ccccCCcccccHHHHHHHHHH
Q psy672 58 QIFTGDSHGVSQPTMCRLVKE 78 (314)
Q Consensus 58 ~~~l~~~fgis~stv~~~~~~ 78 (314)
..++|+.+|||.+|+.+|.++
T Consensus 3 ~~eva~~~gvs~~tlr~w~~~ 23 (68)
T cd01104 3 IGAVARLTGVSPDTLRAWERR 23 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 357888999999999998765
No 382
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=34.32 E-value=28 Score=28.35 Aligned_cols=29 Identities=10% Similarity=0.083 Sum_probs=24.9
Q ss_pred cCCcccccCCcccccHHHHHHHHHHHHHH
Q psy672 54 TGNFQIFTGDSHGVSQPTMCRLVKEVSKA 82 (314)
Q Consensus 54 ~g~~~~~l~~~fgis~stv~~~~~~v~~~ 82 (314)
.-.++.++|+..|+|++||.+-+++..+.
T Consensus 27 ~R~s~~eiA~~lglS~~tv~~Ri~rL~~~ 55 (164)
T PRK11169 27 GRISNVELSKRVGLSPTPCLERVRRLERQ 55 (164)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 34788999999999999999988887764
No 383
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=34.26 E-value=12 Score=34.05 Aligned_cols=22 Identities=23% Similarity=0.200 Sum_probs=19.2
Q ss_pred cccccCCcccccHHHHHHHHHH
Q psy672 57 FQIFTGDSHGVSQPTMCRLVKE 78 (314)
Q Consensus 57 ~~~~l~~~fgis~stv~~~~~~ 78 (314)
+..++|+.-|||.+||+++++.
T Consensus 3 ti~dIA~~aGVS~~TVSrvLn~ 24 (343)
T PRK10727 3 TIKDVARLAGVSVATVSRVINN 24 (343)
T ss_pred CHHHHHHHhCCCHHHHHHHhCC
Confidence 4578999999999999999863
No 384
>PRK13348 chromosome replication initiation inhibitor protein; Provisional
Probab=34.14 E-value=33 Score=30.38 Aligned_cols=38 Identities=11% Similarity=0.082 Sum_probs=30.9
Q ss_pred HHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 48 VIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 48 ~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
++.-++...++...|+..++|++++++.+++.-+.+-.
T Consensus 9 ~f~~v~~~gs~t~AA~~L~iSQ~avS~~i~~LE~~lg~ 46 (294)
T PRK13348 9 ALAAVVETGSFERAARRLHVTPSAVSQRIKALEESLGQ 46 (294)
T ss_pred HHHHHHHcCCHHHHHHHhCCCchHHHHHHHHHHHHhCc
Confidence 33344445688999999999999999999999988774
No 385
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=34.14 E-value=31 Score=30.40 Aligned_cols=41 Identities=12% Similarity=0.055 Sum_probs=33.3
Q ss_pred HHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 45 LLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 45 l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
.+-++.-++...++...|+..+||++++++.+++.-..+..
T Consensus 7 ~L~~f~~v~e~~s~t~AA~~L~isqpavS~~I~~LE~~lg~ 47 (290)
T PRK10837 7 QLEVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGV 47 (290)
T ss_pred HHHHHHHHHHcCCHHHHHHHhCCCccHHHHHHHHHHHHhCC
Confidence 34445555556689999999999999999999999988763
No 386
>PF07453 NUMOD1: NUMOD1 domain; InterPro: IPR010896 This helix-turn-helix-containing DNA-binding domain is found associated in homing nucleases [].
Probab=34.12 E-value=10 Score=22.37 Aligned_cols=22 Identities=14% Similarity=0.090 Sum_probs=17.6
Q ss_pred cCCcccccCCcccccHHHHHHH
Q psy672 54 TGNFQIFTGDSHGVSQPTMCRL 75 (314)
Q Consensus 54 ~g~~~~~l~~~fgis~stv~~~ 75 (314)
...+.++.++.+|++++|++++
T Consensus 15 ~F~Si~eAa~~l~i~~~~I~~~ 36 (37)
T PF07453_consen 15 SFDSIREAARYLGISHSTISKY 36 (37)
T ss_pred EEcCHHHHHHHhCCCHHHHHHh
Confidence 3456678888999999998876
No 387
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=34.08 E-value=27 Score=29.72 Aligned_cols=33 Identities=15% Similarity=0.151 Sum_probs=26.6
Q ss_pred HHHHHhhcC---CcccccCCcccccHHHHHHHHHHH
Q psy672 47 AVIQFYATG---NFQIFTGDSHGVSQPTMCRLVKEV 79 (314)
Q Consensus 47 ~~L~~L~~g---~~~~~l~~~fgis~stv~~~~~~v 79 (314)
-.|..++.| .+..++|+..+||..||.+++...
T Consensus 166 ~Vl~~~~~g~~g~s~~eIa~~l~iS~~Tv~~~~~~~ 201 (225)
T PRK10046 166 AVRKLFKEPGVQHTAETVAQALTISRTTARRYLEYC 201 (225)
T ss_pred HHHHHHHcCCCCcCHHHHHHHhCccHHHHHHHHHHH
Confidence 345666764 688999999999999999998643
No 388
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=34.00 E-value=37 Score=29.88 Aligned_cols=40 Identities=10% Similarity=0.037 Sum_probs=33.7
Q ss_pred HHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 46 LAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 46 ~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
+-++..++...++...|+..++|++++++.+++.-..+-.
T Consensus 6 l~~f~~v~~~gs~s~AA~~L~isqpavS~~I~~LE~~lG~ 45 (275)
T PRK03601 6 LKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGV 45 (275)
T ss_pred HHHHHHHHHcCCHHHHHHHhCCChHHHHHHHHHHHHHhCC
Confidence 4455566777788899999999999999999999998774
No 389
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=33.67 E-value=31 Score=30.48 Aligned_cols=37 Identities=19% Similarity=0.231 Sum_probs=30.5
Q ss_pred HHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 49 IQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 49 L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
+..+....+++..|+..++|+|+|++.+++.-..+..
T Consensus 9 f~~v~~~gs~s~AA~~L~isqsavS~~i~~LE~~lg~ 45 (296)
T PRK11242 9 FLAVAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGV 45 (296)
T ss_pred HHHHHHhCCHHHHHHHcCCCchHHHHHHHHHHHHhCC
Confidence 3344445688999999999999999999999988774
No 390
>PRK09191 two-component response regulator; Provisional
Probab=33.46 E-value=41 Score=29.04 Aligned_cols=49 Identities=14% Similarity=0.149 Sum_probs=38.8
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHhc
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAH 87 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~ 87 (314)
.+|+.++-.+.|.++ .|.++.++|+..|+|.+||...+.+....+.+..
T Consensus 88 ~L~~~~r~v~~l~~~-~~~s~~eIA~~l~~s~~tV~~~l~ra~~~l~~~~ 136 (261)
T PRK09191 88 GLTPLPRQAFLLTAL-EGFSVEEAAEILGVDPAEAEALLDDARAEIARQV 136 (261)
T ss_pred hCCHHHhHHHHHHHH-hcCCHHHHHHHHCCCHHHHHHHHHHHHHHHhccC
Confidence 466676666665554 5677999999999999999999999888888643
No 391
>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=33.37 E-value=46 Score=22.62 Aligned_cols=26 Identities=15% Similarity=0.127 Sum_probs=19.1
Q ss_pred CCcccccCCccccc-HHHHHHHHHHHH
Q psy672 55 GNFQIFTGDSHGVS-QPTMCRLVKEVS 80 (314)
Q Consensus 55 g~~~~~l~~~fgis-~stv~~~~~~v~ 80 (314)
..+.+++++.||++ .+||+.++....
T Consensus 25 ~Pt~rEIa~~~g~~S~~tv~~~L~~Le 51 (65)
T PF01726_consen 25 PPTVREIAEALGLKSTSTVQRHLKALE 51 (65)
T ss_dssp ---HHHHHHHHTSSSHHHHHHHHHHHH
T ss_pred CCCHHHHHHHhCCCChHHHHHHHHHHH
Confidence 36778999999996 889988876544
No 392
>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=33.19 E-value=35 Score=30.28 Aligned_cols=39 Identities=13% Similarity=0.186 Sum_probs=31.5
Q ss_pred HHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 47 AVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 47 ~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
-.+.-+....++...|+..+||++++++.+++.-..+..
T Consensus 9 ~~f~~v~~~gS~s~AA~~L~isq~avS~~I~~LE~~lg~ 47 (300)
T TIGR02424 9 QCFVEVARQGSVKRAAEALHITQPAVSKTLRELEEILGT 47 (300)
T ss_pred HHHHHHHHhCCHHHHHHHhCCChHHHHHHHHHHHHHhCC
Confidence 333444455588999999999999999999999998874
No 393
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=33.13 E-value=15 Score=33.81 Aligned_cols=22 Identities=23% Similarity=0.212 Sum_probs=18.9
Q ss_pred cccccCCcccccHHHHHHHHHH
Q psy672 57 FQIFTGDSHGVSQPTMCRLVKE 78 (314)
Q Consensus 57 ~~~~l~~~fgis~stv~~~~~~ 78 (314)
+..++|+.-|||.+|||++++.
T Consensus 2 TikDVA~~AGVS~sTVSrvln~ 23 (333)
T COG1609 2 TIKDVAKLAGVSKATVSRVLNG 23 (333)
T ss_pred CHHHHHHHhCCCHHHHHHHHcC
Confidence 4568899999999999999874
No 394
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=32.80 E-value=24 Score=27.69 Aligned_cols=28 Identities=11% Similarity=-0.058 Sum_probs=23.3
Q ss_pred HhhcCCcccccCCcccccHHHHHHHHHH
Q psy672 51 FYATGNFQIFTGDSHGVSQPTMCRLVKE 78 (314)
Q Consensus 51 ~L~~g~~~~~l~~~fgis~stv~~~~~~ 78 (314)
+-..|.++.++|...|||.+|+++|.+.
T Consensus 14 R~~~gltq~~lA~~~gvs~~~is~~E~g 41 (135)
T PRK09706 14 RKQLKLSQRSLAKAVKVSHVSISQWERD 41 (135)
T ss_pred HHHcCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 3456788899999999999999987653
No 395
>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=32.54 E-value=24 Score=28.92 Aligned_cols=37 Identities=16% Similarity=0.140 Sum_probs=30.2
Q ss_pred HHHHHHHHHHhhcCCcccccCCccc-ccHHHHHHHHHH
Q psy672 42 MTRLLAVIQFYATGNFQIFTGDSHG-VSQPTMCRLVKE 78 (314)
Q Consensus 42 ~~~l~~~L~~L~~g~~~~~l~~~fg-is~stv~~~~~~ 78 (314)
++++...-.+++.|.+..+||..+| +|+..|.-.+++
T Consensus 5 de~~~~L~~lw~~G~SasqIA~~lg~vsRnAViGk~hR 42 (162)
T PF07750_consen 5 DERVERLRKLWAEGLSASQIARQLGGVSRNAVIGKAHR 42 (162)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHhCCcchhhhhhhhhc
Confidence 5566666667899999999999999 999988766665
No 396
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=32.43 E-value=43 Score=24.78 Aligned_cols=27 Identities=15% Similarity=0.069 Sum_probs=22.4
Q ss_pred cCCcccccCCcccccHHHHHHHHHHHH
Q psy672 54 TGNFQIFTGDSHGVSQPTMCRLVKEVS 80 (314)
Q Consensus 54 ~g~~~~~l~~~fgis~stv~~~~~~v~ 80 (314)
...+..++|+.+|+|.+++.+.|++..
T Consensus 20 ~~~~~~~lA~~~~~S~~~l~r~f~~~~ 46 (107)
T PRK10219 20 QPLNIDVVAKKSGYSKWYLQRMFRTVT 46 (107)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 335667889999999999999999874
No 397
>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=31.92 E-value=28 Score=30.29 Aligned_cols=37 Identities=19% Similarity=0.213 Sum_probs=31.2
Q ss_pred HHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 49 IQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 49 L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
+.-++...++...|+..+||+|+|++.+++.-..+-.
T Consensus 5 f~~v~~~gs~~~AA~~L~isqsavS~~i~~LE~~lg~ 41 (279)
T TIGR03339 5 FHAVARCGSFTRAAERLGLSQPTVTDQVRKLEERYGV 41 (279)
T ss_pred hHHHHhcCCHHHHHHHhcCCchHHHHHHHHHHHHhCC
Confidence 3445566788999999999999999999999988774
No 398
>PRK10632 transcriptional regulator; Provisional
Probab=31.91 E-value=36 Score=30.56 Aligned_cols=38 Identities=11% Similarity=0.014 Sum_probs=31.7
Q ss_pred HHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 48 VIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 48 ~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
++..++...++...|+..++|+++|++.+++.-..+-.
T Consensus 9 ~F~~v~e~gS~t~AA~~L~isQpavS~~I~~LE~~lg~ 46 (309)
T PRK10632 9 VFAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQV 46 (309)
T ss_pred HHHHHHhcCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 34455667788899999999999999999999988764
No 399
>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=31.52 E-value=18 Score=25.41 Aligned_cols=24 Identities=25% Similarity=0.167 Sum_probs=18.1
Q ss_pred CCcccccCCcccccHHHHHHHHHH
Q psy672 55 GNFQIFTGDSHGVSQPTMCRLVKE 78 (314)
Q Consensus 55 g~~~~~l~~~fgis~stv~~~~~~ 78 (314)
..+..++|+..|||.+||.|..+.
T Consensus 34 ~~si~elA~~~~vS~sti~Rf~kk 57 (77)
T PF01418_consen 34 FMSISELAEKAGVSPSTIVRFCKK 57 (77)
T ss_dssp T--HHHHHHHCTS-HHHHHHHHHH
T ss_pred HccHHHHHHHcCCCHHHHHHHHHH
Confidence 466789999999999999988765
No 400
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=31.34 E-value=43 Score=26.42 Aligned_cols=26 Identities=12% Similarity=0.181 Sum_probs=20.9
Q ss_pred CcccccCCcccccHHHHHHHHHHHHH
Q psy672 56 NFQIFTGDSHGVSQPTMCRLVKEVSK 81 (314)
Q Consensus 56 ~~~~~l~~~fgis~stv~~~~~~v~~ 81 (314)
.+..++++.+++|.+||++.+++...
T Consensus 23 ~~~~ela~~l~vs~~svs~~l~~L~~ 48 (142)
T PRK03902 23 ARVSDIAEALSVHPSSVTKMVQKLDK 48 (142)
T ss_pred cCHHHHHHHhCCChhHHHHHHHHHHH
Confidence 45578999999999999988776544
No 401
>PRK11482 putative DNA-binding transcriptional regulator; Provisional
Probab=31.23 E-value=42 Score=30.36 Aligned_cols=43 Identities=5% Similarity=0.100 Sum_probs=34.9
Q ss_pred HHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 43 TRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 43 ~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
.+.+-++.-+....+++..|+..++|++++++.+++.-..+-.
T Consensus 31 l~~L~~f~av~e~gs~s~AA~~L~isQpavS~~I~~LE~~lG~ 73 (317)
T PRK11482 31 LNLLTIFEAVYVHKGIVNAAKILNLTPSAISQSIQKLRVIFPD 73 (317)
T ss_pred hhHHHHHHHHHHcCCHHHHHHHhCCChHHHHHHHHHHHHHhCC
Confidence 3445555556666799999999999999999999999988764
No 402
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=31.18 E-value=49 Score=29.13 Aligned_cols=42 Identities=12% Similarity=0.114 Sum_probs=32.6
Q ss_pred HHHHHHHHHHHhhcC--CcccccCCcccccHHHHHHHHHHHHHH
Q psy672 41 PMTRLLAVIQFYATG--NFQIFTGDSHGVSQPTMCRLVKEVSKA 82 (314)
Q Consensus 41 ~~~~l~~~L~~L~~g--~~~~~l~~~fgis~stv~~~~~~v~~~ 82 (314)
.+++....|-+|... .+..++++.||||..|+.|-+....+.
T Consensus 3 ~~eR~~~Il~~L~~~~~v~v~eLa~~l~VS~~TIRRDL~~Le~~ 46 (256)
T PRK10434 3 PRQRQAAILEYLQKQGKTSVEELAQYFDTTGTTIRKDLVILEHA 46 (256)
T ss_pred HHHHHHHHHHHHHHcCCEEHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 356666667777754 466899999999999999998886554
No 403
>PRK10086 DNA-binding transcriptional regulator DsdC; Provisional
Probab=30.94 E-value=42 Score=30.15 Aligned_cols=41 Identities=10% Similarity=0.157 Sum_probs=34.2
Q ss_pred HHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 45 LLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 45 l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
-+-++..++...+++..|+..|+|++||++.+++.-+.+-.
T Consensus 18 ~L~~f~~va~~gs~s~AA~~L~iSQpavS~~I~~LE~~lG~ 58 (311)
T PRK10086 18 KLHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGI 58 (311)
T ss_pred HHHHHHHHHHcCCHHHHHHHHCCCHHHHHHHHHHHHHHhCC
Confidence 34555566677788999999999999999999999998864
No 404
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=30.86 E-value=48 Score=24.42 Aligned_cols=27 Identities=19% Similarity=0.101 Sum_probs=22.3
Q ss_pred hhcCCcccccCCcccccHHHHHHHHHH
Q psy672 52 YATGNFQIFTGDSHGVSQPTMCRLVKE 78 (314)
Q Consensus 52 L~~g~~~~~l~~~fgis~stv~~~~~~ 78 (314)
-.++......|+..|||++|+.+..++
T Consensus 65 ~~~~gn~s~AAr~LGIsRsTL~rKLkr 91 (95)
T PRK00430 65 QYTRGNQTRAALMLGINRGTLRKKLKK 91 (95)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 346677888999999999999988775
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=30.51 E-value=24 Score=30.39 Aligned_cols=46 Identities=17% Similarity=0.214 Sum_probs=28.4
Q ss_pred hhHHhhhhhhccc-CCCCCCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHH
Q psy672 20 IIFPLARNVLETN-TMQGVKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSK 81 (314)
Q Consensus 20 ~L~~~l~~~~~~~-~~~~~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~ 81 (314)
.|.+.|+..+... -..+..+|.|.+| ++.||||+.||.+.+.....
T Consensus 4 qi~~~l~~~I~~g~~~~G~~LPsE~eL----------------a~~~gVSR~TVR~Al~~L~~ 50 (233)
T TIGR02404 4 QIYQDLEQKITHGQYKEGDYLPSEHEL----------------MDQYGASRETVRKALNLLTE 50 (233)
T ss_pred HHHHHHHHHHHhCCCCCCCCCcCHHHH----------------HHHHCCCHHHHHHHHHHHHH
Confidence 3444455444321 1234567777665 55899999999877766554
No 406
>smart00497 IENR1 Intron encoded nuclease repeat motif. Repeat of unknown function, but possibly DNA-binding via helix-turn-helix motif (Ponting, unpublished).
Probab=30.48 E-value=20 Score=22.76 Aligned_cols=24 Identities=8% Similarity=0.076 Sum_probs=19.3
Q ss_pred CCcccccCCcccccHHHHHHHHHH
Q psy672 55 GNFQIFTGDSHGVSQPTMCRLVKE 78 (314)
Q Consensus 55 g~~~~~l~~~fgis~stv~~~~~~ 78 (314)
..+..++++.+|++.++++++++.
T Consensus 17 f~S~~eAa~~lg~~~~~I~~~~~~ 40 (53)
T smart00497 17 FSSIREAAKYLGISHSSISKYLNT 40 (53)
T ss_pred ecCHHHHHHHhCCCHHHHHHHHhC
Confidence 346678888999999999988764
No 407
>PF01526 DDE_Tnp_Tn3: Tn3 transposase DDE domain; InterPro: IPR002513 Proteins containing this domain include transposases of Tn3, Tn21, Tn1721, Tn2501, Tn3926 transposons from Escherichia coli. The specific binding of the Tn3 transposase to DNA has been demonstrated. Sequence analysis has suggested that the invariant triad of Asp689, Asp765, Glu895 (numbering as in Tn3) may correspond to the D-D-35-E motif previously implicated in the catalytic performance of numerous transposases [].; GO: 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=30.47 E-value=4.7e+02 Score=24.70 Aligned_cols=121 Identities=15% Similarity=0.073 Sum_probs=67.1
Q ss_pred CCCCHHHHHHHHHHHhhcCCcccccCC-cccccHHHHHHHHHHHHH------HHHHhccccccCCCchhhhHHHhhhcCC
Q psy672 37 VKQPPMTRLLAVIQFYATGNFQIFTGD-SHGVSQPTMCRLVKEVSK------ALAQAHVNYVKFPEQLAPTKVAFQGIGN 109 (314)
Q Consensus 37 ~~~s~~~~l~~~L~~L~~g~~~~~l~~-~fgis~stv~~~~~~v~~------~l~~~~~~~i~~P~~~~~~~~~f~~~~~ 109 (314)
..-+....|+++|+=++++.....+|+ .-|+|...+..+-++.+. |...+...+-+.|-. +.+|
T Consensus 25 k~~~~~~~llA~l~A~GtNlGl~~mA~~~~~is~~~L~~v~~~~i~~etl~~An~~ivna~~~lpl~---------~~wG 95 (388)
T PF01526_consen 25 KPKDDQRRLLAALFAYGTNLGLKRMARASPGISYDQLSWVNRWYIREETLRAANARIVNAQHKLPLA---------KYWG 95 (388)
T ss_pred CccchHHHHHHHHHHhhhCCChHHHhhcCCCCCHHHHHHHHHHHHhHHHHHHHHHHHHHHHHhCChH---------HHcC
Confidence 345677888899988999988888888 668887766655544432 222222222233322 1223
Q ss_pred CCCceeeeeceEEEEecCCCCCCCcccCCCC-ceeeeeeeecCCcccEEEeecCCCCCcChh
Q psy672 110 FPGVVGCVDCTHVPIQLPSVENGENFRNRKG-TFSLNVQVIGGPNLEIWDVVSGWPGSVHDS 170 (314)
Q Consensus 110 ~p~~~g~iDgt~i~i~~P~~~~~~~y~~~k~-~~s~~~q~v~d~~g~i~~~~~~~pGs~~D~ 170 (314)
.+.....||+.+++..++- .+ .|+-|-+ .+++.+--.++.+.-.++..+- +++.+++
T Consensus 96 -~g~~aSsDGq~f~~~~~~~-~a-~~~~rY~~~~Gv~~Yt~vsd~~~~~~s~vI-~~~~~Ea 153 (388)
T PF01526_consen 96 -DGTTASSDGQKFETSDQNL-NA-RYNPRYGRGPGVSIYTHVSDQYIPFHSQVI-SCNEREA 153 (388)
T ss_pred -CCceeccceeEEEeecCcc-ch-hcCcccCCCCceEEEEeeccceeeeeeEEe-cCcchHH
Confidence 3556699999999987632 22 3333333 3344444444443333333332 4555554
No 408
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=30.36 E-value=1e+02 Score=26.66 Aligned_cols=49 Identities=12% Similarity=0.133 Sum_probs=30.7
Q ss_pred HHHHhhHHhhhhhhccc-CCCCCCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHH
Q psy672 16 VVLNIIFPLARNVLETN-TMQGVKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSK 81 (314)
Q Consensus 16 ~f~~~L~~~l~~~~~~~-~~~~~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~ 81 (314)
.+. .|.+.|+..+... -..+.++|.|.+| ++.||||+.||.+.+.....
T Consensus 10 ~y~-qI~~~i~~~I~~G~~~~g~kLPsE~eL----------------a~~~~VSR~TvR~Al~~L~~ 59 (241)
T PRK11402 10 LYA-TVRQRLLDDIAQGVYQAGQQIPTENEL----------------CTQYNVSRITIRKAISDLVA 59 (241)
T ss_pred HHH-HHHHHHHHHHHcCCCCCCCcCcCHHHH----------------HHHHCCCHHHHHHHHHHHHH
Confidence 345 5666666555321 1224467777655 55899999999877766554
No 409
>PRK13832 plasmid partitioning protein; Provisional
Probab=29.74 E-value=53 Score=32.03 Aligned_cols=43 Identities=12% Similarity=0.040 Sum_probs=37.1
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHH
Q psy672 35 QGVKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVK 77 (314)
Q Consensus 35 ~~~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~ 77 (314)
.+..+++.++...+-.....|.+..+||..||+|+++|.+...
T Consensus 98 QRedL~PiEea~AfkrLie~G~T~EeIA~~lG~S~~~V~rlll 140 (520)
T PRK13832 98 AREPLNPVDQWRAIERLVALGWTEEAIAVALALPVRQIRKLRL 140 (520)
T ss_pred CcCCCCHHHHHHHHHHHHhcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 4567889999888888889999999999999999999998543
No 410
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=29.62 E-value=50 Score=26.96 Aligned_cols=45 Identities=11% Similarity=0.079 Sum_probs=36.3
Q ss_pred CCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHH
Q psy672 38 KQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALA 84 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~ 84 (314)
.++..+. -.|.+|..|.+...+|+..++|..||..++.+...-|.
T Consensus 149 ~lt~re~--~vl~~l~~g~s~~eIa~~l~~s~~tv~~~~~~~~~kl~ 193 (210)
T PRK09935 149 VLSNREV--TILRYLVSGLSNKEIADQLLLSNKTVSAHKSNIYGKLG 193 (210)
T ss_pred cCCHHHH--HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence 3455554 44567989999999999999999999999998877664
No 411
>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=29.44 E-value=47 Score=29.34 Aligned_cols=38 Identities=11% Similarity=0.097 Sum_probs=30.9
Q ss_pred HHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 48 VIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 48 ~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
++..++...++...|+..++|++++++.+++.-+.|-.
T Consensus 8 ~f~~v~~~~s~t~AA~~L~isQpavS~~I~~LE~~lg~ 45 (292)
T TIGR03298 8 ALAAVVEEGSFERAAAALSVTPSAVSQRIKALEERLGQ 45 (292)
T ss_pred HHHHHHHcCCHHHHHHHhCCCHHHHHHHHHHHHHHhCc
Confidence 33344445589999999999999999999999988774
No 412
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=29.42 E-value=20 Score=26.99 Aligned_cols=26 Identities=23% Similarity=0.012 Sum_probs=20.1
Q ss_pred HhhcCCcccccCCcccccHHHHHHHH
Q psy672 51 FYATGNFQIFTGDSHGVSQPTMCRLV 76 (314)
Q Consensus 51 ~L~~g~~~~~l~~~fgis~stv~~~~ 76 (314)
+=+.+.++...|..+|+|.+||..|=
T Consensus 53 Re~~~lSQ~vFA~~L~vs~~Tv~~WE 78 (104)
T COG2944 53 REKLGLSQPVFARYLGVSVSTVRKWE 78 (104)
T ss_pred HHHhCCCHHHHHHHHCCCHHHHHHHH
Confidence 44567888888888899988888653
No 413
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=29.41 E-value=59 Score=28.58 Aligned_cols=41 Identities=17% Similarity=0.111 Sum_probs=30.0
Q ss_pred HHHHHHHHHHhhcC--CcccccCCcccccHHHHHHHHHHHHHH
Q psy672 42 MTRLLAVIQFYATG--NFQIFTGDSHGVSQPTMCRLVKEVSKA 82 (314)
Q Consensus 42 ~~~l~~~L~~L~~g--~~~~~l~~~fgis~stv~~~~~~v~~~ 82 (314)
.++....|.+|... .+..++++.|+||..|+.|.+....+.
T Consensus 4 ~~R~~~Il~~l~~~~~~~~~ela~~l~vS~~TiRRdL~~Le~~ 46 (252)
T PRK10906 4 TQRHDAIIELVKQQGYVSTEELVEHFSVSPQTIRRDLNDLAEQ 46 (252)
T ss_pred HHHHHHHHHHHHHcCCEeHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence 34555555566544 466789999999999999988877663
No 414
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=29.38 E-value=54 Score=28.12 Aligned_cols=32 Identities=3% Similarity=-0.151 Sum_probs=28.7
Q ss_pred hcCCcccccCCcccccHHHHHHHHHHHHHHHH
Q psy672 53 ATGNFQIFTGDSHGVSQPTMCRLVKEVSKALA 84 (314)
Q Consensus 53 ~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~ 84 (314)
+.|.+..++|..+++|..||..++.+......
T Consensus 176 ~~g~s~~eIA~~l~iS~~Tv~~~~~~~~~~~~ 207 (239)
T PRK10430 176 DYEFSTDELANAVNISRVSCRKYLIWLVNCHI 207 (239)
T ss_pred CCCcCHHHHHHHhCchHHHHHHHHHHHHhCCE
Confidence 58899999999999999999999998877655
No 415
>PRK13503 transcriptional activator RhaS; Provisional
Probab=29.06 E-value=74 Score=27.86 Aligned_cols=26 Identities=19% Similarity=0.078 Sum_probs=22.0
Q ss_pred CCcccccCCcccccHHHHHHHHHHHH
Q psy672 55 GNFQIFTGDSHGVSQPTMCRLVKEVS 80 (314)
Q Consensus 55 g~~~~~l~~~fgis~stv~~~~~~v~ 80 (314)
..+..++|+.+|+|+++++++|++..
T Consensus 187 ~~tl~~lA~~~~lS~~~l~r~Fk~~~ 212 (278)
T PRK13503 187 EVNWEALADQFSLSLRTLHRQLKQQT 212 (278)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHh
Confidence 45567889999999999999998875
No 416
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=29.05 E-value=31 Score=20.80 Aligned_cols=26 Identities=27% Similarity=0.270 Sum_probs=20.2
Q ss_pred hhcCCcccccCCcccccHHHHHHHHH
Q psy672 52 YATGNFQIFTGDSHGVSQPTMCRLVK 77 (314)
Q Consensus 52 L~~g~~~~~l~~~fgis~stv~~~~~ 77 (314)
-..+.+..+++...|++.++++++..
T Consensus 7 ~~~~~s~~~la~~~~i~~~~i~~~~~ 32 (56)
T smart00530 7 EEKGLTQEELAEKLGVSRSTLSRIEN 32 (56)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHC
Confidence 34567788899999999998887543
No 417
>PRK10216 DNA-binding transcriptional regulator YidZ; Provisional
Probab=28.83 E-value=45 Score=30.05 Aligned_cols=41 Identities=10% Similarity=0.134 Sum_probs=32.5
Q ss_pred HHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 45 LLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 45 l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
.+-++.-+..-.++...|+.+++|+|++++.+.+.-..+..
T Consensus 12 ~L~~f~av~e~gs~t~AA~~L~iSQpavS~~I~~LE~~lg~ 52 (319)
T PRK10216 12 LLLCLQLLMQERSVTKAAKRMNVTPSAVSKSLAKLRAWFDD 52 (319)
T ss_pred HHHHHHHHHHhCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 33344444555588999999999999999999999998874
No 418
>PRK11564 stationary phase inducible protein CsiE; Provisional
Probab=28.77 E-value=80 Score=29.96 Aligned_cols=50 Identities=10% Similarity=0.073 Sum_probs=36.9
Q ss_pred CCCCHHHHHHHHH-HHhh--cCCcccccCCcccccHHHHHHHHHHHHHHHHHh
Q psy672 37 VKQPPMTRLLAVI-QFYA--TGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQA 86 (314)
Q Consensus 37 ~~~s~~~~l~~~L-~~L~--~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 86 (314)
+.++++++....+ ..|- .+.+..++++.++||++|+.+-++++-..|.+.
T Consensus 9 ~~~s~~ER~~~il~~LL~~~~~v~l~~Lae~l~VSrsTi~~DLk~l~~~L~~y 61 (426)
T PRK11564 9 SVLSAPQRRCQILLMLFQPGLTVTLETFSQLNGVDDDTARQDIAETGREIQRY 61 (426)
T ss_pred cCCCHHHHHHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHHHHHHHHHHHh
Confidence 4566777655444 3343 335678999999999999999999998888763
No 419
>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=28.75 E-value=26 Score=28.29 Aligned_cols=38 Identities=18% Similarity=0.038 Sum_probs=29.4
Q ss_pred CCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHH
Q psy672 39 QPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKE 78 (314)
Q Consensus 39 ~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~ 78 (314)
.|+...+ --.+-..|.+..++|+..|||++++++|-+.
T Consensus 24 ~p~~~~I--r~~R~~lGmTq~eLAerlGVS~~tIs~iE~G 61 (150)
T TIGR02612 24 TPKEGWV--RAIRKALGMSGAQLAGRLGVTPQRVEALEKS 61 (150)
T ss_pred cCcHHHH--HHHHHHcCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 4444443 3346778999999999999999999988774
No 420
>PRK11139 DNA-binding transcriptional activator GcvA; Provisional
Probab=28.39 E-value=44 Score=29.62 Aligned_cols=42 Identities=17% Similarity=0.053 Sum_probs=32.8
Q ss_pred HHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 43 TRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 43 ~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
.+|-+ +.-+....++...|+..++|++++++.+++.-+.+-.
T Consensus 9 ~~l~~-f~~v~~~gs~s~AA~~L~isq~avS~~i~~LE~~lg~ 50 (297)
T PRK11139 9 NALRA-FEAAARHLSFTRAAEELFVTQAAVSHQIKALEDFLGL 50 (297)
T ss_pred HHHHH-HHHHHHhCCHHHHHHHhCCChHHHHHHHHHHHHHhCc
Confidence 34444 4444455778899999999999999999999988774
No 421
>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=27.99 E-value=36 Score=20.68 Aligned_cols=25 Identities=28% Similarity=0.312 Sum_probs=20.4
Q ss_pred hcCCcccccCCcccccHHHHHHHHH
Q psy672 53 ATGNFQIFTGDSHGVSQPTMCRLVK 77 (314)
Q Consensus 53 ~~g~~~~~l~~~fgis~stv~~~~~ 77 (314)
..+.+..+++...|+|.++++++.+
T Consensus 10 ~~~~s~~~~a~~~~~~~~~v~~~~~ 34 (58)
T cd00093 10 EKGLTQEELAEKLGVSRSTISRIEN 34 (58)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHc
Confidence 4577888999999999998887654
No 422
>PRK10082 cell density-dependent motility repressor; Provisional
Probab=27.87 E-value=50 Score=29.43 Aligned_cols=41 Identities=20% Similarity=0.159 Sum_probs=33.5
Q ss_pred HHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 45 LLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 45 l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
.+-++.-++...++...|+..+||++++++.+++.-..|-.
T Consensus 15 ~l~~F~av~e~gS~t~AA~~L~iSQpavS~~I~~LE~~lG~ 55 (303)
T PRK10082 15 WLYDFLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGV 55 (303)
T ss_pred HHHHHHHHHhcCCHHHHHHHhCCChHHHHHHHHHHHHHcCC
Confidence 33445555666788899999999999999999999998874
No 423
>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=27.86 E-value=60 Score=29.85 Aligned_cols=45 Identities=11% Similarity=0.042 Sum_probs=36.0
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHH
Q psy672 35 QGVKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEV 79 (314)
Q Consensus 35 ~~~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v 79 (314)
.+..+|..++.......+..|.+...++..+|+++++|++++.-.
T Consensus 157 ~R~dLS~iE~A~~~~~L~~~G~~~~~ia~~Lg~~ks~vSr~lsl~ 201 (325)
T TIGR03454 157 ARRDLSFIERALFAQRLEDRGFDRDTIMAALSVDKTELSRMISVA 201 (325)
T ss_pred cccCCCHHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 345688888877666667788888889999999999999887644
No 424
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=27.76 E-value=63 Score=25.89 Aligned_cols=34 Identities=12% Similarity=-0.003 Sum_probs=29.1
Q ss_pred HhhcCCcccccCCcccccHHHHHHHHHHHHHHHH
Q psy672 51 FYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALA 84 (314)
Q Consensus 51 ~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~ 84 (314)
.+..|.+...+++.+|+|..||..++.+...-|.
T Consensus 152 ~~~~~~~~~~ia~~l~~s~~tv~~~~~~~~~kl~ 185 (202)
T PRK09390 152 GLVAGLSNKVIARDLDISPRTVEVYRANVMTKMQ 185 (202)
T ss_pred HHHccCchHHHHHHcCCCHHHHHHHHHHHHHHHc
Confidence 4666788899999999999999999988887764
No 425
>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=27.72 E-value=25 Score=23.60 Aligned_cols=26 Identities=15% Similarity=0.135 Sum_probs=21.8
Q ss_pred hcCCcccccCCcccccHHHHHHHHHH
Q psy672 53 ATGNFQIFTGDSHGVSQPTMCRLVKE 78 (314)
Q Consensus 53 ~~g~~~~~l~~~fgis~stv~~~~~~ 78 (314)
.++..+..+|...++++.||.+|...
T Consensus 14 ~~~GnqtEvaR~l~c~R~TVrKY~~D 39 (64)
T PF06322_consen 14 ETYGNQTEVARRLGCNRATVRKYSRD 39 (64)
T ss_pred HHhCcHHHHHHHhcccHHHHHHHhcc
Confidence 45677889999999999999988754
No 426
>PRK11074 putative DNA-binding transcriptional regulator; Provisional
Probab=27.69 E-value=49 Score=29.44 Aligned_cols=39 Identities=13% Similarity=0.033 Sum_probs=31.9
Q ss_pred HHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 47 AVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 47 ~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
-++..++.-.++...|+..+||++++++.+++.-..+-.
T Consensus 8 ~~f~~v~e~~s~s~AA~~L~isQpavS~~I~~LE~~lg~ 46 (300)
T PRK11074 8 EVVDAVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAV 46 (300)
T ss_pred HHHHHHHHhCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 344445555588999999999999999999999988875
No 427
>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=27.61 E-value=27 Score=28.67 Aligned_cols=26 Identities=31% Similarity=0.473 Sum_probs=21.9
Q ss_pred CcccccCCcccccHHHHHHHHHHHHH
Q psy672 56 NFQIFTGDSHGVSQPTMCRLVKEVSK 81 (314)
Q Consensus 56 ~~~~~l~~~fgis~stv~~~~~~v~~ 81 (314)
.+++.+++.+|+|++||++.+....+
T Consensus 76 ~t~~~ia~~l~iS~~Tv~r~ik~L~e 101 (165)
T PF05732_consen 76 ATQKEIAEKLGISKPTVSRAIKELEE 101 (165)
T ss_pred eeHHHHHHHhCCCHHHHHHHHHHHHh
Confidence 46678999999999999998887665
No 428
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=27.37 E-value=50 Score=30.04 Aligned_cols=37 Identities=16% Similarity=0.407 Sum_probs=27.5
Q ss_pred HHHHHHHhhcC--CcccccCCcccccHHHHHHHHHHHHH
Q psy672 45 LLAVIQFYATG--NFQIFTGDSHGVSQPTMCRLVKEVSK 81 (314)
Q Consensus 45 l~~~L~~L~~g--~~~~~l~~~fgis~stv~~~~~~v~~ 81 (314)
..-.|..|..+ .+..++|+.+|+|++||++.++...+
T Consensus 6 ~~~il~~L~~~~~~s~~~LA~~lgvsr~tV~~~l~~L~~ 44 (319)
T PRK11886 6 MLQLLSLLADGDFHSGEQLGEELGISRAAIWKHIQTLEE 44 (319)
T ss_pred HHHHHHHHHcCCCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 33344444543 45568999999999999999998886
No 429
>PRK03635 chromosome replication initiation inhibitor protein; Validated
Probab=27.37 E-value=53 Score=29.14 Aligned_cols=37 Identities=8% Similarity=0.087 Sum_probs=30.8
Q ss_pred HHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 49 IQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 49 L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
+.-++...+++..|+..++|++++++.+++.-..+-.
T Consensus 10 f~~v~e~gs~s~AA~~L~isq~avS~~I~~LE~~lg~ 46 (294)
T PRK03635 10 LAAVVREGSFERAAQKLHITQSAVSQRIKALEERVGQ 46 (294)
T ss_pred HHHHHHcCCHHHHHHHhCCChHHHHHHHHHHHHHhCc
Confidence 3344445588999999999999999999999988875
No 430
>PF03050 DDE_Tnp_IS66: Transposase IS66 family ; InterPro: IPR004291 Transposase proteins are necessary for efficient DNA transposition. This family includes the bacterial insertion sequence (IS) element, IS66, from Agrobacterium tumefaciens []. IS66 may cause genetic and structural variations of the T region and the vir region of the octopine Ti plasmids []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=27.31 E-value=73 Score=28.05 Aligned_cols=73 Identities=16% Similarity=0.019 Sum_probs=47.2
Q ss_pred CCHHHHHHHHHHHhhcCCcccccCCcc-----cccHHHHHHHHHHHHHHHHHhccccccCCCchhhhHHHhhhcCCCCCc
Q psy672 39 QPPMTRLLAVIQFYATGNFQIFTGDSH-----GVSQPTMCRLVKEVSKALAQAHVNYVKFPEQLAPTKVAFQGIGNFPGV 113 (314)
Q Consensus 39 ~s~~~~l~~~L~~L~~g~~~~~l~~~f-----gis~stv~~~~~~v~~~l~~~~~~~i~~P~~~~~~~~~f~~~~~~p~~ 113 (314)
+++.-.-.+++.....+.++..+.+.| .||.+|+.+++.++.+.+..+...... ... ..-
T Consensus 4 ~g~~~~a~i~~l~~~~~lp~~r~~~~~~~~G~~is~~ti~~~~~~~~~~l~~~~~~l~~----------~~~-----~~~ 68 (271)
T PF03050_consen 4 YGPSLLALIAYLKYVYHLPLYRIQQMLEDLGITISRGTIANWIKRVAEALKPLYEALKE----------ELR-----SSP 68 (271)
T ss_pred CCHHHHHHHHHHHhcCCCCHHHHhhhhhccceeeccchhHhHhhhhhhhhhhhhhhhhh----------hcc-----ccc
Confidence 344445555566666777777666665 689999999999999997754433221 111 112
Q ss_pred eeeeeceEEEEec
Q psy672 114 VGCVDCTHVPIQL 126 (314)
Q Consensus 114 ~g~iDgt~i~i~~ 126 (314)
+--+|-|.+++..
T Consensus 69 ~~~~DET~~~vl~ 81 (271)
T PF03050_consen 69 VVHADETGWRVLD 81 (271)
T ss_pred eeccCCceEEEec
Confidence 2368999888766
No 431
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=27.29 E-value=58 Score=25.16 Aligned_cols=27 Identities=15% Similarity=0.065 Sum_probs=22.6
Q ss_pred cCCcccccCCcccccHHHHHHHHHHHH
Q psy672 54 TGNFQIFTGDSHGVSQPTMCRLVKEVS 80 (314)
Q Consensus 54 ~g~~~~~l~~~fgis~stv~~~~~~v~ 80 (314)
...+..++|+.+|+|++++.+.|++..
T Consensus 24 ~~~sl~~lA~~~g~S~~~l~r~Fk~~~ 50 (127)
T PRK11511 24 SPLSLEKVSERSGYSKWHLQRMFKKET 50 (127)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 445667889999999999999999874
No 432
>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=27.11 E-value=22 Score=25.91 Aligned_cols=24 Identities=17% Similarity=0.003 Sum_probs=17.0
Q ss_pred cCCcccccCCcccccHHHHHHHHH
Q psy672 54 TGNFQIFTGDSHGVSQPTMCRLVK 77 (314)
Q Consensus 54 ~g~~~~~l~~~fgis~stv~~~~~ 77 (314)
.|.+..+||..+|.|++.|++++.
T Consensus 2 ~G~tq~eIA~~lGks~s~Vs~~l~ 25 (93)
T PF08535_consen 2 FGWTQEEIAKRLGKSRSWVSNHLA 25 (93)
T ss_dssp TT--HHHHHHHTT--HHHHHHHHG
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHH
Confidence 477888999999999999887765
No 433
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=27.04 E-value=44 Score=23.68 Aligned_cols=32 Identities=9% Similarity=0.057 Sum_probs=24.8
Q ss_pred hcCCcccccCCcccccHHHHHHHHHHHHHHHH
Q psy672 53 ATGNFQIFTGDSHGVSQPTMCRLVKEVSKALA 84 (314)
Q Consensus 53 ~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~ 84 (314)
....++..+.+..|++.+++++.+....++=+
T Consensus 12 ~~~~~f~~L~~~l~lt~g~Ls~hL~~Le~~Gy 43 (80)
T PF13601_consen 12 NEEATFSELKEELGLTDGNLSKHLKKLEEAGY 43 (80)
T ss_dssp HSEEEHHHHHHHTT--HHHHHHHHHHHHHTTS
T ss_pred cCCCCHHHHHHHhCcCHHHHHHHHHHHHHCCC
Confidence 35588999999999999999998887776544
No 434
>PRK09986 DNA-binding transcriptional activator XapR; Provisional
Probab=26.99 E-value=46 Score=29.29 Aligned_cols=41 Identities=17% Similarity=0.121 Sum_probs=32.3
Q ss_pred HHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 44 RLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 44 ~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
+|-+++....+ .++...|+..+||+|+|++.+++.-..+..
T Consensus 11 ~l~~f~~v~~~-gs~t~AA~~L~itq~avS~~i~~LE~~lg~ 51 (294)
T PRK09986 11 LLRYFLAVAEE-LHFGRAAARLNISQPPLSIHIKELEDQLGT 51 (294)
T ss_pred HHHHHHHHHHh-cCHHHHHHHhCCCCCHHHHHHHHHHHHhCC
Confidence 44444444444 488899999999999999999999998874
No 435
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=26.76 E-value=1.2e+02 Score=26.26 Aligned_cols=51 Identities=22% Similarity=0.242 Sum_probs=32.8
Q ss_pred HHHHHhhHHhhhhhhccc-CCCCCCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHH
Q psy672 15 DVVLNIIFPLARNVLETN-TMQGVKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKA 82 (314)
Q Consensus 15 ~~f~~~L~~~l~~~~~~~-~~~~~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~ 82 (314)
+-+. .|.+.|+..+... -..+.++|.|.. |++.||||+.||.+.+......
T Consensus 7 plY~-qI~~~i~~~I~~G~~~~G~~LPsE~e----------------La~~f~VSR~TvRkAL~~L~~e 58 (236)
T COG2188 7 PLYQ-QIAEDIRQRIESGELPPGDKLPSERE----------------LAEQFGVSRMTVRKALDELVEE 58 (236)
T ss_pred ccHH-HHHHHHHHHHHhCCCCCCCCCCCHHH----------------HHHHHCCcHHHHHHHHHHHHHC
Confidence 3445 5666666655431 123455666655 5669999999999888776653
No 436
>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=26.57 E-value=64 Score=24.18 Aligned_cols=17 Identities=18% Similarity=0.270 Sum_probs=13.1
Q ss_pred ccccHHHHHHHHHHHHH
Q psy672 65 HGVSQPTMCRLVKEVSK 81 (314)
Q Consensus 65 fgis~stv~~~~~~v~~ 81 (314)
.++|.+||+|.++.+.+
T Consensus 31 ~~i~~~TVYR~L~~L~~ 47 (116)
T cd07153 31 PSISLATVYRTLELLEE 47 (116)
T ss_pred CCCCHHHHHHHHHHHHh
Confidence 37899999988776554
No 437
>PRK11062 nhaR transcriptional activator NhaR; Provisional
Probab=26.52 E-value=55 Score=29.10 Aligned_cols=40 Identities=10% Similarity=0.066 Sum_probs=32.2
Q ss_pred HHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 46 LAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 46 ~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
+-++..++...+++..|+..|+|++++++-+++.-..+..
T Consensus 9 L~~F~~v~e~gs~s~AA~~L~isqpavS~~I~~LE~~lg~ 48 (296)
T PRK11062 9 LYYFWMVCKEGSVVGAAEALFLTPQTITGQIKALEERLQG 48 (296)
T ss_pred HHHHHHHHhcCCHHHHHHHhCCChHHHHHHHHHHHHHcCc
Confidence 3344445566778899999999999999999999888774
No 438
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=26.33 E-value=54 Score=26.59 Aligned_cols=26 Identities=8% Similarity=-0.074 Sum_probs=22.6
Q ss_pred hhcCCcccccCCcccccHHHHHHHHH
Q psy672 52 YATGNFQIFTGDSHGVSQPTMCRLVK 77 (314)
Q Consensus 52 L~~g~~~~~l~~~fgis~stv~~~~~ 77 (314)
-..|.++.++|+..|++++++++|-+
T Consensus 79 e~~glSqeeLA~~lgvs~s~IsriE~ 104 (154)
T TIGR00270 79 EKRGWSQEQLAKKIQEKESLIKKIEN 104 (154)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHC
Confidence 34789999999999999999998764
No 439
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=26.29 E-value=60 Score=28.32 Aligned_cols=27 Identities=19% Similarity=0.116 Sum_probs=23.7
Q ss_pred CCcccccCCcccccHHHHHHHHHHHHH
Q psy672 55 GNFQIFTGDSHGVSQPTMCRLVKEVSK 81 (314)
Q Consensus 55 g~~~~~l~~~fgis~stv~~~~~~v~~ 81 (314)
..+..++++.||||++|+.|.+.....
T Consensus 18 ~~~~~eLa~~l~VS~~TiRRdL~~L~~ 44 (240)
T PRK10411 18 SLTTEALAEQLNVSKETIRRDLNELQT 44 (240)
T ss_pred CCcHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 466789999999999999999998866
No 440
>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=26.15 E-value=60 Score=32.10 Aligned_cols=42 Identities=14% Similarity=0.065 Sum_probs=35.5
Q ss_pred CCCCCHHHHHHHHHHHhhcCC-cccccCCcccccHHHHHHHHH
Q psy672 36 GVKQPPMTRLLAVIQFYATGN-FQIFTGDSHGVSQPTMCRLVK 77 (314)
Q Consensus 36 ~~~~s~~~~l~~~L~~L~~g~-~~~~l~~~fgis~stv~~~~~ 77 (314)
+..+++.++...+...+..+. +..+++..||+|+++|.+.+.
T Consensus 89 RedLtP~EeA~A~~rLl~~g~~t~eeIA~~lG~S~~~V~rrLk 131 (554)
T TIGR03734 89 RADMSPAEEAEAAARLLGRCKGDREEAARRLGWSPATLDRRLA 131 (554)
T ss_pred cCCCCHHHHHHHHHHHhhhcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 467889999888777777665 788999999999999998876
No 441
>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=26.00 E-value=33 Score=29.53 Aligned_cols=23 Identities=17% Similarity=0.333 Sum_probs=17.7
Q ss_pred cccCCcccccHHHHHHHHHHHHH
Q psy672 59 IFTGDSHGVSQPTMCRLVKEVSK 81 (314)
Q Consensus 59 ~~l~~~fgis~stv~~~~~~v~~ 81 (314)
.+|++.||||+.||.+.+.....
T Consensus 36 ~eLa~~~~VSR~TvR~Al~~L~~ 58 (238)
T TIGR02325 36 MQLAERFGVNRHTVRRAIAALVE 58 (238)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHH
Confidence 34566999999999887776654
No 442
>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=25.90 E-value=29 Score=26.74 Aligned_cols=21 Identities=24% Similarity=0.259 Sum_probs=17.7
Q ss_pred ccccCCcccccHHHHHHHHHH
Q psy672 58 QIFTGDSHGVSQPTMCRLVKE 78 (314)
Q Consensus 58 ~~~l~~~fgis~stv~~~~~~ 78 (314)
...||+..|+|+.|+++|+++
T Consensus 3 ~eELA~~tG~srQTINrWvRk 23 (122)
T PF07037_consen 3 PEELAELTGYSRQTINRWVRK 23 (122)
T ss_pred HHHHHHHhCccHHHHHHHHHh
Confidence 457888999999999998864
No 443
>COG4941 Predicted RNA polymerase sigma factor containing a TPR repeat domain [Transcription]
Probab=25.63 E-value=86 Score=29.01 Aligned_cols=51 Identities=12% Similarity=0.143 Sum_probs=42.1
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 34 MQGVKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 34 ~~~~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
..++.++++.|++++|..+ +|.+-.+++..|-|+++|+..-+.+--..|.+
T Consensus 116 ccHPal~~~~riALtLR~v-~GLs~~eIArAFLv~e~am~QRivRAK~ri~~ 166 (415)
T COG4941 116 CCHPALPPEQRIALTLRLV-GGLSTAEIARAFLVPEAAMAQRIVRAKARIRE 166 (415)
T ss_pred hcCCCCChhhHHHHHHHHH-cCCcHHHHHHHHcCCcHHHHHHHHHHHHHHHh
Confidence 3567899999999999755 68888899999999999988777766666665
No 444
>TIGR02395 rpoN_sigma RNA polymerase sigma-54 factor. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called sigma-54, or RpoN (unrelated to sigma 70-type factors such as RpoD/SigA). RpoN is responsible for enhancer-dependent transcription, and its presence characteristically is associated with varied panels of activators, most of which are enhancer-binding proteins (but see Brahmachary, et al., PubMed:15231786). RpoN may be responsible for transcription of nitrogen fixation genes, flagellins, pilins, etc., and synonyms for the gene symbol rpoN, such as ntrA, reflect these observations
Probab=25.34 E-value=18 Score=34.59 Aligned_cols=31 Identities=16% Similarity=0.278 Sum_probs=24.0
Q ss_pred CcccccCCcccccHHHHHHHHHHHHHHHHHhccccccCCCc
Q psy672 56 NFQIFTGDSHGVSQPTMCRLVKEVSKALAQAHVNYVKFPEQ 96 (314)
Q Consensus 56 ~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~~~~i~~P~~ 96 (314)
.+..++|+..|++.|||||.++ ..|+..|..
T Consensus 319 LtlkdiA~~lglheSTVSRav~----------~Kyi~tp~G 349 (429)
T TIGR02395 319 LTLREVAEELGLHESTISRAIN----------NKYLQTPRG 349 (429)
T ss_pred CcHHHHHHHhCCCccchhhhhc----------CceEecCCc
Confidence 4668999999999999999854 466665544
No 445
>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=25.15 E-value=39 Score=23.03 Aligned_cols=31 Identities=6% Similarity=0.096 Sum_probs=19.4
Q ss_pred HHHhhcC--CcccccCCcccccHHHHHHHHHHH
Q psy672 49 IQFYATG--NFQIFTGDSHGVSQPTMCRLVKEV 79 (314)
Q Consensus 49 L~~L~~g--~~~~~l~~~fgis~stv~~~~~~v 79 (314)
+.+++.. .+..+||..|++|.++|...+..+
T Consensus 6 ~~~l~~~~~~S~~eLa~~~~~s~~~ve~mL~~l 38 (69)
T PF09012_consen 6 RDYLRERGRVSLAELAREFGISPEAVEAMLEQL 38 (69)
T ss_dssp HHHHHHS-SEEHHHHHHHTT--HHHHHHHHHHH
T ss_pred HHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence 3445433 577899999999999776554443
No 446
>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=24.84 E-value=19 Score=21.63 Aligned_cols=19 Identities=21% Similarity=0.034 Sum_probs=13.3
Q ss_pred cccCCcccccHHHHHHHHH
Q psy672 59 IFTGDSHGVSQPTMCRLVK 77 (314)
Q Consensus 59 ~~l~~~fgis~stv~~~~~ 77 (314)
.++|+.+|||.+|+..|-.
T Consensus 3 ~e~A~~~gvs~~tlR~ye~ 21 (38)
T PF00376_consen 3 GEVAKLLGVSPRTLRYYER 21 (38)
T ss_dssp HHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHCCCHHHHHHHHH
Confidence 4577888999998876643
No 447
>PRK14997 LysR family transcriptional regulator; Provisional
Probab=24.80 E-value=53 Score=29.14 Aligned_cols=38 Identities=8% Similarity=0.059 Sum_probs=31.3
Q ss_pred HHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 48 VIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 48 ~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
++.-++...++...|+..+||+++|++.+++.-+.+-.
T Consensus 9 ~f~~va~~gs~s~AA~~L~isQpavS~~I~~LE~~lG~ 46 (301)
T PRK14997 9 WFVHVVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGV 46 (301)
T ss_pred HHHHHHHcCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 33445556678899999999999999999999998874
No 448
>PRK06474 hypothetical protein; Provisional
Probab=24.71 E-value=67 Score=26.62 Aligned_cols=27 Identities=15% Similarity=0.071 Sum_probs=21.0
Q ss_pred CcccccCCcc-cccHHHHHHHHHHHHHH
Q psy672 56 NFQIFTGDSH-GVSQPTMCRLVKEVSKA 82 (314)
Q Consensus 56 ~~~~~l~~~f-gis~stv~~~~~~v~~~ 82 (314)
.+..+++..+ ++|++|+++.++...++
T Consensus 27 ~ta~el~~~l~~is~aTvYrhL~~L~e~ 54 (178)
T PRK06474 27 LTPLELVKILKDVPQATLYRHLQTMVDS 54 (178)
T ss_pred CCHHHHHHHhcCCCHHHHHHHHHHHHHC
Confidence 5667777777 79999999988876654
No 449
>PRK14999 histidine utilization repressor; Provisional
Probab=24.71 E-value=36 Score=29.53 Aligned_cols=23 Identities=22% Similarity=0.219 Sum_probs=18.4
Q ss_pred cccCCcccccHHHHHHHHHHHHH
Q psy672 59 IFTGDSHGVSQPTMCRLVKEVSK 81 (314)
Q Consensus 59 ~~l~~~fgis~stv~~~~~~v~~ 81 (314)
.+|++.||||+.||.+.+.....
T Consensus 40 ~eLa~~~gVSR~TVR~Al~~L~~ 62 (241)
T PRK14999 40 AELVAQYGFSRMTINRALRELTD 62 (241)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHH
Confidence 45677999999999987776654
No 450
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=24.68 E-value=66 Score=26.82 Aligned_cols=41 Identities=17% Similarity=0.024 Sum_probs=30.2
Q ss_pred HHHHHHHHHHHhhcC--CcccccCCcccccHHHHHHHHHHHHH
Q psy672 41 PMTRLLAVIQFYATG--NFQIFTGDSHGVSQPTMCRLVKEVSK 81 (314)
Q Consensus 41 ~~~~l~~~L~~L~~g--~~~~~l~~~fgis~stv~~~~~~v~~ 81 (314)
..++....|.+|... .+..++++.||+|.+|+.|=+.....
T Consensus 5 ~~~R~~~Il~~l~~~~~~~~~~La~~~~vS~~TiRRDl~~L~~ 47 (185)
T PRK04424 5 KKERQKALQELIEENPFITDEELAEKFGVSIQTIRLDRMELGI 47 (185)
T ss_pred HHHHHHHHHHHHHHCCCEEHHHHHHHHCcCHHHHHHHHHHHhc
Confidence 345555556666654 45578999999999999998887664
No 451
>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=24.65 E-value=26 Score=23.17 Aligned_cols=27 Identities=19% Similarity=0.218 Sum_probs=19.3
Q ss_pred hhcCCcccccCCcccccHHHHHHHHHH
Q psy672 52 YATGNFQIFTGDSHGVSQPTMCRLVKE 78 (314)
Q Consensus 52 L~~g~~~~~l~~~fgis~stv~~~~~~ 78 (314)
-..|.++.++|...|++++++++|.+.
T Consensus 9 ~~~~lt~~~~a~~~~i~~~~i~~~e~g 35 (64)
T PF12844_consen 9 EEKGLTQKDLAEKLGISRSTISKIENG 35 (64)
T ss_dssp HHCT--HHHHHHHHTS-HHHHHHHHTT
T ss_pred HHcCCCHHHHHHHHCcCHHHHHHHHCC
Confidence 446778889999999999999888753
No 452
>PRK13558 bacterio-opsin activator; Provisional
Probab=24.63 E-value=93 Score=31.32 Aligned_cols=48 Identities=10% Similarity=0.019 Sum_probs=36.7
Q ss_pred CCCHHHHHHHHHHHhhcC------CcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 38 KQPPMTRLLAVIQFYATG------NFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 38 ~~s~~~~l~~~L~~L~~g------~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
.++..++=++-+-|...+ .+..++|+.+|||++|++..+++...-|.+
T Consensus 607 ~lt~~q~e~l~~a~~~gyf~~pr~~~~~e~a~~l~is~~t~~~~lr~a~~~l~~ 660 (665)
T PRK13558 607 DLTDRQLTALQKAYVSGYFEWPRRVEGEELAESMGISRSTFHQHLRAAERKLVG 660 (665)
T ss_pred hCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 477666655555554433 567899999999999999999998887775
No 453
>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=24.62 E-value=36 Score=29.23 Aligned_cols=46 Identities=20% Similarity=0.179 Sum_probs=28.4
Q ss_pred hhHHhhhhhhccc-CCCCCCCCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHH
Q psy672 20 IIFPLARNVLETN-TMQGVKQPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSK 81 (314)
Q Consensus 20 ~L~~~l~~~~~~~-~~~~~~~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~ 81 (314)
.|.+.|+..+... -..+..+|.+.+| ++.||||+.||.+.+.....
T Consensus 5 qi~~~l~~~I~~g~~~~g~~LPsE~eL----------------a~~~~VSR~TVR~Al~~L~~ 51 (230)
T TIGR02018 5 RIKQDILERIRSGEWPPGHRIPSEHEL----------------VAQYGCSRMTVNRALRELTD 51 (230)
T ss_pred HHHHHHHHHHHhCCCCCCCcCcCHHHH----------------HHHHCCCHHHHHHHHHHHHH
Confidence 4445555444321 1223456666655 56899999999887776554
No 454
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=24.43 E-value=22 Score=23.91 Aligned_cols=22 Identities=23% Similarity=0.058 Sum_probs=18.1
Q ss_pred cccCCcccccHHHHHHHHHHHH
Q psy672 59 IFTGDSHGVSQPTMCRLVKEVS 80 (314)
Q Consensus 59 ~~l~~~fgis~stv~~~~~~v~ 80 (314)
.++|+.+|||.+|+..|.++..
T Consensus 4 ~eva~~~gvs~~tlr~y~~~gl 25 (69)
T PF13411_consen 4 KEVAKLLGVSPSTLRYYEREGL 25 (69)
T ss_dssp HHHHHHTTTTHHHHHHHHHTTS
T ss_pred HHHHHHHCcCHHHHHHHHHhcC
Confidence 5678899999999998877654
No 455
>TIGR03384 betaine_BetI transcriptional repressor BetI. BetI is a DNA-binding transcriptional repressor of the bet (betaine) regulon. In sequence, it is related to TetR (pfam00440). Choline, through BetI, induces the expression of the betaine biosynthesis genes betA and betB by derepression. The choline porter gene betT is also part of this regulon in Escherichia coli. Note that a different transcriptional regulator, ArcA, controls the expression of bet regulon genes in response to oxygen, as BetA is an oxygen-dependent enzyme.
Probab=24.11 E-value=24 Score=28.79 Aligned_cols=33 Identities=12% Similarity=0.001 Sum_probs=26.4
Q ss_pred CCcccccCCcccccHHHHHHHHHHHHHHHHHhc
Q psy672 55 GNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAH 87 (314)
Q Consensus 55 g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~ 87 (314)
+.+.+++++..|||+++++.+|..--..+..+.
T Consensus 28 ~~s~~~IA~~agvsk~~ly~~F~sK~~L~~~~~ 60 (189)
T TIGR03384 28 DVTIAQIARRAGVSSGIISHYFGGKQGLLEATM 60 (189)
T ss_pred cCCHHHHHHHhCCCHHHHHHHcCCHHHHHHHHH
Confidence 467889999999999999999976655555543
No 456
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=23.56 E-value=74 Score=27.38 Aligned_cols=27 Identities=19% Similarity=0.203 Sum_probs=23.6
Q ss_pred CcccccCCcccccHHHHHHHHHHHHHH
Q psy672 56 NFQIFTGDSHGVSQPTMCRLVKEVSKA 82 (314)
Q Consensus 56 ~~~~~l~~~fgis~stv~~~~~~v~~~ 82 (314)
.+..++++.+++|++|+++.+.+..+.
T Consensus 22 IS~~eLA~~L~iS~~Tvsr~Lk~LEe~ 48 (217)
T PRK14165 22 ISSSEFANHTGTSSKTAARILKQLEDE 48 (217)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 567899999999999999999888654
No 457
>PF05598 DUF772: Transposase domain (DUF772); InterPro: IPR008490 This presumed domain is found at the N terminus of transposase insH and other related transposases.
Probab=23.56 E-value=1.9e+02 Score=19.73 Aligned_cols=45 Identities=20% Similarity=0.169 Sum_probs=25.9
Q ss_pred CCCCHHHHHHHHHHHhhcCC-cccccCCc-----------------ccccHHHHHHHHHHHHH
Q psy672 37 VKQPPMTRLLAVIQFYATGN-FQIFTGDS-----------------HGVSQPTMCRLVKEVSK 81 (314)
Q Consensus 37 ~~~s~~~~l~~~L~~L~~g~-~~~~l~~~-----------------fgis~stv~~~~~~v~~ 81 (314)
++.++...+.+.|.-...|. +.+.+.+. -..+.+|+++..+++..
T Consensus 3 p~~~~~~ml~~ll~~~~~~~~S~r~l~~~l~~~~~~r~~~g~~~~~~~pd~stl~rfr~rl~~ 65 (77)
T PF05598_consen 3 PAYPPRMMLKALLLKYLFGLRSDRELEERLRDNLSFRYFCGLSLEEPVPDHSTLSRFRKRLIQ 65 (77)
T ss_pred CCCCHHHHHHHHHHHHHHhcchHHHHHhhHhhhhHHHHHHhcccCCCCCChHHHHHHHHHHhh
Confidence 35666666666666555554 44443332 23456777777766665
No 458
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=23.33 E-value=40 Score=29.24 Aligned_cols=22 Identities=18% Similarity=0.271 Sum_probs=17.1
Q ss_pred ccCCcccccHHHHHHHHHHHHH
Q psy672 60 FTGDSHGVSQPTMCRLVKEVSK 81 (314)
Q Consensus 60 ~l~~~fgis~stv~~~~~~v~~ 81 (314)
+|++.||||+.||.+.+.....
T Consensus 34 eL~~~~~VSR~TvR~Al~~L~~ 55 (240)
T PRK09764 34 ALQTEFGVSRVTVRQALRQLVE 55 (240)
T ss_pred HHHHHHCCCHHHHHHHHHHHHH
Confidence 4566999999999887766554
No 459
>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family. This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferble copper resistance) of an Enterocuccus faecium plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this model are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI.
Probab=22.63 E-value=1.4e+02 Score=23.19 Aligned_cols=39 Identities=10% Similarity=0.011 Sum_probs=25.3
Q ss_pred HHHHHHHHHHhhcCCcccc----cCCcccccHHHHHHHHHHHHH
Q psy672 42 MTRLLAVIQFYATGNFQIF----TGDSHGVSQPTMCRLVKEVSK 81 (314)
Q Consensus 42 ~~~l~~~L~~L~~g~~~~~----l~~~fgis~stv~~~~~~v~~ 81 (314)
+.+++-.||- ....+.++ +++..+.+.+|+..++++...
T Consensus 6 E~~VM~vlW~-~~~~t~~eI~~~l~~~~~~~~tTv~T~L~rL~~ 48 (130)
T TIGR02698 6 EWEVMRVVWT-LGETTSRDIIRILAEKKDWSDSTIKTLLGRLVD 48 (130)
T ss_pred HHHHHHHHHc-CCCCCHHHHHHHHhhccCCcHHHHHHHHHHHHH
Confidence 4455555553 33455566 555568899999888887765
No 460
>PRK06424 transcription factor; Provisional
Probab=22.54 E-value=49 Score=26.53 Aligned_cols=27 Identities=4% Similarity=-0.225 Sum_probs=23.2
Q ss_pred HhhcCCcccccCCcccccHHHHHHHHH
Q psy672 51 FYATGNFQIFTGDSHGVSQPTMCRLVK 77 (314)
Q Consensus 51 ~L~~g~~~~~l~~~fgis~stv~~~~~ 77 (314)
+-..|.++.+||+..|++++++++|-+
T Consensus 93 Re~~GLSQ~eLA~~iGvs~stIskiE~ 119 (144)
T PRK06424 93 RERLSMSQADLAAKIFERKNVIASIER 119 (144)
T ss_pred HHHcCCCHHHHHHHhCCCHHHHHHHHC
Confidence 344789999999999999999998765
No 461
>PRK15243 transcriptional regulator SpvR; Provisional
Probab=22.49 E-value=80 Score=28.44 Aligned_cols=42 Identities=12% Similarity=0.228 Sum_probs=32.2
Q ss_pred HHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 43 TRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 43 ~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
.+|-.++... ...+++..|+..++|+||+++.+++.-..|-.
T Consensus 7 rqL~~F~aVa-e~gSfs~AA~~L~isQpavS~~Ik~LE~eLG~ 48 (297)
T PRK15243 7 KKLKIFITLM-ETGSFSIATSVLYITRTPLSRVISDLERELKQ 48 (297)
T ss_pred HHHHHHHHHH-HcCCHHHHHHHHCcCHHHHHHHHHHHHHHhCC
Confidence 3444444433 44578999999999999999999999988774
No 462
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=22.30 E-value=24 Score=34.27 Aligned_cols=31 Identities=16% Similarity=0.220 Sum_probs=24.2
Q ss_pred CcccccCCcccccHHHHHHHHHHHHHHHHHhccccccCCCc
Q psy672 56 NFQIFTGDSHGVSQPTMCRLVKEVSKALAQAHVNYVKFPEQ 96 (314)
Q Consensus 56 ~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~~~~i~~P~~ 96 (314)
.+.+++|+..|++.|||||++. .+|+..|..
T Consensus 370 LtlkdVAe~lglHeSTVSRa~~----------~KY~~tp~G 400 (481)
T PRK12469 370 LVLRDVAEELGLHESTISRATG----------NKYMATPRG 400 (481)
T ss_pred CcHHHHHHHhCCCcchhhHHhc----------CceeecCCc
Confidence 3567899999999999999864 466666654
No 463
>PRK13698 plasmid-partitioning protein; Provisional
Probab=22.07 E-value=63 Score=29.58 Aligned_cols=40 Identities=13% Similarity=0.108 Sum_probs=28.8
Q ss_pred CCHHHHHHHHHH-Hh-hcCCcccccCCcccccHHHHHHHHHH
Q psy672 39 QPPMTRLLAVIQ-FY-ATGNFQIFTGDSHGVSQPTMCRLVKE 78 (314)
Q Consensus 39 ~s~~~~l~~~L~-~L-~~g~~~~~l~~~fgis~stv~~~~~~ 78 (314)
.++.+.=..... .. ..|.++.++|+.+|+|+++|++.++-
T Consensus 158 ls~iE~A~ay~~~L~~~~~~tQeeLA~~lG~SRs~Vsn~Lrl 199 (323)
T PRK13698 158 TSAYERGLRYASRLQNEFAGNISALADAENISRKIITRCINT 199 (323)
T ss_pred CCHHHHHHHHHHHHHHhcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 455555443322 23 45689999999999999999988763
No 464
>PRK13500 transcriptional activator RhaR; Provisional
Probab=22.05 E-value=1.5e+02 Score=26.75 Aligned_cols=38 Identities=16% Similarity=-0.014 Sum_probs=27.4
Q ss_pred HHHHHHHHHhhc----CCcccccCCcccccHHHHHHHHHHHH
Q psy672 43 TRLLAVIQFYAT----GNFQIFTGDSHGVSQPTMCRLVKEVS 80 (314)
Q Consensus 43 ~~l~~~L~~L~~----g~~~~~l~~~fgis~stv~~~~~~v~ 80 (314)
..+.-++.|+.. ..+..++|+.+|+|.++++++|++.+
T Consensus 206 ~~l~~i~~yI~~~~~e~isl~~lA~~~~iS~~~L~r~FK~~t 247 (312)
T PRK13500 206 TLLDKLITRLAASLKSPFALDKFCDEASCSERVLRQQFRQQT 247 (312)
T ss_pred HHHHHHHHHHHHcccCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 334444445443 35667899999999999999999874
No 465
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=21.86 E-value=41 Score=27.89 Aligned_cols=27 Identities=11% Similarity=0.140 Sum_probs=23.3
Q ss_pred HhhcCCcccccCCcccccHHHHHHHHH
Q psy672 51 FYATGNFQIFTGDSHGVSQPTMCRLVK 77 (314)
Q Consensus 51 ~L~~g~~~~~l~~~fgis~stv~~~~~ 77 (314)
+-..|.+..++|+..|+|++|+++|-+
T Consensus 16 R~~~glt~~elA~~~gis~~~is~~E~ 42 (185)
T PRK09943 16 RQQQGLSQRRAAELSGLTHSAISTIEQ 42 (185)
T ss_pred HHHcCCCHHHHHHHHCCCHHHHHHHHc
Confidence 345788999999999999999998875
No 466
>COG5606 Uncharacterized conserved small protein [Function unknown]
Probab=21.81 E-value=16 Score=26.38 Aligned_cols=63 Identities=17% Similarity=0.177 Sum_probs=39.7
Q ss_pred CHHHHHHhhHHhhhhhhcccCCCCCCCCHHHHHHHHHHH--hhcCCcccccCCcccccHHHHHHHHHHHH
Q psy672 13 SKDVVLNIIFPLARNVLETNTMQGVKQPPMTRLLAVIQF--YATGNFQIFTGDSHGVSQPTMCRLVKEVS 80 (314)
Q Consensus 13 sr~~f~~~L~~~l~~~~~~~~~~~~~~s~~~~l~~~L~~--L~~g~~~~~l~~~fgis~stv~~~~~~v~ 80 (314)
+-++|. .+++.+.+.-... ..+-...+|++.+.. =-.+.++..++..+||++|.++...+-=+
T Consensus 2 ~~~vF~-s~~~~~~D~~e~a----~~m~ir~~l~~~i~~~i~q~~l~Q~qiae~lgV~qprvS~l~~gk~ 66 (91)
T COG5606 2 SNEVFT-SVWDAIEDTPEAA----ENMKIRSALMMAIKQWIEQAALSQAQIAELLGVTQPRVSDLARGKI 66 (91)
T ss_pred CCchhh-hHHHHHhccHHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCchHHHHHhcch
Confidence 446677 7777766543211 113345555544433 33568889999999999999987765433
No 467
>PF09182 PuR_N: Bacterial purine repressor, N-terminal; InterPro: IPR015265 The N-terminal domain of the bacterial purine repressor PuR is a winged-helix domain, a subdivision of the HTH structural family. It consists of a canonical arrangement of secondary structures: a1-b1-a2-T-a3-b2-W-b3, where a2-T-a3 is the HTH motif, a3 is the recognition helix, and W is the wing. The domain allows for recognition of a conserved CGAA sequence in the centre of a DNA PurBox, resulting in binding to the major groove of DNA []. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1O57_B 1P4A_D.
Probab=21.79 E-value=1.1e+02 Score=21.18 Aligned_cols=43 Identities=9% Similarity=0.302 Sum_probs=26.3
Q ss_pred HHHHHHHHHhhcCC----cccccCCcccccHHHHHHHHHHHHHHHHH
Q psy672 43 TRLLAVIQFYATGN----FQIFTGDSHGVSQPTMCRLVKEVSKALAQ 85 (314)
Q Consensus 43 ~~l~~~L~~L~~g~----~~~~l~~~fgis~stv~~~~~~v~~~l~~ 85 (314)
++|.....+|-... +....+++|+.++||++.=+.-+-+++.+
T Consensus 4 eRlv~it~~L~~~P~~lisL~~Fae~f~~AKSsISEDl~iik~~~~~ 50 (70)
T PF09182_consen 4 ERLVAITKYLLENPNKLISLTYFAERFGAAKSSISEDLSIIKETFEK 50 (70)
T ss_dssp HHHHHHHHHHHTSTT--EEHHHHHHHHT--HHHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHcCCcceEcHHHHHHHhcccccchHHHHHHHHHHHHH
Confidence 44554445554442 34567889999999999766666666654
No 468
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=21.68 E-value=24 Score=34.10 Aligned_cols=31 Identities=16% Similarity=0.228 Sum_probs=23.9
Q ss_pred CcccccCCcccccHHHHHHHHHHHHHHHHHhccccccCCCc
Q psy672 56 NFQIFTGDSHGVSQPTMCRLVKEVSKALAQAHVNYVKFPEQ 96 (314)
Q Consensus 56 ~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~~~~i~~P~~ 96 (314)
.+..++|+..|++.|||||.+. ..|+..|..
T Consensus 344 LtlkdvAe~lglheSTVSRav~----------~Kyv~tp~G 374 (455)
T PRK05932 344 LVLKDIAEELGMHESTISRATT----------NKYMATPRG 374 (455)
T ss_pred ccHHHHHHHhCCCccchhhhhc----------CceeecCCc
Confidence 4568999999999999998754 466665544
No 469
>PRK09744 DNA-binding transcriptional regulator DicC; Provisional
Probab=21.38 E-value=31 Score=24.18 Aligned_cols=20 Identities=10% Similarity=0.130 Sum_probs=16.9
Q ss_pred CcccccCCcccccHHHHHHH
Q psy672 56 NFQIFTGDSHGVSQPTMCRL 75 (314)
Q Consensus 56 ~~~~~l~~~fgis~stv~~~ 75 (314)
.+...+|..+|||.++|+.|
T Consensus 11 Gs~~kvA~aLGIs~~AVsQW 30 (75)
T PRK09744 11 GSKTKLANAAGVRLASVAAW 30 (75)
T ss_pred CcHHHHHHHHCCCHHHHHHH
Confidence 44567899999999999988
No 470
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=21.07 E-value=93 Score=27.64 Aligned_cols=42 Identities=19% Similarity=-0.040 Sum_probs=33.6
Q ss_pred CHHHHHHHHHHHhhcC--CcccccCCcccccHHHHHHHHHHHHH
Q psy672 40 PPMTRLLAVIQFYATG--NFQIFTGDSHGVSQPTMCRLVKEVSK 81 (314)
Q Consensus 40 s~~~~l~~~L~~L~~g--~~~~~l~~~fgis~stv~~~~~~v~~ 81 (314)
...++....|.+|... .+..++++.||||..|+.|-+.....
T Consensus 14 ~~~eR~~~Il~~L~~~~~vtv~eLa~~l~VS~~TIRRDL~~Le~ 57 (269)
T PRK09802 14 GTSERREQIIQRLRQQGSVQVNDLSALYGVSTVTIRNDLAFLEK 57 (269)
T ss_pred cHHHHHHHHHHHHHHcCCEeHHHHHHHHCCCHHHHHHHHHHHHh
Confidence 3467778888888765 46678999999999999999888754
No 471
>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=20.82 E-value=68 Score=24.68 Aligned_cols=28 Identities=11% Similarity=0.214 Sum_probs=22.7
Q ss_pred CCcccccCCcccccHHHHHHHHHHHHHH
Q psy672 55 GNFQIFTGDSHGVSQPTMCRLVKEVSKA 82 (314)
Q Consensus 55 g~~~~~l~~~fgis~stv~~~~~~v~~~ 82 (314)
..+..++++.++++.+++.+++.....+
T Consensus 25 ~~s~~eia~~~~i~~~~v~~il~~L~~~ 52 (132)
T TIGR00738 25 PVSVKEIAERQGISRSYLEKILRTLRRA 52 (132)
T ss_pred cCcHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 3566789999999999998888776653
No 472
>COG5566 Uncharacterized conserved protein [Function unknown]
Probab=20.68 E-value=47 Score=25.86 Aligned_cols=28 Identities=11% Similarity=0.211 Sum_probs=23.1
Q ss_pred cCCcccccCCcccccHHHHHHHHHHHHH
Q psy672 54 TGNFQIFTGDSHGVSQPTMCRLVKEVSK 81 (314)
Q Consensus 54 ~g~~~~~l~~~fgis~stv~~~~~~v~~ 81 (314)
.|.++.+++..+.+|..++.++++++..
T Consensus 101 dG~n~~eLaKkYrlS~~~Iy~VIrr~~t 128 (137)
T COG5566 101 DGSNYVELAKKYRLSENHIYRVIRRTHT 128 (137)
T ss_pred CCccHHHHHHHhcccHHHHHHHHHHHHH
Confidence 4677788899999999999999986543
No 473
>PF05584 Sulfolobus_pRN: Sulfolobus plasmid regulatory protein; InterPro: IPR008848 This family consists of several plasmid regulatory proteins from the extreme thermophilic and acidophilic archaea Sulfolobus.
Probab=20.44 E-value=1.2e+02 Score=21.21 Aligned_cols=41 Identities=12% Similarity=0.122 Sum_probs=29.1
Q ss_pred CCHHHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHH
Q psy672 39 QPPMTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSK 81 (314)
Q Consensus 39 ~s~~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~ 81 (314)
++..+.+++.|-.= ..+...+-...|+++.++..+..+..+
T Consensus 4 lt~~~~IL~~ls~~--c~TLeeL~ekTgi~k~~LlV~LsrL~k 44 (72)
T PF05584_consen 4 LTVTQKILIILSKR--CCTLEELEEKTGISKNTLLVYLSRLAK 44 (72)
T ss_pred hhHHHHHHHHHHhc--cCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 44455555544333 678888999999999999888777654
No 474
>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=20.36 E-value=92 Score=25.56 Aligned_cols=38 Identities=21% Similarity=0.022 Sum_probs=29.1
Q ss_pred HHHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHH
Q psy672 42 MTRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEV 79 (314)
Q Consensus 42 ~~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v 79 (314)
+.+-.+==.|.-.+.+...+|..+|||.+|+.+|=.+-
T Consensus 6 e~R~~~R~~YV~~~~sLe~aA~~~gVs~~TarrWK~~A 43 (165)
T PF08822_consen 6 ETRDAVRRAYVFDRLSLEQAAAKCGVSYATARRWKREA 43 (165)
T ss_pred HHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 44444444566678888999999999999999887654
No 475
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=20.34 E-value=1.5e+02 Score=26.91 Aligned_cols=31 Identities=23% Similarity=0.209 Sum_probs=25.8
Q ss_pred cCCcccccCCcccccHHHHHHHHHHHHHHHH
Q psy672 54 TGNFQIFTGDSHGVSQPTMCRLVKEVSKALA 84 (314)
Q Consensus 54 ~g~~~~~l~~~fgis~stv~~~~~~v~~~l~ 84 (314)
...++.+++...||+..|+.+..++....+.
T Consensus 275 ~~~t~keIa~v~~Vs~~tI~~~ykel~~~l~ 305 (310)
T PRK00423 275 ERRTQREVAEVAGVTEVTVRNRYKELAEKLD 305 (310)
T ss_pred CCCCHHHHHHHcCCCHHHHHHHHHHHHHHhC
Confidence 4468889999999999999988888887653
No 476
>PRK12423 LexA repressor; Provisional
Probab=20.21 E-value=87 Score=26.42 Aligned_cols=26 Identities=12% Similarity=0.124 Sum_probs=21.0
Q ss_pred CcccccCCccc-ccHHHHHHHHHHHHH
Q psy672 56 NFQIFTGDSHG-VSQPTMCRLVKEVSK 81 (314)
Q Consensus 56 ~~~~~l~~~fg-is~stv~~~~~~v~~ 81 (314)
.+.+++|+.|| +|++++++.+.....
T Consensus 26 Ps~~eia~~~g~~s~~~v~~~l~~L~~ 52 (202)
T PRK12423 26 PSLAEIAQAFGFASRSVARKHVQALAE 52 (202)
T ss_pred CCHHHHHHHhCCCChHHHHHHHHHHHH
Confidence 57889999999 599999976666555
No 477
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=20.21 E-value=38 Score=26.14 Aligned_cols=25 Identities=16% Similarity=0.084 Sum_probs=21.8
Q ss_pred hcCCcccccCCcccccHHHHHHHHH
Q psy672 53 ATGNFQIFTGDSHGVSQPTMCRLVK 77 (314)
Q Consensus 53 ~~g~~~~~l~~~fgis~stv~~~~~ 77 (314)
..|.+..++|...|||+++++++.+
T Consensus 16 ~~Glsq~eLA~~~Gis~~~is~iE~ 40 (120)
T PRK13890 16 ERHMTKKELSERSGVSISFLSDLTT 40 (120)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHc
Confidence 4678888999999999999998775
No 478
>PRK15183 Vi polysaccharide biosynthesis protein TviA; Provisional
Probab=20.10 E-value=74 Score=23.86 Aligned_cols=53 Identities=17% Similarity=0.226 Sum_probs=33.1
Q ss_pred HHHHHHHHHhhcCCcccccCCcccccHHHHHHHHHHHHHHHHHhccccccCCC
Q psy672 43 TRLLAVIQFYATGNFQIFTGDSHGVSQPTMCRLVKEVSKALAQAHVNYVKFPE 95 (314)
Q Consensus 43 ~~l~~~L~~L~~g~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~~~~i~~P~ 95 (314)
.+=.+-+-|+-+-....++.++|--|.||+++|-++..--.--.-++|+-.|.
T Consensus 86 ~kdi~kmkyflsesgmeelqdrfmns~st~yrwrke~a~kfgvr~prylllpd 138 (143)
T PRK15183 86 RKDIVKMKYFLSESGMEELQDRFMNSSSTMYRWRKELAVKFGVREPRYLLLPD 138 (143)
T ss_pred hhhhhHhhhhhhhccHHHHHHHHccChHHHHHHHHHHHHHhcCCCCceEecCc
Confidence 33344555555566667777888788888888777765544444555555554
No 479
>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=20.02 E-value=41 Score=22.53 Aligned_cols=20 Identities=25% Similarity=0.137 Sum_probs=16.5
Q ss_pred cccCCcccccHHHHHHHHHH
Q psy672 59 IFTGDSHGVSQPTMCRLVKE 78 (314)
Q Consensus 59 ~~l~~~fgis~stv~~~~~~ 78 (314)
.++|+.+|||.+|+..|..+
T Consensus 4 ~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 4 KEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred HHHHHHHCcCHHHHHHHHHh
Confidence 46788999999999887665
Done!