Query 015913
Match_columns 398
No_of_seqs 255 out of 1661
Neff 8.4
Searched_HMMs 46136
Date Fri Mar 29 02:04:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/015913.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/015913hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4585 Predicted transposase 100.0 9.3E-44 2E-48 339.2 18.6 311 54-393 7-324 (326)
2 PF04827 Plant_tran: Plant tra 100.0 1.1E-42 2.5E-47 298.6 5.1 187 131-330 2-204 (205)
3 PF13359 DDE_Tnp_4: DDE superf 100.0 1.3E-37 2.8E-42 270.9 3.2 153 161-321 1-158 (158)
4 PF13613 HTH_Tnp_4: Helix-turn 98.9 7.2E-10 1.6E-14 77.6 2.8 50 80-129 2-51 (53)
5 PF13612 DDE_Tnp_1_3: Transpos 98.8 1.9E-09 4E-14 92.6 1.6 126 155-299 4-149 (155)
6 PF01609 DDE_Tnp_1: Transposas 97.9 3.3E-07 7.2E-12 82.2 -5.0 161 156-322 4-213 (213)
7 PF13586 DDE_Tnp_1_2: Transpos 96.8 0.00064 1.4E-08 52.8 2.1 49 270-319 36-84 (88)
8 PF13936 HTH_38: Helix-turn-he 95.8 0.0029 6.2E-08 42.2 0.5 41 79-120 3-43 (44)
9 PF04545 Sigma70_r4: Sigma-70, 95.8 0.0078 1.7E-07 41.2 2.6 45 80-125 4-48 (50)
10 PF04218 CENP-B_N: CENP-B N-te 95.1 0.011 2.5E-07 41.0 1.5 43 77-120 3-45 (53)
11 PF08281 Sigma70_r4_2: Sigma-7 94.6 0.026 5.7E-07 39.1 2.4 44 80-124 10-53 (54)
12 PF02796 HTH_7: Helix-turn-hel 94.1 0.0082 1.8E-07 40.2 -1.1 35 86-120 10-44 (45)
13 PF13384 HTH_23: Homeodomain-l 93.6 0.016 3.5E-07 39.5 -0.5 29 94-122 14-42 (50)
14 PF13340 DUF4096: Putative tra 93.1 0.19 4.1E-06 37.5 4.7 66 57-123 1-66 (75)
15 PF13518 HTH_28: Helix-turn-he 93.0 0.04 8.6E-07 37.7 0.8 37 86-123 2-38 (52)
16 PF12116 SpoIIID: Stage III sp 92.9 0.041 9E-07 41.0 0.8 43 84-126 5-48 (82)
17 smart00351 PAX Paired Box doma 92.2 0.1 2.2E-06 43.3 2.3 45 78-123 15-59 (125)
18 PF05225 HTH_psq: helix-turn-h 91.8 0.064 1.4E-06 35.9 0.5 37 84-120 2-39 (45)
19 PF13011 LZ_Tnp_IS481: leucine 91.7 0.097 2.1E-06 40.0 1.6 45 79-123 7-51 (85)
20 COG3415 Transposase and inacti 91.5 0.084 1.8E-06 44.4 1.1 44 80-123 4-47 (138)
21 smart00421 HTH_LUXR helix_turn 91.3 0.19 4.2E-06 34.5 2.7 44 80-125 3-46 (58)
22 cd00131 PAX Paired Box domain 91.1 0.16 3.4E-06 42.3 2.4 45 78-123 15-59 (128)
23 PRK09413 IS2 repressor TnpA; R 90.9 0.18 3.8E-06 41.5 2.5 46 77-122 9-54 (121)
24 PRK04217 hypothetical protein; 90.4 0.24 5.2E-06 40.0 2.7 49 79-128 41-89 (110)
25 PF01527 HTH_Tnp_1: Transposas 90.1 0.11 2.3E-06 38.7 0.4 45 78-122 4-48 (76)
26 cd06171 Sigma70_r4 Sigma70, re 89.7 0.27 5.9E-06 33.1 2.2 43 81-124 11-53 (55)
27 TIGR01321 TrpR trp operon repr 89.3 0.19 4.2E-06 39.1 1.4 41 80-120 32-78 (94)
28 PRK09639 RNA polymerase sigma 88.9 0.34 7.3E-06 41.7 2.8 48 80-129 112-159 (166)
29 PF02209 VHP: Villin headpiece 88.7 0.27 5.8E-06 31.1 1.4 22 46-67 2-23 (36)
30 PRK00118 putative DNA-binding 88.1 0.42 9.1E-06 38.1 2.5 48 79-127 16-63 (104)
31 TIGR02531 yecD_yerC TrpR-relat 88.0 0.29 6.2E-06 37.9 1.5 31 88-118 41-71 (88)
32 cd06170 LuxR_C_like C-terminal 87.1 0.53 1.2E-05 32.3 2.4 43 82-126 2-44 (57)
33 smart00153 VHP Villin headpiec 87.0 0.46 1E-05 30.1 1.8 21 46-66 2-22 (36)
34 PRK12529 RNA polymerase sigma 87.0 0.51 1.1E-05 41.4 2.7 49 79-128 126-174 (178)
35 TIGR03879 near_KaiC_dom probab 86.8 0.32 7E-06 36.0 1.1 42 80-121 15-56 (73)
36 PRK08301 sporulation sigma fac 86.7 0.59 1.3E-05 42.9 3.1 52 79-130 177-231 (234)
37 PRK09652 RNA polymerase sigma 86.7 0.5 1.1E-05 41.1 2.5 50 80-130 128-177 (182)
38 PRK12519 RNA polymerase sigma 86.3 0.53 1.1E-05 41.8 2.5 50 80-130 141-190 (194)
39 PF00356 LacI: Bacterial regul 85.7 0.29 6.4E-06 32.9 0.4 21 100-120 2-22 (46)
40 PF13542 HTH_Tnp_ISL3: Helix-t 85.7 0.3 6.4E-06 33.4 0.4 28 94-121 24-51 (52)
41 PRK09638 RNA polymerase sigma 85.6 0.68 1.5E-05 40.3 2.8 48 79-127 125-172 (176)
42 PRK05911 RNA polymerase sigma 85.1 0.69 1.5E-05 43.3 2.8 51 80-131 205-255 (257)
43 PRK12522 RNA polymerase sigma 84.8 0.69 1.5E-05 40.2 2.5 54 80-134 119-172 (173)
44 cd00569 HTH_Hin_like Helix-tur 84.6 0.43 9.3E-06 29.1 0.8 37 81-118 6-42 (42)
45 PRK01381 Trp operon repressor; 84.4 0.61 1.3E-05 36.7 1.6 39 81-119 33-77 (99)
46 PRK07037 extracytoplasmic-func 84.3 0.82 1.8E-05 39.2 2.7 48 80-128 109-156 (163)
47 cd06571 Bac_DnaA_C C-terminal 84.2 0.86 1.9E-05 35.3 2.5 48 79-126 26-74 (90)
48 PRK09415 RNA polymerase factor 84.2 0.85 1.9E-05 39.9 2.8 49 80-129 127-175 (179)
49 TIGR00721 tfx DNA-binding prot 84.2 0.82 1.8E-05 38.4 2.5 45 80-126 6-50 (137)
50 TIGR02952 Sig70_famx2 RNA poly 83.9 0.89 1.9E-05 39.1 2.8 48 79-127 121-168 (170)
51 PRK05803 sporulation sigma fac 83.9 0.97 2.1E-05 41.5 3.2 50 79-128 174-226 (233)
52 PF04967 HTH_10: HTH DNA bindi 83.8 0.64 1.4E-05 32.2 1.4 30 97-126 23-52 (53)
53 PRK09047 RNA polymerase factor 83.8 1 2.2E-05 38.5 3.0 49 79-128 105-153 (161)
54 TIGR02950 SigM_subfam RNA poly 83.7 0.64 1.4E-05 39.4 1.7 48 80-128 105-152 (154)
55 TIGR02999 Sig-70_X6 RNA polyme 83.5 0.98 2.1E-05 39.5 2.9 47 80-127 134-180 (183)
56 PRK12537 RNA polymerase sigma 83.4 0.96 2.1E-05 39.7 2.8 48 79-127 132-179 (182)
57 TIGR02989 Sig-70_gvs1 RNA poly 83.4 1.6 3.4E-05 37.1 4.1 48 79-127 110-157 (159)
58 PRK12533 RNA polymerase sigma 83.2 1 2.3E-05 40.9 3.0 50 79-129 133-182 (216)
59 PRK12530 RNA polymerase sigma 83.1 0.82 1.8E-05 40.5 2.2 48 80-128 134-181 (189)
60 TIGR02937 sigma70-ECF RNA poly 83.0 1 2.3E-05 37.3 2.8 46 80-126 110-155 (158)
61 PRK12511 RNA polymerase sigma 83.0 1 2.2E-05 39.7 2.8 50 80-130 111-160 (182)
62 PRK12514 RNA polymerase sigma 82.9 1.1 2.3E-05 39.2 2.9 48 80-128 129-176 (179)
63 PF00872 Transposase_mut: Tran 82.9 0.89 1.9E-05 45.2 2.6 132 91-251 108-248 (381)
64 TIGR02985 Sig70_bacteroi1 RNA 82.7 0.93 2E-05 38.4 2.4 46 80-126 113-158 (161)
65 PF12802 MarR_2: MarR family; 82.7 0.9 2E-05 32.0 1.9 26 98-123 22-47 (62)
66 PRK03975 tfx putative transcri 82.6 1.3 2.7E-05 37.5 3.0 46 79-126 5-50 (141)
67 PRK12525 RNA polymerase sigma 82.6 1.1 2.4E-05 38.7 2.8 47 80-127 118-164 (168)
68 PRK11923 algU RNA polymerase s 82.6 0.96 2.1E-05 40.0 2.5 52 80-132 138-189 (193)
69 COG1595 RpoE DNA-directed RNA 82.4 1.2 2.6E-05 39.2 3.0 49 80-129 127-175 (182)
70 PRK09641 RNA polymerase sigma 82.3 1.1 2.4E-05 39.3 2.7 48 80-128 136-183 (187)
71 PRK12528 RNA polymerase sigma 82.3 0.92 2E-05 38.8 2.2 46 80-126 113-158 (161)
72 PF01022 HTH_5: Bacterial regu 82.1 0.79 1.7E-05 30.7 1.3 37 87-123 5-41 (47)
73 TIGR02392 rpoH_proteo alternat 81.9 1.3 2.9E-05 41.7 3.3 48 80-127 218-266 (270)
74 PRK13919 putative RNA polymera 81.7 1.3 2.8E-05 38.9 2.9 48 80-128 135-182 (186)
75 PRK12547 RNA polymerase sigma 81.7 1.2 2.7E-05 38.3 2.8 48 80-128 112-159 (164)
76 TIGR02939 RpoE_Sigma70 RNA pol 81.6 1.3 2.8E-05 38.9 2.9 50 80-130 138-187 (190)
77 PRK12524 RNA polymerase sigma 81.6 1.2 2.6E-05 39.7 2.7 48 80-128 136-183 (196)
78 PRK12516 RNA polymerase sigma 81.6 1.2 2.6E-05 39.4 2.7 50 80-130 116-165 (187)
79 PRK11924 RNA polymerase sigma 81.4 1.2 2.5E-05 38.6 2.5 48 80-128 125-172 (179)
80 PRK09642 RNA polymerase sigma 81.4 1.2 2.7E-05 38.0 2.6 48 80-128 106-153 (160)
81 TIGR02835 spore_sigmaE RNA pol 81.3 1.4 3.1E-05 40.4 3.2 50 79-128 177-229 (234)
82 PF13730 HTH_36: Helix-turn-he 81.1 1.4 3E-05 30.4 2.3 43 81-123 3-51 (55)
83 TIGR03697 NtcA_cyano global ni 81.1 0.57 1.2E-05 41.3 0.5 78 46-123 73-169 (193)
84 TIGR02983 SigE-fam_strep RNA p 81.0 1.4 3E-05 37.7 2.9 48 80-128 110-157 (162)
85 PRK09651 RNA polymerase sigma 80.8 1.4 3.1E-05 38.2 2.9 49 80-129 119-167 (172)
86 TIGR02947 SigH_actino RNA poly 80.2 1.2 2.7E-05 39.4 2.3 50 80-130 131-180 (193)
87 PRK15320 transcriptional activ 80.2 0.72 1.6E-05 40.9 0.7 38 89-126 171-208 (251)
88 PF00196 GerE: Bacterial regul 80.2 0.67 1.4E-05 32.5 0.5 44 81-126 4-47 (58)
89 PRK07408 RNA polymerase sigma 80.2 1.5 3.2E-05 41.1 2.9 48 80-128 203-250 (256)
90 PRK09637 RNA polymerase sigma 80.1 1.6 3.5E-05 38.4 3.0 51 80-131 106-156 (181)
91 PF13751 DDE_Tnp_1_6: Transpos 80.1 0.78 1.7E-05 37.7 0.9 49 275-324 74-123 (125)
92 PRK12515 RNA polymerase sigma 79.9 1.4 2.9E-05 39.0 2.5 48 80-128 131-178 (189)
93 TIGR02844 spore_III_D sporulat 79.8 0.75 1.6E-05 34.8 0.6 24 97-120 19-42 (80)
94 PRK06759 RNA polymerase factor 79.8 1.4 2.9E-05 37.4 2.4 46 80-126 106-151 (154)
95 PF01325 Fe_dep_repress: Iron 79.7 1.2 2.7E-05 31.6 1.7 40 84-123 6-48 (60)
96 PRK12531 RNA polymerase sigma 79.7 1.5 3.2E-05 39.0 2.7 47 80-127 141-187 (194)
97 PF13412 HTH_24: Winged helix- 79.5 1.3 2.8E-05 29.7 1.7 28 96-123 16-43 (48)
98 TIGR02393 RpoD_Cterm RNA polym 79.3 1.5 3.3E-05 40.4 2.7 48 80-127 176-226 (238)
99 PRK12536 RNA polymerase sigma 79.3 1.5 3.3E-05 38.3 2.6 47 80-127 129-175 (181)
100 PRK12534 RNA polymerase sigma 79.2 1.8 3.9E-05 38.0 3.0 48 80-128 137-184 (187)
101 PRK12532 RNA polymerase sigma 79.1 1.5 3.3E-05 38.9 2.6 49 80-129 136-184 (195)
102 PRK09645 RNA polymerase sigma 79.0 1.7 3.8E-05 37.6 2.9 48 80-128 118-165 (173)
103 PRK05572 sporulation sigma fac 79.0 1.8 4E-05 40.2 3.2 48 80-128 202-249 (252)
104 PF01371 Trp_repressor: Trp re 78.9 1 2.2E-05 34.7 1.1 33 87-119 39-71 (87)
105 PF00325 Crp: Bacterial regula 78.9 0.98 2.1E-05 27.8 0.8 25 98-122 3-27 (32)
106 PRK12541 RNA polymerase sigma 78.8 1.6 3.4E-05 37.4 2.5 47 80-127 112-158 (161)
107 PRK12535 RNA polymerase sigma 78.8 1.9 4.2E-05 38.5 3.1 53 80-133 133-185 (196)
108 PRK12523 RNA polymerase sigma 78.7 1.7 3.7E-05 37.6 2.7 46 80-126 119-164 (172)
109 PRK12520 RNA polymerase sigma 78.7 1.7 3.6E-05 38.4 2.7 48 80-128 131-178 (191)
110 TIGR02984 Sig-70_plancto1 RNA 78.7 1.9 4E-05 37.8 3.0 48 80-128 140-187 (189)
111 PRK09649 RNA polymerase sigma 78.6 1.4 3.1E-05 38.8 2.2 48 79-127 129-176 (185)
112 TIGR02954 Sig70_famx3 RNA poly 78.5 1.9 4.1E-05 37.2 2.9 48 80-128 119-166 (169)
113 PRK05602 RNA polymerase sigma 78.5 1.7 3.8E-05 38.1 2.7 49 80-129 128-176 (186)
114 PRK06596 RNA polymerase factor 78.4 1.9 4.2E-05 40.9 3.2 48 80-127 230-278 (284)
115 PRK12545 RNA polymerase sigma 78.3 1.6 3.5E-05 39.0 2.5 49 80-129 139-187 (201)
116 TIGR02959 SigZ RNA polymerase 78.3 1.7 3.8E-05 37.7 2.6 52 80-132 100-151 (170)
117 PRK12546 RNA polymerase sigma 78.3 1.9 4.2E-05 38.2 2.9 50 79-129 112-161 (188)
118 PRK12513 RNA polymerase sigma 78.2 1.8 3.8E-05 38.4 2.7 48 80-128 139-186 (194)
119 TIGR02948 SigW_bacill RNA poly 78.1 2 4.3E-05 37.6 3.0 49 79-128 135-183 (187)
120 TIGR03001 Sig-70_gmx1 RNA poly 77.7 1.6 3.5E-05 40.5 2.4 47 80-127 161-207 (244)
121 PRK12512 RNA polymerase sigma 77.6 1.9 4.2E-05 37.7 2.7 48 80-128 131-178 (184)
122 PRK09644 RNA polymerase sigma 77.6 1.8 3.9E-05 37.2 2.5 50 79-129 107-156 (165)
123 TIGR02846 spore_sigmaK RNA pol 77.5 2.1 4.6E-05 39.1 3.1 49 79-127 173-224 (227)
124 PRK12542 RNA polymerase sigma 77.4 2.1 4.5E-05 37.6 2.9 50 80-130 122-171 (185)
125 PRK12543 RNA polymerase sigma 77.3 1.8 3.8E-05 37.9 2.4 47 80-127 117-163 (179)
126 PRK07500 rpoH2 RNA polymerase 76.9 2.2 4.8E-05 40.7 3.1 50 80-129 227-277 (289)
127 PRK12540 RNA polymerase sigma 76.9 2.1 4.5E-05 37.7 2.7 50 80-130 111-160 (182)
128 PRK09643 RNA polymerase sigma 76.8 2 4.4E-05 38.1 2.7 49 80-129 134-182 (192)
129 PRK06930 positive control sigm 76.7 2.1 4.5E-05 37.5 2.6 48 80-128 114-161 (170)
130 TIGR02394 rpoS_proteo RNA poly 76.6 2.3 5E-05 40.4 3.1 50 80-129 222-274 (285)
131 PRK12539 RNA polymerase sigma 76.5 2.3 5E-05 37.3 2.9 49 79-128 130-178 (184)
132 PRK12538 RNA polymerase sigma 76.4 2 4.2E-05 39.6 2.5 49 80-129 171-219 (233)
133 cd00092 HTH_CRP helix_turn_hel 76.3 1 2.3E-05 32.1 0.5 27 97-123 25-51 (67)
134 TIGR02980 SigBFG RNA polymeras 76.1 2.3 5E-05 38.8 2.9 47 80-127 178-224 (227)
135 PRK12527 RNA polymerase sigma 76.1 2.2 4.8E-05 36.3 2.6 49 80-129 105-153 (159)
136 PRK12526 RNA polymerase sigma 76.1 2.2 4.7E-05 38.3 2.7 48 80-128 153-200 (206)
137 PF07374 DUF1492: Protein of u 76.0 1.7 3.7E-05 34.4 1.7 43 82-125 57-99 (100)
138 PRK08583 RNA polymerase sigma 76.0 2.3 5E-05 39.6 2.9 47 80-127 205-251 (257)
139 PF01047 MarR: MarR family; I 75.9 1.7 3.7E-05 30.3 1.6 28 96-123 16-43 (59)
140 PRK06986 fliA flagellar biosyn 75.8 2.6 5.7E-05 38.7 3.2 49 80-129 184-232 (236)
141 PRK11753 DNA-binding transcrip 75.6 1.2 2.6E-05 39.9 0.8 45 79-123 137-194 (211)
142 PRK12544 RNA polymerase sigma 75.4 2.1 4.6E-05 38.6 2.4 49 79-128 147-195 (206)
143 PF08279 HTH_11: HTH domain; 74.9 1.9 4.1E-05 29.7 1.5 29 96-124 14-42 (55)
144 PRK11922 RNA polymerase sigma 74.8 2.5 5.5E-05 38.7 2.8 51 80-131 149-199 (231)
145 PRK06811 RNA polymerase factor 74.6 2.2 4.7E-05 37.7 2.3 47 79-126 130-176 (189)
146 PRK09646 RNA polymerase sigma 74.5 2.7 5.9E-05 37.3 2.9 48 80-128 142-189 (194)
147 PRK08215 sporulation sigma fac 74.4 2.8 6E-05 39.2 3.0 47 80-127 209-255 (258)
148 TIGR02997 Sig70-cyanoRpoD RNA 74.4 2.3 4.9E-05 40.8 2.4 46 80-125 249-297 (298)
149 PF13551 HTH_29: Winged helix- 74.3 1.2 2.7E-05 35.3 0.5 34 90-123 4-38 (112)
150 PHA00675 hypothetical protein 74.3 1.4 3.1E-05 32.7 0.8 39 81-119 23-61 (78)
151 PRK10402 DNA-binding transcrip 74.3 4.7 0.0001 36.7 4.4 44 80-123 148-195 (226)
152 PRK12518 RNA polymerase sigma 74.0 2 4.4E-05 37.2 1.8 48 80-128 120-167 (175)
153 TIGR02960 SigX5 RNA polymerase 73.9 2.5 5.4E-05 40.8 2.6 51 80-131 142-192 (324)
154 TIGR02943 Sig70_famx1 RNA poly 73.8 2.6 5.5E-05 37.3 2.5 49 80-129 131-179 (188)
155 PF09339 HTH_IclR: IclR helix- 73.5 2.1 4.5E-05 29.3 1.4 28 96-123 17-44 (52)
156 smart00342 HTH_ARAC helix_turn 73.4 3.9 8.4E-05 30.0 3.1 72 48-123 4-77 (84)
157 PRK06704 RNA polymerase factor 73.2 3.6 7.7E-05 37.8 3.3 56 80-136 116-171 (228)
158 PF05344 DUF746: Domain of Unk 73.1 2 4.3E-05 31.0 1.3 43 86-128 2-44 (65)
159 COG2739 Uncharacterized protei 72.9 2.6 5.6E-05 33.1 1.9 41 85-126 22-62 (105)
160 TIGR02850 spore_sigG RNA polym 72.7 2.9 6.3E-05 39.0 2.7 46 80-126 206-251 (254)
161 TIGR02885 spore_sigF RNA polym 72.6 2.7 5.8E-05 38.5 2.4 46 80-126 183-228 (231)
162 PRK07670 RNA polymerase sigma 72.2 3.6 7.7E-05 38.3 3.2 47 80-127 201-247 (251)
163 PF08299 Bac_DnaA_C: Bacterial 72.1 1.5 3.3E-05 32.2 0.5 42 80-121 28-70 (70)
164 PF04297 UPF0122: Putative hel 71.9 3.4 7.5E-05 32.7 2.5 46 81-127 18-63 (101)
165 PRK08295 RNA polymerase factor 71.9 3.3 7.1E-05 37.0 2.8 47 80-128 155-201 (208)
166 PRK07405 RNA polymerase sigma 71.8 3.1 6.7E-05 40.3 2.7 48 80-127 256-306 (317)
167 TIGR02941 Sigma_B RNA polymera 71.0 3.7 8.1E-05 38.2 3.0 47 80-127 205-251 (255)
168 PF01710 HTH_Tnp_IS630: Transp 70.7 6.2 0.00013 32.2 3.9 72 46-120 19-94 (119)
169 COG1191 FliA DNA-directed RNA 70.6 3.7 8.1E-05 38.1 2.8 48 80-128 196-243 (247)
170 PRK09647 RNA polymerase sigma 70.1 3.4 7.5E-05 37.1 2.5 49 80-129 138-186 (203)
171 PRK09391 fixK transcriptional 70.0 5.4 0.00012 36.4 3.8 44 80-123 152-205 (230)
172 PRK06030 hypothetical protein; 69.8 3.5 7.7E-05 34.0 2.2 47 79-125 51-97 (124)
173 TIGR02479 FliA_WhiG RNA polyme 69.1 4.4 9.4E-05 36.9 3.0 47 80-127 175-221 (224)
174 PRK07122 RNA polymerase sigma 69.1 4.6 0.0001 37.9 3.2 47 80-127 215-261 (264)
175 PRK15201 fimbriae regulatory p 68.8 2.2 4.7E-05 37.3 0.8 47 78-126 131-177 (198)
176 PRK12517 RNA polymerase sigma 68.8 3.6 7.8E-05 36.4 2.3 49 80-129 128-176 (188)
177 PRK09648 RNA polymerase sigma 68.4 4.6 9.9E-05 35.5 2.9 47 80-127 139-185 (189)
178 PRK11161 fumarate/nitrate redu 68.2 5.3 0.00011 36.4 3.3 44 80-123 153-210 (235)
179 PF09862 DUF2089: Protein of u 68.1 3.3 7.1E-05 33.5 1.6 46 80-126 33-78 (113)
180 PHA00542 putative Cro-like pro 67.8 1.6 3.4E-05 33.2 -0.2 29 92-120 26-54 (82)
181 COG2963 Transposase and inacti 67.7 4 8.7E-05 33.0 2.2 46 78-123 5-51 (116)
182 COG5421 Transposase [DNA repli 67.6 7.4 0.00016 39.3 4.4 58 183-241 153-210 (480)
183 smart00550 Zalpha Z-DNA-bindin 66.9 4.2 9.1E-05 29.6 1.9 41 82-122 6-47 (68)
184 PRK15411 rcsA colanic acid cap 66.7 2.5 5.5E-05 38.1 0.9 45 80-126 137-181 (207)
185 PRK03573 transcriptional regul 66.4 5 0.00011 33.7 2.6 43 81-123 29-72 (144)
186 PF01381 HTH_3: Helix-turn-hel 66.3 2.5 5.3E-05 29.0 0.6 26 95-120 7-32 (55)
187 PF01710 HTH_Tnp_IS630: Transp 66.0 1.7 3.7E-05 35.5 -0.3 27 93-119 14-40 (119)
188 PF00165 HTH_AraC: Bacterial r 66.0 2.6 5.6E-05 27.3 0.6 29 94-122 5-33 (42)
189 smart00345 HTH_GNTR helix_turn 65.8 5.6 0.00012 27.3 2.4 25 99-123 22-46 (60)
190 PF00126 HTH_1: Bacterial regu 65.7 3.3 7.2E-05 29.2 1.2 29 98-126 14-42 (60)
191 TIGR03209 P21_Cbot clostridium 65.6 3 6.4E-05 34.8 1.0 37 79-116 106-142 (142)
192 PRK09640 RNA polymerase sigma 65.6 2.9 6.4E-05 36.8 1.1 49 80-129 134-182 (188)
193 PF13309 HTH_22: HTH domain 65.1 6.3 0.00014 28.4 2.5 22 98-119 43-64 (64)
194 PRK13870 transcriptional regul 65.0 2.6 5.7E-05 38.8 0.7 46 79-126 172-217 (234)
195 smart00346 HTH_ICLR helix_turn 64.8 3.8 8.2E-05 31.2 1.4 27 97-123 20-46 (91)
196 TIGR01610 phage_O_Nterm phage 64.8 3.9 8.5E-05 32.0 1.5 30 94-123 44-73 (95)
197 PRK07406 RNA polymerase sigma 64.4 5.3 0.00012 39.5 2.7 47 80-126 311-360 (373)
198 PRK06288 RNA polymerase sigma 64.2 5 0.00011 37.7 2.4 47 80-127 212-258 (268)
199 TIGR01636 phage_rinA phage tra 63.7 7.4 0.00016 32.5 3.1 47 81-127 83-130 (134)
200 PRK08241 RNA polymerase factor 63.6 6.6 0.00014 38.1 3.2 50 80-130 153-202 (339)
201 PRK12427 flagellar biosynthesi 63.5 5.5 0.00012 36.6 2.4 46 80-126 183-228 (231)
202 PF12840 HTH_20: Helix-turn-he 63.2 4 8.7E-05 28.8 1.2 30 94-123 21-50 (61)
203 smart00419 HTH_CRP helix_turn_ 63.1 3.9 8.4E-05 26.8 1.1 28 96-123 7-34 (48)
204 PRK10840 transcriptional regul 62.9 4.5 9.7E-05 36.3 1.8 45 80-126 150-194 (216)
205 PRK07598 RNA polymerase sigma 62.7 5.8 0.00012 39.8 2.6 47 80-126 350-399 (415)
206 PRK09392 ftrB transcriptional 62.4 10 0.00022 34.5 4.1 45 79-123 145-199 (236)
207 TIGR02957 SigX4 RNA polymerase 62.2 7.4 0.00016 36.8 3.2 50 80-130 108-157 (281)
208 PRK05949 RNA polymerase sigma 62.1 6.5 0.00014 38.2 2.8 48 80-127 266-316 (327)
209 PRK09210 RNA polymerase sigma 61.5 6.4 0.00014 38.9 2.7 47 80-126 305-354 (367)
210 PRK05657 RNA polymerase sigma 61.4 7.5 0.00016 37.8 3.1 50 80-129 262-314 (325)
211 PRK09636 RNA polymerase sigma 60.5 7.3 0.00016 37.0 2.8 50 80-130 115-164 (293)
212 COG2197 CitB Response regulato 60.3 3.6 7.8E-05 37.2 0.6 45 80-126 148-192 (211)
213 PRK13918 CRP/FNR family transc 60.1 4.6 9.9E-05 35.8 1.3 44 80-123 118-175 (202)
214 TIGR02859 spore_sigH RNA polym 60.0 5.8 0.00013 35.0 2.0 44 82-127 152-195 (198)
215 PF04703 FaeA: FaeA-like prote 59.8 3.5 7.5E-05 29.6 0.3 38 85-122 3-40 (62)
216 TIGR03541 reg_near_HchA LuxR f 59.8 15 0.00033 33.7 4.7 46 79-126 170-215 (232)
217 PF02001 DUF134: Protein of un 58.7 8.9 0.00019 30.7 2.5 46 80-126 41-86 (106)
218 smart00418 HTH_ARSR helix_turn 58.2 5.4 0.00012 27.6 1.2 29 95-123 8-36 (66)
219 TIGR02337 HpaR homoprotocatech 58.0 12 0.00025 30.2 3.3 29 95-123 40-68 (118)
220 PRK13719 conjugal transfer tra 57.8 4.6 0.0001 36.6 0.9 45 80-126 143-187 (217)
221 PF13545 HTH_Crp_2: Crp-like h 57.2 5.4 0.00012 29.3 1.0 27 97-123 28-54 (76)
222 PF05269 Phage_CII: Bacterioph 56.9 8.1 0.00018 30.0 2.0 29 98-126 24-52 (91)
223 PF07638 Sigma70_ECF: ECF sigm 56.8 9.8 0.00021 33.5 2.8 45 81-126 136-180 (185)
224 PF10654 DUF2481: Protein of u 56.2 4.3 9.4E-05 32.5 0.4 30 96-125 79-108 (126)
225 smart00354 HTH_LACI helix_turn 56.2 4.4 9.4E-05 29.6 0.4 22 99-120 2-23 (70)
226 PF13463 HTH_27: Winged helix 56.2 9.2 0.0002 27.2 2.1 28 96-123 17-44 (68)
227 PF13560 HTH_31: Helix-turn-he 56.1 4 8.8E-05 29.1 0.2 27 93-119 10-36 (64)
228 PF01978 TrmB: Sugar-specific 55.7 5.7 0.00012 28.7 0.9 38 85-123 11-48 (68)
229 COG2771 CsgD DNA-binding HTH d 55.4 5.6 0.00012 27.9 0.8 35 91-125 13-47 (65)
230 PF06056 Terminase_5: Putative 55.3 6.5 0.00014 27.8 1.1 32 87-120 5-36 (58)
231 cd01392 HTH_LacI Helix-turn-he 55.2 4.2 9.2E-05 27.4 0.2 20 102-121 2-21 (52)
232 PRK15418 transcriptional regul 54.9 5.3 0.00012 38.6 0.8 35 89-123 21-55 (318)
233 TIGR03020 EpsA transcriptional 54.2 10 0.00022 35.2 2.6 46 79-126 189-234 (247)
234 PRK11475 DNA-binding transcrip 54.2 5.3 0.00011 36.1 0.6 45 80-126 134-178 (207)
235 PRK11512 DNA-binding transcrip 54.2 10 0.00022 31.9 2.3 43 80-123 37-80 (144)
236 PF03333 PapB: Adhesin biosynt 54.0 12 0.00025 29.1 2.4 57 56-123 22-79 (91)
237 PF13744 HTH_37: Helix-turn-he 52.4 5.9 0.00013 29.8 0.6 25 95-119 29-53 (80)
238 COG3355 Predicted transcriptio 52.2 18 0.00039 29.9 3.4 48 53-123 21-68 (126)
239 PRK10188 DNA-binding transcrip 52.0 6.3 0.00014 36.5 0.8 46 79-126 178-223 (240)
240 PRK07921 RNA polymerase sigma 51.7 12 0.00025 36.5 2.6 48 80-127 262-312 (324)
241 PRK05901 RNA polymerase sigma 51.5 12 0.00025 38.7 2.7 48 80-127 447-497 (509)
242 smart00347 HTH_MARR helix_turn 51.1 12 0.00027 28.5 2.3 28 96-123 23-50 (101)
243 cd04762 HTH_MerR-trunc Helix-T 50.8 6.2 0.00013 25.7 0.4 22 99-120 2-23 (49)
244 TIGR03070 couple_hipB transcri 50.7 6.4 0.00014 26.8 0.5 25 95-119 13-37 (58)
245 PRK09492 treR trehalose repres 49.6 12 0.00026 35.5 2.4 23 98-120 5-27 (315)
246 cd00090 HTH_ARSR Arsenical Res 49.4 9.4 0.0002 27.2 1.3 27 97-123 20-46 (78)
247 PF12964 DUF3853: Protein of u 49.3 7 0.00015 30.4 0.5 57 54-119 10-67 (96)
248 PRK09483 response regulator; P 49.2 7 0.00015 34.5 0.6 45 79-125 147-191 (217)
249 PHA02591 hypothetical protein; 48.8 6.3 0.00014 29.4 0.2 32 89-120 51-82 (83)
250 PRK12469 RNA polymerase factor 48.6 17 0.00037 37.3 3.3 31 97-137 369-399 (481)
251 TIGR01889 Staph_reg_Sar staphy 48.6 15 0.00033 29.3 2.4 28 96-123 42-69 (109)
252 smart00420 HTH_DEOR helix_turn 48.5 10 0.00022 25.1 1.2 27 97-123 14-40 (53)
253 PF08220 HTH_DeoR: DeoR-like h 48.2 9.5 0.00021 26.6 1.0 26 97-122 14-39 (57)
254 TIGR02405 trehalos_R_Ecol treh 48.1 11 0.00024 35.7 1.9 21 99-119 3-23 (311)
255 PRK13413 mpi multiple promoter 48.0 7 0.00015 34.9 0.4 27 93-119 168-194 (200)
256 TIGR01764 excise DNA binding d 47.9 7.4 0.00016 25.4 0.4 21 99-119 3-23 (49)
257 PF04552 Sigma54_DBD: Sigma-54 47.8 6.1 0.00013 34.2 0.0 23 97-119 49-71 (160)
258 PF00440 TetR_N: Bacterial reg 47.8 12 0.00026 24.8 1.5 31 96-126 15-45 (47)
259 PRK09635 sigI RNA polymerase s 47.6 17 0.00036 34.7 2.9 50 80-130 118-167 (290)
260 PRK10100 DNA-binding transcrip 47.6 8.3 0.00018 35.0 0.8 45 80-126 155-199 (216)
261 PRK05932 RNA polymerase factor 47.3 19 0.00041 36.7 3.5 58 49-119 306-365 (455)
262 COG3413 Predicted DNA binding 47.0 14 0.00029 33.5 2.2 48 80-127 155-208 (215)
263 PHA00738 putative HTH transcri 46.9 10 0.00022 30.3 1.2 27 98-124 27-53 (108)
264 PRK09191 two-component respons 46.8 13 0.00028 34.1 2.1 47 80-127 88-134 (261)
265 PF12728 HTH_17: Helix-turn-he 46.4 8.2 0.00018 26.0 0.5 21 99-119 3-23 (51)
266 PF13610 DDE_Tnp_IS240: DDE do 46.0 20 0.00044 30.0 2.9 46 279-326 94-139 (140)
267 PF13404 HTH_AsnC-type: AsnC-t 45.9 9.2 0.0002 25.0 0.6 24 97-120 17-40 (42)
268 PF13551 HTH_29: Winged helix- 45.7 37 0.0008 26.6 4.3 73 48-120 15-110 (112)
269 TIGR02395 rpoN_sigma RNA polym 45.4 21 0.00046 36.0 3.5 58 49-119 281-340 (429)
270 PRK14987 gluconate operon tran 45.2 8.1 0.00017 37.0 0.4 23 98-120 6-28 (331)
271 smart00352 POU Found in Pit-Oc 45.2 6.8 0.00015 29.2 -0.1 27 93-119 20-52 (75)
272 PF05043 Mga: Mga helix-turn-h 45.0 15 0.00032 27.8 1.8 34 94-127 27-60 (87)
273 PRK12682 transcriptional regul 44.8 12 0.00026 35.5 1.6 42 85-126 4-45 (309)
274 PRK10014 DNA-binding transcrip 44.8 8.2 0.00018 37.1 0.4 24 97-120 6-29 (342)
275 PRK10870 transcriptional repre 44.7 36 0.00078 29.7 4.4 44 80-123 52-97 (176)
276 PHA01976 helix-turn-helix prot 44.3 9.3 0.0002 27.2 0.5 26 94-119 12-37 (67)
277 PRK09526 lacI lac repressor; R 44.0 8.6 0.00019 36.9 0.4 23 98-120 6-28 (342)
278 COG4496 Uncharacterized protei 44.0 36 0.00078 26.1 3.6 28 92-119 51-78 (100)
279 cd07377 WHTH_GntR Winged helix 43.8 12 0.00027 26.1 1.1 25 99-123 27-51 (66)
280 PF13443 HTH_26: Cro/C1-type H 43.5 9.3 0.0002 26.9 0.4 27 95-121 8-34 (63)
281 COG4565 CitB Response regulato 43.5 29 0.00063 31.4 3.6 39 85-123 161-199 (224)
282 COG2522 Predicted transcriptio 43.2 11 0.00024 30.8 0.8 25 96-120 21-45 (119)
283 PF00392 GntR: Bacterial regul 42.7 21 0.00046 25.3 2.2 25 99-123 26-50 (64)
284 COG1508 RpoN DNA-directed RNA 42.0 16 0.00034 36.9 1.8 22 98-119 331-352 (444)
285 PRK10339 DNA-binding transcrip 41.9 9.7 0.00021 36.4 0.4 23 99-121 3-25 (327)
286 PRK11303 DNA-binding transcrip 41.1 10 0.00022 36.2 0.4 22 99-120 2-23 (328)
287 PRK10401 DNA-binding transcrip 40.9 17 0.00037 35.0 1.9 22 99-120 3-24 (346)
288 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 40.5 15 0.00032 25.2 1.0 40 79-119 3-42 (50)
289 PRK10141 DNA-binding transcrip 40.0 13 0.00029 30.2 0.9 39 85-123 17-56 (117)
290 smart00344 HTH_ASNC helix_turn 39.7 21 0.00045 28.1 2.0 27 97-123 17-43 (108)
291 PRK12683 transcriptional regul 39.7 16 0.00035 34.8 1.5 42 85-126 4-45 (309)
292 COG2390 DeoR Transcriptional r 39.6 12 0.00026 36.2 0.7 32 91-122 20-51 (321)
293 PRK15215 fimbriae biosynthesis 39.5 43 0.00093 26.4 3.5 58 56-124 30-88 (100)
294 PRK14086 dnaA chromosomal repl 39.4 24 0.00051 37.4 2.8 48 79-126 551-598 (617)
295 PRK10703 DNA-binding transcrip 39.3 11 0.00025 36.1 0.4 22 99-120 3-24 (341)
296 PRK10651 transcriptional regul 38.9 12 0.00027 32.5 0.6 45 80-126 155-199 (216)
297 PRK10403 transcriptional regul 38.4 13 0.00028 32.3 0.7 45 80-126 153-197 (215)
298 cd00131 PAX Paired Box domain 38.4 72 0.0016 26.3 5.1 75 46-120 34-126 (128)
299 PRK14088 dnaA chromosomal repl 38.3 23 0.00051 35.9 2.5 47 79-125 369-415 (440)
300 PRK10360 DNA-binding transcrip 37.8 14 0.00031 31.8 0.8 45 80-126 137-181 (196)
301 PRK10423 transcriptional repre 37.4 12 0.00026 35.6 0.3 19 101-119 2-20 (327)
302 PRK00149 dnaA chromosomal repl 37.3 26 0.00056 35.6 2.7 48 79-126 384-432 (450)
303 PF00382 TFIIB: Transcription 36.8 49 0.0011 23.9 3.4 62 50-114 3-71 (71)
304 COG4974 XerD Site-specific rec 36.8 58 0.0013 31.0 4.6 80 48-129 210-293 (300)
305 PRK12679 cbl transcriptional r 36.8 20 0.00043 34.3 1.7 42 85-126 4-45 (316)
306 TIGR00122 birA_repr_reg BirA b 36.6 16 0.00035 26.3 0.8 26 98-123 14-39 (69)
307 TIGR02417 fruct_sucro_rep D-fr 36.5 13 0.00029 35.4 0.4 21 100-120 2-22 (327)
308 PRK00215 LexA repressor; Valid 36.4 22 0.00048 31.8 1.8 28 96-123 22-50 (205)
309 COG3316 Transposase and inacti 36.4 1.3E+02 0.0028 27.3 6.6 184 84-327 12-202 (215)
310 TIGR00180 parB_part ParB-like 35.9 20 0.00043 31.7 1.4 41 79-119 101-142 (187)
311 PRK10072 putative transcriptio 35.7 16 0.00034 28.7 0.6 25 95-119 44-68 (96)
312 PRK05658 RNA polymerase sigma 35.6 31 0.00068 36.7 3.0 47 80-126 556-605 (619)
313 PF05263 DUF722: Protein of un 35.5 28 0.0006 29.0 2.1 45 81-125 82-127 (130)
314 PRK09958 DNA-binding transcrip 35.5 16 0.00034 31.8 0.7 45 80-126 143-187 (204)
315 PRK15369 two component system 35.5 31 0.00067 29.6 2.6 45 80-126 149-193 (211)
316 TIGR01481 ccpA catabolite cont 34.9 15 0.00032 35.1 0.4 22 99-120 3-24 (329)
317 PRK11233 nitrogen assimilation 34.5 22 0.00047 33.7 1.5 33 94-126 12-44 (305)
318 PRK10727 DNA-binding transcrip 34.4 15 0.00033 35.3 0.4 22 99-120 3-24 (343)
319 TIGR02431 pcaR_pcaU beta-ketoa 34.3 22 0.00049 32.8 1.5 43 81-123 5-50 (248)
320 PRK09834 DNA-binding transcrip 33.8 22 0.00047 33.3 1.4 44 80-123 6-52 (263)
321 PF01726 LexA_DNA_bind: LexA D 33.5 24 0.00051 25.5 1.2 27 95-121 23-50 (65)
322 PF10668 Phage_terminase: Phag 33.5 19 0.00041 25.6 0.7 21 97-117 22-42 (60)
323 TIGR00637 ModE_repress ModE mo 33.2 21 0.00045 28.1 1.0 33 94-126 13-45 (99)
324 COG3293 Transposase and inacti 33.0 64 0.0014 26.1 3.9 93 188-299 2-99 (124)
325 COG1609 PurR Transcriptional r 32.6 16 0.00035 35.5 0.3 23 99-121 2-24 (333)
326 TIGR02607 antidote_HigA addict 32.5 19 0.00042 26.4 0.7 26 94-119 15-40 (78)
327 PRK10163 DNA-binding transcrip 32.4 29 0.00063 32.6 2.0 45 79-123 19-66 (271)
328 smart00529 HTH_DTXR Helix-turn 32.3 24 0.00053 27.0 1.2 24 100-123 2-25 (96)
329 PRK12684 transcriptional regul 32.2 26 0.00056 33.4 1.6 41 86-126 5-45 (313)
330 COG5606 Uncharacterized conser 32.1 9.6 0.00021 29.1 -1.1 64 58-123 2-67 (91)
331 TIGR03830 CxxCG_CxxCG_HTH puta 31.3 35 0.00076 27.7 2.1 28 93-120 74-101 (127)
332 PF02954 HTH_8: Bacterial regu 31.2 23 0.00049 22.9 0.7 25 96-120 17-41 (42)
333 PRK11050 manganese transport r 31.1 28 0.00061 29.6 1.5 28 96-123 50-77 (152)
334 PRK14087 dnaA chromosomal repl 30.9 38 0.00082 34.5 2.6 48 79-126 383-431 (450)
335 TIGR02702 SufR_cyano iron-sulf 30.8 34 0.00074 30.6 2.1 39 84-123 3-41 (203)
336 PF01418 HTH_6: Helix-turn-hel 30.6 20 0.00043 26.7 0.4 24 97-120 34-57 (77)
337 PF07453 NUMOD1: NUMOD1 domain 30.3 21 0.00045 22.3 0.4 22 97-118 16-37 (37)
338 PF05930 Phage_AlpA: Prophage 29.4 22 0.00049 24.0 0.5 21 99-119 5-25 (51)
339 PRK13777 transcriptional regul 29.4 42 0.00092 29.7 2.4 42 80-121 42-83 (185)
340 PRK09726 antitoxin HipB; Provi 29.1 22 0.00047 27.1 0.4 27 94-120 22-48 (88)
341 PF08535 KorB: KorB domain; I 28.3 25 0.00054 27.2 0.6 24 96-119 2-25 (93)
342 PF00292 PAX: 'Paired box' dom 28.3 43 0.00094 27.6 2.0 46 76-123 13-59 (125)
343 COG1342 Predicted DNA-binding 27.8 57 0.0012 25.5 2.4 46 80-126 33-78 (99)
344 PRK11151 DNA-binding transcrip 27.5 34 0.00074 32.3 1.5 40 86-126 5-44 (305)
345 PRK12422 chromosomal replicati 27.4 44 0.00095 34.0 2.4 47 79-125 379-425 (445)
346 cd04761 HTH_MerR-SF Helix-Turn 27.0 25 0.00054 23.0 0.4 21 99-119 2-22 (49)
347 PF08765 Mor: Mor transcriptio 26.8 28 0.00062 27.7 0.7 29 97-125 72-100 (108)
348 PRK11569 transcriptional repre 26.8 42 0.00091 31.6 2.0 45 79-123 22-69 (274)
349 TIGR01884 cas_HTH CRISPR locus 26.8 47 0.001 29.7 2.2 27 97-123 157-183 (203)
350 PF14493 HTH_40: Helix-turn-he 26.7 30 0.00065 26.6 0.8 36 89-124 5-40 (91)
351 PF05732 RepL: Firmicute plasm 26.5 32 0.0007 29.9 1.1 26 98-123 76-101 (165)
352 PRK00423 tfb transcription ini 26.1 1.3E+02 0.0029 28.8 5.4 76 50-125 225-304 (310)
353 COG2186 FadR Transcriptional r 26.0 67 0.0015 29.6 3.2 45 57-118 11-55 (241)
354 PRK10219 DNA-binding transcrip 25.8 50 0.0011 25.9 2.0 29 95-123 19-47 (107)
355 PRK12681 cysB transcriptional 25.6 39 0.00084 32.5 1.6 41 86-126 5-45 (324)
356 PRK11511 DNA-binding transcrip 25.6 36 0.00077 27.9 1.1 30 94-123 22-51 (127)
357 PRK15090 DNA-binding transcrip 25.5 46 0.00099 30.9 2.0 45 79-123 8-54 (257)
358 PRK09706 transcriptional repre 24.9 30 0.00065 28.7 0.6 26 95-120 16-41 (135)
359 PRK10430 DNA-binding transcrip 24.8 39 0.00085 30.7 1.4 34 93-126 174-207 (239)
360 PRK11013 DNA-binding transcrip 24.2 41 0.00088 31.9 1.4 39 87-126 9-47 (309)
361 PRK09935 transcriptional regul 24.2 31 0.00068 29.9 0.6 45 80-126 149-193 (210)
362 TIGR03418 chol_sulf_TF putativ 24.1 41 0.0009 31.4 1.4 39 87-126 6-44 (291)
363 PRK09791 putative DNA-binding 23.9 44 0.00094 31.5 1.6 33 94-126 16-48 (302)
364 COG0593 DnaA ATPase involved i 23.7 60 0.0013 32.6 2.5 49 78-126 346-394 (408)
365 COG3139 Uncharacterized protei 23.6 1.5E+02 0.0032 22.5 3.9 43 56-99 9-55 (90)
366 PF07022 Phage_CI_repr: Bacter 23.6 31 0.00066 24.8 0.3 22 99-120 14-36 (66)
367 PRK09906 DNA-binding transcrip 23.6 40 0.00086 31.6 1.2 36 91-126 9-44 (296)
368 COG1846 MarR Transcriptional r 23.5 48 0.001 26.1 1.5 23 101-123 40-62 (126)
369 PRK10094 DNA-binding transcrip 23.1 43 0.00093 31.8 1.3 33 94-126 13-45 (308)
370 COG2973 TrpR Trp operon repres 23.0 42 0.00091 26.3 1.0 26 93-118 56-81 (103)
371 cd01104 HTH_MlrA-CarA Helix-Tu 22.8 36 0.00078 24.1 0.6 22 99-120 2-23 (68)
372 COG0664 Crp cAMP-binding prote 22.7 43 0.00094 29.1 1.2 45 79-123 139-197 (214)
373 PRK12680 transcriptional regul 22.7 49 0.0011 31.9 1.6 38 89-126 8-45 (327)
374 COG1414 IclR Transcriptional r 22.6 53 0.0011 30.4 1.8 26 98-123 20-45 (246)
375 PRK11179 DNA-binding transcrip 22.4 69 0.0015 27.2 2.3 27 97-123 23-49 (153)
376 smart00497 IENR1 Intron encode 22.4 38 0.00082 22.7 0.6 24 97-120 17-40 (53)
377 PRK09940 transcriptional regul 22.3 91 0.002 29.1 3.3 89 33-121 82-174 (253)
378 PF14549 P22_Cro: DNA-binding 22.2 33 0.00071 24.4 0.2 26 99-125 11-36 (60)
379 TIGR03454 partition_RepB plasm 21.8 51 0.0011 32.0 1.5 42 79-120 159-200 (325)
380 PRK15421 DNA-binding transcrip 21.6 51 0.0011 31.5 1.5 39 87-126 7-45 (317)
381 smart00530 HTH_XRE Helix-turn- 21.6 41 0.00088 21.5 0.6 24 96-119 9-32 (56)
382 PRK10046 dpiA two-component re 21.4 36 0.00078 30.6 0.4 29 91-119 168-199 (225)
383 PF01476 LysM: LysM domain; I 21.3 41 0.00089 21.4 0.6 24 93-116 2-25 (44)
384 TIGR02944 suf_reg_Xantho FeS a 21.2 42 0.00091 27.5 0.7 26 98-123 26-51 (130)
385 PF09607 BrkDBD: Brinker DNA-b 21.1 45 0.00097 23.5 0.7 42 79-120 4-48 (58)
386 PF12844 HTH_19: Helix-turn-he 21.1 40 0.00086 23.6 0.5 26 95-120 10-35 (64)
387 PHA02701 ORF020 dsRNA-binding 21.0 65 0.0014 28.4 1.9 40 84-123 6-45 (183)
388 PRK08558 adenine phosphoribosy 21.0 47 0.001 30.7 1.1 36 84-119 10-45 (238)
389 cd07153 Fur_like Ferric uptake 20.9 78 0.0017 25.1 2.3 27 97-123 16-47 (116)
390 PRK11242 DNA-binding transcrip 20.9 53 0.0011 30.6 1.4 32 95-126 13-44 (296)
391 TIGR00498 lexA SOS regulatory 20.8 62 0.0013 28.7 1.8 27 97-123 25-52 (199)
392 PF13022 HTH_Tnp_1_2: Helix-tu 20.6 53 0.0011 27.6 1.2 36 98-133 35-73 (142)
393 PRK13832 plasmid partitioning 20.6 69 0.0015 33.0 2.2 41 78-118 99-139 (520)
394 TIGR02612 mob_myst_A mobile my 20.5 41 0.0009 28.7 0.6 27 93-119 34-60 (150)
395 COG2944 Predicted transcriptio 20.5 39 0.00085 26.9 0.4 23 95-117 55-77 (104)
396 TIGR03384 betaine_BetI transcr 20.3 47 0.001 28.6 0.9 34 96-129 27-60 (189)
No 1
>KOG4585 consensus Predicted transposase [Replication, recombination and repair]
Probab=100.00 E-value=9.3e-44 Score=339.21 Aligned_cols=311 Identities=31% Similarity=0.521 Sum_probs=257.3
Q ss_pred hcCCCHHHHHHHHHHHhcCCcccc-----CCCCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHh
Q 015913 54 NFRMDKKVFYKLCDILQSKGLLRH-----TNRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 128 (398)
Q Consensus 54 ~frms~~~F~~L~~~l~~~~~~~~-----~~~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~ 128 (398)
.|++++.+|..++........... ...+++...+++.++.++++.+.+.++..||...+|+ .+.......
T Consensus 7 ~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~i~~~fg~~~~~~-----~~~~~~~~~ 81 (326)
T KOG4585|consen 7 EFRKSYTTFDKICSLVQSLNVVKNSGFMLSSLLPADTLVAVALWRLKTGESLRTVEKKFGLGQSTC-----KFLEEKEDL 81 (326)
T ss_pred HHHHHHHHHHHHhhhhhhhhhhcccchhhhccccHHhhhhhhhccccccchHHHHHHHcCCcchhh-----hHHHhhhcc
Confidence 678899999999988765432222 1223389999999999999999999999999999999 556666678
Q ss_pred hccccCCCCCCCccccccCCccccccccceeeecceEEEEEeCCCCCCCCCCCCCccccceeeeecCCcceEEeecCccc
Q 015913 129 SLDFFQPPGPDVPPEISLDPRLYPYFKDCVGAVDGIHIPVMVGVDEQGPFRNKSGLLSQNVLAACSFDLKFHYVLAGWEG 208 (398)
Q Consensus 129 ~~~~i~~P~~~~~~~i~~~~~~~~~fp~~iG~IDgt~i~i~~P~~~~~~y~~~k~~~s~~~q~v~d~~~~~~~v~~g~~G 208 (398)
++.++.||......++.+..+. ||+|+|+||+|||++..|+.....|.|+ .++.|+|+|||+|++|++|.+||||
T Consensus 82 ~~~~~~~p~~~~~~~i~~~~~~---~~~~~g~~d~~hi~~~~~~~~~~~~~n~--~~~~Nvlav~n~d~~f~~v~vg~~G 156 (326)
T KOG4585|consen 82 APHFLKWPSRRILYEIRERFES---LPNCVGAIDTTHIPIRVPPKSGSVYFNK--EQSKNLLAVCNFDMRFIYVDVGWPG 156 (326)
T ss_pred cchhhcCchhhhhhhhcccccc---ccchhccccccccceecCcccccccccc--ccchhhhheecCCceEEEEEccCCC
Confidence 9999999997666666654443 8999999999999999999999999998 8899999999999999999999999
Q ss_pred ccccHHHHHHHHhh-cCCCCCCCCceeeccCCCCCCCCccccccCcccCcccccCCC-CchhHHHHHHHHHHHHHhHHHH
Q 015913 209 SASDLRVLNSALTR-RNKLQVPEGKYYLVDNKYANMPGFIAPYQAVSYHTNQTTTGY-HPQDAKELFNQRHSLLRNATDR 286 (398)
Q Consensus 209 s~~D~~vl~~sl~~-~~~~~~~~g~~~l~D~gYp~~~~ll~P~~~~~~~l~~~~~~~-~~~~~~~~fN~~~s~~R~~VE~ 286 (398)
|.||+.|++.++.. ......+. +|+|.|.||++.++++.|+..+.++...|..++ .|+..++.||++|+.+|.++|+
T Consensus 157 s~~D~kvl~~~~~~~~~~~~~~~-k~yl~d~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~elFN~rh~~~r~v~e~ 235 (326)
T KOG4585|consen 157 SAHDTKVLQDSLLYKRNFPHPPL-KYYLVDSGYPLRPGLLGPIGFPLYSLLMFPYGGPQPTNSQELFNKRHSSLRSVAER 235 (326)
T ss_pred CccHHHHHHhhcccccccccCCc-cccccccCcccccccccccccccchhhhcccCCCCCCchHHHHhhhhhhHHHHHHH
Confidence 99999999988654 23334455 999999999999999999999999999998777 4889999999999999999999
Q ss_pred HHHHHHhhhhhhccCCCCCccchhHHhHHHHHHHhhhhccCCCcccccccccCCcccccccCCCCCCCCCCCCccccccc
Q 015913 287 IFGALKERFPILLSAPPYPLQTQVKLVVAACALHNYIQREKPDDWLFRMYEQDTLLPMAESLLPLEGEQPIVHVDTRALE 366 (398)
Q Consensus 287 ~fg~LK~rf~iL~~~~~~~~~~~~~ii~ac~~LHN~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~p~~~~~~~~~~ 366 (398)
+||+||.||+||.....+...+...||.|||+|||++++.+.++..+..++... .+. .....
T Consensus 236 ~fg~lk~rw~il~~~~~~~~~~~~~iV~a~caLHN~~~~~~~~~~~~~~~e~~~--------------d~~----~~~~~ 297 (326)
T KOG4585|consen 236 AFGVLKAKWRILQRREKYDLKKLPKIVTACCALHNIIRDSDEEDPDDPKWEKFD--------------DYG----ENVAH 297 (326)
T ss_pred HHHHhhhhhHHHhhcccccccchHHHHHHHHHHHHHHHhhcccccccccccccc--------------ccc----ccchh
Confidence 999999999999977778899999999999999999999887664433222111 000 01112
Q ss_pred cccchHhHHHHHHHHHHHHHHHHHHhh
Q 015913 367 FGFQTEQLELASHFRDSIATEMWDDYI 393 (398)
Q Consensus 367 ~~~~~~~~~~~~~lRd~ia~~lw~~~~ 393 (398)
.....+.++.|+.+|+.|+..||+...
T Consensus 298 ~~~~~~~~~~~~~~r~~l~~~l~~~~~ 324 (326)
T KOG4585|consen 298 LRYAPQQRDYMEKIRDNLLSELWNGTR 324 (326)
T ss_pred cccchhHHHHHHHHHHHHHHHHHhccc
Confidence 233456778899999999999998753
No 2
>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=1.1e-42 Score=298.56 Aligned_cols=187 Identities=22% Similarity=0.360 Sum_probs=163.5
Q ss_pred cccCCCCCCCccccccCCccccccccceeeecceEEEEE-eCCCCCCCCC-CCCCccccceeeeecCCcceEEeecCccc
Q 015913 131 DFFQPPGPDVPPEISLDPRLYPYFKDCVGAVDGIHIPVM-VGVDEQGPFR-NKSGLLSQNVLAACSFDLKFHYVLAGWEG 208 (398)
Q Consensus 131 ~~i~~P~~~~~~~i~~~~~~~~~fp~~iG~IDgt~i~i~-~P~~~~~~y~-~~k~~~s~~~q~v~d~~~~~~~v~~g~~G 208 (398)
+|++-|+.++.++++...+ ..||||++|+|||+|+.++ +|..++.+|. |++|.+|+.++||+++|++|++++.|.||
T Consensus 2 ~YLr~P~~~d~~rll~~~e-~rGFpGmlGSIDCmHw~WkncP~aw~g~~~~G~~g~pTiiLEaVAs~dlwIWhaffG~~G 80 (205)
T PF04827_consen 2 EYLRRPTNEDLERLLQIGE-ARGFPGMLGSIDCMHWEWKNCPTAWKGQYTRGKEGVPTIILEAVASHDLWIWHAFFGMPG 80 (205)
T ss_pred cccCCCChhHHHHHHHhhh-hcCCCccccceeEEEeehhcchHHhhhcccCCCCCCCeehhhhhhccchhhhheeeccCC
Confidence 6899999999888875333 2499999999999999998 8999999997 99999999999999999999999999999
Q ss_pred ccccHHHHHHH-Hhhc--CC------CCCCC----CceeeccCCCCCCCCccccccCcccCcccccCCCCchhHHHHHHH
Q 015913 209 SASDLRVLNSA-LTRR--NK------LQVPE----GKYYLVDNKYANMPGFIAPYQAVSYHTNQTTTGYHPQDAKELFNQ 275 (398)
Q Consensus 209 s~~D~~vl~~s-l~~~--~~------~~~~~----g~~~l~D~gYp~~~~ll~P~~~~~~~l~~~~~~~~~~~~~~~fN~ 275 (398)
|.||.+||+.| +... .+ +.+.. -.|||+|++||.+..++++++.|. +.+++.|.+
T Consensus 81 S~NDiNVL~~Splf~~~~~G~ap~v~f~VNg~~Y~~gYYLaDGiYP~watfvktI~~p~------------~~k~k~fa~ 148 (205)
T PF04827_consen 81 SNNDINVLDRSPLFDDLLQGQAPRVQFTVNGHEYNMGYYLADGIYPEWATFVKTISLPQ------------GEKRKLFAK 148 (205)
T ss_pred cccccccccccHHHHHHhcCcCCceEEEecCeecccceeeccCcCcchHhHhhhcchhh------------chhhHHHHH
Confidence 99999999966 3321 11 11111 279999999999999999998863 468899999
Q ss_pred HHHHHHhHHHHHHHHHHhhhhhhccC-CCCCccchhHHhHHHHHHHhhhhccCCCc
Q 015913 276 RHSLLRNATDRIFGALKERFPILLSA-PPYPLQTQVKLVVAACALHNYIQREKPDD 330 (398)
Q Consensus 276 ~~s~~R~~VE~~fg~LK~rf~iL~~~-~~~~~~~~~~ii~ac~~LHN~~~~~~~~~ 330 (398)
+++++|+.||||||+|++||+|++.+ +.|+.+++..|+.||++|||||++++++.
T Consensus 149 ~QE~~RKDVErAFGVLQaRfaIi~~p~r~w~~~~l~~Im~aCiILHNMIvEDEr~~ 204 (205)
T PF04827_consen 149 HQESARKDVERAFGVLQARFAIIRGPARLWDREDLANIMRACIILHNMIVEDERDM 204 (205)
T ss_pred hCHHHHHHHHHHHHHHHHHHHHhcCchhccCHHHHHHHHHHHHHhhheeEeccccC
Confidence 99999999999999999999999966 66899999999999999999999998764
No 3
>PF13359 DDE_Tnp_4: DDE superfamily endonuclease
Probab=100.00 E-value=1.3e-37 Score=270.87 Aligned_cols=153 Identities=31% Similarity=0.534 Sum_probs=136.5
Q ss_pred ecceEEEEEeCCC---CCCCCCCCCCccccceeeeecCCcceEEeecCcccccccHHHHHHHH-hhcCCCCCCCCceeec
Q 015913 161 VDGIHIPVMVGVD---EQGPFRNKSGLLSQNVLAACSFDLKFHYVLAGWEGSASDLRVLNSAL-TRRNKLQVPEGKYYLV 236 (398)
Q Consensus 161 IDgt~i~i~~P~~---~~~~y~~~k~~~s~~~q~v~d~~~~~~~v~~g~~Gs~~D~~vl~~sl-~~~~~~~~~~g~~~l~ 236 (398)
||||||++.+|.. ....|+|+|+.+++|+|+|||++|+|++++++||||+||+++|+++. .......+++|.|+||
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 7999999999997 67789999999999999999999999999999999999999999883 2211112678899999
Q ss_pred cCCCCCCCCccccccCcccCcccccCCCCchhHHHHHHHHHHHHHhHHHHHHHHHHhhhhhhccCCCCC-ccchhHHhHH
Q 015913 237 DNKYANMPGFIAPYQAVSYHTNQTTTGYHPQDAKELFNQRHSLLRNATDRIFGALKERFPILLSAPPYP-LQTQVKLVVA 315 (398)
Q Consensus 237 D~gYp~~~~ll~P~~~~~~~l~~~~~~~~~~~~~~~fN~~~s~~R~~VE~~fg~LK~rf~iL~~~~~~~-~~~~~~ii~a 315 (398)
|+|||+.+++++||+.+ ++..++.+++.||++|+++|.+||++||+||+||+||......+ .+.+.++|.|
T Consensus 81 D~gy~~~~~~~~P~~~~--------~~~~l~~~e~~~N~~~s~~R~~vE~~~~~lK~rf~~l~~~~~~~~~~~~~~ii~~ 152 (158)
T PF13359_consen 81 DSGYPLSPYLLTPYKKP--------KGRELTPEEKEFNRRHSSARIIVERAFGRLKSRFRILRGRLRLSRPEKAPQIILA 152 (158)
T ss_pred ccccccccccccccccc--------ccccccccccchhccccceeeeeHHHHHHHHHhcccCCcccCCCcHhHHHHHHhe
Confidence 99999999999999853 23456788999999999999999999999999999998777777 8999999999
Q ss_pred HHHHHh
Q 015913 316 ACALHN 321 (398)
Q Consensus 316 c~~LHN 321 (398)
||+|||
T Consensus 153 ~~~LhN 158 (158)
T PF13359_consen 153 CCVLHN 158 (158)
T ss_pred eEEEEC
Confidence 999999
No 4
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=98.91 E-value=7.2e-10 Score=77.64 Aligned_cols=50 Identities=22% Similarity=0.363 Sum_probs=47.2
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHhh
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAIS 129 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~~ 129 (398)
.+++++|++++|.+|++|.++.++|..||||+|||+++++++++.|....
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 58999999999999999999999999999999999999999999998543
No 5
>PF13612 DDE_Tnp_1_3: Transposase DDE domain
Probab=98.78 E-value=1.9e-09 Score=92.64 Aligned_cols=126 Identities=15% Similarity=0.125 Sum_probs=92.7
Q ss_pred ccceeeecceEEEEEeCCCC-------C---CCCCCCCCccccceeeeecCCcceEEeecCcccccccHHHHHHHHhhcC
Q 015913 155 KDCVGAVDGIHIPVMVGVDE-------Q---GPFRNKSGLLSQNVLAACSFDLKFHYVLAGWEGSASDLRVLNSALTRRN 224 (398)
Q Consensus 155 p~~iG~IDgt~i~i~~P~~~-------~---~~y~~~k~~~s~~~q~v~d~~~~~~~v~~g~~Gs~~D~~vl~~sl~~~~ 224 (398)
+..+.+||.|.||++.+... . ..|+..+-++++++.++|+..|.++.+.. .||++||..++.....
T Consensus 4 ~~~i~~iDS~Pi~vC~~~R~~r~k~~~~~a~~G~~a~~~fyGfKlHllv~~~G~i~~~~l-T~an~~D~~~~~~l~~--- 79 (155)
T PF13612_consen 4 CTGIYIIDSFPIPVCHNIRIKRHKVFKGLAYRGYCAMGWFYGFKLHLLVNDSGEIVAFTL-TPANVHDRKVLEELSE--- 79 (155)
T ss_pred ccEEEEEecCChhHhCccchhhhccccCccccceeccceeEeeeeeeEEccCCcEEEEEE-cccccccccccccccc---
Confidence 45788999999999866422 1 11444445699999999999999998755 5999999999853322
Q ss_pred CCCCCCCceeeccCCCCCCC----------CccccccCcccCcccccCCCCchhHHHHHHHHHHHHHhHHHHHHHHHHhh
Q 015913 225 KLQVPEGKYYLVDNKYANMP----------GFIAPYQAVSYHTNQTTTGYHPQDAKELFNQRHSLLRNATDRIFGALKER 294 (398)
Q Consensus 225 ~~~~~~g~~~l~D~gYp~~~----------~ll~P~~~~~~~l~~~~~~~~~~~~~~~fN~~~s~~R~~VE~~fg~LK~r 294 (398)
. ....++||.||-... .|+||.+... -......+++.+.+.|..||-+|+.||++
T Consensus 80 --~--~~g~l~gDkGYis~~L~~~L~~~gI~L~t~~RkNm-----------k~~~~~~~~~~l~~~R~~IETvfs~Lk~~ 144 (155)
T PF13612_consen 80 --N--LKGKLFGDKGYISKELKDELKEQGIKLITPRRKNM-----------KNKLMPLFDKLLLRKRRIIETVFSQLKNQ 144 (155)
T ss_pred --c--cccceecchhhhcchHHhhhhhceEEEeccccccc-----------cccccchhhhhhhheeeEeehHHHHHHHh
Confidence 1 134799999996554 2677776532 01123457888999999999999999999
Q ss_pred hhhhc
Q 015913 295 FPILL 299 (398)
Q Consensus 295 f~iL~ 299 (398)
|.|=+
T Consensus 145 ~~ie~ 149 (155)
T PF13612_consen 145 FNIEH 149 (155)
T ss_pred hceEe
Confidence 98765
No 6
>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=97.93 E-value=3.3e-07 Score=82.22 Aligned_cols=161 Identities=15% Similarity=0.034 Sum_probs=87.8
Q ss_pred cceeeecceEEEEEeCCCC-CCCCCCCCCccccceeeee-cCCcceEEeecCcccccccHHHHHHHHhhcCCCCCCCCce
Q 015913 156 DCVGAVDGIHIPVMVGVDE-QGPFRNKSGLLSQNVLAAC-SFDLKFHYVLAGWEGSASDLRVLNSALTRRNKLQVPEGKY 233 (398)
Q Consensus 156 ~~iG~IDgt~i~i~~P~~~-~~~y~~~k~~~s~~~q~v~-d~~~~~~~v~~g~~Gs~~D~~vl~~sl~~~~~~~~~~g~~ 233 (398)
..+-+||+|+|+.. +... ...+.+++.....++++++ +..+.++.+... +|+.+|+..+...+.. .....+.+
T Consensus 4 ~~~~~iD~T~i~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~d~~~~~~ll~~---~~~~~~~~ 78 (213)
T PF01609_consen 4 RRVVAIDGTTIRTP-HDKSARRYKKGKKRGFGYKLHLAVDDNSGLPLSVKVT-PGNVHDSKALPELLER---KPGRKPDL 78 (213)
T ss_dssp EEEEEEETTT--EE-EEEEE-B-SSGGGHSSHGGHHHHHHHHHGGGGGGEEE-EEEGG-HHHHHHHHTT--------EEE
T ss_pred CeEEEEECcEEEee-cchhhhcccCCCCcCCCEeEEEEEeecccceeeeecc-ccccceeecccccccc---cccccccc
Confidence 45779999999988 2111 2234555666777999998 456667776666 9999999999986542 23445689
Q ss_pred eeccCCCCCCCC----------ccccccCcccCcccccCCC-----------------------CchhHHHHHHHH----
Q 015913 234 YLVDNKYANMPG----------FIAPYQAVSYHTNQTTTGY-----------------------HPQDAKELFNQR---- 276 (398)
Q Consensus 234 ~l~D~gYp~~~~----------ll~P~~~~~~~l~~~~~~~-----------------------~~~~~~~~fN~~---- 276 (398)
+++|+||...+. ++.|.+........-.... ......+.....
T Consensus 79 vv~D~gy~s~~~~~~l~~~~~~~vi~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 158 (213)
T PF01609_consen 79 VVADRGYDSAENLEALKERGIHFVIRLKKNRKKKIQKIENKFWKSFDRRSARKKPKQKSKRVRVVIRKEQKKKGYFLVTN 158 (213)
T ss_dssp EEE-S--BBTTHHHHHHTS---EEEEE--EEEE-TTS-EEEE--EEEEEEEEEEETGGGEEEEEEEEEECS--TTS---E
T ss_pred eeecccccceeccccccccccccccccccccccccccchhhccccccccccccccccccccccccccccccccccccccc
Confidence 999999976541 3445444332210000000 000001111112
Q ss_pred ----------HHHHHhHHHHHHHHHHhhhhhhccCCCCCccchhHHhHHHHHHHhh
Q 015913 277 ----------HSLLRNATDRIFGALKERFPILLSAPPYPLQTQVKLVVAACALHNY 322 (398)
Q Consensus 277 ----------~s~~R~~VE~~fg~LK~rf~iL~~~~~~~~~~~~~ii~ac~~LHN~ 322 (398)
..+.|-.||+.|..||+.|. +......+...+...+.++++-.|+
T Consensus 159 ~~~~~~~~~~~Y~~Rw~IE~~f~~lK~~~~-l~~~~~~~~~~~~~~~~~~~la~nl 213 (213)
T PF01609_consen 159 ITTLPRDTAALYRRRWQIERFFRELKQFLG-LERLRVRSPERIEAHLFLTLLAYNL 213 (213)
T ss_dssp EEEEESS--SHHHCGGHHHHHHHHHTTTTT-GGGS--SSHHHHHHHHHHHHHH---
T ss_pred ccccccccceeecccchhhHHHHHHHhcCC-CchhcccCHHHHHHHHHHHHhhCcC
Confidence 88999999999999998655 4444455666677777777776664
No 7
>PF13586 DDE_Tnp_1_2: Transposase DDE domain
Probab=96.84 E-value=0.00064 Score=52.75 Aligned_cols=49 Identities=24% Similarity=0.248 Sum_probs=33.5
Q ss_pred HHHHHHHHHHHHhHHHHHHHHHHhhhhhhccCCCCCccchhHHhHHHHHH
Q 015913 270 KELFNQRHSLLRNATDRIFGALKERFPILLSAPPYPLQTQVKLVVAACAL 319 (398)
Q Consensus 270 ~~~fN~~~s~~R~~VE~~fg~LK~rf~iL~~~~~~~~~~~~~ii~ac~~L 319 (398)
...+.....+.|.+|||+|+.||. |+.|.........+....+.-+|++
T Consensus 36 ~~~~d~~~~~~Rw~VEr~f~wlk~-~Rrl~~ryek~~~s~~~~v~la~~~ 84 (88)
T PF13586_consen 36 PRKFDFRLYKRRWVVERTFAWLKR-FRRLATRYEKLASSFLAFVHLACIV 84 (88)
T ss_pred cCccchhhhccceehhhhhHHHHH-cCccccccccCHHHHHHHHHHHHHH
Confidence 446677888999999999999995 7777755444445444444444443
No 8
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=95.84 E-value=0.0029 Score=42.24 Aligned_cols=41 Identities=20% Similarity=0.297 Sum_probs=22.8
Q ss_pred CCCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhh
Q 015913 79 NRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNN 120 (398)
Q Consensus 79 ~~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~ 120 (398)
+.++.+++..+.-+ +..|.+.+.||..+|+|++||++.+++
T Consensus 3 ~~Lt~~eR~~I~~l-~~~G~s~~~IA~~lg~s~sTV~relkR 43 (44)
T PF13936_consen 3 KHLTPEERNQIEAL-LEQGMSIREIAKRLGRSRSTVSRELKR 43 (44)
T ss_dssp ---------HHHHH-HCS---HHHHHHHTT--HHHHHHHHHH
T ss_pred cchhhhHHHHHHHH-HHcCCCHHHHHHHHCcCcHHHHHHHhc
Confidence 35777777776644 678999999999999999999998864
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=95.82 E-value=0.0078 Score=41.17 Aligned_cols=45 Identities=18% Similarity=0.197 Sum_probs=38.4
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHH
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAI 125 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l 125 (398)
.++++++-.+.++| ..|.++.++|..+|+|.+||+++.++.+.-|
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 58899999999988 5689999999999999999999998887765
No 10
>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=95.09 E-value=0.011 Score=41.04 Aligned_cols=43 Identities=23% Similarity=0.326 Sum_probs=31.6
Q ss_pred cCCCCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhh
Q 015913 77 HTNRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNN 120 (398)
Q Consensus 77 ~~~~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~ 120 (398)
.+..+++++++.+.-. +-.|.+..+||..|||+.|||+.++..
T Consensus 3 kR~~LTl~eK~~iI~~-~e~g~s~~~ia~~fgv~~sTv~~I~K~ 45 (53)
T PF04218_consen 3 KRKSLTLEEKLEIIKR-LEEGESKRDIAREFGVSRSTVSTILKN 45 (53)
T ss_dssp SSSS--HHHHHHHHHH-HHCTT-HHHHHHHHT--CCHHHHHHHC
T ss_pred CCccCCHHHHHHHHHH-HHcCCCHHHHHHHhCCCHHHHHHHHHh
Confidence 3567899999987554 677889999999999999999998765
No 11
>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=94.64 E-value=0.026 Score=39.11 Aligned_cols=44 Identities=9% Similarity=0.196 Sum_probs=33.8
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHH
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNA 124 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~ 124 (398)
.+|+.++.++.|.++. |.++.++|..+|+|.+||...+.+....
T Consensus 10 ~L~~~~r~i~~l~~~~-g~s~~eIa~~l~~s~~~v~~~l~ra~~~ 53 (54)
T PF08281_consen 10 QLPERQREIFLLRYFQ-GMSYAEIAEILGISESTVKRRLRRARKK 53 (54)
T ss_dssp CS-HHHHHHHHHHHTS----HHHHHHHCTS-HHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHH-CcCHHHHHHHHCcCHHHHHHHHHHHHhh
Confidence 5888899988888876 9999999999999999999988876654
No 12
>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=94.13 E-value=0.0082 Score=40.20 Aligned_cols=35 Identities=17% Similarity=0.235 Sum_probs=26.5
Q ss_pred HHHhheeccccccchhhhhcccccccchhhhhhhh
Q 015913 86 QLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNN 120 (398)
Q Consensus 86 ~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~ 120 (398)
++.-.+..+..|.+..++|..||||++||.|+++.
T Consensus 10 ~~~~i~~l~~~G~si~~IA~~~gvsr~TvyR~l~~ 44 (45)
T PF02796_consen 10 QIEEIKELYAEGMSIAEIAKQFGVSRSTVYRYLNK 44 (45)
T ss_dssp CHHHHHHHHHTT--HHHHHHHTTS-HHHHHHHHCC
T ss_pred HHHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 45555667788999999999999999999998753
No 13
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=93.59 E-value=0.016 Score=39.49 Aligned_cols=29 Identities=14% Similarity=0.168 Sum_probs=20.8
Q ss_pred cccccchhhhhcccccccchhhhhhhhHH
Q 015913 94 VGHNLRTRAVQELFRYSGETISRHFNNVL 122 (398)
Q Consensus 94 L~~~~~~~~l~~~fgis~stv~r~~~~v~ 122 (398)
+..|.+.+++|..+|+|++||+++++++.
T Consensus 14 ~~~G~s~~~ia~~lgvs~~Tv~~w~kr~~ 42 (50)
T PF13384_consen 14 LREGWSIREIAKRLGVSRSTVYRWIKRYR 42 (50)
T ss_dssp HHHT--HHHHHHHHTS-HHHHHHHHT---
T ss_pred HHCCCCHHHHHHHHCcCHHHHHHHHHHcc
Confidence 33499999999999999999999998764
No 14
>PF13340 DUF4096: Putative transposase of IS4/5 family (DUF4096)
Probab=93.09 E-value=0.19 Score=37.54 Aligned_cols=66 Identities=17% Similarity=0.239 Sum_probs=51.1
Q ss_pred CCHHHHHHHHHHHhcCCccccCCCCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHH
Q 015913 57 MDKKVFYKLCDILQSKGLLRHTNRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLN 123 (398)
Q Consensus 57 ms~~~F~~L~~~l~~~~~~~~~~~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~ 123 (398)
||-+....|-..|.........+..+..+-+-..|+.+.+|++++.|-..|| +.+||++.+++...
T Consensus 1 lsD~~W~~i~p~lp~~~~~~~~~~~~~R~v~~ail~~lrtG~~Wr~LP~~fg-~~~tv~~~f~rW~~ 66 (75)
T PF13340_consen 1 LSDEEWALIEPLLPPRKPRGGRPRIDLREVLNAILYVLRTGCPWRDLPEDFG-PWSTVYRRFRRWSR 66 (75)
T ss_pred CCHHHHHHHHhhCCCCCCCCCCCccchHHHHhcccccceecceecccchhcc-CcCcHHHHHHHHHH
Confidence 3445555666666554333334578888889999999999999999999999 89999998887765
No 15
>PF13518 HTH_28: Helix-turn-helix domain
Probab=93.01 E-value=0.04 Score=37.70 Aligned_cols=37 Identities=19% Similarity=0.249 Sum_probs=30.5
Q ss_pred HHHhheeccccccchhhhhcccccccchhhhhhhhHHH
Q 015913 86 QLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLN 123 (398)
Q Consensus 86 ~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~ 123 (398)
++.+...++ .|.++..+|..||||.+||.+++..+-.
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 345555566 5779999999999999999999988776
No 16
>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=92.88 E-value=0.041 Score=41.02 Aligned_cols=43 Identities=23% Similarity=0.370 Sum_probs=31.3
Q ss_pred HHH-HHhheeccccccchhhhhcccccccchhhhhhhhHHHHHH
Q 015913 84 EEQ-LAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 126 (398)
Q Consensus 84 e~~-l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~ 126 (398)
+++ +-++-|.+.++.+.+..|..||||+|||++=+.+=+..|.
T Consensus 5 eeR~i~i~~yIi~~~aTVR~~Ak~FGvSKSTVHkDvteRL~~in 48 (82)
T PF12116_consen 5 EERVIEIANYIIETKATVRQAAKVFGVSKSTVHKDVTERLPKIN 48 (82)
T ss_dssp HHHHHHHHHHHHHH---HHHHHHHHTS-HHHHHHHHTTHHHHH-
T ss_pred HHHHHHHHHHHHHcccHHHHHHHHHCCcHHHHHHHHHHHHHhcC
Confidence 444 4577788899999999999999999999998877666665
No 17
>smart00351 PAX Paired Box domain.
Probab=92.20 E-value=0.1 Score=43.28 Aligned_cols=45 Identities=13% Similarity=0.145 Sum_probs=38.4
Q ss_pred CCCCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHH
Q 015913 78 TNRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLN 123 (398)
Q Consensus 78 ~~~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~ 123 (398)
...+|.+++.-+.+.+. .|.+.+++|..||||++||+++++++-.
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 35689988888877765 7999999999999999999999988744
No 18
>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=91.77 E-value=0.064 Score=35.89 Aligned_cols=37 Identities=19% Similarity=0.274 Sum_probs=27.5
Q ss_pred HHHHHhheeccccc-cchhhhhcccccccchhhhhhhh
Q 015913 84 EEQLAIFMFIVGHN-LRTRAVQELFRYSGETISRHFNN 120 (398)
Q Consensus 84 e~~l~~~L~~L~~~-~~~~~l~~~fgis~stv~r~~~~ 120 (398)
++.+..+|-.+..| .|++..|..|||+++|+++.++.
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 56666777777777 99999999999999999976653
No 19
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=91.75 E-value=0.097 Score=39.96 Aligned_cols=45 Identities=13% Similarity=0.115 Sum_probs=41.6
Q ss_pred CCCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHH
Q 015913 79 NRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLN 123 (398)
Q Consensus 79 ~~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~ 123 (398)
-.+++.-++.++-..+..|.+...++..||||..|+++++.++-.
T Consensus 7 A~Lt~~gR~~lv~~vv~~g~~~a~aA~~~gVS~~Ta~kW~~Ryra 51 (85)
T PF13011_consen 7 ARLTPRGRLRLVRRVVEQGWPVAHAAAEFGVSRRTAYKWLARYRA 51 (85)
T ss_pred CCCCHHHHHHHHHHHHHcCCcHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 468999999999999999999999999999999999999988765
No 20
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=91.55 E-value=0.084 Score=44.36 Aligned_cols=44 Identities=18% Similarity=0.175 Sum_probs=38.2
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHH
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLN 123 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~ 123 (398)
..+.+.+.+++..++..|.|.+++|.+||+|.+|+.+++++.-+
T Consensus 4 ~~s~~~R~~~~~~~~~~G~S~re~Ak~~gvs~sTvy~wv~r~~e 47 (138)
T COG3415 4 PFSNDLRERVVDAVVGEGLSCREAAKRFGVSISTVYRWVRRYRE 47 (138)
T ss_pred hhhHHHHHHHHHHHHHcCccHHHHHHHhCccHHHHHHHHHHhcc
Confidence 34667788888899999999999999999999999999887654
No 21
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=91.31 E-value=0.19 Score=34.51 Aligned_cols=44 Identities=16% Similarity=0.375 Sum_probs=35.0
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHH
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAI 125 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l 125 (398)
.++..++-++.+ +..|.++.++|..+|+|.+||.+++.+....+
T Consensus 3 ~l~~~e~~i~~~--~~~g~s~~eia~~l~is~~tv~~~~~~~~~kl 46 (58)
T smart00421 3 SLTPREREVLRL--LAEGLTNKEIAERLGISEKTVKTHLSNIMRKL 46 (58)
T ss_pred CCCHHHHHHHHH--HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 356666654433 46899999999999999999999999887766
No 22
>cd00131 PAX Paired Box domain
Probab=91.10 E-value=0.16 Score=42.33 Aligned_cols=45 Identities=13% Similarity=0.150 Sum_probs=38.7
Q ss_pred CCCCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHH
Q 015913 78 TNRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLN 123 (398)
Q Consensus 78 ~~~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~ 123 (398)
.+.+|.+.+..+.+.+ ..|.+.+.+|.+||||.+||.++++++-+
T Consensus 15 ~~~lS~d~R~rIv~~~-~~G~s~~~iA~~~~Vs~~tV~r~i~r~~e 59 (128)
T cd00131 15 GRPLPDSIRQRIVELA-QSGIRPCDISRQLRVSHGCVSKILNRYYE 59 (128)
T ss_pred CCcCCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4678888888777665 68999999999999999999999987765
No 23
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=90.94 E-value=0.18 Score=41.54 Aligned_cols=46 Identities=11% Similarity=0.055 Sum_probs=41.9
Q ss_pred cCCCCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHH
Q 015913 77 HTNRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVL 122 (398)
Q Consensus 77 ~~~~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~ 122 (398)
.++..+.+.++.++...+..|.+..++|..||||.+|+++|++.+.
T Consensus 9 ~rr~ys~EfK~~aV~~~~~~g~sv~evA~e~gIs~~tl~~W~r~y~ 54 (121)
T PRK09413 9 KRRRRTTQEKIAIVQQSFEPGMTVSLVARQHGVAASQLFLWRKQYQ 54 (121)
T ss_pred CCCCCCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHh
Confidence 3567999999999999999999999999999999999999988764
No 24
>PRK04217 hypothetical protein; Provisional
Probab=90.37 E-value=0.24 Score=39.97 Aligned_cols=49 Identities=14% Similarity=0.073 Sum_probs=40.0
Q ss_pred CCCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHh
Q 015913 79 NRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 128 (398)
Q Consensus 79 ~~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~ 128 (398)
..++.+++-++.+++ -.|.++.++|..+|+|.+||.+.+++....|.+.
T Consensus 41 ~~Lt~eereai~l~~-~eGlS~~EIAk~LGIS~sTV~r~L~RArkkLre~ 89 (110)
T PRK04217 41 IFMTYEEFEALRLVD-YEGLTQEEAGKRMGVSRGTVWRALTSARKKVAQM 89 (110)
T ss_pred ccCCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 468888875554444 3689999999999999999999999988888643
No 25
>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=90.06 E-value=0.11 Score=38.72 Aligned_cols=45 Identities=13% Similarity=0.006 Sum_probs=37.5
Q ss_pred CCCCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHH
Q 015913 78 TNRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVL 122 (398)
Q Consensus 78 ~~~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~ 122 (398)
++..|++.+..+.-.++..|.+..+++..+||+.+|+++++..+.
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 457899999999888899999999999999999999999999887
No 26
>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=89.67 E-value=0.27 Score=33.08 Aligned_cols=43 Identities=16% Similarity=0.274 Sum_probs=34.1
Q ss_pred CCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHH
Q 015913 81 IKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNA 124 (398)
Q Consensus 81 ~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~ 124 (398)
++++++-++-+.++ .|.++.+++..+|+|.+|+.+++++....
T Consensus 11 l~~~~~~~~~~~~~-~~~~~~~ia~~~~~s~~~i~~~~~~~~~~ 53 (55)
T cd06171 11 LPEREREVILLRFG-EGLSYEEIAEILGISRSTVRQRLHRALKK 53 (55)
T ss_pred CCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 56666666655554 68999999999999999999998876543
No 27
>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=89.33 E-value=0.19 Score=39.11 Aligned_cols=41 Identities=24% Similarity=0.183 Sum_probs=31.8
Q ss_pred CCCHHHHHHhheec------cccccchhhhhcccccccchhhhhhhh
Q 015913 80 RIKIEEQLAIFMFI------VGHNLRTRAVQELFRYSGETISRHFNN 120 (398)
Q Consensus 80 ~~s~e~~l~~~L~~------L~~~~~~~~l~~~fgis~stv~r~~~~ 120 (398)
-+++.|+-++.+++ +..+.+++.|+...|||.+||+|+-+.
T Consensus 32 lLTp~E~~~l~~R~~i~~~Ll~~~~tQrEIa~~lGiS~atIsR~sn~ 78 (94)
T TIGR01321 32 ILTRSEREDLGDRIRIVNELLNGNMSQREIASKLGVSIATITRGSNN 78 (94)
T ss_pred hCCHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHhCCChhhhhHHHhh
Confidence 36677776666653 356799999999999999999986543
No 28
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=88.86 E-value=0.34 Score=41.72 Aligned_cols=48 Identities=4% Similarity=0.163 Sum_probs=43.3
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHhh
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAIS 129 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~~ 129 (398)
.+++.++-++.|++ .|.++.+||..+|+|.+||...+.+....|....
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 68999999999987 8999999999999999999999999998887543
No 29
>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=88.73 E-value=0.27 Score=31.13 Aligned_cols=22 Identities=32% Similarity=0.413 Sum_probs=16.9
Q ss_pred CChhHHHhhcCCCHHHHHHHHH
Q 015913 46 GQSERCLENFRMDKKVFYKLCD 67 (398)
Q Consensus 46 ~~d~~f~~~frms~~~F~~L~~ 67 (398)
.+|++|.+.|+|+|+.|..|=.
T Consensus 2 Lsd~dF~~vFgm~~~eF~~lP~ 23 (36)
T PF02209_consen 2 LSDEDFEKVFGMSREEFYKLPK 23 (36)
T ss_dssp S-HHHHHHHHSS-HHHHHHS-H
T ss_pred cCHHHHHHHHCCCHHHHHHChH
Confidence 4789999999999999998743
No 30
>PRK00118 putative DNA-binding protein; Validated
Probab=88.08 E-value=0.42 Score=38.14 Aligned_cols=48 Identities=6% Similarity=0.146 Sum_probs=39.3
Q ss_pred CCCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHH
Q 015913 79 NRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMA 127 (398)
Q Consensus 79 ~~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~ 127 (398)
+.++..++-++.++++ .|.++.++|..+|+|++||++.+++....+.+
T Consensus 16 ~~L~ekqRevl~L~y~-eg~S~~EIAe~lGIS~~TV~r~L~RArkkLr~ 63 (104)
T PRK00118 16 SLLTEKQRNYMELYYL-DDYSLGEIAEEFNVSRQAVYDNIKRTEKLLED 63 (104)
T ss_pred ccCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 3467777777766544 49999999999999999999999988887754
No 31
>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=87.99 E-value=0.29 Score=37.86 Aligned_cols=31 Identities=16% Similarity=-0.009 Sum_probs=26.2
Q ss_pred Hhheeccccccchhhhhcccccccchhhhhh
Q 015913 88 AIFMFIVGHNLRTRAVQELFRYSGETISRHF 118 (398)
Q Consensus 88 ~~~L~~L~~~~~~~~l~~~fgis~stv~r~~ 118 (398)
...+.++..|.+..++|..+|+|++||+++.
T Consensus 41 ~~I~~ll~~G~S~~eIA~~LgISrsTIyRi~ 71 (88)
T TIGR02531 41 LQVAKMLKQGKTYSDIEAETGASTATISRVK 71 (88)
T ss_pred HHHHHHHHCCCCHHHHHHHHCcCHHHHHHHH
Confidence 3444568889999999999999999999955
No 32
>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=87.08 E-value=0.53 Score=32.25 Aligned_cols=43 Identities=12% Similarity=0.317 Sum_probs=33.0
Q ss_pred CHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHH
Q 015913 82 KIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 126 (398)
Q Consensus 82 s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~ 126 (398)
+..++-++.+ +..|.++.++|..+++|.+||...+++....+.
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 357899999999999999999999998877653
No 33
>smart00153 VHP Villin headpiece domain.
Probab=87.00 E-value=0.46 Score=30.08 Aligned_cols=21 Identities=38% Similarity=0.455 Sum_probs=18.4
Q ss_pred CChhHHHhhcCCCHHHHHHHH
Q 015913 46 GQSERCLENFRMDKKVFYKLC 66 (398)
Q Consensus 46 ~~d~~f~~~frms~~~F~~L~ 66 (398)
.+|++|...|+|+|+.|..|=
T Consensus 2 LsdeeF~~vfgmsr~eF~~LP 22 (36)
T smart00153 2 LSDEDFEEVFGMTREEFYKLP 22 (36)
T ss_pred CCHHHHHHHHCCCHHHHHhCc
Confidence 378999999999999998863
No 34
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=86.97 E-value=0.51 Score=41.38 Aligned_cols=49 Identities=6% Similarity=0.236 Sum_probs=42.3
Q ss_pred CCCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHh
Q 015913 79 NRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 128 (398)
Q Consensus 79 ~~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~ 128 (398)
..+|++++.++.|.++ .|.++.++|..+|+|.+||...+++.+..+...
T Consensus 126 ~~Lp~~~R~v~~L~~~-~g~s~~EIA~~lgis~~tVk~~l~rAl~~~~~~ 174 (178)
T PRK12529 126 DTLRPRVKQAFLMATL-DGMKQKDIAQALDIALPTVKKYIHQAYVTCLSL 174 (178)
T ss_pred HhCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 3689999999999888 699999999999999999999888777766543
No 35
>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=86.82 E-value=0.32 Score=36.04 Aligned_cols=42 Identities=10% Similarity=0.071 Sum_probs=36.4
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhH
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNV 121 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v 121 (398)
.++...+.+..|.+.-.|.++.++|...|+|.+||..+++..
T Consensus 15 ~l~~~~r~af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~~ 56 (73)
T TIGR03879 15 WVDSLAEAAAALAREEAGKTASEIAEELGRTEQTVRNHLKGE 56 (73)
T ss_pred cCCHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhcC
Confidence 577778888778777789999999999999999999988763
No 36
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=86.70 E-value=0.59 Score=42.95 Aligned_cols=52 Identities=13% Similarity=0.157 Sum_probs=44.3
Q ss_pred CCCCHHHHHHhheecc---ccccchhhhhcccccccchhhhhhhhHHHHHHHhhc
Q 015913 79 NRIKIEEQLAIFMFIV---GHNLRTRAVQELFRYSGETISRHFNNVLNAIMAISL 130 (398)
Q Consensus 79 ~~~s~e~~l~~~L~~L---~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~~~ 130 (398)
..+|+.++-++.|++. -.|.++.++|..+|+|.+||....++....|-+...
T Consensus 177 ~~Lp~~~R~v~~L~y~l~~~eg~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~~l~ 231 (234)
T PRK08301 177 KKLSDREKQIMELRFGLNGGEEKTQKEVADMLGISQSYISRLEKRIIKRLKKEIN 231 (234)
T ss_pred HhCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 3688999988888774 579999999999999999999999998888865443
No 37
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=86.68 E-value=0.5 Score=41.08 Aligned_cols=50 Identities=16% Similarity=0.102 Sum_probs=42.6
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHhhc
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAISL 130 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~~~ 130 (398)
.+++.++.++.|.++ .|.++.++|..+|+|.+||...+++...-|.+...
T Consensus 128 ~L~~~~r~vl~l~~~-~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 177 (182)
T PRK09652 128 SLPEELRTAITLREI-EGLSYEEIAEIMGCPIGTVRSRIFRAREALRAKLQ 177 (182)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 588888888888776 58999999999999999999999988887765443
No 38
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=86.31 E-value=0.53 Score=41.75 Aligned_cols=50 Identities=6% Similarity=0.022 Sum_probs=42.9
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHhhc
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAISL 130 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~~~ 130 (398)
.++++++-++.|+++. |.++.++|..+|+|.+||...+++....|.+...
T Consensus 141 ~L~~~~~~v~~l~~~~-g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~ 190 (194)
T PRK12519 141 QLPESQRQVLELAYYE-GLSQSEIAKRLGIPLGTVKARARQGLLKLRELLQ 190 (194)
T ss_pred hCCHHHhhhhhhhhhc-CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence 5788888888888766 8999999999999999999999998888875443
No 39
>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=85.72 E-value=0.29 Score=32.85 Aligned_cols=21 Identities=24% Similarity=0.254 Sum_probs=18.8
Q ss_pred hhhhhcccccccchhhhhhhh
Q 015913 100 TRAVQELFRYSGETISRHFNN 120 (398)
Q Consensus 100 ~~~l~~~fgis~stv~r~~~~ 120 (398)
..+||...|+|.+|||++++.
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 578999999999999998874
No 40
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=85.66 E-value=0.3 Score=33.39 Aligned_cols=28 Identities=18% Similarity=0.184 Sum_probs=23.9
Q ss_pred cccccchhhhhcccccccchhhhhhhhH
Q 015913 94 VGHNLRTRAVQELFRYSGETISRHFNNV 121 (398)
Q Consensus 94 L~~~~~~~~l~~~fgis~stv~r~~~~v 121 (398)
|..+.++..+|..+|+|.+||.+++++.
T Consensus 24 ~~~~~s~~~vA~~~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 24 LRESRSFKDVARELGVSWSTVRRIFDRY 51 (52)
T ss_pred HhhcCCHHHHHHHHCCCHHHHHHHHHhh
Confidence 3444699999999999999999999864
No 41
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=85.60 E-value=0.68 Score=40.26 Aligned_cols=48 Identities=4% Similarity=0.128 Sum_probs=42.2
Q ss_pred CCCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHH
Q 015913 79 NRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMA 127 (398)
Q Consensus 79 ~~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~ 127 (398)
..+|+.++.++.|.++ .|.++.++|..+|+|.+||...+.+....|..
T Consensus 125 ~~L~~~~r~v~~l~~~-~g~s~~eIA~~l~is~~~V~~~l~ra~~~l~~ 172 (176)
T PRK09638 125 SKLDPEFRAPVILKHY-YGYTYEEIAKMLNIPEGTVKSRVHHGIKQLRK 172 (176)
T ss_pred HcCCHHHhheeeehhh-cCCCHHHHHHHHCCChhHHHHHHHHHHHHHHH
Confidence 3688888888888877 59999999999999999999999888888764
No 42
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=85.12 E-value=0.69 Score=43.31 Aligned_cols=51 Identities=12% Similarity=0.189 Sum_probs=43.5
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHhhcc
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAISLD 131 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~~~~ 131 (398)
.+++.++..+.|+++ .|.++.++|..+|+|.++|++..++....|......
T Consensus 205 ~L~~~er~vi~l~y~-e~~t~~EIA~~lgis~~~V~~~~~ral~kLr~~l~~ 255 (257)
T PRK05911 205 ALEEKERKVMALYYY-EELVLKEIGKILGVSESRVSQIHSKALLKLRATLSA 255 (257)
T ss_pred cCCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHh
Confidence 588888888888875 689999999999999999999999998888755443
No 43
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=84.81 E-value=0.69 Score=40.21 Aligned_cols=54 Identities=7% Similarity=0.142 Sum_probs=43.3
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHhhccccC
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAISLDFFQ 134 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~~~~~i~ 134 (398)
.+|+..+-++.|.++ .|.++.++|...|+|.+||...+.+....|.+....+|+
T Consensus 119 ~L~~~~r~i~~l~~~-~~~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~~~~~ 172 (173)
T PRK12522 119 LLNEKYKTVLVLYYY-EQYSYKEMSEILNIPIGTVKYRLNYAKKQMREHLEGFVH 172 (173)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 467766655555544 599999999999999999999999999999876666553
No 44
>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=84.61 E-value=0.43 Score=29.07 Aligned_cols=37 Identities=11% Similarity=0.055 Sum_probs=26.8
Q ss_pred CCHHHHHHhheeccccccchhhhhcccccccchhhhhh
Q 015913 81 IKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHF 118 (398)
Q Consensus 81 ~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~ 118 (398)
++.+++..+... +..+.+..+++..+|+|.+|+++++
T Consensus 6 ~~~~~~~~i~~~-~~~~~s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 6 LTPEQIEEARRL-LAAGESVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred CCHHHHHHHHHH-HHcCCCHHHHHHHHCCCHHHHHHhC
Confidence 455444444333 4467899999999999999999864
No 45
>PRK01381 Trp operon repressor; Provisional
Probab=84.36 E-value=0.61 Score=36.67 Aligned_cols=39 Identities=21% Similarity=0.215 Sum_probs=28.7
Q ss_pred CCHHHHHHhheec------cccccchhhhhcccccccchhhhhhh
Q 015913 81 IKIEEQLAIFMFI------VGHNLRTRAVQELFRYSGETISRHFN 119 (398)
Q Consensus 81 ~s~e~~l~~~L~~------L~~~~~~~~l~~~fgis~stv~r~~~ 119 (398)
+++.|+-++..++ +..+.|+++|+...|||.+||+|.-+
T Consensus 33 lTp~Er~al~~R~~I~~~L~~g~~sQREIa~~lGvSiaTITRgsn 77 (99)
T PRK01381 33 LTPDEREALGTRVRIVEELLRGELSQREIKQELGVGIATITRGSN 77 (99)
T ss_pred CCHHHHHHHHHHHHHHHHHHcCCcCHHHHHHHhCCceeeehhhHH
Confidence 5566665555542 33458999999999999999998544
No 46
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=84.32 E-value=0.82 Score=39.16 Aligned_cols=48 Identities=8% Similarity=0.070 Sum_probs=41.3
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHh
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 128 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~ 128 (398)
.++++++-.+.|.++. |.++.++|..+|+|.+||...+.+...-|...
T Consensus 109 ~L~~~~r~v~~l~~~~-~~s~~EIA~~lgis~~tV~~~l~ra~~~lr~~ 156 (163)
T PRK07037 109 ELPARTRYAFEMYRLH-GETQKDIARELGVSPTLVNFMIRDALVHCRKC 156 (163)
T ss_pred hCCHHHHHHHHHHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 5788888888777665 99999999999999999999988888877654
No 47
>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=84.18 E-value=0.86 Score=35.29 Aligned_cols=48 Identities=13% Similarity=0.190 Sum_probs=43.6
Q ss_pred CCCCHHHHHHhheeccccccchhhhhcccc-cccchhhhhhhhHHHHHH
Q 015913 79 NRIKIEEQLAIFMFIVGHNLRTRAVQELFR-YSGETISRHFNNVLNAIM 126 (398)
Q Consensus 79 ~~~s~e~~l~~~L~~L~~~~~~~~l~~~fg-is~stv~r~~~~v~~~l~ 126 (398)
+.+...-+++|.|..--.|.++.++|..|| .+.|||+..++++-..+.
T Consensus 26 ~~~~~aR~ia~yl~~~~~~~s~~~Ig~~fg~r~hStV~~a~~ri~~~~~ 74 (90)
T cd06571 26 KEIALARQIAMYLARELTGLSLPEIGRAFGGRDHSTVLHAVRKIEELLE 74 (90)
T ss_pred cCcchHHHHHHHHHHHHhCCCHHHHHHHhCCCCHhHHHHHHHHHHHHHH
Confidence 468888899999998888999999999999 999999999999988775
No 48
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=84.17 E-value=0.85 Score=39.95 Aligned_cols=49 Identities=12% Similarity=0.228 Sum_probs=43.4
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHhh
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAIS 129 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~~ 129 (398)
.+|+.++-++.|.++. |.++.++|..+|+|.+||...+.+....|.+..
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 6888888888888877 999999999999999999999999888887543
No 49
>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=84.15 E-value=0.82 Score=38.43 Aligned_cols=45 Identities=7% Similarity=0.082 Sum_probs=38.5
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHH
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 126 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~ 126 (398)
.++..++-.+.|+ ..|.++.++|..+|+|++||+++.++..+-|.
T Consensus 6 ~Lte~qr~VL~Lr--~~GlTq~EIAe~LgiS~stV~~~e~ra~kkLr 50 (137)
T TIGR00721 6 FLTERQIKVLELR--EKGLSQKEIAKELKTTRANVSAIEKRAMENIE 50 (137)
T ss_pred CCCHHHHHHHHHH--HcCCCHHHHHHHHCcCHHHHHHHHHhHHHHHH
Confidence 4677777777773 69999999999999999999999998888775
No 50
>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=83.94 E-value=0.89 Score=39.13 Aligned_cols=48 Identities=10% Similarity=0.074 Sum_probs=42.2
Q ss_pred CCCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHH
Q 015913 79 NRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMA 127 (398)
Q Consensus 79 ~~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~ 127 (398)
..+|+.++.++.|+++. |.++.++|..+|+|.+||...+++....|-+
T Consensus 121 ~~L~~~~r~vl~l~~~~-g~s~~eIA~~l~is~~tv~~~l~ra~~~Lr~ 168 (170)
T TIGR02952 121 KILTPKQQHVIALRFGQ-NLPIAEVARILGKTEGAVKILQFRAIKKLAR 168 (170)
T ss_pred HhCCHHHHHHHHHHHhc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 37999999999997775 8999999999999999999999888877753
No 51
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=83.93 E-value=0.97 Score=41.53 Aligned_cols=50 Identities=18% Similarity=0.165 Sum_probs=43.0
Q ss_pred CCCCHHHHHHhheecc---ccccchhhhhcccccccchhhhhhhhHHHHHHHh
Q 015913 79 NRIKIEEQLAIFMFIV---GHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 128 (398)
Q Consensus 79 ~~~s~e~~l~~~L~~L---~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~ 128 (398)
..+|+.++..+.|.++ -.|.|+.++|..+|+|.+||.+..++....|...
T Consensus 174 ~~Lp~~~R~i~~l~y~~~~~e~~S~~EIA~~lgis~~tV~~~~~rA~~kLr~~ 226 (233)
T PRK05803 174 DILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRALKKLFKE 226 (233)
T ss_pred HhCCHHHHHHHHHHhCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 3699999999999875 4789999999999999999999888888777643
No 52
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=83.83 E-value=0.64 Score=32.23 Aligned_cols=30 Identities=17% Similarity=0.283 Sum_probs=25.9
Q ss_pred ccchhhhhcccccccchhhhhhhhHHHHHH
Q 015913 97 NLRTRAVQELFRYSGETISRHFNNVLNAIM 126 (398)
Q Consensus 97 ~~~~~~l~~~fgis~stv~r~~~~v~~~l~ 126 (398)
..+..+||..+|||++|++..+++...-|.
T Consensus 23 ~~tl~elA~~lgis~st~~~~LRrae~kli 52 (53)
T PF04967_consen 23 RITLEELAEELGISKSTVSEHLRRAERKLI 52 (53)
T ss_pred cCCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Confidence 467889999999999999999998877653
No 53
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=83.76 E-value=1 Score=38.45 Aligned_cols=49 Identities=8% Similarity=0.166 Sum_probs=42.8
Q ss_pred CCCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHh
Q 015913 79 NRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 128 (398)
Q Consensus 79 ~~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~ 128 (398)
..+|+.++-++.|.++. |.++.++|..+|+|.+||...+++....|...
T Consensus 105 ~~Lp~~~r~v~~l~~~~-g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~ 153 (161)
T PRK09047 105 QKLPARQREAFLLRYWE-DMDVAETAAAMGCSEGSVKTHCSRATHALAKA 153 (161)
T ss_pred HhCCHHHHHHHHHHHHh-cCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 36888888888887765 99999999999999999999999999988753
No 54
>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=83.74 E-value=0.64 Score=39.37 Aligned_cols=48 Identities=8% Similarity=0.170 Sum_probs=40.7
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHh
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 128 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~ 128 (398)
.+|+.++-++.|.++ .|.++.++|..+|+|.+||...+++....|.+.
T Consensus 105 ~L~~~~r~i~~l~~~-~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~~ 152 (154)
T TIGR02950 105 RLPENYRTVLILREF-KEFSYKEIAELLNLSLAKVKSNLFRARKELKKL 152 (154)
T ss_pred hCCHhheeeeeehhh-ccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 577777777777767 699999999999999999999999888877643
No 55
>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=83.49 E-value=0.98 Score=39.53 Aligned_cols=47 Identities=13% Similarity=0.171 Sum_probs=41.2
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHH
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMA 127 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~ 127 (398)
.+|+.++-++.|.++. |.++.++|..+|+|.+||...+++....|.+
T Consensus 134 ~Lp~~~r~v~~l~~~~-g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 180 (183)
T TIGR02999 134 QVDPRQAEVVELRFFA-GLTVEEIAELLGVSVRTVERDWRFARAWLAD 180 (183)
T ss_pred cCCHHHHHHHHHHHHc-CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 4888888888887775 8999999999999999999999998888764
No 56
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=83.44 E-value=0.96 Score=39.70 Aligned_cols=48 Identities=8% Similarity=0.071 Sum_probs=41.0
Q ss_pred CCCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHH
Q 015913 79 NRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMA 127 (398)
Q Consensus 79 ~~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~ 127 (398)
..+|+..+.++.|.+ -.|.++.++|+.+|+|.+||...+++....|.+
T Consensus 132 ~~L~~~~r~i~~l~~-~~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 179 (182)
T PRK12537 132 EQLEPARRNCILHAY-VDGCSHAEIAQRLGAPLGTVKAWIKRSLKALRE 179 (182)
T ss_pred HhCCHHHHHHHHHHH-HcCCCHHHHHHHHCCChhhHHHHHHHHHHHHHH
Confidence 368888887777775 469999999999999999999999999888764
No 57
>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=83.39 E-value=1.6 Score=37.14 Aligned_cols=48 Identities=4% Similarity=0.073 Sum_probs=41.6
Q ss_pred CCCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHH
Q 015913 79 NRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMA 127 (398)
Q Consensus 79 ~~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~ 127 (398)
..+|+.++-.+.|.++ .|.++.++|..+|+|.+||...+++....|.+
T Consensus 110 ~~L~~~~r~v~~l~~~-~g~~~~eIA~~l~is~~tv~~~l~Rar~~Lr~ 157 (159)
T TIGR02989 110 EKLPERQRELLQLRYQ-RGVSLTALAEQLGRTVNAVYKALSRLRVRLRD 157 (159)
T ss_pred HHCCHHHHHHHHHHHh-cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Confidence 3689999988888776 59999999999999999999998888777653
No 58
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=83.18 E-value=1 Score=40.92 Aligned_cols=50 Identities=8% Similarity=0.167 Sum_probs=43.9
Q ss_pred CCCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHhh
Q 015913 79 NRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAIS 129 (398)
Q Consensus 79 ~~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~~ 129 (398)
..+++.++-++.|+++ .|.++.+||..+|+|.+||...+++....|.+..
T Consensus 133 ~~Lp~~~R~v~~L~y~-eg~s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l 182 (216)
T PRK12533 133 AKLPVEYREVLVLREL-EDMSYREIAAIADVPVGTVMSRLARARRRLAALL 182 (216)
T ss_pred HcCCHHHHhHhhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3688888888888887 5999999999999999999999999988887544
No 59
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=83.08 E-value=0.82 Score=40.51 Aligned_cols=48 Identities=8% Similarity=0.016 Sum_probs=42.6
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHh
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 128 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~ 128 (398)
.+|+..+-++.|+++. |.++.++|..+|+|.+||...+++....|.+.
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 5788888888888876 99999999999999999999999988888653
No 60
>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=83.02 E-value=1 Score=37.34 Aligned_cols=46 Identities=13% Similarity=0.257 Sum_probs=39.0
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHH
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 126 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~ 126 (398)
.+++.++-.+.+.++ .|.++.++|..+|+|.+||++...++...|-
T Consensus 110 ~L~~~~~~ii~~~~~-~g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~ 155 (158)
T TIGR02937 110 KLPEREREVLVLRYL-EGLSYKEIAEILGISVGTVKRRLKRARKKLR 155 (158)
T ss_pred hCCHHHHHHHhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 578888877766655 5899999999999999999999999877664
No 61
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=82.99 E-value=1 Score=39.71 Aligned_cols=50 Identities=12% Similarity=0.164 Sum_probs=44.1
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHhhc
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAISL 130 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~~~ 130 (398)
.+|+..+-++.|+++ .|.++.++|..+|+|.+||...+++....|.....
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 688889988888887 49999999999999999999999999988876544
No 62
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=82.95 E-value=1.1 Score=39.21 Aligned_cols=48 Identities=10% Similarity=0.094 Sum_probs=41.8
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHh
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 128 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~ 128 (398)
.++++++-.+.|.++ .|.++.+||..+|+|..||...+++....|-+.
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 588888888888876 689999999999999999999999888887643
No 63
>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=82.93 E-value=0.89 Score=45.21 Aligned_cols=132 Identities=13% Similarity=0.010 Sum_probs=69.8
Q ss_pred eeccccccchhhhhc----ccc---cccchhhhhhhhHHHHHHHhhccccCCCCCCCccccccCCccccccccceeeecc
Q 015913 91 MFIVGHNLRTRAVQE----LFR---YSGETISRHFNNVLNAIMAISLDFFQPPGPDVPPEISLDPRLYPYFKDCVGAVDG 163 (398)
Q Consensus 91 L~~L~~~~~~~~l~~----~fg---is~stv~r~~~~v~~~l~~~~~~~i~~P~~~~~~~i~~~~~~~~~fp~~iG~IDg 163 (398)
+..+..|.|.++++. .+| +|++|||+++..+...+..+...-+ . ..|-++-.|||
T Consensus 108 ~~ly~~G~Str~i~~~l~~l~g~~~~S~s~vSri~~~~~~~~~~w~~R~L------------~------~~~y~~l~iD~ 169 (381)
T PF00872_consen 108 ISLYLKGVSTRDIEEALEELYGEVAVSKSTVSRITKQLDEEVEAWRNRPL------------E------SEPYPYLWIDG 169 (381)
T ss_pred hhhhccccccccccchhhhhhcccccCchhhhhhhhhhhhhHHHHhhhcc------------c------cccccceeeee
Confidence 334566777777655 456 8999999999888877764432211 1 11224668999
Q ss_pred eEEEEEeCCCCCCCCCCCCCccccceeeeecCCcc--eEEeecCcccccccHHHHHHHHhhcCCCCCCCCceeeccCCCC
Q 015913 164 IHIPVMVGVDEQGPFRNKSGLLSQNVLAACSFDLK--FHYVLAGWEGSASDLRVLNSALTRRNKLQVPEGKYYLVDNKYA 241 (398)
Q Consensus 164 t~i~i~~P~~~~~~y~~~k~~~s~~~q~v~d~~~~--~~~v~~g~~Gs~~D~~vl~~sl~~~~~~~~~~g~~~l~D~gYp 241 (398)
+++.+..- ++-...++-+-+.+|.+|+ ++.+..+ ..-....|.+-+.......+.....+++|+.=.
T Consensus 170 ~~~kvr~~--------~~~~~~~~~v~iGi~~dG~r~vLg~~~~---~~Es~~~W~~~l~~L~~RGl~~~~lvv~Dg~~g 238 (381)
T PF00872_consen 170 TYFKVRED--------GRVVKKAVYVAIGIDEDGRREVLGFWVG---DRESAASWREFLQDLKERGLKDILLVVSDGHKG 238 (381)
T ss_pred eecccccc--------cccccchhhhhhhhhcccccceeeeecc---cCCccCEeeecchhhhhccccccceeecccccc
Confidence 99988511 1111233444555777776 4544444 222333333222211111222335677776554
Q ss_pred CCCCcccccc
Q 015913 242 NMPGFIAPYQ 251 (398)
Q Consensus 242 ~~~~ll~P~~ 251 (398)
+...+-.-|+
T Consensus 239 l~~ai~~~fp 248 (381)
T PF00872_consen 239 LKEAIREVFP 248 (381)
T ss_pred cccccccccc
Confidence 4444433333
No 64
>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=82.73 E-value=0.93 Score=38.38 Aligned_cols=46 Identities=11% Similarity=0.156 Sum_probs=39.9
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHH
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 126 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~ 126 (398)
.+++.++-++.|+++ .|.++.++|..+|+|.+||....++....|-
T Consensus 113 ~L~~~~r~il~l~~~-~~~~~~eIA~~lgis~~tv~~~~~ra~~~Lr 158 (161)
T TIGR02985 113 KLPEQCRKIFILSRF-EGKSYKEIAEELGISVKTVEYHISKALKELR 158 (161)
T ss_pred HCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 578888888888776 5999999999999999999999888777664
No 65
>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=82.71 E-value=0.9 Score=32.03 Aligned_cols=26 Identities=23% Similarity=0.252 Sum_probs=22.3
Q ss_pred cchhhhhcccccccchhhhhhhhHHH
Q 015913 98 LRTRAVQELFRYSGETISRHFNNVLN 123 (398)
Q Consensus 98 ~~~~~l~~~fgis~stv~r~~~~v~~ 123 (398)
.+..+|+..++++++|+++++++...
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 69999999999999999998877654
No 66
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=82.62 E-value=1.3 Score=37.48 Aligned_cols=46 Identities=9% Similarity=0.083 Sum_probs=39.0
Q ss_pred CCCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHH
Q 015913 79 NRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 126 (398)
Q Consensus 79 ~~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~ 126 (398)
..+++.++-.+.| ...|.++.++|..+|+|++||+.+.++...-|.
T Consensus 5 ~~Lt~rqreVL~l--r~~GlTq~EIAe~LGiS~~tVs~ie~ra~kkLr 50 (141)
T PRK03975 5 SFLTERQIEVLRL--RERGLTQQEIADILGTSRANVSSIEKRARENIE 50 (141)
T ss_pred cCCCHHHHHHHHH--HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 3578888877777 368999999999999999999999988777764
No 67
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=82.56 E-value=1.1 Score=38.74 Aligned_cols=47 Identities=13% Similarity=0.094 Sum_probs=41.0
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHH
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMA 127 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~ 127 (398)
.+|+.++.++.|+++ .|.++.++|..+|+|.+||...+.+....+..
T Consensus 118 ~L~~~~r~v~~L~~~-eg~s~~EIA~~l~is~~tV~~~l~ra~~~~~~ 164 (168)
T PRK12525 118 GLSGKARAAFLMSQL-EGLTYVEIGERLGVSLSRIHQYMVEAFKCCYQ 164 (168)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 588888888888765 59999999999999999999999888887764
No 68
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=82.55 E-value=0.96 Score=40.03 Aligned_cols=52 Identities=10% Similarity=0.068 Sum_probs=44.5
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHhhccc
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAISLDF 132 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~~~~~ 132 (398)
.++++++-.+.|.++ .|.++.++|..+|+|..||...+.+....|-+....+
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 588888888888776 5999999999999999999999999998887655443
No 69
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=82.42 E-value=1.2 Score=39.15 Aligned_cols=49 Identities=12% Similarity=0.177 Sum_probs=43.1
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHhh
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAIS 129 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~~ 129 (398)
.+|++++-++.|.++. |.|+.++|...|||.+||...+++....|.+..
T Consensus 127 ~Lp~~~R~~~~l~~~~-gls~~EIA~~l~i~~~tVks~l~ra~~~l~~~l 175 (182)
T COG1595 127 RLPPRQREAFLLRYLE-GLSYEEIAEILGISVGTVKSRLHRARKKLREQL 175 (182)
T ss_pred hCCHHHhHHhhhHhhc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 5888888888888776 999999999999999999999999999887543
No 70
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=82.34 E-value=1.1 Score=39.30 Aligned_cols=48 Identities=10% Similarity=0.186 Sum_probs=41.7
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHh
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 128 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~ 128 (398)
.++..++-++.|.++ .|.++.++|..+|+|.+||...+++....|...
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 578888888888777 599999999999999999999999888887643
No 71
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=82.31 E-value=0.92 Score=38.84 Aligned_cols=46 Identities=15% Similarity=0.067 Sum_probs=39.9
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHH
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 126 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~ 126 (398)
.+|++++-++.|.++. |.++.++|..+|+|.+||...+++....+.
T Consensus 113 ~L~~~~r~v~~L~~~~-g~s~~EIA~~l~is~~tV~~~l~ra~~~~~ 158 (161)
T PRK12528 113 GLPPLVKRAFLLAQVD-GLGYGEIATELGISLATVKRYLNKAAMRCY 158 (161)
T ss_pred HCCHHHHHHHHHHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 6888888888887765 999999999999999999998888877663
No 72
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=82.09 E-value=0.79 Score=30.71 Aligned_cols=37 Identities=22% Similarity=0.322 Sum_probs=26.8
Q ss_pred HHhheeccccccchhhhhcccccccchhhhhhhhHHH
Q 015913 87 LAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLN 123 (398)
Q Consensus 87 l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~ 123 (398)
+-+.........+..++++.+|+|++||+++++...+
T Consensus 5 ~~Il~~L~~~~~~~~el~~~l~~s~~~vs~hL~~L~~ 41 (47)
T PF01022_consen 5 LRILKLLSEGPLTVSELAEELGLSQSTVSHHLKKLRE 41 (47)
T ss_dssp HHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHHhCCCchhhHHHhccccchHHHHHHHHHHH
Confidence 3333333345688999999999999999999876554
No 73
>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=81.90 E-value=1.3 Score=41.70 Aligned_cols=48 Identities=15% Similarity=0.153 Sum_probs=41.8
Q ss_pred CCCHHHHHHhheeccc-cccchhhhhcccccccchhhhhhhhHHHHHHH
Q 015913 80 RIKIEEQLAIFMFIVG-HNLRTRAVQELFRYSGETISRHFNNVLNAIMA 127 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~-~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~ 127 (398)
.++..++..+.|+|+. .|.++.++|..+|||.++|+++.++.+.-|-.
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 4888889889998874 48999999999999999999999988887754
No 74
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=81.70 E-value=1.3 Score=38.94 Aligned_cols=48 Identities=15% Similarity=0.187 Sum_probs=41.8
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHh
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 128 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~ 128 (398)
.+|..++..+.|+++. |.++.++|..+|+|.+||...+++....|...
T Consensus 135 ~L~~~~r~vl~l~~~~-~~s~~eIA~~lgis~~~V~~~l~ra~~~Lr~~ 182 (186)
T PRK13919 135 ALSPEERRVIEVLYYQ-GYTHREAAQLLGLPLGTLKTRARRALSRLKEV 182 (186)
T ss_pred hCCHHHHHHHHHHHHc-CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 5888888888887765 99999999999999999999999988888643
No 75
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=81.67 E-value=1.2 Score=38.28 Aligned_cols=48 Identities=10% Similarity=0.151 Sum_probs=42.4
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHh
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 128 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~ 128 (398)
.+|+.++-++.|.++ .|.++.++|..+|+|.+||...+++....|.+.
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 688888888888877 699999999999999999999999998888643
No 76
>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=81.62 E-value=1.3 Score=38.94 Aligned_cols=50 Identities=12% Similarity=0.062 Sum_probs=42.3
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHhhc
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAISL 130 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~~~ 130 (398)
.++++++-++.|.++ .|.++.+||..+|+|..||...+++....|.+...
T Consensus 138 ~L~~~~r~v~~l~~~-~~~s~~EIA~~lgis~~tv~~~l~rar~~Lr~~l~ 187 (190)
T TIGR02939 138 ALPEDLRTAITLREL-EGLSYEDIARIMDCPVGTVRSRIFRAREAIAIRLR 187 (190)
T ss_pred cCCHHHhhhhhhhhh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhh
Confidence 577777777777766 69999999999999999999999999988876543
No 77
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=81.60 E-value=1.2 Score=39.65 Aligned_cols=48 Identities=13% Similarity=0.180 Sum_probs=42.8
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHh
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 128 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~ 128 (398)
.+++.++-++.|.++ .|.++.++|..+|+|.+||...+++....|...
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 688888888888877 699999999999999999999999999888653
No 78
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=81.58 E-value=1.2 Score=39.42 Aligned_cols=50 Identities=14% Similarity=0.144 Sum_probs=43.7
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHhhc
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAISL 130 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~~~ 130 (398)
.+|+.++-++.|.++ .|.++.+||..+|+|.+||...+.+....|.+...
T Consensus 116 ~Lp~~~r~i~~L~~~-~g~s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l~ 165 (187)
T PRK12516 116 QLPDDQREAIILVGA-SGFAYEEAAEICGCAVGTIKSRVNRARQRLQEILQ 165 (187)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 688888888888877 69999999999999999999999999988875443
No 79
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=81.40 E-value=1.2 Score=38.60 Aligned_cols=48 Identities=10% Similarity=0.215 Sum_probs=41.4
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHh
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 128 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~ 128 (398)
.+|+.++-.+.|.++ .|.++.+||..+|+|.+||.+.+++....|.+.
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 588888887777776 599999999999999999999999988888643
No 80
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=81.36 E-value=1.2 Score=37.99 Aligned_cols=48 Identities=4% Similarity=-0.040 Sum_probs=41.2
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHh
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 128 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~ 128 (398)
.+|+.++-++.|.++. |.++.++|..+|+|.+||...+++....|.+.
T Consensus 106 ~Lp~~~r~v~~l~~~~-g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 153 (160)
T PRK09642 106 ELPENYRDVVLAHYLE-EKSYQEIALQEKIEVKTVEMKLYRARKWIKKH 153 (160)
T ss_pred hCCHHHHHHHHHHHHh-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 5888888877777664 99999999999999999999999888888653
No 81
>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=81.27 E-value=1.4 Score=40.45 Aligned_cols=50 Identities=16% Similarity=0.193 Sum_probs=43.7
Q ss_pred CCCCHHHHHHhheecc---ccccchhhhhcccccccchhhhhhhhHHHHHHHh
Q 015913 79 NRIKIEEQLAIFMFIV---GHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 128 (398)
Q Consensus 79 ~~~s~e~~l~~~L~~L---~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~ 128 (398)
..+|+.++-.+.|+++ ..|.++.++|...|+|.+||....++....|-+.
T Consensus 177 ~~Lp~~~R~ii~L~~~l~~~eg~s~~EIA~~Lgis~~tV~~~l~ra~~~LR~~ 229 (234)
T TIGR02835 177 AKLNDREKKIMELRFGLVGGTEKTQKEVADMLGISQSYISRLEKRILKRLKKE 229 (234)
T ss_pred HhCCHHHHHHHHHHHccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3699999999999885 4789999999999999999999988888877653
No 82
>PF13730 HTH_36: Helix-turn-helix domain
Probab=81.14 E-value=1.4 Score=30.41 Aligned_cols=43 Identities=7% Similarity=0.157 Sum_probs=30.3
Q ss_pred CCHHHH-HHhheecccc--c---cchhhhhcccccccchhhhhhhhHHH
Q 015913 81 IKIEEQ-LAIFMFIVGH--N---LRTRAVQELFRYSGETISRHFNNVLN 123 (398)
Q Consensus 81 ~s~e~~-l~~~L~~L~~--~---~~~~~l~~~fgis~stv~r~~~~v~~ 123 (398)
+++.++ |.+.|..++. + .|+..++...|+|+.||.+++++..+
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 455443 4455555542 2 37899999999999999999887654
No 83
>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=81.07 E-value=0.57 Score=41.25 Aligned_cols=78 Identities=19% Similarity=0.212 Sum_probs=51.0
Q ss_pred CChhHHHhhcCCCHHHHHHHHHHHhcCCcc-----ccCCCCCHHHHHHhheecccc--------------ccchhhhhcc
Q 015913 46 GQSERCLENFRMDKKVFYKLCDILQSKGLL-----RHTNRIKIEEQLAIFMFIVGH--------------NLRTRAVQEL 106 (398)
Q Consensus 46 ~~d~~f~~~frms~~~F~~L~~~l~~~~~~-----~~~~~~s~e~~l~~~L~~L~~--------------~~~~~~l~~~ 106 (398)
.+-..|+..+.-.+..-..++..+...... ..-...+++++|+-+|..|+. ..+..++|+.
T Consensus 73 i~~~~~~~l~~~~p~l~~~~~~~l~~~l~~~~~~~~~l~~~~~~~Rla~~L~~l~~~~~~~~~~~~~~~~~~t~~~iA~~ 152 (193)
T TIGR03697 73 VPIEQVEKAIEEDPDLSMLLLQGLSSRILQTEMMIETLAHRDMGSRLVSFLLILCRDFGVPGQRGVTIDLRLSHQAIAEA 152 (193)
T ss_pred eeHHHHHHHHHHChHHHHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhCCCCCCeEEecCCCCHHHHHHH
Confidence 445555555555555444444444432110 011356889999999876532 2478999999
Q ss_pred cccccchhhhhhhhHHH
Q 015913 107 FRYSGETISRHFNNVLN 123 (398)
Q Consensus 107 fgis~stv~r~~~~v~~ 123 (398)
.|+++.||+|+++++.+
T Consensus 153 lG~tretvsR~l~~l~~ 169 (193)
T TIGR03697 153 IGSTRVTITRLLGDLRK 169 (193)
T ss_pred hCCcHHHHHHHHHHHHH
Confidence 99999999999887766
No 84
>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=80.95 E-value=1.4 Score=37.67 Aligned_cols=48 Identities=15% Similarity=0.248 Sum_probs=41.5
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHh
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 128 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~ 128 (398)
.+++.++.++.|.++ .|.++.++|..+|+|.+||...+.+....|-+.
T Consensus 110 ~L~~~~r~i~~l~~~-~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 157 (162)
T TIGR02983 110 RLPARQRAVVVLRYY-EDLSEAQVAEALGISVGTVKSRLSRALARLREL 157 (162)
T ss_pred hCCHHHHHHhhhHHH-hcCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 578888888777774 499999999999999999999999998888653
No 85
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=80.83 E-value=1.4 Score=38.19 Aligned_cols=49 Identities=6% Similarity=0.083 Sum_probs=40.3
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHhh
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAIS 129 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~~ 129 (398)
.++++++-++.|.++ .|.++.++|..+|+|.+||...+++....+....
T Consensus 119 ~L~~~~r~i~~l~~~-~g~s~~EIA~~lgis~~tV~~~l~Ra~~~~~~~~ 167 (172)
T PRK09651 119 GLNGKTREAFLLSQL-DGLTYSEIAHKLGVSVSSVKKYVAKATEHCLLFR 167 (172)
T ss_pred hCCHHHhHHhhhhhc-cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 677777766665555 4899999999999999999999999888876543
No 86
>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=80.21 E-value=1.2 Score=39.41 Aligned_cols=50 Identities=10% Similarity=0.113 Sum_probs=42.1
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHhhc
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAISL 130 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~~~ 130 (398)
.+|+..+-++.|.++ .|.++.+||..+|+|.+||...+.+....|.+...
T Consensus 131 ~Lp~~~r~i~~L~~~-~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~ 180 (193)
T TIGR02947 131 GLPEEFRQAVYLADV-EGFAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQLV 180 (193)
T ss_pred hCCHHHhhheeehhh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 577777877777665 48999999999999999999999999998875443
No 87
>PRK15320 transcriptional activator SprB; Provisional
Probab=80.20 E-value=0.72 Score=40.93 Aligned_cols=38 Identities=11% Similarity=0.159 Sum_probs=34.2
Q ss_pred hheeccccccchhhhhcccccccchhhhhhhhHHHHHH
Q 015913 89 IFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 126 (398)
Q Consensus 89 ~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~ 126 (398)
-.|..|+.|.+.++||+.+++|.+||+.+.++...-+.
T Consensus 171 EVL~LLAkG~SNKEIAekL~LS~KTVSTYKnRLLeKLg 208 (251)
T PRK15320 171 ALLILLSSGHPAIELAKKFGLGTKTVSIYRKKVMYRLG 208 (251)
T ss_pred HHHHHHHcCCCHHHHHHHhccchhhHHHHHHHHHHHcC
Confidence 56678999999999999999999999999998888764
No 88
>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=80.20 E-value=0.67 Score=32.54 Aligned_cols=44 Identities=11% Similarity=0.252 Sum_probs=34.0
Q ss_pred CCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHH
Q 015913 81 IKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 126 (398)
Q Consensus 81 ~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~ 126 (398)
+|..|.- .|..++.|.+..++|...++|.+||..+..++..-+.
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 3444433 5567888999999999999999999999988887663
No 89
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=80.19 E-value=1.5 Score=41.06 Aligned_cols=48 Identities=17% Similarity=0.290 Sum_probs=41.8
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHh
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 128 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~ 128 (398)
.+++.++..+.|+|+ .|.++.++|..+|+|.++|++..++...-|...
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 478888888888886 599999999999999999999999998888643
No 90
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=80.08 E-value=1.6 Score=38.39 Aligned_cols=51 Identities=8% Similarity=-0.020 Sum_probs=43.4
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHhhcc
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAISLD 131 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~~~~ 131 (398)
.++++++.++.|.++. |.++.++|..+|+|.+||...+.+....|.+....
T Consensus 106 ~L~~~~r~i~~l~~~~-g~~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 156 (181)
T PRK09637 106 ALPEKYAEALRLTELE-GLSQKEIAEKLGLSLSGAKSRVQRGRVKLKELLEG 156 (181)
T ss_pred hCCHHHHHHHHHHHhc-CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 6888888888777654 99999999999999999999999999888765544
No 91
>PF13751 DDE_Tnp_1_6: Transposase DDE domain
Probab=80.08 E-value=0.78 Score=37.66 Aligned_cols=49 Identities=16% Similarity=0.058 Sum_probs=36.8
Q ss_pred HHHHHHHh-HHHHHHHHHHhhhhhhccCCCCCccchhHHhHHHHHHHhhhh
Q 015913 275 QRHSLLRN-ATDRIFGALKERFPILLSAPPYPLQTQVKLVVAACALHNYIQ 324 (398)
Q Consensus 275 ~~~s~~R~-~VE~~fg~LK~rf~iL~~~~~~~~~~~~~ii~ac~~LHN~~~ 324 (398)
+...+.|. .||++||.+|. +.-+.........++..-+...++-|||-.
T Consensus 74 k~~y~~R~~~VE~~fg~~K~-~~g~~r~~~rG~~kv~~~~~l~a~a~Nl~r 123 (125)
T PF13751_consen 74 KELYKQRSIKVEGVFGTIKR-NHGLRRFRYRGLEKVRIEFLLAAIAYNLKR 123 (125)
T ss_pred hhhhheeecccccccccchh-ccCCccccccchhhhHHHHHHHHHHHHHHH
Confidence 45567787 99999999996 455555556667777777777888899854
No 92
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=79.91 E-value=1.4 Score=38.97 Aligned_cols=48 Identities=10% Similarity=0.143 Sum_probs=42.7
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHh
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 128 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~ 128 (398)
.++++++-++.|+++ .|.++.++|..+|+|.+||...+.+....|.+.
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 688888888888887 699999999999999999999999988888754
No 93
>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=79.79 E-value=0.75 Score=34.84 Aligned_cols=24 Identities=17% Similarity=0.322 Sum_probs=20.7
Q ss_pred ccchhhhhcccccccchhhhhhhh
Q 015913 97 NLRTRAVQELFRYSGETISRHFNN 120 (398)
Q Consensus 97 ~~~~~~l~~~fgis~stv~r~~~~ 120 (398)
..+..++|..+|+|.+||++.++.
T Consensus 19 ~~ti~dvA~~~gvS~~TVsr~L~~ 42 (80)
T TIGR02844 19 KATVRETAKVFGVSKSTVHKDVTE 42 (80)
T ss_pred CCCHHHHHHHhCCCHHHHHHHhcC
Confidence 357889999999999999998753
No 94
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=79.79 E-value=1.4 Score=37.36 Aligned_cols=46 Identities=9% Similarity=0.038 Sum_probs=39.7
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHH
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 126 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~ 126 (398)
.+++.++-++.|.++. |.++.++|..+|+|.+||...+.+....|-
T Consensus 106 ~L~~~~r~ii~l~~~~-~~s~~EIA~~l~is~~tV~~~~~ra~~~Lr 151 (154)
T PRK06759 106 VLDEKEKYIIFERFFV-GKTMGEIALETEMTYYQVRWIYRQALEKMR 151 (154)
T ss_pred hCCHHHHHHHHHHHhc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHh
Confidence 6888888888887765 899999999999999999999888777663
No 95
>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=79.74 E-value=1.2 Score=31.64 Aligned_cols=40 Identities=18% Similarity=0.283 Sum_probs=29.7
Q ss_pred HHHHHhheeccc---cccchhhhhcccccccchhhhhhhhHHH
Q 015913 84 EEQLAIFMFIVG---HNLRTRAVQELFRYSGETISRHFNNVLN 123 (398)
Q Consensus 84 e~~l~~~L~~L~---~~~~~~~l~~~fgis~stv~r~~~~v~~ 123 (398)
.+.-+-+++.|. ...+..+||..+|+|++||+..+++..+
T Consensus 6 ~e~YL~~Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~ 48 (60)
T PF01325_consen 6 EEDYLKAIYELSEEGGPVRTKDIAERLGVSPPTVTEMLKRLAE 48 (60)
T ss_dssp HHHHHHHHHHHHHCTSSBBHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCCCccHHHHHHHHCCChHHHHHHHHHHHH
Confidence 445555666665 5678899999999999999998877654
No 96
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=79.70 E-value=1.5 Score=38.97 Aligned_cols=47 Identities=13% Similarity=0.208 Sum_probs=41.0
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHH
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMA 127 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~ 127 (398)
.+|++++-++.|+++ .|.++.++|..+|+|.+||...+++....|..
T Consensus 141 ~Lp~~~r~v~~l~~~-eg~s~~EIA~~lgis~~tVk~rl~ra~~~Lr~ 187 (194)
T PRK12531 141 RLPKAQRDVLQAVYL-EELPHQQVAEMFDIPLGTVKSRLRLAVEKLRH 187 (194)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHH
Confidence 578888888888777 59999999999999999999988888888764
No 97
>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=79.51 E-value=1.3 Score=29.66 Aligned_cols=28 Identities=14% Similarity=0.261 Sum_probs=22.8
Q ss_pred cccchhhhhcccccccchhhhhhhhHHH
Q 015913 96 HNLRTRAVQELFRYSGETISRHFNNVLN 123 (398)
Q Consensus 96 ~~~~~~~l~~~fgis~stv~r~~~~v~~ 123 (398)
.+.+..++|..+|+|.+||++++++..+
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 3588999999999999999999988764
No 98
>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=79.31 E-value=1.5 Score=40.40 Aligned_cols=48 Identities=17% Similarity=0.138 Sum_probs=42.3
Q ss_pred CCCHHHHHHhheecc---ccccchhhhhcccccccchhhhhhhhHHHHHHH
Q 015913 80 RIKIEEQLAIFMFIV---GHNLRTRAVQELFRYSGETISRHFNNVLNAIMA 127 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L---~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~ 127 (398)
.+++.++..+.|++. ..+.++.++|..+|+|.++|+++..+.+.-|-.
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 588889999999884 578999999999999999999999988888764
No 99
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=79.29 E-value=1.5 Score=38.34 Aligned_cols=47 Identities=17% Similarity=0.203 Sum_probs=40.6
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHH
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMA 127 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~ 127 (398)
.+|+.++.++.|+++. |.++.++|..+|+|.+||...+++....|.+
T Consensus 129 ~L~~~~r~v~~l~~~~-g~s~~EIA~~l~is~~tV~~~l~rar~~Lr~ 175 (181)
T PRK12536 129 QLPDRQRLPIVHVKLE-GLSVAETAQLTGLSESAVKVGIHRGLKALAA 175 (181)
T ss_pred HCCHHHHHHHHHHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 5788888877777654 9999999999999999999999998888764
No 100
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=79.19 E-value=1.8 Score=38.04 Aligned_cols=48 Identities=8% Similarity=-0.012 Sum_probs=40.7
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHh
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 128 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~ 128 (398)
.+++.++-++.|.++ .|.++.++|..+|+|.+||...+++....|...
T Consensus 137 ~L~~~~r~i~~l~~~-~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 184 (187)
T PRK12534 137 ELEPPRSELIRTAFF-EGITYEELAARTDTPIGTVKSWIRRGLAKLKAC 184 (187)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Confidence 577877777777764 799999999999999999999999988887653
No 101
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=79.14 E-value=1.5 Score=38.88 Aligned_cols=49 Identities=4% Similarity=0.040 Sum_probs=42.6
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHhh
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAIS 129 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~~ 129 (398)
.+++.++-++.|.++ .|.++.++|..+|+|.+||...+++....|.+..
T Consensus 136 ~L~~~~r~i~~L~~~-~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 184 (195)
T PRK12532 136 NLPENTARVFTLKEI-LGFSSDEIQQMCGISTSNYHTIMHRARESLRQCL 184 (195)
T ss_pred hCCHHHHHHhhhHHH-hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 678888888888776 5999999999999999999999999999887543
No 102
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=79.03 E-value=1.7 Score=37.56 Aligned_cols=48 Identities=10% Similarity=0.105 Sum_probs=41.7
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHh
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 128 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~ 128 (398)
.+++.++-++.|.++. |.++.++|..+|+|.+||...+++....|.+.
T Consensus 118 ~L~~~~r~vl~L~~~~-g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~ 165 (173)
T PRK09645 118 QLSPEHRAVLVRSYYR-GWSTAQIAADLGIPEGTVKSRLHYALRALRLA 165 (173)
T ss_pred hCCHHHHHHHHHHHHc-CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 5888888888777665 99999999999999999999999888888754
No 103
>PRK05572 sporulation sigma factor SigF; Validated
Probab=79.03 E-value=1.8 Score=40.25 Aligned_cols=48 Identities=15% Similarity=0.220 Sum_probs=42.3
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHh
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 128 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~ 128 (398)
.+++.++..+.++++ .|.++.++|..+|+|.++|+++.++.+..|...
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 688888888888776 589999999999999999999999999888643
No 104
>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=78.93 E-value=1 Score=34.70 Aligned_cols=33 Identities=18% Similarity=0.062 Sum_probs=26.6
Q ss_pred HHhheeccccccchhhhhcccccccchhhhhhh
Q 015913 87 LAIFMFIVGHNLRTRAVQELFRYSGETISRHFN 119 (398)
Q Consensus 87 l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~ 119 (398)
+.++=-.|..|.+|++|+...|+|.+||+|+-+
T Consensus 39 ~~va~~lL~~g~syreIa~~tgvS~aTItRvsr 71 (87)
T PF01371_consen 39 WQVAKELLDEGKSYREIAEETGVSIATITRVSR 71 (87)
T ss_dssp HHHHHHHHHTTSSHHHHHHHHTSTHHHHHHHHH
T ss_pred HHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 334433677899999999999999999998544
No 105
>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=78.91 E-value=0.98 Score=27.77 Aligned_cols=25 Identities=16% Similarity=0.364 Sum_probs=19.5
Q ss_pred cchhhhhcccccccchhhhhhhhHH
Q 015913 98 LRTRAVQELFRYSGETISRHFNNVL 122 (398)
Q Consensus 98 ~~~~~l~~~fgis~stv~r~~~~v~ 122 (398)
.+..++|+..|.+..||||.+.++-
T Consensus 3 mtr~diA~~lG~t~ETVSR~l~~l~ 27 (32)
T PF00325_consen 3 MTRQDIADYLGLTRETVSRILKKLE 27 (32)
T ss_dssp --HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred cCHHHHHHHhCCcHHHHHHHHHHHH
Confidence 4568999999999999999987754
No 106
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=78.84 E-value=1.6 Score=37.39 Aligned_cols=47 Identities=6% Similarity=0.066 Sum_probs=41.0
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHH
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMA 127 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~ 127 (398)
.+|+.++.++.|.++. |.++.++|..+|+|.+||...+++....|.+
T Consensus 112 ~L~~~~r~v~~l~~~~-~~s~~eIA~~lgis~~tv~~~l~Rar~~L~~ 158 (161)
T PRK12541 112 SLPLERRNVLLLRDYY-GFSYKEIAEMTGLSLAKVKIELHRGRKETKS 158 (161)
T ss_pred HCCHHHHHHhhhHHhc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 6888888888887765 8999999999999999999999888887754
No 107
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=78.79 E-value=1.9 Score=38.45 Aligned_cols=53 Identities=11% Similarity=0.026 Sum_probs=45.0
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHhhcccc
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAISLDFF 133 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~~~~~i 133 (398)
.+|+..+-++.|.++. |.++.++|+.+|+|.+||...+++....|.+....+.
T Consensus 133 ~Lp~~~r~v~~l~~~~-g~s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l~~~~ 185 (196)
T PRK12535 133 ALPPERREALILTQVL-GYTYEEAAKIADVRVGTIRSRVARARADLIAATATGQ 185 (196)
T ss_pred cCCHHHHHHhhhHHHh-CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhcccc
Confidence 5778788777777665 8999999999999999999999999999987666554
No 108
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=78.69 E-value=1.7 Score=37.65 Aligned_cols=46 Identities=9% Similarity=0.114 Sum_probs=40.3
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHH
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 126 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~ 126 (398)
.+|+.++-++.|.++. |.++.++|+.+|+|.+||...+++.+..+.
T Consensus 119 ~Lp~~~r~v~~L~~~~-g~s~~EIA~~lgis~~tV~~~l~ra~~~~~ 164 (172)
T PRK12523 119 KLSSKARAAFLYNRLD-GMGHAEIAERLGVSVSRVRQYLAQGLRQCY 164 (172)
T ss_pred hCCHHHHHHHHHHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 6888888888888775 999999999999999999998888777765
No 109
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=78.68 E-value=1.7 Score=38.45 Aligned_cols=48 Identities=8% Similarity=-0.022 Sum_probs=42.0
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHh
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 128 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~ 128 (398)
.+|+.++-++.|.++. |.++.+||..+|+|.+||...+.+....|.+.
T Consensus 131 ~Lp~~~r~v~~l~~~~-g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 178 (191)
T PRK12520 131 RLPPRTGRVFMMREWL-ELETEEICQELQITATNAWVLLYRARMRLREC 178 (191)
T ss_pred hCCHHHHHHHHHHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 5888888888887765 89999999999999999999999998888643
No 110
>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=78.66 E-value=1.9 Score=37.83 Aligned_cols=48 Identities=17% Similarity=0.151 Sum_probs=41.6
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHh
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 128 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~ 128 (398)
.+++.++-++.|.++ .|.++.++|..+|+|.+||...+++....|-+.
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 688888888888776 699999999999999999999999988877643
No 111
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=78.59 E-value=1.4 Score=38.76 Aligned_cols=48 Identities=13% Similarity=0.158 Sum_probs=41.7
Q ss_pred CCCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHH
Q 015913 79 NRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMA 127 (398)
Q Consensus 79 ~~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~ 127 (398)
..+|+.++-++.|.++. |.++.+||..+|+|.+||...+++....|.+
T Consensus 129 ~~Lp~~~r~v~~L~~~~-g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 176 (185)
T PRK09649 129 ADLTTDQREALLLTQLL-GLSYADAAAVCGCPVGTIRSRVARARDALLA 176 (185)
T ss_pred HhCCHHHhHHhhhHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 36888888888888775 8999999999999999999999888888764
No 112
>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=78.51 E-value=1.9 Score=37.19 Aligned_cols=48 Identities=15% Similarity=0.198 Sum_probs=41.2
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHh
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 128 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~ 128 (398)
.+++.++-++.|.++. |.++.++|..+|+|.+||...+++....|...
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 5788888777777776 89999999999999999999999988888653
No 113
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=78.50 E-value=1.7 Score=38.12 Aligned_cols=49 Identities=12% Similarity=0.070 Sum_probs=42.5
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHhh
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAIS 129 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~~ 129 (398)
.+|+.++-++.|.++. |.++.++|..+|+|..||...+++....|.+..
T Consensus 128 ~L~~~~r~i~~l~~~~-g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 176 (186)
T PRK05602 128 ALPERQREAIVLQYYQ-GLSNIEAAAVMDISVDALESLLARGRRALRAQL 176 (186)
T ss_pred hCCHHHHHHhhHHHhc-CCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHH
Confidence 5788888888888775 999999999999999999999999888887543
No 114
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=78.38 E-value=1.9 Score=40.95 Aligned_cols=48 Identities=10% Similarity=0.073 Sum_probs=42.0
Q ss_pred CCCHHHHHHhheeccc-cccchhhhhcccccccchhhhhhhhHHHHHHH
Q 015913 80 RIKIEEQLAIFMFIVG-HNLRTRAVQELFRYSGETISRHFNNVLNAIMA 127 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~-~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~ 127 (398)
.++..++..+.++|+. .+.++.++|..+|+|+++|+++.++.+.-|-.
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 5788888888888875 58999999999999999999999988887754
No 115
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=78.33 E-value=1.6 Score=39.04 Aligned_cols=49 Identities=4% Similarity=-0.047 Sum_probs=42.1
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHhh
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAIS 129 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~~ 129 (398)
.+|+.++-++.|.++. |.++.+||..+|+|.+||...+.+....|.+..
T Consensus 139 ~Lp~~~r~v~~L~~~e-g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l 187 (201)
T PRK12545 139 HLPEQIGRVFMMREFL-DFEIDDICTELTLTANHCSVLLYRARTRLRTCL 187 (201)
T ss_pred hCCHHHHHHHHHHHHc-CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 5888888888887754 899999999999999999999999888887543
No 116
>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=78.28 E-value=1.7 Score=37.65 Aligned_cols=52 Identities=12% Similarity=0.020 Sum_probs=44.3
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHhhccc
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAISLDF 132 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~~~~~ 132 (398)
.+|+.++.++.|.++. |.++.++|..+|+|.+||...+.+....|.......
T Consensus 100 ~L~~~~r~v~~l~~~~-g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~ 151 (170)
T TIGR02959 100 ELPDEYREAIRLTELE-GLSQQEIAEKLGLSLSGAKSRVQRGRKKLKELLETC 151 (170)
T ss_pred hCCHHHHHHHHHHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 6888888888887765 899999999999999999999999998887655443
No 117
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=78.25 E-value=1.9 Score=38.17 Aligned_cols=50 Identities=10% Similarity=0.115 Sum_probs=44.4
Q ss_pred CCCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHhh
Q 015913 79 NRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAIS 129 (398)
Q Consensus 79 ~~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~~ 129 (398)
..+|++++-++.|+++ .|.++.++|..+|+|.+||...+.+....|-+..
T Consensus 112 ~~Lp~~~r~v~~L~~~-~g~s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l 161 (188)
T PRK12546 112 AQLPDEQREALILVGA-SGFSYEEAAEMCGVAVGTVKSRANRARARLAELL 161 (188)
T ss_pred HhCCHHHhHHhhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3689999999999888 6999999999999999999999999999887544
No 118
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=78.24 E-value=1.8 Score=38.37 Aligned_cols=48 Identities=15% Similarity=0.205 Sum_probs=40.3
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHh
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 128 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~ 128 (398)
.+++.++.++.|+++ .|.++.++|...|+|.+||...+++....|...
T Consensus 139 ~L~~~~r~i~~l~~~-~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~ 186 (194)
T PRK12513 139 TLPDEQREVFLLREH-GDLELEEIAELTGVPEETVKSRLRYALQKLREL 186 (194)
T ss_pred hCCHhHhhheeeehc-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 578888887777764 599999999999999999998888888877643
No 119
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=78.12 E-value=2 Score=37.62 Aligned_cols=49 Identities=10% Similarity=0.191 Sum_probs=42.1
Q ss_pred CCCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHh
Q 015913 79 NRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 128 (398)
Q Consensus 79 ~~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~ 128 (398)
..+|+.++-++.|.++ .|.++.++|..+|+|.+||...+++....|...
T Consensus 135 ~~L~~~~r~v~~l~~~-~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T TIGR02948 135 QALPPKYRMVIVLKYM-EDLSLKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred HhCCHHHhHHhhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3688888888888766 489999999999999999999999988887653
No 120
>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=77.72 E-value=1.6 Score=40.51 Aligned_cols=47 Identities=13% Similarity=0.265 Sum_probs=41.9
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHH
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMA 127 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~ 127 (398)
.+|..++-++.|.++ .|.++.+||..+|+|.+||...+++....|.+
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 588888888888777 69999999999999999999999999998864
No 121
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=77.58 E-value=1.9 Score=37.74 Aligned_cols=48 Identities=10% Similarity=0.075 Sum_probs=42.3
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHh
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 128 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~ 128 (398)
.+|+.++-.+.|.++. |.++.++|..+|+|.+||...+++....|.+.
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 6888888888887776 99999999999999999999999999888743
No 122
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=77.57 E-value=1.8 Score=37.19 Aligned_cols=50 Identities=16% Similarity=0.159 Sum_probs=42.1
Q ss_pred CCCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHhh
Q 015913 79 NRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAIS 129 (398)
Q Consensus 79 ~~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~~ 129 (398)
..+|+.++-++.|+++. |.++.++|..+|+|.+||...+++....|.+..
T Consensus 107 ~~L~~~~r~v~~l~~~~-g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l 156 (165)
T PRK09644 107 HTLPVIEAQAILLCDVH-ELTYEEAASVLDLKLNTYKSHLFRGRKRLKALL 156 (165)
T ss_pred HhCCHHHHHHHHhHHHh-cCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 36888888877777654 899999999999999999999999998887543
No 123
>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=77.48 E-value=2.1 Score=39.11 Aligned_cols=49 Identities=18% Similarity=0.158 Sum_probs=42.8
Q ss_pred CCCCHHHHHHhheecc---ccccchhhhhcccccccchhhhhhhhHHHHHHH
Q 015913 79 NRIKIEEQLAIFMFIV---GHNLRTRAVQELFRYSGETISRHFNNVLNAIMA 127 (398)
Q Consensus 79 ~~~s~e~~l~~~L~~L---~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~ 127 (398)
..+++.++-++.|+++ ..|.|+.++|+..|+|.+||.+..++....|..
T Consensus 173 ~~L~~~~r~il~l~y~~~~~e~~S~~EIAe~lgis~~tV~~~~~rAl~~Lr~ 224 (227)
T TIGR02846 173 SVLDGREREVIEMRYGLGDGRRKTQREIAKILGISRSYVSRIEKRALMKLYK 224 (227)
T ss_pred HhCCHHHHHHHHHHHcCCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3688999988888876 489999999999999999999999888887753
No 124
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=77.38 E-value=2.1 Score=37.64 Aligned_cols=50 Identities=6% Similarity=0.139 Sum_probs=41.7
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHhhc
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAISL 130 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~~~ 130 (398)
.+|+.++-++.|.++. |.++.++|..+|+|.+||...+.+....|.....
T Consensus 122 ~L~~~~r~i~~l~~~~-g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~ 171 (185)
T PRK12542 122 ELNESNRQVFKYKVFY-NLTYQEISSVMGITEANVRKQFERARKRVQNMIG 171 (185)
T ss_pred hCCHHHHHHHHHHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHc
Confidence 5788877777776654 8999999999999999999999988888875443
No 125
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=77.34 E-value=1.8 Score=37.89 Aligned_cols=47 Identities=11% Similarity=0.261 Sum_probs=40.0
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHH
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMA 127 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~ 127 (398)
.+|+.++-++.|.++ .|.++.+||..+|+|.+||...+++....|-+
T Consensus 117 ~Lp~~~r~i~~l~~~-e~~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~ 163 (179)
T PRK12543 117 KLPYKLRQVIILRYL-HDYSQEEIAQLLQIPIGTVKSRIHAALKKLRQ 163 (179)
T ss_pred hCCHHHHHHHHHHHH-ccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 688888888777655 48999999999999999999988888887754
No 126
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=76.90 E-value=2.2 Score=40.66 Aligned_cols=50 Identities=14% Similarity=0.016 Sum_probs=43.5
Q ss_pred CCCHHHHHHhheecc-ccccchhhhhcccccccchhhhhhhhHHHHHHHhh
Q 015913 80 RIKIEEQLAIFMFIV-GHNLRTRAVQELFRYSGETISRHFNNVLNAIMAIS 129 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L-~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~~ 129 (398)
.+++.++..+.|+|+ ..|.++.++|..+|+|.++|+.+.++.+.-|....
T Consensus 227 ~L~~rer~vl~lr~~~~~~~t~~EIa~~lgvs~~~V~q~~~~Al~kLr~~l 277 (289)
T PRK07500 227 TLNERELRIIRERRLREDGATLEALGEELGISKERVRQIEARALEKLRRAL 277 (289)
T ss_pred cCCHHHHHHHHHHhcCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 588888988888875 36899999999999999999999999999887543
No 127
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=76.88 E-value=2.1 Score=37.73 Aligned_cols=50 Identities=10% Similarity=0.152 Sum_probs=43.4
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHhhc
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAISL 130 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~~~ 130 (398)
.+++.++-++.|.++ .|.++.++|..+|+|.+||...+++....|-+...
T Consensus 111 ~Lp~~~R~v~~L~~~-~g~s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l~ 160 (182)
T PRK12540 111 KLPQDQREALILVGA-SGFSYEDAAAICGCAVGTIKSRVNRARSKLSALLY 160 (182)
T ss_pred hCCHHHHHHhhHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 578888888888776 69999999999999999999999999999875443
No 128
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=76.84 E-value=2 Score=38.07 Aligned_cols=49 Identities=8% Similarity=0.157 Sum_probs=41.5
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHhh
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAIS 129 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~~ 129 (398)
.+|+.++.++.|+++ .|.++.+||..+|+|.+||...+++....|.+..
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 588888888877777 5899999999999999999988888877776543
No 129
>PRK06930 positive control sigma-like factor; Validated
Probab=76.74 E-value=2.1 Score=37.50 Aligned_cols=48 Identities=13% Similarity=0.155 Sum_probs=40.6
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHh
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 128 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~ 128 (398)
.+|+.++-++.|.+ ..|.++.++|..+|+|.+||...+.+....|...
T Consensus 114 ~L~~rer~V~~L~~-~eg~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~ 161 (170)
T PRK06930 114 VLTEREKEVYLMHR-GYGLSYSEIADYLNIKKSTVQSMIERAEKKIARQ 161 (170)
T ss_pred hCCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 57777777766654 6799999999999999999999999998888743
No 130
>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=76.61 E-value=2.3 Score=40.41 Aligned_cols=50 Identities=8% Similarity=0.019 Sum_probs=43.8
Q ss_pred CCCHHHHHHhheec-c--ccccchhhhhcccccccchhhhhhhhHHHHHHHhh
Q 015913 80 RIKIEEQLAIFMFI-V--GHNLRTRAVQELFRYSGETISRHFNNVLNAIMAIS 129 (398)
Q Consensus 80 ~~s~e~~l~~~L~~-L--~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~~ 129 (398)
.+|..++..+.|+| | -.|.++.++|..+|+|.+||....++....|-...
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 68999999998887 3 56899999999999999999999999998887543
No 131
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=76.48 E-value=2.3 Score=37.33 Aligned_cols=49 Identities=18% Similarity=0.165 Sum_probs=43.2
Q ss_pred CCCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHh
Q 015913 79 NRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 128 (398)
Q Consensus 79 ~~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~ 128 (398)
..+|+.++-++.|.++. |.++.++|..+|+|..||...+++....|.+.
T Consensus 130 ~~L~~~~r~v~~l~~~~-g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 178 (184)
T PRK12539 130 ARLPEKMRLAIQAVKLE-GLSVAEAATRSGMSESAVKVSVHRGLKALAAL 178 (184)
T ss_pred HhCCHHHHHHHHHHHHc-CCcHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 36888888888888775 99999999999999999999999999988753
No 132
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=76.40 E-value=2 Score=39.63 Aligned_cols=49 Identities=8% Similarity=0.193 Sum_probs=41.7
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHhh
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAIS 129 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~~ 129 (398)
.+|..++-++.|+++. |.++.++|..+|+|.+||...+++....|.+..
T Consensus 171 ~Lp~~~R~v~~L~~~e-g~s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~l 219 (233)
T PRK12538 171 RLPEQQRIAVILSYHE-NMSNGEIAEVMDTTVAAVESLLKRGRQQLRDLL 219 (233)
T ss_pred hCCHHHHHHhhhHHhc-CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 5778888877777664 999999999999999999999999998887543
No 133
>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=76.27 E-value=1 Score=32.14 Aligned_cols=27 Identities=19% Similarity=0.380 Sum_probs=23.4
Q ss_pred ccchhhhhcccccccchhhhhhhhHHH
Q 015913 97 NLRTRAVQELFRYSGETISRHFNNVLN 123 (398)
Q Consensus 97 ~~~~~~l~~~fgis~stv~r~~~~v~~ 123 (398)
..+..++++.+|+|++||+++++...+
T Consensus 25 ~~s~~ela~~~g~s~~tv~r~l~~L~~ 51 (67)
T cd00092 25 PLTRQEIADYLGLTRETVSRTLKELEE 51 (67)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 468889999999999999998877665
No 134
>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=76.08 E-value=2.3 Score=38.78 Aligned_cols=47 Identities=13% Similarity=0.192 Sum_probs=40.7
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHH
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMA 127 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~ 127 (398)
.+|+.++-++.++++ .|.++.++|..+|+|.+||....++....|..
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 588888888877765 58999999999999999999999998887753
No 135
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=76.07 E-value=2.2 Score=36.35 Aligned_cols=49 Identities=10% Similarity=0.093 Sum_probs=41.1
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHhh
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAIS 129 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~~ 129 (398)
.+|++++-++.|.+ -.|.++.++|..+|+|.+||...+.+....|....
T Consensus 105 ~L~~~~r~v~~l~~-~~~~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~l 153 (159)
T PRK12527 105 ELPPACRDSFLLRK-LEGLSHQQIAEHLGISRSLVEKHIVNAMKHCRVRM 153 (159)
T ss_pred hCCHHHHHHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 58888777777765 45999999999999999999999999888887543
No 136
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=76.05 E-value=2.2 Score=38.35 Aligned_cols=48 Identities=8% Similarity=0.083 Sum_probs=40.8
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHh
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 128 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~ 128 (398)
.+|++++.++.|.++. |.++.++|..+|+|.+||...+++....|.+.
T Consensus 153 ~L~~~~r~vl~l~~~~-g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 200 (206)
T PRK12526 153 KLPEAQQTVVKGVYFQ-ELSQEQLAQQLNVPLGTVKSRLRLALAKLKVQ 200 (206)
T ss_pred hCCHHHHHHHHHHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 5888888887777664 89999999999999999999988888877643
No 137
>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=76.03 E-value=1.7 Score=34.37 Aligned_cols=43 Identities=21% Similarity=0.257 Sum_probs=36.8
Q ss_pred CHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHH
Q 015913 82 KIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAI 125 (398)
Q Consensus 82 s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l 125 (398)
.++++..+.++|+ .+.++.+++...++|++|++++-++.+..|
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 4678888888888 578999999999999999999888776644
No 138
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=76.01 E-value=2.3 Score=39.64 Aligned_cols=47 Identities=17% Similarity=0.167 Sum_probs=41.0
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHH
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMA 127 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~ 127 (398)
.+++.++-++.|+++ .|.++.++|..+|+|.+||.+..++....|-.
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 578888888877775 69999999999999999999999999888864
No 139
>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=75.91 E-value=1.7 Score=30.30 Aligned_cols=28 Identities=14% Similarity=0.213 Sum_probs=23.1
Q ss_pred cccchhhhhcccccccchhhhhhhhHHH
Q 015913 96 HNLRTRAVQELFRYSGETISRHFNNVLN 123 (398)
Q Consensus 96 ~~~~~~~l~~~fgis~stv~r~~~~v~~ 123 (398)
.+.+..+++..++++++++++++++...
T Consensus 16 ~~~~~~~la~~~~~~~~~~t~~i~~L~~ 43 (59)
T PF01047_consen 16 GGITQSELAEKLGISRSTVTRIIKRLEK 43 (59)
T ss_dssp SSEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHCCChhHHHHHHHHHHH
Confidence 4578999999999999999998876654
No 140
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=75.77 E-value=2.6 Score=38.69 Aligned_cols=49 Identities=14% Similarity=0.248 Sum_probs=41.7
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHhh
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAIS 129 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~~ 129 (398)
.+++.++-.+.|.++ .|.++.++|..+|+|.+||...+++....|....
T Consensus 184 ~L~~~~r~vl~l~~~-~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l 232 (236)
T PRK06986 184 SLPEREQLVLSLYYQ-EELNLKEIGAVLGVSESRVSQIHSQAIKRLRARL 232 (236)
T ss_pred hCCHHHHHHHHhHhc-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 578888888877775 5899999999999999999999999988886543
No 141
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=75.61 E-value=1.2 Score=39.86 Aligned_cols=45 Identities=9% Similarity=0.219 Sum_probs=35.7
Q ss_pred CCCCHHHHHHhheecccc-------------ccchhhhhcccccccchhhhhhhhHHH
Q 015913 79 NRIKIEEQLAIFMFIVGH-------------NLRTRAVQELFRYSGETISRHFNNVLN 123 (398)
Q Consensus 79 ~~~s~e~~l~~~L~~L~~-------------~~~~~~l~~~fgis~stv~r~~~~v~~ 123 (398)
...++.++++-+|..|+. ..+..++|...|+++.|++|+++++.+
T Consensus 137 ~~~~~~~Rl~~~L~~l~~~~~~~~~~~~~~~~~t~~~lA~~lG~tr~tvsR~l~~l~~ 194 (211)
T PRK11753 137 AFLDVTGRIAQTLLDLAKQPDAMTHPDGMQIKITRQEIGRIVGCSREMVGRVLKMLED 194 (211)
T ss_pred HhcChhhHHHHHHHHHHHhcCCcCCCCceecCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 357888999988876642 245688999999999999998877655
No 142
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=75.40 E-value=2.1 Score=38.56 Aligned_cols=49 Identities=8% Similarity=-0.012 Sum_probs=42.9
Q ss_pred CCCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHh
Q 015913 79 NRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 128 (398)
Q Consensus 79 ~~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~ 128 (398)
..+++.++-++.|.++. |.++.++|..+|+|.+||...+++....|.+.
T Consensus 147 ~~L~~~~r~v~~L~~~~-g~s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~ 195 (206)
T PRK12544 147 DGLPAKYARVFMMREFI-ELETNEICHAVDLSVSNLNVLLYRARLRLREC 195 (206)
T ss_pred HhCCHHHHHHHHHHHHc-CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 36888888888887765 99999999999999999999999999998754
No 143
>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=74.95 E-value=1.9 Score=29.68 Aligned_cols=29 Identities=17% Similarity=0.235 Sum_probs=23.3
Q ss_pred cccchhhhhcccccccchhhhhhhhHHHH
Q 015913 96 HNLRTRAVQELFRYSGETISRHFNNVLNA 124 (398)
Q Consensus 96 ~~~~~~~l~~~fgis~stv~r~~~~v~~~ 124 (398)
.+.+..++|+.++||..||.+.+...-..
T Consensus 14 ~~it~~eLa~~l~vS~rTi~~~i~~L~~~ 42 (55)
T PF08279_consen 14 EPITAKELAEELGVSRRTIRRDIKELREW 42 (55)
T ss_dssp TSBEHHHHHHHCTS-HHHHHHHHHHHHHT
T ss_pred CCcCHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence 34789999999999999999988776443
No 144
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=74.78 E-value=2.5 Score=38.69 Aligned_cols=51 Identities=8% Similarity=0.085 Sum_probs=43.1
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHhhcc
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAISLD 131 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~~~~ 131 (398)
.+++.++-++.|+++. |.++.+||..+|+|.+||...+++....|-+....
T Consensus 149 ~L~~~~r~i~~l~~~~-g~s~~EIAe~lgis~~tVk~~l~Rar~kLr~~l~~ 199 (231)
T PRK11922 149 ALPDAFRAVFVLRVVE-ELSVEETAQALGLPEETVKTRLHRARRLLRESLAR 199 (231)
T ss_pred hCCHHHhhhheeehhc-CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 5788888777777665 99999999999999999999999999888765543
No 145
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=74.61 E-value=2.2 Score=37.70 Aligned_cols=47 Identities=4% Similarity=0.068 Sum_probs=41.7
Q ss_pred CCCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHH
Q 015913 79 NRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 126 (398)
Q Consensus 79 ~~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~ 126 (398)
..+|++++-.+.|+++ .|.++.++|+.+|+|.+||...+.+....|.
T Consensus 130 ~~L~~~~r~i~~l~~~-~g~s~~EIAe~lgis~~~V~~~l~Ra~~~Lr 176 (189)
T PRK06811 130 NDLEKLDREIFIRRYL-LGEKIEEIAKKLGLTRSAIDNRLSRGRKKLQ 176 (189)
T ss_pred HhCCHHHHHHHHHHHH-ccCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 3689999999988887 4899999999999999999999988888775
No 146
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=74.53 E-value=2.7 Score=37.27 Aligned_cols=48 Identities=15% Similarity=0.144 Sum_probs=41.2
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHh
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 128 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~ 128 (398)
.+|+.++-++.|+++. |.++.++|...|+|.+||...+++....|...
T Consensus 142 ~L~~~~r~vl~l~~~~-~~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~ 189 (194)
T PRK09646 142 ALTDTQRESVTLAYYG-GLTYREVAERLAVPLGTVKTRMRDGLIRLRDC 189 (194)
T ss_pred hCCHHHHHHHHHHHHc-CCCHHHHHHHhCCChHhHHHHHHHHHHHHHHH
Confidence 6888888877777654 89999999999999999999999988888653
No 147
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=74.43 E-value=2.8 Score=39.19 Aligned_cols=47 Identities=17% Similarity=0.164 Sum_probs=40.3
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHH
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMA 127 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~ 127 (398)
.+++.++..+.++++ .|.++.++|..+|+|.++|+++.++.+..|-.
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 577888878888775 58999999999999999999999998887754
No 148
>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=74.38 E-value=2.3 Score=40.77 Aligned_cols=46 Identities=13% Similarity=0.164 Sum_probs=39.9
Q ss_pred CCCHHHHHHhheecc---ccccchhhhhcccccccchhhhhhhhHHHHH
Q 015913 80 RIKIEEQLAIFMFIV---GHNLRTRAVQELFRYSGETISRHFNNVLNAI 125 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L---~~~~~~~~l~~~fgis~stv~r~~~~v~~~l 125 (398)
.+++.++..+.|+|. ..+.++.++|..+|+|+++|..+.++.+.-|
T Consensus 249 ~L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVrq~~~rAl~kL 297 (298)
T TIGR02997 249 ELTPRERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKALRKL 297 (298)
T ss_pred cCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHc
Confidence 589999999999885 6789999999999999999999888776543
No 149
>PF13551 HTH_29: Winged helix-turn helix
Probab=74.31 E-value=1.2 Score=35.34 Aligned_cols=34 Identities=9% Similarity=0.231 Sum_probs=29.1
Q ss_pred heeccccccc-hhhhhcccccccchhhhhhhhHHH
Q 015913 90 FMFIVGHNLR-TRAVQELFRYSGETISRHFNNVLN 123 (398)
Q Consensus 90 ~L~~L~~~~~-~~~l~~~fgis~stv~r~~~~v~~ 123 (398)
.|..+..|.+ ...+|..+|+|..||+++++++..
T Consensus 4 ~l~l~~~g~~~~~~ia~~lg~s~~Tv~r~~~~~~~ 38 (112)
T PF13551_consen 4 ILLLLAEGVSTIAEIARRLGISRRTVYRWLKRYRE 38 (112)
T ss_pred HHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHc
Confidence 3455778885 999999999999999999988765
No 150
>PHA00675 hypothetical protein
Probab=74.28 E-value=1.4 Score=32.68 Aligned_cols=39 Identities=15% Similarity=0.062 Sum_probs=27.5
Q ss_pred CCHHHHHHhheeccccccchhhhhcccccccchhhhhhh
Q 015913 81 IKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFN 119 (398)
Q Consensus 81 ~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~ 119 (398)
++..+--.+....-..|.++..||..||+|++||..|.+
T Consensus 23 Lt~~qV~~IR~l~~r~G~s~~~IA~~fGVsrstV~~I~~ 61 (78)
T PHA00675 23 LTDAEVERIRELHEVEGMSYAVLAEKFEQSKGAIAKICR 61 (78)
T ss_pred cCHHHHHHHHHHHHhcCccHHHHHHHhCCCHHHHHHHHc
Confidence 444333333333336688999999999999999998654
No 151
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=74.27 E-value=4.7 Score=36.69 Aligned_cols=44 Identities=14% Similarity=0.248 Sum_probs=36.8
Q ss_pred CCCHHHHHHhheeccccc----cchhhhhcccccccchhhhhhhhHHH
Q 015913 80 RIKIEEQLAIFMFIVGHN----LRTRAVQELFRYSGETISRHFNNVLN 123 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~----~~~~~l~~~fgis~stv~r~~~~v~~ 123 (398)
..+++++++-+|..++.+ .+..++|...|+++.|++|.++++.+
T Consensus 148 ~~~~~~Rla~~L~~~~~~~~~~~t~~~lA~~lG~sretvsR~L~~L~~ 195 (226)
T PRK10402 148 SFPLENRLAAFILLTQEGDLYHEKHTQAAEYLGVSYRHLLYVLAQFIQ 195 (226)
T ss_pred cChHHHHHHHHHHhcccCCcccchHHHHHHHHCCcHHHHHHHHHHHHH
Confidence 458999999999866432 46789999999999999999888776
No 152
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=73.95 E-value=2 Score=37.20 Aligned_cols=48 Identities=8% Similarity=0.227 Sum_probs=39.0
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHh
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 128 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~ 128 (398)
.+|..++-++.|+++ .|.++.++|..+|+|.+||...+++....|.+.
T Consensus 120 ~L~~~~r~vl~l~~~-~g~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~ 167 (175)
T PRK12518 120 TLSLEHRAVLVLHDL-EDLPQKEIAEILNIPVGTVKSRLFYARRQLRKF 167 (175)
T ss_pred hCCHHHeeeeeehHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 466666666666555 488999999999999999999999998888754
No 153
>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=73.90 E-value=2.5 Score=40.75 Aligned_cols=51 Identities=10% Similarity=0.143 Sum_probs=44.2
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHhhcc
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAISLD 131 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~~~~ 131 (398)
.+|+.++.++.|.++ .|.++.+||..+|+|.+||...+++....|.+....
T Consensus 142 ~Lp~~~R~v~~L~~~-~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 192 (324)
T TIGR02960 142 YLPPRQRAVLLLRDV-LGWRAAETAELLGTSTASVNSALQRARATLDEVGPS 192 (324)
T ss_pred hCCHHHhhHhhhHHH-hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhccc
Confidence 688888888888876 689999999999999999999999999998765443
No 154
>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=73.78 E-value=2.6 Score=37.30 Aligned_cols=49 Identities=8% Similarity=-0.008 Sum_probs=41.2
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHhh
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAIS 129 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~~ 129 (398)
.+++.++-++.|.++. |.++.++|..+|+|.+||...+.+....|.+..
T Consensus 131 ~L~~~~r~v~~l~~~~-g~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l 179 (188)
T TIGR02943 131 HLPEQTARVFMMREVL-GFESDEICQELEISTSNCHVLLYRARLSLRACL 179 (188)
T ss_pred hCCHHHHHHHHHHHHh-CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 5777777777777665 999999999999999999999999988886543
No 155
>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=73.51 E-value=2.1 Score=29.29 Aligned_cols=28 Identities=11% Similarity=0.222 Sum_probs=22.5
Q ss_pred cccchhhhhcccccccchhhhhhhhHHH
Q 015913 96 HNLRTRAVQELFRYSGETISRHFNNVLN 123 (398)
Q Consensus 96 ~~~~~~~l~~~fgis~stv~r~~~~v~~ 123 (398)
.+.+..+++...|++++|++|++.....
T Consensus 17 ~~~t~~eia~~~gl~~stv~r~L~tL~~ 44 (52)
T PF09339_consen 17 GPLTLSEIARALGLPKSTVHRLLQTLVE 44 (52)
T ss_dssp SCEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 3457999999999999999998876554
No 156
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=73.39 E-value=3.9 Score=30.04 Aligned_cols=72 Identities=14% Similarity=0.152 Sum_probs=49.9
Q ss_pred hhHHHhhcCCCHHHHHHHHHHHhcCCccccCCCCCHHHHHHhheeccccc-cchhhhhccccc-ccchhhhhhhhHHH
Q 015913 48 SERCLENFRMDKKVFYKLCDILQSKGLLRHTNRIKIEEQLAIFMFIVGHN-LRTRAVQELFRY-SGETISRHFNNVLN 123 (398)
Q Consensus 48 d~~f~~~frms~~~F~~L~~~l~~~~~~~~~~~~s~e~~l~~~L~~L~~~-~~~~~l~~~fgi-s~stv~r~~~~v~~ 123 (398)
-++.-+.++++...|.+++........ ...-...++.-++.+|..+ .+..++|..+|. |.++.++.|++...
T Consensus 4 ~~~la~~~~~s~~~l~~~f~~~~~~s~----~~~~~~~r~~~a~~~l~~~~~~~~~ia~~~g~~s~~~f~r~Fk~~~g 77 (84)
T smart00342 4 LEDLAEALGMSPRHLQRLFKKETGTTP----KQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFG 77 (84)
T ss_pred HHHHHHHhCCCHHHHHHHHHHHhCcCH----HHHHHHHHHHHHHHHHHcCCCCHHHHHHHhCCCChHHHHHHHHHHHC
Confidence 355667788888888887776542211 1112234555566666655 899999999999 99999999987653
No 157
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=73.20 E-value=3.6 Score=37.83 Aligned_cols=56 Identities=7% Similarity=0.078 Sum_probs=46.2
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHhhccccCCC
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAISLDFFQPP 136 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~~~~~i~~P 136 (398)
.+++.++.++.|.++- |.++.++|+..|+|.+||...+++....|.+...+....+
T Consensus 116 ~Lp~~~R~v~lL~~~e-g~S~~EIAe~LgiS~~tVksrL~Rark~Lr~~l~~~~~~~ 171 (228)
T PRK06704 116 SLNVQQSAILLLKDVF-QYSIADIAKVCSVSEGAVKASLFRSRNRLKTVSEEGIEIV 171 (228)
T ss_pred hCCHHHhhHhhhHHhh-CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhcCCCC
Confidence 6888888887777655 8999999999999999999999999999987655544433
No 158
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=73.13 E-value=2 Score=30.97 Aligned_cols=43 Identities=7% Similarity=0.174 Sum_probs=38.2
Q ss_pred HHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHh
Q 015913 86 QLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 128 (398)
Q Consensus 86 ~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~ 128 (398)
+.-.|+.+|+...+..+.|+..|+...+|.+++..+-..+.++
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 3456788999999999999999999999999999999988765
No 159
>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=72.92 E-value=2.6 Score=33.12 Aligned_cols=41 Identities=12% Similarity=0.224 Sum_probs=34.0
Q ss_pred HHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHH
Q 015913 85 EQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 126 (398)
Q Consensus 85 ~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~ 126 (398)
++--+-|+++ -..|...+|+.|+||++.|+..++++...+.
T Consensus 22 Q~~Y~~lyy~-dDlSl~EIAee~~VSRqAIyDnIKr~~~~L~ 62 (105)
T COG2739 22 QKNYLELYYL-DDLSLSEIAEEFNVSRQAIYDNIKRTEKILE 62 (105)
T ss_pred HHHHHHHHHH-hhccHHHHHHHhCccHHHHHHHHHHHHHHHH
Confidence 4444555554 4789999999999999999999999999885
No 160
>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=72.69 E-value=2.9 Score=38.97 Aligned_cols=46 Identities=20% Similarity=0.190 Sum_probs=40.0
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHH
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 126 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~ 126 (398)
.+++.++..+.++++ .|.++.++|..+|+|.++|+++.++.+.-|.
T Consensus 206 ~L~~rer~vi~~~~~-~~~t~~eIA~~lgis~~~V~~~~~ral~kLr 251 (254)
T TIGR02850 206 RLNEREKMILNMRFF-EGKTQMEVAEEIGISQAQVSRLEKAALKHMR 251 (254)
T ss_pred cCCHHHHHHHHHHHc-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 578888888888775 5889999999999999999999998887764
No 161
>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=72.63 E-value=2.7 Score=38.45 Aligned_cols=46 Identities=17% Similarity=0.237 Sum_probs=39.7
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHH
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 126 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~ 126 (398)
.++..++-.+.++++ .|.++.++|..+|+|+++|+++.++.+.-|-
T Consensus 183 ~L~~~e~~i~~~~~~-~~~t~~eIA~~lgis~~~V~~~~~~al~~Lr 228 (231)
T TIGR02885 183 KLDERERQIIMLRYF-KDKTQTEVANMLGISQVQVSRLEKKVLKKMK 228 (231)
T ss_pred cCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 578888888777664 5889999999999999999999999888775
No 162
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=72.18 E-value=3.6 Score=38.26 Aligned_cols=47 Identities=21% Similarity=0.308 Sum_probs=40.8
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHH
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMA 127 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~ 127 (398)
.+++.++-.+.|.++ .|.++.++|..+|+|.+||...+++....|-.
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 578888888888775 69999999999999999999999988887754
No 163
>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=72.05 E-value=1.5 Score=32.20 Aligned_cols=42 Identities=14% Similarity=0.210 Sum_probs=31.5
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccc-cccchhhhhhhhH
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFR-YSGETISRHFNNV 121 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fg-is~stv~r~~~~v 121 (398)
.+.-.-+++|.|..--.+.++.++|..|| .+.|||...++++
T Consensus 28 ~i~~aR~va~yL~r~~~~~sl~~Ig~~fg~rdHstV~~a~~ki 70 (70)
T PF08299_consen 28 KIVEARQVAMYLARELTGLSLSEIGRYFGGRDHSTVIHAIRKI 70 (70)
T ss_dssp HHHHHHHHHHHHHHHHS---HHHHHHHCTSSTHHHHHHHHHHH
T ss_pred hhcchHHHHHHHHHHHhCCCHHHHHHHhCCCCHHHHHHHHHhC
Confidence 34446678888777778999999999999 9999999877654
No 164
>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=71.92 E-value=3.4 Score=32.71 Aligned_cols=46 Identities=7% Similarity=0.102 Sum_probs=32.7
Q ss_pred CCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHH
Q 015913 81 IKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMA 127 (398)
Q Consensus 81 ~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~ 127 (398)
++..++-.+-| ++-.+.|...+|+.+|||+.+|+..+++....|..
T Consensus 18 LT~kQ~~~l~l-yy~eDlSlsEIAe~~~iSRqaV~d~ikr~~~~L~~ 63 (101)
T PF04297_consen 18 LTEKQREILEL-YYEEDLSLSEIAEELGISRQAVYDSIKRAEKKLEE 63 (101)
T ss_dssp S-HHHHHHHHH-HCTS---HHHHHHHCTS-HHHHHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHH-HHccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 44445555554 45569999999999999999999999999998863
No 165
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=71.91 E-value=3.3 Score=36.96 Aligned_cols=47 Identities=9% Similarity=0.072 Sum_probs=40.3
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHh
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 128 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~ 128 (398)
.+++.++-.+.| ++ .|.+++++|..+|+|.+||...+++....|.+.
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 577888888877 55 699999999999999999999999888887653
No 166
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=71.76 E-value=3.1 Score=40.25 Aligned_cols=48 Identities=15% Similarity=0.169 Sum_probs=42.8
Q ss_pred CCCHHHHHHhheecc---ccccchhhhhcccccccchhhhhhhhHHHHHHH
Q 015913 80 RIKIEEQLAIFMFIV---GHNLRTRAVQELFRYSGETISRHFNNVLNAIMA 127 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L---~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~ 127 (398)
.+++.++..+.|+|. ..+.++.++|..+|+|+++|..+..+.+.-|-.
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 589999999999886 577999999999999999999999998888864
No 167
>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=71.02 E-value=3.7 Score=38.19 Aligned_cols=47 Identities=17% Similarity=0.157 Sum_probs=41.0
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHH
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMA 127 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~ 127 (398)
.+++.++-.+.|+++ .|.++.++|..+|+|.+||+...++....|-.
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 688888888888875 58999999999999999999999988887753
No 168
>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=70.73 E-value=6.2 Score=32.19 Aligned_cols=72 Identities=17% Similarity=0.237 Sum_probs=45.8
Q ss_pred CChhHHHhhcCCCHHHHHHHHHHHhcCCccccC----CCCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhh
Q 015913 46 GQSERCLENFRMDKKVFYKLCDILQSKGLLRHT----NRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNN 120 (398)
Q Consensus 46 ~~d~~f~~~frms~~~F~~L~~~l~~~~~~~~~----~~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~ 120 (398)
.+-.+--..|++++.+....+.... .+..... ..+. .+.| ..+.---...+..+++..||||.+|+++.+++
T Consensus 19 ~s~~eaa~~F~VS~~Tv~~W~k~~~-~G~~~~k~r~~~Kid-~~~L-~~~v~~~pd~tl~Ela~~l~Vs~~ti~~~Lkr 94 (119)
T PF01710_consen 19 KSIREAAKRFGVSRNTVYRWLKRKE-TGDLEPKPRGRKKID-RDEL-KALVEENPDATLRELAERLGVSPSTIWRALKR 94 (119)
T ss_pred chHHHHHHHhCcHHHHHHHHHHhcc-ccccccccccccccc-HHHH-HHHHHHCCCcCHHHHHHHcCCCHHHHHHHHHH
Confidence 3556677899999999999988433 2222211 1332 2222 22222234567889999999999999986654
No 169
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=70.63 E-value=3.7 Score=38.12 Aligned_cols=48 Identities=15% Similarity=0.259 Sum_probs=41.9
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHh
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 128 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~ 128 (398)
.++-.+|+.+.|+|. .+.+...+|...|||++.||++..+.+..|.+.
T Consensus 196 ~L~EREk~Vl~l~y~-eelt~kEI~~~LgISes~VSql~kkai~kLr~~ 243 (247)
T COG1191 196 PLPEREKLVLVLRYK-EELTQKEIAEVLGISESRVSRLHKKAIKKLRKE 243 (247)
T ss_pred ccCHHHHHHHHHHHH-hccCHHHHHHHhCccHHHHHHHHHHHHHHHHHH
Confidence 577788899999885 489999999999999999999999999888643
No 170
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=70.09 E-value=3.4 Score=37.06 Aligned_cols=49 Identities=10% Similarity=0.068 Sum_probs=40.6
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHhh
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAIS 129 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~~ 129 (398)
.+++..+-.+.|.++ .|.++.++|..+|+|.+||...+.+....|.+..
T Consensus 138 ~L~~~~r~v~~L~~~-~g~s~~EIA~~Lgis~~tV~~~l~RArk~Lr~~l 186 (203)
T PRK09647 138 SLPPEFRAAVVLCDI-EGLSYEEIAATLGVKLGTVRSRIHRGRQQLRAAL 186 (203)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 577777766666654 5999999999999999999999999998887543
No 171
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=69.98 E-value=5.4 Score=36.43 Aligned_cols=44 Identities=20% Similarity=0.383 Sum_probs=36.1
Q ss_pred CCCHHHHHHhheecccc----------ccchhhhhcccccccchhhhhhhhHHH
Q 015913 80 RIKIEEQLAIFMFIVGH----------NLRTRAVQELFRYSGETISRHFNNVLN 123 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~----------~~~~~~l~~~fgis~stv~r~~~~v~~ 123 (398)
..+++++++-+|..++. ..+..++|...|+++.|++|+++++-+
T Consensus 152 ~~~~~~Rla~~Ll~l~~~~g~~~~i~i~lt~~~IA~~lGisretlsR~L~~L~~ 205 (230)
T PRK09391 152 RKTAMERVAAFLLEMDERLGGAGMMALPMSRRDIADYLGLTIETVSRALSQLQD 205 (230)
T ss_pred CCCHHHHHHHHHHHHHHHhCCCCEEEecCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 47899999999887643 246789999999999999998876654
No 172
>PRK06030 hypothetical protein; Provisional
Probab=69.84 E-value=3.5 Score=33.99 Aligned_cols=47 Identities=15% Similarity=0.150 Sum_probs=41.8
Q ss_pred CCCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHH
Q 015913 79 NRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAI 125 (398)
Q Consensus 79 ~~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l 125 (398)
+.+...-|++|.|..--.+.++.++|..||.+.|||+..++.+-+.+
T Consensus 51 k~i~~aRqIAMYL~r~~~~~sl~~IG~~FGRDHSTV~haikkIe~~~ 97 (124)
T PRK06030 51 REVSRIRQIAMYVAHVSLGWPMNEVALAFGRDRTTVGHACHTVEDLR 97 (124)
T ss_pred cccchHHHHHHHHHHHHcCCCHHHHHHHHCCChhHHHHHHHHHHHHh
Confidence 46888899999999999999999999999999999999888666644
No 173
>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=69.10 E-value=4.4 Score=36.89 Aligned_cols=47 Identities=17% Similarity=0.336 Sum_probs=40.1
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHH
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMA 127 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~ 127 (398)
.+++.++-++.|+++ .|.++.++|..+|+|.+||.+..++....|-.
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 578888888877775 58999999999999999999999888887754
No 174
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=69.06 E-value=4.6 Score=37.92 Aligned_cols=47 Identities=13% Similarity=0.189 Sum_probs=40.1
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHH
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMA 127 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~ 127 (398)
.+++.++-.+.|+++ .|.++.++|..+|+|.++|+++.++....|..
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 477777878888775 59999999999999999999999988887754
No 175
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=68.78 E-value=2.2 Score=37.34 Aligned_cols=47 Identities=11% Similarity=0.223 Sum_probs=39.1
Q ss_pred CCCCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHH
Q 015913 78 TNRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 126 (398)
Q Consensus 78 ~~~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~ 126 (398)
+..+|+.|+= .|..++.|.+..++|...++|.+||..++.++..-|.
T Consensus 131 ~~~LSpRErE--VLrLLAqGkTnKEIAe~L~IS~rTVkth~srImkKLg 177 (198)
T PRK15201 131 TRHFSVTERH--LLKLIASGYHLSETAALLSLSEEQTKSLRRSIMRKLH 177 (198)
T ss_pred CCCCCHHHHH--HHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 3568887763 4556889999999999999999999999998888764
No 176
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=68.77 E-value=3.6 Score=36.38 Aligned_cols=49 Identities=10% Similarity=0.261 Sum_probs=40.6
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHhh
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAIS 129 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~~ 129 (398)
.++...+-++.|.++. |.++.++|...|+|.+||...+++....|.+..
T Consensus 128 ~Lp~~~r~v~~l~~~~-g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 176 (188)
T PRK12517 128 KLDPEYREPLLLQVIG-GFSGEEIAEILDLNKNTVMTRLFRARNQLKEAL 176 (188)
T ss_pred hCCHHHHHHHHHHHHh-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 5777777766666554 999999999999999999999999988887544
No 177
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=68.35 E-value=4.6 Score=35.52 Aligned_cols=47 Identities=11% Similarity=0.121 Sum_probs=40.1
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHH
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMA 127 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~ 127 (398)
.+|+.++-++.|.++. |.++.++|..+|+|.+||...+++....|-+
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 6888888777777666 8999999999999999999988888877754
No 178
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=68.20 E-value=5.3 Score=36.40 Aligned_cols=44 Identities=23% Similarity=0.383 Sum_probs=35.9
Q ss_pred CCCHHHHHHhheecccc--------------ccchhhhhcccccccchhhhhhhhHHH
Q 015913 80 RIKIEEQLAIFMFIVGH--------------NLRTRAVQELFRYSGETISRHFNNVLN 123 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~--------------~~~~~~l~~~fgis~stv~r~~~~v~~ 123 (398)
..+++++++-+|..++. ..+..++|+..|+++.|++|+++++-+
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 56899999999987652 246789999999999999998765544
No 179
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=68.07 E-value=3.3 Score=33.53 Aligned_cols=46 Identities=11% Similarity=0.187 Sum_probs=36.1
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHH
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 126 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~ 126 (398)
.++.+++-++-+ ++.+..+..+++..+|||-+||..-+.+++.+|-
T Consensus 33 ~L~~E~~~Fi~~-Fi~~rGnlKe~e~~lgiSYPTvR~rLd~ii~~lg 78 (113)
T PF09862_consen 33 RLSPEQLEFIKL-FIKNRGNLKEMEKELGISYPTVRNRLDKIIEKLG 78 (113)
T ss_pred cCCHHHHHHHHH-HHHhcCCHHHHHHHHCCCcHHHHHHHHHHHHHhC
Confidence 466666555544 4455678999999999999999999999888885
No 180
>PHA00542 putative Cro-like protein
Probab=67.82 E-value=1.6 Score=33.19 Aligned_cols=29 Identities=14% Similarity=0.214 Sum_probs=25.4
Q ss_pred eccccccchhhhhcccccccchhhhhhhh
Q 015913 92 FIVGHNLRTRAVQELFRYSGETISRHFNN 120 (398)
Q Consensus 92 ~~L~~~~~~~~l~~~fgis~stv~r~~~~ 120 (398)
.+...|.+..++|...|||++|++++.+.
T Consensus 26 ~l~~~glTq~elA~~lgIs~~tIsr~e~g 54 (82)
T PHA00542 26 ALIRAGWSQEQIADATDVSQPTICRIYSG 54 (82)
T ss_pred HHHHCCCCHHHHHHHHCcCHHHHHHHHcC
Confidence 34678999999999999999999998754
No 181
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=67.67 E-value=4 Score=32.98 Aligned_cols=46 Identities=11% Similarity=0.059 Sum_probs=41.0
Q ss_pred CCCCCHHHHHHhheeccccccchhhhhccccc-ccchhhhhhhhHHH
Q 015913 78 TNRIKIEEQLAIFMFIVGHNLRTRAVQELFRY-SGETISRHFNNVLN 123 (398)
Q Consensus 78 ~~~~s~e~~l~~~L~~L~~~~~~~~l~~~fgi-s~stv~r~~~~v~~ 123 (398)
.+..|.|.|+-++-.++..|.+...+|..||| +.+++++++....+
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~sv~~vAr~~gv~~~~~l~~W~~~~~~ 51 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGDTVSEVAREFGIVSATQLYKWRIQLQK 51 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCccHHHHHHHhCCCChHHHHHHHHHHHH
Confidence 45789999999999999999999999999996 99999988876665
No 182
>COG5421 Transposase [DNA replication, recombination, and repair]
Probab=67.65 E-value=7.4 Score=39.27 Aligned_cols=58 Identities=19% Similarity=0.218 Sum_probs=41.4
Q ss_pred CccccceeeeecCCcceEEeecCcccccccHHHHHHHHhhcCCCCCCCCceeeccCCCC
Q 015913 183 GLLSQNVLAACSFDLKFHYVLAGWEGSASDLRVLNSALTRRNKLQVPEGKYYLVDNKYA 241 (398)
Q Consensus 183 ~~~s~~~q~v~d~~~~~~~v~~g~~Gs~~D~~vl~~sl~~~~~~~~~~g~~~l~D~gYp 241 (398)
...-+|+..+++.+|.-+++. -++|+.+|...+-.++..........+.|+++|+|+-
T Consensus 153 dl~QI~vsMi~~~~gIPl~~~-v~~Gni~D~~~~~~ti~kl~~~l~~~~~~~V~Dkgf~ 210 (480)
T COG5421 153 DLPQINVSMIVNQKGIPLFVR-VYSGNISDKNTLIKTIQKLKSVLVKDEVYLVADKGFN 210 (480)
T ss_pred CcceeEEEEEEcCCCCceEEE-ccCCCccchHHHHHHHHHHHHhcccceEEEEEccccc
Confidence 356789999999996555444 4799999999998775432222233347889999994
No 183
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=66.90 E-value=4.2 Score=29.62 Aligned_cols=41 Identities=12% Similarity=0.200 Sum_probs=31.9
Q ss_pred CHHHHHHhheecccc-ccchhhhhcccccccchhhhhhhhHH
Q 015913 82 KIEEQLAIFMFIVGH-NLRTRAVQELFRYSGETISRHFNNVL 122 (398)
Q Consensus 82 s~e~~l~~~L~~L~~-~~~~~~l~~~fgis~stv~r~~~~v~ 122 (398)
+.+++++.+|..-+. +.+..+|+...|++.++|++++....
T Consensus 6 ~~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~ 47 (68)
T smart00550 6 SLEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLE 47 (68)
T ss_pred HHHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 456777777776655 58999999999999999998665443
No 184
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=66.75 E-value=2.5 Score=38.07 Aligned_cols=45 Identities=16% Similarity=0.166 Sum_probs=37.9
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHH
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 126 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~ 126 (398)
.+|+.|+ =.|.+++.|.+++++|...++|..||..+.+++..-|.
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 3777665 34567899999999999999999999999998888774
No 185
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=66.38 E-value=5 Score=33.68 Aligned_cols=43 Identities=2% Similarity=0.004 Sum_probs=29.3
Q ss_pred CCHHH-HHHhheeccccccchhhhhcccccccchhhhhhhhHHH
Q 015913 81 IKIEE-QLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLN 123 (398)
Q Consensus 81 ~s~e~-~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~ 123 (398)
+++.+ .++.+|+....+.+..+|+..++++++|+++.+.+..+
T Consensus 29 lt~~q~~vL~~l~~~~~~~t~~eLa~~l~~~~~tvt~~v~~Le~ 72 (144)
T PRK03573 29 LTQTHWVTLHNIHQLPPEQSQIQLAKAIGIEQPSLVRTLDQLEE 72 (144)
T ss_pred CCHHHHHHHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHHHHHH
Confidence 44433 23344433334567899999999999999987766554
No 186
>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=66.28 E-value=2.5 Score=28.95 Aligned_cols=26 Identities=31% Similarity=0.296 Sum_probs=21.6
Q ss_pred ccccchhhhhcccccccchhhhhhhh
Q 015913 95 GHNLRTRAVQELFRYSGETISRHFNN 120 (398)
Q Consensus 95 ~~~~~~~~l~~~fgis~stv~r~~~~ 120 (398)
..|.++.++|...|+|++|++++.+.
T Consensus 7 ~~gls~~~la~~~gis~~~i~~~~~g 32 (55)
T PF01381_consen 7 EKGLSQKELAEKLGISRSTISRIENG 32 (55)
T ss_dssp HTTS-HHHHHHHHTS-HHHHHHHHTT
T ss_pred HcCCCHHHHHHHhCCCcchhHHHhcC
Confidence 56889999999999999999998865
No 187
>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=66.05 E-value=1.7 Score=35.53 Aligned_cols=27 Identities=19% Similarity=0.257 Sum_probs=24.0
Q ss_pred ccccccchhhhhcccccccchhhhhhh
Q 015913 93 IVGHNLRTRAVQELFRYSGETISRHFN 119 (398)
Q Consensus 93 ~L~~~~~~~~l~~~fgis~stv~r~~~ 119 (398)
++..|.+.+.++..|+||.+||.+++.
T Consensus 14 ~~~~g~s~~eaa~~F~VS~~Tv~~W~k 40 (119)
T PF01710_consen 14 YIEKGKSIREAAKRFGVSRNTVYRWLK 40 (119)
T ss_pred HHHccchHHHHHHHhCcHHHHHHHHHH
Confidence 556688999999999999999999876
No 188
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=65.95 E-value=2.6 Score=27.31 Aligned_cols=29 Identities=21% Similarity=0.259 Sum_probs=22.0
Q ss_pred cccccchhhhhcccccccchhhhhhhhHH
Q 015913 94 VGHNLRTRAVQELFRYSGETISRHFNNVL 122 (398)
Q Consensus 94 L~~~~~~~~l~~~fgis~stv~r~~~~v~ 122 (398)
+.++.+..++|..+|+|.+..+|.|++.+
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 45678899999999999999999998764
No 189
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=65.84 E-value=5.6 Score=27.30 Aligned_cols=25 Identities=12% Similarity=0.166 Sum_probs=21.3
Q ss_pred chhhhhcccccccchhhhhhhhHHH
Q 015913 99 RTRAVQELFRYSGETISRHFNNVLN 123 (398)
Q Consensus 99 ~~~~l~~~fgis~stv~r~~~~v~~ 123 (398)
+.+++++.||+|++||.+.+....+
T Consensus 22 s~~~la~~~~vs~~tv~~~l~~L~~ 46 (60)
T smart00345 22 SERELAAQLGVSRTTVREALSRLEA 46 (60)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 6889999999999999997766554
No 190
>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=65.69 E-value=3.3 Score=29.18 Aligned_cols=29 Identities=17% Similarity=0.150 Sum_probs=26.0
Q ss_pred cchhhhhcccccccchhhhhhhhHHHHHH
Q 015913 98 LRTRAVQELFRYSGETISRHFNNVLNAIM 126 (398)
Q Consensus 98 ~~~~~l~~~fgis~stv~r~~~~v~~~l~ 126 (398)
.++...|...++|+++|++.+++.-..+.
T Consensus 14 gs~~~AA~~l~is~~~vs~~i~~LE~~lg 42 (60)
T PF00126_consen 14 GSISAAAEELGISQSAVSRQIKQLEEELG 42 (60)
T ss_dssp SSHHHHHHHCTSSHHHHHHHHHHHHHHHT
T ss_pred CCHHHHHHHhhccchHHHHHHHHHHHHhC
Confidence 38999999999999999999998888774
No 191
>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=65.62 E-value=3 Score=34.82 Aligned_cols=37 Identities=8% Similarity=0.244 Sum_probs=31.7
Q ss_pred CCCCHHHHHHhheeccccccchhhhhcccccccchhhh
Q 015913 79 NRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISR 116 (398)
Q Consensus 79 ~~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r 116 (398)
..+|+..+-++.|.++. |.++.++|..+|+|.+||.+
T Consensus 106 ~~Lp~~~r~v~~l~~~~-~~s~~EIA~~l~is~~tV~~ 142 (142)
T TIGR03209 106 SILPNKQKKIIYMKFFE-DMKEIDIAKKLHISRQSVYK 142 (142)
T ss_pred HhCCHHHHHHHHHHHHc-CCCHHHHHHHHCcCHHhhcC
Confidence 36888888888887664 89999999999999999863
No 192
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=65.56 E-value=2.9 Score=36.79 Aligned_cols=49 Identities=6% Similarity=0.168 Sum_probs=38.4
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHhh
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAIS 129 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~~ 129 (398)
.+|+.++=++.|.++ .|.++.+||..+|+|.+||...+++....|-...
T Consensus 134 ~L~~~~r~v~~l~~~-~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 182 (188)
T PRK09640 134 HVNPIDREILVLRFV-AELEFQEIADIMHMGLSATKMRYKRALDKLREKF 182 (188)
T ss_pred hcChhheeeeeeHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 456665555555544 6899999999999999999999999888886543
No 193
>PF13309 HTH_22: HTH domain
Probab=65.14 E-value=6.3 Score=28.37 Aligned_cols=22 Identities=23% Similarity=0.122 Sum_probs=18.7
Q ss_pred cchhhhhcccccccchhhhhhh
Q 015913 98 LRTRAVQELFRYSGETISRHFN 119 (398)
Q Consensus 98 ~~~~~l~~~fgis~stv~r~~~ 119 (398)
.+...+|..+|||+.||+++++
T Consensus 43 gav~~vA~~L~iS~~TVY~YLr 64 (64)
T PF13309_consen 43 GAVEYVAEKLGISRATVYRYLR 64 (64)
T ss_pred cHHHHHHHHHCCCHHHHHHHcC
Confidence 3567899999999999999864
No 194
>PRK13870 transcriptional regulator TraR; Provisional
Probab=65.04 E-value=2.6 Score=38.82 Aligned_cols=46 Identities=2% Similarity=0.076 Sum_probs=39.3
Q ss_pred CCCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHH
Q 015913 79 NRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 126 (398)
Q Consensus 79 ~~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~ 126 (398)
..+|+.|+= +|.|.+.|.+..++|...|||++||.-+++++..-|.
T Consensus 172 ~~LT~RE~E--~L~W~A~GKT~~EIa~ILgISe~TV~~Hl~na~~KLg 217 (234)
T PRK13870 172 AWLDPKEAT--YLRWIAVGKTMEEIADVEGVKYNSVRVKLREAMKRFD 217 (234)
T ss_pred CCCCHHHHH--HHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence 357776654 5678999999999999999999999999999888764
No 195
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=64.78 E-value=3.8 Score=31.25 Aligned_cols=27 Identities=22% Similarity=0.240 Sum_probs=23.6
Q ss_pred ccchhhhhcccccccchhhhhhhhHHH
Q 015913 97 NLRTRAVQELFRYSGETISRHFNNVLN 123 (398)
Q Consensus 97 ~~~~~~l~~~fgis~stv~r~~~~v~~ 123 (398)
+.+..+++..+|++++||++++....+
T Consensus 20 ~~t~~~ia~~l~i~~~tv~r~l~~L~~ 46 (91)
T smart00346 20 GLTLAELAERLGLSKSTAHRLLNTLQE 46 (91)
T ss_pred CcCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 478999999999999999998876654
No 196
>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=64.78 E-value=3.9 Score=31.96 Aligned_cols=30 Identities=13% Similarity=0.180 Sum_probs=24.5
Q ss_pred cccccchhhhhcccccccchhhhhhhhHHH
Q 015913 94 VGHNLRTRAVQELFRYSGETISRHFNNVLN 123 (398)
Q Consensus 94 L~~~~~~~~l~~~fgis~stv~r~~~~v~~ 123 (398)
..-+.+..++|...|+|++||++.+++..+
T Consensus 44 ~~~~is~~eLa~~~g~sr~tVsr~L~~Le~ 73 (95)
T TIGR01610 44 KQDRVTATVIAELTGLSRTHVSDAIKSLAR 73 (95)
T ss_pred cCCccCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 344678899999999999999997776554
No 197
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=64.40 E-value=5.3 Score=39.55 Aligned_cols=47 Identities=13% Similarity=0.145 Sum_probs=41.1
Q ss_pred CCCHHHHHHhheecc---ccccchhhhhcccccccchhhhhhhhHHHHHH
Q 015913 80 RIKIEEQLAIFMFIV---GHNLRTRAVQELFRYSGETISRHFNNVLNAIM 126 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L---~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~ 126 (398)
.+++.++..+.++|+ +.+.++..||..+|||+++|+.+-.+.+.-|-
T Consensus 311 ~L~~rEr~IL~lrygl~~~~~~Tl~EIA~~lgiS~eRVRQie~rAL~KLR 360 (373)
T PRK07406 311 TLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLR 360 (373)
T ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHh
Confidence 588899999999875 34689999999999999999999998888775
No 198
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=64.18 E-value=5 Score=37.68 Aligned_cols=47 Identities=11% Similarity=0.253 Sum_probs=39.9
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHH
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMA 127 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~ 127 (398)
.+++.++-++.|+++ .|.++.++|..+|+|.+||.+..++....|-.
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 588888888877775 58999999999999999999888888777754
No 199
>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=63.72 E-value=7.4 Score=32.49 Aligned_cols=47 Identities=15% Similarity=0.145 Sum_probs=38.7
Q ss_pred CCHHHHHHhheeccc-cccchhhhhcccccccchhhhhhhhHHHHHHH
Q 015913 81 IKIEEQLAIFMFIVG-HNLRTRAVQELFRYSGETISRHFNNVLNAIMA 127 (398)
Q Consensus 81 ~s~e~~l~~~L~~L~-~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~ 127 (398)
++.+++-.+-+.|+. ...++..+|..+|+|++|+++.-+.++..+..
T Consensus 83 Ld~~er~II~~rY~~~~~~t~~~Ia~~l~iS~~t~~r~r~~~l~kla~ 130 (134)
T TIGR01636 83 ADEQTRVIIQELYMKKRPLTLVGLAQQLFISKSTAYRLRNHIIEAVAE 130 (134)
T ss_pred CCHHHHHHHHHHHccCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 667788888888774 34599999999999999999998888877763
No 200
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=63.61 E-value=6.6 Score=38.15 Aligned_cols=50 Identities=10% Similarity=0.105 Sum_probs=42.4
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHhhc
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAISL 130 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~~~ 130 (398)
.+++.++-++.|+++ .|.++.+||..+|+|.+||...+++....|.+..+
T Consensus 153 ~Lp~~~R~v~~L~~~-~g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~~~ 202 (339)
T PRK08241 153 HLPPRQRAVLILRDV-LGWSAAEVAELLDTSVAAVNSALQRARATLAERGP 202 (339)
T ss_pred hCCHHHhhhhhhHHh-hCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhhcCC
Confidence 578888888877765 48999999999999999999999999988876433
No 201
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=63.46 E-value=5.5 Score=36.61 Aligned_cols=46 Identities=13% Similarity=0.309 Sum_probs=38.5
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHH
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 126 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~ 126 (398)
.+++.++-.+.|+++ .|.++..+|..+|+|+++|+++-++...-|-
T Consensus 183 ~L~~~er~vi~l~~~-~~~t~~EIA~~lgis~~~V~q~~~~~~~kLr 228 (231)
T PRK12427 183 QLDEREQLILHLYYQ-HEMSLKEIALVLDLTEARICQLNKKIAQKIK 228 (231)
T ss_pred cCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 567777777777774 6899999999999999999998888877664
No 202
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=63.17 E-value=4 Score=28.83 Aligned_cols=30 Identities=17% Similarity=0.214 Sum_probs=25.3
Q ss_pred cccccchhhhhcccccccchhhhhhhhHHH
Q 015913 94 VGHNLRTRAVQELFRYSGETISRHFNNVLN 123 (398)
Q Consensus 94 L~~~~~~~~l~~~fgis~stv~r~~~~v~~ 123 (398)
-..+.+..++++.+|++++|+++.++...+
T Consensus 21 ~~~~~t~~ela~~l~~~~~t~s~hL~~L~~ 50 (61)
T PF12840_consen 21 SNGPMTVSELAEELGISQSTVSYHLKKLEE 50 (61)
T ss_dssp HCSTBEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred cCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 466789999999999999999999887655
No 203
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=63.08 E-value=3.9 Score=26.85 Aligned_cols=28 Identities=25% Similarity=0.394 Sum_probs=23.5
Q ss_pred cccchhhhhcccccccchhhhhhhhHHH
Q 015913 96 HNLRTRAVQELFRYSGETISRHFNNVLN 123 (398)
Q Consensus 96 ~~~~~~~l~~~fgis~stv~r~~~~v~~ 123 (398)
-..+..++++.+|+|++|+++.++...+
T Consensus 7 ~~~s~~~la~~l~~s~~tv~~~l~~L~~ 34 (48)
T smart00419 7 LPLTRQEIAELLGLTRETVSRTLKRLEK 34 (48)
T ss_pred eccCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3567889999999999999998876655
No 204
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=62.94 E-value=4.5 Score=36.26 Aligned_cols=45 Identities=13% Similarity=0.149 Sum_probs=38.2
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHH
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 126 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~ 126 (398)
.+|+.|+ -.|..++.|.+..++|...++|..||..+..+...-|.
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 5888776 55667789999999999999999999999988877663
No 205
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=62.74 E-value=5.8 Score=39.81 Aligned_cols=47 Identities=17% Similarity=0.187 Sum_probs=41.0
Q ss_pred CCCHHHHHHhheecc---ccccchhhhhcccccccchhhhhhhhHHHHHH
Q 015913 80 RIKIEEQLAIFMFIV---GHNLRTRAVQELFRYSGETISRHFNNVLNAIM 126 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L---~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~ 126 (398)
.+++.++-.+.|+|. +.+.++.+||..+|+|.++|..+.++.+..|-
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 588888888888875 35689999999999999999999998888775
No 206
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=62.44 E-value=10 Score=34.52 Aligned_cols=45 Identities=18% Similarity=0.276 Sum_probs=35.4
Q ss_pred CCCCHHHHHHhheeccccc----------cchhhhhcccccccchhhhhhhhHHH
Q 015913 79 NRIKIEEQLAIFMFIVGHN----------LRTRAVQELFRYSGETISRHFNNVLN 123 (398)
Q Consensus 79 ~~~s~e~~l~~~L~~L~~~----------~~~~~l~~~fgis~stv~r~~~~v~~ 123 (398)
...+++++++-+|..++.. .+..++|...|+++.||+|++++..+
T Consensus 145 ~~~~~~~Rla~~Ll~~~~~~~~~~~~~i~~t~~~iA~~lG~tretvsR~l~~L~~ 199 (236)
T PRK09392 145 KLRSSAERLANYLLKQSLRQGGADVVTLPYEKRVLASYLGMTPENLSRAFAALAS 199 (236)
T ss_pred hcCCHHHHHHHHHHHhccccCCCcEEEeeCCHHHHHHHhCCChhHHHHHHHHHHh
Confidence 3568999999988866531 23468999999999999998877554
No 207
>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=62.17 E-value=7.4 Score=36.83 Aligned_cols=50 Identities=10% Similarity=0.011 Sum_probs=42.2
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHhhc
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAISL 130 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~~~ 130 (398)
.+|+.++-++.|.++- |.++.++|..+|+|.+||...+++....|.+..+
T Consensus 108 ~L~~~~R~v~~L~~~~-g~s~~EIA~~lg~s~~tVr~~l~RAr~~Lr~~~~ 157 (281)
T TIGR02957 108 RLSPLERAVFVLREVF-DYPYEEIASIVGKSEANCRQLVSRARRHLDARRP 157 (281)
T ss_pred hCCHHHHHHHHHHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCC
Confidence 6788888887776554 8999999999999999999999999998876433
No 208
>PRK05949 RNA polymerase sigma factor; Validated
Probab=62.10 E-value=6.5 Score=38.24 Aligned_cols=48 Identities=15% Similarity=0.176 Sum_probs=41.6
Q ss_pred CCCHHHHHHhheecc---ccccchhhhhcccccccchhhhhhhhHHHHHHH
Q 015913 80 RIKIEEQLAIFMFIV---GHNLRTRAVQELFRYSGETISRHFNNVLNAIMA 127 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L---~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~ 127 (398)
.+++.++-.+.|+|. ..+.++.++|..+|+|.++|..+.++.+..|-.
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 588888888888873 356899999999999999999999998888864
No 209
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=61.51 E-value=6.4 Score=38.93 Aligned_cols=47 Identities=13% Similarity=0.112 Sum_probs=40.1
Q ss_pred CCCHHHHHHhheecc-c--cccchhhhhcccccccchhhhhhhhHHHHHH
Q 015913 80 RIKIEEQLAIFMFIV-G--HNLRTRAVQELFRYSGETISRHFNNVLNAIM 126 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L-~--~~~~~~~l~~~fgis~stv~r~~~~v~~~l~ 126 (398)
.++..++..+.|+|. . .+.++..||..||+|++.|+.+-.+.+.-|-
T Consensus 305 ~L~~rEr~Vl~lrygl~~~~~~tl~EIa~~lgvs~erVrQi~~~Al~kLr 354 (367)
T PRK09210 305 TLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 354 (367)
T ss_pred hCCHHHHHHHHHHhccCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHh
Confidence 588888888899885 2 5689999999999999999999887777664
No 210
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=61.42 E-value=7.5 Score=37.76 Aligned_cols=50 Identities=8% Similarity=0.026 Sum_probs=42.7
Q ss_pred CCCHHHHHHhheec-c--ccccchhhhhcccccccchhhhhhhhHHHHHHHhh
Q 015913 80 RIKIEEQLAIFMFI-V--GHNLRTRAVQELFRYSGETISRHFNNVLNAIMAIS 129 (398)
Q Consensus 80 ~~s~e~~l~~~L~~-L--~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~~ 129 (398)
.+++.++..+.++| | -.|.++..+|...|+|.+||..+.++....|.+..
T Consensus 262 ~L~~~~R~vl~lrygL~~~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l 314 (325)
T PRK05657 262 ELNDKQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQIQVEALRRLREIL 314 (325)
T ss_pred cCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 68888888888665 3 46899999999999999999999999999887543
No 211
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=60.49 E-value=7.3 Score=37.04 Aligned_cols=50 Identities=12% Similarity=0.037 Sum_probs=42.6
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHhhc
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAISL 130 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~~~ 130 (398)
.+|+.++-++.|+++- |.++.++|+.+|+|.+||...+++....|.+..+
T Consensus 115 ~L~~~~R~v~~L~~~~-g~s~~EIA~~lg~s~~tVk~~l~RAr~~Lr~~~~ 164 (293)
T PRK09636 115 RLSPLERAAFLLHDVF-GVPFDEIASTLGRSPAACRQLASRARKHVRAARP 164 (293)
T ss_pred hCCHHHHHHHHHHHHh-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCC
Confidence 5888888877777665 8999999999999999999999998888876544
No 212
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=60.29 E-value=3.6 Score=37.24 Aligned_cols=45 Identities=18% Similarity=0.309 Sum_probs=37.1
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHH
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 126 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~ 126 (398)
.+|..|.- .|..|+.|.+..++|...++|.+||..++.+...-|.
T Consensus 148 ~LT~RE~e--VL~lla~G~snkeIA~~L~iS~~TVk~h~~~i~~KL~ 192 (211)
T COG2197 148 LLTPRELE--VLRLLAEGLSNKEIAEELNLSEKTVKTHVSNILRKLG 192 (211)
T ss_pred CCCHHHHH--HHHHHHCCCCHHHHHHHHCCCHhHHHHHHHHHHHHcC
Confidence 35665543 4567899999999999999999999999988887663
No 213
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=60.08 E-value=4.6 Score=35.76 Aligned_cols=44 Identities=7% Similarity=0.145 Sum_probs=35.8
Q ss_pred CCCHHHHHHhheecccc--------------ccchhhhhcccccccchhhhhhhhHHH
Q 015913 80 RIKIEEQLAIFMFIVGH--------------NLRTRAVQELFRYSGETISRHFNNVLN 123 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~--------------~~~~~~l~~~fgis~stv~r~~~~v~~ 123 (398)
..+++++|+-+|..|+. ..+..++|+..|+++.||+|+++++.+
T Consensus 118 ~~~~~~Rla~~Ll~l~~~~~~~~~~~~~~~~~~t~~~iA~~lG~tretvsR~l~~l~~ 175 (202)
T PRK13918 118 GQRLKNRIAAALLELSDTPLATQEDSGETMIYATHDELAAAVGSVRETVTKVIGELSR 175 (202)
T ss_pred hCchHHHHHHHHHHHHHHhCCCCCCCCeEEecCCHHHHHHHhCccHHHHHHHHHHHHH
Confidence 45788999988876542 246889999999999999999988776
No 214
>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=60.03 E-value=5.8 Score=34.97 Aligned_cols=44 Identities=7% Similarity=-0.037 Sum_probs=33.5
Q ss_pred CHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHH
Q 015913 82 KIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMA 127 (398)
Q Consensus 82 s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~ 127 (398)
+...+.++ +.++ .|.++.+||..+|+|.+||...+++....|-.
T Consensus 152 ~~~~~~i~-~~~~-~~~s~~eIA~~l~~s~~tV~~~l~r~r~~L~~ 195 (198)
T TIGR02859 152 SDLEWKVL-QSYL-DGKSYQEIACDLNRHVKSIDNALQRVKRKLEK 195 (198)
T ss_pred CHHHHHHH-HHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 33344444 4454 79999999999999999999888887776653
No 215
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=59.85 E-value=3.5 Score=29.60 Aligned_cols=38 Identities=13% Similarity=0.127 Sum_probs=27.4
Q ss_pred HHHHhheeccccccchhhhhcccccccchhhhhhhhHH
Q 015913 85 EQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVL 122 (398)
Q Consensus 85 ~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~ 122 (398)
+++.-+|-....+.+.++||+.+|+|..++.+++....
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 34455555557789999999999999999998765443
No 216
>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=59.81 E-value=15 Score=33.67 Aligned_cols=46 Identities=11% Similarity=0.159 Sum_probs=39.6
Q ss_pred CCCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHH
Q 015913 79 NRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 126 (398)
Q Consensus 79 ~~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~ 126 (398)
..+|+.|+=.+.+ .+.|.++.++|..+|+|.+||..++++...-|.
T Consensus 170 ~~Lt~re~evl~~--~a~G~t~~eIa~~l~is~~Tv~~~l~~~~~kl~ 215 (232)
T TIGR03541 170 GVLSEREREVLAW--TALGRRQADIAAILGISERTVENHLRSARRKLG 215 (232)
T ss_pred ccCCHHHHHHHHH--HHCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHC
Confidence 4788888776666 479999999999999999999999999887764
No 217
>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function.
Probab=58.69 E-value=8.9 Score=30.67 Aligned_cols=46 Identities=20% Similarity=0.176 Sum_probs=37.0
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHH
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 126 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~ 126 (398)
.++++|-=++-|..+- |.++.+.|...|||++|+.++++..-.-|.
T Consensus 41 ~L~~dElEAiRL~D~e-gl~QeeaA~~MgVSR~T~~ril~~ARkKiA 86 (106)
T PF02001_consen 41 VLTVDELEAIRLVDYE-GLSQEEAAERMGVSRPTFQRILESARKKIA 86 (106)
T ss_pred EeeHHHHHHHHHHHHc-CCCHHHHHHHcCCcHHHHHHHHHHHHHHHH
Confidence 5677777666666554 799999999999999999999987666655
No 218
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=58.18 E-value=5.4 Score=27.56 Aligned_cols=29 Identities=21% Similarity=0.314 Sum_probs=24.1
Q ss_pred ccccchhhhhcccccccchhhhhhhhHHH
Q 015913 95 GHNLRTRAVQELFRYSGETISRHFNNVLN 123 (398)
Q Consensus 95 ~~~~~~~~l~~~fgis~stv~r~~~~v~~ 123 (398)
....+..+++..+|+|.+|+++.++...+
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~ 36 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLRE 36 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 44578889999999999999998876554
No 219
>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=57.97 E-value=12 Score=30.23 Aligned_cols=29 Identities=0% Similarity=-0.054 Sum_probs=23.9
Q ss_pred ccccchhhhhcccccccchhhhhhhhHHH
Q 015913 95 GHNLRTRAVQELFRYSGETISRHFNNVLN 123 (398)
Q Consensus 95 ~~~~~~~~l~~~fgis~stv~r~~~~v~~ 123 (398)
..+.+..+++...+++++|+++.+++..+
T Consensus 40 ~~~~t~~ela~~~~~~~~tvs~~l~~Le~ 68 (118)
T TIGR02337 40 QGSMEFTQLANQACILRPSLTGILARLER 68 (118)
T ss_pred cCCcCHHHHHHHhCCCchhHHHHHHHHHH
Confidence 34677899999999999999987766554
No 220
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=57.84 E-value=4.6 Score=36.61 Aligned_cols=45 Identities=4% Similarity=0.139 Sum_probs=36.8
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHH
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 126 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~ 126 (398)
.+++.|+- .|..++.|.+..++|...++|.+||..++.++..-+.
T Consensus 143 ~LS~RE~e--VL~Lia~G~SnkEIA~~L~IS~~TVk~hvs~I~~KLg 187 (217)
T PRK13719 143 KVTKYQND--VFILYSFGFSHEYIAQLLNITVGSSKNKISEILKFFG 187 (217)
T ss_pred CCCHHHHH--HHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 46665543 3456788999999999999999999999999888774
No 221
>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=57.23 E-value=5.4 Score=29.26 Aligned_cols=27 Identities=22% Similarity=0.393 Sum_probs=23.4
Q ss_pred ccchhhhhcccccccchhhhhhhhHHH
Q 015913 97 NLRTRAVQELFRYSGETISRHFNNVLN 123 (398)
Q Consensus 97 ~~~~~~l~~~fgis~stv~r~~~~v~~ 123 (398)
+.+..++|+..|+|+.||+++++++.+
T Consensus 28 ~lt~~~iA~~~g~sr~tv~r~l~~l~~ 54 (76)
T PF13545_consen 28 PLTQEEIADMLGVSRETVSRILKRLKD 54 (76)
T ss_dssp ESSHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 467889999999999999998887665
No 222
>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=56.95 E-value=8.1 Score=29.99 Aligned_cols=29 Identities=24% Similarity=0.330 Sum_probs=23.4
Q ss_pred cchhhhhcccccccchhhhhhhhHHHHHH
Q 015913 98 LRTRAVQELFRYSGETISRHFNNVLNAIM 126 (398)
Q Consensus 98 ~~~~~l~~~fgis~stv~r~~~~v~~~l~ 126 (398)
.++..+|+..|++.|||||+-..++.-+.
T Consensus 24 ~gq~~vA~~~Gv~eStISR~k~~~~~~~a 52 (91)
T PF05269_consen 24 VGQKKVAEAMGVDESTISRWKNDFIEKMA 52 (91)
T ss_dssp HHHHHHHHHHTSSTTTHHHHHHHHHHHHH
T ss_pred HhhHHHHHHhCCCHHHHHHHHhhHHHHHH
Confidence 46789999999999999998766555444
No 223
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=56.82 E-value=9.8 Score=33.54 Aligned_cols=45 Identities=11% Similarity=0.164 Sum_probs=34.0
Q ss_pred CCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHH
Q 015913 81 IKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 126 (398)
Q Consensus 81 ~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~ 126 (398)
+++++.=.+.|+++ .|.++.++|...|||..||.+-....-..|.
T Consensus 136 l~~~~~~~v~l~~~-~Gls~~EIA~~lgiS~~tV~r~l~~aR~~l~ 180 (185)
T PF07638_consen 136 LDPRQRRVVELRFF-EGLSVEEIAERLGISERTVRRRLRRARAWLR 180 (185)
T ss_pred cCHHHHHHHHHHHH-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 44554445555555 6899999999999999999998877665554
No 224
>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=56.21 E-value=4.3 Score=32.48 Aligned_cols=30 Identities=20% Similarity=0.229 Sum_probs=24.8
Q ss_pred cccchhhhhcccccccchhhhhhhhHHHHH
Q 015913 96 HNLRTRAVQELFRYSGETISRHFNNVLNAI 125 (398)
Q Consensus 96 ~~~~~~~l~~~fgis~stv~r~~~~v~~~l 125 (398)
-|.+...+|+.|+||+||+..++.+.-..-
T Consensus 79 AGlt~~aIAd~F~iS~s~~~nft~~n~~eY 108 (126)
T PF10654_consen 79 AGLTCYAIADYFKISKSTVFNFTQNNKKEY 108 (126)
T ss_pred cCCChHHHHHHHhHHHHHHHHHHHHhHHHH
Confidence 478999999999999999998876655443
No 225
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=56.21 E-value=4.4 Score=29.63 Aligned_cols=22 Identities=32% Similarity=0.344 Sum_probs=18.7
Q ss_pred chhhhhcccccccchhhhhhhh
Q 015913 99 RTRAVQELFRYSGETISRHFNN 120 (398)
Q Consensus 99 ~~~~l~~~fgis~stv~r~~~~ 120 (398)
+.+++|...|+|.+|||++++.
T Consensus 2 t~~~iA~~~gvS~~TVSr~ln~ 23 (70)
T smart00354 2 TIKDVARLAGVSKATVSRVLNG 23 (70)
T ss_pred CHHHHHHHHCCCHHHHHHHHCC
Confidence 4678999999999999997754
No 226
>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=56.17 E-value=9.2 Score=27.22 Aligned_cols=28 Identities=18% Similarity=0.207 Sum_probs=21.6
Q ss_pred cccchhhhhcccccccchhhhhhhhHHH
Q 015913 96 HNLRTRAVQELFRYSGETISRHFNNVLN 123 (398)
Q Consensus 96 ~~~~~~~l~~~fgis~stv~r~~~~v~~ 123 (398)
...+..+|+..++++++++++.+++.+.
T Consensus 17 ~~~t~~~l~~~~~~~~~~vs~~i~~L~~ 44 (68)
T PF13463_consen 17 GPMTQSDLAERLGISKSTVSRIIKKLEE 44 (68)
T ss_dssp S-BEHHHHHHHTT--HHHHHHHHHHHHH
T ss_pred CCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4577899999999999999998877665
No 227
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=56.13 E-value=4 Score=29.05 Aligned_cols=27 Identities=19% Similarity=0.094 Sum_probs=21.2
Q ss_pred ccccccchhhhhcccccccchhhhhhh
Q 015913 93 IVGHNLRTRAVQELFRYSGETISRHFN 119 (398)
Q Consensus 93 ~L~~~~~~~~l~~~fgis~stv~r~~~ 119 (398)
+-+.|.++.++|...|+|.+|++++-+
T Consensus 10 R~~~gls~~~lA~~~g~s~s~v~~iE~ 36 (64)
T PF13560_consen 10 RERAGLSQAQLADRLGVSQSTVSRIER 36 (64)
T ss_dssp HHCHTS-HHHHHHHHTS-HHHHHHHHT
T ss_pred HHHcCCCHHHHHHHHCcCHHHHHHHHC
Confidence 345689999999999999999998654
No 228
>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=55.75 E-value=5.7 Score=28.66 Aligned_cols=38 Identities=11% Similarity=0.169 Sum_probs=27.8
Q ss_pred HHHHhheeccccccchhhhhcccccccchhhhhhhhHHH
Q 015913 85 EQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLN 123 (398)
Q Consensus 85 ~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~ 123 (398)
.++...|. -..+.+..+|+...|+++++|++++++..+
T Consensus 11 ~~vy~~Ll-~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~ 48 (68)
T PF01978_consen 11 AKVYLALL-KNGPATAEEIAEELGISRSTVYRALKSLEE 48 (68)
T ss_dssp HHHHHHHH-HHCHEEHHHHHHHHTSSHHHHHHHHHHHHH
T ss_pred HHHHHHHH-HcCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 34444443 233578999999999999999998876654
No 229
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=55.39 E-value=5.6 Score=27.93 Aligned_cols=35 Identities=17% Similarity=0.416 Sum_probs=30.1
Q ss_pred eeccccccchhhhhcccccccchhhhhhhhHHHHH
Q 015913 91 MFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAI 125 (398)
Q Consensus 91 L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l 125 (398)
+.+++.|.+..++|...++|..||..+..++..-+
T Consensus 13 ~~l~~~G~s~~eia~~l~is~~tV~~h~~~i~~Kl 47 (65)
T COG2771 13 LRLVAQGKSNKEIARILGISEETVKTHLRNIYRKL 47 (65)
T ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 44567789999999999999999999988886655
No 230
>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=55.34 E-value=6.5 Score=27.77 Aligned_cols=32 Identities=9% Similarity=0.150 Sum_probs=25.6
Q ss_pred HHhheeccccccchhhhhcccccccchhhhhhhh
Q 015913 87 LAIFMFIVGHNLRTRAVQELFRYSGETISRHFNN 120 (398)
Q Consensus 87 l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~ 120 (398)
.|..||. .|.+..+||...|++.+||+.+..+
T Consensus 5 ~A~~LY~--~G~~~~eIA~~Lg~~~~TV~~W~~r 36 (58)
T PF06056_consen 5 QARSLYL--QGWSIKEIAEELGVPRSTVYSWKDR 36 (58)
T ss_pred HHHHHHH--cCCCHHHHHHHHCCChHHHHHHHHh
Confidence 3445554 5899999999999999999987654
No 231
>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=55.19 E-value=4.2 Score=27.38 Aligned_cols=20 Identities=25% Similarity=0.190 Sum_probs=17.1
Q ss_pred hhhcccccccchhhhhhhhH
Q 015913 102 AVQELFRYSGETISRHFNNV 121 (398)
Q Consensus 102 ~l~~~fgis~stv~r~~~~v 121 (398)
++|...|+|.+||+++++.-
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~ 21 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGK 21 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCC
Confidence 68899999999999987653
No 232
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=54.86 E-value=5.3 Score=38.64 Aligned_cols=35 Identities=17% Similarity=0.175 Sum_probs=28.6
Q ss_pred hheeccccccchhhhhcccccccchhhhhhhhHHH
Q 015913 89 IFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLN 123 (398)
Q Consensus 89 ~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~ 123 (398)
++=+|+-.|.++.++|.++|+|+++|+|.+.+.-+
T Consensus 21 vA~lYY~~g~tQ~eIA~~lgiSR~~VsRlL~~Ar~ 55 (318)
T PRK15418 21 IAWFYYHDGLTQSEIGERLGLTRLKVSRLLEKGRQ 55 (318)
T ss_pred HHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 34445566999999999999999999998876554
No 233
>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=54.24 E-value=10 Score=35.25 Aligned_cols=46 Identities=13% Similarity=0.219 Sum_probs=39.3
Q ss_pred CCCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHH
Q 015913 79 NRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 126 (398)
Q Consensus 79 ~~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~ 126 (398)
..+|+.|+=.+.+ ++.|.++.++|..++||..||..++++...-+.
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 4688888877775 579999999999999999999999988877663
No 234
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=54.18 E-value=5.3 Score=36.08 Aligned_cols=45 Identities=16% Similarity=0.163 Sum_probs=36.4
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHH
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 126 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~ 126 (398)
.+|+.|+ =.|..++.|.+.+++|+..++|..||..+..++..-|.
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 3666555 34556789999999999999999999999988877663
No 235
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=54.16 E-value=10 Score=31.88 Aligned_cols=43 Identities=5% Similarity=0.108 Sum_probs=30.6
Q ss_pred CCCHHHH-HHhheeccccccchhhhhcccccccchhhhhhhhHHH
Q 015913 80 RIKIEEQ-LAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLN 123 (398)
Q Consensus 80 ~~s~e~~-l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~ 123 (398)
++++.+- ++..|+ -..+.+..+|+..++++++|+++.+++..+
T Consensus 37 glt~~q~~vL~~l~-~~~~~t~~eLa~~l~i~~~tvsr~l~~Le~ 80 (144)
T PRK11512 37 DITAAQFKVLCSIR-CAACITPVELKKVLSVDLGALTRMLDRLVC 80 (144)
T ss_pred CCCHHHHHHHHHHH-HcCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4555544 333333 345688999999999999999998766554
No 236
>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=54.01 E-value=12 Score=29.12 Aligned_cols=57 Identities=14% Similarity=0.208 Sum_probs=34.7
Q ss_pred CCCHHHHHHHHHHHhcCCccccCCCCCHHHHHHhhee-ccccccchhhhhcccccccchhhhhhhhHHH
Q 015913 56 RMDKKVFYKLCDILQSKGLLRHTNRIKIEEQLAIFMF-IVGHNLRTRAVQELFRYSGETISRHFNNVLN 123 (398)
Q Consensus 56 rms~~~F~~L~~~l~~~~~~~~~~~~s~e~~l~~~L~-~L~~~~~~~~l~~~fgis~stv~r~~~~v~~ 123 (398)
.++.+.|.-|++.-.- .. +++..+|+ +|-.|.+-..+++++||+++-.++.+++.-.
T Consensus 22 ~vs~e~F~lLl~ls~I----------rS-~kiI~AL~dyLV~G~srkeac~~~gV~~syfs~~L~rL~~ 79 (91)
T PF03333_consen 22 KVSEEHFWLLLELSSI----------RS-EKIIAALRDYLVDGLSRKEACERHGVNQSYFSRALNRLNR 79 (91)
T ss_dssp -S-HHHHHHHHHHS---------------HHHHHHHHHHHTT---HHHHHHHTT--HHHHHHHHHHHHH
T ss_pred CcCHHHHHHHHHHCCC----------Cc-HHHHHHHHHHHHcCCcHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 4566777776665432 22 45555555 8889999999999999999999988776544
No 237
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=52.39 E-value=5.9 Score=29.79 Aligned_cols=25 Identities=24% Similarity=0.204 Sum_probs=19.7
Q ss_pred ccccchhhhhcccccccchhhhhhh
Q 015913 95 GHNLRTRAVQELFRYSGETISRHFN 119 (398)
Q Consensus 95 ~~~~~~~~l~~~fgis~stv~r~~~ 119 (398)
..|.++.++|...|+++++|+++.+
T Consensus 29 ~~~ltQ~e~A~~lgisq~~vS~l~~ 53 (80)
T PF13744_consen 29 ERGLTQAELAERLGISQPRVSRLEN 53 (80)
T ss_dssp CCT--HHHHHHHHTS-HHHHHHHHT
T ss_pred HcCCCHHHHHHHHCCChhHHHHHHc
Confidence 4688999999999999999999875
No 238
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=52.20 E-value=18 Score=29.90 Aligned_cols=48 Identities=17% Similarity=0.231 Sum_probs=35.7
Q ss_pred hhcCCCHHHHHHHHHHHhcCCccccCCCCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHH
Q 015913 53 ENFRMDKKVFYKLCDILQSKGLLRHTNRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLN 123 (398)
Q Consensus 53 ~~frms~~~F~~L~~~l~~~~~~~~~~~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~ 123 (398)
-.|+++...+.-+...|... .+.+..+||...++|+|||++.+++.+.
T Consensus 21 c~~GLs~~Dv~v~~~LL~~~-----------------------~~~tvdelae~lnr~rStv~rsl~~L~~ 68 (126)
T COG3355 21 CVYGLSELDVEVYKALLEEN-----------------------GPLTVDELAEILNRSRSTVYRSLQNLLE 68 (126)
T ss_pred HHhCCcHHHHHHHHHHHhhc-----------------------CCcCHHHHHHHHCccHHHHHHHHHHHHH
Confidence 35677776666666666422 2567789999999999999998877665
No 239
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=52.02 E-value=6.3 Score=36.47 Aligned_cols=46 Identities=11% Similarity=0.105 Sum_probs=38.2
Q ss_pred CCCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHH
Q 015913 79 NRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 126 (398)
Q Consensus 79 ~~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~ 126 (398)
..+|+.|+=.+ .+++.|.+..++|...+||..||..++.++.+-|.
T Consensus 178 ~~LT~rE~evl--~~~a~G~t~~eIa~~l~is~~TV~~h~~~~~~KL~ 223 (240)
T PRK10188 178 MNFSKREKEIL--KWTAEGKTSAEIAMILSISENTVNFHQKNMQKKFN 223 (240)
T ss_pred CCCCHHHHHHH--HHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 36787776544 45589999999999999999999999998888764
No 240
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=51.74 E-value=12 Score=36.45 Aligned_cols=48 Identities=19% Similarity=0.219 Sum_probs=40.6
Q ss_pred CCCHHHHHHhheecc---ccccchhhhhcccccccchhhhhhhhHHHHHHH
Q 015913 80 RIKIEEQLAIFMFIV---GHNLRTRAVQELFRYSGETISRHFNNVLNAIMA 127 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L---~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~ 127 (398)
.++..++..+.++|. +.+.++.+||..+|||++.|+.+-.+.+.-|-.
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 478888888888874 345899999999999999999999888887753
No 241
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=51.49 E-value=12 Score=38.71 Aligned_cols=48 Identities=15% Similarity=0.139 Sum_probs=42.1
Q ss_pred CCCHHHHHHhheecc---ccccchhhhhcccccccchhhhhhhhHHHHHHH
Q 015913 80 RIKIEEQLAIFMFIV---GHNLRTRAVQELFRYSGETISRHFNNVLNAIMA 127 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L---~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~ 127 (398)
.++..++..+.++|. ..+.++..||..+|||++.|+++-.+.+.-|-.
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 588889999999884 467999999999999999999999988887753
No 242
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=51.11 E-value=12 Score=28.50 Aligned_cols=28 Identities=14% Similarity=0.201 Sum_probs=24.1
Q ss_pred cccchhhhhcccccccchhhhhhhhHHH
Q 015913 96 HNLRTRAVQELFRYSGETISRHFNNVLN 123 (398)
Q Consensus 96 ~~~~~~~l~~~fgis~stv~r~~~~v~~ 123 (398)
.+.+..+++..+++|++|+++.+++..+
T Consensus 23 ~~~~~~~la~~~~~s~~~i~~~l~~L~~ 50 (101)
T smart00347 23 GPLSVSELAKRLGVSPSTVTRVLDRLEK 50 (101)
T ss_pred CCcCHHHHHHHHCCCchhHHHHHHHHHH
Confidence 3578899999999999999998877766
No 243
>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=50.84 E-value=6.2 Score=25.68 Aligned_cols=22 Identities=27% Similarity=0.365 Sum_probs=18.6
Q ss_pred chhhhhcccccccchhhhhhhh
Q 015913 99 RTRAVQELFRYSGETISRHFNN 120 (398)
Q Consensus 99 ~~~~l~~~fgis~stv~r~~~~ 120 (398)
+..++|..+|||.+|+.+++..
T Consensus 2 s~~e~a~~lgvs~~tl~~~~~~ 23 (49)
T cd04762 2 TTKEAAELLGVSPSTLRRWVKE 23 (49)
T ss_pred CHHHHHHHHCcCHHHHHHHHHc
Confidence 4578999999999999987764
No 244
>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=50.70 E-value=6.4 Score=26.81 Aligned_cols=25 Identities=16% Similarity=0.021 Sum_probs=22.0
Q ss_pred ccccchhhhhcccccccchhhhhhh
Q 015913 95 GHNLRTRAVQELFRYSGETISRHFN 119 (398)
Q Consensus 95 ~~~~~~~~l~~~fgis~stv~r~~~ 119 (398)
..|.++.++|...|+|++|++++.+
T Consensus 13 ~~gltq~~lA~~~gvs~~~vs~~e~ 37 (58)
T TIGR03070 13 ALGLTQADLADLAGVGLRFIRDVEN 37 (58)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHC
Confidence 4588899999999999999999764
No 245
>PRK09492 treR trehalose repressor; Provisional
Probab=49.57 E-value=12 Score=35.45 Aligned_cols=23 Identities=30% Similarity=0.401 Sum_probs=21.2
Q ss_pred cchhhhhcccccccchhhhhhhh
Q 015913 98 LRTRAVQELFRYSGETISRHFNN 120 (398)
Q Consensus 98 ~~~~~l~~~fgis~stv~r~~~~ 120 (398)
.+.++||...|+|.+||||+++.
T Consensus 5 ~ti~dIA~~agVS~~TVSrvLn~ 27 (315)
T PRK09492 5 LTIKDIARLSGVGKSTVSRVLNN 27 (315)
T ss_pred CcHHHHHHHhCCCHHHHhHHhCC
Confidence 47889999999999999999985
No 246
>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=49.36 E-value=9.4 Score=27.19 Aligned_cols=27 Identities=26% Similarity=0.373 Sum_probs=22.5
Q ss_pred ccchhhhhcccccccchhhhhhhhHHH
Q 015913 97 NLRTRAVQELFRYSGETISRHFNNVLN 123 (398)
Q Consensus 97 ~~~~~~l~~~fgis~stv~r~~~~v~~ 123 (398)
+.+..+++..+|++.+|+++.++....
T Consensus 20 ~~~~~ei~~~~~i~~~~i~~~l~~L~~ 46 (78)
T cd00090 20 PLTVSELAERLGLSQSTVSRHLKKLEE 46 (78)
T ss_pred CcCHHHHHHHHCcCHhHHHHHHHHHHH
Confidence 388999999999999999988766533
No 247
>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=49.26 E-value=7 Score=30.45 Aligned_cols=57 Identities=16% Similarity=0.167 Sum_probs=35.1
Q ss_pred hcCCCHHHHHHHHHHHhcCCccccC-CCCCHHHHHHhheeccccccchhhhhcccccccchhhhhhh
Q 015913 54 NFRMDKKVFYKLCDILQSKGLLRHT-NRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFN 119 (398)
Q Consensus 54 ~frms~~~F~~L~~~l~~~~~~~~~-~~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~ 119 (398)
.+-|+=+.|..|............. .....+.+ |. ..+..+|..||+|.+|++|+-.
T Consensus 10 v~qmTg~ell~L~~~~~~~~~~~~~~~~~~~~~~-----yv----yG~~GlAklfgcSv~Ta~RiK~ 67 (96)
T PF12964_consen 10 VWQMTGEELLFLLKEGKTNSEKQTSQKAKKDEKK-----YV----YGLKGLAKLFGCSVPTANRIKK 67 (96)
T ss_pred HHHhhHHHHHHHHHHHhcCCCccCCccccCcccc-----ee----ehHHHHHHHhCCCchhHHHHHh
Confidence 4567778888888777543222111 11222222 11 2367899999999999999875
No 248
>PRK09483 response regulator; Provisional
Probab=49.19 E-value=7 Score=34.49 Aligned_cols=45 Identities=9% Similarity=0.203 Sum_probs=37.3
Q ss_pred CCCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHH
Q 015913 79 NRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAI 125 (398)
Q Consensus 79 ~~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l 125 (398)
..+++.|.-.+ .+++.|.+..++|..+++|.+||..++++...-|
T Consensus 147 ~~Lt~rE~~vl--~~~~~G~~~~~Ia~~l~is~~TV~~~~~~i~~Kl 191 (217)
T PRK09483 147 ASLSERELQIM--LMITKGQKVNEISEQLNLSPKTVNSYRYRMFSKL 191 (217)
T ss_pred cccCHHHHHHH--HHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHc
Confidence 35788776554 4568899999999999999999999998887766
No 249
>PHA02591 hypothetical protein; Provisional
Probab=48.84 E-value=6.3 Score=29.39 Aligned_cols=32 Identities=9% Similarity=0.169 Sum_probs=26.1
Q ss_pred hheeccccccchhhhhcccccccchhhhhhhh
Q 015913 89 IFMFIVGHNLRTRAVQELFRYSGETISRHFNN 120 (398)
Q Consensus 89 ~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~ 120 (398)
++=.....|.+...+|...|+++++|+++++.
T Consensus 51 vA~eL~eqGlSqeqIA~~LGVsqetVrKYL~~ 82 (83)
T PHA02591 51 VTHELARKGFTVEKIASLLGVSVRKVRRYLES 82 (83)
T ss_pred HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHhc
Confidence 33334567899999999999999999998764
No 250
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=48.64 E-value=17 Score=37.25 Aligned_cols=31 Identities=29% Similarity=0.323 Sum_probs=25.3
Q ss_pred ccchhhhhcccccccchhhhhhhhHHHHHHHhhccccCCCC
Q 015913 97 NLRTRAVQELFRYSGETISRHFNNVLNAIMAISLDFFQPPG 137 (398)
Q Consensus 97 ~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~~~~~i~~P~ 137 (398)
+...++||+..|++.|||||+++ ..|+..|.
T Consensus 369 PLtlkdVAe~lglHeSTVSRa~~----------~KY~~tp~ 399 (481)
T PRK12469 369 PLVLRDVAEELGLHESTISRATG----------NKYMATPR 399 (481)
T ss_pred CCcHHHHHHHhCCCcchhhHHhc----------CceeecCC
Confidence 57899999999999999999774 45666553
No 251
>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=48.58 E-value=15 Score=29.26 Aligned_cols=28 Identities=4% Similarity=0.093 Sum_probs=24.0
Q ss_pred cccchhhhhcccccccchhhhhhhhHHH
Q 015913 96 HNLRTRAVQELFRYSGETISRHFNNVLN 123 (398)
Q Consensus 96 ~~~~~~~l~~~fgis~stv~r~~~~v~~ 123 (398)
.+.+..+++...+++++||++.+++..+
T Consensus 42 ~~~t~~eL~~~l~~~~stvs~~i~~Le~ 69 (109)
T TIGR01889 42 GKLTLKEIIKEILIKQSALVKIIKKLSK 69 (109)
T ss_pred CcCcHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3588999999999999999998876654
No 252
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=48.46 E-value=10 Score=25.14 Aligned_cols=27 Identities=26% Similarity=0.362 Sum_probs=23.0
Q ss_pred ccchhhhhcccccccchhhhhhhhHHH
Q 015913 97 NLRTRAVQELFRYSGETISRHFNNVLN 123 (398)
Q Consensus 97 ~~~~~~l~~~fgis~stv~r~~~~v~~ 123 (398)
+.+..+++..|++|.+|+++.+..+..
T Consensus 14 ~~s~~~l~~~l~~s~~tv~~~l~~L~~ 40 (53)
T smart00420 14 KVSVEELAELLGVSEMTIRRDLNKLEE 40 (53)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 467889999999999999998876654
No 253
>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=48.16 E-value=9.5 Score=26.64 Aligned_cols=26 Identities=27% Similarity=0.371 Sum_probs=21.5
Q ss_pred ccchhhhhcccccccchhhhhhhhHH
Q 015913 97 NLRTRAVQELFRYSGETISRHFNNVL 122 (398)
Q Consensus 97 ~~~~~~l~~~fgis~stv~r~~~~v~ 122 (398)
..+..++++.||||..|+.|-+....
T Consensus 14 ~~s~~ela~~~~VS~~TiRRDl~~L~ 39 (57)
T PF08220_consen 14 KVSVKELAEEFGVSEMTIRRDLNKLE 39 (57)
T ss_pred CEEHHHHHHHHCcCHHHHHHHHHHHH
Confidence 46788999999999999999776543
No 254
>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=48.07 E-value=11 Score=35.73 Aligned_cols=21 Identities=24% Similarity=0.324 Sum_probs=19.5
Q ss_pred chhhhhcccccccchhhhhhh
Q 015913 99 RTRAVQELFRYSGETISRHFN 119 (398)
Q Consensus 99 ~~~~l~~~fgis~stv~r~~~ 119 (398)
+..+||...|+|++||||+++
T Consensus 3 ti~dIA~~agVS~sTVSr~Ln 23 (311)
T TIGR02405 3 TIKDIARLAGVGKSTVSRVLN 23 (311)
T ss_pred cHHHHHHHhCCCHHHHHHHhC
Confidence 568999999999999999997
No 255
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=47.96 E-value=7 Score=34.94 Aligned_cols=27 Identities=11% Similarity=0.250 Sum_probs=24.5
Q ss_pred ccccccchhhhhcccccccchhhhhhh
Q 015913 93 IVGHNLRTRAVQELFRYSGETISRHFN 119 (398)
Q Consensus 93 ~L~~~~~~~~l~~~fgis~stv~r~~~ 119 (398)
++..|.++..+|..+|||.+|+.|+.+
T Consensus 168 ~~~~g~s~~~iak~lgis~~Tv~r~~k 194 (200)
T PRK13413 168 LLDKGTSKSEIARKLGVSRTTLARFLK 194 (200)
T ss_pred HHHCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 467789999999999999999999886
No 256
>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=47.89 E-value=7.4 Score=25.45 Aligned_cols=21 Identities=19% Similarity=0.257 Sum_probs=17.9
Q ss_pred chhhhhcccccccchhhhhhh
Q 015913 99 RTRAVQELFRYSGETISRHFN 119 (398)
Q Consensus 99 ~~~~l~~~fgis~stv~r~~~ 119 (398)
+..+++..+|+|.+|+.++++
T Consensus 3 t~~e~a~~lgis~~ti~~~~~ 23 (49)
T TIGR01764 3 TVEEAAEYLGVSKDTVYRLIH 23 (49)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 567899999999999998663
No 257
>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=47.82 E-value=6.1 Score=34.18 Aligned_cols=23 Identities=17% Similarity=0.296 Sum_probs=0.0
Q ss_pred ccchhhhhcccccccchhhhhhh
Q 015913 97 NLRTRAVQELFRYSGETISRHFN 119 (398)
Q Consensus 97 ~~~~~~l~~~fgis~stv~r~~~ 119 (398)
..+..++|+..|++.|||||+++
T Consensus 49 PLt~~~iA~~lgl~~STVSRav~ 71 (160)
T PF04552_consen 49 PLTMKDIADELGLHESTVSRAVK 71 (160)
T ss_dssp -----------------------
T ss_pred CCCHHHHHHHhCCCHhHHHHHHc
Confidence 46788999999999999999775
No 258
>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=47.81 E-value=12 Score=24.79 Aligned_cols=31 Identities=13% Similarity=0.099 Sum_probs=25.7
Q ss_pred cccchhhhhcccccccchhhhhhhhHHHHHH
Q 015913 96 HNLRTRAVQELFRYSGETISRHFNNVLNAIM 126 (398)
Q Consensus 96 ~~~~~~~l~~~fgis~stv~r~~~~v~~~l~ 126 (398)
.+.+.++|+...|+|+++++++|..--..+.
T Consensus 15 ~~~s~~~Ia~~~gvs~~~~y~~f~~k~~l~~ 45 (47)
T PF00440_consen 15 EAVSIRDIARRAGVSKGSFYRYFPSKDDLLR 45 (47)
T ss_dssp TTSSHHHHHHHHTSCHHHHHHHCSSHHHHHH
T ss_pred HhCCHHHHHHHHccchhhHHHHcCCHHHHHh
Confidence 3578999999999999999999987655543
No 259
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=47.57 E-value=17 Score=34.70 Aligned_cols=50 Identities=10% Similarity=0.093 Sum_probs=41.6
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHHhhc
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAISL 130 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~~~ 130 (398)
.+|+.++-++.|+++- |.++.++|...|+|.+||...+++....|....+
T Consensus 118 ~L~p~~R~vf~L~~~~-g~s~~EIA~~Lgis~~tVr~~l~RAr~~Lr~~~~ 167 (290)
T PRK09635 118 RLGPAERVVFVLHEIF-GLPYQQIATTIGSQASTCRQLAHRARRKINESRI 167 (290)
T ss_pred hCCHHHHHHhhHHHHh-CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHhhCC
Confidence 5778877777766554 9999999999999999999999998888876433
No 260
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=47.57 E-value=8.3 Score=35.03 Aligned_cols=45 Identities=13% Similarity=0.161 Sum_probs=35.6
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHH
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 126 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~ 126 (398)
.+|+.|+=.+ ..++.|.++.++|..+++|..||..++.+.+.-+.
T Consensus 155 ~Lt~rE~~Vl--~l~~~G~s~~eIA~~L~iS~~TVk~~~~~i~~Kl~ 199 (216)
T PRK10100 155 LLTHREKEIL--NKLRIGASNNEIARSLFISENTVKTHLYNLFKKIA 199 (216)
T ss_pred CCCHHHHHHH--HHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 3676555443 34556999999999999999999999998887764
No 261
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=47.33 E-value=19 Score=36.69 Aligned_cols=58 Identities=17% Similarity=0.177 Sum_probs=35.9
Q ss_pred hHHHhhcCCCHHHHHHHHHHHhcCCccccCCCCCHHHHHHhheecc--ccccchhhhhcccccccchhhhhhh
Q 015913 49 ERCLENFRMDKKVFYKLCDILQSKGLLRHTNRIKIEEQLAIFMFIV--GHNLRTRAVQELFRYSGETISRHFN 119 (398)
Q Consensus 49 ~~f~~~frms~~~F~~L~~~l~~~~~~~~~~~~s~e~~l~~~L~~L--~~~~~~~~l~~~fgis~stv~r~~~ 119 (398)
..+.+.....+.|..++...|-. .|-..|+.-- =.+.+.++||+..|++.|||||+++
T Consensus 306 ~~li~~i~~R~~TL~~v~~~Iv~-------------~Q~~Ff~~G~~~LkPLtlkdvAe~lglheSTVSRav~ 365 (455)
T PRK05932 306 KWLIKSLEQRKETLLKVARCIVE-------------QQRDFFEHGEEALKPLVLKDIAEELGMHESTISRATT 365 (455)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH-------------HHHHHHhCCcccCcCccHHHHHHHhCCCccchhhhhc
Confidence 34445555555555555555532 2333333211 1257899999999999999999774
No 262
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=46.99 E-value=14 Score=33.53 Aligned_cols=48 Identities=8% Similarity=0.171 Sum_probs=34.6
Q ss_pred CCCHHHHHHhh-ee---ccc--cccchhhhhcccccccchhhhhhhhHHHHHHH
Q 015913 80 RIKIEEQLAIF-MF---IVG--HNLRTRAVQELFRYSGETISRHFNNVLNAIMA 127 (398)
Q Consensus 80 ~~s~e~~l~~~-L~---~L~--~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~ 127 (398)
.++..|.-++. =+ |+- ...+..+||..||||++|++.++++...-|..
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 57776553322 22 332 23678899999999999999999998887764
No 263
>PHA00738 putative HTH transcription regulator
Probab=46.87 E-value=10 Score=30.30 Aligned_cols=27 Identities=19% Similarity=0.212 Sum_probs=23.5
Q ss_pred cchhhhhcccccccchhhhhhhhHHHH
Q 015913 98 LRTRAVQELFRYSGETISRHFNNVLNA 124 (398)
Q Consensus 98 ~~~~~l~~~fgis~stv~r~~~~v~~~ 124 (398)
.+..++++.|++|++|||++++-.-+|
T Consensus 27 ~~V~eLae~l~lSQptVS~HLKvLreA 53 (108)
T PHA00738 27 LSASLISHTLLLSYTTVLRHLKILNEQ 53 (108)
T ss_pred ccHHHHHHhhCCCHHHHHHHHHHHHHC
Confidence 788899999999999999998766654
No 264
>PRK09191 two-component response regulator; Provisional
Probab=46.85 E-value=13 Score=34.10 Aligned_cols=47 Identities=6% Similarity=0.097 Sum_probs=40.1
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHHH
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMA 127 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~ 127 (398)
.+++.++-.+.|.++. |.++.++|...|+|.+||...+.+....+..
T Consensus 88 ~L~~~~r~v~~l~~~~-~~s~~eIA~~l~~s~~tV~~~l~ra~~~l~~ 134 (261)
T PRK09191 88 GLTPLPRQAFLLTALE-GFSVEEAAEILGVDPAEAEALLDDARAEIAR 134 (261)
T ss_pred hCCHHHhHHHHHHHHh-cCCHHHHHHHHCCCHHHHHHHHHHHHHHHhc
Confidence 5788888777777765 8999999999999999999999888887764
No 265
>PF12728 HTH_17: Helix-turn-helix domain
Probab=46.41 E-value=8.2 Score=25.98 Aligned_cols=21 Identities=24% Similarity=0.328 Sum_probs=18.1
Q ss_pred chhhhhcccccccchhhhhhh
Q 015913 99 RTRAVQELFRYSGETISRHFN 119 (398)
Q Consensus 99 ~~~~l~~~fgis~stv~r~~~ 119 (398)
+..++|+.+|||.+|+.++++
T Consensus 3 t~~e~a~~l~is~~tv~~~~~ 23 (51)
T PF12728_consen 3 TVKEAAELLGISRSTVYRWIR 23 (51)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 567899999999999998764
No 266
>PF13610 DDE_Tnp_IS240: DDE domain
Probab=46.01 E-value=20 Score=29.95 Aligned_cols=46 Identities=17% Similarity=0.206 Sum_probs=37.0
Q ss_pred HHHhHHHHHHHHHHhhhhhhccCCCCCccchhHHhHHHHHHHhhhhcc
Q 015913 279 LLRNATDRIFGALKERFPILLSAPPYPLQTQVKLVVAACALHNYIQRE 326 (398)
Q Consensus 279 ~~R~~VE~~fg~LK~rf~iL~~~~~~~~~~~~~ii~ac~~LHN~~~~~ 326 (398)
-.++.||+-+..+|.|.+...+- .+.+.....+.+-.+.||+...+
T Consensus 94 ~~nN~iE~~h~~~K~r~r~~~gF--ks~~~A~~~l~~~~~~~n~~r~~ 139 (140)
T PF13610_consen 94 YLNNRIERDHRTIKRRTRPMNGF--KSFRSAQRTLSGFEAYHNFRRPH 139 (140)
T ss_pred hhhChhhHhhhhhhhhcccccCc--CCHHHHHHHHHHHHHHHHHhCCC
Confidence 45789999999999988666543 45678888999999999998754
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=45.86 E-value=9.2 Score=24.98 Aligned_cols=24 Identities=17% Similarity=0.178 Sum_probs=18.6
Q ss_pred ccchhhhhcccccccchhhhhhhh
Q 015913 97 NLRTRAVQELFRYSGETISRHFNN 120 (398)
Q Consensus 97 ~~~~~~l~~~fgis~stv~r~~~~ 120 (398)
-.++.++|...|+|.+||.+-+.+
T Consensus 17 r~s~~~la~~lglS~~~v~~Ri~r 40 (42)
T PF13404_consen 17 RRSYAELAEELGLSESTVRRRIRR 40 (42)
T ss_dssp TS-HHHHHHHHTS-HHHHHHHHHH
T ss_pred CccHHHHHHHHCcCHHHHHHHHHH
Confidence 468999999999999999876654
No 268
>PF13551 HTH_29: Winged helix-turn helix
Probab=45.68 E-value=37 Score=26.57 Aligned_cols=73 Identities=12% Similarity=0.196 Sum_probs=46.2
Q ss_pred hhHHHhhcCCCHHHHHHHHHHHhcCC--ccc------cCC-C-CCHHHHHHhheeccccc------cchhhhhcc-----
Q 015913 48 SERCLENFRMDKKVFYKLCDILQSKG--LLR------HTN-R-IKIEEQLAIFMFIVGHN------LRTRAVQEL----- 106 (398)
Q Consensus 48 d~~f~~~frms~~~F~~L~~~l~~~~--~~~------~~~-~-~s~e~~l~~~L~~L~~~------~~~~~l~~~----- 106 (398)
..+.-+.+++++.++.+.+......+ .+. +++ . +++++.-.+.=+..... .+...++..
T Consensus 15 ~~~ia~~lg~s~~Tv~r~~~~~~~~G~~~l~~~~~~~g~~~~~l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~ 94 (112)
T PF13551_consen 15 IAEIARRLGISRRTVYRWLKRYREGGIEGLLPRKPRGGRPRKRLSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEE 94 (112)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHcccHHHHHhccccCCCCCCCCCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhc
Confidence 67888999999999999999987654 111 111 2 56655543332222221 345566553
Q ss_pred --cccccchhhhhhhh
Q 015913 107 --FRYSGETISRHFNN 120 (398)
Q Consensus 107 --fgis~stv~r~~~~ 120 (398)
..+|.+||.+++++
T Consensus 95 ~~~~~s~~ti~r~L~~ 110 (112)
T PF13551_consen 95 FGIDVSPSTIRRILKR 110 (112)
T ss_pred cCccCCHHHHHHHHHH
Confidence 36789999998865
No 269
>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=45.37 E-value=21 Score=36.05 Aligned_cols=58 Identities=21% Similarity=0.229 Sum_probs=36.1
Q ss_pred hHHHhhcCCCHHHHHHHHHHHhcCCccccCCCCCHHHHHHhheecc--ccccchhhhhcccccccchhhhhhh
Q 015913 49 ERCLENFRMDKKVFYKLCDILQSKGLLRHTNRIKIEEQLAIFMFIV--GHNLRTRAVQELFRYSGETISRHFN 119 (398)
Q Consensus 49 ~~f~~~frms~~~F~~L~~~l~~~~~~~~~~~~s~e~~l~~~L~~L--~~~~~~~~l~~~fgis~stv~r~~~ 119 (398)
..+.+...+.+.|..++...|-. .|-..|..-- =.+.+.++||+..|++.|||||+++
T Consensus 281 ~~li~~i~~R~~TL~~v~~~Iv~-------------~Q~~Ff~~G~~~LkPLtlkdiA~~lglheSTVSRav~ 340 (429)
T TIGR02395 281 RWLIKALEQREETLLKVAEAIVE-------------HQKDFFLGGPAALKPLTLREVAEELGLHESTISRAIN 340 (429)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH-------------HHHHHHhcCcccCcCCcHHHHHHHhCCCccchhhhhc
Confidence 34445555566666666655543 2222222211 1357899999999999999999774
No 270
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=45.22 E-value=8.1 Score=37.03 Aligned_cols=23 Identities=22% Similarity=0.208 Sum_probs=20.6
Q ss_pred cchhhhhcccccccchhhhhhhh
Q 015913 98 LRTRAVQELFRYSGETISRHFNN 120 (398)
Q Consensus 98 ~~~~~l~~~fgis~stv~r~~~~ 120 (398)
.+..+||...|||.+||||+++.
T Consensus 6 ~ti~dIA~~agVS~~TVSrvLn~ 28 (331)
T PRK14987 6 PVLQDVADRVGVTKMTVSRFLRN 28 (331)
T ss_pred CcHHHHHHHhCCCHHHhhhhhCC
Confidence 46789999999999999999865
No 271
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=45.18 E-value=6.8 Score=29.17 Aligned_cols=27 Identities=19% Similarity=0.145 Sum_probs=22.8
Q ss_pred ccccccchhhhhcccc------cccchhhhhhh
Q 015913 93 IVGHNLRTRAVQELFR------YSGETISRHFN 119 (398)
Q Consensus 93 ~L~~~~~~~~l~~~fg------is~stv~r~~~ 119 (398)
+..-|.++.++|...| +|++||||+-+
T Consensus 20 R~~lGLTQ~dvA~~lg~~~g~i~SQstISR~Es 52 (75)
T smart00352 20 RIKLGFTQADVGLALGALYGPDFSQTTICRFEA 52 (75)
T ss_pred HHHcCCCHHHHHHHhcccccCcCCHHHHHHHHh
Confidence 4556899999999999 59999999655
No 272
>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=44.98 E-value=15 Score=27.85 Aligned_cols=34 Identities=15% Similarity=0.109 Sum_probs=27.6
Q ss_pred cccccchhhhhcccccccchhhhhhhhHHHHHHH
Q 015913 94 VGHNLRTRAVQELFRYSGETISRHFNNVLNAIMA 127 (398)
Q Consensus 94 L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~ 127 (398)
...+.+..++++.+.+|++|+.+.++.+-+.|..
T Consensus 27 ~~~~~s~~~la~~~~iS~sti~~~i~~l~~~l~~ 60 (87)
T PF05043_consen 27 NNEYVSIEDLAEELFISRSTIYRDIKKLNKYLKK 60 (87)
T ss_dssp H-SEEEHHHHHHHHT--HHHHHHHHHHHHHHHHC
T ss_pred cCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4667899999999999999999999999888864
No 273
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=44.76 E-value=12 Score=35.53 Aligned_cols=42 Identities=17% Similarity=0.143 Sum_probs=35.6
Q ss_pred HHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHH
Q 015913 85 EQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 126 (398)
Q Consensus 85 ~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~ 126 (398)
.++-.|+....+|.++...|...++|+++||+.+++.-..+.
T Consensus 4 ~~L~~F~~v~~~~~s~s~AA~~L~isq~avSr~I~~LE~~lg 45 (309)
T PRK12682 4 QQLRFVREAVRRNLNLTEAAKALHTSQPGVSKAIIELEEELG 45 (309)
T ss_pred HHHHHHHHHHHccCCHHHHHHHhcCccHHHHHHHHHHHHHhC
Confidence 345556666667889999999999999999999999999885
No 274
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=44.75 E-value=8.2 Score=37.09 Aligned_cols=24 Identities=17% Similarity=0.057 Sum_probs=21.8
Q ss_pred ccchhhhhcccccccchhhhhhhh
Q 015913 97 NLRTRAVQELFRYSGETISRHFNN 120 (398)
Q Consensus 97 ~~~~~~l~~~fgis~stv~r~~~~ 120 (398)
..+.++||...|+|.+||||+++.
T Consensus 6 ~~Ti~dIA~~agVS~~TVSr~Ln~ 29 (342)
T PRK10014 6 KITIHDVALAAGVSVSTVSLVLSG 29 (342)
T ss_pred CCcHHHHHHHhCCCHHHHHHHHCC
Confidence 357899999999999999999987
No 275
>PRK10870 transcriptional repressor MprA; Provisional
Probab=44.75 E-value=36 Score=29.74 Aligned_cols=44 Identities=9% Similarity=0.003 Sum_probs=29.6
Q ss_pred CCCHHH-HHHhheecccc-ccchhhhhcccccccchhhhhhhhHHH
Q 015913 80 RIKIEE-QLAIFMFIVGH-NLRTRAVQELFRYSGETISRHFNNVLN 123 (398)
Q Consensus 80 ~~s~e~-~l~~~L~~L~~-~~~~~~l~~~fgis~stv~r~~~~v~~ 123 (398)
++++.+ .++..|+.... +.+..+|+..++++++|+++++++..+
T Consensus 52 gLt~~q~~iL~~L~~~~~~~it~~eLa~~l~l~~~tvsr~v~rLe~ 97 (176)
T PRK10870 52 GINETLFMALITLESQENHSIQPSELSCALGSSRTNATRIADELEK 97 (176)
T ss_pred CCCHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 355543 34444443322 467799999999999999998776554
No 276
>PHA01976 helix-turn-helix protein
Probab=44.32 E-value=9.3 Score=27.25 Aligned_cols=26 Identities=4% Similarity=-0.151 Sum_probs=22.7
Q ss_pred cccccchhhhhcccccccchhhhhhh
Q 015913 94 VGHNLRTRAVQELFRYSGETISRHFN 119 (398)
Q Consensus 94 L~~~~~~~~l~~~fgis~stv~r~~~ 119 (398)
-..|.+..++|...|+|++|++++-+
T Consensus 12 ~~~glt~~~lA~~~gvs~~~v~~~e~ 37 (67)
T PHA01976 12 NARAWSAPELSRRAGVRHSLIYDFEA 37 (67)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 45688999999999999999999764
No 277
>PRK09526 lacI lac repressor; Reviewed
Probab=44.01 E-value=8.6 Score=36.94 Aligned_cols=23 Identities=26% Similarity=0.209 Sum_probs=20.9
Q ss_pred cchhhhhcccccccchhhhhhhh
Q 015913 98 LRTRAVQELFRYSGETISRHFNN 120 (398)
Q Consensus 98 ~~~~~l~~~fgis~stv~r~~~~ 120 (398)
.+..+||...|||.+||||+++.
T Consensus 6 ~ti~dIA~~aGVS~~TVSrvLn~ 28 (342)
T PRK09526 6 VTLYDVARYAGVSYQTVSRVLNQ 28 (342)
T ss_pred CcHHHHHHHhCCCHHHHHHHhcC
Confidence 46889999999999999999984
No 278
>COG4496 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=43.98 E-value=36 Score=26.15 Aligned_cols=28 Identities=21% Similarity=0.116 Sum_probs=24.4
Q ss_pred eccccccchhhhhcccccccchhhhhhh
Q 015913 92 FIVGHNLRTRAVQELFRYSGETISRHFN 119 (398)
Q Consensus 92 ~~L~~~~~~~~l~~~fgis~stv~r~~~ 119 (398)
.+|..|.+|+++...-|.|-.|++|+-+
T Consensus 51 ~mL~eg~tY~~I~~eTGaStaTIsRVkR 78 (100)
T COG4496 51 KMLKEGRTYRDIEDETGASTATISRVKR 78 (100)
T ss_pred HHHHcCCCcchhhhccCcchhhHHHHHH
Confidence 4678899999999999999999998543
No 279
>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=43.78 E-value=12 Score=26.11 Aligned_cols=25 Identities=16% Similarity=0.198 Sum_probs=20.7
Q ss_pred chhhhhcccccccchhhhhhhhHHH
Q 015913 99 RTRAVQELFRYSGETISRHFNNVLN 123 (398)
Q Consensus 99 ~~~~l~~~fgis~stv~r~~~~v~~ 123 (398)
+..+++..||+|.+||++.+.+..+
T Consensus 27 ~~~~la~~~~is~~~v~~~l~~L~~ 51 (66)
T cd07377 27 SERELAEELGVSRTTVREALRELEA 51 (66)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 5778999999999999987766554
No 280
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=43.53 E-value=9.3 Score=26.86 Aligned_cols=27 Identities=19% Similarity=0.213 Sum_probs=19.8
Q ss_pred ccccchhhhhcccccccchhhhhhhhH
Q 015913 95 GHNLRTRAVQELFRYSGETISRHFNNV 121 (398)
Q Consensus 95 ~~~~~~~~l~~~fgis~stv~r~~~~v 121 (398)
..|.+..+++..-|+|++|++++++.-
T Consensus 8 ~~~it~~~La~~~gis~~tl~~~~~~~ 34 (63)
T PF13443_consen 8 ERGITQKDLARKTGISRSTLSRILNGK 34 (63)
T ss_dssp HTT--HHHHHHHHT--HHHHHHHHTTT
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHhcc
Confidence 357789999999999999999988764
No 281
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=43.48 E-value=29 Score=31.41 Aligned_cols=39 Identities=10% Similarity=0.114 Sum_probs=28.7
Q ss_pred HHHHhheeccccccchhhhhcccccccchhhhhhhhHHH
Q 015913 85 EQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLN 123 (398)
Q Consensus 85 ~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~ 123 (398)
.+|.-.|---..+.+..++|...|+|+.|+.|++.....
T Consensus 161 ~~i~~~~~~~~~~~Taeela~~~giSRvTaRRYLeyl~~ 199 (224)
T COG4565 161 QKVREALKEPDQELTAEELAQALGISRVTARRYLEYLVS 199 (224)
T ss_pred HHHHHHHhCcCCccCHHHHHHHhCccHHHHHHHHHHHHh
Confidence 334444444456788899999999999999998765443
No 282
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=43.17 E-value=11 Score=30.81 Aligned_cols=25 Identities=12% Similarity=0.272 Sum_probs=22.6
Q ss_pred cccchhhhhcccccccchhhhhhhh
Q 015913 96 HNLRTRAVQELFRYSGETISRHFNN 120 (398)
Q Consensus 96 ~~~~~~~l~~~fgis~stv~r~~~~ 120 (398)
.|.++..+|...|+|++.||.|++.
T Consensus 21 eG~Sq~~iA~LLGltqaAVS~Yls~ 45 (119)
T COG2522 21 EGLSQYRIAKLLGLTQAAVSQYLSG 45 (119)
T ss_pred cCCcHHHHHHHhCCCHHHHHHHHcc
Confidence 3899999999999999999998753
No 283
>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=42.69 E-value=21 Score=25.26 Aligned_cols=25 Identities=16% Similarity=0.239 Sum_probs=18.4
Q ss_pred chhhhhcccccccchhhhhhhhHHH
Q 015913 99 RTRAVQELFRYSGETISRHFNNVLN 123 (398)
Q Consensus 99 ~~~~l~~~fgis~stv~r~~~~v~~ 123 (398)
+-.+++..||+|++||.+.+.....
T Consensus 26 s~~~la~~~~vsr~tvr~al~~L~~ 50 (64)
T PF00392_consen 26 SERELAERYGVSRTTVREALRRLEA 50 (64)
T ss_dssp -HHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CHHHHHHHhccCCcHHHHHHHHHHH
Confidence 5678999999999999987665443
No 284
>COG1508 RpoN DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription]
Probab=41.99 E-value=16 Score=36.89 Aligned_cols=22 Identities=32% Similarity=0.324 Sum_probs=19.4
Q ss_pred cchhhhhcccccccchhhhhhh
Q 015913 98 LRTRAVQELFRYSGETISRHFN 119 (398)
Q Consensus 98 ~~~~~l~~~fgis~stv~r~~~ 119 (398)
...++||+..|+++|||||++.
T Consensus 331 L~LrdvA~~i~~HESTISRai~ 352 (444)
T COG1508 331 LVLRDVADEIGMHESTISRAIT 352 (444)
T ss_pred ccHHHHHHHhCccHHHHHHHHh
Confidence 4569999999999999999774
No 285
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=41.92 E-value=9.7 Score=36.42 Aligned_cols=23 Identities=22% Similarity=0.108 Sum_probs=20.5
Q ss_pred chhhhhcccccccchhhhhhhhH
Q 015913 99 RTRAVQELFRYSGETISRHFNNV 121 (398)
Q Consensus 99 ~~~~l~~~fgis~stv~r~~~~v 121 (398)
+..+||...|+|++||||+++.-
T Consensus 3 ti~dIA~~agVS~~TVSrvln~~ 25 (327)
T PRK10339 3 TLKDIAIEAGVSLATVSRVLNDD 25 (327)
T ss_pred CHHHHHHHhCCCHHhhhhhhcCC
Confidence 56899999999999999999853
No 286
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=41.11 E-value=10 Score=36.18 Aligned_cols=22 Identities=23% Similarity=0.160 Sum_probs=19.9
Q ss_pred chhhhhcccccccchhhhhhhh
Q 015913 99 RTRAVQELFRYSGETISRHFNN 120 (398)
Q Consensus 99 ~~~~l~~~fgis~stv~r~~~~ 120 (398)
+.++||...|||.+||||+++.
T Consensus 2 ti~dIA~~aGVS~~TVSrvLn~ 23 (328)
T PRK11303 2 KLDEIARLAGVSRTTASYVING 23 (328)
T ss_pred CHHHHHHHhCCCHHHHHHHHcC
Confidence 4679999999999999999886
No 287
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=40.86 E-value=17 Score=35.03 Aligned_cols=22 Identities=36% Similarity=0.308 Sum_probs=20.0
Q ss_pred chhhhhcccccccchhhhhhhh
Q 015913 99 RTRAVQELFRYSGETISRHFNN 120 (398)
Q Consensus 99 ~~~~l~~~fgis~stv~r~~~~ 120 (398)
+..+||...|||.+||||+++.
T Consensus 3 ti~dIA~~aGVS~~TVSrvLn~ 24 (346)
T PRK10401 3 TIRDVARQAGVSVATVSRVLNN 24 (346)
T ss_pred CHHHHHHHhCCCHHHHHHHHCC
Confidence 5789999999999999999973
No 288
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=40.51 E-value=15 Score=25.16 Aligned_cols=40 Identities=18% Similarity=0.152 Sum_probs=24.2
Q ss_pred CCCCHHHHHHhheeccccccchhhhhcccccccchhhhhhh
Q 015913 79 NRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFN 119 (398)
Q Consensus 79 ~~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~ 119 (398)
+.++..||.-+-++. .-|.+..+++.+.|.|+..|.++++
T Consensus 3 ~~Lt~~Eqaqid~m~-qlG~s~~~isr~i~RSr~~Ir~yl~ 42 (50)
T PF11427_consen 3 KTLTDAEQAQIDVMH-QLGMSLREISRRIGRSRTCIRRYLK 42 (50)
T ss_dssp ----HHHHHHHHHHH-HTT--HHHHHHHHT--HHHHHHHHH
T ss_pred CcCCHHHHHHHHHHH-HhchhHHHHHHHhCccHHHHHHHhc
Confidence 356777776554443 3488999999999999999998765
No 289
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=40.04 E-value=13 Score=30.25 Aligned_cols=39 Identities=21% Similarity=0.246 Sum_probs=27.4
Q ss_pred HHHHhheeccc-cccchhhhhcccccccchhhhhhhhHHH
Q 015913 85 EQLAIFMFIVG-HNLRTRAVQELFRYSGETISRHFNNVLN 123 (398)
Q Consensus 85 ~~l~~~L~~L~-~~~~~~~l~~~fgis~stv~r~~~~v~~ 123 (398)
.++.|...... ...+..++++.++++++|||++++..-+
T Consensus 17 tRl~IL~~L~~~~~~~v~ela~~l~lsqstvS~HL~~L~~ 56 (117)
T PRK10141 17 TRLGIVLLLRESGELCVCDLCTALDQSQPKISRHLALLRE 56 (117)
T ss_pred HHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 44444433333 3467889999999999999998865554
No 290
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=39.72 E-value=21 Score=28.11 Aligned_cols=27 Identities=7% Similarity=0.113 Sum_probs=23.6
Q ss_pred ccchhhhhcccccccchhhhhhhhHHH
Q 015913 97 NLRTRAVQELFRYSGETISRHFNNVLN 123 (398)
Q Consensus 97 ~~~~~~l~~~fgis~stv~r~~~~v~~ 123 (398)
..++.+++..+|+|++|+.+.+++..+
T Consensus 17 ~~~~~~la~~l~~s~~tv~~~l~~L~~ 43 (108)
T smart00344 17 RISLAELAKKVGLSPSTVHNRVKRLEE 43 (108)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 578999999999999999998776655
No 291
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=39.70 E-value=16 Score=34.82 Aligned_cols=42 Identities=19% Similarity=0.238 Sum_probs=36.2
Q ss_pred HHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHH
Q 015913 85 EQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 126 (398)
Q Consensus 85 ~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~ 126 (398)
.++-.|+....+|.|+...|+..++|+++||+.+++.-..+.
T Consensus 4 ~~L~~F~~v~~~~~S~s~AA~~L~isQpavS~~I~~LE~~lg 45 (309)
T PRK12683 4 QQLRIIREAVRQNFNLTEVANALYTSQSGVSKQIKDLEDELG 45 (309)
T ss_pred HHHHHHHHHHHccCCHHHHHHHhcCCcHHHHHHHHHHHHHhC
Confidence 356666667777889999999999999999999999999885
No 292
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=39.63 E-value=12 Score=36.21 Aligned_cols=32 Identities=19% Similarity=0.180 Sum_probs=26.8
Q ss_pred eeccccccchhhhhcccccccchhhhhhhhHH
Q 015913 91 MFIVGHNLRTRAVQELFRYSGETISRHFNNVL 122 (398)
Q Consensus 91 L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~ 122 (398)
=.|+-.|.++.++|+++|+|+.+|+|.+.+.-
T Consensus 20 ~lYY~~gltQ~eIA~~LgiSR~~v~rlL~~Ar 51 (321)
T COG2390 20 WLYYVEGLTQSEIAERLGISRATVSRLLAKAR 51 (321)
T ss_pred HHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 34567899999999999999999999776543
No 293
>PRK15215 fimbriae biosynthesis regulatory protein; Provisional
Probab=39.51 E-value=43 Score=26.36 Aligned_cols=58 Identities=14% Similarity=0.220 Sum_probs=43.1
Q ss_pred CCCHHHHHHHHHHHhcCCccccCCCCCHHHHHHhhee-ccccccchhhhhcccccccchhhhhhhhHHHH
Q 015913 56 RMDKKVFYKLCDILQSKGLLRHTNRIKIEEQLAIFMF-IVGHNLRTRAVQELFRYSGETISRHFNNVLNA 124 (398)
Q Consensus 56 rms~~~F~~L~~~l~~~~~~~~~~~~s~e~~l~~~L~-~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~ 124 (398)
.|+.+.|.-|++.-.-+ -+++..+|+ +|-.|.+-.++.++.+|+++-.+-.++++-..
T Consensus 30 ~v~eehF~LLieIS~Ir-----------S~KvI~AL~dyLV~G~trkevCe~~~Vn~gYfS~~L~rL~~i 88 (100)
T PRK15215 30 KVNEEHFWLLIGISSIH-----------SEKIIQALRDYLVFGVSRKDVCERYEVNNGYFSTSLNRLSRI 88 (100)
T ss_pred ccCHHHHHHHHHHcccc-----------hHHHHHHHHHHHHcCccHHHHHHccCCCHHHHHHHHHHHHHH
Confidence 35667776666654321 167777776 78899999999999999999988777665543
No 294
>PRK14086 dnaA chromosomal replication initiation protein; Provisional
Probab=39.41 E-value=24 Score=37.35 Aligned_cols=48 Identities=10% Similarity=0.129 Sum_probs=43.6
Q ss_pred CCCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHH
Q 015913 79 NRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 126 (398)
Q Consensus 79 ~~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~ 126 (398)
+.+...-+++|.|.+--++.++..|+..||.+.|||...++++-+.|.
T Consensus 551 ~~i~~aRqiAMYL~r~lt~~Sl~~IG~~FgRdHSTV~~A~~kI~~~~~ 598 (617)
T PRK14086 551 RVLVTARQIAMYLCRELTDLSLPKIGQQFGRDHTTVMHADRKIRALMA 598 (617)
T ss_pred cccchHHHHHHHHHHHHcCCCHHHHHHHhCCChhHHHHHHHHHHHHHH
Confidence 467778899999999999999999999999999999999999988775
No 295
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=39.25 E-value=11 Score=36.12 Aligned_cols=22 Identities=23% Similarity=0.190 Sum_probs=20.3
Q ss_pred chhhhhcccccccchhhhhhhh
Q 015913 99 RTRAVQELFRYSGETISRHFNN 120 (398)
Q Consensus 99 ~~~~l~~~fgis~stv~r~~~~ 120 (398)
+..+||...|+|.+||||+++.
T Consensus 3 Ti~dIA~~agVS~~TVSrvLn~ 24 (341)
T PRK10703 3 TIKDVAKRAGVSTTTVSHVINK 24 (341)
T ss_pred CHHHHHHHhCCCHHHHHHHHcC
Confidence 5789999999999999999985
No 296
>PRK10651 transcriptional regulator NarL; Provisional
Probab=38.86 E-value=12 Score=32.53 Aligned_cols=45 Identities=11% Similarity=0.279 Sum_probs=36.3
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHH
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 126 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~ 126 (398)
.+++.|.=. |.+++.|.+.++++...++|..||..++.+...-|.
T Consensus 155 ~Lt~rE~~v--l~~l~~g~~~~~ia~~l~is~~tV~~~~~~l~~Kl~ 199 (216)
T PRK10651 155 QLTPRERDI--LKLIAQGLPNKMIARRLDITESTVKVHVKHMLKKMK 199 (216)
T ss_pred cCCHHHHHH--HHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHHHHcC
Confidence 477766533 345778999999999999999999999988877663
No 297
>PRK10403 transcriptional regulator NarP; Provisional
Probab=38.39 E-value=13 Score=32.30 Aligned_cols=45 Identities=16% Similarity=0.284 Sum_probs=36.8
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHH
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 126 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~ 126 (398)
.++..+.-. |..++.|.+...++...++|..||..++.++.+-|.
T Consensus 153 ~Lt~~e~~v--l~~~~~g~s~~~ia~~l~~s~~tv~~~~~~i~~kl~ 197 (215)
T PRK10403 153 VLTERELDV--LHELAQGLSNKQIASVLNISEQTVKVHIRNLLRKLN 197 (215)
T ss_pred cCCHHHHHH--HHHHHCCCCHHHHHHHcCCCHHHHHHHHHHHHHHcC
Confidence 467666644 456678999999999999999999999999888763
No 298
>cd00131 PAX Paired Box domain
Probab=38.39 E-value=72 Score=26.31 Aligned_cols=75 Identities=13% Similarity=0.098 Sum_probs=45.7
Q ss_pred CChhHHHhhcCCCHHHHHHHHHHHhcCCcccc------CCC-CCHHH-HHHhheeccccccchhhhhccc---cc-----
Q 015913 46 GQSERCLENFRMDKKVFYKLCDILQSKGLLRH------TNR-IKIEE-QLAIFMFIVGHNLRTRAVQELF---RY----- 109 (398)
Q Consensus 46 ~~d~~f~~~frms~~~F~~L~~~l~~~~~~~~------~~~-~s~e~-~l~~~L~~L~~~~~~~~l~~~f---gi----- 109 (398)
.+..+.-+.|++++.+...++......+.... ++. ++.+. ...+.+..-.-..+..++++.+ |+
T Consensus 34 ~s~~~iA~~~~Vs~~tV~r~i~r~~e~G~v~pk~~gg~rpr~~~~~~~~~i~~~v~~~p~~Tl~El~~~L~~~gv~~~~~ 113 (128)
T cd00131 34 IRPCDISRQLRVSHGCVSKILNRYYETGSIRPGAIGGSKPRVATPEVVKKIEIYKQENPGMFAWEIRDRLLQEGVCDKSN 113 (128)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCCCCCCCCCCcCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCCcccCC
Confidence 46778889999999999999998876543221 122 33322 2222222222224555655553 55
Q ss_pred --ccchhhhhhhh
Q 015913 110 --SGETISRHFNN 120 (398)
Q Consensus 110 --s~stv~r~~~~ 120 (398)
|.|||+|+++.
T Consensus 114 ~~s~stI~R~L~~ 126 (128)
T cd00131 114 VPSVSSINRILRN 126 (128)
T ss_pred CCCHHHHHHHHHh
Confidence 99999998654
No 299
>PRK14088 dnaA chromosomal replication initiation protein; Provisional
Probab=38.26 E-value=23 Score=35.88 Aligned_cols=47 Identities=11% Similarity=0.181 Sum_probs=42.1
Q ss_pred CCCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHH
Q 015913 79 NRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAI 125 (398)
Q Consensus 79 ~~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l 125 (398)
+.+...-|++|.|..=-++.++.++|..||.+.|||+..++++-..+
T Consensus 369 ~~i~~aR~iamyl~r~~~~~s~~~Ig~~fgr~hstV~~a~~~i~~~~ 415 (440)
T PRK14088 369 VKALLARRIGMYVAKNYLGSSLRTIAEKFNRSHPVVVDSVKKVKDSL 415 (440)
T ss_pred ccccHHHHHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 46777888999998888899999999999999999999999998865
No 300
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=37.81 E-value=14 Score=31.85 Aligned_cols=45 Identities=11% Similarity=0.172 Sum_probs=35.4
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHH
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 126 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~ 126 (398)
.+++.|.-. |..|+.|.+..+++..+++|.+||..++.++..-+.
T Consensus 137 ~Lt~~E~~i--l~~l~~g~~~~~Ia~~l~~s~~tv~~~~~~l~~Kl~ 181 (196)
T PRK10360 137 PLTKRERQV--AEKLAQGMAVKEIAAELGLSPKTVHVHRANLMEKLG 181 (196)
T ss_pred CCCHHHHHH--HHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 466555533 444778899999999999999999999988877653
No 301
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=37.43 E-value=12 Score=35.57 Aligned_cols=19 Identities=32% Similarity=0.319 Sum_probs=17.7
Q ss_pred hhhhcccccccchhhhhhh
Q 015913 101 RAVQELFRYSGETISRHFN 119 (398)
Q Consensus 101 ~~l~~~fgis~stv~r~~~ 119 (398)
++||...|+|.+||||+++
T Consensus 2 ~dIA~~agVS~~TVSrvLn 20 (327)
T PRK10423 2 KDVARLAGVSTSTVSHVIN 20 (327)
T ss_pred hhHHHHhCCcHHHHHHHhC
Confidence 5899999999999999997
No 302
>PRK00149 dnaA chromosomal replication initiation protein; Reviewed
Probab=37.29 E-value=26 Score=35.59 Aligned_cols=48 Identities=13% Similarity=0.158 Sum_probs=43.4
Q ss_pred CCCCHHHHHHhheeccccccchhhhhccc-ccccchhhhhhhhHHHHHH
Q 015913 79 NRIKIEEQLAIFMFIVGHNLRTRAVQELF-RYSGETISRHFNNVLNAIM 126 (398)
Q Consensus 79 ~~~s~e~~l~~~L~~L~~~~~~~~l~~~f-gis~stv~r~~~~v~~~l~ 126 (398)
+.+...-|++|.|.+--++.|+.++|..| |.+.|||+..++++-+.+.
T Consensus 384 ~~~~~aR~iamyl~~~~~~~s~~~Ig~~fg~rdhstV~~a~~~i~~~~~ 432 (450)
T PRK00149 384 RNIARPRQIAMYLAKELTDLSLPEIGRAFGGRDHTTVLHAVRKIEKLLE 432 (450)
T ss_pred cccChHHHHHHHHHHHhcCCCHHHHHHHcCCCCHhHHHHHHHHHHHHHH
Confidence 46888889999999999999999999999 5999999999999988774
No 303
>PF00382 TFIIB: Transcription factor TFIIB repeat; InterPro: IPR013150 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. In eukaryotes, transcription initiation of all protein encoding genes involves the polymerase II system. This sytem is modulated by both general and specific transcription factors. The general factors (which include TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIG and TFIIH) operate through common promoter elements, such as the TATA box. Transcription factor IIB (TFIIB) is of central importance in transcription of class II genes. It associates with TFIID-TFIIA bound to DNA (the DA complex) to form a ternary TFIID-IIA-IBB (DAB) complex, which is recognised by RNA polymerase II [, ]. TFIIB comprises ~315-340 residues and contains an imperfect C-terminal repeat of a 75-residue domain that may contribute to the symmetry of the folded protein. The basal archaeal transcription machinery resembles that of the eukaryotic polymerase II system and includes a homologue of TFIIB []. This entry represents a cyclin-like domain which is found repeated in the C-terminal region of a variety of eukaryotic TFIIB's and their archaeal counterparts. These domains individually form the typical cyclin fold, and in the transcription complex they straddle the C-terminal region of the TATA-binding protein - an interaction essential for the formation of the transcription initiation complex [, ].; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2PHG_A 1C9B_Q 1TFB_A 1VOL_A 3K7A_M 1AIS_B 1D3U_B.
Probab=36.82 E-value=49 Score=23.93 Aligned_cols=62 Identities=19% Similarity=0.194 Sum_probs=35.5
Q ss_pred HHHhhcCCCHHHHHHH---HHHHhcCCccccCCCCCHHHHHHhhee----ccccccchhhhhcccccccchh
Q 015913 50 RCLENFRMDKKVFYKL---CDILQSKGLLRHTNRIKIEEQLAIFMF----IVGHNLRTRAVQELFRYSGETI 114 (398)
Q Consensus 50 ~f~~~frms~~~F~~L---~~~l~~~~~~~~~~~~s~e~~l~~~L~----~L~~~~~~~~l~~~fgis~stv 114 (398)
.|-..++++...-..= +........ .++-++..-.+.++| ..+...+.+++++..||+..|+
T Consensus 3 r~~~~L~L~~~v~~~A~~i~~~~~~~~~---~~Gr~~~~iaAA~iY~acr~~~~~~t~~eIa~~~~Vs~~tI 71 (71)
T PF00382_consen 3 RICSKLGLPEDVRERAKEIYKKAQERGL---LKGRSPESIAAACIYLACRLNGVPRTLKEIAEAAGVSEKTI 71 (71)
T ss_dssp HHHHHTT--HHHHHHHHHHHHHHHHTTT---STTS-HHHHHHHHHHHHHHHTTSSSSHHHHHHHCTSSHHHH
T ss_pred HHHhHcCCCHHHHHHHHHHHHHHHHcCC---cccCCHHHHHHHHHHHHHHHcCCCcCHHHHHHHhCCCCCcC
Confidence 4555667766544443 333333322 234555555555554 4567789999999999998875
No 304
>COG4974 XerD Site-specific recombinase XerD [DNA replication, recombination, and repair]
Probab=36.76 E-value=58 Score=31.04 Aligned_cols=80 Identities=11% Similarity=0.062 Sum_probs=56.3
Q ss_pred hhHHHh--hcCCCHHHHHHHHHHHhcCCccccCCCCCH-HHHHHhheeccccccchhhhhcccccc-cchhhhhhhhHHH
Q 015913 48 SERCLE--NFRMDKKVFYKLCDILQSKGLLRHTNRIKI-EEQLAIFMFIVGHNLRTRAVQELFRYS-GETISRHFNNVLN 123 (398)
Q Consensus 48 d~~f~~--~frms~~~F~~L~~~l~~~~~~~~~~~~s~-e~~l~~~L~~L~~~~~~~~l~~~fgis-~stv~r~~~~v~~ 123 (398)
|.-|.+ --+|||..|..++..+....... ..+|| --+=+.+-..|.+|...+.|++..|++ .||...+++-...
T Consensus 210 ~~LF~n~~g~~ltrq~~w~~lk~~a~~Agi~--~~isPH~LRHsFATHLL~~GADlRvVQeLLGHadisTTQIYTHV~~e 287 (300)
T COG4974 210 DALFPNQRGGGLTRQGFWKRLKDYAERAGID--KKISPHTLRHSFATHLLENGADLRVVQELLGHADISTTQIYTHVTKE 287 (300)
T ss_pred CeeeecCCCCCCCHHHHHHHHHHHHHHhCCC--CCcCchhhHHHHHHHHHhCCccHHHHHHHhCccccchhHHHHHHHHH
Confidence 445543 34689999999998887654433 33444 445567778899999999999999995 6777777665555
Q ss_pred HHHHhh
Q 015913 124 AIMAIS 129 (398)
Q Consensus 124 ~l~~~~ 129 (398)
.|-++.
T Consensus 288 ~L~~~~ 293 (300)
T COG4974 288 RLRDLY 293 (300)
T ss_pred HHHHHH
Confidence 555443
No 305
>PRK12679 cbl transcriptional regulator Cbl; Reviewed
Probab=36.75 E-value=20 Score=34.27 Aligned_cols=42 Identities=19% Similarity=0.245 Sum_probs=35.7
Q ss_pred HHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHH
Q 015913 85 EQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 126 (398)
Q Consensus 85 ~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~ 126 (398)
+++-.|+....++.++...|+..++|++|||+.+++.-..+.
T Consensus 4 ~~l~~f~~v~~~~~s~s~AA~~L~iSQ~avSr~I~~LE~~lg 45 (316)
T PRK12679 4 QQLKIIREAARQDYNLTEVANMLFTSQSGVSRHIRELEDELG 45 (316)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHhcCCchHHHHHHHHHHHHhC
Confidence 345566666667789999999999999999999999999886
No 306
>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=36.64 E-value=16 Score=26.33 Aligned_cols=26 Identities=12% Similarity=0.281 Sum_probs=21.8
Q ss_pred cchhhhhcccccccchhhhhhhhHHH
Q 015913 98 LRTRAVQELFRYSGETISRHFNNVLN 123 (398)
Q Consensus 98 ~~~~~l~~~fgis~stv~r~~~~v~~ 123 (398)
.+..+++..+|+|.+||++.+...-.
T Consensus 14 ~~~~eLa~~l~vS~~tv~~~l~~L~~ 39 (69)
T TIGR00122 14 FSGEKLGEALGMSRTAVNKHIQTLRE 39 (69)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 45789999999999999998876543
No 307
>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=36.46 E-value=13 Score=35.37 Aligned_cols=21 Identities=24% Similarity=0.132 Sum_probs=19.0
Q ss_pred hhhhhcccccccchhhhhhhh
Q 015913 100 TRAVQELFRYSGETISRHFNN 120 (398)
Q Consensus 100 ~~~l~~~fgis~stv~r~~~~ 120 (398)
..+||..-|+|.+||||+++.
T Consensus 2 i~dIA~~aGVS~~TVSrvLn~ 22 (327)
T TIGR02417 2 LSDIAKLAGVSKTTASYVING 22 (327)
T ss_pred HHHHHHHhCCCHHHHHHHHcC
Confidence 568999999999999999876
No 308
>PRK00215 LexA repressor; Validated
Probab=36.43 E-value=22 Score=31.78 Aligned_cols=28 Identities=11% Similarity=0.202 Sum_probs=23.7
Q ss_pred cccchhhhhccccc-ccchhhhhhhhHHH
Q 015913 96 HNLRTRAVQELFRY-SGETISRHFNNVLN 123 (398)
Q Consensus 96 ~~~~~~~l~~~fgi-s~stv~r~~~~v~~ 123 (398)
.+.+..+++..+|+ +++|+++++.....
T Consensus 22 ~~~s~~ela~~~~~~~~~tv~~~l~~L~~ 50 (205)
T PRK00215 22 YPPSRREIADALGLRSPSAVHEHLKALER 50 (205)
T ss_pred CCCCHHHHHHHhCCCChHHHHHHHHHHHH
Confidence 34588899999999 99999998877665
No 309
>COG3316 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=36.38 E-value=1.3e+02 Score=27.30 Aligned_cols=184 Identities=15% Similarity=0.085 Sum_probs=104.6
Q ss_pred HHHHHhheeccccccchhhhhcc-----cccccchhhhhhhhHHHHHHHhhccccCCCCCCCccccccCCccccccccce
Q 015913 84 EEQLAIFMFIVGHNLRTRAVQEL-----FRYSGETISRHFNNVLNAIMAISLDFFQPPGPDVPPEISLDPRLYPYFKDCV 158 (398)
Q Consensus 84 e~~l~~~L~~L~~~~~~~~l~~~-----fgis~stv~r~~~~v~~~l~~~~~~~i~~P~~~~~~~i~~~~~~~~~fp~~i 158 (398)
.-+...+-++|+.+.+++.+.+. ..++.+|+++++.+.-..+....+..=+- ++-.
T Consensus 12 ~vi~~~V~~yl~~~Ls~r~v~e~l~~rgi~v~h~Ti~rwv~k~~~~~~~~~~~r~~~-------------------~~~~ 72 (215)
T COG3316 12 NIIAVAVWLYLRYGLSLRDVEEMLAERGIEVDHETIHRWVQKYGPLLARRLKRRKRK-------------------AGDS 72 (215)
T ss_pred hhHHHHHHHHhhcchhhccHHHHHHHcCcchhHHHHHHHHHHHhHHHHHHhhhhccc-------------------cccc
Confidence 33344455677889999998875 45678899999999888887543322100 1223
Q ss_pred eeecceEEEEEeCCCCCCCCCCCCCccccceeeeecCCcceEEeecCcccccccHHHHH-HHHhhcCCCCCCCCceeecc
Q 015913 159 GAVDGIHIPVMVGVDEQGPFRNKSGLLSQNVLAACSFDLKFHYVLAGWEGSASDLRVLN-SALTRRNKLQVPEGKYYLVD 237 (398)
Q Consensus 159 G~IDgt~i~i~~P~~~~~~y~~~k~~~s~~~q~v~d~~~~~~~v~~g~~Gs~~D~~vl~-~sl~~~~~~~~~~g~~~l~D 237 (398)
-.||-|.|.|. |+.. -+=.++|.+|..+.+...---+...+..|- .++... ..+.-++.|
T Consensus 73 w~vDEt~ikv~----------gkw~----ylyrAid~~g~~Ld~~L~~rRn~~aAk~Fl~kllk~~-----g~p~v~vtD 133 (215)
T COG3316 73 WRVDETYIKVN----------GKWH----YLYRAIDADGLTLDVWLSKRRNALAAKAFLKKLLKKH-----GEPRVFVTD 133 (215)
T ss_pred eeeeeeEEeec----------cEee----ehhhhhccCCCeEEEEEEcccCcHHHHHHHHHHHHhc-----CCCceEEec
Confidence 36888988873 1111 122467777888888776444455555443 445421 334567888
Q ss_pred CCCCCCCCccccccCcccCcccccCCCCchhHHHHHHHHHHHH-HhHHHHHHHHHHhhhhhhccCCCCCccchhHHhHHH
Q 015913 238 NKYANMPGFIAPYQAVSYHTNQTTTGYHPQDAKELFNQRHSLL-RNATDRIFGALKERFPILLSAPPYPLQTQVKLVVAA 316 (398)
Q Consensus 238 ~gYp~~~~ll~P~~~~~~~l~~~~~~~~~~~~~~~fN~~~s~~-R~~VE~~fg~LK~rf~iL~~~~~~~~~~~~~ii~ac 316 (398)
++=.....+ +.. .. .+-++.++- .+.||+-+..+|.|=+-.. ...+.......+...
T Consensus 134 ka~s~~~A~----~~l-------------~~---~~ehr~~~ylnN~iE~dh~~iKrr~~~~~--~f~~~~sa~~~~~gi 191 (215)
T COG3316 134 KAPSYTAAL----RKL-------------GS---EVEHRTSKYLNNRIEQDHRPIKRRTRPMK--RFKSLSSAASTISGI 191 (215)
T ss_pred CccchHHHH----Hhc-------------Cc---chheecccccccchhhcchhHHHHhcccc--cCCChHHHHHHHHhH
Confidence 653222111 000 00 111122222 4788999999987555432 123445556666777
Q ss_pred HHHHhhhhccC
Q 015913 317 CALHNYIQREK 327 (398)
Q Consensus 317 ~~LHN~~~~~~ 327 (398)
=.+|++-....
T Consensus 192 e~i~~~~~~~~ 202 (215)
T COG3316 192 ESIHMLYKRQR 202 (215)
T ss_pred HHHHHHHhhhh
Confidence 77788755543
No 310
>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=35.91 E-value=20 Score=31.72 Aligned_cols=41 Identities=7% Similarity=0.122 Sum_probs=32.1
Q ss_pred CCCCHHHHHHhheeccc-cccchhhhhcccccccchhhhhhh
Q 015913 79 NRIKIEEQLAIFMFIVG-HNLRTRAVQELFRYSGETISRHFN 119 (398)
Q Consensus 79 ~~~s~e~~l~~~L~~L~-~~~~~~~l~~~fgis~stv~r~~~ 119 (398)
..+++.++...+...+. .|.+...+|..+|+|+++|++++.
T Consensus 101 ~~lt~~e~a~~~~~l~~~~g~s~~~iA~~lg~s~~~V~r~l~ 142 (187)
T TIGR00180 101 EDLSPIEEAQAYKRLLEKFSMTQEDLAKKIGKSRAHITNLLR 142 (187)
T ss_pred cCCCHHHHHHHHHHHHHHhCCCHHHHHHHHCcCHHHHHHHHH
Confidence 46788777665555453 688999999999999999998764
No 311
>PRK10072 putative transcriptional regulator; Provisional
Probab=35.70 E-value=16 Score=28.74 Aligned_cols=25 Identities=12% Similarity=0.166 Sum_probs=22.2
Q ss_pred ccccchhhhhcccccccchhhhhhh
Q 015913 95 GHNLRTRAVQELFRYSGETISRHFN 119 (398)
Q Consensus 95 ~~~~~~~~l~~~fgis~stv~r~~~ 119 (398)
..|.++..+|..+|+|.+||++|.+
T Consensus 44 ~~glTQ~elA~~lGvS~~TVs~WE~ 68 (96)
T PRK10072 44 GTGLKIDDFARVLGVSVAMVKEWES 68 (96)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 4588999999999999999999865
No 312
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=35.57 E-value=31 Score=36.67 Aligned_cols=47 Identities=15% Similarity=0.115 Sum_probs=40.2
Q ss_pred CCCHHHHHHhheecc---ccccchhhhhcccccccchhhhhhhhHHHHHH
Q 015913 80 RIKIEEQLAIFMFIV---GHNLRTRAVQELFRYSGETISRHFNNVLNAIM 126 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L---~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~ 126 (398)
.++..++..+.++|. ..+.++..+|..||||++.|+.+-.+.+.-|-
T Consensus 556 ~L~~rE~~Vl~~r~g~~~~~~~tl~ei~~~lgvs~eRVrQie~~al~kLr 605 (619)
T PRK05658 556 SLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 605 (619)
T ss_pred cCCHHHHHHHHHhcCCCCCCCccHHHHHHHhCCCHHHHHHHHHHHHHHHh
Confidence 578888888888885 46789999999999999999998888777764
No 313
>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=35.55 E-value=28 Score=28.99 Aligned_cols=45 Identities=18% Similarity=0.059 Sum_probs=36.2
Q ss_pred CCHHHHHHhheecccc-ccchhhhhcccccccchhhhhhhhHHHHH
Q 015913 81 IKIEEQLAIFMFIVGH-NLRTRAVQELFRYSGETISRHFNNVLNAI 125 (398)
Q Consensus 81 ~s~e~~l~~~L~~L~~-~~~~~~l~~~fgis~stv~r~~~~v~~~l 125 (398)
+..+++-.+-|+|-.. +.++..||..+++|.+|+.++..+|=+.|
T Consensus 82 l~de~k~Ii~lry~~r~~~TW~~IA~~l~i~erta~r~~~~fK~~i 127 (130)
T PF05263_consen 82 LIDEEKRIIKLRYDRRSRRTWYQIAQKLHISERTARRWRDRFKNDI 127 (130)
T ss_pred hCHHHHHHHHHHHcccccchHHHHHHHhCccHHHHHHHHHHHHHHh
Confidence 3445676777777766 79999999999999999999988776544
No 314
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=35.53 E-value=16 Score=31.80 Aligned_cols=45 Identities=13% Similarity=0.116 Sum_probs=36.4
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHH
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 126 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~ 126 (398)
.++..|. -+|..|..|.+..+++..+++|.+||..++.+...-|.
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 4666654 35666778889999999999999999999988887663
No 315
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=35.47 E-value=31 Score=29.58 Aligned_cols=45 Identities=16% Similarity=0.218 Sum_probs=35.5
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHH
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 126 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~ 126 (398)
.+++.++=.+.+ +..|.+.+++|+..++|..||..++.+..+-+.
T Consensus 149 ~lt~~e~~vl~l--~~~g~~~~~Ia~~l~~s~~tv~~~~~~~~~kl~ 193 (211)
T PRK15369 149 LLTPRERQILKL--ITEGYTNRDIAEQLSISIKTVETHRLNMMRKLD 193 (211)
T ss_pred CCCHHHHHHHHH--HHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 366655544333 688999999999999999999999988777664
No 316
>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=34.86 E-value=15 Score=35.08 Aligned_cols=22 Identities=27% Similarity=0.108 Sum_probs=19.8
Q ss_pred chhhhhcccccccchhhhhhhh
Q 015913 99 RTRAVQELFRYSGETISRHFNN 120 (398)
Q Consensus 99 ~~~~l~~~fgis~stv~r~~~~ 120 (398)
+.++||..-|+|.+||||+++.
T Consensus 3 ti~dIA~~agvS~~TVSrvLn~ 24 (329)
T TIGR01481 3 TIYDVAREAGVSMATVSRVVNG 24 (329)
T ss_pred cHHHHHHHhCCCHHHHHHHhCC
Confidence 5679999999999999999875
No 317
>PRK11233 nitrogen assimilation transcriptional regulator; Provisional
Probab=34.47 E-value=22 Score=33.72 Aligned_cols=33 Identities=6% Similarity=0.068 Sum_probs=28.8
Q ss_pred cccccchhhhhcccccccchhhhhhhhHHHHHH
Q 015913 94 VGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 126 (398)
Q Consensus 94 L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~ 126 (398)
++...++...|...++|++|||+.+++.-..+.
T Consensus 12 v~~~~S~s~AA~~L~isQ~avS~~I~~LE~~lg 44 (305)
T PRK11233 12 IVDIGSLTQAAEVLHIAQPALSQQVATLEGELN 44 (305)
T ss_pred HHHcCCHHHHHHHhCCCchHHHHHHHHHHHHhC
Confidence 344459999999999999999999999998885
No 318
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=34.38 E-value=15 Score=35.35 Aligned_cols=22 Identities=36% Similarity=0.347 Sum_probs=19.9
Q ss_pred chhhhhcccccccchhhhhhhh
Q 015913 99 RTRAVQELFRYSGETISRHFNN 120 (398)
Q Consensus 99 ~~~~l~~~fgis~stv~r~~~~ 120 (398)
+..+||..-|+|.+||||+++.
T Consensus 3 ti~dIA~~aGVS~~TVSrvLn~ 24 (343)
T PRK10727 3 TIKDVARLAGVSVATVSRVINN 24 (343)
T ss_pred CHHHHHHHhCCCHHHHHHHhCC
Confidence 5789999999999999999974
No 319
>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=34.33 E-value=22 Score=32.78 Aligned_cols=43 Identities=12% Similarity=0.081 Sum_probs=32.2
Q ss_pred CCHHHHHHhheeccc---cccchhhhhcccccccchhhhhhhhHHH
Q 015913 81 IKIEEQLAIFMFIVG---HNLRTRAVQELFRYSGETISRHFNNVLN 123 (398)
Q Consensus 81 ~s~e~~l~~~L~~L~---~~~~~~~l~~~fgis~stv~r~~~~v~~ 123 (398)
++.-++.+-.|..++ .+.+..+|+...|+++||++|++.....
T Consensus 5 v~sl~ral~IL~~l~~~~~~~~l~eia~~lglpksT~~RlL~tL~~ 50 (248)
T TIGR02431 5 VASLARGLAVIEAFGAERPRLTLTDVAEATGLTRAAARRFLLTLVE 50 (248)
T ss_pred HHHHHHHHHHHHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 444555555566554 3578999999999999999998876654
No 320
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=33.84 E-value=22 Score=33.25 Aligned_cols=44 Identities=9% Similarity=0.099 Sum_probs=33.2
Q ss_pred CCCHHHHHHhheecccc---ccchhhhhcccccccchhhhhhhhHHH
Q 015913 80 RIKIEEQLAIFMFIVGH---NLRTRAVQELFRYSGETISRHFNNVLN 123 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~---~~~~~~l~~~fgis~stv~r~~~~v~~ 123 (398)
.+..-++.+-.|..|+. +.+..+|+...|++++|++|+++....
T Consensus 6 ~v~sl~ral~iL~~l~~~~~~ls~~eia~~lgl~kstv~RlL~tL~~ 52 (263)
T PRK09834 6 TVRGLSRGLMVLRALNRLDGGATVGLLAELTGLHRTTVRRLLETLQE 52 (263)
T ss_pred hHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 45555666666666643 368999999999999999998876654
No 321
>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=33.52 E-value=24 Score=25.48 Aligned_cols=27 Identities=22% Similarity=0.396 Sum_probs=19.1
Q ss_pred ccccchhhhhcccccc-cchhhhhhhhH
Q 015913 95 GHNLRTRAVQELFRYS-GETISRHFNNV 121 (398)
Q Consensus 95 ~~~~~~~~l~~~fgis-~stv~r~~~~v 121 (398)
+...+.++|++.||++ .+||+.++...
T Consensus 23 G~~Pt~rEIa~~~g~~S~~tv~~~L~~L 50 (65)
T PF01726_consen 23 GYPPTVREIAEALGLKSTSTVQRHLKAL 50 (65)
T ss_dssp SS---HHHHHHHHTSSSHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHhCCCChHHHHHHHHHH
Confidence 3456899999999996 88888876543
No 322
>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=33.49 E-value=19 Score=25.62 Aligned_cols=21 Identities=19% Similarity=0.343 Sum_probs=18.8
Q ss_pred ccchhhhhcccccccchhhhh
Q 015913 97 NLRTRAVQELFRYSGETISRH 117 (398)
Q Consensus 97 ~~~~~~l~~~fgis~stv~r~ 117 (398)
...+.+||+.+|||.+||.++
T Consensus 22 ~i~lkdIA~~Lgvs~~tIr~W 42 (60)
T PF10668_consen 22 KIKLKDIAEKLGVSESTIRKW 42 (60)
T ss_pred CccHHHHHHHHCCCHHHHHHH
Confidence 468999999999999999974
No 323
>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=33.19 E-value=21 Score=28.12 Aligned_cols=33 Identities=6% Similarity=-0.192 Sum_probs=27.8
Q ss_pred cccccchhhhhcccccccchhhhhhhhHHHHHH
Q 015913 94 VGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 126 (398)
Q Consensus 94 L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~ 126 (398)
+....|+...|...|+|++|+++.++..-+.+-
T Consensus 13 v~~~gSis~AA~~L~iS~stvs~~I~~LE~~lg 45 (99)
T TIGR00637 13 IARMGSISQAAKDAGISYKSAWDYIRAMNNLSG 45 (99)
T ss_pred HHHhCCHHHHHHHHCCCHHHHHHHHHHHHHHhC
Confidence 444678899999999999999999988877764
No 324
>COG3293 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=32.96 E-value=64 Score=26.14 Aligned_cols=93 Identities=19% Similarity=0.069 Sum_probs=52.9
Q ss_pred ceeeeecCCcceEEeecC-----cccccccHHHHHHHHhhcCCCCCCCCceeeccCCCCCCCCccccccCcccCcccccC
Q 015913 188 NVLAACSFDLKFHYVLAG-----WEGSASDLRVLNSALTRRNKLQVPEGKYYLVDNKYANMPGFIAPYQAVSYHTNQTTT 262 (398)
Q Consensus 188 ~~q~v~d~~~~~~~v~~g-----~~Gs~~D~~vl~~sl~~~~~~~~~~g~~~l~D~gYp~~~~ll~P~~~~~~~l~~~~~ 262 (398)
+.++++|..|+++....+ .+...+...- ..-.-.|+|.+|...++-..|-..+... .
T Consensus 2 ~~~~l~D~~~~~i~~~lp~~~~~~~~~~~~~~~-------------~~v~~~i~~~~~~g~~wr~~p~~~~~~~-----~ 63 (124)
T COG3293 2 KLHALVDAEWRPVEPLLPPAKYGGPPGVTLLRD-------------REVLNGIADLLYTGCAWRALPADFPPAT-----T 63 (124)
T ss_pred CcccccccccceeeccCCCcccCCCCCCccccc-------------HHHHHHHHHHhccchHHHHhHHHhCCCc-----e
Confidence 346788888888877765 1111111110 0012246677777666655443321110 0
Q ss_pred CCCchhHHHHHHHHHHHHHhHHHHHHHHHHhhhhhhc
Q 015913 263 GYHPQDAKELFNQRHSLLRNATDRIFGALKERFPILL 299 (398)
Q Consensus 263 ~~~~~~~~~~fN~~~s~~R~~VE~~fg~LK~rf~iL~ 299 (398)
.-.+...+.-++......|..||+.|+.+|. |+.+.
T Consensus 64 ~~~~~~~~~~~~~g~~~~~~~~~~~f~~~~~-~r~~~ 99 (124)
T COG3293 64 VIPYRRFRRWFKRGLWKRRNLVERTFGRLKQ-FRRTA 99 (124)
T ss_pred EeCCCcchhhHHHHHHHHHHHHHHHHHHHhc-cccee
Confidence 0011123677888999999999999998884 66555
No 325
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=32.61 E-value=16 Score=35.45 Aligned_cols=23 Identities=30% Similarity=0.326 Sum_probs=19.9
Q ss_pred chhhhhcccccccchhhhhhhhH
Q 015913 99 RTRAVQELFRYSGETISRHFNNV 121 (398)
Q Consensus 99 ~~~~l~~~fgis~stv~r~~~~v 121 (398)
+..++|..-|||.+||||+++.-
T Consensus 2 TikDVA~~AGVS~sTVSrvln~~ 24 (333)
T COG1609 2 TIKDVAKLAGVSKATVSRVLNGS 24 (333)
T ss_pred CHHHHHHHhCCCHHHHHHHHcCC
Confidence 46789999999999999998753
No 326
>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=32.53 E-value=19 Score=26.36 Aligned_cols=26 Identities=31% Similarity=0.285 Sum_probs=22.7
Q ss_pred cccccchhhhhcccccccchhhhhhh
Q 015913 94 VGHNLRTRAVQELFRYSGETISRHFN 119 (398)
Q Consensus 94 L~~~~~~~~l~~~fgis~stv~r~~~ 119 (398)
-..|.+..++|...|+|++|++++.+
T Consensus 15 ~~~~~t~~~lA~~~gis~~tis~~~~ 40 (78)
T TIGR02607 15 EPLGLSIRALAKALGVSRSTLSRIVN 40 (78)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 45678899999999999999999765
No 327
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=32.44 E-value=29 Score=32.59 Aligned_cols=45 Identities=7% Similarity=-0.042 Sum_probs=35.9
Q ss_pred CCCCHHHHHHhheecccc---ccchhhhhcccccccchhhhhhhhHHH
Q 015913 79 NRIKIEEQLAIFMFIVGH---NLRTRAVQELFRYSGETISRHFNNVLN 123 (398)
Q Consensus 79 ~~~s~e~~l~~~L~~L~~---~~~~~~l~~~fgis~stv~r~~~~v~~ 123 (398)
..++.-++.+-.|..++. +.+..+|+...|+++||++|+++..+.
T Consensus 19 ~~~~sl~r~l~IL~~~~~~~~~~tl~eIa~~lglpkStv~RlL~tL~~ 66 (271)
T PRK10163 19 KGAQALERGIAILQYLEKSGGSSSVSDISLNLDLPLSTTFRLLKVLQA 66 (271)
T ss_pred ccchHHHHHHHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 357777777777777753 467999999999999999998876665
No 328
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=32.33 E-value=24 Score=27.01 Aligned_cols=24 Identities=17% Similarity=0.260 Sum_probs=20.1
Q ss_pred hhhhhcccccccchhhhhhhhHHH
Q 015913 100 TRAVQELFRYSGETISRHFNNVLN 123 (398)
Q Consensus 100 ~~~l~~~fgis~stv~r~~~~v~~ 123 (398)
..+++..+|+|++|+++.+.....
T Consensus 2 ~~ela~~l~is~stvs~~l~~L~~ 25 (96)
T smart00529 2 TSEIAERLNVSPPTVTQMLKKLEK 25 (96)
T ss_pred HHHHHHHhCCChHHHHHHHHHHHH
Confidence 468899999999999998876655
No 329
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=32.18 E-value=26 Score=33.40 Aligned_cols=41 Identities=15% Similarity=0.113 Sum_probs=34.6
Q ss_pred HHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHH
Q 015913 86 QLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 126 (398)
Q Consensus 86 ~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~ 126 (398)
++-+|+....+|.|+...|...++|++|||+.+++.-..+.
T Consensus 5 ~L~~f~~v~~~g~S~s~AA~~L~isQpavS~~ik~LE~~lg 45 (313)
T PRK12684 5 QLRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEDELG 45 (313)
T ss_pred HHHHHHHHHHcCCCHHHHHHHhcCCChHHHHHHHHHHHHhC
Confidence 45555555666779999999999999999999999999886
No 330
>COG5606 Uncharacterized conserved small protein [Function unknown]
Probab=32.05 E-value=9.6 Score=29.10 Aligned_cols=64 Identities=19% Similarity=0.264 Sum_probs=40.7
Q ss_pred CHHHHHHHHHHHhcCCccccCCCCCHHHHHH--hheeccccccchhhhhcccccccchhhhhhhhHHH
Q 015913 58 DKKVFYKLCDILQSKGLLRHTNRIKIEEQLA--IFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLN 123 (398)
Q Consensus 58 s~~~F~~L~~~l~~~~~~~~~~~~s~e~~l~--~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~ 123 (398)
+-++|..+.+.+.+.... ...+-...++. +.+|.=-.+.++..++..+||+++.||...+--+.
T Consensus 2 ~~~vF~s~~~~~~D~~e~--a~~m~ir~~l~~~i~~~i~q~~l~Q~qiae~lgV~qprvS~l~~gk~~ 67 (91)
T COG5606 2 SNEVFTSVWDAIEDTPEA--AENMKIRSALMMAIKQWIEQAALSQAQIAELLGVTQPRVSDLARGKIQ 67 (91)
T ss_pred CCchhhhHHHHHhccHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCchHHHHHhcchh
Confidence 345677777777653211 12233334443 44444566789999999999999999987665444
No 331
>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=31.27 E-value=35 Score=27.68 Aligned_cols=28 Identities=21% Similarity=0.090 Sum_probs=23.8
Q ss_pred ccccccchhhhhcccccccchhhhhhhh
Q 015913 93 IVGHNLRTRAVQELFRYSGETISRHFNN 120 (398)
Q Consensus 93 ~L~~~~~~~~l~~~fgis~stv~r~~~~ 120 (398)
+-..|.++.++|..+|+|++|++++-+-
T Consensus 74 r~~~gltq~~lA~~lg~~~~tis~~e~g 101 (127)
T TIGR03830 74 RKKLGLSQREAAELLGGGVNAFSRYERG 101 (127)
T ss_pred HHHcCCCHHHHHHHhCCCHHHHHHHHCC
Confidence 4456899999999999999999997653
No 332
>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=31.25 E-value=23 Score=22.93 Aligned_cols=25 Identities=16% Similarity=0.174 Sum_probs=18.7
Q ss_pred cccchhhhhcccccccchhhhhhhh
Q 015913 96 HNLRTRAVQELFRYSGETISRHFNN 120 (398)
Q Consensus 96 ~~~~~~~l~~~fgis~stv~r~~~~ 120 (398)
++......|...|||++|+.+-+.+
T Consensus 17 ~~gn~~~aA~~Lgisr~tL~~klkk 41 (42)
T PF02954_consen 17 CGGNVSKAARLLGISRRTLYRKLKK 41 (42)
T ss_dssp TTT-HHHHHHHHTS-HHHHHHHHHH
T ss_pred hCCCHHHHHHHHCCCHHHHHHHHHh
Confidence 3556779999999999999987654
No 333
>PRK11050 manganese transport regulator MntR; Provisional
Probab=31.10 E-value=28 Score=29.63 Aligned_cols=28 Identities=11% Similarity=0.170 Sum_probs=24.2
Q ss_pred cccchhhhhcccccccchhhhhhhhHHH
Q 015913 96 HNLRTRAVQELFRYSGETISRHFNNVLN 123 (398)
Q Consensus 96 ~~~~~~~l~~~fgis~stv~r~~~~v~~ 123 (398)
.+.+..+++..+++|++||++.+.+...
T Consensus 50 ~~~t~~eLA~~l~is~stVsr~l~~Le~ 77 (152)
T PRK11050 50 GEARQVDIAARLGVSQPTVAKMLKRLAR 77 (152)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4678999999999999999998876654
No 334
>PRK14087 dnaA chromosomal replication initiation protein; Provisional
Probab=30.91 E-value=38 Score=34.51 Aligned_cols=48 Identities=13% Similarity=0.106 Sum_probs=43.6
Q ss_pred CCCCHHHHHHhheeccccccchhhhhcccc-cccchhhhhhhhHHHHHH
Q 015913 79 NRIKIEEQLAIFMFIVGHNLRTRAVQELFR-YSGETISRHFNNVLNAIM 126 (398)
Q Consensus 79 ~~~s~e~~l~~~L~~L~~~~~~~~l~~~fg-is~stv~r~~~~v~~~l~ 126 (398)
+.+...-|+||.|.+=-++.|+.++|..|| .+.|||...++++-+.+.
T Consensus 383 ~~i~~~RqiamyL~r~~t~~sl~~IG~~FggrdHsTV~~a~~ki~~~~~ 431 (450)
T PRK14087 383 KSIVTARHIAMYLTKEILNHTLAQIGEEFGGRDHTTVINAERKIEKMLK 431 (450)
T ss_pred ccccHHHHHHHHHHHHHcCCCHHHHHHHhCCCChHHHHHHHHHHHHHHH
Confidence 468888999999999889999999999997 999999999999888774
No 335
>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=30.79 E-value=34 Score=30.57 Aligned_cols=39 Identities=15% Similarity=0.324 Sum_probs=29.1
Q ss_pred HHHHHhheeccccccchhhhhcccccccchhhhhhhhHHH
Q 015913 84 EEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLN 123 (398)
Q Consensus 84 e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~ 123 (398)
..+++..|..- .+.+..+|+..+|++.+||++++....+
T Consensus 3 r~~IL~~L~~~-~~~t~~eLA~~lgis~~tV~~~L~~Le~ 41 (203)
T TIGR02702 3 KEDILSYLLKQ-GQATAAALAEALAISPQAVRRHLKDLET 41 (203)
T ss_pred HHHHHHHHHHc-CCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 34555555543 3588999999999999999998766544
No 336
>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=30.63 E-value=20 Score=26.67 Aligned_cols=24 Identities=21% Similarity=0.128 Sum_probs=18.0
Q ss_pred ccchhhhhcccccccchhhhhhhh
Q 015913 97 NLRTRAVQELFRYSGETISRHFNN 120 (398)
Q Consensus 97 ~~~~~~l~~~fgis~stv~r~~~~ 120 (398)
..+..++|...|+|++||.|..+.
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 467889999999999999986543
No 337
>PF07453 NUMOD1: NUMOD1 domain; InterPro: IPR010896 This helix-turn-helix-containing DNA-binding domain is found associated in homing nucleases [].
Probab=30.26 E-value=21 Score=22.33 Aligned_cols=22 Identities=23% Similarity=0.147 Sum_probs=18.4
Q ss_pred ccchhhhhcccccccchhhhhh
Q 015913 97 NLRTRAVQELFRYSGETISRHF 118 (398)
Q Consensus 97 ~~~~~~l~~~fgis~stv~r~~ 118 (398)
-.|.++.+..+|++.+|+++++
T Consensus 16 F~Si~eAa~~l~i~~~~I~~~l 37 (37)
T PF07453_consen 16 FDSIREAARYLGISHSTISKYL 37 (37)
T ss_pred EcCHHHHHHHhCCCHHHHHHhC
Confidence 3578889999999999998764
No 338
>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=29.45 E-value=22 Score=24.03 Aligned_cols=21 Identities=38% Similarity=0.447 Sum_probs=16.8
Q ss_pred chhhhhcccccccchhhhhhh
Q 015913 99 RTRAVQELFRYSGETISRHFN 119 (398)
Q Consensus 99 ~~~~l~~~fgis~stv~r~~~ 119 (398)
+..+++...|+|++|+.+.++
T Consensus 5 ~~~ev~~~~g~s~~ti~~~~k 25 (51)
T PF05930_consen 5 RIKEVAELLGVSRSTIYRLIK 25 (51)
T ss_dssp -HHHHHHHHSS-HHHHHHHHH
T ss_pred cHHHHHHHHCCCHHHHHHHHh
Confidence 457899999999999999776
No 339
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=29.40 E-value=42 Score=29.72 Aligned_cols=42 Identities=7% Similarity=0.032 Sum_probs=28.0
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhH
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNV 121 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v 121 (398)
++++.+-..+...+-..|.++.+|+...+++++|+++++.+.
T Consensus 42 gLt~~q~~iL~~L~~~~~itq~eLa~~l~l~~sTvtr~l~rL 83 (185)
T PRK13777 42 DLNINEHHILWIAYHLKGASISEIAKFGVMHVSTAFNFSKKL 83 (185)
T ss_pred CCCHHHHHHHHHHHhCCCcCHHHHHHHHCCCHhhHHHHHHHH
Confidence 355544433322223347889999999999999998866543
No 340
>PRK09726 antitoxin HipB; Provisional
Probab=29.11 E-value=22 Score=27.15 Aligned_cols=27 Identities=19% Similarity=0.122 Sum_probs=23.3
Q ss_pred cccccchhhhhcccccccchhhhhhhh
Q 015913 94 VGHNLRTRAVQELFRYSGETISRHFNN 120 (398)
Q Consensus 94 L~~~~~~~~l~~~fgis~stv~r~~~~ 120 (398)
-..|.+..++|...|+|++|++++.+.
T Consensus 22 ~~~gltq~elA~~~gvs~~tis~~e~g 48 (88)
T PRK09726 22 QQNGWTQSELAKKIGIKQATISNFENN 48 (88)
T ss_pred HHcCCCHHHHHHHHCcCHHHHHHHHCC
Confidence 356889999999999999999998763
No 341
>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=28.28 E-value=25 Score=27.15 Aligned_cols=24 Identities=13% Similarity=0.166 Sum_probs=17.6
Q ss_pred cccchhhhhcccccccchhhhhhh
Q 015913 96 HNLRTRAVQELFRYSGETISRHFN 119 (398)
Q Consensus 96 ~~~~~~~l~~~fgis~stv~r~~~ 119 (398)
.|.+..+||.++|.|++.|++++.
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 578899999999999999998664
No 342
>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=28.26 E-value=43 Score=27.62 Aligned_cols=46 Identities=13% Similarity=0.138 Sum_probs=32.3
Q ss_pred ccCCCCCHHHHHHhh-eeccccccchhhhhcccccccchhhhhhhhHHH
Q 015913 76 RHTNRIKIEEQLAIF-MFIVGHNLRTRAVQELFRYSGETISRHFNNVLN 123 (398)
Q Consensus 76 ~~~~~~s~e~~l~~~-L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~ 123 (398)
.+++.++-+.+.-+. |. ..|.+..+++..+.||.++|++++.++-+
T Consensus 13 ~nGrPLp~~~R~rIvela--~~G~rp~~Isr~l~Vs~gcVsKIl~Ry~e 59 (125)
T PF00292_consen 13 INGRPLPNELRQRIVELA--KEGVRPCDISRQLRVSHGCVSKILSRYRE 59 (125)
T ss_dssp ETTSSS-HHHHHHHHHHH--HTT--HHHHHHHHT--HHHHHHHHHHHHH
T ss_pred eCCccCcHHHHHHHHHHh--hhcCCHHHHHHHHccchhHHHHHHHHHHH
Confidence 356778888876655 43 35999999999999999999999988754
No 343
>COG1342 Predicted DNA-binding proteins [General function prediction only]
Probab=27.78 E-value=57 Score=25.51 Aligned_cols=46 Identities=17% Similarity=0.126 Sum_probs=33.4
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHH
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 126 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~ 126 (398)
.++++|-=++=|.-+ .|.++.+.|.+.|||+.|+.+.++..-.-+.
T Consensus 33 ~lt~eElEAlRLvD~-~~l~QeeAA~rMgISr~Tfwr~l~sAR~KvA 78 (99)
T COG1342 33 ILTIEELEALRLVDY-EGLTQEEAALRMGISRQTFWRLLTSARKKVA 78 (99)
T ss_pred eecHHHHHHHHHHhH-hhccHHHHHHHhcccHHHHHHHHHHHHHHHH
Confidence 355666555555444 2788999999999999999998876555443
No 344
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=27.49 E-value=34 Score=32.28 Aligned_cols=40 Identities=15% Similarity=0.223 Sum_probs=32.2
Q ss_pred HHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHH
Q 015913 86 QLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 126 (398)
Q Consensus 86 ~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~ 126 (398)
++-+|+....+| |+...|+..++|+++||+.+++.-..+.
T Consensus 5 ~L~~f~~v~~~g-S~s~AA~~L~itQpavS~~i~~LE~~lg 44 (305)
T PRK11151 5 DLEYLVALAEHR-HFRRAADSCHVSQPTLSGQIRKLEDELG 44 (305)
T ss_pred HHHHHHHHHHhC-CHHHHHHHhCCCchHHHHHHHHHHHHhC
Confidence 344444445555 9999999999999999999999998885
No 345
>PRK12422 chromosomal replication initiation protein; Provisional
Probab=27.40 E-value=44 Score=34.00 Aligned_cols=47 Identities=11% Similarity=0.217 Sum_probs=42.8
Q ss_pred CCCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHH
Q 015913 79 NRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAI 125 (398)
Q Consensus 79 ~~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l 125 (398)
+.+...-|++|.|.+=-++.|+.++|..||.+.|||...++++-+.+
T Consensus 379 ~~i~~~Rqiamyl~r~~t~~s~~~IG~~fgrdHsTV~~a~~ki~~~~ 425 (445)
T PRK12422 379 REYVLPRQVAMYLCRQKLSLSYVKIGDVFSRDHSTVISSIRAISQKL 425 (445)
T ss_pred cccccHHHHHHHHHHHhcCCCHHHHHHHhCCChHHHHHHHHHHHHHH
Confidence 46778889999999988999999999999999999999998888777
No 346
>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=26.98 E-value=25 Score=23.03 Aligned_cols=21 Identities=14% Similarity=-0.013 Sum_probs=17.2
Q ss_pred chhhhhcccccccchhhhhhh
Q 015913 99 RTRAVQELFRYSGETISRHFN 119 (398)
Q Consensus 99 ~~~~l~~~fgis~stv~r~~~ 119 (398)
+..++|..+|++.+|+..+..
T Consensus 2 ~~~e~a~~~gv~~~tlr~~~~ 22 (49)
T cd04761 2 TIGELAKLTGVSPSTLRYYER 22 (49)
T ss_pred cHHHHHHHHCcCHHHHHHHHH
Confidence 456789999999999998753
No 347
>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=26.85 E-value=28 Score=27.75 Aligned_cols=29 Identities=17% Similarity=0.219 Sum_probs=22.0
Q ss_pred ccchhhhhcccccccchhhhhhhhHHHHH
Q 015913 97 NLRTRAVQELFRYSGETISRHFNNVLNAI 125 (398)
Q Consensus 97 ~~~~~~l~~~fgis~stv~r~~~~v~~~l 125 (398)
|.+..+||..||+|..+|.++++++-...
T Consensus 72 G~n~~eLA~kyglS~r~I~~Ii~~~~~~~ 100 (108)
T PF08765_consen 72 GMNVRELARKYGLSERQIYRIIKRVRRRE 100 (108)
T ss_dssp SS-HHHHHHHHT--HHHHHHHHHHHHH--
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 88899999999999999999998876543
No 348
>PRK11569 transcriptional repressor IclR; Provisional
Probab=26.85 E-value=42 Score=31.56 Aligned_cols=45 Identities=4% Similarity=0.053 Sum_probs=34.8
Q ss_pred CCCCHHHHHHhheecccc---ccchhhhhcccccccchhhhhhhhHHH
Q 015913 79 NRIKIEEQLAIFMFIVGH---NLRTRAVQELFRYSGETISRHFNNVLN 123 (398)
Q Consensus 79 ~~~s~e~~l~~~L~~L~~---~~~~~~l~~~fgis~stv~r~~~~v~~ 123 (398)
..++.-++.+-.|..|+. +.+..+|+...|+++||++|+++..+.
T Consensus 22 ~~v~sl~ral~IL~~l~~~~~~~~lseia~~lglpksTv~RlL~tL~~ 69 (274)
T PRK11569 22 GQVQSLTRGLKLLEWIAESNGSVALTELAQQAGLPNSTTHRLLTTMQQ 69 (274)
T ss_pred cCccHHHHHHHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 346666776666766653 468999999999999999998876555
No 349
>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=26.79 E-value=47 Score=29.67 Aligned_cols=27 Identities=22% Similarity=0.277 Sum_probs=22.9
Q ss_pred ccchhhhhcccccccchhhhhhhhHHH
Q 015913 97 NLRTRAVQELFRYSGETISRHFNNVLN 123 (398)
Q Consensus 97 ~~~~~~l~~~fgis~stv~r~~~~v~~ 123 (398)
+.+..++++.+|+|++|+++.+....+
T Consensus 157 ~~s~~eia~~l~is~stv~r~L~~Le~ 183 (203)
T TIGR01884 157 EKSVKNIAKKLGKSLSTISRHLRELEK 183 (203)
T ss_pred CcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 468999999999999999988776543
No 350
>PF14493 HTH_40: Helix-turn-helix domain
Probab=26.70 E-value=30 Score=26.57 Aligned_cols=36 Identities=14% Similarity=0.235 Sum_probs=29.9
Q ss_pred hheeccccccchhhhhcccccccchhhhhhhhHHHH
Q 015913 89 IFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNA 124 (398)
Q Consensus 89 ~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~ 124 (398)
.++.++..|.+..++|..-|++.+||..++-+....
T Consensus 5 ~T~~l~~~G~si~eIA~~R~L~~sTI~~HL~~~~~~ 40 (91)
T PF14493_consen 5 ITYELFQKGLSIEEIAKIRGLKESTIYGHLAELIES 40 (91)
T ss_pred HHHHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHHHh
Confidence 456667789999999999999999999887666554
No 351
>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=26.52 E-value=32 Score=29.86 Aligned_cols=26 Identities=19% Similarity=0.270 Sum_probs=22.0
Q ss_pred cchhhhhcccccccchhhhhhhhHHH
Q 015913 98 LRTRAVQELFRYSGETISRHFNNVLN 123 (398)
Q Consensus 98 ~~~~~l~~~fgis~stv~r~~~~v~~ 123 (398)
.++++++..+|+|++||+|.+....+
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 46889999999999999998876554
No 352
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=26.13 E-value=1.3e+02 Score=28.83 Aligned_cols=76 Identities=17% Similarity=0.204 Sum_probs=45.2
Q ss_pred HHHhhcCCCHHHHHHHHHHHhcCCccccCCCCCHHHHHHhhee----ccccccchhhhhcccccccchhhhhhhhHHHHH
Q 015913 50 RCLENFRMDKKVFYKLCDILQSKGLLRHTNRIKIEEQLAIFMF----IVGHNLRTRAVQELFRYSGETISRHFNNVLNAI 125 (398)
Q Consensus 50 ~f~~~frms~~~F~~L~~~l~~~~~~~~~~~~s~e~~l~~~L~----~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l 125 (398)
.|-..++++...-..-...++......-..+-+|.--.+.++| ..+...++++++...||+..|+.+..++....+
T Consensus 225 r~~~~L~L~~~v~~~A~~i~~~a~~~~l~~Gr~P~sIAAAaIYlA~~~~g~~~t~keIa~v~~Vs~~tI~~~ykel~~~l 304 (310)
T PRK00423 225 RFASELGLSGEVQKKAIEILQKAKEKGLTSGKGPTGLAAAAIYIASLLLGERRTQREVAEVAGVTEVTVRNRYKELAEKL 304 (310)
T ss_pred HHHHHcCCCHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHHHHHh
Confidence 3445566665544443433332111011123444444444443 456678999999999999999998888887755
No 353
>COG2186 FadR Transcriptional regulators [Transcription]
Probab=26.04 E-value=67 Score=29.62 Aligned_cols=45 Identities=20% Similarity=0.276 Sum_probs=28.7
Q ss_pred CCHHHHHHHHHHHhcCCccccCCCCCHHHHHHhheeccccccchhhhhcccccccchhhhhh
Q 015913 57 MDKKVFYKLCDILQSKGLLRHTNRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHF 118 (398)
Q Consensus 57 ms~~~F~~L~~~l~~~~~~~~~~~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~ 118 (398)
+....+..|-..|... .++.+..+|.| +++++.||||+++|...+
T Consensus 11 l~~~v~~~i~~~I~~g-~~~~G~~LP~E----------------reLae~fgVSR~~vREAl 55 (241)
T COG2186 11 LADEVAEQIGALIVSG-ELPPGDRLPSE----------------RELAERFGVSRTVVREAL 55 (241)
T ss_pred hHHHHHHHHHHHHHcC-CCCCCCCCCCH----------------HHHHHHHCCCcHHHHHHH
Confidence 4445556666666542 33344445554 678899999999987644
No 354
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=25.78 E-value=50 Score=25.88 Aligned_cols=29 Identities=24% Similarity=0.261 Sum_probs=24.4
Q ss_pred ccccchhhhhcccccccchhhhhhhhHHH
Q 015913 95 GHNLRTRAVQELFRYSGETISRHFNNVLN 123 (398)
Q Consensus 95 ~~~~~~~~l~~~fgis~stv~r~~~~v~~ 123 (398)
....+..++|..+|+|..+++|.|++.+.
T Consensus 19 ~~~~~~~~lA~~~~~S~~~l~r~f~~~~g 47 (107)
T PRK10219 19 DQPLNIDVVAKKSGYSKWYLQRMFRTVTH 47 (107)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHC
Confidence 34567889999999999999999998743
No 355
>PRK12681 cysB transcriptional regulator CysB; Reviewed
Probab=25.64 E-value=39 Score=32.48 Aligned_cols=41 Identities=27% Similarity=0.270 Sum_probs=33.4
Q ss_pred HHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHH
Q 015913 86 QLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 126 (398)
Q Consensus 86 ~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~ 126 (398)
++-.|+....+|.|+...|...++|++|||+.+++.-..+.
T Consensus 5 ~L~~f~avae~g~S~s~AA~~L~iSQpavS~~I~~LE~~lG 45 (324)
T PRK12681 5 QLRYIVEVVNHNLNVSATAEGLYTSQPGISKQVRMLEDELG 45 (324)
T ss_pred HHHHHHHHHHccCCHHHHHHHhcCCcHHHHHHHHHHHHHhC
Confidence 34444444556679999999999999999999999999885
No 356
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=25.61 E-value=36 Score=27.94 Aligned_cols=30 Identities=23% Similarity=0.225 Sum_probs=25.4
Q ss_pred cccccchhhhhcccccccchhhhhhhhHHH
Q 015913 94 VGHNLRTRAVQELFRYSGETISRHFNNVLN 123 (398)
Q Consensus 94 L~~~~~~~~l~~~fgis~stv~r~~~~v~~ 123 (398)
+....+..++|..+|+|+.++.+.|++.+.
T Consensus 22 ~~~~~sl~~lA~~~g~S~~~l~r~Fk~~~G 51 (127)
T PRK11511 22 LESPLSLEKVSERSGYSKWHLQRMFKKETG 51 (127)
T ss_pred cCCCCCHHHHHHHHCcCHHHHHHHHHHHHC
Confidence 445678889999999999999999998844
No 357
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=25.54 E-value=46 Score=30.91 Aligned_cols=45 Identities=9% Similarity=0.141 Sum_probs=33.1
Q ss_pred CCCCHHHHHHhheecccc--ccchhhhhcccccccchhhhhhhhHHH
Q 015913 79 NRIKIEEQLAIFMFIVGH--NLRTRAVQELFRYSGETISRHFNNVLN 123 (398)
Q Consensus 79 ~~~s~e~~l~~~L~~L~~--~~~~~~l~~~fgis~stv~r~~~~v~~ 123 (398)
..++.-++.+-.|..|+. +.+..+|+...|+++||++|+++..+.
T Consensus 8 ~~v~sl~r~l~IL~~l~~~~~l~l~eia~~lgl~kstv~Rll~tL~~ 54 (257)
T PRK15090 8 DSVSSVLKVFGILQALGEEREIGITELSQRVMMSKSTVYRFLQTMKT 54 (257)
T ss_pred cccHHHHHHHHHHHHhhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 345666666666655543 367899999999999999998776554
No 358
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=24.94 E-value=30 Score=28.69 Aligned_cols=26 Identities=19% Similarity=0.216 Sum_probs=22.4
Q ss_pred ccccchhhhhcccccccchhhhhhhh
Q 015913 95 GHNLRTRAVQELFRYSGETISRHFNN 120 (398)
Q Consensus 95 ~~~~~~~~l~~~fgis~stv~r~~~~ 120 (398)
..|.++.++|...|||++||+++.+.
T Consensus 16 ~~gltq~~lA~~~gvs~~~is~~E~g 41 (135)
T PRK09706 16 QLKLSQRSLAKAVKVSHVSISQWERD 41 (135)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 45788999999999999999997644
No 359
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=24.75 E-value=39 Score=30.66 Aligned_cols=34 Identities=9% Similarity=0.041 Sum_probs=29.7
Q ss_pred ccccccchhhhhcccccccchhhhhhhhHHHHHH
Q 015913 93 IVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 126 (398)
Q Consensus 93 ~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~ 126 (398)
.++.|.+..++|..+++|..||..++....+...
T Consensus 174 ~~~~g~s~~eIA~~l~iS~~Tv~~~~~~~~~~~~ 207 (239)
T PRK10430 174 HQDYEFSTDELANAVNISRVSCRKYLIWLVNCHI 207 (239)
T ss_pred CCCCCcCHHHHHHHhCchHHHHHHHHHHHHhCCE
Confidence 3578999999999999999999999988877653
No 360
>PRK11013 DNA-binding transcriptional regulator LysR; Provisional
Probab=24.23 E-value=41 Score=31.90 Aligned_cols=39 Identities=21% Similarity=0.230 Sum_probs=30.5
Q ss_pred HHhheeccccccchhhhhcccccccchhhhhhhhHHHHHH
Q 015913 87 LAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 126 (398)
Q Consensus 87 l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~ 126 (398)
+-+|+.... ..|+...|+..++|+++||+.+++.-+-+.
T Consensus 9 L~~f~av~~-~gS~s~AAe~L~isqsavS~~Ik~LE~~lg 47 (309)
T PRK11013 9 IEIFHAVMT-AGSLTEAARLLHTSQPTVSRELARFEKVIG 47 (309)
T ss_pred HHHHHHHHH-hCcHHHHHHHHCCCcHHHHHHHHHHHHHhC
Confidence 333333333 348999999999999999999999998875
No 361
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=24.20 E-value=31 Score=29.87 Aligned_cols=45 Identities=16% Similarity=0.207 Sum_probs=36.4
Q ss_pred CCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHH
Q 015913 80 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 126 (398)
Q Consensus 80 ~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~ 126 (398)
.++..|... |.+|+.|.+..+++...++|..||..++.+...-|.
T Consensus 149 ~lt~re~~v--l~~l~~g~s~~eIa~~l~~s~~tv~~~~~~~~~kl~ 193 (210)
T PRK09935 149 VLSNREVTI--LRYLVSGLSNKEIADQLLLSNKTVSAHKSNIYGKLG 193 (210)
T ss_pred cCCHHHHHH--HHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence 456655544 456888999999999999999999999988877663
No 362
>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=24.11 E-value=41 Score=31.35 Aligned_cols=39 Identities=10% Similarity=0.072 Sum_probs=30.8
Q ss_pred HHhheeccccccchhhhhcccccccchhhhhhhhHHHHHH
Q 015913 87 LAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 126 (398)
Q Consensus 87 l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~ 126 (398)
+-.|+.... ..++...|+..++|++++|+.+++.-+.+.
T Consensus 6 L~~f~~v~~-~gs~s~AA~~L~itqpavS~~Ik~LE~~lg 44 (291)
T TIGR03418 6 LRVFESAAR-LASFTAAARELGSTQPAVSQQVKRLEEELG 44 (291)
T ss_pred HHHHHHHHH-hCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 333443333 448999999999999999999999998875
No 363
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=23.89 E-value=44 Score=31.47 Aligned_cols=33 Identities=9% Similarity=0.244 Sum_probs=28.5
Q ss_pred cccccchhhhhcccccccchhhhhhhhHHHHHH
Q 015913 94 VGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 126 (398)
Q Consensus 94 L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~ 126 (398)
++...++...|+..++|++|||+.+++.-..+.
T Consensus 16 v~~~gs~s~AA~~L~isQ~avS~~i~~LE~~lG 48 (302)
T PRK09791 16 VARQGSIRGASRMLNMSQPALTKSIQELEEGLA 48 (302)
T ss_pred HHHcCCHHHHHHHhCCChHHHHHHHHHHHHHhC
Confidence 333448999999999999999999999999885
No 364
>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]
Probab=23.65 E-value=60 Score=32.56 Aligned_cols=49 Identities=18% Similarity=0.185 Sum_probs=44.3
Q ss_pred CCCCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhhHHHHHH
Q 015913 78 TNRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 126 (398)
Q Consensus 78 ~~~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~ 126 (398)
++.+...-|++|.|.+--++.|+..+|..||...+||...++++.+.+.
T Consensus 346 ~~~i~~~RqiamyL~r~lt~~Slp~IG~~FgrdHtTV~~a~~kI~~~~~ 394 (408)
T COG0593 346 TRNIVRPRQIAMYLARELTNLSLPEIGKAFGRDHTTVLHAVRKIEQLIE 394 (408)
T ss_pred ccccchHHHHHHHHHHHHccCcHHHHHHHhCCCccHHHHHHHHHHHHHh
Confidence 3578888899999999999999999999999999999999988888775
No 365
>COG3139 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.63 E-value=1.5e+02 Score=22.46 Aligned_cols=43 Identities=14% Similarity=0.289 Sum_probs=30.6
Q ss_pred CCCHHHHHHHHHHHhcCCccccCCCCCHHHH----HHhheeccccccc
Q 015913 56 RMDKKVFYKLCDILQSKGLLRHTNRIKIEEQ----LAIFMFIVGHNLR 99 (398)
Q Consensus 56 rms~~~F~~L~~~l~~~~~~~~~~~~s~e~~----l~~~L~~L~~~~~ 99 (398)
-|+++.+.+|...+.--.+ .++..++.|++ =++.||-+.||..
T Consensus 9 ~mtPEiYQrL~~AvElGKW-PdG~~LtqeQke~clQaVmlwqarhN~~ 55 (90)
T COG3139 9 SMTPEIYQRLSTAVELGKW-PDGVALTQEQKENCLQAVMLWQARHNTE 55 (90)
T ss_pred hcCHHHHHHHHHHHHhcCC-CCCCcCCHHHHHHHHHHHHHHHHhcCCh
Confidence 5889999999988875333 46677888777 2456777777654
No 366
>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=23.60 E-value=31 Score=24.79 Aligned_cols=22 Identities=18% Similarity=0.182 Sum_probs=15.8
Q ss_pred chhhhhcccccccchhh-hhhhh
Q 015913 99 RTRAVQELFRYSGETIS-RHFNN 120 (398)
Q Consensus 99 ~~~~l~~~fgis~stv~-r~~~~ 120 (398)
+..++|+..|||++|++ .+.++
T Consensus 14 ~~~~lA~~lgis~st~s~~~~~r 36 (66)
T PF07022_consen 14 SDKELAERLGISKSTLSNNWKKR 36 (66)
T ss_dssp SCHHHHCCTT--HHHHH-HHHHS
T ss_pred CHHHHHHHhCcCHHHhhHHHHhC
Confidence 44599999999999999 55543
No 367
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=23.60 E-value=40 Score=31.56 Aligned_cols=36 Identities=14% Similarity=0.237 Sum_probs=30.4
Q ss_pred eeccccccchhhhhcccccccchhhhhhhhHHHHHH
Q 015913 91 MFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 126 (398)
Q Consensus 91 L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~ 126 (398)
+..++...++...|...++|+++||+.+++.-+.+.
T Consensus 9 f~~v~~~gs~s~AA~~L~isQ~avSr~i~~LE~~lg 44 (296)
T PRK09906 9 FVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVG 44 (296)
T ss_pred HHHHHhhCCHHHHHHHhCCCCcHHHHHHHHHHHHhC
Confidence 344455569999999999999999999999999875
No 368
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=23.53 E-value=48 Score=26.08 Aligned_cols=23 Identities=13% Similarity=0.300 Sum_probs=20.3
Q ss_pred hhhhcccccccchhhhhhhhHHH
Q 015913 101 RAVQELFRYSGETISRHFNNVLN 123 (398)
Q Consensus 101 ~~l~~~fgis~stv~r~~~~v~~ 123 (398)
.+++...+++++|+++.+++...
T Consensus 40 ~~la~~l~i~~~~vt~~l~~Le~ 62 (126)
T COG1846 40 KELAERLGLDRSTVTRLLKRLED 62 (126)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHH
Confidence 89999999999999998876654
No 369
>PRK10094 DNA-binding transcriptional activator AllS; Provisional
Probab=23.05 E-value=43 Score=31.81 Aligned_cols=33 Identities=15% Similarity=-0.012 Sum_probs=28.5
Q ss_pred cccccchhhhhcccccccchhhhhhhhHHHHHH
Q 015913 94 VGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 126 (398)
Q Consensus 94 L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~ 126 (398)
++...++...|...++|+++||+.+++.-..+.
T Consensus 13 v~e~gs~s~AA~~L~iSQpavS~~I~~LE~~lg 45 (308)
T PRK10094 13 VAETGSFSKAAERLCKTTATISYRIKLLEENTG 45 (308)
T ss_pred HHHhCCHHHHHHHhcCCHHHHHHHHHHHHHHhC
Confidence 334458999999999999999999999988875
No 370
>COG2973 TrpR Trp operon repressor [Transcription]
Probab=23.00 E-value=42 Score=26.29 Aligned_cols=26 Identities=23% Similarity=0.261 Sum_probs=22.7
Q ss_pred ccccccchhhhhcccccccchhhhhh
Q 015913 93 IVGHNLRTRAVQELFRYSGETISRHF 118 (398)
Q Consensus 93 ~L~~~~~~~~l~~~fgis~stv~r~~ 118 (398)
.|....|+|+++..+|+|.+|+-|=-
T Consensus 56 LL~ge~sQREi~~~LgvsiAtITRGS 81 (103)
T COG2973 56 LLRGELSQREIAQKLGVSIATITRGS 81 (103)
T ss_pred HHhccccHHHHHHHhCcchhhhccch
Confidence 47788999999999999999997743
No 371
>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=22.78 E-value=36 Score=24.13 Aligned_cols=22 Identities=23% Similarity=0.117 Sum_probs=18.3
Q ss_pred chhhhhcccccccchhhhhhhh
Q 015913 99 RTRAVQELFRYSGETISRHFNN 120 (398)
Q Consensus 99 ~~~~l~~~fgis~stv~r~~~~ 120 (398)
+..++|..+|||.+|+.++.++
T Consensus 2 s~~eva~~~gvs~~tlr~w~~~ 23 (68)
T cd01104 2 TIGAVARLTGVSPDTLRAWERR 23 (68)
T ss_pred CHHHHHHHHCcCHHHHHHHHHh
Confidence 4568999999999999987653
No 372
>COG0664 Crp cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]
Probab=22.69 E-value=43 Score=29.14 Aligned_cols=45 Identities=31% Similarity=0.497 Sum_probs=36.1
Q ss_pred CCCCHHHHHHhheecccc--------------ccchhhhhcccccccchhhhhhhhHHH
Q 015913 79 NRIKIEEQLAIFMFIVGH--------------NLRTRAVQELFRYSGETISRHFNNVLN 123 (398)
Q Consensus 79 ~~~s~e~~l~~~L~~L~~--------------~~~~~~l~~~fgis~stv~r~~~~v~~ 123 (398)
...++.++++.+|..++. ..+...++...|+++.|+++.+.++..
T Consensus 139 ~~~~~~~r~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~ia~~~g~~~~~vsr~l~~l~~ 197 (214)
T COG0664 139 ARKDVEERLARFLLNLGRRLGIATEDGILIPLPLTHKDLAEYLGLSRETVSRILKELRK 197 (214)
T ss_pred hhccHHHHHHHHHHHHhhccCCCCCCCcEEeccCCHHHHHHHhCCchhhHHHHHHHHHh
Confidence 357888999988888763 467888999999999999998876654
No 373
>PRK12680 transcriptional regulator CysB-like protein; Reviewed
Probab=22.66 E-value=49 Score=31.87 Aligned_cols=38 Identities=8% Similarity=0.135 Sum_probs=30.9
Q ss_pred hheeccccccchhhhhcccccccchhhhhhhhHHHHHH
Q 015913 89 IFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 126 (398)
Q Consensus 89 ~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~ 126 (398)
+|+....++.|+...|...++|++|||+.+++.-+.+.
T Consensus 8 ~F~~vae~~gS~s~AA~~L~isQpavS~~I~~LE~~lG 45 (327)
T PRK12680 8 YLVAIADAELNITLAAARVHATQPGLSKQLKQLEDELG 45 (327)
T ss_pred HHHHHHHccCCHHHHHHHhcCCchHHHHHHHHHHHHhC
Confidence 33333333578999999999999999999999999886
No 374
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=22.57 E-value=53 Score=30.44 Aligned_cols=26 Identities=15% Similarity=0.275 Sum_probs=22.1
Q ss_pred cchhhhhcccccccchhhhhhhhHHH
Q 015913 98 LRTRAVQELFRYSGETISRHFNNVLN 123 (398)
Q Consensus 98 ~~~~~l~~~fgis~stv~r~~~~v~~ 123 (398)
.+..+++...|+++||++|++.....
T Consensus 20 l~l~ela~~~glpksT~~RlL~tL~~ 45 (246)
T COG1414 20 LSLAELAERLGLPKSTVHRLLQTLVE 45 (246)
T ss_pred CCHHHHHHHhCcCHHHHHHHHHHHHH
Confidence 45999999999999999998766554
No 375
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=22.40 E-value=69 Score=27.16 Aligned_cols=27 Identities=15% Similarity=0.106 Sum_probs=23.0
Q ss_pred ccchhhhhcccccccchhhhhhhhHHH
Q 015913 97 NLRTRAVQELFRYSGETISRHFNNVLN 123 (398)
Q Consensus 97 ~~~~~~l~~~fgis~stv~r~~~~v~~ 123 (398)
-.|+.++|...|+|++||.+-+++..+
T Consensus 23 R~s~~eiA~~lglS~~tV~~Ri~rL~~ 49 (153)
T PRK11179 23 RTPYAELAKQFGVSPGTIHVRVEKMKQ 49 (153)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 478999999999999999987766554
No 376
>smart00497 IENR1 Intron encoded nuclease repeat motif. Repeat of unknown function, but possibly DNA-binding via helix-turn-helix motif (Ponting, unpublished).
Probab=22.37 E-value=38 Score=22.67 Aligned_cols=24 Identities=21% Similarity=0.218 Sum_probs=20.1
Q ss_pred ccchhhhhcccccccchhhhhhhh
Q 015913 97 NLRTRAVQELFRYSGETISRHFNN 120 (398)
Q Consensus 97 ~~~~~~l~~~fgis~stv~r~~~~ 120 (398)
-.|..+.+..+|++.++++++++.
T Consensus 17 f~S~~eAa~~lg~~~~~I~~~~~~ 40 (53)
T smart00497 17 FSSIREAAKYLGISHSSISKYLNT 40 (53)
T ss_pred ecCHHHHHHHhCCCHHHHHHHHhC
Confidence 357888999999999999987753
No 377
>PRK09940 transcriptional regulator YdeO; Provisional
Probab=22.30 E-value=91 Score=29.12 Aligned_cols=89 Identities=6% Similarity=0.139 Sum_probs=53.6
Q ss_pred CcchhhHHHHHhcCChhHHHhhcCCCHHHHHHHHHHHhcCCcc---ccCCCCCHHHHHH-hheeccccccchhhhhcccc
Q 015913 33 PSNGMKFVDEVLNGQSERCLENFRMDKKVFYKLCDILQSKGLL---RHTNRIKIEEQLA-IFMFIVGHNLRTRAVQELFR 108 (398)
Q Consensus 33 ~~~~~~~~~~i~~~~d~~f~~~frms~~~F~~L~~~l~~~~~~---~~~~~~s~e~~l~-~~L~~L~~~~~~~~l~~~fg 108 (398)
......|+..++..-..+-...-+++...|..|+..+...... ......+...++. +....+....+..++|..+|
T Consensus 82 ~~~~~~~L~~ll~~l~~e~~~~~~l~~~ll~~lL~~l~~~~~~~~~l~~~~~~~~~kv~~~I~~~~~~~~tl~~LA~~~g 161 (253)
T PRK09940 82 SNVPTGLLNEMIAYLNSEERNHHNFSELLLFSCLSIFAACKGFITLLTNGVLSVSGKVRNIVNMKLAHPWKLKDICDCLY 161 (253)
T ss_pred CCCCHHHHHHHHHHHHhcchhhhHHHHHHHHHHHHHHHhCccHHHhhccccccHHHHHHHHHHHhhcCCCCHHHHHHHHC
Confidence 4445566666554322222122267777777777766542211 1123344444443 33345677789999999999
Q ss_pred cccchhhhhhhhH
Q 015913 109 YSGETISRHFNNV 121 (398)
Q Consensus 109 is~stv~r~~~~v 121 (398)
+|+++.+|.|++.
T Consensus 162 mS~s~l~R~FK~~ 174 (253)
T PRK09940 162 ISESLLKKKLKQE 174 (253)
T ss_pred cCHHHHHHHHHHc
Confidence 9999999999863
No 378
>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B.
Probab=22.23 E-value=33 Score=24.38 Aligned_cols=26 Identities=12% Similarity=0.127 Sum_probs=18.9
Q ss_pred chhhhhcccccccchhhhhhhhHHHHH
Q 015913 99 RTRAVQELFRYSGETISRHFNNVLNAI 125 (398)
Q Consensus 99 ~~~~l~~~fgis~stv~r~~~~v~~~l 125 (398)
+...+|..+|||+++|+.+ ...+.+.
T Consensus 11 ~~~~lAkalGVs~~aVs~W-~~~IP~~ 36 (60)
T PF14549_consen 11 GQSKLAKALGVSPQAVSQW-GERIPAE 36 (60)
T ss_dssp SHHHHHHHHTS-HHHHHHH-HTS--HH
T ss_pred CHHHHHHHHCCCHHHHHHh-cCccCHH
Confidence 5678999999999999999 5555543
No 379
>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=21.76 E-value=51 Score=32.01 Aligned_cols=42 Identities=7% Similarity=0.090 Sum_probs=34.0
Q ss_pred CCCCHHHHHHhheeccccccchhhhhcccccccchhhhhhhh
Q 015913 79 NRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNN 120 (398)
Q Consensus 79 ~~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~ 120 (398)
..+|+.|+.......+..|.+...++..+|+++++|++++.-
T Consensus 159 ~dLS~iE~A~~~~~L~~~G~~~~~ia~~Lg~~ks~vSr~lsl 200 (325)
T TIGR03454 159 RDLSFIERALFAQRLEDRGFDRDTIMAALSVDKTELSRMISV 200 (325)
T ss_pred cCCCHHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 468887876655666678888889999999999999997753
No 380
>PRK15421 DNA-binding transcriptional regulator MetR; Provisional
Probab=21.63 E-value=51 Score=31.53 Aligned_cols=39 Identities=10% Similarity=0.159 Sum_probs=31.2
Q ss_pred HHhheeccccccchhhhhcccccccchhhhhhhhHHHHHH
Q 015913 87 LAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 126 (398)
Q Consensus 87 l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~ 126 (398)
+-.|+....+| ++...|+..++|++|||+.+++.-+.+.
T Consensus 7 L~~f~av~~~g-s~s~AA~~L~iSqpaVS~~Ik~LE~~lg 45 (317)
T PRK15421 7 LKTLQALRNCG-SLAAAAATLHQTQSALSHQFSDLEQRLG 45 (317)
T ss_pred HHHHHHHHHcC-CHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 34444444444 8999999999999999999999988885
No 381
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=21.63 E-value=41 Score=21.46 Aligned_cols=24 Identities=29% Similarity=0.272 Sum_probs=20.3
Q ss_pred cccchhhhhcccccccchhhhhhh
Q 015913 96 HNLRTRAVQELFRYSGETISRHFN 119 (398)
Q Consensus 96 ~~~~~~~l~~~fgis~stv~r~~~ 119 (398)
.+.+..+++...|++.++++++.+
T Consensus 9 ~~~s~~~la~~~~i~~~~i~~~~~ 32 (56)
T smart00530 9 KGLTQEELAEKLGVSRSTLSRIEN 32 (56)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHC
Confidence 577889999999999999987654
No 382
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=21.41 E-value=36 Score=30.64 Aligned_cols=29 Identities=14% Similarity=0.119 Sum_probs=24.2
Q ss_pred eecccc---ccchhhhhcccccccchhhhhhh
Q 015913 91 MFIVGH---NLRTRAVQELFRYSGETISRHFN 119 (398)
Q Consensus 91 L~~L~~---~~~~~~l~~~fgis~stv~r~~~ 119 (398)
|..++. |.+.+++|...++|..||.+++.
T Consensus 168 l~~~~~g~~g~s~~eIa~~l~iS~~Tv~~~~~ 199 (225)
T PRK10046 168 RKLFKEPGVQHTAETVAQALTISRTTARRYLE 199 (225)
T ss_pred HHHHHcCCCCcCHHHHHHHhCccHHHHHHHHH
Confidence 444455 58999999999999999999885
No 383
>PF01476 LysM: LysM domain; InterPro: IPR018392 This domain is about 40 residues long and is found in a variety of enzymes involved in bacterial cell wall degradation []. This domain may have a general peptidoglycan binding function.; GO: 0016998 cell wall macromolecule catabolic process; PDB: 2DJP_A 3ZQD_A 1Y7M_B 4A52_A 2L9Y_A 1E0G_A.
Probab=21.28 E-value=41 Score=21.43 Aligned_cols=24 Identities=8% Similarity=0.054 Sum_probs=16.2
Q ss_pred ccccccchhhhhcccccccchhhh
Q 015913 93 IVGHNLRTRAVQELFRYSGETISR 116 (398)
Q Consensus 93 ~L~~~~~~~~l~~~fgis~stv~r 116 (398)
....|.+...||.+||++...+.+
T Consensus 2 ~V~~gDtl~~IA~~~~~~~~~l~~ 25 (44)
T PF01476_consen 2 TVQPGDTLWSIAKRYGISVDELME 25 (44)
T ss_dssp EE-TT--HHHHHHHTTS-HHHHHH
T ss_pred EECcCCcHHHHHhhhhhhHhHHHH
Confidence 456788999999999998877765
No 384
>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=21.20 E-value=42 Score=27.52 Aligned_cols=26 Identities=12% Similarity=0.142 Sum_probs=22.2
Q ss_pred cchhhhhcccccccchhhhhhhhHHH
Q 015913 98 LRTRAVQELFRYSGETISRHFNNVLN 123 (398)
Q Consensus 98 ~~~~~l~~~fgis~stv~r~~~~v~~ 123 (398)
.+..+++..+|+|++++.+++....+
T Consensus 26 ~s~~eia~~l~is~~~v~~~l~~L~~ 51 (130)
T TIGR02944 26 YSAAEIAEQTGLNAPTVSKILKQLSL 51 (130)
T ss_pred ccHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 58899999999999999997766554
No 385
>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=21.09 E-value=45 Score=23.54 Aligned_cols=42 Identities=17% Similarity=0.190 Sum_probs=28.2
Q ss_pred CCCCHHHHHHhheecccccc---chhhhhcccccccchhhhhhhh
Q 015913 79 NRIKIEEQLAIFMFIVGHNL---RTRAVQELFRYSGETISRHFNN 120 (398)
Q Consensus 79 ~~~s~e~~l~~~L~~L~~~~---~~~~l~~~fgis~stv~r~~~~ 120 (398)
+..+++-+|-+.-+...++. .++..|..|+|++..|.++...
T Consensus 4 rsy~~~FKL~Vv~~a~~~~nc~~~~RAaarkf~V~r~~Vr~W~kq 48 (58)
T PF09607_consen 4 RSYTAEFKLKVVEYAEKDNNCKGNQRAAARKFNVSRRQVRKWRKQ 48 (58)
T ss_dssp ----HHHHHHHHHHHHH-TTTTT-HHHHHHHTTS-HHHHHHHHTT
T ss_pred cccChHHHHHHHHHHHHccchhhhHHHHHHHhCccHHHHHHHHHH
Confidence 45677778877777777765 5699999999999998877643
No 386
>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=21.07 E-value=40 Score=23.60 Aligned_cols=26 Identities=27% Similarity=0.267 Sum_probs=19.6
Q ss_pred ccccchhhhhcccccccchhhhhhhh
Q 015913 95 GHNLRTRAVQELFRYSGETISRHFNN 120 (398)
Q Consensus 95 ~~~~~~~~l~~~fgis~stv~r~~~~ 120 (398)
..|.++.++|...|+++++++++.+.
T Consensus 10 ~~~lt~~~~a~~~~i~~~~i~~~e~g 35 (64)
T PF12844_consen 10 EKGLTQKDLAEKLGISRSTISKIENG 35 (64)
T ss_dssp HCT--HHHHHHHHTS-HHHHHHHHTT
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHCC
Confidence 45788999999999999999988754
No 387
>PHA02701 ORF020 dsRNA-binding PKR inhibitor; Provisional
Probab=20.99 E-value=65 Score=28.40 Aligned_cols=40 Identities=13% Similarity=0.223 Sum_probs=29.3
Q ss_pred HHHHHhheeccccccchhhhhcccccccchhhhhhhhHHH
Q 015913 84 EEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLN 123 (398)
Q Consensus 84 e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~~v~~ 123 (398)
+.+++-+|..-+.+.+..+|+..+|+++++|.|.+.+..+
T Consensus 6 ~~~i~~~l~~~~~~~~a~~i~k~l~i~k~~vNr~LY~L~~ 45 (183)
T PHA02701 6 ASLILTLLSSSGDKLPAKRIAKELGISKHEANRCLYRLLE 45 (183)
T ss_pred HHHHHHHHHhcCCCCcHHHHHHHhCccHHHHHHHHHHHhh
Confidence 4455556665555578889999999999999887655433
No 388
>PRK08558 adenine phosphoribosyltransferase; Provisional
Probab=20.98 E-value=47 Score=30.71 Aligned_cols=36 Identities=6% Similarity=0.063 Sum_probs=30.5
Q ss_pred HHHHHhheeccccccchhhhhcccccccchhhhhhh
Q 015913 84 EEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFN 119 (398)
Q Consensus 84 e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~~ 119 (398)
.-++.-.|..|....+|++++..+|++.+.++||++
T Consensus 10 ~~~~v~~lr~lk~~~ty~el~~~~g~p~~~l~RYv~ 45 (238)
T PRK08558 10 QLRAVRVLRSLKKTYTYEELSSITGLPESVLNRYVN 45 (238)
T ss_pred HHHHHHHHHHHhcccCHHHHHHHHCCCHHHHHHHHc
Confidence 344566777888888999999999999999999875
No 389
>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=20.89 E-value=78 Score=25.11 Aligned_cols=27 Identities=19% Similarity=0.194 Sum_probs=17.7
Q ss_pred ccchhhhhccc-----ccccchhhhhhhhHHH
Q 015913 97 NLRTRAVQELF-----RYSGETISRHFNNVLN 123 (398)
Q Consensus 97 ~~~~~~l~~~f-----gis~stv~r~~~~v~~ 123 (398)
..+..+|.+.. ++|.+||+|.++.+.+
T Consensus 16 ~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~ 47 (116)
T cd07153 16 HLTAEEIYERLRKKGPSISLATVYRTLELLEE 47 (116)
T ss_pred CCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHh
Confidence 34455554443 7999999997765544
No 390
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=20.86 E-value=53 Score=30.64 Aligned_cols=32 Identities=13% Similarity=0.127 Sum_probs=28.1
Q ss_pred ccccchhhhhcccccccchhhhhhhhHHHHHH
Q 015913 95 GHNLRTRAVQELFRYSGETISRHFNNVLNAIM 126 (398)
Q Consensus 95 ~~~~~~~~l~~~fgis~stv~r~~~~v~~~l~ 126 (398)
....++...|+..++|+++||+.+++.-+.+.
T Consensus 13 ~~~gs~s~AA~~L~isqsavS~~i~~LE~~lg 44 (296)
T PRK11242 13 AEHGNFTRAAEALHVSQPTLSQQIRQLEESLG 44 (296)
T ss_pred HHhCCHHHHHHHcCCCchHHHHHHHHHHHHhC
Confidence 34458999999999999999999999998875
No 391
>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=20.80 E-value=62 Score=28.67 Aligned_cols=27 Identities=7% Similarity=0.107 Sum_probs=22.0
Q ss_pred ccchhhhhcccccc-cchhhhhhhhHHH
Q 015913 97 NLRTRAVQELFRYS-GETISRHFNNVLN 123 (398)
Q Consensus 97 ~~~~~~l~~~fgis-~stv~r~~~~v~~ 123 (398)
+.+.+++|..+|++ ++||++.+....+
T Consensus 25 ~~~~~ela~~~~~~s~~tv~~~l~~L~~ 52 (199)
T TIGR00498 25 PPSIREIARAVGLRSPSAAEEHLKALER 52 (199)
T ss_pred CCcHHHHHHHhCCCChHHHHHHHHHHHH
Confidence 46788999999998 9999987765544
No 392
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=20.60 E-value=53 Score=27.65 Aligned_cols=36 Identities=14% Similarity=0.113 Sum_probs=26.4
Q ss_pred cchhhhhcccccccchhhhhhh--h-HHHHHHHhhcccc
Q 015913 98 LRTRAVQELFRYSGETISRHFN--N-VLNAIMAISLDFF 133 (398)
Q Consensus 98 ~~~~~l~~~fgis~stv~r~~~--~-v~~~l~~~~~~~i 133 (398)
.++..+|...||+++|+++|-+ + |+..+..+..+++
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 6799999999999999999984 3 6666665555443
No 393
>PRK13832 plasmid partitioning protein; Provisional
Probab=20.56 E-value=69 Score=32.99 Aligned_cols=41 Identities=10% Similarity=0.044 Sum_probs=36.1
Q ss_pred CCCCCHHHHHHhheeccccccchhhhhcccccccchhhhhh
Q 015913 78 TNRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHF 118 (398)
Q Consensus 78 ~~~~s~e~~l~~~L~~L~~~~~~~~l~~~fgis~stv~r~~ 118 (398)
+..+++-++...+-..+..|.+..+||..||+|+++|.+..
T Consensus 99 RedL~PiEea~AfkrLie~G~T~EeIA~~lG~S~~~V~rll 139 (520)
T PRK13832 99 REPLNPVDQWRAIERLVALGWTEEAIAVALALPVRQIRKLR 139 (520)
T ss_pred cCCCCHHHHHHHHHHHHhcCCCHHHHHHHHCCCHHHHHHHH
Confidence 35789999988888888999999999999999999999743
No 394
>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=20.50 E-value=41 Score=28.70 Aligned_cols=27 Identities=0% Similarity=-0.081 Sum_probs=23.7
Q ss_pred ccccccchhhhhcccccccchhhhhhh
Q 015913 93 IVGHNLRTRAVQELFRYSGETISRHFN 119 (398)
Q Consensus 93 ~L~~~~~~~~l~~~fgis~stv~r~~~ 119 (398)
+-..|.+..++|.+.|||++||+++-+
T Consensus 34 R~~lGmTq~eLAerlGVS~~tIs~iE~ 60 (150)
T TIGR02612 34 RKALGMSGAQLAGRLGVTPQRVEALEK 60 (150)
T ss_pred HHHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 556689999999999999999998664
No 395
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=20.46 E-value=39 Score=26.90 Aligned_cols=23 Identities=13% Similarity=0.104 Sum_probs=18.9
Q ss_pred ccccchhhhhcccccccchhhhh
Q 015913 95 GHNLRTRAVQELFRYSGETISRH 117 (398)
Q Consensus 95 ~~~~~~~~l~~~fgis~stv~r~ 117 (398)
+.|.|+.+.|..+|+|.+||..|
T Consensus 55 ~~~lSQ~vFA~~L~vs~~Tv~~W 77 (104)
T COG2944 55 KLGLSQPVFARYLGVSVSTVRKW 77 (104)
T ss_pred HhCCCHHHHHHHHCCCHHHHHHH
Confidence 45788888899999999998864
No 396
>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=20.30 E-value=47 Score=28.61 Aligned_cols=34 Identities=15% Similarity=0.080 Sum_probs=28.0
Q ss_pred cccchhhhhcccccccchhhhhhhhHHHHHHHhh
Q 015913 96 HNLRTRAVQELFRYSGETISRHFNNVLNAIMAIS 129 (398)
Q Consensus 96 ~~~~~~~l~~~fgis~stv~r~~~~v~~~l~~~~ 129 (398)
++.+.++|+..-|+|++|++++|..--..+....
T Consensus 27 ~~~s~~~IA~~agvsk~~ly~~F~sK~~L~~~~~ 60 (189)
T TIGR03384 27 LDVTIAQIARRAGVSSGIISHYFGGKQGLLEATM 60 (189)
T ss_pred ccCCHHHHHHHhCCCHHHHHHHcCCHHHHHHHHH
Confidence 4688999999999999999999977666655433
Done!