Query 016400
Match_columns 390
No_of_seqs 254 out of 1666
Neff 8.5
Searched_HMMs 46136
Date Fri Mar 29 06:31:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/016400.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/016400hhsearch_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 2.1E-43 4.5E-48 334.6 19.3 311 46-385 7-324 (326)
2 PF04827 Plant_tran: Plant tra 100.0 2.7E-43 5.8E-48 300.3 5.8 187 123-322 2-204 (205)
3 PF13359 DDE_Tnp_4: DDE superf 100.0 3E-37 6.6E-42 267.0 3.2 153 153-313 1-158 (158)
4 PF13613 HTH_Tnp_4: Helix-turn 98.9 1.1E-09 2.4E-14 76.1 4.7 49 72-120 2-50 (53)
5 PF13612 DDE_Tnp_1_3: Transpos 98.9 3.2E-10 6.9E-15 96.7 0.9 126 147-291 4-149 (155)
6 PF01609 DDE_Tnp_1: Transposas 98.1 9.9E-08 2.2E-12 85.2 -5.4 162 148-314 4-213 (213)
7 PF13586 DDE_Tnp_1_2: Transpos 97.2 0.00017 3.6E-09 55.7 1.4 48 262-310 36-84 (88)
8 PF13936 HTH_38: Helix-turn-he 96.3 0.0033 7.2E-08 41.6 2.4 41 71-112 3-43 (44)
9 PF04545 Sigma70_r4: Sigma-70, 96.2 0.01 2.2E-07 40.3 4.6 45 72-117 4-48 (50)
10 PF04218 CENP-B_N: CENP-B N-te 95.6 0.014 3.1E-07 40.2 3.2 42 70-112 4-45 (53)
11 PF08281 Sigma70_r4_2: Sigma-7 95.5 0.028 6.1E-07 38.7 4.5 44 72-116 10-53 (54)
12 PF02796 HTH_7: Helix-turn-hel 95.4 0.0052 1.1E-07 40.9 0.6 35 78-112 10-44 (45)
13 PF13384 HTH_23: Homeodomain-l 95.0 0.014 3E-07 39.6 1.6 30 85-114 13-42 (50)
14 PF12116 SpoIIID: Stage III sp 94.7 0.028 6E-07 41.6 2.6 43 76-118 5-48 (82)
15 PF13518 HTH_28: Helix-turn-he 94.5 0.036 7.9E-07 37.6 2.9 37 78-115 2-38 (52)
16 PF05225 HTH_psq: helix-turn-h 94.0 0.056 1.2E-06 35.9 2.8 37 76-112 2-39 (45)
17 smart00351 PAX Paired Box doma 93.8 0.094 2E-06 43.2 4.4 44 71-115 16-59 (125)
18 COG3415 Transposase and inacti 93.5 0.073 1.6E-06 44.4 3.2 43 73-115 5-47 (138)
19 PF13011 LZ_Tnp_IS481: leucine 93.4 0.11 2.4E-06 39.4 3.7 45 71-115 7-51 (85)
20 PF13340 DUF4096: Putative tra 93.3 0.17 3.7E-06 37.5 4.6 66 50-116 2-67 (75)
21 cd00131 PAX Paired Box domain 93.0 0.15 3.2E-06 42.2 4.3 45 70-115 15-59 (128)
22 PRK09413 IS2 repressor TnpA; R 92.7 0.18 3.9E-06 41.2 4.4 46 69-114 9-54 (121)
23 PF01527 HTH_Tnp_1: Transposas 92.7 0.11 2.3E-06 38.5 2.7 45 70-114 4-48 (76)
24 smart00421 HTH_LUXR helix_turn 92.6 0.23 4.9E-06 33.9 4.3 43 73-117 4-46 (58)
25 PRK04217 hypothetical protein; 92.6 0.23 5.1E-06 39.7 4.8 48 71-119 41-88 (110)
26 TIGR02531 yecD_yerC TrpR-relat 92.3 0.17 3.8E-06 38.8 3.6 34 76-110 38-71 (88)
27 cd06171 Sigma70_r4 Sigma70, re 91.7 0.29 6.3E-06 32.7 3.9 43 73-116 11-53 (55)
28 PRK00118 putative DNA-binding 91.3 0.4 8.7E-06 38.0 4.7 47 72-119 17-63 (104)
29 PRK09639 RNA polymerase sigma 91.0 0.36 7.9E-06 41.3 4.7 48 72-121 112-159 (166)
30 PF02209 VHP: Villin headpiece 90.5 0.18 3.8E-06 31.7 1.6 21 38-58 2-22 (36)
31 PF13542 HTH_Tnp_ISL3: Helix-t 90.0 0.28 6.1E-06 33.3 2.5 31 83-113 21-51 (52)
32 PRK12529 RNA polymerase sigma 89.9 0.54 1.2E-05 41.0 4.8 48 72-120 127-174 (178)
33 TIGR03879 near_KaiC_dom probab 89.6 0.4 8.6E-06 35.3 3.1 42 72-113 15-56 (73)
34 cd06170 LuxR_C_like C-terminal 89.6 0.72 1.6E-05 31.4 4.4 32 86-117 12-43 (57)
35 PRK09652 RNA polymerase sigma 89.2 0.57 1.2E-05 40.4 4.5 50 72-122 128-177 (182)
36 PRK08301 sporulation sigma fac 89.0 0.69 1.5E-05 42.2 5.0 50 72-121 178-230 (234)
37 cd00569 HTH_Hin_like Helix-tur 88.9 0.48 1E-05 28.7 2.8 37 73-110 6-42 (42)
38 PF12802 MarR_2: MarR family; 88.8 0.81 1.8E-05 32.1 4.2 38 78-115 9-47 (62)
39 smart00153 VHP Villin headpiec 88.7 0.31 6.8E-06 30.6 1.7 20 38-57 2-21 (36)
40 PRK12519 RNA polymerase sigma 88.6 0.56 1.2E-05 41.3 4.0 50 72-122 141-190 (194)
41 PF01022 HTH_5: Bacterial regu 88.4 0.7 1.5E-05 30.7 3.5 38 78-115 4-41 (47)
42 PRK12522 RNA polymerase sigma 88.0 0.77 1.7E-05 39.7 4.4 53 72-125 119-171 (173)
43 PRK05911 RNA polymerase sigma 88.0 0.81 1.8E-05 42.6 4.8 51 72-123 205-255 (257)
44 TIGR02989 Sig-70_gvs1 RNA poly 87.6 1.5 3.3E-05 37.0 6.0 47 72-119 111-157 (159)
45 PRK07037 extracytoplasmic-func 87.6 0.97 2.1E-05 38.5 4.8 48 72-120 109-156 (163)
46 TIGR02999 Sig-70_X6 RNA polyme 87.5 1 2.2E-05 39.2 4.9 47 72-119 134-180 (183)
47 TIGR02952 Sig70_famx2 RNA poly 87.5 0.98 2.1E-05 38.6 4.8 47 72-119 122-168 (170)
48 PRK09415 RNA polymerase factor 87.5 0.91 2E-05 39.5 4.6 49 72-121 127-175 (179)
49 cd06571 Bac_DnaA_C C-terminal 87.4 1 2.2E-05 34.6 4.3 48 71-118 26-74 (90)
50 PRK09047 RNA polymerase factor 87.3 0.98 2.1E-05 38.3 4.7 48 72-120 106-153 (161)
51 PRK12537 RNA polymerase sigma 87.3 1 2.2E-05 39.3 4.8 47 72-119 133-179 (182)
52 COG1595 RpoE DNA-directed RNA 87.2 1.5 3.4E-05 38.2 6.0 49 72-121 127-175 (182)
53 TIGR00721 tfx DNA-binding prot 87.2 0.94 2E-05 37.8 4.2 45 72-118 6-50 (137)
54 PF00356 LacI: Bacterial regul 87.2 0.34 7.4E-06 32.3 1.3 21 92-112 2-22 (46)
55 PF01325 Fe_dep_repress: Iron 87.2 1.1 2.4E-05 31.7 4.0 41 75-115 5-48 (60)
56 PF04967 HTH_10: HTH DNA bindi 87.1 0.59 1.3E-05 32.1 2.5 30 89-118 23-52 (53)
57 PRK12530 RNA polymerase sigma 87.0 0.87 1.9E-05 40.1 4.3 48 72-120 134-181 (189)
58 PF00196 GerE: Bacterial regul 87.0 0.64 1.4E-05 32.4 2.7 37 82-118 11-47 (58)
59 PRK12511 RNA polymerase sigma 87.0 1 2.3E-05 39.4 4.7 51 72-123 111-161 (182)
60 PF13412 HTH_24: Winged helix- 86.8 1.2 2.5E-05 29.6 3.9 37 78-115 7-43 (48)
61 PRK12528 RNA polymerase sigma 86.7 0.96 2.1E-05 38.5 4.3 46 72-118 113-158 (161)
62 PRK12514 RNA polymerase sigma 86.7 1.1 2.5E-05 38.8 4.8 48 72-120 129-176 (179)
63 PRK05803 sporulation sigma fac 86.7 1.1 2.5E-05 40.8 5.0 48 72-119 175-225 (233)
64 PRK12547 RNA polymerase sigma 86.6 1.2 2.6E-05 38.2 4.8 47 72-119 112-158 (164)
65 PRK15320 transcriptional activ 86.6 0.57 1.2E-05 41.3 2.7 38 81-118 171-208 (251)
66 TIGR02983 SigE-fam_strep RNA p 86.5 1.1 2.5E-05 38.0 4.7 48 72-120 110-157 (162)
67 PF13751 DDE_Tnp_1_6: Transpos 86.5 0.3 6.5E-06 39.9 0.9 50 266-316 73-123 (125)
68 TIGR02985 Sig70_bacteroi1 RNA 86.5 1.1 2.3E-05 37.8 4.4 46 72-118 113-158 (161)
69 PRK12533 RNA polymerase sigma 86.4 1.1 2.4E-05 40.5 4.7 49 72-121 134-182 (216)
70 PRK12525 RNA polymerase sigma 86.4 1.3 2.8E-05 38.1 4.9 47 72-119 118-164 (168)
71 TIGR01321 TrpR trp operon repr 86.3 0.77 1.7E-05 35.6 3.0 40 73-112 33-78 (94)
72 TIGR02937 sigma70-ECF RNA poly 86.2 1.2 2.5E-05 36.8 4.5 46 72-118 110-155 (158)
73 PRK09642 RNA polymerase sigma 86.2 1.2 2.7E-05 37.7 4.7 48 72-120 106-153 (160)
74 PRK12516 RNA polymerase sigma 86.1 1.2 2.6E-05 39.1 4.7 50 72-122 116-165 (187)
75 PRK09638 RNA polymerase sigma 86.1 0.82 1.8E-05 39.5 3.5 47 72-119 126-172 (176)
76 PRK09641 RNA polymerase sigma 85.6 1.3 2.8E-05 38.6 4.6 48 72-120 136-183 (187)
77 PRK12524 RNA polymerase sigma 85.6 1.3 2.9E-05 39.1 4.7 48 72-120 136-183 (196)
78 TIGR02950 SigM_subfam RNA poly 85.5 0.65 1.4E-05 39.1 2.6 48 72-120 105-152 (154)
79 PRK13919 putative RNA polymera 85.5 1.5 3.2E-05 38.3 4.9 47 72-119 135-181 (186)
80 TIGR03697 NtcA_cyano global ni 85.4 0.58 1.3E-05 41.0 2.3 80 37-116 72-170 (193)
81 PF05344 DUF746: Domain of Unk 85.3 1.1 2.5E-05 31.9 3.2 43 78-120 2-44 (65)
82 PRK03975 tfx putative transcri 85.3 1.5 3.2E-05 36.8 4.5 46 71-118 5-50 (141)
83 PRK11923 algU RNA polymerase s 85.3 1.2 2.7E-05 39.1 4.3 52 72-124 138-189 (193)
84 TIGR02844 spore_III_D sporulat 85.1 0.82 1.8E-05 34.4 2.6 37 76-112 5-42 (80)
85 TIGR02835 spore_sigmaE RNA pol 85.1 1.6 3.5E-05 39.9 5.1 49 72-120 178-229 (234)
86 PRK07408 RNA polymerase sigma 85.0 1.5 3.2E-05 40.8 4.9 48 72-120 203-250 (256)
87 PRK11924 RNA polymerase sigma 85.0 1.4 3E-05 37.8 4.5 48 72-120 125-172 (179)
88 PF01047 MarR: MarR family; I 84.9 1.5 3.3E-05 30.3 3.9 36 79-115 8-43 (59)
89 TIGR02392 rpoH_proteo alternat 84.8 1.6 3.4E-05 40.9 5.1 48 72-119 218-266 (270)
90 PRK06759 RNA polymerase factor 84.8 1.4 3.1E-05 37.0 4.4 46 72-118 106-151 (154)
91 PRK12515 RNA polymerase sigma 84.7 1.5 3.3E-05 38.4 4.6 48 72-120 131-178 (189)
92 PRK12531 RNA polymerase sigma 84.6 1.6 3.5E-05 38.5 4.7 47 72-119 141-187 (194)
93 PRK09637 RNA polymerase sigma 84.5 1.7 3.8E-05 37.9 4.9 51 72-123 106-156 (181)
94 TIGR02939 RpoE_Sigma70 RNA pol 84.4 1.5 3.3E-05 38.3 4.5 50 72-122 138-187 (190)
95 PRK12534 RNA polymerase sigma 84.4 1.8 3.8E-05 37.9 4.9 48 72-120 137-184 (187)
96 PRK09645 RNA polymerase sigma 84.4 1.8 3.8E-05 37.3 4.9 48 72-120 118-165 (173)
97 PF08279 HTH_11: HTH domain; 84.4 1.6 3.5E-05 29.8 3.7 39 79-117 5-43 (55)
98 PHA00675 hypothetical protein 84.3 1.1 2.3E-05 33.1 2.8 40 72-111 22-61 (78)
99 PF01371 Trp_repressor: Trp re 84.3 1.3 2.7E-05 33.9 3.4 36 77-112 37-72 (87)
100 PRK12523 RNA polymerase sigma 84.2 1.8 3.8E-05 37.4 4.8 46 72-118 119-164 (172)
101 PRK12536 RNA polymerase sigma 84.2 1.7 3.6E-05 37.9 4.7 47 72-119 129-175 (181)
102 PRK12520 RNA polymerase sigma 84.1 1.7 3.7E-05 38.1 4.8 48 72-120 131-178 (191)
103 PF13730 HTH_36: Helix-turn-he 84.1 1.5 3.3E-05 29.9 3.5 43 73-115 3-51 (55)
104 PF07374 DUF1492: Protein of u 84.1 1.5 3.2E-05 34.5 3.8 43 74-117 57-99 (100)
105 PF00872 Transposase_mut: Tran 83.8 0.72 1.6E-05 45.6 2.4 132 82-242 107-247 (381)
106 TIGR02984 Sig-70_plancto1 RNA 83.7 2 4.3E-05 37.4 5.0 48 72-120 140-187 (189)
107 TIGR02959 SigZ RNA polymerase 83.7 1.9 4.1E-05 37.2 4.7 51 72-123 100-150 (170)
108 PRK09651 RNA polymerase sigma 83.6 1.7 3.7E-05 37.5 4.4 49 72-121 119-167 (172)
109 COG2739 Uncharacterized protei 83.6 1.9 4.2E-05 33.6 4.0 42 76-118 21-62 (105)
110 PRK12541 RNA polymerase sigma 83.5 1.7 3.6E-05 37.0 4.3 47 72-119 112-158 (161)
111 PRK09649 RNA polymerase sigma 83.5 1.5 3.3E-05 38.4 4.1 47 72-119 130-176 (185)
112 PF13551 HTH_29: Winged helix- 83.4 0.98 2.1E-05 35.7 2.6 34 82-115 4-38 (112)
113 PRK12545 RNA polymerase sigma 83.4 1.8 3.8E-05 38.5 4.5 49 72-121 139-187 (201)
114 PRK12532 RNA polymerase sigma 83.3 1.8 3.8E-05 38.2 4.5 48 72-120 136-183 (195)
115 TIGR02393 RpoD_Cterm RNA polym 83.2 1.8 3.8E-05 39.7 4.6 48 72-119 176-226 (238)
116 TIGR03001 Sig-70_gmx1 RNA poly 83.2 1.8 3.8E-05 40.0 4.5 47 72-119 161-207 (244)
117 PRK12512 RNA polymerase sigma 83.0 2 4.4E-05 37.4 4.7 48 72-120 131-178 (184)
118 PRK12543 RNA polymerase sigma 82.9 1.9 4.2E-05 37.4 4.5 47 72-119 117-163 (179)
119 cd00092 HTH_CRP helix_turn_hel 82.8 1.2 2.6E-05 31.6 2.7 27 89-115 25-51 (67)
120 PRK12546 RNA polymerase sigma 82.8 2.1 4.5E-05 37.7 4.7 49 72-121 113-161 (188)
121 TIGR02954 Sig70_famx3 RNA poly 82.8 2.2 4.7E-05 36.6 4.8 48 72-120 119-166 (169)
122 PF00325 Crp: Bacterial regula 82.8 1.1 2.5E-05 27.3 2.0 25 90-114 3-27 (32)
123 PRK12535 RNA polymerase sigma 82.8 2.2 4.8E-05 37.8 4.9 53 72-125 133-185 (196)
124 PRK05572 sporulation sigma fac 82.7 2.2 4.8E-05 39.5 5.0 48 72-120 202-249 (252)
125 PRK12542 RNA polymerase sigma 82.6 2.2 4.8E-05 37.2 4.8 49 72-121 122-170 (185)
126 PRK11753 DNA-binding transcrip 82.5 1.1 2.3E-05 39.9 2.8 45 71-115 137-194 (211)
127 PRK09644 RNA polymerase sigma 82.5 2 4.4E-05 36.6 4.5 48 72-120 108-155 (165)
128 smart00342 HTH_ARAC helix_turn 82.4 3.3 7.2E-05 30.2 5.1 72 40-115 4-77 (84)
129 PRK09643 RNA polymerase sigma 82.4 2.2 4.7E-05 37.6 4.7 49 72-121 134-182 (192)
130 PF09339 HTH_IclR: IclR helix- 82.4 1.6 3.4E-05 29.7 2.9 28 88-115 17-44 (52)
131 TIGR02947 SigH_actino RNA poly 82.3 1.3 2.8E-05 39.1 3.2 50 72-122 131-180 (193)
132 PRK05602 RNA polymerase sigma 82.3 2.2 4.7E-05 37.3 4.6 48 72-120 128-175 (186)
133 PRK06930 positive control sigm 82.3 2.3 5.1E-05 36.9 4.7 47 72-119 114-160 (170)
134 PRK12540 RNA polymerase sigma 82.3 2.3 4.9E-05 37.3 4.7 50 72-122 111-160 (182)
135 PRK12527 RNA polymerase sigma 82.2 2.4 5.1E-05 36.0 4.7 48 72-120 105-152 (159)
136 TIGR02846 spore_sigmaK RNA pol 82.2 2.1 4.5E-05 39.0 4.5 48 72-119 174-224 (227)
137 PF01710 HTH_Tnp_IS630: Transp 82.1 3.2 6.9E-05 33.7 5.2 73 38-113 19-95 (119)
138 TIGR02948 SigW_bacill RNA poly 82.1 2.2 4.8E-05 37.1 4.6 48 72-120 136-183 (187)
139 PRK06596 RNA polymerase factor 82.0 2.4 5.2E-05 40.1 5.1 48 72-119 230-278 (284)
140 PRK12526 RNA polymerase sigma 81.9 2.3 5.1E-05 37.9 4.7 48 72-120 153-200 (206)
141 PRK12538 RNA polymerase sigma 81.7 2 4.3E-05 39.3 4.3 49 72-121 171-219 (233)
142 PRK12544 RNA polymerase sigma 81.7 2.3 4.9E-05 38.1 4.6 48 72-120 148-195 (206)
143 PRK12539 RNA polymerase sigma 81.5 2.5 5.5E-05 36.8 4.8 48 72-120 131-178 (184)
144 TIGR02980 SigBFG RNA polymeras 81.5 2.5 5.5E-05 38.2 4.9 47 72-119 178-224 (227)
145 PRK08583 RNA polymerase sigma 81.2 2.6 5.6E-05 39.1 4.9 47 72-119 205-251 (257)
146 TIGR02394 rpoS_proteo RNA poly 81.0 2.6 5.7E-05 39.8 5.0 50 72-121 222-274 (285)
147 PRK07500 rpoH2 RNA polymerase 81.0 2.6 5.6E-05 39.9 4.9 50 72-121 227-277 (289)
148 PRK06811 RNA polymerase factor 81.0 2.3 5E-05 37.3 4.3 46 72-118 131-176 (189)
149 PF04297 UPF0122: Putative hel 80.7 3.4 7.3E-05 32.5 4.6 46 73-119 18-63 (101)
150 PRK09646 RNA polymerase sigma 80.4 3 6.4E-05 36.8 4.8 48 72-120 142-189 (194)
151 TIGR02943 Sig70_famx1 RNA poly 80.3 2.7 5.9E-05 36.9 4.6 49 72-121 131-179 (188)
152 PRK10402 DNA-binding transcrip 79.9 2.2 4.8E-05 38.6 3.9 91 38-128 109-209 (226)
153 PRK08215 sporulation sigma fac 79.8 3.1 6.7E-05 38.6 5.0 47 72-119 209-255 (258)
154 PRK06986 fliA flagellar biosyn 79.7 3.2 6.9E-05 37.9 4.9 48 72-120 184-231 (236)
155 PRK06704 RNA polymerase factor 79.6 3.6 7.9E-05 37.5 5.2 56 72-128 116-171 (228)
156 PF00126 HTH_1: Bacterial regu 79.6 2.6 5.7E-05 29.5 3.4 39 79-118 4-42 (60)
157 PRK12513 RNA polymerase sigma 79.2 2 4.3E-05 37.8 3.3 48 72-120 139-186 (194)
158 smart00550 Zalpha Z-DNA-bindin 79.2 3.2 6.9E-05 30.1 3.8 42 74-115 6-48 (68)
159 TIGR02960 SigX5 RNA polymerase 78.9 2.8 6E-05 40.2 4.5 51 72-123 142-192 (324)
160 COG5421 Transposase [DNA repli 78.7 3.2 7E-05 41.5 4.8 58 174-232 152-209 (480)
161 PRK01381 Trp operon repressor; 78.5 2.1 4.5E-05 33.5 2.7 40 73-112 33-78 (99)
162 PRK15201 fimbriae regulatory p 78.5 2 4.4E-05 37.3 2.9 46 71-118 132-177 (198)
163 TIGR02997 Sig70-cyanoRpoD RNA 78.4 2.8 6E-05 39.9 4.3 46 72-117 249-297 (298)
164 TIGR02885 spore_sigF RNA polym 78.4 3.2 6.9E-05 37.7 4.5 46 72-118 183-228 (231)
165 PRK09647 RNA polymerase sigma 78.4 3.4 7.3E-05 36.9 4.6 49 72-121 138-186 (203)
166 PRK08295 RNA polymerase factor 78.4 3.3 7.2E-05 36.7 4.5 47 72-120 155-201 (208)
167 TIGR02850 spore_sigG RNA polym 77.9 3.4 7.4E-05 38.2 4.6 46 72-118 206-251 (254)
168 PF08299 Bac_DnaA_C: Bacterial 77.6 2.4 5.3E-05 30.9 2.8 41 73-113 29-70 (70)
169 PRK07670 RNA polymerase sigma 77.6 4.1 9E-05 37.6 5.1 47 72-119 201-247 (251)
170 PRK12517 RNA polymerase sigma 77.3 3.7 8E-05 36.1 4.4 49 72-121 128-176 (188)
171 PF13545 HTH_Crp_2: Crp-like h 76.8 2.7 5.9E-05 30.7 3.0 27 89-115 28-54 (76)
172 PRK12518 RNA polymerase sigma 76.8 2.2 4.7E-05 36.8 2.8 48 72-120 120-167 (175)
173 PRK07405 RNA polymerase sigma 76.7 3.8 8.2E-05 39.4 4.6 48 72-119 256-306 (317)
174 PF01710 HTH_Tnp_IS630: Transp 76.6 1.6 3.4E-05 35.5 1.7 29 84-112 13-41 (119)
175 TIGR02941 Sigma_B RNA polymera 76.5 4.4 9.6E-05 37.5 4.9 47 72-119 205-251 (255)
176 PRK09391 fixK transcriptional 76.4 6.3 0.00014 35.8 5.9 78 38-115 113-205 (230)
177 PRK15411 rcsA colanic acid cap 76.4 2.3 5E-05 38.1 2.9 44 73-118 138-181 (207)
178 PRK11922 RNA polymerase sigma 76.4 2.8 6.1E-05 38.1 3.5 51 72-123 149-199 (231)
179 PF12840 HTH_20: Helix-turn-he 76.3 2.9 6.3E-05 29.4 2.9 31 86-116 21-51 (61)
180 TIGR02479 FliA_WhiG RNA polyme 76.3 4.6 0.0001 36.5 4.9 47 72-119 175-221 (224)
181 smart00346 HTH_ICLR helix_turn 76.2 3.5 7.6E-05 31.2 3.5 39 77-115 5-46 (91)
182 PRK09648 RNA polymerase sigma 76.0 4.8 0.0001 35.1 4.8 47 72-119 139-185 (189)
183 COG1191 FliA DNA-directed RNA 75.7 4.9 0.00011 37.1 4.9 47 72-119 196-242 (247)
184 PRK07122 RNA polymerase sigma 75.4 4.8 0.00011 37.5 4.9 47 72-119 215-261 (264)
185 COG2963 Transposase and inacti 75.4 4.7 0.0001 32.4 4.2 47 70-116 5-52 (116)
186 PHA00542 putative Cro-like pro 75.4 2 4.4E-05 32.4 1.9 30 83-112 25-54 (82)
187 PRK06030 hypothetical protein; 74.4 5.3 0.00012 32.7 4.2 47 71-117 51-97 (124)
188 PF00165 HTH_AraC: Bacterial r 74.3 2.3 5E-05 27.4 1.7 29 86-114 5-33 (42)
189 TIGR01610 phage_O_Nterm phage 74.3 4.1 8.8E-05 31.6 3.4 30 86-115 44-73 (95)
190 PRK11161 fumarate/nitrate redu 74.1 7 0.00015 35.4 5.5 44 72-115 153-210 (235)
191 PRK13870 transcriptional regul 74.1 2.7 5.8E-05 38.6 2.7 45 72-118 173-217 (234)
192 TIGR02337 HpaR homoprotocatech 73.9 7.4 0.00016 31.2 5.1 42 73-115 26-68 (118)
193 TIGR01636 phage_rinA phage tra 73.9 7.2 0.00016 32.4 5.0 47 73-119 83-130 (134)
194 TIGR03209 P21_Cbot clostridium 73.0 2.9 6.3E-05 34.6 2.6 36 71-107 106-141 (142)
195 PF01381 HTH_3: Helix-turn-hel 72.7 2.2 4.7E-05 29.0 1.4 27 86-112 6-32 (55)
196 PF04703 FaeA: FaeA-like prote 72.4 4.3 9.3E-05 28.9 2.8 38 77-114 3-40 (62)
197 TIGR02859 spore_sigH RNA polym 72.3 5.3 0.00011 35.1 4.2 45 74-119 151-195 (198)
198 PRK06288 RNA polymerase sigma 72.3 5.6 0.00012 37.1 4.5 47 72-119 212-258 (268)
199 PRK09392 ftrB transcriptional 72.3 4 8.7E-05 37.0 3.5 45 71-115 145-199 (236)
200 PF01978 TrmB: Sugar-specific 72.1 4.5 9.7E-05 29.0 3.0 39 76-115 10-48 (68)
201 smart00419 HTH_CRP helix_turn_ 71.8 3.5 7.6E-05 26.9 2.2 28 88-115 7-34 (48)
202 PRK03573 transcriptional regul 71.7 4.8 0.0001 33.6 3.6 44 72-115 28-72 (144)
203 PRK12427 flagellar biosynthesi 71.7 5.9 0.00013 36.2 4.4 46 72-118 183-228 (231)
204 PF02001 DUF134: Protein of un 71.7 8.2 0.00018 30.7 4.6 46 72-118 41-86 (106)
205 PF13309 HTH_22: HTH domain 71.4 5.5 0.00012 28.5 3.3 40 72-111 20-64 (64)
206 PF09862 DUF2089: Protein of u 71.3 5.7 0.00012 31.9 3.6 46 72-118 33-78 (113)
207 smart00345 HTH_GNTR helix_turn 71.3 3.4 7.4E-05 28.2 2.2 25 91-115 22-46 (60)
208 PRK08241 RNA polymerase factor 71.2 6.2 0.00013 38.1 4.7 50 72-122 153-202 (339)
209 COG2197 CitB Response regulato 70.2 3.6 7.8E-05 37.0 2.6 44 73-118 149-192 (211)
210 smart00418 HTH_ARSR helix_turn 70.1 4.7 0.0001 27.7 2.8 29 87-115 8-36 (66)
211 PF13463 HTH_27: Winged helix 70.1 7.4 0.00016 27.5 3.8 28 88-115 17-44 (68)
212 PRK13719 conjugal transfer tra 69.7 4.3 9.4E-05 36.5 2.9 45 72-118 143-187 (217)
213 COG3316 Transposase and inacti 69.5 28 0.0006 31.4 7.9 186 73-318 9-201 (215)
214 PRK09636 RNA polymerase sigma 69.5 7.8 0.00017 36.6 4.9 50 72-122 115-164 (293)
215 PRK07406 RNA polymerase sigma 69.4 6.9 0.00015 38.5 4.6 47 72-118 311-360 (373)
216 PRK09640 RNA polymerase sigma 69.3 3.4 7.4E-05 36.1 2.2 48 72-120 134-181 (188)
217 PRK05657 RNA polymerase sigma 69.2 8 0.00017 37.3 4.9 50 72-121 262-314 (325)
218 PRK07598 RNA polymerase sigma 69.1 6.9 0.00015 39.0 4.5 47 72-118 350-399 (415)
219 TIGR02957 SigX4 RNA polymerase 68.7 9.1 0.0002 36.0 5.1 49 72-121 108-156 (281)
220 PRK11512 DNA-binding transcrip 68.2 8.4 0.00018 32.1 4.3 43 72-115 37-80 (144)
221 PF07638 Sigma70_ECF: ECF sigm 68.0 9.6 0.00021 33.4 4.8 45 73-118 136-180 (185)
222 PRK10840 transcriptional regul 68.0 4.4 9.5E-05 36.1 2.7 44 72-117 150-193 (216)
223 PRK05949 RNA polymerase sigma 67.8 7.9 0.00017 37.4 4.6 48 72-119 266-316 (327)
224 PF06056 Terminase_5: Putative 67.8 6.8 0.00015 27.5 3.0 33 79-113 5-37 (58)
225 COG2771 CsgD DNA-binding HTH d 66.9 6.5 0.00014 27.4 2.9 36 82-117 12-47 (65)
226 PRK13918 CRP/FNR family transc 66.8 6 0.00013 34.8 3.3 44 72-115 118-175 (202)
227 PF13560 HTH_31: Helix-turn-he 66.4 4.2 9.1E-05 28.8 1.8 27 85-111 10-36 (64)
228 PF12964 DUF3853: Protein of u 66.1 5.5 0.00012 30.8 2.4 57 46-111 10-67 (96)
229 PRK09210 RNA polymerase sigma 65.9 8.6 0.00019 37.8 4.5 47 72-118 305-354 (367)
230 cd00090 HTH_ARSR Arsenical Res 65.9 8.4 0.00018 27.3 3.5 28 88-115 19-46 (78)
231 PRK11475 DNA-binding transcrip 65.5 5.3 0.00012 35.8 2.7 43 73-117 135-177 (207)
232 PHA02517 putative transposase 65.0 96 0.0021 28.8 11.3 75 143-234 105-181 (277)
233 PF10654 DUF2481: Protein of u 64.7 6.2 0.00013 31.4 2.5 31 88-118 79-109 (126)
234 TIGR03541 reg_near_HchA LuxR f 64.4 17 0.00037 33.1 5.9 46 71-118 170-215 (232)
235 PHA00738 putative HTH transcri 64.2 8.4 0.00018 30.6 3.2 28 89-116 26-53 (108)
236 TIGR01889 Staph_reg_Sar staphy 64.0 13 0.00027 29.5 4.4 44 72-115 22-69 (109)
237 smart00347 HTH_MARR helix_turn 63.2 13 0.00028 28.3 4.2 29 87-115 22-50 (101)
238 PRK10188 DNA-binding transcrip 63.0 6.5 0.00014 36.1 2.9 45 72-118 179-223 (240)
239 PF05043 Mga: Mga helix-turn-h 62.7 12 0.00026 28.2 3.9 34 86-119 27-60 (87)
240 smart00420 HTH_DEOR helix_turn 62.7 13 0.00029 24.4 3.7 27 89-115 14-40 (53)
241 PRK15418 transcriptional regul 62.5 5.8 0.00012 38.2 2.5 35 81-115 21-55 (318)
242 PF05269 Phage_CII: Bacterioph 61.7 9 0.00019 29.5 2.9 29 90-118 24-52 (91)
243 smart00354 HTH_LACI helix_turn 61.4 4.6 0.0001 29.3 1.3 22 91-112 2-23 (70)
244 PRK09483 response regulator; P 61.3 6.9 0.00015 34.3 2.7 44 72-117 148-191 (217)
245 PRK13413 mpi multiple promoter 61.2 5 0.00011 35.6 1.7 29 84-112 167-195 (200)
246 PF13551 HTH_29: Winged helix- 61.2 32 0.00068 26.8 6.3 74 39-112 14-110 (112)
247 PRK10100 DNA-binding transcrip 60.7 7.9 0.00017 35.0 2.9 45 72-118 155-199 (216)
248 PRK10141 DNA-binding transcrip 60.7 16 0.00036 29.5 4.5 41 76-116 16-57 (117)
249 PF05263 DUF722: Protein of un 60.3 15 0.00031 30.4 4.1 45 73-117 82-127 (130)
250 PF13404 HTH_AsnC-type: AsnC-t 60.2 7 0.00015 25.4 1.8 24 89-112 17-40 (42)
251 TIGR03020 EpsA transcriptional 59.7 13 0.00028 34.4 4.2 45 71-117 189-233 (247)
252 cd04762 HTH_MerR-trunc Helix-T 59.6 5.7 0.00012 25.7 1.4 22 91-112 2-23 (49)
253 PHA02591 hypothetical protein; 59.4 8.6 0.00019 28.5 2.3 36 77-112 47-82 (83)
254 cd01392 HTH_LacI Helix-turn-he 59.2 4.4 9.5E-05 27.1 0.8 19 94-112 2-20 (52)
255 PRK07921 RNA polymerase sigma 58.7 15 0.00032 35.5 4.6 48 72-119 262-312 (324)
256 PRK09191 two-component respons 58.1 13 0.00029 33.8 4.1 47 72-119 88-134 (261)
257 TIGR01764 excise DNA binding d 58.1 6.3 0.00014 25.6 1.4 21 91-111 3-23 (49)
258 COG1508 RpoN DNA-directed RNA 57.9 10 0.00022 38.0 3.3 56 43-111 295-352 (444)
259 PF13744 HTH_37: Helix-turn-he 57.8 6.4 0.00014 29.4 1.5 34 78-111 18-53 (80)
260 PF13610 DDE_Tnp_IS240: DDE do 57.8 11 0.00023 31.5 3.0 131 152-318 5-139 (140)
261 PRK12469 RNA polymerase factor 57.6 13 0.00027 38.0 4.0 23 89-111 369-391 (481)
262 PRK05901 RNA polymerase sigma 57.3 15 0.00033 37.7 4.6 48 72-119 447-497 (509)
263 PRK15215 fimbriae biosynthesis 57.2 36 0.00078 26.6 5.5 57 49-116 31-88 (100)
264 PF08220 HTH_DeoR: DeoR-like h 57.0 9.2 0.0002 26.5 2.1 27 89-115 14-40 (57)
265 PRK12682 transcriptional regul 57.0 11 0.00025 35.5 3.5 42 77-118 4-45 (309)
266 PRK05932 RNA polymerase factor 56.9 13 0.00027 37.8 3.9 58 41-111 306-365 (455)
267 COG3413 Predicted DNA binding 56.8 12 0.00025 33.8 3.3 48 72-119 155-208 (215)
268 PF10668 Phage_terminase: Phag 56.3 8.3 0.00018 27.2 1.7 22 89-110 22-43 (60)
269 PRK09635 sigI RNA polymerase s 55.8 20 0.00043 34.0 4.8 50 72-122 118-167 (290)
270 TIGR03070 couple_hipB transcri 55.7 7 0.00015 26.4 1.4 26 86-111 12-37 (58)
271 PF03333 PapB: Adhesin biosynt 55.6 38 0.00083 26.1 5.4 58 48-116 22-80 (91)
272 PF12728 HTH_17: Helix-turn-he 55.4 7.4 0.00016 26.0 1.4 21 91-111 3-23 (51)
273 COG5606 Uncharacterized conser 55.3 5.3 0.00012 30.2 0.7 65 49-115 1-67 (91)
274 smart00344 HTH_ASNC helix_turn 55.0 20 0.00042 28.1 4.0 38 77-115 6-43 (108)
275 TIGR02395 rpoN_sigma RNA polym 54.9 14 0.00031 37.1 3.9 58 41-111 281-340 (429)
276 COG2522 Predicted transcriptio 54.0 13 0.00028 30.2 2.8 25 87-111 20-44 (119)
277 PRK09492 treR trehalose repres 53.8 12 0.00027 35.1 3.2 23 90-112 5-27 (315)
278 smart00352 POU Found in Pit-Oc 53.4 8.5 0.00018 28.5 1.5 28 84-111 19-52 (75)
279 PRK00215 LexA repressor; Valid 53.3 17 0.00036 32.4 3.7 29 88-116 22-51 (205)
280 cd07377 WHTH_GntR Winged helix 53.1 12 0.00025 26.1 2.2 25 91-115 27-51 (66)
281 TIGR02405 trehalos_R_Ecol treh 53.0 12 0.00026 35.3 2.9 21 91-111 3-23 (311)
282 PF13443 HTH_26: Cro/C1-type H 52.9 8.3 0.00018 26.9 1.4 27 87-113 8-34 (63)
283 PRK10360 DNA-binding transcrip 52.7 13 0.00028 32.0 2.9 44 72-117 137-180 (196)
284 PRK12683 transcriptional regul 52.5 15 0.00032 34.9 3.5 42 77-118 4-45 (309)
285 PRK10403 transcriptional regul 52.4 12 0.00026 32.3 2.7 44 72-117 153-196 (215)
286 TIGR00122 birA_repr_reg BirA b 52.4 19 0.00041 25.8 3.2 26 90-115 14-39 (69)
287 PF00382 TFIIB: Transcription 52.3 40 0.00087 24.2 5.0 62 42-106 3-71 (71)
288 COG3355 Predicted transcriptio 51.3 22 0.00047 29.2 3.7 29 88-116 41-69 (126)
289 PRK10651 transcriptional regul 51.2 13 0.00027 32.3 2.6 44 72-117 155-198 (216)
290 PHA01976 helix-turn-helix prot 51.1 11 0.00024 26.6 1.9 27 85-111 11-37 (67)
291 PF00440 TetR_N: Bacterial reg 50.7 28 0.00061 22.8 3.6 30 88-117 15-44 (47)
292 PRK10870 transcriptional repre 50.4 20 0.00043 31.2 3.6 44 72-115 52-97 (176)
293 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 50.1 24 0.00052 23.9 3.2 40 71-111 3-42 (50)
294 PF00665 rve: Integrase core d 50.0 30 0.00065 27.1 4.5 16 272-287 105-120 (120)
295 TIGR00637 ModE_repress ModE mo 49.9 19 0.00041 28.2 3.1 34 85-118 12-45 (99)
296 PRK09958 DNA-binding transcrip 49.8 14 0.00031 31.9 2.7 44 72-117 143-186 (204)
297 PRK12679 cbl transcriptional r 49.6 18 0.00039 34.3 3.6 42 77-118 4-45 (316)
298 PRK09834 DNA-binding transcrip 49.4 18 0.00039 33.6 3.4 44 72-115 6-52 (263)
299 TIGR02431 pcaR_pcaU beta-ketoa 49.2 19 0.00042 33.0 3.6 43 73-115 5-50 (248)
300 COG4565 CitB Response regulato 49.0 31 0.00067 31.0 4.6 68 48-115 129-199 (224)
301 cd00131 PAX Paired Box domain 48.8 83 0.0018 25.8 6.9 75 38-112 34-126 (128)
302 PRK10014 DNA-binding transcrip 48.5 8.9 0.00019 36.6 1.3 23 90-112 7-29 (342)
303 PRK09526 lacI lac repressor; R 48.4 9.2 0.0002 36.5 1.3 23 90-112 6-28 (342)
304 PRK11233 nitrogen assimilation 48.2 19 0.00041 33.9 3.5 40 78-118 5-44 (305)
305 PRK10163 DNA-binding transcrip 48.2 24 0.00052 33.0 4.1 45 71-115 19-66 (271)
306 PF04552 Sigma54_DBD: Sigma-54 48.0 6 0.00013 34.0 0.0 58 41-111 12-71 (160)
307 PF00392 GntR: Bacterial regul 47.8 16 0.00034 25.8 2.2 25 91-115 26-50 (64)
308 PRK14987 gluconate operon tran 47.3 8.9 0.00019 36.5 1.1 23 90-112 6-28 (331)
309 COG2390 DeoR Transcriptional r 47.1 14 0.00031 35.5 2.4 34 82-115 19-52 (321)
310 COG1342 Predicted DNA-binding 47.0 41 0.00088 26.1 4.3 46 72-118 33-78 (99)
311 PRK10401 DNA-binding transcrip 46.6 17 0.00038 34.8 3.0 21 91-111 3-23 (346)
312 PRK14088 dnaA chromosomal repl 46.5 29 0.00062 35.0 4.6 47 71-117 369-415 (440)
313 PRK11050 manganese transport r 46.0 25 0.00054 29.8 3.5 28 88-115 50-77 (152)
314 PF00292 PAX: 'Paired box' dom 46.0 37 0.00081 27.8 4.3 46 68-115 13-59 (125)
315 PRK15369 two component system 45.5 19 0.00042 30.7 2.9 44 73-118 150-193 (211)
316 PRK11303 DNA-binding transcrip 45.3 11 0.00024 35.8 1.3 22 91-112 2-23 (328)
317 PRK13777 transcriptional regul 45.2 34 0.00074 30.1 4.3 43 72-114 42-84 (185)
318 PF02954 HTH_8: Bacterial regu 44.9 18 0.00039 23.3 1.9 25 88-112 17-41 (42)
319 PRK14086 dnaA chromosomal repl 44.8 33 0.00071 36.1 4.7 48 71-118 551-598 (617)
320 PRK00149 dnaA chromosomal repl 44.4 33 0.00071 34.6 4.7 48 71-118 384-432 (450)
321 PRK10339 DNA-binding transcrip 44.3 11 0.00023 36.0 1.1 22 91-112 3-24 (327)
322 TIGR00180 parB_part ParB-like 44.0 26 0.00056 30.7 3.4 42 71-112 101-143 (187)
323 PF09607 BrkDBD: Brinker DNA-b 43.9 27 0.00059 24.4 2.7 42 71-112 4-48 (58)
324 PRK10703 DNA-binding transcrip 43.9 12 0.00025 35.8 1.3 22 91-112 3-24 (341)
325 PRK12684 transcriptional regul 43.9 25 0.00053 33.4 3.5 42 77-118 4-45 (313)
326 PF05930 Phage_AlpA: Prophage 43.7 16 0.00036 24.5 1.7 21 91-111 5-25 (51)
327 PRK14087 dnaA chromosomal repl 43.6 42 0.00091 34.0 5.3 48 71-118 383-431 (450)
328 TIGR02702 SufR_cyano iron-sulf 43.0 33 0.00072 30.5 4.0 39 76-115 3-41 (203)
329 PRK11569 transcriptional repre 42.3 34 0.00073 32.0 4.1 45 71-115 22-69 (274)
330 PRK10423 transcriptional repre 42.2 12 0.00026 35.4 1.1 19 93-111 2-20 (327)
331 TIGR03830 CxxCG_CxxCG_HTH puta 41.6 29 0.00063 28.0 3.2 27 85-111 74-100 (127)
332 PRK00423 tfb transcription ini 41.5 99 0.0022 29.5 7.2 76 42-117 225-304 (310)
333 PRK10072 putative transcriptio 41.2 17 0.00036 28.4 1.5 25 87-111 44-68 (96)
334 PRK11151 DNA-binding transcrip 41.1 29 0.00062 32.6 3.5 40 78-118 5-44 (305)
335 smart00529 HTH_DTXR Helix-turn 41.1 21 0.00046 27.2 2.2 24 92-115 2-25 (96)
336 COG1846 MarR Transcriptional r 40.9 35 0.00075 26.8 3.5 38 77-115 25-62 (126)
337 TIGR02417 fruct_sucro_rep D-fr 40.3 14 0.00031 35.0 1.3 21 92-112 2-22 (327)
338 TIGR03418 chol_sulf_TF putativ 40.2 31 0.00067 32.0 3.6 40 78-118 5-44 (291)
339 PRK15090 DNA-binding transcrip 39.2 39 0.00085 31.2 4.0 45 71-115 8-54 (257)
340 TIGR01884 cas_HTH CRISPR locus 39.2 46 0.00099 29.6 4.3 27 89-115 157-183 (203)
341 PRK05658 RNA polymerase sigma 39.1 41 0.00089 35.6 4.6 47 72-118 556-605 (619)
342 TIGR01481 ccpA catabolite cont 38.9 15 0.00033 34.7 1.3 22 91-112 3-24 (329)
343 PF08765 Mor: Mor transcriptio 38.7 22 0.00048 28.2 1.9 30 88-117 71-100 (108)
344 PF07453 NUMOD1: NUMOD1 domain 38.7 18 0.0004 22.4 1.2 22 89-110 16-37 (37)
345 PF14493 HTH_40: Helix-turn-he 38.6 33 0.00072 26.1 2.9 37 80-116 4-40 (91)
346 PF01418 HTH_6: Helix-turn-hel 38.5 22 0.00049 26.2 1.8 24 89-112 34-57 (77)
347 TIGR02607 antidote_HigA addict 38.4 20 0.00044 26.1 1.6 27 85-111 14-40 (78)
348 PRK10219 DNA-binding transcrip 38.4 47 0.001 25.9 3.8 30 86-115 18-47 (107)
349 PRK10727 DNA-binding transcrip 38.1 16 0.00035 35.0 1.2 22 91-112 3-24 (343)
350 COG3293 Transposase and inacti 37.7 50 0.0011 26.6 4.0 93 180-291 2-99 (124)
351 PRK12681 cysB transcriptional 37.5 36 0.00077 32.6 3.5 42 77-118 4-45 (324)
352 PRK11179 DNA-binding transcrip 37.4 57 0.0012 27.5 4.4 28 88-115 22-49 (153)
353 COG3139 Uncharacterized protei 37.1 91 0.002 23.4 4.7 44 48-92 9-56 (90)
354 COG2964 Uncharacterized protei 37.0 54 0.0012 29.6 4.3 22 92-113 194-215 (220)
355 PRK09791 putative DNA-binding 36.9 38 0.00082 31.7 3.6 41 77-118 8-48 (302)
356 PRK11511 DNA-binding transcrip 36.8 35 0.00076 27.8 2.9 31 85-115 21-51 (127)
357 PRK11013 DNA-binding transcrip 36.8 36 0.00078 32.1 3.4 40 78-118 8-47 (309)
358 COG1609 PurR Transcriptional r 36.8 18 0.00039 34.9 1.4 22 91-112 2-23 (333)
359 COG1414 IclR Transcriptional r 36.6 44 0.00095 30.8 3.8 36 80-115 7-45 (246)
360 PRK10094 DNA-binding transcrip 36.3 37 0.0008 32.1 3.4 40 78-118 6-45 (308)
361 PF05732 RepL: Firmicute plasm 36.1 26 0.00057 30.2 2.1 26 90-115 76-101 (165)
362 PRK09935 transcriptional regul 35.7 31 0.00068 29.7 2.6 43 73-117 150-192 (210)
363 PRK08558 adenine phosphoribosy 35.6 34 0.00073 31.4 2.9 37 75-111 9-45 (238)
364 PF13022 HTH_Tnp_1_2: Helix-tu 35.6 46 0.00099 27.8 3.3 36 90-125 35-73 (142)
365 PHA02701 ORF020 dsRNA-binding 35.3 50 0.0011 28.9 3.7 41 75-115 5-45 (183)
366 PF13701 DDE_Tnp_1_4: Transpos 34.8 53 0.0011 33.2 4.4 125 101-239 103-234 (448)
367 PRK09726 antitoxin HipB; Provi 34.7 23 0.0005 26.8 1.4 26 86-111 22-47 (88)
368 PRK09906 DNA-binding transcrip 34.6 36 0.00078 31.7 3.0 37 82-118 8-44 (296)
369 PRK15421 DNA-binding transcrip 34.6 44 0.00095 31.8 3.7 40 78-118 6-45 (317)
370 PF08280 HTH_Mga: M protein tr 34.3 63 0.0014 22.4 3.5 37 78-115 9-45 (59)
371 PF01726 LexA_DNA_bind: LexA D 34.2 73 0.0016 22.8 3.8 27 88-114 24-51 (65)
372 PF14294 DUF4372: Domain of un 34.0 1.3E+02 0.0027 22.3 5.2 53 49-104 14-67 (76)
373 TIGR00498 lexA SOS regulatory 33.9 53 0.0011 28.9 3.8 40 76-115 8-52 (199)
374 PRK13348 chromosome replicatio 33.9 44 0.00095 31.1 3.5 39 79-118 7-45 (294)
375 PRK12680 transcriptional regul 33.6 45 0.00098 31.9 3.6 40 79-118 6-45 (327)
376 PRK04140 hypothetical protein; 33.5 36 0.00079 32.7 2.8 62 49-111 98-161 (317)
377 cd04761 HTH_MerR-SF Helix-Turn 33.4 25 0.00055 22.8 1.3 21 91-111 2-22 (49)
378 PRK11242 DNA-binding transcrip 33.3 44 0.00094 31.0 3.4 39 79-118 6-44 (296)
379 PF13556 HTH_30: PucR C-termin 32.6 48 0.001 23.0 2.6 34 84-117 7-40 (59)
380 TIGR02944 suf_reg_Xantho FeS a 32.4 54 0.0012 26.7 3.4 26 90-115 26-51 (130)
381 COG1522 Lrp Transcriptional re 32.1 64 0.0014 26.8 3.9 37 78-115 12-48 (154)
382 PRK12422 chromosomal replicati 31.8 64 0.0014 32.6 4.4 47 71-117 379-425 (445)
383 COG0664 Crp cAMP-binding prote 31.7 48 0.001 28.7 3.2 44 72-115 140-197 (214)
384 smart00497 IENR1 Intron encode 31.2 33 0.00071 22.8 1.6 24 89-112 17-40 (53)
385 TIGR02424 TF_pcaQ pca operon t 31.1 51 0.0011 30.7 3.4 32 87-118 15-46 (300)
386 TIGR03298 argP transcriptional 31.0 53 0.0011 30.5 3.5 39 79-118 6-44 (292)
387 PF06530 Phage_antitermQ: Phag 30.9 63 0.0014 26.4 3.5 40 78-117 67-106 (125)
388 COG1654 BirA Biotin operon rep 30.9 78 0.0017 23.7 3.6 39 77-115 6-45 (79)
389 PRK10046 dpiA two-component re 30.7 39 0.00085 30.2 2.5 32 82-113 167-201 (225)
390 cd07153 Fur_like Ferric uptake 30.4 80 0.0017 24.9 4.0 27 89-115 16-47 (116)
391 PF02650 HTH_WhiA: WhiA C-term 30.3 1E+02 0.0022 23.4 4.2 42 73-115 38-82 (85)
392 COG4974 XerD Site-specific rec 30.2 1.2E+02 0.0026 28.7 5.6 80 40-121 210-293 (300)
393 PRK06474 hypothetical protein; 30.2 56 0.0012 28.5 3.2 26 90-115 27-53 (178)
394 PRK11169 leucine-responsive tr 30.1 70 0.0015 27.3 3.8 29 87-115 26-54 (164)
395 COG2512 Predicted membrane-ass 30.0 71 0.0015 29.7 4.0 44 72-115 192-236 (258)
396 cd01104 HTH_MlrA-CarA Helix-Tu 30.0 35 0.00075 24.1 1.6 22 91-112 2-23 (68)
397 PF08535 KorB: KorB domain; I 29.8 34 0.00074 26.2 1.6 24 88-111 2-25 (93)
398 PF07750 GcrA: GcrA cell cycle 29.6 43 0.00092 28.8 2.3 37 76-112 5-42 (162)
399 TIGR01637 phage_arpU phage tra 29.4 1.2E+02 0.0025 24.8 4.9 47 73-119 80-127 (132)
400 PRK11074 putative DNA-binding 29.4 59 0.0013 30.4 3.6 39 79-118 7-45 (300)
401 PRK10216 DNA-binding transcrip 29.1 59 0.0013 30.8 3.5 32 87-118 20-51 (319)
402 PRK11564 stationary phase indu 29.0 96 0.0021 30.9 5.2 51 70-120 8-61 (426)
403 COG2973 TrpR Trp operon repres 29.0 55 0.0012 25.5 2.5 27 85-111 56-82 (103)
404 PRK09706 transcriptional repre 29.0 32 0.0007 28.3 1.5 26 86-111 15-40 (135)
405 COG3677 Transposase and inacti 28.5 45 0.00097 27.5 2.2 44 76-119 76-119 (129)
406 PF08148 DSHCT: DSHCT (NUC185) 28.5 57 0.0012 28.5 3.0 46 78-123 103-148 (180)
407 PRK09508 leuO leucine transcri 28.5 54 0.0012 31.0 3.1 39 80-118 27-65 (314)
408 PRK09986 DNA-binding transcrip 28.4 59 0.0013 30.1 3.4 40 78-118 11-50 (294)
409 PRK03902 manganese transport t 28.2 74 0.0016 26.4 3.5 27 89-115 22-48 (142)
410 COG5566 Uncharacterized conser 28.0 49 0.0011 27.0 2.2 28 88-115 101-128 (137)
411 PRK09801 transcriptional activ 27.9 57 0.0012 30.8 3.2 41 77-118 9-49 (310)
412 PF13601 HTH_34: Winged helix 27.8 74 0.0016 23.7 3.1 30 87-116 12-41 (80)
413 PF07022 Phage_CI_repr: Bacter 27.8 29 0.00063 24.7 0.8 22 91-112 14-36 (66)
414 PRK10341 DNA-binding transcrip 27.7 55 0.0012 30.9 3.0 36 83-118 15-50 (312)
415 PF12844 HTH_19: Helix-turn-he 27.6 37 0.00079 23.6 1.4 26 87-112 10-35 (64)
416 TIGR03454 partition_RepB plasm 27.6 69 0.0015 30.9 3.6 43 71-113 159-201 (325)
417 smart00530 HTH_XRE Helix-turn- 27.4 45 0.00098 21.1 1.8 25 87-111 8-32 (56)
418 PRK10430 DNA-binding transcrip 27.4 74 0.0016 28.6 3.7 33 86-118 175-207 (239)
419 PRK09940 transcriptional regul 27.4 1.1E+02 0.0025 28.3 4.9 85 29-113 86-174 (253)
420 PRK13509 transcriptional repre 27.3 70 0.0015 29.5 3.6 27 89-115 19-45 (251)
421 TIGR03339 phn_lysR aminoethylp 27.3 48 0.0011 30.3 2.5 34 85-118 7-40 (279)
422 CHL00180 rbcR LysR transcripti 27.2 60 0.0013 30.4 3.2 33 86-118 16-48 (305)
423 PRK03635 chromosome replicatio 26.8 70 0.0015 29.8 3.5 33 86-118 13-45 (294)
424 TIGR02684 dnstrm_HI1420 probab 26.6 48 0.001 25.4 1.9 20 92-111 46-65 (89)
425 PRK15092 DNA-binding transcrip 26.5 50 0.0011 31.3 2.5 42 77-118 13-54 (310)
426 COG4496 Uncharacterized protei 26.5 44 0.00095 25.5 1.6 29 83-111 50-78 (100)
427 COG3311 AlpA Predicted transcr 26.5 38 0.00081 24.8 1.2 23 91-113 15-37 (70)
428 COG0593 DnaA ATPase involved i 26.4 92 0.002 31.1 4.3 48 71-118 347-394 (408)
429 PF02082 Rrf2: Transcriptional 26.4 77 0.0017 23.5 3.1 26 90-115 26-51 (83)
430 PRK10837 putative DNA-binding 26.2 62 0.0013 29.9 3.0 37 82-118 10-46 (290)
431 COG2826 Tra8 Transposase and i 25.7 64 0.0014 30.6 2.9 40 72-112 7-46 (318)
432 PRK10434 srlR DNA-bindng trans 25.4 77 0.0017 29.3 3.5 41 76-116 4-46 (256)
433 TIGR02036 dsdC D-serine deamin 25.2 54 0.0012 30.8 2.5 36 83-118 16-51 (302)
434 PF11198 DUF2857: Protein of u 25.1 4.4E+02 0.0095 23.0 8.0 82 32-114 80-178 (180)
435 PRK10632 transcriptional regul 25.0 59 0.0013 30.6 2.7 34 85-118 12-45 (309)
436 PRK13832 plasmid partitioning 24.8 90 0.002 32.0 4.0 41 71-111 100-140 (520)
437 TIGR03384 betaine_BetI transcr 24.7 73 0.0016 27.2 3.1 33 88-120 27-59 (189)
438 PF13411 MerR_1: MerR HTH fami 24.3 47 0.001 23.4 1.5 23 91-113 2-24 (69)
439 PRK04841 transcriptional regul 24.1 60 0.0013 35.7 2.9 45 72-118 838-882 (903)
440 PF09182 PuR_N: Bacterial puri 24.0 1.5E+02 0.0033 21.6 3.9 30 90-119 21-50 (70)
441 PF14549 P22_Cro: DNA-binding 24.0 46 0.00099 23.5 1.3 25 91-116 11-35 (60)
442 PF02295 z-alpha: Adenosine de 23.7 87 0.0019 22.5 2.7 38 75-113 5-44 (66)
443 cd00093 HTH_XRE Helix-turn-hel 23.7 53 0.0012 20.9 1.6 25 87-111 10-34 (58)
444 PRK03601 transcriptional regul 23.6 79 0.0017 29.2 3.3 37 82-118 8-44 (275)
445 COG2944 Predicted transcriptio 23.5 46 0.001 26.3 1.3 23 87-109 55-77 (104)
446 TIGR02404 trehalos_R_Bsub treh 23.3 56 0.0012 29.5 2.1 23 93-115 28-50 (233)
447 PRK09480 slmA division inhibit 23.2 53 0.0012 28.3 1.9 32 88-119 29-60 (194)
448 PF12833 HTH_18: Helix-turn-he 23.1 1.5E+02 0.0032 21.5 4.1 66 45-114 3-71 (81)
449 PRK09390 fixJ response regulat 23.1 76 0.0016 26.7 2.8 33 85-117 152-184 (202)
450 PRK15340 transcriptional regul 23.1 81 0.0018 28.5 3.0 29 87-115 123-151 (216)
451 TIGR02612 mob_myst_A mobile my 23.1 49 0.0011 28.1 1.5 27 85-111 34-60 (150)
452 PRK01905 DNA-binding protein F 22.9 97 0.0021 22.8 2.9 26 88-113 49-74 (77)
453 PF05584 Sulfolobus_pRN: Sulfo 22.7 1.6E+02 0.0035 21.6 3.9 41 73-115 4-44 (72)
454 TIGR03734 PRTRC_parB PRTRC sys 22.7 92 0.002 32.4 3.6 42 71-112 90-132 (554)
455 TIGR00738 rrf2_super rrf2 fami 22.6 93 0.002 25.2 3.1 27 89-115 25-51 (132)
456 PF07900 DUF1670: Protein of u 22.6 4.3E+02 0.0094 23.9 7.4 81 38-119 106-193 (220)
457 PRK15121 right oriC-binding tr 22.5 1.1E+02 0.0025 28.6 4.1 29 86-114 18-46 (289)
458 PF00376 MerR: MerR family reg 22.4 54 0.0012 20.6 1.2 19 92-110 2-20 (38)
459 PRK04424 fatty acid biosynthes 22.1 96 0.0021 27.2 3.3 27 90-116 22-48 (185)
460 PRK13698 plasmid-partitioning 22.1 75 0.0016 30.6 2.7 39 73-111 158-198 (323)
461 PRK10086 DNA-binding transcrip 22.1 85 0.0018 29.6 3.2 38 81-118 20-57 (311)
462 PF07506 RepB: RepB plasmid pa 22.0 1.4E+02 0.0029 26.1 4.2 41 71-111 3-43 (185)
463 PRK14165 winged helix-turn-hel 21.9 1E+02 0.0022 27.9 3.4 26 90-115 22-47 (217)
464 PRK11482 putative DNA-binding 21.9 86 0.0019 29.7 3.2 33 86-118 40-72 (317)
465 PF02575 YbaB_DNA_bd: YbaB/Ebf 21.7 3.5E+02 0.0077 20.3 7.4 58 180-286 31-89 (93)
466 PF04492 Phage_rep_O: Bacterio 21.7 1.4E+02 0.0029 23.5 3.7 39 77-115 35-80 (100)
467 PRK13890 conjugal transfer pro 21.6 55 0.0012 26.5 1.5 25 87-111 16-40 (120)
468 PRK11886 bifunctional biotin-- 21.5 1.2E+02 0.0026 28.9 4.1 27 89-115 18-44 (319)
469 PRK00423 tfb transcription ini 21.3 3.3E+02 0.0071 26.0 7.0 75 43-117 132-210 (310)
470 PRK15243 transcriptional regul 21.3 1E+02 0.0023 29.1 3.6 41 77-118 7-47 (297)
471 PF12298 Bot1p: Eukaryotic mit 21.2 1.4E+02 0.0031 25.9 4.0 42 70-111 14-55 (172)
472 PRK10906 DNA-binding transcrip 21.1 1.1E+02 0.0024 28.3 3.6 27 90-116 20-46 (252)
473 PF09012 FeoC: FeoC like trans 21.0 82 0.0018 22.5 2.2 26 88-113 13-38 (69)
474 COG1510 Predicted transcriptio 21.0 87 0.0019 27.2 2.6 40 77-116 29-68 (177)
475 PRK15183 Vi polysaccharide bio 20.4 96 0.0021 24.4 2.5 50 81-130 90-139 (143)
476 COG4941 Predicted RNA polymera 20.3 1.7E+02 0.0037 28.5 4.5 48 71-119 119-166 (415)
477 PRK10411 DNA-binding transcrip 20.3 1.3E+02 0.0027 27.6 3.7 27 89-115 18-44 (240)
478 PRK09943 DNA-binding transcrip 20.1 59 0.0013 28.3 1.5 26 86-111 17-42 (185)
479 PRK11062 nhaR transcriptional 20.1 78 0.0017 29.5 2.5 34 85-118 14-47 (296)
480 TIGR00270 conserved hypothetic 20.1 62 0.0014 27.6 1.6 26 86-111 79-104 (154)
No 1
>KOG4585 consensus Predicted transposase [Replication, recombination and repair]
Probab=100.00 E-value=2.1e-43 Score=334.56 Aligned_cols=311 Identities=31% Similarity=0.518 Sum_probs=257.1
Q ss_pred hcCCCHHHHHHHHHHhccCCccccC-----CCCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHHh
Q 016400 46 NFRMDKKVFYKLCDILQSKGLLRHT-----NRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 120 (390)
Q Consensus 46 ~frms~~~F~~L~~~L~~~~~~~~~-----~~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 120 (390)
.|++++.+|..++............ ..+++...+++.++.++++.+.+.++..||...+|+ .+.......
T Consensus 7 ~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~i~~~fg~~~~~~-----~~~~~~~~~ 81 (326)
T KOG4585|consen 7 EFRKSYTTFDKICSLVQSLNVVKNSGFMLSSLLPADTLVAVALWRLKTGESLRTVEKKFGLGQSTC-----KFLEEKEDL 81 (326)
T ss_pred HHHHHHHHHHHHhhhhhhhhhhcccchhhhccccHHhhhhhhhccccccchHHHHHHHcCCcchhh-----hHHHhhhcc
Confidence 7888999999999987654322111 123388999999999999999999999999999999 555566678
Q ss_pred hccccCCCCCCCchhhccCCcccCCCccccccccceEEEEEeCCCCCCCCCCCCCCceeeeeeeecCCcceeEeccCccc
Q 016400 121 SLDFFQPPGPDVPPEISLDPRLYPYFKDCVGAVDGIHIPVMVGVDEQGPFRNKSGLLSQNVLAACSFDLKFHYVLAGWEG 200 (390)
Q Consensus 121 ~~~~i~~P~~~~~~~i~~~~~~~~~fp~~iG~IDgt~i~i~~P~~~~~~y~~~k~~~s~~~q~v~d~d~~~~~v~~g~~G 200 (390)
+..++.||.......+.+.++. +|+|+|+||+|||++..|......|.|+ .++.|+|+|||+|++|++|.+||||
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 9999999997666777665543 9999999999999999999999999988 8899999999999999999999999
Q ss_pred ccccHHHHHHHHhh-cCCCCCCCCceeeccCCCCCCCCccccccCcccCcccccCCCC-ChhhHHHHHHHHHHHHhHHHH
Q 016400 201 SASDLRVLNSALTR-RNKLQVPEGKYYLVDNKYANMPGFIAPYQAVSYHTNQTTTGYH-PQDAKELFNQRHSLLRNATDR 278 (390)
Q Consensus 201 s~~D~~vl~~sl~~-~~~~~~p~g~~~l~D~gYp~~~~ll~P~~~~~~~~~~~~~~~~-~~~~~~~fN~~~s~~R~~VE~ 278 (390)
|.||+.|++.++.. ......|. +|+|.|.||++.++++.|+..+.++.-.+..+++ |+..+++||++|+.+|.++|+
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 33334455 9999999999999999999999999988887774 889999999999999999999
Q ss_pred HHHHHHhhchhhhcCCCCCccchhHHHHHHHHHHhhhhccCCCcccccccccCCcccccccCCCCCCCCCCCCCCccccc
Q 016400 279 IFGALKERFPILLSAPPYPLQTQVKLVVAACALHNYIQREKPDDWLFRMYEQDTLLPMAESLLPLEGEQPIVHVDTRALE 358 (390)
Q Consensus 279 ~fg~LK~rf~iL~~~~~~~~~~~~~ii~a~~~LhN~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 358 (390)
+||+||+||+||.+...+...+..+||.|||+|||++++.+..+..+..++... .+. .+...
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 999999999999977778899999999999999999999887664433221111 000 01111
Q ss_pred cccchHHHHHHHHHHHHHHHHHHHHhh
Q 016400 359 FGFQTEQLELASHFRDSIATEMWDDYI 385 (390)
Q Consensus 359 ~~~~~~~~~~~~~~Rd~ia~~lw~~~~ 385 (390)
.....+.++.++.+|+.|+..||+...
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=2.7e-43 Score=300.32 Aligned_cols=187 Identities=23% Similarity=0.361 Sum_probs=164.0
Q ss_pred cccCCCCCCCchhhccCCcccCCCccccccccceEEEEE-eCCCCCCCCC-CCCCCceeeeeeeecCCcceeEeccCccc
Q 016400 123 DFFQPPGPDVPPEISLDPRLYPYFKDCVGAVDGIHIPVM-VGVDEQGPFR-NKSGLLSQNVLAACSFDLKFHYVLAGWEG 200 (390)
Q Consensus 123 ~~i~~P~~~~~~~i~~~~~~~~~fp~~iG~IDgt~i~i~-~P~~~~~~y~-~~k~~~s~~~q~v~d~d~~~~~v~~g~~G 200 (390)
+|++.|+.++..+++...+. .||||++|+|||+|+.++ +|..++.+|. |++|.+|+.++||+++|++|++++.|.||
T Consensus 2 ~YLr~P~~~d~~rll~~~e~-rGFpGmlGSIDCmHw~WkncP~aw~g~~~~G~~g~pTiiLEaVAs~dlwIWhaffG~~G 80 (205)
T PF04827_consen 2 EYLRRPTNEDLERLLQIGEA-RGFPGMLGSIDCMHWEWKNCPTAWKGQYTRGKEGVPTIILEAVASHDLWIWHAFFGMPG 80 (205)
T ss_pred cccCCCChhHHHHHHHhhhh-cCCCccccceeEEEeehhcchHHhhhcccCCCCCCCeehhhhhhccchhhhheeeccCC
Confidence 68999999998888864433 499999999999999997 8999999997 99999999999999999999999999999
Q ss_pred ccccHHHHHHH-Hhh-cCCCCCCC-----------CceeeccCCCCCCCCccccccCcccCcccccCCCCChhhHHHHHH
Q 016400 201 SASDLRVLNSA-LTR-RNKLQVPE-----------GKYYLVDNKYANMPGFIAPYQAVSYHTNQTTTGYHPQDAKELFNQ 267 (390)
Q Consensus 201 s~~D~~vl~~s-l~~-~~~~~~p~-----------g~~~l~D~gYp~~~~ll~P~~~~~~~~~~~~~~~~~~~~~~~fN~ 267 (390)
|.||.+||..| +.. ......|+ -.|||+|++||.+..++++++.|. +.++++|.+
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 332 11112222 279999999999999999998763 568899999
Q ss_pred HHHHHHhHHHHHHHHHHhhchhhhcC-CCCCccchhHHHHHHHHHHhhhhccCCCc
Q 016400 268 RHSLLRNATDRIFGALKERFPILLSA-PPYPLQTQVKLVVAACALHNYIQREKPDD 322 (390)
Q Consensus 268 ~~s~~R~~VE~~fg~LK~rf~iL~~~-~~~~~~~~~~ii~a~~~LhN~~~~~~~~~ 322 (390)
+++++|+.||||||+|++||+|++.+ ..|+.+.+..|+.||+||||||++++++.
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 99999999999999999999999976 66899999999999999999999998764
No 3
>PF13359 DDE_Tnp_4: DDE superfamily endonuclease
Probab=100.00 E-value=3e-37 Score=266.96 Aligned_cols=153 Identities=32% Similarity=0.552 Sum_probs=136.5
Q ss_pred ccceEEEEEeCCC---CCCCCCCCCCCceeeeeeeecCCcceeEeccCcccccccHHHHHHH-HhhcCCCCCCCCceeec
Q 016400 153 VDGIHIPVMVGVD---EQGPFRNKSGLLSQNVLAACSFDLKFHYVLAGWEGSASDLRVLNSA-LTRRNKLQVPEGKYYLV 228 (390)
Q Consensus 153 IDgt~i~i~~P~~---~~~~y~~~k~~~s~~~q~v~d~d~~~~~v~~g~~Gs~~D~~vl~~s-l~~~~~~~~p~g~~~l~ 228 (390)
||||||++++|.. ....|+++|+.+++|+|+|||++|+|+++.+++|||+||+++|+++ +.......+++|.++||
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 5677999999999999999999999999999999999999999987 33211112678899999
Q ss_pred cCCCCCCCCccccccCcccCcccccCCCCChhhHHHHHHHHHHHHhHHHHHHHHHHhhchhhhcCCCCC-ccchhHHHHH
Q 016400 229 DNKYANMPGFIAPYQAVSYHTNQTTTGYHPQDAKELFNQRHSLLRNATDRIFGALKERFPILLSAPPYP-LQTQVKLVVA 307 (390)
Q Consensus 229 D~gYp~~~~ll~P~~~~~~~~~~~~~~~~~~~~~~~fN~~~s~~R~~VE~~fg~LK~rf~iL~~~~~~~-~~~~~~ii~a 307 (390)
|+|||+.+++++||+.+ .+.+++.+++.||++|+++|..||++||.||+||+||......+ .+.+.++|.|
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 016400 308 ACALHN 313 (390)
Q Consensus 308 ~~~LhN 313 (390)
||+|||
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=98.94 E-value=1.1e-09 Score=76.13 Aligned_cols=49 Identities=22% Similarity=0.385 Sum_probs=46.8
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHHh
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 120 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 120 (390)
.++++++++++|.+|++|.++.++|..||||+|||+++++++++.|...
T Consensus 2 kLs~~d~lll~L~~LR~~~~~~~La~~FgIs~stvsri~~~~~~~L~~~ 50 (53)
T PF13613_consen 2 KLSLEDQLLLTLMYLRLNLTFQDLAYRFGISQSTVSRIFHEWIPLLYQV 50 (53)
T ss_pred CCCHHHHHHHHHHHHHcCCcHhHHhhheeecHHHHHHHHHHHHHHHHHh
Confidence 5799999999999999999999999999999999999999999999854
No 5
>PF13612 DDE_Tnp_1_3: Transposase DDE domain
Probab=98.90 E-value=3.2e-10 Score=96.71 Aligned_cols=126 Identities=15% Similarity=0.121 Sum_probs=92.5
Q ss_pred ccccccccceEEEEEeCCCC-------CCC---CCCCCCCceeeeeeeecCCcceeEeccCcccccccHHHHHHHHhhcC
Q 016400 147 KDCVGAVDGIHIPVMVGVDE-------QGP---FRNKSGLLSQNVLAACSFDLKFHYVLAGWEGSASDLRVLNSALTRRN 216 (390)
Q Consensus 147 p~~iG~IDgt~i~i~~P~~~-------~~~---y~~~k~~~s~~~q~v~d~d~~~~~v~~g~~Gs~~D~~vl~~sl~~~~ 216 (390)
+..+.+||.|.||++.+... +.. |+..+-+++++++++|+..|.++.+.. .||++||..++.....
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 45688999999999866432 111 333345699999999999999988755 6999999999853322
Q ss_pred CCCCCCCceeeccCCCCCCC----------CccccccCcccCcccccCCCCChhhHHHHHHHHHHHHhHHHHHHHHHHhh
Q 016400 217 KLQVPEGKYYLVDNKYANMP----------GFIAPYQAVSYHTNQTTTGYHPQDAKELFNQRHSLLRNATDRIFGALKER 286 (390)
Q Consensus 217 ~~~~p~g~~~l~D~gYp~~~----------~ll~P~~~~~~~~~~~~~~~~~~~~~~~fN~~~s~~R~~VE~~fg~LK~r 286 (390)
. ....++||.||-... .|+||.+.+- -......+++.+.+.|..||-+|+.||+.
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 135799999995433 3677776542 01123457888999999999999999999
Q ss_pred chhhh
Q 016400 287 FPILL 291 (390)
Q Consensus 287 f~iL~ 291 (390)
|.|-.
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=98.09 E-value=9.9e-08 Score=85.20 Aligned_cols=162 Identities=15% Similarity=0.031 Sum_probs=87.3
Q ss_pred cccccccceEEEEEeCCCCCCCCCCCCCCceeeeeeee-cCCcceeEeccCcccccccHHHHHHHHhhcCCCCCCCCcee
Q 016400 148 DCVGAVDGIHIPVMVGVDEQGPFRNKSGLLSQNVLAAC-SFDLKFHYVLAGWEGSASDLRVLNSALTRRNKLQVPEGKYY 226 (390)
Q Consensus 148 ~~iG~IDgt~i~i~~P~~~~~~y~~~k~~~s~~~q~v~-d~d~~~~~v~~g~~Gs~~D~~vl~~sl~~~~~~~~p~g~~~ 226 (390)
..+-+||+|+|+..........+.+++.....++++++ +..+.++.+.+. +|+.+|...+...+.. .....+.++
T Consensus 4 ~~~~~iD~T~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~d~~~~~~ll~~---~~~~~~~~v 79 (213)
T PF01609_consen 4 RRVVAIDGTTIRTPHDKSARRYKKGKKRGFGYKLHLAVDDNSGLPLSVKVT-PGNVHDSKALPELLER---KPGRKPDLV 79 (213)
T ss_dssp EEEEEEETTT--EEEEEEE-B-SSGGGHSSHGGHHHHHHHHHGGGGGGEEE-EEEGG-HHHHHHHHTT--------EEEE
T ss_pred CeEEEEECcEEEeecchhhhcccCCCCcCCCEeEEEEEeecccceeeeecc-ccccceeecccccccc---cccccccce
Confidence 35678999999988111112234455666777999998 455666666666 9999999999986552 234456899
Q ss_pred eccCCCCCCC----------CccccccCcccCcccccCCC-----------------------CChhhHHHHHHH-----
Q 016400 227 LVDNKYANMP----------GFIAPYQAVSYHTNQTTTGY-----------------------HPQDAKELFNQR----- 268 (390)
Q Consensus 227 l~D~gYp~~~----------~ll~P~~~~~~~~~~~~~~~-----------------------~~~~~~~~fN~~----- 268 (390)
++|+||.... .++.|.+........-.... ......+.....
T Consensus 80 v~D~gy~s~~~~~~l~~~~~~~vi~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 159 (213)
T PF01609_consen 80 VADRGYDSAENLEALKERGIHFVIRLKKNRKKKIQKIENKFWKSFDRRSARKKPKQKSKRVRVVIRKEQKKKGYFLVTNI 159 (213)
T ss_dssp EE-S--BBTTHHHHHHTS---EEEEE--EEEE-TTS-EEEE--EEEEEEEEEEETGGGEEEEEEEEEECS--TTS---EE
T ss_pred eecccccceeccccccccccccccccccccccccccchhhcccccccccccccccccccccccccccccccccccccccc
Confidence 9999996443 22444444332210000000 000001111111
Q ss_pred ---------HHHHHhHHHHHHHHHHhhchhhhcCCCCCccchhHHHHHHHHHHhh
Q 016400 269 ---------HSLLRNATDRIFGALKERFPILLSAPPYPLQTQVKLVVAACALHNY 314 (390)
Q Consensus 269 ---------~s~~R~~VE~~fg~LK~rf~iL~~~~~~~~~~~~~ii~a~~~LhN~ 314 (390)
..+.|..||+.|..||..|. +......+...+...+.++++..|+
T Consensus 160 ~~~~~~~~~~Y~~Rw~IE~~f~~lK~~~~-l~~~~~~~~~~~~~~~~~~~la~nl 213 (213)
T PF01609_consen 160 TTLPRDTAALYRRRWQIERFFRELKQFLG-LERLRVRSPERIEAHLFLTLLAYNL 213 (213)
T ss_dssp EEEESS--SHHHCGGHHHHHHHHHTTTTT-GGGS--SSHHHHHHHHHHHHHH---
T ss_pred cccccccceeecccchhhHHHHHHHhcCC-CchhcccCHHHHHHHHHHHHhhCcC
Confidence 89999999999999998765 3434556677777777777777764
No 7
>PF13586 DDE_Tnp_1_2: Transposase DDE domain
Probab=97.16 E-value=0.00017 Score=55.66 Aligned_cols=48 Identities=21% Similarity=0.108 Sum_probs=32.4
Q ss_pred HHHHHHHHHHHHhHHHHHHHHHHhhchhhhcCCCCCcc-chhHHHHHHHH
Q 016400 262 KELFNQRHSLLRNATDRIFGALKERFPILLSAPPYPLQ-TQVKLVVAACA 310 (390)
Q Consensus 262 ~~~fN~~~s~~R~~VE~~fg~LK~rf~iL~~~~~~~~~-~~~~ii~a~~~ 310 (390)
...+.....+.|.+|||+|+.||. |+.|......... ....+.+||++
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 456778889999999999999996 5655543333334 44444555544
No 8
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=96.28 E-value=0.0033 Score=41.61 Aligned_cols=41 Identities=20% Similarity=0.297 Sum_probs=23.0
Q ss_pred CCCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHH
Q 016400 71 NRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNN 112 (390)
Q Consensus 71 ~~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~ 112 (390)
+.++.+++..+.-+ +..|.+.+.+|..+|+|+|||++.+++
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 678999999999999999999998875
No 9
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=96.20 E-value=0.01 Score=40.30 Aligned_cols=45 Identities=18% Similarity=0.197 Sum_probs=38.4
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHH
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAI 117 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l 117 (390)
.++++++-.+.++| ..+.++.++|..+|+|.+||+++.++.+.-|
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 58889999999998 5689999999999999999999999887765
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=95.59 E-value=0.014 Score=40.25 Aligned_cols=42 Identities=24% Similarity=0.329 Sum_probs=31.0
Q ss_pred CCCCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHH
Q 016400 70 TNRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNN 112 (390)
Q Consensus 70 ~~~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~ 112 (390)
+..+++++++-+.-. +-.|.+..++|..|||+.|||+.+++.
T Consensus 4 R~~LTl~eK~~iI~~-~e~g~s~~~ia~~fgv~~sTv~~I~K~ 45 (53)
T PF04218_consen 4 RKSLTLEEKLEIIKR-LEEGESKRDIAREFGVSRSTVSTILKN 45 (53)
T ss_dssp SSS--HHHHHHHHHH-HHCTT-HHHHHHHHT--CCHHHHHHHC
T ss_pred CccCCHHHHHHHHHH-HHcCCCHHHHHHHhCCCHHHHHHHHHh
Confidence 457899999887555 677889999999999999999998865
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=95.50 E-value=0.028 Score=38.71 Aligned_cols=44 Identities=9% Similarity=0.196 Sum_probs=33.9
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHH
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNA 116 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~ 116 (390)
.+|+.++.++.|.++. |.++.++|..+|+|.+||...+.+....
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 4788899888888876 8999999999999999999988877654
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=95.42 E-value=0.0052 Score=40.86 Aligned_cols=35 Identities=17% Similarity=0.235 Sum_probs=27.1
Q ss_pred HHHHHhhhcccccchhhhhhhcccchhhhhhhhHH
Q 016400 78 QLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNN 112 (390)
Q Consensus 78 ~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~ 112 (390)
++.-.+.++..|.+..++|..||||++||.|++++
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 45566677889999999999999999999998753
No 13
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=94.98 E-value=0.014 Score=39.56 Aligned_cols=30 Identities=13% Similarity=0.193 Sum_probs=21.3
Q ss_pred hcccccchhhhhhhcccchhhhhhhhHHHH
Q 016400 85 IVGHNLRTRAVQELFRYSGETISRHFNNVL 114 (390)
Q Consensus 85 ~L~~~~~~~~l~~~fgis~stv~~~~~~v~ 114 (390)
.+..|.+..++|..+|+|++||+++++++.
T Consensus 13 l~~~G~s~~~ia~~lgvs~~Tv~~w~kr~~ 42 (50)
T PF13384_consen 13 LLREGWSIREIAKRLGVSRSTVYRWIKRYR 42 (50)
T ss_dssp HHHHT--HHHHHHHHTS-HHHHHHHHT---
T ss_pred HHHCCCCHHHHHHHHCcCHHHHHHHHHHcc
Confidence 333499999999999999999999998874
No 14
>PF12116 SpoIIID: Stage III sporulation protein D; InterPro: IPR014208 Members of this entry represent the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if, and only if, the species is capable of endospore formation. In Bacillus subtilis SpoIIID is a DNA binding protein that is involved in gene repression as well as activation [].; PDB: 2L0K_A.
Probab=94.68 E-value=0.028 Score=41.60 Aligned_cols=43 Identities=23% Similarity=0.370 Sum_probs=31.3
Q ss_pred HHH-HHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 76 EEQ-LAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 76 ~~~-l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
+++ +-+.-|.+.++.+.+.+|..||||+|||++=+.+=+..|.
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 344 4567788899999999999999999999998877666665
No 15
>PF13518 HTH_28: Helix-turn-helix domain
Probab=94.55 E-value=0.036 Score=37.64 Aligned_cols=37 Identities=19% Similarity=0.249 Sum_probs=30.9
Q ss_pred HHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHH
Q 016400 78 QLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 78 ~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
++.+...++ .|.++.++|..||||.+||.++++.+..
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 445566666 5779999999999999999999988876
No 16
>PF05225 HTH_psq: helix-turn-helix, Psq domain; InterPro: IPR007889 This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster []. In pipsqueak this domain binds to GAGA sequence []. The pipsqueak family, which includes proteins from fungi, sea urchins, nematodes, insects, and vertebrates appear to be proteins essential for sequence-specific targeting of a polycomb group protein complex [].; GO: 0003677 DNA binding; PDB: 2COB_A.
Probab=93.99 E-value=0.056 Score=35.88 Aligned_cols=37 Identities=19% Similarity=0.274 Sum_probs=28.1
Q ss_pred HHHHHHHhhhcccc-cchhhhhhhcccchhhhhhhhHH
Q 016400 76 EEQLAIFMFIVGHN-LRTRAVQELFRYSGETISRHFNN 112 (390)
Q Consensus 76 ~~~l~~~L~~L~~~-~~~~~l~~~fgis~stv~~~~~~ 112 (390)
++.+..+|-.+..| .|++..|..|||+++|+++.++.
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 56677777777778 99999999999999999987653
No 17
>smart00351 PAX Paired Box domain.
Probab=93.83 E-value=0.094 Score=43.18 Aligned_cols=44 Identities=14% Similarity=0.157 Sum_probs=38.2
Q ss_pred CCCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHH
Q 016400 71 NRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 71 ~~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
+.++.+.+.-+.+.+. .|.+.+++|..||||.+||+++++++-.
T Consensus 16 ~~~s~~~R~riv~~~~-~G~s~~~iA~~~gvs~~tV~kwi~r~~~ 59 (125)
T smart00351 16 RPLPDEERQRIVELAQ-NGVRPCDISRQLCVSHGCVSKILGRYYE 59 (125)
T ss_pred CCCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4688988888877765 7999999999999999999999998744
No 18
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=93.53 E-value=0.073 Score=44.42 Aligned_cols=43 Identities=19% Similarity=0.186 Sum_probs=38.4
Q ss_pred CCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHH
Q 016400 73 IKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 73 ~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
.+.+.+.+++..++..|.|.+++|.+||||.+|+.++++++-+
T Consensus 5 ~s~~~R~~~~~~~~~~G~S~re~Ak~~gvs~sTvy~wv~r~~e 47 (138)
T COG3415 5 FSNDLRERVVDAVVGEGLSCREAAKRFGVSISTVYRWVRRYRE 47 (138)
T ss_pred hhHHHHHHHHHHHHHcCccHHHHHHHhCccHHHHHHHHHHhcc
Confidence 4567888899999999999999999999999999999988754
No 19
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=93.42 E-value=0.11 Score=39.42 Aligned_cols=45 Identities=13% Similarity=0.115 Sum_probs=41.7
Q ss_pred CCCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHH
Q 016400 71 NRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 71 ~~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
-.+++.-++.+.-..+..|.+...++..||||..|+++++.++-.
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 468999999999999999999999999999999999999988864
No 20
>PF13340 DUF4096: Putative transposase of IS4/5 family (DUF4096)
Probab=93.29 E-value=0.17 Score=37.53 Aligned_cols=66 Identities=17% Similarity=0.230 Sum_probs=49.0
Q ss_pred CHHHHHHHHHHhccCCccccCCCCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHH
Q 016400 50 DKKVFYKLCDILQSKGLLRHTNRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNA 116 (390)
Q Consensus 50 s~~~F~~L~~~L~~~~~~~~~~~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~ 116 (390)
|-+....|-..|.+.......+..+..+-+-..|+.+.+|++++.|...|| +.+||++.|++....
T Consensus 2 sD~~W~~i~p~lp~~~~~~~~~~~~~R~v~~ail~~lrtG~~Wr~LP~~fg-~~~tv~~~f~rW~~~ 67 (75)
T PF13340_consen 2 SDEEWALIEPLLPPRKPRGGRPRIDLREVLNAILYVLRTGCPWRDLPEDFG-PWSTVYRRFRRWSRS 67 (75)
T ss_pred CHHHHHHHHhhCCCCCCCCCCCccchHHHHhcccccceecceecccchhcc-CcCcHHHHHHHHHHc
Confidence 334445555555543322233567888888899999999999999999999 889999999887663
No 21
>cd00131 PAX Paired Box domain
Probab=93.02 E-value=0.15 Score=42.21 Aligned_cols=45 Identities=13% Similarity=0.150 Sum_probs=38.8
Q ss_pred CCCCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHH
Q 016400 70 TNRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 70 ~~~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
.+.+|.+.+..+.+.+ ..|.+.+++|..||||.+||.++++++-+
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 68999999999999999999999988765
No 22
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=92.68 E-value=0.18 Score=41.23 Aligned_cols=46 Identities=11% Similarity=0.055 Sum_probs=42.0
Q ss_pred cCCCCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHH
Q 016400 69 HTNRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVL 114 (390)
Q Consensus 69 ~~~~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~ 114 (390)
.++..+.+.++.+....+..|.+..++|..||||.+|+++|++.+.
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 3467999999999999999999999999999999999999988764
No 23
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=92.65 E-value=0.11 Score=38.47 Aligned_cols=45 Identities=13% Similarity=0.006 Sum_probs=37.5
Q ss_pred CCCCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHH
Q 016400 70 TNRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVL 114 (390)
Q Consensus 70 ~~~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~ 114 (390)
.+..|++.+.-+.-.++..|.+..+++..+||+.+|++++++.+.
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 356899999999888899999999999999999999999999887
No 24
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=92.61 E-value=0.23 Score=33.92 Aligned_cols=43 Identities=16% Similarity=0.386 Sum_probs=34.2
Q ss_pred CCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHH
Q 016400 73 IKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAI 117 (390)
Q Consensus 73 ~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l 117 (390)
++..+.-.+.+ +..|.++.++|..+|+|.+||.++++++...|
T Consensus 4 l~~~e~~i~~~--~~~g~s~~eia~~l~is~~tv~~~~~~~~~kl 46 (58)
T smart00421 4 LTPREREVLRL--LAEGLTNKEIAERLGISEKTVKTHLSNIMRKL 46 (58)
T ss_pred CCHHHHHHHHH--HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 55555543333 46899999999999999999999999887765
No 25
>PRK04217 hypothetical protein; Provisional
Probab=92.60 E-value=0.23 Score=39.73 Aligned_cols=48 Identities=15% Similarity=0.077 Sum_probs=39.4
Q ss_pred CCCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHH
Q 016400 71 NRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMA 119 (390)
Q Consensus 71 ~~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 119 (390)
..++.+++-++.|+++ .|.++.++|..+|+|.+||.+++++....|.+
T Consensus 41 ~~Lt~eereai~l~~~-eGlS~~EIAk~LGIS~sTV~r~L~RArkkLre 88 (110)
T PRK04217 41 IFMTYEEFEALRLVDY-EGLTQEEAGKRMGVSRGTVWRALTSARKKVAQ 88 (110)
T ss_pred ccCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 4678888755544443 68999999999999999999999998888864
No 26
>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=92.32 E-value=0.17 Score=38.77 Aligned_cols=34 Identities=15% Similarity=0.023 Sum_probs=28.0
Q ss_pred HHHHHHHhhhcccccchhhhhhhcccchhhhhhhh
Q 016400 76 EEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHF 110 (390)
Q Consensus 76 ~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~ 110 (390)
.++ ...+.+++.|.++.++|..+|+|++||+++.
T Consensus 38 s~R-~~I~~ll~~G~S~~eIA~~LgISrsTIyRi~ 71 (88)
T TIGR02531 38 AQR-LQVAKMLKQGKTYSDIEAETGASTATISRVK 71 (88)
T ss_pred hHH-HHHHHHHHCCCCHHHHHHHHCcCHHHHHHHH
Confidence 344 4455568889999999999999999999955
No 27
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=91.72 E-value=0.29 Score=32.69 Aligned_cols=43 Identities=16% Similarity=0.274 Sum_probs=34.1
Q ss_pred CCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHH
Q 016400 73 IKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNA 116 (390)
Q Consensus 73 ~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~ 116 (390)
++..++-++-+.++ .|.++.+++..+|+|.+|+.+++++....
T Consensus 11 l~~~~~~~~~~~~~-~~~~~~~ia~~~~~s~~~i~~~~~~~~~~ 53 (55)
T cd06171 11 LPEREREVILLRFG-EGLSYEEIAEILGISRSTVRQRLHRALKK 53 (55)
T ss_pred CCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 55666666655554 68999999999999999999999886543
No 28
>PRK00118 putative DNA-binding protein; Validated
Probab=91.26 E-value=0.4 Score=37.97 Aligned_cols=47 Identities=6% Similarity=0.142 Sum_probs=38.8
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHH
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMA 119 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 119 (390)
.++..++-++.++++ .|.++..+|..+|+|++||++.+++....+.+
T Consensus 17 ~L~ekqRevl~L~y~-eg~S~~EIAe~lGIS~~TV~r~L~RArkkLr~ 63 (104)
T PRK00118 17 LLTEKQRNYMELYYL-DDYSLGEIAEEFNVSRQAVYDNIKRTEKLLED 63 (104)
T ss_pred cCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 467777777666655 49999999999999999999999988887764
No 29
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=91.04 E-value=0.36 Score=41.26 Aligned_cols=48 Identities=4% Similarity=0.163 Sum_probs=43.1
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHHhh
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAIS 121 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~ 121 (390)
.+|..++-++.|++ .|.++.++|..+|+|.+||...+.+....|....
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 58888999988887 8999999999999999999999999998887543
No 30
>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=90.47 E-value=0.18 Score=31.69 Aligned_cols=21 Identities=33% Similarity=0.425 Sum_probs=16.6
Q ss_pred CChhHHHhhcCCCHHHHHHHH
Q 016400 38 GQSERCLENFRMDKKVFYKLC 58 (390)
Q Consensus 38 ~~d~~f~~~frms~~~F~~L~ 58 (390)
.+|++|...|+|+|+.|..|=
T Consensus 2 Lsd~dF~~vFgm~~~eF~~lP 22 (36)
T PF02209_consen 2 LSDEDFEKVFGMSREEFYKLP 22 (36)
T ss_dssp S-HHHHHHHHSS-HHHHHHS-
T ss_pred cCHHHHHHHHCCCHHHHHHCh
Confidence 478999999999999999873
No 31
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=89.96 E-value=0.28 Score=33.27 Aligned_cols=31 Identities=16% Similarity=0.191 Sum_probs=25.3
Q ss_pred hhhcccccchhhhhhhcccchhhhhhhhHHH
Q 016400 83 MFIVGHNLRTRAVQELFRYSGETISRHFNNV 113 (390)
Q Consensus 83 L~~L~~~~~~~~l~~~fgis~stv~~~~~~v 113 (390)
+..|..+.++.++|..+|+|.+||.+++++.
T Consensus 21 ~~~~~~~~s~~~vA~~~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 21 LKLLRESRSFKDVARELGVSWSTVRRIFDRY 51 (52)
T ss_pred HHHHhhcCCHHHHHHHHCCCHHHHHHHHHhh
Confidence 3344444699999999999999999999875
No 32
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=89.87 E-value=0.54 Score=40.96 Aligned_cols=48 Identities=6% Similarity=0.225 Sum_probs=41.7
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHHh
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 120 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 120 (390)
.+|++++.++.|.++ .|.++.++|..+|+|.+||...+++.+..+.+.
T Consensus 127 ~Lp~~~R~v~~L~~~-~g~s~~EIA~~lgis~~tVk~~l~rAl~~~~~~ 174 (178)
T PRK12529 127 TLRPRVKQAFLMATL-DGMKQKDIAQALDIALPTVKKYIHQAYVTCLSL 174 (178)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 688999999999888 699999999999999999998888777766543
No 33
>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=89.61 E-value=0.4 Score=35.32 Aligned_cols=42 Identities=10% Similarity=0.071 Sum_probs=36.0
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHH
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNV 113 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v 113 (390)
.++...+.+..|.+.-.|.++.++|...|+|.+||..+++..
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 477777777777777789999999999999999999988763
No 34
>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=89.61 E-value=0.72 Score=31.37 Aligned_cols=32 Identities=13% Similarity=0.433 Sum_probs=28.6
Q ss_pred cccccchhhhhhhcccchhhhhhhhHHHHHHH
Q 016400 86 VGHNLRTRAVQELFRYSGETISRHFNNVLNAI 117 (390)
Q Consensus 86 L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l 117 (390)
+..|.++.++|..+++|.+||...+++....+
T Consensus 12 ~~~~~s~~eia~~l~~s~~tv~~~~~~~~~~l 43 (57)
T cd06170 12 LAEGKTNKEIADILGISEKTVKTHLRNIMRKL 43 (57)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHh
Confidence 45789999999999999999999999887765
No 35
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=89.16 E-value=0.57 Score=40.42 Aligned_cols=50 Identities=16% Similarity=0.102 Sum_probs=42.1
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHHhhc
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAISL 122 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~~ 122 (390)
.+++.++.++.|.++ .|.++.++|..+|+|.+||...+++...-|.....
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 58999999999999999999999988887765433
No 36
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=88.98 E-value=0.69 Score=42.23 Aligned_cols=50 Identities=14% Similarity=0.178 Sum_probs=43.2
Q ss_pred CCCHHHHHHHHhhhc---ccccchhhhhhhcccchhhhhhhhHHHHHHHHHhh
Q 016400 72 RIKIEEQLAIFMFIV---GHNLRTRAVQELFRYSGETISRHFNNVLNAIMAIS 121 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L---~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~ 121 (390)
.+|+.++-++.|++. -.|.++.++|..+|+|.+||....++....|-...
T Consensus 178 ~Lp~~~R~v~~L~y~l~~~eg~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~~l 230 (234)
T PRK08301 178 KLSDREKQIMELRFGLNGGEEKTQKEVADMLGISQSYISRLEKRIIKRLKKEI 230 (234)
T ss_pred hCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 688888888888874 57999999999999999999999999888886543
No 37
>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=88.88 E-value=0.48 Score=28.66 Aligned_cols=37 Identities=11% Similarity=0.055 Sum_probs=27.1
Q ss_pred CCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhh
Q 016400 73 IKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHF 110 (390)
Q Consensus 73 ~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~ 110 (390)
++.+++..+... +..+.+..+++..+|+|.+|+++++
T Consensus 6 ~~~~~~~~i~~~-~~~~~s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 6 LTPEQIEEARRL-LAAGESVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred CCHHHHHHHHHH-HHcCCCHHHHHHHHCCCHHHHHHhC
Confidence 455444444333 4567899999999999999999864
No 38
>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=88.76 E-value=0.81 Score=32.05 Aligned_cols=38 Identities=16% Similarity=0.141 Sum_probs=28.1
Q ss_pred HHHHHhhhcccc-cchhhhhhhcccchhhhhhhhHHHHH
Q 016400 78 QLAIFMFIVGHN-LRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 78 ~l~~~L~~L~~~-~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
.++.+|..-..+ .+..+|+..++++++|+++++++...
T Consensus 9 ~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~ 47 (62)
T PF12802_consen 9 RVLMALARHPGEELTQSELAERLGISKSTVSRIVKRLEK 47 (62)
T ss_dssp HHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 344455444433 79999999999999999999988755
No 39
>smart00153 VHP Villin headpiece domain.
Probab=88.72 E-value=0.31 Score=30.60 Aligned_cols=20 Identities=40% Similarity=0.529 Sum_probs=18.2
Q ss_pred CChhHHHhhcCCCHHHHHHH
Q 016400 38 GQSERCLENFRMDKKVFYKL 57 (390)
Q Consensus 38 ~~d~~f~~~frms~~~F~~L 57 (390)
.+|++|...|+|+|+.|..|
T Consensus 2 LsdeeF~~vfgmsr~eF~~L 21 (36)
T smart00153 2 LSDEDFEEVFGMTREEFYKL 21 (36)
T ss_pred CCHHHHHHHHCCCHHHHHhC
Confidence 37899999999999999886
No 40
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=88.58 E-value=0.56 Score=41.34 Aligned_cols=50 Identities=6% Similarity=0.022 Sum_probs=42.4
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHHhhc
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAISL 122 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~~ 122 (390)
.+|++++-++.|+++. |.++.++|..+|+|.+||...+++....|.....
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 5788888888787766 8999999999999999999999998888875443
No 41
>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=88.44 E-value=0.7 Score=30.74 Aligned_cols=38 Identities=21% Similarity=0.327 Sum_probs=28.0
Q ss_pred HHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHH
Q 016400 78 QLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 78 ~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
++-+.........+..++++.+|+|++||+++++...+
T Consensus 4 R~~Il~~L~~~~~~~~el~~~l~~s~~~vs~hL~~L~~ 41 (47)
T PF01022_consen 4 RLRILKLLSEGPLTVSELAEELGLSQSTVSHHLKKLRE 41 (47)
T ss_dssp HHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHHHhCCCchhhHHHhccccchHHHHHHHHHHH
Confidence 34443344446688999999999999999999887654
No 42
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=87.97 E-value=0.77 Score=39.66 Aligned_cols=53 Identities=8% Similarity=0.137 Sum_probs=42.7
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHHhhcccc
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAISLDFF 125 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~~~~i 125 (390)
.+|+..+-++.|.++ .|.++.++|..+|+|.+||...+.+....|......+|
T Consensus 119 ~L~~~~r~i~~l~~~-~~~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~~~~ 171 (173)
T PRK12522 119 LLNEKYKTVLVLYYY-EQYSYKEMSEILNIPIGTVKYRLNYAKKQMREHLEGFV 171 (173)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHHh
Confidence 466666655555555 48999999999999999999999999999987666554
No 43
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=87.96 E-value=0.81 Score=42.56 Aligned_cols=51 Identities=12% Similarity=0.189 Sum_probs=42.9
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHHhhcc
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAISLD 123 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~~~ 123 (390)
.+++.++..+.|+++ .+.++.++|..+|+|.++|+.+.++....|......
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 577778878888875 589999999999999999999999998888754433
No 44
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=87.60 E-value=1.5 Score=37.03 Aligned_cols=47 Identities=4% Similarity=0.068 Sum_probs=41.3
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHH
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMA 119 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 119 (390)
.+|+.++-.+.|.++ .|.++.++|..+|+|.+||...+++....|.+
T Consensus 111 ~L~~~~r~v~~l~~~-~g~~~~eIA~~l~is~~tv~~~l~Rar~~Lr~ 157 (159)
T TIGR02989 111 KLPERQRELLQLRYQ-RGVSLTALAEQLGRTVNAVYKALSRLRVRLRD 157 (159)
T ss_pred HCCHHHHHHHHHHHh-cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Confidence 688889988888776 59999999999999999999999888877753
No 45
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=87.57 E-value=0.97 Score=38.49 Aligned_cols=48 Identities=8% Similarity=0.070 Sum_probs=40.9
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHHh
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 120 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 120 (390)
.+++.++-.+.|.++. |.++.++|..+|+|.+||...+.+...-|...
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 5788888877777765 89999999999999999999988888877653
No 46
>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=87.52 E-value=1 Score=39.22 Aligned_cols=47 Identities=13% Similarity=0.171 Sum_probs=41.0
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHH
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMA 119 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 119 (390)
.+|+..+-++.|+++. |.++.++|..+|+|.+||...+++....|..
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 3888888888887775 8999999999999999999999998887764
No 47
>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=87.47 E-value=0.98 Score=38.64 Aligned_cols=47 Identities=11% Similarity=0.070 Sum_probs=41.7
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHH
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMA 119 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 119 (390)
.+|+.++.++.|+++. |.++.++|..+|+|.+||...+++....|-+
T Consensus 122 ~L~~~~r~vl~l~~~~-g~s~~eIA~~l~is~~tv~~~l~ra~~~Lr~ 168 (170)
T TIGR02952 122 ILTPKQQHVIALRFGQ-NLPIAEVARILGKTEGAVKILQFRAIKKLAR 168 (170)
T ss_pred hCCHHHHHHHHHHHhc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 6899999999998775 8999999999999999999999988877753
No 48
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=87.46 E-value=0.91 Score=39.52 Aligned_cols=49 Identities=12% Similarity=0.228 Sum_probs=43.1
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHHhh
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAIS 121 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~ 121 (390)
.+|..++-++.|.++. |.++.++|..+|+|.+||...+.+....|.+..
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 6888888888888887 899999999999999999999999888887543
No 49
>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=87.40 E-value=1 Score=34.60 Aligned_cols=48 Identities=13% Similarity=0.190 Sum_probs=43.4
Q ss_pred CCCCHHHHHHHHhhhcccccchhhhhhhcc-cchhhhhhhhHHHHHHHH
Q 016400 71 NRIKIEEQLAIFMFIVGHNLRTRAVQELFR-YSGETISRHFNNVLNAIM 118 (390)
Q Consensus 71 ~~~~~~~~l~~~L~~L~~~~~~~~l~~~fg-is~stv~~~~~~v~~~l~ 118 (390)
+.+...-++++.|-.--.|.++.++|..|| .+.|||+..++++-..+.
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 367888889999988888999999999999 999999999999988775
No 50
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=87.30 E-value=0.98 Score=38.28 Aligned_cols=48 Identities=8% Similarity=0.164 Sum_probs=42.3
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHHh
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 120 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 120 (390)
.+|..++-++.|.++. |.++.++|..+|+|.+||...+.+....|...
T Consensus 106 ~Lp~~~r~v~~l~~~~-g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~ 153 (161)
T PRK09047 106 KLPARQREAFLLRYWE-DMDVAETAAAMGCSEGSVKTHCSRATHALAKA 153 (161)
T ss_pred hCCHHHHHHHHHHHHh-cCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 6888888888887765 89999999999999999999999999988753
No 51
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=87.25 E-value=1 Score=39.34 Aligned_cols=47 Identities=9% Similarity=0.066 Sum_probs=40.2
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHH
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMA 119 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 119 (390)
.+|+..+.++.|.+ -.|.++.++|..+|+|.+||...+++....|-.
T Consensus 133 ~L~~~~r~i~~l~~-~~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 179 (182)
T PRK12537 133 QLEPARRNCILHAY-VDGCSHAEIAQRLGAPLGTVKAWIKRSLKALRE 179 (182)
T ss_pred hCCHHHHHHHHHHH-HcCCCHHHHHHHHCCChhhHHHHHHHHHHHHHH
Confidence 57888887777775 459999999999999999999999999888754
No 52
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=87.23 E-value=1.5 Score=38.16 Aligned_cols=49 Identities=12% Similarity=0.177 Sum_probs=43.1
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHHhh
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAIS 121 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~ 121 (390)
.+|++++-++.|.++. |.||.++|...|||.+||...+++....|.+..
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 5888888888888876 899999999999999999999999999887543
No 53
>TIGR00721 tfx DNA-binding protein, Tfx family. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.
Probab=87.22 E-value=0.94 Score=37.79 Aligned_cols=45 Identities=7% Similarity=0.082 Sum_probs=37.9
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
.++..++-.+.|+ ..|.++.++|..+|+|++||+++.++..+.|.
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 4666677666663 68999999999999999999999998888775
No 54
>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=87.21 E-value=0.34 Score=32.29 Aligned_cols=21 Identities=24% Similarity=0.254 Sum_probs=18.7
Q ss_pred hhhhhhhcccchhhhhhhhHH
Q 016400 92 TRAVQELFRYSGETISRHFNN 112 (390)
Q Consensus 92 ~~~l~~~fgis~stv~~~~~~ 112 (390)
..++|...|+|.+|||++++.
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 578999999999999998864
No 55
>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=87.19 E-value=1.1 Score=31.68 Aligned_cols=41 Identities=17% Similarity=0.262 Sum_probs=32.0
Q ss_pred HHHHHHHHhhhcc---cccchhhhhhhcccchhhhhhhhHHHHH
Q 016400 75 IEEQLAIFMFIVG---HNLRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 75 ~~~~l~~~L~~L~---~~~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
..+.-+-+++.|. ...+..+||..+++|++||+..+++..+
T Consensus 5 ~~e~YL~~Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~ 48 (60)
T PF01325_consen 5 SEEDYLKAIYELSEEGGPVRTKDIAERLGVSPPTVTEMLKRLAE 48 (60)
T ss_dssp HHHHHHHHHHHHHHCTSSBBHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHcCCCCccHHHHHHHHCCChHHHHHHHHHHHH
Confidence 3455666777776 5688999999999999999999887754
No 56
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=87.14 E-value=0.59 Score=32.15 Aligned_cols=30 Identities=17% Similarity=0.283 Sum_probs=26.2
Q ss_pred ccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 89 NLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 89 ~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
..+..+||..+|||++|++..+++...-|.
T Consensus 23 ~~tl~elA~~lgis~st~~~~LRrae~kli 52 (53)
T PF04967_consen 23 RITLEELAEELGISKSTVSEHLRRAERKLI 52 (53)
T ss_pred cCCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Confidence 477899999999999999999998877653
No 57
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=87.00 E-value=0.87 Score=40.09 Aligned_cols=48 Identities=8% Similarity=0.016 Sum_probs=42.3
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHHh
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 120 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 120 (390)
.+|+..+-++.|+++. |.++.++|..+|+|.+||...+++....|...
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 58
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=86.97 E-value=0.64 Score=32.39 Aligned_cols=37 Identities=11% Similarity=0.301 Sum_probs=32.0
Q ss_pred HhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 82 FMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 82 ~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
.|..++.|.+..++|...++|.+||..+...+..-+.
T Consensus 11 vl~~l~~G~~~~eIA~~l~is~~tV~~~~~~i~~Kl~ 47 (58)
T PF00196_consen 11 VLRLLAQGMSNKEIAEELGISEKTVKSHRRRIMKKLG 47 (58)
T ss_dssp HHHHHHTTS-HHHHHHHHTSHHHHHHHHHHHHHHHHT
T ss_pred HHHHHHhcCCcchhHHhcCcchhhHHHHHHHHHHHhC
Confidence 5677889999999999999999999999998887763
No 59
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=86.96 E-value=1 Score=39.40 Aligned_cols=51 Identities=12% Similarity=0.161 Sum_probs=44.2
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHHhhcc
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAISLD 123 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~~~ 123 (390)
.+|...+-++.|+++ .|.++.++|..+|+|.+||...+.+....|..+...
T Consensus 111 ~Lp~~~R~v~~L~~~-eg~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~~~~ 161 (182)
T PRK12511 111 DLPEEQRAALHLVAI-EGLSYQEAAAVLGIPIGTLMSRIGRARAALRAFEEG 161 (182)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHHh
Confidence 688888888888887 499999999999999999999999999888765543
No 60
>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=86.81 E-value=1.2 Score=29.64 Aligned_cols=37 Identities=11% Similarity=0.222 Sum_probs=26.7
Q ss_pred HHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHH
Q 016400 78 QLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 78 ~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
+++-.|.- ..+.+..++|..+|+|.+||++++++..+
T Consensus 7 ~Il~~l~~-~~~~t~~ela~~~~is~~tv~~~l~~L~~ 43 (48)
T PF13412_consen 7 KILNYLRE-NPRITQKELAEKLGISRSTVNRYLKKLEE 43 (48)
T ss_dssp HHHHHHHH-CTTS-HHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHH-cCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 34444443 34589999999999999999999988764
No 61
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=86.71 E-value=0.96 Score=38.49 Aligned_cols=46 Identities=15% Similarity=0.067 Sum_probs=39.8
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
.+|+.++-++.|.++. |.++.++|..+|+|.+||...+++....+.
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 6888888888888775 899999999999999999999888877663
No 62
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=86.69 E-value=1.1 Score=38.75 Aligned_cols=48 Identities=10% Similarity=0.094 Sum_probs=41.6
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHHh
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 120 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 120 (390)
.+|++++-.+.|.++ .|.++.++|..+|+|.+||...+.+....|.+.
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 578888888888876 689999999999999999999999988887643
No 63
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=86.67 E-value=1.1 Score=40.84 Aligned_cols=48 Identities=19% Similarity=0.175 Sum_probs=42.1
Q ss_pred CCCHHHHHHHHhhhc---ccccchhhhhhhcccchhhhhhhhHHHHHHHHH
Q 016400 72 RIKIEEQLAIFMFIV---GHNLRTRAVQELFRYSGETISRHFNNVLNAIMA 119 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L---~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 119 (390)
.+|+.++..+.|+++ -.|.|+.++|..+|+|.+||.+..++....|..
T Consensus 175 ~Lp~~~R~i~~l~y~~~~~e~~S~~EIA~~lgis~~tV~~~~~rA~~kLr~ 225 (233)
T PRK05803 175 ILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRALKKLFK 225 (233)
T ss_pred hCCHHHHHHHHHHhCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 689999999999875 468999999999999999999998888877764
No 64
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=86.61 E-value=1.2 Score=38.16 Aligned_cols=47 Identities=11% Similarity=0.134 Sum_probs=41.9
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHH
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMA 119 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 119 (390)
.+|+.++-++.|.++ .|.++.++|..+|+|.+||...+.+....|.+
T Consensus 112 ~L~~~~r~v~~l~~~-~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 158 (164)
T PRK12547 112 LLSADQREAIILIGA-SGFSYEDAAAICGCAVGTIKSRVSRARNRLQE 158 (164)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 588888888888877 69999999999999999999999999888864
No 65
>PRK15320 transcriptional activator SprB; Provisional
Probab=86.56 E-value=0.57 Score=41.27 Aligned_cols=38 Identities=11% Similarity=0.159 Sum_probs=34.7
Q ss_pred HHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 81 IFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 81 ~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
-.|..|+.|.+.++||+.+++|.+||+.+.+++.+-+.
T Consensus 171 EVL~LLAkG~SNKEIAekL~LS~KTVSTYKnRLLeKLg 208 (251)
T PRK15320 171 ALLILLSSGHPAIELAKKFGLGTKTVSIYRKKVMYRLG 208 (251)
T ss_pred HHHHHHHcCCCHHHHHHHhccchhhHHHHHHHHHHHcC
Confidence 56788999999999999999999999999999888764
No 66
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=86.53 E-value=1.1 Score=37.98 Aligned_cols=48 Identities=15% Similarity=0.248 Sum_probs=41.2
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHHh
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 120 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 120 (390)
.+|+.++.++.|.++ .|.++.++|..+|+|.+||...+.+....|...
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 577888888777775 499999999999999999999999998888653
No 67
>PF13751 DDE_Tnp_1_6: Transposase DDE domain
Probab=86.52 E-value=0.3 Score=39.91 Aligned_cols=50 Identities=16% Similarity=0.060 Sum_probs=38.3
Q ss_pred HHHHHHHHh-HHHHHHHHHHhhchhhhcCCCCCccchhHHHHHHHHHHhhhh
Q 016400 266 NQRHSLLRN-ATDRIFGALKERFPILLSAPPYPLQTQVKLVVAACALHNYIQ 316 (390)
Q Consensus 266 N~~~s~~R~-~VE~~fg~LK~rf~iL~~~~~~~~~~~~~ii~a~~~LhN~~~ 316 (390)
.+...+.|. .||.+||.||. +.-++........++..-+...|+.|||..
T Consensus 73 ~k~~y~~R~~~VE~~fg~~K~-~~g~~r~~~rG~~kv~~~~~l~a~a~Nl~r 123 (125)
T PF13751_consen 73 GKELYKQRSIKVEGVFGTIKR-NHGLRRFRYRGLEKVRIEFLLAAIAYNLKR 123 (125)
T ss_pred hhhhhheeecccccccccchh-ccCCccccccchhhhHHHHHHHHHHHHHHH
Confidence 345677788 99999999995 444555566677888888888889999864
No 68
>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=86.48 E-value=1.1 Score=37.76 Aligned_cols=46 Identities=11% Similarity=0.156 Sum_probs=39.8
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
.+++.++-++.|+++ .|.++.++|..+|+|.+||....++....|-
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 578888888888777 5999999999999999999999988777664
No 69
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=86.42 E-value=1.1 Score=40.46 Aligned_cols=49 Identities=8% Similarity=0.172 Sum_probs=43.1
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHHhh
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAIS 121 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~ 121 (390)
.+++.++-++.|+++ .|.++.++|..+|||.+||...+++....|....
T Consensus 134 ~Lp~~~R~v~~L~y~-eg~s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l 182 (216)
T PRK12533 134 KLPVEYREVLVLREL-EDMSYREIAAIADVPVGTVMSRLARARRRLAALL 182 (216)
T ss_pred cCCHHHHhHhhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 688888888888888 5999999999999999999999999988887543
No 70
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=86.37 E-value=1.3 Score=38.12 Aligned_cols=47 Identities=13% Similarity=0.094 Sum_probs=40.8
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHH
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMA 119 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 119 (390)
.+|+..+.++.|+++ .|.++.++|..+|+|.+||...+.+....+..
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 48999999999999999999999888887754
No 71
>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=86.26 E-value=0.77 Score=35.56 Aligned_cols=40 Identities=23% Similarity=0.198 Sum_probs=30.8
Q ss_pred CCHHHHHHHHhh------hcccccchhhhhhhcccchhhhhhhhHH
Q 016400 73 IKIEEQLAIFMF------IVGHNLRTRAVQELFRYSGETISRHFNN 112 (390)
Q Consensus 73 ~~~~~~l~~~L~------~L~~~~~~~~l~~~fgis~stv~~~~~~ 112 (390)
+++.|+-++..+ .+..+.+++.++...|||.+||+|+-+.
T Consensus 33 LTp~E~~~l~~R~~i~~~Ll~~~~tQrEIa~~lGiS~atIsR~sn~ 78 (94)
T TIGR01321 33 LTRSEREDLGDRIRIVNELLNGNMSQREIASKLGVSIATITRGSNN 78 (94)
T ss_pred CCHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHhCCChhhhhHHHhh
Confidence 566666665555 3356799999999999999999986554
No 72
>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=86.24 E-value=1.2 Score=36.83 Aligned_cols=46 Identities=13% Similarity=0.257 Sum_probs=38.8
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
.++..++-.+.+.++ .|.++.++|..+|+|.+||++..++....|-
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 577777777766655 5899999999999999999999999877764
No 73
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=86.15 E-value=1.2 Score=37.70 Aligned_cols=48 Identities=4% Similarity=-0.040 Sum_probs=40.9
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHHh
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 120 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 120 (390)
.+|+..+-++.|.++. |.++.++|..+|+|.+||...+.+....|...
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 5788888877777764 89999999999999999999998888887643
No 74
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=86.10 E-value=1.2 Score=39.15 Aligned_cols=50 Identities=14% Similarity=0.144 Sum_probs=43.4
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHHhhc
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAISL 122 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~~ 122 (390)
.+|+.++-++.|.++ .|.++.++|..+|+|.+||...+.+....|.+...
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 578888888888877 59999999999999999999999999988875443
No 75
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=86.06 E-value=0.82 Score=39.51 Aligned_cols=47 Identities=4% Similarity=0.124 Sum_probs=41.4
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHH
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMA 119 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 119 (390)
.+|+.++.++.|+++ .|.++.++|..+|+|.+||...+.+....|..
T Consensus 126 ~L~~~~r~v~~l~~~-~g~s~~eIA~~l~is~~~V~~~l~ra~~~l~~ 172 (176)
T PRK09638 126 KLDPEFRAPVILKHY-YGYTYEEIAKMLNIPEGTVKSRVHHGIKQLRK 172 (176)
T ss_pred cCCHHHhheeeehhh-cCCCHHHHHHHHCCChhHHHHHHHHHHHHHHH
Confidence 588888888888877 59999999999999999999999888887764
No 76
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=85.64 E-value=1.3 Score=38.61 Aligned_cols=48 Identities=10% Similarity=0.186 Sum_probs=41.5
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHHh
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 120 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 120 (390)
.+|..++-++.|.++ .|.++.++|..+|+|.+||...+++....|...
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 578888888888877 599999999999999999999999888877643
No 77
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=85.61 E-value=1.3 Score=39.09 Aligned_cols=48 Identities=13% Similarity=0.180 Sum_probs=42.4
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHHh
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 120 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 120 (390)
.+|..++-++.|.++ .|.++.++|..+|+|.+||...+++....|...
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 588888888888877 699999999999999999999999999888643
No 78
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.
Probab=85.55 E-value=0.65 Score=39.09 Aligned_cols=48 Identities=8% Similarity=0.170 Sum_probs=40.2
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHHh
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 120 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 120 (390)
.+|+.++-++.|.++ .|.++.++|..+|+|.+||...+++....|.+.
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 477777777777766 599999999999999999999999988877643
No 79
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=85.50 E-value=1.5 Score=38.31 Aligned_cols=47 Identities=15% Similarity=0.169 Sum_probs=41.1
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHH
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMA 119 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 119 (390)
.+|..++..+.|+++. |.++.++|..+|+|.+||...+++....|..
T Consensus 135 ~L~~~~r~vl~l~~~~-~~s~~eIA~~lgis~~~V~~~l~ra~~~Lr~ 181 (186)
T PRK13919 135 ALSPEERRVIEVLYYQ-GYTHREAAQLLGLPLGTLKTRARRALSRLKE 181 (186)
T ss_pred hCCHHHHHHHHHHHHc-CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 5788888888887765 8999999999999999999999998888764
No 80
>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=85.35 E-value=0.58 Score=40.98 Aligned_cols=80 Identities=19% Similarity=0.204 Sum_probs=54.4
Q ss_pred cCChhHHHhhcCCCHHHHHHHHHHhccCCcc-----ccCCCCCHHHHHHHHhhhccc--------------ccchhhhhh
Q 016400 37 NGQSERCLENFRMDKKVFYKLCDILQSKGLL-----RHTNRIKIEEQLAIFMFIVGH--------------NLRTRAVQE 97 (390)
Q Consensus 37 ~~~d~~f~~~frms~~~F~~L~~~L~~~~~~-----~~~~~~~~~~~l~~~L~~L~~--------------~~~~~~l~~ 97 (390)
..+-+.|...+.-.++.-..++..+...... ..-...+++++|+-+|..|+. ..+..++|.
T Consensus 72 ~i~~~~~~~l~~~~p~l~~~~~~~l~~~l~~~~~~~~~l~~~~~~~Rla~~L~~l~~~~~~~~~~~~~~~~~~t~~~iA~ 151 (193)
T TIGR03697 72 AVPIEQVEKAIEEDPDLSMLLLQGLSSRILQTEMMIETLAHRDMGSRLVSFLLILCRDFGVPGQRGVTIDLRLSHQAIAE 151 (193)
T ss_pred EeeHHHHHHHHHHChHHHHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhCCCCCCeEEecCCCCHHHHHH
Confidence 4556666666666655555555555432111 011346889999999877632 257899999
Q ss_pred hcccchhhhhhhhHHHHHH
Q 016400 98 LFRYSGETISRHFNNVLNA 116 (390)
Q Consensus 98 ~fgis~stv~~~~~~v~~~ 116 (390)
..|+++.||+|+++++.+.
T Consensus 152 ~lG~tretvsR~l~~l~~~ 170 (193)
T TIGR03697 152 AIGSTRVTITRLLGDLRKK 170 (193)
T ss_pred HhCCcHHHHHHHHHHHHHC
Confidence 9999999999999888663
No 81
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=85.34 E-value=1.1 Score=31.92 Aligned_cols=43 Identities=7% Similarity=0.174 Sum_probs=38.9
Q ss_pred HHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHHh
Q 016400 78 QLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 120 (390)
Q Consensus 78 ~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 120 (390)
+.-.|+.+|+...+..+.|+..|+...+|.+++..|-..+.++
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 4557889999999999999999999999999999999988765
No 82
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=85.33 E-value=1.5 Score=36.80 Aligned_cols=46 Identities=9% Similarity=0.074 Sum_probs=38.3
Q ss_pred CCCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 71 NRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 71 ~~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
..+++.++-.+.|+ ..|.++.++|..+|+|++||+.+.+...+-|.
T Consensus 5 ~~Lt~rqreVL~lr--~~GlTq~EIAe~LGiS~~tVs~ie~ra~kkLr 50 (141)
T PRK03975 5 SFLTERQIEVLRLR--ERGLTQQEIADILGTSRANVSSIEKRARENIE 50 (141)
T ss_pred cCCCHHHHHHHHHH--HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 35777777777663 58999999999999999999999998777664
No 83
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=85.26 E-value=1.2 Score=39.08 Aligned_cols=52 Identities=10% Similarity=0.068 Sum_probs=44.0
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHHhhccc
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAISLDF 124 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~~~~ 124 (390)
.++.+++-.+.|.++ .|.++.++|..+|+|..||...+.+....|-+....+
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 578888888888777 5999999999999999999999999988887654443
No 84
>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=85.08 E-value=0.82 Score=34.39 Aligned_cols=37 Identities=16% Similarity=0.213 Sum_probs=26.1
Q ss_pred HHHHHHHhhhccc-ccchhhhhhhcccchhhhhhhhHH
Q 016400 76 EEQLAIFMFIVGH-NLRTRAVQELFRYSGETISRHFNN 112 (390)
Q Consensus 76 ~~~l~~~L~~L~~-~~~~~~l~~~fgis~stv~~~~~~ 112 (390)
++++..-+-+|.. ..+..+++..+|+|.+||++.++.
T Consensus 5 ~~R~~~I~e~l~~~~~ti~dvA~~~gvS~~TVsr~L~~ 42 (80)
T TIGR02844 5 EERVLEIGKYIVETKATVRETAKVFGVSKSTVHKDVTE 42 (80)
T ss_pred HHHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHhcC
Confidence 3444444444433 367899999999999999997753
No 85
>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=85.08 E-value=1.6 Score=39.89 Aligned_cols=49 Identities=16% Similarity=0.198 Sum_probs=43.2
Q ss_pred CCCHHHHHHHHhhhc---ccccchhhhhhhcccchhhhhhhhHHHHHHHHHh
Q 016400 72 RIKIEEQLAIFMFIV---GHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 120 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L---~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 120 (390)
.+|+.++..+.|+++ ..|.++.++|...|+|.+||....++....|-+.
T Consensus 178 ~Lp~~~R~ii~L~~~l~~~eg~s~~EIA~~Lgis~~tV~~~l~ra~~~LR~~ 229 (234)
T TIGR02835 178 KLNDREKKIMELRFGLVGGTEKTQKEVADMLGISQSYISRLEKRILKRLKKE 229 (234)
T ss_pred hCCHHHHHHHHHHHccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 689999999999985 3789999999999999999999998888877643
No 86
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=84.98 E-value=1.5 Score=40.77 Aligned_cols=48 Identities=17% Similarity=0.290 Sum_probs=41.6
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHHh
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 120 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 120 (390)
.++..++..+.|+|+ .|.++.++|..+|+|.+||++..++....|...
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 477788888888886 489999999999999999999999998888643
No 87
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=84.96 E-value=1.4 Score=37.85 Aligned_cols=48 Identities=10% Similarity=0.215 Sum_probs=40.9
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHHh
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 120 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 120 (390)
.+|+.++-.+.|.++ .|.++.+||..+|+|.+||.+.+.+....|.+.
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 577777777777776 589999999999999999999999988887643
No 88
>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=84.94 E-value=1.5 Score=30.34 Aligned_cols=36 Identities=11% Similarity=0.195 Sum_probs=26.8
Q ss_pred HHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHH
Q 016400 79 LAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 79 l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
++..|+.. .+.+..+++..++++++|+++++++...
T Consensus 8 iL~~l~~~-~~~~~~~la~~~~~~~~~~t~~i~~L~~ 43 (59)
T PF01047_consen 8 ILRILYEN-GGITQSELAEKLGISRSTVTRIIKRLEK 43 (59)
T ss_dssp HHHHHHHH-SSEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHc-CCCCHHHHHHHHCCChhHHHHHHHHHHH
Confidence 33444433 4589999999999999999999887654
No 89
>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=84.84 E-value=1.6 Score=40.93 Aligned_cols=48 Identities=15% Similarity=0.153 Sum_probs=41.4
Q ss_pred CCCHHHHHHHHhhhcc-cccchhhhhhhcccchhhhhhhhHHHHHHHHH
Q 016400 72 RIKIEEQLAIFMFIVG-HNLRTRAVQELFRYSGETISRHFNNVLNAIMA 119 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~-~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 119 (390)
.++..++..+.|+|+. .+.++.++|..+|||.++|+++.++.+.-|-.
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 4778888888888874 47999999999999999999999988887754
No 90
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=84.81 E-value=1.4 Score=36.98 Aligned_cols=46 Identities=9% Similarity=0.038 Sum_probs=39.5
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
.+|+.++-++.|.++. |.++.++|..+|+|.+||...+.+....|-
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 5788888888787765 899999999999999999999988877663
No 91
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=84.67 E-value=1.5 Score=38.43 Aligned_cols=48 Identities=10% Similarity=0.143 Sum_probs=42.3
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHHh
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 120 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 120 (390)
.+|++++-++.|+++ .|.++.++|..+|+|.+||...+.+....|...
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 588888888888887 699999999999999999999999988888653
No 92
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=84.56 E-value=1.6 Score=38.52 Aligned_cols=47 Identities=13% Similarity=0.208 Sum_probs=40.7
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHH
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMA 119 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 119 (390)
.+|.+.+-++.|+++ .|.++.++|..+|+|.+||...+++....|..
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 59999999999999999999988888887764
No 93
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=84.51 E-value=1.7 Score=37.91 Aligned_cols=51 Identities=8% Similarity=-0.020 Sum_probs=43.1
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHHhhcc
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAISLD 123 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~~~ 123 (390)
.+|+.++.++.|.++- |.++.++|..+|+|.+||...+.+....|.+....
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 5788888877777654 89999999999999999999999999888765544
No 94
>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=84.43 E-value=1.5 Score=38.27 Aligned_cols=50 Identities=12% Similarity=0.062 Sum_probs=41.9
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHHhhc
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAISL 122 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~~ 122 (390)
.++.+++-.+.|.++ .|.++.+||..+|+|.+||...+++....|.+...
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 477777777777766 69999999999999999999999999888876443
No 95
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=84.39 E-value=1.8 Score=37.87 Aligned_cols=48 Identities=8% Similarity=-0.012 Sum_probs=40.6
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHHh
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 120 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 120 (390)
.+++.++-++.|.++ .|.++.++|..+|+|.+||...+++....|...
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 577777777777765 699999999999999999999999988887653
No 96
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=84.39 E-value=1.8 Score=37.29 Aligned_cols=48 Identities=10% Similarity=0.105 Sum_probs=41.4
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHHh
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 120 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 120 (390)
.+|+..+-++.|.++. |.++.++|..+|+|.+||...+++....|.+.
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 5788888888777765 89999999999999999999999888888753
No 97
>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=84.35 E-value=1.6 Score=29.85 Aligned_cols=39 Identities=13% Similarity=0.150 Sum_probs=27.7
Q ss_pred HHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHH
Q 016400 79 LAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAI 117 (390)
Q Consensus 79 l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l 117 (390)
++..|.--..+.+..++|+.++||..||.+.++..-...
T Consensus 5 il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i~~L~~~~ 43 (55)
T PF08279_consen 5 ILKLLLESKEPITAKELAEELGVSRRTIRRDIKELREWG 43 (55)
T ss_dssp HHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHHHHHHHTT
T ss_pred HHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence 333333334448999999999999999999998775433
No 98
>PHA00675 hypothetical protein
Probab=84.32 E-value=1.1 Score=33.13 Aligned_cols=40 Identities=15% Similarity=0.083 Sum_probs=28.6
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhH
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFN 111 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~ 111 (390)
.++..+--.+....-..|.++..||..||+|+|||..|.+
T Consensus 22 KLt~~qV~~IR~l~~r~G~s~~~IA~~fGVsrstV~~I~~ 61 (78)
T PHA00675 22 KLTDAEVERIRELHEVEGMSYAVLAEKFEQSKGAIAKICR 61 (78)
T ss_pred ccCHHHHHHHHHHHHhcCccHHHHHHHhCCCHHHHHHHHc
Confidence 3444443344444336788999999999999999998764
No 99
>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=84.32 E-value=1.3 Score=33.92 Aligned_cols=36 Identities=17% Similarity=0.070 Sum_probs=28.6
Q ss_pred HHHHHHhhhcccccchhhhhhhcccchhhhhhhhHH
Q 016400 77 EQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNN 112 (390)
Q Consensus 77 ~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~ 112 (390)
.++.++=-.|..|.+|++|+...|+|-.||+|+-+.
T Consensus 37 ~R~~va~~lL~~g~syreIa~~tgvS~aTItRvsr~ 72 (87)
T PF01371_consen 37 QRWQVAKELLDEGKSYREIAEETGVSIATITRVSRC 72 (87)
T ss_dssp HHHHHHHHHHHTTSSHHHHHHHHTSTHHHHHHHHHH
T ss_pred HHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 344444447789999999999999999999986544
No 100
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=84.23 E-value=1.8 Score=37.36 Aligned_cols=46 Identities=9% Similarity=0.114 Sum_probs=40.1
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
.+|+.++-++.|.++. |.++.++|+.+|+|.+||...+.+.+..+.
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 6788888888888775 899999999999999999998888777765
No 101
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=84.23 E-value=1.7 Score=37.90 Aligned_cols=47 Identities=17% Similarity=0.203 Sum_probs=40.1
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHH
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMA 119 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 119 (390)
.+|+.++.++.|.++. |.++.++|..+|+|.+||...+++....|..
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 5777788777777664 8999999999999999999999998888764
No 102
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=84.14 E-value=1.7 Score=38.13 Aligned_cols=48 Identities=8% Similarity=-0.022 Sum_probs=41.7
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHHh
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 120 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 120 (390)
.+|+.++-++.|.++- |.++.++|..+|+|.+||...+.+....|.+.
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 79999999999999999999999998888653
No 103
>PF13730 HTH_36: Helix-turn-helix domain
Probab=84.10 E-value=1.5 Score=29.95 Aligned_cols=43 Identities=7% Similarity=0.142 Sum_probs=31.5
Q ss_pred CCHH-HHHHHHhhhccc--c---cchhhhhhhcccchhhhhhhhHHHHH
Q 016400 73 IKIE-EQLAIFMFIVGH--N---LRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 73 ~~~~-~~l~~~L~~L~~--~---~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
+++. ..|.++|..++. + -|+..++...|+|+.||.+.+++..+
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 4553 345566666652 2 26899999999999999999987654
No 104
>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=84.08 E-value=1.5 Score=34.48 Aligned_cols=43 Identities=21% Similarity=0.257 Sum_probs=36.7
Q ss_pred CHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHH
Q 016400 74 KIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAI 117 (390)
Q Consensus 74 ~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l 117 (390)
.++++..+.++|+ .+.++.+++..+++|++|++++-++.+..|
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 4568888888888 579999999999999999999988876644
No 105
>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=83.77 E-value=0.72 Score=45.55 Aligned_cols=132 Identities=13% Similarity=0.019 Sum_probs=70.3
Q ss_pred Hhhhcccccchhhhhh----hcc---cchhhhhhhhHHHHHHHHHhhccccCCCCCCCchhhccCCcccCCCcccccccc
Q 016400 82 FMFIVGHNLRTRAVQE----LFR---YSGETISRHFNNVLNAIMAISLDFFQPPGPDVPPEISLDPRLYPYFKDCVGAVD 154 (390)
Q Consensus 82 ~L~~L~~~~~~~~l~~----~fg---is~stv~~~~~~v~~~l~~~~~~~i~~P~~~~~~~i~~~~~~~~~fp~~iG~ID 154 (390)
.+..+..|.|.++++. .+| +|.+|||+++..+...+..+...-+ ...|-.+-.||
T Consensus 107 i~~ly~~G~Str~i~~~l~~l~g~~~~S~s~vSri~~~~~~~~~~w~~R~L------------------~~~~y~~l~iD 168 (381)
T PF00872_consen 107 IISLYLKGVSTRDIEEALEELYGEVAVSKSTVSRITKQLDEEVEAWRNRPL------------------ESEPYPYLWID 168 (381)
T ss_pred hhhhhccccccccccchhhhhhcccccCchhhhhhhhhhhhhHHHHhhhcc------------------ccccccceeee
Confidence 3344566777777655 456 9999999999888877654432211 11122356799
Q ss_pred ceEEEEEeCCCCCCCCCCCCCCceeeeeeeecCCcc--eeEeccCcccccccHHHHHHHHhhcCCCCCCCCceeeccCCC
Q 016400 155 GIHIPVMVGVDEQGPFRNKSGLLSQNVLAACSFDLK--FHYVLAGWEGSASDLRVLNSALTRRNKLQVPEGKYYLVDNKY 232 (390)
Q Consensus 155 gt~i~i~~P~~~~~~y~~~k~~~s~~~q~v~d~d~~--~~~v~~g~~Gs~~D~~vl~~sl~~~~~~~~p~g~~~l~D~gY 232 (390)
|+|+.+..- ++-...++-+-+.++.||+ ++.+..+ ..-....|.+.+.+...--+.....+++|+.=
T Consensus 169 ~~~~kvr~~--------~~~~~~~~~v~iGi~~dG~r~vLg~~~~---~~Es~~~W~~~l~~L~~RGl~~~~lvv~Dg~~ 237 (381)
T PF00872_consen 169 GTYFKVRED--------GRVVKKAVYVAIGIDEDGRREVLGFWVG---DRESAASWREFLQDLKERGLKDILLVVSDGHK 237 (381)
T ss_pred eeecccccc--------cccccchhhhhhhhhcccccceeeeecc---cCCccCEeeecchhhhhccccccceeeccccc
Confidence 999988511 1111233444455777785 4444443 33333333333221111112234577888765
Q ss_pred CCCCCccccc
Q 016400 233 ANMPGFIAPY 242 (390)
Q Consensus 233 p~~~~ll~P~ 242 (390)
.+...+-.-|
T Consensus 238 gl~~ai~~~f 247 (381)
T PF00872_consen 238 GLKEAIREVF 247 (381)
T ss_pred cccccccccc
Confidence 5555444433
No 106
>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=83.72 E-value=2 Score=37.41 Aligned_cols=48 Identities=17% Similarity=0.151 Sum_probs=41.2
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHHh
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 120 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 120 (390)
.+++.++-++.|.++ .|.++.++|..+|+|.+||...+++....|.+.
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 578888877777776 699999999999999999999999988877643
No 107
>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=83.69 E-value=1.9 Score=37.15 Aligned_cols=51 Identities=12% Similarity=0.025 Sum_probs=43.7
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHHhhcc
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAISLD 123 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~~~ 123 (390)
.+|+.++.++.|.++. |.++.++|..+|+|.+||...+.+....|......
T Consensus 100 ~L~~~~r~v~~l~~~~-g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 150 (170)
T TIGR02959 100 ELPDEYREAIRLTELE-GLSQQEIAEKLGLSLSGAKSRVQRGRKKLKELLET 150 (170)
T ss_pred hCCHHHHHHHHHHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 5888888888887765 89999999999999999999999999888765544
No 108
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=83.64 E-value=1.7 Score=37.51 Aligned_cols=49 Identities=6% Similarity=0.081 Sum_probs=39.7
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHHhh
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAIS 121 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~ 121 (390)
.++++.+-++.|.++. |.++.++|..+|+|.+||...+++....+..+.
T Consensus 119 ~L~~~~r~i~~l~~~~-g~s~~EIA~~lgis~~tV~~~l~Ra~~~~~~~~ 167 (172)
T PRK09651 119 GLNGKTREAFLLSQLD-GLTYSEIAHKLGVSVSSVKKYVAKATEHCLLFR 167 (172)
T ss_pred hCCHHHhHHhhhhhcc-CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 5777777666665554 899999999999999999999998888876543
No 109
>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=83.56 E-value=1.9 Score=33.57 Aligned_cols=42 Identities=12% Similarity=0.228 Sum_probs=35.1
Q ss_pred HHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 76 EEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 76 ~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
.++..+-|+++ ...|...+|+.|+||++.|+..+++++..|.
T Consensus 21 KQ~~Y~~lyy~-dDlSl~EIAee~~VSRqAIyDnIKr~~~~L~ 62 (105)
T COG2739 21 KQKNYLELYYL-DDLSLSEIAEEFNVSRQAIYDNIKRTEKILE 62 (105)
T ss_pred HHHHHHHHHHH-hhccHHHHHHHhCccHHHHHHHHHHHHHHHH
Confidence 34555666655 4789999999999999999999999999885
No 110
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=83.54 E-value=1.7 Score=36.96 Aligned_cols=47 Identities=6% Similarity=0.066 Sum_probs=41.0
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHH
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMA 119 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 119 (390)
.+|+.++.++.|.++. |.++.++|..+|+|.+||...+++....|.+
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 5888888888888765 8999999999999999999999988887754
No 111
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=83.53 E-value=1.5 Score=38.35 Aligned_cols=47 Identities=13% Similarity=0.164 Sum_probs=41.3
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHH
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMA 119 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 119 (390)
.+|+.++-++.|.++. |.++.++|..+|+|.+||...+.+....|.+
T Consensus 130 ~Lp~~~r~v~~L~~~~-g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 176 (185)
T PRK09649 130 DLTTDQREALLLTQLL-GLSYADAAAVCGCPVGTIRSRVARARDALLA 176 (185)
T ss_pred hCCHHHhHHhhhHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 5788888888888776 8999999999999999999999988888764
No 112
>PF13551 HTH_29: Winged helix-turn helix
Probab=83.44 E-value=0.98 Score=35.69 Aligned_cols=34 Identities=9% Similarity=0.231 Sum_probs=29.9
Q ss_pred Hhhhcccccc-hhhhhhhcccchhhhhhhhHHHHH
Q 016400 82 FMFIVGHNLR-TRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 82 ~L~~L~~~~~-~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
.|..+..|.+ ...+|..+|+|..||+++++++..
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 4566788996 999999999999999999999865
No 113
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=83.39 E-value=1.8 Score=38.54 Aligned_cols=49 Identities=4% Similarity=-0.047 Sum_probs=41.8
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHHhh
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAIS 121 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~ 121 (390)
.+|+..+-++.|.++. |.++.++|..+|+|.+||...+.+....|....
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 5788888888887764 899999999999999999999999888887543
No 114
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=83.31 E-value=1.8 Score=38.22 Aligned_cols=48 Identities=4% Similarity=0.055 Sum_probs=41.9
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHHh
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 120 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 120 (390)
.+|...+-++.|+++ .|.++.++|..+|+|.+||...+++....|.+.
T Consensus 136 ~L~~~~r~i~~L~~~-~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 183 (195)
T PRK12532 136 NLPENTARVFTLKEI-LGFSSDEIQQMCGISTSNYHTIMHRARESLRQC 183 (195)
T ss_pred hCCHHHHHHhhhHHH-hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 578888888888777 589999999999999999999999999988753
No 115
>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain. This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc.
Probab=83.23 E-value=1.8 Score=39.73 Aligned_cols=48 Identities=17% Similarity=0.138 Sum_probs=42.1
Q ss_pred CCCHHHHHHHHhhhc---ccccchhhhhhhcccchhhhhhhhHHHHHHHHH
Q 016400 72 RIKIEEQLAIFMFIV---GHNLRTRAVQELFRYSGETISRHFNNVLNAIMA 119 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L---~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 119 (390)
.++..++..+.|+|. ..+.++.++|..+|+|.++|+++.++.+.-|-.
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 578888888988884 578999999999999999999999998888764
No 116
>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=83.19 E-value=1.8 Score=40.02 Aligned_cols=47 Identities=13% Similarity=0.265 Sum_probs=41.6
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHH
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMA 119 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 119 (390)
.+|...+-++.|.++ .|.++.++|..+|||.+||...+.+....|.+
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 578888888888877 58999999999999999999999999998864
No 117
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=83.02 E-value=2 Score=37.36 Aligned_cols=48 Identities=10% Similarity=0.075 Sum_probs=41.8
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHHh
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 120 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 120 (390)
.+|..++-.+.|.++. |.++.++|..+|+|.+||...+++....|.+.
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 5788888888887776 99999999999999999999999998888753
No 118
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=82.92 E-value=1.9 Score=37.39 Aligned_cols=47 Identities=9% Similarity=0.209 Sum_probs=39.6
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHH
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMA 119 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 119 (390)
.+|+.++-++.|.++. |.++.++|..+|+|.+||...+++....|-.
T Consensus 117 ~Lp~~~r~i~~l~~~e-~~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~ 163 (179)
T PRK12543 117 KLPYKLRQVIILRYLH-DYSQEEIAQLLQIPIGTVKSRIHAALKKLRQ 163 (179)
T ss_pred hCCHHHHHHHHHHHHc-cCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 5888888777776654 8899999999999999999888888877754
No 119
>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=82.83 E-value=1.2 Score=31.59 Aligned_cols=27 Identities=19% Similarity=0.380 Sum_probs=23.8
Q ss_pred ccchhhhhhhcccchhhhhhhhHHHHH
Q 016400 89 NLRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 89 ~~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
..+..++++.+|+|++|++++++.+.+
T Consensus 25 ~~s~~ela~~~g~s~~tv~r~l~~L~~ 51 (67)
T cd00092 25 PLTRQEIADYLGLTRETVSRTLKELEE 51 (67)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 368899999999999999999887765
No 120
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=82.82 E-value=2.1 Score=37.72 Aligned_cols=49 Identities=10% Similarity=0.119 Sum_probs=43.8
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHHhh
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAIS 121 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~ 121 (390)
.+|+.++-++.|+++ .|.++.++|..+|+|.+||...+.+....|-+..
T Consensus 113 ~Lp~~~r~v~~L~~~-~g~s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l 161 (188)
T PRK12546 113 QLPDEQREALILVGA-SGFSYEEAAEMCGVAVGTVKSRANRARARLAELL 161 (188)
T ss_pred hCCHHHhHHhhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 688889988889888 6999999999999999999999999998887544
No 121
>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=82.78 E-value=2.2 Score=36.58 Aligned_cols=48 Identities=15% Similarity=0.198 Sum_probs=41.1
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHHh
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 120 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 120 (390)
.++..++-++.|.++. |.++.++|..+|+|.+||...+.+....|...
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 5777778777777776 89999999999999999999999988887653
No 122
>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=82.78 E-value=1.1 Score=27.28 Aligned_cols=25 Identities=16% Similarity=0.364 Sum_probs=19.9
Q ss_pred cchhhhhhhcccchhhhhhhhHHHH
Q 016400 90 LRTRAVQELFRYSGETISRHFNNVL 114 (390)
Q Consensus 90 ~~~~~l~~~fgis~stv~~~~~~v~ 114 (390)
.+..++|+..|.+..||+|++.++-
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 4578999999999999999998764
No 123
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=82.77 E-value=2.2 Score=37.79 Aligned_cols=53 Identities=11% Similarity=0.026 Sum_probs=44.5
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHHhhcccc
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAISLDFF 125 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~~~~i 125 (390)
.+|+..+-++.|.++. |.++.++|+.+|+|.+||...+++....|.+....+.
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 5777777777777765 8999999999999999999999999999887665553
No 124
>PRK05572 sporulation sigma factor SigF; Validated
Probab=82.74 E-value=2.2 Score=39.45 Aligned_cols=48 Identities=15% Similarity=0.220 Sum_probs=42.1
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHHh
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 120 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 120 (390)
.++..++..+.++++ .|.++.++|..+|+|.+||+++.++.+..|...
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 125
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=82.63 E-value=2.2 Score=37.23 Aligned_cols=49 Identities=6% Similarity=0.172 Sum_probs=40.9
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHHhh
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAIS 121 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~ 121 (390)
.+|+..+-++.|.++. |.++.++|..+|+|.+||...+.+....|....
T Consensus 122 ~L~~~~r~i~~l~~~~-g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 170 (185)
T PRK12542 122 ELNESNRQVFKYKVFY-NLTYQEISSVMGITEANVRKQFERARKRVQNMI 170 (185)
T ss_pred hCCHHHHHHHHHHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 5777777777776664 899999999999999999999998888886544
No 126
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=82.54 E-value=1.1 Score=39.91 Aligned_cols=45 Identities=9% Similarity=0.219 Sum_probs=36.4
Q ss_pred CCCCHHHHHHHHhhhccc-------------ccchhhhhhhcccchhhhhhhhHHHHH
Q 016400 71 NRIKIEEQLAIFMFIVGH-------------NLRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 71 ~~~~~~~~l~~~L~~L~~-------------~~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
...++.++++-+|..|+. ..+..++|...|+++.|++|+++++.+
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 357888999988877643 245689999999999999999987765
No 127
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=82.51 E-value=2 Score=36.63 Aligned_cols=48 Identities=17% Similarity=0.171 Sum_probs=41.0
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHHh
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 120 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 120 (390)
.+|+.++-++.|+++. |.++.++|..+|+|.+||...+.+....|...
T Consensus 108 ~L~~~~r~v~~l~~~~-g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~ 155 (165)
T PRK09644 108 TLPVIEAQAILLCDVH-ELTYEEAASVLDLKLNTYKSHLFRGRKRLKAL 155 (165)
T ss_pred hCCHHHHHHHHhHHHh-cCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 5788888777777664 89999999999999999999999998888654
No 128
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=82.40 E-value=3.3 Score=30.24 Aligned_cols=72 Identities=14% Similarity=0.152 Sum_probs=51.0
Q ss_pred hhHHHhhcCCCHHHHHHHHHHhccCCccccCCCCCHHHHHHHHhhhcccc-cchhhhhhhccc-chhhhhhhhHHHHH
Q 016400 40 SERCLENFRMDKKVFYKLCDILQSKGLLRHTNRIKIEEQLAIFMFIVGHN-LRTRAVQELFRY-SGETISRHFNNVLN 115 (390)
Q Consensus 40 d~~f~~~frms~~~F~~L~~~L~~~~~~~~~~~~~~~~~l~~~L~~L~~~-~~~~~l~~~fgi-s~stv~~~~~~v~~ 115 (390)
-++.-..++++...|.+++........ ...-...++.-++.+|..+ .+..++|..+|. |.+..++.|++...
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 356667888998888888776543211 1112234566666666665 899999999999 99999999987643
No 129
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=82.37 E-value=2.2 Score=37.62 Aligned_cols=49 Identities=8% Similarity=0.157 Sum_probs=41.2
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHHhh
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAIS 121 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~ 121 (390)
.+|+.++.++.|+++ .|.++.++|..+|+|.+||...+.+....|.+..
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 5899999999999999999988888877776533
No 130
>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=82.37 E-value=1.6 Score=29.68 Aligned_cols=28 Identities=11% Similarity=0.222 Sum_probs=23.0
Q ss_pred cccchhhhhhhcccchhhhhhhhHHHHH
Q 016400 88 HNLRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 88 ~~~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
.+.+..+++...|++++|++|+++....
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 4467999999999999999999887654
No 131
>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=82.35 E-value=1.3 Score=39.06 Aligned_cols=50 Identities=10% Similarity=0.105 Sum_probs=41.6
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHHhhc
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAISL 122 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~~ 122 (390)
.+|...+-++.|.++. |.++.++|..+|+|.+||...+.+....|.+...
T Consensus 131 ~Lp~~~r~i~~L~~~~-g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~ 180 (193)
T TIGR02947 131 GLPEEFRQAVYLADVE-GFAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQLV 180 (193)
T ss_pred hCCHHHhhheeehhhc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 5777777777776654 8999999999999999999999999888875443
No 132
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=82.31 E-value=2.2 Score=37.26 Aligned_cols=48 Identities=13% Similarity=0.086 Sum_probs=41.8
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHHh
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 120 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 120 (390)
.+|+.++-++.|.++. |.++.++|..+|+|..||...+++....|...
T Consensus 128 ~L~~~~r~i~~l~~~~-g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 175 (186)
T PRK05602 128 ALPERQREAIVLQYYQ-GLSNIEAAAVMDISVDALESLLARGRRALRAQ 175 (186)
T ss_pred hCCHHHHHHhhHHHhc-CCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHH
Confidence 5788888888888775 99999999999999999999999988888653
No 133
>PRK06930 positive control sigma-like factor; Validated
Probab=82.29 E-value=2.3 Score=36.89 Aligned_cols=47 Identities=13% Similarity=0.171 Sum_probs=39.7
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHH
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMA 119 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 119 (390)
.+|+.++-++.|++ ..|.++.++|..+|+|.+||...+.+....|..
T Consensus 114 ~L~~rer~V~~L~~-~eg~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~ 160 (170)
T PRK06930 114 VLTEREKEVYLMHR-GYGLSYSEIADYLNIKKSTVQSMIERAEKKIAR 160 (170)
T ss_pred hCCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 57777776666654 669999999999999999999999999888864
No 134
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=82.27 E-value=2.3 Score=37.25 Aligned_cols=50 Identities=10% Similarity=0.152 Sum_probs=43.0
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHHhhc
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAISL 122 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~~ 122 (390)
.+|+..+-++.|.++ .|.++.++|..+|+|.+||...+++..+.|-+...
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 69999999999999999999999999998875433
No 135
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=82.25 E-value=2.4 Score=35.96 Aligned_cols=48 Identities=10% Similarity=0.104 Sum_probs=40.2
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHHh
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 120 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 120 (390)
.+|++++-++.|.+ -.|.++.++|..+|+|.+||...+.+....|...
T Consensus 105 ~L~~~~r~v~~l~~-~~~~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~ 152 (159)
T PRK12527 105 ELPPACRDSFLLRK-LEGLSHQQIAEHLGISRSLVEKHIVNAMKHCRVR 152 (159)
T ss_pred hCCHHHHHHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 57777777776765 4589999999999999999999999988888654
No 136
>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=82.17 E-value=2.1 Score=38.97 Aligned_cols=48 Identities=19% Similarity=0.155 Sum_probs=42.2
Q ss_pred CCCHHHHHHHHhhhc---ccccchhhhhhhcccchhhhhhhhHHHHHHHHH
Q 016400 72 RIKIEEQLAIFMFIV---GHNLRTRAVQELFRYSGETISRHFNNVLNAIMA 119 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L---~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 119 (390)
.+|+.++-.+.|+++ ..|.++.++|+..|+|.+||.+..++....|..
T Consensus 174 ~L~~~~r~il~l~y~~~~~e~~S~~EIAe~lgis~~tV~~~~~rAl~~Lr~ 224 (227)
T TIGR02846 174 VLDGREREVIEMRYGLGDGRRKTQREIAKILGISRSYVSRIEKRALMKLYK 224 (227)
T ss_pred hCCHHHHHHHHHHHcCCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 688889988888876 478999999999999999999999988887753
No 137
>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=82.13 E-value=3.2 Score=33.71 Aligned_cols=73 Identities=15% Similarity=0.194 Sum_probs=47.2
Q ss_pred CChhHHHhhcCCCHHHHHHHHHHhccCCccccC-C---CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHH
Q 016400 38 GQSERCLENFRMDKKVFYKLCDILQSKGLLRHT-N---RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNV 113 (390)
Q Consensus 38 ~~d~~f~~~frms~~~F~~L~~~L~~~~~~~~~-~---~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v 113 (390)
.+-.+--..|++++.+....+...+. +..... + .+. ...+..+.---...+..+++..||||.+|+++.+++.
T Consensus 19 ~s~~eaa~~F~VS~~Tv~~W~k~~~~-G~~~~k~r~~~Kid--~~~L~~~v~~~pd~tl~Ela~~l~Vs~~ti~~~Lkrl 95 (119)
T PF01710_consen 19 KSIREAAKRFGVSRNTVYRWLKRKET-GDLEPKPRGRKKID--RDELKALVEENPDATLRELAERLGVSPSTIWRALKRL 95 (119)
T ss_pred chHHHHHHHhCcHHHHHHHHHHhccc-cccccccccccccc--HHHHHHHHHHCCCcCHHHHHHHcCCCHHHHHHHHHHc
Confidence 35567778999999999999884333 222211 1 232 2222222222345778899999999999999877654
No 138
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=82.09 E-value=2.2 Score=37.07 Aligned_cols=48 Identities=10% Similarity=0.190 Sum_probs=41.5
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHHh
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 120 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 120 (390)
.+|+.++-++.|.++ .|.++.++|..+|+|.+||...+++....|...
T Consensus 136 ~L~~~~r~v~~l~~~-~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T TIGR02948 136 ALPPKYRMVIVLKYM-EDLSLKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred hCCHHHhHHhhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 688888888888776 489999999999999999999999988887653
No 139
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=82.01 E-value=2.4 Score=40.07 Aligned_cols=48 Identities=10% Similarity=0.073 Sum_probs=41.5
Q ss_pred CCCHHHHHHHHhhhcc-cccchhhhhhhcccchhhhhhhhHHHHHHHHH
Q 016400 72 RIKIEEQLAIFMFIVG-HNLRTRAVQELFRYSGETISRHFNNVLNAIMA 119 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~-~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 119 (390)
.++..++..+.++|+. .+.++.++|..+|||+++|+++.++.+.-|-.
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 4777788888888875 58999999999999999999999998887754
No 140
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=81.85 E-value=2.3 Score=37.92 Aligned_cols=48 Identities=8% Similarity=0.083 Sum_probs=40.5
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHHh
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 120 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 120 (390)
.+|..++.++.|.++. |.++.++|..+|+|.+||...+++....|.+.
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 5778888887777665 89999999999999999999988888877643
No 141
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=81.68 E-value=2 Score=39.35 Aligned_cols=49 Identities=8% Similarity=0.193 Sum_probs=41.4
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHHhh
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAIS 121 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~ 121 (390)
.+|..++-++.|+++. |.++.++|..+|+|.+||...+++....|....
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 5777777777777765 899999999999999999999999988887543
No 142
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=81.65 E-value=2.3 Score=38.09 Aligned_cols=48 Identities=8% Similarity=-0.028 Sum_probs=42.4
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHHh
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 120 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 120 (390)
.+|+.++.++.|.++. |.++.++|..+|+|.+||...+++..+.|.+.
T Consensus 148 ~L~~~~r~v~~L~~~~-g~s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~ 195 (206)
T PRK12544 148 GLPAKYARVFMMREFI-ELETNEICHAVDLSVSNLNVLLYRARLRLREC 195 (206)
T ss_pred hCCHHHHHHHHHHHHc-CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 5788888888888776 99999999999999999999999999988753
No 143
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=81.53 E-value=2.5 Score=36.83 Aligned_cols=48 Identities=19% Similarity=0.170 Sum_probs=42.4
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHHh
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 120 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 120 (390)
.+|...+-++.|.++. |.++.++|..+|+|.+||...+++....|.+.
T Consensus 131 ~L~~~~r~v~~l~~~~-g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 178 (184)
T PRK12539 131 RLPEKMRLAIQAVKLE-GLSVAEAATRSGMSESAVKVSVHRGLKALAAL 178 (184)
T ss_pred hCCHHHHHHHHHHHHc-CCcHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 5888888888888875 99999999999999999999999999888653
No 144
>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=81.46 E-value=2.5 Score=38.23 Aligned_cols=47 Identities=13% Similarity=0.192 Sum_probs=40.4
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHH
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMA 119 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 119 (390)
.+|..++-++.++++ .|.++.++|..+|+|.+||....++....|..
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 578878877777765 58999999999999999999999999887753
No 145
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=81.22 E-value=2.6 Score=39.08 Aligned_cols=47 Identities=17% Similarity=0.167 Sum_probs=40.7
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHH
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMA 119 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 119 (390)
.+|+.++-++.|+++ .|.++.++|..+|+|.+||.+..++....|-.
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 578888877777775 58999999999999999999999999888764
No 146
>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=81.03 E-value=2.6 Score=39.77 Aligned_cols=50 Identities=8% Similarity=0.019 Sum_probs=43.7
Q ss_pred CCCHHHHHHHHhhh-c--ccccchhhhhhhcccchhhhhhhhHHHHHHHHHhh
Q 016400 72 RIKIEEQLAIFMFI-V--GHNLRTRAVQELFRYSGETISRHFNNVLNAIMAIS 121 (390)
Q Consensus 72 ~~~~~~~l~~~L~~-L--~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~ 121 (390)
.+|..++..+.|+| | -.|.++.++|..+|+|.+||....++....|....
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 68888998999887 4 46899999999999999999999999998887543
No 147
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=81.02 E-value=2.6 Score=39.94 Aligned_cols=50 Identities=14% Similarity=0.016 Sum_probs=43.1
Q ss_pred CCCHHHHHHHHhhhc-ccccchhhhhhhcccchhhhhhhhHHHHHHHHHhh
Q 016400 72 RIKIEEQLAIFMFIV-GHNLRTRAVQELFRYSGETISRHFNNVLNAIMAIS 121 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L-~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~ 121 (390)
.++..++..+.|+|+ ..|.++.++|..+|+|.++|..+.++.+.-|....
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 478888888888875 36899999999999999999999999999887533
No 148
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=80.95 E-value=2.3 Score=37.28 Aligned_cols=46 Identities=2% Similarity=0.042 Sum_probs=41.1
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
.+|+.++-++.|+++ .|.++.++|+.+|+|.+||...+.+....|.
T Consensus 131 ~L~~~~r~i~~l~~~-~g~s~~EIAe~lgis~~~V~~~l~Ra~~~Lr 176 (189)
T PRK06811 131 DLEKLDREIFIRRYL-LGEKIEEIAKKLGLTRSAIDNRLSRGRKKLQ 176 (189)
T ss_pred hCCHHHHHHHHHHHH-ccCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 688889988888887 4899999999999999999999988888775
No 149
>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=80.71 E-value=3.4 Score=32.52 Aligned_cols=46 Identities=7% Similarity=0.096 Sum_probs=32.3
Q ss_pred CCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHH
Q 016400 73 IKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMA 119 (390)
Q Consensus 73 ~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 119 (390)
++..++-.+- .++-.+.|...+|+.+|||+.+|+..+++....|..
T Consensus 18 LT~kQ~~~l~-lyy~eDlSlsEIAe~~~iSRqaV~d~ikr~~~~L~~ 63 (101)
T PF04297_consen 18 LTEKQREILE-LYYEEDLSLSEIAEELGISRQAVYDSIKRAEKKLEE 63 (101)
T ss_dssp S-HHHHHHHH-HHCTS---HHHHHHHCTS-HHHHHHHHHHHHHHHHH
T ss_pred CCHHHHHHHH-HHHccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3334444444 555668999999999999999999999999998864
No 150
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=80.38 E-value=3 Score=36.78 Aligned_cols=48 Identities=15% Similarity=0.144 Sum_probs=40.8
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHHh
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 120 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 120 (390)
.+|..++-++.|+++. |.++.++|...|+|.+||...+++....|...
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 5788888877777654 89999999999999999999999988888643
No 151
>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=80.34 E-value=2.7 Score=36.88 Aligned_cols=49 Identities=8% Similarity=-0.008 Sum_probs=40.9
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHHhh
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAIS 121 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~ 121 (390)
.+++.++-++.|.++. |.++.++|..+|+|.+||...+.+..+.|.+..
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 899999999999999999999999888886543
No 152
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=79.86 E-value=2.2 Score=38.63 Aligned_cols=91 Identities=16% Similarity=0.227 Sum_probs=55.3
Q ss_pred CChhHHHhhcCCCHHHHHHHHHHhccCCc-----cccCCCCCHHHHHHHHhhhcccc----cchhhhhhhcccchhhhhh
Q 016400 38 GQSERCLENFRMDKKVFYKLCDILQSKGL-----LRHTNRIKIEEQLAIFMFIVGHN----LRTRAVQELFRYSGETISR 108 (390)
Q Consensus 38 ~~d~~f~~~frms~~~F~~L~~~L~~~~~-----~~~~~~~~~~~~l~~~L~~L~~~----~~~~~l~~~fgis~stv~~ 108 (390)
.+-..|...+.-.+..-..++..+..... .......+++++++-+|..++.+ .+..++|...|+++.|++|
T Consensus 109 i~~~~~~~ll~~~p~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~Rla~~L~~~~~~~~~~~t~~~lA~~lG~sretvsR 188 (226)
T PRK10402 109 LPMKDCRPLLLNDALFLRKLCKFLSHKNYRNIVSLTQNQSFPLENRLAAFILLTQEGDLYHEKHTQAAEYLGVSYRHLLY 188 (226)
T ss_pred EEHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHhccChHHHHHHHHHHhcccCCcccchHHHHHHHHCCcHHHHHH
Confidence 44445555554444444444443432210 01112458999999999876532 4678999999999999999
Q ss_pred hhHHHHHH-HHHhhccccCCC
Q 016400 109 HFNNVLNA-IMAISLDFFQPP 128 (390)
Q Consensus 109 ~~~~v~~~-l~~~~~~~i~~P 128 (390)
.++++.+. +.+.....|..+
T Consensus 189 ~L~~L~~~G~I~~~~~~i~I~ 209 (226)
T PRK10402 189 VLAQFIQDGYLKKSKRGYLIK 209 (226)
T ss_pred HHHHHHHCCCEEeeCCEEEEe
Confidence 99988773 444333334333
No 153
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=79.84 E-value=3.1 Score=38.60 Aligned_cols=47 Identities=17% Similarity=0.164 Sum_probs=40.1
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHH
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMA 119 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 119 (390)
.++..++..+.++++ .|.++.++|..+|+|.++|+++.++.+..|-.
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 577778877878775 58899999999999999999999998887754
No 154
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=79.70 E-value=3.2 Score=37.94 Aligned_cols=48 Identities=15% Similarity=0.268 Sum_probs=40.8
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHHh
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 120 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 120 (390)
.+|+.++-.+.|.++ .|.++.++|..+|+|.+||...+++....|...
T Consensus 184 ~L~~~~r~vl~l~~~-~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~ 231 (236)
T PRK06986 184 SLPEREQLVLSLYYQ-EELNLKEIGAVLGVSESRVSQIHSQAIKRLRAR 231 (236)
T ss_pred hCCHHHHHHHHhHhc-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 577777777777765 589999999999999999999999998888653
No 155
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=79.60 E-value=3.6 Score=37.54 Aligned_cols=56 Identities=7% Similarity=0.078 Sum_probs=46.3
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHHhhccccCCC
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAISLDFFQPP 128 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~~~~i~~P 128 (390)
.+++.++.++.|.++- |.++.++|+..|+|.+||...+.+....|.+...+....+
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 5788888888777765 8999999999999999999999999999987655544433
No 156
>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=79.55 E-value=2.6 Score=29.50 Aligned_cols=39 Identities=18% Similarity=0.258 Sum_probs=30.2
Q ss_pred HHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 79 LAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 79 l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
+-+|+....+| ++...|...++|+++|++.++++-..+.
T Consensus 4 l~~f~~v~~~g-s~~~AA~~l~is~~~vs~~i~~LE~~lg 42 (60)
T PF00126_consen 4 LRYFLAVAETG-SISAAAEELGISQSAVSRQIKQLEEELG 42 (60)
T ss_dssp HHHHHHHHHHS-SHHHHHHHCTSSHHHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHhC-CHHHHHHHhhccchHHHHHHHHHHHHhC
Confidence 33344444444 8999999999999999999999888774
No 157
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=79.22 E-value=2 Score=37.80 Aligned_cols=48 Identities=15% Similarity=0.205 Sum_probs=39.1
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHHh
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 120 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 120 (390)
.+|+.++.++.|+++ .|.++.++|...|+|.+||...+.+....|...
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 477777777766654 589999999999999999998888888877643
No 158
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=79.20 E-value=3.2 Score=30.06 Aligned_cols=42 Identities=12% Similarity=0.202 Sum_probs=33.6
Q ss_pred CHHHHHHHHhhhccc-ccchhhhhhhcccchhhhhhhhHHHHH
Q 016400 74 KIEEQLAIFMFIVGH-NLRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 74 ~~~~~l~~~L~~L~~-~~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
+.+++++.+|..-+. +.+..+|+...|++.++|++.+.....
T Consensus 6 ~~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~ 48 (68)
T smart00550 6 SLEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEK 48 (68)
T ss_pred HHHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 456778888877665 589999999999999999987766543
No 159
>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=78.94 E-value=2.8 Score=40.17 Aligned_cols=51 Identities=10% Similarity=0.143 Sum_probs=44.0
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHHhhcc
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAISLD 123 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~~~ 123 (390)
.+|+.++.++.|.++ .|.++.++|..+|+|.+||...+.+....|.+....
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 578888888888876 589999999999999999999999999998765443
No 160
>COG5421 Transposase [DNA replication, recombination, and repair]
Probab=78.66 E-value=3.2 Score=41.50 Aligned_cols=58 Identities=19% Similarity=0.227 Sum_probs=42.8
Q ss_pred CCCceeeeeeeecCCcceeEeccCcccccccHHHHHHHHhhcCCCCCCCCceeeccCCC
Q 016400 174 SGLLSQNVLAACSFDLKFHYVLAGWEGSASDLRVLNSALTRRNKLQVPEGKYYLVDNKY 232 (390)
Q Consensus 174 k~~~s~~~q~v~d~d~~~~~v~~g~~Gs~~D~~vl~~sl~~~~~~~~p~g~~~l~D~gY 232 (390)
...+-+++..+++.+|--+++.+ ++|+.+|.+.+-.++........+.+.++++|+|+
T Consensus 152 ~dl~QI~vsMi~~~~gIPl~~~v-~~Gni~D~~~~~~ti~kl~~~l~~~~~~~V~Dkgf 209 (480)
T COG5421 152 LDLPQINVSMIVNQKGIPLFVRV-YSGNISDKNTLIKTIQKLKSVLVKDEVYLVADKGF 209 (480)
T ss_pred CCcceeEEEEEEcCCCCceEEEc-cCCCccchHHHHHHHHHHHHhcccceEEEEEcccc
Confidence 34578899999999977766665 79999999998877553222223334789999998
No 161
>PRK01381 Trp operon repressor; Provisional
Probab=78.51 E-value=2.1 Score=33.47 Aligned_cols=40 Identities=20% Similarity=0.215 Sum_probs=28.3
Q ss_pred CCHHHHHHHHhh------hcccccchhhhhhhcccchhhhhhhhHH
Q 016400 73 IKIEEQLAIFMF------IVGHNLRTRAVQELFRYSGETISRHFNN 112 (390)
Q Consensus 73 ~~~~~~l~~~L~------~L~~~~~~~~l~~~fgis~stv~~~~~~ 112 (390)
+++.|+-++..+ .+..+.||++|+...|||.+||+|.-+.
T Consensus 33 lTp~Er~al~~R~~I~~~L~~g~~sQREIa~~lGvSiaTITRgsn~ 78 (99)
T PRK01381 33 LTPDEREALGTRVRIVEELLRGELSQREIKQELGVGIATITRGSNS 78 (99)
T ss_pred CCHHHHHHHHHHHHHHHHHHcCCcCHHHHHHHhCCceeeehhhHHH
Confidence 445555444443 2344589999999999999999986543
No 162
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=78.46 E-value=2 Score=37.29 Aligned_cols=46 Identities=9% Similarity=0.208 Sum_probs=38.5
Q ss_pred CCCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 71 NRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 71 ~~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
..+|+.|. =.|.+++.|.+..++|...++|.+||..++.++..-|.
T Consensus 132 ~~LSpREr--EVLrLLAqGkTnKEIAe~L~IS~rTVkth~srImkKLg 177 (198)
T PRK15201 132 RHFSVTER--HLLKLIASGYHLSETAALLSLSEEQTKSLRRSIMRKLH 177 (198)
T ss_pred CCCCHHHH--HHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 46777665 34567889999999999999999999999999888763
No 163
>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=78.45 E-value=2.8 Score=39.90 Aligned_cols=46 Identities=13% Similarity=0.164 Sum_probs=39.9
Q ss_pred CCCHHHHHHHHhhhc---ccccchhhhhhhcccchhhhhhhhHHHHHHH
Q 016400 72 RIKIEEQLAIFMFIV---GHNLRTRAVQELFRYSGETISRHFNNVLNAI 117 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L---~~~~~~~~l~~~fgis~stv~~~~~~v~~~l 117 (390)
.+++.++..+.|+|. ..+.++.++|..+|+|+++|..+.++.+.-|
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 588889989999885 5789999999999999999999988876543
No 164
>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=78.40 E-value=3.2 Score=37.75 Aligned_cols=46 Identities=17% Similarity=0.237 Sum_probs=39.4
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
.++..++..+.++++ .|.++.++|..+|+|.++|+++.++.+.-|-
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 577777877777764 5889999999999999999999999888775
No 165
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=78.39 E-value=3.4 Score=36.89 Aligned_cols=49 Identities=10% Similarity=0.068 Sum_probs=40.2
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHHhh
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAIS 121 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~ 121 (390)
.+++..+-.+.|.++ .|.++.++|..+|+|.+||...+.+....|.+..
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 466766666666654 5899999999999999999999999998887543
No 166
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=78.38 E-value=3.3 Score=36.72 Aligned_cols=47 Identities=9% Similarity=0.072 Sum_probs=39.7
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHHh
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 120 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 120 (390)
.+++.++-++.| ++ .|.+++++|..+|+|.+||...+++....|.+.
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 577777777777 55 699999999999999999999999888887653
No 167
>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=77.88 E-value=3.4 Score=38.24 Aligned_cols=46 Identities=20% Similarity=0.190 Sum_probs=39.7
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
.++..++..+.++++ .|.++.++|..+|+|.++|+++.++.+.-|.
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 577778878888775 5889999999999999999999999888765
No 168
>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=77.57 E-value=2.4 Score=30.88 Aligned_cols=41 Identities=15% Similarity=0.193 Sum_probs=31.2
Q ss_pred CCHHHHHHHHhhhcccccchhhhhhhcc-cchhhhhhhhHHH
Q 016400 73 IKIEEQLAIFMFIVGHNLRTRAVQELFR-YSGETISRHFNNV 113 (390)
Q Consensus 73 ~~~~~~l~~~L~~L~~~~~~~~l~~~fg-is~stv~~~~~~v 113 (390)
+.-.-++++.|-.--.+.++.+++..|| .+.|||...++++
T Consensus 29 i~~aR~va~yL~r~~~~~sl~~Ig~~fg~rdHstV~~a~~ki 70 (70)
T PF08299_consen 29 IVEARQVAMYLARELTGLSLSEIGRYFGGRDHSTVIHAIRKI 70 (70)
T ss_dssp HHHHHHHHHHHHHHHS---HHHHHHHCTSSTHHHHHHHHHHH
T ss_pred hcchHHHHHHHHHHHhCCCHHHHHHHhCCCCHHHHHHHHHhC
Confidence 4445678887777778999999999999 9999999877764
No 169
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=77.55 E-value=4.1 Score=37.58 Aligned_cols=47 Identities=21% Similarity=0.308 Sum_probs=40.6
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHH
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMA 119 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 119 (390)
.+|+.++-.+.|.++ .|.++.++|..+|+|.+||...+++....|-.
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 577888888888775 68999999999999999999999988887754
No 170
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=77.28 E-value=3.7 Score=36.08 Aligned_cols=49 Identities=10% Similarity=0.261 Sum_probs=40.3
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHHhh
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAIS 121 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~ 121 (390)
.+|...+-++.|.++. |.++.++|...|+|.+||...+.+....|....
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 5677777766666554 899999999999999999999999988887543
No 171
>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=76.78 E-value=2.7 Score=30.67 Aligned_cols=27 Identities=22% Similarity=0.393 Sum_probs=23.6
Q ss_pred ccchhhhhhhcccchhhhhhhhHHHHH
Q 016400 89 NLRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 89 ~~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
+.+..++|...|+|+.||+++++++.+
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 356889999999999999999988765
No 172
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=76.78 E-value=2.2 Score=36.77 Aligned_cols=48 Identities=8% Similarity=0.227 Sum_probs=37.9
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHHh
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 120 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 120 (390)
.+|..++-++.|+++ .|.++.++|..+|+|.+||...+++....|...
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 355555555555554 488999999999999999999999998888753
No 173
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=76.70 E-value=3.8 Score=39.41 Aligned_cols=48 Identities=15% Similarity=0.169 Sum_probs=42.8
Q ss_pred CCCHHHHHHHHhhhc---ccccchhhhhhhcccchhhhhhhhHHHHHHHHH
Q 016400 72 RIKIEEQLAIFMFIV---GHNLRTRAVQELFRYSGETISRHFNNVLNAIMA 119 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L---~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 119 (390)
.+++.++..+.|+|. ..+.++.++|..+|+|+++|..+.++.+.-|-.
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 588889999999886 567999999999999999999999998888864
No 174
>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=76.56 E-value=1.6 Score=35.54 Aligned_cols=29 Identities=17% Similarity=0.217 Sum_probs=25.2
Q ss_pred hhcccccchhhhhhhcccchhhhhhhhHH
Q 016400 84 FIVGHNLRTRAVQELFRYSGETISRHFNN 112 (390)
Q Consensus 84 ~~L~~~~~~~~l~~~fgis~stv~~~~~~ 112 (390)
-++..|.+...++..|+||.+||.+++.+
T Consensus 13 ~~~~~g~s~~eaa~~F~VS~~Tv~~W~k~ 41 (119)
T PF01710_consen 13 AYIEKGKSIREAAKRFGVSRNTVYRWLKR 41 (119)
T ss_pred HHHHccchHHHHHHHhCcHHHHHHHHHHh
Confidence 35666889999999999999999998873
No 175
>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=76.52 E-value=4.4 Score=37.46 Aligned_cols=47 Identities=17% Similarity=0.157 Sum_probs=40.7
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHH
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMA 119 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 119 (390)
.+|+.++-.+.|+++ .|.++.++|..+|+|.+||....++....|-.
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 578888888878775 58999999999999999999999988887753
No 176
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=76.43 E-value=6.3 Score=35.75 Aligned_cols=78 Identities=15% Similarity=0.165 Sum_probs=50.0
Q ss_pred CChhHHHhhcCCCHHHHHHHHHHhccCCc-----cccCCCCCHHHHHHHHhhhccc----------ccchhhhhhhcccc
Q 016400 38 GQSERCLENFRMDKKVFYKLCDILQSKGL-----LRHTNRIKIEEQLAIFMFIVGH----------NLRTRAVQELFRYS 102 (390)
Q Consensus 38 ~~d~~f~~~frms~~~F~~L~~~L~~~~~-----~~~~~~~~~~~~l~~~L~~L~~----------~~~~~~l~~~fgis 102 (390)
.+-+.|...+.-.++....++..+..... .......+++++++-+|..++. ..+..++|...|++
T Consensus 113 i~~~~f~~l~~~~p~l~~~l~~~l~~~l~~~~~~~~~l~~~~~~~Rla~~Ll~l~~~~g~~~~i~i~lt~~~IA~~lGis 192 (230)
T PRK09391 113 IKRRSLEQAAATDVDVARALLSLTAGGLRHAQDHMLLLGRKTAMERVAAFLLEMDERLGGAGMMALPMSRRDIADYLGLT 192 (230)
T ss_pred EEHHHHHHHHhhChHHHHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhCCCCEEEecCCHHHHHHHHCCC
Confidence 34455555554444444444444332211 0111347899999999987743 24678999999999
Q ss_pred hhhhhhhhHHHHH
Q 016400 103 GETISRHFNNVLN 115 (390)
Q Consensus 103 ~stv~~~~~~v~~ 115 (390)
+.|++|+++++-+
T Consensus 193 retlsR~L~~L~~ 205 (230)
T PRK09391 193 IETVSRALSQLQD 205 (230)
T ss_pred HHHHHHHHHHHHH
Confidence 9999999887755
No 177
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=76.36 E-value=2.3 Score=38.07 Aligned_cols=44 Identities=16% Similarity=0.171 Sum_probs=37.3
Q ss_pred CCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 73 IKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 73 ~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
+++.|. =.|.+++.|.+++++|...++|.+||..++++++.-|.
T Consensus 138 LT~RE~--eVL~lla~G~snkeIA~~L~iS~~TVk~h~~~I~~KL~ 181 (207)
T PRK15411 138 LSRTES--SMLRMWMAGQGTIQISDQMNIKAKTVSSHKGNIKRKIK 181 (207)
T ss_pred CCHHHH--HHHHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHHHHhC
Confidence 666554 45677899999999999999999999999999888774
No 178
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=76.35 E-value=2.8 Score=38.14 Aligned_cols=51 Identities=8% Similarity=0.085 Sum_probs=42.2
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHHhhcc
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAISLD 123 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~~~ 123 (390)
.+|..++-++.|+++. |.++.++|..+|+|.+||...+.+....|......
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 4777777777776655 99999999999999999999999999888765443
No 179
>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=76.32 E-value=2.9 Score=29.35 Aligned_cols=31 Identities=19% Similarity=0.233 Sum_probs=26.3
Q ss_pred cccccchhhhhhhcccchhhhhhhhHHHHHH
Q 016400 86 VGHNLRTRAVQELFRYSGETISRHFNNVLNA 116 (390)
Q Consensus 86 L~~~~~~~~l~~~fgis~stv~~~~~~v~~~ 116 (390)
-..+.+..+++..+|++.+|+++.++...++
T Consensus 21 ~~~~~t~~ela~~l~~~~~t~s~hL~~L~~a 51 (61)
T PF12840_consen 21 SNGPMTVSELAEELGISQSTVSYHLKKLEEA 51 (61)
T ss_dssp HCSTBEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred cCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 5678999999999999999999999877653
No 180
>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=76.31 E-value=4.6 Score=36.49 Aligned_cols=47 Identities=17% Similarity=0.336 Sum_probs=39.8
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHH
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMA 119 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 119 (390)
.+++.++-.+.|+++ .|.++.++|..+|+|.+||.+..++....|-.
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 577777877777775 58999999999999999999999888887754
No 181
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=76.21 E-value=3.5 Score=31.23 Aligned_cols=39 Identities=18% Similarity=0.154 Sum_probs=29.3
Q ss_pred HHHHHHhhhcc---cccchhhhhhhcccchhhhhhhhHHHHH
Q 016400 77 EQLAIFMFIVG---HNLRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 77 ~~l~~~L~~L~---~~~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
++..-.|.+|+ .+.+..+++..+|++++||+++++....
T Consensus 5 ~r~~~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~~ 46 (91)
T smart00346 5 ERGLAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQE 46 (91)
T ss_pred HHHHHHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 34444444454 3588999999999999999999887755
No 182
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=75.99 E-value=4.8 Score=35.14 Aligned_cols=47 Identities=11% Similarity=0.121 Sum_probs=39.5
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHH
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMA 119 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 119 (390)
.+|+.++-++.|.++. |.++.++|..+|+|.+||...+++....|-.
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 5777777777777666 8999999999999999999998888877754
No 183
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=75.67 E-value=4.9 Score=37.09 Aligned_cols=47 Identities=15% Similarity=0.283 Sum_probs=41.1
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHH
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMA 119 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 119 (390)
.++-.+|+.+.|+|. .+.+...+|...|||+|.||++.++.+..|..
T Consensus 196 ~L~EREk~Vl~l~y~-eelt~kEI~~~LgISes~VSql~kkai~kLr~ 242 (247)
T COG1191 196 PLPEREKLVLVLRYK-EELTQKEIAEVLGISESRVSRLHKKAIKKLRK 242 (247)
T ss_pred ccCHHHHHHHHHHHH-hccCHHHHHHHhCccHHHHHHHHHHHHHHHHH
Confidence 567778888999885 47999999999999999999999999988864
No 184
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=75.42 E-value=4.8 Score=37.55 Aligned_cols=47 Identities=13% Similarity=0.189 Sum_probs=39.3
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHH
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMA 119 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 119 (390)
.++..++-.+.|+|+ .|.++.++|..+|+|.+||+++.++....|..
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 466667777777775 58999999999999999999999988887754
No 185
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=75.37 E-value=4.7 Score=32.36 Aligned_cols=47 Identities=11% Similarity=0.061 Sum_probs=41.5
Q ss_pred CCCCCHHHHHHHHhhhcccccchhhhhhhccc-chhhhhhhhHHHHHH
Q 016400 70 TNRIKIEEQLAIFMFIVGHNLRTRAVQELFRY-SGETISRHFNNVLNA 116 (390)
Q Consensus 70 ~~~~~~~~~l~~~L~~L~~~~~~~~l~~~fgi-s~stv~~~~~~v~~~ 116 (390)
.+..|.|.++-+.-.++..|.++..+|..||| +.+++++++..+.+.
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~sv~~vAr~~gv~~~~~l~~W~~~~~~~ 52 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGDTVSEVAREFGIVSATQLYKWRIQLQKG 52 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCccHHHHHHHhCCCChHHHHHHHHHHHHc
Confidence 45789999999999999999999999999996 999999988877653
No 186
>PHA00542 putative Cro-like protein
Probab=75.36 E-value=2 Score=32.38 Aligned_cols=30 Identities=13% Similarity=0.197 Sum_probs=25.8
Q ss_pred hhhcccccchhhhhhhcccchhhhhhhhHH
Q 016400 83 MFIVGHNLRTRAVQELFRYSGETISRHFNN 112 (390)
Q Consensus 83 L~~L~~~~~~~~l~~~fgis~stv~~~~~~ 112 (390)
..+...|.+..++|...|||++|++++.+-
T Consensus 25 ~~l~~~glTq~elA~~lgIs~~tIsr~e~g 54 (82)
T PHA00542 25 CALIRAGWSQEQIADATDVSQPTICRIYSG 54 (82)
T ss_pred HHHHHCCCCHHHHHHHHCcCHHHHHHHHcC
Confidence 345678999999999999999999998753
No 187
>PRK06030 hypothetical protein; Provisional
Probab=74.37 E-value=5.3 Score=32.71 Aligned_cols=47 Identities=15% Similarity=0.150 Sum_probs=41.9
Q ss_pred CCCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHH
Q 016400 71 NRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAI 117 (390)
Q Consensus 71 ~~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l 117 (390)
+.+...-|++|.|-.--.+.++.++|..||.+-|||...++.+-+.+
T Consensus 51 k~i~~aRqIAMYL~r~~~~~sl~~IG~~FGRDHSTV~haikkIe~~~ 97 (124)
T PRK06030 51 REVSRIRQIAMYVAHVSLGWPMNEVALAFGRDRTTVGHACHTVEDLR 97 (124)
T ss_pred cccchHHHHHHHHHHHHcCCCHHHHHHHHCCChhHHHHHHHHHHHHh
Confidence 45788899999999999999999999999999999999888776654
No 188
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=74.32 E-value=2.3 Score=27.36 Aligned_cols=29 Identities=21% Similarity=0.259 Sum_probs=22.2
Q ss_pred cccccchhhhhhhcccchhhhhhhhHHHH
Q 016400 86 VGHNLRTRAVQELFRYSGETISRHFNNVL 114 (390)
Q Consensus 86 L~~~~~~~~l~~~fgis~stv~~~~~~v~ 114 (390)
+.++.+..++|..+|+|.+..+|.|++.+
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
>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=74.29 E-value=4.1 Score=31.64 Aligned_cols=30 Identities=13% Similarity=0.180 Sum_probs=25.2
Q ss_pred cccccchhhhhhhcccchhhhhhhhHHHHH
Q 016400 86 VGHNLRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 86 L~~~~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
..-+.+..++|...|+|++||++.++++.+
T Consensus 44 ~~~~is~~eLa~~~g~sr~tVsr~L~~Le~ 73 (95)
T TIGR01610 44 KQDRVTATVIAELTGLSRTHVSDAIKSLAR 73 (95)
T ss_pred cCCccCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 345678999999999999999998877754
No 190
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=74.12 E-value=7 Score=35.36 Aligned_cols=44 Identities=23% Similarity=0.383 Sum_probs=36.7
Q ss_pred CCCHHHHHHHHhhhccc--------------ccchhhhhhhcccchhhhhhhhHHHHH
Q 016400 72 RIKIEEQLAIFMFIVGH--------------NLRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~--------------~~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
..+++++++-+|..++. ..+..++|...|+++.|++|+++++-+
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 46889999999988752 246789999999999999999887654
No 191
>PRK13870 transcriptional regulator TraR; Provisional
Probab=74.09 E-value=2.7 Score=38.56 Aligned_cols=45 Identities=2% Similarity=0.085 Sum_probs=38.3
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
.+|+.|+ =.|.|++.|.+..++|...|||++||.-+++.+..-|.
T Consensus 173 ~LT~RE~--E~L~W~A~GKT~~EIa~ILgISe~TV~~Hl~na~~KLg 217 (234)
T PRK13870 173 WLDPKEA--TYLRWIAVGKTMEEIADVEGVKYNSVRVKLREAMKRFD 217 (234)
T ss_pred CCCHHHH--HHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence 4666554 45789999999999999999999999999999888764
No 192
>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=73.86 E-value=7.4 Score=31.22 Aligned_cols=42 Identities=0% Similarity=-0.045 Sum_probs=30.2
Q ss_pred CCHHHH-HHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHH
Q 016400 73 IKIEEQ-LAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 73 ~~~~~~-l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
+++.+- ++..|.. ..+.+..+++...+++++|+++.+++..+
T Consensus 26 lt~~q~~iL~~l~~-~~~~t~~ela~~~~~~~~tvs~~l~~Le~ 68 (118)
T TIGR02337 26 LTEQQWRILRILAE-QGSMEFTQLANQACILRPSLTGILARLER 68 (118)
T ss_pred CCHHHHHHHHHHHH-cCCcCHHHHHHHhCCCchhHHHHHHHHHH
Confidence 454443 3334432 44678999999999999999998877755
No 193
>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=73.85 E-value=7.2 Score=32.36 Aligned_cols=47 Identities=15% Similarity=0.145 Sum_probs=39.0
Q ss_pred CCHHHHHHHHhhhcc-cccchhhhhhhcccchhhhhhhhHHHHHHHHH
Q 016400 73 IKIEEQLAIFMFIVG-HNLRTRAVQELFRYSGETISRHFNNVLNAIMA 119 (390)
Q Consensus 73 ~~~~~~l~~~L~~L~-~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 119 (390)
++.+++-.+-++|+. ...++..+|..+|+|++|+++.-+.++..+..
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 666788888888874 34599999999999999999998888887764
No 194
>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=73.03 E-value=2.9 Score=34.64 Aligned_cols=36 Identities=8% Similarity=0.226 Sum_probs=31.3
Q ss_pred CCCCHHHHHHHHhhhcccccchhhhhhhcccchhhhh
Q 016400 71 NRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETIS 107 (390)
Q Consensus 71 ~~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~ 107 (390)
..+|+..+-++.|.++. |.++.++|..+|+|.+||.
T Consensus 106 ~~Lp~~~r~v~~l~~~~-~~s~~EIA~~l~is~~tV~ 141 (142)
T TIGR03209 106 SILPNKQKKIIYMKFFE-DMKEIDIAKKLHISRQSVY 141 (142)
T ss_pred HhCCHHHHHHHHHHHHc-CCCHHHHHHHHCcCHHhhc
Confidence 36888888888887765 8999999999999999985
No 195
>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=72.73 E-value=2.2 Score=29.01 Aligned_cols=27 Identities=30% Similarity=0.265 Sum_probs=22.0
Q ss_pred cccccchhhhhhhcccchhhhhhhhHH
Q 016400 86 VGHNLRTRAVQELFRYSGETISRHFNN 112 (390)
Q Consensus 86 L~~~~~~~~l~~~fgis~stv~~~~~~ 112 (390)
...|.++.++|...|+|++|++++.+.
T Consensus 6 ~~~gls~~~la~~~gis~~~i~~~~~g 32 (55)
T PF01381_consen 6 KEKGLSQKELAEKLGISRSTISRIENG 32 (55)
T ss_dssp HHTTS-HHHHHHHHTS-HHHHHHHHTT
T ss_pred HHcCCCHHHHHHHhCCCcchhHHHhcC
Confidence 357899999999999999999998764
No 196
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=72.40 E-value=4.3 Score=28.90 Aligned_cols=38 Identities=13% Similarity=0.127 Sum_probs=29.7
Q ss_pred HHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHH
Q 016400 77 EQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVL 114 (390)
Q Consensus 77 ~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~ 114 (390)
++++-+|.....+.+-+++|+.+|+|..++.+++....
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 45666777778899999999999999999998876553
No 197
>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=72.34 E-value=5.3 Score=35.05 Aligned_cols=45 Identities=4% Similarity=0.012 Sum_probs=34.0
Q ss_pred CHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHH
Q 016400 74 KIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMA 119 (390)
Q Consensus 74 ~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 119 (390)
+++.+-.+++.++ .|.++.++|..+|+|.+||...+++....|-.
T Consensus 151 l~~~~~~i~~~~~-~~~s~~eIA~~l~~s~~tV~~~l~r~r~~L~~ 195 (198)
T TIGR02859 151 LSDLEWKVLQSYL-DGKSYQEIACDLNRHVKSIDNALQRVKRKLEK 195 (198)
T ss_pred cCHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3333333445555 79999999999999999999888888777653
No 198
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=72.28 E-value=5.6 Score=37.10 Aligned_cols=47 Identities=11% Similarity=0.253 Sum_probs=39.7
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHH
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMA 119 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 119 (390)
.+|+.++-++.|+++ .|.++.++|..+|+|.+||....++....|..
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 578888888877775 58999999999999999999888887777754
No 199
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=72.25 E-value=4 Score=37.03 Aligned_cols=45 Identities=18% Similarity=0.276 Sum_probs=36.2
Q ss_pred CCCCHHHHHHHHhhhcccc----------cchhhhhhhcccchhhhhhhhHHHHH
Q 016400 71 NRIKIEEQLAIFMFIVGHN----------LRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 71 ~~~~~~~~l~~~L~~L~~~----------~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
...+++++++-+|..++.. .+..++|...|+++.||+|+++++.+
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 3568999999999876531 23578999999999999999988655
No 200
>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=72.14 E-value=4.5 Score=29.02 Aligned_cols=39 Identities=13% Similarity=0.195 Sum_probs=29.5
Q ss_pred HHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHH
Q 016400 76 EEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 76 ~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
|.++...|. -..+.+..+|+...|++++||++++++..+
T Consensus 10 E~~vy~~Ll-~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~ 48 (68)
T PF01978_consen 10 EAKVYLALL-KNGPATAEEIAEELGISRSTVYRALKSLEE 48 (68)
T ss_dssp HHHHHHHHH-HHCHEEHHHHHHHHTSSHHHHHHHHHHHHH
T ss_pred HHHHHHHHH-HcCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 344555554 234588999999999999999998887755
No 201
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=71.76 E-value=3.5 Score=26.88 Aligned_cols=28 Identities=25% Similarity=0.394 Sum_probs=24.0
Q ss_pred cccchhhhhhhcccchhhhhhhhHHHHH
Q 016400 88 HNLRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 88 ~~~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
-..+..++++.+|+|.+|+++.++.+.+
T Consensus 7 ~~~s~~~la~~l~~s~~tv~~~l~~L~~ 34 (48)
T smart00419 7 LPLTRQEIAELLGLTRETVSRTLKRLEK 34 (48)
T ss_pred eccCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4567889999999999999998887755
No 202
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=71.71 E-value=4.8 Score=33.56 Aligned_cols=44 Identities=2% Similarity=0.007 Sum_probs=31.9
Q ss_pred CCCHHH-HHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHH
Q 016400 72 RIKIEE-QLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 72 ~~~~~~-~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
++++.+ .++.+|.....+.+..+|+..++++++|+++.+++..+
T Consensus 28 glt~~q~~vL~~l~~~~~~~t~~eLa~~l~~~~~tvt~~v~~Le~ 72 (144)
T PRK03573 28 ELTQTHWVTLHNIHQLPPEQSQIQLAKAIGIEQPSLVRTLDQLEE 72 (144)
T ss_pred CCCHHHHHHHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHHHHHH
Confidence 355444 34455554444678899999999999999998877754
No 203
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=71.67 E-value=5.9 Score=36.17 Aligned_cols=46 Identities=13% Similarity=0.309 Sum_probs=38.3
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
.++..++-.+.|++. .|.++.++|..+|+|.++|+++-++...-|-
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 467777777777764 5899999999999999999999988877664
No 204
>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function.
Probab=71.67 E-value=8.2 Score=30.65 Aligned_cols=46 Identities=20% Similarity=0.176 Sum_probs=37.4
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
.++++|-=++=|..+- |.++.+.|...|||++|+.++++..-.-|.
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 4677777777666664 799999999999999999999987766654
No 205
>PF13309 HTH_22: HTH domain
Probab=71.37 E-value=5.5 Score=28.47 Aligned_cols=40 Identities=23% Similarity=0.183 Sum_probs=26.4
Q ss_pred CCCHHHHHHHHhhhcccc-----cchhhhhhhcccchhhhhhhhH
Q 016400 72 RIKIEEQLAIFMFIVGHN-----LRTRAVQELFRYSGETISRHFN 111 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~-----~~~~~l~~~fgis~stv~~~~~ 111 (390)
.++.++++.+.-..-..| .+...+|..+|||+.||+++++
T Consensus 20 ~l~~~~k~~iV~~L~~~G~F~lKgav~~vA~~L~iS~~TVY~YLr 64 (64)
T PF13309_consen 20 RLSKEEKKEIVRQLYEKGIFLLKGAVEYVAEKLGISRATVYRYLR 64 (64)
T ss_pred hCCHHHHHHHHHHHHHCCCcccCcHHHHHHHHHCCCHHHHHHHcC
Confidence 344455544433333333 4567899999999999999864
No 206
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=71.35 E-value=5.7 Score=31.91 Aligned_cols=46 Identities=11% Similarity=0.195 Sum_probs=35.8
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
.++.+++-.+ ..++.+..+..+++..+|||-+||..-+.+++.+|-
T Consensus 33 ~L~~E~~~Fi-~~Fi~~rGnlKe~e~~lgiSYPTvR~rLd~ii~~lg 78 (113)
T PF09862_consen 33 RLSPEQLEFI-KLFIKNRGNLKEMEKELGISYPTVRNRLDKIIEKLG 78 (113)
T ss_pred cCCHHHHHHH-HHHHHhcCCHHHHHHHHCCCcHHHHHHHHHHHHHhC
Confidence 4555555444 445555678999999999999999999999988884
No 207
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=71.28 E-value=3.4 Score=28.24 Aligned_cols=25 Identities=12% Similarity=0.166 Sum_probs=21.8
Q ss_pred chhhhhhhcccchhhhhhhhHHHHH
Q 016400 91 RTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 91 ~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
+.+++++.||+|++||.+.++...+
T Consensus 22 s~~~la~~~~vs~~tv~~~l~~L~~ 46 (60)
T smart00345 22 SERELAAQLGVSRTTVREALSRLEA 46 (60)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 6889999999999999998877654
No 208
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=71.18 E-value=6.2 Score=38.11 Aligned_cols=50 Identities=10% Similarity=0.088 Sum_probs=42.2
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHHhhc
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAISL 122 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~~ 122 (390)
.+|..++-++.|+++- |.++.++|..+|+|.+||...+.+....|.+..+
T Consensus 153 ~Lp~~~R~v~~L~~~~-g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~~~ 202 (339)
T PRK08241 153 HLPPRQRAVLILRDVL-GWSAAEVAELLDTSVAAVNSALQRARATLAERGP 202 (339)
T ss_pred hCCHHHhhhhhhHHhh-CCCHHHHHHHhCCCHHHHHHHHHHHHHHHhhcCC
Confidence 5777788877777654 8999999999999999999999999988876433
No 209
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=70.19 E-value=3.6 Score=37.01 Aligned_cols=44 Identities=18% Similarity=0.336 Sum_probs=36.4
Q ss_pred CCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 73 IKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 73 ~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
+|..| .-.|..|+.|.+.+++|...++|.+||..++.....-|.
T Consensus 149 LT~RE--~eVL~lla~G~snkeIA~~L~iS~~TVk~h~~~i~~KL~ 192 (211)
T COG2197 149 LTPRE--LEVLRLLAEGLSNKEIAEELNLSEKTVKTHVSNILRKLG 192 (211)
T ss_pred CCHHH--HHHHHHHHCCCCHHHHHHHHCCCHhHHHHHHHHHHHHcC
Confidence 44444 345678899999999999999999999999998887663
No 210
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=70.08 E-value=4.7 Score=27.70 Aligned_cols=29 Identities=21% Similarity=0.314 Sum_probs=24.7
Q ss_pred ccccchhhhhhhcccchhhhhhhhHHHHH
Q 016400 87 GHNLRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 87 ~~~~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
....+..+++..+|+|.+|+++.+++...
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~ 36 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLRE 36 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 45578999999999999999998877654
No 211
>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=70.08 E-value=7.4 Score=27.54 Aligned_cols=28 Identities=18% Similarity=0.207 Sum_probs=22.1
Q ss_pred cccchhhhhhhcccchhhhhhhhHHHHH
Q 016400 88 HNLRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 88 ~~~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
...+..+|+..++++++++++.+++.+.
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 4578899999999999999999888765
No 212
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=69.74 E-value=4.3 Score=36.53 Aligned_cols=45 Identities=4% Similarity=0.141 Sum_probs=36.5
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
.+++.|+ -.|..++.|.+..++|...++|.+||..++.++..-+.
T Consensus 143 ~LS~RE~--eVL~Lia~G~SnkEIA~~L~IS~~TVk~hvs~I~~KLg 187 (217)
T PRK13719 143 KVTKYQN--DVFILYSFGFSHEYIAQLLNITVGSSKNKISEILKFFG 187 (217)
T ss_pred CCCHHHH--HHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 3444443 44567788999999999999999999999999988774
No 213
>COG3316 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=69.53 E-value=28 Score=31.38 Aligned_cols=186 Identities=15% Similarity=0.082 Sum_probs=106.9
Q ss_pred CCHHHHHHHHhhhcccccchhhhhhh-----cccchhhhhhhhHHHHHHHHHhhccccCCCCCCCchhhccCCcccCCCc
Q 016400 73 IKIEEQLAIFMFIVGHNLRTRAVQEL-----FRYSGETISRHFNNVLNAIMAISLDFFQPPGPDVPPEISLDPRLYPYFK 147 (390)
Q Consensus 73 ~~~~~~l~~~L~~L~~~~~~~~l~~~-----fgis~stv~~~~~~v~~~l~~~~~~~i~~P~~~~~~~i~~~~~~~~~fp 147 (390)
.+..-.....=++|+.+.+++.+.+. ..++.+|+++++.+.-..+....+..=+- +
T Consensus 9 f~~~vi~~~V~~yl~~~Ls~r~v~e~l~~rgi~v~h~Ti~rwv~k~~~~~~~~~~~r~~~-------------------~ 69 (215)
T COG3316 9 FPRNIIAVAVWLYLRYGLSLRDVEEMLAERGIEVDHETIHRWVQKYGPLLARRLKRRKRK-------------------A 69 (215)
T ss_pred cchhhHHHHHHHHhhcchhhccHHHHHHHcCcchhHHHHHHHHHHHhHHHHHHhhhhccc-------------------c
Confidence 33334444555677889999998886 35678999999999988887544332110 1
Q ss_pred cccccccceEEEEEeCCCCCCCCCCCCCCceeeeeeeecCCcceeEeccCcccccccHHHH-HHHHhhcCCCCCCCCcee
Q 016400 148 DCVGAVDGIHIPVMVGVDEQGPFRNKSGLLSQNVLAACSFDLKFHYVLAGWEGSASDLRVL-NSALTRRNKLQVPEGKYY 226 (390)
Q Consensus 148 ~~iG~IDgt~i~i~~P~~~~~~y~~~k~~~s~~~q~v~d~d~~~~~v~~g~~Gs~~D~~vl-~~sl~~~~~~~~p~g~~~ 226 (390)
+-.=.||-|.|.|. |+. .-+=.++|.+|..+.+...-.-+...+..| ..++.. ...+.-+
T Consensus 70 ~~~w~vDEt~ikv~----------gkw----~ylyrAid~~g~~Ld~~L~~rRn~~aAk~Fl~kllk~-----~g~p~v~ 130 (215)
T COG3316 70 GDSWRVDETYIKVN----------GKW----HYLYRAIDADGLTLDVWLSKRRNALAAKAFLKKLLKK-----HGEPRVF 130 (215)
T ss_pred ccceeeeeeEEeec----------cEe----eehhhhhccCCCeEEEEEEcccCcHHHHHHHHHHHHh-----cCCCceE
Confidence 11225788888873 111 112246777788888877644455555444 455553 2345667
Q ss_pred eccCCCCCCCCccccccCcccCcccccCCCCChhhHHHHHHHHHHH-HhHHHHHHHHHHhhchhhhcCCCCCccchhHHH
Q 016400 227 LVDNKYANMPGFIAPYQAVSYHTNQTTTGYHPQDAKELFNQRHSLL-RNATDRIFGALKERFPILLSAPPYPLQTQVKLV 305 (390)
Q Consensus 227 l~D~gYp~~~~ll~P~~~~~~~~~~~~~~~~~~~~~~~fN~~~s~~-R~~VE~~fg~LK~rf~iL~~~~~~~~~~~~~ii 305 (390)
+.|++=.....+ +.. .. .+-++.++. .+.||+-+..+|.|=+-.. ...+.......+
T Consensus 131 vtDka~s~~~A~----~~l-------------~~---~~ehr~~~ylnN~iE~dh~~iKrr~~~~~--~f~~~~sa~~~~ 188 (215)
T COG3316 131 VTDKAPSYTAAL----RKL-------------GS---EVEHRTSKYLNNRIEQDHRPIKRRTRPMK--RFKSLSSAASTI 188 (215)
T ss_pred EecCccchHHHH----Hhc-------------Cc---chheecccccccchhhcchhHHHHhcccc--cCCChHHHHHHH
Confidence 888763222111 000 00 111222233 4889999999997555332 223445566666
Q ss_pred HHHHHHHhhhhcc
Q 016400 306 VAACALHNYIQRE 318 (390)
Q Consensus 306 ~a~~~LhN~~~~~ 318 (390)
...=.+|++-...
T Consensus 189 ~gie~i~~~~~~~ 201 (215)
T COG3316 189 SGIESIHMLYKRQ 201 (215)
T ss_pred HhHHHHHHHHhhh
Confidence 7777788875554
No 214
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=69.52 E-value=7.8 Score=36.62 Aligned_cols=50 Identities=12% Similarity=0.037 Sum_probs=42.3
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHHhhc
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAISL 122 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~~ 122 (390)
.+|+.++-++.|+++- |.++.++|+.+|+|.+||...+++....|.+..+
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 5788888877777665 8999999999999999999999998888876543
No 215
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=69.41 E-value=6.9 Score=38.50 Aligned_cols=47 Identities=13% Similarity=0.145 Sum_probs=40.9
Q ss_pred CCCHHHHHHHHhhhc---ccccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 72 RIKIEEQLAIFMFIV---GHNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L---~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
.++..++..+.|+|+ ..+.++..+|..+|||+++|..+..+.+.-|-
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 588888888888875 34689999999999999999999999888875
No 216
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=69.29 E-value=3.4 Score=36.15 Aligned_cols=48 Identities=6% Similarity=0.191 Sum_probs=37.4
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHHh
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 120 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 120 (390)
.+|..++=++.|.++ .|.++.++|..+|+|.+||...+.+....|-..
T Consensus 134 ~L~~~~r~v~~l~~~-~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 181 (188)
T PRK09640 134 HVNPIDREILVLRFV-AELEFQEIADIMHMGLSATKMRYKRALDKLREK 181 (188)
T ss_pred hcChhheeeeeeHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 355555555555554 589999999999999999999999988888653
No 217
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=69.22 E-value=8 Score=37.30 Aligned_cols=50 Identities=8% Similarity=0.026 Sum_probs=42.8
Q ss_pred CCCHHHHHHHHhhh-c--ccccchhhhhhhcccchhhhhhhhHHHHHHHHHhh
Q 016400 72 RIKIEEQLAIFMFI-V--GHNLRTRAVQELFRYSGETISRHFNNVLNAIMAIS 121 (390)
Q Consensus 72 ~~~~~~~l~~~L~~-L--~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~ 121 (390)
.++..++..+.++| | -.|.++..+|...|+|.+||..+.++....|....
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 68888888888776 3 46899999999999999999999999999887543
No 218
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=69.06 E-value=6.9 Score=39.01 Aligned_cols=47 Identities=17% Similarity=0.187 Sum_probs=40.7
Q ss_pred CCCHHHHHHHHhhhc---ccccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 72 RIKIEEQLAIFMFIV---GHNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L---~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
.+++.++-.+.|+|. +.+.++.++|..+|+|.++|..+.++.+..|-
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 35689999999999999999999999888775
No 219
>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=68.73 E-value=9.1 Score=36.00 Aligned_cols=49 Identities=10% Similarity=0.027 Sum_probs=41.3
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHHhh
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAIS 121 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~ 121 (390)
.+|+.++-++.|.++- |.++.++|..+|+|.+||...+++....|.+..
T Consensus 108 ~L~~~~R~v~~L~~~~-g~s~~EIA~~lg~s~~tVr~~l~RAr~~Lr~~~ 156 (281)
T TIGR02957 108 RLSPLERAVFVLREVF-DYPYEEIASIVGKSEANCRQLVSRARRHLDARR 156 (281)
T ss_pred hCCHHHHHHHHHHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhC
Confidence 5777777777776554 899999999999999999999999998887643
No 220
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=68.19 E-value=8.4 Score=32.15 Aligned_cols=43 Identities=5% Similarity=0.108 Sum_probs=31.9
Q ss_pred CCCHHHH-HHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHH
Q 016400 72 RIKIEEQ-LAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 72 ~~~~~~~-l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
++++.+- ++..|+ -..+.+..+++..++++++|+++.+++..+
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 4555444 444443 345689999999999999999998887654
No 221
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=68.02 E-value=9.6 Score=33.36 Aligned_cols=45 Identities=11% Similarity=0.164 Sum_probs=34.0
Q ss_pred CCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 73 IKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 73 ~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
+++++.=.+.|+++ .|.++.++|...|||..||.+-+...-..|.
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 44444444555555 5899999999999999999998887765554
No 222
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=67.98 E-value=4.4 Score=36.10 Aligned_cols=44 Identities=14% Similarity=0.179 Sum_probs=37.6
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHH
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAI 117 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l 117 (390)
.+++.|+ -.|..++.|.+..++|...++|.+||..+..++..-|
T Consensus 150 ~Lt~rE~--evl~~~~~G~s~~eIA~~l~iS~~TV~~h~~~i~~Kl 193 (216)
T PRK10840 150 RLSPKES--EVLRLFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKL 193 (216)
T ss_pred cCCHHHH--HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHc
Confidence 4777665 5667788999999999999999999999998887766
No 223
>PRK05949 RNA polymerase sigma factor; Validated
Probab=67.79 E-value=7.9 Score=37.39 Aligned_cols=48 Identities=15% Similarity=0.176 Sum_probs=41.4
Q ss_pred CCCHHHHHHHHhhhc---ccccchhhhhhhcccchhhhhhhhHHHHHHHHH
Q 016400 72 RIKIEEQLAIFMFIV---GHNLRTRAVQELFRYSGETISRHFNNVLNAIMA 119 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L---~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 119 (390)
.+++.++-.+.|+|. ..+.++.++|..+|+|.++|..+.++.+..|..
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 588888888888874 356899999999999999999999998888864
No 224
>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=67.78 E-value=6.8 Score=27.46 Aligned_cols=33 Identities=9% Similarity=0.134 Sum_probs=26.5
Q ss_pred HHHHhhhcccccchhhhhhhcccchhhhhhhhHHH
Q 016400 79 LAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNV 113 (390)
Q Consensus 79 l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v 113 (390)
.+..||+ .|.+..++|+..|++.+||+.+..+.
T Consensus 5 ~A~~LY~--~G~~~~eIA~~Lg~~~~TV~~W~~r~ 37 (58)
T PF06056_consen 5 QARSLYL--QGWSIKEIAEELGVPRSTVYSWKDRY 37 (58)
T ss_pred HHHHHHH--cCCCHHHHHHHHCCChHHHHHHHHhh
Confidence 3455554 58999999999999999999877653
No 225
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=66.85 E-value=6.5 Score=27.39 Aligned_cols=36 Identities=17% Similarity=0.414 Sum_probs=30.9
Q ss_pred HhhhcccccchhhhhhhcccchhhhhhhhHHHHHHH
Q 016400 82 FMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAI 117 (390)
Q Consensus 82 ~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l 117 (390)
.+.+++.|.+..+++...++|..||......+..-+
T Consensus 12 v~~l~~~G~s~~eia~~l~is~~tV~~h~~~i~~Kl 47 (65)
T COG2771 12 ILRLVAQGKSNKEIARILGISEETVKTHLRNIYRKL 47 (65)
T ss_pred HHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 355677889999999999999999999988886655
No 226
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=66.76 E-value=6 Score=34.76 Aligned_cols=44 Identities=7% Similarity=0.145 Sum_probs=36.5
Q ss_pred CCCHHHHHHHHhhhccc--------------ccchhhhhhhcccchhhhhhhhHHHHH
Q 016400 72 RIKIEEQLAIFMFIVGH--------------NLRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~--------------~~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
..+++++|+-+|..|+. ..+..++|...|+++.||+|+++++.+
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 45788999998876653 246889999999999999999998876
No 227
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=66.42 E-value=4.2 Score=28.77 Aligned_cols=27 Identities=19% Similarity=0.094 Sum_probs=21.4
Q ss_pred hcccccchhhhhhhcccchhhhhhhhH
Q 016400 85 IVGHNLRTRAVQELFRYSGETISRHFN 111 (390)
Q Consensus 85 ~L~~~~~~~~l~~~fgis~stv~~~~~ 111 (390)
+-+.|.++.++|...|+|.+|++++-+
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 446789999999999999999998654
No 228
>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=66.12 E-value=5.5 Score=30.81 Aligned_cols=57 Identities=16% Similarity=0.167 Sum_probs=35.7
Q ss_pred hcCCCHHHHHHHHHHhccCCccccC-CCCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhH
Q 016400 46 NFRMDKKVFYKLCDILQSKGLLRHT-NRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFN 111 (390)
Q Consensus 46 ~frms~~~F~~L~~~L~~~~~~~~~-~~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~ 111 (390)
.+-|+-+.|..|..........+.. .....+.+ |. ..+..+|..||+|.+|++|+-.
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 4567778888888777543322211 11222222 11 2367899999999999999875
No 229
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=65.93 E-value=8.6 Score=37.76 Aligned_cols=47 Identities=13% Similarity=0.112 Sum_probs=39.8
Q ss_pred CCCHHHHHHHHhhhc-c--cccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 72 RIKIEEQLAIFMFIV-G--HNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L-~--~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
.++..++..+.|+|. . .+.++..||..||||++.|+.+-.+.+.-|-
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 578888888888885 2 5589999999999999999999888777664
No 230
>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=65.92 E-value=8.4 Score=27.29 Aligned_cols=28 Identities=25% Similarity=0.343 Sum_probs=23.6
Q ss_pred cccchhhhhhhcccchhhhhhhhHHHHH
Q 016400 88 HNLRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 88 ~~~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
++.+..+++..++++.+|+++.++.+..
T Consensus 19 ~~~~~~ei~~~~~i~~~~i~~~l~~L~~ 46 (78)
T cd00090 19 GPLTVSELAERLGLSQSTVSRHLKKLEE 46 (78)
T ss_pred CCcCHHHHHHHHCcCHhHHHHHHHHHHH
Confidence 3488999999999999999998877543
No 231
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=65.55 E-value=5.3 Score=35.82 Aligned_cols=43 Identities=16% Similarity=0.211 Sum_probs=35.6
Q ss_pred CCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHH
Q 016400 73 IKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAI 117 (390)
Q Consensus 73 ~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l 117 (390)
+|+.|+ =.|..++.|.+.+++|...++|..||..+..++..-|
T Consensus 135 LT~RE~--eVL~ll~~G~snkeIA~~L~iS~~TV~~h~~~I~~KL 177 (207)
T PRK11475 135 LSPTER--EILRFMSRGYSMPQIAEQLERNIKTIRAHKFNVMSKL 177 (207)
T ss_pred CCHHHH--HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHc
Confidence 555444 3456778999999999999999999999998887766
No 232
>PHA02517 putative transposase OrfB; Reviewed
Probab=65.01 E-value=96 Score=28.75 Aligned_cols=75 Identities=15% Similarity=-0.009 Sum_probs=37.0
Q ss_pred cCCCccccccccceEEEEEeCCCCCCCCCCCCCCceeeeeeeec-CCcceeEeccCcccccccHHHHHHHHhh-cCCCCC
Q 016400 143 YPYFKDCVGAVDGIHIPVMVGVDEQGPFRNKSGLLSQNVLAACS-FDLKFHYVLAGWEGSASDLRVLNSALTR-RNKLQV 220 (390)
Q Consensus 143 ~~~fp~~iG~IDgt~i~i~~P~~~~~~y~~~k~~~s~~~q~v~d-~d~~~~~v~~g~~Gs~~D~~vl~~sl~~-~~~~~~ 220 (390)
...-|+-+-+.|.|++++. +|. .. +.+|.| .+..++...+. ...++.....++.. ......
T Consensus 105 ~~~~pn~~w~~D~t~~~~~------------~g~-~y-l~~iiD~~sr~i~~~~~~---~~~~~~~~~~~l~~a~~~~~~ 167 (277)
T PHA02517 105 VATRPNQLWVADFTYVSTW------------QGW-VY-VAFIIDVFARRIVGWRVS---SSMDTDFVLDALEQALWARGR 167 (277)
T ss_pred CCCCCCCeEEeceeEEEeC------------CCC-EE-EEEecccCCCeeeecccC---CCCChHHHHHHHHHHHHhcCC
Confidence 3456887778999998742 121 12 344444 55555543332 12233333333221 011124
Q ss_pred CCCceeeccCCCCC
Q 016400 221 PEGKYYLVDNKYAN 234 (390)
Q Consensus 221 p~g~~~l~D~gYp~ 234 (390)
|.+..+..|.|-.-
T Consensus 168 ~~~~i~~sD~G~~y 181 (277)
T PHA02517 168 PGGLIHHSDKGSQY 181 (277)
T ss_pred CcCcEeeccccccc
Confidence 44456678998753
No 233
>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=64.74 E-value=6.2 Score=31.41 Aligned_cols=31 Identities=19% Similarity=0.220 Sum_probs=25.4
Q ss_pred cccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 88 HNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 88 ~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
-|.+...+|+.|+||+||+..+..+.-..-.
T Consensus 79 AGlt~~aIAd~F~iS~s~~~nft~~n~~eYy 109 (126)
T PF10654_consen 79 AGLTCYAIADYFKISKSTVFNFTQNNKKEYY 109 (126)
T ss_pred cCCChHHHHHHHhHHHHHHHHHHHHhHHHHH
Confidence 3899999999999999999988766555443
No 234
>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=64.41 E-value=17 Score=33.07 Aligned_cols=46 Identities=11% Similarity=0.159 Sum_probs=38.6
Q ss_pred CCCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 71 NRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 71 ~~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
..++..++=.+.+ .+.|.++.++|..+|+|.+||..++++...-|.
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 4688877766655 479999999999999999999999999887764
No 235
>PHA00738 putative HTH transcription regulator
Probab=64.22 E-value=8.4 Score=30.59 Aligned_cols=28 Identities=18% Similarity=0.171 Sum_probs=24.8
Q ss_pred ccchhhhhhhcccchhhhhhhhHHHHHH
Q 016400 89 NLRTRAVQELFRYSGETISRHFNNVLNA 116 (390)
Q Consensus 89 ~~~~~~l~~~fgis~stv~~~~~~v~~~ 116 (390)
.++..++++.|++|++|||++++-.-+|
T Consensus 26 ~~~V~eLae~l~lSQptVS~HLKvLreA 53 (108)
T PHA00738 26 ILSASLISHTLLLSYTTVLRHLKILNEQ 53 (108)
T ss_pred CccHHHHHHhhCCCHHHHHHHHHHHHHC
Confidence 3788999999999999999999877665
No 236
>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=64.03 E-value=13 Score=29.54 Aligned_cols=44 Identities=7% Similarity=0.166 Sum_probs=31.1
Q ss_pred CCCHHHH-HHHHhhhc---ccccchhhhhhhcccchhhhhhhhHHHHH
Q 016400 72 RIKIEEQ-LAIFMFIV---GHNLRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 72 ~~~~~~~-l~~~L~~L---~~~~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
++++.+- ++..|+.+ ..+.+..+++...+++++|+++.+++..+
T Consensus 22 ~ls~~q~~vL~~l~~~~~~~~~~t~~eL~~~l~~~~stvs~~i~~Le~ 69 (109)
T TIGR01889 22 NLSLEELLILYYLGKLENNEGKLTLKEIIKEILIKQSALVKIIKKLSK 69 (109)
T ss_pred CCCHHHHHHHHHHHhhhccCCcCcHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3555433 44444432 23588999999999999999998887755
No 237
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=63.16 E-value=13 Score=28.27 Aligned_cols=29 Identities=14% Similarity=0.185 Sum_probs=25.1
Q ss_pred ccccchhhhhhhcccchhhhhhhhHHHHH
Q 016400 87 GHNLRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 87 ~~~~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
..+.+..+++..+++|++|+++.+++..+
T Consensus 22 ~~~~~~~~la~~~~~s~~~i~~~l~~L~~ 50 (101)
T smart00347 22 EGPLSVSELAKRLGVSPSTVTRVLDRLEK 50 (101)
T ss_pred cCCcCHHHHHHHHCCCchhHHHHHHHHHH
Confidence 34578999999999999999998888766
No 238
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=63.03 E-value=6.5 Score=36.14 Aligned_cols=45 Identities=11% Similarity=0.124 Sum_probs=37.1
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
.++..|.=. |.+++.|.+..++|...+||..||..++..+.+-|.
T Consensus 179 ~LT~rE~ev--l~~~a~G~t~~eIa~~l~is~~TV~~h~~~~~~KL~ 223 (240)
T PRK10188 179 NFSKREKEI--LKWTAEGKTSAEIAMILSISENTVNFHQKNMQKKFN 223 (240)
T ss_pred CCCHHHHHH--HHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 567666544 455689999999999999999999999998887763
No 239
>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=62.72 E-value=12 Score=28.17 Aligned_cols=34 Identities=15% Similarity=0.109 Sum_probs=28.0
Q ss_pred cccccchhhhhhhcccchhhhhhhhHHHHHHHHH
Q 016400 86 VGHNLRTRAVQELFRYSGETISRHFNNVLNAIMA 119 (390)
Q Consensus 86 L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 119 (390)
...+.+..++++.+.+|+||+.+.++.+-+.|..
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 5677899999999999999999999999888864
No 240
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=62.65 E-value=13 Score=24.37 Aligned_cols=27 Identities=26% Similarity=0.362 Sum_probs=23.6
Q ss_pred ccchhhhhhhcccchhhhhhhhHHHHH
Q 016400 89 NLRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 89 ~~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
+.+..+++..|++|.+|+++.+..+..
T Consensus 14 ~~s~~~l~~~l~~s~~tv~~~l~~L~~ 40 (53)
T smart00420 14 KVSVEELAELLGVSEMTIRRDLNKLEE 40 (53)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 578899999999999999999877655
No 241
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=62.46 E-value=5.8 Score=38.17 Aligned_cols=35 Identities=17% Similarity=0.175 Sum_probs=29.1
Q ss_pred HHhhhcccccchhhhhhhcccchhhhhhhhHHHHH
Q 016400 81 IFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 81 ~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
++=.|+-.|.++.++|..+|+|+++|+|++.+.-+
T Consensus 21 vA~lYY~~g~tQ~eIA~~lgiSR~~VsRlL~~Ar~ 55 (318)
T PRK15418 21 IAWFYYHDGLTQSEIGERLGLTRLKVSRLLEKGRQ 55 (318)
T ss_pred HHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 34445566999999999999999999999887655
No 242
>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=61.73 E-value=9 Score=29.53 Aligned_cols=29 Identities=24% Similarity=0.330 Sum_probs=23.3
Q ss_pred cchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 90 LRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 90 ~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
.++..+|+..|++.|||||+-..+..-+.
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 56889999999999999998766554433
No 243
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=61.42 E-value=4.6 Score=29.29 Aligned_cols=22 Identities=32% Similarity=0.344 Sum_probs=18.6
Q ss_pred chhhhhhhcccchhhhhhhhHH
Q 016400 91 RTRAVQELFRYSGETISRHFNN 112 (390)
Q Consensus 91 ~~~~l~~~fgis~stv~~~~~~ 112 (390)
+.+++|...|+|.+||+++++.
T Consensus 2 t~~~iA~~~gvS~~TVSr~ln~ 23 (70)
T smart00354 2 TIKDVARLAGVSKATVSRVLNG 23 (70)
T ss_pred CHHHHHHHHCCCHHHHHHHHCC
Confidence 4678999999999999997753
No 244
>PRK09483 response regulator; Provisional
Probab=61.33 E-value=6.9 Score=34.31 Aligned_cols=44 Identities=9% Similarity=0.210 Sum_probs=36.3
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHH
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAI 117 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l 117 (390)
.++..+.-.+ .+++.|.+..++|..+++|.+||..+++++..-|
T Consensus 148 ~Lt~rE~~vl--~~~~~G~~~~~Ia~~l~is~~TV~~~~~~i~~Kl 191 (217)
T PRK09483 148 SLSERELQIM--LMITKGQKVNEISEQLNLSPKTVNSYRYRMFSKL 191 (217)
T ss_pred ccCHHHHHHH--HHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHc
Confidence 4777665444 4568899999999999999999999998887766
No 245
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=61.23 E-value=5 Score=35.62 Aligned_cols=29 Identities=10% Similarity=0.201 Sum_probs=25.5
Q ss_pred hhcccccchhhhhhhcccchhhhhhhhHH
Q 016400 84 FIVGHNLRTRAVQELFRYSGETISRHFNN 112 (390)
Q Consensus 84 ~~L~~~~~~~~l~~~fgis~stv~~~~~~ 112 (390)
.++..|.++..+|..+|||.+|++++++.
T Consensus 167 ~~~~~g~s~~~iak~lgis~~Tv~r~~k~ 195 (200)
T PRK13413 167 KLLDKGTSKSEIARKLGVSRTTLARFLKT 195 (200)
T ss_pred HHHHCCCCHHHHHHHHCCCHHHHHHHHHh
Confidence 34677899999999999999999998863
No 246
>PF13551 HTH_29: Winged helix-turn helix
Probab=61.20 E-value=32 Score=26.78 Aligned_cols=74 Identities=12% Similarity=0.200 Sum_probs=47.8
Q ss_pred ChhHHHhhcCCCHHHHHHHHHHhccCC--cccc------C-CC-CCHHHHHHHHhhhcccc------cchhhhhhh----
Q 016400 39 QSERCLENFRMDKKVFYKLCDILQSKG--LLRH------T-NR-IKIEEQLAIFMFIVGHN------LRTRAVQEL---- 98 (390)
Q Consensus 39 ~d~~f~~~frms~~~F~~L~~~L~~~~--~~~~------~-~~-~~~~~~l~~~L~~L~~~------~~~~~l~~~---- 98 (390)
+..+.-+.+++++.++.+.+......+ .+.+ + .. ++.++.-.+.=+...+. .+...++..
T Consensus 14 ~~~~ia~~lg~s~~Tv~r~~~~~~~~G~~~l~~~~~~~g~~~~~l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~ 93 (112)
T PF13551_consen 14 TIAEIARRLGISRRTVYRWLKRYREGGIEGLLPRKPRGGRPRKRLSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEE 93 (112)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHHcccHHHHHhccccCCCCCCCCCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHh
Confidence 378899999999999999999987654 1111 1 12 56555543332222221 345666653
Q ss_pred ---cccchhhhhhhhHH
Q 016400 99 ---FRYSGETISRHFNN 112 (390)
Q Consensus 99 ---fgis~stv~~~~~~ 112 (390)
..+|.+||.+++++
T Consensus 94 ~~~~~~s~~ti~r~L~~ 110 (112)
T PF13551_consen 94 EFGIDVSPSTIRRILKR 110 (112)
T ss_pred ccCccCCHHHHHHHHHH
Confidence 27899999998875
No 247
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=60.68 E-value=7.9 Score=34.96 Aligned_cols=45 Identities=13% Similarity=0.160 Sum_probs=35.1
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
.+++.|+=. |..++.|.++.++|..+++|..||..++.+.+.-+.
T Consensus 155 ~Lt~rE~~V--l~l~~~G~s~~eIA~~L~iS~~TVk~~~~~i~~Kl~ 199 (216)
T PRK10100 155 LLTHREKEI--LNKLRIGASNNEIARSLFISENTVKTHLYNLFKKIA 199 (216)
T ss_pred CCCHHHHHH--HHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 356544433 344566999999999999999999999998887764
No 248
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=60.68 E-value=16 Score=29.53 Aligned_cols=41 Identities=22% Similarity=0.272 Sum_probs=29.7
Q ss_pred HHHHHHHhhhcc-cccchhhhhhhcccchhhhhhhhHHHHHH
Q 016400 76 EEQLAIFMFIVG-HNLRTRAVQELFRYSGETISRHFNNVLNA 116 (390)
Q Consensus 76 ~~~l~~~L~~L~-~~~~~~~l~~~fgis~stv~~~~~~v~~~ 116 (390)
+.++.++..... .+.+..++++.++++++||+++++...++
T Consensus 16 ptRl~IL~~L~~~~~~~v~ela~~l~lsqstvS~HL~~L~~A 57 (117)
T PRK10141 16 ETRLGIVLLLRESGELCVCDLCTALDQSQPKISRHLALLRES 57 (117)
T ss_pred HHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 345555444333 34678999999999999999998776554
No 249
>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=60.28 E-value=15 Score=30.43 Aligned_cols=45 Identities=18% Similarity=0.059 Sum_probs=37.3
Q ss_pred CCHHHHHHHHhhhccc-ccchhhhhhhcccchhhhhhhhHHHHHHH
Q 016400 73 IKIEEQLAIFMFIVGH-NLRTRAVQELFRYSGETISRHFNNVLNAI 117 (390)
Q Consensus 73 ~~~~~~l~~~L~~L~~-~~~~~~l~~~fgis~stv~~~~~~v~~~l 117 (390)
+..+++-.+-|+|... +.+|-.||..+++|.+|+.++..+|-+.|
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 4445777778888876 79999999999999999999998886654
No 250
>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=60.23 E-value=7 Score=25.36 Aligned_cols=24 Identities=17% Similarity=0.178 Sum_probs=19.2
Q ss_pred ccchhhhhhhcccchhhhhhhhHH
Q 016400 89 NLRTRAVQELFRYSGETISRHFNN 112 (390)
Q Consensus 89 ~~~~~~l~~~fgis~stv~~~~~~ 112 (390)
..++.++|...|+|.+||.+-+++
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 478999999999999999887665
No 251
>TIGR03020 EpsA transcriptional regulator EpsA. Proteins in this family include a C-terminal LuxR transcriptional regulator domain (pfam00196). These proteins are positioned proximal to either EpsH-containing exopolysaccharide biosynthesis operons of the Methylobacillus type, or the associated PEP-CTERM-containing genes.
Probab=59.73 E-value=13 Score=34.37 Aligned_cols=45 Identities=13% Similarity=0.246 Sum_probs=38.2
Q ss_pred CCCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHH
Q 016400 71 NRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAI 117 (390)
Q Consensus 71 ~~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l 117 (390)
..+|..++=.+.+ ++.|.++.++|..++||..||..+++++..-+
T Consensus 189 ~~LT~RE~evl~l--~a~G~s~~eIA~~L~IS~~TVk~hl~~i~~KL 233 (247)
T TIGR03020 189 GLITAREAEILAW--VRDGKTNEEIAAILGISSLTVKNHLQHIFKKL 233 (247)
T ss_pred cCCCHHHHHHHHH--HHCCCCHHHHHHHHCcCHHHHHHHHHHHHHHh
Confidence 3688877766665 57999999999999999999999999887765
No 252
>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=59.56 E-value=5.7 Score=25.68 Aligned_cols=22 Identities=27% Similarity=0.365 Sum_probs=18.8
Q ss_pred chhhhhhhcccchhhhhhhhHH
Q 016400 91 RTRAVQELFRYSGETISRHFNN 112 (390)
Q Consensus 91 ~~~~l~~~fgis~stv~~~~~~ 112 (390)
+..++|..+|||.+|+.+++..
T Consensus 2 s~~e~a~~lgvs~~tl~~~~~~ 23 (49)
T cd04762 2 TTKEAAELLGVSPSTLRRWVKE 23 (49)
T ss_pred CHHHHHHHHCcCHHHHHHHHHc
Confidence 4578999999999999998764
No 253
>PHA02591 hypothetical protein; Provisional
Probab=59.43 E-value=8.6 Score=28.48 Aligned_cols=36 Identities=8% Similarity=0.196 Sum_probs=28.8
Q ss_pred HHHHHHhhhcccccchhhhhhhcccchhhhhhhhHH
Q 016400 77 EQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNN 112 (390)
Q Consensus 77 ~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~ 112 (390)
+-+-++=.....|.+...+|...|+++.+|+++++.
T Consensus 47 d~~~vA~eL~eqGlSqeqIA~~LGVsqetVrKYL~~ 82 (83)
T PHA02591 47 DLISVTHELARKGFTVEKIASLLGVSVRKVRRYLES 82 (83)
T ss_pred hHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHhc
Confidence 344455555677999999999999999999998763
No 254
>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=59.16 E-value=4.4 Score=27.13 Aligned_cols=19 Identities=26% Similarity=0.230 Sum_probs=16.5
Q ss_pred hhhhhcccchhhhhhhhHH
Q 016400 94 AVQELFRYSGETISRHFNN 112 (390)
Q Consensus 94 ~l~~~fgis~stv~~~~~~ 112 (390)
++|...|+|.+||+++++.
T Consensus 2 ~lA~~~gvs~~tvs~~l~g 20 (52)
T cd01392 2 DIARAAGVSVATVSRVLNG 20 (52)
T ss_pred cHHHHHCcCHHHHHHHHcC
Confidence 6889999999999998764
No 255
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=58.73 E-value=15 Score=35.49 Aligned_cols=48 Identities=19% Similarity=0.219 Sum_probs=40.3
Q ss_pred CCCHHHHHHHHhhhc---ccccchhhhhhhcccchhhhhhhhHHHHHHHHH
Q 016400 72 RIKIEEQLAIFMFIV---GHNLRTRAVQELFRYSGETISRHFNNVLNAIMA 119 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L---~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 119 (390)
.++..++..+.++|. +.+.++.+||..+|||++.|+.+-.+.+.-|-.
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 477778888888874 345899999999999999999999988887753
No 256
>PRK09191 two-component response regulator; Provisional
Probab=58.11 E-value=13 Score=33.83 Aligned_cols=47 Identities=6% Similarity=0.097 Sum_probs=40.1
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHH
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMA 119 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 119 (390)
.++...+-.+.|.++. |.++.++|...|+|.+||...+.+....+..
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 5777777777777765 8999999999999999999999988887764
No 257
>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=58.07 E-value=6.3 Score=25.62 Aligned_cols=21 Identities=19% Similarity=0.257 Sum_probs=18.1
Q ss_pred chhhhhhhcccchhhhhhhhH
Q 016400 91 RTRAVQELFRYSGETISRHFN 111 (390)
Q Consensus 91 ~~~~l~~~fgis~stv~~~~~ 111 (390)
+..+++..+|+|.+|+.++++
T Consensus 3 t~~e~a~~lgis~~ti~~~~~ 23 (49)
T TIGR01764 3 TVEEAAEYLGVSKDTVYRLIH 23 (49)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 567899999999999998764
No 258
>COG1508 RpoN DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription]
Probab=57.94 E-value=10 Score=37.98 Aligned_cols=56 Identities=20% Similarity=0.164 Sum_probs=34.5
Q ss_pred HHhhcCCCHHHHHHHHHHhccCCccccCCCCCHHHHHHHHhhhcccc--cchhhhhhhcccchhhhhhhhH
Q 016400 43 CLENFRMDKKVFYKLCDILQSKGLLRHTNRIKIEEQLAIFMFIVGHN--LRTRAVQELFRYSGETISRHFN 111 (390)
Q Consensus 43 f~~~frms~~~F~~L~~~L~~~~~~~~~~~~~~~~~l~~~L~~L~~~--~~~~~l~~~fgis~stv~~~~~ 111 (390)
..+..+...+|..++...|-+ .|-..|..--++- ...+++|+..|+++|||||++.
T Consensus 295 LiksL~qR~~TLlkV~~~Iv~-------------~Q~~Ff~~g~~~l~PL~LrdvA~~i~~HESTISRai~ 352 (444)
T COG1508 295 LIKSLEQREETLLKVAEEIVE-------------YQKAFFEGGEEALKPLVLRDVADEIGMHESTISRAIT 352 (444)
T ss_pred HHHHHHHHHHHHHHHHHHHHH-------------HHHHHHhCCcccCCcccHHHHHHHhCccHHHHHHHHh
Confidence 334455555555555554443 3444443332322 5569999999999999999774
No 259
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=57.78 E-value=6.4 Score=29.37 Aligned_cols=34 Identities=24% Similarity=0.164 Sum_probs=23.6
Q ss_pred HHHHHhhhc--ccccchhhhhhhcccchhhhhhhhH
Q 016400 78 QLAIFMFIV--GHNLRTRAVQELFRYSGETISRHFN 111 (390)
Q Consensus 78 ~l~~~L~~L--~~~~~~~~l~~~fgis~stv~~~~~ 111 (390)
+++..|..+ ..|.++.++|...|+++++|+++.+
T Consensus 18 ~l~~~i~~~~~~~~ltQ~e~A~~lgisq~~vS~l~~ 53 (80)
T PF13744_consen 18 QLMAAIRELREERGLTQAELAERLGISQPRVSRLEN 53 (80)
T ss_dssp HHHHHHHHHHHCCT--HHHHHHHHTS-HHHHHHHHT
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHCCChhHHHHHHc
Confidence 344444433 5689999999999999999999875
No 260
>PF13610 DDE_Tnp_IS240: DDE domain
Probab=57.75 E-value=11 Score=31.50 Aligned_cols=131 Identities=16% Similarity=0.155 Sum_probs=73.7
Q ss_pred cccceEEEEEeCCCCCCCCCCCCCCceeeeeeeecCCcceeEeccCcccccccH-HHHHHHHhhcCCCCC-CCCceeecc
Q 016400 152 AVDGIHIPVMVGVDEQGPFRNKSGLLSQNVLAACSFDLKFHYVLAGWEGSASDL-RVLNSALTRRNKLQV-PEGKYYLVD 229 (390)
Q Consensus 152 ~IDgt~i~i~~P~~~~~~y~~~k~~~s~~~q~v~d~d~~~~~v~~g~~Gs~~D~-~vl~~sl~~~~~~~~-p~g~~~l~D 229 (390)
.||-|.|.|. |++ .=+-.++|.+|+++.+.+.-.-...++ ..|+.++. .. ..+..++.|
T Consensus 5 ~~DEt~iki~----------G~~----~yl~~aiD~~~~~l~~~ls~~Rd~~aA~~Fl~~~l~-----~~~~~p~~ivtD 65 (140)
T PF13610_consen 5 HVDETYIKIK----------GKW----HYLWRAIDAEGNILDFYLSKRRDTAAAKRFLKRALK-----RHRGEPRVIVTD 65 (140)
T ss_pred EEeeEEEEEC----------CEE----EEEEEeecccccchhhhhhhhcccccceeeccccce-----eeccccceeecc
Confidence 5788888873 111 223578999999877766532222222 22233333 12 344567777
Q ss_pred CC--CCCCCCccccccCcccCcccccCCCCChhhHHHHHHHHHHHHhHHHHHHHHHHhhchhhhcCCCCCccchhHHHHH
Q 016400 230 NK--YANMPGFIAPYQAVSYHTNQTTTGYHPQDAKELFNQRHSLLRNATDRIFGALKERFPILLSAPPYPLQTQVKLVVA 307 (390)
Q Consensus 230 ~g--Yp~~~~ll~P~~~~~~~~~~~~~~~~~~~~~~~fN~~~s~~R~~VE~~fg~LK~rf~iL~~~~~~~~~~~~~ii~a 307 (390)
++ |+.--.-+.+-.. .+...+ -....-.++.||+-+..+|.|.+..... -+.+.+...+.+
T Consensus 66 k~~aY~~A~~~l~~~~~------------~~~~v~---~~~~k~~nN~iE~~h~~~K~r~r~~~gF--ks~~~A~~~l~~ 128 (140)
T PF13610_consen 66 KLPAYPAAIKELNPEGR------------LHDKVE---HRQRKYLNNRIERDHRTIKRRTRPMNGF--KSFRSAQRTLSG 128 (140)
T ss_pred cCCccchhhhhcccccc------------cccccc---eeechhhhChhhHhhhhhhhhcccccCc--CCHHHHHHHHHH
Confidence 74 3221111111000 000000 0011235789999999999988666543 456788889999
Q ss_pred HHHHHhhhhcc
Q 016400 308 ACALHNYIQRE 318 (390)
Q Consensus 308 ~~~LhN~~~~~ 318 (390)
-.+.||+...+
T Consensus 129 ~~~~~n~~r~~ 139 (140)
T PF13610_consen 129 FEAYHNFRRPH 139 (140)
T ss_pred HHHHHHHhCCC
Confidence 99999998754
No 261
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=57.57 E-value=13 Score=37.95 Aligned_cols=23 Identities=35% Similarity=0.280 Sum_probs=20.7
Q ss_pred ccchhhhhhhcccchhhhhhhhH
Q 016400 89 NLRTRAVQELFRYSGETISRHFN 111 (390)
Q Consensus 89 ~~~~~~l~~~fgis~stv~~~~~ 111 (390)
+...++||+..|++.|||||+++
T Consensus 369 PLtlkdVAe~lglHeSTVSRa~~ 391 (481)
T PRK12469 369 PLVLRDVAEELGLHESTISRATG 391 (481)
T ss_pred CCcHHHHHHHhCCCcchhhHHhc
Confidence 57799999999999999999774
No 262
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=57.34 E-value=15 Score=37.67 Aligned_cols=48 Identities=15% Similarity=0.139 Sum_probs=41.8
Q ss_pred CCCHHHHHHHHhhhc---ccccchhhhhhhcccchhhhhhhhHHHHHHHHH
Q 016400 72 RIKIEEQLAIFMFIV---GHNLRTRAVQELFRYSGETISRHFNNVLNAIMA 119 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L---~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 119 (390)
.++..++..+.++|. ..+.++..||..+|||++.|+++-.+.+.-|-.
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 588888888999884 467999999999999999999999998888763
No 263
>PRK15215 fimbriae biosynthesis regulatory protein; Provisional
Probab=57.25 E-value=36 Score=26.59 Aligned_cols=57 Identities=14% Similarity=0.205 Sum_probs=43.1
Q ss_pred CCHHHHHHHHHHhccCCccccCCCCCHHHHHHHHhh-hcccccchhhhhhhcccchhhhhhhhHHHHHH
Q 016400 49 MDKKVFYKLCDILQSKGLLRHTNRIKIEEQLAIFMF-IVGHNLRTRAVQELFRYSGETISRHFNNVLNA 116 (390)
Q Consensus 49 ms~~~F~~L~~~L~~~~~~~~~~~~~~~~~l~~~L~-~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~ 116 (390)
|+.+.|.-|++.-.-+ + +++..+|+ +|-.|.+-++++++.+|+++-.+-.++++-..
T Consensus 31 v~eehF~LLieIS~Ir----S-------~KvI~AL~dyLV~G~trkevCe~~~Vn~gYfS~~L~rL~~i 88 (100)
T PRK15215 31 VNEEHFWLLIGISSIH----S-------EKIIQALRDYLVFGVSRKDVCERYEVNNGYFSTSLNRLSRI 88 (100)
T ss_pred cCHHHHHHHHHHcccc----h-------HHHHHHHHHHHHcCccHHHHHHccCCCHHHHHHHHHHHHHH
Confidence 6667777666654321 2 67777776 88899999999999999999998777766543
No 264
>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=57.04 E-value=9.2 Score=26.50 Aligned_cols=27 Identities=26% Similarity=0.367 Sum_probs=22.7
Q ss_pred ccchhhhhhhcccchhhhhhhhHHHHH
Q 016400 89 NLRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 89 ~~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
..+..++++.|+||..|+.|-++...+
T Consensus 14 ~~s~~ela~~~~VS~~TiRRDl~~L~~ 40 (57)
T PF08220_consen 14 KVSVKELAEEFGVSEMTIRRDLNKLEK 40 (57)
T ss_pred CEEHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 477899999999999999998776543
No 265
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=57.03 E-value=11 Score=35.49 Aligned_cols=42 Identities=17% Similarity=0.143 Sum_probs=36.5
Q ss_pred HHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 77 EQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 77 ~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
.+|-.|+....+|.++...|+..+||+++||+.+++.-..|-
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 456666677777889999999999999999999999999885
No 266
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=56.86 E-value=13 Score=37.76 Aligned_cols=58 Identities=17% Similarity=0.177 Sum_probs=37.2
Q ss_pred hHHHhhcCCCHHHHHHHHHHhccCCccccCCCCCHHHHHHHHhhhc--ccccchhhhhhhcccchhhhhhhhH
Q 016400 41 ERCLENFRMDKKVFYKLCDILQSKGLLRHTNRIKIEEQLAIFMFIV--GHNLRTRAVQELFRYSGETISRHFN 111 (390)
Q Consensus 41 ~~f~~~frms~~~F~~L~~~L~~~~~~~~~~~~~~~~~l~~~L~~L--~~~~~~~~l~~~fgis~stv~~~~~ 111 (390)
..|.+...+.+.|..++...|-. .|-..|+.-- =.+.+.+++|+..|++.|||||+++
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 44555566666666666666543 2222332211 1257899999999999999999764
No 267
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=56.85 E-value=12 Score=33.78 Aligned_cols=48 Identities=10% Similarity=0.220 Sum_probs=35.5
Q ss_pred CCCHHHH-HHHHhhhccc-----ccchhhhhhhcccchhhhhhhhHHHHHHHHH
Q 016400 72 RIKIEEQ-LAIFMFIVGH-----NLRTRAVQELFRYSGETISRHFNNVLNAIMA 119 (390)
Q Consensus 72 ~~~~~~~-l~~~L~~L~~-----~~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 119 (390)
.++..|. ++..-+-+|+ ..+..+||..||||++|++.++++...-|..
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 4666554 3333333442 4789999999999999999999998887764
No 268
>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=56.27 E-value=8.3 Score=27.24 Aligned_cols=22 Identities=18% Similarity=0.277 Sum_probs=19.3
Q ss_pred ccchhhhhhhcccchhhhhhhh
Q 016400 89 NLRTRAVQELFRYSGETISRHF 110 (390)
Q Consensus 89 ~~~~~~l~~~fgis~stv~~~~ 110 (390)
...+.+||..+|||.+||.++=
T Consensus 22 ~i~lkdIA~~Lgvs~~tIr~WK 43 (60)
T PF10668_consen 22 KIKLKDIAEKLGVSESTIRKWK 43 (60)
T ss_pred CccHHHHHHHHCCCHHHHHHHh
Confidence 4789999999999999998753
No 269
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=55.79 E-value=20 Score=33.99 Aligned_cols=50 Identities=10% Similarity=0.093 Sum_probs=40.9
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHHhhc
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAISL 122 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~~ 122 (390)
.+|+.++-++.|+++- |.++.++|...|+|.+||...+++....|....+
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 5777777777666554 8999999999999999999999998888876433
No 270
>TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
Probab=55.73 E-value=7 Score=26.44 Aligned_cols=26 Identities=15% Similarity=-0.001 Sum_probs=22.5
Q ss_pred cccccchhhhhhhcccchhhhhhhhH
Q 016400 86 VGHNLRTRAVQELFRYSGETISRHFN 111 (390)
Q Consensus 86 L~~~~~~~~l~~~fgis~stv~~~~~ 111 (390)
-..|.++.++|...|+|++|++++.+
T Consensus 12 ~~~gltq~~lA~~~gvs~~~vs~~e~ 37 (58)
T TIGR03070 12 KALGLTQADLADLAGVGLRFIRDVEN 37 (58)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHC
Confidence 34688999999999999999999764
No 271
>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=55.57 E-value=38 Score=26.09 Aligned_cols=58 Identities=16% Similarity=0.238 Sum_probs=35.6
Q ss_pred CCCHHHHHHHHHHhccCCccccCCCCCHHHHHHHHhh-hcccccchhhhhhhcccchhhhhhhhHHHHHH
Q 016400 48 RMDKKVFYKLCDILQSKGLLRHTNRIKIEEQLAIFMF-IVGHNLRTRAVQELFRYSGETISRHFNNVLNA 116 (390)
Q Consensus 48 rms~~~F~~L~~~L~~~~~~~~~~~~~~~~~l~~~L~-~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~ 116 (390)
.|+.+.|.-|++.-. +.. +++..+|+ +|-.|.+-..+++.+||+++-.++.++++-..
T Consensus 22 ~vs~e~F~lLl~ls~----------IrS-~kiI~AL~dyLV~G~srkeac~~~gV~~syfs~~L~rL~~v 80 (91)
T PF03333_consen 22 KVSEEHFWLLLELSS----------IRS-EKIIAALRDYLVDGLSRKEACERHGVNQSYFSRALNRLNRV 80 (91)
T ss_dssp -S-HHHHHHHHHHS---------------HHHHHHHHHHHTT---HHHHHHHTT--HHHHHHHHHHHHHH
T ss_pred CcCHHHHHHHHHHCC----------CCc-HHHHHHHHHHHHcCCcHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 456677777766543 222 45555555 88899999999999999999999888776543
No 272
>PF12728 HTH_17: Helix-turn-helix domain
Probab=55.36 E-value=7.4 Score=26.00 Aligned_cols=21 Identities=24% Similarity=0.328 Sum_probs=18.2
Q ss_pred chhhhhhhcccchhhhhhhhH
Q 016400 91 RTRAVQELFRYSGETISRHFN 111 (390)
Q Consensus 91 ~~~~l~~~fgis~stv~~~~~ 111 (390)
+..++|+.+|||.+|+.++++
T Consensus 3 t~~e~a~~l~is~~tv~~~~~ 23 (51)
T PF12728_consen 3 TVKEAAELLGISRSTVYRWIR 23 (51)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 567899999999999998774
No 273
>COG5606 Uncharacterized conserved small protein [Function unknown]
Probab=55.31 E-value=5.3 Score=30.24 Aligned_cols=65 Identities=20% Similarity=0.282 Sum_probs=42.2
Q ss_pred CCHHHHHHHHHHhccCCccccCCCCCHHHHHH--HHhhhcccccchhhhhhhcccchhhhhhhhHHHHH
Q 016400 49 MDKKVFYKLCDILQSKGLLRHTNRIKIEEQLA--IFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 49 ms~~~F~~L~~~L~~~~~~~~~~~~~~~~~l~--~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
|+-++|..+.+.+...... ...+-...+|+ +.+|.=-.+.++..++..+||+++.+|...+--+.
T Consensus 1 ~~~~vF~s~~~~~~D~~e~--a~~m~ir~~l~~~i~~~i~q~~l~Q~qiae~lgV~qprvS~l~~gk~~ 67 (91)
T COG5606 1 MSNEVFTSVWDAIEDTPEA--AENMKIRSALMMAIKQWIEQAALSQAQIAELLGVTQPRVSDLARGKIQ 67 (91)
T ss_pred CCCchhhhHHHHHhccHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCchHHHHHhcchh
Confidence 3456778777777754311 11233334444 44444456789999999999999999987665444
No 274
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=54.97 E-value=20 Score=28.10 Aligned_cols=38 Identities=5% Similarity=0.005 Sum_probs=28.7
Q ss_pred HHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHH
Q 016400 77 EQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 77 ~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
.+++..|..- ...++.+++..+|+|++|+.+.+++..+
T Consensus 6 ~~il~~L~~~-~~~~~~~la~~l~~s~~tv~~~l~~L~~ 43 (108)
T smart00344 6 RKILEELQKD-ARISLAELAKKVGLSPSTVHNRVKRLEE 43 (108)
T ss_pred HHHHHHHHHh-CCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 3444444432 3588999999999999999998887755
No 275
>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=54.87 E-value=14 Score=37.06 Aligned_cols=58 Identities=21% Similarity=0.229 Sum_probs=37.0
Q ss_pred hHHHhhcCCCHHHHHHHHHHhccCCccccCCCCCHHHHHHHHhhhc--ccccchhhhhhhcccchhhhhhhhH
Q 016400 41 ERCLENFRMDKKVFYKLCDILQSKGLLRHTNRIKIEEQLAIFMFIV--GHNLRTRAVQELFRYSGETISRHFN 111 (390)
Q Consensus 41 ~~f~~~frms~~~F~~L~~~L~~~~~~~~~~~~~~~~~l~~~L~~L--~~~~~~~~l~~~fgis~stv~~~~~ 111 (390)
..+.+...+++.|..++...|-. .|-..|..-- =.+.+.+++|+..|++.|||||+++
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 44555566666666666666543 2222222211 1357899999999999999999774
No 276
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=54.02 E-value=13 Score=30.19 Aligned_cols=25 Identities=12% Similarity=0.256 Sum_probs=22.6
Q ss_pred ccccchhhhhhhcccchhhhhhhhH
Q 016400 87 GHNLRTRAVQELFRYSGETISRHFN 111 (390)
Q Consensus 87 ~~~~~~~~l~~~fgis~stv~~~~~ 111 (390)
..|.++..+|...|+|++.||.|++
T Consensus 20 eeG~Sq~~iA~LLGltqaAVS~Yls 44 (119)
T COG2522 20 EEGLSQYRIAKLLGLTQAAVSQYLS 44 (119)
T ss_pred HcCCcHHHHHHHhCCCHHHHHHHHc
Confidence 3499999999999999999999875
No 277
>PRK09492 treR trehalose repressor; Provisional
Probab=53.85 E-value=12 Score=35.13 Aligned_cols=23 Identities=30% Similarity=0.401 Sum_probs=21.1
Q ss_pred cchhhhhhhcccchhhhhhhhHH
Q 016400 90 LRTRAVQELFRYSGETISRHFNN 112 (390)
Q Consensus 90 ~~~~~l~~~fgis~stv~~~~~~ 112 (390)
.+.++||...|+|.+||||+++.
T Consensus 5 ~ti~dIA~~agVS~~TVSrvLn~ 27 (315)
T PRK09492 5 LTIKDIARLSGVGKSTVSRVLNN 27 (315)
T ss_pred CcHHHHHHHhCCCHHHHhHHhCC
Confidence 47889999999999999999984
No 278
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=53.39 E-value=8.5 Score=28.47 Aligned_cols=28 Identities=18% Similarity=0.102 Sum_probs=23.5
Q ss_pred hhcccccchhhhhhhcc------cchhhhhhhhH
Q 016400 84 FIVGHNLRTRAVQELFR------YSGETISRHFN 111 (390)
Q Consensus 84 ~~L~~~~~~~~l~~~fg------is~stv~~~~~ 111 (390)
.+..-|.++.++|...| +|++||||+-+
T Consensus 19 ~R~~lGLTQ~dvA~~lg~~~g~i~SQstISR~Es 52 (75)
T smart00352 19 RRIKLGFTQADVGLALGALYGPDFSQTTICRFEA 52 (75)
T ss_pred HHHHcCCCHHHHHHHhcccccCcCCHHHHHHHHh
Confidence 35567899999999999 59999999654
No 279
>PRK00215 LexA repressor; Validated
Probab=53.27 E-value=17 Score=32.37 Aligned_cols=29 Identities=10% Similarity=0.190 Sum_probs=24.5
Q ss_pred cccchhhhhhhccc-chhhhhhhhHHHHHH
Q 016400 88 HNLRTRAVQELFRY-SGETISRHFNNVLNA 116 (390)
Q Consensus 88 ~~~~~~~l~~~fgi-s~stv~~~~~~v~~~ 116 (390)
.+.+..+++..+|+ +++|++++++.....
T Consensus 22 ~~~s~~ela~~~~~~~~~tv~~~l~~L~~~ 51 (205)
T PRK00215 22 YPPSRREIADALGLRSPSAVHEHLKALERK 51 (205)
T ss_pred CCCCHHHHHHHhCCCChHHHHHHHHHHHHC
Confidence 34588999999999 999999998877653
No 280
>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=53.11 E-value=12 Score=26.08 Aligned_cols=25 Identities=16% Similarity=0.198 Sum_probs=21.4
Q ss_pred chhhhhhhcccchhhhhhhhHHHHH
Q 016400 91 RTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 91 ~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
+..+++..+++|.+||++.+++..+
T Consensus 27 ~~~~la~~~~is~~~v~~~l~~L~~ 51 (66)
T cd07377 27 SERELAEELGVSRTTVREALRELEA 51 (66)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4778999999999999988877655
No 281
>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=53.04 E-value=12 Score=35.33 Aligned_cols=21 Identities=24% Similarity=0.324 Sum_probs=19.5
Q ss_pred chhhhhhhcccchhhhhhhhH
Q 016400 91 RTRAVQELFRYSGETISRHFN 111 (390)
Q Consensus 91 ~~~~l~~~fgis~stv~~~~~ 111 (390)
+.+++|...|+|++||||+++
T Consensus 3 ti~dIA~~agVS~sTVSr~Ln 23 (311)
T TIGR02405 3 TIKDIARLAGVGKSTVSRVLN 23 (311)
T ss_pred cHHHHHHHhCCCHHHHHHHhC
Confidence 568999999999999999996
No 282
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=52.86 E-value=8.3 Score=26.94 Aligned_cols=27 Identities=19% Similarity=0.213 Sum_probs=19.7
Q ss_pred ccccchhhhhhhcccchhhhhhhhHHH
Q 016400 87 GHNLRTRAVQELFRYSGETISRHFNNV 113 (390)
Q Consensus 87 ~~~~~~~~l~~~fgis~stv~~~~~~v 113 (390)
..|.+..+++..-|+|++|++++++.-
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 457789999999999999999988754
No 283
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=52.71 E-value=13 Score=31.97 Aligned_cols=44 Identities=11% Similarity=0.200 Sum_probs=34.9
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHH
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAI 117 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l 117 (390)
.+++.+. -.|..|+.|.+..+++..+++|.+||..++.++..-+
T Consensus 137 ~Lt~~E~--~il~~l~~g~~~~~Ia~~l~~s~~tv~~~~~~l~~Kl 180 (196)
T PRK10360 137 PLTKRER--QVAEKLAQGMAVKEIAAELGLSPKTVHVHRANLMEKL 180 (196)
T ss_pred CCCHHHH--HHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence 3454444 3455577899999999999999999999999887765
No 284
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=52.50 E-value=15 Score=34.85 Aligned_cols=42 Identities=19% Similarity=0.238 Sum_probs=37.0
Q ss_pred HHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 77 EQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 77 ~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
.+|-.|+....+|.|+...|+..++|+++||+.+++.-..+-
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 456677777778889999999999999999999999999885
No 285
>PRK10403 transcriptional regulator NarP; Provisional
Probab=52.41 E-value=12 Score=32.32 Aligned_cols=44 Identities=16% Similarity=0.307 Sum_probs=36.0
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHH
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAI 117 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l 117 (390)
.++..+.- .|.+++.|.++.+++...++|..||..++.++.+-|
T Consensus 153 ~Lt~~e~~--vl~~~~~g~s~~~ia~~l~~s~~tv~~~~~~i~~kl 196 (215)
T PRK10403 153 VLTERELD--VLHELAQGLSNKQIASVLNISEQTVKVHIRNLLRKL 196 (215)
T ss_pred cCCHHHHH--HHHHHHCCCCHHHHHHHcCCCHHHHHHHHHHHHHHc
Confidence 35655554 355678899999999999999999999999988876
No 286
>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=52.39 E-value=19 Score=25.79 Aligned_cols=26 Identities=12% Similarity=0.281 Sum_probs=22.4
Q ss_pred cchhhhhhhcccchhhhhhhhHHHHH
Q 016400 90 LRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 90 ~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
.+..+++..+|+|.+||++.+...-.
T Consensus 14 ~~~~eLa~~l~vS~~tv~~~l~~L~~ 39 (69)
T TIGR00122 14 FSGEKLGEALGMSRTAVNKHIQTLRE 39 (69)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 55889999999999999998887644
No 287
>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=52.32 E-value=40 Score=24.20 Aligned_cols=62 Identities=21% Similarity=0.233 Sum_probs=35.4
Q ss_pred HHHhhcCCCHHHHHHHHHHh---ccCCccccCCCCCHHHHHHHHhh----hcccccchhhhhhhcccchhhh
Q 016400 42 RCLENFRMDKKVFYKLCDIL---QSKGLLRHTNRIKIEEQLAIFMF----IVGHNLRTRAVQELFRYSGETI 106 (390)
Q Consensus 42 ~f~~~frms~~~F~~L~~~L---~~~~~~~~~~~~~~~~~l~~~L~----~L~~~~~~~~l~~~fgis~stv 106 (390)
.|-..++++...-+.-.+.+ ..... .++-++..-.+..|| ..+...+.+++++..+|++.|+
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 45566777765554433333 33322 233445444444444 4457789999999999999875
No 288
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=51.34 E-value=22 Score=29.21 Aligned_cols=29 Identities=28% Similarity=0.402 Sum_probs=24.9
Q ss_pred cccchhhhhhhcccchhhhhhhhHHHHHH
Q 016400 88 HNLRTRAVQELFRYSGETISRHFNNVLNA 116 (390)
Q Consensus 88 ~~~~~~~l~~~fgis~stv~~~~~~v~~~ 116 (390)
.+.+..++|...++++|||++.+++.+.+
T Consensus 41 ~~~tvdelae~lnr~rStv~rsl~~L~~~ 69 (126)
T COG3355 41 GPLTVDELAEILNRSRSTVYRSLQNLLEA 69 (126)
T ss_pred CCcCHHHHHHHHCccHHHHHHHHHHHHHc
Confidence 45778899999999999999998887664
No 289
>PRK10651 transcriptional regulator NarL; Provisional
Probab=51.23 E-value=13 Score=32.30 Aligned_cols=44 Identities=11% Similarity=0.311 Sum_probs=35.7
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHH
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAI 117 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l 117 (390)
.+++.+. =.|.+++.|.+.++++...++|..||..++.+...-|
T Consensus 155 ~Lt~rE~--~vl~~l~~g~~~~~ia~~l~is~~tV~~~~~~l~~Kl 198 (216)
T PRK10651 155 QLTPRER--DILKLIAQGLPNKMIARRLDITESTVKVHVKHMLKKM 198 (216)
T ss_pred cCCHHHH--HHHHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHHHHc
Confidence 3666554 3345578899999999999999999999999887766
No 290
>PHA01976 helix-turn-helix protein
Probab=51.08 E-value=11 Score=26.61 Aligned_cols=27 Identities=4% Similarity=-0.175 Sum_probs=23.2
Q ss_pred hcccccchhhhhhhcccchhhhhhhhH
Q 016400 85 IVGHNLRTRAVQELFRYSGETISRHFN 111 (390)
Q Consensus 85 ~L~~~~~~~~l~~~fgis~stv~~~~~ 111 (390)
+-..|.+..++|...|+|++|++++.+
T Consensus 11 R~~~glt~~~lA~~~gvs~~~v~~~e~ 37 (67)
T PHA01976 11 RNARAWSAPELSRRAGVRHSLIYDFEA 37 (67)
T ss_pred HHHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 345688999999999999999998764
No 291
>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=50.69 E-value=28 Score=22.77 Aligned_cols=30 Identities=13% Similarity=0.121 Sum_probs=25.3
Q ss_pred cccchhhhhhhcccchhhhhhhhHHHHHHH
Q 016400 88 HNLRTRAVQELFRYSGETISRHFNNVLNAI 117 (390)
Q Consensus 88 ~~~~~~~l~~~fgis~stv~~~~~~v~~~l 117 (390)
.+.+.++++...|+|+++++++|..--..+
T Consensus 15 ~~~s~~~Ia~~~gvs~~~~y~~f~~k~~l~ 44 (47)
T PF00440_consen 15 EAVSIRDIARRAGVSKGSFYRYFPSKDDLL 44 (47)
T ss_dssp TTSSHHHHHHHHTSCHHHHHHHCSSHHHHH
T ss_pred HhCCHHHHHHHHccchhhHHHHcCCHHHHH
Confidence 468899999999999999999987665544
No 292
>PRK10870 transcriptional repressor MprA; Provisional
Probab=50.42 E-value=20 Score=31.23 Aligned_cols=44 Identities=9% Similarity=0.003 Sum_probs=30.7
Q ss_pred CCCHHH-HHHHHhhhccc-ccchhhhhhhcccchhhhhhhhHHHHH
Q 016400 72 RIKIEE-QLAIFMFIVGH-NLRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 72 ~~~~~~-~l~~~L~~L~~-~~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
+++..+ .++..|+.... +.+..+|+..++++++|+++++++..+
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 34444543332 467899999999999999998887654
No 293
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=50.10 E-value=24 Score=23.91 Aligned_cols=40 Identities=18% Similarity=0.152 Sum_probs=24.0
Q ss_pred CCCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhH
Q 016400 71 NRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFN 111 (390)
Q Consensus 71 ~~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~ 111 (390)
+.++..||--+-++. .-|.+..+++...|.|+.+|.++++
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 346666775554432 3478999999999999999998765
No 294
>PF00665 rve: Integrase core domain; InterPro: IPR001584 Integrase comprises three domains capable of folding independently and whose three-dimensional structures are known. However, the manner in which the N-terminal, catalytic, and C-terminal domains interact in the holoenzyme remains obscure. Numerous studies indicate that the enzyme functions as a multimer, minimally a dimer. The integrase proteins from Human immunodeficiency virus 1 (HIV-1) and Avian sarcoma virus (ASV) have been studied most carefully with respect to the structural basis of catalysis. Although the active site of ASV integrase does not undergo significant conformational changes on binding the required metal cofactor, that of HIV-1 does. This active site-mediated conformational change in HIV-1 reorganises the catalytic core and C-terminal domains and appears to promote an interaction that is favourable for catalysis []. Retroviral integrase is synthesised as part of the POL polyprotein that contains; an aspartyl protease, a reverse transcriptase, RNase H and integrase. POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. The presence of retrovirus integrase-related gene sequences in eukaryotes is known. Bacterial transposases involved in the transposition of the insertion sequence also belong to this group. HIV integrase catalyses the incorporation of virally derived DNA into the human genome. This unique step in the virus life cycle provides a variety of points for intervention and hence is an attractive target for the development of new therapeutics for the treatment of AIDS []. Substrate recognition by the retroviral integrase enzyme is critical for retroviral integration. To catalyse this recombination event, integrase must recognise and act on two types of substrates, viral DNA and host DNA, yet the necessary interactions exhibit markedly different degrees of specificity [].; GO: 0015074 DNA integration; PDB: 3AO3_A 3OVN_A 3AO5_A 3AO4_A 3AO1_A 1C6V_D 3HPG_A 3HPH_A 3OYD_A 3OYF_B ....
Probab=49.95 E-value=30 Score=27.15 Aligned_cols=16 Identities=25% Similarity=0.314 Sum_probs=13.3
Q ss_pred HHhHHHHHHHHHHhhc
Q 016400 272 LRNATDRIFGALKERF 287 (390)
Q Consensus 272 ~R~~VE~~fg~LK~rf 287 (390)
....|||.++.||.+|
T Consensus 105 ~ng~vEr~~~~l~~~~ 120 (120)
T PF00665_consen 105 QNGFVERFNRTLKRRI 120 (120)
T ss_dssp HHHHHHHHHHHHHHHH
T ss_pred hccHHHHHHHHHHHhC
Confidence 4568999999999876
No 295
>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=49.87 E-value=19 Score=28.17 Aligned_cols=34 Identities=6% Similarity=-0.194 Sum_probs=28.4
Q ss_pred hcccccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 85 IVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 85 ~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
-+....|+...|...|+|++|+++.+++.-+.+-
T Consensus 12 av~~~gSis~AA~~L~iS~stvs~~I~~LE~~lg 45 (99)
T TIGR00637 12 AIARMGSISQAAKDAGISYKSAWDYIRAMNNLSG 45 (99)
T ss_pred HHHHhCCHHHHHHHHCCCHHHHHHHHHHHHHHhC
Confidence 3444567999999999999999999998887764
No 296
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=49.84 E-value=14 Score=31.90 Aligned_cols=44 Identities=14% Similarity=0.134 Sum_probs=36.0
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHH
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAI 117 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l 117 (390)
.++..+. -.|..|+.|.+..+++..+++|.+||..++.+...-|
T Consensus 143 ~lt~~E~--~vl~~l~~g~~~~~I~~~l~~s~~tv~~~~~~l~~Kl 186 (204)
T PRK09958 143 SLSKQEI--SVMRYILDGKDNNDIAEKMFISNKTVSTYKSRLMEKL 186 (204)
T ss_pred cCCHHHH--HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHc
Confidence 3666554 3666777889999999999999999999999888766
No 297
>PRK12679 cbl transcriptional regulator Cbl; Reviewed
Probab=49.62 E-value=18 Score=34.34 Aligned_cols=42 Identities=19% Similarity=0.245 Sum_probs=36.7
Q ss_pred HHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 77 EQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 77 ~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
.++-.|+....++.++...|+..++|++|||+.+++.-..+.
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 456667777777789999999999999999999999999886
No 298
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=49.45 E-value=18 Score=33.61 Aligned_cols=44 Identities=9% Similarity=0.099 Sum_probs=34.1
Q ss_pred CCCHHHHHHHHhhhccc---ccchhhhhhhcccchhhhhhhhHHHHH
Q 016400 72 RIKIEEQLAIFMFIVGH---NLRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~---~~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
.+..-++.+-.|..|+. +.+..+++...|+++||++|+++....
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 45555666666776643 368999999999999999998887655
No 299
>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family. Member of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.
Probab=49.23 E-value=19 Score=33.03 Aligned_cols=43 Identities=12% Similarity=0.081 Sum_probs=33.5
Q ss_pred CCHHHHHHHHhhhcc---cccchhhhhhhcccchhhhhhhhHHHHH
Q 016400 73 IKIEEQLAIFMFIVG---HNLRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 73 ~~~~~~l~~~L~~L~---~~~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
++.-++.+-.|..++ .+.+..+|+...|+++||++|++.....
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 445566666666665 3578999999999999999999887755
No 300
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=49.00 E-value=31 Score=31.04 Aligned_cols=68 Identities=10% Similarity=0.114 Sum_probs=40.6
Q ss_pred CCCHHHHHHHHHHhccCCcccc-CCCCCH--HHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHH
Q 016400 48 RMDKKVFYKLCDILQSKGLLRH-TNRIKI--EEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 48 rms~~~F~~L~~~L~~~~~~~~-~~~~~~--~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
.++.+..+.|...-.......+ .++++. ..+|.-.|---..+.+..++|...|+|+.|+.|++.....
T Consensus 129 ~~sQ~~lD~l~~~~~k~~~~~~LPkGi~~~Tl~~i~~~~~~~~~~~Taeela~~~giSRvTaRRYLeyl~~ 199 (224)
T COG4565 129 QLSQKELDQLFNIQSKEQPPDDLPKGLDELTLQKVREALKEPDQELTAEELAQALGISRVTARRYLEYLVS 199 (224)
T ss_pred ccCHHHHHHHHhccccccCcccCCCCcCHHHHHHHHHHHhCcCCccCHHHHHHHhCccHHHHHHHHHHHHh
Confidence 4455555555544322111111 133433 3444445554556788999999999999999999876544
No 301
>cd00131 PAX Paired Box domain
Probab=48.76 E-value=83 Score=25.76 Aligned_cols=75 Identities=12% Similarity=0.063 Sum_probs=46.6
Q ss_pred CChhHHHhhcCCCHHHHHHHHHHhccCCccccC------C-CCCHHH-HHHHHhhhcccccchhhhhhhc---cc-----
Q 016400 38 GQSERCLENFRMDKKVFYKLCDILQSKGLLRHT------N-RIKIEE-QLAIFMFIVGHNLRTRAVQELF---RY----- 101 (390)
Q Consensus 38 ~~d~~f~~~frms~~~F~~L~~~L~~~~~~~~~------~-~~~~~~-~l~~~L~~L~~~~~~~~l~~~f---gi----- 101 (390)
.+..+.-..|++++.+..+++............ + .++.+. ...+.+..---..+..++++.+ |+
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 577888899999999999999998765432211 1 223322 2222222222235566666653 55
Q ss_pred --chhhhhhhhHH
Q 016400 102 --SGETISRHFNN 112 (390)
Q Consensus 102 --s~stv~~~~~~ 112 (390)
|.||++|+++.
T Consensus 114 ~~s~stI~R~L~~ 126 (128)
T cd00131 114 VPSVSSINRILRN 126 (128)
T ss_pred CCCHHHHHHHHHh
Confidence 99999998764
No 302
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=48.45 E-value=8.9 Score=36.62 Aligned_cols=23 Identities=17% Similarity=0.047 Sum_probs=21.4
Q ss_pred cchhhhhhhcccchhhhhhhhHH
Q 016400 90 LRTRAVQELFRYSGETISRHFNN 112 (390)
Q Consensus 90 ~~~~~l~~~fgis~stv~~~~~~ 112 (390)
.+.++||...|||.+||||+++.
T Consensus 7 ~Ti~dIA~~agVS~~TVSr~Ln~ 29 (342)
T PRK10014 7 ITIHDVALAAGVSVSTVSLVLSG 29 (342)
T ss_pred CcHHHHHHHhCCCHHHHHHHHCC
Confidence 57899999999999999999986
No 303
>PRK09526 lacI lac repressor; Reviewed
Probab=48.44 E-value=9.2 Score=36.54 Aligned_cols=23 Identities=26% Similarity=0.209 Sum_probs=20.8
Q ss_pred cchhhhhhhcccchhhhhhhhHH
Q 016400 90 LRTRAVQELFRYSGETISRHFNN 112 (390)
Q Consensus 90 ~~~~~l~~~fgis~stv~~~~~~ 112 (390)
.+.+++|...|||.+||||+++.
T Consensus 6 ~ti~dIA~~aGVS~~TVSrvLn~ 28 (342)
T PRK09526 6 VTLYDVARYAGVSYQTVSRVLNQ 28 (342)
T ss_pred CcHHHHHHHhCCCHHHHHHHhcC
Confidence 46889999999999999999984
No 304
>PRK11233 nitrogen assimilation transcriptional regulator; Provisional
Probab=48.22 E-value=19 Score=33.93 Aligned_cols=40 Identities=15% Similarity=0.198 Sum_probs=32.0
Q ss_pred HHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 78 QLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 78 ~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
+|-.|+.... ..++...|+..++|++|||+.+++.-..+.
T Consensus 5 ~L~~F~~v~~-~~S~s~AA~~L~isQ~avS~~I~~LE~~lg 44 (305)
T PRK11233 5 RLKYFVKIVD-IGSLTQAAEVLHIAQPALSQQVATLEGELN 44 (305)
T ss_pred HHHHHHHHHH-cCCHHHHHHHhCCCchHHHHHHHHHHHHhC
Confidence 3444444444 449999999999999999999999999885
No 305
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=48.17 E-value=24 Score=32.98 Aligned_cols=45 Identities=7% Similarity=-0.042 Sum_probs=36.5
Q ss_pred CCCCHHHHHHHHhhhccc---ccchhhhhhhcccchhhhhhhhHHHHH
Q 016400 71 NRIKIEEQLAIFMFIVGH---NLRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 71 ~~~~~~~~l~~~L~~L~~---~~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
..++.-++.+-.|..++. +.+..+|+...|+++||++|+++..+.
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 468999999999999999999887766
No 306
>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=48.03 E-value=6 Score=33.98 Aligned_cols=58 Identities=10% Similarity=0.194 Sum_probs=0.0
Q ss_pred hHHHhhcCCCHHHHHHHHHHhccCCccccCCCCCHHHHHHHHhhh--cccccchhhhhhhcccchhhhhhhhH
Q 016400 41 ERCLENFRMDKKVFYKLCDILQSKGLLRHTNRIKIEEQLAIFMFI--VGHNLRTRAVQELFRYSGETISRHFN 111 (390)
Q Consensus 41 ~~f~~~frms~~~F~~L~~~L~~~~~~~~~~~~~~~~~l~~~L~~--L~~~~~~~~l~~~fgis~stv~~~~~ 111 (390)
..+.....+.+++...+...|-.. |-..|+.- --.+.+..++|+..|++.|||||.++
T Consensus 12 ~~l~~~l~~R~~TL~~v~~~iv~~-------------Q~~ff~~g~~~l~PLt~~~iA~~lgl~~STVSRav~ 71 (160)
T PF04552_consen 12 KWLIRALEQRNETLLRVAQAIVER-------------QKDFFLGGPGALKPLTMKDIADELGLHESTVSRAVK 71 (160)
T ss_dssp -------------------------------------------------------------------------
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH-------------HHHHHhcCcccCcCCCHHHHHHHhCCCHhHHHHHHc
Confidence 344455566666666666666542 11222210 11246788999999999999999875
No 307
>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=47.78 E-value=16 Score=25.79 Aligned_cols=25 Identities=16% Similarity=0.239 Sum_probs=18.9
Q ss_pred chhhhhhhcccchhhhhhhhHHHHH
Q 016400 91 RTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 91 ~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
+-.+++..|++|++||.+.+.....
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 5678999999999999987766543
No 308
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=47.28 E-value=8.9 Score=36.50 Aligned_cols=23 Identities=22% Similarity=0.208 Sum_probs=20.4
Q ss_pred cchhhhhhhcccchhhhhhhhHH
Q 016400 90 LRTRAVQELFRYSGETISRHFNN 112 (390)
Q Consensus 90 ~~~~~l~~~fgis~stv~~~~~~ 112 (390)
.+..++|...|||.+||||+++.
T Consensus 6 ~ti~dIA~~agVS~~TVSrvLn~ 28 (331)
T PRK14987 6 PVLQDVADRVGVTKMTVSRFLRN 28 (331)
T ss_pred CcHHHHHHHhCCCHHHhhhhhCC
Confidence 46789999999999999999854
No 309
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=47.07 E-value=14 Score=35.48 Aligned_cols=34 Identities=18% Similarity=0.156 Sum_probs=27.9
Q ss_pred HhhhcccccchhhhhhhcccchhhhhhhhHHHHH
Q 016400 82 FMFIVGHNLRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 82 ~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
+=.|+-.|.++.++|+.+|||+.||+|.+.+.-+
T Consensus 19 A~lYY~~gltQ~eIA~~LgiSR~~v~rlL~~Ar~ 52 (321)
T COG2390 19 AWLYYVEGLTQSEIAERLGISRATVSRLLAKARE 52 (321)
T ss_pred HHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 3345677999999999999999999998876543
No 310
>COG1342 Predicted DNA-binding proteins [General function prediction only]
Probab=46.97 E-value=41 Score=26.09 Aligned_cols=46 Identities=17% Similarity=0.117 Sum_probs=34.0
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
.+++++-=++=|.-+- +.++.+.|.+.|||+.|+.+.++..-.-+.
T Consensus 33 ~lt~eElEAlRLvD~~-~l~QeeAA~rMgISr~Tfwr~l~sAR~KvA 78 (99)
T COG1342 33 ILTIEELEALRLVDYE-GLTQEEAALRMGISRQTFWRLLTSARKKVA 78 (99)
T ss_pred eecHHHHHHHHHHhHh-hccHHHHHHHhcccHHHHHHHHHHHHHHHH
Confidence 3566666555555443 788999999999999999998877655443
No 311
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=46.63 E-value=17 Score=34.77 Aligned_cols=21 Identities=33% Similarity=0.262 Sum_probs=19.6
Q ss_pred chhhhhhhcccchhhhhhhhH
Q 016400 91 RTRAVQELFRYSGETISRHFN 111 (390)
Q Consensus 91 ~~~~l~~~fgis~stv~~~~~ 111 (390)
+.++||...|||.+||||+++
T Consensus 3 ti~dIA~~aGVS~~TVSrvLn 23 (346)
T PRK10401 3 TIRDVARQAGVSVATVSRVLN 23 (346)
T ss_pred CHHHHHHHhCCCHHHHHHHHC
Confidence 578999999999999999997
No 312
>PRK14088 dnaA chromosomal replication initiation protein; Provisional
Probab=46.48 E-value=29 Score=35.05 Aligned_cols=47 Identities=11% Similarity=0.181 Sum_probs=42.2
Q ss_pred CCCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHH
Q 016400 71 NRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAI 117 (390)
Q Consensus 71 ~~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l 117 (390)
+.+...-+++|.|..=-++.++.++|..||.+.|||...++++-+.+
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 46778888999888888899999999999999999999999998866
No 313
>PRK11050 manganese transport regulator MntR; Provisional
Probab=45.98 E-value=25 Score=29.78 Aligned_cols=28 Identities=11% Similarity=0.170 Sum_probs=24.7
Q ss_pred cccchhhhhhhcccchhhhhhhhHHHHH
Q 016400 88 HNLRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 88 ~~~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
.+.+..+++..+++|++||++.+.+...
T Consensus 50 ~~~t~~eLA~~l~is~stVsr~l~~Le~ 77 (152)
T PRK11050 50 GEARQVDIAARLGVSQPTVAKMLKRLAR 77 (152)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 5678999999999999999998887754
No 314
>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=45.96 E-value=37 Score=27.82 Aligned_cols=46 Identities=13% Similarity=0.138 Sum_probs=32.3
Q ss_pred ccCCCCCHHHHHHHH-hhhcccccchhhhhhhcccchhhhhhhhHHHHH
Q 016400 68 RHTNRIKIEEQLAIF-MFIVGHNLRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 68 ~~~~~~~~~~~l~~~-L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
.+.+.+|.+.+.-+. |. ..|.+-.+++..++||.++|++++.++-+
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 345678888776655 43 35999999999999999999999998854
No 315
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=45.54 E-value=19 Score=30.72 Aligned_cols=44 Identities=16% Similarity=0.240 Sum_probs=34.5
Q ss_pred CCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 73 IKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 73 ~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
++..+.=. |.++..|.+.+++|+..++|..||..++.+..+-+.
T Consensus 150 lt~~e~~v--l~l~~~g~~~~~Ia~~l~~s~~tv~~~~~~~~~kl~ 193 (211)
T PRK15369 150 LTPRERQI--LKLITEGYTNRDIAEQLSISIKTVETHRLNMMRKLD 193 (211)
T ss_pred CCHHHHHH--HHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 55544433 334688999999999999999999999998877663
No 316
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=45.32 E-value=11 Score=35.78 Aligned_cols=22 Identities=23% Similarity=0.160 Sum_probs=19.8
Q ss_pred chhhhhhhcccchhhhhhhhHH
Q 016400 91 RTRAVQELFRYSGETISRHFNN 112 (390)
Q Consensus 91 ~~~~l~~~fgis~stv~~~~~~ 112 (390)
+.+++|...|||.+||||+++.
T Consensus 2 ti~dIA~~aGVS~~TVSrvLn~ 23 (328)
T PRK11303 2 KLDEIARLAGVSRTTASYVING 23 (328)
T ss_pred CHHHHHHHhCCCHHHHHHHHcC
Confidence 4679999999999999999876
No 317
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=45.24 E-value=34 Score=30.09 Aligned_cols=43 Identities=7% Similarity=0.009 Sum_probs=29.9
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHH
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVL 114 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~ 114 (390)
++++.+-..+...+-..|.+..+||...+++++|+++++.+..
T Consensus 42 gLt~~q~~iL~~L~~~~~itq~eLa~~l~l~~sTvtr~l~rLE 84 (185)
T PRK13777 42 DLNINEHHILWIAYHLKGASISEIAKFGVMHVSTAFNFSKKLE 84 (185)
T ss_pred CCCHHHHHHHHHHHhCCCcCHHHHHHHHCCCHhhHHHHHHHHH
Confidence 4555444333322334578999999999999999999776653
No 318
>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=44.86 E-value=18 Score=23.27 Aligned_cols=25 Identities=16% Similarity=0.174 Sum_probs=19.0
Q ss_pred cccchhhhhhhcccchhhhhhhhHH
Q 016400 88 HNLRTRAVQELFRYSGETISRHFNN 112 (390)
Q Consensus 88 ~~~~~~~l~~~fgis~stv~~~~~~ 112 (390)
++......|...|||++|+++-+++
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 3556789999999999999987754
No 319
>PRK14086 dnaA chromosomal replication initiation protein; Provisional
Probab=44.83 E-value=33 Score=36.10 Aligned_cols=48 Identities=10% Similarity=0.129 Sum_probs=43.6
Q ss_pred CCCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 71 NRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 71 ~~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
+.+...-+++|.|-+--++.++..|+..||.+.|||...++++-+.|.
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 467778899999999899999999999999999999999999988775
No 320
>PRK00149 dnaA chromosomal replication initiation protein; Reviewed
Probab=44.41 E-value=33 Score=34.64 Aligned_cols=48 Identities=13% Similarity=0.158 Sum_probs=43.4
Q ss_pred CCCCHHHHHHHHhhhcccccchhhhhhhc-ccchhhhhhhhHHHHHHHH
Q 016400 71 NRIKIEEQLAIFMFIVGHNLRTRAVQELF-RYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 71 ~~~~~~~~l~~~L~~L~~~~~~~~l~~~f-gis~stv~~~~~~v~~~l~ 118 (390)
+.+...-+++|.|..--++.|+.++|..| |.+.|||...++++-+.+.
T Consensus 384 ~~~~~aR~iamyl~~~~~~~s~~~Ig~~fg~rdhstV~~a~~~i~~~~~ 432 (450)
T PRK00149 384 RNIARPRQIAMYLAKELTDLSLPEIGRAFGGRDHTTVLHAVRKIEKLLE 432 (450)
T ss_pred cccChHHHHHHHHHHHhcCCCHHHHHHHcCCCCHhHHHHHHHHHHHHHH
Confidence 46778889999999988999999999999 6999999999999988774
No 321
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=44.28 E-value=11 Score=35.96 Aligned_cols=22 Identities=23% Similarity=0.157 Sum_probs=20.0
Q ss_pred chhhhhhhcccchhhhhhhhHH
Q 016400 91 RTRAVQELFRYSGETISRHFNN 112 (390)
Q Consensus 91 ~~~~l~~~fgis~stv~~~~~~ 112 (390)
+.+++|...|+|.+||||+++.
T Consensus 3 ti~dIA~~agVS~~TVSrvln~ 24 (327)
T PRK10339 3 TLKDIAIEAGVSLATVSRVLND 24 (327)
T ss_pred CHHHHHHHhCCCHHhhhhhhcC
Confidence 5689999999999999999875
No 322
>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=44.04 E-value=26 Score=30.75 Aligned_cols=42 Identities=7% Similarity=0.096 Sum_probs=32.6
Q ss_pred CCCCHHHHHHHHhhhcc-cccchhhhhhhcccchhhhhhhhHH
Q 016400 71 NRIKIEEQLAIFMFIVG-HNLRTRAVQELFRYSGETISRHFNN 112 (390)
Q Consensus 71 ~~~~~~~~l~~~L~~L~-~~~~~~~l~~~fgis~stv~~~~~~ 112 (390)
..+++.++...+...+. .|.+..++|..+|+|+++|++++.-
T Consensus 101 ~~lt~~e~a~~~~~l~~~~g~s~~~iA~~lg~s~~~V~r~l~l 143 (187)
T TIGR00180 101 EDLSPIEEAQAYKRLLEKFSMTQEDLAKKIGKSRAHITNLLRL 143 (187)
T ss_pred cCCCHHHHHHHHHHHHHHhCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 36777777665555554 6889999999999999999987653
No 323
>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=43.95 E-value=27 Score=24.41 Aligned_cols=42 Identities=17% Similarity=0.190 Sum_probs=29.4
Q ss_pred CCCCHHHHHHHHhhhccccc---chhhhhhhcccchhhhhhhhHH
Q 016400 71 NRIKIEEQLAIFMFIVGHNL---RTRAVQELFRYSGETISRHFNN 112 (390)
Q Consensus 71 ~~~~~~~~l~~~L~~L~~~~---~~~~l~~~fgis~stv~~~~~~ 112 (390)
+..+++-+|-+.-+...++. .++..|..|+|++..|.++...
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 46788888888888877775 4699999999999999887653
No 324
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=43.95 E-value=12 Score=35.83 Aligned_cols=22 Identities=23% Similarity=0.190 Sum_probs=20.2
Q ss_pred chhhhhhhcccchhhhhhhhHH
Q 016400 91 RTRAVQELFRYSGETISRHFNN 112 (390)
Q Consensus 91 ~~~~l~~~fgis~stv~~~~~~ 112 (390)
+..+||...|+|.+||||+++.
T Consensus 3 Ti~dIA~~agVS~~TVSrvLn~ 24 (341)
T PRK10703 3 TIKDVAKRAGVSTTTVSHVINK 24 (341)
T ss_pred CHHHHHHHhCCCHHHHHHHHcC
Confidence 5789999999999999999985
No 325
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=43.90 E-value=25 Score=33.37 Aligned_cols=42 Identities=14% Similarity=0.113 Sum_probs=35.8
Q ss_pred HHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 77 EQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 77 ~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
.++-+|+....+|.++...|+..++|++|||+.+++.-..+.
T Consensus 4 ~~L~~f~~v~~~g~S~s~AA~~L~isQpavS~~ik~LE~~lg 45 (313)
T PRK12684 4 HQLRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEDELG 45 (313)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHhcCCChHHHHHHHHHHHHhC
Confidence 355566666667779999999999999999999999999886
No 326
>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=43.73 E-value=16 Score=24.54 Aligned_cols=21 Identities=38% Similarity=0.447 Sum_probs=17.1
Q ss_pred chhhhhhhcccchhhhhhhhH
Q 016400 91 RTRAVQELFRYSGETISRHFN 111 (390)
Q Consensus 91 ~~~~l~~~fgis~stv~~~~~ 111 (390)
+..+++...|+|++|+.+.++
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 467899999999999999877
No 327
>PRK14087 dnaA chromosomal replication initiation protein; Provisional
Probab=43.64 E-value=42 Score=33.95 Aligned_cols=48 Identities=13% Similarity=0.106 Sum_probs=43.6
Q ss_pred CCCCHHHHHHHHhhhcccccchhhhhhhcc-cchhhhhhhhHHHHHHHH
Q 016400 71 NRIKIEEQLAIFMFIVGHNLRTRAVQELFR-YSGETISRHFNNVLNAIM 118 (390)
Q Consensus 71 ~~~~~~~~l~~~L~~L~~~~~~~~l~~~fg-is~stv~~~~~~v~~~l~ 118 (390)
+.+...-|++|.|-+=-++.|+.++|..|| .+-|||..-++++-+.+.
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 468889999999999889999999999997 999999999999988774
No 328
>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=42.97 E-value=33 Score=30.45 Aligned_cols=39 Identities=15% Similarity=0.324 Sum_probs=30.2
Q ss_pred HHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHH
Q 016400 76 EEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 76 ~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
..+++..|..- .+.+..+|+..+|++.+||++.+....+
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 35566666554 4589999999999999999998877654
No 329
>PRK11569 transcriptional repressor IclR; Provisional
Probab=42.33 E-value=34 Score=32.01 Aligned_cols=45 Identities=4% Similarity=0.053 Sum_probs=35.9
Q ss_pred CCCCHHHHHHHHhhhccc---ccchhhhhhhcccchhhhhhhhHHHHH
Q 016400 71 NRIKIEEQLAIFMFIVGH---NLRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 71 ~~~~~~~~l~~~L~~L~~---~~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
..+..-++.+-.|..|+. +.+..+|+...|+++||++|+++....
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 346667777777777753 478999999999999999998887665
No 330
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=42.16 E-value=12 Score=35.40 Aligned_cols=19 Identities=32% Similarity=0.319 Sum_probs=17.7
Q ss_pred hhhhhhcccchhhhhhhhH
Q 016400 93 RAVQELFRYSGETISRHFN 111 (390)
Q Consensus 93 ~~l~~~fgis~stv~~~~~ 111 (390)
+++|...|||.+||||+++
T Consensus 2 ~dIA~~agVS~~TVSrvLn 20 (327)
T PRK10423 2 KDVARLAGVSTSTVSHVIN 20 (327)
T ss_pred hhHHHHhCCcHHHHHHHhC
Confidence 5899999999999999997
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=41.64 E-value=29 Score=27.97 Aligned_cols=27 Identities=22% Similarity=0.089 Sum_probs=23.3
Q ss_pred hcccccchhhhhhhcccchhhhhhhhH
Q 016400 85 IVGHNLRTRAVQELFRYSGETISRHFN 111 (390)
Q Consensus 85 ~L~~~~~~~~l~~~fgis~stv~~~~~ 111 (390)
+-..|.+..++|..+|+|++|++++-+
T Consensus 74 r~~~gltq~~lA~~lg~~~~tis~~e~ 100 (127)
T TIGR03830 74 RKKLGLSQREAAELLGGGVNAFSRYER 100 (127)
T ss_pred HHHcCCCHHHHHHHhCCCHHHHHHHHC
Confidence 445689999999999999999999765
No 332
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=41.50 E-value=99 Score=29.54 Aligned_cols=76 Identities=17% Similarity=0.190 Sum_probs=45.4
Q ss_pred HHHhhcCCCHHHHHHHHHHhccCCccccCCCCCHHHHHHHHh----hhcccccchhhhhhhcccchhhhhhhhHHHHHHH
Q 016400 42 RCLENFRMDKKVFYKLCDILQSKGLLRHTNRIKIEEQLAIFM----FIVGHNLRTRAVQELFRYSGETISRHFNNVLNAI 117 (390)
Q Consensus 42 ~f~~~frms~~~F~~L~~~L~~~~~~~~~~~~~~~~~l~~~L----~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l 117 (390)
.|-..++++...-..-...++......-..+-+|.--.+.++ ...+...++++++...||+..|+.+..+++...+
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 344556676655544444443211111112334433333333 3456678999999999999999999988888765
No 333
>PRK10072 putative transcriptional regulator; Provisional
Probab=41.17 E-value=17 Score=28.39 Aligned_cols=25 Identities=12% Similarity=0.166 Sum_probs=22.2
Q ss_pred ccccchhhhhhhcccchhhhhhhhH
Q 016400 87 GHNLRTRAVQELFRYSGETISRHFN 111 (390)
Q Consensus 87 ~~~~~~~~l~~~fgis~stv~~~~~ 111 (390)
..|.++..+|..+|+|.+||++|.+
T Consensus 44 ~~glTQ~elA~~lGvS~~TVs~WE~ 68 (96)
T PRK10072 44 GTGLKIDDFARVLGVSVAMVKEWES 68 (96)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 4588999999999999999999864
No 334
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=41.14 E-value=29 Score=32.60 Aligned_cols=40 Identities=15% Similarity=0.223 Sum_probs=33.5
Q ss_pred HHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 78 QLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 78 ~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
++-+|+....+| |+...|+..++|+++||+.+++.-..+.
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 455566666665 9999999999999999999999999875
No 335
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=41.09 E-value=21 Score=27.15 Aligned_cols=24 Identities=17% Similarity=0.260 Sum_probs=20.7
Q ss_pred hhhhhhhcccchhhhhhhhHHHHH
Q 016400 92 TRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 92 ~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
..+++..+|++++|+++.+.....
T Consensus 2 ~~ela~~l~is~stvs~~l~~L~~ 25 (96)
T smart00529 2 TSEIAERLNVSPPTVTQMLKKLEK 25 (96)
T ss_pred HHHHHHHhCCChHHHHHHHHHHHH
Confidence 468999999999999998877655
No 336
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=40.86 E-value=35 Score=26.76 Aligned_cols=38 Identities=13% Similarity=0.231 Sum_probs=26.9
Q ss_pred HHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHH
Q 016400 77 EQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 77 ~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
..++.+|+....... .+++...+++++|+++.+++...
T Consensus 25 ~~~L~~l~~~~~~~~-~~la~~l~i~~~~vt~~l~~Le~ 62 (126)
T COG1846 25 YQVLLALYEAGGITV-KELAERLGLDRSTVTRLLKRLED 62 (126)
T ss_pred HHHHHHHHHhCCCcH-HHHHHHHCCCHHHHHHHHHHHHH
Confidence 334444444433222 89999999999999998887755
No 337
>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=40.35 E-value=14 Score=34.97 Aligned_cols=21 Identities=24% Similarity=0.132 Sum_probs=18.9
Q ss_pred hhhhhhhcccchhhhhhhhHH
Q 016400 92 TRAVQELFRYSGETISRHFNN 112 (390)
Q Consensus 92 ~~~l~~~fgis~stv~~~~~~ 112 (390)
.+++|..-|||.+||||+++.
T Consensus 2 i~dIA~~aGVS~~TVSrvLn~ 22 (327)
T TIGR02417 2 LSDIAKLAGVSKTTASYVING 22 (327)
T ss_pred HHHHHHHhCCCHHHHHHHHcC
Confidence 578999999999999999865
No 338
>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=40.16 E-value=31 Score=32.02 Aligned_cols=40 Identities=10% Similarity=0.078 Sum_probs=32.1
Q ss_pred HHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 78 QLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 78 ~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
+|-.|+....+ .++...|+..++|++++++.+++.-+.+.
T Consensus 5 ~L~~f~~v~~~-gs~s~AA~~L~itqpavS~~Ik~LE~~lg 44 (291)
T TIGR03418 5 ALRVFESAARL-ASFTAAARELGSTQPAVSQQVKRLEEELG 44 (291)
T ss_pred HHHHHHHHHHh-CCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 34444444444 48999999999999999999999999875
No 339
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=39.24 E-value=39 Score=31.16 Aligned_cols=45 Identities=9% Similarity=0.141 Sum_probs=34.3
Q ss_pred CCCCHHHHHHHHhhhccc--ccchhhhhhhcccchhhhhhhhHHHHH
Q 016400 71 NRIKIEEQLAIFMFIVGH--NLRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 71 ~~~~~~~~l~~~L~~L~~--~~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
..++.-++.+-.|..|+. +.+..+++...|+++||++|+++..+.
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 356666666666666653 367999999999999999998877655
No 340
>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=39.24 E-value=46 Score=29.57 Aligned_cols=27 Identities=22% Similarity=0.277 Sum_probs=23.6
Q ss_pred ccchhhhhhhcccchhhhhhhhHHHHH
Q 016400 89 NLRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 89 ~~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
+.+..++++.+++|++|+++.+....+
T Consensus 157 ~~s~~eia~~l~is~stv~r~L~~Le~ 183 (203)
T TIGR01884 157 EKSVKNIAKKLGKSLSTISRHLRELEK 183 (203)
T ss_pred CcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 468999999999999999998887654
No 341
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=39.12 E-value=41 Score=35.56 Aligned_cols=47 Identities=15% Similarity=0.115 Sum_probs=39.8
Q ss_pred CCCHHHHHHHHhhhc---ccccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 72 RIKIEEQLAIFMFIV---GHNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L---~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
.++..++..+.++|. ..+.++..+|..||||++.|+.+-.+.+.-|-
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 477888888888885 36789999999999999999999888877764
No 342
>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=38.91 E-value=15 Score=34.73 Aligned_cols=22 Identities=27% Similarity=0.108 Sum_probs=19.7
Q ss_pred chhhhhhhcccchhhhhhhhHH
Q 016400 91 RTRAVQELFRYSGETISRHFNN 112 (390)
Q Consensus 91 ~~~~l~~~fgis~stv~~~~~~ 112 (390)
+.+++|..-|+|.+||||+++.
T Consensus 3 ti~dIA~~agvS~~TVSrvLn~ 24 (329)
T TIGR01481 3 TIYDVAREAGVSMATVSRVVNG 24 (329)
T ss_pred cHHHHHHHhCCCHHHHHHHhCC
Confidence 5679999999999999999865
No 343
>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=38.68 E-value=22 Score=28.21 Aligned_cols=30 Identities=17% Similarity=0.225 Sum_probs=22.3
Q ss_pred cccchhhhhhhcccchhhhhhhhHHHHHHH
Q 016400 88 HNLRTRAVQELFRYSGETISRHFNNVLNAI 117 (390)
Q Consensus 88 ~~~~~~~l~~~fgis~stv~~~~~~v~~~l 117 (390)
.|....+||..||+|..+|.+|++++-...
T Consensus 71 ~G~n~~eLA~kyglS~r~I~~Ii~~~~~~~ 100 (108)
T PF08765_consen 71 NGMNVRELARKYGLSERQIYRIIKRVRRRE 100 (108)
T ss_dssp -SS-HHHHHHHHT--HHHHHHHHHHHHH--
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 488999999999999999999999876543
No 344
>PF07453 NUMOD1: NUMOD1 domain; InterPro: IPR010896 This helix-turn-helix-containing DNA-binding domain is found associated in homing nucleases [].
Probab=38.66 E-value=18 Score=22.40 Aligned_cols=22 Identities=23% Similarity=0.147 Sum_probs=18.5
Q ss_pred ccchhhhhhhcccchhhhhhhh
Q 016400 89 NLRTRAVQELFRYSGETISRHF 110 (390)
Q Consensus 89 ~~~~~~l~~~fgis~stv~~~~ 110 (390)
-.|.++.+..+|++.+|+++++
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 345
>PF14493 HTH_40: Helix-turn-helix domain
Probab=38.60 E-value=33 Score=26.14 Aligned_cols=37 Identities=14% Similarity=0.227 Sum_probs=31.0
Q ss_pred HHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHH
Q 016400 80 AIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNA 116 (390)
Q Consensus 80 ~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~ 116 (390)
..++.++..|.+..++|..-+++.+||..++-+....
T Consensus 4 ~~T~~l~~~G~si~eIA~~R~L~~sTI~~HL~~~~~~ 40 (91)
T PF14493_consen 4 QITYELFQKGLSIEEIAKIRGLKESTIYGHLAELIES 40 (91)
T ss_pred HHHHHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHHHh
Confidence 4567777789999999999999999999887666554
No 346
>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=38.51 E-value=22 Score=26.18 Aligned_cols=24 Identities=21% Similarity=0.128 Sum_probs=18.4
Q ss_pred ccchhhhhhhcccchhhhhhhhHH
Q 016400 89 NLRTRAVQELFRYSGETISRHFNN 112 (390)
Q Consensus 89 ~~~~~~l~~~fgis~stv~~~~~~ 112 (390)
..+..++|...|+|.+||.|.++.
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 478899999999999999987654
No 347
>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=38.41 E-value=20 Score=26.07 Aligned_cols=27 Identities=30% Similarity=0.309 Sum_probs=23.1
Q ss_pred hcccccchhhhhhhcccchhhhhhhhH
Q 016400 85 IVGHNLRTRAVQELFRYSGETISRHFN 111 (390)
Q Consensus 85 ~L~~~~~~~~l~~~fgis~stv~~~~~ 111 (390)
+-..|.+..++|...|+|++|++++.+
T Consensus 14 ~~~~~~t~~~lA~~~gis~~tis~~~~ 40 (78)
T TIGR02607 14 LEPLGLSIRALAKALGVSRSTLSRIVN 40 (78)
T ss_pred HHHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 345688999999999999999999764
No 348
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=38.40 E-value=47 Score=25.87 Aligned_cols=30 Identities=23% Similarity=0.287 Sum_probs=25.1
Q ss_pred cccccchhhhhhhcccchhhhhhhhHHHHH
Q 016400 86 VGHNLRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 86 L~~~~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
+....+..++|..+|+|.+++++.|++.+.
T Consensus 18 ~~~~~~~~~lA~~~~~S~~~l~r~f~~~~g 47 (107)
T PRK10219 18 IDQPLNIDVVAKKSGYSKWYLQRMFRTVTH 47 (107)
T ss_pred cCCCCCHHHHHHHHCCCHHHHHHHHHHHHC
Confidence 344568889999999999999999999743
No 349
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=38.07 E-value=16 Score=34.98 Aligned_cols=22 Identities=36% Similarity=0.347 Sum_probs=19.8
Q ss_pred chhhhhhhcccchhhhhhhhHH
Q 016400 91 RTRAVQELFRYSGETISRHFNN 112 (390)
Q Consensus 91 ~~~~l~~~fgis~stv~~~~~~ 112 (390)
+.+++|..-|+|.+||||+++.
T Consensus 3 ti~dIA~~aGVS~~TVSrvLn~ 24 (343)
T PRK10727 3 TIKDVARLAGVSVATVSRVINN 24 (343)
T ss_pred CHHHHHHHhCCCHHHHHHHhCC
Confidence 5789999999999999999864
No 350
>COG3293 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=37.73 E-value=50 Score=26.60 Aligned_cols=93 Identities=19% Similarity=0.069 Sum_probs=52.7
Q ss_pred eeeeeecCCcceeEeccC-----cccccccHHHHHHHHhhcCCCCCCCCceeeccCCCCCCCCccccccCcccCcccccC
Q 016400 180 NVLAACSFDLKFHYVLAG-----WEGSASDLRVLNSALTRRNKLQVPEGKYYLVDNKYANMPGFIAPYQAVSYHTNQTTT 254 (390)
Q Consensus 180 ~~q~v~d~d~~~~~v~~g-----~~Gs~~D~~vl~~sl~~~~~~~~p~g~~~l~D~gYp~~~~ll~P~~~~~~~~~~~~~ 254 (390)
+.++++|..|+++....+ .+...+...- ..-.-.|+|.+|...++-..|-..+... .
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 356788888888877765 1111111110 0112356677776666655443221100 0
Q ss_pred CCCChhhHHHHHHHHHHHHhHHHHHHHHHHhhchhhh
Q 016400 255 GYHPQDAKELFNQRHSLLRNATDRIFGALKERFPILL 291 (390)
Q Consensus 255 ~~~~~~~~~~fN~~~s~~R~~VE~~fg~LK~rf~iL~ 291 (390)
.-.+...+..++......|..||+.|+.+|. |+.+.
T Consensus 64 ~~~~~~~~~~~~~g~~~~~~~~~~~f~~~~~-~r~~~ 99 (124)
T COG3293 64 VIPYRRFRRWFKRGLWKRRNLVERTFGRLKQ-FRRTA 99 (124)
T ss_pred EeCCCcchhhHHHHHHHHHHHHHHHHHHHhc-cccee
Confidence 0011123677899999999999999998884 55554
No 351
>PRK12681 cysB transcriptional regulator CysB; Reviewed
Probab=37.52 E-value=36 Score=32.55 Aligned_cols=42 Identities=26% Similarity=0.277 Sum_probs=34.9
Q ss_pred HHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 77 EQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 77 ~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
.+|-.|+....+|.|+...|...++|++|||+.+++.-..+-
T Consensus 4 ~~L~~f~avae~g~S~s~AA~~L~iSQpavS~~I~~LE~~lG 45 (324)
T PRK12681 4 QQLRYIVEVVNHNLNVSATAEGLYTSQPGISKQVRMLEDELG 45 (324)
T ss_pred HHHHHHHHHHHccCCHHHHHHHhcCCcHHHHHHHHHHHHHhC
Confidence 345555655556679999999999999999999999999885
No 352
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=37.36 E-value=57 Score=27.48 Aligned_cols=28 Identities=14% Similarity=0.093 Sum_probs=24.3
Q ss_pred cccchhhhhhhcccchhhhhhhhHHHHH
Q 016400 88 HNLRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 88 ~~~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
.-.|+.++|...|+|++||.+-+++..+
T Consensus 22 ~R~s~~eiA~~lglS~~tV~~Ri~rL~~ 49 (153)
T PRK11179 22 ARTPYAELAKQFGVSPGTIHVRVEKMKQ 49 (153)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 3588999999999999999998877655
No 353
>COG3139 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=37.09 E-value=91 Score=23.36 Aligned_cols=44 Identities=14% Similarity=0.280 Sum_probs=32.2
Q ss_pred CCCHHHHHHHHHHhccCCccccCCCCCHHHH----HHHHhhhcccccch
Q 016400 48 RMDKKVFYKLCDILQSKGLLRHTNRIKIEEQ----LAIFMFIVGHNLRT 92 (390)
Q Consensus 48 rms~~~F~~L~~~L~~~~~~~~~~~~~~~~~----l~~~L~~L~~~~~~ 92 (390)
-|+++.+.+|...++-- .-+++..++.+++ =++.||-+.|+...
T Consensus 9 ~mtPEiYQrL~~AvElG-KWPdG~~LtqeQke~clQaVmlwqarhN~~a 56 (90)
T COG3139 9 SMTPEIYQRLSTAVELG-KWPDGVALTQEQKENCLQAVMLWQARHNTEA 56 (90)
T ss_pred hcCHHHHHHHHHHHHhc-CCCCCCcCCHHHHHHHHHHHHHHHHhcCChh
Confidence 48899999999998853 2356777888777 25677888876543
No 354
>COG2964 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=36.98 E-value=54 Score=29.55 Aligned_cols=22 Identities=18% Similarity=0.212 Sum_probs=19.2
Q ss_pred hhhhhhhcccchhhhhhhhHHH
Q 016400 92 TRAVQELFRYSGETISRHFNNV 113 (390)
Q Consensus 92 ~~~l~~~fgis~stv~~~~~~v 113 (390)
...+|...|+|+.||+++++++
T Consensus 194 i~~VA~~L~iSr~TVY~YL~~~ 215 (220)
T COG2964 194 INIVADRLGISRHTVYRYLRKF 215 (220)
T ss_pred HHHHHHHhCCChHHHHHHHHHh
Confidence 4568999999999999999865
No 355
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=36.90 E-value=38 Score=31.70 Aligned_cols=41 Identities=10% Similarity=0.257 Sum_probs=32.4
Q ss_pred HHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 77 EQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 77 ~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
.++-.|+....+ .++...|+..++|++|||+.+++.-..+-
T Consensus 8 ~~L~~f~~v~~~-gs~s~AA~~L~isQ~avS~~i~~LE~~lG 48 (302)
T PRK09791 8 HQIRAFVEVARQ-GSIRGASRMLNMSQPALTKSIQELEEGLA 48 (302)
T ss_pred HHHHHHHHHHHc-CCHHHHHHHhCCChHHHHHHHHHHHHHhC
Confidence 344444444444 48999999999999999999999999885
No 356
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=36.84 E-value=35 Score=27.81 Aligned_cols=31 Identities=23% Similarity=0.188 Sum_probs=26.2
Q ss_pred hcccccchhhhhhhcccchhhhhhhhHHHHH
Q 016400 85 IVGHNLRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 85 ~L~~~~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
-+....+..++|..+|+|++++.+.|++.+.
T Consensus 21 ~~~~~~sl~~lA~~~g~S~~~l~r~Fk~~~G 51 (127)
T PRK11511 21 NLESPLSLEKVSERSGYSKWHLQRMFKKETG 51 (127)
T ss_pred hcCCCCCHHHHHHHHCcCHHHHHHHHHHHHC
Confidence 3445678899999999999999999998844
No 357
>PRK11013 DNA-binding transcriptional regulator LysR; Provisional
Probab=36.80 E-value=36 Score=32.09 Aligned_cols=40 Identities=20% Similarity=0.230 Sum_probs=32.2
Q ss_pred HHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 78 QLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 78 ~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
++-+|+....+ .|+...|+..++|+|+||+.+++.-+-+-
T Consensus 8 ~L~~f~av~~~-gS~s~AAe~L~isqsavS~~Ik~LE~~lg 47 (309)
T PRK11013 8 HIEIFHAVMTA-GSLTEAARLLHTSQPTVSRELARFEKVIG 47 (309)
T ss_pred HHHHHHHHHHh-CcHHHHHHHHCCCcHHHHHHHHHHHHHhC
Confidence 44445554444 48999999999999999999999998875
No 358
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=36.76 E-value=18 Score=34.88 Aligned_cols=22 Identities=32% Similarity=0.356 Sum_probs=19.4
Q ss_pred chhhhhhhcccchhhhhhhhHH
Q 016400 91 RTRAVQELFRYSGETISRHFNN 112 (390)
Q Consensus 91 ~~~~l~~~fgis~stv~~~~~~ 112 (390)
+..++|..-|||.+||||+++.
T Consensus 2 TikDVA~~AGVS~sTVSrvln~ 23 (333)
T COG1609 2 TIKDVAKLAGVSKATVSRVLNG 23 (333)
T ss_pred CHHHHHHHhCCCHHHHHHHHcC
Confidence 4678999999999999998864
No 359
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=36.55 E-value=44 Score=30.76 Aligned_cols=36 Identities=11% Similarity=0.212 Sum_probs=26.8
Q ss_pred HHHhhhcc-c--ccchhhhhhhcccchhhhhhhhHHHHH
Q 016400 80 AIFMFIVG-H--NLRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 80 ~~~L~~L~-~--~~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
+-.|.+|+ + +.+..++++..|+++||++|+++....
T Consensus 7 l~iL~~l~~~~~~l~l~ela~~~glpksT~~RlL~tL~~ 45 (246)
T COG1414 7 LAILDLLAEGPGGLSLAELAERLGLPKSTVHRLLQTLVE 45 (246)
T ss_pred HHHHHHHHhCCCCCCHHHHHHHhCcCHHHHHHHHHHHHH
Confidence 33444444 2 345999999999999999998877655
No 360
>PRK10094 DNA-binding transcriptional activator AllS; Provisional
Probab=36.34 E-value=37 Score=32.08 Aligned_cols=40 Identities=15% Similarity=0.058 Sum_probs=31.8
Q ss_pred HHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 78 QLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 78 ~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
+|-+|+.... ..++...|...++|+++||+.+++.-..+-
T Consensus 6 ~L~~f~~v~e-~gs~s~AA~~L~iSQpavS~~I~~LE~~lg 45 (308)
T PRK10094 6 TLRTFIAVAE-TGSFSKAAERLCKTTATISYRIKLLEENTG 45 (308)
T ss_pred HHHHHHHHHH-hCCHHHHHHHhcCCHHHHHHHHHHHHHHhC
Confidence 3444444444 458999999999999999999999998875
No 361
>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=36.14 E-value=26 Score=30.18 Aligned_cols=26 Identities=19% Similarity=0.270 Sum_probs=22.7
Q ss_pred cchhhhhhhcccchhhhhhhhHHHHH
Q 016400 90 LRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 90 ~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
+++++++..+|+|.+||++.++...+
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 46899999999999999998887655
No 362
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=35.67 E-value=31 Score=29.69 Aligned_cols=43 Identities=16% Similarity=0.278 Sum_probs=35.2
Q ss_pred CCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHH
Q 016400 73 IKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAI 117 (390)
Q Consensus 73 ~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l 117 (390)
++..+. -.|.+|+.|.+..+++...++|..||..++.+...-|
T Consensus 150 lt~re~--~vl~~l~~g~s~~eIa~~l~~s~~tv~~~~~~~~~kl 192 (210)
T PRK09935 150 LSNREV--TILRYLVSGLSNKEIADQLLLSNKTVSAHKSNIYGKL 192 (210)
T ss_pred CCHHHH--HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHc
Confidence 444444 3456788899999999999999999999999887766
No 363
>PRK08558 adenine phosphoribosyltransferase; Provisional
Probab=35.63 E-value=34 Score=31.43 Aligned_cols=37 Identities=5% Similarity=0.087 Sum_probs=31.6
Q ss_pred HHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhH
Q 016400 75 IEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFN 111 (390)
Q Consensus 75 ~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~ 111 (390)
...++.-.|+.|....+|++++..+|++.|.++|+++
T Consensus 9 ~~~~~v~~lr~lk~~~ty~el~~~~g~p~~~l~RYv~ 45 (238)
T PRK08558 9 LQLRAVRVLRSLKKTYTYEELSSITGLPESVLNRYVN 45 (238)
T ss_pred HHHHHHHHHHHHhcccCHHHHHHHHCCCHHHHHHHHc
Confidence 3445566788899889999999999999999999875
No 364
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=35.61 E-value=46 Score=27.83 Aligned_cols=36 Identities=14% Similarity=0.113 Sum_probs=26.5
Q ss_pred cchhhhhhhcccchhhhhhhhH--H-HHHHHHHhhcccc
Q 016400 90 LRTRAVQELFRYSGETISRHFN--N-VLNAIMAISLDFF 125 (390)
Q Consensus 90 ~~~~~l~~~fgis~stv~~~~~--~-v~~~l~~~~~~~i 125 (390)
.++..+|...||+++|+++|-+ + |...+..+..+++
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 6666665555543
No 365
>PHA02701 ORF020 dsRNA-binding PKR inhibitor; Provisional
Probab=35.32 E-value=50 Score=28.89 Aligned_cols=41 Identities=12% Similarity=0.208 Sum_probs=31.4
Q ss_pred HHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHH
Q 016400 75 IEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 75 ~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
.+.+++-||..-+.+.+..+|+..+|+++++|.|.+.+..+
T Consensus 5 ~~~~i~~~l~~~~~~~~a~~i~k~l~i~k~~vNr~LY~L~~ 45 (183)
T PHA02701 5 CASLILTLLSSSGDKLPAKRIAKELGISKHEANRCLYRLLE 45 (183)
T ss_pred HHHHHHHHHHhcCCCCcHHHHHHHhCccHHHHHHHHHHHhh
Confidence 34566667776665688999999999999999887665533
No 366
>PF13701 DDE_Tnp_1_4: Transposase DDE domain group 1
Probab=34.80 E-value=53 Score=33.23 Aligned_cols=125 Identities=16% Similarity=0.055 Sum_probs=63.1
Q ss_pred cchhhhhhhhHHHHHHHH-HhhccccCCCCCCCchhhccCCcccCCCccccccccceEEEEEeCCCCCCCCCCCCCCcee
Q 016400 101 YSGETISRHFNNVLNAIM-AISLDFFQPPGPDVPPEISLDPRLYPYFKDCVGAVDGIHIPVMVGVDEQGPFRNKSGLLSQ 179 (390)
Q Consensus 101 is~stv~~~~~~v~~~l~-~~~~~~i~~P~~~~~~~i~~~~~~~~~fp~~iG~IDgt~i~i~~P~~~~~~y~~~k~~~s~ 179 (390)
-|++|++|..+.+...-. .+...++.+ .....+ ..-..++-=||.|+.++.- ...+..|.+++|.++.
T Consensus 103 as~~t~sR~e~~~~~~~~~~~~~~~~~~--------~~~~~~--~~~~~i~LDiD~T~~~~~G-~Qe~~~~n~y~g~~gY 171 (448)
T PF13701_consen 103 ASQPTLSRLENRPDERDLKRLRRALVDL--------FLASYK--KPPKEIVLDIDSTVDDVHG-EQEGAVFNTYYGEDGY 171 (448)
T ss_pred cchhhHHHHHccccHHHHHHHHHHHHHH--------HHHHhc--cccceEEEecccccccchh-hcccccccccCCCccc
Confidence 467889988876655432 222222110 000000 0112345557888766531 1112235555555555
Q ss_pred eeeeee-cCCcceeEeccCcccccccHHHH----HHHHhhcCCCCCCCCce-eeccCCCCCCCCcc
Q 016400 180 NVLAAC-SFDLKFHYVLAGWEGSASDLRVL----NSALTRRNKLQVPEGKY-YLVDNKYANMPGFI 239 (390)
Q Consensus 180 ~~q~v~-d~d~~~~~v~~g~~Gs~~D~~vl----~~sl~~~~~~~~p~g~~-~l~D~gYp~~~~ll 239 (390)
.-+++- ...|.++.+. -.||+.|-++=. +..+.+. .-..|...- +=||+|| ..+.++
T Consensus 172 ~PL~~f~g~~G~~l~a~-LRpGn~~sa~g~~~fL~~~l~~l-r~~~~~~~ILvR~DSgF-~~~el~ 234 (448)
T PF13701_consen 172 HPLVAFDGQTGYLLAAE-LRPGNVHSAKGAAEFLKRVLRRL-RQRWPDTRILVRGDSGF-ASPELM 234 (448)
T ss_pred ccceeccCCCCceEEEE-ccCCCCChHHHHHHHHHHHHHHH-hhhCccceEEEEecCcc-CcHHHH
Confidence 544444 4578888764 469998887543 3333321 113444333 4599999 334333
No 367
>PRK09726 antitoxin HipB; Provisional
Probab=34.70 E-value=23 Score=26.81 Aligned_cols=26 Identities=15% Similarity=0.078 Sum_probs=23.1
Q ss_pred cccccchhhhhhhcccchhhhhhhhH
Q 016400 86 VGHNLRTRAVQELFRYSGETISRHFN 111 (390)
Q Consensus 86 L~~~~~~~~l~~~fgis~stv~~~~~ 111 (390)
-..|.+..++|...|+|++|++++.+
T Consensus 22 ~~~gltq~elA~~~gvs~~tis~~e~ 47 (88)
T PRK09726 22 QQNGWTQSELAKKIGIKQATISNFEN 47 (88)
T ss_pred HHcCCCHHHHHHHHCcCHHHHHHHHC
Confidence 35689999999999999999999766
No 368
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=34.60 E-value=36 Score=31.67 Aligned_cols=37 Identities=14% Similarity=0.276 Sum_probs=31.1
Q ss_pred HhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 82 FMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 82 ~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
.+..++...++...|+..++|+|+||+.+++.-+.+-
T Consensus 8 ~f~~v~~~gs~s~AA~~L~isQ~avSr~i~~LE~~lg 44 (296)
T PRK09906 8 YFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVG 44 (296)
T ss_pred HHHHHHhhCCHHHHHHHhCCCCcHHHHHHHHHHHHhC
Confidence 3444555569999999999999999999999999875
No 369
>PRK15421 DNA-binding transcriptional regulator MetR; Provisional
Probab=34.58 E-value=44 Score=31.77 Aligned_cols=40 Identities=10% Similarity=0.165 Sum_probs=32.9
Q ss_pred HHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 78 QLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 78 ~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
+|-.|+....+| ++...|+..++|++|||+.++..-..+.
T Consensus 6 ~L~~f~av~~~g-s~s~AA~~L~iSqpaVS~~Ik~LE~~lg 45 (317)
T PRK15421 6 HLKTLQALRNCG-SLAAAAATLHQTQSALSHQFSDLEQRLG 45 (317)
T ss_pred HHHHHHHHHHcC-CHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 445555555555 8999999999999999999999998885
No 370
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [].; PDB: 2WTE_A 3SQN_A.
Probab=34.29 E-value=63 Score=22.39 Aligned_cols=37 Identities=14% Similarity=0.222 Sum_probs=27.5
Q ss_pred HHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHH
Q 016400 78 QLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 78 ~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
+++-.|.- ....++.+++...|+|..|+...+.+.-.
T Consensus 9 ~Ll~~L~~-~~~~~~~ela~~l~~S~rti~~~i~~L~~ 45 (59)
T PF08280_consen 9 KLLELLLK-NKWITLKELAKKLNISERTIKNDINELNE 45 (59)
T ss_dssp HHHHHHHH-HTSBBHHHHHHHCTS-HHHHHHHHHHHHT
T ss_pred HHHHHHHc-CCCCcHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 34444555 56688999999999999999988876644
No 371
>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=34.18 E-value=73 Score=22.76 Aligned_cols=27 Identities=19% Similarity=0.281 Sum_probs=19.7
Q ss_pred cccchhhhhhhcccc-hhhhhhhhHHHH
Q 016400 88 HNLRTRAVQELFRYS-GETISRHFNNVL 114 (390)
Q Consensus 88 ~~~~~~~l~~~fgis-~stv~~~~~~v~ 114 (390)
..-+.+++++.||++ .+||+.++....
T Consensus 24 ~~Pt~rEIa~~~g~~S~~tv~~~L~~Le 51 (65)
T PF01726_consen 24 YPPTVREIAEALGLKSTSTVQRHLKALE 51 (65)
T ss_dssp S---HHHHHHHHTSSSHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHhCCCChHHHHHHHHHHH
Confidence 446799999999996 999988776543
No 372
>PF14294 DUF4372: Domain of unknown function (DUF4372)
Probab=33.99 E-value=1.3e+02 Score=22.31 Aligned_cols=53 Identities=11% Similarity=0.237 Sum_probs=38.0
Q ss_pred CCHHHHHHHHHHhccCCccccCCCCCHHHHHHHHhh-hcccccchhhhhhhcccchh
Q 016400 49 MDKKVFYKLCDILQSKGLLRHTNRIKIEEQLAIFMF-IVGHNLRTRAVQELFRYSGE 104 (390)
Q Consensus 49 ms~~~F~~L~~~L~~~~~~~~~~~~~~~~~l~~~L~-~L~~~~~~~~l~~~fgis~s 104 (390)
+.+..|..++...... ...+.++...++.+.|+ -|..-.|.++|...+....+
T Consensus 14 i~~~~f~~~v~k~~~d---~~~k~f~~~~ql~~mlfaQL~~~~SLRdI~~~l~a~~~ 67 (76)
T PF14294_consen 14 IPRHEFERIVKKYGGD---RYVKKFTCWDQLVAMLFAQLTGRESLRDIEDCLNAHSS 67 (76)
T ss_pred CCHHHHHHHHHHhCCC---CCCCCCCHHHHHHHHHHHHHcccCcHHHHHHHHHHhHH
Confidence 4788888888886643 23467899888765555 78888899988877654443
No 373
>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=33.88 E-value=53 Score=28.93 Aligned_cols=40 Identities=8% Similarity=0.113 Sum_probs=28.4
Q ss_pred HHHHHHHhhhc----ccccchhhhhhhcccc-hhhhhhhhHHHHH
Q 016400 76 EEQLAIFMFIV----GHNLRTRAVQELFRYS-GETISRHFNNVLN 115 (390)
Q Consensus 76 ~~~l~~~L~~L----~~~~~~~~l~~~fgis-~stv~~~~~~v~~ 115 (390)
+.+++-+|.-. +.+.+.+++|..+|++ ++||++.+....+
T Consensus 8 q~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~~L~~ 52 (199)
T TIGR00498 8 QQEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLKALER 52 (199)
T ss_pred HHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHHHHHH
Confidence 34455555532 2346788999999998 9999988776654
No 374
>PRK13348 chromosome replication initiation inhibitor protein; Provisional
Probab=33.85 E-value=44 Score=31.08 Aligned_cols=39 Identities=8% Similarity=0.095 Sum_probs=30.9
Q ss_pred HHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 79 LAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 79 l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
+-.|+.... ..++...|+..++|+++||+.+++.-+.+-
T Consensus 7 L~~f~~v~~-~gs~t~AA~~L~iSQ~avS~~i~~LE~~lg 45 (294)
T PRK13348 7 LEALAAVVE-TGSFERAARRLHVTPSAVSQRIKALEESLG 45 (294)
T ss_pred HHHHHHHHH-cCCHHHHHHHhCCCchHHHHHHHHHHHHhC
Confidence 333333333 458999999999999999999999999875
No 375
>PRK12680 transcriptional regulator CysB-like protein; Reviewed
Probab=33.57 E-value=45 Score=31.89 Aligned_cols=40 Identities=10% Similarity=0.157 Sum_probs=32.3
Q ss_pred HHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 79 LAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 79 l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
+-+|+....++.|+...|+..++|++|||+.+++.-+.+.
T Consensus 6 L~~F~~vae~~gS~s~AA~~L~isQpavS~~I~~LE~~lG 45 (327)
T PRK12680 6 LRYLVAIADAELNITLAAARVHATQPGLSKQLKQLEDELG 45 (327)
T ss_pred HHHHHHHHHccCCHHHHHHHhcCCchHHHHHHHHHHHHhC
Confidence 3344443334578999999999999999999999999886
No 376
>PRK04140 hypothetical protein; Provisional
Probab=33.54 E-value=36 Score=32.68 Aligned_cols=62 Identities=13% Similarity=-0.013 Sum_probs=38.8
Q ss_pred CCHHH-HHHHHHHhccCCc-cccCCCCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhH
Q 016400 49 MDKKV-FYKLCDILQSKGL-LRHTNRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFN 111 (390)
Q Consensus 49 ms~~~-F~~L~~~L~~~~~-~~~~~~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~ 111 (390)
|+.+| |..+++-..|-.. .+++--+...-..+-. .+-..|.++.++|...|+|++|+++|.+
T Consensus 98 ~~~~tl~~~~~~g~~p~v~~~~Gg~~v~i~GerLk~-lRe~~GlSq~eLA~~lGVSr~tIskyE~ 161 (317)
T PRK04140 98 LSPDTLYDDFVEGEPPLIYAAPGGFYVKIDGDVLRE-AREELGLSLGELASELGVSRRTISKYEN 161 (317)
T ss_pred ecHHHHHHHHhCCCCceEEEcCCCeeehhhHHHHHH-HHHHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 45667 6666655554221 1222223333222222 3566799999999999999999999765
No 377
>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=33.44 E-value=25 Score=22.82 Aligned_cols=21 Identities=14% Similarity=-0.013 Sum_probs=17.4
Q ss_pred chhhhhhhcccchhhhhhhhH
Q 016400 91 RTRAVQELFRYSGETISRHFN 111 (390)
Q Consensus 91 ~~~~l~~~fgis~stv~~~~~ 111 (390)
+..++|..+|++.+|+..+..
T Consensus 2 ~~~e~a~~~gv~~~tlr~~~~ 22 (49)
T cd04761 2 TIGELAKLTGVSPSTLRYYER 22 (49)
T ss_pred cHHHHHHHHCcCHHHHHHHHH
Confidence 356889999999999998754
No 378
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=33.27 E-value=44 Score=31.03 Aligned_cols=39 Identities=13% Similarity=0.194 Sum_probs=30.9
Q ss_pred HHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 79 LAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 79 l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
+-+|+.... ..++...|+..++|+|+||+.+++.-+.+.
T Consensus 6 L~~f~~v~~-~gs~s~AA~~L~isqsavS~~i~~LE~~lg 44 (296)
T PRK11242 6 IRYFLAVAE-HGNFTRAAEALHVSQPTLSQQIRQLEESLG 44 (296)
T ss_pred HHHHHHHHH-hCCHHHHHHHcCCCchHHHHHHHHHHHHhC
Confidence 333444444 458999999999999999999999999875
No 379
>PF13556 HTH_30: PucR C-terminal helix-turn-helix domain; PDB: 3ONQ_B.
Probab=32.60 E-value=48 Score=22.97 Aligned_cols=34 Identities=6% Similarity=0.086 Sum_probs=28.4
Q ss_pred hhcccccchhhhhhhcccchhhhhhhhHHHHHHH
Q 016400 84 FIVGHNLRTRAVQELFRYSGETISRHFNNVLNAI 117 (390)
Q Consensus 84 ~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l 117 (390)
.|+.+|.+....|...+|++.|+.--++++.+.+
T Consensus 7 ~yl~~~~n~~~tA~~L~iHrNTl~yRl~ki~~l~ 40 (59)
T PF13556_consen 7 AYLENNGNISKTARALHIHRNTLRYRLKKIEELL 40 (59)
T ss_dssp HHHHTTT-HHHHHHHHTS-HHHHHHHHHHHHHHH
T ss_pred HHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 4788999999999999999999998888887765
No 380
>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=32.38 E-value=54 Score=26.67 Aligned_cols=26 Identities=12% Similarity=0.142 Sum_probs=22.9
Q ss_pred cchhhhhhhcccchhhhhhhhHHHHH
Q 016400 90 LRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 90 ~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
.+..+++..+|+|++++.+++....+
T Consensus 26 ~s~~eia~~l~is~~~v~~~l~~L~~ 51 (130)
T TIGR02944 26 YSAAEIAEQTGLNAPTVSKILKQLSL 51 (130)
T ss_pred ccHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 68999999999999999998877655
No 381
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=32.07 E-value=64 Score=26.83 Aligned_cols=37 Identities=11% Similarity=0.134 Sum_probs=28.0
Q ss_pred HHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHH
Q 016400 78 QLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 78 ~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
+++-.|..=+. .++..+|+..|+|.+|+++.+++..+
T Consensus 12 ~IL~~L~~d~r-~~~~eia~~lglS~~~v~~Ri~~L~~ 48 (154)
T COG1522 12 RILRLLQEDAR-ISNAELAERVGLSPSTVLRRIKRLEE 48 (154)
T ss_pred HHHHHHHHhCC-CCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 34444443343 78999999999999999998887755
No 382
>PRK12422 chromosomal replication initiation protein; Provisional
Probab=31.81 E-value=64 Score=32.62 Aligned_cols=47 Identities=11% Similarity=0.217 Sum_probs=42.9
Q ss_pred CCCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHH
Q 016400 71 NRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAI 117 (390)
Q Consensus 71 ~~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l 117 (390)
+.+...-|++|.|-+=-++.|+.++|..||.+-|||..-++++-+.+
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 46788889999999988999999999999999999999999888777
No 383
>COG0664 Crp cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]
Probab=31.72 E-value=48 Score=28.67 Aligned_cols=44 Identities=32% Similarity=0.511 Sum_probs=36.8
Q ss_pred CCCHHHHHHHHhhhccc--------------ccchhhhhhhcccchhhhhhhhHHHHH
Q 016400 72 RIKIEEQLAIFMFIVGH--------------NLRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~--------------~~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
..++.++++.+|..++. ..+...++...|++..|+++.+.++..
T Consensus 140 ~~~~~~r~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~ia~~~g~~~~~vsr~l~~l~~ 197 (214)
T COG0664 140 RKDVEERLARFLLNLGRRLGIATEDGILIPLPLTHKDLAEYLGLSRETVSRILKELRK 197 (214)
T ss_pred hccHHHHHHHHHHHHhhccCCCCCCCcEEeccCCHHHHHHHhCCchhhHHHHHHHHHh
Confidence 56888999999888873 467888999999999999998887754
No 384
>smart00497 IENR1 Intron encoded nuclease repeat motif. Repeat of unknown function, but possibly DNA-binding via helix-turn-helix motif (Ponting, unpublished).
Probab=31.15 E-value=33 Score=22.84 Aligned_cols=24 Identities=21% Similarity=0.218 Sum_probs=20.2
Q ss_pred ccchhhhhhhcccchhhhhhhhHH
Q 016400 89 NLRTRAVQELFRYSGETISRHFNN 112 (390)
Q Consensus 89 ~~~~~~l~~~fgis~stv~~~~~~ 112 (390)
-.|..+.+..+|++.++++++++.
T Consensus 17 f~S~~eAa~~lg~~~~~I~~~~~~ 40 (53)
T smart00497 17 FSSIREAAKYLGISHSSISKYLNT 40 (53)
T ss_pred ecCHHHHHHHhCCCHHHHHHHHhC
Confidence 357889999999999999987753
No 385
>TIGR02424 TF_pcaQ pca operon transcription factor PcaQ. Members of this family are LysR-family transcription factors associated with operons for catabolism of protocatechuate. Members occur only in Proteobacteria.
Probab=31.13 E-value=51 Score=30.72 Aligned_cols=32 Identities=6% Similarity=0.142 Sum_probs=28.3
Q ss_pred ccccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 87 GHNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 87 ~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
+...|+...|+..++|+++||+.+++.-+.+.
T Consensus 15 ~~~gS~s~AA~~L~isq~avS~~I~~LE~~lg 46 (300)
T TIGR02424 15 ARQGSVKRAAEALHITQPAVSKTLRELEEILG 46 (300)
T ss_pred HHhCCHHHHHHHhCCChHHHHHHHHHHHHHhC
Confidence 33458999999999999999999999999885
No 386
>TIGR03298 argP transcriptional regulator, ArgP family. ArgP used to be known as IciA. ArgP is a positive regulator of argK. It is a negative autoregulator in presence of arginine. It competes with DnaA for oriC iteron (13-mer) binding. It activates dnaA and nrd transcription. It has been demonstrated to be part of the pho regulon (PubMed:10589831). ArgP mutants convey canavanine (an L-arginine structural homolog) sensitivity (PubMed: 15150242).
Probab=30.98 E-value=53 Score=30.51 Aligned_cols=39 Identities=10% Similarity=0.103 Sum_probs=31.2
Q ss_pred HHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 79 LAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 79 l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
+-.|+.... -.++...|+..++|+++||+.+++.-+.|.
T Consensus 6 l~~f~~v~~-~~s~t~AA~~L~isQpavS~~I~~LE~~lg 44 (292)
T TIGR03298 6 LAALAAVVE-EGSFERAAAALSVTPSAVSQRIKALEERLG 44 (292)
T ss_pred HHHHHHHHH-cCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 334444444 448999999999999999999999999875
No 387
>PF06530 Phage_antitermQ: Phage antitermination protein Q; InterPro: IPR010534 This entry is represented by Bacteriophage 933W, GpQ. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several phage antitermination protein Q and related bacterial sequences. Phage 993W gene Q encodes a phage-specific positive regulator of late gene expression, thought, by analogy to the corresponding gene of phage lambda, to be a transcription antiterminator. GpQ positively regulates expression of the phage late gene operons. Bacterial host RNA polymerase modified by antitermination proteins transcribes through termination sites that otherwise prevent expression of the regulated genes [, ].; GO: 0003677 DNA binding, 0060567 negative regulation of transcription termination, DNA-dependent
Probab=30.92 E-value=63 Score=26.37 Aligned_cols=40 Identities=10% Similarity=0.194 Sum_probs=29.8
Q ss_pred HHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHH
Q 016400 78 QLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAI 117 (390)
Q Consensus 78 ~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l 117 (390)
..-+++.++.+|.|.+.+|...++|..++.+.+..-...|
T Consensus 67 ~~~ll~~~Yv~g~s~r~IA~~~~~s~~~ir~~l~~ae~~i 106 (125)
T PF06530_consen 67 EYDLLILYYVYGWSKRQIARKLKCSEGKIRKRLQRAEGFI 106 (125)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHhhhhH
Confidence 3444455555799999999999999999988776544433
No 388
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=30.90 E-value=78 Score=23.70 Aligned_cols=39 Identities=10% Similarity=0.244 Sum_probs=28.2
Q ss_pred HHHHHHhhhccc-ccchhhhhhhcccchhhhhhhhHHHHH
Q 016400 77 EQLAIFMFIVGH-NLRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 77 ~~l~~~L~~L~~-~~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
..+.+.|..+.. ..|-..+++..|+|+.+|.+.+...-+
T Consensus 6 ~~~~~ll~~~~~~~~SGe~La~~LgiSRtaVwK~Iq~Lr~ 45 (79)
T COG1654 6 QMLLLLLLLLTGNFVSGEKLAEELGISRTAVWKHIQQLRE 45 (79)
T ss_pred HHHHHHHHHcCCCcccHHHHHHHHCccHHHHHHHHHHHHH
Confidence 344444444443 378899999999999999988876654
No 389
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=30.70 E-value=39 Score=30.21 Aligned_cols=32 Identities=13% Similarity=0.095 Sum_probs=25.9
Q ss_pred Hhhhccc---ccchhhhhhhcccchhhhhhhhHHH
Q 016400 82 FMFIVGH---NLRTRAVQELFRYSGETISRHFNNV 113 (390)
Q Consensus 82 ~L~~L~~---~~~~~~l~~~fgis~stv~~~~~~v 113 (390)
.|..++. |.+.+++|...++|..||.+++...
T Consensus 167 Vl~~~~~g~~g~s~~eIa~~l~iS~~Tv~~~~~~~ 201 (225)
T PRK10046 167 VRKLFKEPGVQHTAETVAQALTISRTTARRYLEYC 201 (225)
T ss_pred HHHHHHcCCCCcCHHHHHHHhCccHHHHHHHHHHH
Confidence 3455555 5899999999999999999988643
No 390
>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=30.38 E-value=80 Score=24.87 Aligned_cols=27 Identities=19% Similarity=0.194 Sum_probs=18.9
Q ss_pred ccchhhhhhhc-----ccchhhhhhhhHHHHH
Q 016400 89 NLRTRAVQELF-----RYSGETISRHFNNVLN 115 (390)
Q Consensus 89 ~~~~~~l~~~f-----gis~stv~~~~~~v~~ 115 (390)
..+..+|.+.. ++|.+||+|.++.+.+
T Consensus 16 ~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~ 47 (116)
T cd07153 16 HLTAEEIYERLRKKGPSISLATVYRTLELLEE 47 (116)
T ss_pred CCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHh
Confidence 34555555554 7999999998877654
No 391
>PF02650 HTH_WhiA: WhiA C-terminal HTH domain; InterPro: IPR023054 This domain is found at the C terminus of the sporulation regulator WhiA. It is predicted to form a DNA binding helix-turn-helix structure []. ; PDB: 3HYI_A.
Probab=30.31 E-value=1e+02 Score=23.43 Aligned_cols=42 Identities=7% Similarity=0.097 Sum_probs=27.4
Q ss_pred CCHHHHHHHHhhhcccc-cchhhhhhhc--ccchhhhhhhhHHHHH
Q 016400 73 IKIEEQLAIFMFIVGHN-LRTRAVQELF--RYSGETISRHFNNVLN 115 (390)
Q Consensus 73 ~~~~~~l~~~L~~L~~~-~~~~~l~~~f--gis~stv~~~~~~v~~ 115 (390)
+|...+. ++..+|.++ .|..++++.+ .||+|+|...++++.+
T Consensus 38 l~~~l~~-~a~lRl~~Pd~SL~EL~~~~~~~iSKSgvnhrlrKl~~ 82 (85)
T PF02650_consen 38 LPEKLRE-FAELRLENPDASLKELGELLEPPISKSGVNHRLRKLKK 82 (85)
T ss_dssp S-HHHHH-HHHHHHH-TTS-HHHHHHTT--T--HHHHHHHHHHHHH
T ss_pred CCHHHHH-HHHHHHHCccccHHHHHHHHcCcCcHHHHHHHHHHHHH
Confidence 5555554 444455554 8999999999 9999999988887654
No 392
>COG4974 XerD Site-specific recombinase XerD [DNA replication, recombination, and repair]
Probab=30.21 E-value=1.2e+02 Score=28.73 Aligned_cols=80 Identities=11% Similarity=0.145 Sum_probs=54.2
Q ss_pred hhHHHh--hcCCCHHHHHHHHHHhccCCccccCCCCCH-HHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHH-
Q 016400 40 SERCLE--NFRMDKKVFYKLCDILQSKGLLRHTNRIKI-EEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLN- 115 (390)
Q Consensus 40 d~~f~~--~frms~~~F~~L~~~L~~~~~~~~~~~~~~-~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~- 115 (390)
|.-|.. --+||+..|.+++..+.....+. ..++| -.+=+.+-..|.+|...+.+++..|++.=+...|-..|++
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 344543 34689999999999988755544 33443 5556677788999999999999999875444444444444
Q ss_pred HHHHhh
Q 016400 116 AIMAIS 121 (390)
Q Consensus 116 ~l~~~~ 121 (390)
.|-++.
T Consensus 288 ~L~~~~ 293 (300)
T COG4974 288 RLRDLY 293 (300)
T ss_pred HHHHHH
Confidence 343443
No 393
>PRK06474 hypothetical protein; Provisional
Probab=30.16 E-value=56 Score=28.51 Aligned_cols=26 Identities=15% Similarity=0.372 Sum_probs=22.4
Q ss_pred cchhhhhhhc-ccchhhhhhhhHHHHH
Q 016400 90 LRTRAVQELF-RYSGETISRHFNNVLN 115 (390)
Q Consensus 90 ~~~~~l~~~f-gis~stv~~~~~~v~~ 115 (390)
.+..+++..+ ++|++||+++++.+.+
T Consensus 27 ~ta~el~~~l~~is~aTvYrhL~~L~e 53 (178)
T PRK06474 27 LTPLELVKILKDVPQATLYRHLQTMVD 53 (178)
T ss_pred CCHHHHHHHhcCCCHHHHHHHHHHHHH
Confidence 6888888888 7999999999887765
No 394
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=30.11 E-value=70 Score=27.32 Aligned_cols=29 Identities=3% Similarity=-0.013 Sum_probs=24.7
Q ss_pred ccccchhhhhhhcccchhhhhhhhHHHHH
Q 016400 87 GHNLRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 87 ~~~~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
-...++.++|...|+|.+||.+-+++..+
T Consensus 26 d~R~s~~eiA~~lglS~~tv~~Ri~rL~~ 54 (164)
T PRK11169 26 DGRISNVELSKRVGLSPTPCLERVRRLER 54 (164)
T ss_pred CCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 33578999999999999999998877755
No 395
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=30.01 E-value=71 Score=29.74 Aligned_cols=44 Identities=11% Similarity=0.152 Sum_probs=34.4
Q ss_pred CCCHHHHHHHHhhhcccc-cchhhhhhhcccchhhhhhhhHHHHH
Q 016400 72 RIKIEEQLAIFMFIVGHN-LRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~-~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
.++.+++-.+-+-.=..| ..+.++....|.|++|+||++++..+
T Consensus 192 ~L~~~e~~il~~i~~~GGri~Q~eL~r~lglsktTvsR~L~~LEk 236 (258)
T COG2512 192 DLNEDEKEILDLIRERGGRITQAELRRALGLSKTTVSRILRRLEK 236 (258)
T ss_pred CCCHHHHHHHHHHHHhCCEEeHHHHHHhhCCChHHHHHHHHHHHh
Confidence 566777766555544445 78999999999999999999988765
No 396
>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=30.00 E-value=35 Score=24.06 Aligned_cols=22 Identities=23% Similarity=0.117 Sum_probs=18.5
Q ss_pred chhhhhhhcccchhhhhhhhHH
Q 016400 91 RTRAVQELFRYSGETISRHFNN 112 (390)
Q Consensus 91 ~~~~l~~~fgis~stv~~~~~~ 112 (390)
+..++|..+|||.+|+.++.++
T Consensus 2 s~~eva~~~gvs~~tlr~w~~~ 23 (68)
T cd01104 2 TIGAVARLTGVSPDTLRAWERR 23 (68)
T ss_pred CHHHHHHHHCcCHHHHHHHHHh
Confidence 4578999999999999987753
No 397
>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=29.78 E-value=34 Score=26.19 Aligned_cols=24 Identities=13% Similarity=0.166 Sum_probs=17.6
Q ss_pred cccchhhhhhhcccchhhhhhhhH
Q 016400 88 HNLRTRAVQELFRYSGETISRHFN 111 (390)
Q Consensus 88 ~~~~~~~l~~~fgis~stv~~~~~ 111 (390)
.|.+..+||..+|.|++.|++++.
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 398
>PF07750 GcrA: GcrA cell cycle regulator; InterPro: IPR011681 GcrA, together with CtrA (see IPR001789 from INTERPRO and IPR001867 from INTERPRO), form a master cell cycle regulator. These bacterial regulators are involved in controlling the progression and asymmetric polar morphogenesis []. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes []. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery [].
Probab=29.57 E-value=43 Score=28.82 Aligned_cols=37 Identities=8% Similarity=0.129 Sum_probs=29.8
Q ss_pred HHHHHHHhhhcccccchhhhhhhcc-cchhhhhhhhHH
Q 016400 76 EEQLAIFMFIVGHNLRTRAVQELFR-YSGETISRHFNN 112 (390)
Q Consensus 76 ~~~l~~~L~~L~~~~~~~~l~~~fg-is~stv~~~~~~ 112 (390)
++++...-.+++.|.|..+||..+| +|+..|.-.+++
T Consensus 5 de~~~~L~~lw~~G~SasqIA~~lg~vsRnAViGk~hR 42 (162)
T PF07750_consen 5 DERVERLRKLWAEGLSASQIARQLGGVSRNAVIGKAHR 42 (162)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHhCCcchhhhhhhhhc
Confidence 3555555566788999999999999 999988876665
No 399
>TIGR01637 phage_arpU phage transcriptional regulator, ArpU family. This model represents a family of phage proteins, including ArpU, called a putative autolysin regulatory protein. ArpU was described as a regulator of cellular muramidase-2 of Enterococcus hirae but appears to have been cloned from a prophage. This family appears related to the RinA family of bacteriophage transcriptional activators and to some sporulation-specific sigma factors. We propose that this is a phage transcriptional activator family.
Probab=29.40 E-value=1.2e+02 Score=24.76 Aligned_cols=47 Identities=9% Similarity=0.007 Sum_probs=37.8
Q ss_pred CCHHHHHHHHhhhcc-cccchhhhhhhcccchhhhhhhhHHHHHHHHH
Q 016400 73 IKIEEQLAIFMFIVG-HNLRTRAVQELFRYSGETISRHFNNVLNAIMA 119 (390)
Q Consensus 73 ~~~~~~l~~~L~~L~-~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 119 (390)
++..++-.+...|+. .+.+...++..+|+|+++..++-++.+..+..
T Consensus 80 l~~~~r~Il~~~Yl~~~~~~~~~I~~~l~~s~~~~y~~k~~Al~~fA~ 127 (132)
T TIGR01637 80 LDEISRQILYDKYLEPDQKYDYQIMMELGYSHRQYYRIKKRALLRFAT 127 (132)
T ss_pred CCHHHHHHHHHHHcCccccchHHHHHHhCCcHHHHHHHHHHHHHHHHH
Confidence 666788888888886 36778899999999999999887777666654
No 400
>PRK11074 putative DNA-binding transcriptional regulator; Provisional
Probab=29.36 E-value=59 Score=30.39 Aligned_cols=39 Identities=10% Similarity=0.026 Sum_probs=30.9
Q ss_pred HHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 79 LAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 79 l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
+-+|+. ++.-.++...|...++|+++||+.+++.-+.+.
T Consensus 7 L~~f~~-v~e~~s~s~AA~~L~isQpavS~~I~~LE~~lg 45 (300)
T PRK11074 7 LEVVDA-VARTGSFSAAAQELHRVPSAVSYTVRQLEEWLA 45 (300)
T ss_pred HHHHHH-HHHhCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 333333 333458999999999999999999999998885
No 401
>PRK10216 DNA-binding transcriptional regulator YidZ; Provisional
Probab=29.10 E-value=59 Score=30.78 Aligned_cols=32 Identities=3% Similarity=0.003 Sum_probs=28.2
Q ss_pred ccccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 87 GHNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 87 ~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
+.-.++...|+..++|+|+||+.+++.-..+.
T Consensus 20 ~e~gs~t~AA~~L~iSQpavS~~I~~LE~~lg 51 (319)
T PRK10216 20 MQERSVTKAAKRMNVTPSAVSKSLAKLRAWFD 51 (319)
T ss_pred HHhCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 33458999999999999999999999999885
No 402
>PRK11564 stationary phase inducible protein CsiE; Provisional
Probab=29.01 E-value=96 Score=30.92 Aligned_cols=51 Identities=8% Similarity=0.150 Sum_probs=38.1
Q ss_pred CCCCCHHHHHHH-Hhhhc--ccccchhhhhhhcccchhhhhhhhHHHHHHHHHh
Q 016400 70 TNRIKIEEQLAI-FMFIV--GHNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 120 (390)
Q Consensus 70 ~~~~~~~~~l~~-~L~~L--~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 120 (390)
..-++.+++... .+..| ..+.+..++++.+.||++|+.+-++++-..|...
T Consensus 8 ~~~~s~~ER~~~il~~LL~~~~~v~l~~Lae~l~VSrsTi~~DLk~l~~~L~~y 61 (426)
T PRK11564 8 PSVLSAPQRRCQILLMLFQPGLTVTLETFSQLNGVDDDTARQDIAETGREIQRY 61 (426)
T ss_pred CcCCCHHHHHHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHHHHHHHHHHHh
Confidence 345777776443 33333 3457899999999999999999999998887654
No 403
>COG2973 TrpR Trp operon repressor [Transcription]
Probab=28.97 E-value=55 Score=25.47 Aligned_cols=27 Identities=26% Similarity=0.298 Sum_probs=23.1
Q ss_pred hcccccchhhhhhhcccchhhhhhhhH
Q 016400 85 IVGHNLRTRAVQELFRYSGETISRHFN 111 (390)
Q Consensus 85 ~L~~~~~~~~l~~~fgis~stv~~~~~ 111 (390)
.|....|+++++..+|+|-.|+.|=-+
T Consensus 56 LL~ge~sQREi~~~LgvsiAtITRGSN 82 (103)
T COG2973 56 LLRGELSQREIAQKLGVSIATITRGSN 82 (103)
T ss_pred HHhccccHHHHHHHhCcchhhhccchh
Confidence 577889999999999999999977433
No 404
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=28.95 E-value=32 Score=28.31 Aligned_cols=26 Identities=19% Similarity=0.166 Sum_probs=22.4
Q ss_pred cccccchhhhhhhcccchhhhhhhhH
Q 016400 86 VGHNLRTRAVQELFRYSGETISRHFN 111 (390)
Q Consensus 86 L~~~~~~~~l~~~fgis~stv~~~~~ 111 (390)
-..|.++.++|...|||.+||+++.+
T Consensus 15 ~~~gltq~~lA~~~gvs~~~is~~E~ 40 (135)
T PRK09706 15 KQLKLSQRSLAKAVKVSHVSISQWER 40 (135)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 34588899999999999999998764
No 405
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=28.50 E-value=45 Score=27.50 Aligned_cols=44 Identities=11% Similarity=-0.004 Sum_probs=35.7
Q ss_pred HHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHH
Q 016400 76 EEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMA 119 (390)
Q Consensus 76 ~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 119 (390)
.+....+..++..|.+.++++...||+.+++.++.+++...+..
T Consensus 76 ~~~~~~~~~~~~~~~~i~~~a~~l~i~~~~~~r~~~r~~~~~~~ 119 (129)
T COG3677 76 YKIKLQAVTLYMLGLGIRDIARTLGISINTVNRWSKRFGSRVEG 119 (129)
T ss_pred hHHHHHHHHHHHcCCCcccHHHHhcccHHHHHHHHHhhcchhhc
Confidence 44455556666778899999999999999999999999887753
No 406
>PF08148 DSHCT: DSHCT (NUC185) domain; InterPro: IPR012961 This C-terminal domain is found in DOB1/SK12/helY-like DEAD box helicases [].; GO: 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides; PDB: 4A4Z_A 2XGJ_B 3L9O_A.
Probab=28.48 E-value=57 Score=28.46 Aligned_cols=46 Identities=9% Similarity=0.119 Sum_probs=36.0
Q ss_pred HHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHHhhcc
Q 016400 78 QLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAISLD 123 (390)
Q Consensus 78 ~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~~~ 123 (390)
.++-..+.++.|.++.++-..-++..+.+-|+++++.+.|.++...
T Consensus 103 ~l~~~v~~Wa~G~~~~~i~~~t~l~EGdiVR~~rRl~dlLrql~~a 148 (180)
T PF08148_consen 103 GLMEVVYAWASGASFAEILEMTDLFEGDIVRWIRRLIDLLRQLANA 148 (180)
T ss_dssp TTHHHHHHHHCT--HHHHCCT-SS-HHHHHHHHHHHHHHHHHHHHH
T ss_pred cHHHHHHHHHCCCCHHHHHhcCCCCchHHHHHHHHHHHHHHHHHHH
Confidence 4556678889999999999999999999999999999999866544
No 407
>PRK09508 leuO leucine transcriptional activator; Reviewed
Probab=28.47 E-value=54 Score=30.95 Aligned_cols=39 Identities=8% Similarity=-0.050 Sum_probs=31.7
Q ss_pred HHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 80 AIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 80 ~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
+-.+..++...++...|+..++|++||++.+++.-..+.
T Consensus 27 L~~f~avae~gs~s~AA~~L~isQpavS~~I~~LE~~lg 65 (314)
T PRK09508 27 LTVFDAVMQEQNITRAAHNLGMSQPAVSNAVARLKVMFN 65 (314)
T ss_pred HHHHHHHHhcCCHHHHHHHhCCCHHHHHHHHHHHHHhhC
Confidence 334444455567999999999999999999999999885
No 408
>PRK09986 DNA-binding transcriptional activator XapR; Provisional
Probab=28.37 E-value=59 Score=30.06 Aligned_cols=40 Identities=15% Similarity=0.201 Sum_probs=31.9
Q ss_pred HHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 78 QLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 78 ~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
++-+|+....+ .++...|...+||+++||+.+++.-..+.
T Consensus 11 ~l~~f~~v~~~-gs~t~AA~~L~itq~avS~~i~~LE~~lg 50 (294)
T PRK09986 11 LLRYFLAVAEE-LHFGRAAARLNISQPPLSIHIKELEDQLG 50 (294)
T ss_pred HHHHHHHHHHh-cCHHHHHHHhCCCCCHHHHHHHHHHHHhC
Confidence 44444444444 48999999999999999999999999875
No 409
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=28.18 E-value=74 Score=26.37 Aligned_cols=27 Identities=7% Similarity=0.171 Sum_probs=22.4
Q ss_pred ccchhhhhhhcccchhhhhhhhHHHHH
Q 016400 89 NLRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 89 ~~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
..+..+++..+++|.+||++.+++...
T Consensus 22 ~~~~~ela~~l~vs~~svs~~l~~L~~ 48 (142)
T PRK03902 22 YARVSDIAEALSVHPSSVTKMVQKLDK 48 (142)
T ss_pred CcCHHHHHHHhCCChhHHHHHHHHHHH
Confidence 356788999999999999998876543
No 410
>COG5566 Uncharacterized conserved protein [Function unknown]
Probab=27.98 E-value=49 Score=27.02 Aligned_cols=28 Identities=14% Similarity=0.152 Sum_probs=24.8
Q ss_pred cccchhhhhhhcccchhhhhhhhHHHHH
Q 016400 88 HNLRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 88 ~~~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
.|..+.+++..+.+|..+|.++++++..
T Consensus 101 dG~n~~eLaKkYrlS~~~Iy~VIrr~~t 128 (137)
T COG5566 101 DGSNYVELAKKYRLSENHIYRVIRRTHT 128 (137)
T ss_pred CCccHHHHHHHhcccHHHHHHHHHHHHH
Confidence 3889999999999999999999996643
No 411
>PRK09801 transcriptional activator TtdR; Provisional
Probab=27.88 E-value=57 Score=30.85 Aligned_cols=41 Identities=10% Similarity=0.154 Sum_probs=32.5
Q ss_pred HHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 77 EQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 77 ~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
.++-.|+. ++.-.++...|+..++|++|||+.+++.-+.|-
T Consensus 9 ~~L~~F~~-v~~~gs~t~AA~~L~iSQpavS~~I~~LE~~LG 49 (310)
T PRK09801 9 KDLQVLVE-IVHSGSFSAAAATLGQTPAFVTKRIQILENTLA 49 (310)
T ss_pred HHHHHHHH-HHHcCCHHHHHHHhCcCHHHHHHHHHHHHHHhC
Confidence 44444444 444567999999999999999999999999885
No 412
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=27.80 E-value=74 Score=23.67 Aligned_cols=30 Identities=13% Similarity=0.267 Sum_probs=23.7
Q ss_pred ccccchhhhhhhcccchhhhhhhhHHHHHH
Q 016400 87 GHNLRTRAVQELFRYSGETISRHFNNVLNA 116 (390)
Q Consensus 87 ~~~~~~~~l~~~fgis~stv~~~~~~v~~~ 116 (390)
....++..+.+..|++.+++++.++...++
T Consensus 12 ~~~~~f~~L~~~l~lt~g~Ls~hL~~Le~~ 41 (80)
T PF13601_consen 12 NEEATFSELKEELGLTDGNLSKHLKKLEEA 41 (80)
T ss_dssp HSEEEHHHHHHHTT--HHHHHHHHHHHHHT
T ss_pred cCCCCHHHHHHHhCcCHHHHHHHHHHHHHC
Confidence 356899999999999999999988777653
No 413
>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=27.80 E-value=29 Score=24.75 Aligned_cols=22 Identities=18% Similarity=0.182 Sum_probs=15.9
Q ss_pred chhhhhhhcccchhhhh-hhhHH
Q 016400 91 RTRAVQELFRYSGETIS-RHFNN 112 (390)
Q Consensus 91 ~~~~l~~~fgis~stv~-~~~~~ 112 (390)
+..++|+..|||++|++ .+.++
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 45699999999999999 55544
No 414
>PRK10341 DNA-binding transcriptional activator TdcA; Provisional
Probab=27.70 E-value=55 Score=30.87 Aligned_cols=36 Identities=8% Similarity=0.022 Sum_probs=30.7
Q ss_pred hhhcccccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 83 MFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 83 L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
+.-++.-.++...|+..++|+++||+.+++.-+.+.
T Consensus 15 F~av~e~gs~s~AA~~L~iSQpavS~~I~~LE~~lg 50 (312)
T PRK10341 15 FQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFG 50 (312)
T ss_pred HHHHHHcCCHHHHHHHhCCChHHHHHHHHHHHHHhC
Confidence 344455678999999999999999999999999885
No 415
>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=27.59 E-value=37 Score=23.62 Aligned_cols=26 Identities=27% Similarity=0.267 Sum_probs=19.5
Q ss_pred ccccchhhhhhhcccchhhhhhhhHH
Q 016400 87 GHNLRTRAVQELFRYSGETISRHFNN 112 (390)
Q Consensus 87 ~~~~~~~~l~~~fgis~stv~~~~~~ 112 (390)
..|.++.++|...|+++++++++.+-
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 45788999999999999999987753
No 416
>TIGR03454 partition_RepB plasmid partitioning protein RepB. Members of this family are the RepB protein involved in replicon partitioning. RepB is found, in general, as part of a repABC operon in plasmids and small chromosomes, separate from the main chromosome, in various bacteria. This model describes a rather narrow clade of proteins; it should be noted that additional homologs scoring below the trusted cutoff have very similar functions, although they may be named differently.
Probab=27.58 E-value=69 Score=30.93 Aligned_cols=43 Identities=7% Similarity=0.089 Sum_probs=34.2
Q ss_pred CCCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHH
Q 016400 71 NRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNV 113 (390)
Q Consensus 71 ~~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v 113 (390)
..+|..++......++..|.+...++..+|+++++|++++.-.
T Consensus 159 ~dLS~iE~A~~~~~L~~~G~~~~~ia~~Lg~~ks~vSr~lsl~ 201 (325)
T TIGR03454 159 RDLSFIERALFAQRLEDRGFDRDTIMAALSVDKTELSRMISVA 201 (325)
T ss_pred cCCCHHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 3577777766666667788888899999999999999987543
No 417
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=27.39 E-value=45 Score=21.08 Aligned_cols=25 Identities=28% Similarity=0.251 Sum_probs=20.7
Q ss_pred ccccchhhhhhhcccchhhhhhhhH
Q 016400 87 GHNLRTRAVQELFRYSGETISRHFN 111 (390)
Q Consensus 87 ~~~~~~~~l~~~fgis~stv~~~~~ 111 (390)
..+.+..+++...|++.++++++.+
T Consensus 8 ~~~~s~~~la~~~~i~~~~i~~~~~ 32 (56)
T smart00530 8 EKGLTQEELAEKLGVSRSTLSRIEN 32 (56)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHC
Confidence 3577899999999999999987543
No 418
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=27.38 E-value=74 Score=28.65 Aligned_cols=33 Identities=9% Similarity=0.064 Sum_probs=29.2
Q ss_pred cccccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 86 VGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 86 L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
++.|.+..++|..+++|..||..++....+...
T Consensus 175 ~~~g~s~~eIA~~l~iS~~Tv~~~~~~~~~~~~ 207 (239)
T PRK10430 175 QDYEFSTDELANAVNISRVSCRKYLIWLVNCHI 207 (239)
T ss_pred CCCCcCHHHHHHHhCchHHHHHHHHHHHHhCCE
Confidence 468999999999999999999999998877643
No 419
>PRK09940 transcriptional regulator YdeO; Provisional
Probab=27.36 E-value=1.1e+02 Score=28.28 Aligned_cols=85 Identities=6% Similarity=0.156 Sum_probs=51.1
Q ss_pred HHHHHHHhcCChhHHHhhcCCCHHHHHHHHHHhccCCcc---ccCCCCCHHHHHH-HHhhhcccccchhhhhhhcccchh
Q 016400 29 MKFVDEVLNGQSERCLENFRMDKKVFYKLCDILQSKGLL---RHTNRIKIEEQLA-IFMFIVGHNLRTRAVQELFRYSGE 104 (390)
Q Consensus 29 ~~~~~~~~~~~d~~f~~~frms~~~F~~L~~~L~~~~~~---~~~~~~~~~~~l~-~~L~~L~~~~~~~~l~~~fgis~s 104 (390)
..|++.++..-..+-...-+++...|..|+..+...... ......+...++. +....++...+..++|..+|+|++
T Consensus 86 ~~~L~~ll~~l~~e~~~~~~l~~~ll~~lL~~l~~~~~~~~~l~~~~~~~~~kv~~~I~~~~~~~~tl~~LA~~~gmS~s 165 (253)
T PRK09940 86 TGLLNEMIAYLNSEERNHHNFSELLLFSCLSIFAACKGFITLLTNGVLSVSGKVRNIVNMKLAHPWKLKDICDCLYISES 165 (253)
T ss_pred HHHHHHHHHHHHhcchhhhHHHHHHHHHHHHHHHhCccHHHhhccccccHHHHHHHHHHHhhcCCCCHHHHHHHHCcCHH
Confidence 456666554222222222267777777777666542211 1122334334443 334456777899999999999999
Q ss_pred hhhhhhHHH
Q 016400 105 TISRHFNNV 113 (390)
Q Consensus 105 tv~~~~~~v 113 (390)
+.+|.|++.
T Consensus 166 ~l~R~FK~~ 174 (253)
T PRK09940 166 LLKKKLKQE 174 (253)
T ss_pred HHHHHHHHc
Confidence 999999873
No 420
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=27.29 E-value=70 Score=29.49 Aligned_cols=27 Identities=22% Similarity=0.165 Sum_probs=23.7
Q ss_pred ccchhhhhhhcccchhhhhhhhHHHHH
Q 016400 89 NLRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 89 ~~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
..+..++++.||+|++|+.|.++...+
T Consensus 19 ~~~~~ela~~l~vS~~TirRdL~~Le~ 45 (251)
T PRK13509 19 FVTVEKVIERLGISPATARRDINKLDE 45 (251)
T ss_pred CcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 367899999999999999999988655
No 421
>TIGR03339 phn_lysR aminoethylphosphonate catabolism associated LysR family transcriptional regulator. This group of sequences represents a number of related clades with numerous examples of members adjacent to operons for the degradation of 2-aminoethylphosphonate (AEP) in Pseudomonas, Ralstonia, Bordetella and Burkholderia species. These are transcriptional regulators of the LysR family which contain a helix-turn-helix (HTH) domain (pfam00126) and a periplasmic substrate-binding protein-like domain (pfam03466).
Probab=27.28 E-value=48 Score=30.27 Aligned_cols=34 Identities=12% Similarity=0.018 Sum_probs=29.4
Q ss_pred hcccccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 85 IVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 85 ~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
.++...++...|+..++|+|+||+.+++.-+.+.
T Consensus 7 ~v~~~gs~~~AA~~L~isqsavS~~i~~LE~~lg 40 (279)
T TIGR03339 7 AVARCGSFTRAAERLGLSQPTVTDQVRKLEERYG 40 (279)
T ss_pred HHHhcCCHHHHHHHhcCCchHHHHHHHHHHHHhC
Confidence 3444568999999999999999999999999875
No 422
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=27.16 E-value=60 Score=30.42 Aligned_cols=33 Identities=12% Similarity=0.123 Sum_probs=28.8
Q ss_pred cccccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 86 VGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 86 L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
++...++...|...++|+++||+.+++.-+.|.
T Consensus 16 v~e~gs~s~AA~~L~isqpavS~~i~~LE~~lg 48 (305)
T CHL00180 16 IATEGSFKKAAESLYISQPAVSLQIKNLEKQLN 48 (305)
T ss_pred HHHcCCHHHHHHHhcCCChHHHHHHHHHHHHhC
Confidence 333458999999999999999999999999885
No 423
>PRK03635 chromosome replication initiation inhibitor protein; Validated
Probab=26.76 E-value=70 Score=29.81 Aligned_cols=33 Identities=6% Similarity=0.054 Sum_probs=28.7
Q ss_pred cccccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 86 VGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 86 L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
++...++...|+..++|++++|+.+++.-..+-
T Consensus 13 v~e~gs~s~AA~~L~isq~avS~~I~~LE~~lg 45 (294)
T PRK03635 13 VVREGSFERAAQKLHITQSAVSQRIKALEERVG 45 (294)
T ss_pred HHHcCCHHHHHHHhCCChHHHHHHHHHHHHHhC
Confidence 333458999999999999999999999999885
No 424
>TIGR02684 dnstrm_HI1420 probable addiction module antidote protein. gene pairs, when found on the bacterial chromosome, are located often with prophage regions, but also both in integrated plasmid regions and in housekeeping gene regions. Analysis suggests that the gene pair may serve as an addiction module.
Probab=26.57 E-value=48 Score=25.36 Aligned_cols=20 Identities=10% Similarity=0.130 Sum_probs=16.7
Q ss_pred hhhhhhhcccchhhhhhhhH
Q 016400 92 TRAVQELFRYSGETISRHFN 111 (390)
Q Consensus 92 ~~~l~~~fgis~stv~~~~~ 111 (390)
+.++|..-|||++|++++.+
T Consensus 46 lSqLAe~~GIs~stLs~iE~ 65 (89)
T TIGR02684 46 MTQLARKTGLSRESLYKALS 65 (89)
T ss_pred hHHHHHHHCCCHHHHHHHHc
Confidence 33699999999999998764
No 425
>PRK15092 DNA-binding transcriptional repressor LrhA; Provisional
Probab=26.49 E-value=50 Score=31.32 Aligned_cols=42 Identities=10% Similarity=0.000 Sum_probs=34.3
Q ss_pred HHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 77 EQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 77 ~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
.+.+-.+..++...++...|+..+||++|||+.+++.-..+.
T Consensus 13 l~~L~~F~~v~e~gs~s~AA~~L~iSQpavS~~I~~LE~~lG 54 (310)
T PRK15092 13 LDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVG 54 (310)
T ss_pred HHHHHHHHHHHHcCCHHHHHHHhCCChHHHHHHHHHHHHHhC
Confidence 344445555666778999999999999999999999999885
No 426
>COG4496 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.46 E-value=44 Score=25.50 Aligned_cols=29 Identities=21% Similarity=0.104 Sum_probs=25.1
Q ss_pred hhhcccccchhhhhhhcccchhhhhhhhH
Q 016400 83 MFIVGHNLRTRAVQELFRYSGETISRHFN 111 (390)
Q Consensus 83 L~~L~~~~~~~~l~~~fgis~stv~~~~~ 111 (390)
..+|..|.+|+++...-|.|-.|++|+-+
T Consensus 50 a~mL~eg~tY~~I~~eTGaStaTIsRVkR 78 (100)
T COG4496 50 AKMLKEGRTYRDIEDETGASTATISRVKR 78 (100)
T ss_pred HHHHHcCCCcchhhhccCcchhhHHHHHH
Confidence 35678899999999999999999998543
No 427
>COG3311 AlpA Predicted transcriptional regulator [Transcription]
Probab=26.45 E-value=38 Score=24.76 Aligned_cols=23 Identities=30% Similarity=0.258 Sum_probs=19.4
Q ss_pred chhhhhhhcccchhhhhhhhHHH
Q 016400 91 RTRAVQELFRYSGETISRHFNNV 113 (390)
Q Consensus 91 ~~~~l~~~fgis~stv~~~~~~v 113 (390)
...++....|+|++|+++.++.-
T Consensus 15 rl~ev~~~~GlSrstiYr~i~~~ 37 (70)
T COG3311 15 RLPEVAQLTGLSRSTIYRLIKDG 37 (70)
T ss_pred hHHHHHHHHCccHHHHHHHHccC
Confidence 46788999999999999987654
No 428
>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]
Probab=26.44 E-value=92 Score=31.09 Aligned_cols=48 Identities=17% Similarity=0.171 Sum_probs=44.0
Q ss_pred CCCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 71 NRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 71 ~~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
+.+...-|++|.|-+--++.|+..++..||..-+||...++++.+.+.
T Consensus 347 ~~i~~~RqiamyL~r~lt~~Slp~IG~~FgrdHtTV~~a~~kI~~~~~ 394 (408)
T COG0593 347 RNIVRPRQIAMYLARELTNLSLPEIGKAFGRDHTTVLHAVRKIEQLIE 394 (408)
T ss_pred cccchHHHHHHHHHHHHccCcHHHHHHHhCCCccHHHHHHHHHHHHHh
Confidence 578888999999999999999999999999999999999999888775
No 429
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=26.40 E-value=77 Score=23.52 Aligned_cols=26 Identities=8% Similarity=0.212 Sum_probs=22.0
Q ss_pred cchhhhhhhcccchhhhhhhhHHHHH
Q 016400 90 LRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 90 ~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
.+..++|+..+++.+.+.+++....+
T Consensus 26 ~s~~eiA~~~~i~~~~l~kil~~L~~ 51 (83)
T PF02082_consen 26 VSSKEIAERLGISPSYLRKILQKLKK 51 (83)
T ss_dssp BEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHhh
Confidence 68999999999999999998877655
No 430
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=26.17 E-value=62 Score=29.88 Aligned_cols=37 Identities=11% Similarity=0.060 Sum_probs=30.4
Q ss_pred HhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 82 FMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 82 ~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
.+..++...++...|+..++|+++||+.+++.-..+.
T Consensus 10 ~f~~v~e~~s~t~AA~~L~isqpavS~~I~~LE~~lg 46 (290)
T PRK10837 10 VFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLG 46 (290)
T ss_pred HHHHHHHcCCHHHHHHHhCCCccHHHHHHHHHHHHhC
Confidence 3334444568999999999999999999999998875
No 431
>COG2826 Tra8 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]
Probab=25.67 E-value=64 Score=30.62 Aligned_cols=40 Identities=18% Similarity=0.283 Sum_probs=32.3
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHH
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNN 112 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~ 112 (390)
.++.+++..+-=+ +..|.|.++||...|.+.|||+|=+++
T Consensus 7 hLT~~eR~~I~~l-~~~~~S~reIA~~LgRh~sTIsRElkR 46 (318)
T COG2826 7 HLTLFERYEIERL-LKAKMSIREIAKQLNRHHSTISRELKR 46 (318)
T ss_pred hCCHHHHHHHHHH-HHcCCCHHHHHHHhCCCcchhhHHHhc
Confidence 5677777666433 478999999999999999999987654
No 432
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=25.41 E-value=77 Score=29.34 Aligned_cols=41 Identities=15% Similarity=0.237 Sum_probs=29.9
Q ss_pred HHHHHHHhhhccc--ccchhhhhhhcccchhhhhhhhHHHHHH
Q 016400 76 EEQLAIFMFIVGH--NLRTRAVQELFRYSGETISRHFNNVLNA 116 (390)
Q Consensus 76 ~~~l~~~L~~L~~--~~~~~~l~~~fgis~stv~~~~~~v~~~ 116 (390)
+++...-|-+|.. -.+..++++.|++|..||.|-+....+.
T Consensus 4 ~eR~~~Il~~L~~~~~v~v~eLa~~l~VS~~TIRRDL~~Le~~ 46 (256)
T PRK10434 4 RQRQAAILEYLQKQGKTSVEELAQYFDTTGTTIRKDLVILEHA 46 (256)
T ss_pred HHHHHHHHHHHHHcCCEEHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 3444444445543 2689999999999999999998886554
No 433
>TIGR02036 dsdC D-serine deaminase transcriptional activator. This family, part of the LysR family of transcriptional regulators, activates transcription of the gene for D-serine deaminase, dsdA. Trusted members of this family so far are found adjacent to dsdA and only in Gammaproteobacteria, including E. coli, Vibrio cholerae, and Colwellia psychrerythraea.
Probab=25.18 E-value=54 Score=30.79 Aligned_cols=36 Identities=11% Similarity=0.123 Sum_probs=30.3
Q ss_pred hhhcccccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 83 MFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 83 L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
+..++.-.++...|+..++|++|||+.++..-..|-
T Consensus 16 F~~va~~gs~s~AA~~L~isQpavS~~I~~LE~~lg 51 (302)
T TIGR02036 16 FEVAARHQSFSLAAEELSLTPSAISHRINQLEEELG 51 (302)
T ss_pred HHHHHHhCCHHHHHHHHCCCHHHHHHHHHHHHHHhC
Confidence 334455677999999999999999999999998885
No 434
>PF11198 DUF2857: Protein of unknown function (DUF2857); InterPro: IPR021364 This is a bacterial family of uncharacterised proteins.
Probab=25.05 E-value=4.4e+02 Score=22.95 Aligned_cols=82 Identities=15% Similarity=0.022 Sum_probs=53.5
Q ss_pred HHHHhc--CChhHHHhhcCCCHHHHHHHHHHhccCCccccC-CCCCHHHHHHHHhhhc----cccc----------chhh
Q 016400 32 VDEVLN--GQSERCLENFRMDKKVFYKLCDILQSKGLLRHT-NRIKIEEQLAIFMFIV----GHNL----------RTRA 94 (390)
Q Consensus 32 ~~~~~~--~~d~~f~~~frms~~~F~~L~~~L~~~~~~~~~-~~~~~~~~l~~~L~~L----~~~~----------~~~~ 94 (390)
+++.+. .+-+--..+||||...+...=..|.-... +++ +.++.++...+--.|- ..+. -+..
T Consensus 80 idr~L~lGAS~~mm~~~FGls~~ev~~rR~llgi~~~-~GR~~~~~ee~~~~iW~~W~~~~~~~~~~~~~~~~~Le~~m~ 158 (180)
T PF11198_consen 80 IDRALRLGASIEMMQRLFGLSSAEVAARRRLLGIPVR-KGRPPALSEEEEAAIWRRWQQLMKKRGVDNLDSPDALELMML 158 (180)
T ss_pred HHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHhCCCCC-CCCCCCcCHHHHHHHHHHHHHHHhhcCCCCccchHHHHHHHH
Confidence 444443 56677778999999999888888865432 223 3455555555544443 1221 1334
Q ss_pred hhhhcccchhhhhhhhHHHH
Q 016400 95 VQELFRYSGETISRHFNNVL 114 (390)
Q Consensus 95 l~~~fgis~stv~~~~~~v~ 114 (390)
+|+..++|-++|...++.+.
T Consensus 159 ~Ae~~~isL~~iW~~i~~w~ 178 (180)
T PF11198_consen 159 LAEETNISLTVIWSLIQEWE 178 (180)
T ss_pred HHHHhCCCHHHHHHHHHHHH
Confidence 88999999999988887765
No 435
>PRK10632 transcriptional regulator; Provisional
Probab=24.98 E-value=59 Score=30.65 Aligned_cols=34 Identities=15% Similarity=0.056 Sum_probs=29.5
Q ss_pred hcccccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 85 IVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 85 ~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
.++...++...|+..++|+++||+.+++.-+.+-
T Consensus 12 ~v~e~gS~t~AA~~L~isQpavS~~I~~LE~~lg 45 (309)
T PRK10632 12 KVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQ 45 (309)
T ss_pred HHHhcCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 3445678999999999999999999999998874
No 436
>PRK13832 plasmid partitioning protein; Provisional
Probab=24.81 E-value=90 Score=31.97 Aligned_cols=41 Identities=10% Similarity=0.021 Sum_probs=36.1
Q ss_pred CCCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhH
Q 016400 71 NRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFN 111 (390)
Q Consensus 71 ~~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~ 111 (390)
..+++.++...+-.++..|.+..+||..||+|+++|.+...
T Consensus 100 edL~PiEea~AfkrLie~G~T~EeIA~~lG~S~~~V~rlll 140 (520)
T PRK13832 100 EPLNPVDQWRAIERLVALGWTEEAIAVALALPVRQIRKLRL 140 (520)
T ss_pred CCCCHHHHHHHHHHHHhcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 46889899888888889999999999999999999997433
No 437
>TIGR03384 betaine_BetI transcriptional repressor BetI. BetI is a DNA-binding transcriptional repressor of the bet (betaine) regulon. In sequence, it is related to TetR (pfam00440). Choline, through BetI, induces the expression of the betaine biosynthesis genes betA and betB by derepression. The choline porter gene betT is also part of this regulon in Escherichia coli. Note that a different transcriptional regulator, ArcA, controls the expression of bet regulon genes in response to oxygen, as BetA is an oxygen-dependent enzyme.
Probab=24.72 E-value=73 Score=27.19 Aligned_cols=33 Identities=15% Similarity=0.096 Sum_probs=27.3
Q ss_pred cccchhhhhhhcccchhhhhhhhHHHHHHHHHh
Q 016400 88 HNLRTRAVQELFRYSGETISRHFNNVLNAIMAI 120 (390)
Q Consensus 88 ~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~ 120 (390)
++.+.++|+..-|+|+++++++|..--..+.++
T Consensus 27 ~~~s~~~IA~~agvsk~~ly~~F~sK~~L~~~~ 59 (189)
T TIGR03384 27 LDVTIAQIARRAGVSSGIISHYFGGKQGLLEAT 59 (189)
T ss_pred ccCCHHHHHHHhCCCHHHHHHHcCCHHHHHHHH
Confidence 468999999999999999999997666655443
No 438
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=24.31 E-value=47 Score=23.42 Aligned_cols=23 Identities=17% Similarity=0.091 Sum_probs=18.6
Q ss_pred chhhhhhhcccchhhhhhhhHHH
Q 016400 91 RTRAVQELFRYSGETISRHFNNV 113 (390)
Q Consensus 91 ~~~~l~~~fgis~stv~~~~~~v 113 (390)
+..++|..+|||.+|+..+.++.
T Consensus 2 ti~eva~~~gvs~~tlr~y~~~g 24 (69)
T PF13411_consen 2 TIKEVAKLLGVSPSTLRYYEREG 24 (69)
T ss_dssp EHHHHHHHTTTTHHHHHHHHHTT
T ss_pred cHHHHHHHHCcCHHHHHHHHHhc
Confidence 35689999999999999876543
No 439
>PRK04841 transcriptional regulator MalT; Provisional
Probab=24.09 E-value=60 Score=35.68 Aligned_cols=45 Identities=11% Similarity=0.153 Sum_probs=35.8
Q ss_pred CCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 72 RIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 72 ~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
.+|..|.- .|.+++.|.++++|+...+||.+||..+++++..-|.
T Consensus 838 ~lt~~e~~--v~~~~~~g~~~~~ia~~l~~s~~tv~~h~~~~~~kl~ 882 (903)
T PRK04841 838 PLTQREWQ--VLGLIYSGYSNEQIAGELDVAATTIKTHIRNLYQKLG 882 (903)
T ss_pred CCCHHHHH--HHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 35554443 3445889999999999999999999999998877663
No 440
>PF09182 PuR_N: Bacterial purine repressor, N-terminal; InterPro: IPR015265 The N-terminal domain of the bacterial purine repressor PuR is a winged-helix domain, a subdivision of the HTH structural family. It consists of a canonical arrangement of secondary structures: a1-b1-a2-T-a3-b2-W-b3, where a2-T-a3 is the HTH motif, a3 is the recognition helix, and W is the wing. The domain allows for recognition of a conserved CGAA sequence in the centre of a DNA PurBox, resulting in binding to the major groove of DNA []. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1O57_B 1P4A_D.
Probab=24.01 E-value=1.5e+02 Score=21.62 Aligned_cols=30 Identities=13% Similarity=0.156 Sum_probs=21.7
Q ss_pred cchhhhhhhcccchhhhhhhhHHHHHHHHH
Q 016400 90 LRTRAVQELFRYSGETISRHFNNVLNAIMA 119 (390)
Q Consensus 90 ~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 119 (390)
.+....+++|+.++||+|+=+.-+-+++.+
T Consensus 21 isL~~Fae~f~~AKSsISEDl~iik~~~~~ 50 (70)
T PF09182_consen 21 ISLTYFAERFGAAKSSISEDLSIIKETFEK 50 (70)
T ss_dssp EEHHHHHHHHT--HHHHHHHHHHHHHHHHH
T ss_pred EcHHHHHHHhcccccchHHHHHHHHHHHHH
Confidence 467788999999999999877666666543
No 441
>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B.
Probab=24.00 E-value=46 Score=23.48 Aligned_cols=25 Identities=12% Similarity=0.167 Sum_probs=18.2
Q ss_pred chhhhhhhcccchhhhhhhhHHHHHH
Q 016400 91 RTRAVQELFRYSGETISRHFNNVLNA 116 (390)
Q Consensus 91 ~~~~l~~~fgis~stv~~~~~~v~~~ 116 (390)
+...+|..+|||+++|+.+ ...+.+
T Consensus 11 ~~~~lAkalGVs~~aVs~W-~~~IP~ 35 (60)
T PF14549_consen 11 GQSKLAKALGVSPQAVSQW-GERIPA 35 (60)
T ss_dssp SHHHHHHHHTS-HHHHHHH-HTS--H
T ss_pred CHHHHHHHHCCCHHHHHHh-cCccCH
Confidence 4678999999999999999 444444
No 442
>PF02295 z-alpha: Adenosine deaminase z-alpha domain; InterPro: IPR000607 Double-stranded RNA-specific adenosine deaminase (3.5 from EC) converts multiple adenosines to inosines and creates I/U mismatched base pairs in double-helical RNA substrates without apparent sequence specificity. DRADA has been found to modify adenosines in AU-rich regions more frequently, probably due to the relative ease of melting A/U base pairs compared to G/C base pairs. The protein functions to modify viral RNA genomes, and may be responsible for hypermutation of certain negative-stranded viruses. DRADA edits the mRNAs for the glutamate receptor subunits by site-selective adenosine deamination. The DRADA repeat is also found in viral E3 proteins, which contain a double-stranded RNA-binding domain.; GO: 0003723 RNA binding, 0003726 double-stranded RNA adenosine deaminase activity; PDB: 1OYI_A 3EYI_A 2L4M_A 2HEO_D 1J75_A 1SFU_B 3IRR_B 2ACJ_C 3F22_B 2L54_A ....
Probab=23.74 E-value=87 Score=22.46 Aligned_cols=38 Identities=18% Similarity=0.334 Sum_probs=27.6
Q ss_pred HHHHHHHHhhhcccccchhhhhhhcccc--hhhhhhhhHHH
Q 016400 75 IEEQLAIFMFIVGHNLRTRAVQELFRYS--GETISRHFNNV 113 (390)
Q Consensus 75 ~~~~l~~~L~~L~~~~~~~~l~~~fgis--~stv~~~~~~v 113 (390)
.+++++-+|.-++ +.+...++...|++ +..|.+++.+.
T Consensus 5 ~ee~Il~~L~~~g-~~~a~~ia~~~~L~~~kk~VN~~LY~L 44 (66)
T PF02295_consen 5 LEEKILDFLKELG-GSTATAIAKALGLSVPKKEVNRVLYRL 44 (66)
T ss_dssp HHHHHHHHHHHHT-SSEEEHHHHHHHHTS-HHHHHHHHHHH
T ss_pred HHHHHHHHHHhcC-CccHHHHHHHhCcchhHHHHHHHHHHH
Confidence 5788999999999 77777777766665 67666655444
No 443
>cd00093 HTH_XRE Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.
Probab=23.68 E-value=53 Score=20.91 Aligned_cols=25 Identities=32% Similarity=0.267 Sum_probs=21.1
Q ss_pred ccccchhhhhhhcccchhhhhhhhH
Q 016400 87 GHNLRTRAVQELFRYSGETISRHFN 111 (390)
Q Consensus 87 ~~~~~~~~l~~~fgis~stv~~~~~ 111 (390)
..|.+..+++...|++..+++++.+
T Consensus 10 ~~~~s~~~~a~~~~~~~~~v~~~~~ 34 (58)
T cd00093 10 EKGLTQEELAEKLGVSRSTISRIEN 34 (58)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHc
Confidence 3578899999999999999988654
No 444
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=23.64 E-value=79 Score=29.15 Aligned_cols=37 Identities=11% Similarity=0.072 Sum_probs=31.2
Q ss_pred HhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 82 FMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 82 ~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
.+..++.-.++...|...++|++++|+.+++.-..+.
T Consensus 8 ~f~~v~~~gs~s~AA~~L~isqpavS~~I~~LE~~lG 44 (275)
T PRK03601 8 TFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLG 44 (275)
T ss_pred HHHHHHHcCCHHHHHHHhCCChHHHHHHHHHHHHHhC
Confidence 3444555678999999999999999999999999885
No 445
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=23.50 E-value=46 Score=26.31 Aligned_cols=23 Identities=13% Similarity=0.104 Sum_probs=18.7
Q ss_pred ccccchhhhhhhcccchhhhhhh
Q 016400 87 GHNLRTRAVQELFRYSGETISRH 109 (390)
Q Consensus 87 ~~~~~~~~l~~~fgis~stv~~~ 109 (390)
+.+.|+.+.|..+|+|.+||..|
T Consensus 55 ~~~lSQ~vFA~~L~vs~~Tv~~W 77 (104)
T COG2944 55 KLGLSQPVFARYLGVSVSTVRKW 77 (104)
T ss_pred HhCCCHHHHHHHHCCCHHHHHHH
Confidence 45788888888889998888864
No 446
>TIGR02404 trehalos_R_Bsub trehalose operon repressor, B. subtilis-type. This family consists of repressors of the GntR family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gram-positive lineages and does not include the TreR from E. coli.
Probab=23.32 E-value=56 Score=29.52 Aligned_cols=23 Identities=17% Similarity=0.302 Sum_probs=17.9
Q ss_pred hhhhhhcccchhhhhhhhHHHHH
Q 016400 93 RAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 93 ~~l~~~fgis~stv~~~~~~v~~ 115 (390)
.+|+..||||+.||.+.+.....
T Consensus 28 ~eLa~~~gVSR~TVR~Al~~L~~ 50 (233)
T TIGR02404 28 HELMDQYGASRETVRKALNLLTE 50 (233)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHH
Confidence 45678999999999987765544
No 447
>PRK09480 slmA division inhibitor protein; Provisional
Probab=23.24 E-value=53 Score=28.26 Aligned_cols=32 Identities=16% Similarity=0.200 Sum_probs=27.4
Q ss_pred cccchhhhhhhcccchhhhhhhhHHHHHHHHH
Q 016400 88 HNLRTRAVQELFRYSGETISRHFNNVLNAIMA 119 (390)
Q Consensus 88 ~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 119 (390)
++.+.++|+..-|||++|++++|..--..+..
T Consensus 29 ~~~ti~~Ia~~agvs~gt~Y~~F~~K~~L~~~ 60 (194)
T PRK09480 29 ERITTAKLAARVGVSEAALYRHFPSKARMFEG 60 (194)
T ss_pred CccCHHHHHHHhCCCHhHHHHHCCCHHHHHHH
Confidence 68999999999999999999999886665433
No 448
>PF12833 HTH_18: Helix-turn-helix domain; PDB: 2K9S_A 3LSG_C 3OIO_A 1D5Y_B 3GBG_A 3OOU_A 1BL0_A 1XS9_A 3MN2_B 3MKL_B ....
Probab=23.15 E-value=1.5e+02 Score=21.47 Aligned_cols=66 Identities=14% Similarity=0.201 Sum_probs=38.7
Q ss_pred hhcCCCHHHHHHHHHHhccCCccccCCCCCHHHHHHHHhhhc-c-cccchhhhhhhcccc-hhhhhhhhHHHH
Q 016400 45 ENFRMDKKVFYKLCDILQSKGLLRHTNRIKIEEQLAIFMFIV-G-HNLRTRAVQELFRYS-GETISRHFNNVL 114 (390)
Q Consensus 45 ~~frms~~~F~~L~~~L~~~~~~~~~~~~~~~~~l~~~L~~L-~-~~~~~~~l~~~fgis-~stv~~~~~~v~ 114 (390)
+.++|++..|.+++........ ...--..++..+...| . .+.+..+++..+|-+ .+..++.|++..
T Consensus 3 ~~~~~s~~~l~~~f~~~~g~s~----~~~~~~~R~~~a~~~L~~~~~~~i~~ia~~~Gf~~~~~f~~~fk~~~ 71 (81)
T PF12833_consen 3 DELGMSERYLSRIFKKETGMSF----KQYLRELRLQRAKELLRQNTDLSIAEIAEECGFSSQSHFSRAFKRYF 71 (81)
T ss_dssp HHCTS-HHHHHHHHHHHHSS-H----HHHHHHHHHHHHHHHHHHHTT--HHHHHHHTT-SSHHHHHHHHHHHH
T ss_pred HHhCcCHHHHHHHHHHHHCcCH----HHHHHHHHHHHHHHHHHHhhcccHHHHHHHcCCCCHHHHHHHHHHHH
Confidence 4567777777777777543211 0122235566666666 3 688999999999977 555667666553
No 449
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=23.12 E-value=76 Score=26.70 Aligned_cols=33 Identities=15% Similarity=0.130 Sum_probs=28.6
Q ss_pred hcccccchhhhhhhcccchhhhhhhhHHHHHHH
Q 016400 85 IVGHNLRTRAVQELFRYSGETISRHFNNVLNAI 117 (390)
Q Consensus 85 ~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l 117 (390)
.+..|.++..++..+++|..||..++.+....|
T Consensus 152 ~~~~~~~~~~ia~~l~~s~~tv~~~~~~~~~kl 184 (202)
T PRK09390 152 GLVAGLSNKVIARDLDISPRTVEVYRANVMTKM 184 (202)
T ss_pred HHHccCchHHHHHHcCCCHHHHHHHHHHHHHHH
Confidence 355678899999999999999999998887776
No 450
>PRK15340 transcriptional regulator InvF; Provisional
Probab=23.10 E-value=81 Score=28.51 Aligned_cols=29 Identities=17% Similarity=0.106 Sum_probs=25.5
Q ss_pred ccccchhhhhhhcccchhhhhhhhHHHHH
Q 016400 87 GHNLRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 87 ~~~~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
....+..++|..+|+|.++++|.|++.+.
T Consensus 123 ~~~~sleeLA~~~gvS~r~f~RlFk~~~G 151 (216)
T PRK15340 123 TSGNTMRMLGEDYGVSYTHFRRLCSRALG 151 (216)
T ss_pred cCCCCHHHHHHHHCcCHHHHHHHHHHHHC
Confidence 45678999999999999999999998754
No 451
>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=23.06 E-value=49 Score=28.09 Aligned_cols=27 Identities=0% Similarity=-0.081 Sum_probs=23.8
Q ss_pred hcccccchhhhhhhcccchhhhhhhhH
Q 016400 85 IVGHNLRTRAVQELFRYSGETISRHFN 111 (390)
Q Consensus 85 ~L~~~~~~~~l~~~fgis~stv~~~~~ 111 (390)
+-..|.+..++|...|||++||+++-+
T Consensus 34 R~~lGmTq~eLAerlGVS~~tIs~iE~ 60 (150)
T TIGR02612 34 RKALGMSGAQLAGRLGVTPQRVEALEK 60 (150)
T ss_pred HHHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 556789999999999999999998764
No 452
>PRK01905 DNA-binding protein Fis; Provisional
Probab=22.85 E-value=97 Score=22.83 Aligned_cols=26 Identities=8% Similarity=0.111 Sum_probs=21.4
Q ss_pred cccchhhhhhhcccchhhhhhhhHHH
Q 016400 88 HNLRTRAVQELFRYSGETISRHFNNV 113 (390)
Q Consensus 88 ~~~~~~~l~~~fgis~stv~~~~~~v 113 (390)
++......|...|||++|+.+.+++.
T Consensus 49 ~~gn~s~aAr~LGIsrstL~rklkk~ 74 (77)
T PRK01905 49 AGGNQSLAAEYLGINRNTLRKKLQQH 74 (77)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHh
Confidence 45568889999999999999887753
No 453
>PF05584 Sulfolobus_pRN: Sulfolobus plasmid regulatory protein; InterPro: IPR008848 This family consists of several plasmid regulatory proteins from the extreme thermophilic and acidophilic archaea Sulfolobus.
Probab=22.69 E-value=1.6e+02 Score=21.62 Aligned_cols=41 Identities=10% Similarity=0.115 Sum_probs=30.8
Q ss_pred CCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHH
Q 016400 73 IKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 73 ~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
+++.+.+++.|..= +.+...+-...|+++.++..++.+..+
T Consensus 4 lt~~~~IL~~ls~~--c~TLeeL~ekTgi~k~~LlV~LsrL~k 44 (72)
T PF05584_consen 4 LTVTQKILIILSKR--CCTLEELEEKTGISKNTLLVYLSRLAK 44 (72)
T ss_pred hhHHHHHHHHHHhc--cCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 45555555555433 788999999999999999988877654
No 454
>TIGR03734 PRTRC_parB PRTRC system ParB family protein. A novel genetic system characterized by six major proteins, included a ParB homolog and a ThiF homolog, is designated PRTRC, or ParB-Related,ThiF-Related Cassette. It is often found on plasmids. This protein family the member related to ParB, and is designated PRTRC system ParB family protein.
Probab=22.69 E-value=92 Score=32.37 Aligned_cols=42 Identities=12% Similarity=0.144 Sum_probs=35.4
Q ss_pred CCCCHHHHHHHHhhhccccc-chhhhhhhcccchhhhhhhhHH
Q 016400 71 NRIKIEEQLAIFMFIVGHNL-RTRAVQELFRYSGETISRHFNN 112 (390)
Q Consensus 71 ~~~~~~~~l~~~L~~L~~~~-~~~~l~~~fgis~stv~~~~~~ 112 (390)
..+++.++...+...+..+. +..+++..||+|+++|.+.+.-
T Consensus 90 edLtP~EeA~A~~rLl~~g~~t~eeIA~~lG~S~~~V~rrLkL 132 (554)
T TIGR03734 90 ADMSPAEEAEAAARLLGRCKGDREEAARRLGWSPATLDRRLAL 132 (554)
T ss_pred CCCCHHHHHHHHHHHhhhcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 46888888888888887776 8899999999999999987653
No 455
>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator). This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.
Probab=22.65 E-value=93 Score=25.15 Aligned_cols=27 Identities=7% Similarity=0.115 Sum_probs=23.7
Q ss_pred ccchhhhhhhcccchhhhhhhhHHHHH
Q 016400 89 NLRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 89 ~~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
..+..+++..++++.+++.+++.....
T Consensus 25 ~~s~~eia~~~~i~~~~v~~il~~L~~ 51 (132)
T TIGR00738 25 PVSVKEIAERQGISRSYLEKILRTLRR 51 (132)
T ss_pred cCcHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 578999999999999999998877665
No 456
>PF07900 DUF1670: Protein of unknown function (DUF1670); InterPro: IPR012872 The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=22.56 E-value=4.3e+02 Score=23.92 Aligned_cols=81 Identities=14% Similarity=0.089 Sum_probs=58.2
Q ss_pred CChhHHHhhcCCCHHHHHHHHHHhccC-CccccC------CCCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhh
Q 016400 38 GQSERCLENFRMDKKVFYKLCDILQSK-GLLRHT------NRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHF 110 (390)
Q Consensus 38 ~~d~~f~~~frms~~~F~~L~~~L~~~-~~~~~~------~~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~ 110 (390)
.+..+.-..++.|..+....+..++.. ...-.+ -+-++-.+-.+.=.+|. |.+..+++..-.+|..+|-|++
T Consensus 106 LT~~Dla~LL~~S~~TI~~~i~~yq~e~g~vvPtrG~i~DiGp~~tHK~~ii~~~l~-g~~~~eiar~t~HS~~av~rYi 184 (220)
T PF07900_consen 106 LTQEDLAMLLGISPRTISKDIKEYQKEHGVVVPTRGTIHDIGPGVTHKKIIIRLYLK-GKPTPEIARRTNHSPEAVDRYI 184 (220)
T ss_pred ccHHHHHHHHCCCHHHHHHHHHHHHHHcCceeccCCcccccCCcchHHHHHHHHHHc-CCCHHHHHHHhccCHHHHHHHH
Confidence 366777788999999999999998865 222111 13333333333222443 7899999999999999999999
Q ss_pred HHHHHHHHH
Q 016400 111 NNVLNAIMA 119 (390)
Q Consensus 111 ~~v~~~l~~ 119 (390)
+.|..+..-
T Consensus 185 ~~F~rV~~l 193 (220)
T PF07900_consen 185 KDFKRVLML 193 (220)
T ss_pred HhhHHhHHH
Confidence 999998753
No 457
>PRK15121 right oriC-binding transcriptional activator; Provisional
Probab=22.47 E-value=1.1e+02 Score=28.58 Aligned_cols=29 Identities=24% Similarity=0.285 Sum_probs=24.3
Q ss_pred cccccchhhhhhhcccchhhhhhhhHHHH
Q 016400 86 VGHNLRTRAVQELFRYSGETISRHFNNVL 114 (390)
Q Consensus 86 L~~~~~~~~l~~~fgis~stv~~~~~~v~ 114 (390)
|..+.+..++|..+|+|+.+++|.|+..+
T Consensus 18 ~~~~~~l~~lA~~~~~S~~~l~r~F~~~~ 46 (289)
T PRK15121 18 LDQPLSLDNVAAKAGYSKWHLQRMFKDVT 46 (289)
T ss_pred ccCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 34457788999999999999999999873
No 458
>PF00376 MerR: MerR family regulatory protein; InterPro: IPR000551 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these is the MerR subfamily. MerR, which is found in many bacterial species mediates the mercuric-dependent induction of the mercury resistance operon. In the absence of mercury merR represses transcription by binding tightly, as a dimer, to the 'mer' operator region; when mercury is present the dimeric complex binds a single ion and becomes a potent transcriptional activator, while remaining bound to the mer site. Members of the family include the mercuric resistance operon regulatory protein merR; Bacillus subtilis bltR and bmrR; Bacillus glnR; Streptomyces coelicolor hspR; Bradyrhizobium japonicum nolA; Escherichia coli superoxide response regulator soxR; and Streptomyces lividans transcriptional activator tipA [, , , , , ]. Other members include hypothetical proteins from E. coli, B. subtilis and Haemophilus influenzae. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3HH0_A 2DG6_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q07_A 1Q06_A 1Q05_B ....
Probab=22.41 E-value=54 Score=20.64 Aligned_cols=19 Identities=21% Similarity=0.088 Sum_probs=14.3
Q ss_pred hhhhhhhcccchhhhhhhh
Q 016400 92 TRAVQELFRYSGETISRHF 110 (390)
Q Consensus 92 ~~~l~~~fgis~stv~~~~ 110 (390)
..++|..+|||.+|+..+-
T Consensus 2 i~e~A~~~gvs~~tlR~ye 20 (38)
T PF00376_consen 2 IGEVAKLLGVSPRTLRYYE 20 (38)
T ss_dssp HHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHCCCHHHHHHHH
Confidence 3578999999999987653
No 459
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=22.14 E-value=96 Score=27.16 Aligned_cols=27 Identities=19% Similarity=0.068 Sum_probs=23.6
Q ss_pred cchhhhhhhcccchhhhhhhhHHHHHH
Q 016400 90 LRTRAVQELFRYSGETISRHFNNVLNA 116 (390)
Q Consensus 90 ~~~~~l~~~fgis~stv~~~~~~v~~~ 116 (390)
.+..++++.|++|.+|+.|=+......
T Consensus 22 ~~~~~La~~~~vS~~TiRRDl~~L~~~ 48 (185)
T PRK04424 22 ITDEELAEKFGVSIQTIRLDRMELGIP 48 (185)
T ss_pred EEHHHHHHHHCcCHHHHHHHHHHHhcc
Confidence 678999999999999999988877653
No 460
>PRK13698 plasmid-partitioning protein; Provisional
Probab=22.14 E-value=75 Score=30.57 Aligned_cols=39 Identities=18% Similarity=0.077 Sum_probs=27.8
Q ss_pred CCHHHH-HHHHhhhc-ccccchhhhhhhcccchhhhhhhhH
Q 016400 73 IKIEEQ-LAIFMFIV-GHNLRTRAVQELFRYSGETISRHFN 111 (390)
Q Consensus 73 ~~~~~~-l~~~L~~L-~~~~~~~~l~~~fgis~stv~~~~~ 111 (390)
+++.|. ....-... ..|.++.++|...|+|+++|++.++
T Consensus 158 ls~iE~A~ay~~~L~~~~~~tQeeLA~~lG~SRs~Vsn~Lr 198 (323)
T PRK13698 158 TSAYERGLRYASRLQNEFAGNISALADAENISRKIITRCIN 198 (323)
T ss_pred CCHHHHHHHHHHHHHHhcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 455444 33322223 5678999999999999999998775
No 461
>PRK10086 DNA-binding transcriptional regulator DsdC; Provisional
Probab=22.05 E-value=85 Score=29.55 Aligned_cols=38 Identities=5% Similarity=0.059 Sum_probs=31.5
Q ss_pred HHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 81 IFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 81 ~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
-.+..++...++...|...++|++|||+.+++.-+.+.
T Consensus 20 ~~f~~va~~gs~s~AA~~L~iSQpavS~~I~~LE~~lG 57 (311)
T PRK10086 20 HTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELG 57 (311)
T ss_pred HHHHHHHHcCCHHHHHHHHCCCHHHHHHHHHHHHHHhC
Confidence 33444555678999999999999999999999999885
No 462
>PF07506 RepB: RepB plasmid partitioning protein; InterPro: IPR011111 This family includes proteins with sequence similarity to the RepB partitioning protein of the large Ti (tumour-inducing) plasmids of Agrobacterium tumefaciens [, ].
Probab=21.98 E-value=1.4e+02 Score=26.15 Aligned_cols=41 Identities=7% Similarity=0.103 Sum_probs=36.8
Q ss_pred CCCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhH
Q 016400 71 NRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFN 111 (390)
Q Consensus 71 ~~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~ 111 (390)
+.+|..|+..+.......|.+-..|+...|++.+++++.+.
T Consensus 3 ~~Ls~IE~~~fa~~l~~~G~~~~~I~~aL~id~~~ls~~~~ 43 (185)
T PF07506_consen 3 RDLSFIERARFARRLEERGFSREEIAAALGIDKSYLSRMLS 43 (185)
T ss_pred ccCcHHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 46889999999999999999999999999999999976644
No 463
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=21.88 E-value=1e+02 Score=27.91 Aligned_cols=26 Identities=12% Similarity=0.150 Sum_probs=23.3
Q ss_pred cchhhhhhhcccchhhhhhhhHHHHH
Q 016400 90 LRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 90 ~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
.+..+++..+++|++|+++.+++..+
T Consensus 22 IS~~eLA~~L~iS~~Tvsr~Lk~LEe 47 (217)
T PRK14165 22 ISSSEFANHTGTSSKTAARILKQLED 47 (217)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 67999999999999999999887754
No 464
>PRK11482 putative DNA-binding transcriptional regulator; Provisional
Probab=21.86 E-value=86 Score=29.75 Aligned_cols=33 Identities=9% Similarity=0.050 Sum_probs=28.4
Q ss_pred cccccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 86 VGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 86 L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
++...++...|+..++|+++||+.+++.-..+-
T Consensus 40 v~e~gs~s~AA~~L~isQpavS~~I~~LE~~lG 72 (317)
T PRK11482 40 VYVHKGIVNAAKILNLTPSAISQSIQKLRVIFP 72 (317)
T ss_pred HHHcCCHHHHHHHhCCChHHHHHHHHHHHHHhC
Confidence 333458999999999999999999999998874
No 465
>PF02575 YbaB_DNA_bd: YbaB/EbfC DNA-binding family; InterPro: IPR004401 The function of this protein is unknown. It is restricted to bacteria and a few plants, such as Arabidopsis. The plant form contains an additional N-terminal region that may serve as a transit peptide and shows a close relationship to the cyanobacterial member, suggesting that it is a chloroplast protein. Members of this family are found in a single copy per bacterial genome, but are broadly distributed. A crystal structure of one member, YbaB from Haemophilus influenzae, revealed a core structure consisting of two layers, alpha/beta; YbaB forms a tight dimer with a 3-layer structure, beta/alpha/beta []. YbaB is co-transcribed with RecR, which appears to protect DNA strands of the replilcation fork when it is blocked by DNA damage. A deletion of the YbaB operon resulted in increased sensitivity to DNA-damaging agents compared with the wild-type strain.; PDB: 1PUG_B 3F42_B 1YBX_B 1J8B_A.
Probab=21.74 E-value=3.5e+02 Score=20.29 Aligned_cols=58 Identities=12% Similarity=0.002 Sum_probs=36.8
Q ss_pred eeeeeecCCcceeEeccCccccc-ccHHHHHHHHhhcCCCCCCCCceeeccCCCCCCCCccccccCcccCcccccCCCCC
Q 016400 180 NVLAACSFDLKFHYVLAGWEGSA-SDLRVLNSALTRRNKLQVPEGKYYLVDNKYANMPGFIAPYQAVSYHTNQTTTGYHP 258 (390)
Q Consensus 180 ~~q~v~d~d~~~~~v~~g~~Gs~-~D~~vl~~sl~~~~~~~~p~g~~~l~D~gYp~~~~ll~P~~~~~~~~~~~~~~~~~ 258 (390)
.|.+++|.+|.++.+.+.-..-. .|...|.+.+
T Consensus 31 ~V~V~v~g~g~v~~i~i~~~~~~~~~~~~L~~~I---------------------------------------------- 64 (93)
T PF02575_consen 31 LVTVTVNGNGEVVDIEIDPSALRPLDPEELEDLI---------------------------------------------- 64 (93)
T ss_dssp TEEEEEETTS-EEEEEE-GGGGCTS-HHHHHHHH----------------------------------------------
T ss_pred EEEEEEecCceEEEEEEehHhhccCCHHHHHHHH----------------------------------------------
Confidence 47788999999999888633333 4545444333
Q ss_pred hhhHHHHHHHHHHHHhHHHHHHHHHHhh
Q 016400 259 QDAKELFNQRHSLLRNATDRIFGALKER 286 (390)
Q Consensus 259 ~~~~~~fN~~~s~~R~~VE~~fg~LK~r 286 (390)
.+.+|.+...++..++..++-+-+-
T Consensus 65 ---~~A~n~A~~~a~~~~~~~~~~~~g~ 89 (93)
T PF02575_consen 65 ---VEAVNDAQKKAREKAQEEMAELTGG 89 (93)
T ss_dssp ---HHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred ---HHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 3467888888888777777666543
No 466
>PF04492 Phage_rep_O: Bacteriophage replication protein O ; InterPro: IPR006497 This entry is represented by the N-terminal domain of Bacteriophage lambda, GpO. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; GO: 0006260 DNA replication
Probab=21.67 E-value=1.4e+02 Score=23.47 Aligned_cols=39 Identities=10% Similarity=0.245 Sum_probs=28.1
Q ss_pred HHHHHHhhhcccc-------cchhhhhhhcccchhhhhhhhHHHHH
Q 016400 77 EQLAIFMFIVGHN-------LRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 77 ~~l~~~L~~L~~~-------~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
.++++++++..+| .+..+++..-|+|+.+|++.++.+++
T Consensus 35 ~ki~~ai~RkTyG~nKk~d~Is~sq~~e~tg~~~~~V~~al~~Li~ 80 (100)
T PF04492_consen 35 LKILLAIIRKTYGWNKKMDRISNSQIAEMTGLSRDHVSKALNELIR 80 (100)
T ss_pred HHHHHHHHHHccCCCCccceeeHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4677777777655 35667888889999988887766654
No 467
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=21.59 E-value=55 Score=26.51 Aligned_cols=25 Identities=12% Similarity=0.025 Sum_probs=22.0
Q ss_pred ccccchhhhhhhcccchhhhhhhhH
Q 016400 87 GHNLRTRAVQELFRYSGETISRHFN 111 (390)
Q Consensus 87 ~~~~~~~~l~~~fgis~stv~~~~~ 111 (390)
..|.+..++|...|+|++|++++.+
T Consensus 16 ~~Glsq~eLA~~~Gis~~~is~iE~ 40 (120)
T PRK13890 16 ERHMTKKELSERSGVSISFLSDLTT 40 (120)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHc
Confidence 4578999999999999999998765
No 468
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=21.49 E-value=1.2e+02 Score=28.91 Aligned_cols=27 Identities=15% Similarity=0.114 Sum_probs=23.3
Q ss_pred ccchhhhhhhcccchhhhhhhhHHHHH
Q 016400 89 NLRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 89 ~~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
..+..++|+.+|+|++||++.++....
T Consensus 18 ~~s~~~LA~~lgvsr~tV~~~l~~L~~ 44 (319)
T PRK11886 18 FHSGEQLGEELGISRAAIWKHIQTLEE 44 (319)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 357779999999999999998887765
No 469
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=21.32 E-value=3.3e+02 Score=25.97 Aligned_cols=75 Identities=15% Similarity=0.118 Sum_probs=46.2
Q ss_pred HHhhcCCCHHHHHHHHHHhccCCccccCCCCCHHHHHHHHhhhc----ccccchhhhhhhcccchhhhhhhhHHHHHHH
Q 016400 43 CLENFRMDKKVFYKLCDILQSKGLLRHTNRIKIEEQLAIFMFIV----GHNLRTRAVQELFRYSGETISRHFNNVLNAI 117 (390)
Q Consensus 43 f~~~frms~~~F~~L~~~L~~~~~~~~~~~~~~~~~l~~~L~~L----~~~~~~~~l~~~fgis~stv~~~~~~v~~~l 117 (390)
+-..+++++.+-+.-+..++........++.+.+.-++..||+- +.+.++++++...++++..+.+.++.+.+.|
T Consensus 132 ~~~~L~Lp~~v~e~A~~iyk~~~~~~~~rgrs~~~i~AAclYiACR~~~~prtl~eI~~~~~v~~k~i~~~~~~l~k~L 210 (310)
T PRK00423 132 IASQLGLPRSVREEAAVIYRKAVEKGLIRGRSIEGVVAAALYAACRRCKVPRTLDEIAEVSRVSRKEIGRCYRFLLREL 210 (310)
T ss_pred HHHHcCCCHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence 33444555444444333333322222234566666555555543 4678899999999999999988887777765
No 470
>PRK15243 transcriptional regulator SpvR; Provisional
Probab=21.26 E-value=1e+02 Score=29.11 Aligned_cols=41 Identities=12% Similarity=0.233 Sum_probs=32.0
Q ss_pred HHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 77 EQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 77 ~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
.++-.|+.... ..|+...|+..++|++|+|+.+++.-..|-
T Consensus 7 rqL~~F~aVae-~gSfs~AA~~L~isQpavS~~Ik~LE~eLG 47 (297)
T PRK15243 7 KKLKIFITLME-TGSFSIATSVLYITRTPLSRVISDLERELK 47 (297)
T ss_pred HHHHHHHHHHH-cCCHHHHHHHHCcCHHHHHHHHHHHHHHhC
Confidence 34444444444 357999999999999999999999999875
No 471
>PF12298 Bot1p: Eukaryotic mitochondrial regulator protein ; InterPro: IPR021036 This entry represents Ribosomal protein S35, which localises to the mitochondria in live cells and co-fractionates with purified mitochondrial ribosomes. This group of proteins have a novel function in the control of cell respiration by acting on the mitochondrial protein synthesis machinery and a role in mitochondrial integrity. Observations also indicate that in Schizosaccharomyces pombe (Fission yeast), alterations of mitochondrial function are linked to changes in cell cycle and cell morphology control mechanisms [].
Probab=21.18 E-value=1.4e+02 Score=25.94 Aligned_cols=42 Identities=10% Similarity=0.091 Sum_probs=36.5
Q ss_pred CCCCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhH
Q 016400 70 TNRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFN 111 (390)
Q Consensus 70 ~~~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~ 111 (390)
...+|-+.+-.|.-.+...|.+.+.|+..|||+...|.-|++
T Consensus 14 ~~~lse~~r~~Iy~~~~~~~~sv~~vS~~ygi~~~RV~AIvr 55 (172)
T PF12298_consen 14 NPVLSEELREQIYEDVMQDGKSVREVSQKYGIKIQRVEAIVR 55 (172)
T ss_pred CCcCCHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 356888888888888889999999999999999999887765
No 472
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=21.13 E-value=1.1e+02 Score=28.26 Aligned_cols=27 Identities=30% Similarity=0.436 Sum_probs=23.5
Q ss_pred cchhhhhhhcccchhhhhhhhHHHHHH
Q 016400 90 LRTRAVQELFRYSGETISRHFNNVLNA 116 (390)
Q Consensus 90 ~~~~~l~~~fgis~stv~~~~~~v~~~ 116 (390)
.+..++++.|+||..|+.|-+....+.
T Consensus 20 ~~~~ela~~l~vS~~TiRRdL~~Le~~ 46 (252)
T PRK10906 20 VSTEELVEHFSVSPQTIRRDLNDLAEQ 46 (252)
T ss_pred EeHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence 678899999999999999988777663
No 473
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=20.98 E-value=82 Score=22.49 Aligned_cols=26 Identities=12% Similarity=0.190 Sum_probs=18.4
Q ss_pred cccchhhhhhhcccchhhhhhhhHHH
Q 016400 88 HNLRTRAVQELFRYSGETISRHFNNV 113 (390)
Q Consensus 88 ~~~~~~~l~~~fgis~stv~~~~~~v 113 (390)
...+..+||..|++|.++|.-++..+
T Consensus 13 ~~~S~~eLa~~~~~s~~~ve~mL~~l 38 (69)
T PF09012_consen 13 GRVSLAELAREFGISPEAVEAMLEQL 38 (69)
T ss_dssp -SEEHHHHHHHTT--HHHHHHHHHHH
T ss_pred CCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence 45789999999999999887655433
No 474
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=20.96 E-value=87 Score=27.16 Aligned_cols=40 Identities=13% Similarity=0.186 Sum_probs=32.2
Q ss_pred HHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHH
Q 016400 77 EQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNA 116 (390)
Q Consensus 77 ~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~ 116 (390)
-++..+|+.=..+.+..++++..|+|+|.||-.+++...+
T Consensus 29 G~iYgilyls~~Pmtl~Ei~E~lg~Sks~vS~~lkkL~~~ 68 (177)
T COG1510 29 GQIYGILYLSRKPLTLDEIAEALGMSKSNVSMGLKKLQDW 68 (177)
T ss_pred HHHhhhheecCCCccHHHHHHHHCCCcchHHHHHHHHHhc
Confidence 3555666665788999999999999999999888776554
No 475
>PRK15183 Vi polysaccharide biosynthesis protein TviA; Provisional
Probab=20.44 E-value=96 Score=24.44 Aligned_cols=50 Identities=14% Similarity=0.086 Sum_probs=36.2
Q ss_pred HHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHHhhccccCCCCC
Q 016400 81 IFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMAISLDFFQPPGP 130 (390)
Q Consensus 81 ~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~~~~~~i~~P~~ 130 (390)
+-+.|.-+-....+++++|--|.||.+|+-++..--.-..-+.|+-.|++
T Consensus 90 ~kmkyflsesgmeelqdrfmns~st~yrwrke~a~kfgvr~prylllpds 139 (143)
T PRK15183 90 VKMKYFLSESGMEELQDRFMNSSSTMYRWRKELAVKFGVREPRYLLLPDS 139 (143)
T ss_pred hHhhhhhhhccHHHHHHHHccChHHHHHHHHHHHHHhcCCCCceEecCcc
Confidence 33444444566889999999999999999888766555556666666653
No 476
>COG4941 Predicted RNA polymerase sigma factor containing a TPR repeat domain [Transcription]
Probab=20.30 E-value=1.7e+02 Score=28.46 Aligned_cols=48 Identities=17% Similarity=0.275 Sum_probs=39.7
Q ss_pred CCCCHHHHHHHHhhhcccccchhhhhhhcccchhhhhhhhHHHHHHHHH
Q 016400 71 NRIKIEEQLAIFMFIVGHNLRTRAVQELFRYSGETISRHFNNVLNAIMA 119 (390)
Q Consensus 71 ~~~~~~~~l~~~L~~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~~ 119 (390)
+.++++.+++++|+.++ |.+..+|+..|=++.+|+-.-+.+.-..|.+
T Consensus 119 Pal~~~~riALtLR~v~-GLs~~eIArAFLv~e~am~QRivRAK~ri~~ 166 (415)
T COG4941 119 PALPPEQRIALTLRLVG-GLSTAEIARAFLVPEAAMAQRIVRAKARIRE 166 (415)
T ss_pred CCCChhhHHHHHHHHHc-CCcHHHHHHHHcCCcHHHHHHHHHHHHHHHh
Confidence 47999999999999887 8999999999999999987655555444543
No 477
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=20.26 E-value=1.3e+02 Score=27.64 Aligned_cols=27 Identities=37% Similarity=0.474 Sum_probs=24.3
Q ss_pred ccchhhhhhhcccchhhhhhhhHHHHH
Q 016400 89 NLRTRAVQELFRYSGETISRHFNNVLN 115 (390)
Q Consensus 89 ~~~~~~l~~~fgis~stv~~~~~~v~~ 115 (390)
..+..++++.|++|++|+.|.+++...
T Consensus 18 ~~~~~eLa~~l~VS~~TiRRdL~~L~~ 44 (240)
T PRK10411 18 SLTTEALAEQLNVSKETIRRDLNELQT 44 (240)
T ss_pred CCcHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 578899999999999999999988766
No 478
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=20.14 E-value=59 Score=28.28 Aligned_cols=26 Identities=23% Similarity=0.158 Sum_probs=22.8
Q ss_pred cccccchhhhhhhcccchhhhhhhhH
Q 016400 86 VGHNLRTRAVQELFRYSGETISRHFN 111 (390)
Q Consensus 86 L~~~~~~~~l~~~fgis~stv~~~~~ 111 (390)
...|.+..++|...|+|++|++++-+
T Consensus 17 ~~~glt~~elA~~~gis~~~is~~E~ 42 (185)
T PRK09943 17 QQQGLSQRRAAELSGLTHSAISTIEQ 42 (185)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHHc
Confidence 35688999999999999999998765
No 479
>PRK11062 nhaR transcriptional activator NhaR; Provisional
Probab=20.13 E-value=78 Score=29.53 Aligned_cols=34 Identities=12% Similarity=0.128 Sum_probs=29.2
Q ss_pred hcccccchhhhhhhcccchhhhhhhhHHHHHHHH
Q 016400 85 IVGHNLRTRAVQELFRYSGETISRHFNNVLNAIM 118 (390)
Q Consensus 85 ~L~~~~~~~~l~~~fgis~stv~~~~~~v~~~l~ 118 (390)
.++...++...|+..++|+++||+-++..-..+.
T Consensus 14 ~v~e~gs~s~AA~~L~isqpavS~~I~~LE~~lg 47 (296)
T PRK11062 14 MVCKEGSVVGAAEALFLTPQTITGQIKALEERLQ 47 (296)
T ss_pred HHHhcCCHHHHHHHhCCChHHHHHHHHHHHHHcC
Confidence 3444678999999999999999999999988875
No 480
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=20.07 E-value=62 Score=27.55 Aligned_cols=26 Identities=8% Similarity=0.009 Sum_probs=22.9
Q ss_pred cccccchhhhhhhcccchhhhhhhhH
Q 016400 86 VGHNLRTRAVQELFRYSGETISRHFN 111 (390)
Q Consensus 86 L~~~~~~~~l~~~fgis~stv~~~~~ 111 (390)
-..|.++.++|...|++++++++|-+
T Consensus 79 e~~glSqeeLA~~lgvs~s~IsriE~ 104 (154)
T TIGR00270 79 EKRGWSQEQLAKKIQEKESLIKKIEN 104 (154)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHC
Confidence 35789999999999999999999764
Done!