Query psy15697
Match_columns 332
No_of_seqs 232 out of 1517
Neff 8.9
Searched_HMMs 46136
Date Fri Aug 16 19:07:51 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy15697.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/15697hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4585|consensus 100.0 5.4E-38 1.2E-42 285.6 12.9 258 9-280 7-280 (326)
2 PF13359 DDE_Tnp_4: DDE superf 100.0 5.5E-39 1.2E-43 267.0 3.9 149 118-270 1-158 (158)
3 PF04827 Plant_tran: Plant tra 100.0 6E-37 1.3E-41 251.0 7.2 186 89-277 2-202 (205)
4 PF13612 DDE_Tnp_1_3: Transpos 99.1 1.9E-11 4.2E-16 99.9 3.0 125 111-248 3-148 (155)
5 PF13613 HTH_Tnp_4: Helix-turn 99.1 7.5E-11 1.6E-15 78.7 4.3 49 37-85 2-50 (53)
6 PF01609 DDE_Tnp_1: Transposas 97.8 5.1E-07 1.1E-11 77.5 -6.1 147 114-271 5-213 (213)
7 PF13586 DDE_Tnp_1_2: Transpos 97.7 2.4E-05 5.1E-10 58.0 2.0 75 195-270 1-86 (88)
8 PF02796 HTH_7: Helix-turn-hel 96.7 0.00056 1.2E-08 43.7 0.9 41 36-77 4-44 (45)
9 PF04545 Sigma70_r4: Sigma-70, 96.4 0.0043 9.2E-08 40.5 3.5 45 37-82 4-48 (50)
10 PF13936 HTH_38: Helix-turn-he 96.3 0.0018 3.9E-08 41.1 1.1 40 37-77 4-43 (44)
11 PF04218 CENP-B_N: CENP-B N-te 96.0 0.0033 7.2E-08 41.6 1.5 42 35-77 4-45 (53)
12 PF13011 LZ_Tnp_IS481: leucine 95.5 0.016 3.4E-07 42.1 3.4 47 34-80 5-51 (85)
13 PF02209 VHP: Villin headpiece 95.3 0.012 2.7E-07 35.3 1.8 22 1-22 2-23 (36)
14 PF08281 Sigma70_r4_2: Sigma-7 95.1 0.024 5.3E-07 37.4 3.2 44 37-81 10-53 (54)
15 PF13384 HTH_23: Homeodomain-l 95.0 0.0082 1.8E-07 39.0 0.5 31 49-79 12-42 (50)
16 PF12116 SpoIIID: Stage III sp 94.7 0.022 4.7E-07 40.4 2.0 46 43-88 8-53 (82)
17 PF13518 HTH_28: Helix-turn-he 94.7 0.021 4.5E-07 37.3 1.8 37 43-80 2-38 (52)
18 smart00153 VHP Villin headpiec 94.6 0.028 6.2E-07 33.8 2.1 20 1-20 2-21 (36)
19 smart00351 PAX Paired Box doma 94.4 0.037 8.1E-07 43.7 3.1 45 35-80 15-59 (125)
20 PF13340 DUF4096: Putative tra 94.4 0.12 2.6E-06 36.8 5.3 46 34-80 21-66 (75)
21 PF05225 HTH_psq: helix-turn-h 94.1 0.031 6.6E-07 35.6 1.6 37 41-77 2-39 (45)
22 cd00131 PAX Paired Box domain 93.8 0.066 1.4E-06 42.5 3.3 45 35-80 15-59 (128)
23 PRK09413 IS2 repressor TnpA; R 93.6 0.081 1.8E-06 41.5 3.5 46 35-80 10-55 (121)
24 COG3415 Transposase and inacti 93.3 0.058 1.3E-06 43.2 2.2 44 37-80 4-47 (138)
25 PF01527 HTH_Tnp_1: Transposas 93.1 0.04 8.8E-07 39.1 1.0 45 35-79 4-48 (76)
26 cd00569 HTH_Hin_like Helix-tur 93.0 0.092 2E-06 30.8 2.4 39 36-75 4-42 (42)
27 smart00421 HTH_LUXR helix_turn 92.5 0.16 3.5E-06 33.3 3.3 44 38-83 4-47 (58)
28 PRK00118 putative DNA-binding 92.4 0.18 3.8E-06 38.4 3.7 48 36-84 16-63 (104)
29 TIGR03879 near_KaiC_dom probab 92.1 0.11 2.5E-06 36.6 2.2 42 36-77 14-55 (73)
30 cd06171 Sigma70_r4 Sigma70, re 92.1 0.17 3.6E-06 32.6 2.9 42 38-80 11-52 (55)
31 PF13542 HTH_Tnp_ISL3: Helix-t 91.6 0.09 2E-06 34.3 1.2 32 47-78 20-51 (52)
32 cd06571 Bac_DnaA_C C-terminal 91.6 0.29 6.3E-06 36.2 4.0 52 33-84 23-75 (90)
33 PRK12529 RNA polymerase sigma 91.4 0.25 5.5E-06 41.3 3.9 47 37-84 127-173 (178)
34 PRK04217 hypothetical protein; 91.2 0.29 6.4E-06 37.6 3.7 48 36-84 41-88 (110)
35 PRK09639 RNA polymerase sigma 90.7 0.28 6.1E-06 40.3 3.5 46 37-84 112-157 (166)
36 TIGR02531 yecD_yerC TrpR-relat 90.4 0.17 3.7E-06 37.2 1.7 32 45-76 41-72 (88)
37 PRK09047 RNA polymerase factor 89.9 0.46 9.9E-06 38.8 4.2 50 37-87 106-155 (161)
38 cd06170 LuxR_C_like C-terminal 89.9 0.38 8.2E-06 31.5 3.0 33 51-83 12-44 (57)
39 PHA00542 putative Cro-like pro 89.2 0.27 5.8E-06 35.7 2.0 31 47-77 24-54 (82)
40 PRK09652 RNA polymerase sigma 89.1 0.4 8.6E-06 39.8 3.2 47 37-84 128-174 (182)
41 PRK12547 RNA polymerase sigma 88.9 0.55 1.2E-05 38.6 4.0 47 37-84 112-158 (164)
42 PHA00675 hypothetical protein 88.8 0.3 6.5E-06 34.5 1.8 41 36-76 21-61 (78)
43 PF01710 HTH_Tnp_IS630: Transp 88.6 1.2 2.7E-05 34.7 5.5 73 4-78 22-95 (119)
44 PRK05911 RNA polymerase sigma 88.5 0.5 1.1E-05 42.2 3.6 47 37-84 205-251 (257)
45 PRK07037 extracytoplasmic-func 88.4 0.62 1.3E-05 38.1 3.9 46 38-84 110-155 (163)
46 TIGR02985 Sig70_bacteroi1 RNA 88.4 0.54 1.2E-05 38.1 3.5 47 37-84 113-159 (161)
47 PRK08301 sporulation sigma fac 88.3 0.55 1.2E-05 41.2 3.8 48 37-84 178-228 (234)
48 PRK12520 RNA polymerase sigma 88.2 0.6 1.3E-05 39.4 3.8 53 37-90 131-183 (191)
49 TIGR02952 Sig70_famx2 RNA poly 88.1 0.53 1.2E-05 38.7 3.4 47 37-84 122-168 (170)
50 PF00356 LacI: Bacterial regul 88.0 0.16 3.5E-06 32.5 0.1 21 57-77 2-22 (46)
51 PRK12532 RNA polymerase sigma 88.0 0.55 1.2E-05 39.8 3.4 50 37-87 136-185 (195)
52 TIGR02844 spore_III_D sporulat 87.9 0.33 7.2E-06 35.0 1.7 37 41-77 5-42 (80)
53 PRK15320 transcriptional activ 87.9 0.3 6.5E-06 41.3 1.7 39 46-84 171-209 (251)
54 PF07374 DUF1492: Protein of u 87.9 0.52 1.1E-05 35.6 2.8 43 39-82 57-99 (100)
55 TIGR00721 tfx DNA-binding prot 87.8 0.57 1.2E-05 37.5 3.2 47 36-84 5-51 (137)
56 PRK12530 RNA polymerase sigma 87.7 0.56 1.2E-05 39.7 3.3 47 37-84 134-180 (189)
57 PF00872 Transposase_mut: Tran 87.7 0.98 2.1E-05 42.9 5.3 130 47-209 107-245 (381)
58 TIGR01321 TrpR trp operon repr 87.6 0.35 7.7E-06 35.9 1.7 40 38-77 33-78 (94)
59 PRK12533 RNA polymerase sigma 87.5 0.64 1.4E-05 40.4 3.6 46 38-84 135-180 (216)
60 PRK12519 RNA polymerase sigma 87.3 0.48 1E-05 40.1 2.7 46 38-84 142-187 (194)
61 PRK12511 RNA polymerase sigma 87.3 0.68 1.5E-05 39.0 3.6 47 37-84 111-157 (182)
62 TIGR02937 sigma70-ECF RNA poly 87.2 0.61 1.3E-05 37.1 3.2 47 37-84 110-156 (158)
63 TIGR02846 spore_sigmaK RNA pol 87.2 0.73 1.6E-05 40.3 3.8 49 36-84 173-224 (227)
64 TIGR02392 rpoH_proteo alternat 87.1 0.62 1.3E-05 41.9 3.4 47 38-84 219-266 (270)
65 PRK11924 RNA polymerase sigma 87.1 0.68 1.5E-05 38.3 3.4 46 38-84 126-171 (179)
66 PF04967 HTH_10: HTH DNA bindi 87.0 0.36 7.9E-06 31.8 1.3 30 54-83 23-52 (53)
67 PRK03975 tfx putative transcri 86.9 0.77 1.7E-05 37.0 3.5 47 36-84 5-51 (141)
68 TIGR02999 Sig-70_X6 RNA polyme 86.9 0.84 1.8E-05 38.1 3.9 46 38-84 135-180 (183)
69 PRK12514 RNA polymerase sigma 86.9 0.75 1.6E-05 38.3 3.6 47 37-84 129-175 (179)
70 PF13412 HTH_24: Winged helix- 86.8 0.65 1.4E-05 29.6 2.5 28 53-80 16-43 (48)
71 PRK05803 sporulation sigma fac 86.7 0.76 1.6E-05 40.3 3.7 48 37-84 175-225 (233)
72 PRK12516 RNA polymerase sigma 86.6 0.83 1.8E-05 38.6 3.8 47 37-84 116-162 (187)
73 PRK12524 RNA polymerase sigma 86.4 0.72 1.6E-05 39.2 3.3 47 37-84 136-182 (196)
74 TIGR02989 Sig-70_gvs1 RNA poly 86.3 0.8 1.7E-05 37.2 3.4 48 36-84 110-157 (159)
75 PRK12528 RNA polymerase sigma 86.1 0.84 1.8E-05 37.3 3.4 47 37-84 113-159 (161)
76 PRK12512 RNA polymerase sigma 86.1 0.96 2.1E-05 37.9 3.9 48 37-85 131-178 (184)
77 PRK09415 RNA polymerase factor 86.1 0.84 1.8E-05 38.2 3.5 47 37-84 127-173 (179)
78 PRK07408 RNA polymerase sigma 86.0 0.95 2.1E-05 40.4 4.0 46 38-84 204-249 (256)
79 PF00196 GerE: Bacterial regul 85.7 0.45 9.7E-06 31.8 1.3 44 38-83 4-47 (58)
80 PRK09638 RNA polymerase sigma 85.5 0.55 1.2E-05 39.0 2.1 47 37-84 126-172 (176)
81 PRK09641 RNA polymerase sigma 85.2 0.91 2E-05 38.0 3.3 47 37-84 136-182 (187)
82 TIGR02984 Sig-70_plancto1 RNA 85.2 1.1 2.5E-05 37.4 3.9 47 37-84 140-186 (189)
83 PRK12544 RNA polymerase sigma 85.2 0.94 2E-05 39.0 3.4 49 37-86 148-196 (206)
84 TIGR02393 RpoD_Cterm RNA polym 85.0 0.91 2E-05 40.0 3.4 48 37-84 176-226 (238)
85 PRK12531 RNA polymerase sigma 85.0 1.2 2.5E-05 37.9 3.9 46 38-84 142-187 (194)
86 PRK12515 RNA polymerase sigma 84.9 1.1 2.3E-05 37.8 3.6 47 37-84 131-177 (189)
87 PRK12540 RNA polymerase sigma 84.9 1.2 2.5E-05 37.5 3.8 50 37-87 111-160 (182)
88 PRK06596 RNA polymerase factor 84.9 0.93 2E-05 41.2 3.4 47 38-84 231-278 (284)
89 PRK12522 RNA polymerase sigma 84.8 0.95 2.1E-05 37.5 3.2 52 38-91 120-171 (173)
90 PRK09645 RNA polymerase sigma 84.8 1.4 3E-05 36.5 4.2 47 38-85 119-165 (173)
91 PRK08583 RNA polymerase sigma 84.8 1.2 2.6E-05 39.6 4.1 47 37-84 205-251 (257)
92 PRK06030 hypothetical protein; 84.8 1.5 3.2E-05 34.5 4.0 47 36-82 51-97 (124)
93 PF12802 MarR_2: MarR family; 84.8 0.9 2E-05 30.5 2.5 37 44-80 10-47 (62)
94 PRK09642 RNA polymerase sigma 84.7 1.2 2.6E-05 36.3 3.7 46 38-84 107-152 (160)
95 PRK06759 RNA polymerase factor 84.6 1.1 2.3E-05 36.3 3.3 46 37-83 106-151 (154)
96 PRK12537 RNA polymerase sigma 84.5 1.1 2.3E-05 37.6 3.4 46 38-84 134-179 (182)
97 TIGR03001 Sig-70_gmx1 RNA poly 84.5 0.94 2E-05 40.1 3.2 48 38-86 162-209 (244)
98 PRK11923 algU RNA polymerase s 84.5 0.93 2E-05 38.3 3.1 46 38-84 139-184 (193)
99 TIGR02980 SigBFG RNA polymeras 84.3 1.2 2.7E-05 38.7 3.8 47 37-84 178-224 (227)
100 PRK12525 RNA polymerase sigma 84.2 1.3 2.8E-05 36.6 3.7 47 37-84 118-164 (168)
101 TIGR02835 spore_sigmaE RNA pol 84.1 1.1 2.4E-05 39.4 3.4 48 37-84 178-228 (234)
102 PF01022 HTH_5: Bacterial regu 84.1 0.69 1.5E-05 29.5 1.6 28 53-80 14-41 (47)
103 PRK12523 RNA polymerase sigma 84.0 1.4 3.1E-05 36.4 3.9 47 37-84 119-165 (172)
104 smart00342 HTH_ARAC helix_turn 84.0 2 4.4E-05 30.1 4.3 73 2-80 3-77 (84)
105 PRK12534 RNA polymerase sigma 84.0 1.4 3E-05 37.0 3.9 46 38-84 138-183 (187)
106 PF13610 DDE_Tnp_IS240: DDE do 83.9 2.7 5.8E-05 33.7 5.3 132 117-274 5-138 (140)
107 PF13730 HTH_36: Helix-turn-he 83.8 1 2.2E-05 29.6 2.4 40 41-80 7-51 (55)
108 PRK05572 sporulation sigma fac 83.8 1.4 3E-05 39.2 4.0 47 37-84 202-248 (252)
109 PRK12539 RNA polymerase sigma 83.7 1.4 3E-05 37.0 3.7 47 37-84 131-177 (184)
110 TIGR02939 RpoE_Sigma70 RNA pol 83.7 1.1 2.5E-05 37.5 3.3 46 38-84 139-184 (190)
111 TIGR02983 SigE-fam_strep RNA p 83.6 1.3 2.8E-05 36.1 3.5 46 38-84 111-156 (162)
112 PRK12546 RNA polymerase sigma 83.6 1.4 3E-05 37.3 3.7 47 37-84 113-159 (188)
113 PRK07500 rpoH2 RNA polymerase 83.6 1.4 3E-05 40.2 3.9 48 37-84 227-275 (289)
114 PF01371 Trp_repressor: Trp re 83.5 0.76 1.6E-05 33.7 1.8 36 42-77 37-72 (87)
115 PRK05602 RNA polymerase sigma 83.5 1.3 2.8E-05 37.2 3.5 46 38-84 129-174 (186)
116 TIGR02885 spore_sigF RNA polym 83.4 1.3 2.9E-05 38.6 3.7 47 37-84 183-229 (231)
117 TIGR02950 SigM_subfam RNA poly 83.4 0.55 1.2E-05 38.0 1.1 46 38-84 106-151 (154)
118 PRK12536 RNA polymerase sigma 83.4 1.5 3.3E-05 36.7 3.8 46 38-84 130-175 (181)
119 PF13551 HTH_29: Winged helix- 83.3 0.69 1.5E-05 35.1 1.6 34 47-80 4-38 (112)
120 TIGR02943 Sig70_famx1 RNA poly 83.3 1.3 2.9E-05 37.3 3.5 46 38-84 132-177 (188)
121 PRK06811 RNA polymerase factor 83.2 1.2 2.7E-05 37.5 3.3 47 37-84 131-177 (189)
122 COG2963 Transposase and inacti 83.2 1.3 2.8E-05 34.2 3.1 47 35-81 5-52 (116)
123 PF13751 DDE_Tnp_1_6: Transpos 83.2 0.69 1.5E-05 36.2 1.6 48 224-272 73-122 (125)
124 PRK03573 transcriptional regul 83.0 2.5 5.4E-05 33.9 4.9 43 38-80 29-72 (144)
125 PRK09649 RNA polymerase sigma 82.9 1.3 2.9E-05 37.2 3.3 47 37-84 130-176 (185)
126 PF01047 MarR: MarR family; I 82.7 1 2.2E-05 30.0 2.1 28 53-80 16-43 (59)
127 TIGR02394 rpoS_proteo RNA poly 82.7 1.5 3.2E-05 39.8 3.8 50 37-86 222-274 (285)
128 PRK08215 sporulation sigma fac 82.5 1.4 3E-05 39.4 3.4 47 37-84 209-255 (258)
129 TIGR02954 Sig70_famx3 RNA poly 82.5 1.7 3.6E-05 35.8 3.7 47 37-84 119-165 (169)
130 PRK09637 RNA polymerase sigma 82.3 1.6 3.5E-05 36.6 3.6 47 37-84 106-152 (181)
131 TIGR02948 SigW_bacill RNA poly 82.3 1.5 3.2E-05 36.7 3.4 47 37-84 136-182 (187)
132 PRK13919 putative RNA polymera 82.3 1.8 3.9E-05 36.2 3.9 46 38-84 136-181 (186)
133 COG1595 RpoE DNA-directed RNA 82.2 1.5 3.2E-05 36.8 3.4 46 38-84 128-173 (182)
134 PF09339 HTH_IclR: IclR helix- 82.0 0.7 1.5E-05 30.1 1.0 35 46-80 7-44 (52)
135 PF08279 HTH_11: HTH domain; 82.0 1.1 2.4E-05 29.4 2.0 29 54-82 15-43 (55)
136 PRK09643 RNA polymerase sigma 82.0 1.6 3.4E-05 37.0 3.5 46 38-84 135-180 (192)
137 PF05344 DUF746: Domain of Unk 82.0 1.4 2.9E-05 30.3 2.4 43 44-87 3-45 (65)
138 PF01325 Fe_dep_repress: Iron 81.9 1.3 2.9E-05 29.9 2.4 40 41-80 6-48 (60)
139 COG1191 FliA DNA-directed RNA 81.8 1.8 3.8E-05 38.4 3.7 47 37-84 196-242 (247)
140 TIGR02850 spore_sigG RNA polym 81.6 1.7 3.7E-05 38.7 3.7 47 37-84 206-252 (254)
141 PRK12545 RNA polymerase sigma 81.4 1.7 3.7E-05 37.1 3.6 47 37-84 139-185 (201)
142 PRK06986 fliA flagellar biosyn 81.4 1.8 3.9E-05 38.0 3.8 46 38-84 185-230 (236)
143 PRK12535 RNA polymerase sigma 81.4 1.9 4.2E-05 36.7 3.8 51 38-90 134-184 (196)
144 TIGR02997 Sig70-cyanoRpoD RNA 81.3 1.4 3E-05 40.3 3.1 45 37-81 249-296 (298)
145 PRK12543 RNA polymerase sigma 81.2 2 4.3E-05 35.8 3.8 46 38-84 118-163 (179)
146 TIGR03697 NtcA_cyano global ni 81.1 0.67 1.4E-05 39.0 0.9 44 38-81 113-170 (193)
147 PF01710 HTH_Tnp_IS630: Transp 80.9 0.62 1.3E-05 36.4 0.5 30 48-77 12-41 (119)
148 TIGR02960 SigX5 RNA polymerase 80.8 1.7 3.7E-05 40.0 3.6 51 37-89 142-192 (324)
149 TIGR02959 SigZ RNA polymerase 80.7 1.9 4.2E-05 35.6 3.5 47 37-84 100-146 (170)
150 PRK06930 positive control sigm 80.6 2 4.3E-05 35.8 3.5 47 37-84 114-160 (170)
151 PF08299 Bac_DnaA_C: Bacterial 80.4 0.99 2.1E-05 31.6 1.4 43 36-78 27-70 (70)
152 PRK12541 RNA polymerase sigma 80.4 1.9 4.1E-05 35.2 3.3 47 37-84 112-158 (161)
153 TIGR02941 Sigma_B RNA polymera 80.2 2.1 4.6E-05 38.0 3.9 47 37-84 205-251 (255)
154 PRK15418 transcriptional regul 80.2 0.93 2E-05 41.9 1.5 68 46-116 21-88 (318)
155 PRK11753 DNA-binding transcrip 80.1 1.1 2.4E-05 38.3 1.9 45 36-80 137-194 (211)
156 PRK12526 RNA polymerase sigma 79.8 2.3 5.1E-05 36.4 3.9 46 38-84 154-199 (206)
157 TIGR01636 phage_rinA phage tra 79.6 2.6 5.7E-05 33.6 3.8 47 38-84 83-130 (134)
158 PRK06704 RNA polymerase factor 79.4 2.7 5.8E-05 36.9 4.1 51 37-89 116-166 (228)
159 PRK07405 RNA polymerase sigma 79.3 2 4.4E-05 39.6 3.5 48 37-84 256-306 (317)
160 cd00092 HTH_CRP helix_turn_hel 79.3 1.3 2.8E-05 30.1 1.7 26 55-80 26-51 (67)
161 PRK12542 RNA polymerase sigma 79.1 2.6 5.6E-05 35.3 3.8 46 38-84 123-168 (185)
162 PRK08295 RNA polymerase factor 78.9 2.7 5.8E-05 35.9 3.9 46 37-84 155-200 (208)
163 PRK09644 RNA polymerase sigma 78.9 2.4 5.1E-05 34.8 3.5 47 37-84 108-154 (165)
164 PRK15201 fimbriae regulatory p 78.8 1.4 3.1E-05 36.7 2.0 45 37-83 133-177 (198)
165 TIGR02947 SigH_actino RNA poly 78.8 1.4 3E-05 37.2 2.1 46 38-84 132-177 (193)
166 PRK07670 RNA polymerase sigma 78.4 2.8 6.1E-05 37.2 4.0 46 38-84 202-247 (251)
167 PRK12527 RNA polymerase sigma 78.3 2.7 5.9E-05 34.2 3.6 46 38-84 106-151 (159)
168 smart00346 HTH_ICLR helix_turn 78.2 2 4.3E-05 31.3 2.5 38 43-80 6-46 (91)
169 PRK09648 RNA polymerase sigma 78.1 2.4 5.2E-05 35.6 3.4 47 37-84 139-185 (189)
170 PRK12538 RNA polymerase sigma 77.9 2.3 5.1E-05 37.3 3.3 46 38-84 172-217 (233)
171 PRK07122 RNA polymerase sigma 77.8 2.3 5E-05 38.1 3.3 46 38-84 216-261 (264)
172 PRK13870 transcriptional regul 77.6 1.4 3E-05 38.8 1.7 47 36-84 172-218 (234)
173 PRK15411 rcsA colanic acid cap 77.5 1.6 3.5E-05 37.5 2.1 45 37-83 137-181 (207)
174 PRK09651 RNA polymerase sigma 77.4 2.4 5.3E-05 35.1 3.1 47 37-84 119-165 (172)
175 COG2197 CitB Response regulato 77.3 5.1 0.00011 34.6 5.2 45 37-83 148-192 (211)
176 TIGR02479 FliA_WhiG RNA polyme 77.3 3.1 6.8E-05 36.1 3.9 46 38-84 176-221 (224)
177 PF00325 Crp: Bacterial regula 77.2 1.1 2.3E-05 26.2 0.6 25 55-79 3-27 (32)
178 PRK01381 Trp operon repressor; 77.0 1.2 2.6E-05 33.4 1.0 26 51-76 52-77 (99)
179 PRK10402 DNA-binding transcrip 76.8 1.9 4.1E-05 37.5 2.4 44 37-80 148-195 (226)
180 smart00550 Zalpha Z-DNA-bindin 76.7 2.6 5.6E-05 29.3 2.6 42 39-80 6-48 (68)
181 PRK09646 RNA polymerase sigma 76.6 3.1 6.8E-05 35.2 3.6 47 37-84 142-188 (194)
182 PF00126 HTH_1: Bacterial regu 76.5 2.5 5.5E-05 28.4 2.5 37 47-84 7-43 (60)
183 COG2739 Uncharacterized protei 76.1 3.1 6.7E-05 31.1 2.9 43 41-84 21-63 (105)
184 PF01381 HTH_3: Helix-turn-hel 75.6 1 2.2E-05 29.5 0.3 26 52-77 7-32 (55)
185 PF02001 DUF134: Protein of un 75.6 4.3 9.3E-05 30.9 3.7 47 37-84 41-87 (106)
186 TIGR03209 P21_Cbot clostridium 75.5 1.5 3.3E-05 35.0 1.3 36 37-73 107-142 (142)
187 PRK07406 RNA polymerase sigma 74.8 3.2 6.8E-05 39.3 3.4 48 37-84 311-361 (373)
188 PRK12513 RNA polymerase sigma 74.6 2 4.4E-05 36.3 2.0 46 38-84 140-185 (194)
189 TIGR02337 HpaR homoprotocatech 74.5 5.7 0.00012 30.6 4.4 42 38-80 26-68 (118)
190 PRK12427 flagellar biosynthesi 74.3 3.3 7.2E-05 36.3 3.3 45 38-83 184-228 (231)
191 PF04297 UPF0122: Putative hel 74.2 3.9 8.4E-05 30.9 3.1 44 40-84 20-63 (101)
192 PF12964 DUF3853: Protein of u 74.1 2.8 6E-05 31.1 2.2 66 9-84 10-77 (96)
193 PF13560 HTH_31: Helix-turn-he 74.1 1.5 3.3E-05 29.8 0.9 28 49-76 9-36 (64)
194 PRK08241 RNA polymerase factor 74.1 2.2 4.7E-05 39.7 2.2 50 38-89 154-203 (339)
195 PF13551 HTH_29: Winged helix- 73.9 14 0.00031 27.7 6.5 74 3-77 15-110 (112)
196 PRK11922 RNA polymerase sigma 73.8 2.1 4.6E-05 37.4 1.9 46 38-84 150-195 (231)
197 TIGR01610 phage_O_Nterm phage 73.8 2.8 6.1E-05 31.2 2.3 29 52-80 45-73 (95)
198 PRK12517 RNA polymerase sigma 73.8 4.2 9.1E-05 34.3 3.7 46 38-84 129-174 (188)
199 PRK09647 RNA polymerase sigma 73.7 4.1 9E-05 34.9 3.7 46 38-84 139-184 (203)
200 PF13463 HTH_27: Winged helix 73.0 2.2 4.7E-05 29.2 1.5 35 47-81 8-45 (68)
201 PRK07598 RNA polymerase sigma 72.6 3.7 8.1E-05 39.3 3.4 48 37-84 350-400 (415)
202 PRK05657 RNA polymerase sigma 72.2 5.2 0.00011 37.1 4.2 50 37-86 262-314 (325)
203 PF07638 Sigma70_ECF: ECF sigm 72.1 4.8 0.0001 33.9 3.6 46 38-84 136-181 (185)
204 PF12840 HTH_20: Helix-turn-he 72.1 2.3 5E-05 28.6 1.4 30 51-80 21-50 (61)
205 PRK06288 RNA polymerase sigma 72.1 4.4 9.6E-05 36.3 3.6 47 37-84 212-258 (268)
206 smart00419 HTH_CRP helix_turn_ 71.8 2 4.3E-05 26.9 1.0 27 54-80 8-34 (48)
207 PRK12518 RNA polymerase sigma 71.6 2.3 5.1E-05 35.1 1.6 47 38-85 121-167 (175)
208 PHA02591 hypothetical protein; 70.8 2.9 6.3E-05 29.6 1.6 38 40-77 45-82 (83)
209 smart00418 HTH_ARSR helix_turn 70.8 2.7 6E-05 27.8 1.6 29 52-80 8-36 (66)
210 smart00345 HTH_GNTR helix_turn 70.7 2.1 4.5E-05 28.2 0.9 25 56-80 22-46 (60)
211 PRK05949 RNA polymerase sigma 70.7 4.5 9.8E-05 37.5 3.4 48 37-84 266-316 (327)
212 TIGR02859 spore_sigH RNA polym 70.3 4.1 8.9E-05 34.3 2.9 38 46-84 158-195 (198)
213 PRK13719 conjugal transfer tra 70.3 3.1 6.7E-05 36.0 2.0 46 36-83 142-187 (217)
214 PRK09210 RNA polymerase sigma 70.0 4.6 0.0001 38.1 3.4 48 37-84 305-355 (367)
215 PRK09391 fixK transcriptional 69.7 3.1 6.6E-05 36.3 2.0 43 38-80 153-205 (230)
216 cd01392 HTH_LacI Helix-turn-he 68.9 2.2 4.8E-05 27.4 0.7 19 59-77 2-20 (52)
217 PF00165 HTH_AraC: Bacterial r 68.9 1.8 3.8E-05 26.7 0.2 29 51-79 5-33 (42)
218 PHA00738 putative HTH transcri 68.8 2.6 5.5E-05 32.1 1.1 33 49-81 19-53 (108)
219 cd00090 HTH_ARSR Arsenical Res 68.7 4.8 0.00011 27.4 2.5 28 53-80 19-46 (78)
220 PF03333 PapB: Adhesin biosynt 68.7 17 0.00037 26.8 5.4 57 11-79 22-78 (91)
221 PRK14086 dnaA chromosomal repl 68.1 7.9 0.00017 39.0 4.7 52 33-84 548-599 (617)
222 PRK10188 DNA-binding transcrip 67.5 3.6 7.8E-05 36.3 2.0 47 36-84 178-224 (240)
223 PF13309 HTH_22: HTH domain 67.2 2 4.3E-05 29.5 0.2 41 36-76 19-64 (64)
224 TIGR02957 SigX4 RNA polymerase 67.1 7.1 0.00015 35.3 3.9 65 38-105 109-173 (281)
225 PRK10840 transcriptional regul 67.1 3.4 7.4E-05 35.3 1.8 46 36-83 149-194 (216)
226 PRK05901 RNA polymerase sigma 66.7 7.1 0.00015 38.5 4.0 48 37-84 447-497 (509)
227 PRK13413 mpi multiple promoter 66.6 2.9 6.3E-05 35.7 1.2 30 48-77 166-195 (200)
228 PRK11512 DNA-binding transcrip 66.6 7.1 0.00015 31.3 3.4 43 37-80 37-80 (144)
229 PRK00149 dnaA chromosomal repl 66.1 9.9 0.00022 36.9 4.9 53 32-84 380-433 (450)
230 cd00131 PAX Paired Box domain 66.0 29 0.00062 27.4 6.7 76 2-77 35-126 (128)
231 PRK11475 DNA-binding transcrip 65.9 3.8 8.3E-05 35.3 1.8 45 37-83 134-178 (207)
232 PRK09640 RNA polymerase sigma 65.5 2.6 5.7E-05 35.4 0.7 45 39-84 136-180 (188)
233 PF04703 FaeA: FaeA-like prote 65.5 3.3 7.1E-05 28.3 1.0 38 42-79 3-40 (62)
234 PF06056 Terminase_5: Putative 65.5 5.3 0.00011 26.8 2.0 25 53-77 12-36 (58)
235 smart00352 POU Found in Pit-Oc 65.4 2.6 5.6E-05 29.9 0.5 29 49-77 19-53 (75)
236 PF01978 TrmB: Sugar-specific 65.1 3.3 7.3E-05 28.5 1.1 39 41-80 10-48 (68)
237 COG3316 Transposase and inacti 64.8 24 0.00052 30.5 6.3 182 38-273 9-199 (215)
238 PRK07921 RNA polymerase sigma 64.8 7.2 0.00016 36.1 3.5 47 38-84 263-312 (324)
239 smart00354 HTH_LACI helix_turn 64.7 2.4 5.3E-05 29.5 0.3 21 56-76 2-22 (70)
240 PRK11161 fumarate/nitrate redu 64.5 4.2 9.1E-05 35.4 1.8 42 38-79 154-209 (235)
241 PRK09636 RNA polymerase sigma 64.4 8.9 0.00019 34.8 4.0 49 38-88 116-164 (293)
242 PRK09392 ftrB transcriptional 64.2 4.5 9.8E-05 35.2 2.0 44 37-80 146-199 (236)
243 COG2771 CsgD DNA-binding HTH d 64.1 5.5 0.00012 26.6 2.0 36 47-82 12-47 (65)
244 COG1342 Predicted DNA-binding 64.1 7.8 0.00017 28.7 2.8 42 37-79 33-74 (99)
245 PF13744 HTH_37: Helix-turn-he 63.5 2.5 5.4E-05 30.4 0.2 35 42-76 17-53 (80)
246 PF09862 DUF2089: Protein of u 63.4 7.2 0.00016 30.0 2.7 47 37-84 33-79 (113)
247 PF09607 BrkDBD: Brinker DNA-b 62.8 6.8 0.00015 26.2 2.1 43 35-77 3-48 (58)
248 PRK09635 sigI RNA polymerase s 62.7 8.8 0.00019 34.9 3.6 65 38-105 119-183 (290)
249 TIGR03541 reg_near_HchA LuxR f 62.5 8.1 0.00018 33.8 3.2 48 35-84 169-216 (232)
250 PF10654 DUF2481: Protein of u 62.3 2.8 6E-05 32.0 0.2 31 53-83 79-109 (126)
251 COG2522 Predicted transcriptio 62.0 5.7 0.00012 30.9 1.9 24 53-76 21-44 (119)
252 smart00420 HTH_DEOR helix_turn 62.0 8.8 0.00019 24.2 2.6 27 54-80 14-40 (53)
253 PRK14088 dnaA chromosomal repl 61.9 9.7 0.00021 36.9 3.9 50 33-82 366-415 (440)
254 TIGR03070 couple_hipB transcri 61.9 3.2 6.8E-05 27.1 0.4 25 52-76 13-37 (58)
255 PRK09483 response regulator; P 61.5 5.2 0.00011 33.8 1.8 46 36-83 147-192 (217)
256 smart00347 HTH_MARR helix_turn 60.9 11 0.00024 27.5 3.3 28 53-80 23-50 (101)
257 PRK10100 DNA-binding transcrip 60.8 5.9 0.00013 34.4 2.0 45 37-83 155-199 (216)
258 PF05043 Mga: Mga helix-turn-h 60.0 6.3 0.00014 28.5 1.8 34 51-84 27-60 (87)
259 PF13404 HTH_AsnC-type: AsnC-t 59.9 3.6 7.7E-05 25.6 0.4 24 54-77 17-40 (42)
260 PF05263 DUF722: Protein of un 59.7 8.6 0.00019 30.5 2.6 46 38-83 82-128 (130)
261 TIGR03020 EpsA transcriptional 59.7 9.7 0.00021 33.8 3.2 47 35-83 188-234 (247)
262 PF10668 Phage_terminase: Phag 59.7 4.4 9.5E-05 27.4 0.8 28 49-76 15-44 (60)
263 COG2390 DeoR Transcriptional r 59.3 5.4 0.00012 36.9 1.6 66 47-115 19-84 (321)
264 PRK09492 treR trehalose repres 59.0 3.5 7.6E-05 37.4 0.3 23 55-77 5-27 (315)
265 smart00344 HTH_ASNC helix_turn 58.7 11 0.00024 28.4 3.0 38 42-80 6-43 (108)
266 cd04762 HTH_MerR-trunc Helix-T 58.6 3.9 8.4E-05 25.4 0.4 21 57-77 3-23 (49)
267 PHA01976 helix-turn-helix prot 58.3 5.3 0.00012 27.2 1.1 27 50-76 11-37 (67)
268 PRK14087 dnaA chromosomal repl 57.9 16 0.00036 35.4 4.7 52 33-84 380-432 (450)
269 TIGR02405 trehalos_R_Ecol treh 57.5 3.8 8.2E-05 37.3 0.3 21 56-76 3-23 (311)
270 TIGR01889 Staph_reg_Sar staphy 57.4 13 0.00027 28.3 3.2 28 53-80 42-69 (109)
271 PRK13918 CRP/FNR family transc 57.3 8.4 0.00018 32.5 2.4 43 38-80 119-175 (202)
272 PF13545 HTH_Crp_2: Crp-like h 57.2 4.5 9.7E-05 28.3 0.6 27 54-80 28-54 (76)
273 PRK00215 LexA repressor; Valid 57.0 9.9 0.00021 32.5 2.8 27 54-80 23-50 (205)
274 PF13701 DDE_Tnp_1_4: Transpos 56.2 15 0.00032 35.7 4.1 124 66-202 103-229 (448)
275 PF04552 Sigma54_DBD: Sigma-54 56.0 3.8 8.2E-05 33.8 0.0 23 54-76 49-71 (160)
276 COG3413 Predicted DNA binding 55.9 7.3 0.00016 33.7 1.8 49 36-84 154-208 (215)
277 PRK10163 DNA-binding transcrip 55.6 12 0.00027 33.5 3.3 45 36-80 19-66 (271)
278 PRK09191 two-component respons 55.2 12 0.00026 32.7 3.2 47 37-84 88-134 (261)
279 COG5421 Transposase [DNA repli 54.6 13 0.00028 36.0 3.2 58 141-203 154-211 (480)
280 PF13443 HTH_26: Cro/C1-type H 54.6 4 8.7E-05 27.4 -0.1 27 52-78 8-34 (63)
281 PRK12682 transcriptional regul 54.2 10 0.00022 34.4 2.5 46 43-88 5-50 (309)
282 PRK10651 transcriptional regul 54.2 8.3 0.00018 32.2 1.8 45 37-83 155-199 (216)
283 TIGR01764 excise DNA binding d 54.0 5 0.00011 25.0 0.3 21 56-76 3-23 (49)
284 PRK10870 transcriptional repre 53.9 11 0.00023 31.6 2.4 43 38-80 53-97 (176)
285 TIGR00122 birA_repr_reg BirA b 53.4 11 0.00025 25.8 2.1 26 55-80 14-39 (69)
286 PRK10014 DNA-binding transcrip 53.4 5.2 0.00011 36.8 0.5 23 55-77 7-29 (342)
287 PRK10141 DNA-binding transcrip 53.3 11 0.00023 29.4 2.1 28 54-81 30-57 (117)
288 PF12728 HTH_17: Helix-turn-he 53.1 5.3 0.00011 25.6 0.3 21 56-76 3-23 (51)
289 PF05269 Phage_CII: Bacterioph 53.1 7.2 0.00016 28.8 1.1 30 55-84 24-53 (91)
290 PRK09526 lacI lac repressor; R 52.4 5 0.00011 36.9 0.2 23 55-77 6-28 (342)
291 PRK11303 DNA-binding transcrip 51.8 5.4 0.00012 36.4 0.3 22 56-77 2-23 (328)
292 TIGR00180 parB_part ParB-like 51.8 12 0.00027 31.5 2.5 42 35-76 100-142 (187)
293 PF00292 PAX: 'Paired box' dom 50.9 15 0.00033 28.9 2.6 44 35-79 15-58 (125)
294 TIGR02431 pcaR_pcaU beta-ketoa 50.8 12 0.00027 32.9 2.5 43 38-80 5-50 (248)
295 PRK14987 gluconate operon tran 50.5 5 0.00011 36.7 -0.1 23 55-77 6-28 (331)
296 PRK10423 transcriptional repre 50.2 6.4 0.00014 35.9 0.5 19 58-76 2-20 (327)
297 PRK10401 DNA-binding transcrip 50.2 5.9 0.00013 36.6 0.3 21 56-76 3-23 (346)
298 cd07377 WHTH_GntR Winged helix 50.1 8 0.00017 25.8 0.9 25 56-80 27-51 (66)
299 COG1508 RpoN DNA-directed RNA 50.0 6.2 0.00013 37.9 0.4 31 55-96 331-361 (444)
300 PF14493 HTH_40: Helix-turn-he 49.9 13 0.00029 27.2 2.1 37 45-81 4-40 (91)
301 PRK10360 DNA-binding transcrip 49.7 11 0.00024 31.0 2.0 45 37-83 137-181 (196)
302 COG3355 Predicted transcriptio 49.7 14 0.00031 29.1 2.3 29 53-81 41-69 (126)
303 PRK10403 transcriptional regul 48.9 11 0.00025 31.2 1.9 45 37-83 153-197 (215)
304 TIGR00637 ModE_repress ModE mo 48.4 12 0.00026 28.1 1.7 37 48-84 10-46 (99)
305 PRK10703 DNA-binding transcrip 48.3 6.6 0.00014 36.1 0.3 22 56-77 3-24 (341)
306 PRK10072 putative transcriptio 48.2 7.5 0.00016 29.1 0.5 25 52-76 44-68 (96)
307 PRK10339 DNA-binding transcrip 47.8 5.9 0.00013 36.2 -0.1 22 56-77 3-24 (327)
308 PRK09834 DNA-binding transcrip 47.4 15 0.00033 32.8 2.5 43 38-80 7-52 (263)
309 PRK12683 transcriptional regul 47.1 15 0.00033 33.4 2.5 45 43-87 5-49 (309)
310 TIGR02702 SufR_cyano iron-sulf 46.6 18 0.0004 30.8 2.8 39 41-80 3-41 (203)
311 PRK04140 hypothetical protein; 46.6 14 0.0003 34.1 2.1 64 11-76 97-161 (317)
312 COG3293 Transposase and inacti 46.5 8.9 0.00019 29.9 0.8 90 145-248 2-98 (124)
313 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 46.2 16 0.00035 23.7 1.8 41 35-76 2-42 (50)
314 PRK10079 phosphonate metabolis 46.1 15 0.00032 32.2 2.2 47 17-79 14-60 (241)
315 PRK11050 manganese transport r 46.0 18 0.00038 29.5 2.5 28 53-80 50-77 (152)
316 PRK09958 DNA-binding transcrip 46.0 14 0.00029 30.8 1.9 45 37-83 143-187 (204)
317 TIGR02417 fruct_sucro_rep D-fr 45.9 7.6 0.00016 35.4 0.3 21 57-77 2-22 (327)
318 PRK11179 DNA-binding transcrip 45.8 25 0.00055 28.5 3.4 28 53-80 22-49 (153)
319 PF08220 HTH_DeoR: DeoR-like h 45.8 17 0.00038 24.0 2.0 25 55-79 15-39 (57)
320 PRK05658 RNA polymerase sigma 45.4 21 0.00045 36.3 3.4 47 38-84 557-606 (619)
321 PF00392 GntR: Bacterial regul 45.2 9.4 0.0002 25.8 0.6 22 58-79 28-49 (64)
322 PF01418 HTH_6: Helix-turn-hel 45.0 8.3 0.00018 27.4 0.3 25 54-78 34-58 (77)
323 TIGR01481 ccpA catabolite cont 44.9 7.9 0.00017 35.3 0.3 22 56-77 3-24 (329)
324 PRK12679 cbl transcriptional r 44.8 18 0.00039 33.0 2.6 45 43-87 5-49 (316)
325 PRK11569 transcriptional repre 44.7 21 0.00045 32.1 2.9 44 37-80 23-69 (274)
326 smart00529 HTH_DTXR Helix-turn 44.2 12 0.00026 27.4 1.1 24 57-80 2-25 (96)
327 PF02954 HTH_8: Bacterial regu 44.0 9.1 0.0002 23.6 0.4 25 53-77 17-41 (42)
328 PRK11233 nitrogen assimilation 44.0 18 0.00039 32.7 2.5 39 48-86 9-47 (305)
329 COG0593 DnaA ATPase involved i 43.7 31 0.00067 33.0 4.0 53 32-84 343-395 (408)
330 PRK10727 DNA-binding transcrip 43.6 8 0.00017 35.6 0.1 21 56-76 3-23 (343)
331 PRK12422 chromosomal replicati 43.6 27 0.00058 33.9 3.7 52 32-83 375-426 (445)
332 TIGR02607 antidote_HigA addict 43.5 9.4 0.0002 26.8 0.4 27 50-76 14-40 (78)
333 smart00760 Bac_DnaA_C Bacteria 43.3 17 0.00037 24.3 1.7 33 33-65 24-56 (60)
334 PF00440 TetR_N: Bacterial reg 43.0 11 0.00025 23.7 0.7 30 53-82 15-44 (47)
335 PRK15369 two component system 42.8 17 0.00036 29.9 2.0 44 38-83 150-193 (211)
336 COG1846 MarR Transcriptional r 41.8 24 0.00051 26.7 2.5 23 58-80 40-62 (126)
337 TIGR02404 trehalos_R_Bsub treh 41.8 20 0.00044 31.2 2.3 21 59-79 29-49 (233)
338 PRK12684 transcriptional regul 41.5 22 0.00047 32.4 2.6 46 43-88 5-50 (313)
339 PRK15090 DNA-binding transcrip 41.4 24 0.00052 31.3 2.8 44 37-80 9-54 (257)
340 COG1609 PurR Transcriptional r 41.0 10 0.00022 35.2 0.3 22 56-77 2-23 (333)
341 COG4496 Uncharacterized protei 40.5 20 0.00044 26.2 1.7 30 47-76 49-78 (100)
342 TIGR01884 cas_HTH CRISPR locus 40.5 31 0.00066 29.5 3.2 35 46-80 147-183 (203)
343 COG1414 IclR Transcriptional r 40.1 27 0.00059 30.9 2.9 35 45-79 7-44 (246)
344 COG1654 BirA Biotin operon rep 39.8 29 0.00063 24.9 2.5 25 55-79 20-44 (79)
345 TIGR02944 suf_reg_Xantho FeS a 39.7 17 0.00038 28.5 1.5 26 55-80 26-51 (130)
346 PF01726 LexA_DNA_bind: LexA D 39.5 15 0.00032 25.2 0.9 27 53-79 24-51 (65)
347 PF08765 Mor: Mor transcriptio 39.4 11 0.00024 28.7 0.3 31 53-83 71-101 (108)
348 PRK09726 antitoxin HipB; Provi 39.1 13 0.00027 27.2 0.5 26 52-77 23-48 (88)
349 PF07022 Phage_CI_repr: Bacter 38.8 16 0.00035 25.0 1.0 23 55-77 13-36 (66)
350 TIGR03830 CxxCG_CxxCG_HTH puta 38.6 15 0.00033 28.5 1.0 28 50-77 74-101 (127)
351 PRK13777 transcriptional regul 38.6 35 0.00075 28.9 3.2 42 38-79 43-84 (185)
352 PRK10219 DNA-binding transcrip 37.9 32 0.0007 25.7 2.7 26 54-79 21-46 (107)
353 TIGR01637 phage_arpU phage tra 37.8 54 0.0012 25.7 4.1 48 37-84 79-127 (132)
354 PRK10430 DNA-binding transcrip 37.7 71 0.0015 27.6 5.2 33 51-83 175-207 (239)
355 PF14549 P22_Cro: DNA-binding 37.6 11 0.00023 25.6 -0.0 26 56-82 11-36 (60)
356 PRK08558 adenine phosphoribosy 37.3 23 0.0005 31.2 2.0 38 39-76 8-45 (238)
357 PF07453 NUMOD1: NUMOD1 domain 37.3 10 0.00022 22.6 -0.2 23 53-75 15-37 (37)
358 TIGR02395 rpoN_sigma RNA polym 36.9 11 0.00023 36.5 -0.2 32 54-96 318-349 (429)
359 COG1522 Lrp Transcriptional re 36.1 35 0.00076 27.3 2.8 38 42-80 11-48 (154)
360 COG2512 Predicted membrane-ass 35.6 37 0.00081 30.3 3.0 45 35-79 190-235 (258)
361 PRK11151 DNA-binding transcrip 35.5 30 0.00064 31.2 2.5 43 44-87 6-48 (305)
362 PRK11169 leucine-responsive tr 35.3 34 0.00073 28.1 2.6 28 53-80 27-54 (164)
363 PF05930 Phage_AlpA: Prophage 35.1 14 0.0003 23.8 0.2 20 57-76 6-25 (51)
364 TIGR02684 dnstrm_HI1420 probab 34.6 20 0.00044 26.3 1.0 34 44-77 33-66 (89)
365 PRK15092 DNA-binding transcrip 34.5 26 0.00057 31.9 2.0 50 37-86 8-57 (310)
366 PRK09706 transcriptional repre 34.1 20 0.00044 28.3 1.0 27 51-77 15-41 (135)
367 TIGR03454 partition_RepB plasm 34.0 35 0.00076 31.6 2.7 44 35-78 158-201 (325)
368 PRK09764 DNA-binding transcrip 34.0 30 0.00065 30.3 2.2 47 17-79 7-54 (240)
369 COG3179 Predicted chitinase [G 34.0 44 0.00096 28.1 3.0 70 1-75 4-74 (206)
370 PRK13503 transcriptional activ 34.0 52 0.0011 29.2 3.8 27 53-79 186-212 (278)
371 PF07900 DUF1670: Protein of u 33.8 1.4E+02 0.003 26.0 6.0 81 1-84 106-193 (220)
372 PRK12681 cysB transcriptional 33.7 33 0.00072 31.5 2.6 45 43-87 5-49 (324)
373 COG2188 PhnF Transcriptional r 33.7 28 0.0006 30.5 1.9 49 15-79 7-56 (236)
374 PRK11402 DNA-binding transcrip 33.4 31 0.00067 30.2 2.2 48 16-79 10-58 (241)
375 PRK11511 DNA-binding transcrip 33.4 41 0.00088 26.3 2.7 28 52-79 23-50 (127)
376 PRK10094 DNA-binding transcrip 33.3 33 0.00071 31.1 2.4 35 50-84 12-46 (308)
377 PRK09935 transcriptional regul 32.7 37 0.0008 28.1 2.5 45 37-83 149-193 (210)
378 PRK09906 DNA-binding transcrip 32.7 31 0.00067 30.9 2.1 40 46-85 7-46 (296)
379 PRK12469 RNA polymerase factor 32.5 15 0.00033 35.9 0.1 32 54-96 369-400 (481)
380 PRK10046 dpiA two-component re 32.4 25 0.00054 30.3 1.4 31 47-77 167-200 (225)
381 TIGR00498 lexA SOS regulatory 32.2 40 0.00086 28.5 2.6 26 55-80 26-52 (199)
382 PRK05932 RNA polymerase factor 32.1 15 0.00032 35.8 -0.1 32 54-96 343-374 (455)
383 PF06530 Phage_antitermQ: Phag 31.8 43 0.00094 26.2 2.6 40 44-83 68-107 (125)
384 smart00351 PAX Paired Box doma 31.7 1.5E+02 0.0032 23.1 5.6 25 3-27 36-60 (125)
385 PF08280 HTH_Mga: M protein tr 31.7 39 0.00084 22.5 2.0 38 43-81 9-46 (59)
386 TIGR03418 chol_sulf_TF putativ 31.6 32 0.00069 30.7 2.0 43 44-87 6-48 (291)
387 PRK15215 fimbriae biosynthesis 31.5 1.5E+02 0.0032 22.3 5.0 40 40-79 47-86 (100)
388 PF08535 KorB: KorB domain; I 31.5 18 0.00038 26.6 0.3 24 53-76 2-25 (93)
389 PF13556 HTH_30: PucR C-termin 31.4 30 0.00066 23.0 1.4 36 48-83 6-41 (59)
390 cd04761 HTH_MerR-SF Helix-Turn 31.4 18 0.00039 22.6 0.2 20 58-77 4-23 (49)
391 CHL00180 rbcR LysR transcripti 31.2 40 0.00087 30.4 2.6 40 47-86 12-51 (305)
392 PRK03902 manganese transport t 30.7 44 0.00096 26.6 2.5 26 55-80 23-48 (142)
393 PF11198 DUF2857: Protein of u 30.6 2.4E+02 0.0051 23.7 7.0 74 4-79 91-178 (180)
394 PRK10341 DNA-binding transcrip 30.5 35 0.00077 30.9 2.2 43 44-86 11-53 (312)
395 COG4941 Predicted RNA polymera 30.3 59 0.0013 30.2 3.4 49 35-84 118-166 (415)
396 smart00530 HTH_XRE Helix-turn- 30.1 27 0.00059 21.3 1.0 25 52-76 8-32 (56)
397 PRK15421 DNA-binding transcrip 30.1 43 0.00094 30.6 2.7 41 43-84 6-46 (317)
398 PRK11013 DNA-binding transcrip 29.7 41 0.00088 30.5 2.4 41 44-85 9-49 (309)
399 PF05391 Lsm_interact: Lsm int 29.6 36 0.00078 17.7 1.1 10 1-10 10-19 (21)
400 PF12844 HTH_19: Helix-turn-he 29.6 18 0.00039 24.2 0.1 26 52-77 10-35 (64)
401 COG1395 Predicted transcriptio 29.4 29 0.00063 31.7 1.3 66 11-78 97-162 (313)
402 COG4565 CitB Response regulato 29.4 1.2E+02 0.0026 26.3 5.0 69 11-79 129-198 (224)
403 PF05732 RepL: Firmicute plasm 29.4 23 0.0005 29.3 0.7 26 55-80 76-101 (165)
404 PRK09508 leuO leucine transcri 29.4 40 0.00087 30.6 2.3 44 43-86 25-68 (314)
405 COG3677 Transposase and inacti 29.1 53 0.0011 26.0 2.6 44 41-84 76-119 (129)
406 smart00497 IENR1 Intron encode 29.1 22 0.00048 22.7 0.4 24 54-77 17-40 (53)
407 TIGR02612 mob_myst_A mobile my 29.0 23 0.00051 28.8 0.6 29 49-77 33-61 (150)
408 COG1725 Predicted transcriptio 28.8 13 0.00028 29.2 -0.9 58 8-80 4-61 (125)
409 PRK09791 putative DNA-binding 28.7 42 0.0009 30.2 2.3 39 47-85 12-50 (302)
410 cd07153 Fur_like Ferric uptake 28.6 59 0.0013 24.6 2.8 17 64-80 31-47 (116)
411 PRK13509 transcriptional repre 28.6 47 0.001 29.5 2.5 39 42-80 5-45 (251)
412 TIGR03298 argP transcriptional 28.6 46 0.00099 29.7 2.5 39 51-89 12-50 (292)
413 cd01104 HTH_MlrA-CarA Helix-Tu 28.5 23 0.0005 24.0 0.4 21 57-77 3-23 (68)
414 PF02650 HTH_WhiA: WhiA C-term 28.4 75 0.0016 23.1 3.1 45 36-80 36-82 (85)
415 PRK12680 transcriptional regul 28.1 48 0.001 30.5 2.6 41 48-88 9-50 (327)
416 COG1476 Predicted transcriptio 27.7 23 0.00051 24.6 0.3 26 51-76 11-36 (68)
417 TIGR03734 PRTRC_parB PRTRC sys 27.6 49 0.0011 33.0 2.6 42 35-76 89-131 (554)
418 cd00093 HTH_XRE Helix-turn-hel 27.5 33 0.00071 21.1 1.0 25 52-76 10-34 (58)
419 COG2964 Uncharacterized protei 27.5 59 0.0013 28.2 2.8 37 42-78 174-215 (220)
420 PRK10837 putative DNA-binding 27.3 44 0.00095 29.7 2.2 41 46-86 9-49 (290)
421 PRK13832 plasmid partitioning 26.9 54 0.0012 32.3 2.7 50 35-84 99-150 (520)
422 PRK00423 tfb transcription ini 26.5 1.1E+02 0.0024 28.1 4.6 78 6-83 226-305 (310)
423 TIGR03339 phn_lysR aminoethylp 26.0 38 0.00083 29.7 1.5 35 50-84 7-41 (279)
424 COG5593 Nucleic-acid-binding p 25.9 1.7E+02 0.0037 29.0 5.8 63 228-296 467-529 (821)
425 COG2944 Predicted transcriptio 25.9 24 0.00053 26.7 0.2 26 51-76 54-79 (104)
426 PRK09801 transcriptional activ 25.8 57 0.0012 29.6 2.6 39 47-85 13-51 (310)
427 COG5566 Uncharacterized conser 25.7 35 0.00076 26.7 1.0 28 53-80 101-128 (137)
428 PRK06474 hypothetical protein; 25.6 53 0.0011 27.5 2.2 27 55-81 27-54 (178)
429 PRK13890 conjugal transfer pro 25.4 28 0.0006 27.1 0.4 25 52-76 16-40 (120)
430 PRK11886 bifunctional biotin-- 25.3 49 0.0011 30.4 2.1 33 48-80 10-44 (319)
431 PRK10632 transcriptional regul 25.0 45 0.00098 30.2 1.8 37 48-84 10-46 (309)
432 PRK03601 transcriptional regul 25.0 55 0.0012 29.1 2.3 40 46-85 7-46 (275)
433 PRK15186 AraC family transcrip 24.9 1.2E+02 0.0026 27.7 4.5 72 2-80 199-272 (291)
434 TIGR00738 rrf2_super rrf2 fami 24.6 54 0.0012 25.5 2.0 27 54-80 25-51 (132)
435 PRK11242 DNA-binding transcrip 24.6 48 0.001 29.6 1.9 36 51-86 12-47 (296)
436 PRK13348 chromosome replicatio 24.5 53 0.0011 29.3 2.2 38 50-87 12-49 (294)
437 PRK09943 DNA-binding transcrip 24.5 30 0.00064 29.0 0.5 26 52-77 18-43 (185)
438 PRK14165 winged helix-turn-hel 24.4 57 0.0012 28.3 2.2 26 55-80 22-47 (217)
439 PRK01905 DNA-binding protein F 24.2 63 0.0014 22.8 2.1 27 52-78 48-74 (77)
440 PRK10434 srlR DNA-bindng trans 24.2 61 0.0013 28.8 2.4 40 41-80 4-45 (256)
441 PF07750 GcrA: GcrA cell cycle 24.1 41 0.00088 27.8 1.2 38 41-78 5-43 (162)
442 PF01526 DDE_Tnp_Tn3: Tn3 tran 24.1 5.6E+02 0.012 24.4 9.0 87 35-132 24-116 (388)
443 PF02082 Rrf2: Transcriptional 24.0 51 0.0011 23.5 1.6 26 55-80 26-51 (83)
444 TIGR02424 TF_pcaQ pca operon t 24.0 53 0.0011 29.4 2.0 36 50-85 13-48 (300)
445 PRK09390 fixJ response regulat 24.0 58 0.0013 26.4 2.2 34 50-83 152-185 (202)
446 PRK04841 transcriptional regul 23.9 48 0.001 35.0 2.0 46 36-83 837-882 (903)
447 PRK06424 transcription factor; 23.9 39 0.00085 27.3 1.0 33 44-76 85-119 (144)
448 PRK09986 DNA-binding transcrip 23.8 59 0.0013 28.9 2.3 41 44-85 12-52 (294)
449 PRK04424 fatty acid biosynthes 23.4 63 0.0014 27.2 2.3 39 41-79 6-46 (185)
450 PRK10086 DNA-binding transcrip 23.4 58 0.0013 29.5 2.2 40 45-84 19-58 (311)
451 COG3093 VapI Plasmid maintenan 23.2 33 0.00072 26.0 0.4 24 54-77 23-46 (104)
452 COG2973 TrpR Trp operon repres 23.1 47 0.001 24.8 1.2 32 43-74 49-80 (103)
453 PRK10906 DNA-binding transcrip 22.8 70 0.0015 28.4 2.5 38 43-80 6-45 (252)
454 TIGR00270 conserved hypothetic 22.6 36 0.00078 27.8 0.6 33 44-76 70-104 (154)
455 PF02001 DUF134: Protein of un 22.5 1E+02 0.0022 23.5 2.9 26 1-26 58-83 (106)
456 TIGR02036 dsdC D-serine deamin 22.4 60 0.0013 29.3 2.1 39 46-84 14-52 (302)
457 PF07037 DUF1323: Putative tra 22.4 37 0.0008 26.3 0.6 21 57-77 3-23 (122)
458 PF13022 HTH_Tnp_1_2: Helix-tu 22.3 60 0.0013 26.0 1.7 34 55-89 35-71 (142)
459 PF13601 HTH_34: Winged helix 22.2 47 0.001 23.7 1.1 29 53-81 13-41 (80)
460 PF00382 TFIIB: Transcription 22.1 71 0.0015 21.9 2.0 67 5-71 3-71 (71)
461 PRK10411 DNA-binding transcrip 21.9 65 0.0014 28.4 2.1 27 54-80 18-44 (240)
462 PF12298 Bot1p: Eukaryotic mit 21.9 90 0.002 26.0 2.8 42 35-76 14-55 (172)
463 PRK11564 stationary phase indu 21.9 1.1E+02 0.0024 29.3 3.9 49 36-84 9-60 (426)
464 COG3311 AlpA Predicted transcr 21.8 30 0.00066 24.2 -0.0 23 56-78 15-37 (70)
465 PRK10216 DNA-binding transcrip 21.4 66 0.0014 29.2 2.2 38 48-85 16-53 (319)
466 PRK15340 transcriptional regul 21.4 63 0.0014 28.1 1.9 28 52-79 123-150 (216)
467 PF08148 DSHCT: DSHCT (NUC185) 21.4 90 0.002 26.1 2.8 45 43-88 103-147 (180)
468 PRK13558 bacterio-opsin activa 21.2 1.2E+02 0.0026 30.8 4.3 48 37-84 607-660 (665)
469 PF04931 DNA_pol_phi: DNA poly 21.0 1.9E+02 0.004 30.4 5.6 16 228-243 603-618 (784)
470 PRK11482 putative DNA-binding 20.9 70 0.0015 29.1 2.2 40 45-84 34-73 (317)
471 TIGR02297 HpaA 4-hydroxyphenyl 20.8 1.1E+02 0.0024 27.2 3.5 30 50-79 198-227 (287)
472 PRK09940 transcriptional regul 20.6 1.7E+02 0.0037 26.1 4.5 72 2-80 152-224 (253)
473 PRK00430 fis global DNA-bindin 20.3 83 0.0018 23.4 2.1 25 53-77 67-91 (95)
474 PF13411 MerR_1: MerR HTH fami 20.3 44 0.00096 22.6 0.6 22 58-79 4-25 (69)
475 PF12759 HTH_Tnp_IS1: InsA C-t 20.2 63 0.0014 20.6 1.2 25 53-77 20-44 (46)
476 PF12833 HTH_18: Helix-turn-he 20.1 57 0.0012 22.8 1.2 19 60-78 1-19 (81)
477 TIGR02325 C_P_lyase_phnF phosp 20.0 50 0.0011 28.6 1.0 47 17-79 10-57 (238)
No 1
>KOG4585|consensus
Probab=100.00 E-value=5.4e-38 Score=285.58 Aligned_cols=258 Identities=26% Similarity=0.444 Sum_probs=211.9
Q ss_pred HhcCCHHHHHHHHHHhccCcCCCCC--CCCC-CCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHHh
Q psy15697 9 AFRLSATQVEFILEEIAPALTTPTE--RNVA-LSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVDT 85 (332)
Q Consensus 9 ~frms~~~F~~L~~~L~~~~~~~~~--~~~~-~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~~ 85 (332)
.+++++.+|..++............ .... ++....+++.++.++++.+.+.++..||...+|+ .+......
T Consensus 7 ~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~i~~~fg~~~~~~-----~~~~~~~~- 80 (326)
T KOG4585|consen 7 EFRKSYTTFDKICSLVQSLNVVKNSGFMLSSLLPADTLVAVALWRLKTGESLRTVEKKFGLGQSTC-----KFLEEKED- 80 (326)
T ss_pred HHHHHHHHHHHHhhhhhhhhhhcccchhhhccccHHhhhhhhhccccccchHHHHHHHcCCcchhh-----hHHHhhhc-
Confidence 6888999999999886654322111 1111 2288899999999999999999999999999998 44444444
Q ss_pred hhccccCCCcc-cccchhhhhhhcCCCCCceeeecceEEEEeCCCCCcccccccCCccccceeeeccCCcceEEeeccCC
Q psy15697 86 FFQRMVKWPEE-NLNDIPMTFLRKGGFPNVAGCVDGTMVLIDAPNEHEDQFVNRNGDHALNVMAICGPNYKFYAVNANWP 164 (332)
Q Consensus 86 l~~~~I~~P~~-~~~~~~~~f~~~~~~p~~~G~iDgt~i~i~~P~~~~~~y~~~k~~~s~~~~~v~d~~g~~~~v~~~~~ 164 (332)
+++.++.||.. .+..+.+.++. +|+|+|++|+||+++..|+.....|.|+ .++.|+|+|||.+++|++|.+|||
T Consensus 81 ~~~~~~~~p~~~~~~~i~~~~~~---~~~~~g~~d~~hi~~~~~~~~~~~~~n~--~~~~Nvlav~n~d~~f~~v~vg~~ 155 (326)
T KOG4585|consen 81 LAPHFLKWPSRRILYEIRERFES---LPNCVGAIDTTHIPIRVPPKSGSVYFNK--EQSKNLLAVCNFDMRFIYVDVGWP 155 (326)
T ss_pred ccchhhcCchhhhhhhhcccccc---ccchhccccccccceecCcccccccccc--ccchhhhheecCCceEEEEEccCC
Confidence 99999999998 77788887765 9999999999999999999999999988 888899999999999999999999
Q ss_pred ccccchhhhccccccccccccCCCCC----------CCceEecCCCCCCCCcCCCCccCCC-CChHHHHHHHHHHHHHHH
Q psy15697 165 GSVHDARVMRNSMVYRKFDEEGWRPF----------PDAVILGDSAYPLKEWLIPPRTRNP-DAAADQRFLRCHKRTRRL 233 (332)
Q Consensus 165 Gs~~D~~v~~~s~l~~~l~~~~~~~~----------~~~~llgD~gY~~~~~l~~P~~~~~-~~~~~~~fN~~~s~~R~~ 233 (332)
||.||+.|+..+.+.... .... +. -..+++|+.+||..+++++| +.++ .+..++.||++|+.+|.+
T Consensus 156 Gs~~D~kvl~~~~~~~~~-~~~~-~~k~yl~d~~~~~~~~~~g~~~~~~~~~~~~~-~~~~~~~~~~elFN~rh~~~r~v 232 (326)
T KOG4585|consen 156 GSAHDTKVLQDSLLYKRN-FPHP-PLKYYLVDSGYPLRPGLLGPIGFPLYSLLMFP-YGGPQPTNSQELFNKRHSSLRSV 232 (326)
T ss_pred CCccHHHHHHhhcccccc-cccC-CccccccccCcccccccccccccccchhhhcc-cCCCCCCchHHHHhhhhhhHHHH
Confidence 999999999999887766 3331 11 02344555555555556666 5555 367888999999999999
Q ss_pred HHHHHHHHhhhcccc-cccccCcccHHHHHHHHHHHHhhcccCCCCCC
Q psy15697 234 IENSFGILKEKFPCL-NYMRLSPQFAGMVVLASTTLHNIALTIDRDNE 280 (332)
Q Consensus 234 vE~~fg~LK~rf~~L-~~~~~~~~~~~~ii~a~~~LhN~~~~~~~~~~ 280 (332)
+|++||+||.||+|| +.......+..+||.|||+|||++++..+.++
T Consensus 233 ~e~~fg~lk~rw~il~~~~~~~~~~~~~iV~a~caLHN~~~~~~~~~~ 280 (326)
T KOG4585|consen 233 AERAFGVLKAKWRILQRREKYDLKKLPKIVTACCALHNIIRDSDEEDP 280 (326)
T ss_pred HHHHHHHhhhhhHHHhhcccccccchHHHHHHHHHHHHHHHhhccccc
Confidence 999999999999999 55778899999999999999999998888766
No 2
>PF13359 DDE_Tnp_4: DDE superfamily endonuclease
Probab=100.00 E-value=5.5e-39 Score=266.99 Aligned_cols=149 Identities=36% Similarity=0.693 Sum_probs=138.4
Q ss_pred ecceEEEEeCCCC---CcccccccCCccccceeeeccCCcceEEeeccCCccccchhhhccccccccccccCCCCCCCce
Q psy15697 118 VDGTMVLIDAPNE---HEDQFVNRNGDHALNVMAICGPNYKFYAVNANWPGSVHDARVMRNSMVYRKFDEEGWRPFPDAV 194 (332)
Q Consensus 118 iDgt~i~i~~P~~---~~~~y~~~k~~~s~~~~~v~d~~g~~~~v~~~~~Gs~~D~~v~~~s~l~~~l~~~~~~~~~~~~ 194 (332)
|||||++|++|.. ....|+++|+.+++|+|+|||++|+|++++++||||+||+.+|++|.+...+ +.. ..++.+
T Consensus 1 iDgt~v~i~~P~~~~~~~~~y~~~k~~~~~~~q~v~d~~g~i~~v~~~~~Gs~~D~~i~~~s~~~~~l-~~~--~~~~~~ 77 (158)
T PF13359_consen 1 IDGTHVPIQRPSDKEEQREFYSGKKKNHSLKVQIVCDPDGRIIYVSVGWPGSVHDSTIFRQSGLLDRL-EQA--FPPGEY 77 (158)
T ss_pred CccEEEEEEeCCccccccccccCCCCcceEeEEEEEeccceeEeeeccccccccccccccccccccee-ecc--cccCcc
Confidence 7999999999987 7889999999999999999999999999999999999999999999999887 422 345899
Q ss_pred EecCCCCCCCCcCCCCccCC----CCChHHHHHHHHHHHHHHHHHHHHHHHhhhcccc-cccccC-cccHHHHHHHHHHH
Q psy15697 195 ILGDSAYPLKEWLIPPRTRN----PDAAADQRFLRCHKRTRRLIENSFGILKEKFPCL-NYMRLS-PQFAGMVVLASTTL 268 (332)
Q Consensus 195 llgD~gY~~~~~l~~P~~~~----~~~~~~~~fN~~~s~~R~~vE~~fg~LK~rf~~L-~~~~~~-~~~~~~ii~a~~~L 268 (332)
+|||+|||+.+++++| ++. +.+.+|+.||++|++.|.+||++||+||+||+|| ..++.+ ++.+.++|.|||+|
T Consensus 78 ~l~D~gy~~~~~~~~P-~~~~~~~~l~~~e~~~N~~~s~~R~~vE~~~~~lK~rf~~l~~~~~~~~~~~~~~ii~~~~~L 156 (158)
T PF13359_consen 78 LLGDSGYPLSPYLLTP-YKKPKGRELTPEEKEFNRRHSSARIIVERAFGRLKSRFRILRGRLRLSRPEKAPQIILACCVL 156 (158)
T ss_pred cccccccccccccccc-ccccccccccccccchhccccceeeeeHHHHHHHHHhcccCCcccCCCcHhHHHHHHheeEEE
Confidence 9999999999999999 963 2378999999999999999999999999999999 689988 99999999999999
Q ss_pred Hh
Q psy15697 269 HN 270 (332)
Q Consensus 269 hN 270 (332)
||
T Consensus 157 hN 158 (158)
T PF13359_consen 157 HN 158 (158)
T ss_pred EC
Confidence 99
No 3
>PF04827 Plant_tran: Plant transposon protein; InterPro: IPR006912 This entry represents a putative Harbinger transposase-derived nuclease, which is thought to have nuclease activity. However it does not have transposase activity [, ]. ; GO: 0016788 hydrolase activity, acting on ester bonds
Probab=100.00 E-value=6e-37 Score=250.96 Aligned_cols=186 Identities=20% Similarity=0.354 Sum_probs=165.7
Q ss_pred cccCCCcc-cccchhhhhhhcCCCCCceeeecceEEEEe-CCCCCccccc-ccCCccccceeeeccCCcceEEeeccCCc
Q psy15697 89 RMVKWPEE-NLNDIPMTFLRKGGFPNVAGCVDGTMVLID-APNEHEDQFV-NRNGDHALNVMAICGPNYKFYAVNANWPG 165 (332)
Q Consensus 89 ~~I~~P~~-~~~~~~~~f~~~~~~p~~~G~iDgt~i~i~-~P~~~~~~y~-~~k~~~s~~~~~v~d~~g~~~~v~~~~~G 165 (332)
+|++-|+. +++++..-. +..|||+.+|+|||+|+.++ .|......|. +++|.+++.+++|++.+++|+.+..|.||
T Consensus 2 ~YLr~P~~~d~~rll~~~-e~rGFpGmlGSIDCmHw~WkncP~aw~g~~~~G~~g~pTiiLEaVAs~dlwIWhaffG~~G 80 (205)
T PF04827_consen 2 EYLRRPTNEDLERLLQIG-EARGFPGMLGSIDCMHWEWKNCPTAWKGQYTRGKEGVPTIILEAVASHDLWIWHAFFGMPG 80 (205)
T ss_pred cccCCCChhHHHHHHHhh-hhcCCCccccceeEEEeehhcchHHhhhcccCCCCCCCeehhhhhhccchhhhheeeccCC
Confidence 68888999 888888555 45699999999999999998 5666666776 99999999999999999999999999999
Q ss_pred cccchhhhccccccccccccCCCCC----------CCceEecCCCCCCCCcCCCCccCCCCChHHHHHHHHHHHHHHHHH
Q psy15697 166 SVHDARVMRNSMVYRKFDEEGWRPF----------PDAVILGDSAYPLKEWLIPPRTRNPDAAADQRFLRCHKRTRRLIE 235 (332)
Q Consensus 166 s~~D~~v~~~s~l~~~l~~~~~~~~----------~~~~llgD~gY~~~~~l~~P~~~~~~~~~~~~fN~~~s~~R~~vE 235 (332)
|.+|++|+..|++...+ .+|..+. .-.|+|+|..||.++.++.+ ++.|.+.+++.|.++++++|..||
T Consensus 81 S~NDiNVL~~Splf~~~-~~G~ap~v~f~VNg~~Y~~gYYLaDGiYP~watfvkt-I~~p~~~k~k~fa~~QE~~RKDVE 158 (205)
T PF04827_consen 81 SNNDINVLDRSPLFDDL-LQGQAPRVQFTVNGHEYNMGYYLADGIYPEWATFVKT-ISLPQGEKRKLFAKHQESARKDVE 158 (205)
T ss_pred cccccccccccHHHHHH-hcCcCCceEEEecCeecccceeeccCcCcchHhHhhh-cchhhchhhHHHHHhCHHHHHHHH
Confidence 99999999999999988 6553221 14699999999999999999 999999999999999999999999
Q ss_pred HHHHHHhhhcccc-cccc-cCcccHHHHHHHHHHHHhhcccCCC
Q psy15697 236 NSFGILKEKFPCL-NYMR-LSPQFAGMVVLASTTLHNIALTIDR 277 (332)
Q Consensus 236 ~~fg~LK~rf~~L-~~~~-~~~~~~~~ii~a~~~LhN~~~~~~~ 277 (332)
||||+|++||+|+ .+.+ ++.+.+..|+.||++||||+++++.
T Consensus 159 rAFGVLQaRfaIi~~p~r~w~~~~l~~Im~aCiILHNMIvEDEr 202 (205)
T PF04827_consen 159 RAFGVLQARFAIIRGPARLWDREDLANIMRACIILHNMIVEDER 202 (205)
T ss_pred HHHHHHHHHHHHhcCchhccCHHHHHHHHHHHHHhhheeEeccc
Confidence 9999999999999 5555 6899999999999999999986654
No 4
>PF13612 DDE_Tnp_1_3: Transposase DDE domain
Probab=99.15 E-value=1.9e-11 Score=99.94 Aligned_cols=125 Identities=21% Similarity=0.231 Sum_probs=93.9
Q ss_pred CCCceeeecceEEEEeCCCC----------CcccccccCCccccceeeeccCCcceEEeeccCCccccchhhhccccccc
Q psy15697 111 FPNVAGCVDGTMVLIDAPNE----------HEDQFVNRNGDHALNVMAICGPNYKFYAVNANWPGSVHDARVMRNSMVYR 180 (332)
Q Consensus 111 ~p~~~G~iDgt~i~i~~P~~----------~~~~y~~~k~~~s~~~~~v~d~~g~~~~v~~~~~Gs~~D~~v~~~s~l~~ 180 (332)
-+..+.+||.|.+|+..|.. ...-|+..+-+|++|++++|+..|.++.+... ||++||..++. .+..
T Consensus 3 ~~~~i~~iDS~Pi~vC~~~R~~r~k~~~~~a~~G~~a~~~fyGfKlHllv~~~G~i~~~~lT-~an~~D~~~~~--~l~~ 79 (155)
T PF13612_consen 3 QCTGIYIIDSFPIPVCHNIRIKRHKVFKGLAYRGYCAMGWFYGFKLHLLVNDSGEIVAFTLT-PANVHDRKVLE--ELSE 79 (155)
T ss_pred CccEEEEEecCChhHhCccchhhhccccCccccceeccceeEeeeeeeEEccCCcEEEEEEc-ccccccccccc--cccc
Confidence 35678899999999976631 11233444456999999999999999998765 99999998883 2222
Q ss_pred cccccCCCCCCCceEecCCCCCCCC----------cCCCCccCCCC-ChHHHHHHHHHHHHHHHHHHHHHHHhhhcccc
Q psy15697 181 KFDEEGWRPFPDAVILGDSAYPLKE----------WLIPPRTRNPD-AAADQRFLRCHKRTRRLIENSFGILKEKFPCL 248 (332)
Q Consensus 181 ~l~~~~~~~~~~~~llgD~gY~~~~----------~l~~P~~~~~~-~~~~~~fN~~~s~~R~~vE~~fg~LK~rf~~L 248 (332)
.+ ...++||+||-... .++|| .+..- ......+++.+.+.|..||-+|+.||+.|.+=
T Consensus 80 ~~---------~g~l~gDkGYis~~L~~~L~~~gI~L~t~-~RkNmk~~~~~~~~~~l~~~R~~IETvfs~Lk~~~~ie 148 (155)
T PF13612_consen 80 NL---------KGKLFGDKGYISKELKDELKEQGIKLITP-RRKNMKNKLMPLFDKLLLRKRRIIETVFSQLKNQFNIE 148 (155)
T ss_pred cc---------ccceecchhhhcchHHhhhhhceEEEecc-ccccccccccchhhhhhhheeeEeehHHHHHHHhhceE
Confidence 11 55799999997533 37888 77543 23345688899999999999999999988775
No 5
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=99.12 E-value=7.5e-11 Score=78.74 Aligned_cols=49 Identities=22% Similarity=0.449 Sum_probs=47.0
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHHh
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVDT 85 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~~ 85 (332)
+++++++++++|.||+.|.++..+|..||||+|||++++++++++|+..
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 5789999999999999999999999999999999999999999999983
No 6
>PF01609 DDE_Tnp_1: Transposase DDE domain; InterPro: IPR002559 Autonomous mobile genetic elements such as transposon or insertion sequences (IS) encode an enzyme, transposase, that is required for excising and inserting the mobile element. Transposases have been grouped into various families [, , ]. This family includes the IS4 transposase. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 3ECP_A 4DM0_A 1MUS_A 1MUH_A 1MM8_A 1B7E_A.
Probab=97.79 E-value=5.1e-07 Score=77.46 Aligned_cols=147 Identities=16% Similarity=0.186 Sum_probs=84.6
Q ss_pred ceeeecceEEEEeCCC-CCcccccccCCccccceeeec-cCCcceEEeeccCCccccchhhhccccccccccccCCCCCC
Q psy15697 114 VAGCVDGTMVLIDAPN-EHEDQFVNRNGDHALNVMAIC-GPNYKFYAVNANWPGSVHDARVMRNSMVYRKFDEEGWRPFP 191 (332)
Q Consensus 114 ~~G~iDgt~i~i~~P~-~~~~~y~~~k~~~s~~~~~v~-d~~g~~~~v~~~~~Gs~~D~~v~~~s~l~~~l~~~~~~~~~ 191 (332)
.+-+||+|.++.. +. .....+.+++...++++++++ +..|.++.+... +|+.+|...+.. +.+.. ....
T Consensus 5 ~~~~iD~T~i~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~d~~~~~~--ll~~~-----~~~~ 75 (213)
T PF01609_consen 5 RVVAIDGTTIRTP-HDKSARRYKKGKKRGFGYKLHLAVDDNSGLPLSVKVT-PGNVHDSKALPE--LLERK-----PGRK 75 (213)
T ss_dssp EEEEEETTT--EE-EEEEE-B-SSGGGHSSHGGHHHHHHHHHGGGGGGEEE-EEEGG-HHHHHH--HHTT----------
T ss_pred eEEEEECcEEEee-cchhhhcccCCCCcCCCEeEEEEEeecccceeeeecc-ccccceeecccc--ccccc-----cccc
Confidence 4568999999988 21 112334445666778999998 457777777777 999999988875 22221 1334
Q ss_pred CceEecCCCCCCCCc----------CCCCccCCCC-C----------------------------------hHHHHHHHH
Q psy15697 192 DAVILGDSAYPLKEW----------LIPPRTRNPD-A----------------------------------AADQRFLRC 226 (332)
Q Consensus 192 ~~~llgD~gY~~~~~----------l~~P~~~~~~-~----------------------------------~~~~~fN~~ 226 (332)
+..+++|+||...+. .+.| .+... . ...+.....
T Consensus 76 ~~~vv~D~gy~s~~~~~~l~~~~~~~vi~-~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 154 (213)
T PF01609_consen 76 PDLVVADRGYDSAENLEALKERGIHFVIR-LKKNRKKKIQKIENKFWKSFDRRSARKKPKQKSKRVRVVIRKEQKKKGYF 154 (213)
T ss_dssp EEEEEE-S--BBTTHHHHHHTS---EEEE-E--EEEE-TTS-EEEE--EEEEEEEEEEETGGGEEEEEEEEEECS--TTS
T ss_pred ccceeecccccceeccccccccccccccc-cccccccccccchhhccccccccccccccccccccccccccccccccccc
Confidence 779999999975432 1223 22111 0 001111122
Q ss_pred --------------HHHHHHHHHHHHHHHhhhcccccccc-cCcccHHHHHHHHHHHHhh
Q psy15697 227 --------------HKRTRRLIENSFGILKEKFPCLNYMR-LSPQFAGMVVLASTTLHNI 271 (332)
Q Consensus 227 --------------~s~~R~~vE~~fg~LK~rf~~L~~~~-~~~~~~~~ii~a~~~LhN~ 271 (332)
+.+.|..||+.|+.||+.|. |..++ .+...+...+.++++..|+
T Consensus 155 ~~~~~~~~~~~~~~~Y~~Rw~IE~~f~~lK~~~~-l~~~~~~~~~~~~~~~~~~~la~nl 213 (213)
T PF01609_consen 155 LVTNITTLPRDTAALYRRRWQIERFFRELKQFLG-LERLRVRSPERIEAHLFLTLLAYNL 213 (213)
T ss_dssp ---EEEEEESS--SHHHCGGHHHHHHHHHTTTTT-GGGS--SSHHHHHHHHHHHHHH---
T ss_pred ccccccccccccceeecccchhhHHHHHHHhcCC-CchhcccCHHHHHHHHHHHHhhCcC
Confidence 88999999999999998654 44444 4677778888888877775
No 7
>PF13586 DDE_Tnp_1_2: Transposase DDE domain
Probab=97.66 E-value=2.4e-05 Score=58.02 Aligned_cols=75 Identities=19% Similarity=0.161 Sum_probs=49.0
Q ss_pred EecCCCCCCCC-------cCCCCccC---CCCChHHHHHHHHHHHHHHHHHHHHHHHhhhcccc-cccccCcccHHHHHH
Q psy15697 195 ILGDSAYPLKE-------WLIPPRTR---NPDAAADQRFLRCHKRTRRLIENSFGILKEKFPCL-NYMRLSPQFAGMVVL 263 (332)
Q Consensus 195 llgD~gY~~~~-------~l~~P~~~---~~~~~~~~~fN~~~s~~R~~vE~~fg~LK~rf~~L-~~~~~~~~~~~~ii~ 263 (332)
+++|+||.... .-+.|.++ .+....+..+...+.+.|..||++|+.||. |+.| ..+...+......+.
T Consensus 1 v~aDkgYd~~~~r~~l~~~gi~~~i~~~~~~~~~~~~~~d~~~~~~Rw~VEr~f~wlk~-~Rrl~~ryek~~~s~~~~v~ 79 (88)
T PF13586_consen 1 VLADKGYDSRALREYLRERGIRPVIPKRGRRKKRRPRKFDFRLYKRRWVVERTFAWLKR-FRRLATRYEKLASSFLAFVH 79 (88)
T ss_pred CcccCCcCCHHHHHHHHHCCCEEecCCCCCccccccCccchhhhccceehhhhhHHHHH-cCccccccccCHHHHHHHHH
Confidence 47899996521 12222122 111223567888999999999999999995 7777 777766666666665
Q ss_pred HHHHHHh
Q psy15697 264 ASTTLHN 270 (332)
Q Consensus 264 a~~~LhN 270 (332)
.+|++-+
T Consensus 80 la~~~i~ 86 (88)
T PF13586_consen 80 LACIVIW 86 (88)
T ss_pred HHHHHHH
Confidence 5555443
No 8
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=96.74 E-value=0.00056 Score=43.73 Aligned_cols=41 Identities=20% Similarity=0.255 Sum_probs=30.6
Q ss_pred CCCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhH
Q psy15697 36 VALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHE 77 (332)
Q Consensus 36 ~~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~ 77 (332)
..++.+ ++.-++..+..|.+..++|..||||++||.|++.+
T Consensus 4 ~~~~~~-~~~~i~~l~~~G~si~~IA~~~gvsr~TvyR~l~~ 44 (45)
T PF02796_consen 4 PKLSKE-QIEEIKELYAEGMSIAEIAKQFGVSRSTVYRYLNK 44 (45)
T ss_dssp SSSSHC-CHHHHHHHHHTT--HHHHHHHTTS-HHHHHHHHCC
T ss_pred CCCCHH-HHHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 445544 45667778899999999999999999999999864
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=96.40 E-value=0.0043 Score=40.48 Aligned_cols=45 Identities=20% Similarity=0.285 Sum_probs=38.2
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHH
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVI 82 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l 82 (332)
.+|++++-.+.++| -.+.++.++|..+|+|.+||+++.++.+.-|
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 57899999999888 6688999999999999999999999887655
No 10
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=96.29 E-value=0.0018 Score=41.14 Aligned_cols=40 Identities=20% Similarity=0.284 Sum_probs=23.0
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhH
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHE 77 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~ 77 (332)
.++++++..+. .++..|.+.+.+|..+|+|++||++.+++
T Consensus 4 ~Lt~~eR~~I~-~l~~~G~s~~~IA~~lg~s~sTV~relkR 43 (44)
T PF13936_consen 4 HLTPEERNQIE-ALLEQGMSIREIAKRLGRSRSTVSRELKR 43 (44)
T ss_dssp --------HHH-HHHCS---HHHHHHHTT--HHHHHHHHHH
T ss_pred chhhhHHHHHH-HHHHcCCCHHHHHHHHCcCcHHHHHHHhc
Confidence 46666666655 44789999999999999999999999875
No 11
>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=96.03 E-value=0.0033 Score=41.64 Aligned_cols=42 Identities=19% Similarity=0.284 Sum_probs=31.4
Q ss_pred CCCCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhH
Q psy15697 35 NVALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHE 77 (332)
Q Consensus 35 ~~~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~ 77 (332)
+..+++++++-+ +..+-.|.+..+||..|||++|||+.|+..
T Consensus 4 R~~LTl~eK~~i-I~~~e~g~s~~~ia~~fgv~~sTv~~I~K~ 45 (53)
T PF04218_consen 4 RKSLTLEEKLEI-IKRLEEGESKRDIAREFGVSRSTVSTILKN 45 (53)
T ss_dssp SSS--HHHHHHH-HHHHHCTT-HHHHHHHHT--CCHHHHHHHC
T ss_pred CccCCHHHHHHH-HHHHHcCCCHHHHHHHhCCCHHHHHHHHHh
Confidence 467889999876 455788889999999999999999999874
No 12
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=95.54 E-value=0.016 Score=42.12 Aligned_cols=47 Identities=15% Similarity=0.189 Sum_probs=43.1
Q ss_pred CCCCCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHH
Q psy15697 34 RNVALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVP 80 (332)
Q Consensus 34 ~~~~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~ 80 (332)
++..+++..++.++-..+..|.+...++..||||..|+++++.++-.
T Consensus 5 ~nA~Lt~~gR~~lv~~vv~~g~~~a~aA~~~gVS~~Ta~kW~~Ryra 51 (85)
T PF13011_consen 5 KNARLTPRGRLRLVRRVVEQGWPVAHAAAEFGVSRRTAYKWLARYRA 51 (85)
T ss_pred CCCCCCHHHHHHHHHHHHHcCCcHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 45679999999999999999999999999999999999999998764
No 13
>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=95.30 E-value=0.012 Score=35.31 Aligned_cols=22 Identities=14% Similarity=0.255 Sum_probs=17.4
Q ss_pred CChhHHHHHhcCCHHHHHHHHH
Q psy15697 1 MTPFAFKEAFRLSATQVEFILE 22 (332)
Q Consensus 1 ~~d~~f~~~frms~~~F~~L~~ 22 (332)
|+|++|...|+|+++.|..|=.
T Consensus 2 Lsd~dF~~vFgm~~~eF~~lP~ 23 (36)
T PF02209_consen 2 LSDEDFEKVFGMSREEFYKLPK 23 (36)
T ss_dssp S-HHHHHHHHSS-HHHHHHS-H
T ss_pred cCHHHHHHHHCCCHHHHHHChH
Confidence 6899999999999999988743
No 14
>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=95.15 E-value=0.024 Score=37.41 Aligned_cols=44 Identities=20% Similarity=0.339 Sum_probs=32.0
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHH
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPV 81 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~ 81 (332)
.+|+.++.++.|.|+. |.++.++|..+|+|.+||...+.+....
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 4778888877776665 8999999999999999999988876543
No 15
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=95.03 E-value=0.0082 Score=39.04 Aligned_cols=31 Identities=23% Similarity=0.238 Sum_probs=21.7
Q ss_pred hhhccCCcccccccccCCChhhHHhHHhHhH
Q psy15697 49 HWMGVGSPYHIIGATHGPSKSSICRSIHEVV 79 (332)
Q Consensus 49 ~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~ 79 (332)
..+..|.+...+|..+|||++||+++++++.
T Consensus 12 ~l~~~G~s~~~ia~~lgvs~~Tv~~w~kr~~ 42 (50)
T PF13384_consen 12 RLLREGWSIREIAKRLGVSRSTVYRWIKRYR 42 (50)
T ss_dssp HHHHHT--HHHHHHHHTS-HHHHHHHHT---
T ss_pred HHHHCCCCHHHHHHHHCcCHHHHHHHHHHcc
Confidence 3334499999999999999999999998864
No 16
>PF12116 SpoIIID: Stage III sporulation protein D; InterPro: IPR014208 Members of this entry represent the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if, and only if, the species is capable of endospore formation. In Bacillus subtilis SpoIIID is a DNA binding protein that is involved in gene repression as well as activation [].; PDB: 2L0K_A.
Probab=94.72 E-value=0.022 Score=40.44 Aligned_cols=46 Identities=15% Similarity=0.162 Sum_probs=32.6
Q ss_pred HHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHHhhhc
Q psy15697 43 KVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVDTFFQ 88 (332)
Q Consensus 43 ~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~~l~~ 88 (332)
.+-+.=+.+.+..+.+..|..||||+|||++=+.+=+..|...|+.
T Consensus 8 ~i~i~~yIi~~~aTVR~~Ak~FGvSKSTVHkDvteRL~~in~~La~ 53 (82)
T PF12116_consen 8 VIEIANYIIETKATVRQAAKVFGVSKSTVHKDVTERLPKINPELAR 53 (82)
T ss_dssp HHHHHHHHHHH---HHHHHHHHTS-HHHHHHHHTTHHHHH-HHHHH
T ss_pred HHHHHHHHHHcccHHHHHHHHHCCcHHHHHHHHHHHHHhcCHHHHH
Confidence 3555667788899999999999999999999998877776664443
No 17
>PF13518 HTH_28: Helix-turn-helix domain
Probab=94.67 E-value=0.021 Score=37.29 Aligned_cols=37 Identities=19% Similarity=0.246 Sum_probs=30.6
Q ss_pred HHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHH
Q psy15697 43 KVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVP 80 (332)
Q Consensus 43 ~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~ 80 (332)
++.+...++ .|.+...+|..||||.+||.+++..+-.
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 345566666 5779999999999999999999998765
No 18
>smart00153 VHP Villin headpiece domain.
Probab=94.60 E-value=0.028 Score=33.81 Aligned_cols=20 Identities=15% Similarity=0.326 Sum_probs=18.7
Q ss_pred CChhHHHHHhcCCHHHHHHH
Q psy15697 1 MTPFAFKEAFRLSATQVEFI 20 (332)
Q Consensus 1 ~~d~~f~~~frms~~~F~~L 20 (332)
++|++|...|+|+++.|..|
T Consensus 2 LsdeeF~~vfgmsr~eF~~L 21 (36)
T smart00153 2 LSDEDFEEVFGMTREEFYKL 21 (36)
T ss_pred CCHHHHHHHHCCCHHHHHhC
Confidence 68999999999999999877
No 19
>smart00351 PAX Paired Box domain.
Probab=94.42 E-value=0.037 Score=43.71 Aligned_cols=45 Identities=11% Similarity=-0.039 Sum_probs=38.4
Q ss_pred CCCCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHH
Q psy15697 35 NVALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVP 80 (332)
Q Consensus 35 ~~~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~ 80 (332)
..+++.+.+.-+.+.+. .|.+...+|..||||++||+++++++-.
T Consensus 15 ~~~~s~~~R~riv~~~~-~G~s~~~iA~~~gvs~~tV~kwi~r~~~ 59 (125)
T smart00351 15 GRPLPDEERQRIVELAQ-NGVRPCDISRQLCVSHGCVSKILGRYYE 59 (125)
T ss_pred CCCCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 45688888888877665 7999999999999999999999998743
No 20
>PF13340 DUF4096: Putative transposase of IS4/5 family (DUF4096)
Probab=94.38 E-value=0.12 Score=36.83 Aligned_cols=46 Identities=15% Similarity=0.230 Sum_probs=40.6
Q ss_pred CCCCCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHH
Q psy15697 34 RNVALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVP 80 (332)
Q Consensus 34 ~~~~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~ 80 (332)
++...+..+-+-..|+.+++|+.++.|...|| +.+||++.+.++..
T Consensus 21 ~~~~~~~R~v~~ail~~lrtG~~Wr~LP~~fg-~~~tv~~~f~rW~~ 66 (75)
T PF13340_consen 21 GRPRIDLREVLNAILYVLRTGCPWRDLPEDFG-PWSTVYRRFRRWSR 66 (75)
T ss_pred CCCccchHHHHhcccccceecceecccchhcc-CcCcHHHHHHHHHH
Confidence 45668888999999999999999999999999 88899999887754
No 21
>PF05225 HTH_psq: helix-turn-helix, Psq domain; InterPro: IPR007889 This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster []. In pipsqueak this domain binds to GAGA sequence []. The pipsqueak family, which includes proteins from fungi, sea urchins, nematodes, insects, and vertebrates appear to be proteins essential for sequence-specific targeting of a polycomb group protein complex [].; GO: 0003677 DNA binding; PDB: 2COB_A.
Probab=94.10 E-value=0.031 Score=35.62 Aligned_cols=37 Identities=14% Similarity=0.217 Sum_probs=28.5
Q ss_pred HHHHHHHHhhhccC-CcccccccccCCChhhHHhHHhH
Q psy15697 41 KEKVLSCLHWMGVG-SPYHIIGATHGPSKSSICRSIHE 77 (332)
Q Consensus 41 ~~~l~~~L~~L~~g-~~~~~l~~~fgis~sTv~r~~~~ 77 (332)
++.+..+|..+..| .+++..|..|||+++|+++.++.
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 45677777888888 99999999999999999987654
No 22
>cd00131 PAX Paired Box domain
Probab=93.77 E-value=0.066 Score=42.50 Aligned_cols=45 Identities=9% Similarity=-0.064 Sum_probs=38.3
Q ss_pred CCCCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHH
Q psy15697 35 NVALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVP 80 (332)
Q Consensus 35 ~~~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~ 80 (332)
..++|.+.+.-+.+.+ ..|.+.+.+|..||||++||.++++++-.
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 3678888877777665 68999999999999999999999998765
No 23
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=93.59 E-value=0.081 Score=41.51 Aligned_cols=46 Identities=13% Similarity=0.135 Sum_probs=42.0
Q ss_pred CCCCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHH
Q psy15697 35 NVALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVP 80 (332)
Q Consensus 35 ~~~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~ 80 (332)
+...+.+.++-++...+..|.+...+|..||||.+|+++|+.++..
T Consensus 10 rr~ys~EfK~~aV~~~~~~g~sv~evA~e~gIs~~tl~~W~r~y~~ 55 (121)
T PRK09413 10 RRRRTTQEKIAIVQQSFEPGMTVSLVARQHGVAASQLFLWRKQYQE 55 (121)
T ss_pred CCCCCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHhh
Confidence 4668999999999999999999999999999999999999988753
No 24
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=93.29 E-value=0.058 Score=43.18 Aligned_cols=44 Identities=16% Similarity=0.099 Sum_probs=38.9
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHH
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVP 80 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~ 80 (332)
+.+.+.+.+++..++..|.+.+.+|..||||.+|+.+++++.-.
T Consensus 4 ~~s~~~R~~~~~~~~~~G~S~re~Ak~~gvs~sTvy~wv~r~~e 47 (138)
T COG3415 4 PFSNDLRERVVDAVVGEGLSCREAAKRFGVSISTVYRWVRRYRE 47 (138)
T ss_pred hhhHHHHHHHHHHHHHcCccHHHHHHHhCccHHHHHHHHHHhcc
Confidence 45667788889999999999999999999999999999998753
No 25
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=93.11 E-value=0.04 Score=39.11 Aligned_cols=45 Identities=13% Similarity=0.110 Sum_probs=37.9
Q ss_pred CCCCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhH
Q psy15697 35 NVALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVV 79 (332)
Q Consensus 35 ~~~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~ 79 (332)
+...|++.++-++-.++..|.+..+++..+||+.+|+++++.+..
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 466899999999999999999999999999999999999999987
No 26
>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=93.03 E-value=0.092 Score=30.83 Aligned_cols=39 Identities=18% Similarity=0.238 Sum_probs=28.3
Q ss_pred CCCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHH
Q psy15697 36 VALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSI 75 (332)
Q Consensus 36 ~~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~ 75 (332)
..++.+....+. ..+..+.+...++..+|+|.+|+++++
T Consensus 4 ~~~~~~~~~~i~-~~~~~~~s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 4 PKLTPEQIEEAR-RLLAAGESVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred CcCCHHHHHHHH-HHHHcCCCHHHHHHHHCCCHHHHHHhC
Confidence 345555544443 345577899999999999999998864
No 27
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=92.51 E-value=0.16 Score=33.30 Aligned_cols=44 Identities=14% Similarity=0.240 Sum_probs=34.3
Q ss_pred CCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHH
Q psy15697 38 LSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIV 83 (332)
Q Consensus 38 ~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~ 83 (332)
+++.+.-.+ .++..|.++.++|..+|+|.+||.+++.+....+.
T Consensus 4 l~~~e~~i~--~~~~~g~s~~eia~~l~is~~tv~~~~~~~~~kl~ 47 (58)
T smart00421 4 LTPREREVL--RLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLG 47 (58)
T ss_pred CCHHHHHHH--HHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Confidence 555555433 33578999999999999999999999998866553
No 28
>PRK00118 putative DNA-binding protein; Validated
Probab=92.43 E-value=0.18 Score=38.38 Aligned_cols=48 Identities=15% Similarity=0.108 Sum_probs=38.7
Q ss_pred CCCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 36 VALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 36 ~~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
+.+++.++-++.|+ +-.|.++.++|..+|+|++||.+.+.+....+.+
T Consensus 16 ~~L~ekqRevl~L~-y~eg~S~~EIAe~lGIS~~TV~r~L~RArkkLr~ 63 (104)
T PRK00118 16 SLLTEKQRNYMELY-YLDDYSLGEIAEEFNVSRQAVYDNIKRTEKLLED 63 (104)
T ss_pred ccCCHHHHHHHHHH-HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 44667777666555 4459999999999999999999999988777766
No 29
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=92.14 E-value=0.11 Score=36.58 Aligned_cols=42 Identities=10% Similarity=0.131 Sum_probs=37.0
Q ss_pred CCCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhH
Q psy15697 36 VALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHE 77 (332)
Q Consensus 36 ~~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~ 77 (332)
..+|+..+.+..|.+.-.|.++.++|..+|+|.+||..+++.
T Consensus 14 ~~l~~~~r~af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 14 TWVDSLAEAAAALAREEAGKTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred hcCCHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 347788888888888889999999999999999999998885
No 30
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=92.12 E-value=0.17 Score=32.58 Aligned_cols=42 Identities=24% Similarity=0.402 Sum_probs=33.2
Q ss_pred CCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHH
Q psy15697 38 LSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVP 80 (332)
Q Consensus 38 ~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~ 80 (332)
+++.++-++.+.++ .|.++.++|..+|+|.+|+.+++.+...
T Consensus 11 l~~~~~~~~~~~~~-~~~~~~~ia~~~~~s~~~i~~~~~~~~~ 52 (55)
T cd06171 11 LPEREREVILLRFG-EGLSYEEIAEILGISRSTVRQRLHRALK 52 (55)
T ss_pred CCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 45566655555554 7889999999999999999999988654
No 31
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=91.63 E-value=0.09 Score=34.31 Aligned_cols=32 Identities=16% Similarity=0.188 Sum_probs=26.5
Q ss_pred HHhhhccCCcccccccccCCChhhHHhHHhHh
Q psy15697 47 CLHWMGVGSPYHIIGATHGPSKSSICRSIHEV 78 (332)
Q Consensus 47 ~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v 78 (332)
.+..|....++.++|..+|+|.+||.+++++.
T Consensus 20 i~~~~~~~~s~~~vA~~~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 20 ILKLLRESRSFKDVARELGVSWSTVRRIFDRY 51 (52)
T ss_pred HHHHHhhcCCHHHHHHHHCCCHHHHHHHHHhh
Confidence 44455555799999999999999999999864
No 32
>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=91.62 E-value=0.29 Score=36.16 Aligned_cols=52 Identities=13% Similarity=0.257 Sum_probs=45.8
Q ss_pred CCCCCCCHHHHHHHHHhhhccCCcccccccccC-CChhhHHhHHhHhHHHHHH
Q psy15697 33 ERNVALSAKEKVLSCLHWMGVGSPYHIIGATHG-PSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 33 ~~~~~~~~~~~l~~~L~~L~~g~~~~~l~~~fg-is~sTv~r~~~~v~~~l~~ 84 (332)
.+...+..--++++.|..--.|.++.++|..|| .+.|||+..+.++-..+.+
T Consensus 23 ~R~~~~~~aR~ia~yl~~~~~~~s~~~Ig~~fg~r~hStV~~a~~ri~~~~~~ 75 (90)
T cd06571 23 SRKKEIALARQIAMYLARELTGLSLPEIGRAFGGRDHSTVLHAVRKIEELLEE 75 (90)
T ss_pred CCCcCcchHHHHHHHHHHHHhCCCHHHHHHHhCCCCHhHHHHHHHHHHHHHHh
Confidence 345578888899999999989999999999999 9999999999999887764
No 33
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=91.36 E-value=0.25 Score=41.34 Aligned_cols=47 Identities=13% Similarity=0.090 Sum_probs=41.7
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
.+|++.+.++.|+++ .|.++.++|..+|+|.+||...+++-+..+.+
T Consensus 127 ~Lp~~~R~v~~L~~~-~g~s~~EIA~~lgis~~tVk~~l~rAl~~~~~ 173 (178)
T PRK12529 127 TLRPRVKQAFLMATL-DGMKQKDIAQALDIALPTVKKYIHQAYVTCLS 173 (178)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 478888888888888 79999999999999999999999988777776
No 34
>PRK04217 hypothetical protein; Provisional
Probab=91.23 E-value=0.29 Score=37.58 Aligned_cols=48 Identities=15% Similarity=0.118 Sum_probs=38.5
Q ss_pred CCCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 36 VALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 36 ~~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
..++.+++-++.|. .-.+.++.++|..+|||.+||.+.+.+....|.+
T Consensus 41 ~~Lt~eereai~l~-~~eGlS~~EIAk~LGIS~sTV~r~L~RArkkLre 88 (110)
T PRK04217 41 IFMTYEEFEALRLV-DYEGLTQEEAGKRMGVSRGTVWRALTSARKKVAQ 88 (110)
T ss_pred ccCCHHHHHHHHHH-HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 44677776444333 4478899999999999999999999998888877
No 35
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=90.65 E-value=0.28 Score=40.29 Aligned_cols=46 Identities=15% Similarity=0.302 Sum_probs=41.8
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
.+|+..+-++.|++ .|.++.++|..+|+|.+||...+.+....|-.
T Consensus 112 ~L~~~~r~il~l~~--~g~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~ 157 (166)
T PRK09639 112 KMTERDRTVLLLRF--SGYSYKEIAEALGIKESSVGTTLARAKKKFRK 157 (166)
T ss_pred cCCHHHHHHHHHHH--cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 47888888888877 99999999999999999999999998888877
No 36
>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD. This model represents a protein subfamily found mostly in the Firmicutes (Bacillus and allies). This family is similar in sequence to the trp operon repressor TrpR described by TIGR01321, and represents a distinct clade within the broader family described by pfam01371. At least one species, Xylella fastidiosa, in the Proteobacteria, has a member of both this family and TIGR01321. Several genomes with a member of this family do not synthesize tryptophan, and members of this family should not be considered trp operon repressors without new evidence.
Probab=90.38 E-value=0.17 Score=37.24 Aligned_cols=32 Identities=28% Similarity=0.384 Sum_probs=27.5
Q ss_pred HHHHhhhccCCcccccccccCCChhhHHhHHh
Q psy15697 45 LSCLHWMGVGSPYHIIGATHGPSKSSICRSIH 76 (332)
Q Consensus 45 ~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~ 76 (332)
...+.++..|.+...+|..+|||++||+++.+
T Consensus 41 ~~I~~ll~~G~S~~eIA~~LgISrsTIyRi~R 72 (88)
T TIGR02531 41 LQVAKMLKQGKTYSDIEAETGASTATISRVKR 72 (88)
T ss_pred HHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 44566789999999999999999999999553
No 37
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=89.89 E-value=0.46 Score=38.75 Aligned_cols=50 Identities=14% Similarity=0.113 Sum_probs=41.8
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHHhhh
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVDTFF 87 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~~l~ 87 (332)
.+|+..+-++.|+++ .|.++.++|..+|+|.+||...+.+....|...+.
T Consensus 106 ~Lp~~~r~v~~l~~~-~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 155 (161)
T PRK09047 106 KLPARQREAFLLRYW-EDMDVAETAAAMGCSEGSVKTHCSRATHALAKALE 155 (161)
T ss_pred hCCHHHHHHHHHHHH-hcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 367777777777766 48999999999999999999999999988887443
No 38
>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=89.86 E-value=0.38 Score=31.48 Aligned_cols=33 Identities=12% Similarity=0.216 Sum_probs=28.6
Q ss_pred hccCCcccccccccCCChhhHHhHHhHhHHHHH
Q psy15697 51 MGVGSPYHIIGATHGPSKSSICRSIHEVVPVIV 83 (332)
Q Consensus 51 L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~ 83 (332)
+..|.+..++|..+++|.+|+.+.+++....+.
T Consensus 12 ~~~~~s~~eia~~l~~s~~tv~~~~~~~~~~l~ 44 (57)
T cd06170 12 LAEGKTNKEIADILGISEKTVKTHLRNIMRKLG 44 (57)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHhC
Confidence 458899999999999999999999998766544
No 39
>PHA00542 putative Cro-like protein
Probab=89.17 E-value=0.27 Score=35.68 Aligned_cols=31 Identities=19% Similarity=0.262 Sum_probs=26.6
Q ss_pred HHhhhccCCcccccccccCCChhhHHhHHhH
Q psy15697 47 CLHWMGVGSPYHIIGATHGPSKSSICRSIHE 77 (332)
Q Consensus 47 ~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~ 77 (332)
...+...|.++.++|...|||++|++++.+.
T Consensus 24 ~~~l~~~glTq~elA~~lgIs~~tIsr~e~g 54 (82)
T PHA00542 24 VCALIRAGWSQEQIADATDVSQPTICRIYSG 54 (82)
T ss_pred HHHHHHCCCCHHHHHHHHCcCHHHHHHHHcC
Confidence 3445788999999999999999999999863
No 40
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=89.09 E-value=0.4 Score=39.83 Aligned_cols=47 Identities=15% Similarity=0.170 Sum_probs=40.1
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
.+|+.++.++.|.++ .|.++.++|..+|+|.+||...+++...-|-.
T Consensus 128 ~L~~~~r~vl~l~~~-~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 174 (182)
T PRK09652 128 SLPEELRTAITLREI-EGLSYEEIAEIMGCPIGTVRSRIFRAREALRA 174 (182)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 377778887777776 68899999999999999999999988877766
No 41
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=88.94 E-value=0.55 Score=38.63 Aligned_cols=47 Identities=19% Similarity=0.139 Sum_probs=41.1
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
.+|+..+-++.|.++ .|.++.++|..+|+|.+||...+.+....|-.
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 367777777878777 79999999999999999999999999888876
No 42
>PHA00675 hypothetical protein
Probab=88.81 E-value=0.3 Score=34.49 Aligned_cols=41 Identities=17% Similarity=0.127 Sum_probs=29.5
Q ss_pred CCCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHh
Q psy15697 36 VALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIH 76 (332)
Q Consensus 36 ~~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~ 76 (332)
..+...+.-.+....-+.|.++..||..||||++||+.|.+
T Consensus 21 AKLt~~qV~~IR~l~~r~G~s~~~IA~~fGVsrstV~~I~~ 61 (78)
T PHA00675 21 AKLTDAEVERIRELHEVEGMSYAVLAEKFEQSKGAIAKICR 61 (78)
T ss_pred cccCHHHHHHHHHHHHhcCccHHHHHHHhCCCHHHHHHHHc
Confidence 33444444444333337888999999999999999998875
No 43
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=88.60 E-value=1.2 Score=34.67 Aligned_cols=73 Identities=16% Similarity=0.172 Sum_probs=45.0
Q ss_pred hHHHHHhcCCHHHHHHHHHHhccCcCCCCCC-CCCCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHh
Q psy15697 4 FAFKEAFRLSATQVEFILEEIAPALTTPTER-NVALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEV 78 (332)
Q Consensus 4 ~~f~~~frms~~~F~~L~~~L~~~~~~~~~~-~~~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v 78 (332)
.+--..|++++.++...+..-+.-......+ +..++. +.| ..+.---...+..+++..||||.+|+++.++++
T Consensus 22 ~eaa~~F~VS~~Tv~~W~k~~~~G~~~~k~r~~~Kid~-~~L-~~~v~~~pd~tl~Ela~~l~Vs~~ti~~~Lkrl 95 (119)
T PF01710_consen 22 REAAKRFGVSRNTVYRWLKRKETGDLEPKPRGRKKIDR-DEL-KALVEENPDATLRELAERLGVSPSTIWRALKRL 95 (119)
T ss_pred HHHHHHhCcHHHHHHHHHHhcccccccccccccccccH-HHH-HHHHHHCCCcCHHHHHHHcCCCHHHHHHHHHHc
Confidence 3455689999999988887433321111111 124432 222 222222344677899999999999999888764
No 44
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=88.50 E-value=0.5 Score=42.22 Aligned_cols=47 Identities=21% Similarity=0.217 Sum_probs=40.9
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
.+|+.++..+.|+|+ .+.++.++|..+|+|.+||+++.++....|-.
T Consensus 205 ~L~~~er~vi~l~y~-e~~t~~EIA~~lgis~~~V~~~~~ral~kLr~ 251 (257)
T PRK05911 205 ALEEKERKVMALYYY-EELVLKEIGKILGVSESRVSQIHSKALLKLRA 251 (257)
T ss_pred cCCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 377778888888875 68999999999999999999999998888776
No 45
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=88.40 E-value=0.62 Score=38.14 Aligned_cols=46 Identities=15% Similarity=0.101 Sum_probs=38.0
Q ss_pred CCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 38 LSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 38 ~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
+|++.+-.+.|.++. |.++.++|..+|+|.+||...+.+...-|-.
T Consensus 110 L~~~~r~v~~l~~~~-~~s~~EIA~~lgis~~tV~~~l~ra~~~lr~ 155 (163)
T PRK07037 110 LPARTRYAFEMYRLH-GETQKDIARELGVSPTLVNFMIRDALVHCRK 155 (163)
T ss_pred CCHHHHHHHHHHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 566666666666655 9999999999999999999998888877766
No 46
>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=88.37 E-value=0.54 Score=38.08 Aligned_cols=47 Identities=17% Similarity=0.211 Sum_probs=39.7
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
.+|+.++-++.|+++ .|.++.++|..+|+|.+||....++....|-.
T Consensus 113 ~L~~~~r~il~l~~~-~~~~~~eIA~~lgis~~tv~~~~~ra~~~Lr~ 159 (161)
T TIGR02985 113 KLPEQCRKIFILSRF-EGKSYKEIAEELGISVKTVEYHISKALKELRK 159 (161)
T ss_pred HCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 367788888888777 59999999999999999999999988776654
No 47
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=88.35 E-value=0.55 Score=41.16 Aligned_cols=48 Identities=23% Similarity=0.251 Sum_probs=41.7
Q ss_pred CCCHHHHHHHHHhhh---ccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 37 ALSAKEKVLSCLHWM---GVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L---~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
.+|+..+-.+.|+|+ -.|.++.++|..+|+|.+||.+.+++....|-.
T Consensus 178 ~Lp~~~R~v~~L~y~l~~~eg~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~ 228 (234)
T PRK08301 178 KLSDREKQIMELRFGLNGGEEKTQKEVADMLGISQSYISRLEKRIIKRLKK 228 (234)
T ss_pred hCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 377888888888874 579999999999999999999999998888776
No 48
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=88.22 E-value=0.6 Score=39.45 Aligned_cols=53 Identities=4% Similarity=-0.155 Sum_probs=43.2
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHHhhhccc
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVDTFFQRM 90 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~~l~~~~ 90 (332)
.+|+..+-++.|.++- |.++.++|..+|+|.+||...+.+....|...+....
T Consensus 131 ~Lp~~~r~v~~l~~~~-g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~ 183 (191)
T PRK12520 131 RLPPRTGRVFMMREWL-ELETEEICQELQITATNAWVLLYRARMRLRECLDLHW 183 (191)
T ss_pred hCCHHHHHHHHHHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3777788877777765 7999999999999999999999999888877444433
No 49
>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=88.10 E-value=0.53 Score=38.71 Aligned_cols=47 Identities=11% Similarity=0.170 Sum_probs=40.7
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
.+|+.++.++.|+|+. |.++.++|..+|+|.+||...+++....|-.
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 4788888888887775 8999999999999999999999988877654
No 50
>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=88.04 E-value=0.16 Score=32.47 Aligned_cols=21 Identities=29% Similarity=0.368 Sum_probs=18.4
Q ss_pred ccccccccCCChhhHHhHHhH
Q psy15697 57 YHIIGATHGPSKSSICRSIHE 77 (332)
Q Consensus 57 ~~~l~~~fgis~sTv~r~~~~ 77 (332)
..++|...|+|.+|||++++.
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 357899999999999999984
No 51
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=87.95 E-value=0.55 Score=39.84 Aligned_cols=50 Identities=16% Similarity=0.122 Sum_probs=41.9
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHHhhh
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVDTFF 87 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~~l~ 87 (332)
.+|+..+-++.|+++ .|.++.++|..+|+|.+||...+++....|-..+.
T Consensus 136 ~L~~~~r~i~~L~~~-~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~ 185 (195)
T PRK12532 136 NLPENTARVFTLKEI-LGFSSDEIQQMCGISTSNYHTIMHRARESLRQCLQ 185 (195)
T ss_pred hCCHHHHHHhhhHHH-hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 367777777777776 68999999999999999999999999888887443
No 52
>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=87.90 E-value=0.33 Score=34.99 Aligned_cols=37 Identities=22% Similarity=0.301 Sum_probs=27.8
Q ss_pred HHHHHHHHhhhccC-CcccccccccCCChhhHHhHHhH
Q psy15697 41 KEKVLSCLHWMGVG-SPYHIIGATHGPSKSSICRSIHE 77 (332)
Q Consensus 41 ~~~l~~~L~~L~~g-~~~~~l~~~fgis~sTv~r~~~~ 77 (332)
++++...+.+|..| .+..++|..||+|.+||++.++.
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 44555666666653 36778999999999999998763
No 53
>PRK15320 transcriptional activator SprB; Provisional
Probab=87.90 E-value=0.3 Score=41.26 Aligned_cols=39 Identities=13% Similarity=0.120 Sum_probs=35.3
Q ss_pred HHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 46 SCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 46 ~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
-.|..|+.|.+.+++|+.+++|.+||+++..++..-+..
T Consensus 171 EVL~LLAkG~SNKEIAekL~LS~KTVSTYKnRLLeKLgA 209 (251)
T PRK15320 171 ALLILLSSGHPAIELAKKFGLGTKTVSIYRKKVMYRLGM 209 (251)
T ss_pred HHHHHHHcCCCHHHHHHHhccchhhHHHHHHHHHHHcCC
Confidence 578899999999999999999999999999998876653
No 54
>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=87.86 E-value=0.52 Score=35.60 Aligned_cols=43 Identities=9% Similarity=0.197 Sum_probs=36.5
Q ss_pred CHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHH
Q psy15697 39 SAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVI 82 (332)
Q Consensus 39 ~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l 82 (332)
.+.++..+.++|+ .+.++..++..+++|++|++++-++-+..|
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 4678888999999 578899999999999999999988766543
No 55
>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=87.79 E-value=0.57 Score=37.49 Aligned_cols=47 Identities=11% Similarity=0.085 Sum_probs=38.4
Q ss_pred CCCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 36 VALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 36 ~~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
..++..++-.+.|+ ..|.++.++|..+|+|++||+++.++...-|-.
T Consensus 5 ~~Lte~qr~VL~Lr--~~GlTq~EIAe~LgiS~stV~~~e~ra~kkLr~ 51 (137)
T TIGR00721 5 TFLTERQIKVLELR--EKGLSQKEIAKELKTTRANVSAIEKRAMENIEK 51 (137)
T ss_pred CCCCHHHHHHHHHH--HcCCCHHHHHHHHCcCHHHHHHHHHhHHHHHHH
Confidence 34677777777663 699999999999999999999999887766653
No 56
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=87.74 E-value=0.56 Score=39.65 Aligned_cols=47 Identities=11% Similarity=-0.065 Sum_probs=41.0
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
.+|+..+-++.|+++. |.++.++|..+|+|.+||...+++....|-.
T Consensus 134 ~Lp~~~R~v~~L~~~~-g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~ 180 (189)
T PRK12530 134 HLPAQQARVFMMREYL-ELSSEQICQECDISTSNLHVLLYRARLQLQA 180 (189)
T ss_pred hCCHHHHHHHhHHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3677888888888776 9999999999999999999999988888776
No 57
>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=87.71 E-value=0.98 Score=42.85 Aligned_cols=130 Identities=18% Similarity=0.122 Sum_probs=74.9
Q ss_pred HHhhhccCCcccccccc----cC---CChhhHHhHHhHhHHHHHHhhhccccCCCcccccchhhhhhhcCCCCCceeeec
Q psy15697 47 CLHWMGVGSPYHIIGAT----HG---PSKSSICRSIHEVVPVIVDTFFQRMVKWPEENLNDIPMTFLRKGGFPNVAGCVD 119 (332)
Q Consensus 47 ~L~~L~~g~~~~~l~~~----fg---is~sTv~r~~~~v~~~l~~~l~~~~I~~P~~~~~~~~~~f~~~~~~p~~~G~iD 119 (332)
.+..+..|.+.++++.. +| +|++|||+++.++...+.. ...+ ...+.|-.+-.||
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 IISLYLKGVSTRDIEEALEELYGEVAVSKSTVSRITKQLDEEVEA-WRNR-----------------PLESEPYPYLWID 168 (381)
T ss_pred hhhhhccccccccccchhhhhhcccccCchhhhhhhhhhhhhHHH-Hhhh-----------------ccccccccceeee
Confidence 44457778888877644 45 9999999999998877666 2221 1112222345599
Q ss_pred ceEEEEeCCCCCcccccccCCccccceeeeccCCcc--eEEeeccCCccccchhhhccccccccccccCCCCCCCceEec
Q psy15697 120 GTMVLIDAPNEHEDQFVNRNGDHALNVMAICGPNYK--FYAVNANWPGSVHDARVMRNSMVYRKFDEEGWRPFPDAVILG 197 (332)
Q Consensus 120 gt~i~i~~P~~~~~~y~~~k~~~s~~~~~v~d~~g~--~~~v~~~~~Gs~~D~~v~~~s~l~~~l~~~~~~~~~~~~llg 197 (332)
|+++.+..-. .-...++-+.+.++.+|+ ++.+.++ ..-....|. .+...|.+.| ......+++
T Consensus 169 ~~~~kvr~~~--------~~~~~~~~v~iGi~~dG~r~vLg~~~~---~~Es~~~W~--~~l~~L~~RG--l~~~~lvv~ 233 (381)
T PF00872_consen 169 GTYFKVREDG--------RVVKKAVYVAIGIDEDGRREVLGFWVG---DRESAASWR--EFLQDLKERG--LKDILLVVS 233 (381)
T ss_pred eeeccccccc--------ccccchhhhhhhhhcccccceeeeecc---cCCccCEee--ecchhhhhcc--ccccceeec
Confidence 9999986211 112234555667778885 6666554 222233332 3445553555 334567778
Q ss_pred CCCCCCCCcCCC
Q psy15697 198 DSAYPLKEWLIP 209 (332)
Q Consensus 198 D~gY~~~~~l~~ 209 (332)
|.+=.+...+-.
T Consensus 234 Dg~~gl~~ai~~ 245 (381)
T PF00872_consen 234 DGHKGLKEAIRE 245 (381)
T ss_pred cccccccccccc
Confidence 875444444433
No 58
>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=87.62 E-value=0.35 Score=35.86 Aligned_cols=40 Identities=18% Similarity=0.101 Sum_probs=30.8
Q ss_pred CCHHHHHHHHHhh------hccCCcccccccccCCChhhHHhHHhH
Q psy15697 38 LSAKEKVLSCLHW------MGVGSPYHIIGATHGPSKSSICRSIHE 77 (332)
Q Consensus 38 ~~~~~~l~~~L~~------L~~g~~~~~l~~~fgis~sTv~r~~~~ 77 (332)
++|.++-.+.++| +..+.+|+.++...|||.+||+|+=+.
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 5666666665553 356799999999999999999887553
No 59
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=87.48 E-value=0.64 Score=40.37 Aligned_cols=46 Identities=11% Similarity=0.117 Sum_probs=40.8
Q ss_pred CCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 38 LSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 38 ~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
+|+..+-++.|+|+ .|.++.++|..+|||.+||...+++....|..
T Consensus 135 Lp~~~R~v~~L~y~-eg~s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~ 180 (216)
T PRK12533 135 LPVEYREVLVLREL-EDMSYREIAAIADVPVGTVMSRLARARRRLAA 180 (216)
T ss_pred CCHHHHhHhhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 67777787888777 59999999999999999999999998888887
No 60
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=87.34 E-value=0.48 Score=40.09 Aligned_cols=46 Identities=11% Similarity=0.117 Sum_probs=39.1
Q ss_pred CCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 38 LSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 38 ~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
+|++.+-++.|+++. |.++.++|..+|+|.+||...+.+....|-.
T Consensus 142 L~~~~~~v~~l~~~~-g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 187 (194)
T PRK12519 142 LPESQRQVLELAYYE-GLSQSEIAKRLGIPLGTVKARARQGLLKLRE 187 (194)
T ss_pred CCHHHhhhhhhhhhc-CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 567777777777665 8999999999999999999999988887776
No 61
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=87.30 E-value=0.68 Score=38.97 Aligned_cols=47 Identities=15% Similarity=0.167 Sum_probs=41.3
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
.+|+..+-++.|+++ .|.++.++|..+|+|.+||...+.+....|-.
T Consensus 111 ~Lp~~~R~v~~L~~~-eg~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 157 (182)
T PRK12511 111 DLPEEQRAALHLVAI-EGLSYQEAAAVLGIPIGTLMSRIGRARAALRA 157 (182)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHH
Confidence 477888888888877 59999999999999999999999988888777
No 62
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=87.25 E-value=0.61 Score=37.08 Aligned_cols=47 Identities=19% Similarity=0.337 Sum_probs=38.6
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
.+|+.++-.+.+.++ .|.++.++|..+|+|.+||++...+....|-.
T Consensus 110 ~L~~~~~~ii~~~~~-~g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 110 KLPEREREVLVLRYL-EGLSYKEIAEILGISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred hCCHHHHHHHhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 366777776666655 68999999999999999999999998877654
No 63
>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=87.18 E-value=0.73 Score=40.26 Aligned_cols=49 Identities=16% Similarity=0.188 Sum_probs=42.4
Q ss_pred CCCCHHHHHHHHHhhh---ccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 36 VALSAKEKVLSCLHWM---GVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 36 ~~~~~~~~l~~~L~~L---~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
..+|+.++-.+.|+|+ ..|.++.++|..+|+|.+||.+..++....|..
T Consensus 173 ~~L~~~~r~il~l~y~~~~~e~~S~~EIAe~lgis~~tV~~~~~rAl~~Lr~ 224 (227)
T TIGR02846 173 SVLDGREREVIEMRYGLGDGRRKTQREIAKILGISRSYVSRIEKRALMKLYK 224 (227)
T ss_pred HhCCHHHHHHHHHHHcCCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3477888888888886 478999999999999999999999988887765
No 64
>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=87.10 E-value=0.62 Score=41.92 Aligned_cols=47 Identities=15% Similarity=0.200 Sum_probs=41.1
Q ss_pred CCHHHHHHHHHhhhc-cCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 38 LSAKEKVLSCLHWMG-VGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 38 ~~~~~~l~~~L~~L~-~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
+|+.++..+.|+|+. .+.++.++|..+|||+++|+++.++.+.-|-.
T Consensus 219 L~~rer~vl~l~y~~~~~~t~~eIA~~lgvS~~~V~q~~~~Al~kLr~ 266 (270)
T TIGR02392 219 LDARSRRIIEARWLDDDKLTLQELAAEYGVSAERIRQIEKNAMKKLKA 266 (270)
T ss_pred CCHHHHHHHHHHhcCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 777888888998874 47899999999999999999999988887765
No 65
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=87.06 E-value=0.68 Score=38.27 Aligned_cols=46 Identities=15% Similarity=0.299 Sum_probs=39.4
Q ss_pred CCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 38 LSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 38 ~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
+|+..+-.+.|.++ .|.++.+||..+|+|.+||.+.+.+....|-.
T Consensus 126 L~~~~r~i~~l~~~-~~~~~~eIA~~lgis~~tv~~~~~ra~~~lr~ 171 (179)
T PRK11924 126 LPVKQREVFLLRYV-EGLSYREIAEILGVPVGTVKSRLRRARQLLRE 171 (179)
T ss_pred CCHHHHHHhhHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 66777777777776 68999999999999999999999998887766
No 66
>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=86.99 E-value=0.36 Score=31.82 Aligned_cols=30 Identities=13% Similarity=0.203 Sum_probs=24.9
Q ss_pred CCcccccccccCCChhhHHhHHhHhHHHHH
Q psy15697 54 GSPYHIIGATHGPSKSSICRSIHEVVPVIV 83 (332)
Q Consensus 54 g~~~~~l~~~fgis~sTv~r~~~~v~~~l~ 83 (332)
..+..+||..+|||++|++..+++...-|.
T Consensus 23 ~~tl~elA~~lgis~st~~~~LRrae~kli 52 (53)
T PF04967_consen 23 RITLEELAEELGISKSTVSEHLRRAERKLI 52 (53)
T ss_pred cCCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Confidence 356778999999999999999998776553
No 67
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=86.94 E-value=0.77 Score=36.95 Aligned_cols=47 Identities=15% Similarity=0.100 Sum_probs=38.5
Q ss_pred CCCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 36 VALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 36 ~~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
..+++.++-.+.| ...|.++.++|..+|+|++||+++.++....|-.
T Consensus 5 ~~Lt~rqreVL~l--r~~GlTq~EIAe~LGiS~~tVs~ie~ra~kkLr~ 51 (141)
T PRK03975 5 SFLTERQIEVLRL--RERGLTQQEIADILGTSRANVSSIEKRARENIEK 51 (141)
T ss_pred cCCCHHHHHHHHH--HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4577888877777 3699999999999999999999999876665544
No 68
>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=86.90 E-value=0.84 Score=38.13 Aligned_cols=46 Identities=15% Similarity=0.187 Sum_probs=38.9
Q ss_pred CCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 38 LSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 38 ~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
+|+..+-++.|+++. |.++.++|..+|+|.+||...+++....|-.
T Consensus 135 Lp~~~r~v~~l~~~~-g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 180 (183)
T TIGR02999 135 VDPRQAEVVELRFFA-GLTVEEIAELLGVSVRTVERDWRFARAWLAD 180 (183)
T ss_pred CCHHHHHHHHHHHHc-CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 777777766666654 8999999999999999999999998887765
No 69
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=86.89 E-value=0.75 Score=38.33 Aligned_cols=47 Identities=9% Similarity=0.155 Sum_probs=40.2
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
.+|++.+-.+.|.++ .|.++.++|..+|+|.+||...+++....|-+
T Consensus 129 ~L~~~~r~i~~l~~~-~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 175 (179)
T PRK12514 129 ELEKDRAAAVRRAYL-EGLSYKELAERHDVPLNTMRTWLRRSLLKLRE 175 (179)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCChHHHHHHHHHHHHHHHH
Confidence 367777777778776 68999999999999999999999988887766
No 70
>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=86.80 E-value=0.65 Score=29.63 Aligned_cols=28 Identities=14% Similarity=0.167 Sum_probs=22.8
Q ss_pred cCCcccccccccCCChhhHHhHHhHhHH
Q psy15697 53 VGSPYHIIGATHGPSKSSICRSIHEVVP 80 (332)
Q Consensus 53 ~g~~~~~l~~~fgis~sTv~r~~~~v~~ 80 (332)
.+.+..++|..+|+|.+||+++++++..
T Consensus 16 ~~~t~~ela~~~~is~~tv~~~l~~L~~ 43 (48)
T PF13412_consen 16 PRITQKELAEKLGISRSTVNRYLKKLEE 43 (48)
T ss_dssp TTS-HHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 4478999999999999999999998764
No 71
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=86.68 E-value=0.76 Score=40.32 Aligned_cols=48 Identities=19% Similarity=0.225 Sum_probs=41.5
Q ss_pred CCCHHHHHHHHHhhh---ccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 37 ALSAKEKVLSCLHWM---GVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L---~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
.+|+.++..+.|+|+ -.|.++.++|..+|+|.+||.+..++....|..
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 478888999999886 467899999999999999999998887777766
No 72
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=86.64 E-value=0.83 Score=38.60 Aligned_cols=47 Identities=13% Similarity=0.121 Sum_probs=41.1
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
.+|+..+-++.|+++ .|.++.++|..+|+|.+||...+.+....|-.
T Consensus 116 ~Lp~~~r~i~~L~~~-~g~s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~ 162 (187)
T PRK12516 116 QLPDDQREAIILVGA-SGFAYEEAAEICGCAVGTIKSRVNRARQRLQE 162 (187)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 367777877777777 79999999999999999999999999888877
No 73
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=86.44 E-value=0.72 Score=39.21 Aligned_cols=47 Identities=11% Similarity=0.057 Sum_probs=41.1
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
.+|+..+-++.|.++ .|.++.++|..+|+|.+||...+++....|-.
T Consensus 136 ~L~~~~r~i~~L~~~-~g~s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~ 182 (196)
T PRK12524 136 ALPERQRQAVVLRHI-EGLSNPEIAEVMEIGVEAVESLTARGKRALAA 182 (196)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 367777777778777 79999999999999999999999998888876
No 74
>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=86.31 E-value=0.8 Score=37.20 Aligned_cols=48 Identities=13% Similarity=0.260 Sum_probs=41.1
Q ss_pred CCCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 36 VALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 36 ~~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
..+|+.++-.+.|+++ .|.++.++|..+|+|.+||...+++.-..|..
T Consensus 110 ~~L~~~~r~v~~l~~~-~g~~~~eIA~~l~is~~tv~~~l~Rar~~Lr~ 157 (159)
T TIGR02989 110 EKLPERQRELLQLRYQ-RGVSLTALAEQLGRTVNAVYKALSRLRVRLRD 157 (159)
T ss_pred HHCCHHHHHHHHHHHh-cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Confidence 3488888888888776 69999999999999999999999888777654
No 75
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=86.07 E-value=0.84 Score=37.31 Aligned_cols=47 Identities=19% Similarity=0.072 Sum_probs=38.1
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
.+|+..+-++.|.++ .|.++.++|..+|+|.+||...+++....|..
T Consensus 113 ~L~~~~r~v~~L~~~-~g~s~~EIA~~l~is~~tV~~~l~ra~~~~~~ 159 (161)
T PRK12528 113 GLPPLVKRAFLLAQV-DGLGYGEIATELGISLATVKRYLNKAAMRCYF 159 (161)
T ss_pred HCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 367777777766655 48999999999999999999999888776643
No 76
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=86.06 E-value=0.96 Score=37.87 Aligned_cols=48 Identities=10% Similarity=0.145 Sum_probs=41.2
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHHh
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVDT 85 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~~ 85 (332)
.+|+..+-.+.|.|+. |.++.++|..+|+|.+||...+++....|-..
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 3677777777777766 99999999999999999999999998888773
No 77
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=86.06 E-value=0.84 Score=38.17 Aligned_cols=47 Identities=11% Similarity=0.190 Sum_probs=40.9
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
.+|+..+.++.|+++. |.++.++|..+|+|.+||...+.+....|..
T Consensus 127 ~L~~~~r~v~~l~~~~-g~s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~ 173 (179)
T PRK09415 127 SLPIKYREVIYLFYYE-ELSIKEIAEVTGVNENTVKTRLKKAKELLKK 173 (179)
T ss_pred hCCHHHhhHhHhHHhc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3777777877787776 9999999999999999999999998888777
No 78
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=85.98 E-value=0.95 Score=40.39 Aligned_cols=46 Identities=9% Similarity=0.127 Sum_probs=40.6
Q ss_pred CCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 38 LSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 38 ~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
+++.++..+.|+|+ .|.++.++|..+|+|.+||++..++...-|-.
T Consensus 204 L~~~~r~vl~l~y~-~~~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~ 249 (256)
T PRK07408 204 LEERTREVLEFVFL-HDLTQKEAAERLGISPVTVSRRVKKGLDQLKK 249 (256)
T ss_pred CCHHHHHHHHHHHH-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 67777888888886 58999999999999999999999999888776
No 79
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=85.67 E-value=0.45 Score=31.83 Aligned_cols=44 Identities=16% Similarity=0.210 Sum_probs=34.6
Q ss_pred CCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHH
Q psy15697 38 LSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIV 83 (332)
Q Consensus 38 ~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~ 83 (332)
+++.+.- +|.+++.|.+..++|...|||.+||..+...+..-+.
T Consensus 4 LT~~E~~--vl~~l~~G~~~~eIA~~l~is~~tV~~~~~~i~~Kl~ 47 (58)
T PF00196_consen 4 LTERELE--VLRLLAQGMSNKEIAEELGISEKTVKSHRRRIMKKLG 47 (58)
T ss_dssp S-HHHHH--HHHHHHTTS-HHHHHHHHTSHHHHHHHHHHHHHHHHT
T ss_pred cCHHHHH--HHHHHHhcCCcchhHHhcCcchhhHHHHHHHHHHHhC
Confidence 4444433 6788999999999999999999999999988876654
No 80
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=85.55 E-value=0.55 Score=39.00 Aligned_cols=47 Identities=13% Similarity=0.174 Sum_probs=40.8
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
.+|+..+.++.|+++ .|.++.++|..+|+|.+||...+.+....|..
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 377888888888777 69999999999999999999999988887766
No 81
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=85.22 E-value=0.91 Score=37.98 Aligned_cols=47 Identities=13% Similarity=0.138 Sum_probs=40.4
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
.+|+.++-++.|.++ .|.++.++|..+|||.+||...+++....|..
T Consensus 136 ~L~~~~r~il~l~~~-~~~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 182 (187)
T PRK09641 136 QLPEKYRTVIVLKYI-EDLSLKEISEILDLPVGTVKTRIHRGREALRK 182 (187)
T ss_pred hCCHHHHHHhhhHHh-hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 367777787878777 69999999999999999999999988887766
No 82
>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=85.19 E-value=1.1 Score=37.44 Aligned_cols=47 Identities=9% Similarity=0.094 Sum_probs=40.4
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
.+|+.++-++.|.++ .|.++.++|..+|||.+||...+++....|-.
T Consensus 140 ~L~~~~r~vi~l~~~-~g~s~~eIA~~lgis~~~v~~~l~Ra~~~Lr~ 186 (189)
T TIGR02984 140 KLPEDYREVILLRHL-EGLSFAEVAERMDRSEGAVSMLWVRGLARLRQ 186 (189)
T ss_pred cCCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 467877777777776 79999999999999999999999998887765
No 83
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=85.18 E-value=0.94 Score=38.97 Aligned_cols=49 Identities=12% Similarity=-0.060 Sum_probs=41.7
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHHhh
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVDTF 86 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~~l 86 (332)
.+|+..+-++.|+++- |.++.++|..+|+|.+||...+++....|-+.+
T Consensus 148 ~L~~~~r~v~~L~~~~-g~s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l 196 (206)
T PRK12544 148 GLPAKYARVFMMREFI-ELETNEICHAVDLSVSNLNVLLYRARLRLRECL 196 (206)
T ss_pred hCCHHHHHHHHHHHHc-CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4677777877777766 999999999999999999999999988888733
No 84
>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=85.02 E-value=0.91 Score=39.96 Aligned_cols=48 Identities=10% Similarity=0.194 Sum_probs=41.7
Q ss_pred CCCHHHHHHHHHhhh---ccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 37 ALSAKEKVLSCLHWM---GVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L---~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
.+|+.++..+.|+|. ..+.++.++|..+|||.++|+++..+.+.-|-.
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 367888888888884 567899999999999999999999998887766
No 85
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=85.01 E-value=1.2 Score=37.86 Aligned_cols=46 Identities=7% Similarity=0.072 Sum_probs=38.9
Q ss_pred CCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 38 LSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 38 ~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
+|++.+-++.|+++ .|.++.++|..+|+|.+||...+++....|..
T Consensus 142 Lp~~~r~v~~l~~~-eg~s~~EIA~~lgis~~tVk~rl~ra~~~Lr~ 187 (194)
T PRK12531 142 LPKAQRDVLQAVYL-EELPHQQVAEMFDIPLGTVKSRLRLAVEKLRH 187 (194)
T ss_pred CCHHHHHHHHHHHH-cCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHH
Confidence 56667777777766 69999999999999999999998888887776
No 86
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=84.94 E-value=1.1 Score=37.81 Aligned_cols=47 Identities=13% Similarity=0.160 Sum_probs=41.2
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
.+|++.+-++.|+++ .|.++.++|..+|+|.+||...+.+....|-.
T Consensus 131 ~L~~~~r~vl~l~~~-~~~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 177 (189)
T PRK12515 131 KLSPAHREIIDLVYY-HEKSVEEVGEIVGIPESTVKTRMFYARKKLAE 177 (189)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 477788888888877 79999999999999999999999988887776
No 87
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=84.91 E-value=1.2 Score=37.54 Aligned_cols=50 Identities=14% Similarity=0.148 Sum_probs=42.3
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHHhhh
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVDTFF 87 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~~l~ 87 (332)
.+|+..+-++.|+++ .|.++.++|..+|+|.+||...+++....|-+.+.
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 367777777777765 79999999999999999999999999998888443
No 88
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=84.90 E-value=0.93 Score=41.16 Aligned_cols=47 Identities=13% Similarity=0.201 Sum_probs=41.0
Q ss_pred CCHHHHHHHHHhhhc-cCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 38 LSAKEKVLSCLHWMG-VGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 38 ~~~~~~l~~~L~~L~-~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
++..++..+.++|+. .+.++.++|..+|||+++|+++.++.+.-|-.
T Consensus 231 L~~rEr~VL~lry~~~~~~Tl~EIA~~lgvS~~rVrqi~~~Al~kLR~ 278 (284)
T PRK06596 231 LDERSRDIIEARWLDDDKSTLQELAAEYGVSAERVRQIEKNAMKKLKA 278 (284)
T ss_pred CCHHHHHHHHHHhcCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 677788888888875 58899999999999999999999998887765
No 89
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=84.84 E-value=0.95 Score=37.50 Aligned_cols=52 Identities=10% Similarity=0.084 Sum_probs=39.1
Q ss_pred CCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHHhhhcccc
Q psy15697 38 LSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVDTFFQRMV 91 (332)
Q Consensus 38 ~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~~l~~~~I 91 (332)
+|+..+-++. .++-.|.++.++|..+|+|.+||...+.+....|.. ....+|
T Consensus 120 L~~~~r~i~~-l~~~~~~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~-~l~~~~ 171 (173)
T PRK12522 120 LNEKYKTVLV-LYYYEQYSYKEMSEILNIPIGTVKYRLNYAKKQMRE-HLEGFV 171 (173)
T ss_pred CCHHHHHHHH-HHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH-HHHHHh
Confidence 4454554333 344469999999999999999999999999988887 444433
No 90
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=84.79 E-value=1.4 Score=36.47 Aligned_cols=47 Identities=15% Similarity=0.195 Sum_probs=39.4
Q ss_pred CCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHHh
Q psy15697 38 LSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVDT 85 (332)
Q Consensus 38 ~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~~ 85 (332)
+|+..+-++.|+++. |.++.++|..+|+|.+||...+++....|-..
T Consensus 119 L~~~~r~vl~L~~~~-g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~ 165 (173)
T PRK09645 119 LSPEHRAVLVRSYYR-GWSTAQIAADLGIPEGTVKSRLHYALRALRLA 165 (173)
T ss_pred CCHHHHHHHHHHHHc-CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 667777777776655 99999999999999999999999888888773
No 91
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=84.79 E-value=1.2 Score=39.65 Aligned_cols=47 Identities=17% Similarity=0.222 Sum_probs=40.6
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
.+|+.++-++.|+|+ .|.++.++|..+|||.+||.+..++....|-.
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 367777777777775 68999999999999999999999999888776
No 92
>PRK06030 hypothetical protein; Provisional
Probab=84.78 E-value=1.5 Score=34.54 Aligned_cols=47 Identities=13% Similarity=0.264 Sum_probs=42.2
Q ss_pred CCCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHH
Q psy15697 36 VALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVI 82 (332)
Q Consensus 36 ~~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l 82 (332)
..+..--+++|.|..--.+.++.++|..||.+.|||..-++.+-..+
T Consensus 51 k~i~~aRqIAMYL~r~~~~~sl~~IG~~FGRDHSTV~haikkIe~~~ 97 (124)
T PRK06030 51 REVSRIRQIAMYVAHVSLGWPMNEVALAFGRDRTTVGHACHTVEDLR 97 (124)
T ss_pred cccchHHHHHHHHHHHHcCCCHHHHHHHHCCChhHHHHHHHHHHHHh
Confidence 56888999999999999999999999999999999999888766654
No 93
>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=84.76 E-value=0.9 Score=30.50 Aligned_cols=37 Identities=22% Similarity=0.167 Sum_probs=26.4
Q ss_pred HHHHHhhhccC-CcccccccccCCChhhHHhHHhHhHH
Q psy15697 44 VLSCLHWMGVG-SPYHIIGATHGPSKSSICRSIHEVVP 80 (332)
Q Consensus 44 l~~~L~~L~~g-~~~~~l~~~fgis~sTv~r~~~~v~~ 80 (332)
++.+|...... .+..+|+..++++++|+++++++...
T Consensus 10 vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~ 47 (62)
T PF12802_consen 10 VLMALARHPGEELTQSELAERLGISKSTVSRIVKRLEK 47 (62)
T ss_dssp HHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 33344333333 58889999999999999999988754
No 94
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=84.72 E-value=1.2 Score=36.31 Aligned_cols=46 Identities=11% Similarity=0.109 Sum_probs=37.8
Q ss_pred CCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 38 LSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 38 ~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
+|+..+-++.|.++ .|.++.++|..+|+|.+||...+.+....|-.
T Consensus 107 Lp~~~r~v~~l~~~-~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 152 (160)
T PRK09642 107 LPENYRDVVLAHYL-EEKSYQEIALQEKIEVKTVEMKLYRARKWIKK 152 (160)
T ss_pred CCHHHHHHHHHHHH-hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 56666666666554 58999999999999999999999888887776
No 95
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=84.56 E-value=1.1 Score=36.30 Aligned_cols=46 Identities=13% Similarity=0.094 Sum_probs=38.3
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHH
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIV 83 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~ 83 (332)
.+|+.++-++.|.|+. |.++.++|..+|+|.+||...+.+....|-
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 4677788777777765 889999999999999999999998777654
No 96
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=84.51 E-value=1.1 Score=37.60 Aligned_cols=46 Identities=11% Similarity=0.053 Sum_probs=38.1
Q ss_pred CCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 38 LSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 38 ~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
+|+..+.++.|+ +-.|.++.++|..+|+|.+||...+++....|-.
T Consensus 134 L~~~~r~i~~l~-~~~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 179 (182)
T PRK12537 134 LEPARRNCILHA-YVDGCSHAEIAQRLGAPLGTVKAWIKRSLKALRE 179 (182)
T ss_pred CCHHHHHHHHHH-HHcCCCHHHHHHHHCCChhhHHHHHHHHHHHHHH
Confidence 566666666665 4579999999999999999999999998887765
No 97
>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=84.50 E-value=0.94 Score=40.14 Aligned_cols=48 Identities=25% Similarity=0.353 Sum_probs=40.4
Q ss_pred CCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHHhh
Q psy15697 38 LSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVDTF 86 (332)
Q Consensus 38 ~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~~l 86 (332)
+|+..+-++.|+++ .|.++.++|..+|||.+||...+.+....|-..+
T Consensus 162 Lp~~~R~v~~L~~~-eg~S~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~l 209 (244)
T TIGR03001 162 LSERERHLLRLHFV-DGLSMDRIGAMYQVHRSTVSRWVAQARERLLERT 209 (244)
T ss_pred CCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 56667777777766 7899999999999999999999999888887733
No 98
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=84.47 E-value=0.93 Score=38.28 Aligned_cols=46 Identities=15% Similarity=0.105 Sum_probs=39.8
Q ss_pred CCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 38 LSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 38 ~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
+|++.+-.+.|+++ .|.++.++|..+|+|..||...+.+....|-.
T Consensus 139 L~~~~r~v~~l~~~-~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~ 184 (193)
T PRK11923 139 LPEDLRTALTLREF-DGLSYEDIASVMQCPVGTVRSRIFRAREAIDK 184 (193)
T ss_pred CCHHHhHHHhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 66777777777776 69999999999999999999999988888777
No 99
>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily. This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.
Probab=84.30 E-value=1.2 Score=38.70 Aligned_cols=47 Identities=17% Similarity=0.270 Sum_probs=40.6
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
.+|+.++-++.|+|+ .|.++.++|..+|+|.+||.+.+++....|-.
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 477888888878775 58899999999999999999999998887765
No 100
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=84.17 E-value=1.3 Score=36.59 Aligned_cols=47 Identities=26% Similarity=0.208 Sum_probs=39.8
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
.+|+..+.++.|++ -.|.++.++|..+|+|.+||...+.+....+..
T Consensus 118 ~L~~~~r~v~~L~~-~eg~s~~EIA~~l~is~~tV~~~l~ra~~~~~~ 164 (168)
T PRK12525 118 GLSGKARAAFLMSQ-LEGLTYVEIGERLGVSLSRIHQYMVEAFKCCYQ 164 (168)
T ss_pred hCCHHHHHHHHHHH-HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 37788888777775 569999999999999999999999888877765
No 101
>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=84.14 E-value=1.1 Score=39.37 Aligned_cols=48 Identities=21% Similarity=0.245 Sum_probs=42.0
Q ss_pred CCCHHHHHHHHHhhh---ccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 37 ALSAKEKVLSCLHWM---GVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L---~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
.+|+..+..+.|+++ -.|.++.++|...|+|.+||.+..++....|-.
T Consensus 178 ~Lp~~~R~ii~L~~~l~~~eg~s~~EIA~~Lgis~~tV~~~l~ra~~~LR~ 228 (234)
T TIGR02835 178 KLNDREKKIMELRFGLVGGTEKTQKEVADMLGISQSYISRLEKRILKRLKK 228 (234)
T ss_pred hCCHHHHHHHHHHHccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 478888999999885 378999999999999999999999888877766
No 102
>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=84.11 E-value=0.69 Score=29.49 Aligned_cols=28 Identities=11% Similarity=0.116 Sum_probs=22.6
Q ss_pred cCCcccccccccCCChhhHHhHHhHhHH
Q psy15697 53 VGSPYHIIGATHGPSKSSICRSIHEVVP 80 (332)
Q Consensus 53 ~g~~~~~l~~~fgis~sTv~r~~~~v~~ 80 (332)
...+..+++..+|+|++|+++.++....
T Consensus 14 ~~~~~~el~~~l~~s~~~vs~hL~~L~~ 41 (47)
T PF01022_consen 14 GPLTVSELAEELGLSQSTVSHHLKKLRE 41 (47)
T ss_dssp SSEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CCCchhhHHHhccccchHHHHHHHHHHH
Confidence 4467889999999999999999887654
No 103
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=84.01 E-value=1.4 Score=36.42 Aligned_cols=47 Identities=17% Similarity=0.086 Sum_probs=39.6
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
.+|+..+-++.|+++. |.++.++|..+|+|.+||...+.+-..-+..
T Consensus 119 ~Lp~~~r~v~~L~~~~-g~s~~EIA~~lgis~~tV~~~l~ra~~~~~~ 165 (172)
T PRK12523 119 KLSSKARAAFLYNRLD-GMGHAEIAERLGVSVSRVRQYLAQGLRQCYI 165 (172)
T ss_pred hCCHHHHHHHHHHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3677788878777764 8999999999999999999999887777665
No 104
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=83.99 E-value=2 Score=30.15 Aligned_cols=73 Identities=12% Similarity=0.094 Sum_probs=53.0
Q ss_pred ChhHHHHHhcCCHHHHHHHHHHhccCcCCCCCCCCCCCHHHHHHHHHhhhccC-CcccccccccCC-ChhhHHhHHhHhH
Q psy15697 2 TPFAFKEAFRLSATQVEFILEEIAPALTTPTERNVALSAKEKVLSCLHWMGVG-SPYHIIGATHGP-SKSSICRSIHEVV 79 (332)
Q Consensus 2 ~d~~f~~~frms~~~F~~L~~~L~~~~~~~~~~~~~~~~~~~l~~~L~~L~~g-~~~~~l~~~fgi-s~sTv~r~~~~v~ 79 (332)
+-+++-..++++...|..++......-. ...-...++.-++.+|..+ .+..++|..+|. |.++.++.|++..
T Consensus 3 ~~~~la~~~~~s~~~l~~~f~~~~~~s~------~~~~~~~r~~~a~~~l~~~~~~~~~ia~~~g~~s~~~f~r~Fk~~~ 76 (84)
T smart00342 3 TLEDLAEALGMSPRHLQRLFKKETGTTP------KQYLRDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLF 76 (84)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHhCcCH------HHHHHHHHHHHHHHHHHcCCCCHHHHHHHhCCCChHHHHHHHHHHH
Confidence 3456778899999999988876432100 1122345566677777776 789999999999 9999999998765
Q ss_pred H
Q psy15697 80 P 80 (332)
Q Consensus 80 ~ 80 (332)
.
T Consensus 77 g 77 (84)
T smart00342 77 G 77 (84)
T ss_pred C
Confidence 3
No 105
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=83.95 E-value=1.4 Score=36.99 Aligned_cols=46 Identities=13% Similarity=0.143 Sum_probs=38.0
Q ss_pred CCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 38 LSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 38 ~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
+|+..+-++.|.++ .|.++.++|..+|+|.+||...+++....|-.
T Consensus 138 L~~~~r~i~~l~~~-~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 183 (187)
T PRK12534 138 LEPPRSELIRTAFF-EGITYEELAARTDTPIGTVKSWIRRGLAKLKA 183 (187)
T ss_pred CCHHHHHHHHHHHH-cCCCHHHHHHHhCCChhHHHHHHHHHHHHHHH
Confidence 55666666666654 79999999999999999999999998887766
No 106
>PF13610 DDE_Tnp_IS240: DDE domain
Probab=83.92 E-value=2.7 Score=33.74 Aligned_cols=132 Identities=18% Similarity=0.112 Sum_probs=75.5
Q ss_pred eecceEEEEeCCCCCcccccccCCccccceeeeccCCcceEEeeccCCccccchhhhccccccccccccCCCCCCCceEe
Q psy15697 117 CVDGTMVLIDAPNEHEDQFVNRNGDHALNVMAICGPNYKFYAVNANWPGSVHDARVMRNSMVYRKFDEEGWRPFPDAVIL 196 (332)
Q Consensus 117 ~iDgt~i~i~~P~~~~~~y~~~k~~~s~~~~~v~d~~g~~~~v~~~~~Gs~~D~~v~~~s~l~~~l~~~~~~~~~~~~ll 196 (332)
.||=|.|+|. |++ .=+-.++|++|+++++.+.-.-...++..|- ...+ ... ...+..++
T Consensus 5 ~~DEt~iki~----------G~~----~yl~~aiD~~~~~l~~~ls~~Rd~~aA~~Fl----~~~l-~~~--~~~p~~iv 63 (140)
T PF13610_consen 5 HVDETYIKIK----------GKW----HYLWRAIDAEGNILDFYLSKRRDTAAAKRFL----KRAL-KRH--RGEPRVIV 63 (140)
T ss_pred EEeeEEEEEC----------CEE----EEEEEeecccccchhhhhhhhcccccceeec----cccc-eee--ccccceee
Confidence 4788888875 111 1125789999998888776443444443332 2222 111 12245677
Q ss_pred cCCC--CCCCCcCCCCccCCCCChHHHHHHHHHHHHHHHHHHHHHHHhhhcccccccccCcccHHHHHHHHHHHHhhccc
Q psy15697 197 GDSA--YPLKEWLIPPRTRNPDAAADQRFLRCHKRTRRLIENSFGILKEKFPCLNYMRLSPQFAGMVVLASTTLHNIALT 274 (332)
Q Consensus 197 gD~g--Y~~~~~l~~P~~~~~~~~~~~~fN~~~s~~R~~vE~~fg~LK~rf~~L~~~~~~~~~~~~ii~a~~~LhN~~~~ 274 (332)
.|++ |+.--.-+.+.+..+ +..-.....-.++.||+-++.+|.|.+...++. +.+.+...+.+-.+.||+...
T Consensus 64 tDk~~aY~~A~~~l~~~~~~~----~~v~~~~~k~~nN~iE~~h~~~K~r~r~~~gFk-s~~~A~~~l~~~~~~~n~~r~ 138 (140)
T PF13610_consen 64 TDKLPAYPAAIKELNPEGRLH----DKVEHRQRKYLNNRIERDHRTIKRRTRPMNGFK-SFRSAQRTLSGFEAYHNFRRP 138 (140)
T ss_pred cccCCccchhhhhcccccccc----cccceeechhhhChhhHhhhhhhhhcccccCcC-CHHHHHHHHHHHHHHHHHhCC
Confidence 7763 443222222201000 000011112347889999999999887775553 677888899999999999753
No 107
>PF13730 HTH_36: Helix-turn-helix domain
Probab=83.78 E-value=1 Score=29.55 Aligned_cols=40 Identities=18% Similarity=0.180 Sum_probs=29.1
Q ss_pred HHHHHHHHhhhccC-----CcccccccccCCChhhHHhHHhHhHH
Q psy15697 41 KEKVLSCLHWMGVG-----SPYHIIGATHGPSKSSICRSIHEVVP 80 (332)
Q Consensus 41 ~~~l~~~L~~L~~g-----~~~~~l~~~fgis~sTv~r~~~~v~~ 80 (332)
+..|.+.|..++.+ .++..++...|+|+.||.+.+++..+
T Consensus 7 ~~~v~~~l~~~~~~~~~~~pS~~~la~~~g~s~~Tv~~~i~~L~~ 51 (55)
T PF13730_consen 7 AKLVYLYLASYANKNGGCFPSQETLAKDLGVSRRTVQRAIKELEE 51 (55)
T ss_pred HHHHHHHHHHhcCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 33455566666522 25688999999999999999987654
No 108
>PRK05572 sporulation sigma factor SigF; Validated
Probab=83.78 E-value=1.4 Score=39.18 Aligned_cols=47 Identities=13% Similarity=0.286 Sum_probs=41.5
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
.+|+.++.++.|+|+ .|.++..+|..+|+|.+||+++.++.+.-|-.
T Consensus 202 ~L~~~~~~v~~l~~~-~~~s~~eIA~~lgis~~~V~~~~~ral~kLr~ 248 (252)
T PRK05572 202 ELDERERLIVYLRYF-KDKTQSEVAKRLGISQVQVSRLEKKILKQMKE 248 (252)
T ss_pred cCCHHHHHHHHHHHh-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 478888888888776 58999999999999999999999999888766
No 109
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=83.68 E-value=1.4 Score=37.00 Aligned_cols=47 Identities=17% Similarity=0.152 Sum_probs=41.6
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
.+|+..+-++.|.++. |.++.++|..+|+|.+||...+++....|-+
T Consensus 131 ~L~~~~r~v~~l~~~~-g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 177 (184)
T PRK12539 131 RLPEKMRLAIQAVKLE-GLSVAEAATRSGMSESAVKVSVHRGLKALAA 177 (184)
T ss_pred hCCHHHHHHHHHHHHc-CCcHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 4778888888888875 9999999999999999999999999888877
No 110
>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=83.67 E-value=1.1 Score=37.49 Aligned_cols=46 Identities=15% Similarity=0.105 Sum_probs=38.9
Q ss_pred CCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 38 LSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 38 ~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
+|++.+-.+.|+++ .|.++.++|..+|+|.+||...+++....|-+
T Consensus 139 L~~~~r~v~~l~~~-~~~s~~EIA~~lgis~~tv~~~l~rar~~Lr~ 184 (190)
T TIGR02939 139 LPEDLRTAITLREL-EGLSYEDIARIMDCPVGTVRSRIFRAREAIAI 184 (190)
T ss_pred CCHHHhhhhhhhhh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 56666666666665 79999999999999999999999999888877
No 111
>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=83.64 E-value=1.3 Score=36.13 Aligned_cols=46 Identities=11% Similarity=0.190 Sum_probs=39.6
Q ss_pred CCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 38 LSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 38 ~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
+|+..+.++.|.+ -.|.++.++|..+|+|.+||...+.+....|-.
T Consensus 111 L~~~~r~i~~l~~-~~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 156 (162)
T TIGR02983 111 LPARQRAVVVLRY-YEDLSEAQVAEALGISVGTVKSRLSRALARLRE 156 (162)
T ss_pred CCHHHHHHhhhHH-HhcCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 5677777777777 559999999999999999999999999888876
No 112
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=83.60 E-value=1.4 Score=37.33 Aligned_cols=47 Identities=11% Similarity=0.114 Sum_probs=42.4
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
.+|+..+-++.|+++ .|.++.++|..+|+|.+||...+.+....|-.
T Consensus 113 ~Lp~~~r~v~~L~~~-~g~s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~ 159 (188)
T PRK12546 113 QLPDEQREALILVGA-SGFSYEEAAEMCGVAVGTVKSRANRARARLAE 159 (188)
T ss_pred hCCHHHhHHhhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 478888888888888 79999999999999999999999999998887
No 113
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=83.59 E-value=1.4 Score=40.18 Aligned_cols=48 Identities=15% Similarity=0.167 Sum_probs=42.5
Q ss_pred CCCHHHHHHHHHhhh-ccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 37 ALSAKEKVLSCLHWM-GVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L-~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
.+|+.++..+.|+|+ ..+.++.++|..+|||++||.++.++.+.-|-.
T Consensus 227 ~L~~rer~vl~lr~~~~~~~t~~EIa~~lgvs~~~V~q~~~~Al~kLr~ 275 (289)
T PRK07500 227 TLNERELRIIRERRLREDGATLEALGEELGISKERVRQIEARALEKLRR 275 (289)
T ss_pred cCCHHHHHHHHHHhcCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 378888888889886 368899999999999999999999999988877
No 114
>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=83.54 E-value=0.76 Score=33.70 Aligned_cols=36 Identities=19% Similarity=0.240 Sum_probs=28.4
Q ss_pred HHHHHHHhhhccCCcccccccccCCChhhHHhHHhH
Q psy15697 42 EKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHE 77 (332)
Q Consensus 42 ~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~ 77 (332)
.++.++=-.|..|.+|+.++...|+|..||+|+=+.
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 344444447889999999999999999999876543
No 115
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=83.48 E-value=1.3 Score=37.22 Aligned_cols=46 Identities=11% Similarity=0.060 Sum_probs=40.4
Q ss_pred CCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 38 LSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 38 ~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
+|+.++-++.|.++. |.++.++|..+|+|..||...+++....|..
T Consensus 129 L~~~~r~i~~l~~~~-g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 174 (186)
T PRK05602 129 LPERQREAIVLQYYQ-GLSNIEAAAVMDISVDALESLLARGRRALRA 174 (186)
T ss_pred CCHHHHHHhhHHHhc-CCCHHHHHHHhCcCHHHHHHHHHHHHHHHHH
Confidence 577777777787765 9999999999999999999999998888877
No 116
>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=83.41 E-value=1.3 Score=38.62 Aligned_cols=47 Identities=15% Similarity=0.249 Sum_probs=39.6
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
.+|+.++..+.++|+ .|.++.++|..+|+|+++|+++.++.+.-|-.
T Consensus 183 ~L~~~e~~i~~~~~~-~~~t~~eIA~~lgis~~~V~~~~~~al~~Lr~ 229 (231)
T TIGR02885 183 KLDERERQIIMLRYF-KDKTQTEVANMLGISQVQVSRLEKKVLKKMKE 229 (231)
T ss_pred cCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 467777777777664 68899999999999999999999998887754
No 117
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.
Probab=83.38 E-value=0.55 Score=37.96 Aligned_cols=46 Identities=11% Similarity=0.064 Sum_probs=37.9
Q ss_pred CCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 38 LSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 38 ~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
+|+..+-++.|.++ .|.++.++|..+|+|.+||...+++....|-+
T Consensus 106 L~~~~r~i~~l~~~-~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~ 151 (154)
T TIGR02950 106 LPENYRTVLILREF-KEFSYKEIAELLNLSLAKVKSNLFRARKELKK 151 (154)
T ss_pred CCHhheeeeeehhh-ccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 56666666666666 69999999999999999999999988877765
No 118
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=83.37 E-value=1.5 Score=36.66 Aligned_cols=46 Identities=15% Similarity=0.106 Sum_probs=37.8
Q ss_pred CCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 38 LSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 38 ~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
+|+.++.++.|++ -.|.++.++|..+|+|.+||...+++....|..
T Consensus 130 L~~~~r~v~~l~~-~~g~s~~EIA~~l~is~~tV~~~l~rar~~Lr~ 175 (181)
T PRK12536 130 LPDRQRLPIVHVK-LEGLSVAETAQLTGLSESAVKVGIHRGLKALAA 175 (181)
T ss_pred CCHHHHHHHHHHH-HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 5666666555554 459999999999999999999999998888776
No 119
>PF13551 HTH_29: Winged helix-turn helix
Probab=83.26 E-value=0.69 Score=35.11 Aligned_cols=34 Identities=18% Similarity=0.195 Sum_probs=29.5
Q ss_pred HHhhhccCCc-ccccccccCCChhhHHhHHhHhHH
Q psy15697 47 CLHWMGVGSP-YHIIGATHGPSKSSICRSIHEVVP 80 (332)
Q Consensus 47 ~L~~L~~g~~-~~~l~~~fgis~sTv~r~~~~v~~ 80 (332)
+|..+..|.+ ...+|..+|+|.+||+++++++..
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 4566788985 999999999999999999998753
No 120
>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=83.25 E-value=1.3 Score=37.32 Aligned_cols=46 Identities=11% Similarity=-0.080 Sum_probs=38.3
Q ss_pred CCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 38 LSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 38 ~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
+|+..+-++.|+|+. |.++.++|..+|+|.+||...+.+....|-.
T Consensus 132 L~~~~r~v~~l~~~~-g~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~ 177 (188)
T TIGR02943 132 LPEQTARVFMMREVL-GFESDEICQELEISTSNCHVLLYRARLSLRA 177 (188)
T ss_pred CCHHHHHHHHHHHHh-CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 566666666666555 9999999999999999999999998888877
No 121
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=83.22 E-value=1.2 Score=37.46 Aligned_cols=47 Identities=13% Similarity=0.188 Sum_probs=41.2
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
.+|++++-.+.|+++ .|.++.++|..+|+|.+||...+.+....|-.
T Consensus 131 ~L~~~~r~i~~l~~~-~g~s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~ 177 (189)
T PRK06811 131 DLEKLDREIFIRRYL-LGEKIEEIAKKLGLTRSAIDNRLSRGRKKLQK 177 (189)
T ss_pred hCCHHHHHHHHHHHH-ccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 478888888888886 58999999999999999999999988887765
No 122
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=83.18 E-value=1.3 Score=34.20 Aligned_cols=47 Identities=11% Similarity=0.070 Sum_probs=42.0
Q ss_pred CCCCCHHHHHHHHHhhhccCCcccccccccCC-ChhhHHhHHhHhHHH
Q psy15697 35 NVALSAKEKVLSCLHWMGVGSPYHIIGATHGP-SKSSICRSIHEVVPV 81 (332)
Q Consensus 35 ~~~~~~~~~l~~~L~~L~~g~~~~~l~~~fgi-s~sTv~r~~~~v~~~ 81 (332)
+..+|.+.++-++-.++..|.+...+|..||| +.+++++++.+....
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 56789999999999999999999999999996 999999888876653
No 123
>PF13751 DDE_Tnp_1_6: Transposase DDE domain
Probab=83.16 E-value=0.69 Score=36.20 Aligned_cols=48 Identities=19% Similarity=0.178 Sum_probs=35.6
Q ss_pred HHHHHHHHH-HHHHHHHHHhhhcccccccc-cCcccHHHHHHHHHHHHhhc
Q psy15697 224 LRCHKRTRR-LIENSFGILKEKFPCLNYMR-LSPQFAGMVVLASTTLHNIA 272 (332)
Q Consensus 224 N~~~s~~R~-~vE~~fg~LK~rf~~L~~~~-~~~~~~~~ii~a~~~LhN~~ 272 (332)
...+.+.|. .||..||.||. +--++.++ .....+..-+...++.|||.
T Consensus 73 ~k~~y~~R~~~VE~~fg~~K~-~~g~~r~~~rG~~kv~~~~~l~a~a~Nl~ 122 (125)
T PF13751_consen 73 GKELYKQRSIKVEGVFGTIKR-NHGLRRFRYRGLEKVRIEFLLAAIAYNLK 122 (125)
T ss_pred hhhhhheeecccccccccchh-ccCCccccccchhhhHHHHHHHHHHHHHH
Confidence 346667777 99999999996 44443333 46777777788888889985
No 124
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=82.99 E-value=2.5 Score=33.92 Aligned_cols=43 Identities=14% Similarity=0.223 Sum_probs=31.0
Q ss_pred CCHHH-HHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHH
Q psy15697 38 LSAKE-KVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVP 80 (332)
Q Consensus 38 ~~~~~-~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~ 80 (332)
+++.+ .++..|.....+.+..+|+..++++++|+++.+++...
T Consensus 29 lt~~q~~vL~~l~~~~~~~t~~eLa~~l~~~~~tvt~~v~~Le~ 72 (144)
T PRK03573 29 LTQTHWVTLHNIHQLPPEQSQIQLAKAIGIEQPSLVRTLDQLEE 72 (144)
T ss_pred CCHHHHHHHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHHHHHH
Confidence 44443 34455544444578899999999999999988887654
No 125
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=82.91 E-value=1.3 Score=37.21 Aligned_cols=47 Identities=15% Similarity=0.160 Sum_probs=39.2
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
.+|+..+-++.|+++. |.++.++|..+|+|.+||...+.+....|-+
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 3677777777776655 8889999999999999999999988887776
No 126
>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=82.74 E-value=1 Score=29.97 Aligned_cols=28 Identities=21% Similarity=0.251 Sum_probs=23.1
Q ss_pred cCCcccccccccCCChhhHHhHHhHhHH
Q psy15697 53 VGSPYHIIGATHGPSKSSICRSIHEVVP 80 (332)
Q Consensus 53 ~g~~~~~l~~~fgis~sTv~r~~~~v~~ 80 (332)
.+.+..+++..++++++|+++++++...
T Consensus 16 ~~~~~~~la~~~~~~~~~~t~~i~~L~~ 43 (59)
T PF01047_consen 16 GGITQSELAEKLGISRSTVTRIIKRLEK 43 (59)
T ss_dssp SSEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHCCChhHHHHHHHHHHH
Confidence 3478889999999999999999887654
No 127
>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=82.71 E-value=1.5 Score=39.81 Aligned_cols=50 Identities=8% Similarity=0.140 Sum_probs=43.2
Q ss_pred CCCHHHHHHHHHhh-h--ccCCcccccccccCCChhhHHhHHhHhHHHHHHhh
Q psy15697 37 ALSAKEKVLSCLHW-M--GVGSPYHIIGATHGPSKSSICRSIHEVVPVIVDTF 86 (332)
Q Consensus 37 ~~~~~~~l~~~L~~-L--~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~~l 86 (332)
.+|+.++..+.|+| | -.|.++.++|..+|+|.+||....++-...|-..+
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 47888888899887 3 56899999999999999999999999888887733
No 128
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=82.51 E-value=1.4 Score=39.37 Aligned_cols=47 Identities=17% Similarity=0.272 Sum_probs=40.2
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
.+++.++..+.++|+ .|.++.++|..+|+|.+||+++.++.+.-|-.
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 477788888888775 58899999999999999999999998877765
No 129
>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=82.50 E-value=1.7 Score=35.85 Aligned_cols=47 Identities=11% Similarity=0.148 Sum_probs=39.5
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
.+|+..+-++.|.++. |.++.++|..+|+|.+||...+.+....|..
T Consensus 119 ~L~~~~r~i~~l~~~~-g~s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~ 165 (169)
T TIGR02954 119 TLNDKYQTAIILRYYH-DLTIKEIAEVMNKPEGTVKTYLHRALKKLKK 165 (169)
T ss_pred hCCHHHhHHHHHHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3667777666666666 8999999999999999999999998888776
No 130
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=82.34 E-value=1.6 Score=36.62 Aligned_cols=47 Identities=19% Similarity=0.047 Sum_probs=39.3
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
.+|+.++.++.|.++ .|.++.++|..+|+|.+||...+.+....|..
T Consensus 106 ~L~~~~r~i~~l~~~-~g~~~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 152 (181)
T PRK09637 106 ALPEKYAEALRLTEL-EGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKE 152 (181)
T ss_pred hCCHHHHHHHHHHHh-cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 367777776666654 58999999999999999999999998888877
No 131
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=82.31 E-value=1.5 Score=36.70 Aligned_cols=47 Identities=17% Similarity=0.183 Sum_probs=40.0
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
.+|+.++-++.|.++ .|.++.++|..+|+|.+||...+++....|..
T Consensus 136 ~L~~~~r~v~~l~~~-~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 182 (187)
T TIGR02948 136 ALPPKYRMVIVLKYM-EDLSLKEISEILDLPVGTVKTRIHRGREALRK 182 (187)
T ss_pred hCCHHHhHHhhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 467777777777766 58999999999999999999999998888776
No 132
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=82.29 E-value=1.8 Score=36.22 Aligned_cols=46 Identities=11% Similarity=0.122 Sum_probs=39.0
Q ss_pred CCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 38 LSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 38 ~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
+|+.++..+.|+++ .|.++.++|..+|+|.+||...+++....|-.
T Consensus 136 L~~~~r~vl~l~~~-~~~s~~eIA~~lgis~~~V~~~l~ra~~~Lr~ 181 (186)
T PRK13919 136 LSPEERRVIEVLYY-QGYTHREAAQLLGLPLGTLKTRARRALSRLKE 181 (186)
T ss_pred CCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 66777777777664 58999999999999999999999998888776
No 133
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=82.20 E-value=1.5 Score=36.76 Aligned_cols=46 Identities=17% Similarity=0.308 Sum_probs=39.9
Q ss_pred CCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 38 LSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 38 ~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
+|++.+-++.|.++. |.++.++|..+|||.+||...+++-...|..
T Consensus 128 Lp~~~R~~~~l~~~~-gls~~EIA~~l~i~~~tVks~l~ra~~~l~~ 173 (182)
T COG1595 128 LPPRQREAFLLRYLE-GLSYEEIAEILGISVGTVKSRLHRARKKLRE 173 (182)
T ss_pred CCHHHhHHhhhHhhc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 677777777776665 8999999999999999999999999888877
No 134
>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=82.04 E-value=0.7 Score=30.15 Aligned_cols=35 Identities=20% Similarity=0.208 Sum_probs=25.3
Q ss_pred HHHhhhcc---CCcccccccccCCChhhHHhHHhHhHH
Q psy15697 46 SCLHWMGV---GSPYHIIGATHGPSKSSICRSIHEVVP 80 (332)
Q Consensus 46 ~~L~~L~~---g~~~~~l~~~fgis~sTv~r~~~~v~~ 80 (332)
-.|..++. +.+..++++..|++++|++|++.....
T Consensus 7 ~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~~ 44 (52)
T PF09339_consen 7 RILEALAESGGPLTLSEIARALGLPKSTVHRLLQTLVE 44 (52)
T ss_dssp HHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 34444443 346889999999999999999887654
No 135
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=82.01 E-value=1.1 Score=29.39 Aligned_cols=29 Identities=21% Similarity=0.141 Sum_probs=23.1
Q ss_pred CCcccccccccCCChhhHHhHHhHhHHHH
Q psy15697 54 GSPYHIIGATHGPSKSSICRSIHEVVPVI 82 (332)
Q Consensus 54 g~~~~~l~~~fgis~sTv~r~~~~v~~~l 82 (332)
+.+..++|+.++||+.||.+.+...-...
T Consensus 15 ~it~~eLa~~l~vS~rTi~~~i~~L~~~~ 43 (55)
T PF08279_consen 15 PITAKELAEELGVSRRTIRRDIKELREWG 43 (55)
T ss_dssp SBEHHHHHHHCTS-HHHHHHHHHHHHHTT
T ss_pred CcCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence 36778899999999999999998875543
No 136
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=81.96 E-value=1.6 Score=36.98 Aligned_cols=46 Identities=9% Similarity=0.026 Sum_probs=39.4
Q ss_pred CCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 38 LSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 38 ~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
+|+..+.++.|+++ .|.++.++|..+|+|.+||..-+.+....|-.
T Consensus 135 Lp~~~r~i~~l~~~-~g~s~~EIA~~lg~s~~tV~~rl~rar~~Lr~ 180 (192)
T PRK09643 135 LPVEQRAALVAVDM-QGYSVADAARMLGVAEGTVKSRCARGRARLAE 180 (192)
T ss_pred CCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 77888887777776 68999999999999999998888887777766
No 137
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=81.95 E-value=1.4 Score=30.26 Aligned_cols=43 Identities=5% Similarity=0.037 Sum_probs=38.8
Q ss_pred HHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHHhhh
Q psy15697 44 VLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVDTFF 87 (332)
Q Consensus 44 l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~~l~ 87 (332)
+-.+..+|+...+..+.|+..|+...+|.+++..+-..+.+ +-
T Consensus 3 ~~~fIrlLs~~~s~~~Aa~~lG~~~~~v~~wv~~fR~wll~-LD 45 (65)
T PF05344_consen 3 ARAFIRLLSQQISVAQAADRLGTDPGTVRRWVRMFRQWLLQ-LD 45 (65)
T ss_pred HHHHHHHhcccccHHHHHHHHCcCHHHHHHHHHHHHHHHHH-cC
Confidence 44678899999999999999999999999999999999988 54
No 138
>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=81.91 E-value=1.3 Score=29.91 Aligned_cols=40 Identities=13% Similarity=0.118 Sum_probs=28.5
Q ss_pred HHHHHHHHhhhc---cCCcccccccccCCChhhHHhHHhHhHH
Q psy15697 41 KEKVLSCLHWMG---VGSPYHIIGATHGPSKSSICRSIHEVVP 80 (332)
Q Consensus 41 ~~~l~~~L~~L~---~g~~~~~l~~~fgis~sTv~r~~~~v~~ 80 (332)
.+.-+-+++.|. ...+-.+||..+|+|++||+..+++...
T Consensus 6 ~e~YL~~Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~ 48 (60)
T PF01325_consen 6 EEDYLKAIYELSEEGGPVRTKDIAERLGVSPPTVTEMLKRLAE 48 (60)
T ss_dssp HHHHHHHHHHHHHCTSSBBHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCCCccHHHHHHHHCCChHHHHHHHHHHHH
Confidence 344455555555 4456778999999999999999887654
No 139
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=81.80 E-value=1.8 Score=38.42 Aligned_cols=47 Identities=19% Similarity=0.246 Sum_probs=41.2
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
.++-.+++.+.|+| -.+.++..+|...|||++.||++..+.+..|-.
T Consensus 196 ~L~EREk~Vl~l~y-~eelt~kEI~~~LgISes~VSql~kkai~kLr~ 242 (247)
T COG1191 196 PLPEREKLVLVLRY-KEELTQKEIAEVLGISESRVSRLHKKAIKKLRK 242 (247)
T ss_pred ccCHHHHHHHHHHH-HhccCHHHHHHHhCccHHHHHHHHHHHHHHHHH
Confidence 46778889898888 457899999999999999999999999888776
No 140
>TIGR02850 spore_sigG RNA polymerase sigma-G factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigG. It is also desginated stage III sporulation protein G (SpoIIIG). This protein is rather closely related to sigma-F (SpoIIAC), another sporulation sigma factor.
Probab=81.64 E-value=1.7 Score=38.66 Aligned_cols=47 Identities=15% Similarity=0.260 Sum_probs=40.2
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
.+++.++..+.++|+ .|.++.++|..+|+|+++|+++.++.+.-|..
T Consensus 206 ~L~~rer~vi~~~~~-~~~t~~eIA~~lgis~~~V~~~~~ral~kLr~ 252 (254)
T TIGR02850 206 RLNEREKMILNMRFF-EGKTQMEVAEEIGISQAQVSRLEKAALKHMRK 252 (254)
T ss_pred cCCHHHHHHHHHHHc-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHh
Confidence 477788888888775 58899999999999999999999998877654
No 141
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=81.43 E-value=1.7 Score=37.07 Aligned_cols=47 Identities=4% Similarity=-0.107 Sum_probs=39.4
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
.+|+..+-++.|+++ .|.++.++|..+|+|.+||...+.+....|-.
T Consensus 139 ~Lp~~~r~v~~L~~~-eg~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~ 185 (201)
T PRK12545 139 HLPEQIGRVFMMREF-LDFEIDDICTELTLTANHCSVLLYRARTRLRT 185 (201)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 367777777777764 58899999999999999999999988888877
No 142
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=81.42 E-value=1.8 Score=37.98 Aligned_cols=46 Identities=20% Similarity=0.259 Sum_probs=39.8
Q ss_pred CCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 38 LSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 38 ~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
+|+.++-.+.|+|+ .|.++.++|..+|+|.+||...+.+....|-.
T Consensus 185 L~~~~r~vl~l~~~-~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~ 230 (236)
T PRK06986 185 LPEREQLVLSLYYQ-EELNLKEIGAVLGVSESRVSQIHSQAIKRLRA 230 (236)
T ss_pred CCHHHHHHHHhHhc-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 67777777777764 68899999999999999999999998888876
No 143
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=81.39 E-value=1.9 Score=36.67 Aligned_cols=51 Identities=10% Similarity=0.030 Sum_probs=41.3
Q ss_pred CCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHHhhhccc
Q psy15697 38 LSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVDTFFQRM 90 (332)
Q Consensus 38 ~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~~l~~~~ 90 (332)
+|+..+-++.|.++. |.++.++|..+|+|.+||...+++....|-. +...+
T Consensus 134 Lp~~~r~v~~l~~~~-g~s~~EIAe~lgis~~tV~~~l~Rar~~Lr~-~l~~~ 184 (196)
T PRK12535 134 LPPERREALILTQVL-GYTYEEAAKIADVRVGTIRSRVARARADLIA-ATATG 184 (196)
T ss_pred CCHHHHHHhhhHHHh-CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH-Hhccc
Confidence 666666666666554 7889999999999999999999999998888 55443
No 144
>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family. This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393).
Probab=81.32 E-value=1.4 Score=40.30 Aligned_cols=45 Identities=16% Similarity=0.162 Sum_probs=39.0
Q ss_pred CCCHHHHHHHHHhhh---ccCCcccccccccCCChhhHHhHHhHhHHH
Q psy15697 37 ALSAKEKVLSCLHWM---GVGSPYHIIGATHGPSKSSICRSIHEVVPV 81 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L---~~g~~~~~l~~~fgis~sTv~r~~~~v~~~ 81 (332)
.+|+.++..+.|+|. ..+.++.++|..+|||+.+|..+.++.+.-
T Consensus 249 ~L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVrq~~~rAl~k 296 (298)
T TIGR02997 249 ELTPRERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKALRK 296 (298)
T ss_pred cCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 388899999999885 578899999999999999999998876654
No 145
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=81.16 E-value=2 Score=35.84 Aligned_cols=46 Identities=13% Similarity=0.116 Sum_probs=38.0
Q ss_pred CCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 38 LSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 38 ~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
+|+..+-++.|.++ .|.++.++|..+|+|.+||...+++....|-.
T Consensus 118 Lp~~~r~i~~l~~~-e~~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~ 163 (179)
T PRK12543 118 LPYKLRQVIILRYL-HDYSQEEIAQLLQIPIGTVKSRIHAALKKLRQ 163 (179)
T ss_pred CCHHHHHHHHHHHH-ccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 67777777766544 58899999999999999999888888777766
No 146
>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial. Members of this protein family, found in the cyanobacteria, are the global nitrogen regulator NtcA. This DNA-binding transcriptional regulator is required for expressing many different ammonia-repressible genes. The consensus NtcA-binding site is G T A N(8)T A C.
Probab=81.14 E-value=0.67 Score=38.98 Aligned_cols=44 Identities=14% Similarity=0.163 Sum_probs=35.4
Q ss_pred CCHHHHHHHHHhhhcc--------------CCcccccccccCCChhhHHhHHhHhHHH
Q psy15697 38 LSAKEKVLSCLHWMGV--------------GSPYHIIGATHGPSKSSICRSIHEVVPV 81 (332)
Q Consensus 38 ~~~~~~l~~~L~~L~~--------------g~~~~~l~~~fgis~sTv~r~~~~v~~~ 81 (332)
.+++++|+-+|..|+. ..+..++|...|+++.||+|+++++...
T Consensus 113 ~~~~~Rla~~L~~l~~~~~~~~~~~~~~~~~~t~~~iA~~lG~tretvsR~l~~l~~~ 170 (193)
T TIGR03697 113 RDMGSRLVSFLLILCRDFGVPGQRGVTIDLRLSHQAIAEAIGSTRVTITRLLGDLRKK 170 (193)
T ss_pred CCHHHHHHHHHHHHHHHhCCCCCCeEEecCCCCHHHHHHHhCCcHHHHHHHHHHHHHC
Confidence 5788899998877642 2467889999999999999999987653
No 147
>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=80.87 E-value=0.62 Score=36.36 Aligned_cols=30 Identities=17% Similarity=0.340 Sum_probs=26.5
Q ss_pred HhhhccCCcccccccccCCChhhHHhHHhH
Q psy15697 48 LHWMGVGSPYHIIGATHGPSKSSICRSIHE 77 (332)
Q Consensus 48 L~~L~~g~~~~~l~~~fgis~sTv~r~~~~ 77 (332)
|.++..|.+...+|..|+||.+||.+++.+
T Consensus 12 l~~~~~g~s~~eaa~~F~VS~~Tv~~W~k~ 41 (119)
T PF01710_consen 12 LAYIEKGKSIREAAKRFGVSRNTVYRWLKR 41 (119)
T ss_pred HHHHHccchHHHHHHHhCcHHHHHHHHHHh
Confidence 357778899999999999999999999884
No 148
>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=80.77 E-value=1.7 Score=39.97 Aligned_cols=51 Identities=12% Similarity=0.123 Sum_probs=42.3
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHHhhhcc
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVDTFFQR 89 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~~l~~~ 89 (332)
.+|+.++.++.|+++ .|.++.++|..+|+|.+||...+.+....|.+ ....
T Consensus 142 ~Lp~~~R~v~~L~~~-~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~-~l~~ 192 (324)
T TIGR02960 142 YLPPRQRAVLLLRDV-LGWRAAETAELLGTSTASVNSALQRARATLDE-VGPS 192 (324)
T ss_pred hCCHHHhhHhhhHHH-hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH-hccc
Confidence 366777777777766 68999999999999999999999999999888 4443
No 149
>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=80.73 E-value=1.9 Score=35.64 Aligned_cols=47 Identities=15% Similarity=0.051 Sum_probs=40.2
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
.+|+..+.++.|.++ .|.++.++|..+|+|.+||...+.+....|-.
T Consensus 100 ~L~~~~r~v~~l~~~-~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 146 (170)
T TIGR02959 100 ELPDEYREAIRLTEL-EGLSQQEIAEKLGLSLSGAKSRVQRGRKKLKE 146 (170)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 477777777777665 48999999999999999999999998888877
No 150
>PRK06930 positive control sigma-like factor; Validated
Probab=80.64 E-value=2 Score=35.82 Aligned_cols=47 Identities=26% Similarity=0.305 Sum_probs=39.5
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
.+|+.++-++.|+ +..|.++.++|..+|+|.+||...+.+....|..
T Consensus 114 ~L~~rer~V~~L~-~~eg~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~ 160 (170)
T PRK06930 114 VLTEREKEVYLMH-RGYGLSYSEIADYLNIKKSTVQSMIERAEKKIAR 160 (170)
T ss_pred hCCHHHHHHHHHH-HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 4677776666555 4779999999999999999999999998888776
No 151
>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=80.43 E-value=0.99 Score=31.61 Aligned_cols=43 Identities=19% Similarity=0.231 Sum_probs=33.2
Q ss_pred CCCCHHHHHHHHHhhhccCCcccccccccC-CChhhHHhHHhHh
Q psy15697 36 VALSAKEKVLSCLHWMGVGSPYHIIGATHG-PSKSSICRSIHEV 78 (332)
Q Consensus 36 ~~~~~~~~l~~~L~~L~~g~~~~~l~~~fg-is~sTv~r~~~~v 78 (332)
..+.-.-++++.|..-..+.++.++|..|| .+.|||..-++++
T Consensus 27 ~~i~~aR~va~yL~r~~~~~sl~~Ig~~fg~rdHstV~~a~~ki 70 (70)
T PF08299_consen 27 RKIVEARQVAMYLARELTGLSLSEIGRYFGGRDHSTVIHAIRKI 70 (70)
T ss_dssp HHHHHHHHHHHHHHHHHS---HHHHHHHCTSSTHHHHHHHHHHH
T ss_pred hhhcchHHHHHHHHHHHhCCCHHHHHHHhCCCCHHHHHHHHHhC
Confidence 345567788888888888999999999999 9999998877764
No 152
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=80.40 E-value=1.9 Score=35.19 Aligned_cols=47 Identities=17% Similarity=0.120 Sum_probs=39.2
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
.+|+..+.++.|.++. |.++.++|..+|+|.+||...+++....|.+
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 4777777777776654 8899999999999999999999988877765
No 153
>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=80.23 E-value=2.1 Score=37.99 Aligned_cols=47 Identities=17% Similarity=0.203 Sum_probs=40.5
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
.+|+.++-.+.|+++ .|.++.++|..+|+|.+||.+..++....|-.
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 477888887878775 68999999999999999999999988887765
No 154
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=80.16 E-value=0.93 Score=41.87 Aligned_cols=68 Identities=9% Similarity=0.075 Sum_probs=47.0
Q ss_pred HHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHHhhhccccCCCcccccchhhhhhhcCCCCCcee
Q psy15697 46 SCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVDTFFQRMVKWPEENLNDIPMTFLRKGGFPNVAG 116 (332)
Q Consensus 46 ~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~~l~~~~I~~P~~~~~~~~~~f~~~~~~p~~~G 116 (332)
++=.|+-.|.++.++|..+|+|+++|+|.+.+--+. . +-.-.|.-|.....++...++++.++..|+-
T Consensus 21 vA~lYY~~g~tQ~eIA~~lgiSR~~VsRlL~~Ar~~--G-iV~I~I~~~~~~~~~Le~~L~~~fgLk~~iV 88 (318)
T PRK15418 21 IAWFYYHDGLTQSEIGERLGLTRLKVSRLLEKGRQS--G-IIRVQINSRFEGCLELENALRQHFSLQHIRV 88 (318)
T ss_pred HHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHc--C-cEEEEEeCCCccHHHHHHHHHHHhCCCEEEE
Confidence 566778889999999999999999999998875431 0 1222344454434455566666678877763
No 155
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=80.12 E-value=1.1 Score=38.26 Aligned_cols=45 Identities=16% Similarity=0.138 Sum_probs=34.6
Q ss_pred CCCCHHHHHHHHHhhhcc-------------CCcccccccccCCChhhHHhHHhHhHH
Q psy15697 36 VALSAKEKVLSCLHWMGV-------------GSPYHIIGATHGPSKSSICRSIHEVVP 80 (332)
Q Consensus 36 ~~~~~~~~l~~~L~~L~~-------------g~~~~~l~~~fgis~sTv~r~~~~v~~ 80 (332)
...++.++++-+|..|+. ..+..++|...|+++.|++|+++++..
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 346788899888877653 123467899999999999999887654
No 156
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=79.81 E-value=2.3 Score=36.39 Aligned_cols=46 Identities=2% Similarity=-0.023 Sum_probs=37.6
Q ss_pred CCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 38 LSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 38 ~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
+|+..+.++.|.++ .|.++.++|..+|+|.+||...+++....|..
T Consensus 154 L~~~~r~vl~l~~~-~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 199 (206)
T PRK12526 154 LPEAQQTVVKGVYF-QELSQEQLAQQLNVPLGTVKSRLRLALAKLKV 199 (206)
T ss_pred CCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 56666666655554 58999999999999999999999988887776
No 157
>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=79.62 E-value=2.6 Score=33.57 Aligned_cols=47 Identities=13% Similarity=0.080 Sum_probs=40.1
Q ss_pred CCHHHHHHHHHhhhcc-CCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 38 LSAKEKVLSCLHWMGV-GSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 38 ~~~~~~l~~~L~~L~~-g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
++.+++-.+.++|+.. ..++..+|..+|+|++|+++.-++++..+..
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 6778888888888753 3489999999999999999999998888776
No 158
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=79.41 E-value=2.7 Score=36.87 Aligned_cols=51 Identities=10% Similarity=0.020 Sum_probs=42.0
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHHhhhcc
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVDTFFQR 89 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~~l~~~ 89 (332)
.+|+..+.++.|.++- |.++.++|..+|+|.+||...+.+....|.. ...+
T Consensus 116 ~Lp~~~R~v~lL~~~e-g~S~~EIAe~LgiS~~tVksrL~Rark~Lr~-~l~~ 166 (228)
T PRK06704 116 SLNVQQSAILLLKDVF-QYSIADIAKVCSVSEGAVKASLFRSRNRLKT-VSEE 166 (228)
T ss_pred hCCHHHhhHhhhHHhh-CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH-HHHh
Confidence 3677777777776655 7999999999999999999999999998888 4443
No 159
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=79.32 E-value=2 Score=39.64 Aligned_cols=48 Identities=17% Similarity=0.203 Sum_probs=42.2
Q ss_pred CCCHHHHHHHHHhhh---ccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 37 ALSAKEKVLSCLHWM---GVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L---~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
.+|+.++..+.|+|. ..+.++.++|..+|||+.+|..+..+.+.-|-.
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 388888999999986 467899999999999999999999988887765
No 160
>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=79.27 E-value=1.3 Score=30.13 Aligned_cols=26 Identities=15% Similarity=0.272 Sum_probs=22.6
Q ss_pred CcccccccccCCChhhHHhHHhHhHH
Q psy15697 55 SPYHIIGATHGPSKSSICRSIHEVVP 80 (332)
Q Consensus 55 ~~~~~l~~~fgis~sTv~r~~~~v~~ 80 (332)
.+..++|..+|+|++|+++++.....
T Consensus 26 ~s~~ela~~~g~s~~tv~r~l~~L~~ 51 (67)
T cd00092 26 LTRQEIADYLGLTRETVSRTLKELEE 51 (67)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 57778999999999999999887765
No 161
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=79.12 E-value=2.6 Score=35.33 Aligned_cols=46 Identities=9% Similarity=0.178 Sum_probs=37.6
Q ss_pred CCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 38 LSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 38 ~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
+|+..+-++.|.++ .|.++.++|..+|+|.+||...+.+....|-.
T Consensus 123 L~~~~r~i~~l~~~-~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 168 (185)
T PRK12542 123 LNESNRQVFKYKVF-YNLTYQEISSVMGITEANVRKQFERARKRVQN 168 (185)
T ss_pred CCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 56666666555554 58999999999999999999999988888877
No 162
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=78.92 E-value=2.7 Score=35.85 Aligned_cols=46 Identities=24% Similarity=0.258 Sum_probs=38.7
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
.+|+..+-.+.| ++ .|.++.++|..+|+|.+||...+++....|..
T Consensus 155 ~L~~~~r~vl~l-~~-e~~s~~EIA~~lgis~~tV~~~l~rar~~Lr~ 200 (208)
T PRK08295 155 LLSELEKEVLEL-YL-DGKSYQEIAEELNRHVKSIDNALQRVKRKLEK 200 (208)
T ss_pred hCCHHHHHHHHH-HH-ccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 366677777777 55 69999999999999999999999988887776
No 163
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=78.90 E-value=2.4 Score=34.78 Aligned_cols=47 Identities=9% Similarity=-0.074 Sum_probs=38.8
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
.+|+..+-++.|.++ .|.++.++|..+|+|.+||...+++....|-.
T Consensus 108 ~L~~~~r~v~~l~~~-~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~ 154 (165)
T PRK09644 108 TLPVIEAQAILLCDV-HELTYEEAASVLDLKLNTYKSHLFRGRKRLKA 154 (165)
T ss_pred hCCHHHHHHHHhHHH-hcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 366777776655544 58999999999999999999999999888877
No 164
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=78.83 E-value=1.4 Score=36.69 Aligned_cols=45 Identities=13% Similarity=0.073 Sum_probs=37.7
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHH
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIV 83 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~ 83 (332)
.+++.+.= +|.+++.|.+..++|..+++|.+||..++.++..-+.
T Consensus 133 ~LSpRErE--VLrLLAqGkTnKEIAe~L~IS~rTVkth~srImkKLg 177 (198)
T PRK15201 133 HFSVTERH--LLKLIASGYHLSETAALLSLSEEQTKSLRRSIMRKLH 177 (198)
T ss_pred CCCHHHHH--HHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 37776653 6778999999999999999999999999988776554
No 165
>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=78.80 E-value=1.4 Score=37.25 Aligned_cols=46 Identities=15% Similarity=0.162 Sum_probs=37.9
Q ss_pred CCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 38 LSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 38 ~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
+|+..+-++.|+++ .|.++.++|..+|+|.+||...+.+....|-.
T Consensus 132 Lp~~~r~i~~L~~~-~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 177 (193)
T TIGR02947 132 LPEEFRQAVYLADV-EGFAYKEIAEIMGTPIGTVMSRLHRGRKQLRK 177 (193)
T ss_pred CCHHHhhheeehhh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 56666666666554 58999999999999999999999998888877
No 166
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=78.44 E-value=2.8 Score=37.17 Aligned_cols=46 Identities=22% Similarity=0.196 Sum_probs=39.8
Q ss_pred CCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 38 LSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 38 ~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
+|+..+-.+.|+|+ .|.++.++|..+|+|.+||...+++....|-.
T Consensus 202 L~~~~r~vl~l~~~-~~~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~ 247 (251)
T PRK07670 202 LSEKEQLVISLFYK-EELTLTEIGQVLNLSTSRISQIHSKALFKLKK 247 (251)
T ss_pred CCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 67788888888775 78999999999999999999999988887765
No 167
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=78.26 E-value=2.7 Score=34.16 Aligned_cols=46 Identities=17% Similarity=0.013 Sum_probs=38.0
Q ss_pred CCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 38 LSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 38 ~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
+|++.+-++.|.+ -.|.++.++|..+|+|.+||...+.+....|-.
T Consensus 106 L~~~~r~v~~l~~-~~~~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~ 151 (159)
T PRK12527 106 LPPACRDSFLLRK-LEGLSHQQIAEHLGISRSLVEKHIVNAMKHCRV 151 (159)
T ss_pred CCHHHHHHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 6666666665654 569999999999999999999999988888776
No 168
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=78.18 E-value=2 Score=31.29 Aligned_cols=38 Identities=21% Similarity=0.237 Sum_probs=28.9
Q ss_pred HHHHHHhhhcc---CCcccccccccCCChhhHHhHHhHhHH
Q psy15697 43 KVLSCLHWMGV---GSPYHIIGATHGPSKSSICRSIHEVVP 80 (332)
Q Consensus 43 ~l~~~L~~L~~---g~~~~~l~~~fgis~sTv~r~~~~v~~ 80 (332)
+..-.|.+|+. +.+..+++..+|++++|+++++.....
T Consensus 6 r~~~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~~ 46 (91)
T smart00346 6 RGLAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQE 46 (91)
T ss_pred HHHHHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 34445555553 467889999999999999999988754
No 169
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=78.11 E-value=2.4 Score=35.61 Aligned_cols=47 Identities=13% Similarity=0.173 Sum_probs=38.5
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
.+|+.++-++.|.|+. |.++.++|..+|+|.+||...+++....|-.
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 3677777777776666 8999999999999999999998888777665
No 170
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=77.90 E-value=2.3 Score=37.31 Aligned_cols=46 Identities=9% Similarity=0.105 Sum_probs=38.1
Q ss_pred CCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 38 LSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 38 ~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
+|+.++-++.|+++ .|.++.++|..+|+|.+||...+++....|-.
T Consensus 172 Lp~~~R~v~~L~~~-eg~s~~EIA~~Lgis~~tVk~~l~RAr~kLr~ 217 (233)
T PRK12538 172 LPEQQRIAVILSYH-ENMSNGEIAEVMDTTVAAVESLLKRGRQQLRD 217 (233)
T ss_pred CCHHHHHHhhhHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 56666666666554 58999999999999999999999998888877
No 171
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=77.85 E-value=2.3 Score=38.12 Aligned_cols=46 Identities=17% Similarity=0.286 Sum_probs=38.5
Q ss_pred CCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 38 LSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 38 ~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
+|+.++-.+.|+|+ .|.++.++|..+|+|.+||.++.++....|-.
T Consensus 216 L~~rer~vl~l~y~-~~~t~~EIA~~lgis~~~V~~~~~ral~kLr~ 261 (264)
T PRK07122 216 LPERERTVLVLRFF-ESMTQTQIAERVGISQMHVSRLLAKTLARLRD 261 (264)
T ss_pred CCHHHHHHHHHHhc-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 56666667777775 58999999999999999999999988887765
No 172
>PRK13870 transcriptional regulator TraR; Provisional
Probab=77.63 E-value=1.4 Score=38.84 Aligned_cols=47 Identities=23% Similarity=0.338 Sum_probs=40.3
Q ss_pred CCCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 36 VALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 36 ~~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
..+++.++= +|.|.+.|.+..++|...|||++||..+++....-|..
T Consensus 172 ~~LT~RE~E--~L~W~A~GKT~~EIa~ILgISe~TV~~Hl~na~~KLga 218 (234)
T PRK13870 172 AWLDPKEAT--YLRWIAVGKTMEEIADVEGVKYNSVRVKLREAMKRFDV 218 (234)
T ss_pred CCCCHHHHH--HHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCC
Confidence 457777765 78999999999999999999999999999988776543
No 173
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=77.55 E-value=1.6 Score=37.54 Aligned_cols=45 Identities=18% Similarity=0.101 Sum_probs=38.3
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHH
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIV 83 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~ 83 (332)
.+++.+. =.|.+++.|.+..++|...++|.+||..++.++..-|.
T Consensus 137 ~LT~RE~--eVL~lla~G~snkeIA~~L~iS~~TVk~h~~~I~~KL~ 181 (207)
T PRK15411 137 SLSRTES--SMLRMWMAGQGTIQISDQMNIKAKTVSSHKGNIKRKIK 181 (207)
T ss_pred cCCHHHH--HHHHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHHHHhC
Confidence 3777665 36788999999999999999999999999988876654
No 174
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=77.44 E-value=2.4 Score=35.07 Aligned_cols=47 Identities=21% Similarity=0.181 Sum_probs=36.8
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
.+|++.+-++.|.++ .|.++.++|..+|+|.+||...+++....+..
T Consensus 119 ~L~~~~r~i~~l~~~-~g~s~~EIA~~lgis~~tV~~~l~Ra~~~~~~ 165 (172)
T PRK09651 119 GLNGKTREAFLLSQL-DGLTYSEIAHKLGVSVSSVKKYVAKATEHCLL 165 (172)
T ss_pred hCCHHHhHHhhhhhc-cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 366666655555444 58899999999999999999999888877665
No 175
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=77.30 E-value=5.1 Score=34.58 Aligned_cols=45 Identities=13% Similarity=0.185 Sum_probs=38.0
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHH
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIV 83 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~ 83 (332)
.+++.+.- .|..++.|.+..++|...++|.+||..++.+...-|.
T Consensus 148 ~LT~RE~e--VL~lla~G~snkeIA~~L~iS~~TVk~h~~~i~~KL~ 192 (211)
T COG2197 148 LLTPRELE--VLRLLAEGLSNKEIAEELNLSEKTVKTHVSNILRKLG 192 (211)
T ss_pred CCCHHHHH--HHHHHHCCCCHHHHHHHHCCCHhHHHHHHHHHHHHcC
Confidence 46666654 6788999999999999999999999999988876554
No 176
>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family. Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.
Probab=77.26 E-value=3.1 Score=36.10 Aligned_cols=46 Identities=17% Similarity=0.244 Sum_probs=39.0
Q ss_pred CCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 38 LSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 38 ~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
+|+.++-.+.|+|+ .|.++.++|..+|+|.+||.+.+++....|-.
T Consensus 176 L~~~~r~il~l~y~-~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~ 221 (224)
T TIGR02479 176 LSEREQLVLSLYYY-EELNLKEIGEVLGLTESRVSQIHSQALKKLRA 221 (224)
T ss_pred CCHHHHHHHHHHHh-CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 67777777777775 68899999999999999999999988877655
No 177
>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=77.23 E-value=1.1 Score=26.24 Aligned_cols=25 Identities=12% Similarity=0.209 Sum_probs=19.3
Q ss_pred CcccccccccCCChhhHHhHHhHhH
Q psy15697 55 SPYHIIGATHGPSKSSICRSIHEVV 79 (332)
Q Consensus 55 ~~~~~l~~~fgis~sTv~r~~~~v~ 79 (332)
.+..++|+..|.+..||+|++.++-
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 3456899999999999999998764
No 178
>PRK01381 Trp operon repressor; Provisional
Probab=77.00 E-value=1.2 Score=33.37 Aligned_cols=26 Identities=15% Similarity=0.087 Sum_probs=21.6
Q ss_pred hccCCcccccccccCCChhhHHhHHh
Q psy15697 51 MGVGSPYHIIGATHGPSKSSICRSIH 76 (332)
Q Consensus 51 L~~g~~~~~l~~~fgis~sTv~r~~~ 76 (332)
+..+.+|+.|+...|||.+||+|.-+
T Consensus 52 ~~g~~sQREIa~~lGvSiaTITRgsn 77 (99)
T PRK01381 52 LRGELSQREIKQELGVGIATITRGSN 77 (99)
T ss_pred HcCCcCHHHHHHHhCCceeeehhhHH
Confidence 34458999999999999999987644
No 179
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=76.78 E-value=1.9 Score=37.49 Aligned_cols=44 Identities=7% Similarity=0.094 Sum_probs=36.2
Q ss_pred CCCHHHHHHHHHhhhccC----CcccccccccCCChhhHHhHHhHhHH
Q psy15697 37 ALSAKEKVLSCLHWMGVG----SPYHIIGATHGPSKSSICRSIHEVVP 80 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g----~~~~~l~~~fgis~sTv~r~~~~v~~ 80 (332)
..+++++|+-+|..+..+ .+..++|..+|+|+.|++|.++++.+
T Consensus 148 ~~~~~~Rla~~L~~~~~~~~~~~t~~~lA~~lG~sretvsR~L~~L~~ 195 (226)
T PRK10402 148 SFPLENRLAAFILLTQEGDLYHEKHTQAAEYLGVSYRHLLYVLAQFIQ 195 (226)
T ss_pred cChHHHHHHHHHHhcccCCcccchHHHHHHHHCCcHHHHHHHHHHHHH
Confidence 357899999999876533 35678999999999999999998876
No 180
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=76.73 E-value=2.6 Score=29.26 Aligned_cols=42 Identities=24% Similarity=0.229 Sum_probs=31.8
Q ss_pred CHHHHHHHHHhhhcc-CCcccccccccCCChhhHHhHHhHhHH
Q psy15697 39 SAKEKVLSCLHWMGV-GSPYHIIGATHGPSKSSICRSIHEVVP 80 (332)
Q Consensus 39 ~~~~~l~~~L~~L~~-g~~~~~l~~~fgis~sTv~r~~~~v~~ 80 (332)
+.+++++.+|.--+. +.+..+|+..+|++.++|++.+.....
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 356677777665544 478899999999999999888776543
No 181
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=76.58 E-value=3.1 Score=35.17 Aligned_cols=47 Identities=13% Similarity=0.188 Sum_probs=38.7
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
.+|+..+-.+.|+++ .|.++.++|..+|+|.+||...+++....|..
T Consensus 142 ~L~~~~r~vl~l~~~-~~~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~ 188 (194)
T PRK09646 142 ALTDTQRESVTLAYY-GGLTYREVAERLAVPLGTVKTRMRDGLIRLRD 188 (194)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHhCCChHhHHHHHHHHHHHHHH
Confidence 366777776666654 58999999999999999999999988888776
No 182
>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=76.46 E-value=2.5 Score=28.36 Aligned_cols=37 Identities=19% Similarity=0.189 Sum_probs=29.1
Q ss_pred HHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 47 CLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 47 ~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
++....+| ++...|..+++|++++++.++++-..+..
T Consensus 7 f~~v~~~g-s~~~AA~~l~is~~~vs~~i~~LE~~lg~ 43 (60)
T PF00126_consen 7 FLAVAETG-SISAAAEELGISQSAVSRQIKQLEEELGV 43 (60)
T ss_dssp HHHHHHHS-SHHHHHHHCTSSHHHHHHHHHHHHHHHTS
T ss_pred HHHHHHhC-CHHHHHHHhhccchHHHHHHHHHHHHhCC
Confidence 33333344 78889999999999999999998887665
No 183
>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=76.12 E-value=3.1 Score=31.14 Aligned_cols=43 Identities=19% Similarity=0.152 Sum_probs=34.3
Q ss_pred HHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 41 KEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 41 ~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
.++--+-|+| ....|...+|..|+||++.|+..++++...+..
T Consensus 21 KQ~~Y~~lyy-~dDlSl~EIAee~~VSRqAIyDnIKr~~~~L~~ 63 (105)
T COG2739 21 KQKNYLELYY-LDDLSLSEIAEEFNVSRQAIYDNIKRTEKILED 63 (105)
T ss_pred HHHHHHHHHH-HhhccHHHHHHHhCccHHHHHHHHHHHHHHHHH
Confidence 3344444544 457888999999999999999999999988875
No 184
>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=75.63 E-value=1 Score=29.48 Aligned_cols=26 Identities=23% Similarity=0.225 Sum_probs=21.9
Q ss_pred ccCCcccccccccCCChhhHHhHHhH
Q psy15697 52 GVGSPYHIIGATHGPSKSSICRSIHE 77 (332)
Q Consensus 52 ~~g~~~~~l~~~fgis~sTv~r~~~~ 77 (332)
..|.++.++|...|+|++|++++.+.
T Consensus 7 ~~gls~~~la~~~gis~~~i~~~~~g 32 (55)
T PF01381_consen 7 EKGLSQKELAEKLGISRSTISRIENG 32 (55)
T ss_dssp HTTS-HHHHHHHHTS-HHHHHHHHTT
T ss_pred HcCCCHHHHHHHhCCCcchhHHHhcC
Confidence 57899999999999999999999875
No 185
>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function.
Probab=75.61 E-value=4.3 Score=30.93 Aligned_cols=47 Identities=19% Similarity=0.120 Sum_probs=36.6
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
.+++++-=++-|..+- |.++.+.|...|||++|+++++..--.-+..
T Consensus 41 ~L~~dElEAiRL~D~e-gl~QeeaA~~MgVSR~T~~ril~~ARkKiA~ 87 (106)
T PF02001_consen 41 VLTVDELEAIRLVDYE-GLSQEEAAERMGVSRPTFQRILESARKKIAD 87 (106)
T ss_pred EeeHHHHHHHHHHHHc-CCCHHHHHHHcCCcHHHHHHHHHHHHHHHHH
Confidence 4677776667666665 6999999999999999999999865554444
No 186
>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=75.52 E-value=1.5 Score=34.96 Aligned_cols=36 Identities=17% Similarity=0.161 Sum_probs=29.4
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHh
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICR 73 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r 73 (332)
.+|+..+-.+.|+++ .|.++.++|..+|+|.+||.+
T Consensus 107 ~Lp~~~r~v~~l~~~-~~~s~~EIA~~l~is~~tV~~ 142 (142)
T TIGR03209 107 ILPNKQKKIIYMKFF-EDMKEIDIAKKLHISRQSVYK 142 (142)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHhhcC
Confidence 467777777777555 589999999999999999863
No 187
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=74.80 E-value=3.2 Score=39.26 Aligned_cols=48 Identities=17% Similarity=0.190 Sum_probs=41.3
Q ss_pred CCCHHHHHHHHHhhh---ccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 37 ALSAKEKVLSCLHWM---GVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L---~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
.+++.++..+.|+|+ ..+.++..+|..+|||+.+|.++..+.+.-|-.
T Consensus 311 ~L~~rEr~IL~lrygl~~~~~~Tl~EIA~~lgiS~eRVRQie~rAL~KLR~ 361 (373)
T PRK07406 311 TLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRH 361 (373)
T ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHhc
Confidence 378888889999886 246899999999999999999999998887765
No 188
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=74.57 E-value=2 Score=36.25 Aligned_cols=46 Identities=9% Similarity=0.084 Sum_probs=36.2
Q ss_pred CCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 38 LSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 38 ~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
+|+..+..+.|++ -.|.++.++|..+|+|.+||...+.+....|-.
T Consensus 140 L~~~~r~i~~l~~-~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~ 185 (194)
T PRK12513 140 LPDEQREVFLLRE-HGDLELEEIAELTGVPEETVKSRLRYALQKLRE 185 (194)
T ss_pred CCHhHhhheeeeh-ccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 5555555555544 468999999999999999999888888877766
No 189
>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=74.48 E-value=5.7 Score=30.60 Aligned_cols=42 Identities=10% Similarity=0.121 Sum_probs=29.2
Q ss_pred CCHHH-HHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHH
Q psy15697 38 LSAKE-KVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVP 80 (332)
Q Consensus 38 ~~~~~-~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~ 80 (332)
+++.+ .++..|.. ..+.+..+++..++++++|+++.+++...
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 44433 34334432 34677899999999999999988877654
No 190
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=74.33 E-value=3.3 Score=36.30 Aligned_cols=45 Identities=16% Similarity=0.245 Sum_probs=37.4
Q ss_pred CCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHH
Q psy15697 38 LSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIV 83 (332)
Q Consensus 38 ~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~ 83 (332)
+++.++-.+.|+|+ .|.++.++|..+|+|+++|+++.++...-|-
T Consensus 184 L~~~er~vi~l~~~-~~~t~~EIA~~lgis~~~V~q~~~~~~~kLr 228 (231)
T PRK12427 184 LDEREQLILHLYYQ-HEMSLKEIALVLDLTEARICQLNKKIAQKIK 228 (231)
T ss_pred CCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 56677777777764 6899999999999999999999988877654
No 191
>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=74.24 E-value=3.9 Score=30.89 Aligned_cols=44 Identities=14% Similarity=0.154 Sum_probs=32.0
Q ss_pred HHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 40 AKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 40 ~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
..++-.+ -.|+-...|+..+|..+|||+.+|+..+++....|..
T Consensus 20 ~kQ~~~l-~lyy~eDlSlsEIAe~~~iSRqaV~d~ikr~~~~L~~ 63 (101)
T PF04297_consen 20 EKQREIL-ELYYEEDLSLSEIAEELGISRQAVYDSIKRAEKKLEE 63 (101)
T ss_dssp HHHHHHH-HHHCTS---HHHHHHHCTS-HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHH-HHHHccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3444434 4566778999999999999999999999999888865
No 192
>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=74.11 E-value=2.8 Score=31.09 Aligned_cols=66 Identities=17% Similarity=0.187 Sum_probs=39.3
Q ss_pred HhcCCHHHHHHHHHHhccCcCCCCCCCCCCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhH--hHHHHHH
Q psy15697 9 AFRLSATQVEFILEEIAPALTTPTERNVALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHE--VVPVIVD 84 (332)
Q Consensus 9 ~frms~~~F~~L~~~L~~~~~~~~~~~~~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~--v~~~l~~ 84 (332)
.+.|+-+.|..|.......-...+. ......+.+. --.+..+|..||+|.+|++|+-.. .=.||..
T Consensus 10 v~qmTg~ell~L~~~~~~~~~~~~~-~~~~~~~~~y---------vyG~~GlAklfgcSv~Ta~RiK~sG~id~AI~Q 77 (96)
T PF12964_consen 10 VWQMTGEELLFLLKEGKTNSEKQTS-QKAKKDEKKY---------VYGLKGLAKLFGCSVPTANRIKKSGKIDPAITQ 77 (96)
T ss_pred HHHhhHHHHHHHHHHHhcCCCccCC-ccccCcccce---------eehHHHHHHHhCCCchhHHHHHhcCCccHHHHH
Confidence 3667888888888776443222221 1112222211 123567899999999999999863 3355555
No 193
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=74.11 E-value=1.5 Score=29.80 Aligned_cols=28 Identities=18% Similarity=0.136 Sum_probs=22.2
Q ss_pred hhhccCCcccccccccCCChhhHHhHHh
Q psy15697 49 HWMGVGSPYHIIGATHGPSKSSICRSIH 76 (332)
Q Consensus 49 ~~L~~g~~~~~l~~~fgis~sTv~r~~~ 76 (332)
.+-+.|.++..+|...|+|++|++++-+
T Consensus 9 ~R~~~gls~~~lA~~~g~s~s~v~~iE~ 36 (64)
T PF13560_consen 9 LRERAGLSQAQLADRLGVSQSTVSRIER 36 (64)
T ss_dssp HHHCHTS-HHHHHHHHTS-HHHHHHHHT
T ss_pred HHHHcCCCHHHHHHHHCcCHHHHHHHHC
Confidence 3445789999999999999999999876
No 194
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=74.10 E-value=2.2 Score=39.66 Aligned_cols=50 Identities=8% Similarity=0.112 Sum_probs=40.2
Q ss_pred CCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHHhhhcc
Q psy15697 38 LSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVDTFFQR 89 (332)
Q Consensus 38 ~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~~l~~~ 89 (332)
+|+..+-++.|+++ .|.++.++|..+|+|.+||...+.+....|.. ..+.
T Consensus 154 Lp~~~R~v~~L~~~-~g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~-~~~~ 203 (339)
T PRK08241 154 LPPRQRAVLILRDV-LGWSAAEVAELLDTSVAAVNSALQRARATLAE-RGPS 203 (339)
T ss_pred CCHHHhhhhhhHHh-hCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhh-cCCC
Confidence 56666666666554 58999999999999999999999999998887 4443
No 195
>PF13551 HTH_29: Winged helix-turn helix
Probab=73.90 E-value=14 Score=27.66 Aligned_cols=74 Identities=15% Similarity=0.091 Sum_probs=44.7
Q ss_pred hhHHHHHhcCCHHHHHHHHHHhccCc----CC--C-CCCCCC-CCHHHHHHHHHhhhccC-------Ccccccccc----
Q psy15697 3 PFAFKEAFRLSATQVEFILEEIAPAL----TT--P-TERNVA-LSAKEKVLSCLHWMGVG-------SPYHIIGAT---- 63 (332)
Q Consensus 3 d~~f~~~frms~~~F~~L~~~L~~~~----~~--~-~~~~~~-~~~~~~l~~~L~~L~~g-------~~~~~l~~~---- 63 (332)
..+.-+.+++++.++...+......- .. . .++... ++++..- ..+.++... .+...++..
T Consensus 15 ~~~ia~~lg~s~~Tv~r~~~~~~~~G~~~l~~~~~~~g~~~~~l~~~~~~-~l~~~~~~~p~~g~~~~t~~~l~~~l~~~ 93 (112)
T PF13551_consen 15 IAEIARRLGISRRTVYRWLKRYREGGIEGLLPRKPRGGRPRKRLSEEQRA-QLIELLRENPPEGRSRWTLEELAEWLIEE 93 (112)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHcccHHHHHhccccCCCCCCCCCHHHHH-HHHHHHHHCCCCCCCcccHHHHHHHHHHh
Confidence 56778899999999999988866532 11 1 122222 5655544 333344432 233444442
Q ss_pred ---cCCChhhHHhHHhH
Q psy15697 64 ---HGPSKSSICRSIHE 77 (332)
Q Consensus 64 ---fgis~sTv~r~~~~ 77 (332)
..+|.+||.+++++
T Consensus 94 ~~~~~~s~~ti~r~L~~ 110 (112)
T PF13551_consen 94 EFGIDVSPSTIRRILKR 110 (112)
T ss_pred ccCccCCHHHHHHHHHH
Confidence 36789999999875
No 196
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=73.81 E-value=2.1 Score=37.43 Aligned_cols=46 Identities=9% Similarity=0.119 Sum_probs=38.3
Q ss_pred CCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 38 LSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 38 ~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
+|+..+-.+.|+++. |.++.++|..+|+|.+||...+.+....|-.
T Consensus 150 L~~~~r~i~~l~~~~-g~s~~EIAe~lgis~~tVk~~l~Rar~kLr~ 195 (231)
T PRK11922 150 LPDAFRAVFVLRVVE-ELSVEETAQALGLPEETVKTRLHRARRLLRE 195 (231)
T ss_pred CCHHHhhhheeehhc-CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 566666666666554 9999999999999999999999988888877
No 197
>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain. This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.
Probab=73.80 E-value=2.8 Score=31.22 Aligned_cols=29 Identities=14% Similarity=0.209 Sum_probs=24.0
Q ss_pred ccCCcccccccccCCChhhHHhHHhHhHH
Q psy15697 52 GVGSPYHIIGATHGPSKSSICRSIHEVVP 80 (332)
Q Consensus 52 ~~g~~~~~l~~~fgis~sTv~r~~~~v~~ 80 (332)
....+..++|...|+|++||+|.++++..
T Consensus 45 ~~~is~~eLa~~~g~sr~tVsr~L~~Le~ 73 (95)
T TIGR01610 45 QDRVTATVIAELTGLSRTHVSDAIKSLAR 73 (95)
T ss_pred CCccCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 44577888999999999999998887653
No 198
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=73.78 E-value=4.2 Score=34.27 Aligned_cols=46 Identities=11% Similarity=0.065 Sum_probs=37.4
Q ss_pred CCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 38 LSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 38 ~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
+|+..+-++.|+++ .|.++.++|..+|+|.+||...+.+....|..
T Consensus 129 Lp~~~r~v~~l~~~-~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 174 (188)
T PRK12517 129 LDPEYREPLLLQVI-GGFSGEEIAEILDLNKNTVMTRLFRARNQLKE 174 (188)
T ss_pred CCHHHHHHHHHHHH-hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 55666665555544 59999999999999999999999998888877
No 199
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=73.71 E-value=4.1 Score=34.87 Aligned_cols=46 Identities=22% Similarity=0.152 Sum_probs=37.5
Q ss_pred CCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 38 LSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 38 ~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
+|+..+-.+.|.+ -.|.++.++|..+|+|.+||...+.+....|..
T Consensus 139 L~~~~r~v~~L~~-~~g~s~~EIA~~Lgis~~tV~~~l~RArk~Lr~ 184 (203)
T PRK09647 139 LPPEFRAAVVLCD-IEGLSYEEIAATLGVKLGTVRSRIHRGRQQLRA 184 (203)
T ss_pred CCHHHHHHHHHHH-HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 5555555555554 568999999999999999999999999888877
No 200
>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=72.98 E-value=2.2 Score=29.16 Aligned_cols=35 Identities=20% Similarity=0.157 Sum_probs=24.5
Q ss_pred HHhhhc---cCCcccccccccCCChhhHHhHHhHhHHH
Q psy15697 47 CLHWMG---VGSPYHIIGATHGPSKSSICRSIHEVVPV 81 (332)
Q Consensus 47 ~L~~L~---~g~~~~~l~~~fgis~sTv~r~~~~v~~~ 81 (332)
+|++++ ...+..+|+..++++++++++.+++.+..
T Consensus 8 vL~~l~~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~ 45 (68)
T PF13463_consen 8 VLRALAHSDGPMTQSDLAERLGISKSTVSRIIKKLEEK 45 (68)
T ss_dssp HHHHHT--TS-BEHHHHHHHTT--HHHHHHHHHHHHHT
T ss_pred HHHHHHccCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 344455 34567889999999999999998887653
No 201
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=72.60 E-value=3.7 Score=39.27 Aligned_cols=48 Identities=13% Similarity=0.170 Sum_probs=41.0
Q ss_pred CCCHHHHHHHHHhhh---ccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 37 ALSAKEKVLSCLHWM---GVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L---~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
.+++.++-.+.|+|. +.+.++.++|..+|+|.++|..+.++-...|-.
T Consensus 350 ~L~~reR~VI~LRygl~d~~~~Tl~EIA~~LGvS~erVRqie~rAl~KLR~ 400 (415)
T PRK07598 350 DLTSRERDVIRMRFGLADGHTYSLAEIGRALDLSRERVRQIESKALQKLRQ 400 (415)
T ss_pred hCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHhc
Confidence 478888888888885 356899999999999999999999998877764
No 202
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=72.16 E-value=5.2 Score=37.09 Aligned_cols=50 Identities=8% Similarity=0.143 Sum_probs=42.6
Q ss_pred CCCHHHHHHHHHhh-h--ccCCcccccccccCCChhhHHhHHhHhHHHHHHhh
Q psy15697 37 ALSAKEKVLSCLHW-M--GVGSPYHIIGATHGPSKSSICRSIHEVVPVIVDTF 86 (332)
Q Consensus 37 ~~~~~~~l~~~L~~-L--~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~~l 86 (332)
.+|+.++..+.++| | -.|.++..+|..+|||.+||..+.++-...|-..+
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 47888888888876 4 36789999999999999999999999998887733
No 203
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=72.13 E-value=4.8 Score=33.90 Aligned_cols=46 Identities=15% Similarity=0.246 Sum_probs=35.5
Q ss_pred CCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 38 LSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 38 ~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
++++..=.+.|+++ .|.++.++|...|||.+||.+-+...-..|..
T Consensus 136 l~~~~~~~v~l~~~-~Gls~~EIA~~lgiS~~tV~r~l~~aR~~l~~ 181 (185)
T PF07638_consen 136 LDPRQRRVVELRFF-EGLSVEEIAERLGISERTVRRRLRRARAWLRR 181 (185)
T ss_pred cCHHHHHHHHHHHH-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 44555555556555 68899999999999999999998877766554
No 204
>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=72.10 E-value=2.3 Score=28.65 Aligned_cols=30 Identities=10% Similarity=0.077 Sum_probs=25.0
Q ss_pred hccCCcccccccccCCChhhHHhHHhHhHH
Q psy15697 51 MGVGSPYHIIGATHGPSKSSICRSIHEVVP 80 (332)
Q Consensus 51 L~~g~~~~~l~~~fgis~sTv~r~~~~v~~ 80 (332)
-..+.+..+++..+|++++|+++.++...+
T Consensus 21 ~~~~~t~~ela~~l~~~~~t~s~hL~~L~~ 50 (61)
T PF12840_consen 21 SNGPMTVSELAEELGISQSTVSYHLKKLEE 50 (61)
T ss_dssp HCSTBEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred cCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 466778999999999999999999987655
No 205
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=72.07 E-value=4.4 Score=36.32 Aligned_cols=47 Identities=21% Similarity=0.224 Sum_probs=39.5
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
.+|+.++-++.|+|+ .|.++.++|..+|+|.+||.+..++....|-.
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 377788887777775 58999999999999999999888887777665
No 206
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=71.79 E-value=2 Score=26.94 Aligned_cols=27 Identities=11% Similarity=0.213 Sum_probs=22.7
Q ss_pred CCcccccccccCCChhhHHhHHhHhHH
Q psy15697 54 GSPYHIIGATHGPSKSSICRSIHEVVP 80 (332)
Q Consensus 54 g~~~~~l~~~fgis~sTv~r~~~~v~~ 80 (332)
..+..++|..+|+|++|+++.+.....
T Consensus 8 ~~s~~~la~~l~~s~~tv~~~l~~L~~ 34 (48)
T smart00419 8 PLTRQEIAELLGLTRETVSRTLKRLEK 34 (48)
T ss_pred ccCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 456778999999999999998887654
No 207
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=71.57 E-value=2.3 Score=35.09 Aligned_cols=47 Identities=13% Similarity=0.034 Sum_probs=35.1
Q ss_pred CCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHHh
Q psy15697 38 LSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVDT 85 (332)
Q Consensus 38 ~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~~ 85 (332)
+|+.++-++.|++ -.|.++.++|..+|+|.+||...+++....|...
T Consensus 121 L~~~~r~vl~l~~-~~g~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~ 167 (175)
T PRK12518 121 LSLEHRAVLVLHD-LEDLPQKEIAEILNIPVGTVKSRLFYARRQLRKF 167 (175)
T ss_pred CCHHHeeeeeehH-hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3333443333333 3588899999999999999999999998888773
No 208
>PHA02591 hypothetical protein; Provisional
Probab=70.80 E-value=2.9 Score=29.62 Aligned_cols=38 Identities=13% Similarity=0.097 Sum_probs=30.7
Q ss_pred HHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhH
Q psy15697 40 AKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHE 77 (332)
Q Consensus 40 ~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~ 77 (332)
-.+.+.++=...+.|.+...+|...|+++.+|+++++.
T Consensus 45 ~dd~~~vA~eL~eqGlSqeqIA~~LGVsqetVrKYL~~ 82 (83)
T PHA02591 45 EDDLISVTHELARKGFTVEKIASLLGVSVRKVRRYLES 82 (83)
T ss_pred cchHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHhc
Confidence 34445556566678999999999999999999999864
No 209
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=70.80 E-value=2.7 Score=27.78 Aligned_cols=29 Identities=10% Similarity=0.057 Sum_probs=23.8
Q ss_pred ccCCcccccccccCCChhhHHhHHhHhHH
Q psy15697 52 GVGSPYHIIGATHGPSKSSICRSIHEVVP 80 (332)
Q Consensus 52 ~~g~~~~~l~~~fgis~sTv~r~~~~v~~ 80 (332)
....+..+++..+|+|.+|+++.+++...
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~ 36 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLRE 36 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 44567888999999999999999887654
No 210
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=70.74 E-value=2.1 Score=28.17 Aligned_cols=25 Identities=12% Similarity=0.238 Sum_probs=21.0
Q ss_pred cccccccccCCChhhHHhHHhHhHH
Q psy15697 56 PYHIIGATHGPSKSSICRSIHEVVP 80 (332)
Q Consensus 56 ~~~~l~~~fgis~sTv~r~~~~v~~ 80 (332)
+..+++..||+|++||.+.+.....
T Consensus 22 s~~~la~~~~vs~~tv~~~l~~L~~ 46 (60)
T smart00345 22 SERELAAQLGVSRTTVREALSRLEA 46 (60)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 5667899999999999998887654
No 211
>PRK05949 RNA polymerase sigma factor; Validated
Probab=70.73 E-value=4.5 Score=37.52 Aligned_cols=48 Identities=10% Similarity=0.158 Sum_probs=40.9
Q ss_pred CCCHHHHHHHHHhhh-c--cCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 37 ALSAKEKVLSCLHWM-G--VGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L-~--~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
.+++.++-.+.|+|. . .+.++.++|..+|+|.++|..+..+....|-.
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 378888888888874 3 56899999999999999999999988877765
No 212
>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=70.35 E-value=4.1 Score=34.34 Aligned_cols=38 Identities=16% Similarity=0.205 Sum_probs=31.2
Q ss_pred HHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 46 SCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 46 ~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
+.+.++ .|.++.++|..+|+|.+||...+++....|-.
T Consensus 158 i~~~~~-~~~s~~eIA~~l~~s~~tV~~~l~r~r~~L~~ 195 (198)
T TIGR02859 158 VLQSYL-DGKSYQEIACDLNRHVKSIDNALQRVKRKLEK 195 (198)
T ss_pred HHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 345554 79999999999999999999888887776654
No 213
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=70.28 E-value=3.1 Score=35.96 Aligned_cols=46 Identities=11% Similarity=0.042 Sum_probs=37.9
Q ss_pred CCCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHH
Q psy15697 36 VALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIV 83 (332)
Q Consensus 36 ~~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~ 83 (332)
..+++.+.- +|..++.|.+..++|..+++|.+||..++.++..-+-
T Consensus 142 ~~LS~RE~e--VL~Lia~G~SnkEIA~~L~IS~~TVk~hvs~I~~KLg 187 (217)
T PRK13719 142 NKVTKYQND--VFILYSFGFSHEYIAQLLNITVGSSKNKISEILKFFG 187 (217)
T ss_pred CCCCHHHHH--HHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 346665544 5678899999999999999999999999998877654
No 214
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=69.96 E-value=4.6 Score=38.10 Aligned_cols=48 Identities=13% Similarity=0.181 Sum_probs=40.0
Q ss_pred CCCHHHHHHHHHhhh-c--cCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 37 ALSAKEKVLSCLHWM-G--VGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L-~--~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
.+++.++..+.|+|. . .+.++..+|..||||+..|+++-.+.+.-|-.
T Consensus 305 ~L~~rEr~Vl~lrygl~~~~~~tl~EIa~~lgvs~erVrQi~~~Al~kLr~ 355 (367)
T PRK09210 305 TLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRH 355 (367)
T ss_pred hCCHHHHHHHHHHhccCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHhC
Confidence 477888888899885 2 45899999999999999999998887776654
No 215
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=69.68 E-value=3.1 Score=36.34 Aligned_cols=43 Identities=19% Similarity=0.162 Sum_probs=35.1
Q ss_pred CCHHHHHHHHHhhhcc----------CCcccccccccCCChhhHHhHHhHhHH
Q psy15697 38 LSAKEKVLSCLHWMGV----------GSPYHIIGATHGPSKSSICRSIHEVVP 80 (332)
Q Consensus 38 ~~~~~~l~~~L~~L~~----------g~~~~~l~~~fgis~sTv~r~~~~v~~ 80 (332)
.+++++|+-+|..++. ..+..+||...|+++.|++|+++++-+
T Consensus 153 ~~~~~Rla~~Ll~l~~~~g~~~~i~i~lt~~~IA~~lGisretlsR~L~~L~~ 205 (230)
T PRK09391 153 KTAMERVAAFLLEMDERLGGAGMMALPMSRRDIADYLGLTIETVSRALSQLQD 205 (230)
T ss_pred CCHHHHHHHHHHHHHHHhCCCCEEEecCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 5789999999988743 235678999999999999999887654
No 216
>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=68.88 E-value=2.2 Score=27.41 Aligned_cols=19 Identities=21% Similarity=0.316 Sum_probs=16.7
Q ss_pred ccccccCCChhhHHhHHhH
Q psy15697 59 IIGATHGPSKSSICRSIHE 77 (332)
Q Consensus 59 ~l~~~fgis~sTv~r~~~~ 77 (332)
++|...|||.+||+++++.
T Consensus 2 ~lA~~~gvs~~tvs~~l~g 20 (52)
T cd01392 2 DIARAAGVSVATVSRVLNG 20 (52)
T ss_pred cHHHHHCcCHHHHHHHHcC
Confidence 5788999999999999874
No 217
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=68.86 E-value=1.8 Score=26.74 Aligned_cols=29 Identities=17% Similarity=0.080 Sum_probs=21.5
Q ss_pred hccCCcccccccccCCChhhHHhHHhHhH
Q psy15697 51 MGVGSPYHIIGATHGPSKSSICRSIHEVV 79 (332)
Q Consensus 51 L~~g~~~~~l~~~fgis~sTv~r~~~~v~ 79 (332)
|..+.+..++|..+|+|++..+|.|++.+
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 45667788999999999999999998764
No 218
>PHA00738 putative HTH transcription regulator
Probab=68.83 E-value=2.6 Score=32.10 Aligned_cols=33 Identities=12% Similarity=0.052 Sum_probs=25.3
Q ss_pred hhhccC--CcccccccccCCChhhHHhHHhHhHHH
Q psy15697 49 HWMGVG--SPYHIIGATHGPSKSSICRSIHEVVPV 81 (332)
Q Consensus 49 ~~L~~g--~~~~~l~~~fgis~sTv~r~~~~v~~~ 81 (332)
.+|+.+ .+-.+|+..|++|++|||+.++-.-.|
T Consensus 19 ~lL~~~e~~~V~eLae~l~lSQptVS~HLKvLreA 53 (108)
T PHA00738 19 ELIAENYILSASLISHTLLLSYTTVLRHLKILNEQ 53 (108)
T ss_pred HHHHHcCCccHHHHHHhhCCCHHHHHHHHHHHHHC
Confidence 334543 677789999999999999998865543
No 219
>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=68.71 E-value=4.8 Score=27.44 Aligned_cols=28 Identities=14% Similarity=0.165 Sum_probs=23.1
Q ss_pred cCCcccccccccCCChhhHHhHHhHhHH
Q psy15697 53 VGSPYHIIGATHGPSKSSICRSIHEVVP 80 (332)
Q Consensus 53 ~g~~~~~l~~~fgis~sTv~r~~~~v~~ 80 (332)
++.+..+++..++++.+|+++.+..+..
T Consensus 19 ~~~~~~ei~~~~~i~~~~i~~~l~~L~~ 46 (78)
T cd00090 19 GPLTVSELAERLGLSQSTVSRHLKKLEE 46 (78)
T ss_pred CCcCHHHHHHHHCcCHhHHHHHHHHHHH
Confidence 3478889999999999999988877543
No 220
>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=68.69 E-value=17 Score=26.84 Aligned_cols=57 Identities=14% Similarity=0.236 Sum_probs=35.4
Q ss_pred cCCHHHHHHHHHHhccCcCCCCCCCCCCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhH
Q psy15697 11 RLSATQVEFILEEIAPALTTPTERNVALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVV 79 (332)
Q Consensus 11 rms~~~F~~L~~~L~~~~~~~~~~~~~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~ 79 (332)
.|+.+.|.-|++. .++..+.-+...=.+|-.|.+..+++..+||+++-.++.+.+.-
T Consensus 22 ~vs~e~F~lLl~l------------s~IrS~kiI~AL~dyLV~G~srkeac~~~gV~~syfs~~L~rL~ 78 (91)
T PF03333_consen 22 KVSEEHFWLLLEL------------SSIRSEKIIAALRDYLVDGLSRKEACERHGVNQSYFSRALNRLN 78 (91)
T ss_dssp -S-HHHHHHHHHH------------S----HHHHHHHHHHHTT---HHHHHHHTT--HHHHHHHHHHHH
T ss_pred CcCHHHHHHHHHH------------CCCCcHHHHHHHHHHHHcCCcHHHHHHHhCCCHHHHHHHHHHHH
Confidence 4677777777765 23444555666667889999999999999999998888877643
No 221
>PRK14086 dnaA chromosomal replication initiation protein; Provisional
Probab=68.12 E-value=7.9 Score=38.99 Aligned_cols=52 Identities=12% Similarity=0.190 Sum_probs=46.3
Q ss_pred CCCCCCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 33 ERNVALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 33 ~~~~~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
.|...+..--+++|.|.+--.+.++..||..||.+.|||..-++++-..+.+
T Consensus 548 ~R~~~i~~aRqiAMYL~r~lt~~Sl~~IG~~FgRdHSTV~~A~~kI~~~~~~ 599 (617)
T PRK14086 548 SRSRVLVTARQIAMYLCRELTDLSLPKIGQQFGRDHTTVMHADRKIRALMAE 599 (617)
T ss_pred CCCcccchHHHHHHHHHHHHcCCCHHHHHHHhCCChhHHHHHHHHHHHHHHh
Confidence 3456788889999999999999999999999999999999999999887765
No 222
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=67.50 E-value=3.6 Score=36.32 Aligned_cols=47 Identities=17% Similarity=0.204 Sum_probs=39.1
Q ss_pred CCCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 36 VALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 36 ~~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
..+++.+.= +|.+++.|.+..++|..++||..||..++..+..-|..
T Consensus 178 ~~LT~rE~e--vl~~~a~G~t~~eIa~~l~is~~TV~~h~~~~~~KL~~ 224 (240)
T PRK10188 178 MNFSKREKE--ILKWTAEGKTSAEIAMILSISENTVNFHQKNMQKKFNA 224 (240)
T ss_pred CCCCHHHHH--HHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 457777665 67788999999999999999999999999988766543
No 223
>PF13309 HTH_22: HTH domain
Probab=67.23 E-value=2 Score=29.50 Aligned_cols=41 Identities=20% Similarity=0.191 Sum_probs=30.7
Q ss_pred CCCCHHHHHHHHHhhhccCCc-----ccccccccCCChhhHHhHHh
Q psy15697 36 VALSAKEKVLSCLHWMGVGSP-----YHIIGATHGPSKSSICRSIH 76 (332)
Q Consensus 36 ~~~~~~~~l~~~L~~L~~g~~-----~~~l~~~fgis~sTv~r~~~ 76 (332)
..++.++++-+.-.....|.+ -..+|..+|||+.||+++++
T Consensus 19 ~~l~~~~k~~iV~~L~~~G~F~lKgav~~vA~~L~iS~~TVY~YLr 64 (64)
T PF13309_consen 19 SRLSKEEKKEIVRQLYEKGIFLLKGAVEYVAEKLGISRATVYRYLR 64 (64)
T ss_pred hhCCHHHHHHHHHHHHHCCCcccCcHHHHHHHHHCCCHHHHHHHcC
Confidence 446777787776666666654 34688999999999999863
No 224
>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=67.06 E-value=7.1 Score=35.28 Aligned_cols=65 Identities=18% Similarity=0.190 Sum_probs=45.5
Q ss_pred CCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHHhhhccccCCCcccccchhhhh
Q psy15697 38 LSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVDTFFQRMVKWPEENLNDIPMTF 105 (332)
Q Consensus 38 ~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~~l~~~~I~~P~~~~~~~~~~f 105 (332)
+|+.++-++.|+++ .|.++.++|..+|+|.+||...+++....|.+ ..+.+- .|..+.+.+.+.|
T Consensus 109 L~~~~R~v~~L~~~-~g~s~~EIA~~lg~s~~tVr~~l~RAr~~Lr~-~~~~~~-~~~~~~~~~~~~f 173 (281)
T TIGR02957 109 LSPLERAVFVLREV-FDYPYEEIASIVGKSEANCRQLVSRARRHLDA-RRPRFE-VSREESRQLLERF 173 (281)
T ss_pred CCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh-hCCCCC-CChHHHHHHHHHH
Confidence 56666666555544 48899999999999999999999999998887 444321 1211344455555
No 225
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=67.05 E-value=3.4 Score=35.33 Aligned_cols=46 Identities=20% Similarity=0.120 Sum_probs=38.7
Q ss_pred CCCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHH
Q psy15697 36 VALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIV 83 (332)
Q Consensus 36 ~~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~ 83 (332)
..+++.++ -.|..++.|.+..++|...++|.+||..+..++..-|.
T Consensus 149 ~~Lt~rE~--evl~~~~~G~s~~eIA~~l~iS~~TV~~h~~~i~~Kl~ 194 (216)
T PRK10840 149 KRLSPKES--EVLRLFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLG 194 (216)
T ss_pred ccCCHHHH--HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence 34788775 57788899999999999999999999999988776554
No 226
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=66.73 E-value=7.1 Score=38.47 Aligned_cols=48 Identities=17% Similarity=0.207 Sum_probs=42.5
Q ss_pred CCCHHHHHHHHHhhh---ccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 37 ALSAKEKVLSCLHWM---GVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L---~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
.++..++..+.++|. ..+.++..||..||||++.|+++-.+.+.-|-.
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 488999999999995 457899999999999999999999998887766
No 227
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=66.62 E-value=2.9 Score=35.69 Aligned_cols=30 Identities=17% Similarity=0.288 Sum_probs=26.4
Q ss_pred HhhhccCCcccccccccCCChhhHHhHHhH
Q psy15697 48 LHWMGVGSPYHIIGATHGPSKSSICRSIHE 77 (332)
Q Consensus 48 L~~L~~g~~~~~l~~~fgis~sTv~r~~~~ 77 (332)
..++..|.++..+|..+|||.+|+.|+++.
T Consensus 166 ~~~~~~g~s~~~iak~lgis~~Tv~r~~k~ 195 (200)
T PRK13413 166 KKLLDKGTSKSEIARKLGVSRTTLARFLKT 195 (200)
T ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHHHh
Confidence 455788999999999999999999999873
No 228
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=66.60 E-value=7.1 Score=31.31 Aligned_cols=43 Identities=12% Similarity=0.101 Sum_probs=31.3
Q ss_pred CCCHHHH-HHHHHhhhccCCcccccccccCCChhhHHhHHhHhHH
Q psy15697 37 ALSAKEK-VLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVP 80 (332)
Q Consensus 37 ~~~~~~~-l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~ 80 (332)
.+++.+- ++..|+ -..+.+..+|+..++++++|+++.+++...
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 3544443 444443 355689999999999999999999887654
No 229
>PRK00149 dnaA chromosomal replication initiation protein; Reviewed
Probab=66.09 E-value=9.9 Score=36.88 Aligned_cols=53 Identities=9% Similarity=0.192 Sum_probs=46.5
Q ss_pred CCCCCCCCHHHHHHHHHhhhccCCccccccccc-CCChhhHHhHHhHhHHHHHH
Q psy15697 32 TERNVALSAKEKVLSCLHWMGVGSPYHIIGATH-GPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 32 ~~~~~~~~~~~~l~~~L~~L~~g~~~~~l~~~f-gis~sTv~r~~~~v~~~l~~ 84 (332)
..|.+.+..--+++|.|..--.+.++.++|..| |.+.|||...++++-..+..
T Consensus 380 ~~R~~~~~~aR~iamyl~~~~~~~s~~~Ig~~fg~rdhstV~~a~~~i~~~~~~ 433 (450)
T PRK00149 380 KSRTRNIARPRQIAMYLAKELTDLSLPEIGRAFGGRDHTTVLHAVRKIEKLLEE 433 (450)
T ss_pred CCCCcccChHHHHHHHHHHHhcCCCHHHHHHHcCCCCHhHHHHHHHHHHHHHHh
Confidence 345667888999999999999999999999999 59999999999999887654
No 230
>cd00131 PAX Paired Box domain
Probab=66.03 E-value=29 Score=27.38 Aligned_cols=76 Identities=20% Similarity=0.148 Sum_probs=43.0
Q ss_pred ChhHHHHHhcCCHHHHHHHHHHhccC--cCC-C-CCCCCC-CCHHH-HHHHHHhhhccCCccccccccc---CC------
Q psy15697 2 TPFAFKEAFRLSATQVEFILEEIAPA--LTT-P-TERNVA-LSAKE-KVLSCLHWMGVGSPYHIIGATH---GP------ 66 (332)
Q Consensus 2 ~d~~f~~~frms~~~F~~L~~~L~~~--~~~-~-~~~~~~-~~~~~-~l~~~L~~L~~g~~~~~l~~~f---gi------ 66 (332)
+..+.-+.|++++.+...++...... +.. . .++++. ..+.. ..++.+..-.-..+..++++.+ |+
T Consensus 35 s~~~iA~~~~Vs~~tV~r~i~r~~e~G~v~pk~~gg~rpr~~~~~~~~~i~~~v~~~p~~Tl~El~~~L~~~gv~~~~~~ 114 (128)
T cd00131 35 RPCDISRQLRVSHGCVSKILNRYYETGSIRPGAIGGSKPRVATPEVVKKIEIYKQENPGMFAWEIRDRLLQEGVCDKSNV 114 (128)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCCCCCCCCCCcCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCCcccCCC
Confidence 44566788999999999999887653 211 1 122222 33322 2222222222224455555442 55
Q ss_pred -ChhhHHhHHhH
Q psy15697 67 -SKSSICRSIHE 77 (332)
Q Consensus 67 -s~sTv~r~~~~ 77 (332)
|.||+++++++
T Consensus 115 ~s~stI~R~L~~ 126 (128)
T cd00131 115 PSVSSINRILRN 126 (128)
T ss_pred CCHHHHHHHHHh
Confidence 99999999764
No 231
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=65.86 E-value=3.8 Score=35.26 Aligned_cols=45 Identities=20% Similarity=0.211 Sum_probs=37.0
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHH
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIV 83 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~ 83 (332)
.+++.+. =.|..++.|.+..++|...++|..||..+..++..-+.
T Consensus 134 ~LT~RE~--eVL~ll~~G~snkeIA~~L~iS~~TV~~h~~~I~~KLg 178 (207)
T PRK11475 134 MLSPTER--EILRFMSRGYSMPQIAEQLERNIKTIRAHKFNVMSKLG 178 (207)
T ss_pred CCCHHHH--HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence 3666655 36778899999999999999999999999988766543
No 232
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=65.54 E-value=2.6 Score=35.39 Aligned_cols=45 Identities=7% Similarity=0.087 Sum_probs=34.3
Q ss_pred CHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 39 SAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 39 ~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
|+.++=++.|.++ .|.++.++|..+|+|.+||...+.+....|-.
T Consensus 136 ~~~~r~v~~l~~~-~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 180 (188)
T PRK09640 136 NPIDREILVLRFV-AELEFQEIADIMHMGLSATKMRYKRALDKLRE 180 (188)
T ss_pred ChhheeeeeeHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4444333334433 68899999999999999999999988887776
No 233
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=65.52 E-value=3.3 Score=28.27 Aligned_cols=38 Identities=16% Similarity=0.035 Sum_probs=28.1
Q ss_pred HHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhH
Q psy15697 42 EKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVV 79 (332)
Q Consensus 42 ~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~ 79 (332)
++++-+|.-...+.+-+++|+.+|+|..++.+++....
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 44556666667778889999999999999998876543
No 234
>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=65.46 E-value=5.3 Score=26.82 Aligned_cols=25 Identities=16% Similarity=0.153 Sum_probs=22.7
Q ss_pred cCCcccccccccCCChhhHHhHHhH
Q psy15697 53 VGSPYHIIGATHGPSKSSICRSIHE 77 (332)
Q Consensus 53 ~g~~~~~l~~~fgis~sTv~r~~~~ 77 (332)
.|.+..++|..+|++.+||+.+..+
T Consensus 12 ~G~~~~eIA~~Lg~~~~TV~~W~~r 36 (58)
T PF06056_consen 12 QGWSIKEIAEELGVPRSTVYSWKDR 36 (58)
T ss_pred cCCCHHHHHHHHCCChHHHHHHHHh
Confidence 5999999999999999999988764
No 235
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=65.41 E-value=2.6 Score=29.85 Aligned_cols=29 Identities=24% Similarity=0.319 Sum_probs=24.3
Q ss_pred hhhccCCcccccccccC------CChhhHHhHHhH
Q psy15697 49 HWMGVGSPYHIIGATHG------PSKSSICRSIHE 77 (332)
Q Consensus 49 ~~L~~g~~~~~l~~~fg------is~sTv~r~~~~ 77 (332)
.+...|.++.++|...| +|++||+|+-+-
T Consensus 19 ~R~~lGLTQ~dvA~~lg~~~g~i~SQstISR~Es~ 53 (75)
T smart00352 19 RRIKLGFTQADVGLALGALYGPDFSQTTICRFEAL 53 (75)
T ss_pred HHHHcCCCHHHHHHHhcccccCcCCHHHHHHHHhc
Confidence 44567899999999999 599999998773
No 236
>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=65.15 E-value=3.3 Score=28.46 Aligned_cols=39 Identities=21% Similarity=0.221 Sum_probs=27.8
Q ss_pred HHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHH
Q psy15697 41 KEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVP 80 (332)
Q Consensus 41 ~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~ 80 (332)
+.++...|. -..+.+..+|+...|+|++||++++++..+
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 334444443 233467889999999999999999887654
No 237
>COG3316 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=64.79 E-value=24 Score=30.51 Aligned_cols=182 Identities=11% Similarity=0.075 Sum_probs=99.5
Q ss_pred CCHHHHHHHHHhhhccCCcccccccc---c--CCChhhHHhHHhHhHHHHHHhhhccccCCCcccccchhhhhhhcCCCC
Q psy15697 38 LSAKEKVLSCLHWMGVGSPYHIIGAT---H--GPSKSSICRSIHEVVPVIVDTFFQRMVKWPEENLNDIPMTFLRKGGFP 112 (332)
Q Consensus 38 ~~~~~~l~~~L~~L~~g~~~~~l~~~---f--gis~sTv~r~~~~v~~~l~~~l~~~~I~~P~~~~~~~~~~f~~~~~~p 112 (332)
++.......+-+||+.+.+++.|.+. . .++.+|+++++.+....+.. ..+..-+ . +
T Consensus 9 f~~~vi~~~V~~yl~~~Ls~r~v~e~l~~rgi~v~h~Ti~rwv~k~~~~~~~-~~~~r~~-----------------~-~ 69 (215)
T COG3316 9 FPRNIIAVAVWLYLRYGLSLRDVEEMLAERGIEVDHETIHRWVQKYGPLLAR-RLKRRKR-----------------K-A 69 (215)
T ss_pred cchhhHHHHHHHHhhcchhhccHHHHHHHcCcchhHHHHHHHHHHHhHHHHH-Hhhhhcc-----------------c-c
Confidence 44444555566677789999998755 3 45678999999999998888 3321100 0 1
Q ss_pred CceeeecceEEEEeCCCCCcccccccCCccccceeeeccCCcceEEeeccCCccccchhhhccccccccccccCCCCCCC
Q psy15697 113 NVAGCVDGTMVLIDAPNEHEDQFVNRNGDHALNVMAICGPNYKFYAVNANWPGSVHDARVMRNSMVYRKFDEEGWRPFPD 192 (332)
Q Consensus 113 ~~~G~iDgt~i~i~~P~~~~~~y~~~k~~~s~~~~~v~d~~g~~~~v~~~~~Gs~~D~~v~~~s~l~~~l~~~~~~~~~~ 192 (332)
+-.=.||-|.|.|. +...+ +-..||.+|..+++...-.=+.+.+..|-. ..+ +.. ..+
T Consensus 70 ~~~w~vDEt~ikv~-----gkw~y---------lyrAid~~g~~Ld~~L~~rRn~~aAk~Fl~----kll-k~~---g~p 127 (215)
T COG3316 70 GDSWRVDETYIKVN-----GKWHY---------LYRAIDADGLTLDVWLSKRRNALAAKAFLK----KLL-KKH---GEP 127 (215)
T ss_pred ccceeeeeeEEeec-----cEeee---------hhhhhccCCCeEEEEEEcccCcHHHHHHHH----HHH-Hhc---CCC
Confidence 11124888888874 11111 123567778888887765555566655532 233 221 124
Q ss_pred ceEecCCCCCCCCc---CCCCccCCCCChHHHHHHHHHHH-HHHHHHHHHHHHhhhcccccccccCcccHHHHHHHHHHH
Q psy15697 193 AVILGDSAYPLKEW---LIPPRTRNPDAAADQRFLRCHKR-TRRLIENSFGILKEKFPCLNYMRLSPQFAGMVVLASTTL 268 (332)
Q Consensus 193 ~~llgD~gY~~~~~---l~~P~~~~~~~~~~~~fN~~~s~-~R~~vE~~fg~LK~rf~~L~~~~~~~~~~~~ii~a~~~L 268 (332)
..++.|++=-.... +..+ +-++-++ ..+.||+-+..+|.|=+-+...+ ++..+...+...=.+
T Consensus 128 ~v~vtDka~s~~~A~~~l~~~------------~ehr~~~ylnN~iE~dh~~iKrr~~~~~~f~-~~~sa~~~~~gie~i 194 (215)
T COG3316 128 RVFVTDKAPSYTAALRKLGSE------------VEHRTSKYLNNRIEQDHRPIKRRTRPMKRFK-SLSSAASTISGIESI 194 (215)
T ss_pred ceEEecCccchHHHHHhcCcc------------hheecccccccchhhcchhHHHHhcccccCC-ChHHHHHHHHhHHHH
Confidence 56777765322111 1111 1111122 23778888888886544331111 344445555555556
Q ss_pred Hhhcc
Q psy15697 269 HNIAL 273 (332)
Q Consensus 269 hN~~~ 273 (332)
|++-.
T Consensus 195 ~~~~~ 199 (215)
T COG3316 195 HMLYK 199 (215)
T ss_pred HHHHh
Confidence 66654
No 238
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=64.76 E-value=7.2 Score=36.13 Aligned_cols=47 Identities=21% Similarity=0.299 Sum_probs=39.8
Q ss_pred CCHHHHHHHHHhhh---ccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 38 LSAKEKVLSCLHWM---GVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 38 ~~~~~~l~~~L~~L---~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
++..++..+.++|. ....++.++|..||||+..|+++-.+.+.-|-.
T Consensus 263 L~eREr~Vl~~rygl~~~~~~Tl~eIa~~lgvS~eRVrQIe~~Al~KLr~ 312 (324)
T PRK07921 263 LDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLRN 312 (324)
T ss_pred CCHHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 67778888888884 245799999999999999999999988887765
No 239
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=64.70 E-value=2.4 Score=29.51 Aligned_cols=21 Identities=19% Similarity=0.332 Sum_probs=17.8
Q ss_pred cccccccccCCChhhHHhHHh
Q psy15697 56 PYHIIGATHGPSKSSICRSIH 76 (332)
Q Consensus 56 ~~~~l~~~fgis~sTv~r~~~ 76 (332)
+..++|...|+|.+||+++++
T Consensus 2 t~~~iA~~~gvS~~TVSr~ln 22 (70)
T smart00354 2 TIKDVARLAGVSKATVSRVLN 22 (70)
T ss_pred CHHHHHHHHCCCHHHHHHHHC
Confidence 346788999999999999876
No 240
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=64.46 E-value=4.2 Score=35.36 Aligned_cols=42 Identities=17% Similarity=0.143 Sum_probs=34.4
Q ss_pred CCHHHHHHHHHhhhcc--------------CCcccccccccCCChhhHHhHHhHhH
Q psy15697 38 LSAKEKVLSCLHWMGV--------------GSPYHIIGATHGPSKSSICRSIHEVV 79 (332)
Q Consensus 38 ~~~~~~l~~~L~~L~~--------------g~~~~~l~~~fgis~sTv~r~~~~v~ 79 (332)
.+++++++-+|..+.. ..+..++|...|+++.|++|+++++-
T Consensus 154 ~~~~~Rla~~L~~l~~~~~~~~~~~~~~~~~lt~~~iA~~lG~sr~tvsR~l~~l~ 209 (235)
T PRK11161 154 KNAEERLAAFIYNLSRRFAQRGFSPREFRLTMTRGDIGNYLGLTVETISRLLGRFQ 209 (235)
T ss_pred CCHHHHHHHHHHHHHHHHhhcCCCCceeEccccHHHHHHHhCCcHHHHHHHHHHHH
Confidence 5789999999988763 24567899999999999999987654
No 241
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=64.40 E-value=8.9 Score=34.79 Aligned_cols=49 Identities=22% Similarity=0.167 Sum_probs=40.2
Q ss_pred CCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHHhhhc
Q psy15697 38 LSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVDTFFQ 88 (332)
Q Consensus 38 ~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~~l~~ 88 (332)
+|+.++-++.|+++- |.++.++|..+|+|.+||...+++-...|-+ ..+
T Consensus 116 L~~~~R~v~~L~~~~-g~s~~EIA~~lg~s~~tVk~~l~RAr~~Lr~-~~~ 164 (293)
T PRK09636 116 LSPLERAAFLLHDVF-GVPFDEIASTLGRSPAACRQLASRARKHVRA-ARP 164 (293)
T ss_pred CCHHHHHHHHHHHHh-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh-hCC
Confidence 666777666665554 8999999999999999999999999988888 444
No 242
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=64.17 E-value=4.5 Score=35.22 Aligned_cols=44 Identities=11% Similarity=0.175 Sum_probs=34.3
Q ss_pred CCCHHHHHHHHHhhhccC----------CcccccccccCCChhhHHhHHhHhHH
Q psy15697 37 ALSAKEKVLSCLHWMGVG----------SPYHIIGATHGPSKSSICRSIHEVVP 80 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g----------~~~~~l~~~fgis~sTv~r~~~~v~~ 80 (332)
..+++.+++-+|..++.. .+..++|...|+++.||+|+++++..
T Consensus 146 ~~~~~~Rla~~Ll~~~~~~~~~~~~~i~~t~~~iA~~lG~tretvsR~l~~L~~ 199 (236)
T PRK09392 146 LRSSAERLANYLLKQSLRQGGADVVTLPYEKRVLASYLGMTPENLSRAFAALAS 199 (236)
T ss_pred cCCHHHHHHHHHHHhccccCCCcEEEeeCCHHHHHHHhCCChhHHHHHHHHHHh
Confidence 357899999988876542 22357999999999999999988654
No 243
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=64.08 E-value=5.5 Score=26.64 Aligned_cols=36 Identities=14% Similarity=0.223 Sum_probs=30.7
Q ss_pred HHhhhccCCcccccccccCCChhhHHhHHhHhHHHH
Q psy15697 47 CLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVI 82 (332)
Q Consensus 47 ~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l 82 (332)
.+.+++.|.+...+|..+++|..||......+..-+
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 466788899999999999999999998888775544
No 244
>COG1342 Predicted DNA-binding proteins [General function prediction only]
Probab=64.06 E-value=7.8 Score=28.72 Aligned_cols=42 Identities=17% Similarity=0.046 Sum_probs=31.3
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhH
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVV 79 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~ 79 (332)
.+++++-=++-|.-+ .+.++.+.|..+|||++|+++.++.--
T Consensus 33 ~lt~eElEAlRLvD~-~~l~QeeAA~rMgISr~Tfwr~l~sAR 74 (99)
T COG1342 33 ILTIEELEALRLVDY-EGLTQEEAALRMGISRQTFWRLLTSAR 74 (99)
T ss_pred eecHHHHHHHHHHhH-hhccHHHHHHHhcccHHHHHHHHHHHH
Confidence 355666555555444 378899999999999999999988543
No 245
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=63.55 E-value=2.5 Score=30.35 Aligned_cols=35 Identities=11% Similarity=0.187 Sum_probs=24.3
Q ss_pred HHHHHHHhhhc--cCCcccccccccCCChhhHHhHHh
Q psy15697 42 EKVLSCLHWMG--VGSPYHIIGATHGPSKSSICRSIH 76 (332)
Q Consensus 42 ~~l~~~L~~L~--~g~~~~~l~~~fgis~sTv~r~~~ 76 (332)
.+++..|..+. .|.++.++|...|+++++|+++.+
T Consensus 17 ~~l~~~i~~~~~~~~ltQ~e~A~~lgisq~~vS~l~~ 53 (80)
T PF13744_consen 17 AQLMAAIRELREERGLTQAELAERLGISQPRVSRLEN 53 (80)
T ss_dssp HHHHHHHHHHHHCCT--HHHHHHHHTS-HHHHHHHHT
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHCCChhHHHHHHc
Confidence 34444444443 678999999999999999999986
No 246
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=63.40 E-value=7.2 Score=30.05 Aligned_cols=47 Identities=9% Similarity=0.049 Sum_probs=37.5
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
.++++++ .....|+.+..+..+++..+|||=+||..-+.+++.+|--
T Consensus 33 ~L~~E~~-~Fi~~Fi~~rGnlKe~e~~lgiSYPTvR~rLd~ii~~lg~ 79 (113)
T PF09862_consen 33 RLSPEQL-EFIKLFIKNRGNLKEMEKELGISYPTVRNRLDKIIEKLGY 79 (113)
T ss_pred cCCHHHH-HHHHHHHHhcCCHHHHHHHHCCCcHHHHHHHHHHHHHhCC
Confidence 3555554 4556677777789999999999999999999999988753
No 247
>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=62.76 E-value=6.8 Score=26.24 Aligned_cols=43 Identities=7% Similarity=-0.081 Sum_probs=29.3
Q ss_pred CCCCCHHHHHHHHHhhhccCC---cccccccccCCChhhHHhHHhH
Q psy15697 35 NVALSAKEKVLSCLHWMGVGS---PYHIIGATHGPSKSSICRSIHE 77 (332)
Q Consensus 35 ~~~~~~~~~l~~~L~~L~~g~---~~~~l~~~fgis~sTv~r~~~~ 77 (332)
+.+.++..+|-+.-++..++. .++..|..|||++..|.++...
T Consensus 3 rrsy~~~FKL~Vv~~a~~~~nc~~~~RAaarkf~V~r~~Vr~W~kq 48 (58)
T PF09607_consen 3 RRSYTAEFKLKVVEYAEKDNNCKGNQRAAARKFNVSRRQVRKWRKQ 48 (58)
T ss_dssp -----HHHHHHHHHHHHH-TTTTT-HHHHHHHTTS-HHHHHHHHTT
T ss_pred ccccChHHHHHHHHHHHHccchhhhHHHHHHHhCccHHHHHHHHHH
Confidence 456788888888888878776 4599999999999988887654
No 248
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=62.68 E-value=8.8 Score=34.91 Aligned_cols=65 Identities=23% Similarity=0.220 Sum_probs=44.2
Q ss_pred CCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHHhhhccccCCCcccccchhhhh
Q psy15697 38 LSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVDTFFQRMVKWPEENLNDIPMTF 105 (332)
Q Consensus 38 ~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~~l~~~~I~~P~~~~~~~~~~f 105 (332)
+|+.++-++.|++ -.|.++.++|..+|+|.+||...+++....|.. ..+.+- .+..+.+++...|
T Consensus 119 L~p~~R~vf~L~~-~~g~s~~EIA~~Lgis~~tVr~~l~RAr~~Lr~-~~~~~~-~~~~~~~~~~~~f 183 (290)
T PRK09635 119 LGPAERVVFVLHE-IFGLPYQQIATTIGSQASTCRQLAHRARRKINE-SRIAAS-VEPAQHRVVTRAF 183 (290)
T ss_pred CCHHHHHHhhHHH-HhCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHh-hCCCCC-CChHHHHHHHHHH
Confidence 4455555554444 359999999999999999999999999888877 444322 1211344555555
No 249
>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=62.46 E-value=8.1 Score=33.83 Aligned_cols=48 Identities=17% Similarity=0.135 Sum_probs=38.9
Q ss_pred CCCCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 35 NVALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 35 ~~~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
...+++.++=.+.+ .+.|.++.++|..+|+|.+||...+.+...-|..
T Consensus 169 ~~~Lt~re~evl~~--~a~G~t~~eIa~~l~is~~Tv~~~l~~~~~kl~~ 216 (232)
T TIGR03541 169 AGVLSEREREVLAW--TALGRRQADIAAILGISERTVENHLRSARRKLGV 216 (232)
T ss_pred hccCCHHHHHHHHH--HHCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHCC
Confidence 34678877765544 5899999999999999999999999988766543
No 250
>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=62.29 E-value=2.8 Score=31.99 Aligned_cols=31 Identities=16% Similarity=0.023 Sum_probs=25.2
Q ss_pred cCCcccccccccCCChhhHHhHHhHhHHHHH
Q psy15697 53 VGSPYHIIGATHGPSKSSICRSIHEVVPVIV 83 (332)
Q Consensus 53 ~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~ 83 (332)
-|.+..++|+.|+||+||+..+..+.-..-+
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 4789999999999999999988866554433
No 251
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=62.04 E-value=5.7 Score=30.92 Aligned_cols=24 Identities=13% Similarity=0.175 Sum_probs=22.5
Q ss_pred cCCcccccccccCCChhhHHhHHh
Q psy15697 53 VGSPYHIIGATHGPSKSSICRSIH 76 (332)
Q Consensus 53 ~g~~~~~l~~~fgis~sTv~r~~~ 76 (332)
-|.++..+|...|+|++.||++++
T Consensus 21 eG~Sq~~iA~LLGltqaAVS~Yls 44 (119)
T COG2522 21 EGLSQYRIAKLLGLTQAAVSQYLS 44 (119)
T ss_pred cCCcHHHHHHHhCCCHHHHHHHHc
Confidence 399999999999999999999987
No 252
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=61.99 E-value=8.8 Score=24.24 Aligned_cols=27 Identities=15% Similarity=0.186 Sum_probs=22.5
Q ss_pred CCcccccccccCCChhhHHhHHhHhHH
Q psy15697 54 GSPYHIIGATHGPSKSSICRSIHEVVP 80 (332)
Q Consensus 54 g~~~~~l~~~fgis~sTv~r~~~~v~~ 80 (332)
+.+..+++..|++|++|+++.+..+..
T Consensus 14 ~~s~~~l~~~l~~s~~tv~~~l~~L~~ 40 (53)
T smart00420 14 KVSVEELAELLGVSEMTIRRDLNKLEE 40 (53)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 457778899999999999999877654
No 253
>PRK14088 dnaA chromosomal replication initiation protein; Provisional
Probab=61.88 E-value=9.7 Score=36.89 Aligned_cols=50 Identities=18% Similarity=0.188 Sum_probs=44.9
Q ss_pred CCCCCCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHH
Q psy15697 33 ERNVALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVI 82 (332)
Q Consensus 33 ~~~~~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l 82 (332)
.|...+..--+++|.|..=-.+.++.++|..||.+.|||...++++-..+
T Consensus 366 ~R~~~i~~aR~iamyl~r~~~~~s~~~Ig~~fgr~hstV~~a~~~i~~~~ 415 (440)
T PRK14088 366 SRNVKALLARRIGMYVAKNYLGSSLRTIAEKFNRSHPVVVDSVKKVKDSL 415 (440)
T ss_pred CCCccccHHHHHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 45567888889999999888999999999999999999999999998866
No 254
>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=61.85 E-value=3.2 Score=27.07 Aligned_cols=25 Identities=12% Similarity=0.011 Sum_probs=22.3
Q ss_pred ccCCcccccccccCCChhhHHhHHh
Q psy15697 52 GVGSPYHIIGATHGPSKSSICRSIH 76 (332)
Q Consensus 52 ~~g~~~~~l~~~fgis~sTv~r~~~ 76 (332)
..|.++.++|...|+|++|++++.+
T Consensus 13 ~~gltq~~lA~~~gvs~~~vs~~e~ 37 (58)
T TIGR03070 13 ALGLTQADLADLAGVGLRFIRDVEN 37 (58)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHC
Confidence 4688899999999999999999875
No 255
>PRK09483 response regulator; Provisional
Probab=61.50 E-value=5.2 Score=33.78 Aligned_cols=46 Identities=13% Similarity=0.117 Sum_probs=36.7
Q ss_pred CCCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHH
Q psy15697 36 VALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIV 83 (332)
Q Consensus 36 ~~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~ 83 (332)
..+++.+.-. |.+++.|.+..++|..+++|.+||..++.++..-|.
T Consensus 147 ~~Lt~rE~~v--l~~~~~G~~~~~Ia~~l~is~~TV~~~~~~i~~Kl~ 192 (217)
T PRK09483 147 ASLSERELQI--MLMITKGQKVNEISEQLNLSPKTVNSYRYRMFSKLN 192 (217)
T ss_pred cccCHHHHHH--HHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence 3477766554 456789999999999999999999999888776553
No 256
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=60.89 E-value=11 Score=27.50 Aligned_cols=28 Identities=14% Similarity=0.115 Sum_probs=24.0
Q ss_pred cCCcccccccccCCChhhHHhHHhHhHH
Q psy15697 53 VGSPYHIIGATHGPSKSSICRSIHEVVP 80 (332)
Q Consensus 53 ~g~~~~~l~~~fgis~sTv~r~~~~v~~ 80 (332)
.+.+...++..+++|++|+++.+++...
T Consensus 23 ~~~~~~~la~~~~~s~~~i~~~l~~L~~ 50 (101)
T smart00347 23 GPLSVSELAKRLGVSPSTVTRVLDRLEK 50 (101)
T ss_pred CCcCHHHHHHHHCCCchhHHHHHHHHHH
Confidence 3568889999999999999998888766
No 257
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=60.84 E-value=5.9 Score=34.36 Aligned_cols=45 Identities=18% Similarity=0.212 Sum_probs=36.1
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHH
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIV 83 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~ 83 (332)
.+++.++= .|..++.|.+..++|..+++|..||..++.+...-+.
T Consensus 155 ~Lt~rE~~--Vl~l~~~G~s~~eIA~~L~iS~~TVk~~~~~i~~Kl~ 199 (216)
T PRK10100 155 LLTHREKE--ILNKLRIGASNNEIARSLFISENTVKTHLYNLFKKIA 199 (216)
T ss_pred CCCHHHHH--HHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 36665544 4566777999999999999999999999988876654
No 258
>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=59.95 E-value=6.3 Score=28.53 Aligned_cols=34 Identities=15% Similarity=0.039 Sum_probs=27.5
Q ss_pred hccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 51 MGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 51 L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
...+.+..++|+.++||+||+.+.++++-..|..
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 5667788999999999999999999999888775
No 259
>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=59.85 E-value=3.6 Score=25.61 Aligned_cols=24 Identities=25% Similarity=0.371 Sum_probs=18.9
Q ss_pred CCcccccccccCCChhhHHhHHhH
Q psy15697 54 GSPYHIIGATHGPSKSSICRSIHE 77 (332)
Q Consensus 54 g~~~~~l~~~fgis~sTv~r~~~~ 77 (332)
..++.++|...|+|.+||.+-+.+
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 468899999999999999887765
No 260
>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=59.70 E-value=8.6 Score=30.47 Aligned_cols=46 Identities=17% Similarity=0.040 Sum_probs=37.8
Q ss_pred CCHHHHHHHHHhhhcc-CCcccccccccCCChhhHHhHHhHhHHHHH
Q psy15697 38 LSAKEKVLSCLHWMGV-GSPYHIIGATHGPSKSSICRSIHEVVPVIV 83 (332)
Q Consensus 38 ~~~~~~l~~~L~~L~~-g~~~~~l~~~fgis~sTv~r~~~~v~~~l~ 83 (332)
+..+++-.+-|+|-.. +.+|..||..+++|++|+.++..++-..|.
T Consensus 82 l~de~k~Ii~lry~~r~~~TW~~IA~~l~i~erta~r~~~~fK~~i~ 128 (130)
T PF05263_consen 82 LIDEEKRIIKLRYDRRSRRTWYQIAQKLHISERTARRWRDRFKNDIY 128 (130)
T ss_pred hCHHHHHHHHHHHcccccchHHHHHHHhCccHHHHHHHHHHHHHHhc
Confidence 4456666778888876 789999999999999999999988876553
No 261
>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=59.70 E-value=9.7 Score=33.80 Aligned_cols=47 Identities=15% Similarity=0.164 Sum_probs=38.2
Q ss_pred CCCCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHH
Q psy15697 35 NVALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIV 83 (332)
Q Consensus 35 ~~~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~ 83 (332)
...+++.++=.+.+ ++.|.+..++|..+|||..||...+.+...-+.
T Consensus 188 ~~~LT~RE~evl~l--~a~G~s~~eIA~~L~IS~~TVk~hl~~i~~KL~ 234 (247)
T TIGR03020 188 AGLITAREAEILAW--VRDGKTNEEIAAILGISSLTVKNHLQHIFKKLD 234 (247)
T ss_pred ccCCCHHHHHHHHH--HHCCCCHHHHHHHHCcCHHHHHHHHHHHHHHhC
Confidence 34688877765554 679999999999999999999999988766543
No 262
>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=59.67 E-value=4.4 Score=27.43 Aligned_cols=28 Identities=18% Similarity=0.068 Sum_probs=21.7
Q ss_pred hhhcc--CCcccccccccCCChhhHHhHHh
Q psy15697 49 HWMGV--GSPYHIIGATHGPSKSSICRSIH 76 (332)
Q Consensus 49 ~~L~~--g~~~~~l~~~fgis~sTv~r~~~ 76 (332)
.|+.+ ...+.+||..+|||.+||.++=.
T Consensus 15 ~y~~~~g~i~lkdIA~~Lgvs~~tIr~WK~ 44 (60)
T PF10668_consen 15 IYKESNGKIKLKDIAEKLGVSESTIRKWKS 44 (60)
T ss_pred HHHHhCCCccHHHHHHHHCCCHHHHHHHhh
Confidence 34544 36889999999999999987643
No 263
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=59.26 E-value=5.4 Score=36.86 Aligned_cols=66 Identities=12% Similarity=0.147 Sum_probs=42.8
Q ss_pred HHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHHhhhccccCCCcccccchhhhhhhcCCCCCce
Q psy15697 47 CLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVDTFFQRMVKWPEENLNDIPMTFLRKGGFPNVA 115 (332)
Q Consensus 47 ~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~~l~~~~I~~P~~~~~~~~~~f~~~~~~p~~~ 115 (332)
+=.||-.|.++.++|+.+|||+.||+|.+.+--.- =+-.-.|..|....-++....+++.+++.|+
T Consensus 19 A~lYY~~gltQ~eIA~~LgiSR~~v~rlL~~Ar~~---GiV~I~i~~~~~~~~~Le~~L~~~fgL~~a~ 84 (321)
T COG2390 19 AWLYYVEGLTQSEIAERLGISRATVSRLLAKAREE---GIVKISINSPVEGCLELEQQLKERFGLKEAI 84 (321)
T ss_pred HHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHC---CeEEEEeCCCCcchHHHHHHHHHhcCCCeEE
Confidence 44566789999999999999999999998764321 0222234433333333445555666777666
No 264
>PRK09492 treR trehalose repressor; Provisional
Probab=59.01 E-value=3.5 Score=37.41 Aligned_cols=23 Identities=22% Similarity=0.297 Sum_probs=20.7
Q ss_pred CcccccccccCCChhhHHhHHhH
Q psy15697 55 SPYHIIGATHGPSKSSICRSIHE 77 (332)
Q Consensus 55 ~~~~~l~~~fgis~sTv~r~~~~ 77 (332)
.+.++||+..|||.+||||+++.
T Consensus 5 ~ti~dIA~~agVS~~TVSrvLn~ 27 (315)
T PRK09492 5 LTIKDIARLSGVGKSTVSRVLNN 27 (315)
T ss_pred CcHHHHHHHhCCCHHHHhHHhCC
Confidence 46789999999999999999984
No 265
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=58.67 E-value=11 Score=28.35 Aligned_cols=38 Identities=16% Similarity=0.149 Sum_probs=28.4
Q ss_pred HHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHH
Q psy15697 42 EKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVP 80 (332)
Q Consensus 42 ~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~ 80 (332)
.+++..|..- ...++.+++..+|+|++|+.+.+.+...
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 3578999999999999999999888765
No 266
>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=58.60 E-value=3.9 Score=25.43 Aligned_cols=21 Identities=24% Similarity=0.191 Sum_probs=17.9
Q ss_pred ccccccccCCChhhHHhHHhH
Q psy15697 57 YHIIGATHGPSKSSICRSIHE 77 (332)
Q Consensus 57 ~~~l~~~fgis~sTv~r~~~~ 77 (332)
..++|..+|||.+|+.+++.+
T Consensus 3 ~~e~a~~lgvs~~tl~~~~~~ 23 (49)
T cd04762 3 TKEAAELLGVSPSTLRRWVKE 23 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHc
Confidence 457888999999999998875
No 267
>PHA01976 helix-turn-helix protein
Probab=58.26 E-value=5.3 Score=27.19 Aligned_cols=27 Identities=11% Similarity=-0.119 Sum_probs=23.4
Q ss_pred hhccCCcccccccccCCChhhHHhHHh
Q psy15697 50 WMGVGSPYHIIGATHGPSKSSICRSIH 76 (332)
Q Consensus 50 ~L~~g~~~~~l~~~fgis~sTv~r~~~ 76 (332)
+-..|.++.++|...|+|++|++++.+
T Consensus 11 R~~~glt~~~lA~~~gvs~~~v~~~e~ 37 (67)
T PHA01976 11 RNARAWSAPELSRRAGVRHSLIYDFEA 37 (67)
T ss_pred HHHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 345788999999999999999999876
No 268
>PRK14087 dnaA chromosomal replication initiation protein; Provisional
Probab=57.88 E-value=16 Score=35.44 Aligned_cols=52 Identities=10% Similarity=0.179 Sum_probs=45.9
Q ss_pred CCCCCCCHHHHHHHHHhhhccCCcccccccccC-CChhhHHhHHhHhHHHHHH
Q psy15697 33 ERNVALSAKEKVLSCLHWMGVGSPYHIIGATHG-PSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 33 ~~~~~~~~~~~l~~~L~~L~~g~~~~~l~~~fg-is~sTv~r~~~~v~~~l~~ 84 (332)
.|...+...-+++|.|.+=-++.++..+|..|| .+.|||..-++++-..+.+
T Consensus 380 ~R~~~i~~~RqiamyL~r~~t~~sl~~IG~~FggrdHsTV~~a~~ki~~~~~~ 432 (450)
T PRK14087 380 ARSKSIVTARHIAMYLTKEILNHTLAQIGEEFGGRDHTTVINAERKIEKMLKK 432 (450)
T ss_pred CCCccccHHHHHHHHHHHHHcCCCHHHHHHHhCCCChHHHHHHHHHHHHHHHh
Confidence 355678889999999999999999999999997 9999999999988887754
No 269
>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=57.48 E-value=3.8 Score=37.26 Aligned_cols=21 Identities=24% Similarity=0.335 Sum_probs=19.1
Q ss_pred cccccccccCCChhhHHhHHh
Q psy15697 56 PYHIIGATHGPSKSSICRSIH 76 (332)
Q Consensus 56 ~~~~l~~~fgis~sTv~r~~~ 76 (332)
+..++|+.+|||++||||+++
T Consensus 3 ti~dIA~~agVS~sTVSr~Ln 23 (311)
T TIGR02405 3 TIKDIARLAGVGKSTVSRVLN 23 (311)
T ss_pred cHHHHHHHhCCCHHHHHHHhC
Confidence 456899999999999999997
No 270
>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=57.41 E-value=13 Score=28.32 Aligned_cols=28 Identities=11% Similarity=-0.046 Sum_probs=24.4
Q ss_pred cCCcccccccccCCChhhHHhHHhHhHH
Q psy15697 53 VGSPYHIIGATHGPSKSSICRSIHEVVP 80 (332)
Q Consensus 53 ~g~~~~~l~~~fgis~sTv~r~~~~v~~ 80 (332)
.+.+..+++..++++++|+++.+++...
T Consensus 42 ~~~t~~eL~~~l~~~~stvs~~i~~Le~ 69 (109)
T TIGR01889 42 GKLTLKEIIKEILIKQSALVKIIKKLSK 69 (109)
T ss_pred CcCcHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3588999999999999999999887654
No 271
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=57.28 E-value=8.4 Score=32.47 Aligned_cols=43 Identities=14% Similarity=0.182 Sum_probs=34.1
Q ss_pred CCHHHHHHHHHhhhcc--------------CCcccccccccCCChhhHHhHHhHhHH
Q psy15697 38 LSAKEKVLSCLHWMGV--------------GSPYHIIGATHGPSKSSICRSIHEVVP 80 (332)
Q Consensus 38 ~~~~~~l~~~L~~L~~--------------g~~~~~l~~~fgis~sTv~r~~~~v~~ 80 (332)
.+++++|+-+|..|+. ..++.++|...|+++.||+|+++++.+
T Consensus 119 ~~~~~Rla~~Ll~l~~~~~~~~~~~~~~~~~~t~~~iA~~lG~tretvsR~l~~l~~ 175 (202)
T PRK13918 119 QRLKNRIAAALLELSDTPLATQEDSGETMIYATHDELAAAVGSVRETVTKVIGELSR 175 (202)
T ss_pred CchHHHHHHHHHHHHHHhCCCCCCCCeEEecCCHHHHHHHhCccHHHHHHHHHHHHH
Confidence 4578899988876653 135678899999999999999998765
No 272
>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A ....
Probab=57.24 E-value=4.5 Score=28.28 Aligned_cols=27 Identities=15% Similarity=0.185 Sum_probs=22.5
Q ss_pred CCcccccccccCCChhhHHhHHhHhHH
Q psy15697 54 GSPYHIIGATHGPSKSSICRSIHEVVP 80 (332)
Q Consensus 54 g~~~~~l~~~fgis~sTv~r~~~~v~~ 80 (332)
+.+..++|...|+|..||+++++++.+
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 346778999999999999999888754
No 273
>PRK00215 LexA repressor; Validated
Probab=57.01 E-value=9.9 Score=32.47 Aligned_cols=27 Identities=15% Similarity=0.148 Sum_probs=23.3
Q ss_pred CCcccccccccCC-ChhhHHhHHhHhHH
Q psy15697 54 GSPYHIIGATHGP-SKSSICRSIHEVVP 80 (332)
Q Consensus 54 g~~~~~l~~~fgi-s~sTv~r~~~~v~~ 80 (332)
+.+..+|+..+|+ |++|+++++.....
T Consensus 23 ~~s~~ela~~~~~~~~~tv~~~l~~L~~ 50 (205)
T PRK00215 23 PPSRREIADALGLRSPSAVHEHLKALER 50 (205)
T ss_pred CCCHHHHHHHhCCCChHHHHHHHHHHHH
Confidence 3477899999999 99999999887764
No 274
>PF13701 DDE_Tnp_1_4: Transposase DDE domain group 1
Probab=56.18 E-value=15 Score=35.72 Aligned_cols=124 Identities=16% Similarity=0.254 Sum_probs=62.7
Q ss_pred CChhhHHhHHhHhHHHHHHhhhccccCCCcccccchhhhhhhcCCCCCceeeecceEEEEeCCCCCcccccccCCccccc
Q psy15697 66 PSKSSICRSIHEVVPVIVDTFFQRMVKWPEENLNDIPMTFLRKGGFPNVAGCVDGTMVLIDAPNEHEDQFVNRNGDHALN 145 (332)
Q Consensus 66 is~sTv~r~~~~v~~~l~~~l~~~~I~~P~~~~~~~~~~f~~~~~~p~~~G~iDgt~i~i~~P~~~~~~y~~~k~~~s~~ 145 (332)
.|++|++|..+.+...-...+...++ ......+.+ .-..++-=||.|..++.-- .+...|..++|.+++.
T Consensus 103 as~~t~sR~e~~~~~~~~~~~~~~~~-------~~~~~~~~~--~~~~i~LDiD~T~~~~~G~-Qe~~~~n~y~g~~gY~ 172 (448)
T PF13701_consen 103 ASQPTLSRLENRPDERDLKRLRRALV-------DLFLASYKK--PPKEIVLDIDSTVDDVHGE-QEGAVFNTYYGEDGYH 172 (448)
T ss_pred cchhhHHHHHccccHHHHHHHHHHHH-------HHHHHHhcc--ccceEEEecccccccchhh-cccccccccCCCcccc
Confidence 57889999887664333321222111 001111111 1234556688887665421 1223455566666666
Q ss_pred eeeecc-CCcceEEeeccCCccccchhhhcc--ccccccccccCCCCCCCceEecCCCCC
Q psy15697 146 VMAICG-PNYKFYAVNANWPGSVHDARVMRN--SMVYRKFDEEGWRPFPDAVILGDSAYP 202 (332)
Q Consensus 146 ~~~v~d-~~g~~~~v~~~~~Gs~~D~~v~~~--s~l~~~l~~~~~~~~~~~~llgD~gY~ 202 (332)
=+++.+ ..|.++.+ .-.||++|-+.=... ..+...+ ...+ +...-.+-||+||-
T Consensus 173 PL~~f~g~~G~~l~a-~LRpGn~~sa~g~~~fL~~~l~~l-r~~~-~~~~ILvR~DSgF~ 229 (448)
T PF13701_consen 173 PLVAFDGQTGYLLAA-ELRPGNVHSAKGAAEFLKRVLRRL-RQRW-PDTRILVRGDSGFA 229 (448)
T ss_pred cceeccCCCCceEEE-EccCCCCChHHHHHHHHHHHHHHH-hhhC-ccceEEEEecCccC
Confidence 555554 57778776 456999887643221 1112222 1111 11133577999994
No 275
>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=55.98 E-value=3.8 Score=33.80 Aligned_cols=23 Identities=17% Similarity=0.247 Sum_probs=0.0
Q ss_pred CCcccccccccCCChhhHHhHHh
Q psy15697 54 GSPYHIIGATHGPSKSSICRSIH 76 (332)
Q Consensus 54 g~~~~~l~~~fgis~sTv~r~~~ 76 (332)
.+...++|...|+|.|||||.+.
T Consensus 49 PLt~~~iA~~lgl~~STVSRav~ 71 (160)
T PF04552_consen 49 PLTMKDIADELGLHESTVSRAVK 71 (160)
T ss_dssp -----------------------
T ss_pred CCCHHHHHHHhCCCHhHHHHHHc
Confidence 45778999999999999999876
No 276
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=55.86 E-value=7.3 Score=33.67 Aligned_cols=49 Identities=16% Similarity=0.260 Sum_probs=35.1
Q ss_pred CCCCHHHHHHHHHhh-hcc-----CCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 36 VALSAKEKVLSCLHW-MGV-----GSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 36 ~~~~~~~~l~~~L~~-L~~-----g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
..++..+.-++.+-| ++. ..+..+||..||||++|++.++++...-|..
T Consensus 154 ~~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ehLRrAe~Kl~~ 208 (215)
T COG3413 154 NDLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEHLRRAERKLIE 208 (215)
T ss_pred ccCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 357666654443333 222 3567789999999999999999998887776
No 277
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=55.61 E-value=12 Score=33.52 Aligned_cols=45 Identities=16% Similarity=0.123 Sum_probs=36.3
Q ss_pred CCCCHHHHHHHHHhhhcc---CCcccccccccCCChhhHHhHHhHhHH
Q psy15697 36 VALSAKEKVLSCLHWMGV---GSPYHIIGATHGPSKSSICRSIHEVVP 80 (332)
Q Consensus 36 ~~~~~~~~l~~~L~~L~~---g~~~~~l~~~fgis~sTv~r~~~~v~~ 80 (332)
..++.-++.+-.|..++. +.+..+|+...|+++||++|+++..+.
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 346677777777888864 457899999999999999999987764
No 278
>PRK09191 two-component response regulator; Provisional
Probab=55.19 E-value=12 Score=32.75 Aligned_cols=47 Identities=11% Similarity=0.039 Sum_probs=38.9
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
.+|+..+-.+.|.++. |.++.++|..+|+|.+||...+.+....+..
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 3667777767666654 8889999999999999999999988888776
No 279
>COG5421 Transposase [DNA replication, recombination, and repair]
Probab=54.57 E-value=13 Score=35.99 Aligned_cols=58 Identities=14% Similarity=0.175 Sum_probs=39.9
Q ss_pred ccccceeeeccCCcceEEeeccCCccccchhhhccccccccccccCCCCCCCceEecCCCCCC
Q psy15697 141 DHALNVMAICGPNYKFYAVNANWPGSVHDARVMRNSMVYRKFDEEGWRPFPDAVILGDSAYPL 203 (332)
Q Consensus 141 ~~s~~~~~v~d~~g~~~~v~~~~~Gs~~D~~v~~~s~l~~~l~~~~~~~~~~~~llgD~gY~~ 203 (332)
..-+++..+++..|-.+.+.+ ++|+.+|...+-.. .+.+.+.. ...+.++++|+|+-.
T Consensus 154 l~QI~vsMi~~~~gIPl~~~v-~~Gni~D~~~~~~t--i~kl~~~l--~~~~~~~V~Dkgf~S 211 (480)
T COG5421 154 LPQINVSMIVNQKGIPLFVRV-YSGNISDKNTLIKT--IQKLKSVL--VKDEVYLVADKGFNS 211 (480)
T ss_pred cceeEEEEEEcCCCCceEEEc-cCCCccchHHHHHH--HHHHHHhc--ccceEEEEEcccccc
Confidence 477889899998876666655 69999999887543 33331111 222378999999953
No 280
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=54.56 E-value=4 Score=27.42 Aligned_cols=27 Identities=19% Similarity=0.244 Sum_probs=19.7
Q ss_pred ccCCcccccccccCCChhhHHhHHhHh
Q psy15697 52 GVGSPYHIIGATHGPSKSSICRSIHEV 78 (332)
Q Consensus 52 ~~g~~~~~l~~~fgis~sTv~r~~~~v 78 (332)
..|.+..++|...|+|++|++++++.-
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 357788899999999999999999854
No 281
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=54.20 E-value=10 Score=34.45 Aligned_cols=46 Identities=9% Similarity=-0.007 Sum_probs=37.9
Q ss_pred HHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHHhhhc
Q psy15697 43 KVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVDTFFQ 88 (332)
Q Consensus 43 ~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~~l~~ 88 (332)
+|-.++....+|.++...|+..+||+|+||+.+++.-..+-..|..
T Consensus 5 ~L~~F~~v~~~~~s~s~AA~~L~isq~avSr~I~~LE~~lg~~LF~ 50 (309)
T PRK12682 5 QLRFVREAVRRNLNLTEAAKALHTSQPGVSKAIIELEEELGIEIFI 50 (309)
T ss_pred HHHHHHHHHHccCCHHHHHHHhcCccHHHHHHHHHHHHHhCCeeEE
Confidence 4555666667788999999999999999999999999888764443
No 282
>PRK10651 transcriptional regulator NarL; Provisional
Probab=54.19 E-value=8.3 Score=32.20 Aligned_cols=45 Identities=16% Similarity=0.320 Sum_probs=36.4
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHH
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIV 83 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~ 83 (332)
.+++.+. =.|.++..|.+...+|..+++|..||..++.+...-|.
T Consensus 155 ~Lt~rE~--~vl~~l~~g~~~~~ia~~l~is~~tV~~~~~~l~~Kl~ 199 (216)
T PRK10651 155 QLTPRER--DILKLIAQGLPNKMIARRLDITESTVKVHVKHMLKKMK 199 (216)
T ss_pred cCCHHHH--HHHHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHHHHcC
Confidence 3666664 34566889999999999999999999999998876553
No 283
>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=54.00 E-value=5 Score=25.03 Aligned_cols=21 Identities=29% Similarity=0.319 Sum_probs=17.3
Q ss_pred cccccccccCCChhhHHhHHh
Q psy15697 56 PYHIIGATHGPSKSSICRSIH 76 (332)
Q Consensus 56 ~~~~l~~~fgis~sTv~r~~~ 76 (332)
+..++|..+|||.+|+.++++
T Consensus 3 t~~e~a~~lgis~~ti~~~~~ 23 (49)
T TIGR01764 3 TVEEAAEYLGVSKDTVYRLIH 23 (49)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 456788999999999988875
No 284
>PRK10870 transcriptional repressor MprA; Provisional
Probab=53.87 E-value=11 Score=31.56 Aligned_cols=43 Identities=14% Similarity=0.084 Sum_probs=29.2
Q ss_pred CCHH-HHHHHHHhhhcc-CCcccccccccCCChhhHHhHHhHhHH
Q psy15697 38 LSAK-EKVLSCLHWMGV-GSPYHIIGATHGPSKSSICRSIHEVVP 80 (332)
Q Consensus 38 ~~~~-~~l~~~L~~L~~-g~~~~~l~~~fgis~sTv~r~~~~v~~ 80 (332)
+++. ..++..|+.... +.+..+|+..++++++|+++++++...
T Consensus 53 Lt~~q~~iL~~L~~~~~~~it~~eLa~~l~l~~~tvsr~v~rLe~ 97 (176)
T PRK10870 53 INETLFMALITLESQENHSIQPSELSCALGSSRTNATRIADELEK 97 (176)
T ss_pred CCHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4443 334444443322 356789999999999999998887654
No 285
>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=53.44 E-value=11 Score=25.84 Aligned_cols=26 Identities=15% Similarity=0.257 Sum_probs=21.7
Q ss_pred CcccccccccCCChhhHHhHHhHhHH
Q psy15697 55 SPYHIIGATHGPSKSSICRSIHEVVP 80 (332)
Q Consensus 55 ~~~~~l~~~fgis~sTv~r~~~~v~~ 80 (332)
.+...++..+|+|.+||++.+...-.
T Consensus 14 ~~~~eLa~~l~vS~~tv~~~l~~L~~ 39 (69)
T TIGR00122 14 FSGEKLGEALGMSRTAVNKHIQTLRE 39 (69)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 45678899999999999999887644
No 286
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=53.42 E-value=5.2 Score=36.79 Aligned_cols=23 Identities=17% Similarity=0.187 Sum_probs=20.9
Q ss_pred CcccccccccCCChhhHHhHHhH
Q psy15697 55 SPYHIIGATHGPSKSSICRSIHE 77 (332)
Q Consensus 55 ~~~~~l~~~fgis~sTv~r~~~~ 77 (332)
.+.++||..+|||.+||||+++.
T Consensus 7 ~Ti~dIA~~agVS~~TVSr~Ln~ 29 (342)
T PRK10014 7 ITIHDVALAAGVSVSTVSLVLSG 29 (342)
T ss_pred CcHHHHHHHhCCCHHHHHHHHCC
Confidence 46789999999999999999985
No 287
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=53.27 E-value=11 Score=29.38 Aligned_cols=28 Identities=11% Similarity=-0.020 Sum_probs=23.4
Q ss_pred CCcccccccccCCChhhHHhHHhHhHHH
Q psy15697 54 GSPYHIIGATHGPSKSSICRSIHEVVPV 81 (332)
Q Consensus 54 g~~~~~l~~~fgis~sTv~r~~~~v~~~ 81 (332)
..+..+++..++++++||++.++...++
T Consensus 30 ~~~v~ela~~l~lsqstvS~HL~~L~~A 57 (117)
T PRK10141 30 ELCVCDLCTALDQSQPKISRHLALLRES 57 (117)
T ss_pred CcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 4577889999999999999998876554
No 288
>PF12728 HTH_17: Helix-turn-helix domain
Probab=53.12 E-value=5.3 Score=25.63 Aligned_cols=21 Identities=24% Similarity=0.233 Sum_probs=17.4
Q ss_pred cccccccccCCChhhHHhHHh
Q psy15697 56 PYHIIGATHGPSKSSICRSIH 76 (332)
Q Consensus 56 ~~~~l~~~fgis~sTv~r~~~ 76 (332)
+..++|+.+|||.+|+.++++
T Consensus 3 t~~e~a~~l~is~~tv~~~~~ 23 (51)
T PF12728_consen 3 TVKEAAELLGISRSTVYRWIR 23 (51)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 456788999999999998875
No 289
>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=53.11 E-value=7.2 Score=28.82 Aligned_cols=30 Identities=13% Similarity=0.171 Sum_probs=23.2
Q ss_pred CcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 55 SPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 55 ~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
..+..+|...||++|||||+-..++.-+..
T Consensus 24 ~gq~~vA~~~Gv~eStISR~k~~~~~~~a~ 53 (91)
T PF05269_consen 24 VGQKKVAEAMGVDESTISRWKNDFIEKMAM 53 (91)
T ss_dssp HHHHHHHHHHTSSTTTHHHHHHHHHHHHHH
T ss_pred HhhHHHHHHhCCCHHHHHHHHhhHHHHHHH
Confidence 356789999999999999987665544444
No 290
>PRK09526 lacI lac repressor; Reviewed
Probab=52.44 E-value=5 Score=36.87 Aligned_cols=23 Identities=13% Similarity=0.184 Sum_probs=20.4
Q ss_pred CcccccccccCCChhhHHhHHhH
Q psy15697 55 SPYHIIGATHGPSKSSICRSIHE 77 (332)
Q Consensus 55 ~~~~~l~~~fgis~sTv~r~~~~ 77 (332)
.+..++|...|||.+||||+++.
T Consensus 6 ~ti~dIA~~aGVS~~TVSrvLn~ 28 (342)
T PRK09526 6 VTLYDVARYAGVSYQTVSRVLNQ 28 (342)
T ss_pred CcHHHHHHHhCCCHHHHHHHhcC
Confidence 35679999999999999999983
No 291
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=51.85 E-value=5.4 Score=36.40 Aligned_cols=22 Identities=18% Similarity=0.191 Sum_probs=19.5
Q ss_pred cccccccccCCChhhHHhHHhH
Q psy15697 56 PYHIIGATHGPSKSSICRSIHE 77 (332)
Q Consensus 56 ~~~~l~~~fgis~sTv~r~~~~ 77 (332)
+..++|+..|||.+||||+++.
T Consensus 2 ti~dIA~~aGVS~~TVSrvLn~ 23 (328)
T PRK11303 2 KLDEIARLAGVSRTTASYVING 23 (328)
T ss_pred CHHHHHHHhCCCHHHHHHHHcC
Confidence 4568999999999999999985
No 292
>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=51.79 E-value=12 Score=31.50 Aligned_cols=42 Identities=14% Similarity=0.145 Sum_probs=32.7
Q ss_pred CCCCCHHHHHHHHHhhhc-cCCcccccccccCCChhhHHhHHh
Q psy15697 35 NVALSAKEKVLSCLHWMG-VGSPYHIIGATHGPSKSSICRSIH 76 (332)
Q Consensus 35 ~~~~~~~~~l~~~L~~L~-~g~~~~~l~~~fgis~sTv~r~~~ 76 (332)
+..+++.++...+...+. .|.+...+|..+|+|+++|++++.
T Consensus 100 r~~lt~~e~a~~~~~l~~~~g~s~~~iA~~lg~s~~~V~r~l~ 142 (187)
T TIGR00180 100 REDLSPIEEAQAYKRLLEKFSMTQEDLAKKIGKSRAHITNLLR 142 (187)
T ss_pred ccCCCHHHHHHHHHHHHHHhCCCHHHHHHHHCcCHHHHHHHHH
Confidence 356777776665555554 588999999999999999998876
No 293
>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=50.92 E-value=15 Score=28.87 Aligned_cols=44 Identities=9% Similarity=-0.042 Sum_probs=30.3
Q ss_pred CCCCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhH
Q psy15697 35 NVALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVV 79 (332)
Q Consensus 35 ~~~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~ 79 (332)
+.++|.+.+.-+.= ....|..-.+++..+.||.++|++++.++-
T Consensus 15 GrPLp~~~R~rIve-la~~G~rp~~Isr~l~Vs~gcVsKIl~Ry~ 58 (125)
T PF00292_consen 15 GRPLPNELRQRIVE-LAKEGVRPCDISRQLRVSHGCVSKILSRYR 58 (125)
T ss_dssp TSSS-HHHHHHHHH-HHHTT--HHHHHHHHT--HHHHHHHHHHHH
T ss_pred CccCcHHHHHHHHH-HhhhcCCHHHHHHHHccchhHHHHHHHHHH
Confidence 46777777765542 224699999999999999999999999874
No 294
>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=50.81 E-value=12 Score=32.94 Aligned_cols=43 Identities=12% Similarity=0.205 Sum_probs=33.0
Q ss_pred CCHHHHHHHHHhhhcc---CCcccccccccCCChhhHHhHHhHhHH
Q psy15697 38 LSAKEKVLSCLHWMGV---GSPYHIIGATHGPSKSSICRSIHEVVP 80 (332)
Q Consensus 38 ~~~~~~l~~~L~~L~~---g~~~~~l~~~fgis~sTv~r~~~~v~~ 80 (332)
++.-++.+-.|..++. +.+..+|+...|+++||++|++.....
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 3444556666777753 468899999999999999999997653
No 295
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=50.50 E-value=5 Score=36.73 Aligned_cols=23 Identities=13% Similarity=0.235 Sum_probs=20.1
Q ss_pred CcccccccccCCChhhHHhHHhH
Q psy15697 55 SPYHIIGATHGPSKSSICRSIHE 77 (332)
Q Consensus 55 ~~~~~l~~~fgis~sTv~r~~~~ 77 (332)
.+..++|...|||.+||||+++.
T Consensus 6 ~ti~dIA~~agVS~~TVSrvLn~ 28 (331)
T PRK14987 6 PVLQDVADRVGVTKMTVSRFLRN 28 (331)
T ss_pred CcHHHHHHHhCCCHHHhhhhhCC
Confidence 35679999999999999999973
No 296
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=50.24 E-value=6.4 Score=35.86 Aligned_cols=19 Identities=21% Similarity=0.291 Sum_probs=17.6
Q ss_pred cccccccCCChhhHHhHHh
Q psy15697 58 HIIGATHGPSKSSICRSIH 76 (332)
Q Consensus 58 ~~l~~~fgis~sTv~r~~~ 76 (332)
+++|...|||.+||||+++
T Consensus 2 ~dIA~~agVS~~TVSrvLn 20 (327)
T PRK10423 2 KDVARLAGVSTSTVSHVIN 20 (327)
T ss_pred hhHHHHhCCcHHHHHHHhC
Confidence 5789999999999999997
No 297
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=50.18 E-value=5.9 Score=36.56 Aligned_cols=21 Identities=14% Similarity=0.275 Sum_probs=19.2
Q ss_pred cccccccccCCChhhHHhHHh
Q psy15697 56 PYHIIGATHGPSKSSICRSIH 76 (332)
Q Consensus 56 ~~~~l~~~fgis~sTv~r~~~ 76 (332)
+..+||...|||.+||||+++
T Consensus 3 ti~dIA~~aGVS~~TVSrvLn 23 (346)
T PRK10401 3 TIRDVARQAGVSVATVSRVLN 23 (346)
T ss_pred CHHHHHHHhCCCHHHHHHHHC
Confidence 467899999999999999997
No 298
>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=50.13 E-value=8 Score=25.80 Aligned_cols=25 Identities=12% Similarity=0.258 Sum_probs=20.4
Q ss_pred cccccccccCCChhhHHhHHhHhHH
Q psy15697 56 PYHIIGATHGPSKSSICRSIHEVVP 80 (332)
Q Consensus 56 ~~~~l~~~fgis~sTv~r~~~~v~~ 80 (332)
+..+++..|++|++||++.+.+..+
T Consensus 27 ~~~~la~~~~is~~~v~~~l~~L~~ 51 (66)
T cd07377 27 SERELAEELGVSRTTVREALRELEA 51 (66)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4567889999999999988877654
No 299
>COG1508 RpoN DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription]
Probab=50.02 E-value=6.2 Score=37.90 Aligned_cols=31 Identities=19% Similarity=0.267 Sum_probs=24.5
Q ss_pred CcccccccccCCChhhHHhHHhHhHHHHHHhhhccccCCCcc
Q psy15697 55 SPYHIIGATHGPSKSSICRSIHEVVPVIVDTFFQRMVKWPEE 96 (332)
Q Consensus 55 ~~~~~l~~~fgis~sTv~r~~~~v~~~l~~~l~~~~I~~P~~ 96 (332)
...++||+..|+++|||||++. ..|+.-|..
T Consensus 331 L~LrdvA~~i~~HESTISRai~-----------nKy~~tprG 361 (444)
T COG1508 331 LVLRDVADEIGMHESTISRAIT-----------NKYLATPRG 361 (444)
T ss_pred ccHHHHHHHhCccHHHHHHHHh-----------cccccCCcc
Confidence 5568999999999999999864 366666654
No 300
>PF14493 HTH_40: Helix-turn-helix domain
Probab=49.89 E-value=13 Score=27.23 Aligned_cols=37 Identities=16% Similarity=0.194 Sum_probs=32.5
Q ss_pred HHHHhhhccCCcccccccccCCChhhHHhHHhHhHHH
Q psy15697 45 LSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPV 81 (332)
Q Consensus 45 ~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~ 81 (332)
..++..+..|.+..++|..-|++.+||..++-+.+..
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 4678888899999999999999999999888877654
No 301
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=49.68 E-value=11 Score=31.04 Aligned_cols=45 Identities=16% Similarity=0.186 Sum_probs=35.5
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHH
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIV 83 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~ 83 (332)
.+++.+. -.|.+|+.|.+...++..+++|.+||..++.++..-+.
T Consensus 137 ~Lt~~E~--~il~~l~~g~~~~~Ia~~l~~s~~tv~~~~~~l~~Kl~ 181 (196)
T PRK10360 137 PLTKRER--QVAEKLAQGMAVKEIAAELGLSPKTVHVHRANLMEKLG 181 (196)
T ss_pred CCCHHHH--HHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 4555444 35666888999999999999999999999988876543
No 302
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=49.66 E-value=14 Score=29.06 Aligned_cols=29 Identities=14% Similarity=0.188 Sum_probs=23.9
Q ss_pred cCCcccccccccCCChhhHHhHHhHhHHH
Q psy15697 53 VGSPYHIIGATHGPSKSSICRSIHEVVPV 81 (332)
Q Consensus 53 ~g~~~~~l~~~fgis~sTv~r~~~~v~~~ 81 (332)
.+.+-.+||...++++|||+|.+++.+.+
T Consensus 41 ~~~tvdelae~lnr~rStv~rsl~~L~~~ 69 (126)
T COG3355 41 GPLTVDELAEILNRSRSTVYRSLQNLLEA 69 (126)
T ss_pred CCcCHHHHHHHHCccHHHHHHHHHHHHHc
Confidence 34566789999999999999999887653
No 303
>PRK10403 transcriptional regulator NarP; Provisional
Probab=48.93 E-value=11 Score=31.23 Aligned_cols=45 Identities=18% Similarity=0.212 Sum_probs=36.3
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHH
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIV 83 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~ 83 (332)
.+++.+.- .|.++..|.+...++...++|..||..++.++..-+.
T Consensus 153 ~Lt~~e~~--vl~~~~~g~s~~~ia~~l~~s~~tv~~~~~~i~~kl~ 197 (215)
T PRK10403 153 VLTERELD--VLHELAQGLSNKQIASVLNISEQTVKVHIRNLLRKLN 197 (215)
T ss_pred cCCHHHHH--HHHHHHCCCCHHHHHHHcCCCHHHHHHHHHHHHHHcC
Confidence 35665554 4667889999999999999999999999998876653
No 304
>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=48.42 E-value=12 Score=28.12 Aligned_cols=37 Identities=14% Similarity=0.002 Sum_probs=29.9
Q ss_pred HhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 48 LHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 48 L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
|.-+....++...|...|+|++|+++.+++.-+.+-.
T Consensus 10 ~~av~~~gSis~AA~~L~iS~stvs~~I~~LE~~lg~ 46 (99)
T TIGR00637 10 LKAIARMGSISQAAKDAGISYKSAWDYIRAMNNLSGE 46 (99)
T ss_pred HHHHHHhCCHHHHHHHHCCCHHHHHHHHHHHHHHhCC
Confidence 3334456678889999999999999999998887766
No 305
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=48.29 E-value=6.6 Score=36.10 Aligned_cols=22 Identities=14% Similarity=0.270 Sum_probs=19.8
Q ss_pred cccccccccCCChhhHHhHHhH
Q psy15697 56 PYHIIGATHGPSKSSICRSIHE 77 (332)
Q Consensus 56 ~~~~l~~~fgis~sTv~r~~~~ 77 (332)
+..+||...|||.+||||+++.
T Consensus 3 Ti~dIA~~agVS~~TVSrvLn~ 24 (341)
T PRK10703 3 TIKDVAKRAGVSTTTVSHVINK 24 (341)
T ss_pred CHHHHHHHhCCCHHHHHHHHcC
Confidence 4678999999999999999984
No 306
>PRK10072 putative transcriptional regulator; Provisional
Probab=48.18 E-value=7.5 Score=29.08 Aligned_cols=25 Identities=16% Similarity=0.068 Sum_probs=22.9
Q ss_pred ccCCcccccccccCCChhhHHhHHh
Q psy15697 52 GVGSPYHIIGATHGPSKSSICRSIH 76 (332)
Q Consensus 52 ~~g~~~~~l~~~fgis~sTv~r~~~ 76 (332)
..|.++..+|..+|+|.+||++|.+
T Consensus 44 ~~glTQ~elA~~lGvS~~TVs~WE~ 68 (96)
T PRK10072 44 GTGLKIDDFARVLGVSVAMVKEWES 68 (96)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 5689999999999999999999976
No 307
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=47.85 E-value=5.9 Score=36.25 Aligned_cols=22 Identities=18% Similarity=0.317 Sum_probs=19.6
Q ss_pred cccccccccCCChhhHHhHHhH
Q psy15697 56 PYHIIGATHGPSKSSICRSIHE 77 (332)
Q Consensus 56 ~~~~l~~~fgis~sTv~r~~~~ 77 (332)
+..++|+..|||++||||+++.
T Consensus 3 ti~dIA~~agVS~~TVSrvln~ 24 (327)
T PRK10339 3 TLKDIAIEAGVSLATVSRVLND 24 (327)
T ss_pred CHHHHHHHhCCCHHhhhhhhcC
Confidence 4568999999999999999984
No 308
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=47.37 E-value=15 Score=32.78 Aligned_cols=43 Identities=12% Similarity=0.237 Sum_probs=33.2
Q ss_pred CCHHHHHHHHHhhhcc---CCcccccccccCCChhhHHhHHhHhHH
Q psy15697 38 LSAKEKVLSCLHWMGV---GSPYHIIGATHGPSKSSICRSIHEVVP 80 (332)
Q Consensus 38 ~~~~~~l~~~L~~L~~---g~~~~~l~~~fgis~sTv~r~~~~v~~ 80 (332)
++.-++.+-.|..|+. +.+..+|+..+|+++||++|+++....
T Consensus 7 v~sl~ral~iL~~l~~~~~~ls~~eia~~lgl~kstv~RlL~tL~~ 52 (263)
T PRK09834 7 VRGLSRGLMVLRALNRLDGGATVGLLAELTGLHRTTVRRLLETLQE 52 (263)
T ss_pred HHHHHHHHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4445566666777753 368899999999999999999987654
No 309
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=47.12 E-value=15 Score=33.41 Aligned_cols=45 Identities=9% Similarity=0.041 Sum_probs=37.4
Q ss_pred HHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHHhhh
Q psy15697 43 KVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVDTFF 87 (332)
Q Consensus 43 ~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~~l~ 87 (332)
+|-.++.....|.++...|+.+++|+++||+.+++.-..+-..|.
T Consensus 5 ~L~~F~~v~~~~~S~s~AA~~L~isQpavS~~I~~LE~~lg~~Lf 49 (309)
T PRK12683 5 QLRIIREAVRQNFNLTEVANALYTSQSGVSKQIKDLEDELGVEIF 49 (309)
T ss_pred HHHHHHHHHHccCCHHHHHHHhcCCcHHHHHHHHHHHHHhCCeeE
Confidence 455666667778899999999999999999999999888876444
No 310
>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR. All members of this cyanobacterial protein family are the transcriptional regulator SufR and regulate the SUF system, which makes possible iron-sulfur cluster biosynthesis despite exposure to oxygen. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus.
Probab=46.64 E-value=18 Score=30.84 Aligned_cols=39 Identities=18% Similarity=0.182 Sum_probs=29.2
Q ss_pred HHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHH
Q psy15697 41 KEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVP 80 (332)
Q Consensus 41 ~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~ 80 (332)
..+++..|..- .+.+..+|+..+|++++||++.+.+...
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 34555555443 4578899999999999999998887654
No 311
>PRK04140 hypothetical protein; Provisional
Probab=46.62 E-value=14 Score=34.10 Aligned_cols=64 Identities=16% Similarity=0.157 Sum_probs=43.6
Q ss_pred cCCHHH-HHHHHHHhccCcCCCCCCCCCCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHh
Q psy15697 11 RLSATQ-VEFILEEIAPALTTPTERNVALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIH 76 (332)
Q Consensus 11 rms~~~-F~~L~~~L~~~~~~~~~~~~~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~ 76 (332)
-++.+| |..+++-..|.+.... ++--+...-..+ --.+-..|.++.++|...|+|++|+++|.+
T Consensus 97 ~~~~~tl~~~~~~g~~p~v~~~~-Gg~~v~i~GerL-k~lRe~~GlSq~eLA~~lGVSr~tIskyE~ 161 (317)
T PRK04140 97 ALSPDTLYDDFVEGEPPLIYAAP-GGFYVKIDGDVL-REAREELGLSLGELASELGVSRRTISKYEN 161 (317)
T ss_pred eecHHHHHHHHhCCCCceEEEcC-CCeeehhhHHHH-HHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 367788 7777777766543322 223333332222 233566899999999999999999999987
No 312
>COG3293 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=46.48 E-value=8.9 Score=29.85 Aligned_cols=90 Identities=19% Similarity=0.210 Sum_probs=55.5
Q ss_pred ceeeeccCCcceEEeeccCCccccchhhhccccccccccccCCCCCCCceEecCCCCCCCCcCCCCccCCCC-------C
Q psy15697 145 NVMAICGPNYKFYAVNANWPGSVHDARVMRNSMVYRKFDEEGWRPFPDAVILGDSAYPLKEWLIPPRTRNPD-------A 217 (332)
Q Consensus 145 ~~~~v~d~~g~~~~v~~~~~Gs~~D~~v~~~s~l~~~l~~~~~~~~~~~~llgD~gY~~~~~l~~P~~~~~~-------~ 217 (332)
+.+.++|..|+++....+ +|..+ ...-. ..+ .+ ..-.-.+.|.+|...+|...| -..+. .
T Consensus 2 ~~~~l~D~~~~~i~~~lp-~~~~~-~~~~~-----~~~-~~----~~v~~~i~~~~~~g~~wr~~p-~~~~~~~~~~~~~ 68 (124)
T COG3293 2 KLHALVDAEWRPVEPLLP-PAKYG-GPPGV-----TLL-RD----REVLNGIADLLYTGCAWRALP-ADFPPATTVIPYR 68 (124)
T ss_pred CcccccccccceeeccCC-CcccC-CCCCC-----ccc-cc----HHHHHHHHHHhccchHHHHhH-HHhCCCceEeCCC
Confidence 457889999998887776 22222 11000 000 00 001235788888877776655 33321 1
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHhhhcccc
Q psy15697 218 AADQRFLRCHKRTRRLIENSFGILKEKFPCL 248 (332)
Q Consensus 218 ~~~~~fN~~~s~~R~~vE~~fg~LK~rf~~L 248 (332)
..+.-++..+...|..+|+.|+.+|. |+.+
T Consensus 69 ~~~~~~~~g~~~~~~~~~~~f~~~~~-~r~~ 98 (124)
T COG3293 69 RFRRWFKRGLWKRRNLVERTFGRLKQ-FRRT 98 (124)
T ss_pred cchhhHHHHHHHHHHHHHHHHHHHhc-ccce
Confidence 13577899999999999999999984 6666
No 313
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=46.24 E-value=16 Score=23.69 Aligned_cols=41 Identities=20% Similarity=0.230 Sum_probs=22.8
Q ss_pred CCCCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHh
Q psy15697 35 NVALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIH 76 (332)
Q Consensus 35 ~~~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~ 76 (332)
+..++..+|--+-+ +...|.+...++...|.|+..|.++++
T Consensus 2 G~~Lt~~Eqaqid~-m~qlG~s~~~isr~i~RSr~~Ir~yl~ 42 (50)
T PF11427_consen 2 GKTLTDAEQAQIDV-MHQLGMSLREISRRIGRSRTCIRRYLK 42 (50)
T ss_dssp S----HHHHHHHHH-HHHTT--HHHHHHHHT--HHHHHHHHH
T ss_pred CCcCCHHHHHHHHH-HHHhchhHHHHHHHhCccHHHHHHHhc
Confidence 35566666655533 334578888888888988888877765
No 314
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=46.14 E-value=15 Score=32.23 Aligned_cols=47 Identities=17% Similarity=0.205 Sum_probs=29.1
Q ss_pred HHHHHHHhccCcCCCCCCCCCCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhH
Q psy15697 17 VEFILEEIAPALTTPTERNVALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVV 79 (332)
Q Consensus 17 F~~L~~~L~~~~~~~~~~~~~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~ 79 (332)
..+|.+.|+..+...-..+..+|.|. +|++.||||+.||.+-+....
T Consensus 14 Y~qi~~~L~~~I~~~~~~G~~LPsE~----------------eLa~~~~VSR~TVR~Al~~L~ 60 (241)
T PRK10079 14 YQEIAAKLEQELRQHYRCGDYLPAEQ----------------QLAARYEVNRHTLRRAIDQLV 60 (241)
T ss_pred HHHHHHHHHHHHhcccCCCCcCCCHH----------------HHHHHHCCCHHHHHHHHHHHH
Confidence 55555555554432112234566555 567889999999988776654
No 315
>PRK11050 manganese transport regulator MntR; Provisional
Probab=46.00 E-value=18 Score=29.46 Aligned_cols=28 Identities=14% Similarity=0.163 Sum_probs=24.5
Q ss_pred cCCcccccccccCCChhhHHhHHhHhHH
Q psy15697 53 VGSPYHIIGATHGPSKSSICRSIHEVVP 80 (332)
Q Consensus 53 ~g~~~~~l~~~fgis~sTv~r~~~~v~~ 80 (332)
.+.+..+++..+++|++||++.+.+...
T Consensus 50 ~~~t~~eLA~~l~is~stVsr~l~~Le~ 77 (152)
T PRK11050 50 GEARQVDIAARLGVSQPTVAKMLKRLAR 77 (152)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4568899999999999999999887765
No 316
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=45.96 E-value=14 Score=30.77 Aligned_cols=45 Identities=16% Similarity=0.137 Sum_probs=36.9
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHH
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIV 83 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~ 83 (332)
.+++.+. -+|..|..|.+..+++..+++|.+||..++.++..-|.
T Consensus 143 ~lt~~E~--~vl~~l~~g~~~~~I~~~l~~s~~tv~~~~~~l~~Kl~ 187 (204)
T PRK09958 143 SLSKQEI--SVMRYILDGKDNNDIAEKMFISNKTVSTYKSRLMEKLE 187 (204)
T ss_pred cCCHHHH--HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence 4666554 36778889999999999999999999999988876653
No 317
>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=45.89 E-value=7.6 Score=35.44 Aligned_cols=21 Identities=24% Similarity=0.194 Sum_probs=18.6
Q ss_pred ccccccccCCChhhHHhHHhH
Q psy15697 57 YHIIGATHGPSKSSICRSIHE 77 (332)
Q Consensus 57 ~~~l~~~fgis~sTv~r~~~~ 77 (332)
..++|...|||.+||||+++.
T Consensus 2 i~dIA~~aGVS~~TVSrvLn~ 22 (327)
T TIGR02417 2 LSDIAKLAGVSKTTASYVING 22 (327)
T ss_pred HHHHHHHhCCCHHHHHHHHcC
Confidence 457899999999999999975
No 318
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=45.82 E-value=25 Score=28.47 Aligned_cols=28 Identities=18% Similarity=0.341 Sum_probs=24.2
Q ss_pred cCCcccccccccCCChhhHHhHHhHhHH
Q psy15697 53 VGSPYHIIGATHGPSKSSICRSIHEVVP 80 (332)
Q Consensus 53 ~g~~~~~l~~~fgis~sTv~r~~~~v~~ 80 (332)
.-.++.++|...|+|++||.+-+++...
T Consensus 22 ~R~s~~eiA~~lglS~~tV~~Ri~rL~~ 49 (153)
T PRK11179 22 ARTPYAELAKQFGVSPGTIHVRVEKMKQ 49 (153)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 3479999999999999999998887654
No 319
>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=45.77 E-value=17 Score=24.03 Aligned_cols=25 Identities=16% Similarity=0.264 Sum_probs=20.6
Q ss_pred CcccccccccCCChhhHHhHHhHhH
Q psy15697 55 SPYHIIGATHGPSKSSICRSIHEVV 79 (332)
Q Consensus 55 ~~~~~l~~~fgis~sTv~r~~~~v~ 79 (332)
.+..+++..||||..|+.|-+....
T Consensus 15 ~s~~ela~~~~VS~~TiRRDl~~L~ 39 (57)
T PF08220_consen 15 VSVKELAEEFGVSEMTIRRDLNKLE 39 (57)
T ss_pred EEHHHHHHHHCcCHHHHHHHHHHHH
Confidence 4667899999999999998877543
No 320
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=45.41 E-value=21 Score=36.31 Aligned_cols=47 Identities=9% Similarity=0.147 Sum_probs=39.7
Q ss_pred CCHHHHHHHHHhhh---ccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 38 LSAKEKVLSCLHWM---GVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 38 ~~~~~~l~~~L~~L---~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
+++.++..+.++|. ....++..+|..||||++.|+++-.+.+.-|-.
T Consensus 557 L~~rE~~Vl~~r~g~~~~~~~tl~ei~~~lgvs~eRVrQie~~al~kLr~ 606 (619)
T PRK05658 557 LTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 606 (619)
T ss_pred CCHHHHHHHHHhcCCCCCCCccHHHHHHHhCCCHHHHHHHHHHHHHHHhc
Confidence 67788888888885 356789999999999999999999888777655
No 321
>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=45.17 E-value=9.4 Score=25.85 Aligned_cols=22 Identities=9% Similarity=0.268 Sum_probs=16.7
Q ss_pred cccccccCCChhhHHhHHhHhH
Q psy15697 58 HIIGATHGPSKSSICRSIHEVV 79 (332)
Q Consensus 58 ~~l~~~fgis~sTv~r~~~~v~ 79 (332)
..++..|++|.+||.+.+....
T Consensus 28 ~~la~~~~vsr~tvr~al~~L~ 49 (64)
T PF00392_consen 28 RELAERYGVSRTTVREALRRLE 49 (64)
T ss_dssp HHHHHHHTS-HHHHHHHHHHHH
T ss_pred HHHHHHhccCCcHHHHHHHHHH
Confidence 4678899999999988777654
No 322
>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=44.95 E-value=8.3 Score=27.35 Aligned_cols=25 Identities=20% Similarity=0.153 Sum_probs=19.1
Q ss_pred CCcccccccccCCChhhHHhHHhHh
Q psy15697 54 GSPYHIIGATHGPSKSSICRSIHEV 78 (332)
Q Consensus 54 g~~~~~l~~~fgis~sTv~r~~~~v 78 (332)
..+..++|...|||++||.|.+++.
T Consensus 34 ~~si~elA~~~~vS~sti~Rf~kkL 58 (77)
T PF01418_consen 34 FMSISELAEKAGVSPSTIVRFCKKL 58 (77)
T ss_dssp T--HHHHHHHCTS-HHHHHHHHHHC
T ss_pred HccHHHHHHHcCCCHHHHHHHHHHh
Confidence 4677889999999999999988753
No 323
>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=44.88 E-value=7.9 Score=35.33 Aligned_cols=22 Identities=14% Similarity=0.215 Sum_probs=19.4
Q ss_pred cccccccccCCChhhHHhHHhH
Q psy15697 56 PYHIIGATHGPSKSSICRSIHE 77 (332)
Q Consensus 56 ~~~~l~~~fgis~sTv~r~~~~ 77 (332)
+.+++|+..|||.+||||+++.
T Consensus 3 ti~dIA~~agvS~~TVSrvLn~ 24 (329)
T TIGR01481 3 TIYDVAREAGVSMATVSRVVNG 24 (329)
T ss_pred cHHHHHHHhCCCHHHHHHHhCC
Confidence 4568999999999999999984
No 324
>PRK12679 cbl transcriptional regulator Cbl; Reviewed
Probab=44.77 E-value=18 Score=33.02 Aligned_cols=45 Identities=13% Similarity=0.023 Sum_probs=36.9
Q ss_pred HHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHHhhh
Q psy15697 43 KVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVDTFF 87 (332)
Q Consensus 43 ~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~~l~ 87 (332)
++-.++....++.++...|+..++|+||||+.+++.-..+...|.
T Consensus 5 ~l~~f~~v~~~~~s~s~AA~~L~iSQ~avSr~I~~LE~~lg~~LF 49 (316)
T PRK12679 5 QLKIIREAARQDYNLTEVANMLFTSQSGVSRHIRELEDELGIEIF 49 (316)
T ss_pred HHHHHHHHHHcCCCHHHHHHHhcCCchHHHHHHHHHHHHhCCEEE
Confidence 455566666677799999999999999999999999988876443
No 325
>PRK11569 transcriptional repressor IclR; Provisional
Probab=44.68 E-value=21 Score=32.13 Aligned_cols=44 Identities=14% Similarity=0.256 Sum_probs=35.3
Q ss_pred CCCHHHHHHHHHhhhcc---CCcccccccccCCChhhHHhHHhHhHH
Q psy15697 37 ALSAKEKVLSCLHWMGV---GSPYHIIGATHGPSKSSICRSIHEVVP 80 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~---g~~~~~l~~~fgis~sTv~r~~~~v~~ 80 (332)
.++.-++.+-.|.+|+. +.+..+|+...|+++||++|++.....
T Consensus 23 ~v~sl~ral~IL~~l~~~~~~~~lseia~~lglpksTv~RlL~tL~~ 69 (274)
T PRK11569 23 QVQSLTRGLKLLEWIAESNGSVALTELAQQAGLPNSTTHRLLTTMQQ 69 (274)
T ss_pred CccHHHHHHHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 35566777777888874 468899999999999999999987653
No 326
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=44.25 E-value=12 Score=27.45 Aligned_cols=24 Identities=8% Similarity=0.090 Sum_probs=20.3
Q ss_pred ccccccccCCChhhHHhHHhHhHH
Q psy15697 57 YHIIGATHGPSKSSICRSIHEVVP 80 (332)
Q Consensus 57 ~~~l~~~fgis~sTv~r~~~~v~~ 80 (332)
..+++..+|+|++|+++.+.....
T Consensus 2 ~~ela~~l~is~stvs~~l~~L~~ 25 (96)
T smart00529 2 TSEIAERLNVSPPTVTQMLKKLEK 25 (96)
T ss_pred HHHHHHHhCCChHHHHHHHHHHHH
Confidence 357889999999999999887665
No 327
>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=44.01 E-value=9.1 Score=23.62 Aligned_cols=25 Identities=16% Similarity=0.275 Sum_probs=18.6
Q ss_pred cCCcccccccccCCChhhHHhHHhH
Q psy15697 53 VGSPYHIIGATHGPSKSSICRSIHE 77 (332)
Q Consensus 53 ~g~~~~~l~~~fgis~sTv~r~~~~ 77 (332)
++......|...|||++|+++-+.+
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 3456678899999999999987765
No 328
>PRK11233 nitrogen assimilation transcriptional regulator; Provisional
Probab=44.00 E-value=18 Score=32.72 Aligned_cols=39 Identities=0% Similarity=-0.070 Sum_probs=31.1
Q ss_pred HhhhccCCcccccccccCCChhhHHhHHhHhHHHHHHhh
Q psy15697 48 LHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVDTF 86 (332)
Q Consensus 48 L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~~l 86 (332)
+.-++...++...|+..|||+||||+.+++.-..+...|
T Consensus 9 F~~v~~~~S~s~AA~~L~isQ~avS~~I~~LE~~lg~~L 47 (305)
T PRK11233 9 FVKIVDIGSLTQAAEVLHIAQPALSQQVATLEGELNQQL 47 (305)
T ss_pred HHHHHHcCCHHHHHHHhCCCchHHHHHHHHHHHHhCCce
Confidence 333444458999999999999999999999988876633
No 329
>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]
Probab=43.71 E-value=31 Score=33.01 Aligned_cols=53 Identities=11% Similarity=0.204 Sum_probs=46.6
Q ss_pred CCCCCCCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 32 TERNVALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 32 ~~~~~~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
..|.+.+...-|++|.|.+--+..++..+|..||..-|||.--++++...+.+
T Consensus 343 ~~R~~~i~~~RqiamyL~r~lt~~Slp~IG~~FgrdHtTV~~a~~kI~~~~~~ 395 (408)
T COG0593 343 KSRTRNIVRPRQIAMYLARELTNLSLPEIGKAFGRDHTTVLHAVRKIEQLIEE 395 (408)
T ss_pred cccccccchHHHHHHHHHHHHccCcHHHHHHHhCCCccHHHHHHHHHHHHHhc
Confidence 34567788889999999999999999999999999999999998888887765
No 330
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=43.61 E-value=8 Score=35.63 Aligned_cols=21 Identities=19% Similarity=0.273 Sum_probs=19.1
Q ss_pred cccccccccCCChhhHHhHHh
Q psy15697 56 PYHIIGATHGPSKSSICRSIH 76 (332)
Q Consensus 56 ~~~~l~~~fgis~sTv~r~~~ 76 (332)
+..++|...|||.+||||+++
T Consensus 3 ti~dIA~~aGVS~~TVSrvLn 23 (343)
T PRK10727 3 TIKDVARLAGVSVATVSRVIN 23 (343)
T ss_pred CHHHHHHHhCCCHHHHHHHhC
Confidence 457899999999999999998
No 331
>PRK12422 chromosomal replication initiation protein; Provisional
Probab=43.57 E-value=27 Score=33.94 Aligned_cols=52 Identities=15% Similarity=0.176 Sum_probs=45.8
Q ss_pred CCCCCCCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHH
Q psy15697 32 TERNVALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIV 83 (332)
Q Consensus 32 ~~~~~~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~ 83 (332)
..|...+...-|++|.|.+=-++.++.++|..||..-|||..-++++-..+.
T Consensus 375 ~~R~~~i~~~Rqiamyl~r~~t~~s~~~IG~~fgrdHsTV~~a~~ki~~~~~ 426 (445)
T PRK12422 375 RSQSREYVLPRQVAMYLCRQKLSLSYVKIGDVFSRDHSTVISSIRAISQKLE 426 (445)
T ss_pred CCCCcccccHHHHHHHHHHHhcCCCHHHHHHHhCCChHHHHHHHHHHHHHHH
Confidence 3456778888999999999999999999999999999999999988887763
No 332
>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=43.50 E-value=9.4 Score=26.78 Aligned_cols=27 Identities=19% Similarity=0.330 Sum_probs=23.4
Q ss_pred hhccCCcccccccccCCChhhHHhHHh
Q psy15697 50 WMGVGSPYHIIGATHGPSKSSICRSIH 76 (332)
Q Consensus 50 ~L~~g~~~~~l~~~fgis~sTv~r~~~ 76 (332)
.-..|.++.++|...|+|++|++++.+
T Consensus 14 ~~~~~~t~~~lA~~~gis~~tis~~~~ 40 (78)
T TIGR02607 14 LEPLGLSIRALAKALGVSRSTLSRIVN 40 (78)
T ss_pred HHHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 345778899999999999999999876
No 333
>smart00760 Bac_DnaA_C Bacterial dnaA protein helix-turn-helix domain. Could be involved in DNA-binding.
Probab=43.29 E-value=17 Score=24.32 Aligned_cols=33 Identities=15% Similarity=0.120 Sum_probs=28.2
Q ss_pred CCCCCCCHHHHHHHHHhhhccCCcccccccccC
Q psy15697 33 ERNVALSAKEKVLSCLHWMGVGSPYHIIGATHG 65 (332)
Q Consensus 33 ~~~~~~~~~~~l~~~L~~L~~g~~~~~l~~~fg 65 (332)
.+...+..--++++.|..--.|.++.++|..||
T Consensus 24 ~R~~~~~~aR~iamyla~~~~~~sl~~Ig~~fg 56 (60)
T smart00760 24 SRKREIVLARQIAMYLARELTDLSLPEIGKIFG 56 (60)
T ss_pred CCCcchhHHHHHHHHHHHHHHCCCHHHHHHHhC
Confidence 345678888899999988889999999999998
No 334
>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=42.99 E-value=11 Score=23.67 Aligned_cols=30 Identities=20% Similarity=0.141 Sum_probs=24.3
Q ss_pred cCCcccccccccCCChhhHHhHHhHhHHHH
Q psy15697 53 VGSPYHIIGATHGPSKSSICRSIHEVVPVI 82 (332)
Q Consensus 53 ~g~~~~~l~~~fgis~sTv~r~~~~v~~~l 82 (332)
.+.+.++|+...|+|+++++++|..--..+
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 356888999999999999999987654444
No 335
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=42.84 E-value=17 Score=29.93 Aligned_cols=44 Identities=14% Similarity=0.143 Sum_probs=34.4
Q ss_pred CCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHH
Q psy15697 38 LSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIV 83 (332)
Q Consensus 38 ~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~ 83 (332)
+++.+.=. |.++..|.+...+|...++|..||..++.+...-+.
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 455789999999999999999999999988766554
No 336
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=41.83 E-value=24 Score=26.65 Aligned_cols=23 Identities=13% Similarity=0.270 Sum_probs=20.7
Q ss_pred cccccccCCChhhHHhHHhHhHH
Q psy15697 58 HIIGATHGPSKSSICRSIHEVVP 80 (332)
Q Consensus 58 ~~l~~~fgis~sTv~r~~~~v~~ 80 (332)
.+++...+++++|+++.+++...
T Consensus 40 ~~la~~l~i~~~~vt~~l~~Le~ 62 (126)
T COG1846 40 KELAERLGLDRSTVTRLLKRLED 62 (126)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHH
Confidence 89999999999999999887654
No 337
>TIGR02404 trehalos_R_Bsub trehalose operon repressor, B. subtilis-type. This family consists of repressors of the GntR family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gram-positive lineages and does not include the TreR from E. coli.
Probab=41.76 E-value=20 Score=31.18 Aligned_cols=21 Identities=10% Similarity=0.245 Sum_probs=16.3
Q ss_pred ccccccCCChhhHHhHHhHhH
Q psy15697 59 IIGATHGPSKSSICRSIHEVV 79 (332)
Q Consensus 59 ~l~~~fgis~sTv~r~~~~v~ 79 (332)
+|+..||||+.||.+-+....
T Consensus 29 eLa~~~gVSR~TVR~Al~~L~ 49 (233)
T TIGR02404 29 ELMDQYGASRETVRKALNLLT 49 (233)
T ss_pred HHHHHHCCCHHHHHHHHHHHH
Confidence 456789999999988766544
No 338
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=41.49 E-value=22 Score=32.43 Aligned_cols=46 Identities=9% Similarity=-0.008 Sum_probs=36.7
Q ss_pred HHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHHhhhc
Q psy15697 43 KVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVDTFFQ 88 (332)
Q Consensus 43 ~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~~l~~ 88 (332)
+|-.++....+|.++...|+..++|++|||+.+++.-..+...|..
T Consensus 5 ~L~~f~~v~~~g~S~s~AA~~L~isQpavS~~ik~LE~~lg~~Lf~ 50 (313)
T PRK12684 5 QLRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEDELGVEIFT 50 (313)
T ss_pred HHHHHHHHHHcCCCHHHHHHHhcCCChHHHHHHHHHHHHhCCeeEE
Confidence 4555555556666999999999999999999999999988764443
No 339
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=41.44 E-value=24 Score=31.30 Aligned_cols=44 Identities=20% Similarity=0.178 Sum_probs=33.6
Q ss_pred CCCHHHHHHHHHhhhccC--CcccccccccCCChhhHHhHHhHhHH
Q psy15697 37 ALSAKEKVLSCLHWMGVG--SPYHIIGATHGPSKSSICRSIHEVVP 80 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g--~~~~~l~~~fgis~sTv~r~~~~v~~ 80 (332)
.++.-++.+-.|..|+.. .+..+|+...|+++||++|++...+.
T Consensus 9 ~v~sl~r~l~IL~~l~~~~~l~l~eia~~lgl~kstv~Rll~tL~~ 54 (257)
T PRK15090 9 SVSSVLKVFGILQALGEEREIGITELSQRVMMSKSTVYRFLQTMKT 54 (257)
T ss_pred ccHHHHHHHHHHHHhhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 355666666667777643 56788999999999999999987653
No 340
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=40.96 E-value=10 Score=35.20 Aligned_cols=22 Identities=18% Similarity=0.308 Sum_probs=19.1
Q ss_pred cccccccccCCChhhHHhHHhH
Q psy15697 56 PYHIIGATHGPSKSSICRSIHE 77 (332)
Q Consensus 56 ~~~~l~~~fgis~sTv~r~~~~ 77 (332)
+..++|...|||.+||||+++.
T Consensus 2 TikDVA~~AGVS~sTVSrvln~ 23 (333)
T COG1609 2 TIKDVAKLAGVSKATVSRVLNG 23 (333)
T ss_pred CHHHHHHHhCCCHHHHHHHHcC
Confidence 3468899999999999999983
No 341
>COG4496 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=40.53 E-value=20 Score=26.15 Aligned_cols=30 Identities=23% Similarity=0.334 Sum_probs=25.7
Q ss_pred HHhhhccCCcccccccccCCChhhHHhHHh
Q psy15697 47 CLHWMGVGSPYHIIGATHGPSKSSICRSIH 76 (332)
Q Consensus 47 ~L~~L~~g~~~~~l~~~fgis~sTv~r~~~ 76 (332)
+-.+|..|.+|+++...-|.|..|++|+=+
T Consensus 49 Va~mL~eg~tY~~I~~eTGaStaTIsRVkR 78 (100)
T COG4496 49 VAKMLKEGRTYRDIEDETGASTATISRVKR 78 (100)
T ss_pred HHHHHHcCCCcchhhhccCcchhhHHHHHH
Confidence 346788999999999999999999988644
No 342
>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=40.51 E-value=31 Score=29.46 Aligned_cols=35 Identities=23% Similarity=0.260 Sum_probs=26.8
Q ss_pred HHHhhhcc--CCcccccccccCCChhhHHhHHhHhHH
Q psy15697 46 SCLHWMGV--GSPYHIIGATHGPSKSSICRSIHEVVP 80 (332)
Q Consensus 46 ~~L~~L~~--g~~~~~l~~~fgis~sTv~r~~~~v~~ 80 (332)
..|.++.. +.+..++++.+++|++|+++.+.+..+
T Consensus 147 ~IL~~l~~~g~~s~~eia~~l~is~stv~r~L~~Le~ 183 (203)
T TIGR01884 147 KVLEVLKAEGEKSVKNIAKKLGKSLSTISRHLRELEK 183 (203)
T ss_pred HHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 34455543 458999999999999999998887543
No 343
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=40.10 E-value=27 Score=30.88 Aligned_cols=35 Identities=23% Similarity=0.352 Sum_probs=26.7
Q ss_pred HHHHhhhcc---CCcccccccccCCChhhHHhHHhHhH
Q psy15697 45 LSCLHWMGV---GSPYHIIGATHGPSKSSICRSIHEVV 79 (332)
Q Consensus 45 ~~~L~~L~~---g~~~~~l~~~fgis~sTv~r~~~~v~ 79 (332)
+-.|.+|+. +.+..+|++..|+++||++|++....
T Consensus 7 l~iL~~l~~~~~~l~l~ela~~~glpksT~~RlL~tL~ 44 (246)
T COG1414 7 LAILDLLAEGPGGLSLAELAERLGLPKSTVHRLLQTLV 44 (246)
T ss_pred HHHHHHHHhCCCCCCHHHHHHHhCcCHHHHHHHHHHHH
Confidence 344555552 24588999999999999999998765
No 344
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=39.83 E-value=29 Score=24.89 Aligned_cols=25 Identities=12% Similarity=0.239 Sum_probs=21.4
Q ss_pred CcccccccccCCChhhHHhHHhHhH
Q psy15697 55 SPYHIIGATHGPSKSSICRSIHEVV 79 (332)
Q Consensus 55 ~~~~~l~~~fgis~sTv~r~~~~v~ 79 (332)
.|-..||+..|+|+++|.+.+...-
T Consensus 20 ~SGe~La~~LgiSRtaVwK~Iq~Lr 44 (79)
T COG1654 20 VSGEKLAEELGISRTAVWKHIQQLR 44 (79)
T ss_pred ccHHHHHHHHCccHHHHHHHHHHHH
Confidence 6778899999999999998887654
No 345
>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=39.70 E-value=17 Score=28.45 Aligned_cols=26 Identities=8% Similarity=0.148 Sum_probs=21.9
Q ss_pred CcccccccccCCChhhHHhHHhHhHH
Q psy15697 55 SPYHIIGATHGPSKSSICRSIHEVVP 80 (332)
Q Consensus 55 ~~~~~l~~~fgis~sTv~r~~~~v~~ 80 (332)
.+..+++..+|+|++++++++.....
T Consensus 26 ~s~~eia~~l~is~~~v~~~l~~L~~ 51 (130)
T TIGR02944 26 YSAAEIAEQTGLNAPTVSKILKQLSL 51 (130)
T ss_pred ccHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 47788999999999999988877654
No 346
>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=39.46 E-value=15 Score=25.24 Aligned_cols=27 Identities=15% Similarity=0.181 Sum_probs=19.5
Q ss_pred cCCcccccccccCCC-hhhHHhHHhHhH
Q psy15697 53 VGSPYHIIGATHGPS-KSSICRSIHEVV 79 (332)
Q Consensus 53 ~g~~~~~l~~~fgis-~sTv~r~~~~v~ 79 (332)
...+.++++..||++ .+||+..+....
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 446889999999996 888888876543
No 347
>PF08765 Mor: Mor transcription activator family; InterPro: IPR014875 Mor (Middle operon regulator) is a sequence specific DNA binding protein. It mediates transcription activation through its interactions with the C-terminal domains of the alpha and sigma subunits of bacterial RNA polymerase. The N-terminal region of Mor is the dimerisation region, and the C-terminal contains a helix-turn-helix motif which binds DNA []. ; PDB: 1RR7_A.
Probab=39.38 E-value=11 Score=28.67 Aligned_cols=31 Identities=23% Similarity=0.135 Sum_probs=22.1
Q ss_pred cCCcccccccccCCChhhHHhHHhHhHHHHH
Q psy15697 53 VGSPYHIIGATHGPSKSSICRSIHEVVPVIV 83 (332)
Q Consensus 53 ~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~ 83 (332)
.|.....||..||+|..+|.+|+++.-....
T Consensus 71 ~G~n~~eLA~kyglS~r~I~~Ii~~~~~~~~ 101 (108)
T PF08765_consen 71 NGMNVRELARKYGLSERQIYRIIKRVRRRER 101 (108)
T ss_dssp -SS-HHHHHHHHT--HHHHHHHHHHHHH---
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 4888999999999999999999998765443
No 348
>PRK09726 antitoxin HipB; Provisional
Probab=39.15 E-value=13 Score=27.15 Aligned_cols=26 Identities=12% Similarity=0.074 Sum_probs=23.1
Q ss_pred ccCCcccccccccCCChhhHHhHHhH
Q psy15697 52 GVGSPYHIIGATHGPSKSSICRSIHE 77 (332)
Q Consensus 52 ~~g~~~~~l~~~fgis~sTv~r~~~~ 77 (332)
..|.++.++|...|||++|++++.+.
T Consensus 23 ~~gltq~elA~~~gvs~~tis~~e~g 48 (88)
T PRK09726 23 QNGWTQSELAKKIGIKQATISNFENN 48 (88)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHCC
Confidence 56889999999999999999998773
No 349
>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=38.76 E-value=16 Score=24.99 Aligned_cols=23 Identities=17% Similarity=0.128 Sum_probs=16.6
Q ss_pred CcccccccccCCChhhHH-hHHhH
Q psy15697 55 SPYHIIGATHGPSKSSIC-RSIHE 77 (332)
Q Consensus 55 ~~~~~l~~~fgis~sTv~-r~~~~ 77 (332)
.+..++|+.+|||++|++ .+..+
T Consensus 13 ~~~~~lA~~lgis~st~s~~~~~r 36 (66)
T PF07022_consen 13 KSDKELAERLGISKSTLSNNWKKR 36 (66)
T ss_dssp SSCHHHHCCTT--HHHHH-HHHHS
T ss_pred CCHHHHHHHhCcCHHHhhHHHHhC
Confidence 355689999999999999 66654
No 350
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=38.63 E-value=15 Score=28.46 Aligned_cols=28 Identities=11% Similarity=0.026 Sum_probs=24.4
Q ss_pred hhccCCcccccccccCCChhhHHhHHhH
Q psy15697 50 WMGVGSPYHIIGATHGPSKSSICRSIHE 77 (332)
Q Consensus 50 ~L~~g~~~~~l~~~fgis~sTv~r~~~~ 77 (332)
+-..|.++..+|..+|+|++|++++.+.
T Consensus 74 r~~~gltq~~lA~~lg~~~~tis~~e~g 101 (127)
T TIGR03830 74 RKKLGLSQREAAELLGGGVNAFSRYERG 101 (127)
T ss_pred HHHcCCCHHHHHHHhCCCHHHHHHHHCC
Confidence 4456899999999999999999998763
No 351
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=38.60 E-value=35 Score=28.86 Aligned_cols=42 Identities=12% Similarity=0.021 Sum_probs=28.6
Q ss_pred CCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhH
Q psy15697 38 LSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVV 79 (332)
Q Consensus 38 ~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~ 79 (332)
+++.+-..+..-+-..+.++.+||...+++++|+++++.+.-
T Consensus 43 Lt~~q~~iL~~L~~~~~itq~eLa~~l~l~~sTvtr~l~rLE 84 (185)
T PRK13777 43 LNINEHHILWIAYHLKGASISEIAKFGVMHVSTAFNFSKKLE 84 (185)
T ss_pred CCHHHHHHHHHHHhCCCcCHHHHHHHHCCCHhhHHHHHHHHH
Confidence 444443333333334578999999999999999988776543
No 352
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=37.90 E-value=32 Score=25.73 Aligned_cols=26 Identities=19% Similarity=0.176 Sum_probs=21.8
Q ss_pred CCcccccccccCCChhhHHhHHhHhH
Q psy15697 54 GSPYHIIGATHGPSKSSICRSIHEVV 79 (332)
Q Consensus 54 g~~~~~l~~~fgis~sTv~r~~~~v~ 79 (332)
..+..++|..+|+|++++++.|++.+
T Consensus 21 ~~~~~~lA~~~~~S~~~l~r~f~~~~ 46 (107)
T PRK10219 21 PLNIDVVAKKSGYSKWYLQRMFRTVT 46 (107)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 34566789999999999999999863
No 353
>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=37.81 E-value=54 Score=25.69 Aligned_cols=48 Identities=10% Similarity=-0.025 Sum_probs=39.0
Q ss_pred CCCHHHHHHHHHhhhc-cCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 37 ALSAKEKVLSCLHWMG-VGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~-~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
.++..++-.+...|+. .+.+...++..+|+|++++.++-++-+..++.
T Consensus 79 ~l~~~~r~Il~~~Yl~~~~~~~~~I~~~l~~s~~~~y~~k~~Al~~fA~ 127 (132)
T TIGR01637 79 QLDEISRQILYDKYLEPDQKYDYQIMMELGYSHRQYYRIKKRALLRFAT 127 (132)
T ss_pred hCCHHHHHHHHHHHcCccccchHHHHHHhCCcHHHHHHHHHHHHHHHHH
Confidence 4677778888888887 35677889999999999999998887777766
No 354
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=37.65 E-value=71 Score=27.63 Aligned_cols=33 Identities=9% Similarity=-0.047 Sum_probs=29.0
Q ss_pred hccCCcccccccccCCChhhHHhHHhHhHHHHH
Q psy15697 51 MGVGSPYHIIGATHGPSKSSICRSIHEVVPVIV 83 (332)
Q Consensus 51 L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~ 83 (332)
++.|.+...+|..+++|..||..++....+...
T Consensus 175 ~~~g~s~~eIA~~l~iS~~Tv~~~~~~~~~~~~ 207 (239)
T PRK10430 175 QDYEFSTDELANAVNISRVSCRKYLIWLVNCHI 207 (239)
T ss_pred CCCCcCHHHHHHHhCchHHHHHHHHHHHHhCCE
Confidence 468999999999999999999999998876544
No 355
>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B.
Probab=37.58 E-value=11 Score=25.56 Aligned_cols=26 Identities=15% Similarity=0.174 Sum_probs=18.5
Q ss_pred cccccccccCCChhhHHhHHhHhHHHH
Q psy15697 56 PYHIIGATHGPSKSSICRSIHEVVPVI 82 (332)
Q Consensus 56 ~~~~l~~~fgis~sTv~r~~~~v~~~l 82 (332)
+...||..+|||+++|+.+ ...+.+.
T Consensus 11 ~~~~lAkalGVs~~aVs~W-~~~IP~~ 36 (60)
T PF14549_consen 11 GQSKLAKALGVSPQAVSQW-GERIPAE 36 (60)
T ss_dssp SHHHHHHHHTS-HHHHHHH-HTS--HH
T ss_pred CHHHHHHHHCCCHHHHHHh-cCccCHH
Confidence 5567899999999999999 5555443
No 356
>PRK08558 adenine phosphoribosyltransferase; Provisional
Probab=37.34 E-value=23 Score=31.25 Aligned_cols=38 Identities=13% Similarity=0.214 Sum_probs=32.9
Q ss_pred CHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHh
Q psy15697 39 SAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIH 76 (332)
Q Consensus 39 ~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~ 76 (332)
-...++.-.|+.|+..-+|++|+..+|++.|.++|+++
T Consensus 8 ~~~~~~v~~lr~lk~~~ty~el~~~~g~p~~~l~RYv~ 45 (238)
T PRK08558 8 RLQLRAVRVLRSLKKTYTYEELSSITGLPESVLNRYVN 45 (238)
T ss_pred HHHHHHHHHHHHHhcccCHHHHHHHHCCCHHHHHHHHc
Confidence 34455667899999999999999999999999999987
No 357
>PF07453 NUMOD1: NUMOD1 domain; InterPro: IPR010896 This helix-turn-helix-containing DNA-binding domain is found associated in homing nucleases [].
Probab=37.34 E-value=10 Score=22.56 Aligned_cols=23 Identities=17% Similarity=0.080 Sum_probs=18.1
Q ss_pred cCCcccccccccCCChhhHHhHH
Q psy15697 53 VGSPYHIIGATHGPSKSSICRSI 75 (332)
Q Consensus 53 ~g~~~~~l~~~fgis~sTv~r~~ 75 (332)
.-.+.++.+..+|++.+|+++++
T Consensus 15 ~F~Si~eAa~~l~i~~~~I~~~l 37 (37)
T PF07453_consen 15 SFDSIREAARYLGISHSTISKYL 37 (37)
T ss_pred EEcCHHHHHHHhCCCHHHHHHhC
Confidence 34566778888999999998764
No 358
>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=36.92 E-value=11 Score=36.45 Aligned_cols=32 Identities=19% Similarity=0.316 Sum_probs=25.4
Q ss_pred CCcccccccccCCChhhHHhHHhHhHHHHHHhhhccccCCCcc
Q psy15697 54 GSPYHIIGATHGPSKSSICRSIHEVVPVIVDTFFQRMVKWPEE 96 (332)
Q Consensus 54 g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~~l~~~~I~~P~~ 96 (332)
.+...++|...|++.|||||+++ ..|+..|..
T Consensus 318 PLtlkdiA~~lglheSTVSRav~-----------~Kyi~tp~G 349 (429)
T TIGR02395 318 PLTLREVAEELGLHESTISRAIN-----------NKYLQTPRG 349 (429)
T ss_pred CCcHHHHHHHhCCCccchhhhhc-----------CceEecCCc
Confidence 35678999999999999999854 467776654
No 359
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=36.07 E-value=35 Score=27.32 Aligned_cols=38 Identities=18% Similarity=0.176 Sum_probs=28.2
Q ss_pred HHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHH
Q psy15697 42 EKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVP 80 (332)
Q Consensus 42 ~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~ 80 (332)
.+++-.|..=+. .++..+|...|+|.+||++.+.+...
T Consensus 11 ~~IL~~L~~d~r-~~~~eia~~lglS~~~v~~Ri~~L~~ 48 (154)
T COG1522 11 RRILRLLQEDAR-ISNAELAERVGLSPSTVLRRIKRLEE 48 (154)
T ss_pred HHHHHHHHHhCC-CCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 344444444333 78999999999999999999888665
No 360
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=35.57 E-value=37 Score=30.34 Aligned_cols=45 Identities=20% Similarity=0.175 Sum_probs=34.4
Q ss_pred CCCCCHHHHHHHHHhhhccC-CcccccccccCCChhhHHhHHhHhH
Q psy15697 35 NVALSAKEKVLSCLHWMGVG-SPYHIIGATHGPSKSSICRSIHEVV 79 (332)
Q Consensus 35 ~~~~~~~~~l~~~L~~L~~g-~~~~~l~~~fgis~sTv~r~~~~v~ 79 (332)
...++.+++-.+-+-.=..| ..+.++.+..|.|++|+||++++.-
T Consensus 190 ~~~L~~~e~~il~~i~~~GGri~Q~eL~r~lglsktTvsR~L~~LE 235 (258)
T COG2512 190 EYDLNEDEKEILDLIRERGGRITQAELRRALGLSKTTVSRILRRLE 235 (258)
T ss_pred cCCCCHHHHHHHHHHHHhCCEEeHHHHHHhhCCChHHHHHHHHHHH
Confidence 35677777765554444455 6889999999999999999998764
No 361
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=35.50 E-value=30 Score=31.22 Aligned_cols=43 Identities=5% Similarity=0.009 Sum_probs=33.2
Q ss_pred HHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHHhhh
Q psy15697 44 VLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVDTFF 87 (332)
Q Consensus 44 l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~~l~ 87 (332)
|-.++....+| ++...|+..+||+++||+.+++.-..+...|.
T Consensus 6 L~~f~~v~~~g-S~s~AA~~L~itQpavS~~i~~LE~~lg~~LF 48 (305)
T PRK11151 6 LEYLVALAEHR-HFRRAADSCHVSQPTLSGQIRKLEDELGVMLL 48 (305)
T ss_pred HHHHHHHHHhC-CHHHHHHHhCCCchHHHHHHHHHHHHhCchhe
Confidence 44445555555 88899999999999999999998887765333
No 362
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=35.30 E-value=34 Score=28.11 Aligned_cols=28 Identities=7% Similarity=-0.029 Sum_probs=24.0
Q ss_pred cCCcccccccccCCChhhHHhHHhHhHH
Q psy15697 53 VGSPYHIIGATHGPSKSSICRSIHEVVP 80 (332)
Q Consensus 53 ~g~~~~~l~~~fgis~sTv~r~~~~v~~ 80 (332)
...++.+||+..|+|++||.+-+++..+
T Consensus 27 ~R~s~~eiA~~lglS~~tv~~Ri~rL~~ 54 (164)
T PRK11169 27 GRISNVELSKRVGLSPTPCLERVRRLER 54 (164)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 3468899999999999999998887654
No 363
>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=35.15 E-value=14 Score=23.85 Aligned_cols=20 Identities=30% Similarity=0.363 Sum_probs=16.0
Q ss_pred ccccccccCCChhhHHhHHh
Q psy15697 57 YHIIGATHGPSKSSICRSIH 76 (332)
Q Consensus 57 ~~~l~~~fgis~sTv~r~~~ 76 (332)
..+++...|+|++|+.+.++
T Consensus 6 ~~ev~~~~g~s~~ti~~~~k 25 (51)
T PF05930_consen 6 IKEVAELLGVSRSTIYRLIK 25 (51)
T ss_dssp HHHHHHHHSS-HHHHHHHHH
T ss_pred HHHHHHHHCCCHHHHHHHHh
Confidence 34678889999999999887
No 364
>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=34.56 E-value=20 Score=26.30 Aligned_cols=34 Identities=12% Similarity=0.278 Sum_probs=25.0
Q ss_pred HHHHHhhhccCCcccccccccCCChhhHHhHHhH
Q psy15697 44 VLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHE 77 (332)
Q Consensus 44 l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~ 77 (332)
+...|..++.-..+..+|...|||++|++++.+.
T Consensus 33 ~~~~l~~~r~~~glSqLAe~~GIs~stLs~iE~g 66 (89)
T TIGR02684 33 IAHALGYIARARGMTQLARKTGLSRESLYKALSG 66 (89)
T ss_pred HHHHHHHHHHHCChHHHHHHHCCCHHHHHHHHcC
Confidence 4555555554444556999999999999998864
No 365
>PRK15092 DNA-binding transcriptional repressor LrhA; Provisional
Probab=34.51 E-value=26 Score=31.94 Aligned_cols=50 Identities=6% Similarity=0.119 Sum_probs=39.7
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHHhh
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVDTF 86 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~~l 86 (332)
.+....+.+-++.-++...++...|+..+||++|||+.+++.-..+...|
T Consensus 8 ~~~m~l~~L~~F~~v~e~gs~s~AA~~L~iSQpavS~~I~~LE~~lG~~L 57 (310)
T PRK15092 8 IINLDLDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKEL 57 (310)
T ss_pred hhcCCHHHHHHHHHHHHcCCHHHHHHHhCCChHHHHHHHHHHHHHhCcce
Confidence 34445555666677778889999999999999999999999988876633
No 366
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=34.07 E-value=20 Score=28.33 Aligned_cols=27 Identities=11% Similarity=-0.007 Sum_probs=23.2
Q ss_pred hccCCcccccccccCCChhhHHhHHhH
Q psy15697 51 MGVGSPYHIIGATHGPSKSSICRSIHE 77 (332)
Q Consensus 51 L~~g~~~~~l~~~fgis~sTv~r~~~~ 77 (332)
-..|.++..+|...|||++||+++.+.
T Consensus 15 ~~~gltq~~lA~~~gvs~~~is~~E~g 41 (135)
T PRK09706 15 KQLKLSQRSLAKAVKVSHVSISQWERD 41 (135)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 346888999999999999999998764
No 367
>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=34.01 E-value=35 Score=31.62 Aligned_cols=44 Identities=23% Similarity=0.132 Sum_probs=35.8
Q ss_pred CCCCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHh
Q psy15697 35 NVALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEV 78 (332)
Q Consensus 35 ~~~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v 78 (332)
+..+++.++.......+..|.+...++..+|+++++|++++.-.
T Consensus 158 R~dLS~iE~A~~~~~L~~~G~~~~~ia~~Lg~~ks~vSr~lsl~ 201 (325)
T TIGR03454 158 RRDLSFIERALFAQRLEDRGFDRDTIMAALSVDKTELSRMISVA 201 (325)
T ss_pred ccCCCHHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 46688888876666677788888889999999999999988743
No 368
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=33.99 E-value=30 Score=30.27 Aligned_cols=47 Identities=15% Similarity=0.268 Sum_probs=29.0
Q ss_pred HHHHHHHhccCcCCC-CCCCCCCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhH
Q psy15697 17 VEFILEEIAPALTTP-TERNVALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVV 79 (332)
Q Consensus 17 F~~L~~~L~~~~~~~-~~~~~~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~ 79 (332)
..+|.+.|...+... -..+..+|.|. +|+..||||+.||.+.+....
T Consensus 7 y~qi~~~L~~~I~~g~~~~G~~LPsE~----------------eL~~~~~VSR~TvR~Al~~L~ 54 (240)
T PRK09764 7 YRQIADRIREQIARGELKPGDALPTES----------------ALQTEFGVSRVTVRQALRQLV 54 (240)
T ss_pred HHHHHHHHHHHHHcCCCCCCCcCCCHH----------------HHHHHHCCCHHHHHHHHHHHH
Confidence 455555555544321 11234566665 567889999999988776544
No 369
>COG3179 Predicted chitinase [General function prediction only]
Probab=33.98 E-value=44 Score=28.15 Aligned_cols=70 Identities=11% Similarity=0.169 Sum_probs=53.8
Q ss_pred CChhHHHHHhcCCHHHHHHHHHHhccCcCCCCCCCCCCCHHHHHHHHHhhhccCCc-ccccccccCCChhhHHhHH
Q psy15697 1 MTPFAFKEAFRLSATQVEFILEEIAPALTTPTERNVALSAKEKVLSCLHWMGVGSP-YHIIGATHGPSKSSICRSI 75 (332)
Q Consensus 1 ~~d~~f~~~frms~~~F~~L~~~L~~~~~~~~~~~~~~~~~~~l~~~L~~L~~g~~-~~~l~~~fgis~sTv~r~~ 75 (332)
+++.+|.+.+...+..|-..+-.|.+.+.. ..++-..+++++|--+.|-+. +..+.+.++-|..+..+.+
T Consensus 4 i~e~~~~ki~p~a~k~~~~v~~al~~~l~~-----~gi~~p~r~AmFlAQ~~HESggf~rl~EnlnYSaq~L~~tf 74 (206)
T COG3179 4 ITEVDLRKIFPKARKEFVDVIVALQPALDE-----AGITTPLRQAMFLAQVMHESGGFTRLDENLNYSAQGLLQTF 74 (206)
T ss_pred hhHHHHHHhcchhhhhhHHHHHHHHHHHHH-----hcCCCHHHHHHHHHHHhhhcCCceeehhhcchHHHHHHHhc
Confidence 467789999999999988888888887643 335567889999999998776 7888888887766554443
No 370
>PRK13503 transcriptional activator RhaS; Provisional
Probab=33.98 E-value=52 Score=29.18 Aligned_cols=27 Identities=7% Similarity=0.144 Sum_probs=22.8
Q ss_pred cCCcccccccccCCChhhHHhHHhHhH
Q psy15697 53 VGSPYHIIGATHGPSKSSICRSIHEVV 79 (332)
Q Consensus 53 ~g~~~~~l~~~fgis~sTv~r~~~~v~ 79 (332)
...+..++|..+|+|+++++++|++..
T Consensus 186 ~~~tl~~lA~~~~lS~~~l~r~Fk~~~ 212 (278)
T PRK13503 186 EEVNWEALADQFSLSLRTLHRQLKQQT 212 (278)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHh
Confidence 456678899999999999999998763
No 371
>PF07900 DUF1670: Protein of unknown function (DUF1670); InterPro: IPR012872 The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=33.79 E-value=1.4e+02 Score=25.98 Aligned_cols=81 Identities=15% Similarity=0.146 Sum_probs=57.0
Q ss_pred CChhHHHHHhcCCHHHHHHHHHHhccCc----CCCC-C--CCCCCCHHHHHHHHHhhhccCCcccccccccCCChhhHHh
Q psy15697 1 MTPFAFKEAFRLSATQVEFILEEIAPAL----TTPT-E--RNVALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICR 73 (332)
Q Consensus 1 ~~d~~f~~~frms~~~F~~L~~~L~~~~----~~~~-~--~~~~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r 73 (332)
|+.++.-..+++|..+....+..++..- +..+ . -++.++-.. .. +..+-.|.+..++|..-..|..+|-|
T Consensus 106 LT~~Dla~LL~~S~~TI~~~i~~yq~e~g~vvPtrG~i~DiGp~~tHK~-~i--i~~~l~g~~~~eiar~t~HS~~av~r 182 (220)
T PF07900_consen 106 LTQEDLAMLLGISPRTISKDIKEYQKEHGVVVPTRGTIHDIGPGVTHKK-II--IRLYLKGKPTPEIARRTNHSPEAVDR 182 (220)
T ss_pred ccHHHHHHHHCCCHHHHHHHHHHHHHHcCceeccCCcccccCCcchHHH-HH--HHHHHcCCCHHHHHHHhccCHHHHHH
Confidence 4566777889999999999998887651 1111 1 123333222 22 33344488999999999999999999
Q ss_pred HHhHhHHHHHH
Q psy15697 74 SIHEVVPVIVD 84 (332)
Q Consensus 74 ~~~~v~~~l~~ 84 (332)
+++.+..+..-
T Consensus 183 Yi~~F~rV~~l 193 (220)
T PF07900_consen 183 YIKDFKRVLML 193 (220)
T ss_pred HHHhhHHhHHH
Confidence 99999887764
No 372
>PRK12681 cysB transcriptional regulator CysB; Reviewed
Probab=33.74 E-value=33 Score=31.46 Aligned_cols=45 Identities=7% Similarity=0.004 Sum_probs=35.3
Q ss_pred HHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHHhhh
Q psy15697 43 KVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVDTFF 87 (332)
Q Consensus 43 ~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~~l~ 87 (332)
+|-.++....+|.+++..|...++|++|||+.+++.-..+...|.
T Consensus 5 ~L~~f~avae~g~S~s~AA~~L~iSQpavS~~I~~LE~~lG~~LF 49 (324)
T PRK12681 5 QLRYIVEVVNHNLNVSATAEGLYTSQPGISKQVRMLEDELGIQIF 49 (324)
T ss_pred HHHHHHHHHHccCCHHHHHHHhcCCcHHHHHHHHHHHHHhCCEeE
Confidence 344455555566799999999999999999999999888876443
No 373
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=33.66 E-value=28 Score=30.54 Aligned_cols=49 Identities=16% Similarity=0.269 Sum_probs=32.3
Q ss_pred HHHHHHHHHhccCcCCC-CCCCCCCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhH
Q psy15697 15 TQVEFILEEIAPALTTP-TERNVALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVV 79 (332)
Q Consensus 15 ~~F~~L~~~L~~~~~~~-~~~~~~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~ 79 (332)
+-+.+|.+.|+..+... -..+..+|.|. +|+..||||+.||.+-+....
T Consensus 7 plY~qI~~~i~~~I~~G~~~~G~~LPsE~----------------eLa~~f~VSR~TvRkAL~~L~ 56 (236)
T COG2188 7 PLYQQIAEDIRQRIESGELPPGDKLPSER----------------ELAEQFGVSRMTVRKALDELV 56 (236)
T ss_pred ccHHHHHHHHHHHHHhCCCCCCCCCCCHH----------------HHHHHHCCcHHHHHHHHHHHH
Confidence 44566666666655431 22345566666 567889999999998777654
No 374
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=33.41 E-value=31 Score=30.19 Aligned_cols=48 Identities=8% Similarity=0.177 Sum_probs=30.4
Q ss_pred HHHHHHHHhccCcCCC-CCCCCCCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhH
Q psy15697 16 QVEFILEEIAPALTTP-TERNVALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVV 79 (332)
Q Consensus 16 ~F~~L~~~L~~~~~~~-~~~~~~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~ 79 (332)
.+.+|.+.|...+... -..+..+|.|.. |+..||||+.||.+-+....
T Consensus 10 ~y~qI~~~i~~~I~~G~~~~g~kLPsE~e----------------La~~~~VSR~TvR~Al~~L~ 58 (241)
T PRK11402 10 LYATVRQRLLDDIAQGVYQAGQQIPTENE----------------LCTQYNVSRITIRKAISDLV 58 (241)
T ss_pred HHHHHHHHHHHHHHcCCCCCCCcCcCHHH----------------HHHHHCCCHHHHHHHHHHHH
Confidence 4556666666554321 122456777764 56789999999988776544
No 375
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=33.40 E-value=41 Score=26.29 Aligned_cols=28 Identities=14% Similarity=0.077 Sum_probs=23.2
Q ss_pred ccCCcccccccccCCChhhHHhHHhHhH
Q psy15697 52 GVGSPYHIIGATHGPSKSSICRSIHEVV 79 (332)
Q Consensus 52 ~~g~~~~~l~~~fgis~sTv~r~~~~v~ 79 (332)
....+..++|..+|+|++++.+.|++.+
T Consensus 23 ~~~~sl~~lA~~~g~S~~~l~r~Fk~~~ 50 (127)
T PRK11511 23 ESPLSLEKVSERSGYSKWHLQRMFKKET 50 (127)
T ss_pred CCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 3445677899999999999999999874
No 376
>PRK10094 DNA-binding transcriptional activator AllS; Provisional
Probab=33.28 E-value=33 Score=31.15 Aligned_cols=35 Identities=6% Similarity=-0.068 Sum_probs=29.4
Q ss_pred hhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 50 WMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 50 ~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
.++...++...|...++|++++|+.+++.-..+..
T Consensus 12 ~v~e~gs~s~AA~~L~iSQpavS~~I~~LE~~lg~ 46 (308)
T PRK10094 12 AVAETGSFSKAAERLCKTTATISYRIKLLEENTGV 46 (308)
T ss_pred HHHHhCCHHHHHHHhcCCHHHHHHHHHHHHHHhCC
Confidence 33445588899999999999999999998887765
No 377
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=32.75 E-value=37 Score=28.08 Aligned_cols=45 Identities=16% Similarity=0.132 Sum_probs=36.4
Q ss_pred CCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHH
Q psy15697 37 ALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIV 83 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~ 83 (332)
++++.+.. .|.+|..|.+...+|...++|..||...+.+...-|.
T Consensus 149 ~lt~re~~--vl~~l~~g~s~~eIa~~l~~s~~tv~~~~~~~~~kl~ 193 (210)
T PRK09935 149 VLSNREVT--ILRYLVSGLSNKEIADQLLLSNKTVSAHKSNIYGKLG 193 (210)
T ss_pred cCCHHHHH--HHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence 45555544 5678999999999999999999999999988876653
No 378
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=32.73 E-value=31 Score=30.88 Aligned_cols=40 Identities=5% Similarity=0.040 Sum_probs=32.5
Q ss_pred HHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHHh
Q psy15697 46 SCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVDT 85 (332)
Q Consensus 46 ~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~~ 85 (332)
-++..++...++...|...++|+||||+.+++.-..+-..
T Consensus 7 ~~f~~v~~~gs~s~AA~~L~isQ~avSr~i~~LE~~lg~~ 46 (296)
T PRK09906 7 RYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVP 46 (296)
T ss_pred HHHHHHHhhCCHHHHHHHhCCCCcHHHHHHHHHHHHhCCe
Confidence 3445555566999999999999999999999998877653
No 379
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=32.50 E-value=15 Score=35.91 Aligned_cols=32 Identities=16% Similarity=0.188 Sum_probs=25.5
Q ss_pred CCcccccccccCCChhhHHhHHhHhHHHHHHhhhccccCCCcc
Q psy15697 54 GSPYHIIGATHGPSKSSICRSIHEVVPVIVDTFFQRMVKWPEE 96 (332)
Q Consensus 54 g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~~l~~~~I~~P~~ 96 (332)
.+..+++|...|++.|||||++. ..|+..|..
T Consensus 369 PLtlkdVAe~lglHeSTVSRa~~-----------~KY~~tp~G 400 (481)
T PRK12469 369 PLVLRDVAEELGLHESTISRATG-----------NKYMATPRG 400 (481)
T ss_pred CCcHHHHHHHhCCCcchhhHHhc-----------CceeecCCc
Confidence 35678999999999999999854 467777754
No 380
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=32.42 E-value=25 Score=30.26 Aligned_cols=31 Identities=6% Similarity=-0.004 Sum_probs=25.8
Q ss_pred HHhhhcc---CCcccccccccCCChhhHHhHHhH
Q psy15697 47 CLHWMGV---GSPYHIIGATHGPSKSSICRSIHE 77 (332)
Q Consensus 47 ~L~~L~~---g~~~~~l~~~fgis~sTv~r~~~~ 77 (332)
.|..++. |.+..++|...++|..||.+++..
T Consensus 167 Vl~~~~~g~~g~s~~eIa~~l~iS~~Tv~~~~~~ 200 (225)
T PRK10046 167 VRKLFKEPGVQHTAETVAQALTISRTTARRYLEY 200 (225)
T ss_pred HHHHHHcCCCCcCHHHHHHHhCccHHHHHHHHHH
Confidence 4556666 478999999999999999999863
No 381
>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=32.17 E-value=40 Score=28.54 Aligned_cols=26 Identities=12% Similarity=0.080 Sum_probs=21.6
Q ss_pred CcccccccccCCC-hhhHHhHHhHhHH
Q psy15697 55 SPYHIIGATHGPS-KSSICRSIHEVVP 80 (332)
Q Consensus 55 ~~~~~l~~~fgis-~sTv~r~~~~v~~ 80 (332)
.+.+++|..+|++ ++||++.+.....
T Consensus 26 ~~~~ela~~~~~~s~~tv~~~l~~L~~ 52 (199)
T TIGR00498 26 PSIREIARAVGLRSPSAAEEHLKALER 52 (199)
T ss_pred CcHHHHHHHhCCCChHHHHHHHHHHHH
Confidence 5677999999998 9999988876543
No 382
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=32.11 E-value=15 Score=35.81 Aligned_cols=32 Identities=19% Similarity=0.208 Sum_probs=25.4
Q ss_pred CCcccccccccCCChhhHHhHHhHhHHHHHHhhhccccCCCcc
Q psy15697 54 GSPYHIIGATHGPSKSSICRSIHEVVPVIVDTFFQRMVKWPEE 96 (332)
Q Consensus 54 g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~~l~~~~I~~P~~ 96 (332)
.+..+++|...|++.|||||.+. ..||..|..
T Consensus 343 PLtlkdvAe~lglheSTVSRav~-----------~Kyv~tp~G 374 (455)
T PRK05932 343 PLVLKDIAEELGMHESTISRATT-----------NKYMATPRG 374 (455)
T ss_pred CccHHHHHHHhCCCccchhhhhc-----------CceeecCCc
Confidence 35678999999999999999854 467776654
No 383
>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=31.78 E-value=43 Score=26.21 Aligned_cols=40 Identities=13% Similarity=0.005 Sum_probs=30.8
Q ss_pred HHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHH
Q psy15697 44 VLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIV 83 (332)
Q Consensus 44 l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~ 83 (332)
.-+.+.|+.+|.+.+.+|...++|..++.+.+..--..|.
T Consensus 68 ~~ll~~~Yv~g~s~r~IA~~~~~s~~~ir~~l~~ae~~i~ 107 (125)
T PF06530_consen 68 YDLLILYYVYGWSKRQIARKLKCSEGKIRKRLQRAEGFID 107 (125)
T ss_pred HHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHhhhhHh
Confidence 4455566668999999999999999999888775544443
No 384
>smart00351 PAX Paired Box domain.
Probab=31.75 E-value=1.5e+02 Score=23.09 Aligned_cols=25 Identities=20% Similarity=0.167 Sum_probs=19.8
Q ss_pred hhHHHHHhcCCHHHHHHHHHHhccC
Q psy15697 3 PFAFKEAFRLSATQVEFILEEIAPA 27 (332)
Q Consensus 3 d~~f~~~frms~~~F~~L~~~L~~~ 27 (332)
-.+.-+.|++++.+...++......
T Consensus 36 ~~~iA~~~gvs~~tV~kwi~r~~~~ 60 (125)
T smart00351 36 PCDISRQLCVSHGCVSKILGRYYET 60 (125)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHc
Confidence 3456678999999999998876553
No 385
>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=31.73 E-value=39 Score=22.47 Aligned_cols=38 Identities=18% Similarity=0.097 Sum_probs=27.1
Q ss_pred HHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHH
Q psy15697 43 KVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPV 81 (332)
Q Consensus 43 ~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~ 81 (332)
+|+-.|.- ....++.++|...|+|..|+...+.+.-..
T Consensus 9 ~Ll~~L~~-~~~~~~~ela~~l~~S~rti~~~i~~L~~~ 46 (59)
T PF08280_consen 9 KLLELLLK-NKWITLKELAKKLNISERTIKNDINELNEF 46 (59)
T ss_dssp HHHHHHHH-HTSBBHHHHHHHCTS-HHHHHHHHHHHHTT
T ss_pred HHHHHHHc-CCCCcHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 34444444 556788899999999999998888776543
No 386
>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=31.64 E-value=32 Score=30.71 Aligned_cols=43 Identities=5% Similarity=0.105 Sum_probs=32.0
Q ss_pred HHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHHhhh
Q psy15697 44 VLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVDTFF 87 (332)
Q Consensus 44 l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~~l~ 87 (332)
|-.++... ...++...|+.++||+||+++.+++.-..+...|.
T Consensus 6 L~~f~~v~-~~gs~s~AA~~L~itqpavS~~Ik~LE~~lg~~LF 48 (291)
T TIGR03418 6 LRVFESAA-RLASFTAAARELGSTQPAVSQQVKRLEEELGTPLF 48 (291)
T ss_pred HHHHHHHH-HhCCHHHHHHHhCCCHHHHHHHHHHHHHHhCcHHh
Confidence 33344444 44488899999999999999999998877765333
No 387
>PRK15215 fimbriae biosynthesis regulatory protein; Provisional
Probab=31.50 E-value=1.5e+02 Score=22.32 Aligned_cols=40 Identities=5% Similarity=0.086 Sum_probs=30.0
Q ss_pred HHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhH
Q psy15697 40 AKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVV 79 (332)
Q Consensus 40 ~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~ 79 (332)
.+.-+...=.||-.|.+..++.+..+|+++-.+-.+.++-
T Consensus 47 S~KvI~AL~dyLV~G~trkevCe~~~Vn~gYfS~~L~rL~ 86 (100)
T PRK15215 47 SEKIIQALRDYLVFGVSRKDVCERYEVNNGYFSTSLNRLS 86 (100)
T ss_pred hHHHHHHHHHHHHcCccHHHHHHccCCCHHHHHHHHHHHH
Confidence 3333444445888999999999999999998877766543
No 388
>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=31.46 E-value=18 Score=26.65 Aligned_cols=24 Identities=21% Similarity=0.232 Sum_probs=17.8
Q ss_pred cCCcccccccccCCChhhHHhHHh
Q psy15697 53 VGSPYHIIGATHGPSKSSICRSIH 76 (332)
Q Consensus 53 ~g~~~~~l~~~fgis~sTv~r~~~ 76 (332)
.|.++.+||..+|.|++.|++++.
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 478889999999999999998876
No 389
>PF13556 HTH_30: PucR C-terminal helix-turn-helix domain; PDB: 3ONQ_B.
Probab=31.37 E-value=30 Score=22.99 Aligned_cols=36 Identities=0% Similarity=0.020 Sum_probs=29.1
Q ss_pred HhhhccCCcccccccccCCChhhHHhHHhHhHHHHH
Q psy15697 48 LHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIV 83 (332)
Q Consensus 48 L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~ 83 (332)
-.|+.++.+....|...+|++.|+.--+.++.+.+-
T Consensus 6 ~~yl~~~~n~~~tA~~L~iHrNTl~yRl~ki~~l~g 41 (59)
T PF13556_consen 6 RAYLENNGNISKTARALHIHRNTLRYRLKKIEELLG 41 (59)
T ss_dssp HHHHHTTT-HHHHHHHHTS-HHHHHHHHHHHHHHHS
T ss_pred HHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Confidence 357888999999999999999999988888877654
No 390
>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=31.36 E-value=18 Score=22.59 Aligned_cols=20 Identities=15% Similarity=-0.008 Sum_probs=16.1
Q ss_pred cccccccCCChhhHHhHHhH
Q psy15697 58 HIIGATHGPSKSSICRSIHE 77 (332)
Q Consensus 58 ~~l~~~fgis~sTv~r~~~~ 77 (332)
.++|..+||+.+|+..+..+
T Consensus 4 ~e~a~~~gv~~~tlr~~~~~ 23 (49)
T cd04761 4 GELAKLTGVSPSTLRYYERI 23 (49)
T ss_pred HHHHHHHCcCHHHHHHHHHC
Confidence 46788899999999887654
No 391
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=31.16 E-value=40 Score=30.40 Aligned_cols=40 Identities=8% Similarity=0.067 Sum_probs=31.8
Q ss_pred HHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHHhh
Q psy15697 47 CLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVDTF 86 (332)
Q Consensus 47 ~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~~l 86 (332)
++.-+....++...|...++|+++||+.+++.-..+...|
T Consensus 12 ~f~~v~e~gs~s~AA~~L~isqpavS~~i~~LE~~lg~~L 51 (305)
T CHL00180 12 ILKAIATEGSFKKAAESLYISQPAVSLQIKNLEKQLNIPL 51 (305)
T ss_pred HHHHHHHcCCHHHHHHHhcCCChHHHHHHHHHHHHhCCEE
Confidence 3344444558889999999999999999999988887633
No 392
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=30.68 E-value=44 Score=26.60 Aligned_cols=26 Identities=12% Similarity=0.107 Sum_probs=21.2
Q ss_pred CcccccccccCCChhhHHhHHhHhHH
Q psy15697 55 SPYHIIGATHGPSKSSICRSIHEVVP 80 (332)
Q Consensus 55 ~~~~~l~~~fgis~sTv~r~~~~v~~ 80 (332)
.+..+|+..+++|++||++.+.+...
T Consensus 23 ~~~~ela~~l~vs~~svs~~l~~L~~ 48 (142)
T PRK03902 23 ARVSDIAEALSVHPSSVTKMVQKLDK 48 (142)
T ss_pred cCHHHHHHHhCCChhHHHHHHHHHHH
Confidence 45567999999999999998876544
No 393
>PF11198 DUF2857: Protein of unknown function (DUF2857); InterPro: IPR021364 This is a bacterial family of uncharacterised proteins.
Probab=30.63 E-value=2.4e+02 Score=23.67 Aligned_cols=74 Identities=20% Similarity=0.173 Sum_probs=47.0
Q ss_pred hHHHHHhcCCHHHHHHHHHHhccCcCCCCCCCCCCCHHHHHHHHHhhh----ccCC------ccc----ccccccCCChh
Q psy15697 4 FAFKEAFRLSATQVEFILEEIAPALTTPTERNVALSAKEKVLSCLHWM----GVGS------PYH----IIGATHGPSKS 69 (332)
Q Consensus 4 ~~f~~~frms~~~F~~L~~~L~~~~~~~~~~~~~~~~~~~l~~~L~~L----~~g~------~~~----~l~~~fgis~s 69 (332)
+-..+.||||...+...=..|+-. ...+|.+.++.++...+--.|- ..+. .+- .+|+..++|-+
T Consensus 91 ~mm~~~FGls~~ev~~rR~llgi~--~~~GR~~~~~ee~~~~iW~~W~~~~~~~~~~~~~~~~~Le~~m~~Ae~~~isL~ 168 (180)
T PF11198_consen 91 EMMQRLFGLSSAEVAARRRLLGIP--VRKGRPPALSEEEEAAIWRRWQQLMKKRGVDNLDSPDALELMMLLAEETNISLT 168 (180)
T ss_pred HHHHHHHCCCHHHHHHHHHHhCCC--CCCCCCCCcCHHHHHHHHHHHHHHHhhcCCCCccchHHHHHHHHHHHHhCCCHH
Confidence 345678999999998877777543 3344555556655555544443 1221 111 27788899999
Q ss_pred hHHhHHhHhH
Q psy15697 70 SICRSIHEVV 79 (332)
Q Consensus 70 Tv~r~~~~v~ 79 (332)
+|...|..+.
T Consensus 169 ~iW~~i~~w~ 178 (180)
T PF11198_consen 169 VIWSLIQEWE 178 (180)
T ss_pred HHHHHHHHHH
Confidence 8888887765
No 394
>PRK10341 DNA-binding transcriptional activator TdcA; Provisional
Probab=30.53 E-value=35 Score=30.92 Aligned_cols=43 Identities=7% Similarity=0.053 Sum_probs=33.9
Q ss_pred HHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHHhh
Q psy15697 44 VLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVDTF 86 (332)
Q Consensus 44 l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~~l 86 (332)
-+-++.-++...++...|+..+||++|+|+.+++.-..+...|
T Consensus 11 ~L~~F~av~e~gs~s~AA~~L~iSQpavS~~I~~LE~~lg~~L 53 (312)
T PRK10341 11 HLVVFQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVEL 53 (312)
T ss_pred HHHHHHHHHHcCCHHHHHHHhCCChHHHHHHHHHHHHHhCCeE
Confidence 3344455556778889999999999999999999988877633
No 395
>COG4941 Predicted RNA polymerase sigma factor containing a TPR repeat domain [Transcription]
Probab=30.28 E-value=59 Score=30.24 Aligned_cols=49 Identities=16% Similarity=0.227 Sum_probs=39.7
Q ss_pred CCCCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 35 NVALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 35 ~~~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
.+.++++.+++++|+.++ |.+-.+++..|=||++|+..-+.+--..|.+
T Consensus 118 HPal~~~~riALtLR~v~-GLs~~eIArAFLv~e~am~QRivRAK~ri~~ 166 (415)
T COG4941 118 HPALPPEQRIALTLRLVG-GLSTAEIARAFLVPEAAMAQRIVRAKARIRE 166 (415)
T ss_pred CCCCChhhHHHHHHHHHc-CCcHHHHHHHHcCCcHHHHHHHHHHHHHHHh
Confidence 577999999999998776 8999999999999999986555555554444
No 396
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=30.10 E-value=27 Score=21.30 Aligned_cols=25 Identities=20% Similarity=0.232 Sum_probs=20.4
Q ss_pred ccCCcccccccccCCChhhHHhHHh
Q psy15697 52 GVGSPYHIIGATHGPSKSSICRSIH 76 (332)
Q Consensus 52 ~~g~~~~~l~~~fgis~sTv~r~~~ 76 (332)
..+.+..+++...|++.++++++..
T Consensus 8 ~~~~s~~~la~~~~i~~~~i~~~~~ 32 (56)
T smart00530 8 EKGLTQEELAEKLGVSRSTLSRIEN 32 (56)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHC
Confidence 3567888999999999999987654
No 397
>PRK15421 DNA-binding transcriptional regulator MetR; Provisional
Probab=30.07 E-value=43 Score=30.55 Aligned_cols=41 Identities=10% Similarity=0.072 Sum_probs=32.3
Q ss_pred HHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 43 KVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 43 ~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
+|-.++....+| ++...|+..++|++|||+-+++.-..+..
T Consensus 6 ~L~~f~av~~~g-s~s~AA~~L~iSqpaVS~~Ik~LE~~lg~ 46 (317)
T PRK15421 6 HLKTLQALRNCG-SLAAAAATLHQTQSALSHQFSDLEQRLGF 46 (317)
T ss_pred HHHHHHHHHHcC-CHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 344444444555 88899999999999999999998888765
No 398
>PRK11013 DNA-binding transcriptional regulator LysR; Provisional
Probab=29.65 E-value=41 Score=30.48 Aligned_cols=41 Identities=12% Similarity=0.019 Sum_probs=31.3
Q ss_pred HHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHHh
Q psy15697 44 VLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVDT 85 (332)
Q Consensus 44 l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~~ 85 (332)
|-.++....+ .++...|+..++|+||||+.+++.-..+-..
T Consensus 9 L~~f~av~~~-gS~s~AAe~L~isqsavS~~Ik~LE~~lg~~ 49 (309)
T PRK11013 9 IEIFHAVMTA-GSLTEAARLLHTSQPTVSRELARFEKVIGLK 49 (309)
T ss_pred HHHHHHHHHh-CcHHHHHHHHCCCcHHHHHHHHHHHHHhCce
Confidence 3344444444 4888999999999999999999988877653
No 399
>PF05391 Lsm_interact: Lsm interaction motif; InterPro: IPR008669 This short motif is found at the C terminus of Prp24 proteins and probably interacts with the Lsm proteins to promote U4/U6 formation [].
Probab=29.63 E-value=36 Score=17.74 Aligned_cols=10 Identities=20% Similarity=0.388 Sum_probs=7.3
Q ss_pred CChhHHHHHh
Q psy15697 1 MTPFAFKEAF 10 (332)
Q Consensus 1 ~~d~~f~~~f 10 (332)
||.++|+++|
T Consensus 10 ~SNddFrkmf 19 (21)
T PF05391_consen 10 KSNDDFRKMF 19 (21)
T ss_pred cchHHHHHHH
Confidence 5677888776
No 400
>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=29.62 E-value=18 Score=24.17 Aligned_cols=26 Identities=19% Similarity=0.181 Sum_probs=19.9
Q ss_pred ccCCcccccccccCCChhhHHhHHhH
Q psy15697 52 GVGSPYHIIGATHGPSKSSICRSIHE 77 (332)
Q Consensus 52 ~~g~~~~~l~~~fgis~sTv~r~~~~ 77 (332)
..|.++.++|...|+++++++++.+.
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 45788999999999999999998864
No 401
>COG1395 Predicted transcriptional regulator [Transcription]
Probab=29.40 E-value=29 Score=31.74 Aligned_cols=66 Identities=11% Similarity=0.069 Sum_probs=44.7
Q ss_pred cCCHHHHHHHHHHhccCcCCCCCCCCCCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHh
Q psy15697 11 RLSATQVEFILEEIAPALTTPTERNVALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEV 78 (332)
Q Consensus 11 rms~~~F~~L~~~L~~~~~~~~~~~~~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v 78 (332)
=+++.||..+++--.|.+.. ..++--+...-..+=-+ +...|.|...+|...|+|+.||+++=+..
T Consensus 97 ~vs~~Tf~~~~~Ge~P~v~a-~rGG~yV~Idge~Lre~-Ree~glSlG~lA~~lgVSRktV~~YE~G~ 162 (313)
T COG1395 97 AVSPETFYDYVEGEPPYVYA-ARGGFYVKIDGEKLREK-REEMGLSLGDLATMLGVSRKTVYKYEKGL 162 (313)
T ss_pred eeCHHHHHHHhCCCCceEEe-cCCeEEEEechHHHHHH-HHHcCcCHHHHHHHhCccHHHHHHhccCC
Confidence 36889999998844444332 22233333333333222 66789999999999999999999988763
No 402
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=29.39 E-value=1.2e+02 Score=26.28 Aligned_cols=69 Identities=13% Similarity=0.097 Sum_probs=38.0
Q ss_pred cCCHHHHHHHHHHhccCcC-CCCCCCCCCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhH
Q psy15697 11 RLSATQVEFILEEIAPALT-TPTERNVALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVV 79 (332)
Q Consensus 11 rms~~~F~~L~~~L~~~~~-~~~~~~~~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~ 79 (332)
.++.+..+.|...-...-. ....++-.-.-..++.-.+.--..+.+-.++|...|+|+.|+.|++....
T Consensus 129 ~~sQ~~lD~l~~~~~k~~~~~~LPkGi~~~Tl~~i~~~~~~~~~~~Taeela~~~giSRvTaRRYLeyl~ 198 (224)
T COG4565 129 QLSQKELDQLFNIQSKEQPPDDLPKGLDELTLQKVREALKEPDQELTAEELAQALGISRVTARRYLEYLV 198 (224)
T ss_pred ccCHHHHHHHHhccccccCcccCCCCcCHHHHHHHHHHHhCcCCccCHHHHHHHhCccHHHHHHHHHHHH
Confidence 4556666666654322111 11111111112233333343333566778899999999999999987554
No 403
>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=29.39 E-value=23 Score=29.30 Aligned_cols=26 Identities=27% Similarity=0.360 Sum_probs=21.6
Q ss_pred CcccccccccCCChhhHHhHHhHhHH
Q psy15697 55 SPYHIIGATHGPSKSSICRSIHEVVP 80 (332)
Q Consensus 55 ~~~~~l~~~fgis~sTv~r~~~~v~~ 80 (332)
.+++.++..+|+|++||++.+....+
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 36778999999999999998887654
No 404
>PRK09508 leuO leucine transcriptional activator; Reviewed
Probab=29.36 E-value=40 Score=30.60 Aligned_cols=44 Identities=9% Similarity=0.139 Sum_probs=35.0
Q ss_pred HHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHHhh
Q psy15697 43 KVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVDTF 86 (332)
Q Consensus 43 ~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~~l 86 (332)
+.+-++..++...++...|+..+||++||++.+++.-..+...|
T Consensus 25 ~~L~~f~avae~gs~s~AA~~L~isQpavS~~I~~LE~~lg~~L 68 (314)
T PRK09508 25 NLLTVFDAVMQEQNITRAAHNLGMSQPAVSNAVARLKVMFNDEL 68 (314)
T ss_pred HHHHHHHHHHhcCCHHHHHHHhCCCHHHHHHHHHHHHHhhCCCc
Confidence 34455555666677999999999999999999999988887633
No 405
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=29.14 E-value=53 Score=25.98 Aligned_cols=44 Identities=16% Similarity=0.058 Sum_probs=37.2
Q ss_pred HHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 41 KEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 41 ~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
.....-+..++..|.+.+++++..+|+.+|+.++..++...+..
T Consensus 76 ~~~~~~~~~~~~~~~~i~~~a~~l~i~~~~~~r~~~r~~~~~~~ 119 (129)
T COG3677 76 YKIKLQAVTLYMLGLGIRDIARTLGISINTVNRWSKRFGSRVEG 119 (129)
T ss_pred hHHHHHHHHHHHcCCCcccHHHHhcccHHHHHHHHHhhcchhhc
Confidence 44455566777888999999999999999999999999888776
No 406
>smart00497 IENR1 Intron encoded nuclease repeat motif. Repeat of unknown function, but possibly DNA-binding via helix-turn-helix motif (Ponting, unpublished).
Probab=29.11 E-value=22 Score=22.69 Aligned_cols=24 Identities=25% Similarity=0.142 Sum_probs=19.5
Q ss_pred CCcccccccccCCChhhHHhHHhH
Q psy15697 54 GSPYHIIGATHGPSKSSICRSIHE 77 (332)
Q Consensus 54 g~~~~~l~~~fgis~sTv~r~~~~ 77 (332)
-.+..+.|+.+|++.++++++++.
T Consensus 17 f~S~~eAa~~lg~~~~~I~~~~~~ 40 (53)
T smart00497 17 FSSIREAAKYLGISHSSISKYLNT 40 (53)
T ss_pred ecCHHHHHHHhCCCHHHHHHHHhC
Confidence 356677888999999999988764
No 407
>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=29.02 E-value=23 Score=28.80 Aligned_cols=29 Identities=7% Similarity=-0.010 Sum_probs=25.6
Q ss_pred hhhccCCcccccccccCCChhhHHhHHhH
Q psy15697 49 HWMGVGSPYHIIGATHGPSKSSICRSIHE 77 (332)
Q Consensus 49 ~~L~~g~~~~~l~~~fgis~sTv~r~~~~ 77 (332)
.+-..|.++..+|...|||++||+++-+.
T Consensus 33 ~R~~lGmTq~eLAerlGVS~~tIs~iE~G 61 (150)
T TIGR02612 33 IRKALGMSGAQLAGRLGVTPQRVEALEKS 61 (150)
T ss_pred HHHHcCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 35667999999999999999999999874
No 408
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=28.85 E-value=13 Score=29.24 Aligned_cols=58 Identities=17% Similarity=0.230 Sum_probs=38.7
Q ss_pred HHhcCCHHHHHHHHHHhccCcCCCCCCCCCCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHH
Q psy15697 8 EAFRLSATQVEFILEEIAPALTTPTERNVALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVP 80 (332)
Q Consensus 8 ~~frms~~~F~~L~~~L~~~~~~~~~~~~~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~ 80 (332)
-.|..+++.+.+|.+.+...+.+.. +.|.++| .|-+++|...||+.-||+|.....-.
T Consensus 4 i~f~s~~PIY~QI~~qIk~~I~~g~-----l~pGdkL----------PSvRelA~~~~VNpnTv~raY~eLE~ 61 (125)
T COG1725 4 IDFDSSKPIYEQIANQIKEQIASGE-----LKPGDKL----------PSVRELAKDLGVNPNTVQRAYQELER 61 (125)
T ss_pred cCcCCCCCHHHHHHHHHHHHHHhCC-----cCCCCCC----------CcHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 3466778888888888887654321 2222222 35567788899999999987766543
No 409
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=28.68 E-value=42 Score=30.19 Aligned_cols=39 Identities=10% Similarity=0.053 Sum_probs=31.2
Q ss_pred HHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHHh
Q psy15697 47 CLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVDT 85 (332)
Q Consensus 47 ~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~~ 85 (332)
++.-++...++...|+..++|++|||+.+++.-..+-..
T Consensus 12 ~f~~v~~~gs~s~AA~~L~isQ~avS~~i~~LE~~lG~~ 50 (302)
T PRK09791 12 AFVEVARQGSIRGASRMLNMSQPALTKSIQELEEGLAAQ 50 (302)
T ss_pred HHHHHHHcCCHHHHHHHhCCChHHHHHHHHHHHHHhCCe
Confidence 333444445899999999999999999999998887663
No 410
>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=28.63 E-value=59 Score=24.63 Aligned_cols=17 Identities=12% Similarity=0.159 Sum_probs=13.2
Q ss_pred cCCChhhHHhHHhHhHH
Q psy15697 64 HGPSKSSICRSIHEVVP 80 (332)
Q Consensus 64 fgis~sTv~r~~~~v~~ 80 (332)
.++|.+||+|.++.+.+
T Consensus 31 ~~i~~~TVYR~L~~L~~ 47 (116)
T cd07153 31 PSISLATVYRTLELLEE 47 (116)
T ss_pred CCCCHHHHHHHHHHHHh
Confidence 47899999998776554
No 411
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=28.61 E-value=47 Score=29.45 Aligned_cols=39 Identities=13% Similarity=0.059 Sum_probs=28.2
Q ss_pred HHHHHHHhhhccC--CcccccccccCCChhhHHhHHhHhHH
Q psy15697 42 EKVLSCLHWMGVG--SPYHIIGATHGPSKSSICRSIHEVVP 80 (332)
Q Consensus 42 ~~l~~~L~~L~~g--~~~~~l~~~fgis~sTv~r~~~~v~~ 80 (332)
++....|.+|... .+..++++.||||++|+.|.++.+-.
T Consensus 5 ~R~~~Il~~l~~~~~~~~~ela~~l~vS~~TirRdL~~Le~ 45 (251)
T PRK13509 5 QRHQILLELLAQLGFVTVEKVIERLGISPATARRDINKLDE 45 (251)
T ss_pred HHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 3344445555543 56778999999999999999988643
No 412
>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=28.60 E-value=46 Score=29.71 Aligned_cols=39 Identities=10% Similarity=0.150 Sum_probs=30.9
Q ss_pred hccCCcccccccccCCChhhHHhHHhHhHHHHHHhhhcc
Q psy15697 51 MGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVDTFFQR 89 (332)
Q Consensus 51 L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~~l~~~ 89 (332)
++...++...|+..++|+++||+-+++.-..|-..|..+
T Consensus 12 v~~~~s~t~AA~~L~isQpavS~~I~~LE~~lg~~Lf~R 50 (292)
T TIGR03298 12 VVEEGSFERAAAALSVTPSAVSQRIKALEERLGQPLLVR 50 (292)
T ss_pred HHHcCCHHHHHHHhCCCHHHHHHHHHHHHHHhCchheec
Confidence 334458889999999999999999999988776644433
No 413
>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=28.53 E-value=23 Score=23.98 Aligned_cols=21 Identities=10% Similarity=0.032 Sum_probs=17.6
Q ss_pred ccccccccCCChhhHHhHHhH
Q psy15697 57 YHIIGATHGPSKSSICRSIHE 77 (332)
Q Consensus 57 ~~~l~~~fgis~sTv~r~~~~ 77 (332)
..++|..+|||.+|+.++.++
T Consensus 3 ~~eva~~~gvs~~tlr~w~~~ 23 (68)
T cd01104 3 IGAVARLTGVSPDTLRAWERR 23 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 357889999999999998764
No 414
>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=28.36 E-value=75 Score=23.13 Aligned_cols=45 Identities=16% Similarity=0.137 Sum_probs=28.4
Q ss_pred CCCCHHHHHHHHHhhhccCCccccccccc--CCChhhHHhHHhHhHH
Q psy15697 36 VALSAKEKVLSCLHWMGVGSPYHIIGATH--GPSKSSICRSIHEVVP 80 (332)
Q Consensus 36 ~~~~~~~~l~~~L~~L~~g~~~~~l~~~f--gis~sTv~r~~~~v~~ 80 (332)
..+|...+-+.-|+.=--..++.+||..+ .||+|+|...+.++..
T Consensus 36 ~~l~~~l~~~a~lRl~~Pd~SL~EL~~~~~~~iSKSgvnhrlrKl~~ 82 (85)
T PF02650_consen 36 DKLPEKLREFAELRLENPDASLKELGELLEPPISKSGVNHRLRKLKK 82 (85)
T ss_dssp GGS-HHHHHHHHHHHH-TTS-HHHHHHTT--T--HHHHHHHHHHHHH
T ss_pred ccCCHHHHHHHHHHHHCccccHHHHHHHHcCcCcHHHHHHHHHHHHH
Confidence 44666666544444433446999999999 9999999888887654
No 415
>PRK12680 transcriptional regulator CysB-like protein; Reviewed
Probab=28.14 E-value=48 Score=30.49 Aligned_cols=41 Identities=7% Similarity=0.071 Sum_probs=32.8
Q ss_pred Hhhhcc-CCcccccccccCCChhhHHhHHhHhHHHHHHhhhc
Q psy15697 48 LHWMGV-GSPYHIIGATHGPSKSSICRSIHEVVPVIVDTFFQ 88 (332)
Q Consensus 48 L~~L~~-g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~~l~~ 88 (332)
+..++. +.++...|...++|++|||+.+++.-..+...|..
T Consensus 9 F~~vae~~gS~s~AA~~L~isQpavS~~I~~LE~~lG~~LF~ 50 (327)
T PRK12680 9 LVAIADAELNITLAAARVHATQPGLSKQLKQLEDELGFLLFV 50 (327)
T ss_pred HHHHHHccCCHHHHHHHhcCCchHHHHHHHHHHHHhCCeEEE
Confidence 334444 57899999999999999999999999888764443
No 416
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=27.71 E-value=23 Score=24.58 Aligned_cols=26 Identities=15% Similarity=0.134 Sum_probs=22.1
Q ss_pred hccCCcccccccccCCChhhHHhHHh
Q psy15697 51 MGVGSPYHIIGATHGPSKSSICRSIH 76 (332)
Q Consensus 51 L~~g~~~~~l~~~fgis~sTv~r~~~ 76 (332)
-..|.++.++|...|||+.|+..+=+
T Consensus 11 ~~~~ltQ~elA~~vgVsRQTi~~iEk 36 (68)
T COG1476 11 AELGLTQEELAKLVGVSRQTIIAIEK 36 (68)
T ss_pred HHhCcCHHHHHHHcCcCHHHHHHHHc
Confidence 34688999999999999999887765
No 417
>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=27.63 E-value=49 Score=32.99 Aligned_cols=42 Identities=14% Similarity=0.137 Sum_probs=35.8
Q ss_pred CCCCCHHHHHHHHHhhhccCC-cccccccccCCChhhHHhHHh
Q psy15697 35 NVALSAKEKVLSCLHWMGVGS-PYHIIGATHGPSKSSICRSIH 76 (332)
Q Consensus 35 ~~~~~~~~~l~~~L~~L~~g~-~~~~l~~~fgis~sTv~r~~~ 76 (332)
+..++|-++...+...+..+. +...++..||+|+++|++.+.
T Consensus 89 RedLtP~EeA~A~~rLl~~g~~t~eeIA~~lG~S~~~V~rrLk 131 (554)
T TIGR03734 89 RADMSPAEEAEAAARLLGRCKGDREEAARRLGWSPATLDRRLA 131 (554)
T ss_pred cCCCCHHHHHHHHHHHhhhcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 467888888877777777776 788999999999999999886
No 418
>cd00093 HTH_XRE Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.
Probab=27.53 E-value=33 Score=21.09 Aligned_cols=25 Identities=24% Similarity=0.248 Sum_probs=20.8
Q ss_pred ccCCcccccccccCCChhhHHhHHh
Q psy15697 52 GVGSPYHIIGATHGPSKSSICRSIH 76 (332)
Q Consensus 52 ~~g~~~~~l~~~fgis~sTv~r~~~ 76 (332)
..+.+...++...|+|+.+++++.+
T Consensus 10 ~~~~s~~~~a~~~~~~~~~v~~~~~ 34 (58)
T cd00093 10 EKGLTQEELAEKLGVSRSTISRIEN 34 (58)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHc
Confidence 4577888999999999999888765
No 419
>COG2964 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.52 E-value=59 Score=28.18 Aligned_cols=37 Identities=14% Similarity=0.141 Sum_probs=26.7
Q ss_pred HHHHHHHhhhccCCcc-----cccccccCCChhhHHhHHhHh
Q psy15697 42 EKVLSCLHWMGVGSPY-----HIIGATHGPSKSSICRSIHEV 78 (332)
Q Consensus 42 ~~l~~~L~~L~~g~~~-----~~l~~~fgis~sTv~r~~~~v 78 (332)
+..-+++..+..|... ..+|...|+|++||++++++.
T Consensus 174 ~~reiV~~L~EkGiF~lK~Ai~~VA~~L~iSr~TVY~YL~~~ 215 (220)
T COG2964 174 KNREIVKALYEKGIFNLKDAINIVADRLGISRHTVYRYLRKF 215 (220)
T ss_pred HHHHHHHHHHhcCccchhhHHHHHHHHhCCChHHHHHHHHHh
Confidence 3334566666777653 347888999999999999865
No 420
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=27.28 E-value=44 Score=29.68 Aligned_cols=41 Identities=5% Similarity=-0.027 Sum_probs=32.2
Q ss_pred HHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHHhh
Q psy15697 46 SCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVDTF 86 (332)
Q Consensus 46 ~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~~l 86 (332)
-++.-++...++...|+..++|++|||+.+++.-..+...|
T Consensus 9 ~~f~~v~e~~s~t~AA~~L~isqpavS~~I~~LE~~lg~~L 49 (290)
T PRK10837 9 EVFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQL 49 (290)
T ss_pred HHHHHHHHcCCHHHHHHHhCCCccHHHHHHHHHHHHhCCcc
Confidence 34444455568889999999999999999999988776533
No 421
>PRK13832 plasmid partitioning protein; Provisional
Probab=26.86 E-value=54 Score=32.27 Aligned_cols=50 Identities=14% Similarity=0.162 Sum_probs=40.4
Q ss_pred CCCCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHh--HhHHHHHH
Q psy15697 35 NVALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIH--EVVPVIVD 84 (332)
Q Consensus 35 ~~~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~--~v~~~l~~ 84 (332)
+..++|-++...+-.....|.+...||..||+|+++|.+... .+...|.+
T Consensus 99 RedL~PiEea~AfkrLie~G~T~EeIA~~lG~S~~~V~rlllLA~L~P~lLd 150 (520)
T PRK13832 99 REPLNPVDQWRAIERLVALGWTEEAIAVALALPVRQIRKLRLLANVLPAMLD 150 (520)
T ss_pred cCCCCHHHHHHHHHHHHhcCCCHHHHHHHHCCCHHHHHHHHHHcCCCHHHHH
Confidence 467888888888888889999999999999999999988544 24444444
No 422
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=26.51 E-value=1.1e+02 Score=28.09 Aligned_cols=78 Identities=12% Similarity=0.102 Sum_probs=44.2
Q ss_pred HHHHhcCCHHHHHHHHHHhccCcCC-CCCCCCCCCHH-HHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHH
Q psy15697 6 FKEAFRLSATQVEFILEEIAPALTT-PTERNVALSAK-EKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIV 83 (332)
Q Consensus 6 f~~~frms~~~F~~L~~~L~~~~~~-~~~~~~~~~~~-~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~ 83 (332)
|-..++++...-..-...++..... -..++.+.++- -.|.++....+...++.+++...||+..|+.+..+++...+.
T Consensus 226 ~~~~L~L~~~v~~~A~~i~~~a~~~~l~~Gr~P~sIAAAaIYlA~~~~g~~~t~keIa~v~~Vs~~tI~~~ykel~~~l~ 305 (310)
T PRK00423 226 FASELGLSGEVQKKAIEILQKAKEKGLTSGKGPTGLAAAAIYIASLLLGERRTQREVAEVAGVTEVTVRNRYKELAEKLD 305 (310)
T ss_pred HHHHcCCCHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHHHHHhC
Confidence 3445567665554444444332211 11122222221 123333334455678999999999999999998888887653
No 423
>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=26.05 E-value=38 Score=29.75 Aligned_cols=35 Identities=6% Similarity=0.032 Sum_probs=29.4
Q ss_pred hhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 50 WMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 50 ~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
-++...++...|+..++|+|+||+.+++.-..+-.
T Consensus 7 ~v~~~gs~~~AA~~L~isqsavS~~i~~LE~~lg~ 41 (279)
T TIGR03339 7 AVARCGSFTRAAERLGLSQPTVTDQVRKLEERYGV 41 (279)
T ss_pred HHHhcCCHHHHHHHhcCCchHHHHHHHHHHHHhCC
Confidence 34555688899999999999999999998887765
No 424
>COG5593 Nucleic-acid-binding protein possibly involved in ribosomal biogenesis [Translation, ribosomal structure and biogenesis]
Probab=25.92 E-value=1.7e+02 Score=29.02 Aligned_cols=63 Identities=14% Similarity=0.198 Sum_probs=32.8
Q ss_pred HHHHHHHHHHHHHHhhhcccccccccCcccHHHHHHHHHHHHhhcccCCCCCCCCcccCCCCcccCCCc
Q psy15697 228 KRTRRLIENSFGILKEKFPCLNYMRLSPQFAGMVVLASTTLHNIALTIDRDNENQNVEIHDDEAEDDGE 296 (332)
Q Consensus 228 s~~R~~vE~~fg~LK~rf~~L~~~~~~~~~~~~ii~a~~~LhN~~~~~~~~~~~~~~~~~~d~~~~~~~ 296 (332)
.+++..+.++..++-. |..+.......-..-++..||--|-||.-.... +.++++|..|+.++
T Consensus 467 ~rv~af~kr~lQv~S~-w~~~p~~tg~f~~l~ql~~a~~~lk~l~tn~~v-----d~e~e~d~~eeq~d 529 (821)
T COG5593 467 HRVDAFRKRALQVISG-WMVLPFDTGDFMSLLQLEMACGDLKNLLTNTPV-----DYEYESDAEEEQGD 529 (821)
T ss_pred hHHHHHHHHHHHHhhc-cccCCccchHHHHHHHHHHHhHHHHHHhcCCCc-----ccccccchhhhhcc
Confidence 3344444555544443 444422222333456778999999999854333 23444444444433
No 425
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=25.91 E-value=24 Score=26.73 Aligned_cols=26 Identities=15% Similarity=0.115 Sum_probs=20.0
Q ss_pred hccCCcccccccccCCChhhHHhHHh
Q psy15697 51 MGVGSPYHIIGATHGPSKSSICRSIH 76 (332)
Q Consensus 51 L~~g~~~~~l~~~fgis~sTv~r~~~ 76 (332)
=+.+.++..-|..+|+|.+||..|=.
T Consensus 54 e~~~lSQ~vFA~~L~vs~~Tv~~WEq 79 (104)
T COG2944 54 EKLGLSQPVFARYLGVSVSTVRKWEQ 79 (104)
T ss_pred HHhCCCHHHHHHHHCCCHHHHHHHHc
Confidence 34678888888888888888887643
No 426
>PRK09801 transcriptional activator TtdR; Provisional
Probab=25.77 E-value=57 Score=29.62 Aligned_cols=39 Identities=15% Similarity=0.177 Sum_probs=31.0
Q ss_pred HHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHHh
Q psy15697 47 CLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVDT 85 (332)
Q Consensus 47 ~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~~ 85 (332)
++..++...++...|+.+++|++|||+.+++.-..+-..
T Consensus 13 ~F~~v~~~gs~t~AA~~L~iSQpavS~~I~~LE~~LG~~ 51 (310)
T PRK09801 13 VLVEIVHSGSFSAAAATLGQTPAFVTKRIQILENTLATT 51 (310)
T ss_pred HHHHHHHcCCHHHHHHHhCcCHHHHHHHHHHHHHHhCCE
Confidence 334445556788899999999999999999998887653
No 427
>COG5566 Uncharacterized conserved protein [Function unknown]
Probab=25.67 E-value=35 Score=26.73 Aligned_cols=28 Identities=25% Similarity=0.240 Sum_probs=24.0
Q ss_pred cCCcccccccccCCChhhHHhHHhHhHH
Q psy15697 53 VGSPYHIIGATHGPSKSSICRSIHEVVP 80 (332)
Q Consensus 53 ~g~~~~~l~~~fgis~sTv~r~~~~v~~ 80 (332)
.|..+.+|+..+.+|.++|.++++++..
T Consensus 101 dG~n~~eLaKkYrlS~~~Iy~VIrr~~t 128 (137)
T COG5566 101 DGSNYVELAKKYRLSENHIYRVIRRTHT 128 (137)
T ss_pred CCccHHHHHHHhcccHHHHHHHHHHHHH
Confidence 3778889999999999999999996654
No 428
>PRK06474 hypothetical protein; Provisional
Probab=25.60 E-value=53 Score=27.50 Aligned_cols=27 Identities=7% Similarity=0.048 Sum_probs=20.9
Q ss_pred Cccccccccc-CCChhhHHhHHhHhHHH
Q psy15697 55 SPYHIIGATH-GPSKSSICRSIHEVVPV 81 (332)
Q Consensus 55 ~~~~~l~~~f-gis~sTv~r~~~~v~~~ 81 (332)
.+-.+|+..+ ++|++||++.++.+.++
T Consensus 27 ~ta~el~~~l~~is~aTvYrhL~~L~e~ 54 (178)
T PRK06474 27 LTPLELVKILKDVPQATLYRHLQTMVDS 54 (178)
T ss_pred CCHHHHHHHhcCCCHHHHHHHHHHHHHC
Confidence 5666777777 79999999998876653
No 429
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=25.40 E-value=28 Score=27.13 Aligned_cols=25 Identities=12% Similarity=-0.037 Sum_probs=22.4
Q ss_pred ccCCcccccccccCCChhhHHhHHh
Q psy15697 52 GVGSPYHIIGATHGPSKSSICRSIH 76 (332)
Q Consensus 52 ~~g~~~~~l~~~fgis~sTv~r~~~ 76 (332)
..|.++.++|...|||++|++++.+
T Consensus 16 ~~Glsq~eLA~~~Gis~~~is~iE~ 40 (120)
T PRK13890 16 ERHMTKKELSERSGVSISFLSDLTT 40 (120)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHc
Confidence 4678899999999999999999886
No 430
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=25.28 E-value=49 Score=30.39 Aligned_cols=33 Identities=21% Similarity=0.338 Sum_probs=25.0
Q ss_pred HhhhccC--CcccccccccCCChhhHHhHHhHhHH
Q psy15697 48 LHWMGVG--SPYHIIGATHGPSKSSICRSIHEVVP 80 (332)
Q Consensus 48 L~~L~~g--~~~~~l~~~fgis~sTv~r~~~~v~~ 80 (332)
|..|..+ .+..++|..+|+|++||++.+.....
T Consensus 10 l~~L~~~~~~s~~~LA~~lgvsr~tV~~~l~~L~~ 44 (319)
T PRK11886 10 LSLLADGDFHSGEQLGEELGISRAAIWKHIQTLEE 44 (319)
T ss_pred HHHHHcCCCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3444443 45667999999999999999988764
No 431
>PRK10632 transcriptional regulator; Provisional
Probab=25.04 E-value=45 Score=30.20 Aligned_cols=37 Identities=11% Similarity=-0.004 Sum_probs=30.6
Q ss_pred HhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 48 LHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 48 L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
+..++...++...|+..++|+++||+.+++.-..+-.
T Consensus 10 F~~v~e~gS~t~AA~~L~isQpavS~~I~~LE~~lg~ 46 (309)
T PRK10632 10 FAKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQV 46 (309)
T ss_pred HHHHHhcCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 3445566788899999999999999999998887765
No 432
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=24.97 E-value=55 Score=29.06 Aligned_cols=40 Identities=5% Similarity=-0.045 Sum_probs=32.7
Q ss_pred HHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHHh
Q psy15697 46 SCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVDT 85 (332)
Q Consensus 46 ~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~~ 85 (332)
-++..++...++...|+..++|++|+|+.+.+.-..+...
T Consensus 7 ~~f~~v~~~gs~s~AA~~L~isqpavS~~I~~LE~~lG~~ 46 (275)
T PRK03601 7 KTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVN 46 (275)
T ss_pred HHHHHHHHcCCHHHHHHHhCCChHHHHHHHHHHHHHhCCc
Confidence 3455566677888899999999999999999998877653
No 433
>PRK15186 AraC family transcriptional regulator; Provisional
Probab=24.91 E-value=1.2e+02 Score=27.65 Aligned_cols=72 Identities=6% Similarity=0.027 Sum_probs=50.8
Q ss_pred ChhHHHHHhcCCHHHHHHHHHHhccCcCCCCCCCCCCCHHHHHHHHHhhhccC-CcccccccccCCC-hhhHHhHHhHhH
Q psy15697 2 TPFAFKEAFRLSATQVEFILEEIAPALTTPTERNVALSAKEKVLSCLHWMGVG-SPYHIIGATHGPS-KSSICRSIHEVV 79 (332)
Q Consensus 2 ~d~~f~~~frms~~~F~~L~~~L~~~~~~~~~~~~~~~~~~~l~~~L~~L~~g-~~~~~l~~~fgis-~sTv~r~~~~v~ 79 (332)
+-+++-..++||+.+|..++....... ...-...++..++..|..+ .+..++|...|-+ .|..++.|++..
T Consensus 199 sl~~lA~~~gmS~stl~R~Fk~~g~s~-------~~~~~~~Rl~~A~~lL~~~~~sI~~IA~~~GY~s~S~Fsr~FK~~~ 271 (291)
T PRK15186 199 ALKDISDSLYMSCSTLKRKLKQENTSF-------SEVYLNARMNKATKLLRNSEYNITRVAYMCGYDSASYFTCVFKKHF 271 (291)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHcCCCH-------HHHHHHHHHHHHHHHHHcCCCCHHHHHHHhCCCCHHHHHHHHHHHH
Confidence 346677889999999999987632111 1112256777788888775 6999999999974 666788887765
Q ss_pred H
Q psy15697 80 P 80 (332)
Q Consensus 80 ~ 80 (332)
.
T Consensus 272 G 272 (291)
T PRK15186 272 K 272 (291)
T ss_pred C
Confidence 3
No 434
>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=24.58 E-value=54 Score=25.52 Aligned_cols=27 Identities=15% Similarity=0.153 Sum_probs=22.7
Q ss_pred CCcccccccccCCChhhHHhHHhHhHH
Q psy15697 54 GSPYHIIGATHGPSKSSICRSIHEVVP 80 (332)
Q Consensus 54 g~~~~~l~~~fgis~sTv~r~~~~v~~ 80 (332)
..+..+++..++++++++.+++.....
T Consensus 25 ~~s~~eia~~~~i~~~~v~~il~~L~~ 51 (132)
T TIGR00738 25 PVSVKEIAERQGISRSYLEKILRTLRR 51 (132)
T ss_pred cCcHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 457778999999999999998887665
No 435
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=24.56 E-value=48 Score=29.55 Aligned_cols=36 Identities=6% Similarity=0.089 Sum_probs=29.4
Q ss_pred hccCCcccccccccCCChhhHHhHHhHhHHHHHHhh
Q psy15697 51 MGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVDTF 86 (332)
Q Consensus 51 L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~~l 86 (332)
+....++...|+..++|+||||+.+++.-..+...|
T Consensus 12 v~~~gs~s~AA~~L~isqsavS~~i~~LE~~lg~~L 47 (296)
T PRK11242 12 VAEHGNFTRAAEALHVSQPTLSQQIRQLEESLGVQL 47 (296)
T ss_pred HHHhCCHHHHHHHcCCCchHHHHHHHHHHHHhCCee
Confidence 334458889999999999999999999988776533
No 436
>PRK13348 chromosome replication initiation inhibitor protein; Provisional
Probab=24.54 E-value=53 Score=29.32 Aligned_cols=38 Identities=5% Similarity=0.051 Sum_probs=30.5
Q ss_pred hhccCCcccccccccCCChhhHHhHHhHhHHHHHHhhh
Q psy15697 50 WMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVDTFF 87 (332)
Q Consensus 50 ~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~~l~ 87 (332)
-++...++...|+..++|++|||+.+++.-..+-..|.
T Consensus 12 ~v~~~gs~t~AA~~L~iSQ~avS~~i~~LE~~lg~~Lf 49 (294)
T PRK13348 12 AVVETGSFERAARRLHVTPSAVSQRIKALEESLGQPLL 49 (294)
T ss_pred HHHHcCCHHHHHHHhCCCchHHHHHHHHHHHHhCceee
Confidence 33444588899999999999999999999887766443
No 437
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=24.52 E-value=30 Score=29.00 Aligned_cols=26 Identities=15% Similarity=0.132 Sum_probs=23.2
Q ss_pred ccCCcccccccccCCChhhHHhHHhH
Q psy15697 52 GVGSPYHIIGATHGPSKSSICRSIHE 77 (332)
Q Consensus 52 ~~g~~~~~l~~~fgis~sTv~r~~~~ 77 (332)
..|.++..+|...|+|++|++++.+.
T Consensus 18 ~~glt~~elA~~~gis~~~is~~E~g 43 (185)
T PRK09943 18 QQGLSQRRAAELSGLTHSAISTIEQD 43 (185)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHcC
Confidence 46889999999999999999998873
No 438
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=24.36 E-value=57 Score=28.32 Aligned_cols=26 Identities=12% Similarity=0.155 Sum_probs=22.8
Q ss_pred CcccccccccCCChhhHHhHHhHhHH
Q psy15697 55 SPYHIIGATHGPSKSSICRSIHEVVP 80 (332)
Q Consensus 55 ~~~~~l~~~fgis~sTv~r~~~~v~~ 80 (332)
.+..+++..+++|++|+++.+.+...
T Consensus 22 IS~~eLA~~L~iS~~Tvsr~Lk~LEe 47 (217)
T PRK14165 22 ISSSEFANHTGTSSKTAARILKQLED 47 (217)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 56789999999999999999988754
No 439
>PRK01905 DNA-binding protein Fis; Provisional
Probab=24.17 E-value=63 Score=22.84 Aligned_cols=27 Identities=7% Similarity=0.238 Sum_probs=21.7
Q ss_pred ccCCcccccccccCCChhhHHhHHhHh
Q psy15697 52 GVGSPYHIIGATHGPSKSSICRSIHEV 78 (332)
Q Consensus 52 ~~g~~~~~l~~~fgis~sTv~r~~~~v 78 (332)
.++......|...|||++|+.+.+++.
T Consensus 48 ~~~gn~s~aAr~LGIsrstL~rklkk~ 74 (77)
T PRK01905 48 QAGGNQSLAAEYLGINRNTLRKKLQQH 74 (77)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHHh
Confidence 345567788999999999999887763
No 440
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=24.16 E-value=61 Score=28.81 Aligned_cols=40 Identities=5% Similarity=0.145 Sum_probs=30.0
Q ss_pred HHHHHHHHhhhccC--CcccccccccCCChhhHHhHHhHhHH
Q psy15697 41 KEKVLSCLHWMGVG--SPYHIIGATHGPSKSSICRSIHEVVP 80 (332)
Q Consensus 41 ~~~l~~~L~~L~~g--~~~~~l~~~fgis~sTv~r~~~~v~~ 80 (332)
+++....|.+|... .+..+|++.|+||..||.|-+...-.
T Consensus 4 ~eR~~~Il~~L~~~~~v~v~eLa~~l~VS~~TIRRDL~~Le~ 45 (256)
T PRK10434 4 RQRQAAILEYLQKQGKTSVEELAQYFDTTGTTIRKDLVILEH 45 (256)
T ss_pred HHHHHHHHHHHHHcCCEEHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 44555566666643 47788999999999999999887543
No 441
>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=24.15 E-value=41 Score=27.79 Aligned_cols=38 Identities=18% Similarity=0.211 Sum_probs=30.0
Q ss_pred HHHHHHHHhhhccCCcccccccccC-CChhhHHhHHhHh
Q psy15697 41 KEKVLSCLHWMGVGSPYHIIGATHG-PSKSSICRSIHEV 78 (332)
Q Consensus 41 ~~~l~~~L~~L~~g~~~~~l~~~fg-is~sTv~r~~~~v 78 (332)
++++...-..++.|.+...||..+| ||+..|.-.+++.
T Consensus 5 de~~~~L~~lw~~G~SasqIA~~lg~vsRnAViGk~hRl 43 (162)
T PF07750_consen 5 DERVERLRKLWAEGLSASQIARQLGGVSRNAVIGKAHRL 43 (162)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHhCCcchhhhhhhhhcc
Confidence 3455555566789999999999999 9999887777763
No 442
>PF01526 DDE_Tnp_Tn3: Tn3 transposase DDE domain; InterPro: IPR002513 Proteins containing this domain include transposases of Tn3, Tn21, Tn1721, Tn2501, Tn3926 transposons from Escherichia coli. The specific binding of the Tn3 transposase to DNA has been demonstrated. Sequence analysis has suggested that the invariant triad of Asp689, Asp765, Glu895 (numbering as in Tn3) may correspond to the D-D-35-E motif previously implicated in the catalytic performance of numerous transposases [].; GO: 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=24.13 E-value=5.6e+02 Score=24.43 Aligned_cols=87 Identities=13% Similarity=0.104 Sum_probs=53.4
Q ss_pred CCCCCHHHHHHHHHhhhccCCccccccc-ccCCChhhHHhHHhHhH-----HHHHHhhhccccCCCcccccchhhhhhhc
Q psy15697 35 NVALSAKEKVLSCLHWMGVGSPYHIIGA-THGPSKSSICRSIHEVV-----PVIVDTFFQRMVKWPEENLNDIPMTFLRK 108 (332)
Q Consensus 35 ~~~~~~~~~l~~~L~~L~~g~~~~~l~~-~fgis~sTv~r~~~~v~-----~~l~~~l~~~~I~~P~~~~~~~~~~f~~~ 108 (332)
.+.-+....|+++|.=++.+.....+|. .-++|...+..+-.+.+ .+-...+...+.+.|-. +.
T Consensus 24 ~k~~~~~~~llA~l~A~GtNlGl~~mA~~~~~is~~~L~~v~~~~i~~etl~~An~~ivna~~~lpl~----------~~ 93 (388)
T PF01526_consen 24 AKPKDDQRRLLAALFAYGTNLGLKRMARASPGISYDQLSWVNRWYIREETLRAANARIVNAQHKLPLA----------KY 93 (388)
T ss_pred CCccchHHHHHHHHHHhhhCCChHHHhhcCCCCCHHHHHHHHHHHHhHHHHHHHHHHHHHHHHhCChH----------HH
Confidence 3456677888889998888888888888 67888776655544332 11111122222223321 33
Q ss_pred CCCCCceeeecceEEEEeCCCCCc
Q psy15697 109 GGFPNVAGCVDGTMVLIDAPNEHE 132 (332)
Q Consensus 109 ~~~p~~~G~iDgt~i~i~~P~~~~ 132 (332)
+| -+-..+.||+.+++..++-..
T Consensus 94 wG-~g~~aSsDGq~f~~~~~~~~a 116 (388)
T PF01526_consen 94 WG-DGTTASSDGQKFETSDQNLNA 116 (388)
T ss_pred cC-CCceeccceeEEEeecCccch
Confidence 34 244568999999998775543
No 443
>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=24.03 E-value=51 Score=23.52 Aligned_cols=26 Identities=15% Similarity=0.129 Sum_probs=19.9
Q ss_pred CcccccccccCCChhhHHhHHhHhHH
Q psy15697 55 SPYHIIGATHGPSKSSICRSIHEVVP 80 (332)
Q Consensus 55 ~~~~~l~~~fgis~sTv~r~~~~v~~ 80 (332)
.+..++|+..++|++++.+++.....
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 46678999999999988888776544
No 444
>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=24.01 E-value=53 Score=29.41 Aligned_cols=36 Identities=3% Similarity=0.077 Sum_probs=29.5
Q ss_pred hhccCCcccccccccCCChhhHHhHHhHhHHHHHHh
Q psy15697 50 WMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVDT 85 (332)
Q Consensus 50 ~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~~ 85 (332)
-+....++...|+..++|+++||+.+++.-..+...
T Consensus 13 ~v~~~gS~s~AA~~L~isq~avS~~I~~LE~~lg~~ 48 (300)
T TIGR02424 13 EVARQGSVKRAAEALHITQPAVSKTLRELEEILGTP 48 (300)
T ss_pred HHHHhCCHHHHHHHhCCChHHHHHHHHHHHHHhCCe
Confidence 334455888899999999999999999988877653
No 445
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=23.98 E-value=58 Score=26.39 Aligned_cols=34 Identities=12% Similarity=0.037 Sum_probs=28.8
Q ss_pred hhccCCcccccccccCCChhhHHhHHhHhHHHHH
Q psy15697 50 WMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIV 83 (332)
Q Consensus 50 ~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~ 83 (332)
.+..|.+...++..+|+|..||..++.+...-+.
T Consensus 152 ~~~~~~~~~~ia~~l~~s~~tv~~~~~~~~~kl~ 185 (202)
T PRK09390 152 GLVAGLSNKVIARDLDISPRTVEVYRANVMTKMQ 185 (202)
T ss_pred HHHccCchHHHHHHcCCCHHHHHHHHHHHHHHHc
Confidence 4666888999999999999999999888777654
No 446
>PRK04841 transcriptional regulator MalT; Provisional
Probab=23.94 E-value=48 Score=35.03 Aligned_cols=46 Identities=15% Similarity=0.126 Sum_probs=36.7
Q ss_pred CCCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHH
Q psy15697 36 VALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIV 83 (332)
Q Consensus 36 ~~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~ 83 (332)
..+++.+.= .|.+++.|.+.++||...+||.+||...++++..-+.
T Consensus 837 ~~lt~~e~~--v~~~~~~g~~~~~ia~~l~~s~~tv~~h~~~~~~kl~ 882 (903)
T PRK04841 837 SPLTQREWQ--VLGLIYSGYSNEQIAGELDVAATTIKTHIRNLYQKLG 882 (903)
T ss_pred CCCCHHHHH--HHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 346655544 5566999999999999999999999999988776554
No 447
>PRK06424 transcription factor; Provisional
Probab=23.86 E-value=39 Score=27.29 Aligned_cols=33 Identities=9% Similarity=-0.102 Sum_probs=26.1
Q ss_pred HHHHHhhh--ccCCcccccccccCCChhhHHhHHh
Q psy15697 44 VLSCLHWM--GVGSPYHIIGATHGPSKSSICRSIH 76 (332)
Q Consensus 44 l~~~L~~L--~~g~~~~~l~~~fgis~sTv~r~~~ 76 (332)
+.--|..+ ..|.++.+||...|++++|+++|.+
T Consensus 85 ~g~~Ir~lRe~~GLSQ~eLA~~iGvs~stIskiE~ 119 (144)
T PRK06424 85 YAELVKNARERLSMSQADLAAKIFERKNVIASIER 119 (144)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHC
Confidence 33334444 4789999999999999999999886
No 448
>PRK09986 DNA-binding transcriptional activator XapR; Provisional
Probab=23.83 E-value=59 Score=28.89 Aligned_cols=41 Identities=12% Similarity=0.005 Sum_probs=31.5
Q ss_pred HHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHHh
Q psy15697 44 VLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVDT 85 (332)
Q Consensus 44 l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~~ 85 (332)
+-+++....+ .++...|...+||+|+||+.+++.-..+...
T Consensus 12 l~~f~~v~~~-gs~t~AA~~L~itq~avS~~i~~LE~~lg~~ 52 (294)
T PRK09986 12 LRYFLAVAEE-LHFGRAAARLNISQPPLSIHIKELEDQLGTP 52 (294)
T ss_pred HHHHHHHHHh-cCHHHHHHHhCCCCCHHHHHHHHHHHHhCCe
Confidence 3344444444 4888899999999999999999998887653
No 449
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=23.44 E-value=63 Score=27.18 Aligned_cols=39 Identities=15% Similarity=0.049 Sum_probs=27.8
Q ss_pred HHHHHHHHhhhccC--CcccccccccCCChhhHHhHHhHhH
Q psy15697 41 KEKVLSCLHWMGVG--SPYHIIGATHGPSKSSICRSIHEVV 79 (332)
Q Consensus 41 ~~~l~~~L~~L~~g--~~~~~l~~~fgis~sTv~r~~~~v~ 79 (332)
.++....|.+|... .+..+|+..||+|.+|+.|=+....
T Consensus 6 ~~R~~~Il~~l~~~~~~~~~~La~~~~vS~~TiRRDl~~L~ 46 (185)
T PRK04424 6 KERQKALQELIEENPFITDEELAEKFGVSIQTIRLDRMELG 46 (185)
T ss_pred HHHHHHHHHHHHHCCCEEHHHHHHHHCcCHHHHHHHHHHHh
Confidence 34444455555543 3567899999999999999888654
No 450
>PRK10086 DNA-binding transcriptional regulator DsdC; Provisional
Probab=23.42 E-value=58 Score=29.51 Aligned_cols=40 Identities=8% Similarity=0.091 Sum_probs=32.8
Q ss_pred HHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 45 LSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 45 ~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
+-++..++...++...|...|+|++|||+-+++.-..+..
T Consensus 19 L~~f~~va~~gs~s~AA~~L~iSQpavS~~I~~LE~~lG~ 58 (311)
T PRK10086 19 LHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGI 58 (311)
T ss_pred HHHHHHHHHcCCHHHHHHHHCCCHHHHHHHHHHHHHHhCC
Confidence 3445555667788899999999999999999999888755
No 451
>COG3093 VapI Plasmid maintenance system antidote protein [General function prediction only]
Probab=23.15 E-value=33 Score=25.96 Aligned_cols=24 Identities=17% Similarity=0.281 Sum_probs=22.3
Q ss_pred CCcccccccccCCChhhHHhHHhH
Q psy15697 54 GSPYHIIGATHGPSKSSICRSIHE 77 (332)
Q Consensus 54 g~~~~~l~~~fgis~sTv~r~~~~ 77 (332)
|.+...+|...||++.|++++++.
T Consensus 23 glt~~~lA~~lgV~r~~is~ling 46 (104)
T COG3093 23 GLTQTELAEALGVTRNTISELING 46 (104)
T ss_pred cCCHHHHHHHhCCCHHHHHHHHcC
Confidence 789999999999999999999984
No 452
>COG2973 TrpR Trp operon repressor [Transcription]
Probab=23.13 E-value=47 Score=24.79 Aligned_cols=32 Identities=19% Similarity=0.104 Sum_probs=25.0
Q ss_pred HHHHHHhhhccCCcccccccccCCChhhHHhH
Q psy15697 43 KVLSCLHWMGVGSPYHIIGATHGPSKSSICRS 74 (332)
Q Consensus 43 ~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~ 74 (332)
++-+.=-.|....++++++..+|+|..|+.|=
T Consensus 49 Rv~Iv~eLL~ge~sQREi~~~LgvsiAtITRG 80 (103)
T COG2973 49 RVRIVEELLRGELSQREIAQKLGVSIATITRG 80 (103)
T ss_pred HHHHHHHHHhccccHHHHHHHhCcchhhhccc
Confidence 34444455778899999999999999988653
No 453
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=22.77 E-value=70 Score=28.37 Aligned_cols=38 Identities=8% Similarity=0.077 Sum_probs=26.8
Q ss_pred HHHHHHhhhccC--CcccccccccCCChhhHHhHHhHhHH
Q psy15697 43 KVLSCLHWMGVG--SPYHIIGATHGPSKSSICRSIHEVVP 80 (332)
Q Consensus 43 ~l~~~L~~L~~g--~~~~~l~~~fgis~sTv~r~~~~v~~ 80 (332)
+....|.+|... .+..+|++.|+||..|+.|-+....+
T Consensus 6 R~~~Il~~l~~~~~~~~~ela~~l~vS~~TiRRdL~~Le~ 45 (252)
T PRK10906 6 RHDAIIELVKQQGYVSTEELVEHFSVSPQTIRRDLNDLAE 45 (252)
T ss_pred HHHHHHHHHHHcCCEeHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 333344444433 46678999999999999998877654
No 454
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=22.64 E-value=36 Score=27.84 Aligned_cols=33 Identities=9% Similarity=-0.096 Sum_probs=26.4
Q ss_pred HHHHHhhhc--cCCcccccccccCCChhhHHhHHh
Q psy15697 44 VLSCLHWMG--VGSPYHIIGATHGPSKSSICRSIH 76 (332)
Q Consensus 44 l~~~L~~L~--~g~~~~~l~~~fgis~sTv~r~~~ 76 (332)
+.-.|..++ .|.++..||...|+|++++++|-+
T Consensus 70 ~g~~Ir~~Re~~glSqeeLA~~lgvs~s~IsriE~ 104 (154)
T TIGR00270 70 YGIIIRREREKRGWSQEQLAKKIQEKESLIKKIEN 104 (154)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHC
Confidence 334455444 689999999999999999999876
No 455
>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function.
Probab=22.46 E-value=1e+02 Score=23.54 Aligned_cols=26 Identities=19% Similarity=0.169 Sum_probs=21.5
Q ss_pred CChhHHHHHhcCCHHHHHHHHHHhcc
Q psy15697 1 MTPFAFKEAFRLSATQVEFILEEIAP 26 (332)
Q Consensus 1 ~~d~~f~~~frms~~~F~~L~~~L~~ 26 (332)
|+.++.-...++|+.||..++..-+.
T Consensus 58 l~QeeaA~~MgVSR~T~~ril~~ARk 83 (106)
T PF02001_consen 58 LSQEEAAERMGVSRPTFQRILESARK 83 (106)
T ss_pred CCHHHHHHHcCCcHHHHHHHHHHHHH
Confidence 56678888999999999999986543
No 456
>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=22.44 E-value=60 Score=29.26 Aligned_cols=39 Identities=8% Similarity=0.074 Sum_probs=31.7
Q ss_pred HHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 46 SCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 46 ~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
-++.-++...++...|+.+++|++|||+-++..-..+..
T Consensus 14 ~~F~~va~~gs~s~AA~~L~isQpavS~~I~~LE~~lg~ 52 (302)
T TIGR02036 14 HTFEVAARHQSFSLAAEELSLTPSAISHRINQLEEELGI 52 (302)
T ss_pred HHHHHHHHhCCHHHHHHHHCCCHHHHHHHHHHHHHHhCC
Confidence 344445666788889999999999999999998887765
No 457
>PF07037 DUF1323: Putative transcription regulator (DUF1323); InterPro: IPR010749 This family consists of several hypothetical Enterobacterial proteins of around 120 residues in length. The function of this family is unknown.
Probab=22.36 E-value=37 Score=26.35 Aligned_cols=21 Identities=19% Similarity=0.238 Sum_probs=17.6
Q ss_pred ccccccccCCChhhHHhHHhH
Q psy15697 57 YHIIGATHGPSKSSICRSIHE 77 (332)
Q Consensus 57 ~~~l~~~fgis~sTv~r~~~~ 77 (332)
-.+||+..|+|+.||+|++++
T Consensus 3 ~eELA~~tG~srQTINrWvRk 23 (122)
T PF07037_consen 3 PEELAELTGYSRQTINRWVRK 23 (122)
T ss_pred HHHHHHHhCccHHHHHHHHHh
Confidence 346889999999999998864
No 458
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=22.28 E-value=60 Score=26.05 Aligned_cols=34 Identities=18% Similarity=0.185 Sum_probs=23.8
Q ss_pred CcccccccccCCChhhHHhHHh--H-hHHHHHHhhhcc
Q psy15697 55 SPYHIIGATHGPSKSSICRSIH--E-VVPVIVDTFFQR 89 (332)
Q Consensus 55 ~~~~~l~~~fgis~sTv~r~~~--~-v~~~l~~~l~~~ 89 (332)
.++..+|...||+++|+++|-+ + ++..+.. +..+
T Consensus 35 ~T~~eiAee~Gis~~tLYrWr~~~~~Fiey~n~-la~~ 71 (142)
T PF13022_consen 35 RTQAEIAEEVGISRSTLYRWRQQNKAFIEYKNE-LADR 71 (142)
T ss_dssp S-HHHHHHHHTS-HHHHHHHHHH-HHHHHHHHH-HHHH
T ss_pred chHHHHHHHhCCCHHHHHHHHhcCHHHHHHHHH-HHHH
Confidence 5688899999999999999985 2 5555554 4433
No 459
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=22.23 E-value=47 Score=23.73 Aligned_cols=29 Identities=3% Similarity=0.203 Sum_probs=22.4
Q ss_pred cCCcccccccccCCChhhHHhHHhHhHHH
Q psy15697 53 VGSPYHIIGATHGPSKSSICRSIHEVVPV 81 (332)
Q Consensus 53 ~g~~~~~l~~~fgis~sTv~r~~~~v~~~ 81 (332)
...++..|.+..|++.+++++.+....++
T Consensus 13 ~~~~f~~L~~~l~lt~g~Ls~hL~~Le~~ 41 (80)
T PF13601_consen 13 EEATFSELKEELGLTDGNLSKHLKKLEEA 41 (80)
T ss_dssp SEEEHHHHHHHTT--HHHHHHHHHHHHHT
T ss_pred CCCCHHHHHHHhCcCHHHHHHHHHHHHHC
Confidence 45789999999999999999988776553
No 460
>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=22.09 E-value=71 Score=21.91 Aligned_cols=67 Identities=18% Similarity=0.072 Sum_probs=32.9
Q ss_pred HHHHHhcCCHHHHHHHHHHhccCcCCCC-CCCCCCC-HHHHHHHHHhhhccCCcccccccccCCChhhH
Q psy15697 5 AFKEAFRLSATQVEFILEEIAPALTTPT-ERNVALS-AKEKVLSCLHWMGVGSPYHIIGATHGPSKSSI 71 (332)
Q Consensus 5 ~f~~~frms~~~F~~L~~~L~~~~~~~~-~~~~~~~-~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv 71 (332)
.|-..++++.+.-+.=.+..+....... .++.+.+ .--.|.++.+......++.+++...+|++.|+
T Consensus 3 r~~~~L~L~~~v~~~A~~i~~~~~~~~~~~Gr~~~~iaAA~iY~acr~~~~~~t~~eIa~~~~Vs~~tI 71 (71)
T PF00382_consen 3 RICSKLGLPEDVRERAKEIYKKAQERGLLKGRSPESIAAACIYLACRLNGVPRTLKEIAEAAGVSEKTI 71 (71)
T ss_dssp HHHHHTT--HHHHHHHHHHHHHHHHTTTSTTS-HHHHHHHHHHHHHHHTTSSSSHHHHHHHCTSSHHHH
T ss_pred HHHhHcCCCHHHHHHHHHHHHHHHHcCCcccCCHHHHHHHHHHHHHHHcCCCcCHHHHHHHhCCCCCcC
Confidence 3455667776554444444333222111 1111111 11123333344456678899999999998875
No 461
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=21.94 E-value=65 Score=28.36 Aligned_cols=27 Identities=19% Similarity=0.226 Sum_probs=23.6
Q ss_pred CCcccccccccCCChhhHHhHHhHhHH
Q psy15697 54 GSPYHIIGATHGPSKSSICRSIHEVVP 80 (332)
Q Consensus 54 g~~~~~l~~~fgis~sTv~r~~~~v~~ 80 (332)
..+..++++.||||+.|+.|.+.+...
T Consensus 18 ~~~~~eLa~~l~VS~~TiRRdL~~L~~ 44 (240)
T PRK10411 18 SLTTEALAEQLNVSKETIRRDLNELQT 44 (240)
T ss_pred CCcHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 457788999999999999999998765
No 462
>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=21.88 E-value=90 Score=26.04 Aligned_cols=42 Identities=14% Similarity=0.062 Sum_probs=37.4
Q ss_pred CCCCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHh
Q psy15697 35 NVALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIH 76 (332)
Q Consensus 35 ~~~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~ 76 (332)
...+|-+.+-.|.-.+...|.+.+.||..|||+...|.-|++
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 466888999999999999999999999999999999887776
No 463
>PRK11564 stationary phase inducible protein CsiE; Provisional
Probab=21.86 E-value=1.1e+02 Score=29.26 Aligned_cols=49 Identities=16% Similarity=0.136 Sum_probs=35.5
Q ss_pred CCCCHHHHHHH-HHhhhc--cCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 36 VALSAKEKVLS-CLHWMG--VGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 36 ~~~~~~~~l~~-~L~~L~--~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
.-++++++... .+..|- .+.+...+++.++||++|+.+-++++-..|..
T Consensus 9 ~~~s~~ER~~~il~~LL~~~~~v~l~~Lae~l~VSrsTi~~DLk~l~~~L~~ 60 (426)
T PRK11564 9 SVLSAPQRRCQILLMLFQPGLTVTLETFSQLNGVDDDTARQDIAETGREIQR 60 (426)
T ss_pred cCCCHHHHHHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 34566666443 333343 34577889999999999999999998887765
No 464
>COG3311 AlpA Predicted transcriptional regulator [Transcription]
Probab=21.77 E-value=30 Score=24.18 Aligned_cols=23 Identities=26% Similarity=0.293 Sum_probs=18.6
Q ss_pred cccccccccCCChhhHHhHHhHh
Q psy15697 56 PYHIIGATHGPSKSSICRSIHEV 78 (332)
Q Consensus 56 ~~~~l~~~fgis~sTv~r~~~~v 78 (332)
...+++...|+|++|+++.+++-
T Consensus 15 rl~ev~~~~GlSrstiYr~i~~~ 37 (70)
T COG3311 15 RLPEVAQLTGLSRSTIYRLIKDG 37 (70)
T ss_pred hHHHHHHHHCccHHHHHHHHccC
Confidence 34567788999999999988765
No 465
>PRK10216 DNA-binding transcriptional regulator YidZ; Provisional
Probab=21.44 E-value=66 Score=29.25 Aligned_cols=38 Identities=11% Similarity=0.094 Sum_probs=30.7
Q ss_pred HhhhccCCcccccccccCCChhhHHhHHhHhHHHHHHh
Q psy15697 48 LHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVDT 85 (332)
Q Consensus 48 L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~~ 85 (332)
+.-+..-.++...|+.+++|+|+||+.+.+.-..+...
T Consensus 16 f~av~e~gs~t~AA~~L~iSQpavS~~I~~LE~~lg~~ 53 (319)
T PRK10216 16 LQLLMQERSVTKAAKRMNVTPSAVSKSLAKLRAWFDDP 53 (319)
T ss_pred HHHHHHhCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCc
Confidence 33344455888999999999999999999998887763
No 466
>PRK15340 transcriptional regulator InvF; Provisional
Probab=21.43 E-value=63 Score=28.07 Aligned_cols=28 Identities=18% Similarity=0.290 Sum_probs=24.2
Q ss_pred ccCCcccccccccCCChhhHHhHHhHhH
Q psy15697 52 GVGSPYHIIGATHGPSKSSICRSIHEVV 79 (332)
Q Consensus 52 ~~g~~~~~l~~~fgis~sTv~r~~~~v~ 79 (332)
....+..++|..+|+|.++++|.|++.+
T Consensus 123 ~~~~sleeLA~~~gvS~r~f~RlFk~~~ 150 (216)
T PRK15340 123 TSGNTMRMLGEDYGVSYTHFRRLCSRAL 150 (216)
T ss_pred cCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 4567788899999999999999999864
No 467
>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=21.43 E-value=90 Score=26.07 Aligned_cols=45 Identities=11% Similarity=0.166 Sum_probs=35.4
Q ss_pred HHHHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHHhhhc
Q psy15697 43 KVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVDTFFQ 88 (332)
Q Consensus 43 ~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~~l~~ 88 (332)
.++-..+-++.|.++.++-..-++.+..+-|+++++.+.|.. +..
T Consensus 103 ~l~~~v~~Wa~G~~~~~i~~~t~l~EGdiVR~~rRl~dlLrq-l~~ 147 (180)
T PF08148_consen 103 GLMEVVYAWASGASFAEILEMTDLFEGDIVRWIRRLIDLLRQ-LAN 147 (180)
T ss_dssp TTHHHHHHHHCT--HHHHCCT-SS-HHHHHHHHHHHHHHHHH-HHH
T ss_pred cHHHHHHHHHCCCCHHHHHhcCCCCchHHHHHHHHHHHHHHH-HHH
Confidence 456677888999999999999999999999999999999988 443
No 468
>PRK13558 bacterio-opsin activator; Provisional
Probab=21.19 E-value=1.2e+02 Score=30.78 Aligned_cols=48 Identities=10% Similarity=0.106 Sum_probs=36.7
Q ss_pred CCCHHHHHHHHHhhhcc------CCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 37 ALSAKEKVLSCLHWMGV------GSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 37 ~~~~~~~l~~~L~~L~~------g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
.++..++=++-+-|... +.+..+||..+|||++|++..+++-..-|.+
T Consensus 607 ~lt~~q~e~l~~a~~~gyf~~pr~~~~~e~a~~l~is~~t~~~~lr~a~~~l~~ 660 (665)
T PRK13558 607 DLTDRQLTALQKAYVSGYFEWPRRVEGEELAESMGISRSTFHQHLRAAERKLVG 660 (665)
T ss_pred hCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 46776665555555443 3578899999999999999999988877766
No 469
>PF04931 DNA_pol_phi: DNA polymerase phi; InterPro: IPR007015 Proteins of this family are predominantly nucleolar. The majority are described as transcription factor transactivators. The family also includes the fifth essential DNA polymerase (Pol5p) of Schizosaccharomyces pombe (Fission yeast) and Saccharomyces cerevisiae (Baker's yeast) (2.7.7.7 from EC). Pol5p is localized exclusively to the nucleolus and binds near or at the enhancer region of rRNA-encoding DNA repeating units.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=21.04 E-value=1.9e+02 Score=30.44 Aligned_cols=16 Identities=19% Similarity=0.229 Sum_probs=11.9
Q ss_pred HHHHHHHHHHHHHHhh
Q psy15697 228 KRTRRLIENSFGILKE 243 (332)
Q Consensus 228 s~~R~~vE~~fg~LK~ 243 (332)
+-.|.+++.+|+.+-.
T Consensus 603 ~llR~~~~~vf~~~~~ 618 (784)
T PF04931_consen 603 ALLRKVSEQVFEAFCP 618 (784)
T ss_pred hHHHHHHHHHHHHHHh
Confidence 3478888888888764
No 470
>PRK11482 putative DNA-binding transcriptional regulator; Provisional
Probab=20.92 E-value=70 Score=29.15 Aligned_cols=40 Identities=18% Similarity=0.120 Sum_probs=32.2
Q ss_pred HHHHhhhccCCcccccccccCCChhhHHhHHhHhHHHHHH
Q psy15697 45 LSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVVPVIVD 84 (332)
Q Consensus 45 ~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~~~l~~ 84 (332)
+-++.-+....++...|+..++|++|||+.+++.-..+-.
T Consensus 34 L~~f~av~e~gs~s~AA~~L~isQpavS~~I~~LE~~lG~ 73 (317)
T PRK11482 34 LTIFEAVYVHKGIVNAAKILNLTPSAISQSIQKLRVIFPD 73 (317)
T ss_pred HHHHHHHHHcCCHHHHHHHhCCChHHHHHHHHHHHHHhCC
Confidence 3444445556689999999999999999999998887765
No 471
>TIGR02297 HpaA 4-hydroxyphenylacetate catabolism regulatory protein HpaA. This putative transcriptional regulator, which contains both the substrate-binding, dimerization domain (pfam02311) and the helix-turn-helix DNA-binding domain (pfam00165) of the AraC famil, is located proximal to genes of the 4-hydroxyphenylacetate catabolism pathway.
Probab=20.84 E-value=1.1e+02 Score=27.22 Aligned_cols=30 Identities=10% Similarity=-0.107 Sum_probs=25.1
Q ss_pred hhccCCcccccccccCCChhhHHhHHhHhH
Q psy15697 50 WMGVGSPYHIIGATHGPSKSSICRSIHEVV 79 (332)
Q Consensus 50 ~L~~g~~~~~l~~~fgis~sTv~r~~~~v~ 79 (332)
.++...+...+|..+|+|+++++|+|++.+
T Consensus 198 ~~~~~~sl~~lA~~~~~S~~~l~r~Fk~~~ 227 (287)
T TIGR02297 198 NYKQHLRLPEYADRLGISESRLNDICRRFS 227 (287)
T ss_pred hhccCCCHHHHHHHHCCCHHHHHHHHHHHh
Confidence 445567888999999999999999999853
No 472
>PRK09940 transcriptional regulator YdeO; Provisional
Probab=20.56 E-value=1.7e+02 Score=26.07 Aligned_cols=72 Identities=8% Similarity=0.071 Sum_probs=48.2
Q ss_pred ChhHHHHHhcCCHHHHHHHHHHhccCcCCCCCCCCCCCHHHHHHHHHhhhccCCcccccccccCCC-hhhHHhHHhHhHH
Q psy15697 2 TPFAFKEAFRLSATQVEFILEEIAPALTTPTERNVALSAKEKVLSCLHWMGVGSPYHIIGATHGPS-KSSICRSIHEVVP 80 (332)
Q Consensus 2 ~d~~f~~~frms~~~F~~L~~~L~~~~~~~~~~~~~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis-~sTv~r~~~~v~~ 80 (332)
+-+++-..++||+.+|..+....+... ..+=-+.++-.+...|.++.+..++|...|-+ .+..++.|++...
T Consensus 152 tl~~LA~~~gmS~s~l~R~FK~~G~T~-------~eyl~~~Rl~~A~~LL~~~~sI~eIA~~~GF~s~S~Fsr~FKr~~G 224 (253)
T PRK09940 152 KLKDICDCLYISESLLKKKLKQEQTTF-------SQILLDARMQHAKNLIRVEGSVNKIAEQCGYASTSYFIYAFRKHFG 224 (253)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHcCCCH-------HHHHHHHHHHHHHHHHccCCCHHHHHHHhCCCCHHHHHHHHHHHHC
Confidence 345677889999999998887632110 11222445666667777888999999998875 5556777776554
No 473
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=20.29 E-value=83 Score=23.35 Aligned_cols=25 Identities=4% Similarity=0.104 Sum_probs=20.8
Q ss_pred cCCcccccccccCCChhhHHhHHhH
Q psy15697 53 VGSPYHIIGATHGPSKSSICRSIHE 77 (332)
Q Consensus 53 ~g~~~~~l~~~fgis~sTv~r~~~~ 77 (332)
++......|...|||++|+.+.+++
T Consensus 67 ~~gn~s~AAr~LGIsRsTL~rKLkr 91 (95)
T PRK00430 67 TRGNQTRAALMLGINRGTLRKKLKK 91 (95)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 4556778899999999999988876
No 474
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=20.26 E-value=44 Score=22.57 Aligned_cols=22 Identities=18% Similarity=0.076 Sum_probs=18.2
Q ss_pred cccccccCCChhhHHhHHhHhH
Q psy15697 58 HIIGATHGPSKSSICRSIHEVV 79 (332)
Q Consensus 58 ~~l~~~fgis~sTv~r~~~~v~ 79 (332)
.++|..+|||.+|+..+..+..
T Consensus 4 ~eva~~~gvs~~tlr~y~~~gl 25 (69)
T PF13411_consen 4 KEVAKLLGVSPSTLRYYEREGL 25 (69)
T ss_dssp HHHHHHTTTTHHHHHHHHHTTS
T ss_pred HHHHHHHCcCHHHHHHHHHhcC
Confidence 4688999999999998877654
No 475
>PF12759 HTH_Tnp_IS1: InsA C-terminal domain; InterPro: IPR024431 This entry represents the helix-turn-helix domain found at the C-terminal of InsA.
Probab=20.24 E-value=63 Score=20.56 Aligned_cols=25 Identities=16% Similarity=0.127 Sum_probs=21.9
Q ss_pred cCCcccccccccCCChhhHHhHHhH
Q psy15697 53 VGSPYHIIGATHGPSKSSICRSIHE 77 (332)
Q Consensus 53 ~g~~~~~l~~~fgis~sTv~r~~~~ 77 (332)
+|...++.|...+||..||-+.++.
T Consensus 20 nG~GiRdtaRvL~I~~nTVlrtLK~ 44 (46)
T PF12759_consen 20 NGSGIRDTARVLKISINTVLRTLKN 44 (46)
T ss_pred cCCcchhhHhHhcchHHHHHHHHhc
Confidence 7888999999999999999887654
No 476
>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=20.14 E-value=57 Score=22.77 Aligned_cols=19 Identities=16% Similarity=0.233 Sum_probs=15.3
Q ss_pred cccccCCChhhHHhHHhHh
Q psy15697 60 IGATHGPSKSSICRSIHEV 78 (332)
Q Consensus 60 l~~~fgis~sTv~r~~~~v 78 (332)
||+.+|+|.+++++++.+.
T Consensus 1 lA~~~~~s~~~l~~~f~~~ 19 (81)
T PF12833_consen 1 LADELGMSERYLSRIFKKE 19 (81)
T ss_dssp HHHHCTS-HHHHHHHHHHH
T ss_pred ChHHhCcCHHHHHHHHHHH
Confidence 4678999999999999874
No 477
>TIGR02325 C_P_lyase_phnF phosphonates metabolism transcriptional regulator PhnF. All members of the seed alignment for this family are predicted helix-turn-helix transcriptional regulatory proteins of the broader gntR and are found associated with genes for the import and degradation of phosphonates and/or related compounds (e.g. phosphonites) with a direct C-P bond.
Probab=20.01 E-value=50 Score=28.63 Aligned_cols=47 Identities=17% Similarity=0.241 Sum_probs=29.0
Q ss_pred HHHHHHHhccCcCCC-CCCCCCCCHHHHHHHHHhhhccCCcccccccccCCChhhHHhHHhHhH
Q psy15697 17 VEFILEEIAPALTTP-TERNVALSAKEKVLSCLHWMGVGSPYHIIGATHGPSKSSICRSIHEVV 79 (332)
Q Consensus 17 F~~L~~~L~~~~~~~-~~~~~~~~~~~~l~~~L~~L~~g~~~~~l~~~fgis~sTv~r~~~~v~ 79 (332)
+.+|.+.|+..+... -.-+..+|.|. +|+..||||+.||.+-+....
T Consensus 10 y~~i~~~l~~~I~~g~~~~G~~LPsE~----------------eLa~~~~VSR~TvR~Al~~L~ 57 (238)
T TIGR02325 10 WRQIADKIEQEIAAGHLRAGDYLPAEM----------------QLAERFGVNRHTVRRAIAALV 57 (238)
T ss_pred HHHHHHHHHHHHHcCCCCCCCcCcCHH----------------HHHHHHCCCHHHHHHHHHHHH
Confidence 455555555544321 11234566655 567889999999988776544
Done!