Query 046847
Match_columns 88
No_of_seqs 118 out of 220
Neff 6.0
Searched_HMMs 46136
Date Fri Mar 29 05:03:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046847.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046847hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF13613 HTH_Tnp_4: Helix-turn 98.7 2E-08 4.3E-13 58.1 4.5 47 24-70 2-49 (53)
2 PF12116 SpoIIID: Stage III sp 96.9 0.001 2.2E-08 42.2 2.7 45 30-74 8-54 (82)
3 PF13936 HTH_38: Helix-turn-he 96.8 0.0012 2.6E-08 36.7 2.3 39 23-62 3-42 (44)
4 KOG4585 Predicted transposase 96.2 0.005 1.1E-07 47.3 3.3 83 1-87 10-97 (326)
5 cd06571 Bac_DnaA_C C-terminal 95.4 0.036 7.8E-07 34.7 4.4 47 23-69 26-74 (90)
6 PF08299 Bac_DnaA_C: Bacterial 95.1 0.026 5.7E-07 34.1 3.0 42 23-64 27-70 (70)
7 PF04545 Sigma70_r4: Sigma-70, 95.1 0.061 1.3E-06 29.9 4.2 43 25-68 5-48 (50)
8 PRK06030 hypothetical protein; 95.0 0.035 7.6E-07 37.5 3.7 44 23-66 51-95 (124)
9 COG3415 Transposase and inacti 94.4 0.054 1.2E-06 37.2 3.3 41 23-63 3-44 (138)
10 PF04218 CENP-B_N: CENP-B N-te 94.2 0.088 1.9E-06 30.2 3.5 37 23-60 5-41 (53)
11 PRK11753 DNA-binding transcrip 93.6 0.037 8.1E-07 38.1 1.4 62 20-81 134-210 (211)
12 smart00421 HTH_LUXR helix_turn 93.2 0.2 4.3E-06 27.1 3.8 42 25-68 4-46 (58)
13 TIGR03697 NtcA_cyano global ni 92.8 0.13 2.9E-06 34.7 3.1 58 23-80 111-184 (193)
14 PF01371 Trp_repressor: Trp re 92.6 0.22 4.7E-06 31.7 3.7 42 27-68 35-76 (87)
15 PRK10402 DNA-binding transcrip 92.3 0.24 5.2E-06 35.0 4.1 43 24-66 148-195 (226)
16 cd06170 LuxR_C_like C-terminal 91.8 0.37 8.1E-06 26.1 3.7 36 33-69 8-44 (57)
17 PRK00149 dnaA chromosomal repl 91.5 0.26 5.7E-06 38.6 3.8 47 22-68 383-431 (450)
18 PRK13918 CRP/FNR family transc 91.3 0.29 6.3E-06 33.4 3.4 57 24-80 118-190 (202)
19 smart00351 PAX Paired Box doma 90.9 0.37 8.1E-06 31.9 3.6 42 22-64 15-57 (125)
20 cd00092 HTH_CRP helix_turn_hel 90.6 0.35 7.6E-06 27.5 2.9 26 41-66 25-51 (67)
21 PRK14088 dnaA chromosomal repl 90.5 0.36 7.7E-06 38.2 3.7 47 22-68 368-415 (440)
22 PF00325 Crp: Bacterial regula 90.4 0.17 3.6E-06 26.7 1.2 23 42-64 3-26 (32)
23 cd00131 PAX Paired Box domain 90.0 0.48 1E-05 31.6 3.5 43 22-65 15-58 (128)
24 TIGR01321 TrpR trp operon repr 89.9 0.36 7.8E-06 31.3 2.8 41 26-66 40-80 (94)
25 PRK14087 dnaA chromosomal repl 89.7 0.48 1E-05 37.7 3.8 47 22-68 382-430 (450)
26 PRK04217 hypothetical protein; 89.7 0.81 1.7E-05 30.3 4.3 48 22-70 40-88 (110)
27 PRK11161 fumarate/nitrate redu 89.5 0.42 9.1E-06 33.5 3.1 58 23-80 152-225 (235)
28 PF13384 HTH_23: Homeodomain-l 89.5 0.23 4.9E-06 27.2 1.4 27 37-63 13-40 (50)
29 PRK14086 dnaA chromosomal repl 89.4 0.63 1.4E-05 38.9 4.4 48 22-69 550-598 (617)
30 PF13542 HTH_Tnp_ISL3: Helix-t 89.4 0.34 7.4E-06 26.7 2.1 29 36-64 22-51 (52)
31 PRK09391 fixK transcriptional 89.1 0.47 1E-05 33.7 3.1 58 23-80 151-221 (230)
32 TIGR02531 yecD_yerC TrpR-relat 89.0 0.56 1.2E-05 29.8 3.1 37 26-63 36-72 (88)
33 PF02796 HTH_7: Helix-turn-hel 88.9 0.17 3.7E-06 27.8 0.6 27 36-62 16-43 (45)
34 PF13730 HTH_36: Helix-turn-he 88.9 0.72 1.6E-05 25.7 3.2 23 43-65 27-50 (55)
35 PRK12422 chromosomal replicati 88.7 0.59 1.3E-05 37.2 3.7 47 22-68 378-425 (445)
36 PF13545 HTH_Crp_2: Crp-like h 88.6 0.56 1.2E-05 27.5 2.8 38 29-66 1-54 (76)
37 PRK09392 ftrB transcriptional 88.3 0.67 1.5E-05 32.6 3.5 44 22-65 144-198 (236)
38 PF05225 HTH_psq: helix-turn-h 87.4 0.81 1.8E-05 25.4 2.8 35 28-62 2-38 (45)
39 PRK01381 Trp operon repressor; 86.8 0.62 1.3E-05 30.5 2.3 42 27-68 41-82 (99)
40 PRK09492 treR trehalose repres 86.3 0.44 9.6E-06 34.3 1.6 32 41-72 4-47 (315)
41 PF13340 DUF4096: Putative tra 86.2 1.5 3.2E-05 26.4 3.7 63 2-65 2-65 (75)
42 PRK09639 RNA polymerase sigma 85.9 1.5 3.3E-05 29.0 4.0 44 25-70 113-157 (166)
43 PF01022 HTH_5: Bacterial regu 85.7 1.3 2.9E-05 24.2 3.0 38 29-66 3-41 (47)
44 PF13518 HTH_28: Helix-turn-he 85.5 1.5 3.3E-05 23.7 3.2 35 31-66 3-38 (52)
45 PF01325 Fe_dep_repress: Iron 84.8 1.8 3.8E-05 25.3 3.5 39 27-65 5-47 (60)
46 cd06171 Sigma70_r4 Sigma70, re 84.3 2.3 4.9E-05 22.1 3.5 28 39-66 24-52 (55)
47 PF12840 HTH_20: Helix-turn-he 82.9 1.9 4.2E-05 24.6 3.0 39 28-66 10-50 (61)
48 TIGR02937 sigma70-ECF RNA poly 82.6 2.6 5.5E-05 26.4 3.8 44 25-69 111-155 (158)
49 TIGR02985 Sig70_bacteroi1 RNA 82.3 3 6.5E-05 26.9 4.2 44 24-68 113-157 (161)
50 PF08281 Sigma70_r4_2: Sigma-7 82.0 3.8 8.1E-05 22.5 4.0 42 25-67 11-53 (54)
51 PF13412 HTH_24: Winged helix- 81.7 3.2 6.9E-05 22.4 3.5 26 41-66 17-43 (48)
52 COG0593 DnaA ATPase involved i 81.7 2.8 6.1E-05 33.4 4.5 50 20-69 344-394 (408)
53 PRK09047 RNA polymerase factor 81.6 3.8 8.3E-05 26.8 4.5 43 33-75 114-158 (161)
54 cd00569 HTH_Hin_like Helix-tur 81.6 2.2 4.7E-05 19.9 2.6 34 26-60 7-40 (42)
55 PF08279 HTH_11: HTH domain; 81.5 2.9 6.3E-05 23.1 3.4 35 31-65 5-40 (55)
56 smart00760 Bac_DnaA_C Bacteria 81.3 1.9 4.1E-05 24.8 2.6 33 22-54 26-59 (60)
57 PF08220 HTH_DeoR: DeoR-like h 81.2 1.2 2.5E-05 25.6 1.6 26 40-65 13-39 (57)
58 PRK09413 IS2 repressor TnpA; R 80.8 3.4 7.3E-05 27.0 4.0 49 18-66 6-55 (121)
59 TIGR02844 spore_III_D sporulat 80.5 2 4.3E-05 26.9 2.6 24 40-63 18-42 (80)
60 PF00356 LacI: Bacterial regul 79.8 0.79 1.7E-05 25.7 0.6 20 44-63 2-22 (46)
61 PF12802 MarR_2: MarR family; 79.6 4.2 9E-05 22.7 3.7 24 42-65 22-46 (62)
62 PRK10014 DNA-binding transcrip 79.5 1.2 2.7E-05 32.4 1.7 32 41-72 6-49 (342)
63 PF00196 GerE: Bacterial regul 79.4 2.4 5.2E-05 23.9 2.6 35 35-69 12-47 (58)
64 TIGR02392 rpoH_proteo alternat 78.9 3.6 7.8E-05 30.2 4.0 46 25-70 219-266 (270)
65 COG0664 Crp cAMP-binding prote 78.7 3.4 7.3E-05 27.5 3.5 44 23-66 139-197 (214)
66 TIGR02393 RpoD_Cterm RNA polym 78.6 3.7 8.1E-05 29.4 3.9 47 24-70 176-226 (238)
67 PRK07408 RNA polymerase sigma 78.1 4 8.7E-05 29.7 4.0 46 24-70 203-249 (256)
68 PRK05911 RNA polymerase sigma 76.8 6.1 0.00013 28.8 4.7 46 24-70 205-251 (257)
69 COG2826 Tra8 Transposase and i 76.6 3.1 6.6E-05 32.3 3.1 39 23-62 6-45 (318)
70 PRK12524 RNA polymerase sigma 76.1 5.4 0.00012 27.4 4.1 44 26-70 138-182 (196)
71 PF00126 HTH_1: Bacterial regu 75.7 4.2 9.2E-05 23.1 2.9 39 30-69 3-42 (60)
72 PRK00118 putative DNA-binding 75.4 6.1 0.00013 25.8 3.9 43 25-68 18-61 (104)
73 PRK12519 RNA polymerase sigma 74.9 6.1 0.00013 26.8 4.1 38 33-70 149-187 (194)
74 PRK15320 transcriptional activ 74.7 3.4 7.5E-05 30.8 2.9 35 35-69 173-208 (251)
75 PRK09652 RNA polymerase sigma 74.4 8 0.00017 25.4 4.4 33 38-70 141-174 (182)
76 TIGR00721 tfx DNA-binding prot 74.0 6.1 0.00013 27.0 3.8 43 25-69 7-50 (137)
77 smart00345 HTH_GNTR helix_turn 73.6 2.1 4.6E-05 23.3 1.3 23 43-65 22-45 (60)
78 smart00342 HTH_ARAC helix_turn 73.4 7.3 0.00016 22.1 3.6 31 35-65 44-76 (84)
79 PHA00542 putative Cro-like pro 73.4 3.5 7.6E-05 25.3 2.3 50 34-83 24-79 (82)
80 PF05732 RepL: Firmicute plasm 72.9 3.8 8.3E-05 28.6 2.7 39 28-66 55-101 (165)
81 PRK06930 positive control sigm 72.9 6.8 0.00015 27.3 3.9 45 25-70 115-160 (170)
82 PF13463 HTH_27: Winged helix 72.6 7.2 0.00016 22.0 3.4 28 39-66 16-44 (68)
83 PRK12514 RNA polymerase sigma 72.3 8.9 0.00019 25.7 4.3 44 25-69 130-174 (179)
84 PRK08301 sporulation sigma fac 72.1 9.6 0.00021 27.0 4.6 44 27-70 181-228 (234)
85 smart00346 HTH_ICLR helix_turn 71.1 9 0.0002 22.8 3.8 40 26-65 3-45 (91)
86 PRK15411 rcsA colanic acid cap 71.0 5.1 0.00011 28.2 3.0 43 25-69 138-181 (207)
87 PRK12683 transcriptional regul 70.7 6 0.00013 29.0 3.4 40 29-68 4-44 (309)
88 TIGR02835 spore_sigmaE RNA pol 70.6 8.3 0.00018 27.5 4.0 46 24-69 178-227 (234)
89 PF01047 MarR: MarR family; I 70.1 9.8 0.00021 21.0 3.6 27 39-65 15-42 (59)
90 PRK10840 transcriptional regul 70.1 5 0.00011 27.5 2.7 44 24-69 150-194 (216)
91 PRK12529 RNA polymerase sigma 69.9 11 0.00024 25.4 4.4 42 27-69 130-172 (178)
92 PRK12522 RNA polymerase sigma 69.8 12 0.00026 25.0 4.5 45 32-76 126-171 (173)
93 TIGR02983 SigE-fam_strep RNA p 69.7 8.4 0.00018 25.3 3.7 41 30-70 115-156 (162)
94 PRK04424 fatty acid biosynthes 69.6 12 0.00026 26.2 4.6 47 42-88 22-75 (185)
95 TIGR02405 trehalos_R_Ecol treh 69.6 2.2 4.7E-05 30.9 0.9 21 42-62 2-23 (311)
96 COG2771 CsgD DNA-binding HTH d 69.5 6.1 0.00013 21.9 2.6 34 35-68 13-47 (65)
97 PRK12679 cbl transcriptional r 69.5 6.6 0.00014 28.8 3.4 40 29-68 4-44 (316)
98 COG2197 CitB Response regulato 69.5 5.1 0.00011 28.4 2.7 35 35-69 157-192 (211)
99 PRK12532 RNA polymerase sigma 69.2 13 0.00029 25.3 4.7 46 33-78 144-191 (195)
100 smart00418 HTH_ARSR helix_turn 69.0 6.8 0.00015 21.0 2.7 28 39-66 8-36 (66)
101 COG4496 Uncharacterized protei 68.4 4.7 0.0001 26.3 2.1 30 37-66 52-81 (100)
102 PRK12545 RNA polymerase sigma 68.3 13 0.00028 25.8 4.5 48 33-80 147-196 (201)
103 PRK09483 response regulator; P 67.5 6 0.00013 26.4 2.6 43 24-68 148-191 (217)
104 PRK09651 RNA polymerase sigma 67.5 12 0.00026 25.1 4.1 40 32-71 126-166 (172)
105 PRK10703 DNA-binding transcrip 67.3 3.6 7.7E-05 30.0 1.6 30 43-72 3-44 (341)
106 PRK07500 rpoH2 RNA polymerase 67.1 10 0.00022 28.3 4.0 47 24-70 227-275 (289)
107 TIGR02941 Sigma_B RNA polymera 67.0 11 0.00023 27.2 4.0 38 33-70 213-251 (255)
108 PRK08583 RNA polymerase sigma 67.0 12 0.00026 26.9 4.3 38 33-70 213-251 (257)
109 PRK09637 RNA polymerase sigma 67.0 20 0.00044 24.4 5.3 48 25-73 107-155 (181)
110 TIGR02980 SigBFG RNA polymeras 66.8 11 0.00023 26.5 3.9 43 26-69 180-223 (227)
111 TIGR02997 Sig70-cyanoRpoD RNA 66.5 9 0.0002 28.5 3.6 42 25-66 250-295 (298)
112 TIGR01610 phage_O_Nterm phage 66.4 16 0.00035 22.8 4.3 27 39-65 45-72 (95)
113 PRK06596 RNA polymerase factor 66.3 11 0.00023 28.0 4.0 45 25-69 231-277 (284)
114 TIGR02959 SigZ RNA polymerase 66.0 20 0.00043 24.1 5.0 47 32-78 107-154 (170)
115 PRK12547 RNA polymerase sigma 65.8 16 0.00035 24.2 4.5 37 34-70 121-158 (164)
116 PRK05572 sporulation sigma fac 65.7 12 0.00026 27.0 4.0 45 25-70 203-248 (252)
117 PRK03975 tfx putative transcri 65.3 16 0.00035 25.0 4.4 42 25-68 7-49 (141)
118 TIGR02885 spore_sigF RNA polym 65.2 12 0.00026 26.4 3.9 44 25-69 184-228 (231)
119 TIGR03879 near_KaiC_dom probab 65.1 8.4 0.00018 23.7 2.7 41 26-66 17-58 (73)
120 PRK07037 extracytoplasmic-func 65.0 15 0.00032 24.1 4.1 38 33-70 117-155 (163)
121 PRK11923 algU RNA polymerase s 64.4 17 0.00037 24.6 4.5 44 26-70 140-184 (193)
122 PRK12516 RNA polymerase sigma 63.9 14 0.00031 25.3 4.1 44 26-70 118-162 (187)
123 TIGR02850 spore_sigG RNA polym 63.9 14 0.00029 26.8 4.1 45 24-69 206-251 (254)
124 PRK12531 RNA polymerase sigma 63.8 16 0.00034 25.0 4.2 38 33-70 149-187 (194)
125 PRK10360 DNA-binding transcrip 63.4 9.7 0.00021 24.9 3.0 43 25-69 138-181 (196)
126 PRK11511 DNA-binding transcrip 63.3 12 0.00026 24.4 3.4 43 22-64 6-49 (127)
127 smart00419 HTH_CRP helix_turn_ 63.2 6.8 0.00015 20.5 1.9 26 40-65 7-33 (48)
128 PRK02287 hypothetical protein; 63.1 5.4 0.00012 28.4 1.8 43 24-67 106-149 (171)
129 PRK12544 RNA polymerase sigma 62.9 18 0.0004 25.3 4.5 42 33-74 156-199 (206)
130 PHA00738 putative HTH transcri 62.9 11 0.00023 25.1 3.0 35 30-64 14-50 (108)
131 PRK12515 RNA polymerase sigma 62.8 21 0.00046 24.1 4.7 45 25-70 132-177 (189)
132 TIGR01889 Staph_reg_Sar staphy 62.7 30 0.00064 21.8 5.1 66 6-83 10-81 (109)
133 PRK08215 sporulation sigma fac 62.7 14 0.00031 26.7 4.0 44 25-69 210-254 (258)
134 PRK09641 RNA polymerase sigma 62.4 14 0.00031 24.6 3.8 43 26-69 138-181 (187)
135 PRK09526 lacI lac repressor; R 62.4 3.7 8E-05 29.9 0.9 31 42-72 6-48 (342)
136 PRK15201 fimbriae regulatory p 62.2 9.3 0.0002 27.8 2.9 46 22-69 131-177 (198)
137 PRK10651 transcriptional regul 61.8 9 0.0002 25.1 2.6 43 25-69 156-199 (216)
138 PRK05803 sporulation sigma fac 61.7 15 0.00033 26.1 4.0 43 28-70 179-225 (233)
139 cd00090 HTH_ARSR Arsenical Res 61.3 19 0.00042 19.6 3.7 32 34-65 13-45 (78)
140 PRK14987 gluconate operon tran 60.8 3.6 7.8E-05 29.9 0.6 31 42-72 6-48 (331)
141 PRK11475 DNA-binding transcrip 60.8 9.3 0.0002 27.1 2.7 34 35-68 143-177 (207)
142 smart00347 HTH_MARR helix_turn 60.6 23 0.00049 20.9 4.1 36 31-66 13-50 (101)
143 PRK12537 RNA polymerase sigma 60.6 19 0.00041 24.3 4.1 37 33-69 141-178 (182)
144 PRK12512 RNA polymerase sigma 60.5 18 0.00038 24.3 3.9 39 32-70 138-177 (184)
145 TIGR02950 SigM_subfam RNA poly 60.4 7 0.00015 25.3 1.9 33 38-70 118-151 (154)
146 COG1508 RpoN DNA-directed RNA 60.3 5.7 0.00012 32.1 1.7 49 26-84 313-364 (444)
147 PRK10141 DNA-binding transcrip 60.2 13 0.00027 24.7 3.1 39 28-66 16-56 (117)
148 TIGR02859 spore_sigH RNA polym 59.5 18 0.00039 24.4 3.9 37 32-69 157-194 (198)
149 PF09339 HTH_IclR: IclR helix- 59.5 17 0.00037 20.0 3.1 39 26-64 1-42 (52)
150 PRK12527 RNA polymerase sigma 59.1 20 0.00043 23.5 3.9 39 32-70 112-151 (159)
151 PRK06759 RNA polymerase factor 59.1 20 0.00044 23.1 4.0 36 33-68 114-150 (154)
152 PRK07122 RNA polymerase sigma 58.7 18 0.00039 26.5 4.0 44 25-69 216-260 (264)
153 PRK15369 two component system 58.7 13 0.00027 24.0 2.9 32 38-69 161-193 (211)
154 PRK11233 nitrogen assimilation 58.7 14 0.0003 26.8 3.4 37 29-66 4-41 (305)
155 PRK11564 stationary phase indu 58.5 15 0.00032 28.5 3.6 50 19-68 5-58 (426)
156 PRK12530 RNA polymerase sigma 58.3 20 0.00043 24.5 4.0 41 29-70 139-180 (189)
157 PRK11924 RNA polymerase sigma 58.1 20 0.00043 23.4 3.8 38 33-70 133-171 (179)
158 PRK03573 transcriptional regul 58.1 19 0.00042 23.5 3.7 42 24-65 28-71 (144)
159 PRK10401 DNA-binding transcrip 58.0 10 0.00022 27.8 2.6 31 42-72 2-44 (346)
160 PRK12682 transcriptional regul 57.9 15 0.00032 26.7 3.4 40 29-68 4-44 (309)
161 TIGR02999 Sig-70_X6 RNA polyme 57.9 21 0.00045 23.8 3.9 37 33-69 142-179 (183)
162 TIGR02394 rpoS_proteo RNA poly 57.8 24 0.00051 26.0 4.5 49 25-73 223-276 (285)
163 PRK09649 RNA polymerase sigma 57.4 19 0.00041 24.5 3.7 41 30-70 135-176 (185)
164 TIGR02984 Sig-70_plancto1 RNA 57.0 26 0.00057 23.3 4.3 38 33-70 148-186 (189)
165 PRK08295 RNA polymerase factor 56.9 21 0.00046 24.3 3.9 41 28-70 159-200 (208)
166 PRK12684 transcriptional regul 56.9 16 0.00034 26.7 3.4 41 29-69 4-45 (313)
167 PRK10403 transcriptional regul 56.8 14 0.0003 24.1 2.9 43 25-69 154-197 (215)
168 TIGR02989 Sig-70_gvs1 RNA poly 56.6 24 0.00052 22.9 4.0 37 33-69 119-156 (159)
169 PRK10100 DNA-binding transcrip 56.3 13 0.00029 26.5 2.9 43 25-69 156-199 (216)
170 PRK13719 conjugal transfer tra 56.1 13 0.00029 27.3 2.9 44 24-69 143-187 (217)
171 PRK06811 RNA polymerase factor 56.0 26 0.00056 23.8 4.2 44 25-69 132-176 (189)
172 PRK12536 RNA polymerase sigma 56.0 23 0.00049 23.9 3.9 38 33-70 137-175 (181)
173 TIGR02846 spore_sigmaK RNA pol 55.6 23 0.0005 25.1 4.0 42 28-69 178-223 (227)
174 PRK07405 RNA polymerase sigma 55.5 22 0.00048 26.9 4.1 46 25-70 257-306 (317)
175 smart00352 POU Found in Pit-Oc 55.3 14 0.00031 22.9 2.5 38 37-74 20-66 (75)
176 PF00165 HTH_AraC: Bacterial r 55.2 7.8 0.00017 20.3 1.2 27 39-65 6-33 (42)
177 PRK12534 RNA polymerase sigma 55.1 31 0.00066 23.2 4.4 32 39-70 151-183 (187)
178 PRK09646 RNA polymerase sigma 54.6 27 0.00058 23.9 4.1 38 33-70 150-188 (194)
179 PF10799 YliH: Biofilm formati 54.3 13 0.00028 25.1 2.4 30 3-33 43-72 (127)
180 KOG1766 Enhancer of rudimentar 54.3 14 0.0003 24.3 2.4 25 61-85 25-49 (104)
181 PRK12525 RNA polymerase sigma 54.3 26 0.00056 23.3 3.9 38 33-70 126-164 (168)
182 PRK06288 RNA polymerase sigma 54.2 24 0.00051 25.7 4.0 44 25-69 213-257 (268)
183 PRK12533 RNA polymerase sigma 54.1 23 0.0005 25.2 3.8 41 29-70 139-180 (216)
184 TIGR03541 reg_near_HchA LuxR f 53.9 58 0.0013 23.2 5.9 46 22-69 169-215 (232)
185 PRK07670 RNA polymerase sigma 53.9 26 0.00057 25.2 4.1 43 26-69 203-246 (251)
186 TIGR02948 SigW_bacill RNA poly 53.9 23 0.00049 23.6 3.6 33 38-70 149-182 (187)
187 TIGR02939 RpoE_Sigma70 RNA pol 53.6 26 0.00057 23.4 3.9 38 33-70 146-184 (190)
188 PF13551 HTH_29: Winged helix- 53.6 17 0.00036 22.2 2.7 31 35-65 5-37 (112)
189 PRK12528 RNA polymerase sigma 53.4 28 0.00061 22.8 4.0 37 32-68 120-157 (161)
190 PF04967 HTH_10: HTH DNA bindi 53.3 14 0.00031 21.2 2.2 29 41-69 23-52 (53)
191 PRK10423 transcriptional repre 52.9 5.7 0.00012 28.6 0.5 28 45-72 2-41 (327)
192 COG5606 Uncharacterized conser 52.9 10 0.00022 24.4 1.6 60 1-60 1-60 (91)
193 PRK09638 RNA polymerase sigma 52.7 13 0.00028 24.7 2.3 43 26-69 128-171 (176)
194 PRK12541 RNA polymerase sigma 52.7 29 0.00063 22.7 3.9 38 33-70 120-158 (161)
195 PRK10339 DNA-binding transcrip 52.6 6.2 0.00013 28.7 0.7 21 43-63 3-24 (327)
196 PRK10434 srlR DNA-bindng trans 52.5 18 0.0004 26.4 3.1 41 28-69 4-47 (256)
197 PRK12535 RNA polymerase sigma 52.4 30 0.00066 23.9 4.2 44 33-76 141-185 (196)
198 PF13011 LZ_Tnp_IS481: leucine 52.0 23 0.00049 22.5 3.1 42 24-65 8-50 (85)
199 PF01710 HTH_Tnp_IS630: Transp 51.9 11 0.00023 24.5 1.7 23 40-62 17-40 (119)
200 PRK12520 RNA polymerase sigma 51.6 46 0.001 22.5 4.9 43 33-75 139-183 (191)
201 PRK13919 putative RNA polymera 51.5 31 0.00068 23.1 4.0 36 34-69 144-180 (186)
202 PRK09642 RNA polymerase sigma 51.2 31 0.00067 22.5 3.9 38 33-70 114-152 (160)
203 COG1349 GlpR Transcriptional r 50.8 18 0.0004 26.5 2.9 25 42-66 20-45 (253)
204 PRK12546 RNA polymerase sigma 50.7 29 0.00063 23.9 3.8 45 25-70 114-159 (188)
205 PRK12511 RNA polymerase sigma 50.6 40 0.00086 23.0 4.5 37 34-70 120-157 (182)
206 TIGR02952 Sig70_famx2 RNA poly 50.5 34 0.00073 22.3 4.0 45 24-69 122-167 (170)
207 PRK12540 RNA polymerase sigma 50.5 30 0.00065 23.6 3.8 42 33-74 119-162 (182)
208 PF09246 PHAT: PHAT; InterPro 50.0 22 0.00048 23.6 2.9 36 4-39 48-83 (108)
209 PF00392 GntR: Bacterial regul 49.9 12 0.00026 21.4 1.5 22 43-64 26-48 (64)
210 PF04034 DUF367: Domain of unk 49.9 12 0.00026 25.5 1.7 33 24-56 65-97 (127)
211 PRK09647 RNA polymerase sigma 49.9 32 0.00069 24.0 4.0 39 32-70 145-184 (203)
212 PRK06986 fliA flagellar biosyn 49.8 31 0.00067 24.4 3.9 43 27-70 187-230 (236)
213 smart00354 HTH_LACI helix_turn 49.7 8.1 0.00018 22.7 0.8 21 43-63 2-23 (70)
214 PRK09958 DNA-binding transcrip 49.5 22 0.00047 23.4 2.9 42 25-68 144-186 (204)
215 PRK11303 DNA-binding transcrip 49.5 7.8 0.00017 28.0 0.8 21 43-63 2-23 (328)
216 PRK12427 flagellar biosynthesi 49.5 32 0.0007 24.6 4.0 43 25-68 184-227 (231)
217 PRK09644 RNA polymerase sigma 49.3 31 0.00066 22.8 3.6 44 26-70 110-154 (165)
218 COG1595 RpoE DNA-directed RNA 48.9 31 0.00067 23.3 3.7 38 33-70 135-173 (182)
219 PRK09415 RNA polymerase factor 48.7 38 0.00083 22.8 4.1 45 25-70 128-173 (179)
220 PRK09906 DNA-binding transcrip 48.6 18 0.00038 25.8 2.5 38 30-68 5-43 (296)
221 TIGR02337 HpaR homoprotocatech 48.5 45 0.00097 21.0 4.2 27 39-65 40-67 (118)
222 PRK09210 RNA polymerase sigma 48.5 30 0.00065 26.7 3.9 46 24-69 305-354 (367)
223 PRK00215 LexA repressor; Valid 48.3 30 0.00064 24.0 3.6 27 39-65 21-49 (205)
224 TIGR03001 Sig-70_gmx1 RNA poly 48.3 33 0.0007 25.0 3.9 38 33-70 169-207 (244)
225 COG3355 Predicted transcriptio 48.2 34 0.00073 23.2 3.7 52 9-67 15-69 (126)
226 PRK09645 RNA polymerase sigma 48.0 28 0.00062 23.0 3.3 37 34-70 127-164 (173)
227 PRK12681 cysB transcriptional 47.9 26 0.00056 25.9 3.4 40 29-68 4-44 (324)
228 PRK12526 RNA polymerase sigma 47.7 36 0.00079 23.6 4.0 38 33-70 161-199 (206)
229 smart00550 Zalpha Z-DNA-bindin 47.4 40 0.00087 19.7 3.6 39 26-64 6-46 (68)
230 PRK12539 RNA polymerase sigma 47.4 37 0.0008 22.9 3.9 33 38-70 144-177 (184)
231 PRK07406 RNA polymerase sigma 46.7 35 0.00077 26.7 4.1 46 24-69 311-360 (373)
232 PRK12542 RNA polymerase sigma 46.7 43 0.00093 22.5 4.1 39 32-70 129-168 (185)
233 PRK11151 DNA-binding transcrip 46.6 28 0.00061 25.0 3.3 36 29-65 4-40 (305)
234 PRK12680 transcriptional regul 46.6 28 0.00061 25.8 3.4 41 29-69 4-45 (327)
235 cd01392 HTH_LacI Helix-turn-he 46.2 7.8 0.00017 20.9 0.3 18 46-63 2-20 (52)
236 TIGR02943 Sig70_famx1 RNA poly 45.5 41 0.00089 23.0 3.9 38 33-70 139-177 (188)
237 PF01527 HTH_Tnp_1: Transposas 45.3 23 0.00051 20.4 2.3 43 23-65 5-48 (76)
238 TIGR01884 cas_HTH CRISPR locus 44.6 38 0.00083 23.7 3.7 36 30-65 145-182 (203)
239 TIGR02479 FliA_WhiG RNA polyme 44.4 45 0.00097 23.4 4.0 43 26-69 177-220 (224)
240 PRK09643 RNA polymerase sigma 44.0 59 0.0013 22.2 4.5 38 33-70 142-180 (192)
241 TIGR02954 Sig70_famx3 RNA poly 43.9 47 0.001 21.9 3.9 38 33-70 127-165 (169)
242 PRK06704 RNA polymerase factor 43.8 53 0.0012 23.8 4.4 48 26-74 118-166 (228)
243 TIGR02395 rpoN_sigma RNA polym 43.8 17 0.00037 29.0 1.9 48 27-84 302-352 (429)
244 TIGR02404 trehalos_R_Bsub treh 43.8 42 0.0009 23.6 3.8 41 8-65 8-49 (233)
245 PF02936 COX4: Cytochrome c ox 43.6 45 0.00097 22.8 3.8 68 8-82 31-105 (142)
246 PRK05932 RNA polymerase factor 43.4 17 0.00037 29.2 1.9 48 27-84 327-377 (455)
247 TIGR00180 parB_part ParB-like 43.3 32 0.00069 23.9 3.1 39 26-64 105-143 (187)
248 PRK07598 RNA polymerase sigma 43.2 42 0.00092 26.8 4.1 45 25-69 351-399 (415)
249 PRK10906 DNA-binding transcrip 43.0 32 0.00069 25.2 3.2 25 42-66 20-45 (252)
250 COG1725 Predicted transcriptio 43.0 63 0.0014 21.8 4.4 48 3-66 10-61 (125)
251 cd07377 WHTH_GntR Winged helix 42.9 21 0.00047 19.5 1.8 23 43-65 27-50 (66)
252 PRK10681 DNA-binding transcrip 42.9 31 0.00067 25.1 3.1 39 28-67 6-47 (252)
253 PF01381 HTH_3: Helix-turn-hel 42.7 15 0.00032 19.9 1.1 26 38-63 6-32 (55)
254 PRK13509 transcriptional repre 42.7 32 0.00069 25.1 3.1 24 41-64 19-43 (251)
255 PRK15183 Vi polysaccharide bio 42.5 21 0.00046 24.1 2.0 41 42-82 99-140 (143)
256 PRK04841 transcriptional regul 42.4 26 0.00056 29.2 2.9 33 37-69 849-882 (903)
257 PF13972 TetR: Bacterial trans 42.3 93 0.002 20.3 5.1 65 3-69 67-134 (146)
258 PF13921 Myb_DNA-bind_6: Myb-l 42.3 28 0.00061 19.3 2.3 26 40-65 16-43 (60)
259 TIGR02417 fruct_sucro_rep D-fr 42.3 12 0.00025 27.1 0.7 20 44-63 2-22 (327)
260 PRK03341 arginine repressor; P 42.1 39 0.00086 23.7 3.4 42 24-65 10-59 (168)
261 TIGR00362 DnaA chromosomal rep 41.8 28 0.0006 26.8 2.8 33 22-54 371-404 (405)
262 PF06056 Terminase_5: Putative 41.7 33 0.00072 19.9 2.5 30 29-60 3-32 (58)
263 PRK09640 RNA polymerase sigma 41.7 19 0.00042 24.4 1.8 38 33-70 142-180 (188)
264 PRK12518 RNA polymerase sigma 41.7 20 0.00042 23.8 1.7 33 38-70 133-166 (175)
265 PRK10094 DNA-binding transcrip 41.7 34 0.00073 25.0 3.1 36 29-65 5-41 (308)
266 COG0184 RpsO Ribosomal protein 41.2 22 0.00048 22.7 1.8 26 11-36 9-34 (89)
267 PRK09801 transcriptional activ 40.8 35 0.00075 25.0 3.1 40 28-68 8-48 (310)
268 PRK11242 DNA-binding transcrip 40.8 39 0.00084 23.9 3.3 36 29-65 4-40 (296)
269 TIGR00122 birA_repr_reg BirA b 40.7 42 0.00091 19.3 2.9 25 41-65 13-38 (69)
270 TIGR00637 ModE_repress ModE mo 40.5 22 0.00048 22.5 1.8 35 35-69 10-45 (99)
271 PRK05602 RNA polymerase sigma 40.2 52 0.0011 22.1 3.7 33 38-70 141-174 (186)
272 PRK10219 DNA-binding transcrip 40.2 51 0.0011 20.3 3.4 15 3-17 4-18 (107)
273 PF04552 Sigma54_DBD: Sigma-54 40.1 10 0.00022 26.4 0.1 40 24-63 30-72 (160)
274 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 40.1 44 0.00095 19.1 2.8 36 24-60 4-39 (50)
275 PRK00441 argR arginine repress 40.0 35 0.00076 23.4 2.8 23 42-64 19-47 (149)
276 PHA00675 hypothetical protein 40.0 58 0.0013 20.4 3.5 38 23-60 21-58 (78)
277 PRK09648 RNA polymerase sigma 40.0 57 0.0012 21.9 3.9 37 33-69 147-184 (189)
278 PF13560 HTH_31: Helix-turn-he 40.0 16 0.00035 20.7 1.0 25 36-60 9-33 (64)
279 PRK11922 RNA polymerase sigma 40.0 42 0.00091 23.7 3.3 37 34-70 158-195 (231)
280 PF13404 HTH_AsnC-type: AsnC-t 40.0 21 0.00046 19.2 1.4 24 40-63 16-40 (42)
281 PRK12423 LexA repressor; Provi 40.0 45 0.00097 23.4 3.5 24 41-64 25-50 (202)
282 PRK05949 RNA polymerase sigma 39.8 67 0.0014 24.5 4.6 46 25-70 267-316 (327)
283 PRK11013 DNA-binding transcrip 39.8 39 0.00086 24.5 3.2 35 29-64 7-42 (309)
284 TIGR01481 ccpA catabolite cont 39.7 14 0.00029 26.7 0.8 30 43-72 3-44 (329)
285 PF12834 Phage_int_SAM_2: Phag 39.7 81 0.0018 19.7 4.3 48 4-51 27-75 (91)
286 PF04297 UPF0122: Putative hel 39.6 71 0.0015 20.8 4.1 43 27-69 19-62 (101)
287 PRK15421 DNA-binding transcrip 39.5 38 0.00083 24.9 3.2 36 29-65 5-41 (317)
288 COG4974 XerD Site-specific rec 39.3 81 0.0018 24.4 4.9 64 1-66 221-286 (300)
289 PRK12543 RNA polymerase sigma 39.2 56 0.0012 21.9 3.7 37 33-69 125-162 (179)
290 PRK11512 DNA-binding transcrip 39.1 66 0.0014 21.0 4.0 41 24-65 37-79 (144)
291 CHL00180 rbcR LysR transcripti 39.0 44 0.00096 24.1 3.4 39 29-68 8-47 (305)
292 TIGR02957 SigX4 RNA polymerase 38.8 54 0.0012 24.0 3.8 39 32-70 115-154 (281)
293 PRK13348 chromosome replicatio 38.8 45 0.00098 23.7 3.4 39 29-68 5-44 (294)
294 PRK12538 RNA polymerase sigma 38.6 48 0.001 23.8 3.5 38 33-70 179-217 (233)
295 PRK12523 RNA polymerase sigma 38.4 66 0.0014 21.3 4.0 40 28-68 123-163 (172)
296 TIGR03418 chol_sulf_TF putativ 38.2 41 0.0009 23.8 3.1 36 30-66 5-41 (291)
297 PHA02675 ORF104 fusion protein 37.6 50 0.0011 21.2 3.0 46 24-75 32-81 (90)
298 TIGR03764 ICE_PFGI_1_parB inte 36.7 61 0.0013 24.5 3.9 44 25-68 114-168 (258)
299 PF10668 Phage_terminase: Phag 36.7 42 0.00092 19.9 2.5 32 28-60 10-41 (60)
300 TIGR03020 EpsA transcriptional 36.7 62 0.0013 23.9 3.9 44 23-68 189-233 (247)
301 PF07638 Sigma70_ECF: ECF sigm 36.3 52 0.0011 22.6 3.2 27 39-65 149-176 (185)
302 PF08535 KorB: KorB domain; I 36.2 19 0.00041 22.3 0.9 21 40-60 2-22 (93)
303 PRK09935 transcriptional regul 36.0 42 0.0009 21.9 2.6 42 25-68 150-192 (210)
304 PF05043 Mga: Mga helix-turn-h 36.0 41 0.00089 20.1 2.4 33 38-70 27-60 (87)
305 PRK09636 RNA polymerase sigma 35.8 72 0.0016 23.4 4.1 39 32-70 122-161 (293)
306 PRK10727 DNA-binding transcrip 35.7 17 0.00037 26.6 0.7 30 43-72 3-44 (343)
307 TIGR02960 SigX5 RNA polymerase 35.1 59 0.0013 23.9 3.5 38 33-70 150-188 (324)
308 PRK12513 RNA polymerase sigma 34.9 35 0.00075 23.1 2.2 33 38-70 152-185 (194)
309 PF11469 Ribonucleas_3_2: Ribo 34.8 88 0.0019 21.0 4.0 43 24-72 74-118 (120)
310 COG1609 PurR Transcriptional r 34.4 19 0.00041 27.1 0.9 21 43-63 2-23 (333)
311 PRK15418 transcriptional regul 34.2 27 0.00058 26.6 1.6 25 40-64 28-53 (318)
312 KOG0946 ER-Golgi vesicle-tethe 33.7 81 0.0018 28.0 4.5 42 4-47 208-249 (970)
313 PF09862 DUF2089: Protein of u 33.6 93 0.002 20.6 4.0 47 23-70 32-79 (113)
314 PRK08241 RNA polymerase factor 33.4 85 0.0018 23.3 4.2 38 33-70 161-199 (339)
315 PRK10411 DNA-binding transcrip 33.4 54 0.0012 23.8 3.1 26 41-66 18-44 (240)
316 PRK07921 RNA polymerase sigma 32.6 84 0.0018 24.0 4.1 45 25-69 263-311 (324)
317 PRK13698 plasmid-partitioning 32.4 53 0.0011 25.6 3.0 38 25-62 159-198 (323)
318 PRK11050 manganese transport r 31.7 54 0.0012 22.1 2.7 28 39-66 49-77 (152)
319 PRK15340 transcriptional regul 31.5 66 0.0014 23.5 3.2 25 41-65 125-150 (216)
320 PRK12469 RNA polymerase factor 31.4 28 0.00062 28.3 1.5 48 27-84 353-403 (481)
321 smart00420 HTH_DEOR helix_turn 31.4 81 0.0018 16.2 3.4 25 41-65 14-39 (53)
322 PRK10632 transcriptional regul 31.4 42 0.00091 24.4 2.2 37 29-66 5-42 (309)
323 PRK11402 DNA-binding transcrip 31.4 1E+02 0.0022 21.8 4.2 43 6-64 11-57 (241)
324 PRK11074 putative DNA-binding 31.2 62 0.0013 23.3 3.1 37 29-66 5-42 (300)
325 PRK10430 DNA-binding transcrip 31.1 78 0.0017 22.0 3.5 45 25-69 159-207 (239)
326 PF08897 DUF1841: Domain of un 31.0 50 0.0011 22.7 2.4 55 22-81 69-127 (137)
327 PRK10188 DNA-binding transcrip 30.9 2E+02 0.0044 20.7 6.0 45 23-69 178-223 (240)
328 PF05344 DUF746: Domain of Unk 30.9 97 0.0021 18.7 3.4 43 29-71 1-44 (65)
329 PF11740 KfrA_N: Plasmid repli 30.8 44 0.00095 21.1 2.0 37 33-69 11-49 (120)
330 TIGR03298 argP transcriptional 30.8 66 0.0014 22.9 3.1 37 30-67 5-42 (292)
331 PF07750 GcrA: GcrA cell cycle 30.7 53 0.0011 22.8 2.5 36 28-63 5-42 (162)
332 PF09758 FPL: Uncharacterised 30.5 72 0.0016 22.1 3.2 73 1-75 23-107 (149)
333 TIGR02944 suf_reg_Xantho FeS a 30.4 81 0.0018 20.2 3.3 39 27-65 8-50 (130)
334 PRK09791 putative DNA-binding 30.4 72 0.0016 22.8 3.3 39 29-68 8-47 (302)
335 PF01978 TrmB: Sugar-specific 30.3 79 0.0017 18.0 2.9 33 33-65 13-47 (68)
336 TIGR02702 SufR_cyano iron-sulf 30.0 84 0.0018 21.9 3.5 37 28-65 3-40 (203)
337 PRK10837 putative DNA-binding 29.9 49 0.0011 23.3 2.3 38 30-68 7-45 (290)
338 TIGR02947 SigH_actino RNA poly 29.9 67 0.0015 21.7 2.9 38 33-70 139-177 (193)
339 TIGR03339 phn_lysR aminoethylp 29.4 50 0.0011 23.0 2.3 33 35-67 5-38 (279)
340 TIGR02036 dsdC D-serine deamin 29.0 46 0.001 24.1 2.1 38 29-67 11-49 (302)
341 PRK10870 transcriptional repre 28.6 73 0.0016 21.9 3.0 25 41-65 71-96 (176)
342 PF00440 TetR_N: Bacterial reg 28.4 66 0.0014 17.1 2.2 33 31-63 6-39 (47)
343 PF00157 Pou: Pou domain - N-t 28.4 30 0.00065 21.5 0.9 23 53-75 42-67 (75)
344 COG3179 Predicted chitinase [G 28.4 28 0.0006 25.5 0.8 43 22-64 33-77 (206)
345 smart00344 HTH_ASNC helix_turn 28.3 1.2E+02 0.0026 18.5 3.7 27 40-66 16-43 (108)
346 PRK10572 DNA-binding transcrip 28.2 81 0.0017 22.7 3.3 28 37-64 195-223 (290)
347 smart00529 HTH_DTXR Helix-turn 28.1 46 0.00099 20.0 1.7 23 44-66 2-25 (96)
348 PRK15092 DNA-binding transcrip 28.0 52 0.0011 24.2 2.3 35 33-67 17-52 (310)
349 TIGR02424 TF_pcaQ pca operon t 27.9 80 0.0017 22.4 3.2 38 29-67 6-44 (300)
350 TIGR00498 lexA SOS regulatory 27.8 1E+02 0.0022 21.2 3.6 26 39-64 23-50 (199)
351 PF13744 HTH_37: Helix-turn-he 27.4 39 0.00084 20.3 1.3 27 36-62 26-53 (80)
352 TIGR03070 couple_hipB transcri 27.1 43 0.00093 17.7 1.3 26 37-62 11-37 (58)
353 PF05269 Phage_CII: Bacterioph 27.1 82 0.0018 20.1 2.8 25 42-66 24-49 (91)
354 PRK05901 RNA polymerase sigma 27.1 1.1E+02 0.0024 25.2 4.1 46 24-69 447-496 (509)
355 COG2973 TrpR Trp operon repres 27.0 55 0.0012 21.6 1.9 27 37-63 56-83 (103)
356 PRK09834 DNA-binding transcrip 26.9 1.1E+02 0.0024 22.2 3.8 40 26-65 9-51 (263)
357 TIGR00519 asnASE_I L-asparagin 26.8 67 0.0015 24.6 2.7 37 18-54 293-329 (336)
358 PRK12517 RNA polymerase sigma 26.7 1.5E+02 0.0031 20.2 4.2 38 33-70 136-174 (188)
359 PF01316 Arg_repressor: Argini 26.6 34 0.00073 20.7 0.9 29 25-64 19-48 (70)
360 PRK11062 nhaR transcriptional 26.6 64 0.0014 23.2 2.5 35 29-64 7-42 (296)
361 PRK09508 leuO leucine transcri 26.6 60 0.0013 23.6 2.4 35 30-65 26-61 (314)
362 PF12162 STAT1_TAZ2bind: STAT1 26.6 73 0.0016 15.5 1.9 13 1-13 10-22 (23)
363 COG2378 Predicted transcriptio 26.3 92 0.002 23.6 3.4 39 31-69 11-51 (311)
364 PF03623 Focal_AT: Focal adhes 26.0 88 0.0019 21.6 2.9 31 50-80 3-34 (139)
365 PRK13413 mpi multiple promoter 25.7 62 0.0013 22.4 2.2 30 32-62 164-194 (200)
366 PRK09986 DNA-binding transcrip 25.7 1E+02 0.0022 21.8 3.3 39 29-68 10-49 (294)
367 cd04762 HTH_MerR-trunc Helix-T 25.5 40 0.00087 17.1 1.0 21 43-63 2-23 (49)
368 PRK10086 DNA-binding transcrip 25.5 61 0.0013 23.5 2.2 37 30-67 18-55 (311)
369 PRK09802 DNA-binding transcrip 25.3 84 0.0018 23.2 2.9 37 28-64 16-55 (269)
370 PRK12302 bssR biofilm formatio 25.2 72 0.0016 21.4 2.3 30 3-33 43-72 (127)
371 PF03965 Penicillinase_R: Peni 24.7 1.3E+02 0.0029 19.0 3.5 28 26-54 3-30 (115)
372 COG2739 Uncharacterized protei 24.5 83 0.0018 20.8 2.5 32 38-69 30-62 (105)
373 PF01498 HTH_Tnp_Tc3_2: Transp 24.5 48 0.001 19.1 1.3 22 42-63 14-41 (72)
374 PRK03902 manganese transport t 24.5 1.3E+02 0.0029 19.6 3.6 39 27-65 6-47 (142)
375 PRK10341 DNA-binding transcrip 24.4 71 0.0015 23.1 2.4 40 28-68 9-49 (312)
376 PF04591 DUF596: Protein of un 24.4 47 0.001 20.4 1.2 12 24-35 16-27 (70)
377 PF12964 DUF3853: Protein of u 24.3 88 0.0019 20.3 2.5 68 1-76 13-83 (96)
378 PF08858 IDEAL: IDEAL domain; 24.2 72 0.0016 16.8 1.8 12 2-13 26-37 (37)
379 KOG1062 Vesicle coat complex A 24.1 1.2E+02 0.0026 26.8 3.9 47 2-48 26-74 (866)
380 PF07374 DUF1492: Protein of u 23.9 1.6E+02 0.0034 18.4 3.7 40 26-66 57-97 (100)
381 PRK06474 hypothetical protein; 23.8 1.1E+02 0.0024 21.3 3.1 38 29-66 12-53 (178)
382 PHA01976 helix-turn-helix prot 23.5 57 0.0012 18.3 1.4 26 37-62 11-37 (67)
383 COG2042 Uncharacterized conser 23.5 64 0.0014 23.2 1.9 32 24-55 114-145 (179)
384 PF14223 UBN2: gag-polypeptide 23.3 1.8E+02 0.0038 18.1 3.9 58 5-69 49-107 (119)
385 smart00530 HTH_XRE Helix-turn- 23.1 62 0.0013 15.8 1.4 23 38-60 7-29 (56)
386 TIGR01764 excise DNA binding d 22.9 48 0.001 16.9 0.9 20 43-62 3-23 (49)
387 PF04703 FaeA: FaeA-like prote 22.8 98 0.0021 18.2 2.4 32 29-60 3-34 (62)
388 KOG0854 Alkyl hydroperoxide re 22.8 54 0.0012 24.1 1.4 17 55-71 150-167 (224)
389 PF00872 Transposase_mut: Tran 22.7 70 0.0015 24.8 2.2 38 34-71 107-152 (381)
390 TIGR01529 argR_whole arginine 22.6 37 0.00081 23.0 0.6 16 49-64 29-45 (146)
391 PF02001 DUF134: Protein of un 22.6 2E+02 0.0043 18.8 4.0 44 22-66 39-83 (106)
392 PRK03635 chromosome replicatio 22.6 81 0.0017 22.6 2.4 38 30-68 6-44 (294)
393 PF01726 LexA_DNA_bind: LexA D 22.5 1.6E+02 0.0035 17.2 3.3 24 37-60 21-45 (65)
394 PRK09393 ftrA transcriptional 22.3 1.1E+02 0.0025 22.5 3.2 27 38-64 231-258 (322)
395 PF13443 HTH_26: Cro/C1-type H 22.1 49 0.0011 18.3 0.9 26 38-63 7-33 (63)
396 PF15467 SGIII: Secretogranin- 22.1 1.1E+02 0.0023 24.8 3.1 47 2-48 149-196 (453)
397 PRK09461 ansA cytoplasmic aspa 22.0 87 0.0019 24.0 2.5 37 18-54 293-329 (335)
398 COG1740 HyaA Ni,Fe-hydrogenase 21.8 92 0.002 24.7 2.6 29 1-29 13-41 (355)
399 TIGR03209 P21_Cbot clostridium 21.8 83 0.0018 20.1 2.1 27 33-59 115-141 (142)
400 TIGR02325 C_P_lyase_phnF phosp 21.7 60 0.0013 22.7 1.5 43 6-64 10-56 (238)
401 PRK09191 two-component respons 21.7 1.7E+02 0.0036 20.2 3.8 38 32-69 95-133 (261)
402 PRK05657 RNA polymerase sigma 21.5 1.7E+02 0.0037 22.2 4.0 32 39-70 280-312 (325)
403 PRK10216 DNA-binding transcrip 21.4 83 0.0018 22.9 2.2 39 29-68 11-50 (319)
404 PF01418 HTH_6: Helix-turn-hel 21.4 65 0.0014 19.1 1.4 38 26-63 16-57 (77)
405 TIGR03830 CxxCG_CxxCG_HTH puta 21.2 63 0.0014 20.4 1.4 27 36-62 73-100 (127)
406 PRK14997 LysR family transcrip 20.9 87 0.0019 22.3 2.2 38 30-68 6-44 (301)
407 PF06817 RVT_thumb: Reverse tr 20.9 84 0.0018 19.1 1.8 27 7-33 40-66 (70)
408 COG2188 PhnF Transcriptional r 20.7 63 0.0014 23.2 1.5 44 6-65 9-56 (236)
409 KOG4075 Cytochrome c oxidase, 20.7 3.2E+02 0.007 19.4 5.2 69 10-83 58-131 (167)
410 PRK15243 transcriptional regul 20.7 1.3E+02 0.0028 22.4 3.1 39 27-66 5-44 (297)
411 PRK10079 phosphonate metabolis 20.4 76 0.0016 22.5 1.8 44 6-65 14-60 (241)
412 PRK10082 cell density-dependen 20.3 1E+02 0.0022 22.2 2.5 36 30-66 15-51 (303)
413 TIGR02018 his_ut_repres histid 20.3 77 0.0017 22.3 1.8 43 7-65 4-50 (230)
414 PRK10130 transcriptional regul 20.0 1.5E+02 0.0032 22.8 3.5 34 32-65 247-281 (350)
No 1
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=98.74 E-value=2e-08 Score=58.10 Aligned_cols=47 Identities=23% Similarity=0.312 Sum_probs=44.6
Q ss_pred ccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847 24 VVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE 70 (88)
Q Consensus 24 ~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~ 70 (88)
.++.|+|+.+.|..+.+|.++++++.+|+.|.+|||| |+++++.+..
T Consensus 2 kLs~~d~lll~L~~LR~~~~~~~La~~FgIs~stvsri~~~~~~~L~~ 49 (53)
T PF13613_consen 2 KLSLEDQLLLTLMYLRLNLTFQDLAYRFGISQSTVSRIFHEWIPLLYQ 49 (53)
T ss_pred CCCHHHHHHHHHHHHHcCCcHhHHhhheeecHHHHHHHHHHHHHHHHH
Confidence 4689999999999999999999999999999999999 9999998865
No 2
>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=96.86 E-value=0.001 Score=42.17 Aligned_cols=45 Identities=11% Similarity=0.062 Sum_probs=33.6
Q ss_pred HHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH-hhhh
Q 046847 30 QVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE-LQHI 74 (88)
Q Consensus 30 ~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~-L~~~ 74 (88)
.+-+--||+.++++.|+++..||.|.+||++ ..+=|..|.. |+..
T Consensus 8 ~i~i~~yIi~~~aTVR~~Ak~FGvSKSTVHkDvteRL~~in~~La~e 54 (82)
T PF12116_consen 8 VIEIANYIIETKATVRQAAKVFGVSKSTVHKDVTERLPKINPELARE 54 (82)
T ss_dssp HHHHHHHHHHH---HHHHHHHHTS-HHHHHHHHTTHHHHH-HHHHHH
T ss_pred HHHHHHHHHHcccHHHHHHHHHCCcHHHHHHHHHHHHHhcCHHHHHH
Confidence 4567789999999999999999999999999 9887777754 5543
No 3
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=96.78 E-value=0.0012 Score=36.68 Aligned_cols=39 Identities=21% Similarity=0.225 Sum_probs=21.8
Q ss_pred CccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HH
Q 046847 23 SVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FN 62 (88)
Q Consensus 23 ~~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~ 62 (88)
++++.+|...|.-+ ...|.+.+.|+..+++|.+||++ .+
T Consensus 3 ~~Lt~~eR~~I~~l-~~~G~s~~~IA~~lg~s~sTV~relk 42 (44)
T PF13936_consen 3 KHLTPEERNQIEAL-LEQGMSIREIAKRLGRSRSTVSRELK 42 (44)
T ss_dssp ---------HHHHH-HCS---HHHHHHHTT--HHHHHHHHH
T ss_pred cchhhhHHHHHHHH-HHcCCCHHHHHHHHCcCcHHHHHHHh
Confidence 46778888888766 57889999999999999999998 65
No 4
>KOG4585 consensus Predicted transposase [Replication, recombination and repair]
Probab=96.20 E-value=0.005 Score=47.34 Aligned_cols=83 Identities=23% Similarity=0.210 Sum_probs=63.0
Q ss_pred CChHHHHHHHHHHhhCcCCcC-----CCccchhHHHHHHHHHhccccchhhhhhhcccccchhHhHHHHHHHHHHhhhhh
Q 046847 1 MDRKTFGLLFELLCSDERLKT-----DSVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISRFNSILNGVLELQHIL 75 (88)
Q Consensus 1 M~~~~F~~L~~~L~~~~~L~~-----t~~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisrf~~Vl~ai~~L~~~~ 75 (88)
+++.+|.++|........-+. +..+++.+.+|+.+|.++++.+-+.++.+|++..+|+ ..+.+...+++.+
T Consensus 10 ~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~i~~~fg~~~~~~----~~~~~~~~~~~~~ 85 (326)
T KOG4585|consen 10 KSYTTFDKICSLVQSLNVVKNSGFMLSSLLPADTLVAVALWRLKTGESLRTVEKKFGLGQSTC----KFLEEKEDLAPHF 85 (326)
T ss_pred HHHHHHHHHhhhhhhhhhhcccchhhhccccHHhhhhhhhccccccchHHHHHHHcCCcchhh----hHHHhhhcccchh
Confidence 357788899888655322222 1222299999999999999999999999999999998 5666677789999
Q ss_pred ccCCCCCCCCCC
Q 046847 76 LKSPKPMPEYCT 87 (88)
Q Consensus 76 ik~p~~~~~~~i 87 (88)
++.|+...+.+|
T Consensus 86 ~~~p~~~~~~~i 97 (326)
T KOG4585|consen 86 LKWPSRRILYEI 97 (326)
T ss_pred hcCchhhhhhhh
Confidence 999975444433
No 5
>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=95.42 E-value=0.036 Score=34.72 Aligned_cols=47 Identities=15% Similarity=0.167 Sum_probs=42.2
Q ss_pred CccchhHHHHHHHHHhccccchhhhhhhcc-cccchhHh-HHHHHHHHH
Q 046847 23 SVVFVDEQVCMFLHALAHHVKNQTINNRFK-HSGETISR-FNSILNGVL 69 (88)
Q Consensus 23 ~~v~veE~la~FL~i~~~n~~~r~i~~~F~-~S~eTisr-f~~Vl~ai~ 69 (88)
+.+..--++||+|-.--.+.++.+|+..|+ ++.+||+. .+.|=+.+-
T Consensus 26 ~~~~~aR~ia~yl~~~~~~~s~~~Ig~~fg~r~hStV~~a~~ri~~~~~ 74 (90)
T cd06571 26 KEIALARQIAMYLARELTGLSLPEIGRAFGGRDHSTVLHAVRKIEELLE 74 (90)
T ss_pred cCcchHHHHHHHHHHHHhCCCHHHHHHHhCCCCHhHHHHHHHHHHHHHH
Confidence 568889999999999999999999999999 99999999 888866553
No 6
>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=95.13 E-value=0.026 Score=34.06 Aligned_cols=42 Identities=19% Similarity=0.239 Sum_probs=34.5
Q ss_pred CccchhHHHHHHHHHhccccchhhhhhhcc-cccchhHh-HHHH
Q 046847 23 SVVFVDEQVCMFLHALAHHVKNQTINNRFK-HSGETISR-FNSI 64 (88)
Q Consensus 23 ~~v~veE~la~FL~i~~~n~~~r~i~~~F~-~S~eTisr-f~~V 64 (88)
+.+.---++||+|-.--.+.+..+|+..|+ ++.+||.. .++|
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 457778899999999999999999999999 99999988 7765
No 7
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=95.08 E-value=0.061 Score=29.85 Aligned_cols=43 Identities=19% Similarity=0.194 Sum_probs=34.2
Q ss_pred cchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHH
Q 046847 25 VFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGV 68 (88)
Q Consensus 25 v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai 68 (88)
.+.+|+-.+-++. ..+.++.+|+..++.|.+||++ -+..++-+
T Consensus 5 L~~~er~vi~~~y-~~~~t~~eIa~~lg~s~~~V~~~~~~al~kL 48 (50)
T PF04545_consen 5 LPPREREVIRLRY-FEGLTLEEIAERLGISRSTVRRILKRALKKL 48 (50)
T ss_dssp S-HHHHHHHHHHH-TST-SHHHHHHHHTSCHHHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHh-cCCCCHHHHHHHHCCcHHHHHHHHHHHHHHh
Confidence 5667777666666 8889999999999999999999 88877654
No 8
>PRK06030 hypothetical protein; Provisional
Probab=95.05 E-value=0.035 Score=37.47 Aligned_cols=44 Identities=11% Similarity=0.153 Sum_probs=40.1
Q ss_pred CccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHH
Q 046847 23 SVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILN 66 (88)
Q Consensus 23 ~~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ 66 (88)
+.+..--|+||+|-.--.+.++..|+..||++-+||+. ++.|=+
T Consensus 51 k~i~~aRqIAMYL~r~~~~~sl~~IG~~FGRDHSTV~haikkIe~ 95 (124)
T PRK06030 51 REVSRIRQIAMYVAHVSLGWPMNEVALAFGRDRTTVGHACHTVED 95 (124)
T ss_pred cccchHHHHHHHHHHHHcCCCHHHHHHHHCCChhHHHHHHHHHHH
Confidence 46888999999999999999999999999999999999 886644
No 9
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=94.36 E-value=0.054 Score=37.21 Aligned_cols=41 Identities=15% Similarity=0.062 Sum_probs=36.3
Q ss_pred CccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHH
Q 046847 23 SVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNS 63 (88)
Q Consensus 23 ~~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~ 63 (88)
+.-+.+++-+.|-+.++.+.|.|+|+.+|++|.+||-+ .+.
T Consensus 3 k~~s~~~R~~~~~~~~~~G~S~re~Ak~~gvs~sTvy~wv~r 44 (138)
T COG3415 3 KPFSNDLRERVVDAVVGEGLSCREAAKRFGVSISTVYRWVRR 44 (138)
T ss_pred chhhHHHHHHHHHHHHHcCccHHHHHHHhCccHHHHHHHHHH
Confidence 34567899999999999999999999999999999987 654
No 10
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=94.16 E-value=0.088 Score=30.22 Aligned_cols=37 Identities=16% Similarity=0.224 Sum_probs=26.7
Q ss_pred CccchhHHHHHHHHHhccccchhhhhhhcccccchhHh
Q 046847 23 SVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR 60 (88)
Q Consensus 23 ~~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr 60 (88)
+.+|++|++.|--.. -.|.+.++|+..|+.+.+||+.
T Consensus 5 ~~LTl~eK~~iI~~~-e~g~s~~~ia~~fgv~~sTv~~ 41 (53)
T PF04218_consen 5 KSLTLEEKLEIIKRL-EEGESKRDIAREFGVSRSTVST 41 (53)
T ss_dssp SS--HHHHHHHHHHH-HCTT-HHHHHHHHT--CCHHHH
T ss_pred ccCCHHHHHHHHHHH-HcCCCHHHHHHHhCCCHHHHHH
Confidence 458999999996664 4455999999999999999997
No 11
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=93.60 E-value=0.037 Score=38.05 Aligned_cols=62 Identities=16% Similarity=0.174 Sum_probs=44.5
Q ss_pred cCCCccchhHHHHHHHHHhcc-------------ccchhhhhhhcccccchhHh-HHHHHH-HHHHhhhhhccCCCC
Q 046847 20 KTDSVVFVDEQVCMFLHALAH-------------HVKNQTINNRFKHSGETISR-FNSILN-GVLELQHILLKSPKP 81 (88)
Q Consensus 20 ~~t~~v~veE~la~FL~i~~~-------------n~~~r~i~~~F~~S~eTisr-f~~Vl~-ai~~L~~~~ik~p~~ 81 (88)
.+....++++++|-+|+.++. ..+..++++..|-+.+|||| +++.-+ -++.....-|..|++
T Consensus 134 ~~~~~~~~~~Rl~~~L~~l~~~~~~~~~~~~~~~~~t~~~lA~~lG~tr~tvsR~l~~l~~~gii~~~~~~i~i~~~ 210 (211)
T PRK11753 134 GDLAFLDVTGRIAQTLLDLAKQPDAMTHPDGMQIKITRQEIGRIVGCSREMVGRVLKMLEDQGLISAHGKTIVVYGT 210 (211)
T ss_pred HHHHhcChhhHHHHHHHHHHHhcCCcCCCCceecCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEecCCEEEEecC
Confidence 344567899999999987653 34568999999999999999 887764 333444444555543
No 12
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=93.25 E-value=0.2 Score=27.10 Aligned_cols=42 Identities=21% Similarity=0.322 Sum_probs=32.5
Q ss_pred cchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHH
Q 046847 25 VFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGV 68 (88)
Q Consensus 25 v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai 68 (88)
++.+|.- ++.+ ...+.++++|+..++.|..||.+ .+.++..+
T Consensus 4 l~~~e~~-i~~~-~~~g~s~~eia~~l~is~~tv~~~~~~~~~kl 46 (58)
T smart00421 4 LTPRERE-VLRL-LAEGLTNKEIAERLGISEKTVKTHLSNIMRKL 46 (58)
T ss_pred CCHHHHH-HHHH-HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 4445554 4444 46789999999999999999999 98887655
No 13
>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=92.77 E-value=0.13 Score=34.74 Aligned_cols=58 Identities=14% Similarity=0.240 Sum_probs=42.7
Q ss_pred CccchhHHHHHHHHHhcc--------------ccchhhhhhhcccccchhHh-HHHHHHH-HHHhhhhhccCCC
Q 046847 23 SVVFVDEQVCMFLHALAH--------------HVKNQTINNRFKHSGETISR-FNSILNG-VLELQHILLKSPK 80 (88)
Q Consensus 23 ~~v~veE~la~FL~i~~~--------------n~~~r~i~~~F~~S~eTisr-f~~Vl~a-i~~L~~~~ik~p~ 80 (88)
..-+++++||-||..++. +.+..++++.-|-|.+|||| +++.-+. ++.....-|..+|
T Consensus 111 ~~~~~~~Rla~~L~~l~~~~~~~~~~~~~~~~~~t~~~iA~~lG~tretvsR~l~~l~~~g~I~~~~~~i~I~d 184 (193)
T TIGR03697 111 AHRDMGSRLVSFLLILCRDFGVPGQRGVTIDLRLSHQAIAEAIGSTRVTITRLLGDLRKKKLISIHKKKITVHD 184 (193)
T ss_pred HhCCHHHHHHHHHHHHHHHhCCCCCCeEEecCCCCHHHHHHHhCCcHHHHHHHHHHHHHCCCEEecCCEEEEeC
Confidence 445899999999986532 35899999999999999999 9887652 4444444444443
No 14
>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=92.57 E-value=0.22 Score=31.74 Aligned_cols=42 Identities=17% Similarity=0.038 Sum_probs=33.2
Q ss_pred hhHHHHHHHHHhccccchhhhhhhcccccchhHhHHHHHHHH
Q 046847 27 VDEQVCMFLHALAHHVKNQTINNRFKHSGETISRFNSILNGV 68 (88)
Q Consensus 27 veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisrf~~Vl~ai 68 (88)
+..++.++=-++-.+.+||.|+...|.|..||+|....|+..
T Consensus 35 l~~R~~va~~lL~~g~syreIa~~tgvS~aTItRvsr~Lk~~ 76 (87)
T PF01371_consen 35 LAQRWQVAKELLDEGKSYREIAEETGVSIATITRVSRCLKYG 76 (87)
T ss_dssp HHHHHHHHHHHHHTTSSHHHHHHHHTSTHHHHHHHHHHHHHS
T ss_pred HHHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHcC
Confidence 344555554567789999999999999999999987777643
No 15
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=92.34 E-value=0.24 Score=34.99 Aligned_cols=43 Identities=9% Similarity=0.145 Sum_probs=35.8
Q ss_pred ccchhHHHHHHHHHhcc----ccchhhhhhhcccccchhHh-HHHHHH
Q 046847 24 VVFVDEQVCMFLHALAH----HVKNQTINNRFKHSGETISR-FNSILN 66 (88)
Q Consensus 24 ~v~veE~la~FL~i~~~----n~~~r~i~~~F~~S~eTisr-f~~Vl~ 66 (88)
..+++|+||-||...+. +.+..+++...|-|.+|||| +++.-+
T Consensus 148 ~~~~~~Rla~~L~~~~~~~~~~~t~~~lA~~lG~sretvsR~L~~L~~ 195 (226)
T PRK10402 148 SFPLENRLAAFILLTQEGDLYHEKHTQAAEYLGVSYRHLLYVLAQFIQ 195 (226)
T ss_pred cChHHHHHHHHHHhcccCCcccchHHHHHHHHCCcHHHHHHHHHHHHH
Confidence 34899999999986543 24679999999999999999 998654
No 16
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=91.84 E-value=0.37 Score=26.14 Aligned_cols=36 Identities=19% Similarity=0.237 Sum_probs=29.3
Q ss_pred HHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847 33 MFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVL 69 (88)
Q Consensus 33 ~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~ 69 (88)
++.+ +..+.++++|+..++.|..||.+ .+++...+.
T Consensus 8 i~~~-~~~~~s~~eia~~l~~s~~tv~~~~~~~~~~l~ 44 (57)
T cd06170 8 VLRL-LAEGKTNKEIADILGISEKTVKTHLRNIMRKLG 44 (57)
T ss_pred HHHH-HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHhC
Confidence 4444 45889999999999999999999 998876543
No 17
>PRK00149 dnaA chromosomal replication initiation protein; Reviewed
Probab=91.51 E-value=0.26 Score=38.64 Aligned_cols=47 Identities=15% Similarity=0.164 Sum_probs=42.0
Q ss_pred CCccchhHHHHHHHHHhccccchhhhhhhc-ccccchhHh-HHHHHHHH
Q 046847 22 DSVVFVDEQVCMFLHALAHHVKNQTINNRF-KHSGETISR-FNSILNGV 68 (88)
Q Consensus 22 t~~v~veE~la~FL~i~~~n~~~r~i~~~F-~~S~eTisr-f~~Vl~ai 68 (88)
++.+..--|+||+|-.--.+.++.+|+..| +|+.+||+. .+.|=+-+
T Consensus 383 ~~~~~~aR~iamyl~~~~~~~s~~~Ig~~fg~rdhstV~~a~~~i~~~~ 431 (450)
T PRK00149 383 TRNIARPRQIAMYLAKELTDLSLPEIGRAFGGRDHTTVLHAVRKIEKLL 431 (450)
T ss_pred CcccChHHHHHHHHHHHhcCCCHHHHHHHcCCCCHhHHHHHHHHHHHHH
Confidence 377888999999999999999999999999 699999999 98886544
No 18
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=91.28 E-value=0.29 Score=33.43 Aligned_cols=57 Identities=9% Similarity=0.099 Sum_probs=42.1
Q ss_pred ccchhHHHHHHHHHhcc--------------ccchhhhhhhcccccchhHh-HHHHHH-HHHHhhhhhccCCC
Q 046847 24 VVFVDEQVCMFLHALAH--------------HVKNQTINNRFKHSGETISR-FNSILN-GVLELQHILLKSPK 80 (88)
Q Consensus 24 ~v~veE~la~FL~i~~~--------------n~~~r~i~~~F~~S~eTisr-f~~Vl~-ai~~L~~~~ik~p~ 80 (88)
.-+++++||.||+.++. +.+..+|++..|-+.+|||| +++.-+ -++......|..+|
T Consensus 118 ~~~~~~Rla~~Ll~l~~~~~~~~~~~~~~~~~~t~~~iA~~lG~tretvsR~l~~l~~~g~I~~~~~~i~I~d 190 (202)
T PRK13918 118 GQRLKNRIAAALLELSDTPLATQEDSGETMIYATHDELAAAVGSVRETVTKVIGELSREGYIRSGYGKIQLLD 190 (202)
T ss_pred hCchHHHHHHHHHHHHHHhCCCCCCCCeEEecCCHHHHHHHhCccHHHHHHHHHHHHHCCCEEcCCCEEEEEC
Confidence 45689999999987653 24688999999999999999 988765 33344444454444
No 19
>smart00351 PAX Paired Box domain.
Probab=90.90 E-value=0.37 Score=31.88 Aligned_cols=42 Identities=14% Similarity=0.093 Sum_probs=35.6
Q ss_pred CCccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHH
Q 046847 22 DSVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSI 64 (88)
Q Consensus 22 t~~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~V 64 (88)
.+..+.|++..|.+..- .+.+.++|+.+|+.|..||.+ .+..
T Consensus 15 ~~~~s~~~R~riv~~~~-~G~s~~~iA~~~gvs~~tV~kwi~r~ 57 (125)
T smart00351 15 GRPLPDEERQRIVELAQ-NGVRPCDISRQLCVSHGCVSKILGRY 57 (125)
T ss_pred CCCCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 35688889888887664 678999999999999999999 7765
No 20
>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=90.64 E-value=0.35 Score=27.50 Aligned_cols=26 Identities=23% Similarity=0.351 Sum_probs=22.3
Q ss_pred ccchhhhhhhcccccchhHh-HHHHHH
Q 046847 41 HVKNQTINNRFKHSGETISR-FNSILN 66 (88)
Q Consensus 41 n~~~r~i~~~F~~S~eTisr-f~~Vl~ 66 (88)
..+.+++++.++.|.+||+| ++...+
T Consensus 25 ~~s~~ela~~~g~s~~tv~r~l~~L~~ 51 (67)
T cd00092 25 PLTRQEIADYLGLTRETVSRTLKELEE 51 (67)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 36889999999999999999 877653
No 21
>PRK14088 dnaA chromosomal replication initiation protein; Provisional
Probab=90.46 E-value=0.36 Score=38.19 Aligned_cols=47 Identities=11% Similarity=0.228 Sum_probs=41.9
Q ss_pred CCccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHH
Q 046847 22 DSVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGV 68 (88)
Q Consensus 22 t~~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai 68 (88)
++.+..--|+||+|-.=-.+.++..|+..||++..||++ .+.|=+.+
T Consensus 368 ~~~i~~aR~iamyl~r~~~~~s~~~Ig~~fgr~hstV~~a~~~i~~~~ 415 (440)
T PRK14088 368 NVKALLARRIGMYVAKNYLGSSLRTIAEKFNRSHPVVVDSVKKVKDSL 415 (440)
T ss_pred CccccHHHHHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 467888899999999998999999999999999999999 88886644
No 22
>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=90.42 E-value=0.17 Score=26.70 Aligned_cols=23 Identities=26% Similarity=0.437 Sum_probs=17.9
Q ss_pred cchhhhhhhcccccchhHh-HHHH
Q 046847 42 VKNQTINNRFKHSGETISR-FNSI 64 (88)
Q Consensus 42 ~~~r~i~~~F~~S~eTisr-f~~V 64 (88)
.+.++|++..+-+.||||| +.+.
T Consensus 3 mtr~diA~~lG~t~ETVSR~l~~l 26 (32)
T PF00325_consen 3 MTRQDIADYLGLTRETVSRILKKL 26 (32)
T ss_dssp --HHHHHHHHTS-HHHHHHHHHHH
T ss_pred cCHHHHHHHhCCcHHHHHHHHHHH
Confidence 4678999999999999999 8764
No 23
>cd00131 PAX Paired Box domain
Probab=89.97 E-value=0.48 Score=31.63 Aligned_cols=43 Identities=12% Similarity=0.092 Sum_probs=36.5
Q ss_pred CCccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHH
Q 046847 22 DSVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSIL 65 (88)
Q Consensus 22 t~~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl 65 (88)
.+..|.+.+..|.+.. ..+.+.++|+.+|+.|..||.+ .+..-
T Consensus 15 ~~~lS~d~R~rIv~~~-~~G~s~~~iA~~~~Vs~~tV~r~i~r~~ 58 (128)
T cd00131 15 GRPLPDSIRQRIVELA-QSGIRPCDISRQLRVSHGCVSKILNRYY 58 (128)
T ss_pred CCcCCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 4778888988888765 5789999999999999999999 66544
No 24
>TIGR01321 TrpR trp operon repressor, proteobacterial. This model represents TrpR, the repressor of the trp operon. It is found so far only in the gamma subdivision of the proteobacteria and in Chlamydia trachomatis. All members belong to species capable of tryptophan biosynthesis.
Probab=89.93 E-value=0.36 Score=31.25 Aligned_cols=41 Identities=17% Similarity=0.195 Sum_probs=31.4
Q ss_pred chhHHHHHHHHHhccccchhhhhhhcccccchhHhHHHHHH
Q 046847 26 FVDEQVCMFLHALAHHVKNQTINNRFKHSGETISRFNSILN 66 (88)
Q Consensus 26 ~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisrf~~Vl~ 66 (88)
-+..+++++=-.+..+.++|.|+...|.|..||+|.-+.|.
T Consensus 40 ~l~~R~~i~~~Ll~~~~tQrEIa~~lGiS~atIsR~sn~lk 80 (94)
T TIGR01321 40 DLGDRIRIVNELLNGNMSQREIASKLGVSIATITRGSNNLK 80 (94)
T ss_pred HHHHHHHHHHHHHhCCCCHHHHHHHhCCChhhhhHHHhhcc
Confidence 34445555555566889999999999999999999555554
No 25
>PRK14087 dnaA chromosomal replication initiation protein; Provisional
Probab=89.69 E-value=0.48 Score=37.68 Aligned_cols=47 Identities=13% Similarity=0.166 Sum_probs=42.1
Q ss_pred CCccchhHHHHHHHHHhccccchhhhhhhcc-cccchhHh-HHHHHHHH
Q 046847 22 DSVVFVDEQVCMFLHALAHHVKNQTINNRFK-HSGETISR-FNSILNGV 68 (88)
Q Consensus 22 t~~v~veE~la~FL~i~~~n~~~r~i~~~F~-~S~eTisr-f~~Vl~ai 68 (88)
++.+..--|+||+|-.--.+.++..|+..|| |+-+||.. .+.|=+.+
T Consensus 382 ~~~i~~~RqiamyL~r~~t~~sl~~IG~~FggrdHsTV~~a~~ki~~~~ 430 (450)
T PRK14087 382 SKSIVTARHIAMYLTKEILNHTLAQIGEEFGGRDHTTVINAERKIEKML 430 (450)
T ss_pred CccccHHHHHHHHHHHHHcCCCHHHHHHHhCCCChHHHHHHHHHHHHHH
Confidence 5678899999999999999999999999997 99999998 88876554
No 26
>PRK04217 hypothetical protein; Provisional
Probab=89.66 E-value=0.81 Score=30.25 Aligned_cols=48 Identities=15% Similarity=0.060 Sum_probs=37.8
Q ss_pred CCccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847 22 DSVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE 70 (88)
Q Consensus 22 t~~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~ 70 (88)
...++.+|+- ++...--++.++.+|+..++.|..||.+ ++...+.+-.
T Consensus 40 ~~~Lt~eere-ai~l~~~eGlS~~EIAk~LGIS~sTV~r~L~RArkkLre 88 (110)
T PRK04217 40 PIFMTYEEFE-ALRLVDYEGLTQEEAGKRMGVSRGTVWRALTSARKKVAQ 88 (110)
T ss_pred cccCCHHHHH-HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 3667788874 4444455889999999999999999999 9987776643
No 27
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=89.54 E-value=0.42 Score=33.53 Aligned_cols=58 Identities=22% Similarity=0.319 Sum_probs=41.8
Q ss_pred CccchhHHHHHHHHHhcc--------------ccchhhhhhhcccccchhHh-HHHHHH-HHHHhhhhhccCCC
Q 046847 23 SVVFVDEQVCMFLHALAH--------------HVKNQTINNRFKHSGETISR-FNSILN-GVLELQHILLKSPK 80 (88)
Q Consensus 23 ~~v~veE~la~FL~i~~~--------------n~~~r~i~~~F~~S~eTisr-f~~Vl~-ai~~L~~~~ik~p~ 80 (88)
..-+++|++|-||..++. +.+..+|++..|-|.+|||| +++.=+ -++++....|..+|
T Consensus 152 ~~~~~~~Rla~~L~~l~~~~~~~~~~~~~~~~~lt~~~iA~~lG~sr~tvsR~l~~l~~~g~I~~~~~~i~i~d 225 (235)
T PRK11161 152 SKKNAEERLAAFIYNLSRRFAQRGFSPREFRLTMTRGDIGNYLGLTVETISRLLGRFQKSGMLAVKGKYITIEN 225 (235)
T ss_pred hCCCHHHHHHHHHHHHHHHHhhcCCCCceeEccccHHHHHHHhCCcHHHHHHHHHHHHHCCCEEecCCEEEEcC
Confidence 446889999999998753 35778999999999999999 876533 23334444444443
No 28
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=89.50 E-value=0.23 Score=27.22 Aligned_cols=27 Identities=22% Similarity=0.209 Sum_probs=19.5
Q ss_pred HhccccchhhhhhhcccccchhHh-HHH
Q 046847 37 ALAHHVKNQTINNRFKHSGETISR-FNS 63 (88)
Q Consensus 37 i~~~n~~~r~i~~~F~~S~eTisr-f~~ 63 (88)
.+..+.+.++|+..|+.|..||++ .+.
T Consensus 13 l~~~G~s~~~ia~~lgvs~~Tv~~w~kr 40 (50)
T PF13384_consen 13 LLREGWSIREIAKRLGVSRSTVYRWIKR 40 (50)
T ss_dssp HHHHT--HHHHHHHHTS-HHHHHHHHT-
T ss_pred HHHCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 334499999999999999999999 654
No 29
>PRK14086 dnaA chromosomal replication initiation protein; Provisional
Probab=89.43 E-value=0.63 Score=38.90 Aligned_cols=48 Identities=17% Similarity=0.201 Sum_probs=42.8
Q ss_pred CCccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847 22 DSVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVL 69 (88)
Q Consensus 22 t~~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~ 69 (88)
++.+..--|+||||-.--.+.++..|+..|+|+-.||.. +++|=+.+-
T Consensus 550 ~~~i~~aRqiAMYL~r~lt~~Sl~~IG~~FgRdHSTV~~A~~kI~~~~~ 598 (617)
T PRK14086 550 SRVLVTARQIAMYLCRELTDLSLPKIGQQFGRDHTTVMHADRKIRALMA 598 (617)
T ss_pred CcccchHHHHHHHHHHHHcCCCHHHHHHHhCCChhHHHHHHHHHHHHHH
Confidence 467888899999999999999999999999999999999 998866443
No 30
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=89.38 E-value=0.34 Score=26.73 Aligned_cols=29 Identities=17% Similarity=0.217 Sum_probs=24.0
Q ss_pred HHhccccchhhhhhhcccccchhHh-HHHH
Q 046847 36 HALAHHVKNQTINNRFKHSGETISR-FNSI 64 (88)
Q Consensus 36 ~i~~~n~~~r~i~~~F~~S~eTisr-f~~V 64 (88)
..+..+.++..|+..++.|-+||.| |++.
T Consensus 22 ~~~~~~~s~~~vA~~~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 22 KLLRESRSFKDVARELGVSWSTVRRIFDRY 51 (52)
T ss_pred HHHhhcCCHHHHHHHHCCCHHHHHHHHHhh
Confidence 3445556999999999999999999 8763
No 31
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=89.12 E-value=0.47 Score=33.68 Aligned_cols=58 Identities=19% Similarity=0.277 Sum_probs=41.6
Q ss_pred CccchhHHHHHHHHHhcc----------ccchhhhhhhcccccchhHh-HHHHHH-HHHHhhh-hhccCCC
Q 046847 23 SVVFVDEQVCMFLHALAH----------HVKNQTINNRFKHSGETISR-FNSILN-GVLELQH-ILLKSPK 80 (88)
Q Consensus 23 ~~v~veE~la~FL~i~~~----------n~~~r~i~~~F~~S~eTisr-f~~Vl~-ai~~L~~-~~ik~p~ 80 (88)
...+++++||-||...+. ..+..+|++..+-+.+|+|| +++.-+ -++.... ..|...|
T Consensus 151 ~~~~~~~Rla~~Ll~l~~~~g~~~~i~i~lt~~~IA~~lGisretlsR~L~~L~~~GlI~~~~~~~i~I~D 221 (230)
T PRK09391 151 GRKTAMERVAAFLLEMDERLGGAGMMALPMSRRDIADYLGLTIETVSRALSQLQDRGLIGLSGARQIELRN 221 (230)
T ss_pred cCCCHHHHHHHHHHHHHHHhCCCCEEEecCCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEecCCceEEEcC
Confidence 446899999999988643 35678999999999999999 876654 2333332 3444444
No 32
>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=89.00 E-value=0.56 Score=29.79 Aligned_cols=37 Identities=19% Similarity=0.127 Sum_probs=28.9
Q ss_pred chhHHHHHHHHHhccccchhhhhhhcccccchhHhHHH
Q 046847 26 FVDEQVCMFLHALAHHVKNQTINNRFKHSGETISRFNS 63 (88)
Q Consensus 26 ~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisrf~~ 63 (88)
+..++-.|+.| ++.+.+++.|+..++.|..||+|..+
T Consensus 36 ~Ls~R~~I~~l-l~~G~S~~eIA~~LgISrsTIyRi~R 72 (88)
T TIGR02531 36 SLAQRLQVAKM-LKQGKTYSDIEAETGASTATISRVKR 72 (88)
T ss_pred hhhHHHHHHHH-HHCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 35666555555 66778999999999999999999333
No 33
>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=88.93 E-value=0.17 Score=27.84 Aligned_cols=27 Identities=26% Similarity=0.306 Sum_probs=19.7
Q ss_pred HHhccccchhhhhhhcccccchhHh-HH
Q 046847 36 HALAHHVKNQTINNRFKHSGETISR-FN 62 (88)
Q Consensus 36 ~i~~~n~~~r~i~~~F~~S~eTisr-f~ 62 (88)
-+...+.+..+|+..|+.|..||-| ++
T Consensus 16 ~l~~~G~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 16 ELYAEGMSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp HHHHTT--HHHHHHHTTS-HHHHHHHHC
T ss_pred HHHHCCCCHHHHHHHHCcCHHHHHHHHh
Confidence 3445669999999999999999988 54
No 34
>PF13730 HTH_36: Helix-turn-helix domain
Probab=88.87 E-value=0.72 Score=25.65 Aligned_cols=23 Identities=17% Similarity=0.306 Sum_probs=20.5
Q ss_pred chhhhhhhcccccchhHh-HHHHH
Q 046847 43 KNQTINNRFKHSGETISR-FNSIL 65 (88)
Q Consensus 43 ~~r~i~~~F~~S~eTisr-f~~Vl 65 (88)
|++.+++..+.|..||.| +++.-
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~L~ 50 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKELE 50 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHH
Confidence 789999999999999999 87653
No 35
>PRK12422 chromosomal replication initiation protein; Provisional
Probab=88.71 E-value=0.59 Score=37.20 Aligned_cols=47 Identities=17% Similarity=0.235 Sum_probs=42.4
Q ss_pred CCccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHH
Q 046847 22 DSVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGV 68 (88)
Q Consensus 22 t~~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai 68 (88)
++.+..--|+||||-.-=.+.|+..|+..|||+-.||.. .++|=+.+
T Consensus 378 ~~~i~~~Rqiamyl~r~~t~~s~~~IG~~fgrdHsTV~~a~~ki~~~~ 425 (445)
T PRK12422 378 SREYVLPRQVAMYLCRQKLSLSYVKIGDVFSRDHSTVISSIRAISQKL 425 (445)
T ss_pred CcccccHHHHHHHHHHHhcCCCHHHHHHHhCCChHHHHHHHHHHHHHH
Confidence 477888899999999999999999999999999999998 88876555
No 36
>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=88.61 E-value=0.56 Score=27.48 Aligned_cols=38 Identities=26% Similarity=0.428 Sum_probs=28.5
Q ss_pred HHHHHHHHHhcc---------------ccchhhhhhhcccccchhHh-HHHHHH
Q 046847 29 EQVCMFLHALAH---------------HVKNQTINNRFKHSGETISR-FNSILN 66 (88)
Q Consensus 29 E~la~FL~i~~~---------------n~~~r~i~~~F~~S~eTisr-f~~Vl~ 66 (88)
|+||-||..++. +.+..++++..+-|.+||+| +++.-+
T Consensus 1 ~Rla~~Ll~l~~~~~~~~~~~~~~~~~~lt~~~iA~~~g~sr~tv~r~l~~l~~ 54 (76)
T PF13545_consen 1 QRLARFLLELAERFGRRQDGDGIRIPLPLTQEEIADMLGVSRETVSRILKRLKD 54 (76)
T ss_dssp HHHHHHHHHHHHHHEEEEETTEEEEEEESSHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred ChHHHHHHHHHHHHCCCCCCCCceEEecCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 456666666553 34678999999999999999 887654
No 37
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=88.31 E-value=0.67 Score=32.57 Aligned_cols=44 Identities=14% Similarity=0.243 Sum_probs=35.4
Q ss_pred CCccchhHHHHHHHHHhcc----------ccchhhhhhhcccccchhHh-HHHHH
Q 046847 22 DSVVFVDEQVCMFLHALAH----------HVKNQTINNRFKHSGETISR-FNSIL 65 (88)
Q Consensus 22 t~~v~veE~la~FL~i~~~----------n~~~r~i~~~F~~S~eTisr-f~~Vl 65 (88)
...-++++++|-||+..+. +.+..+|+...|-+.+|||| +++.-
T Consensus 144 ~~~~~~~~Rla~~Ll~~~~~~~~~~~~~i~~t~~~iA~~lG~tretvsR~l~~L~ 198 (236)
T PRK09392 144 QKLRSSAERLANYLLKQSLRQGGADVVTLPYEKRVLASYLGMTPENLSRAFAALA 198 (236)
T ss_pred hhcCCHHHHHHHHHHHhccccCCCcEEEeeCCHHHHHHHhCCChhHHHHHHHHHH
Confidence 3456899999999997653 23457899999999999999 98853
No 38
>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=87.43 E-value=0.81 Score=25.37 Aligned_cols=35 Identities=11% Similarity=0.252 Sum_probs=23.0
Q ss_pred hHHHHHHHHHhccc-cchhhhhhhcccccchhHh-HH
Q 046847 28 DEQVCMFLHALAHH-VKNQTINNRFKHSGETISR-FN 62 (88)
Q Consensus 28 eE~la~FL~i~~~n-~~~r~i~~~F~~S~eTisr-f~ 62 (88)
||++.--+--+-.+ .|.|.++..|+.+.+|+++ .+
T Consensus 2 ee~l~~Ai~~v~~g~~S~r~AA~~ygVp~sTL~~r~~ 38 (45)
T PF05225_consen 2 EEDLQKAIEAVKNGKMSIRKAAKKYGVPRSTLRRRLR 38 (45)
T ss_dssp HHHHHHHHHHHHTTSS-HHHHHHHHT--HHHHHHHHH
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHc
Confidence 44444444444444 9999999999999999987 54
No 39
>PRK01381 Trp operon repressor; Provisional
Probab=86.80 E-value=0.62 Score=30.48 Aligned_cols=42 Identities=17% Similarity=0.176 Sum_probs=30.2
Q ss_pred hhHHHHHHHHHhccccchhhhhhhcccccchhHhHHHHHHHH
Q 046847 27 VDEQVCMFLHALAHHVKNQTINNRFKHSGETISRFNSILNGV 68 (88)
Q Consensus 27 veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisrf~~Vl~ai 68 (88)
+..++.|+=.-+....++|.|+...|.|..||+|--..|+..
T Consensus 41 l~~R~~I~~~L~~g~~sQREIa~~lGvSiaTITRgsn~Lk~~ 82 (99)
T PRK01381 41 LGTRVRIVEELLRGELSQREIKQELGVGIATITRGSNSLKTA 82 (99)
T ss_pred HHHHHHHHHHHHcCCcCHHHHHHHhCCceeeehhhHHHhccC
Confidence 334444444444556999999999999999999966665543
No 40
>PRK09492 treR trehalose repressor; Provisional
Probab=86.28 E-value=0.44 Score=34.34 Aligned_cols=32 Identities=16% Similarity=0.121 Sum_probs=26.9
Q ss_pred ccchhhhhhhcccccchhHh-HHH-----------HHHHHHHhh
Q 046847 41 HVKNQTINNRFKHSGETISR-FNS-----------ILNGVLELQ 72 (88)
Q Consensus 41 n~~~r~i~~~F~~S~eTisr-f~~-----------Vl~ai~~L~ 72 (88)
..+.++|+...|.|..|||| ++. |++++-+|.
T Consensus 4 ~~ti~dIA~~agVS~~TVSrvLn~~~~vs~~tr~rV~~~a~elg 47 (315)
T PRK09492 4 KLTIKDIARLSGVGKSTVSRVLNNESGVSEETRERVEAVINQHG 47 (315)
T ss_pred CCcHHHHHHHhCCCHHHHhHHhCCCCCCCHHHHHHHHHHHHHHC
Confidence 35789999999999999999 985 777776664
No 41
>PF13340 DUF4096: Putative transposase of IS4/5 family (DUF4096)
Probab=86.19 E-value=1.5 Score=26.36 Aligned_cols=63 Identities=16% Similarity=0.144 Sum_probs=49.8
Q ss_pred ChHHHHHHHHHHhhCcCCcCCCccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHH
Q 046847 2 DRKTFGLLFELLCSDERLKTDSVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSIL 65 (88)
Q Consensus 2 ~~~~F~~L~~~L~~~~~L~~t~~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl 65 (88)
+-+.+..+...|.....-.....++..+-+--.||++.++..-|.+-..|+ +..||.+ |+.-.
T Consensus 2 sD~~W~~i~p~lp~~~~~~~~~~~~~R~v~~ail~~lrtG~~Wr~LP~~fg-~~~tv~~~f~rW~ 65 (75)
T PF13340_consen 2 SDEEWALIEPLLPPRKPRGGRPRIDLREVLNAILYVLRTGCPWRDLPEDFG-PWSTVYRRFRRWS 65 (75)
T ss_pred CHHHHHHHHhhCCCCCCCCCCCccchHHHHhcccccceecceecccchhcc-CcCcHHHHHHHHH
Confidence 445566666677665543344668888989888999999999999999999 8889999 98743
No 42
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=85.94 E-value=1.5 Score=28.95 Aligned_cols=44 Identities=5% Similarity=0.080 Sum_probs=37.4
Q ss_pred cchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847 25 VFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE 70 (88)
Q Consensus 25 v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~ 70 (88)
++.+++-++.|+. .+.++..|+..++.|..||.. .+.....+-.
T Consensus 113 L~~~~r~il~l~~--~g~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~ 157 (166)
T PRK09639 113 MTERDRTVLLLRF--SGYSYKEIAEALGIKESSVGTTLARAKKKFRK 157 (166)
T ss_pred CCHHHHHHHHHHH--cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 5666777777777 999999999999999999999 8888777654
No 43
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=85.67 E-value=1.3 Score=24.21 Aligned_cols=38 Identities=8% Similarity=0.112 Sum_probs=30.4
Q ss_pred HHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHH
Q 046847 29 EQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILN 66 (88)
Q Consensus 29 E~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ 66 (88)
-++.|-........+..++++.++-|.+|||+ .+...+
T Consensus 3 ~R~~Il~~L~~~~~~~~el~~~l~~s~~~vs~hL~~L~~ 41 (47)
T PF01022_consen 3 TRLRILKLLSEGPLTVSELAEELGLSQSTVSHHLKKLRE 41 (47)
T ss_dssp HHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhCCCchhhHHHhccccchHHHHHHHHHHH
Confidence 35666667777889999999999999999999 877653
No 44
>PF13518 HTH_28: Helix-turn-helix domain
Probab=85.54 E-value=1.5 Score=23.72 Aligned_cols=35 Identities=17% Similarity=0.126 Sum_probs=26.4
Q ss_pred HHHHHHHhccccchhhhhhhcccccchhHh-HHHHHH
Q 046847 31 VCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILN 66 (88)
Q Consensus 31 la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ 66 (88)
+.+-..+. .+.+.+.++..|+.|..||.+ .+....
T Consensus 3 ~~iv~~~~-~g~s~~~~a~~~gis~~tv~~w~~~y~~ 38 (52)
T PF13518_consen 3 LQIVELYL-EGESVREIAREFGISRSTVYRWIKRYRE 38 (52)
T ss_pred HHHHHHHH-cCCCHHHHHHHHCCCHhHHHHHHHHHHh
Confidence 44444455 455999999999999999998 766554
No 45
>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=84.85 E-value=1.8 Score=25.31 Aligned_cols=39 Identities=18% Similarity=0.268 Sum_probs=30.2
Q ss_pred hhHHHHHHHHHhc---cccchhhhhhhcccccchhHh-HHHHH
Q 046847 27 VDEQVCMFLHALA---HHVKNQTINNRFKHSGETISR-FNSIL 65 (88)
Q Consensus 27 veE~la~FL~i~~---~n~~~r~i~~~F~~S~eTisr-f~~Vl 65 (88)
.+|.---.+|.+. ...+..+|+.+++.|..||+. +++.-
T Consensus 5 ~~e~YL~~Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml~~L~ 47 (60)
T PF01325_consen 5 SEEDYLKAIYELSEEGGPVRTKDIAERLGVSPPTVTEMLKRLA 47 (60)
T ss_dssp HHHHHHHHHHHHHHCTSSBBHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHcCCCCccHHHHHHHHCCChHHHHHHHHHHH
Confidence 4455556667666 789999999999999999998 77654
No 46
>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=84.25 E-value=2.3 Score=22.14 Aligned_cols=28 Identities=14% Similarity=0.214 Sum_probs=24.4
Q ss_pred ccccchhhhhhhcccccchhHh-HHHHHH
Q 046847 39 AHHVKNQTINNRFKHSGETISR-FNSILN 66 (88)
Q Consensus 39 ~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ 66 (88)
..+.++.+|+..++.|..||.+ .+....
T Consensus 24 ~~~~~~~~ia~~~~~s~~~i~~~~~~~~~ 52 (55)
T cd06171 24 GEGLSYEEIAEILGISRSTVRQRLHRALK 52 (55)
T ss_pred hcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 3778999999999999999999 877654
No 47
>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=82.85 E-value=1.9 Score=24.63 Aligned_cols=39 Identities=8% Similarity=0.070 Sum_probs=32.3
Q ss_pred hHHHHHHHHH-hccccchhhhhhhcccccchhHh-HHHHHH
Q 046847 28 DEQVCMFLHA-LAHHVKNQTINNRFKHSGETISR-FNSILN 66 (88)
Q Consensus 28 eE~la~FL~i-~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ 66 (88)
.-++.|.-+. .+.+.+..+++..++.+..|+++ .+..-+
T Consensus 10 p~R~~Il~~L~~~~~~t~~ela~~l~~~~~t~s~hL~~L~~ 50 (61)
T PF12840_consen 10 PTRLRILRLLASNGPMTVSELAEELGISQSTVSYHLKKLEE 50 (61)
T ss_dssp HHHHHHHHHHHHCSTBEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4567777777 88899999999999999999999 887654
No 48
>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=82.58 E-value=2.6 Score=26.37 Aligned_cols=44 Identities=14% Similarity=0.095 Sum_probs=34.0
Q ss_pred cchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847 25 VFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVL 69 (88)
Q Consensus 25 v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~ 69 (88)
++-.|+-.+.++. ..+.+..+|+..++.|.+||++ .+.+++.+-
T Consensus 111 L~~~~~~ii~~~~-~~g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~ 155 (158)
T TIGR02937 111 LPEREREVLVLRY-LEGLSYKEIAEILGISVGTVKRRLKRARKKLR 155 (158)
T ss_pred CCHHHHHHHhhHH-hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4555555555543 3689999999999999999999 988877653
No 49
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
Probab=82.35 E-value=3 Score=26.89 Aligned_cols=44 Identities=11% Similarity=0.086 Sum_probs=34.7
Q ss_pred ccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHH
Q 046847 24 VVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGV 68 (88)
Q Consensus 24 ~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai 68 (88)
.++.+++-++-|+.+ .+.++..|+..+|.|.+||.. .+.....+
T Consensus 113 ~L~~~~r~il~l~~~-~~~~~~eIA~~lgis~~tv~~~~~ra~~~L 157 (161)
T TIGR02985 113 KLPEQCRKIFILSRF-EGKSYKEIAEELGISVKTVEYHISKALKEL 157 (161)
T ss_pred HCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 345666777777555 689999999999999999999 77776554
No 50
>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=82.00 E-value=3.8 Score=22.54 Aligned_cols=42 Identities=12% Similarity=0.099 Sum_probs=28.1
Q ss_pred cchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHH
Q 046847 25 VFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNG 67 (88)
Q Consensus 25 v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~a 67 (88)
++.+++-++.| .--.+.++.+|+..++.|.+||.. .+..++.
T Consensus 11 L~~~~r~i~~l-~~~~g~s~~eIa~~l~~s~~~v~~~l~ra~~~ 53 (54)
T PF08281_consen 11 LPERQREIFLL-RYFQGMSYAEIAEILGISESTVKRRLRRARKK 53 (54)
T ss_dssp S-HHHHHHHHH-HHTS---HHHHHHHCTS-HHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHH-HHHHCcCHHHHHHHHCcCHHHHHHHHHHHHhh
Confidence 55566665555 445679999999999999999998 8776543
No 51
>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=81.74 E-value=3.2 Score=22.43 Aligned_cols=26 Identities=12% Similarity=0.349 Sum_probs=21.4
Q ss_pred ccchhhhhhhcccccchhHh-HHHHHH
Q 046847 41 HVKNQTINNRFKHSGETISR-FNSILN 66 (88)
Q Consensus 41 n~~~r~i~~~F~~S~eTisr-f~~Vl~ 66 (88)
+.+.++++...+-|..||++ +++..+
T Consensus 17 ~~t~~ela~~~~is~~tv~~~l~~L~~ 43 (48)
T PF13412_consen 17 RITQKELAEKLGISRSTVNRYLKKLEE 43 (48)
T ss_dssp TS-HHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 39999999999999999999 888763
No 52
>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]
Probab=81.72 E-value=2.8 Score=33.43 Aligned_cols=50 Identities=14% Similarity=0.167 Sum_probs=43.9
Q ss_pred cCCCccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847 20 KTDSVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVL 69 (88)
Q Consensus 20 ~~t~~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~ 69 (88)
+-++++..--|+||+|-.-=.+.|.-.|+..|+|.-.||.. .++|-+-+-
T Consensus 344 ~R~~~i~~~RqiamyL~r~lt~~Slp~IG~~FgrdHtTV~~a~~kI~~~~~ 394 (408)
T COG0593 344 SRTRNIVRPRQIAMYLARELTNLSLPEIGKAFGRDHTTVLHAVRKIEQLIE 394 (408)
T ss_pred ccccccchHHHHHHHHHHHHccCcHHHHHHHhCCCccHHHHHHHHHHHHHh
Confidence 34588889999999999999999999999999999999988 888765553
No 53
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=81.62 E-value=3.8 Score=26.79 Aligned_cols=43 Identities=9% Similarity=0.055 Sum_probs=34.3
Q ss_pred HHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH-hhhhh
Q 046847 33 MFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE-LQHIL 75 (88)
Q Consensus 33 ~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~-L~~~~ 75 (88)
+|+...-.+.+++.|+...+.|..||.. .+..+..+-. |....
T Consensus 114 v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~~ 158 (161)
T PRK09047 114 AFLLRYWEDMDVAETAAAMGCSEGSVKTHCSRATHALAKALEAKG 158 (161)
T ss_pred HHHHHHHhcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhcC
Confidence 4555556889999999999999999999 8888887754 44443
No 54
>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=81.56 E-value=2.2 Score=19.86 Aligned_cols=34 Identities=21% Similarity=0.035 Sum_probs=23.5
Q ss_pred chhHHHHHHHHHhccccchhhhhhhcccccchhHh
Q 046847 26 FVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR 60 (88)
Q Consensus 26 ~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr 60 (88)
+.++...+.. ..-.+.+.++++..|+.|..||++
T Consensus 7 ~~~~~~~i~~-~~~~~~s~~~ia~~~~is~~tv~~ 40 (42)
T cd00569 7 TPEQIEEARR-LLAAGESVAEIARRLGVSRSTLYR 40 (42)
T ss_pred CHHHHHHHHH-HHHcCCCHHHHHHHHCCCHHHHHH
Confidence 3344433333 344566999999999999999975
No 55
>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=81.45 E-value=2.9 Score=23.10 Aligned_cols=35 Identities=14% Similarity=0.224 Sum_probs=25.4
Q ss_pred HHHHHHHhccccchhhhhhhcccccchhHh-HHHHH
Q 046847 31 VCMFLHALAHHVKNQTINNRFKHSGETISR-FNSIL 65 (88)
Q Consensus 31 la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl 65 (88)
+-.+|..-..+.+-..+++.|+.|..||.+ .+++=
T Consensus 5 il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i~~L~ 40 (55)
T PF08279_consen 5 ILKLLLESKEPITAKELAEELGVSRRTIRRDIKELR 40 (55)
T ss_dssp HHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHHHHHH
T ss_pred HHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 333444444458899999999999999999 88763
No 56
>smart00760 Bac_DnaA_C Bacterial dnaA protein helix-turn-helix domain. Could be involved in DNA-binding.
Probab=81.32 E-value=1.9 Score=24.85 Aligned_cols=33 Identities=15% Similarity=0.267 Sum_probs=29.5
Q ss_pred CCccchhHHHHHHHHHhccccchhhhhhhcc-cc
Q 046847 22 DSVVFVDEQVCMFLHALAHHVKNQTINNRFK-HS 54 (88)
Q Consensus 22 t~~v~veE~la~FL~i~~~n~~~r~i~~~F~-~S 54 (88)
++.+..--++||+|-.--.+.++.+|+..|+ ++
T Consensus 26 ~~~~~~aR~iamyla~~~~~~sl~~Ig~~fg~rd 59 (60)
T smart00760 26 KREIVLARQIAMYLARELTDLSLPEIGKIFGGRD 59 (60)
T ss_pred CcchhHHHHHHHHHHHHHHCCCHHHHHHHhCCCC
Confidence 5778889999999999999999999999998 54
No 57
>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=81.24 E-value=1.2 Score=25.63 Aligned_cols=26 Identities=27% Similarity=0.333 Sum_probs=22.0
Q ss_pred cccchhhhhhhcccccchhHh-HHHHH
Q 046847 40 HHVKNQTINNRFKHSGETISR-FNSIL 65 (88)
Q Consensus 40 ~n~~~r~i~~~F~~S~eTisr-f~~Vl 65 (88)
...+..++++.|+.|..||.| +++.-
T Consensus 13 ~~~s~~ela~~~~VS~~TiRRDl~~L~ 39 (57)
T PF08220_consen 13 GKVSVKELAEEFGVSEMTIRRDLNKLE 39 (57)
T ss_pred CCEEHHHHHHHHCcCHHHHHHHHHHHH
Confidence 347888899999999999999 88643
No 58
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=80.78 E-value=3.4 Score=26.98 Aligned_cols=49 Identities=2% Similarity=-0.001 Sum_probs=43.0
Q ss_pred CCcCCCccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHH
Q 046847 18 RLKTDSVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILN 66 (88)
Q Consensus 18 ~L~~t~~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ 66 (88)
+....+.-+.|+++.+-...+..+.+.++++..|+.|..|+.+ .++...
T Consensus 6 ~~~~rr~ys~EfK~~aV~~~~~~g~sv~evA~e~gIs~~tl~~W~r~y~~ 55 (121)
T PRK09413 6 GPEKRRRRTTQEKIAIVQQSFEPGMTVSLVARQHGVAASQLFLWRKQYQE 55 (121)
T ss_pred CCCCCCCCCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHhh
Confidence 4455678899999999999999999999999999999999999 888653
No 59
>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=80.49 E-value=2 Score=26.87 Aligned_cols=24 Identities=13% Similarity=0.165 Sum_probs=21.3
Q ss_pred cccchhhhhhhcccccchhHh-HHH
Q 046847 40 HHVKNQTINNRFKHSGETISR-FNS 63 (88)
Q Consensus 40 ~n~~~r~i~~~F~~S~eTisr-f~~ 63 (88)
+..+-.+++..||.|.+|||| ++.
T Consensus 18 ~~~ti~dvA~~~gvS~~TVsr~L~~ 42 (80)
T TIGR02844 18 TKATVRETAKVFGVSKSTVHKDVTE 42 (80)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHhcC
Confidence 567889999999999999999 864
No 60
>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=79.79 E-value=0.79 Score=25.67 Aligned_cols=20 Identities=30% Similarity=0.297 Sum_probs=17.5
Q ss_pred hhhhhhhcccccchhHh-HHH
Q 046847 44 NQTINNRFKHSGETISR-FNS 63 (88)
Q Consensus 44 ~r~i~~~F~~S~eTisr-f~~ 63 (88)
.++|+..-|.|..|||| ++.
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 46889999999999999 874
No 61
>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=79.65 E-value=4.2 Score=22.68 Aligned_cols=24 Identities=21% Similarity=0.335 Sum_probs=20.8
Q ss_pred cchhhhhhhcccccchhHh-HHHHH
Q 046847 42 VKNQTINNRFKHSGETISR-FNSIL 65 (88)
Q Consensus 42 ~~~r~i~~~F~~S~eTisr-f~~Vl 65 (88)
.+..+|+..++.+..||++ .+..-
T Consensus 22 ~t~~~la~~l~~~~~~vs~~v~~L~ 46 (62)
T PF12802_consen 22 LTQSELAERLGISKSTVSRIVKRLE 46 (62)
T ss_dssp EEHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred cCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 6999999999999999999 87765
No 62
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=79.51 E-value=1.2 Score=32.39 Aligned_cols=32 Identities=16% Similarity=0.129 Sum_probs=26.8
Q ss_pred ccchhhhhhhcccccchhHh-HHH-----------HHHHHHHhh
Q 046847 41 HVKNQTINNRFKHSGETISR-FNS-----------ILNGVLELQ 72 (88)
Q Consensus 41 n~~~r~i~~~F~~S~eTisr-f~~-----------Vl~ai~~L~ 72 (88)
..+.++|+...|.|..|||| ++. |++++-+|.
T Consensus 6 ~~Ti~dIA~~agVS~~TVSr~Ln~~~~vs~~tr~~V~~~a~elg 49 (342)
T PRK10014 6 KITIHDVALAAGVSVSTVSLVLSGKGRISTATGERVNQAIEELG 49 (342)
T ss_pred CCcHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHhC
Confidence 46889999999999999999 987 666666664
No 63
>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=79.44 E-value=2.4 Score=23.93 Aligned_cols=35 Identities=23% Similarity=0.279 Sum_probs=29.1
Q ss_pred HHHhccccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847 35 LHALAHHVKNQTINNRFKHSGETISR-FNSILNGVL 69 (88)
Q Consensus 35 L~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~ 69 (88)
|..++.+.++..|+...+.|..||.. ...+.+-+.
T Consensus 12 l~~l~~G~~~~eIA~~l~is~~tV~~~~~~i~~Kl~ 47 (58)
T PF00196_consen 12 LRLLAQGMSNKEIAEELGISEKTVKSHRRRIMKKLG 47 (58)
T ss_dssp HHHHHTTS-HHHHHHHHTSHHHHHHHHHHHHHHHHT
T ss_pred HHHHHhcCCcchhHHhcCcchhhHHHHHHHHHHHhC
Confidence 45677889999999999999999999 888876653
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=78.88 E-value=3.6 Score=30.17 Aligned_cols=46 Identities=11% Similarity=0.086 Sum_probs=36.7
Q ss_pred cchhHHHHHHHHHh-ccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847 25 VFVDEQVCMFLHAL-AHHVKNQTINNRFKHSGETISR-FNSILNGVLE 70 (88)
Q Consensus 25 v~veE~la~FL~i~-~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~ 70 (88)
.+-.|+..+-|+.. ..+.+++.|+..++.|.++|++ -++.|.-+-.
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 56667777777664 3478999999999999999999 8888776643
No 65
>COG0664 Crp cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]
Probab=78.67 E-value=3.4 Score=27.49 Aligned_cols=44 Identities=23% Similarity=0.338 Sum_probs=37.9
Q ss_pred CccchhHHHHHHHHHhcc--------------ccchhhhhhhcccccchhHh-HHHHHH
Q 046847 23 SVVFVDEQVCMFLHALAH--------------HVKNQTINNRFKHSGETISR-FNSILN 66 (88)
Q Consensus 23 ~~v~veE~la~FL~i~~~--------------n~~~r~i~~~F~~S~eTisr-f~~Vl~ 66 (88)
..-+++++++.+|..++. ..+...++...+-+.+|++| +++.-+
T Consensus 139 ~~~~~~~r~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~ia~~~g~~~~~vsr~l~~l~~ 197 (214)
T COG0664 139 ARKDVEERLARFLLNLGRRLGIATEDGILIPLPLTHKDLAEYLGLSRETVSRILKELRK 197 (214)
T ss_pred hhccHHHHHHHHHHHHhhccCCCCCCCcEEeccCCHHHHHHHhCCchhhHHHHHHHHHh
Confidence 456899999999999884 57889999999999999999 887653
No 66
>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=78.56 E-value=3.7 Score=29.36 Aligned_cols=47 Identities=11% Similarity=0.095 Sum_probs=38.7
Q ss_pred ccchhHHHHHHHHHh---ccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847 24 VVFVDEQVCMFLHAL---AHHVKNQTINNRFKHSGETISR-FNSILNGVLE 70 (88)
Q Consensus 24 ~v~veE~la~FL~i~---~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~ 70 (88)
..+..|+..+.|+.. ..+.+++.|+..++.|.++|++ .+..++-+-.
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 356667777777663 5789999999999999999999 8888877754
No 67
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=78.13 E-value=4 Score=29.74 Aligned_cols=46 Identities=15% Similarity=0.122 Sum_probs=37.1
Q ss_pred ccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847 24 VVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE 70 (88)
Q Consensus 24 ~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~ 70 (88)
.++-.++-.+.|+. ..+.++..|+..+|.|.+||++ .+..+.-+-.
T Consensus 203 ~L~~~~r~vl~l~y-~~~~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~ 249 (256)
T PRK07408 203 QLEERTREVLEFVF-LHDLTQKEAAERLGISPVTVSRRVKKGLDQLKK 249 (256)
T ss_pred cCCHHHHHHHHHHH-HCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 35566677777766 4689999999999999999999 9888876654
No 68
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=76.81 E-value=6.1 Score=28.83 Aligned_cols=46 Identities=15% Similarity=0.062 Sum_probs=36.7
Q ss_pred ccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847 24 VVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE 70 (88)
Q Consensus 24 ~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~ 70 (88)
.++..|+..+-|+. ..+.+++.|+..++.|.+||++ .+..+..+-.
T Consensus 205 ~L~~~er~vi~l~y-~e~~t~~EIA~~lgis~~~V~~~~~ral~kLr~ 251 (257)
T PRK05911 205 ALEEKERKVMALYY-YEELVLKEIGKILGVSESRVSQIHSKALLKLRA 251 (257)
T ss_pred cCCHHHHHHHHHHH-hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 35556666666655 5789999999999999999999 8888776654
No 69
>COG2826 Tra8 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]
Probab=76.59 E-value=3.1 Score=32.34 Aligned_cols=39 Identities=15% Similarity=0.115 Sum_probs=33.8
Q ss_pred CccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HH
Q 046847 23 SVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FN 62 (88)
Q Consensus 23 ~~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~ 62 (88)
.+++.+|+.-|==|- ..+.|+|.|+..-++..+|||| .+
T Consensus 6 ~hLT~~eR~~I~~l~-~~~~S~reIA~~LgRh~sTIsRElk 45 (318)
T COG2826 6 KHLTLFERYEIERLL-KAKMSIREIAKQLNRHHSTISRELK 45 (318)
T ss_pred hhCCHHHHHHHHHHH-HcCCCHHHHHHHhCCCcchhhHHHh
Confidence 378888888776666 7789999999999999999999 75
No 70
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=76.13 E-value=5.4 Score=27.41 Aligned_cols=44 Identities=9% Similarity=0.023 Sum_probs=33.6
Q ss_pred chhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847 26 FVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE 70 (88)
Q Consensus 26 ~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~ 70 (88)
+-+++-++-| ..-++.++..|+..++.|..||.. .+..+..+-.
T Consensus 138 ~~~~r~i~~L-~~~~g~s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~ 182 (196)
T PRK12524 138 PERQRQAVVL-RHIEGLSNPEIAEVMEIGVEAVESLTARGKRALAA 182 (196)
T ss_pred CHHHHHHHHH-HHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 3334444444 444899999999999999999999 9988877754
No 71
>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=75.65 E-value=4.2 Score=23.14 Aligned_cols=39 Identities=15% Similarity=0.140 Sum_probs=29.7
Q ss_pred HHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847 30 QVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVL 69 (88)
Q Consensus 30 ~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~ 69 (88)
++-+|+-++-+ .+...++...+.|.+|||+ .++.=+.+.
T Consensus 3 ~l~~f~~v~~~-gs~~~AA~~l~is~~~vs~~i~~LE~~lg 42 (60)
T PF00126_consen 3 QLRYFLAVAET-GSISAAAEELGISQSAVSRQIKQLEEELG 42 (60)
T ss_dssp HHHHHHHHHHH-SSHHHHHHHCTSSHHHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHh-CCHHHHHHHhhccchHHHHHHHHHHHHhC
Confidence 45555555555 4999999999999999999 888755443
No 72
>PRK00118 putative DNA-binding protein; Validated
Probab=75.44 E-value=6.1 Score=25.80 Aligned_cols=43 Identities=12% Similarity=0.057 Sum_probs=32.3
Q ss_pred cchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHH
Q 046847 25 VFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGV 68 (88)
Q Consensus 25 v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai 68 (88)
++-.++-++-|+ -..+.++..|+..+|.|..||.+ .+.....+
T Consensus 18 L~ekqRevl~L~-y~eg~S~~EIAe~lGIS~~TV~r~L~RArkkL 61 (104)
T PRK00118 18 LTEKQRNYMELY-YLDDYSLGEIAEEFNVSRQAVYDNIKRTEKLL 61 (104)
T ss_pred CCHHHHHHHHHH-HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 445555555444 55689999999999999999999 88665444
No 73
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=74.93 E-value=6.1 Score=26.85 Aligned_cols=38 Identities=16% Similarity=0.053 Sum_probs=31.7
Q ss_pred HHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847 33 MFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE 70 (88)
Q Consensus 33 ~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~ 70 (88)
+|....-++.+++.|+..++-|..||.. .+..++.+-.
T Consensus 149 v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 187 (194)
T PRK12519 149 VLELAYYEGLSQSEIAKRLGIPLGTVKARARQGLLKLRE 187 (194)
T ss_pred hhhhhhhcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 4444456789999999999999999999 8888887765
No 74
>PRK15320 transcriptional activator SprB; Provisional
Probab=74.71 E-value=3.4 Score=30.77 Aligned_cols=35 Identities=14% Similarity=0.133 Sum_probs=30.5
Q ss_pred HHHhccccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847 35 LHALAHHVKNQTINNRFKHSGETISR-FNSILNGVL 69 (88)
Q Consensus 35 L~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~ 69 (88)
|-.++.+.++++|++.|+-|..|||. -..+++.+.
T Consensus 173 L~LLAkG~SNKEIAekL~LS~KTVSTYKnRLLeKLg 208 (251)
T PRK15320 173 LILLSSGHPAIELAKKFGLGTKTVSIYRKKVMYRLG 208 (251)
T ss_pred HHHHHcCCCHHHHHHHhccchhhHHHHHHHHHHHcC
Confidence 45689999999999999999999999 888876553
No 75
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=74.41 E-value=8 Score=25.44 Aligned_cols=33 Identities=6% Similarity=-0.049 Sum_probs=28.1
Q ss_pred hccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847 38 LAHHVKNQTINNRFKHSGETISR-FNSILNGVLE 70 (88)
Q Consensus 38 ~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~ 70 (88)
.-.+.+++.|+..+|.|..||.. .+..+.-+-.
T Consensus 141 ~~~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 174 (182)
T PRK09652 141 EIEGLSYEEIAEIMGCPIGTVRSRIFRAREALRA 174 (182)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 34789999999999999999998 8877766654
No 76
>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=74.02 E-value=6.1 Score=27.00 Aligned_cols=43 Identities=9% Similarity=0.142 Sum_probs=31.9
Q ss_pred cchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847 25 VFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVL 69 (88)
Q Consensus 25 v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~ 69 (88)
.+-.|+-.+-|+ .++.+++.|+..++-|..||++ -+..++.+-
T Consensus 7 Lte~qr~VL~Lr--~~GlTq~EIAe~LgiS~stV~~~e~ra~kkLr 50 (137)
T TIGR00721 7 LTERQIKVLELR--EKGLSQKEIAKELKTTRANVSAIEKRAMENIE 50 (137)
T ss_pred CCHHHHHHHHHH--HcCCCHHHHHHHHCcCHHHHHHHHHhHHHHHH
Confidence 344455555553 6999999999999999999997 666555443
No 77
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=73.60 E-value=2.1 Score=23.31 Aligned_cols=23 Identities=9% Similarity=0.213 Sum_probs=19.6
Q ss_pred chhhhhhhcccccchhHh-HHHHH
Q 046847 43 KNQTINNRFKHSGETISR-FNSIL 65 (88)
Q Consensus 43 ~~r~i~~~F~~S~eTisr-f~~Vl 65 (88)
+.++++.+|+.|.+||.+ ++..-
T Consensus 22 s~~~la~~~~vs~~tv~~~l~~L~ 45 (60)
T smart00345 22 SERELAAQLGVSRTTVREALSRLE 45 (60)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHH
Confidence 678899999999999988 77654
No 78
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=73.44 E-value=7.3 Score=22.07 Aligned_cols=31 Identities=19% Similarity=0.177 Sum_probs=25.5
Q ss_pred HHHhccccchhhhhhhccc-ccchhHh-HHHHH
Q 046847 35 LHALAHHVKNQTINNRFKH-SGETISR-FNSIL 65 (88)
Q Consensus 35 L~i~~~n~~~r~i~~~F~~-S~eTisr-f~~Vl 65 (88)
-|+..++.+..+++...|- |..+.+| |++..
T Consensus 44 ~~l~~~~~~~~~ia~~~g~~s~~~f~r~Fk~~~ 76 (84)
T smart00342 44 RLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLF 76 (84)
T ss_pred HHHHcCCCCHHHHHHHhCCCChHHHHHHHHHHH
Confidence 3444556899999999999 9999999 98764
No 79
>PHA00542 putative Cro-like protein
Probab=73.39 E-value=3.5 Score=25.29 Aligned_cols=50 Identities=18% Similarity=0.183 Sum_probs=36.8
Q ss_pred HHHHhccccchhhhhhhcccccchhHh-HHHH-----HHHHHHhhhhhccCCCCCC
Q 046847 34 FLHALAHHVKNQTINNRFKHSGETISR-FNSI-----LNGVLELQHILLKSPKPMP 83 (88)
Q Consensus 34 FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~V-----l~ai~~L~~~~ik~p~~~~ 83 (88)
.......+.+.++++...+.|..||++ .+.- ++.+..|+..|.+.-+.++
T Consensus 24 ~~~l~~~glTq~elA~~lgIs~~tIsr~e~g~~~~p~~~~l~ki~~~~~~~~~~~~ 79 (82)
T PHA00542 24 VCALIRAGWSQEQIADATDVSQPTICRIYSGRHKDPRYSVVEKLRHLVLNLDDFQQ 79 (82)
T ss_pred HHHHHHCCCCHHHHHHHHCcCHHHHHHHHcCCCCCCCHHHHHHHHHHHHHhchhhh
Confidence 344577889999999999999999999 7542 4456666666666655443
No 80
>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=72.92 E-value=3.8 Score=28.56 Aligned_cols=39 Identities=15% Similarity=0.281 Sum_probs=32.6
Q ss_pred hHHHHHHHHHhccc-------cchhhhhhhcccccchhHh-HHHHHH
Q 046847 28 DEQVCMFLHALAHH-------VKNQTINNRFKHSGETISR-FNSILN 66 (88)
Q Consensus 28 eE~la~FL~i~~~n-------~~~r~i~~~F~~S~eTisr-f~~Vl~ 66 (88)
..+..++.|++.+- .+++.++..++-|..||+| |++.-+
T Consensus 55 ~k~~~Vl~~il~~~d~~N~v~~t~~~ia~~l~iS~~Tv~r~ik~L~e 101 (165)
T PF05732_consen 55 NKAFRVLMYILENMDKDNAVVATQKEIAEKLGISKPTVSRAIKELEE 101 (165)
T ss_pred hhHHHHHHHHHHhcCCCCeEEeeHHHHHHHhCCCHHHHHHHHHHHHh
Confidence 35788888887663 5789999999999999999 998765
No 81
>PRK06930 positive control sigma-like factor; Validated
Probab=72.88 E-value=6.8 Score=27.29 Aligned_cols=45 Identities=9% Similarity=0.098 Sum_probs=35.3
Q ss_pred cchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847 25 VFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE 70 (88)
Q Consensus 25 v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~ 70 (88)
++..|+ .+|+.....+.++..|+..++-|..||.. .+..++.+-.
T Consensus 115 L~~rer-~V~~L~~~eg~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~ 160 (170)
T PRK06930 115 LTEREK-EVYLMHRGYGLSYSEIADYLNIKKSTVQSMIERAEKKIAR 160 (170)
T ss_pred CCHHHH-HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 333333 45555568999999999999999999999 8888877754
No 82
>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=72.60 E-value=7.2 Score=22.01 Aligned_cols=28 Identities=18% Similarity=0.278 Sum_probs=21.7
Q ss_pred ccccchhhhhhhcccccchhHh-HHHHHH
Q 046847 39 AHHVKNQTINNRFKHSGETISR-FNSILN 66 (88)
Q Consensus 39 ~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ 66 (88)
....+..+|++.++.+..|||+ .++..+
T Consensus 16 ~~~~t~~~l~~~~~~~~~~vs~~i~~L~~ 44 (68)
T PF13463_consen 16 DGPMTQSDLAERLGISKSTVSRIIKKLEE 44 (68)
T ss_dssp TS-BEHHHHHHHTT--HHHHHHHHHHHHH
T ss_pred CCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 3668889999999999999999 888773
No 83
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=72.30 E-value=8.9 Score=25.70 Aligned_cols=44 Identities=9% Similarity=0.021 Sum_probs=33.4
Q ss_pred cchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847 25 VFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVL 69 (88)
Q Consensus 25 v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~ 69 (88)
++.+++-.+.|.. -.+.++..|+..+|.|..||.. .+..++.+-
T Consensus 130 L~~~~r~i~~l~~-~~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr 174 (179)
T PRK12514 130 LEKDRAAAVRRAY-LEGLSYKELAERHDVPLNTMRTWLRRSLLKLR 174 (179)
T ss_pred CCHHHHHHHHHHH-HcCCCHHHHHHHHCCChHHHHHHHHHHHHHHH
Confidence 3444555555554 4789999999999999999988 888776654
No 84
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=72.06 E-value=9.6 Score=26.95 Aligned_cols=44 Identities=18% Similarity=0.123 Sum_probs=33.0
Q ss_pred hhHHHHHHHHHh---ccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847 27 VDEQVCMFLHAL---AHHVKNQTINNRFKHSGETISR-FNSILNGVLE 70 (88)
Q Consensus 27 veE~la~FL~i~---~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~ 70 (88)
..++-++-|+.. -++.+++.|+..++.|..||.. .+..++.+-.
T Consensus 181 ~~~R~v~~L~y~l~~~eg~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~ 228 (234)
T PRK08301 181 DREKQIMELRFGLNGGEEKTQKEVADMLGISQSYISRLEKRIIKRLKK 228 (234)
T ss_pred HHHHHHHHHHhccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 344444445432 5899999999999999999988 8887776644
No 85
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=71.15 E-value=9 Score=22.84 Aligned_cols=40 Identities=13% Similarity=0.188 Sum_probs=30.6
Q ss_pred chhHHHHHHHHHhcc--ccchhhhhhhcccccchhHh-HHHHH
Q 046847 26 FVDEQVCMFLHALAH--HVKNQTINNRFKHSGETISR-FNSIL 65 (88)
Q Consensus 26 ~veE~la~FL~i~~~--n~~~r~i~~~F~~S~eTisr-f~~Vl 65 (88)
+++..+.|.-++..+ ..+..+++...+-|..||+| .+...
T Consensus 3 ~~~r~~~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~ 45 (91)
T smart00346 3 SLERGLAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQ 45 (91)
T ss_pred HHHHHHHHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 455666666665543 58999999999999999999 76654
No 86
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=70.97 E-value=5.1 Score=28.21 Aligned_cols=43 Identities=14% Similarity=0.126 Sum_probs=33.8
Q ss_pred cchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847 25 VFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVL 69 (88)
Q Consensus 25 v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~ 69 (88)
.|--|.= -|-.++.+.+|++|+..-+-|..||.. ...+++-+.
T Consensus 138 LT~RE~e--VL~lla~G~snkeIA~~L~iS~~TVk~h~~~I~~KL~ 181 (207)
T PRK15411 138 LSRTESS--MLRMWMAGQGTIQISDQMNIKAKTVSSHKGNIKRKIK 181 (207)
T ss_pred CCHHHHH--HHHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHHHHhC
Confidence 4444432 245578889999999999999999999 999887664
No 87
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=70.69 E-value=6 Score=28.97 Aligned_cols=40 Identities=13% Similarity=0.243 Sum_probs=35.1
Q ss_pred HHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHH
Q 046847 29 EQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGV 68 (88)
Q Consensus 29 E~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai 68 (88)
++|-.|+.++-++.++..++++.+.|..|||+ .++.=+.+
T Consensus 4 ~~L~~F~~v~~~~~S~s~AA~~L~isQpavS~~I~~LE~~l 44 (309)
T PRK12683 4 QQLRIIREAVRQNFNLTEVANALYTSQSGVSKQIKDLEDEL 44 (309)
T ss_pred HHHHHHHHHHHccCCHHHHHHHhcCCcHHHHHHHHHHHHHh
Confidence 57889999999989999999999999999999 98864444
No 88
>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=70.55 E-value=8.3 Score=27.49 Aligned_cols=46 Identities=20% Similarity=0.090 Sum_probs=36.5
Q ss_pred ccchhHHHHHHHHHh---ccccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847 24 VVFVDEQVCMFLHAL---AHHVKNQTINNRFKHSGETISR-FNSILNGVL 69 (88)
Q Consensus 24 ~v~veE~la~FL~i~---~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~ 69 (88)
.++..++..+.|+.. ..+.++..|+..-|.|..||.. .+..+..+-
T Consensus 178 ~Lp~~~R~ii~L~~~l~~~eg~s~~EIA~~Lgis~~tV~~~l~ra~~~LR 227 (234)
T TIGR02835 178 KLNDREKKIMELRFGLVGGTEKTQKEVADMLGISQSYISRLEKRILKRLK 227 (234)
T ss_pred hCCHHHHHHHHHHHccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 355566777777764 4889999999999999999988 777766554
No 89
>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=70.11 E-value=9.8 Score=21.03 Aligned_cols=27 Identities=11% Similarity=0.255 Sum_probs=22.1
Q ss_pred ccccchhhhhhhcccccchhHh-HHHHH
Q 046847 39 AHHVKNQTINNRFKHSGETISR-FNSIL 65 (88)
Q Consensus 39 ~~n~~~r~i~~~F~~S~eTisr-f~~Vl 65 (88)
..+.+..+++..++.+..|+++ .+...
T Consensus 15 ~~~~~~~~la~~~~~~~~~~t~~i~~L~ 42 (59)
T PF01047_consen 15 NGGITQSELAEKLGISRSTVTRIIKRLE 42 (59)
T ss_dssp HSSEEHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred cCCCCHHHHHHHHCCChhHHHHHHHHHH
Confidence 3448999999999999999999 77765
No 90
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=70.10 E-value=5 Score=27.54 Aligned_cols=44 Identities=20% Similarity=0.108 Sum_probs=34.2
Q ss_pred ccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847 24 VVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVL 69 (88)
Q Consensus 24 ~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~ 69 (88)
..|--|+= -|..++.+.++.+|+...+-|..||.. ...+++-+.
T Consensus 150 ~Lt~rE~e--vl~~~~~G~s~~eIA~~l~iS~~TV~~h~~~i~~Kl~ 194 (216)
T PRK10840 150 RLSPKESE--VLRLFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLG 194 (216)
T ss_pred cCCHHHHH--HHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence 35555542 345567889999999999999999998 888876553
No 91
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=69.85 E-value=11 Score=25.45 Aligned_cols=42 Identities=12% Similarity=0.159 Sum_probs=30.7
Q ss_pred hhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847 27 VDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVL 69 (88)
Q Consensus 27 veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~ 69 (88)
.+++.++-| .--.+.++..|+...|.|..||.. .+.-+..+.
T Consensus 130 ~~~R~v~~L-~~~~g~s~~EIA~~lgis~~tVk~~l~rAl~~~~ 172 (178)
T PRK12529 130 PRVKQAFLM-ATLDGMKQKDIAQALDIALPTVKKYIHQAYVTCL 172 (178)
T ss_pred HHHHHHHHH-HHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 333444444 344889999999999999999998 776655444
No 92
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=69.82 E-value=12 Score=24.99 Aligned_cols=45 Identities=7% Similarity=0.008 Sum_probs=36.4
Q ss_pred HHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHHhhhhhc
Q 046847 32 CMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLELQHILL 76 (88)
Q Consensus 32 a~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~L~~~~i 76 (88)
.+|+..--.+.+++.|+...|.|..||.. .+.....+-..-..+|
T Consensus 126 ~i~~l~~~~~~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~~~~ 171 (173)
T PRK12522 126 TVLVLYYYEQYSYKEMSEILNIPIGTVKYRLNYAKKQMREHLEGFV 171 (173)
T ss_pred HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHHh
Confidence 45555556789999999999999999999 9998888876555544
No 93
>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=69.69 E-value=8.4 Score=25.27 Aligned_cols=41 Identities=12% Similarity=0.137 Sum_probs=32.3
Q ss_pred HHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847 30 QVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE 70 (88)
Q Consensus 30 ~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~ 70 (88)
+--+|....-++.++..|+..+|.|..||.. .+.....+-.
T Consensus 115 ~r~i~~l~~~~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 156 (162)
T TIGR02983 115 QRAVVVLRYYEDLSEAQVAEALGISVGTVKSRLSRALARLRE 156 (162)
T ss_pred HHHHhhhHHHhcCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 3344544457799999999999999999998 8887776653
No 94
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=69.64 E-value=12 Score=26.22 Aligned_cols=47 Identities=13% Similarity=0.024 Sum_probs=31.3
Q ss_pred cchhhhhhhcccccchhHh-HHHHHH-----HHHH-hhhhhccCCCCCCCCCCC
Q 046847 42 VKNQTINNRFKHSGETISR-FNSILN-----GVLE-LQHILLKSPKPMPEYCTD 88 (88)
Q Consensus 42 ~~~r~i~~~F~~S~eTisr-f~~Vl~-----ai~~-L~~~~ik~p~~~~~~~i~ 88 (88)
.+..++...|+.|.+||-| +.+.-+ -+-. -...|-|..+-.+++.||
T Consensus 22 ~~~~~La~~~~vS~~TiRRDl~~L~~~g~~~r~~~~~~~~~~~~~~~~~~~~vD 75 (185)
T PRK04424 22 ITDEELAEKFGVSIQTIRLDRMELGIPELRERIKHVAEKNYDKVKSLPEEEVVG 75 (185)
T ss_pred EEHHHHHHHHCcCHHHHHHHHHHHhcchHHHHHHHHHHHhHHhhhcCCccccee
Confidence 6788999999999999999 987643 1111 123455555555555554
No 95
>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=69.63 E-value=2.2 Score=30.95 Aligned_cols=21 Identities=24% Similarity=0.237 Sum_probs=18.9
Q ss_pred cchhhhhhhcccccchhHh-HH
Q 046847 42 VKNQTINNRFKHSGETISR-FN 62 (88)
Q Consensus 42 ~~~r~i~~~F~~S~eTisr-f~ 62 (88)
.+-++|+...|.|..|||| ++
T Consensus 2 ~ti~dIA~~agVS~sTVSr~Ln 23 (311)
T TIGR02405 2 LTIKDIARLAGVGKSTVSRVLN 23 (311)
T ss_pred CcHHHHHHHhCCCHHHHHHHhC
Confidence 3568999999999999999 96
No 96
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=69.54 E-value=6.1 Score=21.89 Aligned_cols=34 Identities=24% Similarity=0.296 Sum_probs=27.3
Q ss_pred HHHhccccchhhhhhhcccccchhHh-HHHHHHHH
Q 046847 35 LHALAHHVKNQTINNRFKHSGETISR-FNSILNGV 68 (88)
Q Consensus 35 L~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai 68 (88)
+..++.+.++..|+...+.|..||.- ...+..-+
T Consensus 13 ~~l~~~G~s~~eia~~l~is~~tV~~h~~~i~~Kl 47 (65)
T COG2771 13 LRLVAQGKSNKEIARILGISEETVKTHLRNIYRKL 47 (65)
T ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 34556679999999999999999988 77775433
No 97
>PRK12679 cbl transcriptional regulator Cbl; Reviewed
Probab=69.52 E-value=6.6 Score=28.78 Aligned_cols=40 Identities=15% Similarity=0.187 Sum_probs=34.7
Q ss_pred HHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHH
Q 046847 29 EQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGV 68 (88)
Q Consensus 29 E~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai 68 (88)
+++-.|+.++.++.++..++.+-..|..|||| .++.=+.+
T Consensus 4 ~~l~~f~~v~~~~~s~s~AA~~L~iSQ~avSr~I~~LE~~l 44 (316)
T PRK12679 4 QQLKIIREAARQDYNLTEVANMLFTSQSGVSRHIRELEDEL 44 (316)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHhcCCchHHHHHHHHHHHHh
Confidence 46888999999989999999999999999999 88764444
No 98
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=69.49 E-value=5.1 Score=28.44 Aligned_cols=35 Identities=26% Similarity=0.348 Sum_probs=31.1
Q ss_pred HHHhccccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847 35 LHALAHHVKNQTINNRFKHSGETISR-FNSILNGVL 69 (88)
Q Consensus 35 L~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~ 69 (88)
|..++.+.+|++|+.+-+.|..||+- ...+++-+.
T Consensus 157 L~lla~G~snkeIA~~L~iS~~TVk~h~~~i~~KL~ 192 (211)
T COG2197 157 LRLLAEGLSNKEIAEELNLSEKTVKTHVSNILRKLG 192 (211)
T ss_pred HHHHHCCCCHHHHHHHHCCCHhHHHHHHHHHHHHcC
Confidence 56789999999999999999999999 888887653
No 99
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=69.22 E-value=13 Score=25.28 Aligned_cols=46 Identities=11% Similarity=0.055 Sum_probs=35.3
Q ss_pred HHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH-hhhhhccC
Q 046847 33 MFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE-LQHILLKS 78 (88)
Q Consensus 33 ~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~-L~~~~ik~ 78 (88)
+|+..--.+.++..|+..+|.|..||.. .+...+.+-. |...++..
T Consensus 144 i~~L~~~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~~~~~~ 191 (195)
T PRK12532 144 VFTLKEILGFSSDEIQQMCGISTSNYHTIMHRARESLRQCLQIKWFNQ 191 (195)
T ss_pred HhhhHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhhccc
Confidence 3433334789999999999999999999 9988888765 55555543
No 100
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=68.96 E-value=6.8 Score=21.02 Aligned_cols=28 Identities=11% Similarity=0.092 Sum_probs=23.4
Q ss_pred ccccchhhhhhhcccccchhHh-HHHHHH
Q 046847 39 AHHVKNQTINNRFKHSGETISR-FNSILN 66 (88)
Q Consensus 39 ~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ 66 (88)
....+..+|+..++.|..|+++ .+...+
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~ 36 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLRE 36 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 5567889999999999999999 877653
No 101
>COG4496 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=68.41 E-value=4.7 Score=26.25 Aligned_cols=30 Identities=30% Similarity=0.284 Sum_probs=26.3
Q ss_pred HhccccchhhhhhhcccccchhHhHHHHHH
Q 046847 37 ALAHHVKNQTINNRFKHSGETISRFNSILN 66 (88)
Q Consensus 37 i~~~n~~~r~i~~~F~~S~eTisrf~~Vl~ 66 (88)
++-.+..|++|...=|-|..||||.+.+|+
T Consensus 52 mL~eg~tY~~I~~eTGaStaTIsRVkRcl~ 81 (100)
T COG4496 52 MLKEGRTYRDIEDETGASTATISRVKRCLN 81 (100)
T ss_pred HHHcCCCcchhhhccCcchhhHHHHHHHHH
Confidence 456788999999999999999999888775
No 102
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=68.28 E-value=13 Score=25.79 Aligned_cols=48 Identities=10% Similarity=0.054 Sum_probs=37.0
Q ss_pred HHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH-hhhhhccCCC
Q 046847 33 MFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE-LQHILLKSPK 80 (88)
Q Consensus 33 ~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~-L~~~~ik~p~ 80 (88)
+|....-.+.++..|+..+|.|..||.. .+.....+-. |......+++
T Consensus 147 v~~L~~~eg~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~~~~~~~~~ 196 (201)
T PRK12545 147 VFMMREFLDFEIDDICTELTLTANHCSVLLYRARTRLRTCLSEKGLTTED 196 (201)
T ss_pred HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHhcchhh
Confidence 4555567889999999999999999998 8888777754 5555555554
No 103
>PRK09483 response regulator; Provisional
Probab=67.48 E-value=6 Score=26.39 Aligned_cols=43 Identities=14% Similarity=0.166 Sum_probs=33.1
Q ss_pred ccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHH
Q 046847 24 VVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGV 68 (88)
Q Consensus 24 ~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai 68 (88)
..|-.|.=.+- .++.+.++++|+..++.|..||.. .+.+++-+
T Consensus 148 ~Lt~rE~~vl~--~~~~G~~~~~Ia~~l~is~~TV~~~~~~i~~Kl 191 (217)
T PRK09483 148 SLSERELQIML--MITKGQKVNEISEQLNLSPKTVNSYRYRMFSKL 191 (217)
T ss_pred ccCHHHHHHHH--HHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHc
Confidence 35555554443 457889999999999999999999 88887654
No 104
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=67.45 E-value=12 Score=25.11 Aligned_cols=40 Identities=13% Similarity=0.142 Sum_probs=33.6
Q ss_pred HHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHHh
Q 046847 32 CMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLEL 71 (88)
Q Consensus 32 a~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~L 71 (88)
.+|+....++.++..|+..+|-|..||.. .+..+..+...
T Consensus 126 ~i~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~~~~~ 166 (172)
T PRK09651 126 EAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKATEHCLLF 166 (172)
T ss_pred HHhhhhhccCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 46666778899999999999999999999 88877766543
No 105
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=67.32 E-value=3.6 Score=30.03 Aligned_cols=30 Identities=23% Similarity=0.317 Sum_probs=24.7
Q ss_pred chhhhhhhcccccchhHh-HHH-----------HHHHHHHhh
Q 046847 43 KNQTINNRFKHSGETISR-FNS-----------ILNGVLELQ 72 (88)
Q Consensus 43 ~~r~i~~~F~~S~eTisr-f~~-----------Vl~ai~~L~ 72 (88)
+.++|+..-|.|..|||| ++. |++++-+|.
T Consensus 3 Ti~dIA~~agVS~~TVSrvLn~~~~vs~~tr~~V~~~a~elg 44 (341)
T PRK10703 3 TIKDVAKRAGVSTTTVSHVINKTRFVAEETRNAVWAAIKELH 44 (341)
T ss_pred CHHHHHHHhCCCHHHHHHHHcCCCCCCHHHHHHHHHHHHHHC
Confidence 678999999999999999 985 666666553
No 106
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=67.07 E-value=10 Score=28.30 Aligned_cols=47 Identities=11% Similarity=0.039 Sum_probs=38.0
Q ss_pred ccchhHHHHHHHHHh-ccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847 24 VVFVDEQVCMFLHAL-AHHVKNQTINNRFKHSGETISR-FNSILNGVLE 70 (88)
Q Consensus 24 ~v~veE~la~FL~i~-~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~ 70 (88)
..+-.|+..+-|+.. ..+.++..|+..++.|.+||++ -+..++.+-.
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 356677777777653 3789999999999999999999 8888877654
No 107
>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=67.03 E-value=11 Score=27.18 Aligned_cols=38 Identities=13% Similarity=0.217 Sum_probs=31.4
Q ss_pred HHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847 33 MFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE 70 (88)
Q Consensus 33 ~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~ 70 (88)
+|...-..+.++..|+..++.|.+||++ .+..+..+-.
T Consensus 213 ii~l~~~~g~s~~eIA~~lgis~~~V~~~~~ra~~~Lr~ 251 (255)
T TIGR02941 213 IIHCTFEENLSQKETGERLGISQMHVSRLQRQAISKLKE 251 (255)
T ss_pred HHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 4444556889999999999999999999 9888876643
No 108
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=67.02 E-value=12 Score=26.91 Aligned_cols=38 Identities=13% Similarity=0.211 Sum_probs=31.0
Q ss_pred HHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847 33 MFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE 70 (88)
Q Consensus 33 ~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~ 70 (88)
+|......+.+++.|+..++.|..||++ .+..++.+-.
T Consensus 213 vl~l~~~~g~s~~eIA~~l~is~~tV~~~~~ra~~kLr~ 251 (257)
T PRK08583 213 IIQCTFIENLSQKETGERLGISQMHVSRLQRQAIKKLRE 251 (257)
T ss_pred HHHHHHhCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3333446889999999999999999999 8888877753
No 109
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=66.96 E-value=20 Score=24.39 Aligned_cols=48 Identities=8% Similarity=-0.083 Sum_probs=35.5
Q ss_pred cchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHHhhh
Q 046847 25 VFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLELQH 73 (88)
Q Consensus 25 v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~L~~ 73 (88)
++.+++. +|....-.+.+++.|+..++.|..||.. ++.....+-..-.
T Consensus 107 L~~~~r~-i~~l~~~~g~~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 155 (181)
T PRK09637 107 LPEKYAE-ALRLTELEGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKELLE 155 (181)
T ss_pred CCHHHHH-HHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence 3333333 4444456889999999999999999998 9988888776433
No 110
>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=66.78 E-value=11 Score=26.50 Aligned_cols=43 Identities=19% Similarity=0.199 Sum_probs=32.3
Q ss_pred chhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847 26 FVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVL 69 (88)
Q Consensus 26 ~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~ 69 (88)
+-.|+-++-| ....+.++++|+..++.|.+||.+ .+.+++.+-
T Consensus 180 ~~~~r~vl~l-~y~~~~s~~eIA~~lgis~~~v~~~~~ra~~~Lr 223 (227)
T TIGR02980 180 PERERRILLL-RFFEDKTQSEIAERLGISQMHVSRLLRRALKKLR 223 (227)
T ss_pred CHHHHHHHHH-HHhcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 3333333333 345789999999999999999999 998887664
No 111
>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=66.49 E-value=9 Score=28.50 Aligned_cols=42 Identities=17% Similarity=0.127 Sum_probs=33.8
Q ss_pred cchhHHHHHHHHHh---ccccchhhhhhhcccccchhHh-HHHHHH
Q 046847 25 VFVDEQVCMFLHAL---AHHVKNQTINNRFKHSGETISR-FNSILN 66 (88)
Q Consensus 25 v~veE~la~FL~i~---~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ 66 (88)
.+-.|+..+-|+.. ..+.++..|+..++.|.+||.. -+..++
T Consensus 250 L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVrq~~~rAl~ 295 (298)
T TIGR02997 250 LTPRERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKALR 295 (298)
T ss_pred CCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 56667777777654 6889999999999999999988 776654
No 112
>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=66.37 E-value=16 Score=22.80 Aligned_cols=27 Identities=19% Similarity=0.158 Sum_probs=23.2
Q ss_pred ccccchhhhhhhcccccchhHh-HHHHH
Q 046847 39 AHHVKNQTINNRFKHSGETISR-FNSIL 65 (88)
Q Consensus 39 ~~n~~~r~i~~~F~~S~eTisr-f~~Vl 65 (88)
....+.++++...+-|.+||+| .++.-
T Consensus 45 ~~~is~~eLa~~~g~sr~tVsr~L~~Le 72 (95)
T TIGR01610 45 QDRVTATVIAELTGLSRTHVSDAIKSLA 72 (95)
T ss_pred CCccCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 4568899999999999999999 77765
No 113
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=66.28 E-value=11 Score=28.05 Aligned_cols=45 Identities=9% Similarity=0.039 Sum_probs=34.7
Q ss_pred cchhHHHHHHHHHhc-cccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847 25 VFVDEQVCMFLHALA-HHVKNQTINNRFKHSGETISR-FNSILNGVL 69 (88)
Q Consensus 25 v~veE~la~FL~i~~-~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~ 69 (88)
.+-.|+..+-++... .+.+...|+..+|.|.++|++ -+..+.-+-
T Consensus 231 L~~rEr~VL~lry~~~~~~Tl~EIA~~lgvS~~rVrqi~~~Al~kLR 277 (284)
T PRK06596 231 LDERSRDIIEARWLDDDKSTLQELAAEYGVSAERVRQIEKNAMKKLK 277 (284)
T ss_pred CCHHHHHHHHHHhcCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 455577677776543 689999999999999999999 777665443
No 114
>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=65.97 E-value=20 Score=24.06 Aligned_cols=47 Identities=11% Similarity=-0.067 Sum_probs=35.5
Q ss_pred HHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHHhhhhhccC
Q 046847 32 CMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLELQHILLKS 78 (88)
Q Consensus 32 a~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~L~~~~ik~ 78 (88)
.+|...--++.+++.|+..++.|..||.. .+.....+-..-.....+
T Consensus 107 ~v~~l~~~~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~~~ 154 (170)
T TIGR02959 107 EAIRLTELEGLSQQEIAEKLGLSLSGAKSRVQRGRKKLKELLETCCHF 154 (170)
T ss_pred HHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHhCCe
Confidence 34444456889999999999999999998 888888776643344333
No 115
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=65.80 E-value=16 Score=24.20 Aligned_cols=37 Identities=14% Similarity=-0.008 Sum_probs=29.7
Q ss_pred HHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847 34 FLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE 70 (88)
Q Consensus 34 FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~ 70 (88)
|+..--.+.++.+|+..++-|..||.. .+.....+-.
T Consensus 121 ~~l~~~~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 158 (164)
T PRK12547 121 IILIGASGFSYEDAAAICGCAVGTIKSRVSRARNRLQE 158 (164)
T ss_pred HHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 333334889999999999999999998 8888776653
No 116
>PRK05572 sporulation sigma factor SigF; Validated
Probab=65.69 E-value=12 Score=27.00 Aligned_cols=45 Identities=20% Similarity=0.239 Sum_probs=35.3
Q ss_pred cchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847 25 VFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE 70 (88)
Q Consensus 25 v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~ 70 (88)
++-.++-.+-|+. ..+.+++.|+..++.|..||++ -+..+..+-.
T Consensus 203 L~~~~~~v~~l~~-~~~~s~~eIA~~lgis~~~V~~~~~ral~kLr~ 248 (252)
T PRK05572 203 LDERERLIVYLRY-FKDKTQSEVAKRLGISQVQVSRLEKKILKQMKE 248 (252)
T ss_pred CCHHHHHHHHHHH-hCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 4555555555544 4689999999999999999999 9888877653
No 117
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=65.28 E-value=16 Score=25.02 Aligned_cols=42 Identities=12% Similarity=0.082 Sum_probs=32.1
Q ss_pred cchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHH
Q 046847 25 VFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGV 68 (88)
Q Consensus 25 v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai 68 (88)
++-.|+-.+-| ...+.++.+|+..++-|..||++ -+..++.+
T Consensus 7 Lt~rqreVL~l--r~~GlTq~EIAe~LGiS~~tVs~ie~ra~kkL 49 (141)
T PRK03975 7 LTERQIEVLRL--RERGLTQQEIADILGTSRANVSSIEKRARENI 49 (141)
T ss_pred CCHHHHHHHHH--HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 44445555555 36999999999999999999999 77765544
No 118
>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=65.24 E-value=12 Score=26.40 Aligned_cols=44 Identities=16% Similarity=0.155 Sum_probs=33.1
Q ss_pred cchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847 25 VFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVL 69 (88)
Q Consensus 25 v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~ 69 (88)
.+-.|+-.+-|+ ...+.+...|+..++.|.+||++ -+.+++-+-
T Consensus 184 L~~~e~~i~~~~-~~~~~t~~eIA~~lgis~~~V~~~~~~al~~Lr 228 (231)
T TIGR02885 184 LDERERQIIMLR-YFKDKTQTEVANMLGISQVQVSRLEKKVLKKMK 228 (231)
T ss_pred CCHHHHHHHHHH-HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 344455444443 45789999999999999999999 888876553
No 119
>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=65.10 E-value=8.4 Score=23.73 Aligned_cols=41 Identities=7% Similarity=0.004 Sum_probs=30.9
Q ss_pred chhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHH
Q 046847 26 FVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILN 66 (88)
Q Consensus 26 ~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ 66 (88)
+.-++.+.-|..--.+.+++.|+...+.|..||+. ++...+
T Consensus 17 ~~~~r~af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~~~~ 58 (73)
T TIGR03879 17 DSLAEAAAALAREEAGKTASEIAEELGRTEQTVRNHLKGETK 58 (73)
T ss_pred CHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhcCcc
Confidence 33444444454555889999999999999999999 887443
No 120
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=65.04 E-value=15 Score=24.12 Aligned_cols=38 Identities=13% Similarity=0.049 Sum_probs=29.8
Q ss_pred HHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847 33 MFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE 70 (88)
Q Consensus 33 ~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~ 70 (88)
+|....-.+.++..|+..++-|..||.+ ....++-+-.
T Consensus 117 v~~l~~~~~~s~~EIA~~lgis~~tV~~~l~ra~~~lr~ 155 (163)
T PRK07037 117 AFEMYRLHGETQKDIARELGVSPTLVNFMIRDALVHCRK 155 (163)
T ss_pred HHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4444455689999999999999999999 7776665543
No 121
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=64.41 E-value=17 Score=24.58 Aligned_cols=44 Identities=9% Similarity=0.037 Sum_probs=33.7
Q ss_pred chhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847 26 FVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE 70 (88)
Q Consensus 26 ~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~ 70 (88)
+.+++-.+.|.. =.+.++..|+..++-|..||.. .+.....+-.
T Consensus 140 ~~~~r~v~~l~~-~~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~ 184 (193)
T PRK11923 140 PEDLRTALTLRE-FDGLSYEDIASVMQCPVGTVRSRIFRAREAIDK 184 (193)
T ss_pred CHHHhHHHhhHH-hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 444444455533 4779999999999999999999 9888877765
No 122
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=63.87 E-value=14 Score=25.32 Aligned_cols=44 Identities=16% Similarity=0.044 Sum_probs=33.2
Q ss_pred chhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847 26 FVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE 70 (88)
Q Consensus 26 ~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~ 70 (88)
+.+++-++.| ..-.+.++..|+..++.|..||.. .+..+..+-.
T Consensus 118 p~~~r~i~~L-~~~~g~s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~ 162 (187)
T PRK12516 118 PDDQREAIIL-VGASGFAYEEAAEICGCAVGTIKSRVNRARQRLQE 162 (187)
T ss_pred CHHHHHHHHH-HHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3334444444 444889999999999999999998 8887777654
No 123
>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=63.87 E-value=14 Score=26.77 Aligned_cols=45 Identities=11% Similarity=0.066 Sum_probs=34.9
Q ss_pred ccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847 24 VVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVL 69 (88)
Q Consensus 24 ~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~ 69 (88)
..+..|+-.+-++. ..+.++..|+..+|.|.++|++ -+..++-+-
T Consensus 206 ~L~~rer~vi~~~~-~~~~t~~eIA~~lgis~~~V~~~~~ral~kLr 251 (254)
T TIGR02850 206 RLNEREKMILNMRF-FEGKTQMEVAEEIGISQAQVSRLEKAALKHMR 251 (254)
T ss_pred cCCHHHHHHHHHHH-cCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 34555666666654 5789999999999999999999 888876553
No 124
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=63.79 E-value=16 Score=25.02 Aligned_cols=38 Identities=8% Similarity=0.134 Sum_probs=30.4
Q ss_pred HHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847 33 MFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE 70 (88)
Q Consensus 33 ~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~ 70 (88)
+|....-.+.++..|+..+|.|..||.. .+..++.+-.
T Consensus 149 v~~l~~~eg~s~~EIA~~lgis~~tVk~rl~ra~~~Lr~ 187 (194)
T PRK12531 149 VLQAVYLEELPHQQVAEMFDIPLGTVKSRLRLAVEKLRH 187 (194)
T ss_pred HHHHHHHcCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHH
Confidence 3443344889999999999999999988 8887776653
No 125
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=63.39 E-value=9.7 Score=24.93 Aligned_cols=43 Identities=14% Similarity=0.118 Sum_probs=32.6
Q ss_pred cchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847 25 VFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVL 69 (88)
Q Consensus 25 v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~ 69 (88)
.+..|.- .|..++.+.++++|+..++-|..||.. ...+.+-+.
T Consensus 138 Lt~~E~~--il~~l~~g~~~~~Ia~~l~~s~~tv~~~~~~l~~Kl~ 181 (196)
T PRK10360 138 LTKRERQ--VAEKLAQGMAVKEIAAELGLSPKTVHVHRANLMEKLG 181 (196)
T ss_pred CCHHHHH--HHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 4444443 344466789999999999999999999 888877653
No 126
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=63.29 E-value=12 Score=24.37 Aligned_cols=43 Identities=12% Similarity=0.122 Sum_probs=28.9
Q ss_pred CCccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHH
Q 046847 22 DSVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSI 64 (88)
Q Consensus 22 t~~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~V 64 (88)
+....+++.+..----...+.+..+++..++-|..+++| |++.
T Consensus 6 ~~~~~i~~~~~~I~~~~~~~~sl~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 6 TDAITIHSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred ccHHHHHHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 344444444444444455667778888888888888888 8886
No 127
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=63.21 E-value=6.8 Score=20.47 Aligned_cols=26 Identities=23% Similarity=0.289 Sum_probs=21.8
Q ss_pred cccchhhhhhhcccccchhHh-HHHHH
Q 046847 40 HHVKNQTINNRFKHSGETISR-FNSIL 65 (88)
Q Consensus 40 ~n~~~r~i~~~F~~S~eTisr-f~~Vl 65 (88)
-..+.+++++.++-|.+|+++ ++...
T Consensus 7 ~~~s~~~la~~l~~s~~tv~~~l~~L~ 33 (48)
T smart00419 7 LPLTRQEIAELLGLTRETVSRTLKRLE 33 (48)
T ss_pred eccCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 346788999999999999999 77665
No 128
>PRK02287 hypothetical protein; Provisional
Probab=63.09 E-value=5.4 Score=28.37 Aligned_cols=43 Identities=19% Similarity=0.145 Sum_probs=33.6
Q ss_pred ccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHH
Q 046847 24 VVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNG 67 (88)
Q Consensus 24 ~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~a 67 (88)
..+.-|++|..|||+|....-..+-+.|..+. |.-+ =+++|++
T Consensus 106 kLs~vEAlAaaLyI~G~~~~A~~ll~~F~WG~-~Fl~lN~elLe~ 149 (171)
T PRK02287 106 KLSSVEALAAALYILGFKEEAEKILSKFKWGH-TFLELNKEPLEA 149 (171)
T ss_pred cccHHHHHHHHHHHcCCHHHHHHHHhhCCChH-HHHHHHHHHHHH
Confidence 58899999999999999999999999998754 3333 4444543
No 129
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=62.89 E-value=18 Score=25.35 Aligned_cols=42 Identities=12% Similarity=0.089 Sum_probs=34.0
Q ss_pred HHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH-hhhh
Q 046847 33 MFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE-LQHI 74 (88)
Q Consensus 33 ~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~-L~~~ 74 (88)
+|+...-.+.+++.|+..++-|..||.. .+..++.+-. |..+
T Consensus 156 v~~L~~~~g~s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l~~~ 199 (206)
T PRK12544 156 VFMMREFIELETNEICHAVDLSVSNLNVLLYRARLRLRECLENK 199 (206)
T ss_pred HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHH
Confidence 4455556799999999999999999999 9988888865 4433
No 130
>PHA00738 putative HTH transcription regulator
Probab=62.85 E-value=11 Score=25.07 Aligned_cols=35 Identities=11% Similarity=0.078 Sum_probs=27.6
Q ss_pred HHHHHHHHhcc-ccchhhhhhhcccccchhHh-HHHH
Q 046847 30 QVCMFLHALAH-HVKNQTINNRFKHSGETISR-FNSI 64 (88)
Q Consensus 30 ~la~FL~i~~~-n~~~r~i~~~F~~S~eTisr-f~~V 64 (88)
+++|+.+...+ ..+..++.+.|+-|..|||+ .+..
T Consensus 14 Rr~IL~lL~~~e~~~V~eLae~l~lSQptVS~HLKvL 50 (108)
T PHA00738 14 RRKILELIAENYILSASLISHTLLLSYTTVLRHLKIL 50 (108)
T ss_pred HHHHHHHHHHcCCccHHHHHHhhCCCHHHHHHHHHHH
Confidence 56676666555 37899999999999999999 6543
No 131
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=62.80 E-value=21 Score=24.14 Aligned_cols=45 Identities=9% Similarity=-0.002 Sum_probs=34.4
Q ss_pred cchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847 25 VFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE 70 (88)
Q Consensus 25 v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~ 70 (88)
++.+++-++-|+.+ ++.++.+|+..++-|..||.. .+..+..+-.
T Consensus 132 L~~~~r~vl~l~~~-~~~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 177 (189)
T PRK12515 132 LSPAHREIIDLVYY-HEKSVEEVGEIVGIPESTVKTRMFYARKKLAE 177 (189)
T ss_pred CCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 34444444445444 899999999999999999999 8888877765
No 132
>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=62.72 E-value=30 Score=21.84 Aligned_cols=66 Identities=11% Similarity=0.090 Sum_probs=41.4
Q ss_pred HHHHHHHHhhCcCCcCCCccchhHHHHH-HHHH---hccccchhhhhhhcccccchhHh-HHHHHHHHHHhhhhhcc-CC
Q 046847 6 FGLLFELLCSDERLKTDSVVFVDEQVCM-FLHA---LAHHVKNQTINNRFKHSGETISR-FNSILNGVLELQHILLK-SP 79 (88)
Q Consensus 6 F~~L~~~L~~~~~L~~t~~v~veE~la~-FL~i---~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~L~~~~ik-~p 79 (88)
+..+-+.++..++| +..|-..+ +|+. -+...+..+++...+.+..||++ .+..- ...||. .|
T Consensus 10 ~~~~~~~l~~~~~l------s~~q~~vL~~l~~~~~~~~~~t~~eL~~~l~~~~stvs~~i~~Le------~kg~I~r~~ 77 (109)
T TIGR01889 10 IKSLKRYLKKEFNL------SLEELLILYYLGKLENNEGKLTLKEIIKEILIKQSALVKIIKKLS------KKGYLSKER 77 (109)
T ss_pred HHHHHHHHHHHcCC------CHHHHHHHHHHHhhhccCCcCcHHHHHHHHCCCHHHHHHHHHHHH------HCCCEeccC
Confidence 45556666666554 44443322 2331 12348999999999999999999 77665 455553 45
Q ss_pred CCCC
Q 046847 80 KPMP 83 (88)
Q Consensus 80 ~~~~ 83 (88)
+++.
T Consensus 78 ~~~D 81 (109)
T TIGR01889 78 SEDD 81 (109)
T ss_pred Cccc
Confidence 5544
No 133
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=62.69 E-value=14 Score=26.67 Aligned_cols=44 Identities=14% Similarity=0.092 Sum_probs=33.4
Q ss_pred cchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847 25 VFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVL 69 (88)
Q Consensus 25 v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~ 69 (88)
.+..|+-.+-++. ..+.++..|+..+|.|.+||++ -+..++.+-
T Consensus 210 L~~~er~vi~~~~-~~~~t~~eIA~~lgis~~~V~~~~~~al~kLr 254 (258)
T PRK08215 210 LNDREKLILNLRF-FQGKTQMEVAEEIGISQAQVSRLEKAALKHMR 254 (258)
T ss_pred CCHHHHHHHHHHH-hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 3444554444443 5789999999999999999999 888877664
No 134
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=62.45 E-value=14 Score=24.60 Aligned_cols=43 Identities=7% Similarity=0.010 Sum_probs=31.5
Q ss_pred chhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847 26 FVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVL 69 (88)
Q Consensus 26 ~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~ 69 (88)
+.+++-++.|.. -.+.++.+|+..+|.|.+||.. .+.....+-
T Consensus 138 ~~~~r~il~l~~-~~~~s~~eIA~~lgis~~~v~~~l~Rar~~Lr 181 (187)
T PRK09641 138 PEKYRTVIVLKY-IEDLSLKEISEILDLPVGTVKTRIHRGREALR 181 (187)
T ss_pred CHHHHHHhhhHH-hhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 333444444433 4789999999999999999988 777766554
No 135
>PRK09526 lacI lac repressor; Reviewed
Probab=62.42 E-value=3.7 Score=29.87 Aligned_cols=31 Identities=26% Similarity=0.241 Sum_probs=25.7
Q ss_pred cchhhhhhhcccccchhHh-HHH-----------HHHHHHHhh
Q 046847 42 VKNQTINNRFKHSGETISR-FNS-----------ILNGVLELQ 72 (88)
Q Consensus 42 ~~~r~i~~~F~~S~eTisr-f~~-----------Vl~ai~~L~ 72 (88)
.+-++|+...|.|..|||| +|. |++++-+|.
T Consensus 6 ~ti~dIA~~aGVS~~TVSrvLn~~~~vs~~tr~rV~~~a~elg 48 (342)
T PRK09526 6 VTLYDVARYAGVSYQTVSRVLNQASHVSAKTREKVEAAMAELN 48 (342)
T ss_pred CcHHHHHHHhCCCHHHHHHHhcCCCCCCHHHHHHHHHHHHHHC
Confidence 5678999999999999999 984 777776653
No 136
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=62.16 E-value=9.3 Score=27.84 Aligned_cols=46 Identities=17% Similarity=0.100 Sum_probs=35.4
Q ss_pred CCccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847 22 DSVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVL 69 (88)
Q Consensus 22 t~~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~ 69 (88)
|..+|.-|.= .|-.++.|.++++|+...+.|..||.. ...+++-+.
T Consensus 131 ~~~LSpRErE--VLrLLAqGkTnKEIAe~L~IS~rTVkth~srImkKLg 177 (198)
T PRK15201 131 TRHFSVTERH--LLKLIASGYHLSETAALLSLSEEQTKSLRRSIMRKLH 177 (198)
T ss_pred CCCCCHHHHH--HHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 3446665543 244578899999999999999999999 888876554
No 137
>PRK10651 transcriptional regulator NarL; Provisional
Probab=61.81 E-value=9 Score=25.14 Aligned_cols=43 Identities=19% Similarity=0.272 Sum_probs=33.5
Q ss_pred cchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847 25 VFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVL 69 (88)
Q Consensus 25 v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~ 69 (88)
.+..|. =.|..++.|.+++.|+...+.|..||.. ..+..+-+.
T Consensus 156 Lt~rE~--~vl~~l~~g~~~~~ia~~l~is~~tV~~~~~~l~~Kl~ 199 (216)
T PRK10651 156 LTPRER--DILKLIAQGLPNKMIARRLDITESTVKVHVKHMLKKMK 199 (216)
T ss_pred CCHHHH--HHHHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHHHHcC
Confidence 555554 3344467889999999999999999999 988876553
No 138
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=61.70 E-value=15 Score=26.06 Aligned_cols=43 Identities=14% Similarity=0.134 Sum_probs=31.7
Q ss_pred hHHHHHHHHHh---ccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847 28 DEQVCMFLHAL---AHHVKNQTINNRFKHSGETISR-FNSILNGVLE 70 (88)
Q Consensus 28 eE~la~FL~i~---~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~ 70 (88)
.++..+=|+.. ..+.|++.|+..+|-|.+||.+ -+.-++.+-.
T Consensus 179 ~~R~i~~l~y~~~~~e~~S~~EIA~~lgis~~tV~~~~~rA~~kLr~ 225 (233)
T PRK05803 179 REKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRALKKLFK 225 (233)
T ss_pred HHHHHHHHHhCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 44444555332 4789999999999999999988 7776666544
No 139
>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=61.34 E-value=19 Score=19.63 Aligned_cols=32 Identities=19% Similarity=0.230 Sum_probs=24.2
Q ss_pred HHHHhccccchhhhhhhcccccchhHh-HHHHH
Q 046847 34 FLHALAHHVKNQTINNRFKHSGETISR-FNSIL 65 (88)
Q Consensus 34 FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl 65 (88)
..++..+..+..+++..++-|..||++ ++...
T Consensus 13 l~~l~~~~~~~~ei~~~~~i~~~~i~~~l~~L~ 45 (78)
T cd00090 13 LRLLLEGPLTVSELAERLGLSQSTVSRHLKKLE 45 (78)
T ss_pred HHHHHHCCcCHHHHHHHHCcCHhHHHHHHHHHH
Confidence 333333448899999999999999988 77753
No 140
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=60.81 E-value=3.6 Score=29.95 Aligned_cols=31 Identities=26% Similarity=0.264 Sum_probs=25.4
Q ss_pred cchhhhhhhcccccchhHh-HHH-----------HHHHHHHhh
Q 046847 42 VKNQTINNRFKHSGETISR-FNS-----------ILNGVLELQ 72 (88)
Q Consensus 42 ~~~r~i~~~F~~S~eTisr-f~~-----------Vl~ai~~L~ 72 (88)
.+-++|+...|.|..|||| ++. |++++-+|.
T Consensus 6 ~ti~dIA~~agVS~~TVSrvLn~~~~vs~~tr~rV~~~a~elg 48 (331)
T PRK14987 6 PVLQDVADRVGVTKMTVSRFLRNPEQVSVALRGKIAAALDELG 48 (331)
T ss_pred CcHHHHHHHhCCCHHHhhhhhCCCCCCCHHHHHHHHHHHHHhC
Confidence 4678999999999999999 965 677776654
No 141
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=60.80 E-value=9.3 Score=27.15 Aligned_cols=34 Identities=12% Similarity=0.171 Sum_probs=29.0
Q ss_pred HHHhccccchhhhhhhcccccchhHh-HHHHHHHH
Q 046847 35 LHALAHHVKNQTINNRFKHSGETISR-FNSILNGV 68 (88)
Q Consensus 35 L~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai 68 (88)
|..++.+.+|++|+...+.|..||.. -..+++-+
T Consensus 143 L~ll~~G~snkeIA~~L~iS~~TV~~h~~~I~~KL 177 (207)
T PRK11475 143 LRFMSRGYSMPQIAEQLERNIKTIRAHKFNVMSKL 177 (207)
T ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHc
Confidence 45577899999999999999999998 88876554
No 142
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=60.64 E-value=23 Score=20.87 Aligned_cols=36 Identities=11% Similarity=0.170 Sum_probs=26.9
Q ss_pred HHHHHHHh-ccccchhhhhhhcccccchhHh-HHHHHH
Q 046847 31 VCMFLHAL-AHHVKNQTINNRFKHSGETISR-FNSILN 66 (88)
Q Consensus 31 la~FL~i~-~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ 66 (88)
+.++..+. ....+...++..++.|..||++ .++..+
T Consensus 13 ~~il~~l~~~~~~~~~~la~~~~~s~~~i~~~l~~L~~ 50 (101)
T smart00347 13 FLVLRILYEEGPLSVSELAKRLGVSPSTVTRVLDRLEK 50 (101)
T ss_pred HHHHHHHHHcCCcCHHHHHHHHCCCchhHHHHHHHHHH
Confidence 33444443 3457999999999999999999 888764
No 143
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=60.63 E-value=19 Score=24.32 Aligned_cols=37 Identities=19% Similarity=0.243 Sum_probs=31.6
Q ss_pred HHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847 33 MFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVL 69 (88)
Q Consensus 33 ~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~ 69 (88)
+|+...-.+.++.+|+..+|.|..||.. .+..++.+-
T Consensus 141 i~~l~~~~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr 178 (182)
T PRK12537 141 CILHAYVDGCSHAEIAQRLGAPLGTVKAWIKRSLKALR 178 (182)
T ss_pred HHHHHHHcCCCHHHHHHHHCCChhhHHHHHHHHHHHHH
Confidence 4666678999999999999999999999 888777664
No 144
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=60.55 E-value=18 Score=24.35 Aligned_cols=39 Identities=5% Similarity=-0.003 Sum_probs=32.0
Q ss_pred HHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847 32 CMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE 70 (88)
Q Consensus 32 a~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~ 70 (88)
-+|....-.+.++..|+..++-|..||.. .+..+..+-.
T Consensus 138 ~v~~l~~~~g~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~ 177 (184)
T PRK12512 138 DVVQSISVEGASIKETAAKLSMSEGAVRVALHRGLAALAA 177 (184)
T ss_pred HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 34555555699999999999999999999 9988877754
No 145
>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=60.38 E-value=7 Score=25.32 Aligned_cols=33 Identities=6% Similarity=-0.029 Sum_probs=27.8
Q ss_pred hccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847 38 LAHHVKNQTINNRFKHSGETISR-FNSILNGVLE 70 (88)
Q Consensus 38 ~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~ 70 (88)
...+.++++|+..+|.|..||.. .+.....+-.
T Consensus 118 ~~~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~ 151 (154)
T TIGR02950 118 EFKEFSYKEIAELLNLSLAKVKSNLFRARKELKK 151 (154)
T ss_pred hhccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 34789999999999999999988 8887766643
No 146
>COG1508 RpoN DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription]
Probab=60.32 E-value=5.7 Score=32.14 Aligned_cols=49 Identities=20% Similarity=0.237 Sum_probs=38.3
Q ss_pred chhHHHHHHHHHhccccch--hhhhhhcccccchhHh-HHHHHHHHHHhhhhhccCCCCCCC
Q 046847 26 FVDEQVCMFLHALAHHVKN--QTINNRFKHSGETISR-FNSILNGVLELQHILLKSPKPMPE 84 (88)
Q Consensus 26 ~veE~la~FL~i~~~n~~~--r~i~~~F~~S~eTisr-f~~Vl~ai~~L~~~~ik~p~~~~~ 84 (88)
=|+.|=+.|.+-.++-... |+|++..+.+-+|||| . +..|++.|.+.++
T Consensus 313 Iv~~Q~~Ff~~g~~~l~PL~LrdvA~~i~~HESTISRai----------~nKy~~tprG~fe 364 (444)
T COG1508 313 IVEYQKAFFEGGEEALKPLVLRDVADEIGMHESTISRAI----------TNKYLATPRGLFE 364 (444)
T ss_pred HHHHHHHHHhCCcccCCcccHHHHHHHhCccHHHHHHHH----------hcccccCCcceee
Confidence 4677888888777776544 9999999999999999 6 4577777766554
No 147
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=60.20 E-value=13 Score=24.66 Aligned_cols=39 Identities=13% Similarity=0.139 Sum_probs=30.3
Q ss_pred hHHHHHHHHHhc-cccchhhhhhhcccccchhHh-HHHHHH
Q 046847 28 DEQVCMFLHALA-HHVKNQTINNRFKHSGETISR-FNSILN 66 (88)
Q Consensus 28 eE~la~FL~i~~-~n~~~r~i~~~F~~S~eTisr-f~~Vl~ 66 (88)
+-++.|+.+... ...+...+.+.++-|..|||+ .+..-+
T Consensus 16 ptRl~IL~~L~~~~~~~v~ela~~l~lsqstvS~HL~~L~~ 56 (117)
T PRK10141 16 ETRLGIVLLLRESGELCVCDLCTALDQSQPKISRHLALLRE 56 (117)
T ss_pred HHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 346677777664 457889999999999999999 876543
No 148
>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=59.52 E-value=18 Score=24.43 Aligned_cols=37 Identities=8% Similarity=0.047 Sum_probs=29.9
Q ss_pred HHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847 32 CMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVL 69 (88)
Q Consensus 32 a~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~ 69 (88)
.+++.. -.+.+++.|+..++.|-.||.. ++...+.+-
T Consensus 157 ~i~~~~-~~~~s~~eIA~~l~~s~~tV~~~l~r~r~~L~ 194 (198)
T TIGR02859 157 KVLQSY-LDGKSYQEIACDLNRHVKSIDNALQRVKRKLE 194 (198)
T ss_pred HHHHHH-HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 344543 4899999999999999999988 888877654
No 149
>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=59.46 E-value=17 Score=19.96 Aligned_cols=39 Identities=8% Similarity=0.099 Sum_probs=28.0
Q ss_pred chhHHHHHHHHHhcccc--chhhhhhhcccccchhHh-HHHH
Q 046847 26 FVDEQVCMFLHALAHHV--KNQTINNRFKHSGETISR-FNSI 64 (88)
Q Consensus 26 ~veE~la~FL~i~~~n~--~~r~i~~~F~~S~eTisr-f~~V 64 (88)
+++..+.+.=+...++. +..+|+...+-+..|++| .+..
T Consensus 1 sl~ral~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL 42 (52)
T PF09339_consen 1 SLERALRILEALAESGGPLTLSEIARALGLPKSTVHRLLQTL 42 (52)
T ss_dssp HHHHHHHHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 35566666666665554 699999999999999988 5443
No 150
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=59.11 E-value=20 Score=23.49 Aligned_cols=39 Identities=13% Similarity=0.108 Sum_probs=32.4
Q ss_pred HHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847 32 CMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE 70 (88)
Q Consensus 32 a~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~ 70 (88)
-+|....-++.++.+|+..++-|..||.. ....+.++-.
T Consensus 112 ~v~~l~~~~~~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~ 151 (159)
T PRK12527 112 DSFLLRKLEGLSHQQIAEHLGISRSLVEKHIVNAMKHCRV 151 (159)
T ss_pred HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 45666678999999999999999999998 8877766654
No 151
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=59.09 E-value=20 Score=23.12 Aligned_cols=36 Identities=6% Similarity=0.019 Sum_probs=28.8
Q ss_pred HHHHHhccccchhhhhhhcccccchhHh-HHHHHHHH
Q 046847 33 MFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGV 68 (88)
Q Consensus 33 ~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai 68 (88)
+|....-.+.+++.|+...|.|..||.. .+..+..+
T Consensus 114 ii~l~~~~~~s~~EIA~~l~is~~tV~~~~~ra~~~L 150 (154)
T PRK06759 114 IIFERFFVGKTMGEIALETEMTYYQVRWIYRQALEKM 150 (154)
T ss_pred HHHHHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 3444456789999999999999999998 88776654
No 152
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=58.74 E-value=18 Score=26.53 Aligned_cols=44 Identities=18% Similarity=0.191 Sum_probs=33.8
Q ss_pred cchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847 25 VFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVL 69 (88)
Q Consensus 25 v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~ 69 (88)
++-.|+-.+-|+. ..+.++..|+..++.|.+||++ .+..+..+-
T Consensus 216 L~~rer~vl~l~y-~~~~t~~EIA~~lgis~~~V~~~~~ral~kLr 260 (264)
T PRK07122 216 LPERERTVLVLRF-FESMTQTQIAERVGISQMHVSRLLAKTLARLR 260 (264)
T ss_pred CCHHHHHHHHHHh-cCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 4444555555544 5789999999999999999999 888776554
No 153
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=58.73 E-value=13 Score=24.05 Aligned_cols=32 Identities=13% Similarity=0.150 Sum_probs=27.9
Q ss_pred hccccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847 38 LAHHVKNQTINNRFKHSGETISR-FNSILNGVL 69 (88)
Q Consensus 38 ~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~ 69 (88)
++.|.++++|+...+-|..||.. ..+.++-+.
T Consensus 161 ~~~g~~~~~Ia~~l~~s~~tv~~~~~~~~~kl~ 193 (211)
T PRK15369 161 ITEGYTNRDIAEQLSISIKTVETHRLNMMRKLD 193 (211)
T ss_pred HHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 67889999999999999999998 888776653
No 154
>PRK11233 nitrogen assimilation transcriptional regulator; Provisional
Probab=58.67 E-value=14 Score=26.79 Aligned_cols=37 Identities=5% Similarity=0.083 Sum_probs=28.8
Q ss_pred HHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHH
Q 046847 29 EQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILN 66 (88)
Q Consensus 29 E~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ 66 (88)
++|..|+-+.- ..++..++.+.+.|.+|||+ +++.=+
T Consensus 4 ~~L~~F~~v~~-~~S~s~AA~~L~isQ~avS~~I~~LE~ 41 (305)
T PRK11233 4 RRLKYFVKIVD-IGSLTQAAEVLHIAQPALSQQVATLEG 41 (305)
T ss_pred HHHHHHHHHHH-cCCHHHHHHHhCCCchHHHHHHHHHHH
Confidence 45666665544 46999999999999999999 887533
No 155
>PRK11564 stationary phase inducible protein CsiE; Provisional
Probab=58.48 E-value=15 Score=28.48 Aligned_cols=50 Identities=16% Similarity=0.155 Sum_probs=35.8
Q ss_pred CcCCCccchhHHHHH-HHH--HhccccchhhhhhhcccccchhHh-HHHHHHHH
Q 046847 19 LKTDSVVFVDEQVCM-FLH--ALAHHVKNQTINNRFKHSGETISR-FNSILNGV 68 (88)
Q Consensus 19 L~~t~~v~veE~la~-FL~--i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai 68 (88)
|.+....+.+|+... .++ ......+..++++.++.|..||.+ .++|=..+
T Consensus 5 ~~~~~~~s~~ER~~~il~~LL~~~~~v~l~~Lae~l~VSrsTi~~DLk~l~~~L 58 (426)
T PRK11564 5 LAPPSVLSAPQRRCQILLMLFQPGLTVTLETFSQLNGVDDDTARQDIAETGREI 58 (426)
T ss_pred CCCCcCCCHHHHHHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 445566777776543 333 334558889999999999999999 88875444
No 156
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=58.33 E-value=20 Score=24.50 Aligned_cols=41 Identities=5% Similarity=0.033 Sum_probs=30.8
Q ss_pred HHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847 29 EQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE 70 (88)
Q Consensus 29 E~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~ 70 (88)
.+-++-|.. -.+.++..|+..++.|..||.. .+.....+-.
T Consensus 139 ~R~v~~L~~-~~g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~ 180 (189)
T PRK12530 139 QARVFMMRE-YLELSSEQICQECDISTSNLHVLLYRARLQLQA 180 (189)
T ss_pred HHHHHhHHH-HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 344444443 4589999999999999999988 7777666653
No 157
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=58.14 E-value=20 Score=23.44 Aligned_cols=38 Identities=13% Similarity=0.113 Sum_probs=29.8
Q ss_pred HHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847 33 MFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE 70 (88)
Q Consensus 33 ~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~ 70 (88)
+|......+.++..|+..++-|..||.+ .+.....+-.
T Consensus 133 i~~l~~~~~~~~~eIA~~lgis~~tv~~~~~ra~~~lr~ 171 (179)
T PRK11924 133 VFLLRYVEGLSYREIAEILGVPVGTVKSRLRRARQLLRE 171 (179)
T ss_pred HhhHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3433344789999999999999999999 8887766543
No 158
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=58.09 E-value=19 Score=23.46 Aligned_cols=42 Identities=7% Similarity=0.084 Sum_probs=29.4
Q ss_pred ccchhH-HHHHHHHHhccccchhhhhhhcccccchhHh-HHHHH
Q 046847 24 VVFVDE-QVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSIL 65 (88)
Q Consensus 24 ~v~veE-~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl 65 (88)
+++..+ .+-++|+..+.+.+..+++..++-+..||++ .+..-
T Consensus 28 glt~~q~~vL~~l~~~~~~~t~~eLa~~l~~~~~tvt~~v~~Le 71 (144)
T PRK03573 28 ELTQTHWVTLHNIHQLPPEQSQIQLAKAIGIEQPSLVRTLDQLE 71 (144)
T ss_pred CCCHHHHHHHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHHHHH
Confidence 355544 3334444444457889999999999999999 77655
No 159
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=58.04 E-value=10 Score=27.76 Aligned_cols=31 Identities=26% Similarity=0.370 Sum_probs=24.6
Q ss_pred cchhhhhhhcccccchhHh-HHH-----------HHHHHHHhh
Q 046847 42 VKNQTINNRFKHSGETISR-FNS-----------ILNGVLELQ 72 (88)
Q Consensus 42 ~~~r~i~~~F~~S~eTisr-f~~-----------Vl~ai~~L~ 72 (88)
.+.++|+...|.|..|||| ++. |++++-+|.
T Consensus 2 ~ti~dIA~~aGVS~~TVSrvLn~~~~Vs~~tr~kV~~~a~elg 44 (346)
T PRK10401 2 ITIRDVARQAGVSVATVSRVLNNSALVSADTREAVMKAVSELG 44 (346)
T ss_pred CCHHHHHHHhCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHC
Confidence 3678999999999999999 973 566665553
No 160
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=57.92 E-value=15 Score=26.69 Aligned_cols=40 Identities=10% Similarity=0.153 Sum_probs=33.4
Q ss_pred HHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHH
Q 046847 29 EQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGV 68 (88)
Q Consensus 29 E~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai 68 (88)
++|-.|+-..-++.+++.++...+.|.+|||| .++.=+.+
T Consensus 4 ~~L~~F~~v~~~~~s~s~AA~~L~isq~avSr~I~~LE~~l 44 (309)
T PRK12682 4 QQLRFVREAVRRNLNLTEAAKALHTSQPGVSKAIIELEEEL 44 (309)
T ss_pred HHHHHHHHHHHccCCHHHHHHHhcCccHHHHHHHHHHHHHh
Confidence 46777877777778999999999999999999 98865544
No 161
>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=57.90 E-value=21 Score=23.84 Aligned_cols=37 Identities=11% Similarity=0.009 Sum_probs=30.8
Q ss_pred HHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847 33 MFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVL 69 (88)
Q Consensus 33 ~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~ 69 (88)
+|+...-.+.++..|+...|.|..||.. .+.....+-
T Consensus 142 v~~l~~~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr 179 (183)
T TIGR02999 142 VVELRFFAGLTVEEIAELLGVSVRTVERDWRFARAWLA 179 (183)
T ss_pred HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 4555566889999999999999999999 888776654
No 162
>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=57.79 E-value=24 Score=25.99 Aligned_cols=49 Identities=8% Similarity=0.051 Sum_probs=36.4
Q ss_pred cchhHHHHHHHHH-h--ccccchhhhhhhcccccchhHh-HHHHHHHHHH-hhh
Q 046847 25 VFVDEQVCMFLHA-L--AHHVKNQTINNRFKHSGETISR-FNSILNGVLE-LQH 73 (88)
Q Consensus 25 v~veE~la~FL~i-~--~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~-L~~ 73 (88)
.+-.++..+.|+. + -.+.+++.|+...+-|.+||+. .+.-++.+-. |..
T Consensus 223 Lp~~~R~Vl~l~ygL~~~e~~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~~l~~ 276 (285)
T TIGR02394 223 LNERQREVLARRFGLLGYEPATLEEVAAEVGLTRERVRQIQVEALKKLRRILER 276 (285)
T ss_pred CCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 3444555666654 2 5789999999999999999999 8888777754 443
No 163
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=57.42 E-value=19 Score=24.54 Aligned_cols=41 Identities=12% Similarity=-0.023 Sum_probs=33.2
Q ss_pred HHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847 30 QVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE 70 (88)
Q Consensus 30 ~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~ 70 (88)
+=.+|....-++.++..|+..++.|..||.. .+..+..+-.
T Consensus 135 ~r~v~~L~~~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 176 (185)
T PRK09649 135 QREALLLTQLLGLSYADAAAVCGCPVGTIRSRVARARDALLA 176 (185)
T ss_pred HhHHhhhHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 3345666677889999999999999999998 8877776654
No 164
>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=57.02 E-value=26 Score=23.29 Aligned_cols=38 Identities=13% Similarity=0.135 Sum_probs=30.7
Q ss_pred HHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847 33 MFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE 70 (88)
Q Consensus 33 ~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~ 70 (88)
+|....-.+.+++.|+...|.|..||.. .+..+..+-.
T Consensus 148 vi~l~~~~g~s~~eIA~~lgis~~~v~~~l~Ra~~~Lr~ 186 (189)
T TIGR02984 148 VILLRHLEGLSFAEVAERMDRSEGAVSMLWVRGLARLRQ 186 (189)
T ss_pred HHHHHHhcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 3444445889999999999999999999 8888776643
No 165
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=56.89 E-value=21 Score=24.30 Aligned_cols=41 Identities=12% Similarity=0.122 Sum_probs=31.9
Q ss_pred hHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847 28 DEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE 70 (88)
Q Consensus 28 eE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~ 70 (88)
.++-.+-| .-.+.+++.|+...|.|..||.. .+.....+-.
T Consensus 159 ~~r~vl~l--~~e~~s~~EIA~~lgis~~tV~~~l~rar~~Lr~ 200 (208)
T PRK08295 159 LEKEVLEL--YLDGKSYQEIAEELNRHVKSIDNALQRVKRKLEK 200 (208)
T ss_pred HHHHHHHH--HHccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 33444444 34789999999999999999999 8888777654
No 166
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=56.88 E-value=16 Score=26.72 Aligned_cols=41 Identities=10% Similarity=0.083 Sum_probs=34.5
Q ss_pred HHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847 29 EQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVL 69 (88)
Q Consensus 29 E~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~ 69 (88)
++|-+|+.++-++.++..++.+-+.|..|||+ .++.=+.+.
T Consensus 4 ~~L~~f~~v~~~g~S~s~AA~~L~isQpavS~~ik~LE~~lg 45 (313)
T PRK12684 4 HQLRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEDELG 45 (313)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHhcCCChHHHHHHHHHHHHhC
Confidence 47778888888877999999999999999999 988655544
No 167
>PRK10403 transcriptional regulator NarP; Provisional
Probab=56.76 E-value=14 Score=24.13 Aligned_cols=43 Identities=23% Similarity=0.288 Sum_probs=33.1
Q ss_pred cchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847 25 VFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVL 69 (88)
Q Consensus 25 v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~ 69 (88)
.+-.|.-. |+.++.|.++++|+...+-|..||.. .+.+.+.+.
T Consensus 154 Lt~~e~~v--l~~~~~g~s~~~ia~~l~~s~~tv~~~~~~i~~kl~ 197 (215)
T PRK10403 154 LTERELDV--LHELAQGLSNKQIASVLNISEQTVKVHIRNLLRKLN 197 (215)
T ss_pred CCHHHHHH--HHHHHCCCCHHHHHHHcCCCHHHHHHHHHHHHHHcC
Confidence 45555543 44556779999999999999999998 888877653
No 168
>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=56.56 E-value=24 Score=22.87 Aligned_cols=37 Identities=3% Similarity=0.097 Sum_probs=29.8
Q ss_pred HHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847 33 MFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVL 69 (88)
Q Consensus 33 ~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~ 69 (88)
+|....-.+.++..|+..++-|..||.. .+.....+-
T Consensus 119 v~~l~~~~g~~~~eIA~~l~is~~tv~~~l~Rar~~Lr 156 (159)
T TIGR02989 119 LLQLRYQRGVSLTALAEQLGRTVNAVYKALSRLRVRLR 156 (159)
T ss_pred HHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 4444455889999999999999999998 888776653
No 169
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=56.25 E-value=13 Score=26.46 Aligned_cols=43 Identities=14% Similarity=0.137 Sum_probs=32.8
Q ss_pred cchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847 25 VFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVL 69 (88)
Q Consensus 25 v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~ 69 (88)
.|--|+=.+.| ++.+.+|++|+...+-|..||.. ...++..+.
T Consensus 156 Lt~rE~~Vl~l--~~~G~s~~eIA~~L~iS~~TVk~~~~~i~~Kl~ 199 (216)
T PRK10100 156 LTHREKEILNK--LRIGASNNEIARSLFISENTVKTHLYNLFKKIA 199 (216)
T ss_pred CCHHHHHHHHH--HHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 55555444444 44589999999999999999999 888877654
No 170
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=56.10 E-value=13 Score=27.32 Aligned_cols=44 Identities=9% Similarity=-0.030 Sum_probs=34.0
Q ss_pred ccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847 24 VVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVL 69 (88)
Q Consensus 24 ~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~ 69 (88)
..|.-|.= -|-.++.+.++++|+...+.|..||.. ...+++-+.
T Consensus 143 ~LS~RE~e--VL~Lia~G~SnkEIA~~L~IS~~TVk~hvs~I~~KLg 187 (217)
T PRK13719 143 KVTKYQND--VFILYSFGFSHEYIAQLLNITVGSSKNKISEILKFFG 187 (217)
T ss_pred CCCHHHHH--HHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 34444433 245578899999999999999999999 988877654
No 171
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=56.03 E-value=26 Score=23.83 Aligned_cols=44 Identities=9% Similarity=0.012 Sum_probs=33.5
Q ss_pred cchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847 25 VFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVL 69 (88)
Q Consensus 25 v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~ 69 (88)
++.+++-.+-|+.+ .+.+++.|+..++.|..||.. .+.....+-
T Consensus 132 L~~~~r~i~~l~~~-~g~s~~EIAe~lgis~~~V~~~l~Ra~~~Lr 176 (189)
T PRK06811 132 LEKLDREIFIRRYL-LGEKIEEIAKKLGLTRSAIDNRLSRGRKKLQ 176 (189)
T ss_pred CCHHHHHHHHHHHH-ccCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 44555555555443 679999999999999999998 887776654
No 172
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=55.96 E-value=23 Score=23.90 Aligned_cols=38 Identities=8% Similarity=0.010 Sum_probs=30.6
Q ss_pred HHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847 33 MFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE 70 (88)
Q Consensus 33 ~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~ 70 (88)
+|...--.+.++++|+..++.|..||.. .+.....+-.
T Consensus 137 v~~l~~~~g~s~~EIA~~l~is~~tV~~~l~rar~~Lr~ 175 (181)
T PRK12536 137 PIVHVKLEGLSVAETAQLTGLSESAVKVGIHRGLKALAA 175 (181)
T ss_pred HHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3444445779999999999999999999 8888776654
No 173
>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=55.59 E-value=23 Score=25.06 Aligned_cols=42 Identities=14% Similarity=0.075 Sum_probs=31.9
Q ss_pred hHHHHHHHHHh---ccccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847 28 DEQVCMFLHAL---AHHVKNQTINNRFKHSGETISR-FNSILNGVL 69 (88)
Q Consensus 28 eE~la~FL~i~---~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~ 69 (88)
.++-++-|+.. ..+.++..|+...+-|..||++ .+..+..+-
T Consensus 178 ~~r~il~l~y~~~~~e~~S~~EIAe~lgis~~tV~~~~~rAl~~Lr 223 (227)
T TIGR02846 178 REREVIEMRYGLGDGRRKTQREIAKILGISRSYVSRIEKRALMKLY 223 (227)
T ss_pred HHHHHHHHHHcCCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 33444444443 3889999999999999999998 888877664
No 174
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=55.50 E-value=22 Score=26.89 Aligned_cols=46 Identities=13% Similarity=0.129 Sum_probs=36.4
Q ss_pred cchhHHHHHHHHHh---ccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847 25 VFVDEQVCMFLHAL---AHHVKNQTINNRFKHSGETISR-FNSILNGVLE 70 (88)
Q Consensus 25 v~veE~la~FL~i~---~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~ 70 (88)
.+-.|+..+-|... +.+.++..|+..++.|.+||.. -+..++-+-.
T Consensus 257 L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVRqi~~rAl~kLr~ 306 (317)
T PRK07405 257 LTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKLRK 306 (317)
T ss_pred CCHHHHHHHHHHhhcCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 55666766777654 5789999999999999999999 8877766643
No 175
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=55.28 E-value=14 Score=22.93 Aligned_cols=38 Identities=16% Similarity=0.269 Sum_probs=28.1
Q ss_pred Hhccccchhhhhhhccc------ccchhHhHHH---HHHHHHHhhhh
Q 046847 37 ALAHHVKNQTINNRFKH------SGETISRFNS---ILNGVLELQHI 74 (88)
Q Consensus 37 i~~~n~~~r~i~~~F~~------S~eTisrf~~---Vl~ai~~L~~~ 74 (88)
...-|.+..+++...+. |..|||||.. -++..++|.+-
T Consensus 20 R~~lGLTQ~dvA~~lg~~~g~i~SQstISR~Es~~ls~~n~~kl~p~ 66 (75)
T smart00352 20 RIKLGFTQADVGLALGALYGPDFSQTTICRFEALQLSFKNMCKLKPL 66 (75)
T ss_pred HHHcCCCHHHHHHHhcccccCcCCHHHHHHHHhcCccHHHHHHHHHH
Confidence 45667888999999995 9999999544 25566666554
No 176
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=55.15 E-value=7.8 Score=20.35 Aligned_cols=27 Identities=19% Similarity=0.193 Sum_probs=19.8
Q ss_pred ccccchhhhhhhcccccchhHh-HHHHH
Q 046847 39 AHHVKNQTINNRFKHSGETISR-FNSIL 65 (88)
Q Consensus 39 ~~n~~~r~i~~~F~~S~eTisr-f~~Vl 65 (88)
..+.+-.+|++..+-|....+| |++.+
T Consensus 6 ~~~~~l~~iA~~~g~S~~~f~r~Fk~~~ 33 (42)
T PF00165_consen 6 QQKLTLEDIAEQAGFSPSYFSRLFKKET 33 (42)
T ss_dssp -SS--HHHHHHHHTS-HHHHHHHHHHHT
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 4567788899999999999999 98874
No 177
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=55.15 E-value=31 Score=23.21 Aligned_cols=32 Identities=9% Similarity=0.049 Sum_probs=27.4
Q ss_pred ccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847 39 AHHVKNQTINNRFKHSGETISR-FNSILNGVLE 70 (88)
Q Consensus 39 ~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~ 70 (88)
-.+.++..|+..+|-|..||.. .+.....+-.
T Consensus 151 ~~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 183 (187)
T PRK12534 151 FEGITYEELAARTDTPIGTVKSWIRRGLAKLKA 183 (187)
T ss_pred HcCCCHHHHHHHhCCChhHHHHHHHHHHHHHHH
Confidence 4899999999999999999998 8877766543
No 178
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=54.64 E-value=27 Score=23.87 Aligned_cols=38 Identities=11% Similarity=0.037 Sum_probs=31.6
Q ss_pred HHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847 33 MFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE 70 (88)
Q Consensus 33 ~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~ 70 (88)
+|+...-.+.++..|+...+.|..||.. .+..+..+-.
T Consensus 150 vl~l~~~~~~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~ 188 (194)
T PRK09646 150 SVTLAYYGGLTYREVAERLAVPLGTVKTRMRDGLIRLRD 188 (194)
T ss_pred HHHHHHHcCCCHHHHHHHhCCChHhHHHHHHHHHHHHHH
Confidence 4555556789999999999999999998 8888877654
No 179
>PF10799 YliH: Biofilm formation protein (YliH/bssR); InterPro: IPR020359 This entry represents Biofilm regulator, BssR (from the gene also known as yliH). It represses Escherichia coli biofilm formation in M9C glu and LB glu media but not in M9C and LB media. It may act as a global regulator of several genes involved in catabolite repression and stress response and regulation of the uptake and export of signalling pathways. It could also be involved the regulation of indole as well as uptake and export of AI-2 through a cAMP-dependent pathway [].
Probab=54.33 E-value=13 Score=25.15 Aligned_cols=30 Identities=10% Similarity=-0.003 Sum_probs=23.3
Q ss_pred hHHHHHHHHHHhhCcCCcCCCccchhHHHHH
Q 046847 3 RKTFGLLFELLCSDERLKTDSVVFVDEQVCM 33 (88)
Q Consensus 3 ~~~F~~L~~~L~~~~~L~~t~~v~veE~la~ 33 (88)
|+.|+.||..+|.+.. +=..++.-||+.|.
T Consensus 43 Rdn~FeLc~e~r~~~~-~l~~~l~~eE~~aL 72 (127)
T PF10799_consen 43 RDNLFELCREMRDKAP-RLKLHLDPEEWEAL 72 (127)
T ss_pred HHHHHHHHHHHHHhhH-hhhhhcCHHHHHHH
Confidence 6889999999999865 33456788887765
No 180
>KOG1766 consensus Enhancer of rudimentary [General function prediction only]
Probab=54.31 E-value=14 Score=24.28 Aligned_cols=25 Identities=16% Similarity=0.270 Sum_probs=21.6
Q ss_pred HHHHHHHHHHhhhhhccCCCCCCCC
Q 046847 61 FNSILNGVLELQHILLKSPKPMPEY 85 (88)
Q Consensus 61 f~~Vl~ai~~L~~~~ik~p~~~~~~ 85 (88)
..+++++||.+..+++|...|+.++
T Consensus 25 v~e~megiCk~yEe~Lkk~nPs~~~ 49 (104)
T KOG1766|consen 25 VTECMEGICKMYEEHLKKKNPSAPP 49 (104)
T ss_pred HHHHHHHHHHHHHHHHHhcCCCCCC
Confidence 5789999999999999988887754
No 181
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=54.28 E-value=26 Score=23.31 Aligned_cols=38 Identities=16% Similarity=0.164 Sum_probs=31.3
Q ss_pred HHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847 33 MFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE 70 (88)
Q Consensus 33 ~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~ 70 (88)
+|....-.+.++..|+..++-|..||.. ....+..+..
T Consensus 126 v~~L~~~eg~s~~EIA~~l~is~~tV~~~l~ra~~~~~~ 164 (168)
T PRK12525 126 AFLMSQLEGLTYVEIGERLGVSLSRIHQYMVEAFKCCYQ 164 (168)
T ss_pred HHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4444567889999999999999999999 8877776653
No 182
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=54.16 E-value=24 Score=25.70 Aligned_cols=44 Identities=11% Similarity=0.071 Sum_probs=32.5
Q ss_pred cchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847 25 VFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVL 69 (88)
Q Consensus 25 v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~ 69 (88)
++..++-.+.|+. ..+.++..|+..++.|.+||.+ .+..++.+-
T Consensus 213 L~~~~r~vl~l~~-~~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr 257 (268)
T PRK06288 213 LPEREKKVLILYY-YEDLTLKEIGKVLGVTESRISQLHTKAVLQLR 257 (268)
T ss_pred CCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 4445555555544 5789999999999999999997 766655443
No 183
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=54.06 E-value=23 Score=25.21 Aligned_cols=41 Identities=10% Similarity=0.058 Sum_probs=31.4
Q ss_pred HHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847 29 EQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE 70 (88)
Q Consensus 29 E~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~ 70 (88)
++-++-|+.+ .+.+++.|+..++-|..||.. .+..+..+-.
T Consensus 139 ~R~v~~L~y~-eg~s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~ 180 (216)
T PRK12533 139 YREVLVLREL-EDMSYREIAAIADVPVGTVMSRLARARRRLAA 180 (216)
T ss_pred HHhHhhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3344444333 789999999999999999999 8887776654
No 184
>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=53.93 E-value=58 Score=23.24 Aligned_cols=46 Identities=15% Similarity=0.060 Sum_probs=36.5
Q ss_pred CCccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847 22 DSVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVL 69 (88)
Q Consensus 22 t~~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~ 69 (88)
...+|..|+=.+.+ .+.+.++.+|+..++.|..||.. .+.+.+.+.
T Consensus 169 ~~~Lt~re~evl~~--~a~G~t~~eIa~~l~is~~Tv~~~l~~~~~kl~ 215 (232)
T TIGR03541 169 AGVLSEREREVLAW--TALGRRQADIAAILGISERTVENHLRSARRKLG 215 (232)
T ss_pred hccCCHHHHHHHHH--HHCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHC
Confidence 34566666655555 47999999999999999999999 888876654
No 185
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=53.92 E-value=26 Score=25.18 Aligned_cols=43 Identities=19% Similarity=0.150 Sum_probs=32.6
Q ss_pred chhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847 26 FVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVL 69 (88)
Q Consensus 26 ~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~ 69 (88)
+..++-.+-|. .-.+.+++.|+..++.|.+||.. .+..++.+-
T Consensus 203 ~~~~r~vl~l~-~~~~~s~~EIA~~lgis~~tV~~~~~ra~~~Lr 246 (251)
T PRK07670 203 SEKEQLVISLF-YKEELTLTEIGQVLNLSTSRISQIHSKALFKLK 246 (251)
T ss_pred CHHHHHHHHHH-HhcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 33444444443 35889999999999999999998 888777664
No 186
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=53.92 E-value=23 Score=23.61 Aligned_cols=33 Identities=6% Similarity=0.040 Sum_probs=28.1
Q ss_pred hccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847 38 LAHHVKNQTINNRFKHSGETISR-FNSILNGVLE 70 (88)
Q Consensus 38 ~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~ 70 (88)
.-.+.++..|+..++.|.+||.. .+.....+-.
T Consensus 149 ~~~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 182 (187)
T TIGR02948 149 YMEDLSLKEISEILDLPVGTVKTRIHRGREALRK 182 (187)
T ss_pred HhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 44789999999999999999999 8888776643
No 187
>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=53.63 E-value=26 Score=23.38 Aligned_cols=38 Identities=5% Similarity=-0.059 Sum_probs=31.1
Q ss_pred HHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847 33 MFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE 70 (88)
Q Consensus 33 ~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~ 70 (88)
+|....-.+.++..|+..+|-|..||.. .+.....+-.
T Consensus 146 v~~l~~~~~~s~~EIA~~lgis~~tv~~~l~rar~~Lr~ 184 (190)
T TIGR02939 146 AITLRELEGLSYEDIARIMDCPVGTVRSRIFRAREAIAI 184 (190)
T ss_pred hhhhhhhcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 3433445889999999999999999998 8888877765
No 188
>PF13551 HTH_29: Winged helix-turn helix
Probab=53.61 E-value=17 Score=22.22 Aligned_cols=31 Identities=29% Similarity=0.258 Sum_probs=25.6
Q ss_pred HHHhccccc-hhhhhhhcccccchhHh-HHHHH
Q 046847 35 LHALAHHVK-NQTINNRFKHSGETISR-FNSIL 65 (88)
Q Consensus 35 L~i~~~n~~-~r~i~~~F~~S~eTisr-f~~Vl 65 (88)
|..+..+.+ ...|+..++.|..||.+ .+..-
T Consensus 5 l~l~~~g~~~~~~ia~~lg~s~~Tv~r~~~~~~ 37 (112)
T PF13551_consen 5 LLLLAEGVSTIAEIARRLGISRRTVYRWLKRYR 37 (112)
T ss_pred HHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHH
Confidence 445667775 99999999999999999 87764
No 189
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=53.39 E-value=28 Score=22.78 Aligned_cols=37 Identities=22% Similarity=0.151 Sum_probs=29.5
Q ss_pred HHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHH
Q 046847 32 CMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGV 68 (88)
Q Consensus 32 a~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai 68 (88)
.+|+...-++.++..|+..++.|..||.. .+...+.+
T Consensus 120 ~v~~L~~~~g~s~~EIA~~l~is~~tV~~~l~ra~~~~ 157 (161)
T PRK12528 120 RAFLLAQVDGLGYGEIATELGISLATVKRYLNKAAMRC 157 (161)
T ss_pred HHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 34555567889999999999999999988 77765543
No 190
>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=53.33 E-value=14 Score=21.23 Aligned_cols=29 Identities=10% Similarity=0.194 Sum_probs=23.9
Q ss_pred ccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847 41 HVKNQTINNRFKHSGETISR-FNSILNGVL 69 (88)
Q Consensus 41 n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~ 69 (88)
..+-.++++.++.|..|++. .+...+-|+
T Consensus 23 ~~tl~elA~~lgis~st~~~~LRrae~kli 52 (53)
T PF04967_consen 23 RITLEELAEELGISKSTVSEHLRRAERKLI 52 (53)
T ss_pred cCCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Confidence 45667799999999999999 988776554
No 191
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=52.87 E-value=5.7 Score=28.64 Aligned_cols=28 Identities=21% Similarity=0.256 Sum_probs=22.3
Q ss_pred hhhhhhcccccchhHh-HHH-----------HHHHHHHhh
Q 046847 45 QTINNRFKHSGETISR-FNS-----------ILNGVLELQ 72 (88)
Q Consensus 45 r~i~~~F~~S~eTisr-f~~-----------Vl~ai~~L~ 72 (88)
++|+...|.|..|||| ++. |++++-+|.
T Consensus 2 ~dIA~~agVS~~TVSrvLn~~~~vs~~tr~rV~~~a~~lg 41 (327)
T PRK10423 2 KDVARLAGVSTSTVSHVINKDRFVSEAITAKVEAAIKELN 41 (327)
T ss_pred hhHHHHhCCcHHHHHHHhCCCCCCCHHHHHHHHHHHHHHC
Confidence 5789999999999999 973 666666553
No 192
>COG5606 Uncharacterized conserved small protein [Function unknown]
Probab=52.86 E-value=10 Score=24.43 Aligned_cols=60 Identities=7% Similarity=0.066 Sum_probs=42.3
Q ss_pred CChHHHHHHHHHHhhCcCCcCCCccchhHHHHHHHHHhccccchhhhhhhcccccchhHh
Q 046847 1 MDRKTFGLLFELLCSDERLKTDSVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR 60 (88)
Q Consensus 1 M~~~~F~~L~~~L~~~~~L~~t~~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr 60 (88)
|.-++|..+-+.......-.++-.+..+=..++-+|+--.+.+.++|...++.+.+-||-
T Consensus 1 ~~~~vF~s~~~~~~D~~e~a~~m~ir~~l~~~i~~~i~q~~l~Q~qiae~lgV~qprvS~ 60 (91)
T COG5606 1 MSNEVFTSVWDAIEDTPEAAENMKIRSALMMAIKQWIEQAALSQAQIAELLGVTQPRVSD 60 (91)
T ss_pred CCCchhhhHHHHHhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCchHHH
Confidence 455677776666654432222333333444567889999999999999999999999986
No 193
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=52.72 E-value=13 Score=24.68 Aligned_cols=43 Identities=7% Similarity=-0.018 Sum_probs=30.6
Q ss_pred chhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847 26 FVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVL 69 (88)
Q Consensus 26 ~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~ 69 (88)
+..++.++-|+. -.+.++.+|+..++-|..||.. .+.....+-
T Consensus 128 ~~~~r~v~~l~~-~~g~s~~eIA~~l~is~~~V~~~l~ra~~~l~ 171 (176)
T PRK09638 128 DPEFRAPVILKH-YYGYTYEEIAKMLNIPEGTVKSRVHHGIKQLR 171 (176)
T ss_pred CHHHhheeeehh-hcCCCHHHHHHHHCCChhHHHHHHHHHHHHHH
Confidence 333344333433 4789999999999999999987 777666554
No 194
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=52.68 E-value=29 Score=22.73 Aligned_cols=38 Identities=8% Similarity=-0.117 Sum_probs=30.6
Q ss_pred HHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847 33 MFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE 70 (88)
Q Consensus 33 ~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~ 70 (88)
+|....-.+.++..|+..+|-|..||.. .+.....+-.
T Consensus 120 v~~l~~~~~~s~~eIA~~lgis~~tv~~~l~Rar~~L~~ 158 (161)
T PRK12541 120 VLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRKETKS 158 (161)
T ss_pred HhhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 4444456789999999999999999998 8887776654
No 195
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=52.60 E-value=6.2 Score=28.70 Aligned_cols=21 Identities=29% Similarity=0.178 Sum_probs=18.7
Q ss_pred chhhhhhhcccccchhHh-HHH
Q 046847 43 KNQTINNRFKHSGETISR-FNS 63 (88)
Q Consensus 43 ~~r~i~~~F~~S~eTisr-f~~ 63 (88)
+-++|+..-|.|..|||| +|.
T Consensus 3 ti~dIA~~agVS~~TVSrvln~ 24 (327)
T PRK10339 3 TLKDIAIEAGVSLATVSRVLND 24 (327)
T ss_pred CHHHHHHHhCCCHHhhhhhhcC
Confidence 568999999999999999 874
No 196
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=52.46 E-value=18 Score=26.43 Aligned_cols=41 Identities=17% Similarity=0.264 Sum_probs=28.6
Q ss_pred hHHHHHHHHHhccc--cchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847 28 DEQVCMFLHALAHH--VKNQTINNRFKHSGETISR-FNSILNGVL 69 (88)
Q Consensus 28 eE~la~FL~i~~~n--~~~r~i~~~F~~S~eTisr-f~~Vl~ai~ 69 (88)
+|+...-|-.+..+ .+..++++.|+.|.+||.| ..+ |+.-.
T Consensus 4 ~eR~~~Il~~L~~~~~v~v~eLa~~l~VS~~TIRRDL~~-Le~~g 47 (256)
T PRK10434 4 RQRQAAILEYLQKQGKTSVEELAQYFDTTGTTIRKDLVI-LEHAG 47 (256)
T ss_pred HHHHHHHHHHHHHcCCEEHHHHHHHHCCCHHHHHHHHHH-HHHCC
Confidence 34444444444433 6788899999999999999 888 44333
No 197
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=52.43 E-value=30 Score=23.91 Aligned_cols=44 Identities=5% Similarity=-0.111 Sum_probs=34.9
Q ss_pred HHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHHhhhhhc
Q 046847 33 MFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLELQHILL 76 (88)
Q Consensus 33 ~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~L~~~~i 76 (88)
+|....-.+.+++.|++.++.|..||.. .+..+..+-.+-..+.
T Consensus 141 v~~l~~~~g~s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l~~~~ 185 (196)
T PRK12535 141 ALILTQVLGYTYEEAAKIADVRVGTIRSRVARARADLIAATATGQ 185 (196)
T ss_pred HhhhHHHhCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhcccc
Confidence 4444556789999999999999999999 9888888776544443
No 198
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=52.00 E-value=23 Score=22.46 Aligned_cols=42 Identities=7% Similarity=-0.009 Sum_probs=35.3
Q ss_pred ccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHH
Q 046847 24 VVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSIL 65 (88)
Q Consensus 24 ~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl 65 (88)
.++..-.+.+---++.++.+...++..||.|..|.++ ...--
T Consensus 8 ~Lt~~gR~~lv~~vv~~g~~~a~aA~~~gVS~~Ta~kW~~Ryr 50 (85)
T PF13011_consen 8 RLTPRGRLRLVRRVVEQGWPVAHAAAEFGVSRRTAYKWLARYR 50 (85)
T ss_pred CCCHHHHHHHHHHHHHcCCcHHHHHHHhCCCHHHHHHHHHHHH
Confidence 3667777777778889999999999999999999999 65543
No 199
>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=51.87 E-value=11 Score=24.54 Aligned_cols=23 Identities=22% Similarity=0.260 Sum_probs=20.4
Q ss_pred cccchhhhhhhcccccchhHh-HH
Q 046847 40 HHVKNQTINNRFKHSGETISR-FN 62 (88)
Q Consensus 40 ~n~~~r~i~~~F~~S~eTisr-f~ 62 (88)
.+.+-+.++.+|+.|..||.+ +.
T Consensus 17 ~g~s~~eaa~~F~VS~~Tv~~W~k 40 (119)
T PF01710_consen 17 KGKSIREAAKRFGVSRNTVYRWLK 40 (119)
T ss_pred ccchHHHHHHHhCcHHHHHHHHHH
Confidence 355889999999999999999 87
No 200
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=51.59 E-value=46 Score=22.50 Aligned_cols=43 Identities=9% Similarity=0.042 Sum_probs=33.2
Q ss_pred HHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH-hhhhh
Q 046847 33 MFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE-LQHIL 75 (88)
Q Consensus 33 ~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~-L~~~~ 75 (88)
+|....-.+.++..|+...|-|..||.. .+..++.+-. |....
T Consensus 139 v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~ 183 (191)
T PRK12520 139 VFMMREWLELETEEICQELQITATNAWVLLYRARMRLRECLDLHW 183 (191)
T ss_pred HHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444445679999999999999999998 8888877754 44444
No 201
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=51.52 E-value=31 Score=23.08 Aligned_cols=36 Identities=6% Similarity=-0.075 Sum_probs=29.4
Q ss_pred HHHHhccccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847 34 FLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVL 69 (88)
Q Consensus 34 FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~ 69 (88)
|....-.+.++..|+..+|-|..||.. .+.....+-
T Consensus 144 l~l~~~~~~s~~eIA~~lgis~~~V~~~l~ra~~~Lr 180 (186)
T PRK13919 144 IEVLYYQGYTHREAAQLLGLPLGTLKTRARRALSRLK 180 (186)
T ss_pred HHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 333446789999999999999999998 888776664
No 202
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=51.24 E-value=31 Score=22.52 Aligned_cols=38 Identities=13% Similarity=0.013 Sum_probs=30.2
Q ss_pred HHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847 33 MFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE 70 (88)
Q Consensus 33 ~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~ 70 (88)
+|....-.+.+++.|+..+|.|..||.. .+.....+-.
T Consensus 114 v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 152 (160)
T PRK09642 114 VVLAHYLEEKSYQEIALQEKIEVKTVEMKLYRARKWIKK 152 (160)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4444456889999999999999999988 8777666544
No 203
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=50.81 E-value=18 Score=26.46 Aligned_cols=25 Identities=28% Similarity=0.339 Sum_probs=21.0
Q ss_pred cchhhhhhhcccccchhHh-HHHHHH
Q 046847 42 VKNQTINNRFKHSGETISR-FNSILN 66 (88)
Q Consensus 42 ~~~r~i~~~F~~S~eTisr-f~~Vl~ 66 (88)
.+..++.++|+.|.+||.| .++.-+
T Consensus 20 v~v~eLa~~~~VS~~TIRRDL~~Le~ 45 (253)
T COG1349 20 VSVEELAELFGVSEMTIRRDLNELEE 45 (253)
T ss_pred EEHHHHHHHhCCCHHHHHHhHHHHHH
Confidence 5667789999999999999 887643
No 204
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=50.73 E-value=29 Score=23.89 Aligned_cols=45 Identities=9% Similarity=0.013 Sum_probs=34.1
Q ss_pred cchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847 25 VFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE 70 (88)
Q Consensus 25 v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~ 70 (88)
++.+++-++-|+.+ .+.++..|+..++.|..||.. .+..+..+-.
T Consensus 114 Lp~~~r~v~~L~~~-~g~s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~ 159 (188)
T PRK12546 114 LPDEQREALILVGA-SGFSYEEAAEMCGVAVGTVKSRANRARARLAE 159 (188)
T ss_pred CCHHHhHHhhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 34444444545444 889999999999999999998 8888777654
No 205
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=50.58 E-value=40 Score=23.04 Aligned_cols=37 Identities=5% Similarity=-0.083 Sum_probs=29.7
Q ss_pred HHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847 34 FLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE 70 (88)
Q Consensus 34 FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~ 70 (88)
|....-.+.++..|+..++.|..||.. .+.....+-.
T Consensus 120 ~~L~~~eg~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 157 (182)
T PRK12511 120 LHLVAIEGLSYQEAAAVLGIPIGTLMSRIGRARAALRA 157 (182)
T ss_pred HHHHHHcCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHH
Confidence 333344789999999999999999998 8877776654
No 206
>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=50.50 E-value=34 Score=22.35 Aligned_cols=45 Identities=4% Similarity=0.056 Sum_probs=33.6
Q ss_pred ccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847 24 VVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVL 69 (88)
Q Consensus 24 ~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~ 69 (88)
.++..++.++-|+. -.+.++..|+..++.|..||.. .+...+.+-
T Consensus 122 ~L~~~~r~vl~l~~-~~g~s~~eIA~~l~is~~tv~~~l~ra~~~Lr 167 (170)
T TIGR02952 122 ILTPKQQHVIALRF-GQNLPIAEVARILGKTEGAVKILQFRAIKKLA 167 (170)
T ss_pred hCCHHHHHHHHHHH-hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 34555555555533 4689999999999999999998 887776653
No 207
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=50.48 E-value=30 Score=23.60 Aligned_cols=42 Identities=12% Similarity=-0.058 Sum_probs=33.2
Q ss_pred HHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH-hhhh
Q 046847 33 MFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE-LQHI 74 (88)
Q Consensus 33 ~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~-L~~~ 74 (88)
+|+...-.+.++..|+..++-|..||.. .+...+.+-. |...
T Consensus 119 v~~L~~~~g~s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l~~~ 162 (182)
T PRK12540 119 ALILVGASGFSYEDAAAICGCAVGTIKSRVNRARSKLSALLYVD 162 (182)
T ss_pred HhhHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhc
Confidence 4444456899999999999999999998 8888877754 4443
No 208
>PF09246 PHAT: PHAT; InterPro: IPR015327 The PHAT (pseudo-HEAT analogous topology) domain assumes a structure consisting of a layer of three parallel helices packed against a layer of two antiparallel helices, into a cylindrical shaped five-helix bundle. It is found in the RNA-binding protein Smaug, where it is essential for high-affinity RNA binding []. ; PDB: 1OXJ_A.
Probab=50.03 E-value=22 Score=23.56 Aligned_cols=36 Identities=25% Similarity=0.439 Sum_probs=23.1
Q ss_pred HHHHHHHHHHhhCcCCcCCCccchhHHHHHHHHHhc
Q 046847 4 KTFGLLFELLCSDERLKTDSVVFVDEQVCMFLHALA 39 (88)
Q Consensus 4 ~~F~~L~~~L~~~~~L~~t~~v~veE~la~FL~i~~ 39 (88)
..|.++-+.+-+...+.+--..-=||.|++|+||+-
T Consensus 48 ~qF~KVL~~v~s~l~~~p~~~~qdde~L~v~~wIle 83 (108)
T PF09246_consen 48 GQFTKVLDLVCSILQQRPYCSPQDDEILCVFMWILE 83 (108)
T ss_dssp HHHHHHHHHHHHHHHT-TTG-GG-HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHhcccccccchhHHHHHHHHHH
Confidence 467777777765544343334557899999999964
No 209
>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=49.94 E-value=12 Score=21.38 Aligned_cols=22 Identities=14% Similarity=0.370 Sum_probs=13.9
Q ss_pred chhhhhhhcccccchhHh-HHHH
Q 046847 43 KNQTINNRFKHSGETISR-FNSI 64 (88)
Q Consensus 43 ~~r~i~~~F~~S~eTisr-f~~V 64 (88)
+-++++.+|+.|..||.+ ++..
T Consensus 26 s~~~la~~~~vsr~tvr~al~~L 48 (64)
T PF00392_consen 26 SERELAERYGVSRTTVREALRRL 48 (64)
T ss_dssp -HHHHHHHHTS-HHHHHHHHHHH
T ss_pred CHHHHHHHhccCCcHHHHHHHHH
Confidence 345567788999999866 5443
No 210
>PF04034 DUF367: Domain of unknown function (DUF367); InterPro: IPR007177 This domain is found in a family of proteins of unknown function. It appears to be found in eukaryotes and archaebacteria, and occurs associated with a potential metal-binding region in RNase L inhibitor, RLI (IPR007209 from INTERPRO).
Probab=49.92 E-value=12 Score=25.45 Aligned_cols=33 Identities=15% Similarity=0.161 Sum_probs=29.4
Q ss_pred ccchhHHHHHHHHHhccccchhhhhhhcccccc
Q 046847 24 VVFVDEQVCMFLHALAHHVKNQTINNRFKHSGE 56 (88)
Q Consensus 24 ~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~e 56 (88)
..|.-|++|--|||+|....-..+-+.|+.+..
T Consensus 65 kLscvEAlAAaLyI~G~~~~A~~lL~~FkWG~~ 97 (127)
T PF04034_consen 65 KLSCVEALAAALYILGFKEQAEELLSKFKWGHT 97 (127)
T ss_pred cccHHHHHHHHHHHcCCHHHHHHHHhcCCCcHH
Confidence 488999999999999999999999999987643
No 211
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=49.85 E-value=32 Score=24.04 Aligned_cols=39 Identities=5% Similarity=-0.054 Sum_probs=32.0
Q ss_pred HHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847 32 CMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE 70 (88)
Q Consensus 32 a~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~ 70 (88)
.+|+-.--.+.++..|+..+|.|..||.. .+.....+-.
T Consensus 145 ~v~~L~~~~g~s~~EIA~~Lgis~~tV~~~l~RArk~Lr~ 184 (203)
T PRK09647 145 AAVVLCDIEGLSYEEIAATLGVKLGTVRSRIHRGRQQLRA 184 (203)
T ss_pred HHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 34555557899999999999999999999 8888776654
No 212
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=49.77 E-value=31 Score=24.44 Aligned_cols=43 Identities=14% Similarity=0.164 Sum_probs=32.6
Q ss_pred hhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847 27 VDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE 70 (88)
Q Consensus 27 veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~ 70 (88)
..++-.+-| .-..+.++..|+..++.|..||.. .+..++.+-.
T Consensus 187 ~~~r~vl~l-~~~~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~ 230 (236)
T PRK06986 187 EREQLVLSL-YYQEELNLKEIGAVLGVSESRVSQIHSQAIKRLRA 230 (236)
T ss_pred HHHHHHHHh-HhccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 334444434 346789999999999999999999 8888776654
No 213
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=49.73 E-value=8.1 Score=22.72 Aligned_cols=21 Identities=24% Similarity=0.226 Sum_probs=15.6
Q ss_pred chhhhhhhcccccchhHh-HHH
Q 046847 43 KNQTINNRFKHSGETISR-FNS 63 (88)
Q Consensus 43 ~~r~i~~~F~~S~eTisr-f~~ 63 (88)
+.++|+.+=|.|.+|||| ++.
T Consensus 2 t~~~iA~~~gvS~~TVSr~ln~ 23 (70)
T smart00354 2 TIKDVARLAGVSKATVSRVLNG 23 (70)
T ss_pred CHHHHHHHHCCCHHHHHHHHCC
Confidence 346677777888888888 765
No 214
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=49.54 E-value=22 Score=23.37 Aligned_cols=42 Identities=14% Similarity=0.188 Sum_probs=32.2
Q ss_pred cchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHH
Q 046847 25 VFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGV 68 (88)
Q Consensus 25 v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai 68 (88)
++..|.- .|..++.|.++.+|+...+-|..||.. ...+.+-+
T Consensus 144 lt~~E~~--vl~~l~~g~~~~~I~~~l~~s~~tv~~~~~~l~~Kl 186 (204)
T PRK09958 144 LSKQEIS--VMRYILDGKDNNDIAEKMFISNKTVSTYKSRLMEKL 186 (204)
T ss_pred CCHHHHH--HHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHc
Confidence 5555553 455556677999999999999999998 88776654
No 215
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=49.53 E-value=7.8 Score=27.99 Aligned_cols=21 Identities=29% Similarity=0.094 Sum_probs=18.2
Q ss_pred chhhhhhhcccccchhHh-HHH
Q 046847 43 KNQTINNRFKHSGETISR-FNS 63 (88)
Q Consensus 43 ~~r~i~~~F~~S~eTisr-f~~ 63 (88)
+-++|+..-|.|..|||| +|.
T Consensus 2 ti~dIA~~aGVS~~TVSrvLn~ 23 (328)
T PRK11303 2 KLDEIARLAGVSRTTASYVING 23 (328)
T ss_pred CHHHHHHHhCCCHHHHHHHHcC
Confidence 457899999999999999 876
No 216
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=49.48 E-value=32 Score=24.64 Aligned_cols=43 Identities=16% Similarity=0.152 Sum_probs=32.5
Q ss_pred cchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHH
Q 046847 25 VFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGV 68 (88)
Q Consensus 25 v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai 68 (88)
++-.|+-.+-|+. ..+.+++.|+..++.|.++|++ -+..++-+
T Consensus 184 L~~~er~vi~l~~-~~~~t~~EIA~~lgis~~~V~q~~~~~~~kL 227 (231)
T PRK12427 184 LDEREQLILHLYY-QHEMSLKEIALVLDLTEARICQLNKKIAQKI 227 (231)
T ss_pred CCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 4445555555554 5789999999999999999999 66666544
No 217
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=49.30 E-value=31 Score=22.77 Aligned_cols=44 Identities=11% Similarity=-0.047 Sum_probs=33.8
Q ss_pred chhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847 26 FVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE 70 (88)
Q Consensus 26 ~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~ 70 (88)
+.+++- +|+...-++.++..|+..++.|..||.. .+...+.+-.
T Consensus 110 ~~~~r~-v~~l~~~~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~ 154 (165)
T PRK09644 110 PVIEAQ-AILLCDVHELTYEEAASVLDLKLNTYKSHLFRGRKRLKA 154 (165)
T ss_pred CHHHHH-HHHhHHHhcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 333343 3444466889999999999999999988 8888877754
No 218
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=48.90 E-value=31 Score=23.29 Aligned_cols=38 Identities=16% Similarity=0.135 Sum_probs=32.3
Q ss_pred HHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847 33 MFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE 70 (88)
Q Consensus 33 ~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~ 70 (88)
+|+..--++.|+..|+...+.|..||.. .+..+..+-.
T Consensus 135 ~~~l~~~~gls~~EIA~~l~i~~~tVks~l~ra~~~l~~ 173 (182)
T COG1595 135 AFLLRYLEGLSYEEIAEILGISVGTVKSRLHRARKKLRE 173 (182)
T ss_pred HhhhHhhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4555666789999999999999999999 8888877765
No 219
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=48.68 E-value=38 Score=22.76 Aligned_cols=45 Identities=7% Similarity=0.079 Sum_probs=33.2
Q ss_pred cchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847 25 VFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE 70 (88)
Q Consensus 25 v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~ 70 (88)
++..++-++-|. .-.+.++..|+..++-|..||.. .+..+..+-.
T Consensus 128 L~~~~r~v~~l~-~~~g~s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~ 173 (179)
T PRK09415 128 LPIKYREVIYLF-YYEELSIKEIAEVTGVNENTVKTRLKKAKELLKK 173 (179)
T ss_pred CCHHHhhHhHhH-HhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 344444444443 34589999999999999999998 8888777654
No 220
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=48.57 E-value=18 Score=25.83 Aligned_cols=38 Identities=16% Similarity=0.320 Sum_probs=29.1
Q ss_pred HHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHH
Q 046847 30 QVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGV 68 (88)
Q Consensus 30 ~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai 68 (88)
+|-.|+ .++...+.+.++.....|.+|||| .++.=+.+
T Consensus 5 ~L~~f~-~v~~~gs~s~AA~~L~isQ~avSr~i~~LE~~l 43 (296)
T PRK09906 5 HLRYFV-AVAEELNFTKAAEKLHTAQPSLSQQIKDLENCV 43 (296)
T ss_pred HHHHHH-HHHhhCCHHHHHHHhCCCCcHHHHHHHHHHHHh
Confidence 444454 555667999999999999999999 88854433
No 221
>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=48.54 E-value=45 Score=21.03 Aligned_cols=27 Identities=4% Similarity=0.016 Sum_probs=23.3
Q ss_pred ccccchhhhhhhcccccchhHh-HHHHH
Q 046847 39 AHHVKNQTINNRFKHSGETISR-FNSIL 65 (88)
Q Consensus 39 ~~n~~~r~i~~~F~~S~eTisr-f~~Vl 65 (88)
..+.+..+++...+.+..||++ .++..
T Consensus 40 ~~~~t~~ela~~~~~~~~tvs~~l~~Le 67 (118)
T TIGR02337 40 QGSMEFTQLANQACILRPSLTGILARLE 67 (118)
T ss_pred cCCcCHHHHHHHhCCCchhHHHHHHHHH
Confidence 3457899999999999999999 87766
No 222
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=48.52 E-value=30 Score=26.72 Aligned_cols=46 Identities=13% Similarity=0.059 Sum_probs=35.6
Q ss_pred ccchhHHHHHHHHHh---ccccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847 24 VVFVDEQVCMFLHAL---AHHVKNQTINNRFKHSGETISR-FNSILNGVL 69 (88)
Q Consensus 24 ~v~veE~la~FL~i~---~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~ 69 (88)
..+-.|+..+-|+.. |.+.++..|+..|+.|.+.|++ =++.|.-+-
T Consensus 305 ~L~~rEr~Vl~lrygl~~~~~~tl~EIa~~lgvs~erVrQi~~~Al~kLr 354 (367)
T PRK09210 305 TLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 354 (367)
T ss_pred hCCHHHHHHHHHHhccCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHh
Confidence 366677777777653 3678999999999999999999 666665543
No 223
>PRK00215 LexA repressor; Validated
Probab=48.34 E-value=30 Score=24.05 Aligned_cols=27 Identities=7% Similarity=0.127 Sum_probs=22.8
Q ss_pred ccccchhhhhhhccc-ccchhHh-HHHHH
Q 046847 39 AHHVKNQTINNRFKH-SGETISR-FNSIL 65 (88)
Q Consensus 39 ~~n~~~r~i~~~F~~-S~eTisr-f~~Vl 65 (88)
+...+.++++..++- |..|++| .+..-
T Consensus 21 ~~~~s~~ela~~~~~~~~~tv~~~l~~L~ 49 (205)
T PRK00215 21 GYPPSRREIADALGLRSPSAVHEHLKALE 49 (205)
T ss_pred CCCCCHHHHHHHhCCCChHHHHHHHHHHH
Confidence 555689999999998 9999999 76654
No 224
>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=48.31 E-value=33 Score=24.97 Aligned_cols=38 Identities=16% Similarity=0.232 Sum_probs=31.2
Q ss_pred HHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847 33 MFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE 70 (88)
Q Consensus 33 ~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~ 70 (88)
+|....-.+.+++.|+..++-|..||.. .+..+..+-.
T Consensus 169 v~~L~~~eg~S~~EIA~~Lgis~~TVk~rl~RAr~~Lr~ 207 (244)
T TIGR03001 169 LLRLHFVDGLSMDRIGAMYQVHRSTVSRWVAQARERLLE 207 (244)
T ss_pred HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 3444455889999999999999999999 9888877654
No 225
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=48.19 E-value=34 Score=23.20 Aligned_cols=52 Identities=15% Similarity=0.162 Sum_probs=36.8
Q ss_pred HHHHHhhCcCCcCCCccchhHHHHHHHHHh--ccccchhhhhhhcccccchhHh-HHHHHHH
Q 046847 9 LFELLCSDERLKTDSVVFVDEQVCMFLHAL--AHHVKNQTINNRFKHSGETISR-FNSILNG 67 (88)
Q Consensus 9 L~~~L~~~~~L~~t~~v~veE~la~FL~i~--~~n~~~r~i~~~F~~S~eTisr-f~~Vl~a 67 (88)
+-+.|+--+||+++- +-.|.-.+ ....+.-.|+..-.+|.+||+| .+..+++
T Consensus 15 ~~dvl~c~~GLs~~D-------v~v~~~LL~~~~~~tvdelae~lnr~rStv~rsl~~L~~~ 69 (126)
T COG3355 15 CEDVLKCVYGLSELD-------VEVYKALLEENGPLTVDELAEILNRSRSTVYRSLQNLLEA 69 (126)
T ss_pred HHHHHHHHhCCcHHH-------HHHHHHHHhhcCCcCHHHHHHHHCccHHHHHHHHHHHHHc
Confidence 345566666666652 12233333 6778899999999999999999 9988764
No 226
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=48.03 E-value=28 Score=23.00 Aligned_cols=37 Identities=8% Similarity=0.079 Sum_probs=30.1
Q ss_pred HHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847 34 FLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE 70 (88)
Q Consensus 34 FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~ 70 (88)
|+...-.+.+++.|+...+.|..||.. .+.-+..+-.
T Consensus 127 l~L~~~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~ 164 (173)
T PRK09645 127 LVRSYYRGWSTAQIAADLGIPEGTVKSRLHYALRALRL 164 (173)
T ss_pred HHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 444456789999999999999999988 8877776654
No 227
>PRK12681 cysB transcriptional regulator CysB; Reviewed
Probab=47.85 E-value=26 Score=25.93 Aligned_cols=40 Identities=13% Similarity=0.221 Sum_probs=32.4
Q ss_pred HHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHH
Q 046847 29 EQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGV 68 (88)
Q Consensus 29 E~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai 68 (88)
++|-.|+.+.-++.|++.++.....|..|||+ .++.=+.+
T Consensus 4 ~~L~~f~avae~g~S~s~AA~~L~iSQpavS~~I~~LE~~l 44 (324)
T PRK12681 4 QQLRYIVEVVNHNLNVSATAEGLYTSQPGISKQVRMLEDEL 44 (324)
T ss_pred HHHHHHHHHHHccCCHHHHHHHhcCCcHHHHHHHHHHHHHh
Confidence 45677777776777999999999999999999 88754433
No 228
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=47.73 E-value=36 Score=23.57 Aligned_cols=38 Identities=5% Similarity=0.072 Sum_probs=30.4
Q ss_pred HHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847 33 MFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE 70 (88)
Q Consensus 33 ~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~ 70 (88)
+|....-.+.+++.|+..++.|-.||.. .+..+..+-.
T Consensus 161 vl~l~~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 199 (206)
T PRK12526 161 VVKGVYFQELSQEQLAQQLNVPLGTVKSRLRLALAKLKV 199 (206)
T ss_pred HHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3444567889999999999999999988 8777666543
No 229
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=47.41 E-value=40 Score=19.72 Aligned_cols=39 Identities=13% Similarity=0.262 Sum_probs=32.5
Q ss_pred chhHHHHHHHHHhcc-ccchhhhhhhcccccchhHh-HHHH
Q 046847 26 FVDEQVCMFLHALAH-HVKNQTINNRFKHSGETISR-FNSI 64 (88)
Q Consensus 26 ~veE~la~FL~i~~~-n~~~r~i~~~F~~S~eTisr-f~~V 64 (88)
..++++.-+|..-|. ..+-.+|+...+-+..||+| ....
T Consensus 6 ~~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L 46 (68)
T smart00550 6 SLEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSL 46 (68)
T ss_pred HHHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHH
Confidence 568888888888876 59999999999999999987 5443
No 230
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=47.38 E-value=37 Score=22.90 Aligned_cols=33 Identities=9% Similarity=0.002 Sum_probs=28.9
Q ss_pred hccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847 38 LAHHVKNQTINNRFKHSGETISR-FNSILNGVLE 70 (88)
Q Consensus 38 ~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~ 70 (88)
.-.+.++..|+..++.|..||.. .+..+..+-.
T Consensus 144 ~~~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 177 (184)
T PRK12539 144 KLEGLSVAEAATRSGMSESAVKVSVHRGLKALAA 177 (184)
T ss_pred HHcCCcHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 34699999999999999999999 9888887764
No 231
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=46.74 E-value=35 Score=26.73 Aligned_cols=46 Identities=15% Similarity=0.068 Sum_probs=36.9
Q ss_pred ccchhHHHHHHHHHh---ccccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847 24 VVFVDEQVCMFLHAL---AHHVKNQTINNRFKHSGETISR-FNSILNGVL 69 (88)
Q Consensus 24 ~v~veE~la~FL~i~---~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~ 69 (88)
..+-.|+..+-|+.. +.+.+...|+..++.|.++|+. -+..++-+-
T Consensus 311 ~L~~rEr~IL~lrygl~~~~~~Tl~EIA~~lgiS~eRVRQie~rAL~KLR 360 (373)
T PRK07406 311 TLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLR 360 (373)
T ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHh
Confidence 467778877777553 3568999999999999999999 887777664
No 232
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=46.71 E-value=43 Score=22.54 Aligned_cols=39 Identities=13% Similarity=0.166 Sum_probs=31.5
Q ss_pred HHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847 32 CMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE 70 (88)
Q Consensus 32 a~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~ 70 (88)
.+|+...-.+.++..|+..++-|..||.. .+.....+-.
T Consensus 129 ~i~~l~~~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 168 (185)
T PRK12542 129 QVFKYKVFYNLTYQEISSVMGITEANVRKQFERARKRVQN 168 (185)
T ss_pred HHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 34555566889999999999999999998 8877766654
No 233
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=46.64 E-value=28 Score=25.00 Aligned_cols=36 Identities=11% Similarity=0.124 Sum_probs=29.5
Q ss_pred HHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHH
Q 046847 29 EQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSIL 65 (88)
Q Consensus 29 E~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl 65 (88)
.++-.|+.++-++ |+..+++.-+.|..|||+ .++.=
T Consensus 4 ~~L~~f~~v~~~g-S~s~AA~~L~itQpavS~~i~~LE 40 (305)
T PRK11151 4 RDLEYLVALAEHR-HFRRAADSCHVSQPTLSGQIRKLE 40 (305)
T ss_pred HHHHHHHHHHHhC-CHHHHHHHhCCCchHHHHHHHHHH
Confidence 4566777777665 999999999999999999 88753
No 234
>PRK12680 transcriptional regulator CysB-like protein; Reviewed
Probab=46.57 E-value=28 Score=25.80 Aligned_cols=41 Identities=7% Similarity=0.103 Sum_probs=32.9
Q ss_pred HHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847 29 EQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVL 69 (88)
Q Consensus 29 E~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~ 69 (88)
++|-+|+.+.=+..|+..++..-+.|.+|||+ .++.=+.+.
T Consensus 4 ~~L~~F~~vae~~gS~s~AA~~L~isQpavS~~I~~LE~~lG 45 (327)
T PRK12680 4 TQLRYLVAIADAELNITLAAARVHATQPGLSKQLKQLEDELG 45 (327)
T ss_pred HHHHHHHHHHHccCCHHHHHHHhcCCchHHHHHHHHHHHHhC
Confidence 46777777666668999999999999999999 888655443
No 235
>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=46.24 E-value=7.8 Score=20.86 Aligned_cols=18 Identities=33% Similarity=0.290 Sum_probs=13.2
Q ss_pred hhhhhcccccchhHh-HHH
Q 046847 46 TINNRFKHSGETISR-FNS 63 (88)
Q Consensus 46 ~i~~~F~~S~eTisr-f~~ 63 (88)
+++.+-+.|..|||+ ++.
T Consensus 2 ~lA~~~gvs~~tvs~~l~g 20 (52)
T cd01392 2 DIARAAGVSVATVSRVLNG 20 (52)
T ss_pred cHHHHHCcCHHHHHHHHcC
Confidence 466777788888888 664
No 236
>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=45.49 E-value=41 Score=22.95 Aligned_cols=38 Identities=8% Similarity=0.035 Sum_probs=31.8
Q ss_pred HHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847 33 MFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE 70 (88)
Q Consensus 33 ~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~ 70 (88)
+|....-.+.+++.|+..++-|..||.. ....++.+-.
T Consensus 139 v~~l~~~~g~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~ 177 (188)
T TIGR02943 139 VFMMREVLGFESDEICQELEISTSNCHVLLYRARLSLRA 177 (188)
T ss_pred HHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 4555566899999999999999999988 8888777754
No 237
>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=45.31 E-value=23 Score=20.38 Aligned_cols=43 Identities=7% Similarity=-0.072 Sum_probs=32.8
Q ss_pred CccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHH
Q 046847 23 SVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSIL 65 (88)
Q Consensus 23 ~~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl 65 (88)
+.-|.|++..+---.+..+.+..++...+|.+..|+++ ..+..
T Consensus 5 ~~ys~e~K~~~v~~~~~~g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 5 RRYSPEFKLQAVREYLESGESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp ----HHHHHHHHHHHHHHHCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHHCCCceEeeecccccccccccHHHHHHh
Confidence 34567777777666678899999999999999999999 77765
No 238
>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=44.61 E-value=38 Score=23.69 Aligned_cols=36 Identities=19% Similarity=0.189 Sum_probs=27.0
Q ss_pred HHHHHHHHhcc-ccchhhhhhhcccccchhHh-HHHHH
Q 046847 30 QVCMFLHALAH-HVKNQTINNRFKHSGETISR-FNSIL 65 (88)
Q Consensus 30 ~la~FL~i~~~-n~~~r~i~~~F~~S~eTisr-f~~Vl 65 (88)
+..+..++..+ ..+..+++..++.|..|++| ....-
T Consensus 145 ~~~IL~~l~~~g~~s~~eia~~l~is~stv~r~L~~Le 182 (203)
T TIGR01884 145 ELKVLEVLKAEGEKSVKNIAKKLGKSLSTISRHLRELE 182 (203)
T ss_pred HHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 34554455443 46999999999999999999 77743
No 239
>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=44.38 E-value=45 Score=23.37 Aligned_cols=43 Identities=14% Similarity=0.123 Sum_probs=32.2
Q ss_pred chhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847 26 FVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVL 69 (88)
Q Consensus 26 ~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~ 69 (88)
+..++-.+-|+. ..+.++..|+..++.|.+||.+ .+..++.+-
T Consensus 177 ~~~~r~il~l~y-~~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr 220 (224)
T TIGR02479 177 SEREQLVLSLYY-YEELNLKEIGEVLGLTESRVSQIHSQALKKLR 220 (224)
T ss_pred CHHHHHHHHHHH-hCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 344444444433 5778999999999999999999 888877664
No 240
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=44.00 E-value=59 Score=22.19 Aligned_cols=38 Identities=5% Similarity=-0.081 Sum_probs=29.5
Q ss_pred HHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847 33 MFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE 70 (88)
Q Consensus 33 ~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~ 70 (88)
+|....-++.+++.|+..++.|..||-. .+.....+-.
T Consensus 142 i~~l~~~~g~s~~EIA~~lg~s~~tV~~rl~rar~~Lr~ 180 (192)
T PRK09643 142 ALVAVDMQGYSVADAARMLGVAEGTVKSRCARGRARLAE 180 (192)
T ss_pred HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 4444455889999999999999999988 8766655543
No 241
>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=43.95 E-value=47 Score=21.90 Aligned_cols=38 Identities=11% Similarity=0.195 Sum_probs=30.4
Q ss_pred HHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847 33 MFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE 70 (88)
Q Consensus 33 ~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~ 70 (88)
+|....-.+.+++.|+..+|.|..||.. .+..+..+-.
T Consensus 127 i~~l~~~~g~s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~ 165 (169)
T TIGR02954 127 AIILRYYHDLTIKEIAEVMNKPEGTVKTYLHRALKKLKK 165 (169)
T ss_pred HHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4444455689999999999999999998 8887776643
No 242
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=43.77 E-value=53 Score=23.82 Aligned_cols=48 Identities=10% Similarity=0.031 Sum_probs=35.7
Q ss_pred chhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHHhhhh
Q 046847 26 FVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLELQHI 74 (88)
Q Consensus 26 ~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~L~~~ 74 (88)
+.+++.++.| .-..+.++++|+...|.|..||.. .+...+.+-.....
T Consensus 118 p~~~R~v~lL-~~~eg~S~~EIAe~LgiS~~tVksrL~Rark~Lr~~l~~ 166 (228)
T PRK06704 118 NVQQSAILLL-KDVFQYSIADIAKVCSVSEGAVKASLFRSRNRLKTVSEE 166 (228)
T ss_pred CHHHhhHhhh-HHhhCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHh
Confidence 4444454444 345579999999999999999998 88888877664444
No 243
>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=43.76 E-value=17 Score=28.98 Aligned_cols=48 Identities=25% Similarity=0.345 Sum_probs=35.0
Q ss_pred hhHHHHHHHHHhc--cccchhhhhhhcccccchhHh-HHHHHHHHHHhhhhhccCCCCCCC
Q 046847 27 VDEQVCMFLHALA--HHVKNQTINNRFKHSGETISR-FNSILNGVLELQHILLKSPKPMPE 84 (88)
Q Consensus 27 veE~la~FL~i~~--~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~L~~~~ik~p~~~~~ 84 (88)
|+-|=+.|..-.+ .+.+.++|++..|.+-+|||| . ...|+..|-+-+|
T Consensus 302 v~~Q~~Ff~~G~~~LkPLtlkdiA~~lglheSTVSRav----------~~Kyi~tp~Gi~~ 352 (429)
T TIGR02395 302 VEHQKDFFLGGPAALKPLTLREVAEELGLHESTISRAI----------NNKYLQTPRGVFE 352 (429)
T ss_pred HHHHHHHHhcCcccCcCCcHHHHHHHhCCCccchhhhh----------cCceEecCCceEE
Confidence 4556666665433 578999999999999999999 6 4566666655543
No 244
>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=43.75 E-value=42 Score=23.64 Aligned_cols=41 Identities=15% Similarity=0.225 Sum_probs=27.2
Q ss_pred HHHHHHhhCcCCcCCCccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHH
Q 046847 8 LLFELLCSDERLKTDSVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSIL 65 (88)
Q Consensus 8 ~L~~~L~~~~~L~~t~~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl 65 (88)
.|-+.+.+ +.+++...++.|..| +.+|+.|..||.+ +.+.-
T Consensus 8 ~l~~~I~~-g~~~~G~~LPsE~eL----------------a~~~gVSR~TVR~Al~~L~ 49 (233)
T TIGR02404 8 DLEQKITH-GQYKEGDYLPSEHEL----------------MDQYGASRETVRKALNLLT 49 (233)
T ss_pred HHHHHHHh-CCCCCCCCCcCHHHH----------------HHHHCCCHHHHHHHHHHHH
Confidence 33344433 345666668887755 6799999999977 66643
No 245
>PF02936 COX4: Cytochrome c oxidase subunit IV; InterPro: IPR004203 Cytochrome c oxidase, a 13 sub-unit complex (1.9.3.1 from EC) is the terminal oxidase in the mitochondrial electron transport chain. This family is composed of cytochrome c oxidase subunit IV. The Dictyostelium discoideum (Slime mould) member of this family is called COX VI. The Saccharomyces cerevisiae protein YGX6_YEAST appears to be the yeast COX IV subunit.; GO: 0004129 cytochrome-c oxidase activity; PDB: 3ABK_Q 3AG1_Q 3ASN_Q 1OCZ_D 2EIN_Q 2OCC_D 2YBB_O 3AG3_D 1OCO_Q 1V55_Q ....
Probab=43.61 E-value=45 Score=22.77 Aligned_cols=68 Identities=15% Similarity=0.128 Sum_probs=33.9
Q ss_pred HHHHHHhhCcCCcCCCccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHH------HhhhhhccCCC
Q 046847 8 LLFELLCSDERLKTDSVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVL------ELQHILLKSPK 80 (88)
Q Consensus 8 ~L~~~L~~~~~L~~t~~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~------~L~~~~ik~p~ 80 (88)
.+-..|+++- ..|-+.+|.||+.|. |.+ +|.+-..|..++..--.. |.-|+-.|. .+...|+.||.
T Consensus 31 ~~~~~LkeKe-kg~Wk~LS~eEKkal--Y~i----sFg~~g~r~~~~~gewk~v~~~~~~~i~~s~~l~~~~r~~~~~~~ 103 (142)
T PF02936_consen 31 EIIEALKEKE-KGDWKKLSLEEKKAL--YRI----SFGQTGPRMKAPTGEWKKVFGGVFIFIGFSVLLFIWQRSYVYPPL 103 (142)
T ss_dssp HHHHHHHHHT-TS-GGGS-HHHHHHH--HHH----H-SS-HHHHT---SHHHHHHHHHHHHHHHHHHHHHHHHHHT----
T ss_pred HHHHHHHHHH-hCCHhhCCHHHHHHH--HHh----hhcCcccccccCCcchHHHHHHHHHHHHHHHHHHHHHHHHhCCCC
Confidence 4556677764 466799999999986 444 444455556666555555 665544332 24566777775
Q ss_pred CC
Q 046847 81 PM 82 (88)
Q Consensus 81 ~~ 82 (88)
|.
T Consensus 104 P~ 105 (142)
T PF02936_consen 104 PH 105 (142)
T ss_dssp -G
T ss_pred CC
Confidence 53
No 246
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=43.38 E-value=17 Score=29.18 Aligned_cols=48 Identities=23% Similarity=0.292 Sum_probs=35.9
Q ss_pred hhHHHHHHHHHhc--cccchhhhhhhcccccchhHh-HHHHHHHHHHhhhhhccCCCCCCC
Q 046847 27 VDEQVCMFLHALA--HHVKNQTINNRFKHSGETISR-FNSILNGVLELQHILLKSPKPMPE 84 (88)
Q Consensus 27 veE~la~FL~i~~--~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~L~~~~ik~p~~~~~ 84 (88)
|+-|=+.|+.-.+ .+.+.++|++.-|.+-+|||| . +..|+..|-+-+|
T Consensus 327 v~~Q~~Ff~~G~~~LkPLtlkdvAe~lglheSTVSRav----------~~Kyv~tp~Gi~~ 377 (455)
T PRK05932 327 VEQQRDFFEHGEEALKPLVLKDIAEELGMHESTISRAT----------TNKYMATPRGIFE 377 (455)
T ss_pred HHHHHHHHhCCcccCcCccHHHHHHHhCCCccchhhhh----------cCceeecCCceEE
Confidence 5566677766443 578999999999999999999 6 4566766665544
No 247
>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=43.31 E-value=32 Score=23.86 Aligned_cols=39 Identities=8% Similarity=0.096 Sum_probs=26.2
Q ss_pred chhHHHHHHHHHhccccchhhhhhhcccccchhHhHHHH
Q 046847 26 FVDEQVCMFLHALAHHVKNQTINNRFKHSGETISRFNSI 64 (88)
Q Consensus 26 ~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisrf~~V 64 (88)
+.|+..++.-..-..+.+...|+..++.|..+|++.-.+
T Consensus 105 ~~e~a~~~~~l~~~~g~s~~~iA~~lg~s~~~V~r~l~l 143 (187)
T TIGR00180 105 PIEEAQAYKRLLEKFSMTQEDLAKKIGKSRAHITNLLRL 143 (187)
T ss_pred HHHHHHHHHHHHHHhCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 344444333322235788999999999999999994333
No 248
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=43.22 E-value=42 Score=26.85 Aligned_cols=45 Identities=13% Similarity=0.088 Sum_probs=34.3
Q ss_pred cchhHHHHHHHHHh---ccccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847 25 VFVDEQVCMFLHAL---AHHVKNQTINNRFKHSGETISR-FNSILNGVL 69 (88)
Q Consensus 25 v~veE~la~FL~i~---~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~ 69 (88)
++..|+-.+-|... +.+.++..|+..++.|.+||.. -+.-+..+-
T Consensus 351 L~~reR~VI~LRygl~d~~~~Tl~EIA~~LGvS~erVRqie~rAl~KLR 399 (415)
T PRK07598 351 LTSRERDVIRMRFGLADGHTYSLAEIGRALDLSRERVRQIESKALQKLR 399 (415)
T ss_pred CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHh
Confidence 45556655666443 4779999999999999999999 887776554
No 249
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=43.03 E-value=32 Score=25.19 Aligned_cols=25 Identities=28% Similarity=0.466 Sum_probs=20.7
Q ss_pred cchhhhhhhcccccchhHh-HHHHHH
Q 046847 42 VKNQTINNRFKHSGETISR-FNSILN 66 (88)
Q Consensus 42 ~~~r~i~~~F~~S~eTisr-f~~Vl~ 66 (88)
.+..+++++|+.|.+||.| ..+.-+
T Consensus 20 ~~~~ela~~l~vS~~TiRRdL~~Le~ 45 (252)
T PRK10906 20 VSTEELVEHFSVSPQTIRRDLNDLAE 45 (252)
T ss_pred EeHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 5777899999999999999 776544
No 250
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=42.98 E-value=63 Score=21.78 Aligned_cols=48 Identities=8% Similarity=0.201 Sum_probs=30.9
Q ss_pred hHHHHHHHHHHhh---CcCCcCCCccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHH
Q 046847 3 RKTFGLLFELLCS---DERLKTDSVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILN 66 (88)
Q Consensus 3 ~~~F~~L~~~L~~---~~~L~~t~~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ 66 (88)
..++..+++.+.. ++.|++.-.+ -|.|..+...+.+..||+| +++.=+
T Consensus 10 ~PIY~QI~~qIk~~I~~g~l~pGdkL----------------PSvRelA~~~~VNpnTv~raY~eLE~ 61 (125)
T COG1725 10 KPIYEQIANQIKEQIASGELKPGDKL----------------PSVRELAKDLGVNPNTVQRAYQELER 61 (125)
T ss_pred CCHHHHHHHHHHHHHHhCCcCCCCCC----------------CcHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 4456666666554 3444444444 4566666677889999999 888643
No 251
>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=42.93 E-value=21 Score=19.49 Aligned_cols=23 Identities=9% Similarity=0.212 Sum_probs=18.4
Q ss_pred chhhhhhhcccccchhHh-HHHHH
Q 046847 43 KNQTINNRFKHSGETISR-FNSIL 65 (88)
Q Consensus 43 ~~r~i~~~F~~S~eTisr-f~~Vl 65 (88)
+.++++..|+-|.+||++ .+..-
T Consensus 27 ~~~~la~~~~is~~~v~~~l~~L~ 50 (66)
T cd07377 27 SERELAEELGVSRTTVREALRELE 50 (66)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHH
Confidence 467888999999999987 66654
No 252
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=42.85 E-value=31 Score=25.12 Aligned_cols=39 Identities=26% Similarity=0.313 Sum_probs=27.0
Q ss_pred hHHHHHHHHHhccc--cchhhhhhhcccccchhHh-HHHHHHH
Q 046847 28 DEQVCMFLHALAHH--VKNQTINNRFKHSGETISR-FNSILNG 67 (88)
Q Consensus 28 eE~la~FL~i~~~n--~~~r~i~~~F~~S~eTisr-f~~Vl~a 67 (88)
+|+..--+-.+..+ .+..++.+.|+.|.+||-| ..+ |+.
T Consensus 6 ~eR~~~I~~~l~~~~~v~v~eLa~~~~VS~~TIRRDL~~-Le~ 47 (252)
T PRK10681 6 DERIGQLLQALKRSDKLHLKDAAALLGVSEMTIRRDLNA-HSA 47 (252)
T ss_pred HHHHHHHHHHHHHcCCCcHHHHHHHhCCCHHHHHHHHHH-hhc
Confidence 34444334444333 6788899999999999999 886 553
No 253
>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=42.72 E-value=15 Score=19.92 Aligned_cols=26 Identities=23% Similarity=0.271 Sum_probs=20.6
Q ss_pred hccccchhhhhhhcccccchhHh-HHH
Q 046847 38 LAHHVKNQTINNRFKHSGETISR-FNS 63 (88)
Q Consensus 38 ~~~n~~~r~i~~~F~~S~eTisr-f~~ 63 (88)
-.+|.+.++++..-+.|..||++ .+.
T Consensus 6 ~~~gls~~~la~~~gis~~~i~~~~~g 32 (55)
T PF01381_consen 6 KEKGLSQKELAEKLGISRSTISRIENG 32 (55)
T ss_dssp HHTTS-HHHHHHHHTS-HHHHHHHHTT
T ss_pred HHcCCCHHHHHHHhCCCcchhHHHhcC
Confidence 45788999999999999999999 765
No 254
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=42.70 E-value=32 Score=25.09 Aligned_cols=24 Identities=25% Similarity=0.308 Sum_probs=21.1
Q ss_pred ccchhhhhhhcccccchhHh-HHHH
Q 046847 41 HVKNQTINNRFKHSGETISR-FNSI 64 (88)
Q Consensus 41 n~~~r~i~~~F~~S~eTisr-f~~V 64 (88)
..+..++++.|+.|.+||.| +++.
T Consensus 19 ~~~~~ela~~l~vS~~TirRdL~~L 43 (251)
T PRK13509 19 FVTVEKVIERLGISPATARRDINKL 43 (251)
T ss_pred CcCHHHHHHHHCcCHHHHHHHHHHH
Confidence 37788899999999999999 8884
No 255
>PRK15183 Vi polysaccharide biosynthesis protein TviA; Provisional
Probab=42.49 E-value=21 Score=24.13 Aligned_cols=41 Identities=17% Similarity=0.172 Sum_probs=32.6
Q ss_pred cchhhhhhhcccccchhHh-HHHHHHHHHHhhhhhccCCCCC
Q 046847 42 VKNQTINNRFKHSGETISR-FNSILNGVLELQHILLKSPKPM 82 (88)
Q Consensus 42 ~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~L~~~~ik~p~~~ 82 (88)
.....+|+||-.|.+|.-| =+|+--....=.+.|+-.||..
T Consensus 99 sgmeelqdrfmns~st~yrwrke~a~kfgvr~prylllpdsv 140 (143)
T PRK15183 99 SGMEELQDRFMNSSSTMYRWRKELAVKFGVREPRYLLLPDSV 140 (143)
T ss_pred ccHHHHHHHHccChHHHHHHHHHHHHHhcCCCCceEecCccc
Confidence 4567899999999999999 7776555555678888888864
No 256
>PRK04841 transcriptional regulator MalT; Provisional
Probab=42.40 E-value=26 Score=29.19 Aligned_cols=33 Identities=12% Similarity=0.176 Sum_probs=29.4
Q ss_pred HhccccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847 37 ALAHHVKNQTINNRFKHSGETISR-FNSILNGVL 69 (88)
Q Consensus 37 i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~ 69 (88)
.++.+.+|++|+.....|..||.. .+++...+.
T Consensus 849 ~~~~g~~~~~ia~~l~~s~~tv~~h~~~~~~kl~ 882 (903)
T PRK04841 849 LIYSGYSNEQIAGELDVAATTIKTHIRNLYQKLG 882 (903)
T ss_pred HHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 388999999999999999999999 999876653
No 257
>PF13972 TetR: Bacterial transcriptional repressor; PDB: 3RH2_A 3NNR_A.
Probab=42.33 E-value=93 Score=20.29 Aligned_cols=65 Identities=14% Similarity=0.091 Sum_probs=39.2
Q ss_pred hHHHHHHHHHHhhCcCCcCCCccchhHHHHHHHHHhccc-cchhhhhhhcc-cccchhHh-HHHHHHHHH
Q 046847 3 RKTFGLLFELLCSDERLKTDSVVFVDEQVCMFLHALAHH-VKNQTINNRFK-HSGETISR-FNSILNGVL 69 (88)
Q Consensus 3 ~~~F~~L~~~L~~~~~L~~t~~v~veE~la~FL~i~~~n-~~~r~i~~~F~-~S~eTisr-f~~Vl~ai~ 69 (88)
...+..+++.|++.+.++.+ -.--+.||--+|+++.. .++..+...=. ...+++.+ ...|+..+.
T Consensus 67 ~~~~~~l~~~l~~~g~l~~~--~~~~~~La~~i~lv~t~Wl~~~~~~~~~~~~~~~~~~~gv~qv~~L~~ 134 (146)
T PF13972_consen 67 REQLRQLLQSLIEAGILRID--DEELQALADNIWLVSTFWLSFLETQHPRDKLTEEDIRRGVYQVLSLLR 134 (146)
T ss_dssp HHHHHHHHHHHHHTTSB-----GHHHHHHHHHHHHHHHCHHHHHHHHSS-----HHCHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHCCCCCCC--HHHHHHHHHHHHHHHHHHHhHHHHhCccccchHHHHHHHHHHHHHHHH
Confidence 35778999999999988844 22233888899998887 44444443221 34566666 666665443
No 258
>PF13921 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 1A5J_A 1MBH_A 1GV5_A 1H89_C 1IDY_A 1MBK_A 1IDZ_A 1H88_C 1GVD_A 1MBG_A ....
Probab=42.27 E-value=28 Score=19.35 Aligned_cols=26 Identities=8% Similarity=0.081 Sum_probs=19.0
Q ss_pred cccchhhhhhhcc-cccchhHh-HHHHH
Q 046847 40 HHVKNQTINNRFK-HSGETISR-FNSIL 65 (88)
Q Consensus 40 ~n~~~r~i~~~F~-~S~eTisr-f~~Vl 65 (88)
++.....|+..|+ ||...+.. +...|
T Consensus 16 ~g~~W~~Ia~~l~~Rt~~~~~~r~~~~l 43 (60)
T PF13921_consen 16 YGNDWKKIAEHLGNRTPKQCRNRWRNHL 43 (60)
T ss_dssp HTS-HHHHHHHSTTS-HHHHHHHHHHTT
T ss_pred HCcCHHHHHHHHCcCCHHHHHHHHHHHC
Confidence 3457899999999 99988877 77744
No 259
>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=42.27 E-value=12 Score=27.15 Aligned_cols=20 Identities=25% Similarity=0.042 Sum_probs=16.6
Q ss_pred hhhhhhhcccccchhHh-HHH
Q 046847 44 NQTINNRFKHSGETISR-FNS 63 (88)
Q Consensus 44 ~r~i~~~F~~S~eTisr-f~~ 63 (88)
.++|+..-|.|..|||| +|.
T Consensus 2 i~dIA~~aGVS~~TVSrvLn~ 22 (327)
T TIGR02417 2 LSDIAKLAGVSKTTASYVING 22 (327)
T ss_pred HHHHHHHhCCCHHHHHHHHcC
Confidence 46788888999999999 865
No 260
>PRK03341 arginine repressor; Provisional
Probab=42.08 E-value=39 Score=23.71 Aligned_cols=42 Identities=10% Similarity=0.128 Sum_probs=27.8
Q ss_pred ccchhHHHHHHHHHhccc--cchhhhhhhc-----ccccchhHh-HHHHH
Q 046847 24 VVFVDEQVCMFLHALAHH--VKNQTINNRF-----KHSGETISR-FNSIL 65 (88)
Q Consensus 24 ~v~veE~la~FL~i~~~n--~~~r~i~~~F-----~~S~eTisr-f~~Vl 65 (88)
.|.-+++....+-++..+ .+..++.+.. +.|..|||| .++.=
T Consensus 10 ~m~k~~R~~~I~~li~~~~i~tQ~eL~~~L~~~Gi~vTQaTiSRDl~eL~ 59 (168)
T PRK03341 10 PATRAARQARIVAILSRQSVRSQAELAALLADEGIEVTQATLSRDLDELG 59 (168)
T ss_pred cCCHHHHHHHHHHHHHHCCCccHHHHHHHHHHcCCcccHHHHHHHHHHhc
Confidence 345555666666655554 4455555555 999999999 98863
No 261
>TIGR00362 DnaA chromosomal replication initiator protein DnaA. DnaA is involved in DNA biosynthesis; initiation of chromosome replication and can also be transcription regulator. The C-terminal of the family hits the pfam bacterial DnaA (bac_dnaA) domain family. For a review, see Kaguni (2006).
Probab=41.77 E-value=28 Score=26.83 Aligned_cols=33 Identities=15% Similarity=0.232 Sum_probs=29.7
Q ss_pred CCccchhHHHHHHHHHhccccchhhhhhhcc-cc
Q 046847 22 DSVVFVDEQVCMFLHALAHHVKNQTINNRFK-HS 54 (88)
Q Consensus 22 t~~v~veE~la~FL~i~~~n~~~r~i~~~F~-~S 54 (88)
++.+..-.|+||+|-.--.+.++..|+..|| |.
T Consensus 371 ~~~~~~~R~~amyl~~~~~~~s~~~ig~~fg~rd 404 (405)
T TIGR00362 371 TRNIVRPRQIAMYLAKELTDLSLPEIGRAFGGRD 404 (405)
T ss_pred CcccchHHHHHHHHHHHHcCCCHHHHHHHhCCCC
Confidence 4778889999999999999999999999997 53
No 262
>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=41.75 E-value=33 Score=19.86 Aligned_cols=30 Identities=10% Similarity=0.013 Sum_probs=25.4
Q ss_pred HHHHHHHHHhccccchhhhhhhcccccchhHh
Q 046847 29 EQVCMFLHALAHHVKNQTINNRFKHSGETISR 60 (88)
Q Consensus 29 E~la~FL~i~~~n~~~r~i~~~F~~S~eTisr 60 (88)
...|..||. .+.+...|+...+.+..||..
T Consensus 3 k~~A~~LY~--~G~~~~eIA~~Lg~~~~TV~~ 32 (58)
T PF06056_consen 3 KEQARSLYL--QGWSIKEIAEELGVPRSTVYS 32 (58)
T ss_pred HHHHHHHHH--cCCCHHHHHHHHCCChHHHHH
Confidence 356788886 578999999999999999987
No 263
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=41.72 E-value=19 Score=24.39 Aligned_cols=38 Identities=11% Similarity=0.179 Sum_probs=30.8
Q ss_pred HHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847 33 MFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE 70 (88)
Q Consensus 33 ~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~ 70 (88)
+|.+..-.+.++..|+..++.|..||.. .+..+..+-.
T Consensus 142 v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 180 (188)
T PRK09640 142 ILVLRFVAELEFQEIADIMHMGLSATKMRYKRALDKLRE 180 (188)
T ss_pred eeeeHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4444556789999999999999999998 8887776654
No 264
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=41.70 E-value=20 Score=23.80 Aligned_cols=33 Identities=6% Similarity=-0.022 Sum_probs=28.7
Q ss_pred hccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847 38 LAHHVKNQTINNRFKHSGETISR-FNSILNGVLE 70 (88)
Q Consensus 38 ~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~ 70 (88)
.-.+.++++|+..+|-|..||.. ++.....+-.
T Consensus 133 ~~~g~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~ 166 (175)
T PRK12518 133 DLEDLPQKEIAEILNIPVGTVKSRLFYARRQLRK 166 (175)
T ss_pred HhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45678999999999999999999 9988877764
No 265
>PRK10094 DNA-binding transcriptional activator AllS; Provisional
Probab=41.68 E-value=34 Score=24.97 Aligned_cols=36 Identities=17% Similarity=0.146 Sum_probs=28.9
Q ss_pred HHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHH
Q 046847 29 EQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSIL 65 (88)
Q Consensus 29 E~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl 65 (88)
++|-+|+.++-+ .++..++.+.+.|..|||+ .++.=
T Consensus 5 ~~L~~f~~v~e~-gs~s~AA~~L~iSQpavS~~I~~LE 41 (308)
T PRK10094 5 ETLRTFIAVAET-GSFSKAAERLCKTTATISYRIKLLE 41 (308)
T ss_pred HHHHHHHHHHHh-CCHHHHHHHhcCCHHHHHHHHHHHH
Confidence 566667655544 6999999999999999999 88753
No 266
>COG0184 RpsO Ribosomal protein S15P/S13E [Translation, ribosomal structure and biogenesis]
Probab=41.23 E-value=22 Score=22.69 Aligned_cols=26 Identities=8% Similarity=0.005 Sum_probs=22.5
Q ss_pred HHHhhCcCCcCCCccchhHHHHHHHH
Q 046847 11 ELLCSDERLKTDSVVFVDEQVCMFLH 36 (88)
Q Consensus 11 ~~L~~~~~L~~t~~v~veE~la~FL~ 36 (88)
..|+..|+.......+.|||||+-..
T Consensus 9 ~~l~~eyg~~~~dtgs~evq~a~Lt~ 34 (89)
T COG0184 9 QELRDEYGIPEVDTGSGEVQLALLTE 34 (89)
T ss_pred HHHHHHhCCCCCCCCCcHHHHHHHHH
Confidence 46888999999999999999999764
No 267
>PRK09801 transcriptional activator TtdR; Provisional
Probab=40.82 E-value=35 Score=24.97 Aligned_cols=40 Identities=5% Similarity=0.169 Sum_probs=30.7
Q ss_pred hHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHH
Q 046847 28 DEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGV 68 (88)
Q Consensus 28 eE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai 68 (88)
-++|-.|+. ++...+++.+++..+.|..|||+ +++.=+.+
T Consensus 8 ~~~L~~F~~-v~~~gs~t~AA~~L~iSQpavS~~I~~LE~~L 48 (310)
T PRK09801 8 AKDLQVLVE-IVHSGSFSAAAATLGQTPAFVTKRIQILENTL 48 (310)
T ss_pred HHHHHHHHH-HHHcCCHHHHHHHhCcCHHHHHHHHHHHHHHh
Confidence 356666665 45558999999999999999999 98854433
No 268
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=40.78 E-value=39 Score=23.95 Aligned_cols=36 Identities=17% Similarity=0.211 Sum_probs=28.1
Q ss_pred HHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHH
Q 046847 29 EQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSIL 65 (88)
Q Consensus 29 E~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl 65 (88)
++|-.|+.++- ..+...++..-+.|.+|||+ .++.=
T Consensus 4 ~~L~~f~~v~~-~gs~s~AA~~L~isqsavS~~i~~LE 40 (296)
T PRK11242 4 RHIRYFLAVAE-HGNFTRAAEALHVSQPTLSQQIRQLE 40 (296)
T ss_pred HHHHHHHHHHH-hCCHHHHHHHcCCCchHHHHHHHHHH
Confidence 44555665554 46999999999999999999 88753
No 269
>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=40.71 E-value=42 Score=19.28 Aligned_cols=25 Identities=4% Similarity=0.223 Sum_probs=21.0
Q ss_pred ccchhhhhhhcccccchhHh-HHHHH
Q 046847 41 HVKNQTINNRFKHSGETISR-FNSIL 65 (88)
Q Consensus 41 n~~~r~i~~~F~~S~eTisr-f~~Vl 65 (88)
..+...++.+|+.|..||++ +...-
T Consensus 13 ~~~~~eLa~~l~vS~~tv~~~l~~L~ 38 (69)
T TIGR00122 13 PFSGEKLGEALGMSRTAVNKHIQTLR 38 (69)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 45678899999999999999 87753
No 270
>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=40.50 E-value=22 Score=22.54 Aligned_cols=35 Identities=14% Similarity=-0.074 Sum_probs=28.3
Q ss_pred HHHhccccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847 35 LHALAHHVKNQTINNRFKHSGETISR-FNSILNGVL 69 (88)
Q Consensus 35 L~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~ 69 (88)
+..+....|++.++...+.|..|||+ .++.=+.+.
T Consensus 10 ~~av~~~gSis~AA~~L~iS~stvs~~I~~LE~~lg 45 (99)
T TIGR00637 10 LKAIARMGSISQAAKDAGISYKSAWDYIRAMNNLSG 45 (99)
T ss_pred HHHHHHhCCHHHHHHHHCCCHHHHHHHHHHHHHHhC
Confidence 44566679999999999999999999 887655443
No 271
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=40.21 E-value=52 Score=22.08 Aligned_cols=33 Identities=6% Similarity=-0.018 Sum_probs=28.0
Q ss_pred hccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847 38 LAHHVKNQTINNRFKHSGETISR-FNSILNGVLE 70 (88)
Q Consensus 38 ~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~ 70 (88)
.-.+.++..|+..+|.|..||.. .+..+..+-.
T Consensus 141 ~~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 174 (186)
T PRK05602 141 YYQGLSNIEAAAVMDISVDALESLLARGRRALRA 174 (186)
T ss_pred HhcCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHH
Confidence 34689999999999999999999 8887766654
No 272
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=40.18 E-value=51 Score=20.34 Aligned_cols=15 Identities=13% Similarity=0.104 Sum_probs=8.9
Q ss_pred hHHHHHHHHHHhhCc
Q 046847 3 RKTFGLLFELLCSDE 17 (88)
Q Consensus 3 ~~~F~~L~~~L~~~~ 17 (88)
.+.+..+..++.+++
T Consensus 4 ~~~~~~~~~~i~~~~ 18 (107)
T PRK10219 4 QKIIQTLIAWIDEHI 18 (107)
T ss_pred HHHHHHHHHHHHHhc
Confidence 355666666666653
No 273
>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=40.08 E-value=10 Score=26.44 Aligned_cols=40 Identities=20% Similarity=0.265 Sum_probs=0.0
Q ss_pred ccchhHHHHHHHHHh--ccccchhhhhhhcccccchhHh-HHH
Q 046847 24 VVFVDEQVCMFLHAL--AHHVKNQTINNRFKHSGETISR-FNS 63 (88)
Q Consensus 24 ~v~veE~la~FL~i~--~~n~~~r~i~~~F~~S~eTisr-f~~ 63 (88)
..=++.|-+.|+.-- =.+.+.++|++.-+.+-+|||| .+.
T Consensus 30 ~~iv~~Q~~ff~~g~~~l~PLt~~~iA~~lgl~~STVSRav~~ 72 (160)
T PF04552_consen 30 QAIVERQKDFFLGGPGALKPLTMKDIADELGLHESTVSRAVKN 72 (160)
T ss_dssp -------------------------------------------
T ss_pred HHHHHHHHHHHhcCcccCcCCCHHHHHHHhCCCHhHHHHHHcC
Confidence 344667777777432 2457899999999999999999 653
No 274
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=40.08 E-value=44 Score=19.07 Aligned_cols=36 Identities=19% Similarity=0.129 Sum_probs=22.2
Q ss_pred ccchhHHHHHHHHHhccccchhhhhhhcccccchhHh
Q 046847 24 VVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR 60 (88)
Q Consensus 24 ~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr 60 (88)
.++..||--+-+ +..-+.+.+.|+.+.+||...|.+
T Consensus 4 ~Lt~~Eqaqid~-m~qlG~s~~~isr~i~RSr~~Ir~ 39 (50)
T PF11427_consen 4 TLTDAEQAQIDV-MHQLGMSLREISRRIGRSRTCIRR 39 (50)
T ss_dssp ---HHHHHHHHH-HHHTT--HHHHHHHHT--HHHHHH
T ss_pred cCCHHHHHHHHH-HHHhchhHHHHHHHhCccHHHHHH
Confidence 356667655544 455678999999999999999977
No 275
>PRK00441 argR arginine repressor; Provisional
Probab=40.04 E-value=35 Score=23.36 Aligned_cols=23 Identities=17% Similarity=0.401 Sum_probs=17.1
Q ss_pred cchhhhhhh-----cccccchhHh-HHHH
Q 046847 42 VKNQTINNR-----FKHSGETISR-FNSI 64 (88)
Q Consensus 42 ~~~r~i~~~-----F~~S~eTisr-f~~V 64 (88)
.+..++... |+.|..|||| +++.
T Consensus 19 ~~q~eL~~~L~~~G~~vSqaTisRDl~~L 47 (149)
T PRK00441 19 ETQEELAEELKKMGFDVTQATVSRDIKEL 47 (149)
T ss_pred CcHHHHHHHHHhcCCCcCHHHHHHHHHHc
Confidence 344555555 6999999999 9875
No 276
>PHA00675 hypothetical protein
Probab=40.04 E-value=58 Score=20.43 Aligned_cols=38 Identities=11% Similarity=0.074 Sum_probs=29.8
Q ss_pred CccchhHHHHHHHHHhccccchhhhhhhcccccchhHh
Q 046847 23 SVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR 60 (88)
Q Consensus 23 ~~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr 60 (88)
-.++-.+--.|+.-....+.|+-.|+..|+.|.+||+.
T Consensus 21 AKLt~~qV~~IR~l~~r~G~s~~~IA~~fGVsrstV~~ 58 (78)
T PHA00675 21 AKLTDAEVERIRELHEVEGMSYAVLAEKFEQSKGAIAK 58 (78)
T ss_pred cccCHHHHHHHHHHHHhcCccHHHHHHHhCCCHHHHHH
Confidence 34566666677777756666999999999999999976
No 277
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=40.03 E-value=57 Score=21.93 Aligned_cols=37 Identities=3% Similarity=0.049 Sum_probs=29.3
Q ss_pred HHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847 33 MFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVL 69 (88)
Q Consensus 33 ~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~ 69 (88)
+|....-.+.+++.|+..+|-|..||.. .+..+..+-
T Consensus 147 i~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr 184 (189)
T PRK09648 147 ILILRVVVGLSAEETAEAVGSTPGAVRVAQHRALARLR 184 (189)
T ss_pred HHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4444455689999999999999999988 877666554
No 278
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=40.02 E-value=16 Score=20.69 Aligned_cols=25 Identities=20% Similarity=0.222 Sum_probs=19.5
Q ss_pred HHhccccchhhhhhhcccccchhHh
Q 046847 36 HALAHHVKNQTINNRFKHSGETISR 60 (88)
Q Consensus 36 ~i~~~n~~~r~i~~~F~~S~eTisr 60 (88)
+.-.++.|..+++.+.+.|.+||++
T Consensus 9 ~R~~~gls~~~lA~~~g~s~s~v~~ 33 (64)
T PF13560_consen 9 LRERAGLSQAQLADRLGVSQSTVSR 33 (64)
T ss_dssp HHHCHTS-HHHHHHHHTS-HHHHHH
T ss_pred HHHHcCCCHHHHHHHHCcCHHHHHH
Confidence 3456688999999999999999998
No 279
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=40.02 E-value=42 Score=23.73 Aligned_cols=37 Identities=11% Similarity=0.149 Sum_probs=30.2
Q ss_pred HHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847 34 FLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE 70 (88)
Q Consensus 34 FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~ 70 (88)
|....-++.+++.|+..++.|.+||.. .+.....+-.
T Consensus 158 ~~l~~~~g~s~~EIAe~lgis~~tVk~~l~Rar~kLr~ 195 (231)
T PRK11922 158 FVLRVVEELSVEETAQALGLPEETVKTRLHRARRLLRE 195 (231)
T ss_pred heeehhcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 333345789999999999999999999 8887776665
No 280
>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=40.00 E-value=21 Score=19.25 Aligned_cols=24 Identities=13% Similarity=0.158 Sum_probs=18.7
Q ss_pred cccchhhhhhhcccccchhHh-HHH
Q 046847 40 HHVKNQTINNRFKHSGETISR-FNS 63 (88)
Q Consensus 40 ~n~~~r~i~~~F~~S~eTisr-f~~ 63 (88)
...+++.++...|-|.+||.+ ++.
T Consensus 16 ~r~s~~~la~~lglS~~~v~~Ri~r 40 (42)
T PF13404_consen 16 GRRSYAELAEELGLSESTVRRRIRR 40 (42)
T ss_dssp TTS-HHHHHHHHTS-HHHHHHHHHH
T ss_pred CCccHHHHHHHHCcCHHHHHHHHHH
Confidence 447899999999999999988 764
No 281
>PRK12423 LexA repressor; Provisional
Probab=40.00 E-value=45 Score=23.44 Aligned_cols=24 Identities=13% Similarity=0.149 Sum_probs=19.7
Q ss_pred ccchhhhhhhcc-cccchhHh-HHHH
Q 046847 41 HVKNQTINNRFK-HSGETISR-FNSI 64 (88)
Q Consensus 41 n~~~r~i~~~F~-~S~eTisr-f~~V 64 (88)
.-+.++++..|+ +|..||++ +...
T Consensus 25 ~Ps~~eia~~~g~~s~~~v~~~l~~L 50 (202)
T PRK12423 25 PPSLAEIAQAFGFASRSVARKHVQAL 50 (202)
T ss_pred CCCHHHHHHHhCCCChHHHHHHHHHH
Confidence 469999999999 79999987 5443
No 282
>PRK05949 RNA polymerase sigma factor; Validated
Probab=39.84 E-value=67 Score=24.52 Aligned_cols=46 Identities=11% Similarity=0.124 Sum_probs=34.5
Q ss_pred cchhHHHHHHHHHh---ccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847 25 VFVDEQVCMFLHAL---AHHVKNQTINNRFKHSGETISR-FNSILNGVLE 70 (88)
Q Consensus 25 v~veE~la~FL~i~---~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~ 70 (88)
.+..|+-.+-|... +.+.++..|+..++.|.+||.. -+..++.+-.
T Consensus 267 L~~rer~Vi~lr~gl~~~e~~Tl~EIa~~lgiS~erVrq~~~rAl~kLr~ 316 (327)
T PRK05949 267 LTPQQREVLTLRFGLEDGKELSLAKVGERLNLSRERVRQLEHQALAHLRR 316 (327)
T ss_pred CCHHHHHHHHHHhccCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 44455555555432 3789999999999999999999 8887776654
No 283
>PRK11013 DNA-binding transcriptional regulator LysR; Provisional
Probab=39.80 E-value=39 Score=24.46 Aligned_cols=35 Identities=14% Similarity=0.191 Sum_probs=29.1
Q ss_pred HHHHHHHHHhccccchhhhhhhcccccchhHh-HHHH
Q 046847 29 EQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSI 64 (88)
Q Consensus 29 E~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~V 64 (88)
.++-+|+-+.-+ .++..+++..+.|.+|||+ .++.
T Consensus 7 ~~L~~f~av~~~-gS~s~AAe~L~isqsavS~~Ik~L 42 (309)
T PRK11013 7 RHIEIFHAVMTA-GSLTEAARLLHTSQPTVSRELARF 42 (309)
T ss_pred HHHHHHHHHHHh-CcHHHHHHHHCCCcHHHHHHHHHH
Confidence 567777766655 5999999999999999999 8874
No 284
>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=39.69 E-value=14 Score=26.73 Aligned_cols=30 Identities=23% Similarity=0.226 Sum_probs=24.3
Q ss_pred chhhhhhhcccccchhHh-HHH-----------HHHHHHHhh
Q 046847 43 KNQTINNRFKHSGETISR-FNS-----------ILNGVLELQ 72 (88)
Q Consensus 43 ~~r~i~~~F~~S~eTisr-f~~-----------Vl~ai~~L~ 72 (88)
+-++|+..=|.|..|||| +|. |++|+-+|.
T Consensus 3 ti~dIA~~agvS~~TVSrvLn~~~~vs~~tr~rV~~~a~~lg 44 (329)
T TIGR01481 3 TIYDVAREAGVSMATVSRVVNGNPNVKPATRKKVLEVIKRLD 44 (329)
T ss_pred cHHHHHHHhCCCHHHHHHHhCCCCCCCHHHHHHHHHHHHHHC
Confidence 567899999999999999 875 666666653
No 285
>PF12834 Phage_int_SAM_2: Phage integrase, N-terminal; InterPro: IPR024457 Phage integrase proteins cleave DNA substrates by a series of staggered cuts, during which the protein becomes covalently linked to the DNA through a catalytic tyrosine residue at the carboxy end of the alignment [, ]. This entry represents the N-terminal predicted alpha-helical domain found in a family of putative prophage DNA-binding integrases.
Probab=39.67 E-value=81 Score=19.70 Aligned_cols=48 Identities=13% Similarity=0.129 Sum_probs=37.6
Q ss_pred HHHHHHHHHHhh-CcCCcCCCccchhHHHHHHHHHhccccchhhhhhhc
Q 046847 4 KTFGLLFELLCS-DERLKTDSVVFVDEQVCMFLHALAHHVKNQTINNRF 51 (88)
Q Consensus 4 ~~F~~L~~~L~~-~~~L~~t~~v~veE~la~FL~i~~~n~~~r~i~~~F 51 (88)
.+...+++.|+. .+.+++..++...---|..=+-...+.+-++|+++.
T Consensus 27 ~~~~~~~~~L~~~g~~i~~~~~lk~kHI~~lv~~w~~~gis~~TiqN~m 75 (91)
T PF12834_consen 27 RILKRFARFLRELGFQIRSIRNLKPKHIEALVQHWKAQGISPRTIQNEM 75 (91)
T ss_pred HHHHHHHHHHHHCCCCcCCHHHhhHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence 455667777765 677788888888877788888888899998888876
No 286
>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=39.57 E-value=71 Score=20.77 Aligned_cols=43 Identities=7% Similarity=0.032 Sum_probs=30.9
Q ss_pred hhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847 27 VDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVL 69 (88)
Q Consensus 27 veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~ 69 (88)
.+.|=-++-+..-.+.|...|++.++.|...|+- ++..-..+.
T Consensus 19 T~kQ~~~l~lyy~eDlSlsEIAe~~~iSRqaV~d~ikr~~~~L~ 62 (101)
T PF04297_consen 19 TEKQREILELYYEEDLSLSEIAEELGISRQAVYDSIKRAEKKLE 62 (101)
T ss_dssp -HHHHHHHHHHCTS---HHHHHHHCTS-HHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 3556666667777899999999999999999999 888766554
No 287
>PRK15421 DNA-binding transcriptional regulator MetR; Provisional
Probab=39.53 E-value=38 Score=24.88 Aligned_cols=36 Identities=6% Similarity=0.086 Sum_probs=29.3
Q ss_pred HHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHH
Q 046847 29 EQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSIL 65 (88)
Q Consensus 29 E~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl 65 (88)
.+|-.|+-++-++ +++.++..-+.|..|||+ +++.=
T Consensus 5 ~~L~~f~av~~~g-s~s~AA~~L~iSqpaVS~~Ik~LE 41 (317)
T PRK15421 5 KHLKTLQALRNCG-SLAAAAATLHQTQSALSHQFSDLE 41 (317)
T ss_pred HHHHHHHHHHHcC-CHHHHHHHhCCCHHHHHHHHHHHH
Confidence 4566777666665 999999999999999999 88753
No 288
>COG4974 XerD Site-specific recombinase XerD [DNA replication, recombination, and repair]
Probab=39.30 E-value=81 Score=24.42 Aligned_cols=64 Identities=8% Similarity=0.148 Sum_probs=48.1
Q ss_pred CChHHHHHHHHHHhhCcCCcCCCccchh-HHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHH
Q 046847 1 MDRKTFGLLFELLCSDERLKTDSVVFVD-EQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILN 66 (88)
Q Consensus 1 M~~~~F~~L~~~L~~~~~L~~t~~v~ve-E~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ 66 (88)
|++..|.++.+....+.|+. +.++.. =+=+.--+.+-+++.-|.+|..-||+.=+.-. .-.|.+
T Consensus 221 ltrq~~w~~lk~~a~~Agi~--~~isPH~LRHsFATHLL~~GADlRvVQeLLGHadisTTQIYTHV~~ 286 (300)
T COG4974 221 LTRQGFWKRLKDYAERAGID--KKISPHTLRHSFATHLLENGADLRVVQELLGHADISTTQIYTHVTK 286 (300)
T ss_pred CCHHHHHHHHHHHHHHhCCC--CCcCchhhHHHHHHHHHhCCccHHHHHHHhCccccchhHHHHHHHH
Confidence 78999999999999888887 233332 24466778899999999999999998644434 555653
No 289
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=39.21 E-value=56 Score=21.89 Aligned_cols=37 Identities=11% Similarity=0.176 Sum_probs=29.7
Q ss_pred HHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847 33 MFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVL 69 (88)
Q Consensus 33 ~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~ 69 (88)
+|+..--.+.+++.|+..+|-|-.||.. .+..+..+-
T Consensus 125 i~~l~~~e~~s~~EIA~~lgis~~tV~~~l~ra~~~Lr 162 (179)
T PRK12543 125 VIILRYLHDYSQEEIAQLLQIPIGTVKSRIHAALKKLR 162 (179)
T ss_pred HHHHHHHccCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 5555566889999999999999999888 777766554
No 290
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=39.14 E-value=66 Score=21.03 Aligned_cols=41 Identities=5% Similarity=0.133 Sum_probs=29.5
Q ss_pred ccchhHHHHHH-HHHhccccchhhhhhhcccccchhHh-HHHHH
Q 046847 24 VVFVDEQVCMF-LHALAHHVKNQTINNRFKHSGETISR-FNSIL 65 (88)
Q Consensus 24 ~v~veE~la~F-L~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl 65 (88)
+++..+-..++ || -..+.+...+++.++.+..||++ .+..-
T Consensus 37 glt~~q~~vL~~l~-~~~~~t~~eLa~~l~i~~~tvsr~l~~Le 79 (144)
T PRK11512 37 DITAAQFKVLCSIR-CAACITPVELKKVLSVDLGALTRMLDRLV 79 (144)
T ss_pred CCCHHHHHHHHHHH-HcCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 45555543333 33 34568999999999999999999 87755
No 291
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=39.03 E-value=44 Score=24.10 Aligned_cols=39 Identities=8% Similarity=0.054 Sum_probs=29.9
Q ss_pred HHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHH
Q 046847 29 EQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGV 68 (88)
Q Consensus 29 E~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai 68 (88)
+++-+|+.++ ...++..++...+.|..+||+ .++.=+.+
T Consensus 8 ~~L~~f~~v~-e~gs~s~AA~~L~isqpavS~~i~~LE~~l 47 (305)
T CHL00180 8 DQLRILKAIA-TEGSFKKAAESLYISQPAVSLQIKNLEKQL 47 (305)
T ss_pred HHHHHHHHHH-HcCCHHHHHHHhcCCChHHHHHHHHHHHHh
Confidence 3465565554 456999999999999999999 98864444
No 292
>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=38.78 E-value=54 Score=24.03 Aligned_cols=39 Identities=8% Similarity=0.027 Sum_probs=32.2
Q ss_pred HHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847 32 CMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE 70 (88)
Q Consensus 32 a~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~ 70 (88)
++|+..--.+.+++.|+..++.|..||.. .+.....+-.
T Consensus 115 ~v~~L~~~~g~s~~EIA~~lg~s~~tVr~~l~RAr~~Lr~ 154 (281)
T TIGR02957 115 AVFVLREVFDYPYEEIASIVGKSEANCRQLVSRARRHLDA 154 (281)
T ss_pred HHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 34555567889999999999999999998 8888777754
No 293
>PRK13348 chromosome replication initiation inhibitor protein; Provisional
Probab=38.77 E-value=45 Score=23.75 Aligned_cols=39 Identities=8% Similarity=0.135 Sum_probs=29.5
Q ss_pred HHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHH
Q 046847 29 EQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGV 68 (88)
Q Consensus 29 E~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai 68 (88)
++|-.|.-+ +...++..++++.+.|..|||+ .++.=+.+
T Consensus 5 ~~L~~f~~v-~~~gs~t~AA~~L~iSQ~avS~~i~~LE~~l 44 (294)
T PRK13348 5 KQLEALAAV-VETGSFERAARRLHVTPSAVSQRIKALEESL 44 (294)
T ss_pred HHHHHHHHH-HHcCCHHHHHHHhCCCchHHHHHHHHHHHHh
Confidence 455555544 4457999999999999999999 88764433
No 294
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=38.59 E-value=48 Score=23.77 Aligned_cols=38 Identities=5% Similarity=0.097 Sum_probs=30.9
Q ss_pred HHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847 33 MFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE 70 (88)
Q Consensus 33 ~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~ 70 (88)
+|+..--.+.+++.|+..++.|..||.. .+..+..+-.
T Consensus 179 v~~L~~~eg~s~~EIA~~Lgis~~tVk~~l~RAr~kLr~ 217 (233)
T PRK12538 179 AVILSYHENMSNGEIAEVMDTTVAAVESLLKRGRQQLRD 217 (233)
T ss_pred HhhhHHhcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 3444456789999999999999999998 8888777654
No 295
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=38.41 E-value=66 Score=21.35 Aligned_cols=40 Identities=10% Similarity=0.140 Sum_probs=29.2
Q ss_pred hHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHH
Q 046847 28 DEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGV 68 (88)
Q Consensus 28 eE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai 68 (88)
+++-++-|+ .-++.+++.|+..++.|..||.. .+.-++.+
T Consensus 123 ~~r~v~~L~-~~~g~s~~EIA~~lgis~~tV~~~l~ra~~~~ 163 (172)
T PRK12523 123 KARAAFLYN-RLDGMGHAEIAERLGVSVSRVRQYLAQGLRQC 163 (172)
T ss_pred HHHHHHHHH-HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 344444443 34789999999999999999988 76655444
No 296
>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=38.21 E-value=41 Score=23.85 Aligned_cols=36 Identities=8% Similarity=0.112 Sum_probs=27.8
Q ss_pred HHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHH
Q 046847 30 QVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILN 66 (88)
Q Consensus 30 ~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ 66 (88)
+|=.|+.++ ...++..++...+.|.+|||+ .++.=+
T Consensus 5 ~L~~f~~v~-~~gs~s~AA~~L~itqpavS~~Ik~LE~ 41 (291)
T TIGR03418 5 ALRVFESAA-RLASFTAAARELGSTQPAVSQQVKRLEE 41 (291)
T ss_pred HHHHHHHHH-HhCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 455555544 445999999999999999999 887533
No 297
>PHA02675 ORF104 fusion protein; Provisional
Probab=37.61 E-value=50 Score=21.17 Aligned_cols=46 Identities=20% Similarity=0.320 Sum_probs=35.2
Q ss_pred ccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHH---HHHHHHHhhhhh
Q 046847 24 VVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNS---ILNGVLELQHIL 75 (88)
Q Consensus 24 ~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~---Vl~ai~~L~~~~ 75 (88)
.=++||+|+-.+ ..+..+.+....+++++.| =++ +-++++.|++.+
T Consensus 32 ~esle~RL~~L~------k~~~~i~~cC~~~~~~L~RLE~H~ETLRk~Ml~L~KKI 81 (90)
T PHA02675 32 KESVEERLVSLL------DSYKTITDCCRETGARLDRLERHLETLREALLKLNTKI 81 (90)
T ss_pred HHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 357889988877 7888999999999999998 332 345778787663
No 298
>TIGR03764 ICE_PFGI_1_parB integrating conjugative element, PFGI_1 class, ParB family protein. Members of this protein family carry the ParB-type nuclease domain and are found in integrating conjugative elements (ICE) in the same class as PFGI-1 of Pseudomonas fluorescens Pf-5.
Probab=36.74 E-value=61 Score=24.49 Aligned_cols=44 Identities=18% Similarity=0.352 Sum_probs=31.7
Q ss_pred cchhHHHHHH----HHH--hccccchhhhhhhccc-----ccchhHhHHHHHHHH
Q 046847 25 VFVDEQVCMF----LHA--LAHHVKNQTINNRFKH-----SGETISRFNSILNGV 68 (88)
Q Consensus 25 v~veE~la~F----L~i--~~~n~~~r~i~~~F~~-----S~eTisrf~~Vl~ai 68 (88)
-.+||++|.- ||- .|.+.+.+.++.+.+. |.+|||+.-.+++.+
T Consensus 114 sfIE~A~~~~~l~~l~e~~~g~~ltq~ela~~lgk~g~~isrs~Isn~lrll~~L 168 (258)
T TIGR03764 114 TFIEKALGVQKARALYEKELGESLSQRELARRLSADGYPISQSHISRMGDTVEYL 168 (258)
T ss_pred CHHHHHHHHHHHHHHHHhhccCCCCHHHHHHHhcccCCCCCHHHHHHHHHHHHhC
Confidence 4678888633 332 3578999999999998 888888855555433
No 299
>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=36.71 E-value=42 Score=19.86 Aligned_cols=32 Identities=19% Similarity=0.284 Sum_probs=24.1
Q ss_pred hHHHHHHHHHhccccchhhhhhhcccccchhHh
Q 046847 28 DEQVCMFLHALAHHVKNQTINNRFKHSGETISR 60 (88)
Q Consensus 28 eE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr 60 (88)
+++--||+- .+....+++|++..+.|..||++
T Consensus 10 dkA~e~y~~-~~g~i~lkdIA~~Lgvs~~tIr~ 41 (60)
T PF10668_consen 10 DKAFEIYKE-SNGKIKLKDIAEKLGVSESTIRK 41 (60)
T ss_pred HHHHHHHHH-hCCCccHHHHHHHHCCCHHHHHH
Confidence 444444432 35568999999999999999987
No 300
>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=36.69 E-value=62 Score=23.91 Aligned_cols=44 Identities=14% Similarity=0.173 Sum_probs=36.5
Q ss_pred CccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHH
Q 046847 23 SVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGV 68 (88)
Q Consensus 23 ~~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai 68 (88)
...|-.|+=.+.| ++.+.++..|+...+-|..||.. .+.+++-+
T Consensus 189 ~~LT~RE~evl~l--~a~G~s~~eIA~~L~IS~~TVk~hl~~i~~KL 233 (247)
T TIGR03020 189 GLITAREAEILAW--VRDGKTNEEIAAILGISSLTVKNHLQHIFKKL 233 (247)
T ss_pred cCCCHHHHHHHHH--HHCCCCHHHHHHHHCcCHHHHHHHHHHHHHHh
Confidence 4577777777776 46899999999999999999999 88887654
No 301
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=36.27 E-value=52 Score=22.58 Aligned_cols=27 Identities=19% Similarity=0.212 Sum_probs=23.6
Q ss_pred ccccchhhhhhhcccccchhHh-HHHHH
Q 046847 39 AHHVKNQTINNRFKHSGETISR-FNSIL 65 (88)
Q Consensus 39 ~~n~~~r~i~~~F~~S~eTisr-f~~Vl 65 (88)
-++.++..|+...|.|..||.| .+..-
T Consensus 149 ~~Gls~~EIA~~lgiS~~tV~r~l~~aR 176 (185)
T PF07638_consen 149 FEGLSVEEIAERLGISERTVRRRLRRAR 176 (185)
T ss_pred HCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 3778999999999999999999 77654
No 302
>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=36.23 E-value=19 Score=22.25 Aligned_cols=21 Identities=19% Similarity=0.200 Sum_probs=15.8
Q ss_pred cccchhhhhhhcccccchhHh
Q 046847 40 HHVKNQTINNRFKHSGETISR 60 (88)
Q Consensus 40 ~n~~~r~i~~~F~~S~eTisr 60 (88)
.|.+..+|+.+.|.|...||+
T Consensus 2 ~G~tq~eIA~~lGks~s~Vs~ 22 (93)
T PF08535_consen 2 FGWTQEEIAKRLGKSRSWVSN 22 (93)
T ss_dssp TT--HHHHHHHTT--HHHHHH
T ss_pred CCCCHHHHHHHHCCCHHHHHH
Confidence 578899999999999999998
No 303
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=36.04 E-value=42 Score=21.91 Aligned_cols=42 Identities=21% Similarity=0.248 Sum_probs=32.1
Q ss_pred cchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHH
Q 046847 25 VFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGV 68 (88)
Q Consensus 25 v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai 68 (88)
.+-.|. -.|..++.|.+++.|+...+-|..||.. ...+.+.+
T Consensus 150 lt~re~--~vl~~l~~g~s~~eIa~~l~~s~~tv~~~~~~~~~kl 192 (210)
T PRK09935 150 LSNREV--TILRYLVSGLSNKEIADQLLLSNKTVSAHKSNIYGKL 192 (210)
T ss_pred CCHHHH--HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHc
Confidence 344443 3345577889999999999999999998 88877655
No 304
>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=36.02 E-value=41 Score=20.10 Aligned_cols=33 Identities=15% Similarity=0.080 Sum_probs=24.8
Q ss_pred hccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847 38 LAHHVKNQTINNRFKHSGETISR-FNSILNGVLE 70 (88)
Q Consensus 38 ~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~ 70 (88)
-..+.+..++++.+..|.+|+.| .+++=+.+-.
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 47778999999999999999999 8887665543
No 305
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=35.84 E-value=72 Score=23.39 Aligned_cols=39 Identities=15% Similarity=0.058 Sum_probs=31.8
Q ss_pred HHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847 32 CMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE 70 (88)
Q Consensus 32 a~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~ 70 (88)
++|+..-..+.+++.|+..++.|..||.. .+.-.+.+-.
T Consensus 122 ~v~~L~~~~g~s~~EIA~~lg~s~~tVk~~l~RAr~~Lr~ 161 (293)
T PRK09636 122 AAFLLHDVFGVPFDEIASTLGRSPAACRQLASRARKHVRA 161 (293)
T ss_pred HHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 35666667889999999999999999998 8876666654
No 306
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=35.71 E-value=17 Score=26.58 Aligned_cols=30 Identities=20% Similarity=0.193 Sum_probs=23.9
Q ss_pred chhhhhhhcccccchhHh-HHH-----------HHHHHHHhh
Q 046847 43 KNQTINNRFKHSGETISR-FNS-----------ILNGVLELQ 72 (88)
Q Consensus 43 ~~r~i~~~F~~S~eTisr-f~~-----------Vl~ai~~L~ 72 (88)
+-++|+..=|.|..|||| +|. |++++-+|.
T Consensus 3 ti~dIA~~aGVS~~TVSrvLn~~~~Vs~~tr~rV~~~a~elg 44 (343)
T PRK10727 3 TIKDVARLAGVSVATVSRVINNSPKASEASRLAVHSAMESLS 44 (343)
T ss_pred CHHHHHHHhCCCHHHHHHHhCCCCCCCHHHHHHHHHHHHHHC
Confidence 567899999999999999 874 666666553
No 307
>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=35.06 E-value=59 Score=23.88 Aligned_cols=38 Identities=8% Similarity=0.017 Sum_probs=31.4
Q ss_pred HHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847 33 MFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE 70 (88)
Q Consensus 33 ~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~ 70 (88)
+|+..--++.+++.|+...+.|..||.. .+...+.+-.
T Consensus 150 v~~L~~~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 188 (324)
T TIGR02960 150 VLLLRDVLGWRAAETAELLGTSTASVNSALQRARATLDE 188 (324)
T ss_pred HhhhHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3444456889999999999999999999 8888877765
No 308
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=34.91 E-value=35 Score=23.13 Aligned_cols=33 Identities=15% Similarity=0.095 Sum_probs=28.0
Q ss_pred hccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847 38 LAHHVKNQTINNRFKHSGETISR-FNSILNGVLE 70 (88)
Q Consensus 38 ~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~ 70 (88)
.-.+.++..|+...|-|..||.. .+..++.+-.
T Consensus 152 ~~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~ 185 (194)
T PRK12513 152 EHGDLELEEIAELTGVPEETVKSRLRYALQKLRE 185 (194)
T ss_pred hccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 46789999999999999999988 7777766654
No 309
>PF11469 Ribonucleas_3_2: Ribonuclease III; InterPro: IPR021568 This archaeal family of proteins has no known function. ; PDB: 1ZTD_A.
Probab=34.83 E-value=88 Score=20.95 Aligned_cols=43 Identities=21% Similarity=0.429 Sum_probs=30.1
Q ss_pred ccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH-hh
Q 046847 24 VVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE-LQ 72 (88)
Q Consensus 24 ~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~-L~ 72 (88)
.+++||+|-| +..|.+.... .|.|-+|.|.+ |-++++.|.+ |.
T Consensus 74 ~it~eEavei----l~~nl~~dv~--~fsrkke~ig~Ala~Ll~~i~Erl~ 118 (120)
T PF11469_consen 74 KITIEEAVEI----LKANLTEDVL--HFSRKKEAIGKALAELLKVIKERLT 118 (120)
T ss_dssp SS-HHHHHHH----HHCT--GGGG---TTTHHHHHHHHHHHHHHHHHHHHH
T ss_pred cccHHHHHHH----HHhcCchhhc--chhHHHHHHHHHHHHHHHHHHHHhc
Confidence 3889999866 4566655443 58899999999 9999998864 44
No 310
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=34.41 E-value=19 Score=27.09 Aligned_cols=21 Identities=24% Similarity=0.233 Sum_probs=17.9
Q ss_pred chhhhhhhcccccchhHh-HHH
Q 046847 43 KNQTINNRFKHSGETISR-FNS 63 (88)
Q Consensus 43 ~~r~i~~~F~~S~eTisr-f~~ 63 (88)
+..+|+.+=|.|..|||| +|.
T Consensus 2 TikDVA~~AGVS~sTVSrvln~ 23 (333)
T COG1609 2 TIKDVAKLAGVSKATVSRVLNG 23 (333)
T ss_pred CHHHHHHHhCCCHHHHHHHHcC
Confidence 456889999999999999 875
No 311
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=34.23 E-value=27 Score=26.58 Aligned_cols=25 Identities=16% Similarity=0.228 Sum_probs=22.4
Q ss_pred cccchhhhhhhcccccchhHh-HHHH
Q 046847 40 HHVKNQTINNRFKHSGETISR-FNSI 64 (88)
Q Consensus 40 ~n~~~r~i~~~F~~S~eTisr-f~~V 64 (88)
.+.+..+|+.+++-|..|||| ..+-
T Consensus 28 ~g~tQ~eIA~~lgiSR~~VsRlL~~A 53 (318)
T PRK15418 28 DGLTQSEIGERLGLTRLKVSRLLEKG 53 (318)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 458899999999999999999 8774
No 312
>KOG0946 consensus ER-Golgi vesicle-tethering protein p115 [Intracellular trafficking, secretion, and vesicular transport]
Probab=33.72 E-value=81 Score=27.96 Aligned_cols=42 Identities=19% Similarity=0.423 Sum_probs=37.2
Q ss_pred HHHHHHHHHHhhCcCCcCCCccchhHHHHHHHHHhccccchhhh
Q 046847 4 KTFGLLFELLCSDERLKTDSVVFVDEQVCMFLHALAHHVKNQTI 47 (88)
Q Consensus 4 ~~F~~L~~~L~~~~~L~~t~~v~veE~la~FL~i~~~n~~~r~i 47 (88)
.+|..|-+++++.+|+.++ +=||+.|-.-+..+-.|.+|++.
T Consensus 208 NaFerLfsIIeeEGg~dGg--IVveDCL~ll~NLLK~N~SNQ~~ 249 (970)
T KOG0946|consen 208 NAFERLFSIIEEEGGLDGG--IVVEDCLILLNNLLKNNISNQNF 249 (970)
T ss_pred HHHHHHHHHHHhcCCCCCc--chHHHHHHHHHHHHhhCcchhhH
Confidence 5799999999999998776 78999999999999999998764
No 313
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=33.62 E-value=93 Score=20.65 Aligned_cols=47 Identities=9% Similarity=0.039 Sum_probs=36.5
Q ss_pred CccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847 23 SVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE 70 (88)
Q Consensus 23 ~~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~ 70 (88)
...+-|++--+-+++.+. .+-..++..++.|=.||-. ++++++++.-
T Consensus 32 ~~L~~E~~~Fi~~Fi~~r-GnlKe~e~~lgiSYPTvR~rLd~ii~~lg~ 79 (113)
T PF09862_consen 32 ARLSPEQLEFIKLFIKNR-GNLKEMEKELGISYPTVRNRLDKIIEKLGY 79 (113)
T ss_pred hcCCHHHHHHHHHHHHhc-CCHHHHHHHHCCCcHHHHHHHHHHHHHhCC
Confidence 445556665555555554 6788999999999999988 9999999874
No 314
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=33.43 E-value=85 Score=23.33 Aligned_cols=38 Identities=5% Similarity=0.028 Sum_probs=31.1
Q ss_pred HHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847 33 MFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE 70 (88)
Q Consensus 33 ~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~ 70 (88)
+|+..--.+.+++.|+..++.|..||.. .+...+.+-.
T Consensus 161 v~~L~~~~g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~ 199 (339)
T PRK08241 161 VLILRDVLGWSAAEVAELLDTSVAAVNSALQRARATLAE 199 (339)
T ss_pred hhhhHHhhCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhh
Confidence 3444456789999999999999999998 8887777765
No 315
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=33.36 E-value=54 Score=23.77 Aligned_cols=26 Identities=23% Similarity=0.432 Sum_probs=22.6
Q ss_pred ccchhhhhhhcccccchhHh-HHHHHH
Q 046847 41 HVKNQTINNRFKHSGETISR-FNSILN 66 (88)
Q Consensus 41 n~~~r~i~~~F~~S~eTisr-f~~Vl~ 66 (88)
..+..+++..|+.|..||.| .++.-.
T Consensus 18 ~~~~~eLa~~l~VS~~TiRRdL~~L~~ 44 (240)
T PRK10411 18 SLTTEALAEQLNVSKETIRRDLNELQT 44 (240)
T ss_pred CCcHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 57888999999999999999 887655
No 316
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=32.60 E-value=84 Score=24.01 Aligned_cols=45 Identities=18% Similarity=0.150 Sum_probs=35.2
Q ss_pred cchhHHHHHHHHH-h--ccccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847 25 VFVDEQVCMFLHA-L--AHHVKNQTINNRFKHSGETISR-FNSILNGVL 69 (88)
Q Consensus 25 v~veE~la~FL~i-~--~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~ 69 (88)
.+--|+..+-++. + +.+.+...|+..||.|.+.|++ =.+.|+-+-
T Consensus 263 L~eREr~Vl~~rygl~~~~~~Tl~eIa~~lgvS~eRVrQIe~~Al~KLr 311 (324)
T PRK07921 263 LDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLR 311 (324)
T ss_pred CCHHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 5666777777755 3 4678999999999999999999 677666554
No 317
>PRK13698 plasmid-partitioning protein; Provisional
Probab=32.42 E-value=53 Score=25.60 Aligned_cols=38 Identities=11% Similarity=-0.022 Sum_probs=31.1
Q ss_pred cchhHHHHH-HHHHhccccchhhhhhhcccccchhHh-HH
Q 046847 25 VFVDEQVCM-FLHALAHHVKNQTINNRFKHSGETISR-FN 62 (88)
Q Consensus 25 v~veE~la~-FL~i~~~n~~~r~i~~~F~~S~eTisr-f~ 62 (88)
-..|+..+. -..+-..+.+...++.+.|.|..+|++ ++
T Consensus 159 s~iE~A~ay~~~L~~~~~~tQeeLA~~lG~SRs~Vsn~Lr 198 (323)
T PRK13698 159 SAYERGLRYASRLQNEFAGNISALADAENISRKIITRCIN 198 (323)
T ss_pred CHHHHHHHHHHHHHHhcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 567888877 434557788999999999999999999 54
No 318
>PRK11050 manganese transport regulator MntR; Provisional
Probab=31.73 E-value=54 Score=22.10 Aligned_cols=28 Identities=14% Similarity=0.272 Sum_probs=23.6
Q ss_pred ccccchhhhhhhcccccchhHh-HHHHHH
Q 046847 39 AHHVKNQTINNRFKHSGETISR-FNSILN 66 (88)
Q Consensus 39 ~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ 66 (88)
+...+.++++..++.|..||++ ....-.
T Consensus 49 ~~~~t~~eLA~~l~is~stVsr~l~~Le~ 77 (152)
T PRK11050 49 VGEARQVDIAARLGVSQPTVAKMLKRLAR 77 (152)
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3568999999999999999999 776543
No 319
>PRK15340 transcriptional regulator InvF; Provisional
Probab=31.51 E-value=66 Score=23.51 Aligned_cols=25 Identities=12% Similarity=0.101 Sum_probs=20.6
Q ss_pred ccchhhhhhhcccccchhHh-HHHHH
Q 046847 41 HVKNQTINNRFKHSGETISR-FNSIL 65 (88)
Q Consensus 41 n~~~r~i~~~F~~S~eTisr-f~~Vl 65 (88)
..+..+++..++.|..+++| |++.+
T Consensus 125 ~~sleeLA~~~gvS~r~f~RlFk~~~ 150 (216)
T PRK15340 125 GNTMRMLGEDYGVSYTHFRRLCSRAL 150 (216)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 45677888899999999999 99863
No 320
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=31.44 E-value=28 Score=28.34 Aligned_cols=48 Identities=19% Similarity=0.166 Sum_probs=35.9
Q ss_pred hhHHHHHHHHHhc--cccchhhhhhhcccccchhHh-HHHHHHHHHHhhhhhccCCCCCCC
Q 046847 27 VDEQVCMFLHALA--HHVKNQTINNRFKHSGETISR-FNSILNGVLELQHILLKSPKPMPE 84 (88)
Q Consensus 27 veE~la~FL~i~~--~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~L~~~~ik~p~~~~~ 84 (88)
|+-|-+.|.+-.+ .+...++|++.-|.+-+|||| . +..|+..|-+-++
T Consensus 353 v~~Q~~Ff~~G~~~LkPLtlkdVAe~lglHeSTVSRa~----------~~KY~~tp~Gife 403 (481)
T PRK12469 353 VARQRDFFRYGEIALKPLVLRDVAEELGLHESTISRAT----------GNKYMATPRGTFE 403 (481)
T ss_pred HHHHHHHHhCCcccCcCCcHHHHHHHhCCCcchhhHHh----------cCceeecCCceEe
Confidence 5566677765543 468899999999999999999 5 4567777665544
No 321
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=31.44 E-value=81 Score=16.18 Aligned_cols=25 Identities=24% Similarity=0.267 Sum_probs=21.0
Q ss_pred ccchhhhhhhcccccchhHh-HHHHH
Q 046847 41 HVKNQTINNRFKHSGETISR-FNSIL 65 (88)
Q Consensus 41 n~~~r~i~~~F~~S~eTisr-f~~Vl 65 (88)
..+..+++..|+.|..|+++ ....-
T Consensus 14 ~~s~~~l~~~l~~s~~tv~~~l~~L~ 39 (53)
T smart00420 14 KVSVEELAELLGVSEMTIRRDLNKLE 39 (53)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 47888999999999999998 76654
No 322
>PRK10632 transcriptional regulator; Provisional
Probab=31.44 E-value=42 Score=24.38 Aligned_cols=37 Identities=11% Similarity=0.204 Sum_probs=28.9
Q ss_pred HHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHH
Q 046847 29 EQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILN 66 (88)
Q Consensus 29 E~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ 66 (88)
+++-.|+ .++...+++.++++.+.|..|||+ .++.=+
T Consensus 5 ~~L~~F~-~v~e~gS~t~AA~~L~isQpavS~~I~~LE~ 42 (309)
T PRK10632 5 KRMSVFA-KVVEFGSFTAAARQLQMSVSSISQTVSKLED 42 (309)
T ss_pred HHHHHHH-HHHhcCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 3455555 455668999999999999999999 887543
No 323
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=31.40 E-value=1e+02 Score=21.79 Aligned_cols=43 Identities=9% Similarity=0.216 Sum_probs=29.3
Q ss_pred HHHHHHHHhh---CcCCcCCCccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHH
Q 046847 6 FGLLFELLCS---DERLKTDSVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSI 64 (88)
Q Consensus 6 F~~L~~~L~~---~~~L~~t~~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~V 64 (88)
+..+.+.|+. .+.+++...++.|..| +..|+.|..||.+ +.+.
T Consensus 11 y~qI~~~i~~~I~~G~~~~g~kLPsE~eL----------------a~~~~VSR~TvR~Al~~L 57 (241)
T PRK11402 11 YATVRQRLLDDIAQGVYQAGQQIPTENEL----------------CTQYNVSRITIRKAISDL 57 (241)
T ss_pred HHHHHHHHHHHHHcCCCCCCCcCcCHHHH----------------HHHHCCCHHHHHHHHHHH
Confidence 4556666665 3455666667777655 6789999999977 6654
No 324
>PRK11074 putative DNA-binding transcriptional regulator; Provisional
Probab=31.25 E-value=62 Score=23.26 Aligned_cols=37 Identities=5% Similarity=-0.010 Sum_probs=28.5
Q ss_pred HHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHH
Q 046847 29 EQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILN 66 (88)
Q Consensus 29 E~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ 66 (88)
++|-.|+. ++...++..++.+.+.|..|||+ .++.=+
T Consensus 5 ~~L~~f~~-v~e~~s~s~AA~~L~isQpavS~~I~~LE~ 42 (300)
T PRK11074 5 YSLEVVDA-VARTGSFSAAAQELHRVPSAVSYTVRQLEE 42 (300)
T ss_pred HHHHHHHH-HHHhCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 45655554 44556999999999999999999 887533
No 325
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=31.05 E-value=78 Score=22.02 Aligned_cols=45 Identities=7% Similarity=-0.009 Sum_probs=32.7
Q ss_pred cchhHHHHHHHHHh---ccccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847 25 VFVDEQVCMFLHAL---AHHVKNQTINNRFKHSGETISR-FNSILNGVL 69 (88)
Q Consensus 25 v~veE~la~FL~i~---~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~ 69 (88)
.+-.|.--+.+|+. +.+.++..|+...+-|..||.. +..+.++.+
T Consensus 159 Lt~re~~~l~~~i~~~~~~g~s~~eIA~~l~iS~~Tv~~~~~~~~~~~~ 207 (239)
T PRK10430 159 LTPQTLRTLCQWIDAHQDYEFSTDELANAVNISRVSCRKYLIWLVNCHI 207 (239)
T ss_pred CCHHHHHHHHHHHHhCCCCCcCHHHHHHHhCchHHHHHHHHHHHHhCCE
Confidence 34444323344554 5789999999999999999999 888766544
No 326
>PF08897 DUF1841: Domain of unknown function (DUF1841); InterPro: IPR014993 This group of proteins are functionally uncharacterised.
Probab=31.02 E-value=50 Score=22.73 Aligned_cols=55 Identities=11% Similarity=0.160 Sum_probs=41.8
Q ss_pred CCccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH-h--hhhhccCCCC
Q 046847 22 DSVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE-L--QHILLKSPKP 81 (88)
Q Consensus 22 t~~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~-L--~~~~ik~p~~ 81 (88)
+-+++|+|||++ .++...|.+-.+-..-+..-+. -|.+.+|+.. | +...=+|||.
T Consensus 69 smHLsI~EQ~si-----dqP~GIr~a~~~L~~r~~~~h~A~H~~mecL~e~iW~aQR~g~~pD~ 127 (137)
T PF08897_consen 69 SMHLSIQEQLSI-----DQPPGIRAAYERLAARGGDRHEAEHAMMECLAEMIWEAQRNGRPPDE 127 (137)
T ss_pred HHHHHHHHHHhc-----cCChHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHcCCCCCH
Confidence 368899999986 6777777777777777777888 8999888876 3 5566666664
No 327
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=30.93 E-value=2e+02 Score=20.66 Aligned_cols=45 Identities=11% Similarity=-0.048 Sum_probs=35.8
Q ss_pred CccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847 23 SVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVL 69 (88)
Q Consensus 23 ~~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~ 69 (88)
...|.-|.=.+.+ ++.+-++.+|+...+.|..||.. ...+.+-+.
T Consensus 178 ~~LT~rE~evl~~--~a~G~t~~eIa~~l~is~~TV~~h~~~~~~KL~ 223 (240)
T PRK10188 178 MNFSKREKEILKW--TAEGKTSAEIAMILSISENTVNFHQKNMQKKFN 223 (240)
T ss_pred CCCCHHHHHHHHH--HHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 3467666655554 38889999999999999999998 888876553
No 328
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=30.93 E-value=97 Score=18.74 Aligned_cols=43 Identities=19% Similarity=0.315 Sum_probs=33.8
Q ss_pred HHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHHh
Q 046847 29 EQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLEL 71 (88)
Q Consensus 29 E~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~L 71 (88)
|+.--|.-.+|+..+..+++++-|.+..||.+ ....-.=+..|
T Consensus 1 ~~~~~fIrlLs~~~s~~~Aa~~lG~~~~~v~~wv~~fR~wll~L 44 (65)
T PF05344_consen 1 EKARAFIRLLSQQISVAQAADRLGTDPGTVRRWVRMFRQWLLQL 44 (65)
T ss_pred CcHHHHHHHhcccccHHHHHHHHCcCHHHHHHHHHHHHHHHHHc
Confidence 34556778899999999999999999999998 66654444433
No 329
>PF11740 KfrA_N: Plasmid replication region DNA-binding N-term; InterPro: IPR021104 The KfrA family of protiens are encoded on plasmids, generally in or near gene clusters invloved in stable inheritance functions. These proteins are thought to form an all-helical structure, consisting of an N-terminal helix-turn-helix DNA binding domain and an extended coiled-coil tail. The best-characterised KfrA protein, encoded on the broad host-range Plasmid RK2, is a site-specific DNA-binding protein whose operator overlaps its own promoter. The DNA-binding domain is essential for function, while the coiled-coil domain is probably responsible for formation of multimers, and may provide an example of a bridge to host structures required for plasmid partitioning []. This entry represents the N-terminal DNA-binding domain.
Probab=30.81 E-value=44 Score=21.14 Aligned_cols=37 Identities=19% Similarity=0.087 Sum_probs=26.0
Q ss_pred HHHHHhccccchhhhhhhcc-cccchhHh-HHHHHHHHH
Q 046847 33 MFLHALAHHVKNQTINNRFK-HSGETISR-FNSILNGVL 69 (88)
Q Consensus 33 ~FL~i~~~n~~~r~i~~~F~-~S~eTisr-f~~Vl~ai~ 69 (88)
-=|+--|.+.+.+.|....| -|..||++ +++.-....
T Consensus 11 ~~L~~~G~~pT~~~Vr~~lG~GS~~ti~~~l~~w~~~~~ 49 (120)
T PF11740_consen 11 DELLAAGKKPTVRAVRERLGGGSMSTISKHLKEWREERE 49 (120)
T ss_pred HHHHHcCCCCCHHHHHHHHCCCCHHHHHHHHHHHHHhhh
Confidence 33445555667777888888 88889998 887765544
No 330
>TIGR03298 argP transcriptional regulator, ArgP family. ArgP used to be known as IciA. ArgP is a positive regulator of argK. It is a negative autoregulator in presence of arginine. It competes with DnaA for oriC iteron (13-mer) binding. It activates dnaA and nrd transcription. It has been demonstrated to be part of the pho regulon (PubMed:10589831). ArgP mutants convey canavanine (an L-arginine structural homolog) sensitivity (PubMed: 15150242).
Probab=30.80 E-value=66 Score=22.86 Aligned_cols=37 Identities=5% Similarity=0.083 Sum_probs=28.1
Q ss_pred HHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHH
Q 046847 30 QVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNG 67 (88)
Q Consensus 30 ~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~a 67 (88)
++-.|+.. +...++..++++.+.|..|||+ .++.=+-
T Consensus 5 ~l~~f~~v-~~~~s~t~AA~~L~isQpavS~~I~~LE~~ 42 (292)
T TIGR03298 5 QLAALAAV-VEEGSFERAAAALSVTPSAVSQRIKALEER 42 (292)
T ss_pred HHHHHHHH-HHcCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 45555544 4456999999999999999999 8876443
No 331
>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=30.69 E-value=53 Score=22.81 Aligned_cols=36 Identities=17% Similarity=0.153 Sum_probs=27.0
Q ss_pred hHHHHHHHHHhccccchhhhhhhcc-cccchhHh-HHH
Q 046847 28 DEQVCMFLHALAHHVKNQTINNRFK-HSGETISR-FNS 63 (88)
Q Consensus 28 eE~la~FL~i~~~n~~~r~i~~~F~-~S~eTisr-f~~ 63 (88)
+|++..---..+.+.|..+|+..++ .|...|-- .|.
T Consensus 5 de~~~~L~~lw~~G~SasqIA~~lg~vsRnAViGk~hR 42 (162)
T PF07750_consen 5 DERVERLRKLWAEGLSASQIARQLGGVSRNAVIGKAHR 42 (162)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHhCCcchhhhhhhhhc
Confidence 4555555555688999999999999 88888765 554
No 332
>PF09758 FPL: Uncharacterised conserved protein; InterPro: IPR019155 The proteins in this family are functionally uncharacterised. They contain a highly conserved FPL motif.
Probab=30.48 E-value=72 Score=22.14 Aligned_cols=73 Identities=15% Similarity=0.248 Sum_probs=51.7
Q ss_pred CChHHHHHHHHHHhhCcCCcCCCccchhHHHHHHH----------HHhccccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847 1 MDRKTFGLLFELLCSDERLKTDSVVFVDEQVCMFL----------HALAHHVKNQTINNRFKHSGETISR-FNSILNGVL 69 (88)
Q Consensus 1 M~~~~F~~L~~~L~~~~~L~~t~~v~veE~la~FL----------~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~ 69 (88)
|+++++..+.+.|+. ....+-.+-+-+.+.|.+ |++++|.-|+-|...|.-+.|-+-- .=..|+++-
T Consensus 23 ~E~nil~~f~~il~~--~~~~~V~~QlLQtlsiLiqNi~~~~slyyllSnn~iN~iI~~~~d~~~ee~l~yYIsfLK~lS 100 (149)
T PF09758_consen 23 MEKNILSTFVRILKQ--SRSSSVKLQLLQTLSILIQNIRSETSLYYLLSNNHINEIITYPFDFSDEEVLSYYISFLKTLS 100 (149)
T ss_pred HHHHHHHHHHHHHHh--cCChHHHHHHHHHHHHHHHhcCCCcceEEEecchHHHHHHhcCCCCCcchhHHHHHHHHHHHH
Confidence 456677777777765 223334455566777766 4678888899999999999998888 888888875
Q ss_pred -Hhhhhh
Q 046847 70 -ELQHIL 75 (88)
Q Consensus 70 -~L~~~~ 75 (88)
+|-++-
T Consensus 101 lkln~~t 107 (149)
T PF09758_consen 101 LKLNKDT 107 (149)
T ss_pred hhcCCCc
Confidence 355443
No 333
>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=30.43 E-value=81 Score=20.24 Aligned_cols=39 Identities=10% Similarity=0.123 Sum_probs=27.7
Q ss_pred hhHHHHHHHHHhcc---ccchhhhhhhcccccchhHh-HHHHH
Q 046847 27 VDEQVCMFLHALAH---HVKNQTINNRFKHSGETISR-FNSIL 65 (88)
Q Consensus 27 veE~la~FL~i~~~---n~~~r~i~~~F~~S~eTisr-f~~Vl 65 (88)
++-.|.+-+|+..+ ..+.++|+.+++-|..+|++ ....-
T Consensus 8 ~~yal~~l~~la~~~~~~~s~~eia~~l~is~~~v~~~l~~L~ 50 (130)
T TIGR02944 8 TDYATLVLTTLAQNDSQPYSAAEIAEQTGLNAPTVSKILKQLS 50 (130)
T ss_pred HhHHHHHHHHHHhCCCCCccHHHHHHHHCcCHHHHHHHHHHHH
Confidence 45566666666543 26889999999999999988 55543
No 334
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=30.40 E-value=72 Score=22.84 Aligned_cols=39 Identities=13% Similarity=0.266 Sum_probs=29.9
Q ss_pred HHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHH
Q 046847 29 EQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGV 68 (88)
Q Consensus 29 E~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai 68 (88)
++|-.|+.+ +...+...+++.-+.|..|||+ .++.=+.+
T Consensus 8 ~~L~~f~~v-~~~gs~s~AA~~L~isQ~avS~~i~~LE~~l 47 (302)
T PRK09791 8 HQIRAFVEV-ARQGSIRGASRMLNMSQPALTKSIQELEEGL 47 (302)
T ss_pred HHHHHHHHH-HHcCCHHHHHHHhCCChHHHHHHHHHHHHHh
Confidence 556666554 4556999999999999999999 88864443
No 335
>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=30.31 E-value=79 Score=17.96 Aligned_cols=33 Identities=21% Similarity=0.304 Sum_probs=25.3
Q ss_pred HHHHHh-ccccchhhhhhhcccccchhHh-HHHHH
Q 046847 33 MFLHAL-AHHVKNQTINNRFKHSGETISR-FNSIL 65 (88)
Q Consensus 33 ~FL~i~-~~n~~~r~i~~~F~~S~eTisr-f~~Vl 65 (88)
++++.+ ....+-++|+...+.|..||++ .+...
T Consensus 13 vy~~Ll~~~~~t~~eIa~~l~i~~~~v~~~L~~L~ 47 (68)
T PF01978_consen 13 VYLALLKNGPATAEEIAEELGISRSTVYRALKSLE 47 (68)
T ss_dssp HHHHHHHHCHEEHHHHHHHHTSSHHHHHHHHHHHH
T ss_pred HHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 344444 5568899999999999999988 76654
No 336
>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR. All members of this cyanobacterial protein family are the transcriptional regulator SufR and regulate the SUF system, which makes possible iron-sulfur cluster biosynthesis despite exposure to oxygen. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus.
Probab=30.04 E-value=84 Score=21.92 Aligned_cols=37 Identities=11% Similarity=0.258 Sum_probs=28.2
Q ss_pred hHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHH
Q 046847 28 DEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSIL 65 (88)
Q Consensus 28 eE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl 65 (88)
.++|-..|+.-+ +.+..+++..++.|..||++ ..+.-
T Consensus 3 r~~IL~~L~~~~-~~t~~eLA~~lgis~~tV~~~L~~Le 40 (203)
T TIGR02702 3 KEDILSYLLKQG-QATAAALAEALAISPQAVRRHLKDLE 40 (203)
T ss_pred HHHHHHHHHHcC-CCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 345555565544 48999999999999999999 77655
No 337
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=29.89 E-value=49 Score=23.34 Aligned_cols=38 Identities=11% Similarity=0.125 Sum_probs=28.3
Q ss_pred HHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHH
Q 046847 30 QVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGV 68 (88)
Q Consensus 30 ~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai 68 (88)
+|-.|+ .++...++..++..-+.|..|||+ .++.=+.+
T Consensus 7 ~L~~f~-~v~e~~s~t~AA~~L~isqpavS~~I~~LE~~l 45 (290)
T PRK10837 7 QLEVFA-EVLKSGSTTQASVMLALSQSAVSAALTDLEGQL 45 (290)
T ss_pred HHHHHH-HHHHcCCHHHHHHHhCCCccHHHHHHHHHHHHh
Confidence 344444 445557999999999999999999 88754333
No 338
>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=29.88 E-value=67 Score=21.73 Aligned_cols=38 Identities=8% Similarity=-0.058 Sum_probs=31.4
Q ss_pred HHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847 33 MFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE 70 (88)
Q Consensus 33 ~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~ 70 (88)
+|+..--.+.+++.|+...+.|..||.. .+.....+-.
T Consensus 139 i~~L~~~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 177 (193)
T TIGR02947 139 AVYLADVEGFAYKEIAEIMGTPIGTVMSRLHRGRKQLRK 177 (193)
T ss_pred heeehhhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4444556789999999999999999999 8888777765
No 339
>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=29.43 E-value=50 Score=22.95 Aligned_cols=33 Identities=18% Similarity=0.192 Sum_probs=26.7
Q ss_pred HHHhccccchhhhhhhcccccchhHh-HHHHHHH
Q 046847 35 LHALAHHVKNQTINNRFKHSGETISR-FNSILNG 67 (88)
Q Consensus 35 L~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~a 67 (88)
+..++...++..+++.-+.|.+|||+ .++.=+.
T Consensus 5 f~~v~~~gs~~~AA~~L~isqsavS~~i~~LE~~ 38 (279)
T TIGR03339 5 FHAVARCGSFTRAAERLGLSQPTVTDQVRKLEER 38 (279)
T ss_pred hHHHHhcCCHHHHHHHhcCCchHHHHHHHHHHHH
Confidence 34566678999999999999999999 8875433
No 340
>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=29.03 E-value=46 Score=24.07 Aligned_cols=38 Identities=16% Similarity=0.185 Sum_probs=29.7
Q ss_pred HHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHH
Q 046847 29 EQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNG 67 (88)
Q Consensus 29 E~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~a 67 (88)
+++-.|+ .++...++..++.+.+.|..|||+ .+..=+.
T Consensus 11 ~~L~~F~-~va~~gs~s~AA~~L~isQpavS~~I~~LE~~ 49 (302)
T TIGR02036 11 SKMHTFE-VAARHQSFSLAAEELSLTPSAISHRINQLEEE 49 (302)
T ss_pred HHHHHHH-HHHHhCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 4455554 566779999999999999999999 9875333
No 341
>PRK10870 transcriptional repressor MprA; Provisional
Probab=28.56 E-value=73 Score=21.93 Aligned_cols=25 Identities=8% Similarity=0.171 Sum_probs=21.7
Q ss_pred ccchhhhhhhcccccchhHh-HHHHH
Q 046847 41 HVKNQTINNRFKHSGETISR-FNSIL 65 (88)
Q Consensus 41 n~~~r~i~~~F~~S~eTisr-f~~Vl 65 (88)
+.+..+++..++.+..||++ ++..-
T Consensus 71 ~it~~eLa~~l~l~~~tvsr~v~rLe 96 (176)
T PRK10870 71 SIQPSELSCALGSSRTNATRIADELE 96 (176)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 46779999999999999999 87765
No 342
>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=28.45 E-value=66 Score=17.09 Aligned_cols=33 Identities=24% Similarity=0.202 Sum_probs=25.5
Q ss_pred HHHHHHHhccccchhhhhhhcccccchhHh-HHH
Q 046847 31 VCMFLHALAHHVKNQTINNRFKHSGETISR-FNS 63 (88)
Q Consensus 31 la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~ 63 (88)
+-+|.-.--.+.+.+.|..+-+.|..++.+ |..
T Consensus 6 ~~l~~~~G~~~~s~~~Ia~~~gvs~~~~y~~f~~ 39 (47)
T PF00440_consen 6 LELFAEKGYEAVSIRDIARRAGVSKGSFYRYFPS 39 (47)
T ss_dssp HHHHHHHHTTTSSHHHHHHHHTSCHHHHHHHCSS
T ss_pred HHHHHHhCHHhCCHHHHHHHHccchhhHHHHcCC
Confidence 334444445678999999999999999999 764
No 343
>PF00157 Pou: Pou domain - N-terminal to homeobox domain; InterPro: IPR000327 POU proteins are eukaryotic transcription factors containing a bipartite DNA binding domain referred to as the POU domain. The acronym POU (pronounced 'pow') is derived from the names of three mammalian transcription factors, the pituitary-specific Pit-1, the octamer-binding proteins Oct-1 and Oct-2, and the neural Unc-86 from Caenorhabditis elegans. POU domain genes have been identified in diverse organisms including nematodes, flies, amphibians, fish and mammals but have not been yet identified in plants and fungi. The various members of the POU family have a wide variety of functions, all of which are related to the function of the neuroendocrine system [] and the development of an organism []. Some other genes are also regulated, including those for immunoglobulin light and heavy chains (Oct-2) [, ], and trophic hormone genes, such as those for prolactin and growth hormone (Pit-1). The POU domain is a bipartite domain composed of two subunits separated by a non-conserved region of 15-55 aa. The N-terminal subunit is known as the POU-specific (POUs) domain (IPR000327 from INTERPRO), while the C-terminal subunit is a homeobox domain (IPR007103 from INTERPRO). 3D structures of complexes including both POU subdomains bound to DNA are available. Both subdomains contain the structural motif 'helix-turn-helix', which directly associates with the two components of bipartite DNA binding sites, and both are required for high affinity sequence-specific DNA-binding. The domain may also be involved in protein-protein interactions []. The subdomains are connected by a flexible linker [, , ]. In proteins a POU-specific domain is always accompanied by a homeodomain. Despite of the lack of sequence homology, 3D structure of POUs is similar to 3D structure of bacteriophage lambda repressor and other members of HTH_3 family [, ]. This entry represents the POU-specific subunit of the POU domain.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3D1N_O 1AU7_A 3L1P_A 2XSD_C 1O4X_A 1HF0_B 1GT0_C 1POU_A 1CQT_B 1E3O_C ....
Probab=28.43 E-value=30 Score=21.47 Aligned_cols=23 Identities=30% Similarity=0.577 Sum_probs=15.7
Q ss_pred cccchhHhHHHH---HHHHHHhhhhh
Q 046847 53 HSGETISRFNSI---LNGVLELQHIL 75 (88)
Q Consensus 53 ~S~eTisrf~~V---l~ai~~L~~~~ 75 (88)
.|..|||||... ++.+++|.+..
T Consensus 42 ~SQttI~RFE~L~LS~kn~~klkP~L 67 (75)
T PF00157_consen 42 FSQTTICRFEALQLSFKNMCKLKPLL 67 (75)
T ss_dssp GSHHHHHHHHTTTSCHHHHHHHHHHH
T ss_pred ccchhhhhhHhcccCHHHHHHHHHHH
Confidence 578899997664 56666665543
No 344
>COG3179 Predicted chitinase [General function prediction only]
Probab=28.40 E-value=28 Score=25.55 Aligned_cols=43 Identities=14% Similarity=0.241 Sum_probs=36.6
Q ss_pred CCccchhHHHHHHHHHhccccc-hhhhhhhcccccchhHh-HHHH
Q 046847 22 DSVVFVDEQVCMFLHALAHHVK-NQTINNRFKHSGETISR-FNSI 64 (88)
Q Consensus 22 t~~v~veE~la~FL~i~~~n~~-~r~i~~~F~~S~eTisr-f~~V 64 (88)
...|+--+++||||=-++|-.. ++.+.+.+--|-++.++ |..=
T Consensus 33 ~~gi~~p~r~AmFlAQ~~HESggf~rl~EnlnYSaq~L~~tf~~r 77 (206)
T COG3179 33 EAGITTPLRQAMFLAQVMHESGGFTRLDENLNYSAQGLLQTFPKR 77 (206)
T ss_pred HhcCCCHHHHHHHHHHHhhhcCCceeehhhcchHHHHHHHhcccc
Confidence 4557778999999999999877 89999999999999888 7653
No 345
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=28.26 E-value=1.2e+02 Score=18.53 Aligned_cols=27 Identities=7% Similarity=0.137 Sum_probs=23.5
Q ss_pred cccchhhhhhhcccccchhHh-HHHHHH
Q 046847 40 HHVKNQTINNRFKHSGETISR-FNSILN 66 (88)
Q Consensus 40 ~n~~~r~i~~~F~~S~eTisr-f~~Vl~ 66 (88)
...++.+++..++-|..||.+ .+...+
T Consensus 16 ~~~~~~~la~~l~~s~~tv~~~l~~L~~ 43 (108)
T smart00344 16 ARISLAELAKKVGLSPSTVHNRVKRLEE 43 (108)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 358999999999999999999 887754
No 346
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=28.15 E-value=81 Score=22.69 Aligned_cols=28 Identities=14% Similarity=0.204 Sum_probs=24.8
Q ss_pred HhccccchhhhhhhcccccchhHh-HHHH
Q 046847 37 ALAHHVKNQTINNRFKHSGETISR-FNSI 64 (88)
Q Consensus 37 i~~~n~~~r~i~~~F~~S~eTisr-f~~V 64 (88)
-.+.+.+..+++..++-|.++++| |++.
T Consensus 195 ~~~~~isl~~lA~~~~lS~~~l~r~Fk~~ 223 (290)
T PRK10572 195 HLASEFDIESVAQHVCLSPSRLAHLFRQQ 223 (290)
T ss_pred cccCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 355678899999999999999999 9996
No 347
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=28.13 E-value=46 Score=19.96 Aligned_cols=23 Identities=17% Similarity=0.336 Sum_probs=18.6
Q ss_pred hhhhhhhcccccchhHh-HHHHHH
Q 046847 44 NQTINNRFKHSGETISR-FNSILN 66 (88)
Q Consensus 44 ~r~i~~~F~~S~eTisr-f~~Vl~ 66 (88)
.++++..++.|..||++ ....-+
T Consensus 2 ~~ela~~l~is~stvs~~l~~L~~ 25 (96)
T smart00529 2 TSEIAERLNVSPPTVTQMLKKLEK 25 (96)
T ss_pred HHHHHHHhCCChHHHHHHHHHHHH
Confidence 46788999999999999 776543
No 348
>PRK15092 DNA-binding transcriptional repressor LrhA; Provisional
Probab=28.00 E-value=52 Score=24.18 Aligned_cols=35 Identities=9% Similarity=-0.009 Sum_probs=28.6
Q ss_pred HHHHHhccccchhhhhhhcccccchhHh-HHHHHHH
Q 046847 33 MFLHALAHHVKNQTINNRFKHSGETISR-FNSILNG 67 (88)
Q Consensus 33 ~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~a 67 (88)
-.++.++...++..++.+...|..|||+ .++.=+.
T Consensus 17 ~~F~~v~e~gs~s~AA~~L~iSQpavS~~I~~LE~~ 52 (310)
T PRK15092 17 RTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQL 52 (310)
T ss_pred HHHHHHHHcCCHHHHHHHhCCChHHHHHHHHHHHHH
Confidence 4455677779999999999999999999 9885433
No 349
>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=27.91 E-value=80 Score=22.45 Aligned_cols=38 Identities=8% Similarity=0.148 Sum_probs=29.2
Q ss_pred HHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHH
Q 046847 29 EQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNG 67 (88)
Q Consensus 29 E~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~a 67 (88)
+++-+|+.+ +...|+..++..-+.|..|||+ .++.=+.
T Consensus 6 ~~l~~f~~v-~~~gS~s~AA~~L~isq~avS~~I~~LE~~ 44 (300)
T TIGR02424 6 RHLQCFVEV-ARQGSVKRAAEALHITQPAVSKTLRELEEI 44 (300)
T ss_pred HHHHHHHHH-HHhCCHHHHHHHhCCChHHHHHHHHHHHHH
Confidence 456666654 4556999999999999999999 8875333
No 350
>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=27.76 E-value=1e+02 Score=21.17 Aligned_cols=26 Identities=4% Similarity=0.004 Sum_probs=21.0
Q ss_pred ccccchhhhhhhcccc-cchhHh-HHHH
Q 046847 39 AHHVKNQTINNRFKHS-GETISR-FNSI 64 (88)
Q Consensus 39 ~~n~~~r~i~~~F~~S-~eTisr-f~~V 64 (88)
+...+.+.++..++-| ..||++ ....
T Consensus 23 ~~~~~~~ela~~~~~~s~~tv~~~l~~L 50 (199)
T TIGR00498 23 GYPPSIREIARAVGLRSPSAAEEHLKAL 50 (199)
T ss_pred CCCCcHHHHHHHhCCCChHHHHHHHHHH
Confidence 3458899999999998 999987 5544
No 351
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=27.43 E-value=39 Score=20.29 Aligned_cols=27 Identities=19% Similarity=0.167 Sum_probs=20.7
Q ss_pred HHhccccchhhhhhhcccccchhHh-HH
Q 046847 36 HALAHHVKNQTINNRFKHSGETISR-FN 62 (88)
Q Consensus 36 ~i~~~n~~~r~i~~~F~~S~eTisr-f~ 62 (88)
++-..+.+.++++.+.|-|.++||+ -+
T Consensus 26 ~~~~~~ltQ~e~A~~lgisq~~vS~l~~ 53 (80)
T PF13744_consen 26 LREERGLTQAELAERLGISQPRVSRLEN 53 (80)
T ss_dssp HHHCCT--HHHHHHHHTS-HHHHHHHHT
T ss_pred HHHHcCCCHHHHHHHHCCChhHHHHHHc
Confidence 4567889999999999999999999 54
No 352
>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=27.15 E-value=43 Score=17.74 Aligned_cols=26 Identities=12% Similarity=-0.081 Sum_probs=20.3
Q ss_pred HhccccchhhhhhhcccccchhHh-HH
Q 046847 37 ALAHHVKNQTINNRFKHSGETISR-FN 62 (88)
Q Consensus 37 i~~~n~~~r~i~~~F~~S~eTisr-f~ 62 (88)
+-..+.+..+++..-+.|.+||++ .+
T Consensus 11 r~~~gltq~~lA~~~gvs~~~vs~~e~ 37 (58)
T TIGR03070 11 RKALGLTQADLADLAGVGLRFIRDVEN 37 (58)
T ss_pred HHHcCCCHHHHHHHhCCCHHHHHHHHC
Confidence 445677888888888899999988 54
No 353
>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=27.13 E-value=82 Score=20.13 Aligned_cols=25 Identities=24% Similarity=0.337 Sum_probs=20.3
Q ss_pred cchhhhhhhcccccchhHh-HHHHHH
Q 046847 42 VKNQTINNRFKHSGETISR-FNSILN 66 (88)
Q Consensus 42 ~~~r~i~~~F~~S~eTisr-f~~Vl~ 66 (88)
...+.+++.-|.+-+|||| -+.-+.
T Consensus 24 ~gq~~vA~~~Gv~eStISR~k~~~~~ 49 (91)
T PF05269_consen 24 VGQKKVAEAMGVDESTISRWKNDFIE 49 (91)
T ss_dssp HHHHHHHHHHTSSTTTHHHHHHHHHH
T ss_pred HhhHHHHHHhCCCHHHHHHHHhhHHH
Confidence 6778999999999999999 545333
No 354
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=27.10 E-value=1.1e+02 Score=25.22 Aligned_cols=46 Identities=11% Similarity=0.026 Sum_probs=36.1
Q ss_pred ccchhHHHHHHHHHh---ccccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847 24 VVFVDEQVCMFLHAL---AHHVKNQTINNRFKHSGETISR-FNSILNGVL 69 (88)
Q Consensus 24 ~v~veE~la~FL~i~---~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~ 69 (88)
..+--|+..|-++.. +.+.+...|+..||.|.+.|++ =...|.-+-
T Consensus 447 ~L~eREr~VI~lRyGL~~~e~~TL~EIa~~lGVSrERVRQIe~kAL~KLR 496 (509)
T PRK05901 447 TLSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESKTLRKLR 496 (509)
T ss_pred hCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 356667777777553 5789999999999999999999 766666554
No 355
>COG2973 TrpR Trp operon repressor [Transcription]
Probab=27.00 E-value=55 Score=21.56 Aligned_cols=27 Identities=30% Similarity=0.308 Sum_probs=23.7
Q ss_pred HhccccchhhhhhhcccccchhHh-HHH
Q 046847 37 ALAHHVKNQTINNRFKHSGETISR-FNS 63 (88)
Q Consensus 37 i~~~n~~~r~i~~~F~~S~eTisr-f~~ 63 (88)
-+-.+.+.|.|+...|.|..||-| =+.
T Consensus 56 LL~ge~sQREi~~~LgvsiAtITRGSN~ 83 (103)
T COG2973 56 LLRGELSQREIAQKLGVSIATITRGSNS 83 (103)
T ss_pred HHhccccHHHHHHHhCcchhhhccchhh
Confidence 467899999999999999999988 554
No 356
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=26.88 E-value=1.1e+02 Score=22.17 Aligned_cols=40 Identities=5% Similarity=-0.016 Sum_probs=28.2
Q ss_pred chhHHHHHHHHHhccc--cchhhhhhhcccccchhHh-HHHHH
Q 046847 26 FVDEQVCMFLHALAHH--VKNQTINNRFKHSGETISR-FNSIL 65 (88)
Q Consensus 26 ~veE~la~FL~i~~~n--~~~r~i~~~F~~S~eTisr-f~~Vl 65 (88)
+++..+.+.-....++ .+..+|....+.+.+|++| .+...
T Consensus 9 sl~ral~iL~~l~~~~~~ls~~eia~~lgl~kstv~RlL~tL~ 51 (263)
T PRK09834 9 GLSRGLMVLRALNRLDGGATVGLLAELTGLHRTTVRRLLETLQ 51 (263)
T ss_pred HHHHHHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 3455555544444433 6899999999999999999 65543
No 357
>TIGR00519 asnASE_I L-asparaginases, type I. Two related families of asparaginase are designated type I and type II according to the terminology in E. coli, which has both: L-asparaginase I is a low-affinity enzyme found in the cytoplasm, while L-asparaginase II is a high-affinity secreted enzyme synthesized with a cleavable signal sequence. This model describes L-asparaginases related to type I of E. coli. Archaeal putative asparaginases are of this type but contain an extra ~ 80 residues in a conserved N-terminal region. These archaeal homologs are included in this model.
Probab=26.77 E-value=67 Score=24.62 Aligned_cols=37 Identities=3% Similarity=0.062 Sum_probs=32.5
Q ss_pred CCcCCCccchhHHHHHHHHHhccccchhhhhhhcccc
Q 046847 18 RLKTDSVVFVDEQVCMFLHALAHHVKNQTINNRFKHS 54 (88)
Q Consensus 18 ~L~~t~~v~veE~la~FL~i~~~n~~~r~i~~~F~~S 54 (88)
|.-+...++.|...+.-+|.++.+.+...++..|+++
T Consensus 293 G~i~~g~lt~e~A~~kL~~~L~~~~~~~~i~~~f~~~ 329 (336)
T TIGR00519 293 GVIGGEDMLPEVALVKLMWLLGQYSDPEEAKKMMSKN 329 (336)
T ss_pred CEEECCCCCHHHHHHHHHHHHcCCCCHHHHHHHHhcc
Confidence 4556678999999999999999999999999999864
No 358
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=26.66 E-value=1.5e+02 Score=20.23 Aligned_cols=38 Identities=13% Similarity=0.100 Sum_probs=30.6
Q ss_pred HHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847 33 MFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVLE 70 (88)
Q Consensus 33 ~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~ 70 (88)
+|......+.+++.|+...|-|..||.. .+.....+-.
T Consensus 136 v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 174 (188)
T PRK12517 136 PLLLQVIGGFSGEEIAEILDLNKNTVMTRLFRARNQLKE 174 (188)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4555566789999999999999999988 7777666554
No 359
>PF01316 Arg_repressor: Arginine repressor, DNA binding domain; InterPro: IPR020900 The arginine dihydrolase (AD) pathway is found in many prokaryotes and some primitive eukaryotes, an example of the latter being Giardia lamblia (Giardia intestinalis) []. The three-enzyme anaerobic pathway breaks down L-arginine to form 1 mol of ATP, carbon dioxide and ammonia. In simpler bacteria, the first enzyme, arginine deiminase, can account for up to 10% of total cell protein []. Most prokaryotic arginine deiminase pathways are under the control of a repressor gene, termed ArgR []. This is a negative regulator, and will only release the arginine deiminase operon for expression in the presence of arginine []. The crystal structure of apo-ArgR from Bacillus stearothermophilus has been determined to 2.5A by means of X-ray crystallography []. The protein exists as a hexamer of identical subunits, and is shown to have six DNA-binding domains, clustered around a central oligomeric core when bound to arginine. It predominantly interacts with A.T residues in ARG boxes. This hexameric protein binds DNA at its N terminus to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbour-joining tree, some of these paralogous sequences show long branches and differ significantly from the well-conserved C-terminal region. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0006525 arginine metabolic process; PDB: 1AOY_A 3V4G_A 3LAJ_D 3FHZ_A 3LAP_B 3ERE_D 2P5L_C 1F9N_D 2P5K_A 1B4A_A ....
Probab=26.62 E-value=34 Score=20.71 Aligned_cols=29 Identities=21% Similarity=0.374 Sum_probs=15.9
Q ss_pred cchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHH
Q 046847 25 VFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSI 64 (88)
Q Consensus 25 v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~V 64 (88)
|+..|.|.=-|- ..-|..+..|||| .++.
T Consensus 19 i~sQ~eL~~~L~-----------~~Gi~vTQaTiSRDLkeL 48 (70)
T PF01316_consen 19 ISSQEELVELLE-----------EEGIEVTQATISRDLKEL 48 (70)
T ss_dssp --SHHHHHHHHH-----------HTT-T--HHHHHHHHHHH
T ss_pred cCCHHHHHHHHH-----------HcCCCcchhHHHHHHHHc
Confidence 555555554442 3356678899999 8875
No 360
>PRK11062 nhaR transcriptional activator NhaR; Provisional
Probab=26.61 E-value=64 Score=23.19 Aligned_cols=35 Identities=9% Similarity=0.133 Sum_probs=28.9
Q ss_pred HHHHHHHHHhccccchhhhhhhcccccchhHh-HHHH
Q 046847 29 EQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSI 64 (88)
Q Consensus 29 E~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~V 64 (88)
++|-.|+. ++...+++.++.+.+.|..|||| .++.
T Consensus 7 ~~L~~F~~-v~e~gs~s~AA~~L~isqpavS~~I~~L 42 (296)
T PRK11062 7 NHLYYFWM-VCKEGSVVGAAEALFLTPQTITGQIKAL 42 (296)
T ss_pred HHHHHHHH-HHhcCCHHHHHHHhCCChHHHHHHHHHH
Confidence 46666664 55678999999999999999999 8874
No 361
>PRK09508 leuO leucine transcriptional activator; Reviewed
Probab=26.59 E-value=60 Score=23.55 Aligned_cols=35 Identities=11% Similarity=0.125 Sum_probs=28.2
Q ss_pred HHHHHHHHhccccchhhhhhhcccccchhHh-HHHHH
Q 046847 30 QVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSIL 65 (88)
Q Consensus 30 ~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl 65 (88)
+|-.|+ .++...++..+++..+.|..|||+ .++.=
T Consensus 26 ~L~~f~-avae~gs~s~AA~~L~isQpavS~~I~~LE 61 (314)
T PRK09508 26 LLTVFD-AVMQEQNITRAAHNLGMSQPAVSNAVARLK 61 (314)
T ss_pred HHHHHH-HHHhcCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 465555 556667899999999999999999 98853
No 362
>PF12162 STAT1_TAZ2bind: STAT1 TAZ2 binding domain; InterPro: IPR022752 This entry represents the C-terminal domain of STAT1, which selectively binds the TAZ2 domain of CRB (CREB-binding protein) []. This group of eukaryotic proteins is approximately 20 amino acids in length, and is found in association with PF02865 from PFAM, PF00017 from PFAM, PF01017 from PFAM, PF02864 from PFAM. By binding to CRB, it becomes a transcriptional activator and can initiate transcription of certain genes. ; GO: 0003700 sequence-specific DNA binding transcription factor activity; PDB: 2KA6_B.
Probab=26.57 E-value=73 Score=15.52 Aligned_cols=13 Identities=15% Similarity=0.307 Sum_probs=9.7
Q ss_pred CChHHHHHHHHHH
Q 046847 1 MDRKTFGLLFELL 13 (88)
Q Consensus 1 M~~~~F~~L~~~L 13 (88)
|+++.|..|+...
T Consensus 10 MSPddy~~l~~~V 22 (23)
T PF12162_consen 10 MSPDDYDELERMV 22 (23)
T ss_dssp S-HHHHHHHHHHH
T ss_pred CCHHHHHHHHHhh
Confidence 8899999988653
No 363
>COG2378 Predicted transcriptional regulator [Transcription]
Probab=26.31 E-value=92 Score=23.59 Aligned_cols=39 Identities=15% Similarity=0.173 Sum_probs=28.8
Q ss_pred HHHHHHHhcccc-chhhhhhhcccccchhHh-HHHHHHHHH
Q 046847 31 VCMFLHALAHHV-KNQTINNRFKHSGETISR-FNSILNGVL 69 (88)
Q Consensus 31 la~FL~i~~~n~-~~r~i~~~F~~S~eTisr-f~~Vl~ai~ 69 (88)
+.|-.+..++.. +-+.++++|+.|..||-| ++....+-+
T Consensus 11 ~~ii~~L~~~~~vta~~lA~~~~VS~RTi~RDi~~L~~~gv 51 (311)
T COG2378 11 LQIIQILRAKETVTAAELADEFEVSVRTIYRDIATLRAAGV 51 (311)
T ss_pred HHHHHHHHhCccchHHHHHHhcCCCHHHHHHHHHHHHHCCC
Confidence 444445555554 788899999999999999 998765443
No 364
>PF03623 Focal_AT: Focal adhesion targeting region; InterPro: IPR005189 Focal adhesion kinase (FAK) is a tyrosine kinase found in focal adhesions, intracellular signalling complexes that are formed following engagement of the extracellular matrix by integrins. The C-terminal "focal adhesion targeting" (FAT) region is necessary and sufficient for localizing FAK to focal adhesions. The crystal structure of FAT shows it forms a four-helix bundle that resembles those found in two other proteins involved in cell adhesion, alpha-catenin and vinculin []. The binding of FAT to the focal adhesion protein, paxillin, requires the integrity of the helical bundle, whereas binding to another focal adhesion protein, talin, does not.; GO: 0004713 protein tyrosine kinase activity, 0004871 signal transducer activity, 0006468 protein phosphorylation, 0007172 signal complex assembly, 0005925 focal adhesion; PDB: 1K05_C 1OW8_C 1OW7_C 3S9O_C 3B71_B 1K04_A 1OW6_C 3GM1_B 3GM3_A 3GM2_A ....
Probab=26.04 E-value=88 Score=21.56 Aligned_cols=31 Identities=6% Similarity=0.278 Sum_probs=27.1
Q ss_pred hcccccchhHh-HHHHHHHHHHhhhhhccCCC
Q 046847 50 RFKHSGETISR-FNSILNGVLELQHILLKSPK 80 (88)
Q Consensus 50 ~F~~S~eTisr-f~~Vl~ai~~L~~~~ik~p~ 80 (88)
.+.|+.++|.+ --.|.+|+..|...+-..|.
T Consensus 3 ~ldR~~D~Vy~at~~VVkaV~~Ls~~v~~~~~ 34 (139)
T PF03623_consen 3 ELDRTNDKVYDATTGVVKAVMQLSNSVQTAKP 34 (139)
T ss_dssp SSTCTTHHHHHHHHHHHHHHHHHHHHTTTSSH
T ss_pred CCCcccChHHHHHHHHHHHHHHHHhhhccCCh
Confidence 47899999999 99999999999998877663
No 365
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=25.74 E-value=62 Score=22.43 Aligned_cols=30 Identities=17% Similarity=0.190 Sum_probs=24.1
Q ss_pred HHHHHHhccccchhhhhhhcccccchhHh-HH
Q 046847 32 CMFLHALAHHVKNQTINNRFKHSGETISR-FN 62 (88)
Q Consensus 32 a~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~ 62 (88)
.++-+ ...+.+.+.|+..++.|..||.| .+
T Consensus 164 ~i~~~-~~~g~s~~~iak~lgis~~Tv~r~~k 194 (200)
T PRK13413 164 KIKKL-LDKGTSKSEIARKLGVSRTTLARFLK 194 (200)
T ss_pred HHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 45555 35568999999999999999988 54
No 366
>PRK09986 DNA-binding transcriptional activator XapR; Provisional
Probab=25.70 E-value=1e+02 Score=21.75 Aligned_cols=39 Identities=13% Similarity=0.164 Sum_probs=31.0
Q ss_pred HHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHH
Q 046847 29 EQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGV 68 (88)
Q Consensus 29 E~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai 68 (88)
+++=+|+-++-+ .++..++...+.|.++||+ .++.=+.+
T Consensus 10 ~~l~~f~~v~~~-gs~t~AA~~L~itq~avS~~i~~LE~~l 49 (294)
T PRK09986 10 KLLRYFLAVAEE-LHFGRAAARLNISQPPLSIHIKELEDQL 49 (294)
T ss_pred HHHHHHHHHHHh-cCHHHHHHHhCCCCCHHHHHHHHHHHHh
Confidence 467777766666 5999999999999999999 98864433
No 367
>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=25.48 E-value=40 Score=17.06 Aligned_cols=21 Identities=14% Similarity=0.164 Sum_probs=16.1
Q ss_pred chhhhhhhcccccchhHh-HHH
Q 046847 43 KNQTINNRFKHSGETISR-FNS 63 (88)
Q Consensus 43 ~~r~i~~~F~~S~eTisr-f~~ 63 (88)
+..+++..++.|..||.+ ..+
T Consensus 2 s~~e~a~~lgvs~~tl~~~~~~ 23 (49)
T cd04762 2 TTKEAAELLGVSPSTLRRWVKE 23 (49)
T ss_pred CHHHHHHHHCcCHHHHHHHHHc
Confidence 456788889999999977 553
No 368
>PRK10086 DNA-binding transcriptional regulator DsdC; Provisional
Probab=25.45 E-value=61 Score=23.53 Aligned_cols=37 Identities=14% Similarity=0.190 Sum_probs=29.1
Q ss_pred HHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHH
Q 046847 30 QVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNG 67 (88)
Q Consensus 30 ~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~a 67 (88)
++-.|+ .++...+++.++...+.|..|||+ .++.=+.
T Consensus 18 ~L~~f~-~va~~gs~s~AA~~L~iSQpavS~~I~~LE~~ 55 (311)
T PRK10086 18 KLHTFE-VAARHQSFALAADELSLTPSAVSHRINQLEEE 55 (311)
T ss_pred HHHHHH-HHHHcCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 444444 566679999999999999999999 9885433
No 369
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=25.27 E-value=84 Score=23.18 Aligned_cols=37 Identities=16% Similarity=0.204 Sum_probs=26.6
Q ss_pred hHHHHHHHHHhcc--ccchhhhhhhcccccchhHh-HHHH
Q 046847 28 DEQVCMFLHALAH--HVKNQTINNRFKHSGETISR-FNSI 64 (88)
Q Consensus 28 eE~la~FL~i~~~--n~~~r~i~~~F~~S~eTisr-f~~V 64 (88)
+|+...-+-.+.. -.+..+++..|+.|.+||-| +.+.
T Consensus 16 ~eR~~~Il~~L~~~~~vtv~eLa~~l~VS~~TIRRDL~~L 55 (269)
T PRK09802 16 SERREQIIQRLRQQGSVQVNDLSALYGVSTVTIRNDLAFL 55 (269)
T ss_pred HHHHHHHHHHHHHcCCEeHHHHHHHHCCCHHHHHHHHHHH
Confidence 3444444433332 37889999999999999999 8875
No 370
>PRK12302 bssR biofilm formation regulatory protein BssR; Reviewed
Probab=25.25 E-value=72 Score=21.43 Aligned_cols=30 Identities=17% Similarity=0.070 Sum_probs=22.4
Q ss_pred hHHHHHHHHHHhhCcCCcCCCccchhHHHHH
Q 046847 3 RKTFGLLFELLCSDERLKTDSVVFVDEQVCM 33 (88)
Q Consensus 3 ~~~F~~L~~~L~~~~~L~~t~~v~veE~la~ 33 (88)
|+-|+.||.+++.+.. .-..++.-||..|.
T Consensus 43 RdN~FeL~re~~~~s~-~l~~h~d~eE~~aL 72 (127)
T PRK12302 43 RDNFFELNRELHDKSL-RLNLHLDQEEWSAL 72 (127)
T ss_pred HHHHHHHHHHHHHhhH-HHhccCCHHHHHHH
Confidence 6789999999998753 44466777777654
No 371
>PF03965 Penicillinase_R: Penicillinase repressor; InterPro: IPR005650 Proteins in this entry are transcriptional regulators found in a variety of bacteria and a small number of archaea. Many are BlaI/MecI proteins which regulate resistance to penicillins (beta-lactams), though at least one protein (Q47839 from SWISSPROT) appears to be involved in the regulation of copper homeostasis []. BlaI regulators repress the expression of penicillin-degrading enzymes (penicillinases) until the cell encounters the antiobiotic, at which point repression ceases and penicillinase expression occurs, allowing cell growth []. MecI regulators repress the expression of MecA, a cell-wall biosynthetic enzyme not inhibited by penicillins at clinically achievable concentrations, until the presence of the antibiotic is detected []. At this point repression ends and MecA expression occurs which, together with the switching off of the penicillin-sensitive enzymes, allows the cell to grow despite the presence of antibiotic.; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2G9W_A 2K4B_A 1XSD_A 1SD4_A 1SD7_A 1SD6_A 2P7C_B 1P6R_A 1OKR_B 2D45_B ....
Probab=24.71 E-value=1.3e+02 Score=18.96 Aligned_cols=28 Identities=7% Similarity=0.109 Sum_probs=24.8
Q ss_pred chhHHHHHHHHHhccccchhhhhhhcccc
Q 046847 26 FVDEQVCMFLHALAHHVKNQTINNRFKHS 54 (88)
Q Consensus 26 ~veE~la~FL~i~~~n~~~r~i~~~F~~S 54 (88)
..|..|-=.||-.|. .+-++|.+.+...
T Consensus 3 ~~E~~IM~~lW~~~~-~t~~eI~~~l~~~ 30 (115)
T PF03965_consen 3 DLELEIMEILWESGE-ATVREIHEALPEE 30 (115)
T ss_dssp HHHHHHHHHHHHHSS-EEHHHHHHHHCTT
T ss_pred HHHHHHHHHHHhCCC-CCHHHHHHHHHhc
Confidence 468888999999999 9999999999877
No 372
>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.53 E-value=83 Score=20.80 Aligned_cols=32 Identities=13% Similarity=0.088 Sum_probs=26.6
Q ss_pred hccccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847 38 LAHHVKNQTINNRFKHSGETISR-FNSILNGVL 69 (88)
Q Consensus 38 ~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~ 69 (88)
..-..|...|++.|+.|...|+- ++.+...+.
T Consensus 30 y~dDlSl~EIAee~~VSRqAIyDnIKr~~~~L~ 62 (105)
T COG2739 30 YLDDLSLSEIAEEFNVSRQAIYDNIKRTEKILE 62 (105)
T ss_pred HHhhccHHHHHHHhCccHHHHHHHHHHHHHHHH
Confidence 34568999999999999999999 888766554
No 373
>PF01498 HTH_Tnp_Tc3_2: Transposase; InterPro: IPR002492 Transposase proteins are necessary for efficient DNA transposition. This family includes the amino-terminal region of Tc1, Tc1A, Tc1B and Tc2B transposases of Caenorhabditis elegans. The region encompasses the specific DNA binding and second DNA recognition domains as well as an amino-terminal region of the catalytic domain of Tc3 as described in []. Tc3 is a member of the Tc1/mariner family of transposable elements. This entry also includes histone-lysine N-methyltransferase SETMAR, which is a SET domain and mariner transposase fusion gene-containing protein. This histone methyltransferase has sequence-specific DNA-binding activity and recognises the 19-mer core of the 5'-terminal inverted repeats (TIRs) of the Hsmar1 element. This protein has DNA nicking activity, and has in vivo end joining activity and may mediate genomic integration of foreign DNA [, , , ]. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated, 0015074 DNA integration; PDB: 3K9K_B 3F2K_B 3K9J_B 1U78_A.
Probab=24.50 E-value=48 Score=19.07 Aligned_cols=22 Identities=23% Similarity=0.365 Sum_probs=10.4
Q ss_pred cchhhhhhhc-----ccccchhHh-HHH
Q 046847 42 VKNQTINNRF-----KHSGETISR-FNS 63 (88)
Q Consensus 42 ~~~r~i~~~F-----~~S~eTisr-f~~ 63 (88)
.+.++|+..+ ..|..||.| +++
T Consensus 14 ~s~~~i~~~l~~~~~~vS~~TI~r~L~~ 41 (72)
T PF01498_consen 14 ISAREIAQELQEAGISVSKSTIRRRLRE 41 (72)
T ss_dssp --HHHHHHHT---T--S-HHHHHHHHHH
T ss_pred CCHHHHHHHHHHccCCcCHHHHHHHHHH
Confidence 5566666665 455555555 443
No 374
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=24.45 E-value=1.3e+02 Score=19.59 Aligned_cols=39 Identities=3% Similarity=0.116 Sum_probs=26.9
Q ss_pred hhHHHHHHHHHhc--cccchhhhhhhcccccchhHh-HHHHH
Q 046847 27 VDEQVCMFLHALA--HHVKNQTINNRFKHSGETISR-FNSIL 65 (88)
Q Consensus 27 veE~la~FL~i~~--~n~~~r~i~~~F~~S~eTisr-f~~Vl 65 (88)
.|+-|..++.... ...+..+++..++.|..||++ .+..-
T Consensus 6 ~edyL~~I~~l~~~~~~~~~~ela~~l~vs~~svs~~l~~L~ 47 (142)
T PRK03902 6 MEDYIEQIYLLIEEKGYARVSDIAEALSVHPSSVTKMVQKLD 47 (142)
T ss_pred HHHHHHHHHHHHhcCCCcCHHHHHHHhCCChhHHHHHHHHHH
Confidence 3444555444443 335777899999999999999 77654
No 375
>PRK10341 DNA-binding transcriptional activator TdcA; Provisional
Probab=24.44 E-value=71 Score=23.14 Aligned_cols=40 Identities=10% Similarity=0.169 Sum_probs=30.6
Q ss_pred hHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHH
Q 046847 28 DEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGV 68 (88)
Q Consensus 28 eE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai 68 (88)
-++|-.|+ .++...+++.+++..+.|..|||+ .++.=+.+
T Consensus 9 ~~~L~~F~-av~e~gs~s~AA~~L~iSQpavS~~I~~LE~~l 49 (312)
T PRK10341 9 TQHLVVFQ-EVIRSGSIGSAAKELGLTQPAVSKIINDIEDYF 49 (312)
T ss_pred HHHHHHHH-HHHHcCCHHHHHHHhCCChHHHHHHHHHHHHHh
Confidence 34555555 455678999999999999999999 88864443
No 376
>PF04591 DUF596: Protein of unknown function, DUF596; InterPro: IPR007670 This family contains several uncharacterised proteins.; PDB: 2O5H_B.
Probab=24.38 E-value=47 Score=20.41 Aligned_cols=12 Identities=42% Similarity=0.310 Sum_probs=7.9
Q ss_pred ccchhHHHHHHH
Q 046847 24 VVFVDEQVCMFL 35 (88)
Q Consensus 24 ~v~veE~la~FL 35 (88)
.-|+||||.||=
T Consensus 16 ~Gt~eEqve~fr 27 (70)
T PF04591_consen 16 EGTTEEQVEMFR 27 (70)
T ss_dssp ---HHHHHHHHH
T ss_pred cCCHHHHHHHHH
Confidence 357999999984
No 377
>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=24.35 E-value=88 Score=20.35 Aligned_cols=68 Identities=13% Similarity=0.128 Sum_probs=38.3
Q ss_pred CChHHHHHHHHHHhhCcCCcCCCccchhHHHHHHHHHhccccchhhhhhhcccccchhHhHHH--HH-HHHHHhhhhhc
Q 046847 1 MDRKTFGLLFELLCSDERLKTDSVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISRFNS--IL-NGVLELQHILL 76 (88)
Q Consensus 1 M~~~~F~~L~~~L~~~~~L~~t~~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisrf~~--Vl-~ai~~L~~~~i 76 (88)
|+-+.|..|.+.......-+..+....+|+- |+ .-+.-++..|+-|.+|++|..+ ++ +||...+..+|
T Consensus 13 mTg~ell~L~~~~~~~~~~~~~~~~~~~~~~----yv----yG~~GlAklfgcSv~Ta~RiK~sG~id~AI~Q~Gr~Ii 83 (96)
T PF12964_consen 13 MTGEELLFLLKEGKTNSEKQTSQKAKKDEKK----YV----YGLKGLAKLFGCSVPTANRIKKSGKIDPAITQIGRKII 83 (96)
T ss_pred hhHHHHHHHHHHHhcCCCccCCccccCcccc----ee----ehHHHHHHHhCCCchhHHHHHhcCCccHHHHHcCCEEE
Confidence 4455666666666444433322222333322 11 3356789999999999999553 23 36665555443
No 378
>PF08858 IDEAL: IDEAL domain; InterPro: IPR014957 This entry represents the C-terminal domain of Bacteriophage SPP1, p90. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. his domain may also be referred to as the IDEAL domain, after the sequence of the most conserved region of the domain.; PDB: 3DO9_A.
Probab=24.19 E-value=72 Score=16.81 Aligned_cols=12 Identities=42% Similarity=0.315 Sum_probs=9.1
Q ss_pred ChHHHHHHHHHH
Q 046847 2 DRKTFGLLFELL 13 (88)
Q Consensus 2 ~~~~F~~L~~~L 13 (88)
+++.|..|++.|
T Consensus 26 D~e~F~~Ls~eL 37 (37)
T PF08858_consen 26 DKEWFYELSEEL 37 (37)
T ss_dssp -HHHHHHHHHHH
T ss_pred CHHHHHHHHhhC
Confidence 478899998875
No 379
>KOG1062 consensus Vesicle coat complex AP-1, gamma subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=24.10 E-value=1.2e+02 Score=26.80 Aligned_cols=47 Identities=13% Similarity=0.150 Sum_probs=34.3
Q ss_pred ChHHHHHHHHHHhhCcCCcCCCccchhHHHH--HHHHHhccccchhhhh
Q 046847 2 DRKTFGLLFELLCSDERLKTDSVVFVDEQVC--MFLHALAHHVKNQTIN 48 (88)
Q Consensus 2 ~~~~F~~L~~~L~~~~~L~~t~~v~veE~la--~FL~i~~~n~~~r~i~ 48 (88)
++.+-.+=|..+|....-.+.-...-.+++| ||++|+|+.+.+-+|.
T Consensus 26 Er~vI~kE~a~IRa~ire~~~d~~~r~rniaKLlYi~MLGypahFGqie 74 (866)
T KOG1062|consen 26 ERAVIQKECAAIRASIREPTNDPRKRHRNIAKLLYIHMLGYPAHFGQIE 74 (866)
T ss_pred HHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHhCCCccchhhH
Confidence 4567788899999886553454455556666 6777899999998874
No 380
>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=23.87 E-value=1.6e+02 Score=18.42 Aligned_cols=40 Identities=18% Similarity=0.220 Sum_probs=30.1
Q ss_pred chhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHH
Q 046847 26 FVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILN 66 (88)
Q Consensus 26 ~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ 66 (88)
..+|+..+.++.+ .+.+..+|++..+-|..|+.| =++-+.
T Consensus 57 d~~~r~iL~~~Yi-~~~~~~~I~~~l~~S~~t~yr~~~~Al~ 97 (100)
T PF07374_consen 57 DPDERLILRMRYI-NKLTWEQIAEELNISRRTYYRIHKKALK 97 (100)
T ss_pred ChhHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3566666666655 568889999999999999998 555444
No 381
>PRK06474 hypothetical protein; Provisional
Probab=23.75 E-value=1.1e+02 Score=21.29 Aligned_cols=38 Identities=5% Similarity=0.145 Sum_probs=25.5
Q ss_pred HHHHHHHHHhccc--cchhhhhhhc-ccccchhHh-HHHHHH
Q 046847 29 EQVCMFLHALAHH--VKNQTINNRF-KHSGETISR-FNSILN 66 (88)
Q Consensus 29 E~la~FL~i~~~n--~~~r~i~~~F-~~S~eTisr-f~~Vl~ 66 (88)
-++.|+-+..+++ .+-.++...+ +.|..||+| .+...+
T Consensus 12 ~R~~Il~~L~~~~~~~ta~el~~~l~~is~aTvYrhL~~L~e 53 (178)
T PRK06474 12 VRMKICQVLMRNKEGLTPLELVKILKDVPQATLYRHLQTMVD 53 (178)
T ss_pred HHHHHHHHHHhCCCCCCHHHHHHHhcCCCHHHHHHHHHHHHH
Confidence 3455555555544 6777777777 678899998 776654
No 382
>PHA01976 helix-turn-helix protein
Probab=23.54 E-value=57 Score=18.26 Aligned_cols=26 Identities=12% Similarity=-0.078 Sum_probs=19.9
Q ss_pred HhccccchhhhhhhcccccchhHh-HH
Q 046847 37 ALAHHVKNQTINNRFKHSGETISR-FN 62 (88)
Q Consensus 37 i~~~n~~~r~i~~~F~~S~eTisr-f~ 62 (88)
.-..+.+..+++..-+.|..||++ -+
T Consensus 11 R~~~glt~~~lA~~~gvs~~~v~~~e~ 37 (67)
T PHA01976 11 RNARAWSAPELSRRAGVRHSLIYDFEA 37 (67)
T ss_pred HHHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 455677788888888888888888 54
No 383
>COG2042 Uncharacterized conserved protein [Function unknown]
Probab=23.52 E-value=64 Score=23.23 Aligned_cols=32 Identities=13% Similarity=0.131 Sum_probs=28.0
Q ss_pred ccchhHHHHHHHHHhccccchhhhhhhccccc
Q 046847 24 VVFVDEQVCMFLHALAHHVKNQTINNRFKHSG 55 (88)
Q Consensus 24 ~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~ 55 (88)
..+.-|++|--|||+|--..-..+-..|..+.
T Consensus 114 kLss~EAlaAaLYI~G~~deA~~lls~F~WG~ 145 (179)
T COG2042 114 KLSSAEALAAALYIVGFKDEASELLSKFKWGH 145 (179)
T ss_pred hhchHHHHHHHHHHhCcHHHHHHHHhhCcccH
Confidence 37889999999999999999999998887653
No 384
>PF14223 UBN2: gag-polypeptide of LTR copia-type
Probab=23.35 E-value=1.8e+02 Score=18.11 Aligned_cols=58 Identities=12% Similarity=0.179 Sum_probs=37.6
Q ss_pred HHHHHHHHHhhCcCCcCCCccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847 5 TFGLLFELLCSDERLKTDSVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVL 69 (88)
Q Consensus 5 ~F~~L~~~L~~~~~L~~t~~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~ 69 (88)
-|..||+.|+..+. .++=++.+...|--+. .+|..+..-+..+...-.. |.++...+.
T Consensus 49 ~~~~i~~~L~~~g~-----~i~d~~~v~~iL~~Lp--~~y~~~~~~i~~~~~~~~~t~~el~~~L~ 107 (119)
T PF14223_consen 49 RLKEIVDELRAIGK-----PISDEDLVSKILRSLP--PSYDTFVTAIRNSKDLPKMTLEELISRLL 107 (119)
T ss_pred HHHHhhhhhhhcCC-----cccchhHHHHHHhcCC--chhHHHHHHHHhcCCCCcCCHHHHHHHHH
Confidence 35667777765533 4566666666665554 7888888877777665555 777766654
No 385
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=23.12 E-value=62 Score=15.84 Aligned_cols=23 Identities=17% Similarity=0.280 Sum_probs=17.1
Q ss_pred hccccchhhhhhhcccccchhHh
Q 046847 38 LAHHVKNQTINNRFKHSGETISR 60 (88)
Q Consensus 38 ~~~n~~~r~i~~~F~~S~eTisr 60 (88)
-..+.+.++++...+.|.+||++
T Consensus 7 ~~~~~s~~~la~~~~i~~~~i~~ 29 (56)
T smart00530 7 EEKGLTQEELAEKLGVSRSTLSR 29 (56)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHH
Confidence 34567777888888888888876
No 386
>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=22.86 E-value=48 Score=16.93 Aligned_cols=20 Identities=15% Similarity=0.182 Sum_probs=15.1
Q ss_pred chhhhhhhcccccchhHh-HH
Q 046847 43 KNQTINNRFKHSGETISR-FN 62 (88)
Q Consensus 43 ~~r~i~~~F~~S~eTisr-f~ 62 (88)
+..+++..++.|..||.+ .+
T Consensus 3 t~~e~a~~lgis~~ti~~~~~ 23 (49)
T TIGR01764 3 TVEEAAEYLGVSKDTVYRLIH 23 (49)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 456788888888888866 53
No 387
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=22.85 E-value=98 Score=18.22 Aligned_cols=32 Identities=13% Similarity=0.129 Sum_probs=24.2
Q ss_pred HHHHHHHHHhccccchhhhhhhcccccchhHh
Q 046847 29 EQVCMFLHALAHHVKNQTINNRFKHSGETISR 60 (88)
Q Consensus 29 E~la~FL~i~~~n~~~r~i~~~F~~S~eTisr 60 (88)
|++-=||-....+.+.++|++.++-|..|+.+
T Consensus 3 e~Il~~i~~~~~p~~T~eiA~~~gls~~~aR~ 34 (62)
T PF04703_consen 3 EKILEYIKEQNGPLKTREIADALGLSIYQARY 34 (62)
T ss_dssp HCHHHHHHHHTS-EEHHHHHHHHTS-HHHHHH
T ss_pred HHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHH
Confidence 44555666667889999999999999999866
No 388
>KOG0854 consensus Alkyl hydroperoxide reductase, thiol specific antioxidant and related enzymes [Posttranslational modification, protein turnover, chaperones]
Probab=22.80 E-value=54 Score=24.11 Aligned_cols=17 Identities=35% Similarity=0.458 Sum_probs=14.6
Q ss_pred cchhHh-HHHHHHHHHHh
Q 046847 55 GETISR-FNSILNGVLEL 71 (88)
Q Consensus 55 ~eTisr-f~~Vl~ai~~L 71 (88)
..|+.| |.|||++|-+|
T Consensus 150 P~ttGRN~dEiLRvidsL 167 (224)
T KOG0854|consen 150 PSTTGRNFDEILRVIDSL 167 (224)
T ss_pred ccccCcCHHHHHHHHHHH
Confidence 468999 99999999874
No 389
>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=22.75 E-value=70 Score=24.79 Aligned_cols=38 Identities=18% Similarity=0.217 Sum_probs=27.0
Q ss_pred HHHHhccccchhhhhhh----cc---cccchhHh-HHHHHHHHHHh
Q 046847 34 FLHALAHHVKNQTINNR----FK---HSGETISR-FNSILNGVLEL 71 (88)
Q Consensus 34 FL~i~~~n~~~r~i~~~----F~---~S~eTisr-f~~Vl~ai~~L 71 (88)
.+.+.+++.|.|+|+.- ++ .|.+|||| .+++...+-.+
T Consensus 107 i~~ly~~G~Str~i~~~l~~l~g~~~~S~s~vSri~~~~~~~~~~w 152 (381)
T PF00872_consen 107 IISLYLKGVSTRDIEEALEELYGEVAVSKSTVSRITKQLDEEVEAW 152 (381)
T ss_pred hhhhhccccccccccchhhhhhcccccCchhhhhhhhhhhhhHHHH
Confidence 34445677787777654 34 79999999 88887776644
No 390
>TIGR01529 argR_whole arginine repressor. This model includes most members of the arginine-responsive transcriptional regulator family ArgR. This hexameric protein binds DNA at its amino end to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbor-joining tree, some of these paralogous sequences show long branches and differ significantly in an otherwise well-conserved C-terminal region motif GT[VIL][AC]GDDT. These paralogs are excluded from the seed and score in the gray zone of this model, between trusted and noise cutoffs.
Probab=22.62 E-value=37 Score=23.04 Aligned_cols=16 Identities=19% Similarity=0.385 Sum_probs=12.5
Q ss_pred hhcccccchhHh-HHHH
Q 046847 49 NRFKHSGETISR-FNSI 64 (88)
Q Consensus 49 ~~F~~S~eTisr-f~~V 64 (88)
.-|..|..|||| +++.
T Consensus 29 ~G~~vsqaTIsRdL~el 45 (146)
T TIGR01529 29 EGIEVTQATVSRDLREL 45 (146)
T ss_pred hCCCcCHHHHHHHHHHc
Confidence 346688899999 8873
No 391
>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function.
Probab=22.61 E-value=2e+02 Score=18.84 Aligned_cols=44 Identities=23% Similarity=0.206 Sum_probs=36.0
Q ss_pred CCccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHH
Q 046847 22 DSVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILN 66 (88)
Q Consensus 22 t~~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ 66 (88)
+-.+++||-=||=|-- -.+.++...+.+-+.|..|++| .+..-+
T Consensus 39 ~V~L~~dElEAiRL~D-~egl~QeeaA~~MgVSR~T~~ril~~ARk 83 (106)
T PF02001_consen 39 PVVLTVDELEAIRLVD-YEGLSQEEAAERMGVSRPTFQRILESARK 83 (106)
T ss_pred eEEeeHHHHHHHHHHH-HcCCCHHHHHHHcCCcHHHHHHHHHHHHH
Confidence 4678999988887744 4569999999999999999999 876444
No 392
>PRK03635 chromosome replication initiation inhibitor protein; Validated
Probab=22.57 E-value=81 Score=22.59 Aligned_cols=38 Identities=11% Similarity=0.170 Sum_probs=28.6
Q ss_pred HHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHH
Q 046847 30 QVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGV 68 (88)
Q Consensus 30 ~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai 68 (88)
++-.|+ .++...+++.++++.+-|..|||| .++.=+-+
T Consensus 6 ~L~~f~-~v~e~gs~s~AA~~L~isq~avS~~I~~LE~~l 44 (294)
T PRK03635 6 QLEALA-AVVREGSFERAAQKLHITQSAVSQRIKALEERV 44 (294)
T ss_pred HHHHHH-HHHHcCCHHHHHHHhCCChHHHHHHHHHHHHHh
Confidence 344444 455567999999999999999999 88764433
No 393
>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=22.46 E-value=1.6e+02 Score=17.20 Aligned_cols=24 Identities=13% Similarity=0.063 Sum_probs=16.4
Q ss_pred Hhccccchhhhhhhcccc-cchhHh
Q 046847 37 ALAHHVKNQTINNRFKHS-GETISR 60 (88)
Q Consensus 37 i~~~n~~~r~i~~~F~~S-~eTisr 60 (88)
.-|..-+.|.|++.|+-+ ..||++
T Consensus 21 ~~G~~Pt~rEIa~~~g~~S~~tv~~ 45 (65)
T PF01726_consen 21 ENGYPPTVREIAEALGLKSTSTVQR 45 (65)
T ss_dssp HHSS---HHHHHHHHTSSSHHHHHH
T ss_pred HcCCCCCHHHHHHHhCCCChHHHHH
Confidence 345667899999999965 777765
No 394
>PRK09393 ftrA transcriptional activator FtrA; Provisional
Probab=22.29 E-value=1.1e+02 Score=22.52 Aligned_cols=27 Identities=26% Similarity=0.262 Sum_probs=23.7
Q ss_pred hccccchhhhhhhcccccchhHh-HHHH
Q 046847 38 LAHHVKNQTINNRFKHSGETISR-FNSI 64 (88)
Q Consensus 38 ~~~n~~~r~i~~~F~~S~eTisr-f~~V 64 (88)
...+.+-.+++..++-|..+++| |++.
T Consensus 231 ~~~~~sl~~lA~~~~~S~~~l~r~fk~~ 258 (322)
T PRK09393 231 LAEPHTVASLAARAAMSPRTFLRRFEAA 258 (322)
T ss_pred cCCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 45567889999999999999999 9986
No 395
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=22.08 E-value=49 Score=18.32 Aligned_cols=26 Identities=19% Similarity=0.299 Sum_probs=14.4
Q ss_pred hccccchhhhhhhcccccchhHh-HHH
Q 046847 38 LAHHVKNQTINNRFKHSGETISR-FNS 63 (88)
Q Consensus 38 ~~~n~~~r~i~~~F~~S~eTisr-f~~ 63 (88)
--++.+...++..=|.|..|+++ ++.
T Consensus 7 ~~~~it~~~La~~~gis~~tl~~~~~~ 33 (63)
T PF13443_consen 7 AERGITQKDLARKTGISRSTLSRILNG 33 (63)
T ss_dssp HHTT--HHHHHHHHT--HHHHHHHHTT
T ss_pred HHcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 34556666777777777777777 654
No 396
>PF15467 SGIII: Secretogranin-3
Probab=22.05 E-value=1.1e+02 Score=24.76 Aligned_cols=47 Identities=17% Similarity=0.251 Sum_probs=39.5
Q ss_pred ChHHHHHHHHHHhhCcCCcCCCccchhHHHHHHHHH-hccccchhhhh
Q 046847 2 DRKTFGLLFELLCSDERLKTDSVVFVDEQVCMFLHA-LAHHVKNQTIN 48 (88)
Q Consensus 2 ~~~~F~~L~~~L~~~~~L~~t~~v~veE~la~FL~i-~~~n~~~r~i~ 48 (88)
+|.+|.++...|-.-+.+.++..-++|.+||=-|-- ++.++.++.+.
T Consensus 149 DRGVFDkIVSKLLnLGLITeSQA~TLEdeVAEaLQ~LIskeAkn~E~e 196 (453)
T PF15467_consen 149 DRGVFDKIVSKLLNLGLITESQAYTLEDEVAEALQKLISKEAKNNEEE 196 (453)
T ss_pred cchHHHHHHHHHHhccccchhhhhHHHHHHHHHHHHHHHhhhccchhh
Confidence 478999999999999999999999999999988864 45556666655
No 397
>PRK09461 ansA cytoplasmic asparaginase I; Provisional
Probab=21.99 E-value=87 Score=24.01 Aligned_cols=37 Identities=8% Similarity=0.188 Sum_probs=32.4
Q ss_pred CCcCCCccchhHHHHHHHHHhccccchhhhhhhcccc
Q 046847 18 RLKTDSVVFVDEQVCMFLHALAHHVKNQTINNRFKHS 54 (88)
Q Consensus 18 ~L~~t~~v~veE~la~FL~i~~~n~~~r~i~~~F~~S 54 (88)
|.-+...++.|...+.-+|.++++.+...++..|.++
T Consensus 293 G~i~~g~lt~ekAr~kL~~~L~~~~~~~~i~~~f~~~ 329 (335)
T PRK09461 293 GVISGADMTVEAALTKLHYLLSQELSTEEIRQAMQQN 329 (335)
T ss_pred CEEECCCCCHHHHHHHHHHHHhCCCCHHHHHHHHhhc
Confidence 4566788999999999999999999999999999863
No 398
>COG1740 HyaA Ni,Fe-hydrogenase I small subunit [Energy production and conversion]
Probab=21.81 E-value=92 Score=24.69 Aligned_cols=29 Identities=17% Similarity=0.181 Sum_probs=23.4
Q ss_pred CChHHHHHHHHHHhhCcCCcCCCccchhH
Q 046847 1 MDRKTFGLLFELLCSDERLKTDSVVFVDE 29 (88)
Q Consensus 1 M~~~~F~~L~~~L~~~~~L~~t~~v~veE 29 (88)
|+|+.|.++|..|....+|..+-.-.+.+
T Consensus 13 ~~Rr~f~k~~~~~~a~l~L~~~~~~~~~~ 41 (355)
T COG1740 13 ITRRDFLKLCGALAASLGLSASYAPEIAK 41 (355)
T ss_pred CcHHHHHHHHHHHHHHhccCccchHHHHH
Confidence 68999999999999999998874444433
No 399
>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=21.77 E-value=83 Score=20.08 Aligned_cols=27 Identities=11% Similarity=0.240 Sum_probs=21.7
Q ss_pred HHHHHhccccchhhhhhhcccccchhH
Q 046847 33 MFLHALAHHVKNQTINNRFKHSGETIS 59 (88)
Q Consensus 33 ~FL~i~~~n~~~r~i~~~F~~S~eTis 59 (88)
+|...--++.+++.|+...|-|..||.
T Consensus 115 v~~l~~~~~~s~~EIA~~l~is~~tV~ 141 (142)
T TIGR03209 115 IIYMKFFEDMKEIDIAKKLHISRQSVY 141 (142)
T ss_pred HHHHHHHcCCCHHHHHHHHCcCHHhhc
Confidence 344455678999999999999999985
No 400
>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=21.67 E-value=60 Score=22.69 Aligned_cols=43 Identities=12% Similarity=0.267 Sum_probs=27.5
Q ss_pred HHHHHHHHhh---CcCCcCCCccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHH
Q 046847 6 FGLLFELLCS---DERLKTDSVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSI 64 (88)
Q Consensus 6 F~~L~~~L~~---~~~L~~t~~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~V 64 (88)
+..+.+.|+. .+.++....++.|. .++.+|+.|.-||.+ +.+.
T Consensus 10 y~~i~~~l~~~I~~g~~~~G~~LPsE~----------------eLa~~~~VSR~TvR~Al~~L 56 (238)
T TIGR02325 10 WRQIADKIEQEIAAGHLRAGDYLPAEM----------------QLAERFGVNRHTVRRAIAAL 56 (238)
T ss_pred HHHHHHHHHHHHHcCCCCCCCcCcCHH----------------HHHHHHCCCHHHHHHHHHHH
Confidence 3445555554 23445555566665 456899999999977 6654
No 401
>PRK09191 two-component response regulator; Provisional
Probab=21.65 E-value=1.7e+02 Score=20.21 Aligned_cols=38 Identities=5% Similarity=-0.004 Sum_probs=29.9
Q ss_pred HHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHHH
Q 046847 32 CMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGVL 69 (88)
Q Consensus 32 a~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~ 69 (88)
.+|+-..=.+.++..|+...+.|..||.. .+.-++.+-
T Consensus 95 ~v~~l~~~~~~s~~eIA~~l~~s~~tV~~~l~ra~~~l~ 133 (261)
T PRK09191 95 QAFLLTALEGFSVEEAAEILGVDPAEAEALLDDARAEIA 133 (261)
T ss_pred HHHHHHHHhcCCHHHHHHHHCCCHHHHHHHHHHHHHHHh
Confidence 34555556789999999999999999998 877665554
No 402
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=21.54 E-value=1.7e+02 Score=22.23 Aligned_cols=32 Identities=9% Similarity=0.077 Sum_probs=28.0
Q ss_pred ccccchhhhhhhcccccchhHh-HHHHHHHHHH
Q 046847 39 AHHVKNQTINNRFKHSGETISR-FNSILNGVLE 70 (88)
Q Consensus 39 ~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai~~ 70 (88)
..+.++..|+...+.|.+||.. .++-++.+-.
T Consensus 280 ~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~ 312 (325)
T PRK05657 280 YEAATLEDVAREIGLTRERVRQIQVEALRRLRE 312 (325)
T ss_pred CCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 4679999999999999999999 8888777654
No 403
>PRK10216 DNA-binding transcriptional regulator YidZ; Provisional
Probab=21.39 E-value=83 Score=22.87 Aligned_cols=39 Identities=8% Similarity=0.086 Sum_probs=29.7
Q ss_pred HHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHH
Q 046847 29 EQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGV 68 (88)
Q Consensus 29 E~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai 68 (88)
++|-.|+- ++...+.+.+++..+.|.++||+ ..+.=+.+
T Consensus 11 ~~L~~f~a-v~e~gs~t~AA~~L~iSQpavS~~I~~LE~~l 50 (319)
T PRK10216 11 NLLLCLQL-LMQERSVTKAAKRMNVTPSAVSKSLAKLRAWF 50 (319)
T ss_pred HHHHHHHH-HHHhCCHHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence 45556654 45556999999999999999999 98854433
No 404
>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=21.37 E-value=65 Score=19.13 Aligned_cols=38 Identities=11% Similarity=0.129 Sum_probs=25.3
Q ss_pred chhHHHHHHHHH---hccccchhhhhhhcccccchhHh-HHH
Q 046847 26 FVDEQVCMFLHA---LAHHVKNQTINNRFKHSGETISR-FNS 63 (88)
Q Consensus 26 ~veE~la~FL~i---~~~n~~~r~i~~~F~~S~eTisr-f~~ 63 (88)
..|.++|=|+.- -..+.+-+.++..-+.|..||.| .++
T Consensus 16 ~~e~~Ia~yil~~~~~~~~~si~elA~~~~vS~sti~Rf~kk 57 (77)
T PF01418_consen 16 PTEKKIADYILENPDEIAFMSISELAEKAGVSPSTIVRFCKK 57 (77)
T ss_dssp HHHHHHHHHHHH-HHHHCT--HHHHHHHCTS-HHHHHHHHHH
T ss_pred HHHHHHHHHHHhCHHHHHHccHHHHHHHcCCCHHHHHHHHHH
Confidence 446666655532 22358889999999999999999 655
No 405
>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=21.24 E-value=63 Score=20.38 Aligned_cols=27 Identities=7% Similarity=-0.054 Sum_probs=22.8
Q ss_pred HHhccccchhhhhhhcccccchhHh-HH
Q 046847 36 HALAHHVKNQTINNRFKHSGETISR-FN 62 (88)
Q Consensus 36 ~i~~~n~~~r~i~~~F~~S~eTisr-f~ 62 (88)
++-..+.+.+.++..++-|..||++ -+
T Consensus 73 ~r~~~gltq~~lA~~lg~~~~tis~~e~ 100 (127)
T TIGR03830 73 IRKKLGLSQREAAELLGGGVNAFSRYER 100 (127)
T ss_pred HHHHcCCCHHHHHHHhCCCHHHHHHHHC
Confidence 3566788999999999999999998 44
No 406
>PRK14997 LysR family transcriptional regulator; Provisional
Probab=20.90 E-value=87 Score=22.34 Aligned_cols=38 Identities=8% Similarity=0.162 Sum_probs=28.9
Q ss_pred HHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHHHH
Q 046847 30 QVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILNGV 68 (88)
Q Consensus 30 ~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ai 68 (88)
+|-+|+ .++...++..++..-+.|..|||+ .++.=+.+
T Consensus 6 ~L~~f~-~va~~gs~s~AA~~L~isQpavS~~I~~LE~~l 44 (301)
T PRK14997 6 DFAWFV-HVVEEGGFAAAGRALDEPKSKLSRRIAQLEERL 44 (301)
T ss_pred HHHHHH-HHHHcCCHHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence 455555 455568999999999999999999 98854333
No 407
>PF06817 RVT_thumb: Reverse transcriptase thumb domain; InterPro: IPR010661 This domain is known as the thumb domain. It is composed of a four helix bundle []. Reverse transcriptase converts the viral RNA genome into double-stranded viral DNA. Reverse transcriptase often occurs in a polyprotein; with integrase, ribonuclease H and/or protease, which is cleaved before the enzyme takes action. The impact of antiretroviral treatment on the first 400 amino acids of HIV reverse transcriptase is good. Little is known, however, of the antiretroviral drug impact on the C-terminal domains of Pol, which includes the thumb, connection and RNase H []. Evidence suggests that these might be well conserved domains.; GO: 0003964 RNA-directed DNA polymerase activity, 0006278 RNA-dependent DNA replication; PDB: 2JLE_A 2WOM_B 1DTQ_A 2OPS_A 3FFI_A 1VRU_B 1FK9_B 3DM2_B 1JLQ_B 3LAM_A ....
Probab=20.89 E-value=84 Score=19.13 Aligned_cols=27 Identities=19% Similarity=0.235 Sum_probs=21.9
Q ss_pred HHHHHHHhhCcCCcCCCccchhHHHHH
Q 046847 7 GLLFELLCSDERLKTDSVVFVDEQVCM 33 (88)
Q Consensus 7 ~~L~~~L~~~~~L~~t~~v~veE~la~ 33 (88)
..||+.||....|.+.+.++-|-..+.
T Consensus 40 k~L~kllrG~~~l~~~~~lT~eA~~eL 66 (70)
T PF06817_consen 40 KQLCKLLRGDKALTSPVELTEEAELEL 66 (70)
T ss_dssp HHHHHCTTSSSSTTSBESTTHHHHHHH
T ss_pred hHHHHHhcCCCCccceecCCHHHHHHH
Confidence 369999999999999988887766554
No 408
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=20.73 E-value=63 Score=23.16 Aligned_cols=44 Identities=11% Similarity=0.237 Sum_probs=28.0
Q ss_pred HHHHHHHHhh---CcCCcCCCccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHH
Q 046847 6 FGLLFELLCS---DERLKTDSVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSIL 65 (88)
Q Consensus 6 F~~L~~~L~~---~~~L~~t~~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl 65 (88)
+.++.+.|+. .+.++....++.|- .++..|+.|..||.+ ..+.-
T Consensus 9 Y~qI~~~i~~~I~~G~~~~G~~LPsE~----------------eLa~~f~VSR~TvRkAL~~L~ 56 (236)
T COG2188 9 YQQIAEDIRQRIESGELPPGDKLPSER----------------ELAEQFGVSRMTVRKALDELV 56 (236)
T ss_pred HHHHHHHHHHHHHhCCCCCCCCCCCHH----------------HHHHHHCCcHHHHHHHHHHHH
Confidence 3344444443 34455565566665 557899999999987 66543
No 409
>KOG4075 consensus Cytochrome c oxidase, subunit IV/COX5b [Energy production and conversion]
Probab=20.67 E-value=3.2e+02 Score=19.44 Aligned_cols=69 Identities=13% Similarity=0.205 Sum_probs=40.0
Q ss_pred HHHHhhCcCCcCCCccchhHHHHHHHHHhcc-ccchhhhhhhcccccchhH--h--HHHHHHHHHHhhhhhccCCCCCC
Q 046847 10 FELLCSDERLKTDSVVFVDEQVCMFLHALAH-HVKNQTINNRFKHSGETIS--R--FNSILNGVLELQHILLKSPKPMP 83 (88)
Q Consensus 10 ~~~L~~~~~L~~t~~v~veE~la~FL~i~~~-n~~~r~i~~~F~~S~eTis--r--f~~Vl~ai~~L~~~~ik~p~~~~ 83 (88)
.+-|+++- ..|-+..|.||+.|..=+-.+. -+..+...+.. .||. . |--..-.+.-+...++-+|.|.+
T Consensus 58 ~~aL~eKe-k~~Wk~LS~~EKkalYrisF~et~ae~~~~~~ew----Ktv~g~~~~f~Gl~~~v~l~~~v~vy~~~P~T 131 (167)
T KOG4075|consen 58 IKALREKE-KAPWKQLSTEEKKALYRISFGETFAERNRGSNEW----KTVFGVAGFFLGLTISVILFGKVRVYGPLPKT 131 (167)
T ss_pred HHHHHHHh-cCChhhcCHHHHHHHHHHHhccccccccCCCCcc----cchhhHHHHHHHHHHHHHHHHhheecCCCCcc
Confidence 34466663 4667899999999865543333 12222222222 3444 2 44445555567788888888765
No 410
>PRK15243 transcriptional regulator SpvR; Provisional
Probab=20.65 E-value=1.3e+02 Score=22.40 Aligned_cols=39 Identities=8% Similarity=0.197 Sum_probs=30.1
Q ss_pred hhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHH
Q 046847 27 VDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILN 66 (88)
Q Consensus 27 veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ 66 (88)
+..+|-.|+-+.- ..|++.++.+-+-|++|||+ +++.=+
T Consensus 5 ~~rqL~~F~aVae-~gSfs~AA~~L~isQpavS~~Ik~LE~ 44 (297)
T PRK15243 5 INKKLKIFITLME-TGSFSIATSVLYITRTPLSRVISDLER 44 (297)
T ss_pred cHHHHHHHHHHHH-cCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 3456766665544 46899999999999999999 887543
No 411
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=20.41 E-value=76 Score=22.51 Aligned_cols=44 Identities=9% Similarity=0.266 Sum_probs=28.8
Q ss_pred HHHHHHHHhhCc--CCcCCCccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHH
Q 046847 6 FGLLFELLCSDE--RLKTDSVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSIL 65 (88)
Q Consensus 6 F~~L~~~L~~~~--~L~~t~~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl 65 (88)
+..+.+.|+.+. .+++...++.|. .++..|+.|.-||.+ +.+.-
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 556666666532 344444566554 567899999999988 76654
No 412
>PRK10082 cell density-dependent motility repressor; Provisional
Probab=20.31 E-value=1e+02 Score=22.16 Aligned_cols=36 Identities=17% Similarity=0.102 Sum_probs=28.0
Q ss_pred HHHHHHHHhccccchhhhhhhcccccchhHh-HHHHHH
Q 046847 30 QVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSILN 66 (88)
Q Consensus 30 ~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl~ 66 (88)
++-.|+ .++...++..++.+.+.|..|||+ .++.=+
T Consensus 15 ~l~~F~-av~e~gS~t~AA~~L~iSQpavS~~I~~LE~ 51 (303)
T PRK10082 15 WLYDFL-TLEKCRNFSQAAVSRNVSQPAFSRRIRALEQ 51 (303)
T ss_pred HHHHHH-HHHhcCCHHHHHHHhCCChHHHHHHHHHHHH
Confidence 454555 455568999999999999999999 887533
No 413
>TIGR02018 his_ut_repres histidine utilization repressor, proteobacterial. This model represents a proteobacterial histidine utilization repressor. It is usually found clustered with the enzymes HutUHIG so that it can regulate its own expression as well. A number of species have several paralogs and may fine-tune the regulation according to levels of degradation intermediates such as urocanate. This family belongs to the larger GntR family of transcriptional regulators.
Probab=20.28 E-value=77 Score=22.26 Aligned_cols=43 Identities=7% Similarity=0.105 Sum_probs=28.0
Q ss_pred HHHHHHHhh---CcCCcCCCccchhHHHHHHHHHhccccchhhhhhhcccccchhHh-HHHHH
Q 046847 7 GLLFELLCS---DERLKTDSVVFVDEQVCMFLHALAHHVKNQTINNRFKHSGETISR-FNSIL 65 (88)
Q Consensus 7 ~~L~~~L~~---~~~L~~t~~v~veE~la~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl 65 (88)
..+.+.|+. .+.+++...++.|..| +..|+.|..||.+ +...-
T Consensus 4 ~qi~~~l~~~I~~g~~~~g~~LPsE~eL----------------a~~~~VSR~TVR~Al~~L~ 50 (230)
T TIGR02018 4 QRIKQDILERIRSGEWPPGHRIPSEHEL----------------VAQYGCSRMTVNRALRELT 50 (230)
T ss_pred HHHHHHHHHHHHhCCCCCCCcCcCHHHH----------------HHHHCCCHHHHHHHHHHHH
Confidence 344455544 2345666667777655 5899999999977 66543
No 414
>PRK10130 transcriptional regulator EutR; Provisional
Probab=20.01 E-value=1.5e+02 Score=22.84 Aligned_cols=34 Identities=24% Similarity=0.349 Sum_probs=27.0
Q ss_pred HHHHHHhccccchhhhhhhcccccchhHh-HHHHH
Q 046847 32 CMFLHALAHHVKNQTINNRFKHSGETISR-FNSIL 65 (88)
Q Consensus 32 a~FL~i~~~n~~~r~i~~~F~~S~eTisr-f~~Vl 65 (88)
..-.-..+...+..+++..++.|..|+++ |++++
T Consensus 247 ~~i~~~~~~~ltv~~lA~~~gvS~r~L~r~Fk~~~ 281 (350)
T PRK10130 247 EYVLENMSEPVTVLDLCNQLHVSRRTLQNAFHAIL 281 (350)
T ss_pred HHHHhhhcCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 33334456678999999999999999999 99974
Done!