Query 036324
Match_columns 91
No_of_seqs 103 out of 223
Neff 6.0
Searched_HMMs 46136
Date Fri Mar 29 11:30:55 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/036324.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/036324hhsearch_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 98.9 2.8E-09 6.1E-14 62.0 5.1 47 44-90 2-48 (53)
2 PF13936 HTH_38: Helix-turn-he 97.3 0.00034 7.3E-09 39.1 3.0 40 43-83 3-42 (44)
3 PF12116 SpoIIID: Stage III sp 96.5 0.0033 7.2E-08 40.0 3.2 39 50-88 8-46 (82)
4 TIGR03697 NtcA_cyano global ni 96.4 0.014 3E-07 39.9 5.9 77 4-86 78-168 (193)
5 COG3415 Transposase and inacti 96.3 0.0064 1.4E-07 42.0 4.1 42 43-84 3-44 (138)
6 PRK10402 DNA-binding transcrip 96.3 0.022 4.8E-07 40.6 7.0 78 4-87 114-195 (226)
7 PF04545 Sigma70_r4: Sigma-70, 96.2 0.02 4.4E-07 32.0 5.2 45 44-89 4-48 (50)
8 smart00421 HTH_LUXR helix_turn 96.1 0.021 4.5E-07 31.4 4.7 43 45-89 4-46 (58)
9 PF02796 HTH_7: Helix-turn-hel 95.9 0.0087 1.9E-07 33.3 2.7 27 57-83 17-43 (45)
10 cd06571 Bac_DnaA_C C-terminal 95.9 0.027 5.9E-07 35.5 5.2 47 43-89 26-73 (90)
11 PRK11753 DNA-binding transcrip 95.9 0.042 9.2E-07 38.0 6.5 78 4-87 104-194 (211)
12 PRK11161 fumarate/nitrate redu 95.8 0.042 9.1E-07 38.9 6.3 77 3-85 118-208 (235)
13 PRK09391 fixK transcriptional 95.7 0.057 1.2E-06 38.7 6.9 77 3-85 117-203 (230)
14 PF04218 CENP-B_N: CENP-B N-te 95.5 0.026 5.7E-07 32.6 3.6 40 43-83 5-44 (53)
15 PF08299 Bac_DnaA_C: Bacterial 95.4 0.033 7.2E-07 33.8 3.9 43 43-85 27-70 (70)
16 PRK09392 ftrB transcriptional 95.3 0.088 1.9E-06 37.4 6.6 76 4-85 112-197 (236)
17 cd06170 LuxR_C_like C-terminal 95.3 0.062 1.3E-06 29.6 4.6 36 53-89 8-43 (57)
18 smart00351 PAX Paired Box doma 95.1 0.055 1.2E-06 36.1 4.9 44 41-85 14-57 (125)
19 cd00131 PAX Paired Box domain 95.1 0.06 1.3E-06 36.2 4.8 46 40-86 13-58 (128)
20 PRK06030 hypothetical protein; 94.8 0.085 1.8E-06 35.8 5.1 45 43-87 51-95 (124)
21 PF13384 HTH_23: Homeodomain-l 94.7 0.03 6.6E-07 31.0 2.3 30 56-85 12-41 (50)
22 TIGR02531 yecD_yerC TrpR-relat 94.5 0.1 2.3E-06 33.3 4.7 36 47-83 37-72 (88)
23 PRK04217 hypothetical protein; 94.4 0.12 2.7E-06 34.3 5.0 47 42-89 40-86 (110)
24 PF05225 HTH_psq: helix-turn-h 94.1 0.11 2.4E-06 29.1 3.7 36 48-83 2-38 (45)
25 PRK13918 CRP/FNR family transc 94.1 0.18 3.9E-06 34.7 5.5 44 44-87 118-175 (202)
26 PF01022 HTH_5: Bacterial regu 93.5 0.19 4.1E-06 27.9 3.9 39 50-88 4-42 (47)
27 PF13518 HTH_28: Helix-turn-he 93.3 0.2 4.4E-06 27.5 3.9 35 51-86 3-37 (52)
28 cd00092 HTH_CRP helix_turn_hel 93.3 0.15 3.3E-06 29.2 3.5 27 61-87 25-51 (67)
29 PF13730 HTH_36: Helix-turn-he 92.8 0.23 4.9E-06 27.9 3.6 24 63-86 27-50 (55)
30 KOG4585 Predicted transposase 92.7 0.15 3.3E-06 39.5 3.7 61 18-78 7-72 (326)
31 PF13542 HTH_Tnp_ISL3: Helix-t 92.7 0.25 5.5E-06 27.4 3.7 28 58-85 24-51 (52)
32 PF12840 HTH_20: Helix-turn-he 92.6 0.27 5.9E-06 28.5 3.9 41 48-88 10-51 (61)
33 cd06171 Sigma70_r4 Sigma70, re 92.5 0.42 9.2E-06 25.3 4.4 30 59-88 24-53 (55)
34 TIGR01321 TrpR trp operon repr 92.5 0.19 4.1E-06 32.7 3.4 38 46-83 40-77 (94)
35 PF13412 HTH_24: Winged helix- 92.3 0.42 9.2E-06 26.2 4.3 36 52-87 7-43 (48)
36 PF00325 Crp: Bacterial regula 92.3 0.11 2.4E-06 27.5 1.8 24 62-85 3-26 (32)
37 cd00569 HTH_Hin_like Helix-tur 92.3 0.24 5.3E-06 23.6 3.0 35 46-81 7-41 (42)
38 PRK09639 RNA polymerase sigma 92.0 0.43 9.4E-06 31.8 4.9 44 44-89 112-155 (166)
39 PF00196 GerE: Bacterial regul 92.0 0.27 6E-06 28.1 3.4 35 55-89 12-46 (58)
40 PF13545 HTH_Crp_2: Crp-like h 91.9 0.28 6.1E-06 29.0 3.4 38 49-86 1-53 (76)
41 PRK00149 dnaA chromosomal repl 91.8 0.34 7.3E-06 38.3 4.7 46 43-88 384-430 (450)
42 PF13551 HTH_29: Winged helix- 91.5 2 4.3E-05 26.7 7.3 73 12-84 15-110 (112)
43 PF01371 Trp_repressor: Trp re 91.2 0.36 7.7E-06 30.9 3.6 37 47-83 35-71 (87)
44 PF08279 HTH_11: HTH domain; 91.2 0.6 1.3E-05 26.1 4.2 36 51-86 5-40 (55)
45 PF08281 Sigma70_r4_2: Sigma-7 91.0 0.9 2E-05 25.3 4.8 44 44-88 10-53 (54)
46 PRK14088 dnaA chromosomal repl 90.9 0.59 1.3E-05 37.2 5.3 48 42-89 368-415 (440)
47 PRK09413 IS2 repressor TnpA; R 90.6 0.89 1.9E-05 29.9 5.2 48 39-86 7-54 (121)
48 PRK14086 dnaA chromosomal repl 90.4 0.62 1.3E-05 39.2 5.2 48 42-89 550-597 (617)
49 TIGR02937 sigma70-ECF RNA poly 90.4 0.75 1.6E-05 29.1 4.6 45 44-89 110-154 (158)
50 PF13340 DUF4096: Putative tra 90.3 0.49 1.1E-05 28.7 3.5 62 24-86 4-65 (75)
51 PF00126 HTH_1: Bacterial regu 90.0 0.77 1.7E-05 26.5 4.0 39 49-88 2-40 (60)
52 PF01710 HTH_Tnp_IS630: Transp 89.7 2.6 5.7E-05 27.6 6.9 72 10-84 19-94 (119)
53 PRK00118 putative DNA-binding 89.4 1.1 2.4E-05 29.5 4.8 44 45-89 18-61 (104)
54 TIGR02985 Sig70_bacteroi1 RNA 89.4 1.2 2.6E-05 29.0 5.1 45 44-89 113-157 (161)
55 PF04967 HTH_10: HTH DNA bindi 89.0 0.72 1.6E-05 26.9 3.3 31 61-91 23-53 (53)
56 PRK15320 transcriptional activ 88.9 0.56 1.2E-05 35.0 3.5 35 55-89 173-207 (251)
57 PRK15411 rcsA colanic acid cap 88.5 0.75 1.6E-05 32.7 3.8 35 55-89 146-180 (207)
58 smart00342 HTH_ARAC helix_turn 88.4 3.3 7.1E-05 23.7 6.2 71 12-86 4-76 (84)
59 TIGR00721 tfx DNA-binding prot 88.2 1.8 3.9E-05 29.8 5.4 43 45-89 7-49 (137)
60 PF01325 Fe_dep_repress: Iron 87.9 1.8 3.9E-05 25.4 4.6 41 46-86 4-47 (60)
61 PRK10840 transcriptional regul 87.9 0.79 1.7E-05 31.8 3.6 44 44-89 150-193 (216)
62 COG2771 CsgD DNA-binding HTH d 87.8 1.2 2.6E-05 25.1 3.8 34 55-88 13-46 (65)
63 PF12802 MarR_2: MarR family; 87.7 1.7 3.7E-05 24.5 4.4 26 62-87 22-47 (62)
64 COG2197 CitB Response regulato 87.6 0.78 1.7E-05 32.8 3.5 35 55-89 157-191 (211)
65 PRK01381 Trp operon repressor; 87.5 0.55 1.2E-05 30.9 2.4 37 47-83 41-77 (99)
66 PRK09483 response regulator; P 87.5 0.9 2E-05 30.7 3.6 44 44-89 148-191 (217)
67 PRK14087 dnaA chromosomal repl 87.5 1.5 3.2E-05 35.1 5.3 47 42-88 382-429 (450)
68 PF00356 LacI: Bacterial regul 87.2 0.39 8.5E-06 27.1 1.4 20 64-83 2-21 (46)
69 PHA00738 putative HTH transcri 87.1 1.3 2.8E-05 29.5 4.0 39 50-88 14-53 (108)
70 TIGR02392 rpoH_proteo alternat 86.9 1.5 3.3E-05 32.3 4.8 45 45-89 219-264 (270)
71 PRK06930 positive control sigm 86.8 1.7 3.8E-05 30.5 4.8 44 45-89 115-158 (170)
72 TIGR02844 spore_III_D sporulat 86.6 1.2 2.7E-05 28.0 3.5 25 60-84 18-42 (80)
73 PRK07408 RNA polymerase sigma 86.4 1.9 4E-05 31.7 5.0 44 45-89 204-247 (256)
74 TIGR02393 RpoD_Cterm RNA polym 86.2 1.8 3.9E-05 31.2 4.8 46 44-89 176-224 (238)
75 smart00346 HTH_ICLR helix_turn 86.1 2.1 4.5E-05 25.9 4.4 42 46-87 3-46 (91)
76 PRK09492 treR trehalose repres 86.0 0.43 9.3E-06 34.7 1.4 23 62-84 5-27 (315)
77 PRK11475 DNA-binding transcrip 85.8 1.2 2.6E-05 32.0 3.6 35 55-89 143-177 (207)
78 PRK12524 RNA polymerase sigma 85.8 2.3 5.1E-05 29.4 5.0 43 46-89 138-180 (196)
79 PRK12683 transcriptional regul 85.3 1.4 3.1E-05 32.5 4.0 37 49-85 4-40 (309)
80 PRK09047 RNA polymerase factor 85.2 2.3 4.9E-05 28.1 4.6 38 52-89 113-150 (161)
81 PRK10141 DNA-binding transcrip 85.0 1.8 4E-05 28.9 4.0 41 48-88 16-57 (117)
82 TIGR02983 SigE-fam_strep RNA p 84.9 2.3 5E-05 28.2 4.5 41 49-89 114-154 (162)
83 PRK12422 chromosomal replicati 84.8 2.2 4.9E-05 34.1 5.1 47 42-88 378-424 (445)
84 smart00760 Bac_DnaA_C Bacteria 84.7 1.3 2.8E-05 25.7 2.8 33 42-74 26-59 (60)
85 PRK10651 transcriptional regul 84.5 1.6 3.6E-05 29.0 3.7 43 45-89 156-198 (216)
86 PRK12679 cbl transcriptional r 84.4 1.7 3.6E-05 32.2 4.0 37 49-85 4-40 (316)
87 PRK08301 sporulation sigma fac 84.3 2.6 5.6E-05 30.1 4.8 45 45-89 179-226 (234)
88 PF13551 HTH_29: Winged helix- 84.3 1.8 3.9E-05 26.9 3.6 32 55-86 5-37 (112)
89 smart00418 HTH_ARSR helix_turn 84.3 1.9 4.2E-05 23.5 3.4 29 59-87 8-36 (66)
90 PRK12514 RNA polymerase sigma 84.0 3.3 7.2E-05 28.0 5.1 44 45-89 130-173 (179)
91 smart00345 HTH_GNTR helix_turn 84.0 1 2.2E-05 24.9 2.1 24 63-86 22-45 (60)
92 PF01047 MarR: MarR family; I 84.0 3.7 8E-05 23.0 4.5 29 59-87 15-43 (59)
93 PRK03975 tfx putative transcri 83.9 3.8 8.3E-05 28.3 5.3 43 45-89 7-49 (141)
94 PF02209 VHP: Villin headpiece 83.6 0.98 2.1E-05 24.5 1.8 24 11-34 3-26 (36)
95 PRK15201 fimbriae regulatory p 83.5 1.9 4E-05 31.6 3.8 46 42-89 131-176 (198)
96 PRK09652 RNA polymerase sigma 83.1 3.3 7.1E-05 27.5 4.7 36 54-89 137-172 (182)
97 PRK05911 RNA polymerase sigma 83.1 3.2 7E-05 30.5 5.0 44 45-89 206-249 (257)
98 PRK12519 RNA polymerase sigma 83.0 2.6 5.6E-05 28.9 4.2 38 52-89 148-185 (194)
99 TIGR02980 SigBFG RNA polymeras 82.7 3.3 7.2E-05 29.3 4.8 43 46-89 180-222 (227)
100 TIGR02835 spore_sigmaE RNA pol 82.6 3.4 7.4E-05 29.7 4.9 46 44-89 178-226 (234)
101 smart00153 VHP Villin headpiec 82.6 1.3 2.8E-05 23.9 2.0 22 11-32 3-24 (36)
102 PRK05572 sporulation sigma fac 82.5 3.5 7.6E-05 30.0 4.9 45 44-89 202-246 (252)
103 TIGR02885 spore_sigF RNA polym 82.4 3.4 7.4E-05 29.4 4.8 43 46-89 185-227 (231)
104 cd07377 WHTH_GntR Winged helix 82.2 5.3 0.00012 22.2 4.8 24 63-86 27-50 (66)
105 smart00419 HTH_CRP helix_turn_ 82.2 1.6 3.4E-05 23.2 2.4 27 61-87 8-34 (48)
106 PRK13719 conjugal transfer tra 82.0 2.3 4.9E-05 31.5 3.8 35 55-89 152-186 (217)
107 PRK10403 transcriptional regul 81.9 2.6 5.7E-05 27.9 3.8 43 45-89 154-196 (215)
108 PHA00542 putative Cro-like pro 81.6 3.2 6.8E-05 25.7 3.9 29 55-83 25-53 (82)
109 PRK08583 RNA polymerase sigma 81.5 3.9 8.4E-05 29.7 4.9 37 53-89 213-249 (257)
110 PHA00675 hypothetical protein 81.2 4.9 0.00011 25.4 4.6 40 43-82 21-60 (78)
111 PF01710 HTH_Tnp_IS630: Transp 81.2 1.5 3.3E-05 28.8 2.4 26 58-83 15-40 (119)
112 TIGR02941 Sigma_B RNA polymera 81.2 3.9 8.5E-05 29.6 4.8 43 46-89 207-249 (255)
113 TIGR01610 phage_O_Nterm phage 81.0 6.5 0.00014 24.8 5.3 53 18-86 20-72 (95)
114 PRK06596 RNA polymerase factor 81.0 3.9 8.4E-05 30.6 4.8 45 45-89 231-276 (284)
115 COG0593 DnaA ATPase involved i 80.8 4.1 8.8E-05 32.7 5.1 48 41-88 345-392 (408)
116 PF05732 RepL: Firmicute plasm 80.8 2.6 5.7E-05 29.6 3.6 39 49-87 56-101 (165)
117 PRK12682 transcriptional regul 80.8 2.8 6.1E-05 30.7 4.0 37 49-85 4-40 (309)
118 TIGR03541 reg_near_HchA LuxR f 80.6 11 0.00023 27.2 6.9 45 43-89 170-214 (232)
119 PRK10360 DNA-binding transcrip 80.6 3.2 7E-05 27.5 3.9 44 44-89 137-180 (196)
120 TIGR02405 trehalos_R_Ecol treh 80.6 1.1 2.3E-05 32.8 1.6 22 62-83 2-23 (311)
121 PRK07500 rpoH2 RNA polymerase 80.5 4.1 8.9E-05 30.6 4.8 45 45-89 228-273 (289)
122 TIGR02850 spore_sigG RNA polym 80.4 4.7 0.0001 29.4 5.0 44 45-89 207-250 (254)
123 TIGR02997 Sig70-cyanoRpoD RNA 80.3 3.8 8.3E-05 30.7 4.6 45 45-89 250-297 (298)
124 TIGR03879 near_KaiC_dom probab 80.2 4.3 9.3E-05 25.2 4.0 38 47-84 18-55 (73)
125 PRK12537 RNA polymerase sigma 80.2 4.9 0.00011 27.4 4.8 37 53-89 141-177 (182)
126 PF13309 HTH_22: HTH domain 80.1 2.6 5.5E-05 25.1 2.9 41 43-83 19-64 (64)
127 PRK12527 RNA polymerase sigma 79.9 5.4 0.00012 26.4 4.8 38 52-89 112-149 (159)
128 PRK10100 DNA-binding transcrip 79.8 3 6.5E-05 30.0 3.8 43 45-89 156-198 (216)
129 PF13463 HTH_27: Winged helix 79.8 4.8 0.0001 22.9 4.0 28 60-87 17-44 (68)
130 PRK08215 sporulation sigma fac 79.7 4.7 0.0001 29.4 4.8 44 45-89 210-253 (258)
131 PF09339 HTH_IclR: IclR helix- 79.7 3.7 8.1E-05 22.9 3.4 40 47-86 2-43 (52)
132 PRK15369 two component system 79.6 3.4 7.4E-05 27.0 3.7 32 58-89 161-192 (211)
133 PRK11233 nitrogen assimilation 79.5 3.4 7.3E-05 30.3 4.0 37 49-86 4-40 (305)
134 PRK09637 RNA polymerase sigma 79.4 5.1 0.00011 27.6 4.7 39 51-89 112-150 (181)
135 PRK12515 RNA polymerase sigma 79.3 6.1 0.00013 27.1 5.1 44 45-89 132-175 (189)
136 COG0664 Crp cAMP-binding prote 79.3 4.2 9.1E-05 27.2 4.2 44 43-86 139-196 (214)
137 PF13011 LZ_Tnp_IS481: leucine 79.2 4.8 0.00011 25.7 4.2 42 44-85 8-49 (85)
138 TIGR02989 Sig-70_gvs1 RNA poly 79.1 5.5 0.00012 26.1 4.7 44 45-89 112-155 (159)
139 PRK12512 RNA polymerase sigma 79.0 5.1 0.00011 27.2 4.6 38 52-89 138-175 (184)
140 cd00090 HTH_ARSR Arsenical Res 79.0 6 0.00013 22.0 4.2 34 53-86 12-45 (78)
141 TIGR02337 HpaR homoprotocatech 78.8 12 0.00026 23.9 6.1 61 19-87 7-68 (118)
142 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 78.7 4.9 0.00011 23.2 3.7 39 44-83 4-42 (50)
143 PF08220 HTH_DeoR: DeoR-like h 78.6 1.8 3.8E-05 25.0 1.9 25 61-85 14-38 (57)
144 TIGR02984 Sig-70_plancto1 RNA 78.3 6.3 0.00014 26.6 4.8 37 53-89 148-184 (189)
145 PRK05803 sporulation sigma fac 78.2 5.6 0.00012 28.5 4.8 45 45-89 176-223 (233)
146 PRK12516 RNA polymerase sigma 78.0 6.4 0.00014 27.3 4.9 43 46-89 118-160 (187)
147 TIGR02999 Sig-70_X6 RNA polyme 77.9 6 0.00013 26.7 4.7 38 52-89 141-178 (183)
148 PRK12547 RNA polymerase sigma 77.9 7.4 0.00016 26.1 5.1 37 53-89 120-156 (164)
149 PRK09649 RNA polymerase sigma 77.7 5.8 0.00012 27.3 4.6 41 49-89 134-174 (185)
150 PRK11924 RNA polymerase sigma 77.6 6.2 0.00013 26.1 4.6 37 53-89 133-169 (179)
151 PRK12536 RNA polymerase sigma 77.5 6.6 0.00014 26.7 4.8 43 46-89 131-173 (181)
152 PRK09641 RNA polymerase sigma 77.4 6.6 0.00014 26.4 4.8 43 46-89 138-180 (187)
153 PRK12684 transcriptional regul 77.3 4 8.8E-05 30.1 3.9 39 49-87 4-42 (313)
154 PRK06759 RNA polymerase factor 77.2 7.4 0.00016 25.4 4.8 37 53-89 114-150 (154)
155 PRK09958 DNA-binding transcrip 77.0 4.5 9.8E-05 26.9 3.8 44 44-89 143-186 (204)
156 PRK12525 RNA polymerase sigma 77.0 6.4 0.00014 26.5 4.6 38 53-90 126-163 (168)
157 PRK12528 RNA polymerase sigma 76.9 7.6 0.00016 25.8 4.9 38 52-89 120-157 (161)
158 PRK10014 DNA-binding transcrip 76.9 1.6 3.5E-05 32.0 1.7 24 61-84 6-29 (342)
159 COG2826 Tra8 Transposase and i 76.4 3.7 8E-05 32.1 3.5 40 43-83 6-45 (318)
160 PF01381 HTH_3: Helix-turn-hel 76.1 2.5 5.4E-05 23.3 2.0 27 58-84 6-32 (55)
161 PRK12530 RNA polymerase sigma 75.8 8.2 0.00018 26.6 4.9 41 48-89 138-178 (189)
162 PF00440 TetR_N: Bacterial reg 75.5 5.2 0.00011 21.8 3.2 34 51-84 6-39 (47)
163 PRK07037 extracytoplasmic-func 75.5 8.8 0.00019 25.4 4.9 36 53-88 117-152 (163)
164 PRK07122 RNA polymerase sigma 75.5 7.4 0.00016 28.8 4.9 43 46-89 217-259 (264)
165 smart00347 HTH_MARR helix_turn 75.5 8.8 0.00019 22.9 4.5 37 51-87 13-50 (101)
166 PRK12544 RNA polymerase sigma 75.4 7.8 0.00017 27.4 4.8 37 53-89 156-192 (206)
167 PRK12531 RNA polymerase sigma 75.2 9.2 0.0002 26.4 5.1 37 53-89 149-185 (194)
168 TIGR02959 SigZ RNA polymerase 75.0 8.9 0.00019 25.9 4.9 44 45-89 101-144 (170)
169 TIGR02950 SigM_subfam RNA poly 74.9 2.8 6.1E-05 27.4 2.3 32 58-89 118-149 (154)
170 TIGR02846 spore_sigmaK RNA pol 74.6 8.4 0.00018 27.5 4.9 44 46-89 176-222 (227)
171 PF01527 HTH_Tnp_1: Transposas 74.5 4.7 0.0001 23.6 3.0 43 44-86 6-48 (76)
172 PRK12533 RNA polymerase sigma 74.2 8.2 0.00018 27.7 4.7 40 49-89 139-178 (216)
173 TIGR02859 spore_sigH RNA polym 73.7 8.9 0.00019 26.1 4.7 37 52-89 157-193 (198)
174 PRK07405 RNA polymerase sigma 73.6 8.8 0.00019 29.3 5.0 46 44-89 256-304 (317)
175 PRK09642 RNA polymerase sigma 73.6 9.1 0.0002 25.3 4.6 37 53-89 114-150 (160)
176 PRK13919 putative RNA polymera 73.5 9.2 0.0002 25.9 4.6 37 53-89 143-179 (186)
177 PRK09651 RNA polymerase sigma 73.4 6.9 0.00015 26.5 4.0 38 52-89 126-163 (172)
178 PRK11923 algU RNA polymerase s 73.3 9.7 0.00021 26.0 4.8 44 45-89 139-182 (193)
179 PRK12529 RNA polymerase sigma 73.2 9 0.0002 26.1 4.6 38 53-90 135-172 (178)
180 PRK13413 mpi multiple promoter 73.2 4.8 0.0001 28.3 3.2 32 52-84 164-195 (200)
181 PRK12532 RNA polymerase sigma 72.8 9.1 0.0002 26.3 4.5 37 53-89 144-180 (195)
182 PRK09526 lacI lac repressor; R 72.7 2.4 5.1E-05 31.1 1.7 23 62-84 6-28 (342)
183 TIGR02952 Sig70_famx2 RNA poly 72.7 11 0.00024 24.9 4.8 45 44-89 122-166 (170)
184 PRK09644 RNA polymerase sigma 72.7 9.3 0.0002 25.5 4.5 44 45-89 109-152 (165)
185 TIGR02948 SigW_bacill RNA poly 72.6 8.8 0.00019 25.8 4.4 32 58-89 149-180 (187)
186 PRK10401 DNA-binding transcrip 72.6 2.3 4.9E-05 31.5 1.5 21 63-83 3-23 (346)
187 smart00420 HTH_DEOR helix_turn 72.5 10 0.00022 20.0 3.9 26 61-86 14-39 (53)
188 PRK12511 RNA polymerase sigma 72.4 10 0.00022 26.2 4.7 37 53-89 119-155 (182)
189 PRK12681 cysB transcriptional 72.4 6.5 0.00014 29.4 4.0 37 49-85 4-40 (324)
190 cd01392 HTH_LacI Helix-turn-he 72.4 2 4.4E-05 23.4 1.0 18 66-83 2-19 (52)
191 PRK12522 RNA polymerase sigma 72.3 10 0.00022 25.5 4.6 38 52-89 126-163 (173)
192 PRK14987 gluconate operon tran 72.1 2 4.3E-05 31.5 1.1 23 62-84 6-28 (331)
193 PRK12540 RNA polymerase sigma 71.9 10 0.00023 26.1 4.7 38 52-89 118-155 (182)
194 PRK12541 RNA polymerase sigma 71.8 10 0.00022 25.1 4.5 38 52-89 119-156 (161)
195 PRK06288 RNA polymerase sigma 71.6 11 0.00024 27.6 5.0 44 45-89 213-256 (268)
196 PRK09647 RNA polymerase sigma 71.4 11 0.00024 26.5 4.8 38 52-89 145-182 (203)
197 PRK11151 DNA-binding transcrip 71.1 7.3 0.00016 28.3 3.9 36 49-85 4-39 (305)
198 PRK12545 RNA polymerase sigma 71.0 12 0.00025 26.2 4.8 37 53-89 147-183 (201)
199 PRK09906 DNA-binding transcrip 70.8 7.2 0.00016 28.1 3.8 36 50-86 5-40 (296)
200 PRK12539 RNA polymerase sigma 70.6 11 0.00023 25.8 4.5 37 53-89 139-175 (184)
201 smart00354 HTH_LACI helix_turn 70.6 3 6.5E-05 24.8 1.5 21 63-83 2-22 (70)
202 PRK09646 RNA polymerase sigma 70.5 13 0.00027 25.7 4.9 38 52-89 149-186 (194)
203 TIGR03020 EpsA transcriptional 70.5 11 0.00025 27.9 4.9 45 43-89 189-233 (247)
204 TIGR03001 Sig-70_gmx1 RNA poly 70.5 11 0.00024 27.6 4.8 37 53-89 169-205 (244)
205 PRK09940 transcriptional regul 70.3 12 0.00026 28.0 5.0 83 2-84 87-173 (253)
206 PRK04841 transcriptional regul 70.2 6.2 0.00013 33.0 3.8 43 45-89 839-881 (903)
207 TIGR01884 cas_HTH CRISPR locus 70.2 9.8 0.00021 26.9 4.3 38 49-86 144-182 (203)
208 PRK06986 fliA flagellar biosyn 70.2 11 0.00025 26.9 4.7 43 46-89 186-228 (236)
209 TIGR01889 Staph_reg_Sar staphy 70.1 25 0.00055 22.3 6.1 55 26-86 10-68 (109)
210 TIGR02943 Sig70_famx1 RNA poly 69.7 13 0.00028 25.6 4.8 37 53-89 139-175 (188)
211 TIGR00637 ModE_repress ModE mo 69.6 5.5 0.00012 25.5 2.7 34 54-87 9-42 (99)
212 PRK12546 RNA polymerase sigma 69.3 13 0.00028 25.9 4.7 44 45-89 114-157 (188)
213 PRK10188 DNA-binding transcrip 69.3 37 0.0008 24.7 7.3 45 43-89 178-222 (240)
214 PF08535 KorB: KorB domain; I 69.1 4 8.7E-05 25.5 1.9 24 60-83 2-25 (93)
215 TIGR00180 parB_part ParB-like 69.1 8.6 0.00019 26.9 3.8 38 46-83 105-142 (187)
216 TIGR00122 birA_repr_reg BirA b 69.1 11 0.00023 22.0 3.7 25 61-85 13-37 (69)
217 TIGR03418 chol_sulf_TF putativ 69.1 8.7 0.00019 27.5 3.9 36 49-85 4-39 (291)
218 PRK12542 RNA polymerase sigma 69.0 14 0.0003 25.2 4.7 38 52-89 129-166 (185)
219 smart00550 Zalpha Z-DNA-bindin 69.0 13 0.00027 22.1 4.0 41 45-85 5-46 (68)
220 PRK11511 DNA-binding transcrip 68.8 10 0.00022 24.9 3.9 30 57-86 21-50 (127)
221 PRK09415 RNA polymerase factor 68.6 12 0.00027 25.4 4.4 44 45-89 128-171 (179)
222 PRK12680 transcriptional regul 68.5 8.7 0.00019 28.7 4.0 38 49-86 4-41 (327)
223 PRK00215 LexA repressor; Valid 68.4 12 0.00025 26.3 4.4 28 59-86 21-49 (205)
224 TIGR02954 Sig70_famx3 RNA poly 68.4 14 0.0003 24.6 4.6 38 52-89 126-163 (169)
225 PRK07670 RNA polymerase sigma 68.3 15 0.00032 26.6 5.0 43 46-89 203-245 (251)
226 PRK13348 chromosome replicatio 68.3 9.4 0.0002 27.5 4.0 36 49-85 5-40 (294)
227 PRK12520 RNA polymerase sigma 68.2 15 0.00032 25.2 4.8 37 53-89 139-175 (191)
228 PRK12427 flagellar biosynthesi 68.0 15 0.00033 26.5 5.0 43 46-89 185-227 (231)
229 CHL00180 rbcR LysR transcripti 68.0 9.1 0.0002 27.9 3.9 39 49-88 8-46 (305)
230 TIGR02394 rpoS_proteo RNA poly 67.9 13 0.00029 27.5 4.8 45 45-89 223-270 (285)
231 PRK09210 RNA polymerase sigma 67.6 13 0.00028 29.0 4.8 46 44-89 305-353 (367)
232 PF06056 Terminase_5: Putative 67.5 12 0.00026 21.8 3.7 33 49-83 3-35 (58)
233 PRK07406 RNA polymerase sigma 66.9 14 0.00031 29.1 5.0 46 44-89 311-359 (373)
234 PF00165 HTH_AraC: Bacterial r 66.9 5.4 0.00012 21.1 1.9 28 59-86 6-33 (42)
235 PRK08295 RNA polymerase factor 66.9 15 0.00033 25.2 4.7 42 46-89 157-198 (208)
236 PRK12423 LexA repressor; Provi 66.5 13 0.00027 26.4 4.3 26 61-86 25-51 (202)
237 PRK12534 RNA polymerase sigma 66.3 17 0.00038 24.6 4.8 31 59-89 151-181 (187)
238 PRK12526 RNA polymerase sigma 66.3 17 0.00036 25.5 4.8 37 53-89 161-197 (206)
239 PRK10094 DNA-binding transcrip 66.3 10 0.00023 27.8 3.9 36 49-85 5-40 (308)
240 PRK10703 DNA-binding transcrip 66.1 3.9 8.4E-05 30.0 1.6 22 63-84 3-24 (341)
241 COG1595 RpoE DNA-directed RNA 66.1 14 0.0003 25.2 4.3 38 52-89 134-171 (182)
242 PRK11242 DNA-binding transcrip 66.0 11 0.00023 27.0 3.9 36 49-85 4-39 (296)
243 PRK06811 RNA polymerase factor 65.6 17 0.00036 25.0 4.6 44 45-89 132-175 (189)
244 PF01978 TrmB: Sugar-specific 65.6 16 0.00035 21.1 4.0 36 52-87 12-48 (68)
245 PRK15421 DNA-binding transcrip 65.6 11 0.00025 27.9 4.0 36 49-85 5-40 (317)
246 PF00392 GntR: Bacterial regul 65.6 23 0.00051 20.2 5.6 45 24-85 4-48 (64)
247 TIGR02939 RpoE_Sigma70 RNA pol 65.5 14 0.00029 25.0 4.1 37 53-89 146-182 (190)
248 PF10799 YliH: Biofilm formati 65.3 7.3 0.00016 26.5 2.6 30 23-53 43-72 (127)
249 PRK05602 RNA polymerase sigma 65.3 15 0.00033 24.9 4.4 37 53-89 136-172 (186)
250 PRK06474 hypothetical protein; 65.1 13 0.00028 26.1 4.1 40 49-88 12-54 (178)
251 PRK10430 DNA-binding transcrip 65.0 14 0.0003 26.0 4.3 44 45-88 159-205 (239)
252 PRK15418 transcriptional regul 64.7 5.8 0.00013 30.4 2.4 26 60-85 28-53 (318)
253 PRK12543 RNA polymerase sigma 64.6 17 0.00038 24.6 4.6 37 53-89 125-161 (179)
254 PRK11013 DNA-binding transcrip 64.5 11 0.00023 27.6 3.7 36 49-85 7-42 (309)
255 PF13560 HTH_31: Helix-turn-he 64.2 5.6 0.00012 22.8 1.8 26 57-82 10-35 (64)
256 PRK09480 slmA division inhibit 64.2 8.4 0.00018 25.9 2.9 25 59-83 28-52 (194)
257 PRK03573 transcriptional regul 63.8 13 0.00028 24.4 3.7 42 45-86 29-71 (144)
258 TIGR02479 FliA_WhiG RNA polyme 63.8 20 0.00043 25.3 4.9 43 46-89 177-219 (224)
259 PRK09643 RNA polymerase sigma 63.3 20 0.00044 24.7 4.8 44 45-89 135-178 (192)
260 COG3355 Predicted transcriptio 63.3 16 0.00035 24.9 4.1 54 28-88 14-69 (126)
261 PRK12535 RNA polymerase sigma 62.3 19 0.00042 25.1 4.5 38 52-89 140-177 (196)
262 PRK07598 RNA polymerase sigma 62.2 19 0.00042 28.9 5.0 45 45-89 351-398 (415)
263 PRK09648 RNA polymerase sigma 62.2 23 0.0005 24.1 4.8 38 52-89 146-183 (189)
264 cd04762 HTH_MerR-trunc Helix-T 62.0 6.7 0.00014 20.3 1.7 22 63-84 2-23 (49)
265 PRK09935 transcriptional regul 62.0 14 0.00029 24.5 3.6 43 45-89 150-192 (210)
266 PRK12523 RNA polymerase sigma 62.0 24 0.00053 23.6 4.9 40 48-88 123-162 (172)
267 PRK09801 transcriptional activ 62.0 9.6 0.00021 28.1 3.1 38 48-86 8-45 (310)
268 PRK13698 plasmid-partitioning 61.7 13 0.00029 29.0 3.9 40 45-84 159-199 (323)
269 TIGR03298 argP transcriptional 61.6 15 0.00033 26.4 4.0 35 50-85 5-39 (292)
270 PRK09638 RNA polymerase sigma 61.4 9.5 0.00021 25.5 2.7 44 45-89 127-170 (176)
271 PRK10339 DNA-binding transcrip 61.1 4.5 9.8E-05 29.6 1.2 22 63-84 3-24 (327)
272 TIGR02404 trehalos_R_Bsub treh 61.1 28 0.00062 24.6 5.3 42 27-85 7-48 (233)
273 PRK11074 putative DNA-binding 61.0 15 0.00033 26.6 3.9 36 49-85 5-40 (300)
274 PF04297 UPF0122: Putative hel 60.9 24 0.00052 23.1 4.5 43 47-89 19-61 (101)
275 TIGR02702 SufR_cyano iron-sulf 60.7 18 0.00038 25.6 4.1 38 48-86 3-40 (203)
276 COG1725 Predicted transcriptio 60.7 34 0.00074 23.2 5.3 51 19-85 6-59 (125)
277 PRK09645 RNA polymerase sigma 60.6 27 0.00058 23.3 4.8 37 53-89 126-162 (173)
278 PF02001 DUF134: Protein of un 60.6 30 0.00065 22.8 4.9 48 42-90 39-90 (106)
279 PHA02591 hypothetical protein; 60.4 9.8 0.00021 24.2 2.4 27 58-84 56-82 (83)
280 PHA02510 X gene X product; Rev 60.3 48 0.001 22.3 5.9 58 25-87 9-67 (116)
281 PRK05949 RNA polymerase sigma 60.0 22 0.00048 27.3 4.8 45 45-89 267-314 (327)
282 PRK12538 RNA polymerase sigma 59.7 20 0.00043 25.9 4.3 37 53-89 179-215 (233)
283 PRK11564 stationary phase indu 58.9 20 0.00043 27.9 4.5 48 39-86 5-55 (426)
284 cd00131 PAX Paired Box domain 58.9 51 0.0011 21.9 8.1 74 11-84 35-126 (128)
285 PRK12518 RNA polymerase sigma 58.8 9.5 0.00021 25.5 2.4 32 58-89 133-164 (175)
286 TIGR02960 SigX5 RNA polymerase 58.6 21 0.00046 26.4 4.4 37 53-89 150-186 (324)
287 PRK09640 RNA polymerase sigma 58.5 10 0.00022 26.0 2.5 37 53-89 142-178 (188)
288 PRK11922 RNA polymerase sigma 58.4 14 0.0003 26.4 3.3 36 54-89 158-193 (231)
289 TIGR02036 dsdC D-serine deamin 58.4 12 0.00025 27.4 3.0 36 49-85 11-46 (302)
290 TIGR03070 couple_hipB transcri 58.4 11 0.00024 20.3 2.3 27 57-83 11-37 (58)
291 TIGR02424 TF_pcaQ pca operon t 58.3 18 0.00039 26.0 3.9 36 49-85 6-41 (300)
292 TIGR02957 SigX4 RNA polymerase 58.2 25 0.00055 25.9 4.8 38 52-89 115-152 (281)
293 PRK10632 transcriptional regul 57.9 13 0.00029 27.2 3.2 36 49-85 5-40 (309)
294 PRK09791 putative DNA-binding 57.8 19 0.00042 26.0 4.0 38 49-87 8-45 (302)
295 PRK11050 manganese transport r 57.4 25 0.00054 23.9 4.3 26 60-85 50-75 (152)
296 PF07900 DUF1670: Protein of u 57.3 78 0.0017 23.6 8.1 74 13-88 109-190 (220)
297 smart00351 PAX Paired Box doma 57.2 53 0.0011 21.6 6.8 72 11-82 35-124 (125)
298 PRK10837 putative DNA-binding 57.1 13 0.00027 26.6 2.9 35 50-85 7-41 (290)
299 PF13972 TetR: Bacterial trans 56.8 38 0.00083 22.3 5.1 84 4-89 45-133 (146)
300 PRK15092 DNA-binding transcrip 56.7 13 0.00029 27.5 3.0 34 52-85 16-49 (310)
301 PRK09636 RNA polymerase sigma 56.4 28 0.00061 25.7 4.7 38 52-89 122-159 (293)
302 TIGR01764 excise DNA binding d 56.2 9.6 0.00021 19.9 1.7 21 63-83 3-23 (49)
303 PF05043 Mga: Mga helix-turn-h 56.2 16 0.00036 22.0 3.0 31 58-88 27-57 (87)
304 PRK10434 srlR DNA-bindng trans 55.7 21 0.00046 26.3 3.9 37 49-85 5-43 (256)
305 smart00497 IENR1 Intron encode 55.6 11 0.00024 20.5 1.9 23 62-84 18-40 (53)
306 TIGR03384 betaine_BetI transcr 55.5 14 0.0003 24.7 2.7 36 48-83 15-50 (189)
307 PRK12513 RNA polymerase sigma 55.4 14 0.0003 25.3 2.8 32 58-89 152-183 (194)
308 PF04703 FaeA: FaeA-like prote 55.4 20 0.00043 21.3 3.1 37 49-85 3-39 (62)
309 PF01726 LexA_DNA_bind: LexA D 54.9 34 0.00074 20.3 4.1 28 58-85 22-50 (65)
310 PRK02287 hypothetical protein; 54.8 11 0.00023 27.0 2.2 33 44-76 106-138 (171)
311 COG3413 Predicted DNA binding 54.8 14 0.0003 26.3 2.8 31 60-90 177-207 (215)
312 PRK13509 transcriptional repre 54.7 24 0.00053 25.9 4.1 24 62-85 20-43 (251)
313 PRK11512 DNA-binding transcrip 54.6 32 0.00069 22.7 4.4 42 44-86 37-79 (144)
314 TIGR03339 phn_lysR aminoethylp 54.5 15 0.00032 25.9 2.9 31 55-85 5-35 (279)
315 TIGR03830 CxxCG_CxxCG_HTH puta 54.4 13 0.00028 23.9 2.3 28 56-83 73-100 (127)
316 PRK10219 DNA-binding transcrip 54.4 33 0.00071 21.4 4.2 23 63-85 23-45 (107)
317 PRK09508 leuO leucine transcri 54.1 17 0.00036 26.7 3.2 40 45-86 22-61 (314)
318 PRK07921 RNA polymerase sigma 53.8 35 0.00076 26.3 5.0 45 45-89 263-310 (324)
319 PF13921 Myb_DNA-bind_6: Myb-l 53.8 25 0.00055 19.7 3.3 27 60-86 16-43 (60)
320 PRK15243 transcriptional regul 53.7 24 0.00051 26.5 4.0 39 47-86 5-43 (297)
321 PF07638 Sigma70_ECF: ECF sigm 53.6 29 0.00062 24.0 4.2 27 59-85 149-175 (185)
322 TIGR00498 lexA SOS regulatory 53.3 28 0.00061 24.2 4.1 26 60-85 24-50 (199)
323 TIGR02947 SigH_actino RNA poly 53.2 17 0.00037 24.9 2.9 37 53-89 139-175 (193)
324 TIGR01481 ccpA catabolite cont 53.1 8.6 0.00019 28.0 1.5 22 63-84 3-24 (329)
325 PRK10086 DNA-binding transcrip 53.0 17 0.00036 26.7 3.0 36 50-86 18-53 (311)
326 PF11740 KfrA_N: Plasmid repli 53.0 16 0.00035 23.3 2.7 33 55-87 13-46 (120)
327 PRK12517 RNA polymerase sigma 52.8 39 0.00083 23.3 4.7 37 53-89 136-172 (188)
328 PRK06704 RNA polymerase factor 52.7 30 0.00066 25.3 4.3 44 45-89 117-160 (228)
329 PRK09764 DNA-binding transcrip 52.5 52 0.0011 23.6 5.5 44 26-85 7-53 (240)
330 PF10668 Phage_terminase: Phag 52.4 25 0.00055 20.9 3.2 35 46-81 8-42 (60)
331 PRK09986 DNA-binding transcrip 52.4 24 0.00051 25.2 3.7 38 49-87 10-47 (294)
332 PHA01976 helix-turn-helix prot 52.3 16 0.00035 20.8 2.4 27 57-83 11-37 (67)
333 PF13443 HTH_26: Cro/C1-type H 51.9 13 0.00027 21.0 1.8 28 57-84 6-33 (63)
334 PRK10216 DNA-binding transcrip 51.7 26 0.00057 25.7 3.9 38 49-87 11-48 (319)
335 TIGR02607 antidote_HigA addict 51.6 35 0.00076 19.8 3.8 38 45-83 3-40 (78)
336 TIGR02018 his_ut_repres histid 51.2 60 0.0013 23.0 5.6 33 37-85 17-49 (230)
337 PF01498 HTH_Tnp_Tc3_2: Transp 50.9 15 0.00032 21.5 2.0 23 62-84 14-41 (72)
338 PF07374 DUF1492: Protein of u 50.8 49 0.0011 20.9 4.6 42 47-89 58-99 (100)
339 PRK10341 DNA-binding transcrip 50.8 19 0.00042 26.3 3.1 39 48-87 9-47 (312)
340 COG0184 RpsO Ribosomal protein 50.5 15 0.00033 23.6 2.2 26 31-56 9-34 (89)
341 KOG0483 Transcription factor H 50.3 12 0.00027 27.2 1.9 51 14-73 50-100 (198)
342 PRK11062 nhaR transcriptional 50.3 20 0.00043 26.0 3.1 36 49-85 7-42 (296)
343 COG4974 XerD Site-specific rec 50.0 99 0.0022 24.1 6.9 59 20-80 220-280 (300)
344 PRK03635 chromosome replicatio 49.7 20 0.00044 25.9 3.0 35 50-85 6-40 (294)
345 TIGR03764 ICE_PFGI_1_parB inte 49.5 33 0.0007 26.1 4.1 42 44-85 113-165 (258)
346 PF07453 NUMOD1: NUMOD1 domain 49.5 10 0.00022 19.7 1.1 20 62-81 17-36 (37)
347 PRK10727 DNA-binding transcrip 49.4 10 0.00022 27.9 1.4 21 63-83 3-23 (343)
348 COG1508 RpoN DNA-directed RNA 49.3 15 0.00032 30.0 2.4 38 46-83 313-352 (444)
349 PRK11402 DNA-binding transcrip 49.3 56 0.0012 23.3 5.2 45 25-85 10-57 (241)
350 PF11469 Ribonucleas_3_2: Ribo 49.3 17 0.00038 24.4 2.3 42 44-91 74-115 (120)
351 COG2739 Uncharacterized protei 49.1 53 0.0011 21.8 4.6 32 57-88 29-60 (105)
352 PRK10046 dpiA two-component re 49.0 19 0.00041 25.2 2.7 24 61-84 177-200 (225)
353 TIGR02944 suf_reg_Xantho FeS a 48.8 43 0.00093 21.7 4.2 40 48-87 9-51 (130)
354 PRK10082 cell density-dependen 48.6 23 0.00051 25.7 3.2 41 43-85 9-49 (303)
355 PRK09834 DNA-binding transcrip 48.5 42 0.00091 24.5 4.5 41 46-86 9-51 (263)
356 COG5606 Uncharacterized conser 48.5 8.9 0.00019 24.9 0.8 58 23-80 3-60 (91)
357 smart00352 POU Found in Pit-Oc 48.5 15 0.00032 23.0 1.8 26 57-82 20-51 (75)
358 PRK10906 DNA-binding transcrip 48.4 36 0.00078 25.1 4.2 24 62-85 20-43 (252)
359 COG2973 TrpR Trp operon repres 47.7 30 0.00065 22.9 3.2 25 57-81 56-80 (103)
360 PF13744 HTH_37: Helix-turn-he 47.6 17 0.00037 22.0 2.0 28 56-83 26-53 (80)
361 TIGR02325 C_P_lyase_phnF phosp 46.8 66 0.0014 22.6 5.2 44 26-85 10-56 (238)
362 PRK03601 transcriptional regul 46.5 26 0.00055 25.2 3.1 36 50-86 5-40 (275)
363 PF02954 HTH_8: Bacterial regu 46.4 22 0.00049 19.0 2.2 25 60-84 17-41 (42)
364 PRK09464 pdhR transcriptional 46.2 37 0.00081 24.3 3.9 42 24-82 14-55 (254)
365 PRK08241 RNA polymerase factor 45.9 40 0.00087 25.2 4.2 37 53-89 161-197 (339)
366 PRK09975 DNA-binding transcrip 45.6 26 0.00057 24.0 3.0 37 47-83 17-53 (213)
367 smart00344 HTH_ASNC helix_turn 45.5 55 0.0012 20.2 4.2 27 61-87 17-43 (108)
368 PRK14997 LysR family transcrip 45.4 27 0.00059 25.2 3.1 36 50-86 6-41 (301)
369 PRK03341 arginine repressor; P 45.4 52 0.0011 23.3 4.4 15 71-85 44-58 (168)
370 PRK11482 putative DNA-binding 45.4 26 0.00057 25.9 3.1 40 44-85 28-67 (317)
371 COG3179 Predicted chitinase [G 45.1 35 0.00077 25.1 3.6 70 11-83 5-75 (206)
372 PRK05901 RNA polymerase sigma 44.6 53 0.0012 27.1 5.0 45 45-89 448-495 (509)
373 PRK13870 transcriptional regul 44.5 35 0.00076 24.8 3.6 44 44-89 173-216 (234)
374 PF12728 HTH_17: Helix-turn-he 44.5 19 0.00041 19.6 1.7 21 63-83 3-23 (51)
375 PRK03902 manganese transport t 44.5 55 0.0012 21.6 4.3 40 47-86 6-47 (142)
376 TIGR00362 DnaA chromosomal rep 44.0 28 0.0006 27.0 3.1 33 42-74 371-404 (405)
377 PRK14999 histidine utilization 43.9 85 0.0018 22.4 5.5 44 26-85 14-60 (241)
378 COG4496 Uncharacterized protei 43.9 18 0.00038 23.7 1.7 25 57-81 52-76 (100)
379 PRK10870 transcriptional repre 43.7 35 0.00075 23.7 3.3 26 61-86 71-96 (176)
380 COG1309 AcrR Transcriptional r 43.6 15 0.00031 23.1 1.3 30 60-89 31-63 (201)
381 TIGR03613 RutR pyrimidine util 43.5 32 0.00069 23.4 3.1 37 47-83 14-50 (202)
382 PF14393 DUF4422: Domain of un 43.3 13 0.00029 27.5 1.2 32 4-35 156-187 (231)
383 smart00530 HTH_XRE Helix-turn- 43.2 30 0.00065 17.2 2.3 25 58-82 7-31 (56)
384 COG2188 PhnF Transcriptional r 43.1 80 0.0017 22.8 5.3 44 26-85 9-55 (236)
385 COG2390 DeoR Transcriptional r 43.0 22 0.00048 27.6 2.4 26 59-84 24-49 (321)
386 PRK04424 fatty acid biosynthes 42.8 53 0.0011 23.1 4.2 24 62-85 22-45 (185)
387 PRK11139 DNA-binding transcrip 42.8 30 0.00065 24.9 3.0 36 49-85 9-44 (297)
388 PF13404 HTH_AsnC-type: AsnC-t 42.6 25 0.00055 19.1 2.0 24 61-84 17-40 (42)
389 PRK09390 fixJ response regulat 42.4 49 0.0011 21.2 3.8 32 58-89 153-184 (202)
390 cd01197 INT_FimBE_C FimB and F 41.8 1E+02 0.0022 20.3 6.3 63 20-84 107-171 (180)
391 PF09862 DUF2089: Protein of u 41.7 79 0.0017 21.1 4.6 46 44-90 33-78 (113)
392 PRK14996 TetR family transcrip 41.4 28 0.00061 23.6 2.5 37 48-84 15-51 (192)
393 PRK10411 DNA-binding transcrip 41.1 48 0.001 24.2 3.9 27 61-87 18-44 (240)
394 PRK00441 argR arginine repress 41.0 54 0.0012 22.6 3.9 24 62-85 19-47 (149)
395 PF01316 Arg_repressor: Argini 40.8 83 0.0018 19.1 5.1 31 44-85 18-48 (70)
396 PF04034 DUF367: Domain of unk 40.4 25 0.00053 24.1 2.1 33 44-76 65-97 (127)
397 PF09246 PHAT: PHAT; InterPro 40.4 37 0.0008 22.6 2.8 37 23-59 47-83 (108)
398 COG2963 Transposase and inacti 40.0 82 0.0018 19.9 4.5 43 43-85 6-49 (116)
399 PRK04984 fatty acid metabolism 39.3 80 0.0017 22.3 4.7 44 24-84 11-54 (239)
400 PF03428 RP-C: Replication pro 39.3 28 0.00061 24.8 2.3 67 21-88 23-98 (177)
401 COG1740 HyaA Ni,Fe-hydrogenase 39.0 38 0.00082 26.9 3.2 36 16-51 8-43 (355)
402 PRK13756 tetracycline represso 38.8 33 0.00072 24.4 2.7 24 60-83 23-46 (205)
403 PRK05657 RNA polymerase sigma 38.7 79 0.0017 24.2 4.9 31 59-89 280-310 (325)
404 PRK10072 putative transcriptio 38.5 26 0.00056 22.5 1.9 27 57-83 42-68 (96)
405 PRK09706 transcriptional repre 38.1 31 0.00067 22.7 2.3 27 57-83 14-40 (135)
406 PRK09191 two-component respons 38.0 83 0.0018 21.9 4.6 40 50-89 93-132 (261)
407 PRK03837 transcriptional regul 38.0 98 0.0021 21.8 5.0 43 24-83 17-59 (241)
408 PRK15340 transcriptional regul 37.7 66 0.0014 23.6 4.1 26 61-86 125-150 (216)
409 PRK10681 DNA-binding transcrip 37.6 64 0.0014 23.6 4.1 23 62-84 22-44 (252)
410 TIGR03209 P21_Cbot clostridium 37.2 35 0.00075 22.0 2.4 28 52-79 114-141 (142)
411 cd00093 HTH_XRE Helix-turn-hel 37.1 32 0.0007 17.2 1.9 25 59-83 10-34 (58)
412 KOG2072 Translation initiation 36.9 32 0.0007 30.5 2.7 34 2-36 150-206 (988)
413 PRK15481 transcriptional regul 36.7 91 0.002 24.1 5.0 47 23-86 8-54 (431)
414 TIGR01636 phage_rinA phage tra 36.4 94 0.002 20.6 4.4 43 47-89 85-128 (134)
415 PF04552 Sigma54_DBD: Sigma-54 36.2 12 0.00026 26.2 0.0 38 47-84 33-72 (160)
416 PF06413 Neugrin: Neugrin; In 36.1 90 0.002 23.1 4.6 43 41-83 7-51 (225)
417 PRK12302 bssR biofilm formatio 36.0 41 0.00089 22.7 2.5 30 23-53 43-72 (127)
418 COG1846 MarR Transcriptional r 35.8 79 0.0017 19.1 3.8 22 65-86 40-61 (126)
419 PF03564 DUF1759: Protein of u 35.3 45 0.00097 21.8 2.7 40 2-41 32-71 (145)
420 PRK09635 sigI RNA polymerase s 35.3 86 0.0019 23.5 4.5 38 52-89 125-162 (290)
421 PRK13824 replication initiatio 35.2 69 0.0015 25.6 4.2 67 21-88 35-110 (404)
422 PRK10668 DNA-binding transcrip 34.9 43 0.00094 23.0 2.7 34 50-83 20-53 (215)
423 PRK10572 DNA-binding transcrip 34.9 1.5E+02 0.0032 21.5 5.6 29 58-86 196-224 (290)
424 PRK09990 DNA-binding transcrip 34.8 1.1E+02 0.0023 21.9 4.8 43 24-83 11-53 (251)
425 PF12964 DUF3853: Protein of u 34.7 54 0.0012 21.4 2.9 58 18-83 10-67 (96)
426 PRK00767 transcriptional regul 34.1 54 0.0012 21.9 3.0 35 49-83 17-51 (197)
427 PF11198 DUF2857: Protein of u 34.0 1.5E+02 0.0033 20.9 5.4 29 52-80 78-106 (180)
428 TIGR02812 fadR_gamma fatty aci 33.7 77 0.0017 22.4 3.9 43 24-83 10-52 (235)
429 PRK11552 putative DNA-binding 33.3 54 0.0012 23.2 3.0 36 47-83 19-54 (225)
430 COG1191 FliA DNA-directed RNA 32.9 97 0.0021 23.2 4.4 43 46-89 198-240 (247)
431 PRK10130 transcriptional regul 32.9 86 0.0019 24.3 4.3 31 56-86 251-281 (350)
432 PF00292 PAX: 'Paired box' dom 32.7 1.1E+02 0.0025 20.7 4.4 43 40-84 13-56 (125)
433 COG2186 FadR Transcriptional r 32.6 1.4E+02 0.0031 21.7 5.2 40 22-78 12-51 (241)
434 COG2378 Predicted transcriptio 32.4 95 0.0021 23.7 4.4 37 51-87 11-48 (311)
435 cd04761 HTH_MerR-SF Helix-Turn 32.3 35 0.00076 17.9 1.5 21 63-83 2-22 (49)
436 PRK11202 DNA-binding transcrip 32.0 26 0.00056 24.3 1.2 24 60-83 31-54 (203)
437 COG1342 Predicted DNA-binding 31.6 61 0.0013 21.3 2.8 47 43-90 32-82 (99)
438 PF06163 DUF977: Bacterial pro 31.4 1.1E+02 0.0024 20.9 4.2 45 43-87 3-52 (127)
439 PRK10421 DNA-binding transcrip 31.1 1.2E+02 0.0025 21.8 4.5 43 24-83 6-48 (253)
440 PF05930 Phage_AlpA: Prophage 31.1 45 0.00098 18.4 1.9 21 63-83 5-25 (51)
441 PF07750 GcrA: GcrA cell cycle 30.8 64 0.0014 22.5 3.0 37 48-84 5-42 (162)
442 PF04591 DUF596: Protein of un 30.7 32 0.00069 21.3 1.3 12 44-55 16-27 (70)
443 COG2996 Predicted RNA-bindinin 30.7 47 0.001 25.7 2.4 28 10-37 247-274 (287)
444 cd01104 HTH_MlrA-CarA Helix-Tu 30.2 48 0.001 18.7 2.0 22 63-84 2-23 (68)
445 PRK10079 phosphonate metabolis 30.0 54 0.0012 23.4 2.6 45 26-86 14-60 (241)
446 COG1414 IclR Transcriptional r 30.0 1.3E+02 0.0028 22.0 4.6 39 47-85 3-43 (246)
447 TIGR02395 rpoN_sigma RNA polym 29.9 38 0.00081 27.2 1.9 37 47-83 302-340 (429)
448 COG1349 GlpR Transcriptional r 29.9 82 0.0018 23.2 3.6 24 62-85 20-43 (253)
449 TIGR03337 phnR transcriptional 29.6 1.8E+02 0.0039 20.2 5.2 42 27-85 8-49 (231)
450 TIGR01529 argR_whole arginine 29.5 38 0.00082 23.1 1.6 15 70-84 30-44 (146)
451 TIGR03734 PRTRC_parB PRTRC sys 29.3 97 0.0021 26.1 4.2 40 44-83 91-131 (554)
452 PRK15008 HTH-type transcriptio 29.2 67 0.0015 22.3 2.9 36 48-83 25-60 (212)
453 PF03965 Penicillinase_R: Peni 29.2 1.3E+02 0.0028 19.1 4.1 39 46-85 3-45 (115)
454 PRK14165 winged helix-turn-hel 29.1 81 0.0018 23.1 3.4 25 62-86 22-46 (217)
455 PRK10225 DNA-binding transcrip 29.1 1.6E+02 0.0034 21.1 4.9 41 26-83 15-55 (257)
456 PF07526 POX: Associated with 29.0 55 0.0012 22.4 2.3 62 19-90 75-139 (140)
457 PF10654 DUF2481: Protein of u 28.8 62 0.0014 22.0 2.5 35 43-81 66-100 (126)
458 COG2522 Predicted transcriptio 28.1 45 0.00098 22.5 1.8 23 61-83 22-44 (119)
459 KOG3414 Component of the U4/U6 28.0 26 0.00057 24.3 0.6 31 61-91 20-50 (142)
460 PRK09393 ftrA transcriptional 28.0 1.2E+02 0.0025 22.6 4.1 29 58-86 231-259 (322)
461 PRK13503 transcriptional activ 27.9 2.2E+02 0.0049 20.1 5.7 27 60-86 186-212 (278)
462 PF06970 RepA_N: Replication i 27.6 47 0.001 20.4 1.7 22 63-84 54-75 (76)
463 COG2909 MalT ATP-dependent tra 27.5 50 0.0011 29.3 2.3 34 55-88 840-873 (894)
464 TIGR02612 mob_myst_A mobile my 27.4 49 0.0011 22.9 1.9 27 57-83 34-60 (150)
465 PF09494 Slx4: Slx4 endonuclea 27.4 1E+02 0.0022 18.0 3.1 44 2-46 3-46 (64)
466 PRK05658 RNA polymerase sigma 27.4 1.3E+02 0.0027 25.1 4.6 44 46-89 558-604 (619)
467 PF01476 LysM: LysM domain; I 27.3 25 0.00054 18.2 0.3 24 57-80 2-25 (44)
468 PRK10336 DNA-binding transcrip 27.3 84 0.0018 20.8 3.0 37 53-89 156-201 (219)
469 cd00167 SANT 'SWI3, ADA2, N-Co 27.2 91 0.002 15.4 3.9 24 62-85 20-44 (45)
470 PRK11523 DNA-binding transcrip 26.8 1.6E+02 0.0036 21.0 4.7 43 24-83 12-54 (253)
471 PF05944 Phage_term_smal: Phag 26.8 71 0.0015 21.7 2.6 38 46-88 63-100 (132)
472 PF01418 HTH_6: Helix-turn-hel 26.7 67 0.0014 19.2 2.2 39 46-84 16-57 (77)
473 PRK09802 DNA-binding transcrip 26.7 91 0.002 23.1 3.4 24 62-85 32-55 (269)
474 PRK05932 RNA polymerase factor 26.6 45 0.00097 27.0 1.8 37 47-83 327-365 (455)
475 PF13565 HTH_32: Homeodomain-l 26.2 46 0.00099 19.3 1.4 35 47-81 33-76 (77)
476 PRK00423 tfb transcription ini 26.0 2.9E+02 0.0064 20.9 8.1 72 18-89 135-210 (310)
477 COG0583 LysR Transcriptional r 25.8 80 0.0017 22.0 2.8 31 55-85 9-39 (297)
478 PF12834 Phage_int_SAM_2: Phag 25.5 1.8E+02 0.0039 18.2 4.7 48 24-71 27-75 (91)
479 PRK00423 tfb transcription ini 25.5 3E+02 0.0065 20.8 8.4 76 14-89 225-304 (310)
480 COG3139 Uncharacterized protei 25.5 1.9E+02 0.0042 18.6 5.5 58 21-79 10-87 (90)
481 cd07153 Fur_like Ferric uptake 25.3 1.4E+02 0.0031 18.6 3.7 16 72-87 32-47 (116)
482 TIGR02297 HpaA 4-hydroxyphenyl 25.2 77 0.0017 22.7 2.7 29 58-86 199-227 (287)
483 PRK09726 antitoxin HipB; Provi 25.2 71 0.0015 19.5 2.2 27 57-83 21-47 (88)
484 PF14291 DUF4371: Domain of un 24.8 56 0.0012 23.6 1.9 45 41-88 159-210 (235)
485 KOG0946 ER-Golgi vesicle-tethe 24.7 1.7E+02 0.0037 26.2 4.9 42 24-67 208-249 (970)
486 PRK10163 DNA-binding transcrip 24.6 1.8E+02 0.0038 21.4 4.6 43 45-87 22-66 (271)
487 PRK11169 leucine-responsive tr 24.6 1E+02 0.0022 21.0 3.1 26 62-87 29-54 (164)
488 PRK15185 transcriptional regul 24.3 2E+02 0.0044 22.3 5.0 44 41-84 201-245 (309)
489 PF06782 UPF0236: Uncharacteri 24.0 1.4E+02 0.003 24.2 4.2 54 27-85 103-163 (470)
490 PRK09943 DNA-binding transcrip 23.8 60 0.0013 22.3 1.9 27 57-83 16-42 (185)
491 PRK11179 DNA-binding transcrip 23.8 1E+02 0.0022 20.7 3.0 26 62-87 24-49 (153)
492 PRK15183 Vi polysaccharide bio 23.8 70 0.0015 21.7 2.1 24 63-86 100-123 (143)
493 PF05344 DUF746: Domain of Unk 23.7 1.8E+02 0.0039 17.7 3.7 36 50-85 2-37 (65)
494 PRK13832 plasmid partitioning 23.6 1.2E+02 0.0025 25.5 3.7 38 44-81 101-138 (520)
495 TIGR02431 pcaR_pcaU beta-ketoa 23.4 1.8E+02 0.004 20.8 4.4 41 46-86 7-49 (248)
496 PF13601 HTH_34: Winged helix 23.4 1.6E+02 0.0035 17.8 3.6 29 59-87 12-40 (80)
497 PHA03078 transcriptional elong 23.3 82 0.0018 23.5 2.5 25 66-90 189-213 (219)
498 COG2207 AraC AraC-type DNA-bin 23.1 1.1E+02 0.0023 18.5 2.8 27 60-86 35-61 (127)
499 PF09758 FPL: Uncharacterised 23.0 1E+02 0.0022 21.5 2.8 76 11-89 14-99 (149)
500 PF08765 Mor: Mor transcriptio 22.9 82 0.0018 20.1 2.2 27 61-87 72-98 (108)
No 1
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=98.92 E-value=2.8e-09 Score=62.00 Aligned_cols=47 Identities=28% Similarity=0.365 Sum_probs=44.7
Q ss_pred CccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHHh
Q 036324 44 TVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAIL 90 (91)
Q Consensus 44 ~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai~ 90 (91)
..+.++|+.+.|..+.+|.++.+++.+||.|.+||||+|+++++.+.
T Consensus 2 kLs~~d~lll~L~~LR~~~~~~~La~~FgIs~stvsri~~~~~~~L~ 48 (53)
T PF13613_consen 2 KLSLEDQLLLTLMYLRLNLTFQDLAYRFGISQSTVSRIFHEWIPLLY 48 (53)
T ss_pred CCCHHHHHHHHHHHHHcCCcHhHHhhheeecHHHHHHHHHHHHHHHH
Confidence 57899999999999999999999999999999999999999998874
No 2
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=97.27 E-value=0.00034 Score=39.14 Aligned_cols=40 Identities=30% Similarity=0.305 Sum_probs=22.9
Q ss_pred CCccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHH
Q 036324 43 GTVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFN 83 (91)
Q Consensus 43 ~~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~ 83 (91)
++.|.+|...|.-+ ...|.+.+.|+..+++|.+||+|.++
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 46778888887766 57889999999999999999999876
No 3
>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=96.50 E-value=0.0033 Score=40.01 Aligned_cols=39 Identities=15% Similarity=0.090 Sum_probs=29.8
Q ss_pred HHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHH
Q 036324 50 QLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNA 88 (91)
Q Consensus 50 ~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~a 88 (91)
.+.+--||+.++++.|+++..||.|.+||++-+.+=|..
T Consensus 8 ~i~i~~yIi~~~aTVR~~Ak~FGvSKSTVHkDvteRL~~ 46 (82)
T PF12116_consen 8 VIEIANYIIETKATVRQAAKVFGVSKSTVHKDVTERLPK 46 (82)
T ss_dssp HHHHHHHHHHH---HHHHHHHHTS-HHHHHHHHTTHHHH
T ss_pred HHHHHHHHHHcccHHHHHHHHHCCcHHHHHHHHHHHHHh
Confidence 456778999999999999999999999999988765543
No 4
>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=96.35 E-value=0.014 Score=39.87 Aligned_cols=77 Identities=16% Similarity=0.115 Sum_probs=50.9
Q ss_pred hHHhhcCChhHHHHHhCCCHHHHHHHHHHHHhCCCCCCCCCccHHHHHHHHHHHhhc--------------Ccchhhhhh
Q 036324 4 LSRSIIGSDIECVNQLRMDKRTFELLCGLLRINGGLKADGTVSIEEQLCMFLHILAH--------------HVKSRTIHS 69 (91)
Q Consensus 4 l~~ll~~~~~~c~~~fRM~~~~F~~L~~~L~~~~~l~~s~~v~veE~vamFL~i~~~--------------~~~~r~i~~ 69 (91)
+.+++..+|.-....++.-...+..+.+.+.. ...-+++++||-||..++. +.+..++++
T Consensus 78 ~~~l~~~~p~l~~~~~~~l~~~l~~~~~~~~~------l~~~~~~~Rla~~L~~l~~~~~~~~~~~~~~~~~~t~~~iA~ 151 (193)
T TIGR03697 78 VEKAIEEDPDLSMLLLQGLSSRILQTEMMIET------LAHRDMGSRLVSFLLILCRDFGVPGQRGVTIDLRLSHQAIAE 151 (193)
T ss_pred HHHHHHHChHHHHHHHHHHHHHHHHHHHHHHH------HHhCCHHHHHHHHHHHHHHHhCCCCCCeEEecCCCCHHHHHH
Confidence 44555556655555554433333333333222 2345789999999987542 358999999
Q ss_pred ccccchhhHHHHHHHHH
Q 036324 70 RFLRSRETISRYFNLVL 86 (91)
Q Consensus 70 ~F~~S~eTisr~f~~Vl 86 (91)
.-|-|++||||.+++.-
T Consensus 152 ~lG~tretvsR~l~~l~ 168 (193)
T TIGR03697 152 AIGSTRVTITRLLGDLR 168 (193)
T ss_pred HhCCcHHHHHHHHHHHH
Confidence 99999999999998754
No 5
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=96.34 E-value=0.0064 Score=41.99 Aligned_cols=42 Identities=17% Similarity=0.139 Sum_probs=38.0
Q ss_pred CCccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHH
Q 036324 43 GTVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNL 84 (91)
Q Consensus 43 ~~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~ 84 (91)
+.-+.+++-+.|-+.++.|.|.|+|+.+|++|.+||.+..+.
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 345778999999999999999999999999999999998764
No 6
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=96.30 E-value=0.022 Score=40.56 Aligned_cols=78 Identities=8% Similarity=-0.000 Sum_probs=52.8
Q ss_pred hHHhhcCChhHHHHHhCCCHHHHHHHHHHHHhCCCCCCCCCccHHHHHHHHHHHhhcC----cchhhhhhccccchhhHH
Q 036324 4 LSRSIIGSDIECVNQLRMDKRTFELLCGLLRINGGLKADGTVSIEEQLCMFLHILAHH----VKSRTIHSRFLRSRETIS 79 (91)
Q Consensus 4 l~~ll~~~~~~c~~~fRM~~~~F~~L~~~L~~~~~l~~s~~v~veE~vamFL~i~~~~----~~~r~i~~~F~~S~eTis 79 (91)
+.+++..+|.-.....++-..-+..+...+.. ....+++++||-||.-.+.+ .+..+++...|-|++|||
T Consensus 114 ~~~ll~~~p~~~~~~~~~l~~~~~~~~~~~~~------~~~~~~~~Rla~~L~~~~~~~~~~~t~~~lA~~lG~sretvs 187 (226)
T PRK10402 114 CRPLLLNDALFLRKLCKFLSHKNYRNIVSLTQ------NQSFPLENRLAAFILLTQEGDLYHEKHTQAAEYLGVSYRHLL 187 (226)
T ss_pred HHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHH------hccChHHHHHHHHHHhcccCCcccchHHHHHHHHCCcHHHHH
Confidence 45566667766666555444443333333332 12348999999999865432 467899999999999999
Q ss_pred HHHHHHHH
Q 036324 80 RYFNLVLN 87 (91)
Q Consensus 80 r~f~~Vl~ 87 (91)
|.+.+.-+
T Consensus 188 R~L~~L~~ 195 (226)
T PRK10402 188 YVLAQFIQ 195 (226)
T ss_pred HHHHHHHH
Confidence 99987643
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=96.22 E-value=0.02 Score=31.99 Aligned_cols=45 Identities=20% Similarity=0.224 Sum_probs=36.4
Q ss_pred CccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 44 TVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 44 ~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
..+.+|+-.+-++. ..+.++.+|+..+|.|.+||++..+..++.+
T Consensus 4 ~L~~~er~vi~~~y-~~~~t~~eIa~~lg~s~~~V~~~~~~al~kL 48 (50)
T PF04545_consen 4 QLPPREREVIRLRY-FEGLTLEEIAERLGISRSTVRRILKRALKKL 48 (50)
T ss_dssp TS-HHHHHHHHHHH-TST-SHHHHHHHHTSCHHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHh-cCCCCHHHHHHHHCCcHHHHHHHHHHHHHHh
Confidence 35667777666666 8899999999999999999999999988765
No 8
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=96.07 E-value=0.021 Score=31.36 Aligned_cols=43 Identities=16% Similarity=0.254 Sum_probs=34.2
Q ss_pred ccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 45 VSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 45 v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
++..|.- ++.+ ...+.++..|+..++.|.+||.++.+.+...+
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 46889999999999999999999999987765
No 9
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=95.93 E-value=0.0087 Score=33.32 Aligned_cols=27 Identities=33% Similarity=0.469 Sum_probs=21.0
Q ss_pred HhhcCcchhhhhhccccchhhHHHHHH
Q 036324 57 ILAHHVKSRTIHSRFLRSRETISRYFN 83 (91)
Q Consensus 57 i~~~~~~~r~i~~~F~~S~eTisr~f~ 83 (91)
....+.+..+|+..|+.|..||+|++.
T Consensus 17 l~~~G~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 17 LYAEGMSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp HHHTT--HHHHHHHTTS-HHHHHHHHC
T ss_pred HHHCCCCHHHHHHHHCcCHHHHHHHHh
Confidence 346679999999999999999999975
No 10
>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=95.92 E-value=0.027 Score=35.49 Aligned_cols=47 Identities=15% Similarity=0.207 Sum_probs=42.1
Q ss_pred CCccHHHHHHHHHHHhhcCcchhhhhhccc-cchhhHHHHHHHHHHHH
Q 036324 43 GTVSIEEQLCMFLHILAHHVKSRTIHSRFL-RSRETISRYFNLVLNAI 89 (91)
Q Consensus 43 ~~v~veE~vamFL~i~~~~~~~r~i~~~F~-~S~eTisr~f~~Vl~ai 89 (91)
+.+..--|+||+|-.--.|.+..+|+..|+ ++.+||+.-.+.|=+.+
T Consensus 26 ~~~~~aR~ia~yl~~~~~~~s~~~Ig~~fg~r~hStV~~a~~ri~~~~ 73 (90)
T cd06571 26 KEIALARQIAMYLARELTGLSLPEIGRAFGGRDHSTVLHAVRKIEELL 73 (90)
T ss_pred cCcchHHHHHHHHHHHHhCCCHHHHHHHhCCCCHhHHHHHHHHHHHHH
Confidence 478999999999999999999999999999 99999999888775543
No 11
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=95.87 E-value=0.042 Score=38.04 Aligned_cols=78 Identities=13% Similarity=0.063 Sum_probs=49.8
Q ss_pred hHHhhcCChhHHHHHhCCCHHHHHHHHHHHHhCCCCCCCCCccHHHHHHHHHHHhhc-------------Ccchhhhhhc
Q 036324 4 LSRSIIGSDIECVNQLRMDKRTFELLCGLLRINGGLKADGTVSIEEQLCMFLHILAH-------------HVKSRTIHSR 70 (91)
Q Consensus 4 l~~ll~~~~~~c~~~fRM~~~~F~~L~~~L~~~~~l~~s~~v~veE~vamFL~i~~~-------------~~~~r~i~~~ 70 (91)
+.+++..+|.-.....+.-.+....+.+.+ .....-++.+++|-+|+.++. ..+..++++.
T Consensus 104 ~~~l~~~~p~~~~~~~~~~~~~l~~~~~~~------~~~~~~~~~~Rl~~~L~~l~~~~~~~~~~~~~~~~~t~~~lA~~ 177 (211)
T PRK11753 104 FRQLIQVNPDILMALSAQMARRLQNTSRKV------GDLAFLDVTGRIAQTLLDLAKQPDAMTHPDGMQIKITRQEIGRI 177 (211)
T ss_pred HHHHHHHCHHHHHHHHHHHHHHHHHHHHHH------HHHHhcChhhHHHHHHHHHHHhcCCcCCCCceecCCCHHHHHHH
Confidence 344555555555444433222222222222 233457899999999987653 3456899999
Q ss_pred cccchhhHHHHHHHHHH
Q 036324 71 FLRSRETISRYFNLVLN 87 (91)
Q Consensus 71 F~~S~eTisr~f~~Vl~ 87 (91)
.|-|++||||.+++.-+
T Consensus 178 lG~tr~tvsR~l~~l~~ 194 (211)
T PRK11753 178 VGCSREMVGRVLKMLED 194 (211)
T ss_pred hCCCHHHHHHHHHHHHH
Confidence 99999999999987643
No 12
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=95.77 E-value=0.042 Score=38.92 Aligned_cols=77 Identities=17% Similarity=0.083 Sum_probs=56.6
Q ss_pred hhHHhhcCChhHHHHHhCCCHHHHHHHHHHHHhCCCCCCCCCccHHHHHHHHHHHhhc--------------Ccchhhhh
Q 036324 3 HLSRSIIGSDIECVNQLRMDKRTFELLCGLLRINGGLKADGTVSIEEQLCMFLHILAH--------------HVKSRTIH 68 (91)
Q Consensus 3 ~l~~ll~~~~~~c~~~fRM~~~~F~~L~~~L~~~~~l~~s~~v~veE~vamFL~i~~~--------------~~~~r~i~ 68 (91)
.+.+++..+|.-.....+.-...+..+...+... ..-++++++|-||..++. +.+..+|+
T Consensus 118 ~f~~l~~~~p~~~~~~~~~~~~~~~~~~~~~~~l------~~~~~~~Rla~~L~~l~~~~~~~~~~~~~~~~~lt~~~iA 191 (235)
T PRK11161 118 TLDDLSGKMPKLRQQIMRLMSGEIKGDQEMILLL------SKKNAEERLAAFIYNLSRRFAQRGFSPREFRLTMTRGDIG 191 (235)
T ss_pred HHHHHHHHChHHHHHHHHHHHHHHHHHHHHHHHH------hCCCHHHHHHHHHHHHHHHHhhcCCCCceeEccccHHHHH
Confidence 3556677777777776666666666555555432 235789999999998763 35778999
Q ss_pred hccccchhhHHHHHHHH
Q 036324 69 SRFLRSRETISRYFNLV 85 (91)
Q Consensus 69 ~~F~~S~eTisr~f~~V 85 (91)
+..|.|++||||.+.+.
T Consensus 192 ~~lG~sr~tvsR~l~~l 208 (235)
T PRK11161 192 NYLGLTVETISRLLGRF 208 (235)
T ss_pred HHhCCcHHHHHHHHHHH
Confidence 99999999999998754
No 13
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=95.72 E-value=0.057 Score=38.71 Aligned_cols=77 Identities=16% Similarity=0.127 Sum_probs=54.8
Q ss_pred hhHHhhcCChhHHHHHhCCCHHHHHHHHHHHHhCCCCCCCCCccHHHHHHHHHHHhhc----------Ccchhhhhhccc
Q 036324 3 HLSRSIIGSDIECVNQLRMDKRTFELLCGLLRINGGLKADGTVSIEEQLCMFLHILAH----------HVKSRTIHSRFL 72 (91)
Q Consensus 3 ~l~~ll~~~~~~c~~~fRM~~~~F~~L~~~L~~~~~l~~s~~v~veE~vamFL~i~~~----------~~~~r~i~~~F~ 72 (91)
.+.+++..+|.-....++.--..+..+.+.+.. ...-+++++||-||...+. ..+..+|++..|
T Consensus 117 ~f~~l~~~~p~l~~~l~~~l~~~l~~~~~~~~~------l~~~~~~~Rla~~Ll~l~~~~g~~~~i~i~lt~~~IA~~lG 190 (230)
T PRK09391 117 SLEQAAATDVDVARALLSLTAGGLRHAQDHMLL------LGRKTAMERVAAFLLEMDERLGGAGMMALPMSRRDIADYLG 190 (230)
T ss_pred HHHHHHhhChHHHHHHHHHHHHHHHHHHHHHHH------HcCCCHHHHHHHHHHHHHHHhCCCCEEEecCCHHHHHHHHC
Confidence 355666667766666665555555555444433 2235899999999998744 256789999999
Q ss_pred cchhhHHHHHHHH
Q 036324 73 RSRETISRYFNLV 85 (91)
Q Consensus 73 ~S~eTisr~f~~V 85 (91)
.|++|+||.+++.
T Consensus 191 isretlsR~L~~L 203 (230)
T PRK09391 191 LTIETVSRALSQL 203 (230)
T ss_pred CCHHHHHHHHHHH
Confidence 9999999998865
No 14
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=95.48 E-value=0.026 Score=32.62 Aligned_cols=40 Identities=28% Similarity=0.376 Sum_probs=29.2
Q ss_pred CCccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHH
Q 036324 43 GTVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFN 83 (91)
Q Consensus 43 ~~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~ 83 (91)
+..|++|++.|--. +-.|.+.++|+..||.+.+||+.+..
T Consensus 5 ~~LTl~eK~~iI~~-~e~g~s~~~ia~~fgv~~sTv~~I~K 44 (53)
T PF04218_consen 5 KSLTLEEKLEIIKR-LEEGESKRDIAREFGVSRSTVSTILK 44 (53)
T ss_dssp SS--HHHHHHHHHH-HHCTT-HHHHHHHHT--CCHHHHHHH
T ss_pred ccCCHHHHHHHHHH-HHcCCCHHHHHHHhCCCHHHHHHHHH
Confidence 46899999998665 45566999999999999999998875
No 15
>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=95.36 E-value=0.033 Score=33.81 Aligned_cols=43 Identities=16% Similarity=0.169 Sum_probs=35.4
Q ss_pred CCccHHHHHHHHHHHhhcCcchhhhhhccc-cchhhHHHHHHHH
Q 036324 43 GTVSIEEQLCMFLHILAHHVKSRTIHSRFL-RSRETISRYFNLV 85 (91)
Q Consensus 43 ~~v~veE~vamFL~i~~~~~~~r~i~~~F~-~S~eTisr~f~~V 85 (91)
+.+.---++||+|-.--.+.+..+|+..|+ ++.+||..-.+.|
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 357778899999999999999999999999 9999998877664
No 16
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=95.31 E-value=0.088 Score=37.37 Aligned_cols=76 Identities=16% Similarity=0.067 Sum_probs=51.7
Q ss_pred hHHhhcCChhHHHHHhCCCHHHHHHHHHHHHhCCCCCCCCCccHHHHHHHHHHHhhc----------Ccchhhhhhcccc
Q 036324 4 LSRSIIGSDIECVNQLRMDKRTFELLCGLLRINGGLKADGTVSIEEQLCMFLHILAH----------HVKSRTIHSRFLR 73 (91)
Q Consensus 4 l~~ll~~~~~~c~~~fRM~~~~F~~L~~~L~~~~~l~~s~~v~veE~vamFL~i~~~----------~~~~r~i~~~F~~ 73 (91)
+.+++..+|.-.....+.-...+..+.+.+.. ...-++++++|-||+..+. +.+..+|++..|-
T Consensus 112 ~~~l~~~~p~l~~~~~~~l~~~~~~~~~~~~~------~~~~~~~~Rla~~Ll~~~~~~~~~~~~~i~~t~~~iA~~lG~ 185 (236)
T PRK09392 112 VREAMSEDPGFMRAVVFELAGCYRGLVKSLKN------QKLRSSAERLANYLLKQSLRQGGADVVTLPYEKRVLASYLGM 185 (236)
T ss_pred HHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHH------hhcCCHHHHHHHHHHHhccccCCCcEEEeeCCHHHHHHHhCC
Confidence 34555566665555554444444444444443 2345899999999997654 2345789999999
Q ss_pred chhhHHHHHHHH
Q 036324 74 SRETISRYFNLV 85 (91)
Q Consensus 74 S~eTisr~f~~V 85 (91)
+++||||.+++.
T Consensus 186 tretvsR~l~~L 197 (236)
T PRK09392 186 TPENLSRAFAAL 197 (236)
T ss_pred ChhHHHHHHHHH
Confidence 999999999875
No 17
>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=95.27 E-value=0.062 Score=29.57 Aligned_cols=36 Identities=14% Similarity=0.171 Sum_probs=30.5
Q ss_pred HHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 53 MFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 53 mFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
++.+ +..+.+.++|+..++.|..||.++.+.+...+
T Consensus 8 i~~~-~~~~~s~~eia~~l~~s~~tv~~~~~~~~~~l 43 (57)
T cd06170 8 VLRL-LAEGKTNKEIADILGISEKTVKTHLRNIMRKL 43 (57)
T ss_pred HHHH-HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHh
Confidence 4444 46889999999999999999999999987754
No 18
>smart00351 PAX Paired Box domain.
Probab=95.15 E-value=0.055 Score=36.11 Aligned_cols=44 Identities=14% Similarity=0.103 Sum_probs=37.7
Q ss_pred CCCCccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHH
Q 036324 41 ADGTVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLV 85 (91)
Q Consensus 41 ~s~~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~V 85 (91)
..+..+.++...|.+..- .|.+.++|+.+|+.|..||+++++..
T Consensus 14 ~~~~~s~~~R~riv~~~~-~G~s~~~iA~~~gvs~~tV~kwi~r~ 57 (125)
T smart00351 14 NGRPLPDEERQRIVELAQ-NGVRPCDISRQLCVSHGCVSKILGRY 57 (125)
T ss_pred CCCCCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 346789999988887664 78899999999999999999998864
No 19
>cd00131 PAX Paired Box domain
Probab=95.06 E-value=0.06 Score=36.24 Aligned_cols=46 Identities=9% Similarity=0.034 Sum_probs=39.2
Q ss_pred CCCCCccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHH
Q 036324 40 KADGTVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVL 86 (91)
Q Consensus 40 ~~s~~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl 86 (91)
...+..|.+..-.|.+.. ..|.+.++|+.+|+.|..||+++.+..-
T Consensus 13 ~m~~~lS~d~R~rIv~~~-~~G~s~~~iA~~~~Vs~~tV~r~i~r~~ 58 (128)
T cd00131 13 VNGRPLPDSIRQRIVELA-QSGIRPCDISRQLRVSHGCVSKILNRYY 58 (128)
T ss_pred cCCCcCCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 345788999999888775 5899999999999999999999987643
No 20
>PRK06030 hypothetical protein; Provisional
Probab=94.82 E-value=0.085 Score=35.79 Aligned_cols=45 Identities=20% Similarity=0.206 Sum_probs=40.6
Q ss_pred CCccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHH
Q 036324 43 GTVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLN 87 (91)
Q Consensus 43 ~~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ 87 (91)
+.+..--|+||||-.--.+.+...|+..||++-+||+--++.|=+
T Consensus 51 k~i~~aRqIAMYL~r~~~~~sl~~IG~~FGRDHSTV~haikkIe~ 95 (124)
T PRK06030 51 REVSRIRQIAMYVAHVSLGWPMNEVALAFGRDRTTVGHACHTVED 95 (124)
T ss_pred cccchHHHHHHHHHHHHcCCCHHHHHHHHCCChhHHHHHHHHHHH
Confidence 468899999999999999999999999999999999988876543
No 21
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=94.71 E-value=0.03 Score=31.03 Aligned_cols=30 Identities=27% Similarity=0.310 Sum_probs=21.2
Q ss_pred HHhhcCcchhhhhhccccchhhHHHHHHHH
Q 036324 56 HILAHHVKSRTIHSRFLRSRETISRYFNLV 85 (91)
Q Consensus 56 ~i~~~~~~~r~i~~~F~~S~eTisr~f~~V 85 (91)
..+..+.+.+.|+..|+.|..||+++.+.-
T Consensus 12 ~l~~~G~s~~~ia~~lgvs~~Tv~~w~kr~ 41 (50)
T PF13384_consen 12 RLLREGWSIREIAKRLGVSRSTVYRWIKRY 41 (50)
T ss_dssp HHHHHT--HHHHHHHHTS-HHHHHHHHT--
T ss_pred HHHHCCCCHHHHHHHHCcCHHHHHHHHHHc
Confidence 333449999999999999999999997653
No 22
>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=94.52 E-value=0.1 Score=33.33 Aligned_cols=36 Identities=22% Similarity=0.124 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHH
Q 036324 47 IEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFN 83 (91)
Q Consensus 47 veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~ 83 (91)
..++-.|+.| ++.+.+++.|+..++.|..||+|+.+
T Consensus 37 Ls~R~~I~~l-l~~G~S~~eIA~~LgISrsTIyRi~R 72 (88)
T TIGR02531 37 LAQRLQVAKM-LKQGKTYSDIEAETGASTATISRVKR 72 (88)
T ss_pred hhHHHHHHHH-HHCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 5566555555 67789999999999999999999543
No 23
>PRK04217 hypothetical protein; Provisional
Probab=94.41 E-value=0.12 Score=34.34 Aligned_cols=47 Identities=15% Similarity=0.021 Sum_probs=38.0
Q ss_pred CCCccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 42 DGTVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 42 s~~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
...++.+|+ .++...--++.++.+|+..++.|..||+++++...+.+
T Consensus 40 ~~~Lt~eer-eai~l~~~eGlS~~EIAk~LGIS~sTV~r~L~RArkkL 86 (110)
T PRK04217 40 PIFMTYEEF-EALRLVDYEGLTQEEAGKRMGVSRGTVWRALTSARKKV 86 (110)
T ss_pred cccCCHHHH-HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 346778887 44455555889999999999999999999999877665
No 24
>PF05225 HTH_psq: helix-turn-helix, Psq domain; InterPro: IPR007889 This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster []. In pipsqueak this domain binds to GAGA sequence []. The pipsqueak family, which includes proteins from fungi, sea urchins, nematodes, insects, and vertebrates appear to be proteins essential for sequence-specific targeting of a polycomb group protein complex [].; GO: 0003677 DNA binding; PDB: 2COB_A.
Probab=94.10 E-value=0.11 Score=29.09 Aligned_cols=36 Identities=19% Similarity=0.278 Sum_probs=25.3
Q ss_pred HHHHHHHHHHhhcC-cchhhhhhccccchhhHHHHHH
Q 036324 48 EEQLCMFLHILAHH-VKSRTIHSRFLRSRETISRYFN 83 (91)
Q Consensus 48 eE~vamFL~i~~~~-~~~r~i~~~F~~S~eTisr~f~ 83 (91)
||++.--+-.+-.| .+.|.++..|+.+.+|++++.+
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 45555555555555 9999999999999999998765
No 25
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=94.06 E-value=0.18 Score=34.68 Aligned_cols=44 Identities=11% Similarity=0.144 Sum_probs=36.2
Q ss_pred CccHHHHHHHHHHHhhc--------------CcchhhhhhccccchhhHHHHHHHHHH
Q 036324 44 TVSIEEQLCMFLHILAH--------------HVKSRTIHSRFLRSRETISRYFNLVLN 87 (91)
Q Consensus 44 ~v~veE~vamFL~i~~~--------------~~~~r~i~~~F~~S~eTisr~f~~Vl~ 87 (91)
.-+++++||.||..++. +.+..+|++.-|-|++||||.+++.-+
T Consensus 118 ~~~~~~Rla~~Ll~l~~~~~~~~~~~~~~~~~~t~~~iA~~lG~tretvsR~l~~l~~ 175 (202)
T PRK13918 118 GQRLKNRIAAALLELSDTPLATQEDSGETMIYATHDELAAAVGSVRETVTKVIGELSR 175 (202)
T ss_pred hCchHHHHHHHHHHHHHHhCCCCCCCCeEEecCCHHHHHHHhCccHHHHHHHHHHHHH
Confidence 34689999999987664 246889999999999999999987643
No 26
>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=93.47 E-value=0.19 Score=27.85 Aligned_cols=39 Identities=13% Similarity=0.124 Sum_probs=31.1
Q ss_pred HHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHH
Q 036324 50 QLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNA 88 (91)
Q Consensus 50 ~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~a 88 (91)
++.|-......+.+..++++.++-|.+|||+|.....++
T Consensus 4 R~~Il~~L~~~~~~~~el~~~l~~s~~~vs~hL~~L~~~ 42 (47)
T PF01022_consen 4 RLRILKLLSEGPLTVSELAEELGLSQSTVSHHLKKLREA 42 (47)
T ss_dssp HHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred HHHHHHHHHhCCCchhhHHHhccccchHHHHHHHHHHHC
Confidence 455666666678999999999999999999999876553
No 27
>PF13518 HTH_28: Helix-turn-helix domain
Probab=93.31 E-value=0.2 Score=27.52 Aligned_cols=35 Identities=26% Similarity=0.222 Sum_probs=27.2
Q ss_pred HHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHH
Q 036324 51 LCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVL 86 (91)
Q Consensus 51 vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl 86 (91)
+.+-..+. .+.+.+.++..|+.|..||+++.....
T Consensus 3 ~~iv~~~~-~g~s~~~~a~~~gis~~tv~~w~~~y~ 37 (52)
T PF13518_consen 3 LQIVELYL-EGESVREIAREFGISRSTVYRWIKRYR 37 (52)
T ss_pred HHHHHHHH-cCCCHHHHHHHHCCCHhHHHHHHHHHH
Confidence 34444444 466999999999999999999987654
No 28
>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=93.30 E-value=0.15 Score=29.21 Aligned_cols=27 Identities=22% Similarity=0.244 Sum_probs=23.3
Q ss_pred CcchhhhhhccccchhhHHHHHHHHHH
Q 036324 61 HVKSRTIHSRFLRSRETISRYFNLVLN 87 (91)
Q Consensus 61 ~~~~r~i~~~F~~S~eTisr~f~~Vl~ 87 (91)
..+..++++.++.|.+||+|.+....+
T Consensus 25 ~~s~~ela~~~g~s~~tv~r~l~~L~~ 51 (67)
T cd00092 25 PLTRQEIADYLGLTRETVSRTLKELEE 51 (67)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 368899999999999999999987543
No 29
>PF13730 HTH_36: Helix-turn-helix domain
Probab=92.77 E-value=0.23 Score=27.93 Aligned_cols=24 Identities=21% Similarity=0.199 Sum_probs=21.9
Q ss_pred chhhhhhccccchhhHHHHHHHHH
Q 036324 63 KSRTIHSRFLRSRETISRYFNLVL 86 (91)
Q Consensus 63 ~~r~i~~~F~~S~eTisr~f~~Vl 86 (91)
|+..+++..+.|..||+|++++.-
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~L~ 50 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKELE 50 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHH
Confidence 789999999999999999998754
No 30
>KOG4585 consensus Predicted transposase [Replication, recombination and repair]
Probab=92.73 E-value=0.15 Score=39.48 Aligned_cols=61 Identities=20% Similarity=0.297 Sum_probs=51.0
Q ss_pred HhCCCHHHHHHHHHHHHhCCCCCC-----CCCccHHHHHHHHHHHhhcCcchhhhhhccccchhhH
Q 036324 18 QLRMDKRTFELLCGLLRINGGLKA-----DGTVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETI 78 (91)
Q Consensus 18 ~fRM~~~~F~~L~~~L~~~~~l~~-----s~~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTi 78 (91)
.|++++.+|.++|........-+. +..++..+.+|+.++.++++...+.++..|++..+|+
T Consensus 7 ~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~i~~~fg~~~~~~ 72 (326)
T KOG4585|consen 7 EFRKSYTTFDKICSLVQSLNVVKNSGFMLSSLLPADTLVAVALWRLKTGESLRTVEKKFGLGQSTC 72 (326)
T ss_pred HHHHHHHHHHHHhhhhhhhhhhcccchhhhccccHHhhhhhhhccccccchHHHHHHHcCCcchhh
Confidence 899999999999999666433222 1223399999999999999999999999999999998
No 31
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=92.68 E-value=0.25 Score=27.41 Aligned_cols=28 Identities=18% Similarity=0.190 Sum_probs=23.8
Q ss_pred hhcCcchhhhhhccccchhhHHHHHHHH
Q 036324 58 LAHHVKSRTIHSRFLRSRETISRYFNLV 85 (91)
Q Consensus 58 ~~~~~~~r~i~~~F~~S~eTisr~f~~V 85 (91)
+..+.++..|+..++.|-+||.|+|++.
T Consensus 24 ~~~~~s~~~vA~~~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 24 LRESRSFKDVARELGVSWSTVRRIFDRY 51 (52)
T ss_pred HhhcCCHHHHHHHHCCCHHHHHHHHHhh
Confidence 3444599999999999999999999863
No 32
>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=92.60 E-value=0.27 Score=28.47 Aligned_cols=41 Identities=12% Similarity=0.083 Sum_probs=33.6
Q ss_pred HHHHHHHHHH-hhcCcchhhhhhccccchhhHHHHHHHHHHH
Q 036324 48 EEQLCMFLHI-LAHHVKSRTIHSRFLRSRETISRYFNLVLNA 88 (91)
Q Consensus 48 eE~vamFL~i-~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~a 88 (91)
.-++.|.-+. ...+.+..++++.++.|.+|+|+++...-+|
T Consensus 10 p~R~~Il~~L~~~~~~t~~ela~~l~~~~~t~s~hL~~L~~a 51 (61)
T PF12840_consen 10 PTRLRILRLLASNGPMTVSELAEELGISQSTVSYHLKKLEEA 51 (61)
T ss_dssp HHHHHHHHHHHHCSTBEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 4456777777 7888999999999999999999999887654
No 33
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=92.55 E-value=0.42 Score=25.28 Aligned_cols=30 Identities=17% Similarity=0.154 Sum_probs=26.6
Q ss_pred hcCcchhhhhhccccchhhHHHHHHHHHHH
Q 036324 59 AHHVKSRTIHSRFLRSRETISRYFNLVLNA 88 (91)
Q Consensus 59 ~~~~~~r~i~~~F~~S~eTisr~f~~Vl~a 88 (91)
..+.++.+|+..++.|..||+++.+.....
T Consensus 24 ~~~~~~~~ia~~~~~s~~~i~~~~~~~~~~ 53 (55)
T cd06171 24 GEGLSYEEIAEILGISRSTVRQRLHRALKK 53 (55)
T ss_pred hcCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 478999999999999999999999887654
No 34
>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=92.50 E-value=0.19 Score=32.72 Aligned_cols=38 Identities=24% Similarity=0.294 Sum_probs=29.1
Q ss_pred cHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHH
Q 036324 46 SIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFN 83 (91)
Q Consensus 46 ~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~ 83 (91)
.+..+++++=-.+..+.++|.|+...|.|..||+|.=+
T Consensus 40 ~l~~R~~i~~~Ll~~~~tQrEIa~~lGiS~atIsR~sn 77 (94)
T TIGR01321 40 DLGDRIRIVNELLNGNMSQREIASKLGVSIATITRGSN 77 (94)
T ss_pred HHHHHHHHHHHHHhCCCCHHHHHHHhCCChhhhhHHHh
Confidence 34445555555556789999999999999999999643
No 35
>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=92.34 E-value=0.42 Score=26.20 Aligned_cols=36 Identities=14% Similarity=0.279 Sum_probs=26.6
Q ss_pred HHHHHHhhcC-cchhhhhhccccchhhHHHHHHHHHH
Q 036324 52 CMFLHILAHH-VKSRTIHSRFLRSRETISRYFNLVLN 87 (91)
Q Consensus 52 amFL~i~~~~-~~~r~i~~~F~~S~eTisr~f~~Vl~ 87 (91)
.|..++-.++ .+.++++...+-|..||++++++..+
T Consensus 7 ~Il~~l~~~~~~t~~ela~~~~is~~tv~~~l~~L~~ 43 (48)
T PF13412_consen 7 KILNYLRENPRITQKELAEKLGISRSTVNRYLKKLEE 43 (48)
T ss_dssp HHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 3444444444 89999999999999999999998765
No 36
>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=92.33 E-value=0.11 Score=27.46 Aligned_cols=24 Identities=25% Similarity=0.340 Sum_probs=18.9
Q ss_pred cchhhhhhccccchhhHHHHHHHH
Q 036324 62 VKSRTIHSRFLRSRETISRYFNLV 85 (91)
Q Consensus 62 ~~~r~i~~~F~~S~eTisr~f~~V 85 (91)
.+..+|++.-|-|.|||||.+...
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 467889999999999999998764
No 37
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=92.33 E-value=0.24 Score=23.63 Aligned_cols=35 Identities=29% Similarity=0.230 Sum_probs=25.3
Q ss_pred cHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHH
Q 036324 46 SIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRY 81 (91)
Q Consensus 46 ~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~ 81 (91)
+.++...+ +...-.+.+...++..|+.|..||+++
T Consensus 7 ~~~~~~~i-~~~~~~~~s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 7 TPEQIEEA-RRLLAAGESVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred CHHHHHHH-HHHHHcCCCHHHHHHHHCCCHHHHHHh
Confidence 44444333 333446679999999999999999986
No 38
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=92.04 E-value=0.43 Score=31.83 Aligned_cols=44 Identities=5% Similarity=0.099 Sum_probs=37.7
Q ss_pred CccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 44 TVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 44 ~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
.++.+++-++.|+. .|.++..|+..+|.|..||....+.....+
T Consensus 112 ~L~~~~r~il~l~~--~g~s~~eIA~~lgis~~tV~~~i~ra~~~L 155 (166)
T PRK09639 112 KMTERDRTVLLLRF--SGYSYKEIAEALGIKESSVGTTLARAKKKF 155 (166)
T ss_pred cCCHHHHHHHHHHH--cCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 35667787777877 999999999999999999999998877665
No 39
>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=91.99 E-value=0.27 Score=28.11 Aligned_cols=35 Identities=17% Similarity=0.277 Sum_probs=30.0
Q ss_pred HHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 55 LHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 55 L~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
|..++.|.++..|+...+.|..||..+...+.+.+
T Consensus 12 l~~l~~G~~~~eIA~~l~is~~tV~~~~~~i~~Kl 46 (58)
T PF00196_consen 12 LRLLAQGMSNKEIAEELGISEKTVKSHRRRIMKKL 46 (58)
T ss_dssp HHHHHTTS-HHHHHHHHTSHHHHHHHHHHHHHHHH
T ss_pred HHHHHhcCCcchhHHhcCcchhhHHHHHHHHHHHh
Confidence 45678899999999999999999999999988754
No 40
>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=91.88 E-value=0.28 Score=28.98 Aligned_cols=38 Identities=32% Similarity=0.373 Sum_probs=29.5
Q ss_pred HHHHHHHHHhhcC---------------cchhhhhhccccchhhHHHHHHHHH
Q 036324 49 EQLCMFLHILAHH---------------VKSRTIHSRFLRSRETISRYFNLVL 86 (91)
Q Consensus 49 E~vamFL~i~~~~---------------~~~r~i~~~F~~S~eTisr~f~~Vl 86 (91)
|+||-||..++.. .+..++++..|-|++||+|.+++.-
T Consensus 1 ~Rla~~Ll~l~~~~~~~~~~~~~~~~~~lt~~~iA~~~g~sr~tv~r~l~~l~ 53 (76)
T PF13545_consen 1 QRLARFLLELAERFGRRQDGDGIRIPLPLTQEEIADMLGVSRETVSRILKRLK 53 (76)
T ss_dssp HHHHHHHHHHHHHHEEEEETTEEEEEEESSHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred ChHHHHHHHHHHHHCCCCCCCCceEEecCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 4567777666533 4678999999999999999998754
No 41
>PRK00149 dnaA chromosomal replication initiation protein; Reviewed
Probab=91.81 E-value=0.34 Score=38.29 Aligned_cols=46 Identities=15% Similarity=0.167 Sum_probs=41.6
Q ss_pred CCccHHHHHHHHHHHhhcCcchhhhhhcc-ccchhhHHHHHHHHHHH
Q 036324 43 GTVSIEEQLCMFLHILAHHVKSRTIHSRF-LRSRETISRYFNLVLNA 88 (91)
Q Consensus 43 ~~v~veE~vamFL~i~~~~~~~r~i~~~F-~~S~eTisr~f~~Vl~a 88 (91)
+.+..--|+||+|-.--.+.+...|+..| +|+.+||+.-.+.|=+.
T Consensus 384 ~~~~~aR~iamyl~~~~~~~s~~~Ig~~fg~rdhstV~~a~~~i~~~ 430 (450)
T PRK00149 384 RNIARPRQIAMYLAKELTDLSLPEIGRAFGGRDHTTVLHAVRKIEKL 430 (450)
T ss_pred cccChHHHHHHHHHHHhcCCCHHHHHHHcCCCCHhHHHHHHHHHHHH
Confidence 57889999999999999999999999999 69999999988877543
No 42
>PF13551 HTH_29: Winged helix-turn helix
Probab=91.51 E-value=2 Score=26.70 Aligned_cols=73 Identities=19% Similarity=0.147 Sum_probs=50.5
Q ss_pred hhHHHHHhCCCHHHHHHHHHHHHhCC--CCCC-C----C--C-ccHHHHHHHHHHHhhcC------cchhhhhhcc----
Q 036324 12 DIECVNQLRMDKRTFELLCGLLRING--GLKA-D----G--T-VSIEEQLCMFLHILAHH------VKSRTIHSRF---- 71 (91)
Q Consensus 12 ~~~c~~~fRM~~~~F~~L~~~L~~~~--~l~~-s----~--~-v~veE~vamFL~i~~~~------~~~r~i~~~F---- 71 (91)
..+.-..+++++.|+.+..+..++.+ ++.+ + + + ++.++.-.+-=++..+. .+...++...
T Consensus 15 ~~~ia~~lg~s~~Tv~r~~~~~~~~G~~~l~~~~~~~g~~~~~l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~ 94 (112)
T PF13551_consen 15 IAEIARRLGISRRTVYRWLKRYREGGIEGLLPRKPRGGRPRKRLSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEE 94 (112)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHcccHHHHHhccccCCCCCCCCCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhc
Confidence 78888999999999999999988766 3433 2 1 2 55555555554555543 3455665532
Q ss_pred ---ccchhhHHHHHHH
Q 036324 72 ---LRSRETISRYFNL 84 (91)
Q Consensus 72 ---~~S~eTisr~f~~ 84 (91)
..|.+||+|++++
T Consensus 95 ~~~~~s~~ti~r~L~~ 110 (112)
T PF13551_consen 95 FGIDVSPSTIRRILKR 110 (112)
T ss_pred cCccCCHHHHHHHHHH
Confidence 6899999999875
No 43
>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=91.25 E-value=0.36 Score=30.91 Aligned_cols=37 Identities=19% Similarity=0.103 Sum_probs=28.9
Q ss_pred HHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHH
Q 036324 47 IEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFN 83 (91)
Q Consensus 47 veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~ 83 (91)
+..++.++=-.+-.+.+||.|+...|.|..||+|.=+
T Consensus 35 l~~R~~va~~lL~~g~syreIa~~tgvS~aTItRvsr 71 (87)
T PF01371_consen 35 LAQRWQVAKELLDEGKSYREIAEETGVSIATITRVSR 71 (87)
T ss_dssp HHHHHHHHHHHHHTTSSHHHHHHHHTSTHHHHHHHHH
T ss_pred HHHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 4445555544667899999999999999999998643
No 44
>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=91.16 E-value=0.6 Score=26.13 Aligned_cols=36 Identities=17% Similarity=0.162 Sum_probs=26.5
Q ss_pred HHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHH
Q 036324 51 LCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVL 86 (91)
Q Consensus 51 vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl 86 (91)
+-.+|..-..+.+-..+++.|+.|..||.+++.+.=
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 333443444447899999999999999999998763
No 45
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=90.99 E-value=0.9 Score=25.29 Aligned_cols=44 Identities=11% Similarity=0.055 Sum_probs=30.1
Q ss_pred CccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHH
Q 036324 44 TVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNA 88 (91)
Q Consensus 44 ~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~a 88 (91)
.+|..++-++.| .--.|.++..|+..++.|.+||.+..+..+..
T Consensus 10 ~L~~~~r~i~~l-~~~~g~s~~eIa~~l~~s~~~v~~~l~ra~~~ 53 (54)
T PF08281_consen 10 QLPERQREIFLL-RYFQGMSYAEIAEILGISESTVKRRLRRARKK 53 (54)
T ss_dssp CS-HHHHHHHHH-HHTS---HHHHHHHCTS-HHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHH-HHHHCcCHHHHHHHHCcCHHHHHHHHHHHHhh
Confidence 355566655554 45568999999999999999999999887654
No 46
>PRK14088 dnaA chromosomal replication initiation protein; Provisional
Probab=90.94 E-value=0.59 Score=37.22 Aligned_cols=48 Identities=17% Similarity=0.208 Sum_probs=42.7
Q ss_pred CCCccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 42 DGTVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 42 s~~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
++.+..--|+||||-.=-.+.++..|+..||++.+||+...+.|=..+
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 357889999999999999999999999999999999999988876543
No 47
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=90.62 E-value=0.89 Score=29.94 Aligned_cols=48 Identities=2% Similarity=-0.011 Sum_probs=42.7
Q ss_pred CCCCCCccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHH
Q 036324 39 LKADGTVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVL 86 (91)
Q Consensus 39 l~~s~~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl 86 (91)
....+.-|.|+++.+-...+..+.+.+.|+..|+.|..||+++.++..
T Consensus 7 ~~~rr~ys~EfK~~aV~~~~~~g~sv~evA~e~gIs~~tl~~W~r~y~ 54 (121)
T PRK09413 7 PEKRRRRTTQEKIAIVQQSFEPGMTVSLVARQHGVAASQLFLWRKQYQ 54 (121)
T ss_pred CCCCCCCCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHh
Confidence 344578899999999999999999999999999999999999988764
No 48
>PRK14086 dnaA chromosomal replication initiation protein; Provisional
Probab=90.42 E-value=0.62 Score=39.17 Aligned_cols=48 Identities=15% Similarity=0.153 Sum_probs=43.1
Q ss_pred CCCccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 42 DGTVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 42 s~~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
++.+..--||||||-.--.+.++..|+..|+|+-.||..-++.|=+.+
T Consensus 550 ~~~i~~aRqiAMYL~r~lt~~Sl~~IG~~FgRdHSTV~~A~~kI~~~~ 597 (617)
T PRK14086 550 SRVLVTARQIAMYLCRELTDLSLPKIGQQFGRDHTTVMHADRKIRALM 597 (617)
T ss_pred CcccchHHHHHHHHHHHHcCCCHHHHHHHhCCChhHHHHHHHHHHHHH
Confidence 457888999999999999999999999999999999999888876544
No 49
>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=90.36 E-value=0.75 Score=29.09 Aligned_cols=45 Identities=13% Similarity=0.116 Sum_probs=35.4
Q ss_pred CccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 44 TVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 44 ~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
.++..++-.+.++. ..|.+...|+..++.|.+||++..+.++..+
T Consensus 110 ~L~~~~~~ii~~~~-~~g~s~~eIA~~l~~s~~~v~~~~~~~~~kl 154 (158)
T TIGR02937 110 KLPEREREVLVLRY-LEGLSYKEIAEILGISVGTVKRRLKRARKKL 154 (158)
T ss_pred hCCHHHHHHHhhHH-hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 34555555555543 4689999999999999999999999988765
No 50
>PF13340 DUF4096: Putative transposase of IS4/5 family (DUF4096)
Probab=90.34 E-value=0.49 Score=28.68 Aligned_cols=62 Identities=19% Similarity=0.176 Sum_probs=47.8
Q ss_pred HHHHHHHHHHHhCCCCCCCCCccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHH
Q 036324 24 RTFELLCGLLRINGGLKADGTVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVL 86 (91)
Q Consensus 24 ~~F~~L~~~L~~~~~l~~s~~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl 86 (91)
+.+..+...|.+...-.....++..+-+--.||++.+|..-|.+-..|+ +..||++.|+.=.
T Consensus 4 ~~W~~i~p~lp~~~~~~~~~~~~~R~v~~ail~~lrtG~~Wr~LP~~fg-~~~tv~~~f~rW~ 65 (75)
T PF13340_consen 4 EEWALIEPLLPPRKPRGGRPRIDLREVLNAILYVLRTGCPWRDLPEDFG-PWSTVYRRFRRWS 65 (75)
T ss_pred HHHHHHHhhCCCCCCCCCCCccchHHHHhcccccceecceecccchhcc-CcCcHHHHHHHHH
Confidence 4445555556554433334568889999888999999999999999999 8899999998643
No 51
>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=89.95 E-value=0.77 Score=26.46 Aligned_cols=39 Identities=18% Similarity=0.181 Sum_probs=30.6
Q ss_pred HHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHH
Q 036324 49 EQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNA 88 (91)
Q Consensus 49 E~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~a 88 (91)
+++-+|+-+.-++ +...++...+.|.+|||+.+++.=+.
T Consensus 2 ~~l~~f~~v~~~g-s~~~AA~~l~is~~~vs~~i~~LE~~ 40 (60)
T PF00126_consen 2 RQLRYFLAVAETG-SISAAAEELGISQSAVSRQIKQLEEE 40 (60)
T ss_dssp HHHHHHHHHHHHS-SHHHHHHHCTSSHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHhC-CHHHHHHHhhccchHHHHHHHHHHHH
Confidence 3555666665555 99999999999999999999876443
No 52
>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=89.72 E-value=2.6 Score=27.62 Aligned_cols=72 Identities=17% Similarity=0.126 Sum_probs=48.3
Q ss_pred CChhHHHHHhCCCHHHHHHHHHHHHhCCCCCCCC----CccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHH
Q 036324 10 GSDIECVNQLRMDKRTFELLCGLLRINGGLKADG----TVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNL 84 (91)
Q Consensus 10 ~~~~~c~~~fRM~~~~F~~L~~~L~~~~~l~~s~----~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~ 84 (91)
++...--..|.+++.|...... -...+.+.+.. .+. .+.|.-+ ..--.+.+...++..|+.|.+||++.++.
T Consensus 19 ~s~~eaa~~F~VS~~Tv~~W~k-~~~~G~~~~k~r~~~Kid-~~~L~~~-v~~~pd~tl~Ela~~l~Vs~~ti~~~Lkr 94 (119)
T PF01710_consen 19 KSIREAAKRFGVSRNTVYRWLK-RKETGDLEPKPRGRKKID-RDELKAL-VEENPDATLRELAERLGVSPSTIWRALKR 94 (119)
T ss_pred chHHHHHHHhCcHHHHHHHHHH-hccccccccccccccccc-HHHHHHH-HHHCCCcCHHHHHHHcCCCHHHHHHHHHH
Confidence 3556777899999999999888 44445443322 232 2233222 22233477789999999999999998865
No 53
>PRK00118 putative DNA-binding protein; Validated
Probab=89.38 E-value=1.1 Score=29.46 Aligned_cols=44 Identities=14% Similarity=0.110 Sum_probs=33.4
Q ss_pred ccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 45 VSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 45 v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
.+..++-++-+ .-..+.++..|+..+|.|..||+++++.....+
T Consensus 18 L~ekqRevl~L-~y~eg~S~~EIAe~lGIS~~TV~r~L~RArkkL 61 (104)
T PRK00118 18 LTEKQRNYMEL-YYLDDYSLGEIAEEFNVSRQAVYDNIKRTEKLL 61 (104)
T ss_pred CCHHHHHHHHH-HHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 34555555544 455699999999999999999999998765543
No 54
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
Probab=89.35 E-value=1.2 Score=28.97 Aligned_cols=45 Identities=11% Similarity=0.079 Sum_probs=36.7
Q ss_pred CccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 44 TVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 44 ~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
..+.+++-++-|+.+ .+.+...|+..+|.|.+||....+.....+
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 356677777777555 689999999999999999999988877654
No 55
>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=88.97 E-value=0.72 Score=26.88 Aligned_cols=31 Identities=10% Similarity=0.169 Sum_probs=26.7
Q ss_pred CcchhhhhhccccchhhHHHHHHHHHHHHhC
Q 036324 61 HVKSRTIHSRFLRSRETISRYFNLVLNAILQ 91 (91)
Q Consensus 61 ~~~~r~i~~~F~~S~eTisr~f~~Vl~ai~e 91 (91)
..+-.++++.++.|.+|++.+++...+.|+|
T Consensus 23 ~~tl~elA~~lgis~st~~~~LRrae~kli~ 53 (53)
T PF04967_consen 23 RITLEELAEELGISKSTVSEHLRRAERKLIE 53 (53)
T ss_pred cCCHHHHHHHhCCCHHHHHHHHHHHHHHHhC
Confidence 4566778999999999999999999888765
No 56
>PRK15320 transcriptional activator SprB; Provisional
Probab=88.92 E-value=0.56 Score=35.04 Aligned_cols=35 Identities=20% Similarity=0.253 Sum_probs=31.3
Q ss_pred HHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 55 LHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 55 L~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
|--++.|.++++|++.|+-|..|||.|-..+++.+
T Consensus 173 L~LLAkG~SNKEIAekL~LS~KTVSTYKnRLLeKL 207 (251)
T PRK15320 173 LILLSSGHPAIELAKKFGLGTKTVSIYRKKVMYRL 207 (251)
T ss_pred HHHHHcCCCHHHHHHHhccchhhHHHHHHHHHHHc
Confidence 45589999999999999999999999999888754
No 57
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=88.54 E-value=0.75 Score=32.70 Aligned_cols=35 Identities=14% Similarity=0.070 Sum_probs=31.3
Q ss_pred HHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 55 LHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 55 L~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
|-.++.|.+|++|+..-+.|..||..|...+++.+
T Consensus 146 L~lla~G~snkeIA~~L~iS~~TVk~h~~~I~~KL 180 (207)
T PRK15411 146 LRMWMAGQGTIQISDQMNIKAKTVSSHKGNIKRKI 180 (207)
T ss_pred HHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHHHHh
Confidence 45578899999999999999999999999998764
No 58
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=88.37 E-value=3.3 Score=23.75 Aligned_cols=71 Identities=17% Similarity=0.102 Sum_probs=48.2
Q ss_pred hhHHHHHhCCCHHHHHHHHHHHHhCCCCCCCCCccHHHHHHH-HHHHhhcCcchhhhhhcccc-chhhHHHHHHHHH
Q 036324 12 DIECVNQLRMDKRTFELLCGLLRINGGLKADGTVSIEEQLCM-FLHILAHHVKSRTIHSRFLR-SRETISRYFNLVL 86 (91)
Q Consensus 12 ~~~c~~~fRM~~~~F~~L~~~L~~~~~l~~s~~v~veE~vam-FL~i~~~~~~~r~i~~~F~~-S~eTisr~f~~Vl 86 (91)
-.+.-..+.+++..|.++..... +..+...+ -+.++.- .-++..++.+..+++...|- |..+.+|.|++..
T Consensus 4 ~~~la~~~~~s~~~l~~~f~~~~---~~s~~~~~-~~~r~~~a~~~l~~~~~~~~~ia~~~g~~s~~~f~r~Fk~~~ 76 (84)
T smart00342 4 LEDLAEALGMSPRHLQRLFKKET---GTTPKQYL-RDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLF 76 (84)
T ss_pred HHHHHHHhCCCHHHHHHHHHHHh---CcCHHHHH-HHHHHHHHHHHHHcCCCCHHHHHHHhCCCChHHHHHHHHHHH
Confidence 34566788899998888777553 23322222 2233433 33444456899999999999 9999999998764
No 59
>TIGR00721 tfx DNA-binding protein, Tfx family. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.
Probab=88.15 E-value=1.8 Score=29.77 Aligned_cols=43 Identities=12% Similarity=0.176 Sum_probs=33.6
Q ss_pred ccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 45 VSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 45 v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
.|-.|+-.+-|+ .+|.++..|+..++-|.+||+++-+..++.+
T Consensus 7 Lte~qr~VL~Lr--~~GlTq~EIAe~LgiS~stV~~~e~ra~kkL 49 (137)
T TIGR00721 7 LTERQIKVLELR--EKGLSQKEIAKELKTTRANVSAIEKRAMENI 49 (137)
T ss_pred CCHHHHHHHHHH--HcCCCHHHHHHHHCcCHHHHHHHHHhHHHHH
Confidence 344455555553 7999999999999999999999888776654
No 60
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....
Probab=87.92 E-value=1.8 Score=25.41 Aligned_cols=41 Identities=20% Similarity=0.206 Sum_probs=32.4
Q ss_pred cHHHHHHHHHHHhh---cCcchhhhhhccccchhhHHHHHHHHH
Q 036324 46 SIEEQLCMFLHILA---HHVKSRTIHSRFLRSRETISRYFNLVL 86 (91)
Q Consensus 46 ~veE~vamFL~i~~---~~~~~r~i~~~F~~S~eTisr~f~~Vl 86 (91)
+.+|.-.-.+|.+. ...+..+|+..++.|.+||+..++..-
T Consensus 4 ~~~e~YL~~Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml~~L~ 47 (60)
T PF01325_consen 4 ESEEDYLKAIYELSEEGGPVRTKDIAERLGVSPPTVTEMLKRLA 47 (60)
T ss_dssp CHHHHHHHHHHHHHHCTSSBBHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred cHHHHHHHHHHHHHcCCCCccHHHHHHHHCCChHHHHHHHHHHH
Confidence 34566666777777 779999999999999999999887654
No 61
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=87.89 E-value=0.79 Score=31.79 Aligned_cols=44 Identities=23% Similarity=0.206 Sum_probs=35.1
Q ss_pred CccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 44 TVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 44 ~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
..|.-|.= =|..++.|.++.+|+...+.|..||..|...+++.+
T Consensus 150 ~Lt~rE~e--vl~~~~~G~s~~eIA~~l~iS~~TV~~h~~~i~~Kl 193 (216)
T PRK10840 150 RLSPKESE--VLRLFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKL 193 (216)
T ss_pred cCCHHHHH--HHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHc
Confidence 35555542 245567999999999999999999999999888754
No 62
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=87.83 E-value=1.2 Score=25.08 Aligned_cols=34 Identities=18% Similarity=0.207 Sum_probs=28.9
Q ss_pred HHHhhcCcchhhhhhccccchhhHHHHHHHHHHH
Q 036324 55 LHILAHHVKSRTIHSRFLRSRETISRYFNLVLNA 88 (91)
Q Consensus 55 L~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~a 88 (91)
+..++.|.++..|+...+.|..||.-+...+..-
T Consensus 13 ~~l~~~G~s~~eia~~l~is~~tV~~h~~~i~~K 46 (65)
T COG2771 13 LRLVAQGKSNKEIARILGISEETVKTHLRNIYRK 46 (65)
T ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 3456777999999999999999999999888653
No 63
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=87.68 E-value=1.7 Score=24.49 Aligned_cols=26 Identities=19% Similarity=0.249 Sum_probs=22.3
Q ss_pred cchhhhhhccccchhhHHHHHHHHHH
Q 036324 62 VKSRTIHSRFLRSRETISRYFNLVLN 87 (91)
Q Consensus 62 ~~~r~i~~~F~~S~eTisr~f~~Vl~ 87 (91)
.+..+|+..++.|+.||++.+...-+
T Consensus 22 ~t~~~la~~l~~~~~~vs~~v~~L~~ 47 (62)
T PF12802_consen 22 LTQSELAERLGISKSTVSRIVKRLEK 47 (62)
T ss_dssp EEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred cCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 69999999999999999999887643
No 64
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=87.58 E-value=0.78 Score=32.84 Aligned_cols=35 Identities=20% Similarity=0.322 Sum_probs=32.1
Q ss_pred HHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 55 LHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 55 L~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
|-.++.|.+|+.|+..-+.|..||+-|...+++.+
T Consensus 157 L~lla~G~snkeIA~~L~iS~~TVk~h~~~i~~KL 191 (211)
T COG2197 157 LRLLAEGLSNKEIAEELNLSEKTVKTHVSNILRKL 191 (211)
T ss_pred HHHHHCCCCHHHHHHHHCCCHhHHHHHHHHHHHHc
Confidence 56789999999999999999999999999998765
No 65
>PRK01381 Trp operon repressor; Provisional
Probab=87.52 E-value=0.55 Score=30.87 Aligned_cols=37 Identities=19% Similarity=0.214 Sum_probs=26.4
Q ss_pred HHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHH
Q 036324 47 IEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFN 83 (91)
Q Consensus 47 veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~ 83 (91)
+..++.|+=--+....++|.|+...|.|..||+|.=+
T Consensus 41 l~~R~~I~~~L~~g~~sQREIa~~lGvSiaTITRgsn 77 (99)
T PRK01381 41 LGTRVRIVEELLRGELSQREIKQELGVGIATITRGSN 77 (99)
T ss_pred HHHHHHHHHHHHcCCcCHHHHHHHhCCceeeehhhHH
Confidence 3334444433344468999999999999999999643
No 66
>PRK09483 response regulator; Provisional
Probab=87.50 E-value=0.9 Score=30.69 Aligned_cols=44 Identities=18% Similarity=0.258 Sum_probs=34.6
Q ss_pred CccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 44 TVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 44 ~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
..|.-|.=-+- .++.|.++++|+...+.|..||..|.+.+++-+
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 457889999999999999999999999988754
No 67
>PRK14087 dnaA chromosomal replication initiation protein; Provisional
Probab=87.46 E-value=1.5 Score=35.11 Aligned_cols=47 Identities=13% Similarity=0.126 Sum_probs=41.3
Q ss_pred CCCccHHHHHHHHHHHhhcCcchhhhhhccc-cchhhHHHHHHHHHHH
Q 036324 42 DGTVSIEEQLCMFLHILAHHVKSRTIHSRFL-RSRETISRYFNLVLNA 88 (91)
Q Consensus 42 s~~v~veE~vamFL~i~~~~~~~r~i~~~F~-~S~eTisr~f~~Vl~a 88 (91)
++.+..--||||||-.--.+.+...|+..|| |+-+||.--.+.|=+.
T Consensus 382 ~~~i~~~RqiamyL~r~~t~~sl~~IG~~FggrdHsTV~~a~~ki~~~ 429 (450)
T PRK14087 382 SKSIVTARHIAMYLTKEILNHTLAQIGEEFGGRDHTTVINAERKIEKM 429 (450)
T ss_pred CccccHHHHHHHHHHHHHcCCCHHHHHHHhCCCChHHHHHHHHHHHHH
Confidence 4578899999999999999999999999997 9999998777766543
No 68
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=87.16 E-value=0.39 Score=27.08 Aligned_cols=20 Identities=30% Similarity=0.300 Sum_probs=17.7
Q ss_pred hhhhhhccccchhhHHHHHH
Q 036324 64 SRTIHSRFLRSRETISRYFN 83 (91)
Q Consensus 64 ~r~i~~~F~~S~eTisr~f~ 83 (91)
-.+|+..-|.|..||||.++
T Consensus 2 i~dIA~~agvS~~TVSr~ln 21 (46)
T PF00356_consen 2 IKDIAREAGVSKSTVSRVLN 21 (46)
T ss_dssp HHHHHHHHTSSHHHHHHHHT
T ss_pred HHHHHHHHCcCHHHHHHHHh
Confidence 46788999999999999986
No 69
>PHA00738 putative HTH transcription regulator
Probab=87.07 E-value=1.3 Score=29.54 Aligned_cols=39 Identities=15% Similarity=0.157 Sum_probs=29.5
Q ss_pred HHHHHHHHhhc-CcchhhhhhccccchhhHHHHHHHHHHH
Q 036324 50 QLCMFLHILAH-HVKSRTIHSRFLRSRETISRYFNLVLNA 88 (91)
Q Consensus 50 ~vamFL~i~~~-~~~~r~i~~~F~~S~eTisr~f~~Vl~a 88 (91)
+++|+.+...+ ..+-..+.+.|+.|++|||+|....-+|
T Consensus 14 Rr~IL~lL~~~e~~~V~eLae~l~lSQptVS~HLKvLreA 53 (108)
T PHA00738 14 RRKILELIAENYILSASLISHTLLLSYTTVLRHLKILNEQ 53 (108)
T ss_pred HHHHHHHHHHcCCccHHHHHHhhCCCHHHHHHHHHHHHHC
Confidence 45566655554 3788899999999999999998765443
No 70
>TIGR02392 rpoH_proteo alternative sigma factor RpoH. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors.
Probab=86.94 E-value=1.5 Score=32.31 Aligned_cols=45 Identities=9% Similarity=0.107 Sum_probs=35.0
Q ss_pred ccHHHHHHHHHHHh-hcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 45 VSIEEQLCMFLHIL-AHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 45 v~veE~vamFL~i~-~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
.+-.|+..+-|+.. ..+.+++.|+..++.|.+||++..+..|..+
T Consensus 219 L~~rer~vl~l~y~~~~~~t~~eIA~~lgvS~~~V~q~~~~Al~kL 264 (270)
T TIGR02392 219 LDARSRRIIEARWLDDDKLTLQELAAEYGVSAERIRQIEKNAMKKL 264 (270)
T ss_pred CCHHHHHHHHHHhcCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 44456666666554 3478999999999999999999988887654
No 71
>PRK06930 positive control sigma-like factor; Validated
Probab=86.78 E-value=1.7 Score=30.46 Aligned_cols=44 Identities=11% Similarity=0.101 Sum_probs=34.9
Q ss_pred ccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 45 VSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 45 v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
.|..|+ .+|+.....|.++..|+..++.|..||..+.+.....+
T Consensus 115 L~~rer-~V~~L~~~eg~s~~EIA~~lgiS~~tVk~~l~Ra~~kL 158 (170)
T PRK06930 115 LTEREK-EVYLMHRGYGLSYSEIADYLNIKKSTVQSMIERAEKKI 158 (170)
T ss_pred CCHHHH-HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 344443 45555578999999999999999999999988877655
No 72
>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=86.55 E-value=1.2 Score=27.95 Aligned_cols=25 Identities=16% Similarity=0.130 Sum_probs=21.7
Q ss_pred cCcchhhhhhccccchhhHHHHHHH
Q 036324 60 HHVKSRTIHSRFLRSRETISRYFNL 84 (91)
Q Consensus 60 ~~~~~r~i~~~F~~S~eTisr~f~~ 84 (91)
+..+-.+|+..||.|.+||||.++.
T Consensus 18 ~~~ti~dvA~~~gvS~~TVsr~L~~ 42 (80)
T TIGR02844 18 TKATVRETAKVFGVSKSTVHKDVTE 42 (80)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHhcC
Confidence 5567889999999999999998864
No 73
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=86.43 E-value=1.9 Score=31.70 Aligned_cols=44 Identities=16% Similarity=0.161 Sum_probs=35.9
Q ss_pred ccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 45 VSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 45 v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
.+..++-.+.|+. ..+.++..|+..+|.|.+||++..+..+..+
T Consensus 204 L~~~~r~vl~l~y-~~~~s~~eIA~~lgvs~~~V~~~~~ra~~kL 247 (256)
T PRK07408 204 LEERTREVLEFVF-LHDLTQKEAAERLGISPVTVSRRVKKGLDQL 247 (256)
T ss_pred CCHHHHHHHHHHH-HCCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 4556666666665 4699999999999999999999999887654
No 74
>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=86.18 E-value=1.8 Score=31.22 Aligned_cols=46 Identities=15% Similarity=0.153 Sum_probs=37.1
Q ss_pred CccHHHHHHHHHHHh---hcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 44 TVSIEEQLCMFLHIL---AHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 44 ~v~veE~vamFL~i~---~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
..+..|+..+.|+.. ..+.++..|+..+|.|.++|++..+..+.-+
T Consensus 176 ~L~~~er~vl~l~ygl~~~~~~t~~EIA~~lgis~~~V~q~~~~al~kL 224 (238)
T TIGR02393 176 TLTERERKVLRMRYGLLDGRPHTLEEVGKEFNVTRERIRQIESKALRKL 224 (238)
T ss_pred hCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 345567777777653 5789999999999999999999998887654
No 75
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=86.10 E-value=2.1 Score=25.90 Aligned_cols=42 Identities=19% Similarity=0.256 Sum_probs=32.6
Q ss_pred cHHHHHHHHHHHhhc--CcchhhhhhccccchhhHHHHHHHHHH
Q 036324 46 SIEEQLCMFLHILAH--HVKSRTIHSRFLRSRETISRYFNLVLN 87 (91)
Q Consensus 46 ~veE~vamFL~i~~~--~~~~r~i~~~F~~S~eTisr~f~~Vl~ 87 (91)
+++..+.|.-++..+ +.+..+++...+.|..||+|++....+
T Consensus 3 ~~~r~~~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~~ 46 (91)
T smart00346 3 SLERGLAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQE 46 (91)
T ss_pred HHHHHHHHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 455666666665544 489999999999999999999987643
No 76
>PRK09492 treR trehalose repressor; Provisional
Probab=86.04 E-value=0.43 Score=34.66 Aligned_cols=23 Identities=22% Similarity=0.174 Sum_probs=21.0
Q ss_pred cchhhhhhccccchhhHHHHHHH
Q 036324 62 VKSRTIHSRFLRSRETISRYFNL 84 (91)
Q Consensus 62 ~~~r~i~~~F~~S~eTisr~f~~ 84 (91)
.+-++|+...|.|..||||.++.
T Consensus 5 ~ti~dIA~~agVS~~TVSrvLn~ 27 (315)
T PRK09492 5 LTIKDIARLSGVGKSTVSRVLNN 27 (315)
T ss_pred CcHHHHHHHhCCCHHHHhHHhCC
Confidence 57789999999999999999984
No 77
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=85.85 E-value=1.2 Score=31.97 Aligned_cols=35 Identities=17% Similarity=0.169 Sum_probs=31.1
Q ss_pred HHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 55 LHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 55 L~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
|-.++.|.+|++|+...+.|..||..|...+++.+
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 45678899999999999999999999999988754
No 78
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=85.75 E-value=2.3 Score=29.43 Aligned_cols=43 Identities=7% Similarity=-0.047 Sum_probs=33.0
Q ss_pred cHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 46 SIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 46 ~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
+.+++- +|+..--++.++..|+..++.|..||...++.....+
T Consensus 138 ~~~~r~-i~~L~~~~g~s~~eIA~~lgis~~tV~~~l~Ra~~~L 180 (196)
T PRK12524 138 PERQRQ-AVVLRHIEGLSNPEIAEVMEIGVEAVESLTARGKRAL 180 (196)
T ss_pred CHHHHH-HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 333443 4444444899999999999999999999998877654
No 79
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=85.32 E-value=1.4 Score=32.47 Aligned_cols=37 Identities=11% Similarity=0.203 Sum_probs=34.3
Q ss_pred HHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHH
Q 036324 49 EQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLV 85 (91)
Q Consensus 49 E~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~V 85 (91)
+++-.|+.++-++.++..++++.+.|++|||+.+.+.
T Consensus 4 ~~L~~F~~v~~~~~S~s~AA~~L~isQpavS~~I~~L 40 (309)
T PRK12683 4 QQLRIIREAVRQNFNLTEVANALYTSQSGVSKQIKDL 40 (309)
T ss_pred HHHHHHHHHHHccCCHHHHHHHhcCCcHHHHHHHHHH
Confidence 5788999999999999999999999999999999875
No 80
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=85.24 E-value=2.3 Score=28.09 Aligned_cols=38 Identities=11% Similarity=0.019 Sum_probs=32.1
Q ss_pred HHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 52 CMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 52 amFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
.+|+...-.|.++..|+...|.|..||....+..+..+
T Consensus 113 ~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~ra~~~L 150 (161)
T PRK09047 113 EAFLLRYWEDMDVAETAAAMGCSEGSVKTHCSRATHAL 150 (161)
T ss_pred HHHHHHHHhcCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 35555566899999999999999999999998887765
No 81
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=85.04 E-value=1.8 Score=28.86 Aligned_cols=41 Identities=20% Similarity=0.232 Sum_probs=31.3
Q ss_pred HHHHHHHHHHhh-cCcchhhhhhccccchhhHHHHHHHHHHH
Q 036324 48 EEQLCMFLHILA-HHVKSRTIHSRFLRSRETISRYFNLVLNA 88 (91)
Q Consensus 48 eE~vamFL~i~~-~~~~~r~i~~~F~~S~eTisr~f~~Vl~a 88 (91)
+-++.|+.+... ...+...+.+.++.|++|||+|+...-+|
T Consensus 16 ptRl~IL~~L~~~~~~~v~ela~~l~lsqstvS~HL~~L~~A 57 (117)
T PRK10141 16 ETRLGIVLLLRESGELCVCDLCTALDQSQPKISRHLALLRES 57 (117)
T ss_pred HHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 345667766654 35778999999999999999999865443
No 82
>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=84.87 E-value=2.3 Score=28.19 Aligned_cols=41 Identities=10% Similarity=0.064 Sum_probs=33.4
Q ss_pred HHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 49 EQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 49 E~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
++--+|....-+|.++..|++.+|.|.+||....+.....+
T Consensus 114 ~~r~i~~l~~~~g~s~~eIA~~lgis~~tV~~~l~ra~~~L 154 (162)
T TIGR02983 114 RQRAVVVLRYYEDLSEAQVAEALGISVGTVKSRLSRALARL 154 (162)
T ss_pred HHHHHhhhHHHhcCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 34445655557899999999999999999999998887654
No 83
>PRK12422 chromosomal replication initiation protein; Provisional
Probab=84.77 E-value=2.2 Score=34.13 Aligned_cols=47 Identities=15% Similarity=0.171 Sum_probs=41.0
Q ss_pred CCCccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHH
Q 036324 42 DGTVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNA 88 (91)
Q Consensus 42 s~~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~a 88 (91)
++.+..--|+||||-.-=++.|+..|+..|||+-+||---++.|=+.
T Consensus 378 ~~~i~~~Rqiamyl~r~~t~~s~~~IG~~fgrdHsTV~~a~~ki~~~ 424 (445)
T PRK12422 378 SREYVLPRQVAMYLCRQKLSLSYVKIGDVFSRDHSTVISSIRAISQK 424 (445)
T ss_pred CcccccHHHHHHHHHHHhcCCCHHHHHHHhCCChHHHHHHHHHHHHH
Confidence 45788899999999999999999999999999999997776666443
No 84
>smart00760 Bac_DnaA_C Bacterial dnaA protein helix-turn-helix domain. Could be involved in DNA-binding.
Probab=84.65 E-value=1.3 Score=25.68 Aligned_cols=33 Identities=18% Similarity=0.243 Sum_probs=29.7
Q ss_pred CCCccHHHHHHHHHHHhhcCcchhhhhhccc-cc
Q 036324 42 DGTVSIEEQLCMFLHILAHHVKSRTIHSRFL-RS 74 (91)
Q Consensus 42 s~~v~veE~vamFL~i~~~~~~~r~i~~~F~-~S 74 (91)
++.++.--++||+|-.--.+.+..+|+..|+ ++
T Consensus 26 ~~~~~~aR~iamyla~~~~~~sl~~Ig~~fg~rd 59 (60)
T smart00760 26 KREIVLARQIAMYLARELTDLSLPEIGKIFGGRD 59 (60)
T ss_pred CcchhHHHHHHHHHHHHHHCCCHHHHHHHhCCCC
Confidence 5688999999999999999999999999998 64
No 85
>PRK10651 transcriptional regulator NarL; Provisional
Probab=84.49 E-value=1.6 Score=28.97 Aligned_cols=43 Identities=16% Similarity=0.274 Sum_probs=34.3
Q ss_pred ccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 45 VSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 45 v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
.|..|. =.|..++.|.++++|+...+.|..||..|+......+
T Consensus 156 Lt~rE~--~vl~~l~~g~~~~~ia~~l~is~~tV~~~~~~l~~Kl 198 (216)
T PRK10651 156 LTPRER--DILKLIAQGLPNKMIARRLDITESTVKVHVKHMLKKM 198 (216)
T ss_pred CCHHHH--HHHHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHHHHc
Confidence 555554 2334467889999999999999999999999987654
No 86
>PRK12679 cbl transcriptional regulator Cbl; Reviewed
Probab=84.38 E-value=1.7 Score=32.16 Aligned_cols=37 Identities=14% Similarity=0.180 Sum_probs=33.9
Q ss_pred HHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHH
Q 036324 49 EQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLV 85 (91)
Q Consensus 49 E~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~V 85 (91)
+++-.|+.++.++.++..++..-..|++||||.+++.
T Consensus 4 ~~l~~f~~v~~~~~s~s~AA~~L~iSQ~avSr~I~~L 40 (316)
T PRK12679 4 QQLKIIREAARQDYNLTEVANMLFTSQSGVSRHIREL 40 (316)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHhcCCchHHHHHHHHH
Confidence 5788999999999999999999999999999999864
No 87
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=84.35 E-value=2.6 Score=30.08 Aligned_cols=45 Identities=18% Similarity=0.149 Sum_probs=33.9
Q ss_pred ccHHHHHHHHHHHh---hcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 45 VSIEEQLCMFLHIL---AHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 45 v~veE~vamFL~i~---~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
.|..++-++-|+.. -.+.++..|+..+|.|..||.+..+..+..+
T Consensus 179 Lp~~~R~v~~L~y~l~~~eg~s~~EIA~~lgis~~tVk~~~~rA~~~L 226 (234)
T PRK08301 179 LSDREKQIMELRFGLNGGEEKTQKEVADMLGISQSYISRLEKRIIKRL 226 (234)
T ss_pred CCHHHHHHHHHHhccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 34444555555432 5899999999999999999999988777654
No 88
>PF13551 HTH_29: Winged helix-turn helix
Probab=84.33 E-value=1.8 Score=26.87 Aligned_cols=32 Identities=31% Similarity=0.327 Sum_probs=26.8
Q ss_pred HHHhhcCcc-hhhhhhccccchhhHHHHHHHHH
Q 036324 55 LHILAHHVK-SRTIHSRFLRSRETISRYFNLVL 86 (91)
Q Consensus 55 L~i~~~~~~-~r~i~~~F~~S~eTisr~f~~Vl 86 (91)
|..+..+.+ ...|+..++.|..||+++.+..-
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 445677885 99999999999999999988753
No 89
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=84.29 E-value=1.9 Score=23.50 Aligned_cols=29 Identities=10% Similarity=0.016 Sum_probs=24.8
Q ss_pred hcCcchhhhhhccccchhhHHHHHHHHHH
Q 036324 59 AHHVKSRTIHSRFLRSRETISRYFNLVLN 87 (91)
Q Consensus 59 ~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ 87 (91)
....+...|+..++.|..|+++.++...+
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~ 36 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLRE 36 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 55678889999999999999999987654
No 90
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=84.04 E-value=3.3 Score=28.02 Aligned_cols=44 Identities=7% Similarity=0.070 Sum_probs=33.7
Q ss_pred ccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 45 VSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 45 v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
++.+++-.+.|. .-.|.++..|+..+|.|..||....+...+.+
T Consensus 130 L~~~~r~i~~l~-~~~g~s~~eIA~~lgis~~tV~~~l~Rar~~L 173 (179)
T PRK12514 130 LEKDRAAAVRRA-YLEGLSYKELAERHDVPLNTMRTWLRRSLLKL 173 (179)
T ss_pred CCHHHHHHHHHH-HHcCCCHHHHHHHHCCChHHHHHHHHHHHHHH
Confidence 334444445555 34789999999999999999999988877655
No 91
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=84.01 E-value=1 Score=24.85 Aligned_cols=24 Identities=17% Similarity=0.213 Sum_probs=20.6
Q ss_pred chhhhhhccccchhhHHHHHHHHH
Q 036324 63 KSRTIHSRFLRSRETISRYFNLVL 86 (91)
Q Consensus 63 ~~r~i~~~F~~S~eTisr~f~~Vl 86 (91)
+.++++..|+.|.+||++.+...-
T Consensus 22 s~~~la~~~~vs~~tv~~~l~~L~ 45 (60)
T smart00345 22 SERELAAQLGVSRTTVREALSRLE 45 (60)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHH
Confidence 677889999999999999987653
No 92
>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=83.98 E-value=3.7 Score=22.96 Aligned_cols=29 Identities=14% Similarity=0.205 Sum_probs=23.6
Q ss_pred hcCcchhhhhhccccchhhHHHHHHHHHH
Q 036324 59 AHHVKSRTIHSRFLRSRETISRYFNLVLN 87 (91)
Q Consensus 59 ~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ 87 (91)
..+.+..+++..++.+..|+++..+...+
T Consensus 15 ~~~~~~~~la~~~~~~~~~~t~~i~~L~~ 43 (59)
T PF01047_consen 15 NGGITQSELAEKLGISRSTVTRIIKRLEK 43 (59)
T ss_dssp HSSEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred cCCCCHHHHHHHHCCChhHHHHHHHHHHH
Confidence 34479999999999999999999887643
No 93
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=83.93 E-value=3.8 Score=28.30 Aligned_cols=43 Identities=14% Similarity=0.078 Sum_probs=33.8
Q ss_pred ccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 45 VSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 45 v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
.|-.|+-.+-| ...|.++.+|+..++.|..||+++-+..+..+
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 44455555555 36999999999999999999999988776643
No 94
>PF02209 VHP: Villin headpiece domain; InterPro: IPR003128 Villin is an F-actin bundling protein involved in the maintenance of the microvilli of the absorptive epithelia. The villin-type "headpiece" domain is a modular motif found at the extreme C terminus of larger "core" domains in over 25 cytoskeletal proteins in plants and animals, often in assocation with the Gelsolin repeat. Although the headpiece is classified as an F-actin-binding domain, it has been shown that not all headpiece domains are intrinsically F-actin-binding motifs, surface charge distribution may be an important element for F-actin recognition []. An autonomously folding, 35 residue, thermostable subdomain (HP36) of the full-length 76 amino acid residue villin headpiece, is the smallest known example of a cooperatively folded domain of a naturally occurring protein. The structure of HP36, as determined by NMR spectroscopy, consists of three short helices surrounding a tightly packed hydrophobic core []. ; GO: 0003779 actin binding, 0007010 cytoskeleton organization; PDB: 1ZV6_A 1QZP_A 1UND_A 2PPZ_A 3TJW_B 1YU8_X 2JM0_A 1WY4_A 3MYC_A 1YU5_X ....
Probab=83.60 E-value=0.98 Score=24.46 Aligned_cols=24 Identities=21% Similarity=0.182 Sum_probs=18.3
Q ss_pred ChhHHHHHhCCCHHHHHHHHHHHH
Q 036324 11 SDIECVNQLRMDKRTFELLCGLLR 34 (91)
Q Consensus 11 ~~~~c~~~fRM~~~~F~~L~~~L~ 34 (91)
+|++....|+|+++.|.+|=.+=+
T Consensus 3 sd~dF~~vFgm~~~eF~~lP~WKq 26 (36)
T PF02209_consen 3 SDEDFEKVFGMSREEFYKLPKWKQ 26 (36)
T ss_dssp -HHHHHHHHSS-HHHHHHS-HHHH
T ss_pred CHHHHHHHHCCCHHHHHHChHHHH
Confidence 578999999999999999876643
No 95
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=83.53 E-value=1.9 Score=31.56 Aligned_cols=46 Identities=13% Similarity=0.158 Sum_probs=36.4
Q ss_pred CCCccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 42 DGTVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 42 s~~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
|...|.-|.= .|-.++.|.++++|+...+.|..||..+...+++.+
T Consensus 131 ~~~LSpRErE--VLrLLAqGkTnKEIAe~L~IS~rTVkth~srImkKL 176 (198)
T PRK15201 131 TRHFSVTERH--LLKLIASGYHLSETAALLSLSEEQTKSLRRSIMRKL 176 (198)
T ss_pred CCCCCHHHHH--HHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence 3456665543 244578899999999999999999999999888754
No 96
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=83.13 E-value=3.3 Score=27.51 Aligned_cols=36 Identities=8% Similarity=-0.114 Sum_probs=28.8
Q ss_pred HHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 54 FLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 54 FL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
|....-.+.+++.|+..+|.|..||+...+..+..+
T Consensus 137 l~l~~~~~~s~~eIA~~lgis~~tV~~~l~ra~~~L 172 (182)
T PRK09652 137 ITLREIEGLSYEEIAEIMGCPIGTVRSRIFRAREAL 172 (182)
T ss_pred HHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 333334789999999999999999999888776554
No 97
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=83.11 E-value=3.2 Score=30.49 Aligned_cols=44 Identities=16% Similarity=0.098 Sum_probs=34.6
Q ss_pred ccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 45 VSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 45 v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
.+..|+-.+-|+. ..+.++..|+..+|.|.+||++..+..+..+
T Consensus 206 L~~~er~vi~l~y-~e~~t~~EIA~~lgis~~~V~~~~~ral~kL 249 (257)
T PRK05911 206 LEEKERKVMALYY-YEELVLKEIGKILGVSESRVSQIHSKALLKL 249 (257)
T ss_pred CCHHHHHHHHHHH-hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 4445555555554 5799999999999999999999988877654
No 98
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=82.98 E-value=2.6 Score=28.93 Aligned_cols=38 Identities=11% Similarity=-0.044 Sum_probs=31.2
Q ss_pred HHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 52 CMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 52 amFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
-+|....-+|.++..|+..+|.|..||...++..+..+
T Consensus 148 ~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~L 185 (194)
T PRK12519 148 QVLELAYYEGLSQSEIAKRLGIPLGTVKARARQGLLKL 185 (194)
T ss_pred hhhhhhhhcCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 34544556799999999999999999999988877655
No 99
>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily. This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.
Probab=82.69 E-value=3.3 Score=29.33 Aligned_cols=43 Identities=19% Similarity=0.213 Sum_probs=33.1
Q ss_pred cHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 46 SIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 46 ~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
+..++-++-| ....+.++..|+..+|.|.+||++..+.++..+
T Consensus 180 ~~~~r~vl~l-~y~~~~s~~eIA~~lgis~~~v~~~~~ra~~~L 222 (227)
T TIGR02980 180 PERERRILLL-RFFEDKTQSEIAERLGISQMHVSRLLRRALKKL 222 (227)
T ss_pred CHHHHHHHHH-HHhcCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 3334433333 345789999999999999999999999988765
No 100
>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=82.60 E-value=3.4 Score=29.69 Aligned_cols=46 Identities=17% Similarity=0.138 Sum_probs=37.6
Q ss_pred CccHHHHHHHHHHHh---hcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 44 TVSIEEQLCMFLHIL---AHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 44 ~v~veE~vamFL~i~---~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
..|..++-.+.|+.. ..+.++..|+..-|.|..||.+..+..+..+
T Consensus 178 ~Lp~~~R~ii~L~~~l~~~eg~s~~EIA~~Lgis~~tV~~~l~ra~~~L 226 (234)
T TIGR02835 178 KLNDREKKIMELRFGLVGGTEKTQKEVADMLGISQSYISRLEKRILKRL 226 (234)
T ss_pred hCCHHHHHHHHHHHccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 456667777888764 4899999999999999999999987766654
No 101
>smart00153 VHP Villin headpiece domain.
Probab=82.57 E-value=1.3 Score=23.93 Aligned_cols=22 Identities=23% Similarity=0.152 Sum_probs=19.6
Q ss_pred ChhHHHHHhCCCHHHHHHHHHH
Q 036324 11 SDIECVNQLRMDKRTFELLCGL 32 (91)
Q Consensus 11 ~~~~c~~~fRM~~~~F~~L~~~ 32 (91)
+|++....|+|+++.|.+|=.+
T Consensus 3 sdeeF~~vfgmsr~eF~~LP~W 24 (36)
T smart00153 3 SDEDFEEVFGMTREEFYKLPLW 24 (36)
T ss_pred CHHHHHHHHCCCHHHHHhCcHh
Confidence 5789999999999999998665
No 102
>PRK05572 sporulation sigma factor SigF; Validated
Probab=82.51 E-value=3.5 Score=29.97 Aligned_cols=45 Identities=18% Similarity=0.258 Sum_probs=35.7
Q ss_pred CccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 44 TVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 44 ~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
..+..++-.+-|+. ..+.++..|+..+|.|.+||+++-+..+..+
T Consensus 202 ~L~~~~~~v~~l~~-~~~~s~~eIA~~lgis~~~V~~~~~ral~kL 246 (252)
T PRK05572 202 ELDERERLIVYLRY-FKDKTQSEVAKRLGISQVQVSRLEKKILKQM 246 (252)
T ss_pred cCCHHHHHHHHHHH-hCCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 34555555555544 4789999999999999999999999988765
No 103
>TIGR02885 spore_sigF RNA polymerase sigma-F factor. Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore.
Probab=82.41 E-value=3.4 Score=29.39 Aligned_cols=43 Identities=16% Similarity=0.156 Sum_probs=33.6
Q ss_pred cHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 46 SIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 46 ~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
+..|+-.+-++ ...+.+...|+..+|.|.+||++.-+.++.-+
T Consensus 185 ~~~e~~i~~~~-~~~~~t~~eIA~~lgis~~~V~~~~~~al~~L 227 (231)
T TIGR02885 185 DERERQIIMLR-YFKDKTQTEVANMLGISQVQVSRLEKKVLKKM 227 (231)
T ss_pred CHHHHHHHHHH-HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 44444444443 46789999999999999999999999988765
No 104
>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=82.24 E-value=5.3 Score=22.21 Aligned_cols=24 Identities=17% Similarity=0.169 Sum_probs=19.9
Q ss_pred chhhhhhccccchhhHHHHHHHHH
Q 036324 63 KSRTIHSRFLRSRETISRYFNLVL 86 (91)
Q Consensus 63 ~~r~i~~~F~~S~eTisr~f~~Vl 86 (91)
+.+++++.|+.|.+||++.+...-
T Consensus 27 ~~~~la~~~~is~~~v~~~l~~L~ 50 (66)
T cd07377 27 SERELAEELGVSRTTVREALRELE 50 (66)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHH
Confidence 466788999999999999887654
No 105
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=82.23 E-value=1.6 Score=23.19 Aligned_cols=27 Identities=22% Similarity=0.241 Sum_probs=23.1
Q ss_pred CcchhhhhhccccchhhHHHHHHHHHH
Q 036324 61 HVKSRTIHSRFLRSRETISRYFNLVLN 87 (91)
Q Consensus 61 ~~~~r~i~~~F~~S~eTisr~f~~Vl~ 87 (91)
..+..++++.++.|.+|+++.+....+
T Consensus 8 ~~s~~~la~~l~~s~~tv~~~l~~L~~ 34 (48)
T smart00419 8 PLTRQEIAELLGLTRETVSRTLKRLEK 34 (48)
T ss_pred ccCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 467889999999999999999887643
No 106
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=81.98 E-value=2.3 Score=31.53 Aligned_cols=35 Identities=6% Similarity=0.011 Sum_probs=31.2
Q ss_pred HHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 55 LHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 55 L~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
|-.++.|.++.+|+...+.|..||..|...+++.+
T Consensus 152 L~Lia~G~SnkEIA~~L~IS~~TVk~hvs~I~~KL 186 (217)
T PRK13719 152 FILYSFGFSHEYIAQLLNITVGSSKNKISEILKFF 186 (217)
T ss_pred HHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence 45578899999999999999999999999988764
No 107
>PRK10403 transcriptional regulator NarP; Provisional
Probab=81.94 E-value=2.6 Score=27.86 Aligned_cols=43 Identities=23% Similarity=0.239 Sum_probs=34.4
Q ss_pred ccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 45 VSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 45 v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
.|..|.-. |..++.|.++..|+...+.|..||..|++.+.+.+
T Consensus 154 Lt~~e~~v--l~~~~~g~s~~~ia~~l~~s~~tv~~~~~~i~~kl 196 (215)
T PRK10403 154 LTERELDV--LHELAQGLSNKQIASVLNISEQTVKVHIRNLLRKL 196 (215)
T ss_pred CCHHHHHH--HHHHHCCCCHHHHHHHcCCCHHHHHHHHHHHHHHc
Confidence 45555543 44456789999999999999999999999988765
No 108
>PHA00542 putative Cro-like protein
Probab=81.61 E-value=3.2 Score=25.65 Aligned_cols=29 Identities=17% Similarity=0.155 Sum_probs=25.4
Q ss_pred HHHhhcCcchhhhhhccccchhhHHHHHH
Q 036324 55 LHILAHHVKSRTIHSRFLRSRETISRYFN 83 (91)
Q Consensus 55 L~i~~~~~~~r~i~~~F~~S~eTisr~f~ 83 (91)
......+.+..+++...|.|.+|||++.+
T Consensus 25 ~~l~~~glTq~elA~~lgIs~~tIsr~e~ 53 (82)
T PHA00542 25 CALIRAGWSQEQIADATDVSQPTICRIYS 53 (82)
T ss_pred HHHHHCCCCHHHHHHHHCcCHHHHHHHHc
Confidence 34567889999999999999999999874
No 109
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=81.48 E-value=3.9 Score=29.70 Aligned_cols=37 Identities=11% Similarity=0.175 Sum_probs=31.0
Q ss_pred HHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 53 MFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 53 mFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
+|...-..+.++..|+..++.|.+||++..+..+..+
T Consensus 213 vl~l~~~~g~s~~eIA~~l~is~~tV~~~~~ra~~kL 249 (257)
T PRK08583 213 IIQCTFIENLSQKETGERLGISQMHVSRLQRQAIKKL 249 (257)
T ss_pred HHHHHHhCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 3444446899999999999999999999999888765
No 110
>PHA00675 hypothetical protein
Probab=81.24 E-value=4.9 Score=25.37 Aligned_cols=40 Identities=10% Similarity=0.058 Sum_probs=33.1
Q ss_pred CCccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHH
Q 036324 43 GTVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYF 82 (91)
Q Consensus 43 ~~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f 82 (91)
-.++-.+--.|+.-....+.++-.|+..||.|.+||+.+-
T Consensus 21 AKLt~~qV~~IR~l~~r~G~s~~~IA~~fGVsrstV~~I~ 60 (78)
T PHA00675 21 AKLTDAEVERIRELHEVEGMSYAVLAEKFEQSKGAIAKIC 60 (78)
T ss_pred cccCHHHHHHHHHHHHhcCccHHHHHHHhCCCHHHHHHHH
Confidence 3567777777888776777899999999999999998764
No 111
>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=81.23 E-value=1.5 Score=28.78 Aligned_cols=26 Identities=27% Similarity=0.387 Sum_probs=22.5
Q ss_pred hhcCcchhhhhhccccchhhHHHHHH
Q 036324 58 LAHHVKSRTIHSRFLRSRETISRYFN 83 (91)
Q Consensus 58 ~~~~~~~r~i~~~F~~S~eTisr~f~ 83 (91)
+-.|.+-+.++.+|+.|..||.+.+.
T Consensus 15 ~~~g~s~~eaa~~F~VS~~Tv~~W~k 40 (119)
T PF01710_consen 15 IEKGKSIREAAKRFGVSRNTVYRWLK 40 (119)
T ss_pred HHccchHHHHHHHhCcHHHHHHHHHH
Confidence 33466999999999999999999987
No 112
>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=81.17 E-value=3.9 Score=29.65 Aligned_cols=43 Identities=14% Similarity=0.178 Sum_probs=34.0
Q ss_pred cHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 46 SIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 46 ~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
+..++- +|...-..|.++..|+..++.|.+||++..+..+..+
T Consensus 207 ~~~~r~-ii~l~~~~g~s~~eIA~~lgis~~~V~~~~~ra~~~L 249 (255)
T TIGR02941 207 SEREKS-IIHCTFEENLSQKETGERLGISQMHVSRLQRQAISKL 249 (255)
T ss_pred CHHHHH-HHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 334443 4555556899999999999999999999999888765
No 113
>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=81.01 E-value=6.5 Score=24.79 Aligned_cols=53 Identities=19% Similarity=0.238 Sum_probs=35.5
Q ss_pred HhCCCHHHHHHHHHHHHhCCCCCCCCCccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHH
Q 036324 18 QLRMDKRTFELLCGLLRINGGLKADGTVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVL 86 (91)
Q Consensus 18 ~fRM~~~~F~~L~~~L~~~~~l~~s~~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl 86 (91)
.+.++...+.-|..+.+..++-.. ...+.+.++++...+.|++||||.+++.-
T Consensus 20 ~~~l~~r~~~vLl~L~~~~~G~~~----------------~~~~is~~eLa~~~g~sr~tVsr~L~~Le 72 (95)
T TIGR01610 20 GADLSGREFRVLLAIIRLTYGWNK----------------KQDRVTATVIAELTGLSRTHVSDAIKSLA 72 (95)
T ss_pred hCCCCHHHHHHHHHHHHHHhCccc----------------cCCccCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 445556666666655543333111 34457888999999999999999888754
No 114
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=80.98 E-value=3.9 Score=30.59 Aligned_cols=45 Identities=7% Similarity=0.053 Sum_probs=34.7
Q ss_pred ccHHHHHHHHHHHhh-cCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 45 VSIEEQLCMFLHILA-HHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 45 v~veE~vamFL~i~~-~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
.+-.|+..+-++... .+.+...|+..+|.|.++|++.-+..+.-+
T Consensus 231 L~~rEr~VL~lry~~~~~~Tl~EIA~~lgvS~~rVrqi~~~Al~kL 276 (284)
T PRK06596 231 LDERSRDIIEARWLDDDKSTLQELAAEYGVSAERVRQIEKNAMKKL 276 (284)
T ss_pred CCHHHHHHHHHHhcCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 444466666665543 689999999999999999999988877643
No 115
>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]
Probab=80.83 E-value=4.1 Score=32.73 Aligned_cols=48 Identities=15% Similarity=0.146 Sum_probs=41.9
Q ss_pred CCCCccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHH
Q 036324 41 ADGTVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNA 88 (91)
Q Consensus 41 ~s~~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~a 88 (91)
-++++..--|+||+|-.-=++.|.-.|+..|||.-.||.--.+.|-+-
T Consensus 345 R~~~i~~~RqiamyL~r~lt~~Slp~IG~~FgrdHtTV~~a~~kI~~~ 392 (408)
T COG0593 345 RTRNIVRPRQIAMYLARELTNLSLPEIGKAFGRDHTTVLHAVRKIEQL 392 (408)
T ss_pred cccccchHHHHHHHHHHHHccCcHHHHHHHhCCCccHHHHHHHHHHHH
Confidence 356899999999999999999999999999999999997766666543
No 116
>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=80.79 E-value=2.6 Score=29.58 Aligned_cols=39 Identities=18% Similarity=0.265 Sum_probs=32.6
Q ss_pred HHHHHHHHHhhcC-------cchhhhhhccccchhhHHHHHHHHHH
Q 036324 49 EQLCMFLHILAHH-------VKSRTIHSRFLRSRETISRYFNLVLN 87 (91)
Q Consensus 49 E~vamFL~i~~~~-------~~~r~i~~~F~~S~eTisr~f~~Vl~ 87 (91)
.+..++.|++.+- .+++.+++.++-|..||+|.|.+.-+
T Consensus 56 k~~~Vl~~il~~~d~~N~v~~t~~~ia~~l~iS~~Tv~r~ik~L~e 101 (165)
T PF05732_consen 56 KAFRVLMYILENMDKDNAVVATQKEIAEKLGISKPTVSRAIKELEE 101 (165)
T ss_pred hHHHHHHHHHHhcCCCCeEEeeHHHHHHHhCCCHHHHHHHHHHHHh
Confidence 4678888887654 57899999999999999999988654
No 117
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=80.78 E-value=2.8 Score=30.66 Aligned_cols=37 Identities=11% Similarity=0.105 Sum_probs=32.8
Q ss_pred HHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHH
Q 036324 49 EQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLV 85 (91)
Q Consensus 49 E~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~V 85 (91)
+++-.|+-..-++.+++.++...+.|++||||.+++.
T Consensus 4 ~~L~~F~~v~~~~~s~s~AA~~L~isq~avSr~I~~L 40 (309)
T PRK12682 4 QQLRFVREAVRRNLNLTEAAKALHTSQPGVSKAIIEL 40 (309)
T ss_pred HHHHHHHHHHHccCCHHHHHHHhcCccHHHHHHHHHH
Confidence 5677888777788899999999999999999999875
No 118
>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=80.64 E-value=11 Score=27.22 Aligned_cols=45 Identities=16% Similarity=0.101 Sum_probs=37.0
Q ss_pred CCccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 43 GTVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 43 ~~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
...|..|+=.+.+ .+.|.++.+|+..++.|..||..+.+.+.+.+
T Consensus 170 ~~Lt~re~evl~~--~a~G~t~~eIa~~l~is~~Tv~~~l~~~~~kl 214 (232)
T TIGR03541 170 GVLSEREREVLAW--TALGRRQADIAAILGISERTVENHLRSARRKL 214 (232)
T ss_pred ccCCHHHHHHHHH--HHCCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 3567666655555 48999999999999999999999999988765
No 119
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=80.61 E-value=3.2 Score=27.47 Aligned_cols=44 Identities=14% Similarity=0.127 Sum_probs=34.1
Q ss_pred CccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 44 TVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 44 ~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
..+..|.-- |..++.|.++.+|+..++.|..||..+...+.+.+
T Consensus 137 ~Lt~~E~~i--l~~l~~g~~~~~Ia~~l~~s~~tv~~~~~~l~~Kl 180 (196)
T PRK10360 137 PLTKRERQV--AEKLAQGMAVKEIAAELGLSPKTVHVHRANLMEKL 180 (196)
T ss_pred CCCHHHHHH--HHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence 355555533 44466789999999999999999999999887654
No 120
>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=80.56 E-value=1.1 Score=32.82 Aligned_cols=22 Identities=23% Similarity=0.235 Sum_probs=19.6
Q ss_pred cchhhhhhccccchhhHHHHHH
Q 036324 62 VKSRTIHSRFLRSRETISRYFN 83 (91)
Q Consensus 62 ~~~r~i~~~F~~S~eTisr~f~ 83 (91)
.+-++|+...|.|..||||.++
T Consensus 2 ~ti~dIA~~agVS~sTVSr~Ln 23 (311)
T TIGR02405 2 LTIKDIARLAGVGKSTVSRVLN 23 (311)
T ss_pred CcHHHHHHHhCCCHHHHHHHhC
Confidence 3568999999999999999996
No 121
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=80.51 E-value=4.1 Score=30.59 Aligned_cols=45 Identities=11% Similarity=0.048 Sum_probs=36.2
Q ss_pred ccHHHHHHHHHHHh-hcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 45 VSIEEQLCMFLHIL-AHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 45 v~veE~vamFL~i~-~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
.+-.|+..+-|+.. ..+.++..|+..+|.|.+||+++.+..++.+
T Consensus 228 L~~rer~vl~lr~~~~~~~t~~EIa~~lgvs~~~V~q~~~~Al~kL 273 (289)
T PRK07500 228 LNERELRIIRERRLREDGATLEALGEELGISKERVRQIEARALEKL 273 (289)
T ss_pred CCHHHHHHHHHHhcCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 45566666666553 3789999999999999999999999888764
No 122
>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=80.42 E-value=4.7 Score=29.39 Aligned_cols=44 Identities=11% Similarity=0.138 Sum_probs=34.9
Q ss_pred ccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 45 VSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 45 v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
.+..|+-.+-++. ..+.++..|+..+|.|.+||+++-+..+.-+
T Consensus 207 L~~rer~vi~~~~-~~~~t~~eIA~~lgis~~~V~~~~~ral~kL 250 (254)
T TIGR02850 207 LNEREKMILNMRF-FEGKTQMEVAEEIGISQAQVSRLEKAALKHM 250 (254)
T ss_pred CCHHHHHHHHHHH-cCCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 4445555555554 5789999999999999999999999888754
No 123
>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=80.27 E-value=3.8 Score=30.69 Aligned_cols=45 Identities=18% Similarity=0.170 Sum_probs=36.6
Q ss_pred ccHHHHHHHHHHHh---hcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 45 VSIEEQLCMFLHIL---AHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 45 v~veE~vamFL~i~---~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
.+..|+-.+-|... ..+.++..|+..+|.|.+||..+.+..+..+
T Consensus 250 L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVrq~~~rAl~kL 297 (298)
T TIGR02997 250 LTPRERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKALRKL 297 (298)
T ss_pred CCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHc
Confidence 56666766777654 6889999999999999999999988877653
No 124
>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=80.16 E-value=4.3 Score=25.17 Aligned_cols=38 Identities=11% Similarity=0.003 Sum_probs=29.1
Q ss_pred HHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHH
Q 036324 47 IEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNL 84 (91)
Q Consensus 47 veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~ 84 (91)
.-.+.+.-|..--.+.+++.|+...+.|..||..+++.
T Consensus 18 ~~~r~af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 18 SLAEAAAALAREEAGKTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 33344444444458999999999999999999999875
No 125
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=80.16 E-value=4.9 Score=27.41 Aligned_cols=37 Identities=19% Similarity=0.253 Sum_probs=32.6
Q ss_pred HHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 53 MFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 53 mFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
+|+...-.|.++..|+..+|.|..||..+.+..+..+
T Consensus 141 i~~l~~~~~~s~~eIA~~lgis~~tV~~~l~ra~~~L 177 (182)
T PRK12537 141 CILHAYVDGCSHAEIAQRLGAPLGTVKAWIKRSLKAL 177 (182)
T ss_pred HHHHHHHcCCCHHHHHHHHCCChhhHHHHHHHHHHHH
Confidence 4666678999999999999999999999999887765
No 126
>PF13309 HTH_22: HTH domain
Probab=80.07 E-value=2.6 Score=25.06 Aligned_cols=41 Identities=20% Similarity=0.237 Sum_probs=27.6
Q ss_pred CCccHHHHHHHHHHHhhcC-----cchhhhhhccccchhhHHHHHH
Q 036324 43 GTVSIEEQLCMFLHILAHH-----VKSRTIHSRFLRSRETISRYFN 83 (91)
Q Consensus 43 ~~v~veE~vamFL~i~~~~-----~~~r~i~~~F~~S~eTisr~f~ 83 (91)
..++-+|++.+--.-=..| .+...+++.++.|..||++|.+
T Consensus 19 ~~l~~~~k~~iV~~L~~~G~F~lKgav~~vA~~L~iS~~TVY~YLr 64 (64)
T PF13309_consen 19 SRLSKEEKKEIVRQLYEKGIFLLKGAVEYVAEKLGISRATVYRYLR 64 (64)
T ss_pred hhCCHHHHHHHHHHHHHCCCcccCcHHHHHHHHHCCCHHHHHHHcC
Confidence 4566666665533332222 4567789999999999999863
No 127
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=79.95 E-value=5.4 Score=26.42 Aligned_cols=38 Identities=13% Similarity=0.067 Sum_probs=32.7
Q ss_pred HHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 52 CMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 52 amFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
.+|....-.+.++.+|+..+|.|..||.......+.++
T Consensus 112 ~v~~l~~~~~~s~~eIA~~lgis~~tv~~~l~ra~~~L 149 (159)
T PRK12527 112 DSFLLRKLEGLSHQQIAEHLGISRSLVEKHIVNAMKHC 149 (159)
T ss_pred HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 46666778999999999999999999999988777665
No 128
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=79.80 E-value=3 Score=30.01 Aligned_cols=43 Identities=14% Similarity=0.145 Sum_probs=33.5
Q ss_pred ccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 45 VSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 45 v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
.|--|+=.+.| ++.|.+|.+|+...+.|..||..+....+..+
T Consensus 156 Lt~rE~~Vl~l--~~~G~s~~eIA~~L~iS~~TVk~~~~~i~~Kl 198 (216)
T PRK10100 156 LTHREKEILNK--LRIGASNNEIARSLFISENTVKTHLYNLFKKI 198 (216)
T ss_pred CCHHHHHHHHH--HHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence 55544444433 44589999999999999999999999988765
No 129
>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=79.79 E-value=4.8 Score=22.93 Aligned_cols=28 Identities=18% Similarity=0.214 Sum_probs=22.4
Q ss_pred cCcchhhhhhccccchhhHHHHHHHHHH
Q 036324 60 HHVKSRTIHSRFLRSRETISRYFNLVLN 87 (91)
Q Consensus 60 ~~~~~r~i~~~F~~S~eTisr~f~~Vl~ 87 (91)
...+..+|++.++.+..||||.+++..+
T Consensus 17 ~~~t~~~l~~~~~~~~~~vs~~i~~L~~ 44 (68)
T PF13463_consen 17 GPMTQSDLAERLGISKSTVSRIIKKLEE 44 (68)
T ss_dssp S-BEHHHHHHHTT--HHHHHHHHHHHHH
T ss_pred CCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 5588899999999999999999988765
No 130
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=79.70 E-value=4.7 Score=29.39 Aligned_cols=44 Identities=16% Similarity=0.154 Sum_probs=34.1
Q ss_pred ccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 45 VSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 45 v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
.+..|+-.+-++. ..|.++..|+..+|.|.+||++..+..++.+
T Consensus 210 L~~~er~vi~~~~-~~~~t~~eIA~~lgis~~~V~~~~~~al~kL 253 (258)
T PRK08215 210 LNDREKLILNLRF-FQGKTQMEVAEEIGISQAQVSRLEKAALKHM 253 (258)
T ss_pred CCHHHHHHHHHHH-hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 4444444444433 5789999999999999999999999888765
No 131
>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=79.66 E-value=3.7 Score=22.86 Aligned_cols=40 Identities=13% Similarity=0.168 Sum_probs=30.0
Q ss_pred HHHHHHHHHHHhhcCc--chhhhhhccccchhhHHHHHHHHH
Q 036324 47 IEEQLCMFLHILAHHV--KSRTIHSRFLRSRETISRYFNLVL 86 (91)
Q Consensus 47 veE~vamFL~i~~~~~--~~r~i~~~F~~S~eTisr~f~~Vl 86 (91)
++..+.+.=+...++. +..+|....+-+++|++|+.....
T Consensus 2 l~ral~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~ 43 (52)
T PF09339_consen 2 LERALRILEALAESGGPLTLSEIARALGLPKSTVHRLLQTLV 43 (52)
T ss_dssp HHHHHHHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 5556666666665554 699999999999999999987654
No 132
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=79.60 E-value=3.4 Score=26.96 Aligned_cols=32 Identities=13% Similarity=0.124 Sum_probs=29.1
Q ss_pred hhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 58 LAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 58 ~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
++.|.+++.|+...+.|..||..+....++.+
T Consensus 161 ~~~g~~~~~Ia~~l~~s~~tv~~~~~~~~~kl 192 (211)
T PRK15369 161 ITEGYTNRDIAEQLSISIKTVETHRLNMMRKL 192 (211)
T ss_pred HHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence 67889999999999999999999999887764
No 133
>PRK11233 nitrogen assimilation transcriptional regulator; Provisional
Probab=79.47 E-value=3.4 Score=30.27 Aligned_cols=37 Identities=11% Similarity=0.087 Sum_probs=29.4
Q ss_pred HHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHH
Q 036324 49 EQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVL 86 (91)
Q Consensus 49 E~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl 86 (91)
++|..|+-+.- ..+++.++...+.|++|||+.+.+.=
T Consensus 4 ~~L~~F~~v~~-~~S~s~AA~~L~isQ~avS~~I~~LE 40 (305)
T PRK11233 4 RRLKYFVKIVD-IGSLTQAAEVLHIAQPALSQQVATLE 40 (305)
T ss_pred HHHHHHHHHHH-cCCHHHHHHHhCCCchHHHHHHHHHH
Confidence 45666665555 45999999999999999999998753
No 134
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=79.35 E-value=5.1 Score=27.58 Aligned_cols=39 Identities=5% Similarity=-0.140 Sum_probs=31.7
Q ss_pred HHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 51 LCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 51 vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
-.+|....-.|.++..|+..++.|..||...++....++
T Consensus 112 r~i~~l~~~~g~~~~EIA~~lgis~~tV~~~l~Rar~~L 150 (181)
T PRK09637 112 AEALRLTELEGLSQKEIAEKLGLSLSGAKSRVQRGRVKL 150 (181)
T ss_pred HHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 344444456789999999999999999999988877665
No 135
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=79.35 E-value=6.1 Score=27.06 Aligned_cols=44 Identities=9% Similarity=0.002 Sum_probs=33.7
Q ss_pred ccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 45 VSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 45 v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
.+.+++-++-|+.+ .+.++..|+..++.|..||...++.....+
T Consensus 132 L~~~~r~vl~l~~~-~~~s~~eIA~~lgis~~tV~~~l~Rar~~L 175 (189)
T PRK12515 132 LSPAHREIIDLVYY-HEKSVEEVGEIVGIPESTVKTRMFYARKKL 175 (189)
T ss_pred CCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 34444444445444 899999999999999999999988777654
No 136
>COG0664 Crp cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]
Probab=79.31 E-value=4.2 Score=27.22 Aligned_cols=44 Identities=27% Similarity=0.351 Sum_probs=38.4
Q ss_pred CCccHHHHHHHHHHHhhc--------------CcchhhhhhccccchhhHHHHHHHHH
Q 036324 43 GTVSIEEQLCMFLHILAH--------------HVKSRTIHSRFLRSRETISRYFNLVL 86 (91)
Q Consensus 43 ~~v~veE~vamFL~i~~~--------------~~~~r~i~~~F~~S~eTisr~f~~Vl 86 (91)
..-++++++|.+|..++. ..+...++...+-|.+|++|.+.+.-
T Consensus 139 ~~~~~~~r~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~ia~~~g~~~~~vsr~l~~l~ 196 (214)
T COG0664 139 ARKDVEERLARFLLNLGRRLGIATEDGILIPLPLTHKDLAEYLGLSRETVSRILKELR 196 (214)
T ss_pred hhccHHHHHHHHHHHHhhccCCCCCCCcEEeccCCHHHHHHHhCCchhhHHHHHHHHH
Confidence 456899999999999984 57889999999999999999998754
No 137
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=79.21 E-value=4.8 Score=25.68 Aligned_cols=42 Identities=12% Similarity=0.138 Sum_probs=35.9
Q ss_pred CccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHH
Q 036324 44 TVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLV 85 (91)
Q Consensus 44 ~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~V 85 (91)
..+..-.+.+---++.++.+...+...||.|..|.+++...-
T Consensus 8 ~Lt~~gR~~lv~~vv~~g~~~a~aA~~~gVS~~Ta~kW~~Ry 49 (85)
T PF13011_consen 8 RLTPRGRLRLVRRVVEQGWPVAHAAAEFGVSRRTAYKWLARY 49 (85)
T ss_pred CCCHHHHHHHHHHHHHcCCcHHHHHHHhCCCHHHHHHHHHHH
Confidence 366777777777788999999999999999999999987653
No 138
>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=79.07 E-value=5.5 Score=26.12 Aligned_cols=44 Identities=5% Similarity=0.070 Sum_probs=34.0
Q ss_pred ccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 45 VSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 45 v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
+|.+++- +|....-.|.++..|+..+|.|..||...++.....+
T Consensus 112 L~~~~r~-v~~l~~~~g~~~~eIA~~l~is~~tv~~~l~Rar~~L 155 (159)
T TIGR02989 112 LPERQRE-LLQLRYQRGVSLTALAEQLGRTVNAVYKALSRLRVRL 155 (159)
T ss_pred CCHHHHH-HHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 4444444 4444456899999999999999999999998877665
No 139
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=79.04 E-value=5.1 Score=27.18 Aligned_cols=38 Identities=11% Similarity=0.064 Sum_probs=32.0
Q ss_pred HHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 52 CMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 52 amFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
.+|....-.|.++..|+..++.|..||...++..+..+
T Consensus 138 ~v~~l~~~~g~s~~eIA~~l~is~~tV~~~l~ra~~~L 175 (184)
T PRK12512 138 DVVQSISVEGASIKETAAKLSMSEGAVRVALHRGLAAL 175 (184)
T ss_pred HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 45555556699999999999999999999999887765
No 140
>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=79.00 E-value=6 Score=21.97 Aligned_cols=34 Identities=18% Similarity=0.213 Sum_probs=26.1
Q ss_pred HHHHHhhcCcchhhhhhccccchhhHHHHHHHHH
Q 036324 53 MFLHILAHHVKSRTIHSRFLRSRETISRYFNLVL 86 (91)
Q Consensus 53 mFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl 86 (91)
+..++..++.+..+++..++.|..||++.+....
T Consensus 12 il~~l~~~~~~~~ei~~~~~i~~~~i~~~l~~L~ 45 (78)
T cd00090 12 ILRLLLEGPLTVSELAERLGLSQSTVSRHLKKLE 45 (78)
T ss_pred HHHHHHHCCcCHHHHHHHHCcCHhHHHHHHHHHH
Confidence 3333333448899999999999999999988753
No 141
>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=78.79 E-value=12 Score=23.89 Aligned_cols=61 Identities=8% Similarity=0.088 Sum_probs=38.4
Q ss_pred hCCCHHHHHHHHHHHHhCCCCCCCCCccHHHHH-HHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHH
Q 036324 19 LRMDKRTFELLCGLLRINGGLKADGTVSIEEQL-CMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLN 87 (91)
Q Consensus 19 fRM~~~~F~~L~~~L~~~~~l~~s~~v~veE~v-amFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ 87 (91)
++........+...+.. .+ ++..+-- -..|+ -..+.+..++++..+.+.+||++.++..-+
T Consensus 7 ~~~~~~~~~~~~~~l~~-~~------lt~~q~~iL~~l~-~~~~~t~~ela~~~~~~~~tvs~~l~~Le~ 68 (118)
T TIGR02337 7 LQAREAAMSFFRPILAQ-HG------LTEQQWRILRILA-EQGSMEFTQLANQACILRPSLTGILARLER 68 (118)
T ss_pred HHHHHHHHHHHHHHHHH-cC------CCHHHHHHHHHHH-HcCCcCHHHHHHHhCCCchhHHHHHHHHHH
Confidence 34444555555666654 32 3444432 22222 234578999999999999999999887543
No 142
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=78.74 E-value=4.9 Score=23.18 Aligned_cols=39 Identities=31% Similarity=0.350 Sum_probs=25.5
Q ss_pred CccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHH
Q 036324 44 TVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFN 83 (91)
Q Consensus 44 ~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~ 83 (91)
..+..||--+-+ +..-|.+.+.|+.+.+||+..|.+|++
T Consensus 4 ~Lt~~Eqaqid~-m~qlG~s~~~isr~i~RSr~~Ir~yl~ 42 (50)
T PF11427_consen 4 TLTDAEQAQIDV-MHQLGMSLREISRRIGRSRTCIRRYLK 42 (50)
T ss_dssp ---HHHHHHHHH-HHHTT--HHHHHHHHT--HHHHHHHHH
T ss_pred cCCHHHHHHHHH-HHHhchhHHHHHHHhCccHHHHHHHhc
Confidence 466777765544 345689999999999999999999976
No 143
>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=78.58 E-value=1.8 Score=24.98 Aligned_cols=25 Identities=28% Similarity=0.311 Sum_probs=21.7
Q ss_pred CcchhhhhhccccchhhHHHHHHHH
Q 036324 61 HVKSRTIHSRFLRSRETISRYFNLV 85 (91)
Q Consensus 61 ~~~~r~i~~~F~~S~eTisr~f~~V 85 (91)
..+..++++.|+.|..||-|-+...
T Consensus 14 ~~s~~ela~~~~VS~~TiRRDl~~L 38 (57)
T PF08220_consen 14 KVSVKELAEEFGVSEMTIRRDLNKL 38 (57)
T ss_pred CEEHHHHHHHHCcCHHHHHHHHHHH
Confidence 4677889999999999999998764
No 144
>TIGR02984 Sig-70_plancto1 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are apparently found only in the Planctomycetaceae family including the genuses Gemmata and Pirellula (in which seven sequences are found).
Probab=78.30 E-value=6.3 Score=26.56 Aligned_cols=37 Identities=16% Similarity=0.127 Sum_probs=30.9
Q ss_pred HHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 53 MFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 53 mFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
+|....-.+.++..|+...|.|..||.+..+.....+
T Consensus 148 vi~l~~~~g~s~~eIA~~lgis~~~v~~~l~Ra~~~L 184 (189)
T TIGR02984 148 VILLRHLEGLSFAEVAERMDRSEGAVSMLWVRGLARL 184 (189)
T ss_pred HHHHHHhcCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 3444445899999999999999999999999887765
No 145
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=78.22 E-value=5.6 Score=28.49 Aligned_cols=45 Identities=18% Similarity=0.138 Sum_probs=32.9
Q ss_pred ccHHHHHHHHHHHh---hcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 45 VSIEEQLCMFLHIL---AHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 45 v~veE~vamFL~i~---~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
.|..++-.+=|+.. ..|.|++.|+..+|.|.+||++..+.-+..+
T Consensus 176 Lp~~~R~i~~l~y~~~~~e~~S~~EIA~~lgis~~tV~~~~~rA~~kL 223 (233)
T PRK05803 176 LDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRALKKL 223 (233)
T ss_pred CCHHHHHHHHHHhCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 33445555555432 4789999999999999999999877666544
No 146
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=78.05 E-value=6.4 Score=27.27 Aligned_cols=43 Identities=9% Similarity=-0.045 Sum_probs=32.6
Q ss_pred cHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 46 SIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 46 ~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
+..++-+ |+..--.|.++..|+..++.|..||....+.....+
T Consensus 118 p~~~r~i-~~L~~~~g~s~~EIA~~Lgis~~tVk~~l~Rar~~L 160 (187)
T PRK12516 118 PDDQREA-IILVGASGFAYEEAAEICGCAVGTIKSRVNRARQRL 160 (187)
T ss_pred CHHHHHH-HHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 3344444 444445899999999999999999999888776654
No 147
>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=77.92 E-value=6 Score=26.68 Aligned_cols=38 Identities=11% Similarity=-0.014 Sum_probs=32.3
Q ss_pred HHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 52 CMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 52 amFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
.+|+..--.|.++..|+...|.|..||....+.....+
T Consensus 141 ~v~~l~~~~g~s~~EIA~~lgis~~tVk~~l~Rar~~L 178 (183)
T TIGR02999 141 EVVELRFFAGLTVEEIAELLGVSVRTVERDWRFARAWL 178 (183)
T ss_pred HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 35666667899999999999999999999998877665
No 148
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=77.89 E-value=7.4 Score=26.07 Aligned_cols=37 Identities=14% Similarity=-0.037 Sum_probs=30.3
Q ss_pred HHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 53 MFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 53 mFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
+|+..--.|.++.+|+..+|.|..||....+.....+
T Consensus 120 v~~l~~~~g~s~~eIA~~lgis~~tV~~~l~Rar~~L 156 (164)
T PRK12547 120 AIILIGASGFSYEDAAAICGCAVGTIKSRVSRARNRL 156 (164)
T ss_pred HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 3444444899999999999999999999998887665
No 149
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=77.73 E-value=5.8 Score=27.30 Aligned_cols=41 Identities=12% Similarity=-0.069 Sum_probs=34.4
Q ss_pred HHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 49 EQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 49 E~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
++=.+|...--++.++..|+..++.|..||....+..+..+
T Consensus 134 ~~r~v~~L~~~~g~s~~EIA~~lgis~~tVk~~l~Rar~~L 174 (185)
T PRK09649 134 DQREALLLTQLLGLSYADAAAVCGCPVGTIRSRVARARDAL 174 (185)
T ss_pred HHhHHhhhHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 34456666777899999999999999999999998887765
No 150
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=77.60 E-value=6.2 Score=26.07 Aligned_cols=37 Identities=14% Similarity=0.094 Sum_probs=30.1
Q ss_pred HHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 53 MFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 53 mFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
+|......+.++..|+..+|.|..||.+..+.....+
T Consensus 133 i~~l~~~~~~~~~eIA~~lgis~~tv~~~~~ra~~~l 169 (179)
T PRK11924 133 VFLLRYVEGLSYREIAEILGVPVGTVKSRLRRARQLL 169 (179)
T ss_pred HhhHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 3444445789999999999999999999998876654
No 151
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=77.46 E-value=6.6 Score=26.75 Aligned_cols=43 Identities=12% Similarity=0.039 Sum_probs=33.2
Q ss_pred cHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 46 SIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 46 ~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
+..++. +|...--.|.++.+|++.++.|..||....+.....+
T Consensus 131 ~~~~r~-v~~l~~~~g~s~~EIA~~l~is~~tV~~~l~rar~~L 173 (181)
T PRK12536 131 PDRQRL-PIVHVKLEGLSVAETAQLTGLSESAVKVGIHRGLKAL 173 (181)
T ss_pred CHHHHH-HHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 333444 4444456789999999999999999999998877665
No 152
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=77.38 E-value=6.6 Score=26.45 Aligned_cols=43 Identities=9% Similarity=0.043 Sum_probs=32.2
Q ss_pred cHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 46 SIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 46 ~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
+.+++-++.|. .-.+.++..|+..+|.|.+||....+.....+
T Consensus 138 ~~~~r~il~l~-~~~~~s~~eIA~~lgis~~~v~~~l~Rar~~L 180 (187)
T PRK09641 138 PEKYRTVIVLK-YIEDLSLKEISEILDLPVGTVKTRIHRGREAL 180 (187)
T ss_pred CHHHHHHhhhH-HhhCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 34444444443 34799999999999999999999888776554
No 153
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=77.34 E-value=4 Score=30.07 Aligned_cols=39 Identities=10% Similarity=0.090 Sum_probs=33.7
Q ss_pred HHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHH
Q 036324 49 EQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLN 87 (91)
Q Consensus 49 E~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ 87 (91)
+++-+|+.++-++.++..++..-+.|++|||+.+++.=+
T Consensus 4 ~~L~~f~~v~~~g~S~s~AA~~L~isQpavS~~ik~LE~ 42 (313)
T PRK12684 4 HQLRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELED 42 (313)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHhcCCChHHHHHHHHHHH
Confidence 478888888888889999999999999999999987533
No 154
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=77.22 E-value=7.4 Score=25.42 Aligned_cols=37 Identities=5% Similarity=-0.006 Sum_probs=30.8
Q ss_pred HHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 53 MFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 53 mFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
+|...--.|.++..|+...|.|..||....+..+..+
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 4444456789999999999999999999998877665
No 155
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=77.05 E-value=4.5 Score=26.92 Aligned_cols=44 Identities=16% Similarity=0.288 Sum_probs=34.6
Q ss_pred CccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 44 TVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 44 ~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
..|..|.- .|..++.|.++.+|+...+.|..||..|...+.+.+
T Consensus 143 ~lt~~E~~--vl~~l~~g~~~~~I~~~l~~s~~tv~~~~~~l~~Kl 186 (204)
T PRK09958 143 SLSKQEIS--VMRYILDGKDNNDIAEKMFISNKTVSTYKSRLMEKL 186 (204)
T ss_pred cCCHHHHH--HHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHc
Confidence 35555543 455666778999999999999999999999887654
No 156
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=76.97 E-value=6.4 Score=26.49 Aligned_cols=38 Identities=18% Similarity=0.146 Sum_probs=32.3
Q ss_pred HHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHHh
Q 036324 53 MFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAIL 90 (91)
Q Consensus 53 mFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai~ 90 (91)
+|....-.|.++..|+..++.|..||.......+.++.
T Consensus 126 v~~L~~~eg~s~~EIA~~l~is~~tV~~~l~ra~~~~~ 163 (168)
T PRK12525 126 AFLMSQLEGLTYVEIGERLGVSLSRIHQYMVEAFKCCY 163 (168)
T ss_pred HHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 45555688999999999999999999999988887653
No 157
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=76.90 E-value=7.6 Score=25.75 Aligned_cols=38 Identities=21% Similarity=0.158 Sum_probs=31.6
Q ss_pred HHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 52 CMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 52 amFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
.+|....-+|.++..|+..+|.|..||....+.....+
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 45555677899999999999999999999988776543
No 158
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=76.89 E-value=1.6 Score=31.98 Aligned_cols=24 Identities=13% Similarity=-0.040 Sum_probs=21.5
Q ss_pred CcchhhhhhccccchhhHHHHHHH
Q 036324 61 HVKSRTIHSRFLRSRETISRYFNL 84 (91)
Q Consensus 61 ~~~~r~i~~~F~~S~eTisr~f~~ 84 (91)
..+-++|+...|.|..||||.++.
T Consensus 6 ~~Ti~dIA~~agVS~~TVSr~Ln~ 29 (342)
T PRK10014 6 KITIHDVALAAGVSVSTVSLVLSG 29 (342)
T ss_pred CCcHHHHHHHhCCCHHHHHHHHCC
Confidence 357899999999999999999875
No 159
>COG2826 Tra8 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]
Probab=76.41 E-value=3.7 Score=32.06 Aligned_cols=40 Identities=20% Similarity=0.224 Sum_probs=34.6
Q ss_pred CCccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHH
Q 036324 43 GTVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFN 83 (91)
Q Consensus 43 ~~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~ 83 (91)
.+.|.+|..-|==|- ..+.|+|.|+..-++..+||||-++
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 388888888776666 7899999999999999999999764
No 160
>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=76.13 E-value=2.5 Score=23.29 Aligned_cols=27 Identities=26% Similarity=0.214 Sum_probs=21.7
Q ss_pred hhcCcchhhhhhccccchhhHHHHHHH
Q 036324 58 LAHHVKSRTIHSRFLRSRETISRYFNL 84 (91)
Q Consensus 58 ~~~~~~~r~i~~~F~~S~eTisr~f~~ 84 (91)
-.+|.+.++++..-+.|..||+++.+.
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 357889999999999999999998753
No 161
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=75.76 E-value=8.2 Score=26.61 Aligned_cols=41 Identities=7% Similarity=0.010 Sum_probs=30.6
Q ss_pred HHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 48 EEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 48 eE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
..+-++-|. --.|.++..|+..+|.|..||....+.....+
T Consensus 138 ~~R~v~~L~-~~~g~s~~EIA~~lgis~~tVk~~l~RAr~~L 178 (189)
T PRK12530 138 QQARVFMMR-EYLELSSEQICQECDISTSNLHVLLYRARLQL 178 (189)
T ss_pred HHHHHHhHH-HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 334444444 44599999999999999999988877666544
No 162
>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=75.52 E-value=5.2 Score=21.77 Aligned_cols=34 Identities=29% Similarity=0.271 Sum_probs=27.0
Q ss_pred HHHHHHHhhcCcchhhhhhccccchhhHHHHHHH
Q 036324 51 LCMFLHILAHHVKSRTIHSRFLRSRETISRYFNL 84 (91)
Q Consensus 51 vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~ 84 (91)
+-+|.-.=-.+.+.+.|..+-+.|..++++||..
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 3444444456789999999999999999999963
No 163
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=75.49 E-value=8.8 Score=25.37 Aligned_cols=36 Identities=14% Similarity=0.018 Sum_probs=29.1
Q ss_pred HHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHH
Q 036324 53 MFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNA 88 (91)
Q Consensus 53 mFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~a 88 (91)
+|....-.+.++..|+..+|.|..||.+.....+.-
T Consensus 117 v~~l~~~~~~s~~EIA~~lgis~~tV~~~l~ra~~~ 152 (163)
T PRK07037 117 AFEMYRLHGETQKDIARELGVSPTLVNFMIRDALVH 152 (163)
T ss_pred HHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 454445569999999999999999999987766554
No 164
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=75.46 E-value=7.4 Score=28.79 Aligned_cols=43 Identities=19% Similarity=0.221 Sum_probs=32.8
Q ss_pred cHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 46 SIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 46 ~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
+..|+-.+-|+. ..+.++..|+..++.|.+||++..+..+..+
T Consensus 217 ~~rer~vl~l~y-~~~~t~~EIA~~lgis~~~V~~~~~ral~kL 259 (264)
T PRK07122 217 PERERTVLVLRF-FESMTQTQIAERVGISQMHVSRLLAKTLARL 259 (264)
T ss_pred CHHHHHHHHHHh-cCCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 333444444443 5799999999999999999999988877654
No 165
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=75.45 E-value=8.8 Score=22.88 Aligned_cols=37 Identities=11% Similarity=0.155 Sum_probs=27.3
Q ss_pred HHHHHHHh-hcCcchhhhhhccccchhhHHHHHHHHHH
Q 036324 51 LCMFLHIL-AHHVKSRTIHSRFLRSRETISRYFNLVLN 87 (91)
Q Consensus 51 vamFL~i~-~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ 87 (91)
+.++..+. ....+...++..++.|..||++.++...+
T Consensus 13 ~~il~~l~~~~~~~~~~la~~~~~s~~~i~~~l~~L~~ 50 (101)
T smart00347 13 FLVLRILYEEGPLSVSELAKRLGVSPSTVTRVLDRLEK 50 (101)
T ss_pred HHHHHHHHHcCCcCHHHHHHHHCCCchhHHHHHHHHHH
Confidence 33444443 33478999999999999999999887644
No 166
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=75.38 E-value=7.8 Score=27.41 Aligned_cols=37 Identities=8% Similarity=-0.003 Sum_probs=31.5
Q ss_pred HHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 53 MFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 53 mFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
+|+...-.|.++..|+..+|.|..||....+..+..+
T Consensus 156 v~~L~~~~g~s~~EIAe~lgis~~tV~~~l~RAr~~L 192 (206)
T PRK12544 156 VFMMREFIELETNEICHAVDLSVSNLNVLLYRARLRL 192 (206)
T ss_pred HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 4555566799999999999999999999998887765
No 167
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=75.25 E-value=9.2 Score=26.36 Aligned_cols=37 Identities=8% Similarity=0.186 Sum_probs=29.8
Q ss_pred HHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 53 MFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 53 mFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
+|....-.|.++..|+..+|.|..||...++...+.+
T Consensus 149 v~~l~~~eg~s~~EIA~~lgis~~tVk~rl~ra~~~L 185 (194)
T PRK12531 149 VLQAVYLEELPHQQVAEMFDIPLGTVKSRLRLAVEKL 185 (194)
T ss_pred HHHHHHHcCCCHHHHHHHhCcCHHHHHHHHHHHHHHH
Confidence 4444445899999999999999999998888776544
No 168
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).
Probab=74.98 E-value=8.9 Score=25.93 Aligned_cols=44 Identities=7% Similarity=-0.130 Sum_probs=33.9
Q ss_pred ccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 45 VSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 45 v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
++..+ -.+|...--+|.+++.|+..++.|..||....+.....+
T Consensus 101 L~~~~-r~v~~l~~~~g~s~~eIA~~lgis~~tV~~~l~Rar~~L 144 (170)
T TIGR02959 101 LPDEY-REAIRLTELEGLSQQEIAEKLGLSLSGAKSRVQRGRKKL 144 (170)
T ss_pred CCHHH-HHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 33333 345555567899999999999999999999988877655
No 169
>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=74.87 E-value=2.8 Score=27.42 Aligned_cols=32 Identities=6% Similarity=-0.053 Sum_probs=27.8
Q ss_pred hhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 58 LAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 58 ~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
-..|.++..|+..+|.|..||....+.....+
T Consensus 118 ~~~g~s~~eIA~~lgis~~tv~~~l~Ra~~~L 149 (154)
T TIGR02950 118 EFKEFSYKEIAELLNLSLAKVKSNLFRARKEL 149 (154)
T ss_pred hhccCcHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 34799999999999999999999988777655
No 170
>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=74.61 E-value=8.4 Score=27.52 Aligned_cols=44 Identities=18% Similarity=0.079 Sum_probs=34.1
Q ss_pred cHHHHHHHHHHHh---hcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 46 SIEEQLCMFLHIL---AHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 46 ~veE~vamFL~i~---~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
+..++-++-|+.. ..+.++..|+...+-|..||++..+..+..+
T Consensus 176 ~~~~r~il~l~y~~~~~e~~S~~EIAe~lgis~~tV~~~~~rAl~~L 222 (227)
T TIGR02846 176 DGREREVIEMRYGLGDGRRKTQREIAKILGISRSYVSRIEKRALMKL 222 (227)
T ss_pred CHHHHHHHHHHHcCCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 3444444445443 3889999999999999999999998888765
No 171
>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=74.47 E-value=4.7 Score=23.59 Aligned_cols=43 Identities=14% Similarity=0.003 Sum_probs=33.6
Q ss_pred CccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHH
Q 036324 44 TVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVL 86 (91)
Q Consensus 44 ~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl 86 (91)
.-|.|++..+---.+..+.+...+...+|.|..|+++...+..
T Consensus 6 ~ys~e~K~~~v~~~~~~g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 6 RYSPEFKLQAVREYLESGESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp ---HHHHHHHHHHHHHHHCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHCCCceEeeecccccccccccHHHHHHh
Confidence 4567777777666678899999999999999999999988764
No 172
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=74.16 E-value=8.2 Score=27.70 Aligned_cols=40 Identities=10% Similarity=-0.014 Sum_probs=30.9
Q ss_pred HHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 49 EQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 49 E~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
++-++-|+ --.+.++..|+..+|.|..||..+.+.....+
T Consensus 139 ~R~v~~L~-y~eg~s~~EIAe~LgiS~~tVk~~L~RAr~~L 178 (216)
T PRK12533 139 YREVLVLR-ELEDMSYREIAAIADVPVGTVMSRLARARRRL 178 (216)
T ss_pred HHhHhhhH-HhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 33334443 34799999999999999999999988776654
No 173
>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=73.66 E-value=8.9 Score=26.11 Aligned_cols=37 Identities=11% Similarity=0.077 Sum_probs=30.4
Q ss_pred HHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 52 CMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 52 amFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
.+++.. -.+.++..|+..++.|..||...++...+.+
T Consensus 157 ~i~~~~-~~~~s~~eIA~~l~~s~~tV~~~l~r~r~~L 193 (198)
T TIGR02859 157 KVLQSY-LDGKSYQEIACDLNRHVKSIDNALQRVKRKL 193 (198)
T ss_pred HHHHHH-HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 344543 4899999999999999999999998877654
No 174
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=73.61 E-value=8.8 Score=29.26 Aligned_cols=46 Identities=15% Similarity=0.170 Sum_probs=36.5
Q ss_pred CccHHHHHHHHHHHh---hcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 44 TVSIEEQLCMFLHIL---AHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 44 ~v~veE~vamFL~i~---~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
..+..|+-.+-|... +.+.+...|+..+|.|.+||..+-+..+..+
T Consensus 256 ~L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVRqi~~rAl~kL 304 (317)
T PRK07405 256 DLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKL 304 (317)
T ss_pred cCCHHHHHHHHHHhhcCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 355666666666654 5789999999999999999999988877654
No 175
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=73.57 E-value=9.1 Score=25.27 Aligned_cols=37 Identities=11% Similarity=-0.058 Sum_probs=29.9
Q ss_pred HHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 53 MFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 53 mFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
+|....-.|.++..|+..+|.|..||...++.....+
T Consensus 114 v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Rar~~L 150 (160)
T PRK09642 114 VVLAHYLEEKSYQEIALQEKIEVKTVEMKLYRARKWI 150 (160)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 4444556899999999999999999988877766544
No 176
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=73.47 E-value=9.2 Score=25.91 Aligned_cols=37 Identities=8% Similarity=-0.023 Sum_probs=30.6
Q ss_pred HHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 53 MFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 53 mFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
+|....-.+.++..|+..+|.|..||....+.....+
T Consensus 143 vl~l~~~~~~s~~eIA~~lgis~~~V~~~l~ra~~~L 179 (186)
T PRK13919 143 VIEVLYYQGYTHREAAQLLGLPLGTLKTRARRALSRL 179 (186)
T ss_pred HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 3444446799999999999999999999988887765
No 177
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=73.42 E-value=6.9 Score=26.48 Aligned_cols=38 Identities=13% Similarity=0.107 Sum_probs=33.1
Q ss_pred HHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 52 CMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 52 amFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
.+|+.....|.++..|+..+|.|..||....+..+..+
T Consensus 126 ~i~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~~ 163 (172)
T PRK09651 126 EAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKATEHC 163 (172)
T ss_pred HHhhhhhccCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 56777778999999999999999999999888877665
No 178
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=73.30 E-value=9.7 Score=26.01 Aligned_cols=44 Identities=14% Similarity=0.024 Sum_probs=33.7
Q ss_pred ccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 45 VSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 45 v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
.+.+++-.+.|.. =.|.++..|+..+|.|..||....+.....+
T Consensus 139 L~~~~r~v~~l~~-~~g~s~~eIA~~lgis~~tv~~~l~Rar~~L 182 (193)
T PRK11923 139 LPEDLRTALTLRE-FDGLSYEDIASVMQCPVGTVRSRIFRAREAI 182 (193)
T ss_pred CCHHHhHHHhhHH-hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 3445555555533 3789999999999999999999988877654
No 179
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=73.18 E-value=9 Score=26.10 Aligned_cols=38 Identities=18% Similarity=0.242 Sum_probs=30.4
Q ss_pred HHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHHh
Q 036324 53 MFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAIL 90 (91)
Q Consensus 53 mFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai~ 90 (91)
+|+..--.|.++..|+...|.|..||....+.-+..+.
T Consensus 135 v~~L~~~~g~s~~EIA~~lgis~~tVk~~l~rAl~~~~ 172 (178)
T PRK12529 135 AFLMATLDGMKQKDIAQALDIALPTVKKYIHQAYVTCL 172 (178)
T ss_pred HHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 34444458999999999999999999998887666543
No 180
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=73.18 E-value=4.8 Score=28.29 Aligned_cols=32 Identities=19% Similarity=0.221 Sum_probs=26.6
Q ss_pred HHHHHHhhcCcchhhhhhccccchhhHHHHHHH
Q 036324 52 CMFLHILAHHVKSRTIHSRFLRSRETISRYFNL 84 (91)
Q Consensus 52 amFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~ 84 (91)
.++-+ ...+.+.+.|+..++.|.+||+|+...
T Consensus 164 ~i~~~-~~~g~s~~~iak~lgis~~Tv~r~~k~ 195 (200)
T PRK13413 164 KIKKL-LDKGTSKSEIARKLGVSRTTLARFLKT 195 (200)
T ss_pred HHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHh
Confidence 45555 456789999999999999999999863
No 181
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=72.78 E-value=9.1 Score=26.31 Aligned_cols=37 Identities=11% Similarity=-0.009 Sum_probs=29.9
Q ss_pred HHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 53 MFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 53 mFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
+|...--.+.++..|+..+|.|..||....+.....+
T Consensus 144 i~~L~~~~g~s~~EIA~~lgis~~tVk~~l~Rar~~L 180 (195)
T PRK12532 144 VFTLKEILGFSSDEIQQMCGISTSNYHTIMHRARESL 180 (195)
T ss_pred HhhhHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 3443344789999999999999999999988776654
No 182
>PRK09526 lacI lac repressor; Reviewed
Probab=72.69 E-value=2.4 Score=31.11 Aligned_cols=23 Identities=26% Similarity=0.131 Sum_probs=20.5
Q ss_pred cchhhhhhccccchhhHHHHHHH
Q 036324 62 VKSRTIHSRFLRSRETISRYFNL 84 (91)
Q Consensus 62 ~~~r~i~~~F~~S~eTisr~f~~ 84 (91)
.+-++|+...|.|..||||.++.
T Consensus 6 ~ti~dIA~~aGVS~~TVSrvLn~ 28 (342)
T PRK09526 6 VTLYDVARYAGVSYQTVSRVLNQ 28 (342)
T ss_pred CcHHHHHHHhCCCHHHHHHHhcC
Confidence 46789999999999999999873
No 183
>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=72.68 E-value=11 Score=24.88 Aligned_cols=45 Identities=4% Similarity=0.090 Sum_probs=34.9
Q ss_pred CccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 44 TVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 44 ~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
..|..++.++-|+. -.|.++..|+..+|.|..||....+.....+
T Consensus 122 ~L~~~~r~vl~l~~-~~g~s~~eIA~~l~is~~tv~~~l~ra~~~L 166 (170)
T TIGR02952 122 ILTPKQQHVIALRF-GQNLPIAEVARILGKTEGAVKILQFRAIKKL 166 (170)
T ss_pred hCCHHHHHHHHHHH-hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 35555555555533 4689999999999999999999998887765
No 184
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=72.67 E-value=9.3 Score=25.47 Aligned_cols=44 Identities=11% Similarity=-0.032 Sum_probs=33.9
Q ss_pred ccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 45 VSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 45 v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
++.+++- +|+....+|.++..|+..+|.|..||....+.....+
T Consensus 109 L~~~~r~-v~~l~~~~g~s~~eIA~~lgis~~tv~~~l~Rar~~L 152 (165)
T PRK09644 109 LPVIEAQ-AILLCDVHELTYEEAASVLDLKLNTYKSHLFRGRKRL 152 (165)
T ss_pred CCHHHHH-HHHhHHHhcCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 3444444 4444567899999999999999999999988877655
No 185
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=72.64 E-value=8.8 Score=25.84 Aligned_cols=32 Identities=9% Similarity=0.021 Sum_probs=27.9
Q ss_pred hhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 58 LAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 58 ~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
.-.+.++..|+..+|.|.+||...++.....+
T Consensus 149 ~~~g~s~~eIA~~lgis~~~v~~~l~Rar~~L 180 (187)
T TIGR02948 149 YMEDLSLKEISEILDLPVGTVKTRIHRGREAL 180 (187)
T ss_pred HhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 44789999999999999999999998877654
No 186
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=72.62 E-value=2.3 Score=31.48 Aligned_cols=21 Identities=29% Similarity=0.245 Sum_probs=19.4
Q ss_pred chhhhhhccccchhhHHHHHH
Q 036324 63 KSRTIHSRFLRSRETISRYFN 83 (91)
Q Consensus 63 ~~r~i~~~F~~S~eTisr~f~ 83 (91)
+.++|+...|.|..||||.++
T Consensus 3 ti~dIA~~aGVS~~TVSrvLn 23 (346)
T PRK10401 3 TIRDVARQAGVSVATVSRVLN 23 (346)
T ss_pred CHHHHHHHhCCCHHHHHHHHC
Confidence 678999999999999999986
No 187
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=72.47 E-value=10 Score=19.98 Aligned_cols=26 Identities=23% Similarity=0.137 Sum_probs=22.4
Q ss_pred CcchhhhhhccccchhhHHHHHHHHH
Q 036324 61 HVKSRTIHSRFLRSRETISRYFNLVL 86 (91)
Q Consensus 61 ~~~~r~i~~~F~~S~eTisr~f~~Vl 86 (91)
..+..+++..|+.|..||++.+...-
T Consensus 14 ~~s~~~l~~~l~~s~~tv~~~l~~L~ 39 (53)
T smart00420 14 KVSVEELAELLGVSEMTIRRDLNKLE 39 (53)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 46888999999999999999987754
No 188
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=72.41 E-value=10 Score=26.18 Aligned_cols=37 Identities=5% Similarity=-0.062 Sum_probs=29.8
Q ss_pred HHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 53 MFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 53 mFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
+|....-.+.++..|+..++.|.+||....+.....+
T Consensus 119 v~~L~~~eg~s~~EIA~~lgis~~tV~~~l~Rar~~L 155 (182)
T PRK12511 119 ALHLVAIEGLSYQEAAAVLGIPIGTLMSRIGRARAAL 155 (182)
T ss_pred HHHHHHHcCCCHHHHHHHhCcCHHHHHHHHHHHHHHH
Confidence 3444344799999999999999999999988776654
No 189
>PRK12681 cysB transcriptional regulator CysB; Reviewed
Probab=72.40 E-value=6.5 Score=29.36 Aligned_cols=37 Identities=16% Similarity=0.334 Sum_probs=32.0
Q ss_pred HHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHH
Q 036324 49 EQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLV 85 (91)
Q Consensus 49 E~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~V 85 (91)
+++-.|+-+.-++.+++.++...+.|++|||+.+.+.
T Consensus 4 ~~L~~f~avae~g~S~s~AA~~L~iSQpavS~~I~~L 40 (324)
T PRK12681 4 QQLRYIVEVVNHNLNVSATAEGLYTSQPGISKQVRML 40 (324)
T ss_pred HHHHHHHHHHHccCCHHHHHHHhcCCcHHHHHHHHHH
Confidence 5677788777777899999999999999999998864
No 190
>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=72.37 E-value=2 Score=23.45 Aligned_cols=18 Identities=33% Similarity=0.207 Sum_probs=14.6
Q ss_pred hhhhccccchhhHHHHHH
Q 036324 66 TIHSRFLRSRETISRYFN 83 (91)
Q Consensus 66 ~i~~~F~~S~eTisr~f~ 83 (91)
+++..-|.|.+|||++++
T Consensus 2 ~lA~~~gvs~~tvs~~l~ 19 (52)
T cd01392 2 DIARAAGVSVATVSRVLN 19 (52)
T ss_pred cHHHHHCcCHHHHHHHHc
Confidence 567778899999998875
No 191
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=72.34 E-value=10 Score=25.48 Aligned_cols=38 Identities=5% Similarity=0.040 Sum_probs=32.2
Q ss_pred HHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 52 CMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 52 amFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
.+|+..--.|.++..|+...|.|..||..+++.....+
T Consensus 126 ~i~~l~~~~~~s~~EIA~~lgis~~tV~~~l~Ra~~~L 163 (173)
T PRK12522 126 TVLVLYYYEQYSYKEMSEILNIPIGTVKYRLNYAKKQM 163 (173)
T ss_pred HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 45666666899999999999999999999988877655
No 192
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=72.06 E-value=2 Score=31.53 Aligned_cols=23 Identities=17% Similarity=0.237 Sum_probs=20.1
Q ss_pred cchhhhhhccccchhhHHHHHHH
Q 036324 62 VKSRTIHSRFLRSRETISRYFNL 84 (91)
Q Consensus 62 ~~~r~i~~~F~~S~eTisr~f~~ 84 (91)
.+-++|+...|.|..||||.++.
T Consensus 6 ~ti~dIA~~agVS~~TVSrvLn~ 28 (331)
T PRK14987 6 PVLQDVADRVGVTKMTVSRFLRN 28 (331)
T ss_pred CcHHHHHHHhCCCHHHhhhhhCC
Confidence 46789999999999999999853
No 193
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=71.91 E-value=10 Score=26.07 Aligned_cols=38 Identities=11% Similarity=-0.060 Sum_probs=31.1
Q ss_pred HHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 52 CMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 52 amFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
.+|+..--.+.++..|+..++.|..||....+...+.+
T Consensus 118 ~v~~L~~~~g~s~~EIA~~Lgis~~tV~~~l~RAr~~L 155 (182)
T PRK12540 118 EALILVGASGFSYEDAAAICGCAVGTIKSRVNRARSKL 155 (182)
T ss_pred HHhhHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 34444456899999999999999999999988776654
No 194
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=71.78 E-value=10 Score=25.11 Aligned_cols=38 Identities=8% Similarity=-0.178 Sum_probs=31.3
Q ss_pred HHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 52 CMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 52 amFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
.+|....-.|.++..|+..+|.|..||....+.....+
T Consensus 119 ~v~~l~~~~~~s~~eIA~~lgis~~tv~~~l~Rar~~L 156 (161)
T PRK12541 119 NVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRKET 156 (161)
T ss_pred HHhhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 34555556789999999999999999999988877655
No 195
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=71.62 E-value=11 Score=27.60 Aligned_cols=44 Identities=11% Similarity=0.112 Sum_probs=32.9
Q ss_pred ccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 45 VSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 45 v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
.+..++-.+.|+. ..+.++..|+..++.|.+||.+..+..+..+
T Consensus 213 L~~~~r~vl~l~~-~~~~s~~eIA~~lgis~~tV~~~~~ra~~~L 256 (268)
T PRK06288 213 LPEREKKVLILYY-YEDLTLKEIGKVLGVTESRISQLHTKAVLQL 256 (268)
T ss_pred CCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 4445555555544 5789999999999999999998877665543
No 196
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=71.41 E-value=11 Score=26.54 Aligned_cols=38 Identities=5% Similarity=-0.074 Sum_probs=31.6
Q ss_pred HHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 52 CMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 52 amFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
.+|+-.--.|.++..|+..+|.|..||....+.....+
T Consensus 145 ~v~~L~~~~g~s~~EIA~~Lgis~~tV~~~l~RArk~L 182 (203)
T PRK09647 145 AAVVLCDIEGLSYEEIAATLGVKLGTVRSRIHRGRQQL 182 (203)
T ss_pred HHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 34555557899999999999999999999988877654
No 197
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=71.10 E-value=7.3 Score=28.27 Aligned_cols=36 Identities=17% Similarity=0.174 Sum_probs=30.4
Q ss_pred HHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHH
Q 036324 49 EQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLV 85 (91)
Q Consensus 49 E~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~V 85 (91)
.++-.|+.++-++ +...+++.-+.|++|||+.+++.
T Consensus 4 ~~L~~f~~v~~~g-S~s~AA~~L~itQpavS~~i~~L 39 (305)
T PRK11151 4 RDLEYLVALAEHR-HFRRAADSCHVSQPTLSGQIRKL 39 (305)
T ss_pred HHHHHHHHHHHhC-CHHHHHHHhCCCchHHHHHHHHH
Confidence 4566777777766 99999999999999999999875
No 198
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=70.96 E-value=12 Score=26.17 Aligned_cols=37 Identities=8% Similarity=0.029 Sum_probs=30.4
Q ss_pred HHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 53 MFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 53 mFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
+|....-.|.++..|+..+|.|..||....+.....+
T Consensus 147 v~~L~~~eg~s~~EIA~~lgis~~tVk~~l~RAr~~L 183 (201)
T PRK12545 147 VFMMREFLDFEIDDICTELTLTANHCSVLLYRARTRL 183 (201)
T ss_pred HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 4555567899999999999999999998887666554
No 199
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=70.78 E-value=7.2 Score=28.08 Aligned_cols=36 Identities=11% Similarity=0.205 Sum_probs=28.6
Q ss_pred HHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHH
Q 036324 50 QLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVL 86 (91)
Q Consensus 50 ~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl 86 (91)
++-.|+ .++...+.+.++...+.|++||||.+++.=
T Consensus 5 ~L~~f~-~v~~~gs~s~AA~~L~isQ~avSr~i~~LE 40 (296)
T PRK09906 5 HLRYFV-AVAEELNFTKAAEKLHTAQPSLSQQIKDLE 40 (296)
T ss_pred HHHHHH-HHHhhCCHHHHHHHhCCCCcHHHHHHHHHH
Confidence 444554 555566999999999999999999998753
No 200
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=70.62 E-value=11 Score=25.75 Aligned_cols=37 Identities=11% Similarity=0.012 Sum_probs=30.4
Q ss_pred HHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 53 MFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 53 mFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
+|....-.|.++..|+..++.|..||....+..+..+
T Consensus 139 v~~l~~~~g~s~~eIA~~lgis~~tV~~~l~ra~~~L 175 (184)
T PRK12539 139 AIQAVKLEGLSVAEAATRSGMSESAVKVSVHRGLKAL 175 (184)
T ss_pred HHHHHHHcCCcHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 3433334699999999999999999999999888765
No 201
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=70.61 E-value=3 Score=24.76 Aligned_cols=21 Identities=24% Similarity=0.229 Sum_probs=16.8
Q ss_pred chhhhhhccccchhhHHHHHH
Q 036324 63 KSRTIHSRFLRSRETISRYFN 83 (91)
Q Consensus 63 ~~r~i~~~F~~S~eTisr~f~ 83 (91)
+.++|+..=|.|.+||||.++
T Consensus 2 t~~~iA~~~gvS~~TVSr~ln 22 (70)
T smart00354 2 TIKDVARLAGVSKATVSRVLN 22 (70)
T ss_pred CHHHHHHHHCCCHHHHHHHHC
Confidence 356777888899999999875
No 202
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=70.51 E-value=13 Score=25.68 Aligned_cols=38 Identities=11% Similarity=-0.029 Sum_probs=32.2
Q ss_pred HHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 52 CMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 52 amFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
.+|+...-.|.++..|+...|.|..||-..++..+..+
T Consensus 149 ~vl~l~~~~~~s~~EIA~~Lgis~~tVk~~l~ra~~~L 186 (194)
T PRK09646 149 ESVTLAYYGGLTYREVAERLAVPLGTVKTRMRDGLIRL 186 (194)
T ss_pred HHHHHHHHcCCCHHHHHHHhCCChHhHHHHHHHHHHHH
Confidence 35555567889999999999999999999998887765
No 203
>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=70.49 E-value=11 Score=27.94 Aligned_cols=45 Identities=11% Similarity=0.134 Sum_probs=38.0
Q ss_pred CCccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 43 GTVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 43 ~~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
...|..|+=.+.| ++.|.++..|+...+.|..||..+.+.+++.+
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 3577777777776 46999999999999999999999999987654
No 204
>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=70.48 E-value=11 Score=27.56 Aligned_cols=37 Identities=14% Similarity=0.214 Sum_probs=31.4
Q ss_pred HHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 53 MFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 53 mFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
+|....-.|.++..|+..++.|..||...++....++
T Consensus 169 v~~L~~~eg~S~~EIA~~Lgis~~TVk~rl~RAr~~L 205 (244)
T TIGR03001 169 LLRLHFVDGLSMDRIGAMYQVHRSTVSRWVAQARERL 205 (244)
T ss_pred HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 4444555899999999999999999999999887765
No 205
>PRK09940 transcriptional regulator YdeO; Provisional
Probab=70.26 E-value=12 Score=28.03 Aligned_cols=83 Identities=17% Similarity=0.137 Sum_probs=49.2
Q ss_pred chhHHhhcCChhHHHHHhCCCHHHHHHHHHHHHh-CCC--CCCCCCccHHHHH-HHHHHHhhcCcchhhhhhccccchhh
Q 036324 2 PHLSRSIIGSDIECVNQLRMDKRTFELLCGLLRI-NGG--LKADGTVSIEEQL-CMFLHILAHHVKSRTIHSRFLRSRET 77 (91)
Q Consensus 2 ~~l~~ll~~~~~~c~~~fRM~~~~F~~L~~~L~~-~~~--l~~s~~v~veE~v-amFL~i~~~~~~~r~i~~~F~~S~eT 77 (91)
.||..++..-..+-...-++..-.|..+...+.. .+. +......+..+++ .+...-.+++.+-.+++..++-|..+
T Consensus 87 ~~L~~ll~~l~~e~~~~~~l~~~ll~~lL~~l~~~~~~~~~l~~~~~~~~~kv~~~I~~~~~~~~tl~~LA~~~gmS~s~ 166 (253)
T PRK09940 87 GLLNEMIAYLNSEERNHHNFSELLLFSCLSIFAACKGFITLLTNGVLSVSGKVRNIVNMKLAHPWKLKDICDCLYISESL 166 (253)
T ss_pred HHHHHHHHHHHhcchhhhHHHHHHHHHHHHHHHhCccHHHhhccccccHHHHHHHHHHHhhcCCCCHHHHHHHHCcCHHH
Confidence 4555555422222212226666677777766654 222 1112223333333 33344567778999999999999999
Q ss_pred HHHHHHH
Q 036324 78 ISRYFNL 84 (91)
Q Consensus 78 isr~f~~ 84 (91)
.+|.|++
T Consensus 167 l~R~FK~ 173 (253)
T PRK09940 167 LKKKLKQ 173 (253)
T ss_pred HHHHHHH
Confidence 9999986
No 206
>PRK04841 transcriptional regulator MalT; Provisional
Probab=70.24 E-value=6.2 Score=33.02 Aligned_cols=43 Identities=12% Similarity=0.078 Sum_probs=34.4
Q ss_pred ccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 45 VSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 45 v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
.|--|.=-+.| ++.|.+|++|+.....|..||-.|++.+...+
T Consensus 839 lt~~e~~v~~~--~~~g~~~~~ia~~l~~s~~tv~~h~~~~~~kl 881 (903)
T PRK04841 839 LTQREWQVLGL--IYSGYSNEQIAGELDVAATTIKTHIRNLYQKL 881 (903)
T ss_pred CCHHHHHHHHH--HHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence 44444433333 88999999999999999999999999988765
No 207
>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=70.16 E-value=9.8 Score=26.88 Aligned_cols=38 Identities=24% Similarity=0.230 Sum_probs=28.6
Q ss_pred HHHHHHHHHhhc-CcchhhhhhccccchhhHHHHHHHHH
Q 036324 49 EQLCMFLHILAH-HVKSRTIHSRFLRSRETISRYFNLVL 86 (91)
Q Consensus 49 E~vamFL~i~~~-~~~~r~i~~~F~~S~eTisr~f~~Vl 86 (91)
.+..+.-++..+ ..+...+++.++.|.+|++|++...-
T Consensus 144 ~~~~IL~~l~~~g~~s~~eia~~l~is~stv~r~L~~Le 182 (203)
T TIGR01884 144 EELKVLEVLKAEGEKSVKNIAKKLGKSLSTISRHLRELE 182 (203)
T ss_pred HHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 344554444443 46999999999999999999988743
No 208
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=70.16 E-value=11 Score=26.87 Aligned_cols=43 Identities=16% Similarity=0.207 Sum_probs=32.8
Q ss_pred cHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 46 SIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 46 ~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
+..++-.+-| .-..+.++..|+..+|.|..||....+..+..+
T Consensus 186 ~~~~r~vl~l-~~~~g~s~~EIA~~lgis~~tV~~~~~ra~~~L 228 (236)
T PRK06986 186 PEREQLVLSL-YYQEELNLKEIGAVLGVSESRVSQIHSQAIKRL 228 (236)
T ss_pred CHHHHHHHHh-HhccCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 3334444444 346889999999999999999999988877654
No 209
>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=70.06 E-value=25 Score=22.30 Aligned_cols=55 Identities=18% Similarity=0.249 Sum_probs=36.2
Q ss_pred HHHHHHHHHhCCCCCCCCCccHHHHHHH-HHHHh---hcCcchhhhhhccccchhhHHHHHHHHH
Q 036324 26 FELLCGLLRINGGLKADGTVSIEEQLCM-FLHIL---AHHVKSRTIHSRFLRSRETISRYFNLVL 86 (91)
Q Consensus 26 F~~L~~~L~~~~~l~~s~~v~veE~vam-FL~i~---~~~~~~r~i~~~F~~S~eTisr~f~~Vl 86 (91)
+..+-+.++..++ ++..|-..+ +|+.+ +.+.+...++...+.+.+|||+.+...-
T Consensus 10 ~~~~~~~l~~~~~------ls~~q~~vL~~l~~~~~~~~~~t~~eL~~~l~~~~stvs~~i~~Le 68 (109)
T TIGR01889 10 IKSLKRYLKKEFN------LSLEELLILYYLGKLENNEGKLTLKEIIKEILIKQSALVKIIKKLS 68 (109)
T ss_pred HHHHHHHHHHHcC------CCHHHHHHHHHHHhhhccCCcCcHHHHHHHHCCCHHHHHHHHHHHH
Confidence 4455566666554 444443322 33321 2348999999999999999999987653
No 210
>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=69.69 E-value=13 Score=25.62 Aligned_cols=37 Identities=11% Similarity=0.016 Sum_probs=31.3
Q ss_pred HHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 53 MFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 53 mFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
+|....-.|.++..|+..+|.|..||........+.+
T Consensus 139 v~~l~~~~g~s~~EIA~~lgis~~tvk~rl~Rar~~L 175 (188)
T TIGR02943 139 VFMMREVLGFESDEICQELEISTSNCHVLLYRARLSL 175 (188)
T ss_pred HHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 5555666899999999999999999999888776655
No 211
>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=69.62 E-value=5.5 Score=25.52 Aligned_cols=34 Identities=15% Similarity=0.034 Sum_probs=28.3
Q ss_pred HHHHhhcCcchhhhhhccccchhhHHHHHHHHHH
Q 036324 54 FLHILAHHVKSRTIHSRFLRSRETISRYFNLVLN 87 (91)
Q Consensus 54 FL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ 87 (91)
.+..+....+.+.++...+.|.+|||+.+++.=+
T Consensus 9 ~~~av~~~gSis~AA~~L~iS~stvs~~I~~LE~ 42 (99)
T TIGR00637 9 LLKAIARMGSISQAAKDAGISYKSAWDYIRAMNN 42 (99)
T ss_pred HHHHHHHhCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3455667889999999999999999999987543
No 212
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=69.30 E-value=13 Score=25.87 Aligned_cols=44 Identities=9% Similarity=-0.067 Sum_probs=33.4
Q ss_pred ccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 45 VSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 45 v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
++.+++-++-|+.+ .+.++..|+..+|.|..||-..++.....+
T Consensus 114 Lp~~~r~v~~L~~~-~g~s~~EIA~~LgiS~~tVk~~l~Rar~~L 157 (188)
T PRK12546 114 LPDEQREALILVGA-SGFSYEEAAEMCGVAVGTVKSRANRARARL 157 (188)
T ss_pred CCHHHhHHhhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 34444444445444 899999999999999999999988877654
No 213
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=69.25 E-value=37 Score=24.72 Aligned_cols=45 Identities=16% Similarity=-0.022 Sum_probs=36.8
Q ss_pred CCccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 43 GTVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 43 ~~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
...|.-|.=.+.+- +.|-++.+|+...+.|..||.-|...+.+.+
T Consensus 178 ~~LT~rE~evl~~~--a~G~t~~eIa~~l~is~~TV~~h~~~~~~KL 222 (240)
T PRK10188 178 MNFSKREKEILKWT--AEGKTSAEIAMILSISENTVNFHQKNMQKKF 222 (240)
T ss_pred CCCCHHHHHHHHHH--HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence 35676666555553 8899999999999999999999999988754
No 214
>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=69.14 E-value=4 Score=25.49 Aligned_cols=24 Identities=21% Similarity=0.189 Sum_probs=18.1
Q ss_pred cCcchhhhhhccccchhhHHHHHH
Q 036324 60 HHVKSRTIHSRFLRSRETISRYFN 83 (91)
Q Consensus 60 ~~~~~r~i~~~F~~S~eTisr~f~ 83 (91)
.|.+..+|+.+.|+|.+.||++..
T Consensus 2 ~G~tq~eIA~~lGks~s~Vs~~l~ 25 (93)
T PF08535_consen 2 FGWTQEEIAKRLGKSRSWVSNHLA 25 (93)
T ss_dssp TT--HHHHHHHTT--HHHHHHHHG
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHH
Confidence 578999999999999999999864
No 215
>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=69.13 E-value=8.6 Score=26.92 Aligned_cols=38 Identities=16% Similarity=0.204 Sum_probs=26.9
Q ss_pred cHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHH
Q 036324 46 SIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFN 83 (91)
Q Consensus 46 ~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~ 83 (91)
+.|+..++.-..-..+.+...|+..+|.|..+|+|+..
T Consensus 105 ~~e~a~~~~~l~~~~g~s~~~iA~~lg~s~~~V~r~l~ 142 (187)
T TIGR00180 105 PIEEAQAYKRLLEKFSMTQEDLAKKIGKSRAHITNLLR 142 (187)
T ss_pred HHHHHHHHHHHHHHhCCCHHHHHHHHCcCHHHHHHHHH
Confidence 34444433332223678999999999999999999875
No 216
>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=69.09 E-value=11 Score=22.00 Aligned_cols=25 Identities=8% Similarity=0.149 Sum_probs=21.7
Q ss_pred CcchhhhhhccccchhhHHHHHHHH
Q 036324 61 HVKSRTIHSRFLRSRETISRYFNLV 85 (91)
Q Consensus 61 ~~~~r~i~~~F~~S~eTisr~f~~V 85 (91)
..+...++..|+.|..||++++...
T Consensus 13 ~~~~~eLa~~l~vS~~tv~~~l~~L 37 (69)
T TIGR00122 13 PFSGEKLGEALGMSRTAVNKHIQTL 37 (69)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHH
Confidence 3567889999999999999999875
No 217
>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=69.09 E-value=8.7 Score=27.55 Aligned_cols=36 Identities=8% Similarity=0.066 Sum_probs=28.5
Q ss_pred HHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHH
Q 036324 49 EQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLV 85 (91)
Q Consensus 49 E~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~V 85 (91)
.++-.|+.++-+ .++..+++..+.|++||||.+++.
T Consensus 4 ~~L~~f~~v~~~-gs~s~AA~~L~itqpavS~~Ik~L 39 (291)
T TIGR03418 4 QALRVFESAARL-ASFTAAARELGSTQPAVSQQVKRL 39 (291)
T ss_pred HHHHHHHHHHHh-CCHHHHHHHhCCCHHHHHHHHHHH
Confidence 355566655544 599999999999999999999874
No 218
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=68.97 E-value=14 Score=25.19 Aligned_cols=38 Identities=11% Similarity=0.105 Sum_probs=31.3
Q ss_pred HHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 52 CMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 52 amFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
.+|+...-.+.++..|+..+|.|..||....+.....+
T Consensus 129 ~i~~l~~~~g~s~~EIA~~lgis~~tVk~~l~Rar~~L 166 (185)
T PRK12542 129 QVFKYKVFYNLTYQEISSVMGITEANVRKQFERARKRV 166 (185)
T ss_pred HHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 45665567889999999999999999999888766554
No 219
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=68.95 E-value=13 Score=22.07 Aligned_cols=41 Identities=15% Similarity=0.206 Sum_probs=34.8
Q ss_pred ccHHHHHHHHHHHhhc-CcchhhhhhccccchhhHHHHHHHH
Q 036324 45 VSIEEQLCMFLHILAH-HVKSRTIHSRFLRSRETISRYFNLV 85 (91)
Q Consensus 45 v~veE~vamFL~i~~~-~~~~r~i~~~F~~S~eTisr~f~~V 85 (91)
-..++++.-+|..-|. +.+-.+|+...|.+..||+|+....
T Consensus 5 ~~~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L 46 (68)
T smart00550 5 DSLEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSL 46 (68)
T ss_pred hHHHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHH
Confidence 3578889888888876 5899999999999999999987654
No 220
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=68.78 E-value=10 Score=24.90 Aligned_cols=30 Identities=17% Similarity=0.106 Sum_probs=21.9
Q ss_pred HhhcCcchhhhhhccccchhhHHHHHHHHH
Q 036324 57 ILAHHVKSRTIHSRFLRSRETISRYFNLVL 86 (91)
Q Consensus 57 i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl 86 (91)
-...+.+..+++..++.|..|++|.|++.+
T Consensus 21 ~~~~~~sl~~lA~~~g~S~~~l~r~Fk~~~ 50 (127)
T PRK11511 21 NLESPLSLEKVSERSGYSKWHLQRMFKKET 50 (127)
T ss_pred hcCCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 344456667777888888888888888763
No 221
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=68.58 E-value=12 Score=25.40 Aligned_cols=44 Identities=9% Similarity=0.132 Sum_probs=32.7
Q ss_pred ccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 45 VSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 45 v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
.|..++-++-| ..-.|.++..|+..++.|..||....+..+..+
T Consensus 128 L~~~~r~v~~l-~~~~g~s~~EIA~~l~is~~tv~~~l~Ra~~~L 171 (179)
T PRK09415 128 LPIKYREVIYL-FYYEELSIKEIAEVTGVNENTVKTRLKKAKELL 171 (179)
T ss_pred CCHHHhhHhHh-HHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 44444444444 444589999999999999999999888777655
No 222
>PRK12680 transcriptional regulator CysB-like protein; Reviewed
Probab=68.55 E-value=8.7 Score=28.74 Aligned_cols=38 Identities=13% Similarity=0.160 Sum_probs=32.0
Q ss_pred HHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHH
Q 036324 49 EQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVL 86 (91)
Q Consensus 49 E~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl 86 (91)
+++-+|+.+.=+..++..++..-+.|++|||+.+++.=
T Consensus 4 ~~L~~F~~vae~~gS~s~AA~~L~isQpavS~~I~~LE 41 (327)
T PRK12680 4 TQLRYLVAIADAELNITLAAARVHATQPGLSKQLKQLE 41 (327)
T ss_pred HHHHHHHHHHHccCCHHHHHHHhcCCchHHHHHHHHHH
Confidence 46777777766668999999999999999999998753
No 223
>PRK00215 LexA repressor; Validated
Probab=68.42 E-value=12 Score=26.28 Aligned_cols=28 Identities=11% Similarity=0.029 Sum_probs=23.8
Q ss_pred hcCcchhhhhhcccc-chhhHHHHHHHHH
Q 036324 59 AHHVKSRTIHSRFLR-SRETISRYFNLVL 86 (91)
Q Consensus 59 ~~~~~~r~i~~~F~~-S~eTisr~f~~Vl 86 (91)
+...+.++++..++. |++|++|++...-
T Consensus 21 ~~~~s~~ela~~~~~~~~~tv~~~l~~L~ 49 (205)
T PRK00215 21 GYPPSRREIADALGLRSPSAVHEHLKALE 49 (205)
T ss_pred CCCCCHHHHHHHhCCCChHHHHHHHHHHH
Confidence 445689999999998 9999999987654
No 224
>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=68.40 E-value=14 Score=24.64 Aligned_cols=38 Identities=13% Similarity=0.260 Sum_probs=31.2
Q ss_pred HHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 52 CMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 52 amFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
.+|....-.|.++..|+..+|.|..||....+.....+
T Consensus 126 ~i~~l~~~~g~s~~eiA~~lgis~~tv~~~l~Ra~~~L 163 (169)
T TIGR02954 126 TAIILRYYHDLTIKEIAEVMNKPEGTVKTYLHRALKKL 163 (169)
T ss_pred HHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 34555556699999999999999999999888777654
No 225
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=68.29 E-value=15 Score=26.61 Aligned_cols=43 Identities=23% Similarity=0.182 Sum_probs=33.1
Q ss_pred cHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 46 SIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 46 ~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
+..++-.+-|. .-.+.++..|+..++.|.+||...++..+..+
T Consensus 203 ~~~~r~vl~l~-~~~~~s~~EIA~~lgis~~tV~~~~~ra~~~L 245 (251)
T PRK07670 203 SEKEQLVISLF-YKEELTLTEIGQVLNLSTSRISQIHSKALFKL 245 (251)
T ss_pred CHHHHHHHHHH-HhcCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 34444444443 35899999999999999999999988877654
No 226
>PRK13348 chromosome replication initiation inhibitor protein; Provisional
Probab=68.25 E-value=9.4 Score=27.48 Aligned_cols=36 Identities=11% Similarity=0.124 Sum_probs=28.8
Q ss_pred HHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHH
Q 036324 49 EQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLV 85 (91)
Q Consensus 49 E~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~V 85 (91)
+++-.|.-++ ...++..+++..+.|++|||+.+++.
T Consensus 5 ~~L~~f~~v~-~~gs~t~AA~~L~iSQ~avS~~i~~L 40 (294)
T PRK13348 5 KQLEALAAVV-ETGSFERAARRLHVTPSAVSQRIKAL 40 (294)
T ss_pred HHHHHHHHHH-HcCCHHHHHHHhCCCchHHHHHHHHH
Confidence 4565555544 45699999999999999999999875
No 227
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=68.19 E-value=15 Score=25.16 Aligned_cols=37 Identities=5% Similarity=-0.021 Sum_probs=30.2
Q ss_pred HHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 53 MFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 53 mFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
+|....-.+.++..|+...|.|..||....+...+.+
T Consensus 139 v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Rar~~L 175 (191)
T PRK12520 139 VFMMREWLELETEEICQELQITATNAWVLLYRARMRL 175 (191)
T ss_pred HHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 4444455789999999999999999999988776655
No 228
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=68.04 E-value=15 Score=26.54 Aligned_cols=43 Identities=19% Similarity=0.185 Sum_probs=33.1
Q ss_pred cHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 46 SIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 46 ~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
+-.|+-.+-|+. ..+.++..|+..+|.|.++|++.-+..+..+
T Consensus 185 ~~~er~vi~l~~-~~~~t~~EIA~~lgis~~~V~q~~~~~~~kL 227 (231)
T PRK12427 185 DEREQLILHLYY-QHEMSLKEIALVLDLTEARICQLNKKIAQKI 227 (231)
T ss_pred CHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 344444454544 6789999999999999999999988877654
No 229
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=67.97 E-value=9.1 Score=27.91 Aligned_cols=39 Identities=13% Similarity=0.096 Sum_probs=30.2
Q ss_pred HHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHH
Q 036324 49 EQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNA 88 (91)
Q Consensus 49 E~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~a 88 (91)
+++-+|+-++- ..++..++...+.|+++||+.+++.=+.
T Consensus 8 ~~L~~f~~v~e-~gs~s~AA~~L~isqpavS~~i~~LE~~ 46 (305)
T CHL00180 8 DQLRILKAIAT-EGSFKKAAESLYISQPAVSLQIKNLEKQ 46 (305)
T ss_pred HHHHHHHHHHH-cCCHHHHHHHhcCCChHHHHHHHHHHHH
Confidence 45656655554 5599999999999999999999876433
No 230
>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=67.92 E-value=13 Score=27.50 Aligned_cols=45 Identities=9% Similarity=0.080 Sum_probs=35.1
Q ss_pred ccHHHHHHHHHHH-h--hcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 45 VSIEEQLCMFLHI-L--AHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 45 v~veE~vamFL~i-~--~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
.+-.++..+.|+. + -.+.+++.|+...|.|.+||.+..+.-+..+
T Consensus 223 Lp~~~R~Vl~l~ygL~~~e~~s~~EIA~~Lgis~~tVk~~l~rAlkkL 270 (285)
T TIGR02394 223 LNERQREVLARRFGLLGYEPATLEEVAAEVGLTRERVRQIQVEALKKL 270 (285)
T ss_pred CCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 4455555666654 2 5789999999999999999999998877654
No 231
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=67.65 E-value=13 Score=28.97 Aligned_cols=46 Identities=17% Similarity=0.130 Sum_probs=35.2
Q ss_pred CccHHHHHHHHHHHh---hcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 44 TVSIEEQLCMFLHIL---AHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 44 ~v~veE~vamFL~i~---~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
..+-.|+..+-|+.. |.+.+...|+..|+.|.++|+++=.+.|.-+
T Consensus 305 ~L~~rEr~Vl~lrygl~~~~~~tl~EIa~~lgvs~erVrQi~~~Al~kL 353 (367)
T PRK09210 305 TLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKL 353 (367)
T ss_pred hCCHHHHHHHHHHhccCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 345556666666553 3668999999999999999999987777654
No 232
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=67.54 E-value=12 Score=21.85 Aligned_cols=33 Identities=12% Similarity=0.115 Sum_probs=27.5
Q ss_pred HHHHHHHHHhhcCcchhhhhhccccchhhHHHHHH
Q 036324 49 EQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFN 83 (91)
Q Consensus 49 E~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~ 83 (91)
...|..||. .|-+...|+...+.+..||+....
T Consensus 3 k~~A~~LY~--~G~~~~eIA~~Lg~~~~TV~~W~~ 35 (58)
T PF06056_consen 3 KEQARSLYL--QGWSIKEIAEELGVPRSTVYSWKD 35 (58)
T ss_pred HHHHHHHHH--cCCCHHHHHHHHCCChHHHHHHHH
Confidence 356788886 578999999999999999988654
No 233
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=66.92 E-value=14 Score=29.10 Aligned_cols=46 Identities=22% Similarity=0.132 Sum_probs=36.4
Q ss_pred CccHHHHHHHHHHHh---hcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 44 TVSIEEQLCMFLHIL---AHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 44 ~v~veE~vamFL~i~---~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
..+..|+..+-|+.. +.+.+...|+..+|.|.++|+++-+..+..+
T Consensus 311 ~L~~rEr~IL~lrygl~~~~~~Tl~EIA~~lgiS~eRVRQie~rAL~KL 359 (373)
T PRK07406 311 TLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKL 359 (373)
T ss_pred cCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 356667767777543 3568999999999999999999988888765
No 234
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=66.87 E-value=5.4 Score=21.12 Aligned_cols=28 Identities=18% Similarity=0.083 Sum_probs=20.8
Q ss_pred hcCcchhhhhhccccchhhHHHHHHHHH
Q 036324 59 AHHVKSRTIHSRFLRSRETISRYFNLVL 86 (91)
Q Consensus 59 ~~~~~~r~i~~~F~~S~eTisr~f~~Vl 86 (91)
.++.+-.+|++..+-|....+|.|++.+
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 4567778899999999999999998863
No 235
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=66.86 E-value=15 Score=25.20 Aligned_cols=42 Identities=17% Similarity=0.103 Sum_probs=32.3
Q ss_pred cHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 46 SIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 46 ~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
+..++-.+-| .-.+.+++.|+...|.|..||....+.....+
T Consensus 157 ~~~~r~vl~l--~~e~~s~~EIA~~lgis~~tV~~~l~rar~~L 198 (208)
T PRK08295 157 SELEKEVLEL--YLDGKSYQEIAEELNRHVKSIDNALQRVKRKL 198 (208)
T ss_pred CHHHHHHHHH--HHccCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 3344444444 34789999999999999999999988877664
No 236
>PRK12423 LexA repressor; Provisional
Probab=66.45 E-value=13 Score=26.43 Aligned_cols=26 Identities=15% Similarity=0.079 Sum_probs=21.7
Q ss_pred Ccchhhhhhccc-cchhhHHHHHHHHH
Q 036324 61 HVKSRTIHSRFL-RSRETISRYFNLVL 86 (91)
Q Consensus 61 ~~~~r~i~~~F~-~S~eTisr~f~~Vl 86 (91)
.-+.++++..|+ +|+.||++++...-
T Consensus 25 ~Ps~~eia~~~g~~s~~~v~~~l~~L~ 51 (202)
T PRK12423 25 PPSLAEIAQAFGFASRSVARKHVQALA 51 (202)
T ss_pred CCCHHHHHHHhCCCChHHHHHHHHHHH
Confidence 358899999999 79999998876543
No 237
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=66.33 E-value=17 Score=24.59 Aligned_cols=31 Identities=10% Similarity=0.093 Sum_probs=27.6
Q ss_pred hcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 59 AHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 59 ~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
-.|.++..|+..+|.|..||....+.....+
T Consensus 151 ~~g~s~~eIA~~lgis~~~v~~~l~Rar~~L 181 (187)
T PRK12534 151 FEGITYEELAARTDTPIGTVKSWIRRGLAKL 181 (187)
T ss_pred HcCCCHHHHHHHhCCChhHHHHHHHHHHHHH
Confidence 5899999999999999999999988776654
No 238
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=66.31 E-value=17 Score=25.46 Aligned_cols=37 Identities=8% Similarity=0.159 Sum_probs=30.2
Q ss_pred HHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 53 MFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 53 mFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
+|....-.|.++..|+..++.|..||....+.-+..+
T Consensus 161 vl~l~~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~L 197 (206)
T PRK12526 161 VVKGVYFQELSQEQLAQQLNVPLGTVKSRLRLALAKL 197 (206)
T ss_pred HHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 3555567899999999999999999998887766544
No 239
>PRK10094 DNA-binding transcriptional activator AllS; Provisional
Probab=66.31 E-value=10 Score=27.85 Aligned_cols=36 Identities=22% Similarity=0.277 Sum_probs=29.4
Q ss_pred HHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHH
Q 036324 49 EQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLV 85 (91)
Q Consensus 49 E~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~V 85 (91)
+++-+|+.++- ..++..++...+.|++|||+.+.+.
T Consensus 5 ~~L~~f~~v~e-~gs~s~AA~~L~iSQpavS~~I~~L 40 (308)
T PRK10094 5 ETLRTFIAVAE-TGSFSKAAERLCKTTATISYRIKLL 40 (308)
T ss_pred HHHHHHHHHHH-hCCHHHHHHHhcCCHHHHHHHHHHH
Confidence 56677765555 4599999999999999999998874
No 240
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=66.10 E-value=3.9 Score=30.04 Aligned_cols=22 Identities=23% Similarity=0.173 Sum_probs=19.8
Q ss_pred chhhhhhccccchhhHHHHHHH
Q 036324 63 KSRTIHSRFLRSRETISRYFNL 84 (91)
Q Consensus 63 ~~r~i~~~F~~S~eTisr~f~~ 84 (91)
+.++|+..-|.|..||||.++.
T Consensus 3 Ti~dIA~~agVS~~TVSrvLn~ 24 (341)
T PRK10703 3 TIKDVAKRAGVSTTTVSHVINK 24 (341)
T ss_pred CHHHHHHHhCCCHHHHHHHHcC
Confidence 5679999999999999999874
No 241
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=66.07 E-value=14 Score=25.19 Aligned_cols=38 Identities=13% Similarity=0.024 Sum_probs=32.6
Q ss_pred HHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 52 CMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 52 amFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
.+|+..--+|.|+..|+...+.|..||....+.-+.++
T Consensus 134 ~~~~l~~~~gls~~EIA~~l~i~~~tVks~l~ra~~~l 171 (182)
T COG1595 134 EAFLLRYLEGLSYEEIAEILGISVGTVKSRLHRARKKL 171 (182)
T ss_pred HHhhhHhhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 35666677899999999999999999999998877765
No 242
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=66.04 E-value=11 Score=27.02 Aligned_cols=36 Identities=17% Similarity=0.210 Sum_probs=28.8
Q ss_pred HHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHH
Q 036324 49 EQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLV 85 (91)
Q Consensus 49 E~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~V 85 (91)
+++-.|+.++-+ .+...++..-+.|++|||+.+++.
T Consensus 4 ~~L~~f~~v~~~-gs~s~AA~~L~isqsavS~~i~~L 39 (296)
T PRK11242 4 RHIRYFLAVAEH-GNFTRAAEALHVSQPTLSQQIRQL 39 (296)
T ss_pred HHHHHHHHHHHh-CCHHHHHHHcCCCchHHHHHHHHH
Confidence 456566655554 599999999999999999999875
No 243
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=65.64 E-value=17 Score=24.96 Aligned_cols=44 Identities=9% Similarity=0.024 Sum_probs=33.5
Q ss_pred ccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 45 VSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 45 v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
+|.+++-.+-|+. -.|.++..|+..+|.|..||....+.....+
T Consensus 132 L~~~~r~i~~l~~-~~g~s~~EIAe~lgis~~~V~~~l~Ra~~~L 175 (189)
T PRK06811 132 LEKLDREIFIRRY-LLGEKIEEIAKKLGLTRSAIDNRLSRGRKKL 175 (189)
T ss_pred CCHHHHHHHHHHH-HccCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 4445555555544 3689999999999999999999888776654
No 244
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=65.60 E-value=16 Score=21.08 Aligned_cols=36 Identities=19% Similarity=0.239 Sum_probs=28.0
Q ss_pred HHHHHHh-hcCcchhhhhhccccchhhHHHHHHHHHH
Q 036324 52 CMFLHIL-AHHVKSRTIHSRFLRSRETISRYFNLVLN 87 (91)
Q Consensus 52 amFL~i~-~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ 87 (91)
.++++.+ -...+...|+...+.|..||++.++...+
T Consensus 12 ~vy~~Ll~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~ 48 (68)
T PF01978_consen 12 KVYLALLKNGPATAEEIAEELGISRSTVYRALKSLEE 48 (68)
T ss_dssp HHHHHHHHHCHEEHHHHHHHHTSSHHHHHHHHHHHHH
T ss_pred HHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4455555 44488999999999999999999887543
No 245
>PRK15421 DNA-binding transcriptional regulator MetR; Provisional
Probab=65.60 E-value=11 Score=27.88 Aligned_cols=36 Identities=8% Similarity=0.118 Sum_probs=30.1
Q ss_pred HHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHH
Q 036324 49 EQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLV 85 (91)
Q Consensus 49 E~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~V 85 (91)
.++-.|+-++-++ +++.+++.-+.|++|||+.++..
T Consensus 5 ~~L~~f~av~~~g-s~s~AA~~L~iSqpaVS~~Ik~L 40 (317)
T PRK15421 5 KHLKTLQALRNCG-SLAAAAATLHQTQSALSHQFSDL 40 (317)
T ss_pred HHHHHHHHHHHcC-CHHHHHHHhCCCHHHHHHHHHHH
Confidence 4666777666666 99999999999999999999875
No 246
>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=65.55 E-value=23 Score=20.23 Aligned_cols=45 Identities=18% Similarity=0.289 Sum_probs=28.5
Q ss_pred HHHHHHHHHHHhCCCCCCCCCccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHH
Q 036324 24 RTFELLCGLLRINGGLKADGTVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLV 85 (91)
Q Consensus 24 ~~F~~L~~~L~~~~~l~~s~~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~V 85 (91)
.+...|.+.+.. +.+++...++.|.+ ++.+|+.|+.||.+-++..
T Consensus 4 ~i~~~l~~~I~~-g~~~~g~~lps~~~----------------la~~~~vsr~tvr~al~~L 48 (64)
T PF00392_consen 4 QIYDQLRQAILS-GRLPPGDRLPSERE----------------LAERYGVSRTTVREALRRL 48 (64)
T ss_dssp HHHHHHHHHHHT-TSS-TTSBE--HHH----------------HHHHHTS-HHHHHHHHHHH
T ss_pred HHHHHHHHHHHc-CCCCCCCEeCCHHH----------------HHHHhccCCcHHHHHHHHH
Confidence 455566666665 55666666766655 4678999999998877654
No 247
>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=65.53 E-value=14 Score=24.97 Aligned_cols=37 Identities=11% Similarity=-0.105 Sum_probs=30.4
Q ss_pred HHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 53 MFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 53 mFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
+|...--.|.++..|+..+|.|..||....+.....+
T Consensus 146 v~~l~~~~~~s~~EIA~~lgis~~tv~~~l~rar~~L 182 (190)
T TIGR02939 146 AITLRELEGLSYEDIARIMDCPVGTVRSRIFRAREAI 182 (190)
T ss_pred hhhhhhhcCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 4444445899999999999999999999988877665
No 248
>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=65.32 E-value=7.3 Score=26.47 Aligned_cols=30 Identities=17% Similarity=0.172 Sum_probs=23.2
Q ss_pred HHHHHHHHHHHHhCCCCCCCCCccHHHHHHH
Q 036324 23 KRTFELLCGLLRINGGLKADGTVSIEEQLCM 53 (91)
Q Consensus 23 ~~~F~~L~~~L~~~~~l~~s~~v~veE~vam 53 (91)
|+.|+.||.+++.++. .-..++..||+.|.
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 5899999999999774 33447888888764
No 249
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=65.28 E-value=15 Score=24.90 Aligned_cols=37 Identities=5% Similarity=-0.045 Sum_probs=29.8
Q ss_pred HHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 53 MFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 53 mFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
+|....-.|.++..|+..+|.|..||....+.....+
T Consensus 136 i~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Rar~~L 172 (186)
T PRK05602 136 AIVLQYYQGLSNIEAAAVMDISVDALESLLARGRRAL 172 (186)
T ss_pred HhhHHHhcCCCHHHHHHHhCcCHHHHHHHHHHHHHHH
Confidence 3333345699999999999999999999988877654
No 250
>PRK06474 hypothetical protein; Provisional
Probab=65.07 E-value=13 Score=26.14 Aligned_cols=40 Identities=5% Similarity=0.126 Sum_probs=26.5
Q ss_pred HHHHHHHHHhhcC--cchhhhhhcc-ccchhhHHHHHHHHHHH
Q 036324 49 EQLCMFLHILAHH--VKSRTIHSRF-LRSRETISRYFNLVLNA 88 (91)
Q Consensus 49 E~vamFL~i~~~~--~~~r~i~~~F-~~S~eTisr~f~~Vl~a 88 (91)
-++.|+-+...++ .+-.++...+ +.|+.||+|+++...++
T Consensus 12 ~R~~Il~~L~~~~~~~ta~el~~~l~~is~aTvYrhL~~L~e~ 54 (178)
T PRK06474 12 VRMKICQVLMRNKEGLTPLELVKILKDVPQATLYRHLQTMVDS 54 (178)
T ss_pred HHHHHHHHHHhCCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHC
Confidence 3444554444443 5666666666 68999999999876553
No 251
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=65.01 E-value=14 Score=26.03 Aligned_cols=44 Identities=11% Similarity=0.123 Sum_probs=32.9
Q ss_pred ccHHHHHHHHHHHh---hcCcchhhhhhccccchhhHHHHHHHHHHH
Q 036324 45 VSIEEQLCMFLHIL---AHHVKSRTIHSRFLRSRETISRYFNLVLNA 88 (91)
Q Consensus 45 v~veE~vamFL~i~---~~~~~~r~i~~~F~~S~eTisr~f~~Vl~a 88 (91)
.+..|.--+.+|+. +.+.++..|+...+-|..||..|+....++
T Consensus 159 Lt~re~~~l~~~i~~~~~~g~s~~eIA~~l~iS~~Tv~~~~~~~~~~ 205 (239)
T PRK10430 159 LTPQTLRTLCQWIDAHQDYEFSTDELANAVNISRVSCRKYLIWLVNC 205 (239)
T ss_pred CCHHHHHHHHHHHHhCCCCCcCHHHHHHHhCchHHHHHHHHHHHHhC
Confidence 44444323344554 578999999999999999999999987654
No 252
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=64.72 E-value=5.8 Score=30.38 Aligned_cols=26 Identities=19% Similarity=0.190 Sum_probs=23.4
Q ss_pred cCcchhhhhhccccchhhHHHHHHHH
Q 036324 60 HHVKSRTIHSRFLRSRETISRYFNLV 85 (91)
Q Consensus 60 ~~~~~r~i~~~F~~S~eTisr~f~~V 85 (91)
.|.++.+|+.+++.|+.||||...+-
T Consensus 28 ~g~tQ~eIA~~lgiSR~~VsRlL~~A 53 (318)
T PRK15418 28 DGLTQSEIGERLGLTRLKVSRLLEKG 53 (318)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 47899999999999999999998764
No 253
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=64.63 E-value=17 Score=24.57 Aligned_cols=37 Identities=11% Similarity=0.130 Sum_probs=30.6
Q ss_pred HHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 53 MFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 53 mFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
+|+..--.+.++..|+..+|.|..||..+.+..+..+
T Consensus 125 i~~l~~~e~~s~~EIA~~lgis~~tV~~~l~ra~~~L 161 (179)
T PRK12543 125 VIILRYLHDYSQEEIAQLLQIPIGTVKSRIHAALKKL 161 (179)
T ss_pred HHHHHHHccCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 5555666889999999999999999998887766544
No 254
>PRK11013 DNA-binding transcriptional regulator LysR; Provisional
Probab=64.47 E-value=11 Score=27.64 Aligned_cols=36 Identities=14% Similarity=0.158 Sum_probs=29.9
Q ss_pred HHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHH
Q 036324 49 EQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLV 85 (91)
Q Consensus 49 E~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~V 85 (91)
.++.+|+-+.-+ .++..+++..+.|++|||+.+++.
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 599999999999999999998864
No 255
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=64.24 E-value=5.6 Score=22.83 Aligned_cols=26 Identities=19% Similarity=0.106 Sum_probs=20.6
Q ss_pred HhhcCcchhhhhhccccchhhHHHHH
Q 036324 57 ILAHHVKSRTIHSRFLRSRETISRYF 82 (91)
Q Consensus 57 i~~~~~~~r~i~~~F~~S~eTisr~f 82 (91)
.-.+|.+..+++...+.|.+||+++-
T Consensus 10 R~~~gls~~~lA~~~g~s~s~v~~iE 35 (64)
T PF13560_consen 10 RERAGLSQAQLADRLGVSQSTVSRIE 35 (64)
T ss_dssp HHCHTS-HHHHHHHHTS-HHHHHHHH
T ss_pred HHHcCCCHHHHHHHHCcCHHHHHHHH
Confidence 34568899999999999999999874
No 256
>PRK09480 slmA division inhibitor protein; Provisional
Probab=64.24 E-value=8.4 Score=25.90 Aligned_cols=25 Identities=16% Similarity=0.267 Sum_probs=23.5
Q ss_pred hcCcchhhhhhccccchhhHHHHHH
Q 036324 59 AHHVKSRTIHSRFLRSRETISRYFN 83 (91)
Q Consensus 59 ~~~~~~r~i~~~F~~S~eTisr~f~ 83 (91)
|++.+.++|..+=|.|+.|+++||.
T Consensus 28 G~~~ti~~Ia~~agvs~gt~Y~~F~ 52 (194)
T PRK09480 28 GERITTAKLAARVGVSEAALYRHFP 52 (194)
T ss_pred CCccCHHHHHHHhCCCHhHHHHHCC
Confidence 6889999999999999999999995
No 257
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=63.80 E-value=13 Score=24.45 Aligned_cols=42 Identities=7% Similarity=0.038 Sum_probs=29.5
Q ss_pred ccHHH-HHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHH
Q 036324 45 VSIEE-QLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVL 86 (91)
Q Consensus 45 v~veE-~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl 86 (91)
++..+ .+-++|+..+.+.+...+++.++.+.+||++.+...-
T Consensus 29 lt~~q~~vL~~l~~~~~~~t~~eLa~~l~~~~~tvt~~v~~Le 71 (144)
T PRK03573 29 LTQTHWVTLHNIHQLPPEQSQIQLAKAIGIEQPSLVRTLDQLE 71 (144)
T ss_pred CCHHHHHHHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHHHHH
Confidence 44444 3334444433456889999999999999999887654
No 258
>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=63.75 E-value=20 Score=25.34 Aligned_cols=43 Identities=19% Similarity=0.186 Sum_probs=32.8
Q ss_pred cHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 46 SIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 46 ~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
+..++-.+-|.. ..+.++..|+...|.|.+||.+..+..+..+
T Consensus 177 ~~~~r~il~l~y-~~~~s~~eIA~~lgis~~tV~~~~~ra~~~L 219 (224)
T TIGR02479 177 SEREQLVLSLYY-YEELNLKEIGEVLGLTESRVSQIHSQALKKL 219 (224)
T ss_pred CHHHHHHHHHHH-hCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 444444444433 5788999999999999999999988877765
No 259
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=63.33 E-value=20 Score=24.67 Aligned_cols=44 Identities=5% Similarity=0.003 Sum_probs=32.3
Q ss_pred ccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 45 VSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 45 v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
++.+.+ .+|....-++.++..|+..++.|..||-...+.....+
T Consensus 135 Lp~~~r-~i~~l~~~~g~s~~EIA~~lg~s~~tV~~rl~rar~~L 178 (192)
T PRK09643 135 LPVEQR-AALVAVDMQGYSVADAARMLGVAEGTVKSRCARGRARL 178 (192)
T ss_pred CCHHHH-HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 343344 34444455899999999999999999988886655543
No 260
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=63.26 E-value=16 Score=24.85 Aligned_cols=54 Identities=20% Similarity=0.214 Sum_probs=38.1
Q ss_pred HHHHHHHhCCCCCCCCCccHHHHHHHHHHHh--hcCcchhhhhhccccchhhHHHHHHHHHHH
Q 036324 28 LLCGLLRINGGLKADGTVSIEEQLCMFLHIL--AHHVKSRTIHSRFLRSRETISRYFNLVLNA 88 (91)
Q Consensus 28 ~L~~~L~~~~~l~~s~~v~veE~vamFL~i~--~~~~~~r~i~~~F~~S~eTisr~f~~Vl~a 88 (91)
.+-+.|+--+||+++- +-.|.-.+ ..+.+.-.|++.-.+|++||+|-.+..+++
T Consensus 14 ~~~dvl~c~~GLs~~D-------v~v~~~LL~~~~~~tvdelae~lnr~rStv~rsl~~L~~~ 69 (126)
T COG3355 14 RCEDVLKCVYGLSELD-------VEVYKALLEENGPLTVDELAEILNRSRSTVYRSLQNLLEA 69 (126)
T ss_pred cHHHHHHHHhCCcHHH-------HHHHHHHHhhcCCcCHHHHHHHHCccHHHHHHHHHHHHHc
Confidence 3456666667766643 22233334 556788899999999999999999988765
No 261
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=62.30 E-value=19 Score=25.07 Aligned_cols=38 Identities=5% Similarity=-0.190 Sum_probs=30.8
Q ss_pred HHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 52 CMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 52 amFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
.+|....-.|.++..|++.++.|..||....+..+..+
T Consensus 140 ~v~~l~~~~g~s~~EIAe~lgis~~tV~~~l~Rar~~L 177 (196)
T PRK12535 140 EALILTQVLGYTYEEAAKIADVRVGTIRSRVARARADL 177 (196)
T ss_pred HHhhhHHHhCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 34545556789999999999999999998888776654
No 262
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=62.19 E-value=19 Score=28.93 Aligned_cols=45 Identities=16% Similarity=0.138 Sum_probs=33.9
Q ss_pred ccHHHHHHHHHHHh---hcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 45 VSIEEQLCMFLHIL---AHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 45 v~veE~vamFL~i~---~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
.+..|+-.+-|... +.+.++..|+..++.|.+||..+.+.-+..+
T Consensus 351 L~~reR~VI~LRygl~d~~~~Tl~EIA~~LGvS~erVRqie~rAl~KL 398 (415)
T PRK07598 351 LTSRERDVIRMRFGLADGHTYSLAEIGRALDLSRERVRQIESKALQKL 398 (415)
T ss_pred CCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 34444545555442 3778999999999999999999988877654
No 263
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=62.18 E-value=23 Score=24.09 Aligned_cols=38 Identities=3% Similarity=-0.024 Sum_probs=30.5
Q ss_pred HHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 52 CMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 52 amFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
.+|....-.|.++..|+..+|.|..||....+..+..+
T Consensus 146 ~i~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~L 183 (189)
T PRK09648 146 EILILRVVVGLSAEETAEAVGSTPGAVRVAQHRALARL 183 (189)
T ss_pred HHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 34555555689999999999999999998888766554
No 264
>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=62.04 E-value=6.7 Score=20.35 Aligned_cols=22 Identities=14% Similarity=0.149 Sum_probs=17.7
Q ss_pred chhhhhhccccchhhHHHHHHH
Q 036324 63 KSRTIHSRFLRSRETISRYFNL 84 (91)
Q Consensus 63 ~~r~i~~~F~~S~eTisr~f~~ 84 (91)
+..+++..++.|..||.++..+
T Consensus 2 s~~e~a~~lgvs~~tl~~~~~~ 23 (49)
T cd04762 2 TTKEAAELLGVSPSTLRRWVKE 23 (49)
T ss_pred CHHHHHHHHCcCHHHHHHHHHc
Confidence 4567888999999999988653
No 265
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=62.02 E-value=14 Score=24.46 Aligned_cols=43 Identities=21% Similarity=0.260 Sum_probs=33.9
Q ss_pred ccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 45 VSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 45 v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
.+..|.- -|..++.|.++..|+...+.|..||..+...+.+.+
T Consensus 150 lt~re~~--vl~~l~~g~s~~eIa~~l~~s~~tv~~~~~~~~~kl 192 (210)
T PRK09935 150 LSNREVT--ILRYLVSGLSNKEIADQLLLSNKTVSAHKSNIYGKL 192 (210)
T ss_pred CCHHHHH--HHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHc
Confidence 4444443 345577889999999999999999999999887654
No 266
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=61.99 E-value=24 Score=23.64 Aligned_cols=40 Identities=13% Similarity=0.127 Sum_probs=30.1
Q ss_pred HHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHH
Q 036324 48 EEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNA 88 (91)
Q Consensus 48 eE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~a 88 (91)
+++-++-| ..-.|.++..|+..+|.|..||-...+.-+..
T Consensus 123 ~~r~v~~L-~~~~g~s~~EIA~~lgis~~tV~~~l~ra~~~ 162 (172)
T PRK12523 123 KARAAFLY-NRLDGMGHAEIAERLGVSVSRVRQYLAQGLRQ 162 (172)
T ss_pred HHHHHHHH-HHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 33443444 34579999999999999999998888776554
No 267
>PRK09801 transcriptional activator TtdR; Provisional
Probab=61.96 E-value=9.6 Score=28.13 Aligned_cols=38 Identities=5% Similarity=0.163 Sum_probs=30.2
Q ss_pred HHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHH
Q 036324 48 EEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVL 86 (91)
Q Consensus 48 eE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl 86 (91)
-+++-.|+. ++...+++.+++..+.|++|||+.+++.=
T Consensus 8 ~~~L~~F~~-v~~~gs~t~AA~~L~iSQpavS~~I~~LE 45 (310)
T PRK09801 8 AKDLQVLVE-IVHSGSFSAAAATLGQTPAFVTKRIQILE 45 (310)
T ss_pred HHHHHHHHH-HHHcCCHHHHHHHhCcCHHHHHHHHHHHH
Confidence 356666664 55567999999999999999999998753
No 268
>PRK13698 plasmid-partitioning protein; Provisional
Probab=61.69 E-value=13 Score=29.04 Aligned_cols=40 Identities=18% Similarity=0.008 Sum_probs=33.2
Q ss_pred ccHHHHHHH-HHHHhhcCcchhhhhhccccchhhHHHHHHH
Q 036324 45 VSIEEQLCM-FLHILAHHVKSRTIHSRFLRSRETISRYFNL 84 (91)
Q Consensus 45 v~veE~vam-FL~i~~~~~~~r~i~~~F~~S~eTisr~f~~ 84 (91)
-.+|+..+. -..+-..+.++..++.+.|.|+++|++.++-
T Consensus 159 s~iE~A~ay~~~L~~~~~~tQeeLA~~lG~SRs~Vsn~Lrl 199 (323)
T PRK13698 159 SAYERGLRYASRLQNEFAGNISALADAENISRKIITRCINT 199 (323)
T ss_pred CHHHHHHHHHHHHHHhcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 668888877 4345577899999999999999999999863
No 269
>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=61.62 E-value=15 Score=26.35 Aligned_cols=35 Identities=9% Similarity=0.100 Sum_probs=27.8
Q ss_pred HHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHH
Q 036324 50 QLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLV 85 (91)
Q Consensus 50 ~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~V 85 (91)
++-.|+.. +...+++.+++..+.|++|||+.+++.
T Consensus 5 ~l~~f~~v-~~~~s~t~AA~~L~isQpavS~~I~~L 39 (292)
T TIGR03298 5 QLAALAAV-VEEGSFERAAAALSVTPSAVSQRIKAL 39 (292)
T ss_pred HHHHHHHH-HHcCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 45555544 445599999999999999999999874
No 270
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=61.35 E-value=9.5 Score=25.53 Aligned_cols=44 Identities=9% Similarity=-0.017 Sum_probs=31.9
Q ss_pred ccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 45 VSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 45 v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
+|..++-++-|+. -.|.++..|+..++.|..||....+.....+
T Consensus 127 L~~~~r~v~~l~~-~~g~s~~eIA~~l~is~~~V~~~l~ra~~~l 170 (176)
T PRK09638 127 LDPEFRAPVILKH-YYGYTYEEIAKMLNIPEGTVKSRVHHGIKQL 170 (176)
T ss_pred CCHHHhheeeehh-hcCCCHHHHHHHHCCChhHHHHHHHHHHHHH
Confidence 3444444444433 4799999999999999999988877766554
No 271
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=61.14 E-value=4.5 Score=29.63 Aligned_cols=22 Identities=27% Similarity=0.108 Sum_probs=19.4
Q ss_pred chhhhhhccccchhhHHHHHHH
Q 036324 63 KSRTIHSRFLRSRETISRYFNL 84 (91)
Q Consensus 63 ~~r~i~~~F~~S~eTisr~f~~ 84 (91)
+-++|+..-|.|..||||.++.
T Consensus 3 ti~dIA~~agVS~~TVSrvln~ 24 (327)
T PRK10339 3 TLKDIAIEAGVSLATVSRVLND 24 (327)
T ss_pred CHHHHHHHhCCCHHhhhhhhcC
Confidence 5678999999999999999873
No 272
>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=61.07 E-value=28 Score=24.65 Aligned_cols=42 Identities=26% Similarity=0.335 Sum_probs=30.9
Q ss_pred HHHHHHHHhCCCCCCCCCccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHH
Q 036324 27 ELLCGLLRINGGLKADGTVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLV 85 (91)
Q Consensus 27 ~~L~~~L~~~~~l~~s~~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~V 85 (91)
..|.+.+.+ +.+++...++.|.+| +..|+.|+.||-+-+.+.
T Consensus 7 ~~l~~~I~~-g~~~~G~~LPsE~eL----------------a~~~gVSR~TVR~Al~~L 48 (233)
T TIGR02404 7 QDLEQKITH-GQYKEGDYLPSEHEL----------------MDQYGASRETVRKALNLL 48 (233)
T ss_pred HHHHHHHHh-CCCCCCCCCcCHHHH----------------HHHHCCCHHHHHHHHHHH
Confidence 344444444 667877789988876 579999999998877654
No 273
>PRK11074 putative DNA-binding transcriptional regulator; Provisional
Probab=60.95 E-value=15 Score=26.65 Aligned_cols=36 Identities=11% Similarity=-0.005 Sum_probs=28.9
Q ss_pred HHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHH
Q 036324 49 EQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLV 85 (91)
Q Consensus 49 E~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~V 85 (91)
+++-.|+. ++...++..++...+.|++|||+.+.+.
T Consensus 5 ~~L~~f~~-v~e~~s~s~AA~~L~isQpavS~~I~~L 40 (300)
T PRK11074 5 YSLEVVDA-VARTGSFSAAAQELHRVPSAVSYTVRQL 40 (300)
T ss_pred HHHHHHHH-HHHhCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 55655554 4555699999999999999999999875
No 274
>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=60.93 E-value=24 Score=23.09 Aligned_cols=43 Identities=12% Similarity=0.067 Sum_probs=31.6
Q ss_pred HHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 47 IEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 47 veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
.+.|=-++-+..-.+.|...|++.++.|+.+|+-.++..-..+
T Consensus 19 T~kQ~~~l~lyy~eDlSlsEIAe~~~iSRqaV~d~ikr~~~~L 61 (101)
T PF04297_consen 19 TEKQREILELYYEEDLSLSEIAEELGISRQAVYDSIKRAEKKL 61 (101)
T ss_dssp -HHHHHHHHHHCTS---HHHHHHHCTS-HHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHccCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 4566677777788899999999999999999999988766544
No 275
>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=60.74 E-value=18 Score=25.58 Aligned_cols=38 Identities=11% Similarity=0.168 Sum_probs=29.4
Q ss_pred HHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHH
Q 036324 48 EEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVL 86 (91)
Q Consensus 48 eE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl 86 (91)
.++|...|+.-+ +.+...++..++.|..||+++....-
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 345555555543 48999999999999999999988754
No 276
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=60.65 E-value=34 Score=23.18 Aligned_cols=51 Identities=16% Similarity=0.276 Sum_probs=37.0
Q ss_pred hCCCHHHHHHHHHHHHh---CCCCCCCCCccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHH
Q 036324 19 LRMDKRTFELLCGLLRI---NGGLKADGTVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLV 85 (91)
Q Consensus 19 fRM~~~~F~~L~~~L~~---~~~l~~s~~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~V 85 (91)
|..++.++.++++.++. ++.|++...+++--.+|+ ..+.+.-||+|-+++.
T Consensus 6 f~s~~PIY~QI~~qIk~~I~~g~l~pGdkLPSvRelA~----------------~~~VNpnTv~raY~eL 59 (125)
T COG1725 6 FDSSKPIYEQIANQIKEQIASGELKPGDKLPSVRELAK----------------DLGVNPNTVQRAYQEL 59 (125)
T ss_pred cCCCCCHHHHHHHHHHHHHHhCCcCCCCCCCcHHHHHH----------------HhCCCHHHHHHHHHHH
Confidence 55666778888887765 467777777776555555 5588889999988875
No 277
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=60.61 E-value=27 Score=23.30 Aligned_cols=37 Identities=11% Similarity=0.140 Sum_probs=29.6
Q ss_pred HHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 53 MFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 53 mFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
+|+...-.|.++..|+...|.|..||....+.-+..+
T Consensus 126 vl~L~~~~g~s~~EIA~~lgis~~tV~~~l~ra~~~L 162 (173)
T PRK09645 126 VLVRSYYRGWSTAQIAADLGIPEGTVKSRLHYALRAL 162 (173)
T ss_pred HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 3444456799999999999999999988877766554
No 278
>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function.
Probab=60.58 E-value=30 Score=22.83 Aligned_cols=48 Identities=17% Similarity=0.182 Sum_probs=38.6
Q ss_pred CCCccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHH----HHHHHh
Q 036324 42 DGTVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNL----VLNAIL 90 (91)
Q Consensus 42 s~~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~----Vl~ai~ 90 (91)
+-.+++||-=||=|-- -.|.++...+.+-|.|+.|++|..+. |-+|++
T Consensus 39 ~V~L~~dElEAiRL~D-~egl~QeeaA~~MgVSR~T~~ril~~ARkKiA~ALv 90 (106)
T PF02001_consen 39 PVVLTVDELEAIRLVD-YEGLSQEEAAERMGVSRPTFQRILESARKKIADALV 90 (106)
T ss_pred eEEeeHHHHHHHHHHH-HcCCCHHHHHHHcCCcHHHHHHHHHHHHHHHHHHHH
Confidence 3478999988888744 45799999999999999999999875 444544
No 279
>PHA02591 hypothetical protein; Provisional
Probab=60.41 E-value=9.8 Score=24.24 Aligned_cols=27 Identities=19% Similarity=0.160 Sum_probs=23.5
Q ss_pred hhcCcchhhhhhccccchhhHHHHHHH
Q 036324 58 LAHHVKSRTIHSRFLRSRETISRYFNL 84 (91)
Q Consensus 58 ~~~~~~~r~i~~~F~~S~eTisr~f~~ 84 (91)
...|.+..+|+..-|.|.+||++|.+.
T Consensus 56 ~eqGlSqeqIA~~LGVsqetVrKYL~~ 82 (83)
T PHA02591 56 ARKGFTVEKIASLLGVSVRKVRRYLES 82 (83)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHhc
Confidence 346789999999999999999999764
No 280
>PHA02510 X gene X product; Reviewed
Probab=60.27 E-value=48 Score=22.30 Aligned_cols=58 Identities=12% Similarity=0.102 Sum_probs=43.8
Q ss_pred HHHHHHHHHHhCCCCCCCCCccHHHHHHHHHHHhhcC-cchhhhhhccccchhhHHHHHHHHHH
Q 036324 25 TFELLCGLLRINGGLKADGTVSIEEQLCMFLHILAHH-VKSRTIHSRFLRSRETISRYFNLVLN 87 (91)
Q Consensus 25 ~F~~L~~~L~~~~~l~~s~~v~veE~vamFL~i~~~~-~~~r~i~~~F~~S~eTisr~f~~Vl~ 87 (91)
+...|++.+-. ..++.+++.-.+...|.|-.|.. ..+..+...+ |..|.+|+..+.++
T Consensus 9 v~~~l~~~~~t---~t~~G~~s~aka~~~f~~y~~l~~~g~~~vk~~l--~k~tFyrhr~~L~~ 67 (116)
T PHA02510 9 VIDAIINKFFS---ITKSGNLSSAKAMRYFGFYRRLVNEGYDNVADTM--SRATFWRHRKVLKE 67 (116)
T ss_pred HHHHHHhhhee---eCCCCCcCHHHHHHHHHHHHhhhhhhHHHHHHHc--cHHHHHHHHHHHHH
Confidence 34445554443 45667899999999999999998 6677788887 66899999877664
No 281
>PRK05949 RNA polymerase sigma factor; Validated
Probab=60.01 E-value=22 Score=27.30 Aligned_cols=45 Identities=16% Similarity=0.249 Sum_probs=33.3
Q ss_pred ccHHHHHHHHHHH-h--hcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 45 VSIEEQLCMFLHI-L--AHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 45 v~veE~vamFL~i-~--~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
.+..|+-.+-|.. + +.+.++..|+..+|.|.+||..+.+.-++.+
T Consensus 267 L~~rer~Vi~lr~gl~~~e~~Tl~EIa~~lgiS~erVrq~~~rAl~kL 314 (327)
T PRK05949 267 LTPQQREVLTLRFGLEDGKELSLAKVGERLNLSRERVRQLEHQALAHL 314 (327)
T ss_pred CCHHHHHHHHHHhccCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 3444454444433 2 3779999999999999999999988877654
No 282
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=59.72 E-value=20 Score=25.94 Aligned_cols=37 Identities=3% Similarity=0.013 Sum_probs=30.7
Q ss_pred HHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 53 MFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 53 mFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
+|+..--.|.++..|+..+|.|..||....+..+..+
T Consensus 179 v~~L~~~eg~s~~EIA~~Lgis~~tVk~~l~RAr~kL 215 (233)
T PRK12538 179 AVILSYHENMSNGEIAEVMDTTVAAVESLLKRGRQQL 215 (233)
T ss_pred HhhhHHhcCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 4444456899999999999999999999988877655
No 283
>PRK11564 stationary phase inducible protein CsiE; Provisional
Probab=58.95 E-value=20 Score=27.93 Aligned_cols=48 Identities=15% Similarity=0.136 Sum_probs=34.8
Q ss_pred CCCCCCccHHHHHH-HHHHHh--hcCcchhhhhhccccchhhHHHHHHHHH
Q 036324 39 LKADGTVSIEEQLC-MFLHIL--AHHVKSRTIHSRFLRSRETISRYFNLVL 86 (91)
Q Consensus 39 l~~s~~v~veE~va-mFL~i~--~~~~~~r~i~~~F~~S~eTisr~f~~Vl 86 (91)
|.++...+.+|+.. +.++.+ ....+.-++++.+++|+.||.+-+.+|=
T Consensus 5 ~~~~~~~s~~ER~~~il~~LL~~~~~v~l~~Lae~l~VSrsTi~~DLk~l~ 55 (426)
T PRK11564 5 LAPPSVLSAPQRRCQILLMLFQPGLTVTLETFSQLNGVDDDTARQDIAETG 55 (426)
T ss_pred CCCCcCCCHHHHHHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHHHHHH
Confidence 45556677777644 333333 3447889999999999999999888773
No 284
>cd00131 PAX Paired Box domain
Probab=58.93 E-value=51 Score=21.90 Aligned_cols=74 Identities=15% Similarity=0.115 Sum_probs=48.2
Q ss_pred ChhHHHHHhCCCHHHHHHHHHHHHhCCCCCCC------CCccHHHHHHHHH-HHhhcC-cchhhhhhc-c--cc------
Q 036324 11 SDIECVNQLRMDKRTFELLCGLLRINGGLKAD------GTVSIEEQLCMFL-HILAHH-VKSRTIHSR-F--LR------ 73 (91)
Q Consensus 11 ~~~~c~~~fRM~~~~F~~L~~~L~~~~~l~~s------~~v~veE~vamFL-~i~~~~-~~~r~i~~~-F--~~------ 73 (91)
.....-..|++++.+-.++....++.+.+.+- .....+++...++ ++-.++ .+-+.+.+. + +.
T Consensus 35 s~~~iA~~~~Vs~~tV~r~i~r~~e~G~v~pk~~gg~rpr~~~~~~~~~i~~~v~~~p~~Tl~El~~~L~~~gv~~~~~~ 114 (128)
T cd00131 35 RPCDISRQLRVSHGCVSKILNRYYETGSIRPGAIGGSKPRVATPEVVKKIEIYKQENPGMFAWEIRDRLLQEGVCDKSNV 114 (128)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCCCCCCCCCCcCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCCcccCCC
Confidence 56677889999999999999999887766542 1222333433333 333333 445555555 2 33
Q ss_pred -chhhHHHHHHH
Q 036324 74 -SRETISRYFNL 84 (91)
Q Consensus 74 -S~eTisr~f~~ 84 (91)
|.+||+|.++.
T Consensus 115 ~s~stI~R~L~~ 126 (128)
T cd00131 115 PSVSSINRILRN 126 (128)
T ss_pred CCHHHHHHHHHh
Confidence 99999998764
No 285
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=58.81 E-value=9.5 Score=25.50 Aligned_cols=32 Identities=6% Similarity=-0.016 Sum_probs=27.9
Q ss_pred hhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 58 LAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 58 ~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
.-.|.++++|+..+|.|..||...++.....+
T Consensus 133 ~~~g~s~~eIA~~lg~s~~tv~~~l~Rar~~L 164 (175)
T PRK12518 133 DLEDLPQKEIAEILNIPVGTVKSRLFYARRQL 164 (175)
T ss_pred HhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 45688999999999999999999998877654
No 286
>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=58.63 E-value=21 Score=26.41 Aligned_cols=37 Identities=5% Similarity=-0.023 Sum_probs=30.8
Q ss_pred HHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 53 MFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 53 mFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
+|+..--++.++..|+...+.|..||...++.....+
T Consensus 150 v~~L~~~~g~s~~EIA~~lgis~~tV~~~l~Rar~~L 186 (324)
T TIGR02960 150 VLLLRDVLGWRAAETAELLGTSTASVNSALQRARATL 186 (324)
T ss_pred HhhhHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 4444556899999999999999999999988777655
No 287
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=58.48 E-value=10 Score=25.98 Aligned_cols=37 Identities=5% Similarity=0.110 Sum_probs=30.3
Q ss_pred HHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 53 MFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 53 mFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
+|.+....|.++..|+..++.|..||....+..+..+
T Consensus 142 v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~L 178 (188)
T PRK09640 142 ILVLRFVAELEFQEIADIMHMGLSATKMRYKRALDKL 178 (188)
T ss_pred eeeeHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 4555556789999999999999999998888766654
No 288
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=58.44 E-value=14 Score=26.40 Aligned_cols=36 Identities=8% Similarity=0.103 Sum_probs=28.9
Q ss_pred HHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 54 FLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 54 FL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
|....-++.++..|+..+|.|.+||....+.....+
T Consensus 158 ~~l~~~~g~s~~EIAe~lgis~~tVk~~l~Rar~kL 193 (231)
T PRK11922 158 FVLRVVEELSVEETAQALGLPEETVKTRLHRARRLL 193 (231)
T ss_pred heeehhcCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 333345699999999999999999999888766543
No 289
>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=58.39 E-value=12 Score=27.40 Aligned_cols=36 Identities=17% Similarity=0.188 Sum_probs=29.4
Q ss_pred HHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHH
Q 036324 49 EQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLV 85 (91)
Q Consensus 49 E~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~V 85 (91)
+++-.|+ .++...++..+++..+.|++||||.++..
T Consensus 11 ~~L~~F~-~va~~gs~s~AA~~L~isQpavS~~I~~L 46 (302)
T TIGR02036 11 SKMHTFE-VAARHQSFSLAAEELSLTPSAISHRINQL 46 (302)
T ss_pred HHHHHHH-HHHHhCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 4555554 56777899999999999999999999875
No 290
>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=58.36 E-value=11 Score=20.31 Aligned_cols=27 Identities=11% Similarity=-0.165 Sum_probs=22.1
Q ss_pred HhhcCcchhhhhhccccchhhHHHHHH
Q 036324 57 ILAHHVKSRTIHSRFLRSRETISRYFN 83 (91)
Q Consensus 57 i~~~~~~~r~i~~~F~~S~eTisr~f~ 83 (91)
.-..+.+..+++..-+.|.+|||++.+
T Consensus 11 r~~~gltq~~lA~~~gvs~~~vs~~e~ 37 (58)
T TIGR03070 11 RKALGLTQADLADLAGVGLRFIRDVEN 37 (58)
T ss_pred HHHcCCCHHHHHHHhCCCHHHHHHHHC
Confidence 345678888899999999999998764
No 291
>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=58.30 E-value=18 Score=26.02 Aligned_cols=36 Identities=8% Similarity=0.184 Sum_probs=28.9
Q ss_pred HHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHH
Q 036324 49 EQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLV 85 (91)
Q Consensus 49 E~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~V 85 (91)
+++-+|+.++ ...+...++..-+.|.+|||+.+++.
T Consensus 6 ~~l~~f~~v~-~~gS~s~AA~~L~isq~avS~~I~~L 41 (300)
T TIGR02424 6 RHLQCFVEVA-RQGSVKRAAEALHITQPAVSKTLREL 41 (300)
T ss_pred HHHHHHHHHH-HhCCHHHHHHHhCCChHHHHHHHHHH
Confidence 4566666554 45599999999999999999999875
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=58.16 E-value=25 Score=25.93 Aligned_cols=38 Identities=11% Similarity=0.043 Sum_probs=31.8
Q ss_pred HHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 52 CMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 52 amFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
++|+..-..+.++..|+..++.|..||...++.....+
T Consensus 115 ~v~~L~~~~g~s~~EIA~~lg~s~~tVr~~l~RAr~~L 152 (281)
T TIGR02957 115 AVFVLREVFDYPYEEIASIVGKSEANCRQLVSRARRHL 152 (281)
T ss_pred HHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 45566667899999999999999999999888776654
No 293
>PRK10632 transcriptional regulator; Provisional
Probab=57.88 E-value=13 Score=27.16 Aligned_cols=36 Identities=11% Similarity=0.134 Sum_probs=28.9
Q ss_pred HHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHH
Q 036324 49 EQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLV 85 (91)
Q Consensus 49 E~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~V 85 (91)
+++-.|+ .++...+++.++++.+.|++|||+.+++.
T Consensus 5 ~~L~~F~-~v~e~gS~t~AA~~L~isQpavS~~I~~L 40 (309)
T PRK10632 5 KRMSVFA-KVVEFGSFTAAARQLQMSVSSISQTVSKL 40 (309)
T ss_pred HHHHHHH-HHHhcCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 3455554 55667899999999999999999999874
No 294
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=57.81 E-value=19 Score=26.02 Aligned_cols=38 Identities=11% Similarity=0.148 Sum_probs=29.8
Q ss_pred HHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHH
Q 036324 49 EQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLN 87 (91)
Q Consensus 49 E~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ 87 (91)
.++-.|+-+. ...+...+++.-+.|++|||+.+++.=+
T Consensus 8 ~~L~~f~~v~-~~gs~s~AA~~L~isQ~avS~~i~~LE~ 45 (302)
T PRK09791 8 HQIRAFVEVA-RQGSIRGASRMLNMSQPALTKSIQELEE 45 (302)
T ss_pred HHHHHHHHHH-HcCCHHHHHHHhCCChHHHHHHHHHHHH
Confidence 5666666554 4559999999999999999999987533
No 295
>PRK11050 manganese transport regulator MntR; Provisional
Probab=57.38 E-value=25 Score=23.91 Aligned_cols=26 Identities=15% Similarity=0.250 Sum_probs=23.3
Q ss_pred cCcchhhhhhccccchhhHHHHHHHH
Q 036324 60 HHVKSRTIHSRFLRSRETISRYFNLV 85 (91)
Q Consensus 60 ~~~~~r~i~~~F~~S~eTisr~f~~V 85 (91)
.+.+.+.++..++.|.+||++.+...
T Consensus 50 ~~~t~~eLA~~l~is~stVsr~l~~L 75 (152)
T PRK11050 50 GEARQVDIAARLGVSQPTVAKMLKRL 75 (152)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 56799999999999999999998764
No 296
>PF07900 DUF1670: Protein of unknown function (DUF1670); InterPro: IPR012872 The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=57.27 E-value=78 Score=23.58 Aligned_cols=74 Identities=15% Similarity=0.087 Sum_probs=53.9
Q ss_pred hHHHHHhCCCHHHHHHHHHHHHhC-CCCCCCCC-------ccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHH
Q 036324 13 IECVNQLRMDKRTFELLCGLLRIN-GGLKADGT-------VSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNL 84 (91)
Q Consensus 13 ~~c~~~fRM~~~~F~~L~~~L~~~-~~l~~s~~-------v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~ 84 (91)
.+---.|..++.|-.+....++.+ +..-|+++ --...+.++=+|.= +....+|+-+=.||+++|-||+..
T Consensus 109 ~Dla~LL~~S~~TI~~~i~~yq~e~g~vvPtrG~i~DiGp~~tHK~~ii~~~l~--g~~~~eiar~t~HS~~av~rYi~~ 186 (220)
T PF07900_consen 109 EDLAMLLGISPRTISKDIKEYQKEHGVVVPTRGTIHDIGPGVTHKKIIIRLYLK--GKPTPEIARRTNHSPEAVDRYIKD 186 (220)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHHcCceeccCCcccccCCcchHHHHHHHHHHc--CCCHHHHHHHhccCHHHHHHHHHh
Confidence 344567899999999999999988 65556542 22334444444443 578889999999999999999876
Q ss_pred HHHH
Q 036324 85 VLNA 88 (91)
Q Consensus 85 Vl~a 88 (91)
.-+.
T Consensus 187 F~rV 190 (220)
T PF07900_consen 187 FKRV 190 (220)
T ss_pred hHHh
Confidence 5543
No 297
>smart00351 PAX Paired Box domain.
Probab=57.25 E-value=53 Score=21.60 Aligned_cols=72 Identities=15% Similarity=0.181 Sum_probs=47.7
Q ss_pred ChhHHHHHhCCCHHHHHHHHHHHHhCCCCCCC-----C-CccHHHHHHHHH-HHhhcC-cchhhhhhcccc---------
Q 036324 11 SDIECVNQLRMDKRTFELLCGLLRINGGLKAD-----G-TVSIEEQLCMFL-HILAHH-VKSRTIHSRFLR--------- 73 (91)
Q Consensus 11 ~~~~c~~~fRM~~~~F~~L~~~L~~~~~l~~s-----~-~v~veE~vamFL-~i~~~~-~~~r~i~~~F~~--------- 73 (91)
+..+.-..|.+++.|-.+..+..++.+.+.+- + ....++.....+ ++..++ .+.+.++.....
T Consensus 35 s~~~iA~~~gvs~~tV~kwi~r~~~~G~~~pk~~gg~rp~~~~~~~~~~I~~~~~~~p~~t~~el~~~L~~~gv~~~~~~ 114 (125)
T smart00351 35 RPCDISRQLCVSHGCVSKILGRYYETGSIRPGAIGGSKPKVATPKVVKKIADYKQENPGIFAWEIRDRLLSEGVCDKDNV 114 (125)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCcCCCCCCCCccCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCCCcCCCC
Confidence 56778889999999999999998887766551 2 233333333333 344443 556666655532
Q ss_pred -chhhHHHHH
Q 036324 74 -SRETISRYF 82 (91)
Q Consensus 74 -S~eTisr~f 82 (91)
|.+||++.+
T Consensus 115 Ps~sti~~~l 124 (125)
T smart00351 115 PSVSSINRIL 124 (125)
T ss_pred CChhhHHHhh
Confidence 889998876
No 298
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=57.07 E-value=13 Score=26.57 Aligned_cols=35 Identities=14% Similarity=0.124 Sum_probs=27.7
Q ss_pred HHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHH
Q 036324 50 QLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLV 85 (91)
Q Consensus 50 ~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~V 85 (91)
++-.|+. ++...+.+.++..-+.|++|||+.+++.
T Consensus 7 ~L~~f~~-v~e~~s~t~AA~~L~isqpavS~~I~~L 41 (290)
T PRK10837 7 QLEVFAE-VLKSGSTTQASVMLALSQSAVSAALTDL 41 (290)
T ss_pred HHHHHHH-HHHcCCHHHHHHHhCCCccHHHHHHHHH
Confidence 4445554 4455699999999999999999999875
No 299
>PF13972 TetR: Bacterial transcriptional repressor; PDB: 3RH2_A 3NNR_A.
Probab=56.77 E-value=38 Score=22.32 Aligned_cols=84 Identities=14% Similarity=0.082 Sum_probs=53.7
Q ss_pred hHHhhcCChh---HHHHHhCCCHHHHHHHHHHHHhCCCCCCCCCccHHHHHHHHHHHhhcC-cchhhhhhccc-cchhhH
Q 036324 4 LSRSIIGSDI---ECVNQLRMDKRTFELLCGLLRINGGLKADGTVSIEEQLCMFLHILAHH-VKSRTIHSRFL-RSRETI 78 (91)
Q Consensus 4 l~~ll~~~~~---~c~~~fRM~~~~F~~L~~~L~~~~~l~~s~~v~veE~vamFL~i~~~~-~~~r~i~~~F~-~S~eTi 78 (91)
+.+|+..+|. +......-....+..+++.|++.|.++.+ .-.+ +.||--+|+++.. .++..+...=. ...+++
T Consensus 45 l~~Ll~~~p~L~~~~~~~~~~~~~~~~~l~~~l~~~g~l~~~-~~~~-~~La~~i~lv~t~Wl~~~~~~~~~~~~~~~~~ 122 (146)
T PF13972_consen 45 LPDLLRRDPELKKRYRQLQQRRREQLRQLLQSLIEAGILRID-DEEL-QALADNIWLVSTFWLSFLETQHPRDKLTEEDI 122 (146)
T ss_dssp HHHHHHC-HHHHHHHHHHHHHHHHHHHHHHHHHHHTTSB----GHHH-HHHHHHHHHHHHCHHHHHHHHSS-----HHCH
T ss_pred HHHHHHhCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC-HHHH-HHHHHHHHHHHHHHHhHHHHhCccccchHHHH
Confidence 4455665553 44555556678999999999999988843 2233 3899999999988 55555443322 456788
Q ss_pred HHHHHHHHHHH
Q 036324 79 SRYFNLVLNAI 89 (91)
Q Consensus 79 sr~f~~Vl~ai 89 (91)
.+.+..|+..+
T Consensus 123 ~~gv~qv~~L~ 133 (146)
T PF13972_consen 123 RRGVYQVLSLL 133 (146)
T ss_dssp HHHHHHHHHHH
T ss_pred HHHHHHHHHHH
Confidence 88888887654
No 300
>PRK15092 DNA-binding transcriptional repressor LrhA; Provisional
Probab=56.65 E-value=13 Score=27.54 Aligned_cols=34 Identities=9% Similarity=0.047 Sum_probs=28.8
Q ss_pred HHHHHHhhcCcchhhhhhccccchhhHHHHHHHH
Q 036324 52 CMFLHILAHHVKSRTIHSRFLRSRETISRYFNLV 85 (91)
Q Consensus 52 amFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~V 85 (91)
.-.++.++...++..++...+.|++|||+.+++.
T Consensus 16 L~~F~~v~e~gs~s~AA~~L~iSQpavS~~I~~L 49 (310)
T PRK15092 16 LRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRL 49 (310)
T ss_pred HHHHHHHHHcCCHHHHHHHhCCChHHHHHHHHHH
Confidence 3455677778899999999999999999999875
No 301
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=56.36 E-value=28 Score=25.72 Aligned_cols=38 Identities=18% Similarity=0.072 Sum_probs=31.9
Q ss_pred HHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 52 CMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 52 amFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
++|+..-..+.++..|++.++.|..||...++.-...+
T Consensus 122 ~v~~L~~~~g~s~~EIA~~lg~s~~tVk~~l~RAr~~L 159 (293)
T PRK09636 122 AAFLLHDVFGVPFDEIASTLGRSPAACRQLASRARKHV 159 (293)
T ss_pred HHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 46666677899999999999999999999888766554
No 302
>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=56.21 E-value=9.6 Score=19.90 Aligned_cols=21 Identities=14% Similarity=0.161 Sum_probs=17.6
Q ss_pred chhhhhhccccchhhHHHHHH
Q 036324 63 KSRTIHSRFLRSRETISRYFN 83 (91)
Q Consensus 63 ~~r~i~~~F~~S~eTisr~f~ 83 (91)
+..+++..++.|..||.+..+
T Consensus 3 t~~e~a~~lgis~~ti~~~~~ 23 (49)
T TIGR01764 3 TVEEAAEYLGVSKDTVYRLIH 23 (49)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 456788999999999988765
No 303
>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=56.20 E-value=16 Score=22.02 Aligned_cols=31 Identities=19% Similarity=0.130 Sum_probs=23.5
Q ss_pred hhcCcchhhhhhccccchhhHHHHHHHHHHH
Q 036324 58 LAHHVKSRTIHSRFLRSRETISRYFNLVLNA 88 (91)
Q Consensus 58 ~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~a 88 (91)
-..+.+..++++.+..|.+|+.|.++++=+.
T Consensus 27 ~~~~~s~~~la~~~~iS~sti~~~i~~l~~~ 57 (87)
T PF05043_consen 27 NNEYVSIEDLAEELFISRSTIYRDIKKLNKY 57 (87)
T ss_dssp H-SEEEHHHHHHHHT--HHHHHHHHHHHHHH
T ss_pred cCCCcCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 3566889999999999999999999876543
No 304
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=55.71 E-value=21 Score=26.26 Aligned_cols=37 Identities=14% Similarity=0.230 Sum_probs=26.5
Q ss_pred HHHHHHHHHhhcC--cchhhhhhccccchhhHHHHHHHH
Q 036324 49 EQLCMFLHILAHH--VKSRTIHSRFLRSRETISRYFNLV 85 (91)
Q Consensus 49 E~vamFL~i~~~~--~~~r~i~~~F~~S~eTisr~f~~V 85 (91)
|+...-|-.+..+ .+..++++.|+.|.+||.|.+.+.
T Consensus 5 eR~~~Il~~L~~~~~v~v~eLa~~l~VS~~TIRRDL~~L 43 (256)
T PRK10434 5 QRQAAILEYLQKQGKTSVEELAQYFDTTGTTIRKDLVIL 43 (256)
T ss_pred HHHHHHHHHHHHcCCEEHHHHHHHHCCCHHHHHHHHHHH
Confidence 3333334444433 577889999999999999998873
No 305
>smart00497 IENR1 Intron encoded nuclease repeat motif. Repeat of unknown function, but possibly DNA-binding via helix-turn-helix motif (Ponting, unpublished).
Probab=55.57 E-value=11 Score=20.49 Aligned_cols=23 Identities=26% Similarity=0.284 Sum_probs=19.5
Q ss_pred cchhhhhhccccchhhHHHHHHH
Q 036324 62 VKSRTIHSRFLRSRETISRYFNL 84 (91)
Q Consensus 62 ~~~r~i~~~F~~S~eTisr~f~~ 84 (91)
.+.+.++..++.+..||+++.+.
T Consensus 18 ~S~~eAa~~lg~~~~~I~~~~~~ 40 (53)
T smart00497 18 SSIREAAKYLGISHSSISKYLNT 40 (53)
T ss_pred cCHHHHHHHhCCCHHHHHHHHhC
Confidence 46788999999999999998763
No 306
>TIGR03384 betaine_BetI transcriptional repressor BetI. BetI is a DNA-binding transcriptional repressor of the bet (betaine) regulon. In sequence, it is related to TetR (pfam00440). Choline, through BetI, induces the expression of the betaine biosynthesis genes betA and betB by derepression. The choline porter gene betT is also part of this regulon in Escherichia coli. Note that a different transcriptional regulator, ArcA, controls the expression of bet regulon genes in response to oxygen, as BetA is an oxygen-dependent enzyme.
Probab=55.48 E-value=14 Score=24.69 Aligned_cols=36 Identities=22% Similarity=0.128 Sum_probs=27.9
Q ss_pred HHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHH
Q 036324 48 EEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFN 83 (91)
Q Consensus 48 eE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~ 83 (91)
+-...+|.=.=-++.+.+.|+..-|.|+.|+++||.
T Consensus 15 ~aA~~lf~~~G~~~~s~~~IA~~agvsk~~ly~~F~ 50 (189)
T TIGR03384 15 DATIESIGERGSLDVTIAQIARRAGVSSGIISHYFG 50 (189)
T ss_pred HHHHHHHHhcCcccCCHHHHHHHhCCCHHHHHHHcC
Confidence 334444544444679999999999999999999994
No 307
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=55.42 E-value=14 Score=25.29 Aligned_cols=32 Identities=13% Similarity=0.073 Sum_probs=27.1
Q ss_pred hhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 58 LAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 58 ~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
.-.|.++..|+...|.|.+||....+..+..+
T Consensus 152 ~~~g~s~~EIA~~lgis~~tV~~~l~ra~~~L 183 (194)
T PRK12513 152 EHGDLELEEIAELTGVPEETVKSRLRYALQKL 183 (194)
T ss_pred hccCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 46789999999999999999988877666554
No 308
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=55.42 E-value=20 Score=21.35 Aligned_cols=37 Identities=16% Similarity=0.183 Sum_probs=27.9
Q ss_pred HHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHH
Q 036324 49 EQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLV 85 (91)
Q Consensus 49 E~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~V 85 (91)
|++-=||-....+.+-++|++.++.|..|+.+|....
T Consensus 3 e~Il~~i~~~~~p~~T~eiA~~~gls~~~aR~yL~~L 39 (62)
T PF04703_consen 3 EKILEYIKEQNGPLKTREIADALGLSIYQARYYLEKL 39 (62)
T ss_dssp HCHHHHHHHHTS-EEHHHHHHHHTS-HHHHHHHHHHH
T ss_pred HHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 4555566666788999999999999999998776553
No 309
>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=54.95 E-value=34 Score=20.28 Aligned_cols=28 Identities=14% Similarity=0.075 Sum_probs=20.4
Q ss_pred hhcCcchhhhhhccccc-hhhHHHHHHHH
Q 036324 58 LAHHVKSRTIHSRFLRS-RETISRYFNLV 85 (91)
Q Consensus 58 ~~~~~~~r~i~~~F~~S-~eTisr~f~~V 85 (91)
=|..-+.|.|++.||-+ ..||+++....
T Consensus 22 ~G~~Pt~rEIa~~~g~~S~~tv~~~L~~L 50 (65)
T PF01726_consen 22 NGYPPTVREIAEALGLKSTSTVQRHLKAL 50 (65)
T ss_dssp HSS---HHHHHHHHTSSSHHHHHHHHHHH
T ss_pred cCCCCCHHHHHHHhCCCChHHHHHHHHHH
Confidence 44557899999999975 99999987653
No 310
>PRK02287 hypothetical protein; Provisional
Probab=54.83 E-value=11 Score=27.02 Aligned_cols=33 Identities=27% Similarity=0.286 Sum_probs=29.3
Q ss_pred CccHHHHHHHHHHHhhcCcchhhhhhccccchh
Q 036324 44 TVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRE 76 (91)
Q Consensus 44 ~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~e 76 (91)
..|.-|++|..|||+|....-..+-+.|..+.+
T Consensus 106 kLs~vEAlAaaLyI~G~~~~A~~ll~~F~WG~~ 138 (171)
T PRK02287 106 KLSSVEALAAALYILGFKEEAEKILSKFKWGHT 138 (171)
T ss_pred cccHHHHHHHHHHHcCCHHHHHHHHhhCCChHH
Confidence 689999999999999999999999999977643
No 311
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=54.75 E-value=14 Score=26.35 Aligned_cols=31 Identities=13% Similarity=0.181 Sum_probs=26.4
Q ss_pred cCcchhhhhhccccchhhHHHHHHHHHHHHh
Q 036324 60 HHVKSRTIHSRFLRSRETISRYFNLVLNAIL 90 (91)
Q Consensus 60 ~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai~ 90 (91)
...+-++++..||.|.+|++.|.+...+-++
T Consensus 177 R~~~l~dLA~~lGISkst~~ehLRrAe~Kl~ 207 (215)
T COG3413 177 RRVSLKDLAKELGISKSTLSEHLRRAERKLI 207 (215)
T ss_pred ccCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 4577788999999999999999998877654
No 312
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=54.73 E-value=24 Score=25.85 Aligned_cols=24 Identities=25% Similarity=0.185 Sum_probs=21.5
Q ss_pred cchhhhhhccccchhhHHHHHHHH
Q 036324 62 VKSRTIHSRFLRSRETISRYFNLV 85 (91)
Q Consensus 62 ~~~r~i~~~F~~S~eTisr~f~~V 85 (91)
.+..++++.|+.|.+||.|.+++.
T Consensus 20 ~~~~ela~~l~vS~~TirRdL~~L 43 (251)
T PRK13509 20 VTVEKVIERLGISPATARRDINKL 43 (251)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHHH
Confidence 677889999999999999998874
No 313
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=54.63 E-value=32 Score=22.71 Aligned_cols=42 Identities=5% Similarity=0.148 Sum_probs=30.1
Q ss_pred CccHHHHHHHH-HHHhhcCcchhhhhhccccchhhHHHHHHHHH
Q 036324 44 TVSIEEQLCMF-LHILAHHVKSRTIHSRFLRSRETISRYFNLVL 86 (91)
Q Consensus 44 ~v~veE~vamF-L~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl 86 (91)
+++..+-..++ |+ -..+.+...+++.++.+++||+|.+...-
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 24568999999999999999999887643
No 314
>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=54.51 E-value=15 Score=25.86 Aligned_cols=31 Identities=16% Similarity=0.125 Sum_probs=26.8
Q ss_pred HHHhhcCcchhhhhhccccchhhHHHHHHHH
Q 036324 55 LHILAHHVKSRTIHSRFLRSRETISRYFNLV 85 (91)
Q Consensus 55 L~i~~~~~~~r~i~~~F~~S~eTisr~f~~V 85 (91)
+..++...++..+++.-+.|++|||+.+++.
T Consensus 5 f~~v~~~gs~~~AA~~L~isqsavS~~i~~L 35 (279)
T TIGR03339 5 FHAVARCGSFTRAAERLGLSQPTVTDQVRKL 35 (279)
T ss_pred hHHHHhcCCHHHHHHHhcCCchHHHHHHHHH
Confidence 4566677899999999999999999999875
No 315
>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=54.39 E-value=13 Score=23.85 Aligned_cols=28 Identities=14% Similarity=0.018 Sum_probs=24.0
Q ss_pred HHhhcCcchhhhhhccccchhhHHHHHH
Q 036324 56 HILAHHVKSRTIHSRFLRSRETISRYFN 83 (91)
Q Consensus 56 ~i~~~~~~~r~i~~~F~~S~eTisr~f~ 83 (91)
+.-..|.+.+.++..+|.|..||+++-+
T Consensus 73 ~r~~~gltq~~lA~~lg~~~~tis~~e~ 100 (127)
T TIGR03830 73 IRKKLGLSQREAAELLGGGVNAFSRYER 100 (127)
T ss_pred HHHHcCCCHHHHHHHhCCCHHHHHHHHC
Confidence 3556789999999999999999999754
No 316
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=54.35 E-value=33 Score=21.36 Aligned_cols=23 Identities=17% Similarity=0.153 Sum_probs=14.5
Q ss_pred chhhhhhccccchhhHHHHHHHH
Q 036324 63 KSRTIHSRFLRSRETISRYFNLV 85 (91)
Q Consensus 63 ~~r~i~~~F~~S~eTisr~f~~V 85 (91)
+-.+++..++.|..+++|.|.+.
T Consensus 23 ~~~~lA~~~~~S~~~l~r~f~~~ 45 (107)
T PRK10219 23 NIDVVAKKSGYSKWYLQRMFRTV 45 (107)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHH
Confidence 33445666667777777777665
No 317
>PRK09508 leuO leucine transcriptional activator; Reviewed
Probab=54.07 E-value=17 Score=26.67 Aligned_cols=40 Identities=13% Similarity=0.102 Sum_probs=30.5
Q ss_pred ccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHH
Q 036324 45 VSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVL 86 (91)
Q Consensus 45 v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl 86 (91)
++. ++|-.|+ .++...++..+++..+.|++|||+.+.+.=
T Consensus 22 ~~l-~~L~~f~-avae~gs~s~AA~~L~isQpavS~~I~~LE 61 (314)
T PRK09508 22 VDL-NLLTVFD-AVMQEQNITRAAHNLGMSQPAVSNAVARLK 61 (314)
T ss_pred cCh-HHHHHHH-HHHhcCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 443 3465555 556667799999999999999999998753
No 318
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=53.83 E-value=35 Score=26.25 Aligned_cols=45 Identities=22% Similarity=0.208 Sum_probs=34.6
Q ss_pred ccHHHHHHHHHHH-h--hcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 45 VSIEEQLCMFLHI-L--AHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 45 v~veE~vamFL~i-~--~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
.+--|+.-+-++. + +.+.+...|+..||.|.+.|+++=...++-+
T Consensus 263 L~eREr~Vl~~rygl~~~~~~Tl~eIa~~lgvS~eRVrQIe~~Al~KL 310 (324)
T PRK07921 263 LDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKL 310 (324)
T ss_pred CCHHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 4555666666654 3 4568999999999999999999888777654
No 319
>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=53.77 E-value=25 Score=19.66 Aligned_cols=27 Identities=11% Similarity=0.032 Sum_probs=20.4
Q ss_pred cCcchhhhhhccc-cchhhHHHHHHHHH
Q 036324 60 HHVKSRTIHSRFL-RSRETISRYFNLVL 86 (91)
Q Consensus 60 ~~~~~r~i~~~F~-~S~eTisr~f~~Vl 86 (91)
+|..-..|+..|+ ||...+...+...|
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 4557899999999 99999988887744
No 320
>PRK15243 transcriptional regulator SpvR; Provisional
Probab=53.73 E-value=24 Score=26.49 Aligned_cols=39 Identities=18% Similarity=0.255 Sum_probs=31.2
Q ss_pred HHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHH
Q 036324 47 IEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVL 86 (91)
Q Consensus 47 veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl 86 (91)
+..|+-.|+-+.-+ .+++.+++.-+.|++|||+.+++.=
T Consensus 5 ~~rqL~~F~aVae~-gSfs~AA~~L~isQpavS~~Ik~LE 43 (297)
T PRK15243 5 INKKLKIFITLMET-GSFSIATSVLYITRTPLSRVISDLE 43 (297)
T ss_pred cHHHHHHHHHHHHc-CCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 45677777655554 6899999999999999999998753
No 321
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=53.59 E-value=29 Score=24.02 Aligned_cols=27 Identities=19% Similarity=0.159 Sum_probs=24.2
Q ss_pred hcCcchhhhhhccccchhhHHHHHHHH
Q 036324 59 AHHVKSRTIHSRFLRSRETISRYFNLV 85 (91)
Q Consensus 59 ~~~~~~r~i~~~F~~S~eTisr~f~~V 85 (91)
-+|.++..|+...|.|..||.|..+..
T Consensus 149 ~~Gls~~EIA~~lgiS~~tV~r~l~~a 175 (185)
T PF07638_consen 149 FEGLSVEEIAERLGISERTVRRRLRRA 175 (185)
T ss_pred HCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 378899999999999999999988765
No 322
>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=53.34 E-value=28 Score=24.21 Aligned_cols=26 Identities=8% Similarity=-0.069 Sum_probs=22.3
Q ss_pred cCcchhhhhhccccc-hhhHHHHHHHH
Q 036324 60 HHVKSRTIHSRFLRS-RETISRYFNLV 85 (91)
Q Consensus 60 ~~~~~r~i~~~F~~S-~eTisr~f~~V 85 (91)
...+.+.++..++.| .+||+++....
T Consensus 24 ~~~~~~ela~~~~~~s~~tv~~~l~~L 50 (199)
T TIGR00498 24 YPPSIREIARAVGLRSPSAAEEHLKAL 50 (199)
T ss_pred CCCcHHHHHHHhCCCChHHHHHHHHHH
Confidence 347899999999998 99999988754
No 323
>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=53.18 E-value=17 Score=24.88 Aligned_cols=37 Identities=5% Similarity=-0.101 Sum_probs=30.4
Q ss_pred HHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 53 MFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 53 mFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
+|+..--.|.++..|+...|.|..||....+.....+
T Consensus 139 i~~L~~~~g~s~~EIA~~lgis~~tVk~~l~Rar~~L 175 (193)
T TIGR02947 139 AVYLADVEGFAYKEIAEIMGTPIGTVMSRLHRGRKQL 175 (193)
T ss_pred heeehhhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 4444556789999999999999999999988776654
No 324
>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=53.07 E-value=8.6 Score=27.98 Aligned_cols=22 Identities=23% Similarity=0.028 Sum_probs=19.0
Q ss_pred chhhhhhccccchhhHHHHHHH
Q 036324 63 KSRTIHSRFLRSRETISRYFNL 84 (91)
Q Consensus 63 ~~r~i~~~F~~S~eTisr~f~~ 84 (91)
+-++|+..=|.|..||||.++.
T Consensus 3 ti~dIA~~agvS~~TVSrvLn~ 24 (329)
T TIGR01481 3 TIYDVAREAGVSMATVSRVVNG 24 (329)
T ss_pred cHHHHHHHhCCCHHHHHHHhCC
Confidence 5678999999999999999863
No 325
>PRK10086 DNA-binding transcriptional regulator DsdC; Provisional
Probab=53.02 E-value=17 Score=26.69 Aligned_cols=36 Identities=17% Similarity=0.192 Sum_probs=29.0
Q ss_pred HHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHH
Q 036324 50 QLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVL 86 (91)
Q Consensus 50 ~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl 86 (91)
++-.| ..++...+++.++..-+.|++|||+.+++.=
T Consensus 18 ~L~~f-~~va~~gs~s~AA~~L~iSQpavS~~I~~LE 53 (311)
T PRK10086 18 KLHTF-EVAARHQSFALAADELSLTPSAVSHRINQLE 53 (311)
T ss_pred HHHHH-HHHHHcCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 44444 4666778999999999999999999998753
No 326
>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=52.96 E-value=16 Score=23.31 Aligned_cols=33 Identities=21% Similarity=0.160 Sum_probs=23.9
Q ss_pred HHHhhcCcchhhhhhccc-cchhhHHHHHHHHHH
Q 036324 55 LHILAHHVKSRTIHSRFL-RSRETISRYFNLVLN 87 (91)
Q Consensus 55 L~i~~~~~~~r~i~~~F~-~S~eTisr~f~~Vl~ 87 (91)
|+--|.+.+.+.|....| -|..||++++++.-.
T Consensus 13 L~~~G~~pT~~~Vr~~lG~GS~~ti~~~l~~w~~ 46 (120)
T PF11740_consen 13 LLAAGKKPTVRAVRERLGGGSMSTISKHLKEWRE 46 (120)
T ss_pred HHHcCCCCCHHHHHHHHCCCCHHHHHHHHHHHHH
Confidence 344444557777777788 889999999987643
No 327
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=52.79 E-value=39 Score=23.29 Aligned_cols=37 Identities=11% Similarity=0.033 Sum_probs=30.5
Q ss_pred HHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 53 MFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 53 mFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
+|......|.++..|+...|.|..||....+.....+
T Consensus 136 v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Rar~~L 172 (188)
T PRK12517 136 PLLLQVIGGFSGEEIAEILDLNKNTVMTRLFRARNQL 172 (188)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 4555667799999999999999999998887766554
No 328
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=52.70 E-value=30 Score=25.26 Aligned_cols=44 Identities=9% Similarity=0.052 Sum_probs=32.9
Q ss_pred ccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 45 VSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 45 v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
.+..++.++.| .-..+.++++|+...|.|..||....+.....+
T Consensus 117 Lp~~~R~v~lL-~~~eg~S~~EIAe~LgiS~~tVksrL~Rark~L 160 (228)
T PRK06704 117 LNVQQSAILLL-KDVFQYSIADIAKVCSVSEGAVKASLFRSRNRL 160 (228)
T ss_pred CCHHHhhHhhh-HHhhCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 34444554444 445689999999999999999999887766654
No 329
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=52.54 E-value=52 Score=23.56 Aligned_cols=44 Identities=23% Similarity=0.376 Sum_probs=31.5
Q ss_pred HHHHHHHHHh---CCCCCCCCCccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHH
Q 036324 26 FELLCGLLRI---NGGLKADGTVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLV 85 (91)
Q Consensus 26 F~~L~~~L~~---~~~l~~s~~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~V 85 (91)
...+.+.|+. .+.+++...++.|..| +..|+.|+.||-+-+.+.
T Consensus 7 y~qi~~~L~~~I~~g~~~~G~~LPsE~eL----------------~~~~~VSR~TvR~Al~~L 53 (240)
T PRK09764 7 YRQIADRIREQIARGELKPGDALPTESAL----------------QTEFGVSRVTVRQALRQL 53 (240)
T ss_pred HHHHHHHHHHHHHcCCCCCCCcCCCHHHH----------------HHHHCCCHHHHHHHHHHH
Confidence 3445555544 3667777788888765 679999999998877654
No 330
>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=52.42 E-value=25 Score=20.94 Aligned_cols=35 Identities=14% Similarity=0.272 Sum_probs=26.1
Q ss_pred cHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHH
Q 036324 46 SIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRY 81 (91)
Q Consensus 46 ~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~ 81 (91)
.-+++--||+- .+.+..+++|++..+.|..||++.
T Consensus 8 ~rdkA~e~y~~-~~g~i~lkdIA~~Lgvs~~tIr~W 42 (60)
T PF10668_consen 8 NRDKAFEIYKE-SNGKIKLKDIAEKLGVSESTIRKW 42 (60)
T ss_pred CHHHHHHHHHH-hCCCccHHHHHHHHCCCHHHHHHH
Confidence 34555556543 344689999999999999999864
No 331
>PRK09986 DNA-binding transcriptional activator XapR; Provisional
Probab=52.36 E-value=24 Score=25.20 Aligned_cols=38 Identities=16% Similarity=0.117 Sum_probs=31.1
Q ss_pred HHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHH
Q 036324 49 EQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLN 87 (91)
Q Consensus 49 E~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ 87 (91)
+++-.|+-++-++ +...++...+.|++|||+.+++.=+
T Consensus 10 ~~l~~f~~v~~~g-s~t~AA~~L~itq~avS~~i~~LE~ 47 (294)
T PRK09986 10 KLLRYFLAVAEEL-HFGRAAARLNISQPPLSIHIKELED 47 (294)
T ss_pred HHHHHHHHHHHhc-CHHHHHHHhCCCCCHHHHHHHHHHH
Confidence 5777777666664 9999999999999999999987533
No 332
>PHA01976 helix-turn-helix protein
Probab=52.34 E-value=16 Score=20.77 Aligned_cols=27 Identities=11% Similarity=-0.061 Sum_probs=22.2
Q ss_pred HhhcCcchhhhhhccccchhhHHHHHH
Q 036324 57 ILAHHVKSRTIHSRFLRSRETISRYFN 83 (91)
Q Consensus 57 i~~~~~~~r~i~~~F~~S~eTisr~f~ 83 (91)
.-..|.+..+++..-+.|.+||+++-+
T Consensus 11 R~~~glt~~~lA~~~gvs~~~v~~~e~ 37 (67)
T PHA01976 11 RNARAWSAPELSRRAGVRHSLIYDFEA 37 (67)
T ss_pred HHHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 456778888999999999999998753
No 333
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=51.86 E-value=13 Score=20.97 Aligned_cols=28 Identities=21% Similarity=0.265 Sum_probs=18.9
Q ss_pred HhhcCcchhhhhhccccchhhHHHHHHH
Q 036324 57 ILAHHVKSRTIHSRFLRSRETISRYFNL 84 (91)
Q Consensus 57 i~~~~~~~r~i~~~F~~S~eTisr~f~~ 84 (91)
+--+|.+...++..=|.|..|++++++.
T Consensus 6 m~~~~it~~~La~~~gis~~tl~~~~~~ 33 (63)
T PF13443_consen 6 MAERGITQKDLARKTGISRSTLSRILNG 33 (63)
T ss_dssp HHHTT--HHHHHHHHT--HHHHHHHHTT
T ss_pred HHHcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 3456778888888899999999998763
No 334
>PRK10216 DNA-binding transcriptional regulator YidZ; Provisional
Probab=51.70 E-value=26 Score=25.67 Aligned_cols=38 Identities=11% Similarity=0.068 Sum_probs=29.6
Q ss_pred HHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHH
Q 036324 49 EQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLN 87 (91)
Q Consensus 49 E~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ 87 (91)
+++-.|+- ++...+.+.+++..+.|+++||+.+.+.=+
T Consensus 11 ~~L~~f~a-v~e~gs~t~AA~~L~iSQpavS~~I~~LE~ 48 (319)
T PRK10216 11 NLLLCLQL-LMQERSVTKAAKRMNVTPSAVSKSLAKLRA 48 (319)
T ss_pred HHHHHHHH-HHHhCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 45656654 455559999999999999999999987533
No 335
>TIGR02607 antidote_HigA addiction module antidote protein, HigA family. Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by Pfam model pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair.
Probab=51.57 E-value=35 Score=19.82 Aligned_cols=38 Identities=24% Similarity=0.142 Sum_probs=27.3
Q ss_pred ccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHH
Q 036324 45 VSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFN 83 (91)
Q Consensus 45 v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~ 83 (91)
.++.|.+... ++-.+|.+...++..-|.|..||+++.+
T Consensus 3 ~~~g~~i~~~-~~~~~~~t~~~lA~~~gis~~tis~~~~ 40 (78)
T TIGR02607 3 AHPGEILREE-FLEPLGLSIRALAKALGVSRSTLSRIVN 40 (78)
T ss_pred CCHHHHHHHH-HHHHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 3445554421 2566778889999999999999998764
No 336
>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=51.20 E-value=60 Score=22.97 Aligned_cols=33 Identities=21% Similarity=0.294 Sum_probs=26.4
Q ss_pred CCCCCCCCccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHH
Q 036324 37 GGLKADGTVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLV 85 (91)
Q Consensus 37 ~~l~~s~~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~V 85 (91)
+.+++...++.|.+| +..|+.|+.||-+-+...
T Consensus 17 g~~~~g~~LPsE~eL----------------a~~~~VSR~TVR~Al~~L 49 (230)
T TIGR02018 17 GEWPPGHRIPSEHEL----------------VAQYGCSRMTVNRALREL 49 (230)
T ss_pred CCCCCCCcCcCHHHH----------------HHHHCCCHHHHHHHHHHH
Confidence 667777778888776 479999999998877654
No 337
>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=50.91 E-value=15 Score=21.50 Aligned_cols=23 Identities=26% Similarity=0.355 Sum_probs=14.5
Q ss_pred cchhhhhhcc-----ccchhhHHHHHHH
Q 036324 62 VKSRTIHSRF-----LRSRETISRYFNL 84 (91)
Q Consensus 62 ~~~r~i~~~F-----~~S~eTisr~f~~ 84 (91)
.+.++|+..+ ..|..||.|.+++
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 4566666655 7888999998876
No 338
>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=50.81 E-value=49 Score=20.93 Aligned_cols=42 Identities=19% Similarity=0.255 Sum_probs=32.5
Q ss_pred HHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 47 IEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 47 veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
.+++..+.++-+ .+.+..+|.+..+-|..|++|.=++-+..+
T Consensus 58 ~~~r~iL~~~Yi-~~~~~~~I~~~l~~S~~t~yr~~~~Al~~L 99 (100)
T PF07374_consen 58 PDERLILRMRYI-NKLTWEQIAEELNISRRTYYRIHKKALKEL 99 (100)
T ss_pred hhHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHhc
Confidence 556655555555 578889999999999999999988777653
No 339
>PRK10341 DNA-binding transcriptional activator TdcA; Provisional
Probab=50.77 E-value=19 Score=26.32 Aligned_cols=39 Identities=10% Similarity=0.139 Sum_probs=30.5
Q ss_pred HHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHH
Q 036324 48 EEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLN 87 (91)
Q Consensus 48 eE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ 87 (91)
-+++-.|+ .++...+.+.+++..+.|++|||+.+++.=+
T Consensus 9 ~~~L~~F~-av~e~gs~s~AA~~L~iSQpavS~~I~~LE~ 47 (312)
T PRK10341 9 TQHLVVFQ-EVIRSGSIGSAAKELGLTQPAVSKIINDIED 47 (312)
T ss_pred HHHHHHHH-HHHHcCCHHHHHHHhCCChHHHHHHHHHHHH
Confidence 34555555 5566789999999999999999999987543
No 340
>COG0184 RpsO Ribosomal protein S15P/S13E [Translation, ribosomal structure and biogenesis]
Probab=50.48 E-value=15 Score=23.55 Aligned_cols=26 Identities=31% Similarity=0.178 Sum_probs=22.2
Q ss_pred HHHHhCCCCCCCCCccHHHHHHHHHH
Q 036324 31 GLLRINGGLKADGTVSIEEQLCMFLH 56 (91)
Q Consensus 31 ~~L~~~~~l~~s~~v~veE~vamFL~ 56 (91)
..|+..|+.......|.|||||+-..
T Consensus 9 ~~l~~eyg~~~~dtgs~evq~a~Lt~ 34 (89)
T COG0184 9 QELRDEYGIPEVDTGSGEVQLALLTE 34 (89)
T ss_pred HHHHHHhCCCCCCCCCcHHHHHHHHH
Confidence 46788899999999999999998654
No 341
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=50.29 E-value=12 Score=27.20 Aligned_cols=51 Identities=12% Similarity=0.194 Sum_probs=41.5
Q ss_pred HHHHHhCCCHHHHHHHHHHHHhCCCCCCCCCccHHHHHHHHHHHhhcCcchhhhhhcccc
Q 036324 14 ECVNQLRMDKRTFELLCGLLRINGGLKADGTVSIEEQLCMFLHILAHHVKSRTIHSRFLR 73 (91)
Q Consensus 14 ~c~~~fRM~~~~F~~L~~~L~~~~~l~~s~~v~veE~vamFL~i~~~~~~~r~i~~~F~~ 73 (91)
......||+.+.+..|=..+.....|.+-+.+.+-.+| |++.|+|+.+||-
T Consensus 50 ~~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~L---------gL~pRQVavWFQN 100 (198)
T KOG0483|consen 50 GKGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKEL---------GLQPRQVAVWFQN 100 (198)
T ss_pred cccccccccHHHHHHhHHhhccccccChHHHHHHHHhh---------CCChhHHHHHHhh
Confidence 56778999999999999999888878777755444444 7899999999983
No 342
>PRK11062 nhaR transcriptional activator NhaR; Provisional
Probab=50.26 E-value=20 Score=26.03 Aligned_cols=36 Identities=11% Similarity=0.152 Sum_probs=29.5
Q ss_pred HHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHH
Q 036324 49 EQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLV 85 (91)
Q Consensus 49 E~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~V 85 (91)
+++-.|+. ++...+++.++...+.|++||||.++..
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 5567799999999999999999998864
No 343
>COG4974 XerD Site-specific recombinase XerD [DNA replication, recombination, and repair]
Probab=50.01 E-value=99 Score=24.07 Aligned_cols=59 Identities=12% Similarity=0.104 Sum_probs=45.9
Q ss_pred CCCHHHHHHHHHHHHhCCCCCCCCCccHH-HHHHHHHHHhhcCcchhhhhhccccch-hhHHH
Q 036324 20 RMDKRTFELLCGLLRINGGLKADGTVSIE-EQLCMFLHILAHHVKSRTIHSRFLRSR-ETISR 80 (91)
Q Consensus 20 RM~~~~F~~L~~~L~~~~~l~~s~~v~ve-E~vamFL~i~~~~~~~r~i~~~F~~S~-eTisr 80 (91)
+|++..|-++.+....+.++. +.+|.- =+=+.--+.+-+|+.-|+||..-|||- +|...
T Consensus 220 ~ltrq~~w~~lk~~a~~Agi~--~~isPH~LRHsFATHLL~~GADlRvVQeLLGHadisTTQI 280 (300)
T COG4974 220 GLTRQGFWKRLKDYAERAGID--KKISPHTLRHSFATHLLENGADLRVVQELLGHADISTTQI 280 (300)
T ss_pred CCCHHHHHHHHHHHHHHhCCC--CCcCchhhHHHHHHHHHhCCccHHHHHHHhCccccchhHH
Confidence 799999999999999998887 233332 244566788999999999999999975 44433
No 344
>PRK03635 chromosome replication initiation inhibitor protein; Validated
Probab=49.74 E-value=20 Score=25.91 Aligned_cols=35 Identities=9% Similarity=0.100 Sum_probs=27.9
Q ss_pred HHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHH
Q 036324 50 QLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLV 85 (91)
Q Consensus 50 ~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~V 85 (91)
++-.|+ .++...+++.+++..+.|++||||.+++.
T Consensus 6 ~L~~f~-~v~e~gs~s~AA~~L~isq~avS~~I~~L 40 (294)
T PRK03635 6 QLEALA-AVVREGSFERAAQKLHITQSAVSQRIKAL 40 (294)
T ss_pred HHHHHH-HHHHcCCHHHHHHHhCCChHHHHHHHHHH
Confidence 444444 45556699999999999999999999875
No 345
>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=49.49 E-value=33 Score=26.10 Aligned_cols=42 Identities=29% Similarity=0.283 Sum_probs=32.1
Q ss_pred CccHHHHHHH----HHHH--hhcCcchhhhhhcccc-----chhhHHHHHHHH
Q 036324 44 TVSIEEQLCM----FLHI--LAHHVKSRTIHSRFLR-----SRETISRYFNLV 85 (91)
Q Consensus 44 ~v~veE~vam----FL~i--~~~~~~~r~i~~~F~~-----S~eTisr~f~~V 85 (91)
--.+||++|. -||- .|.+.+.+.++.+.+. |++|||+..+-+
T Consensus 113 LsfIE~A~~~~~l~~l~e~~~g~~ltq~ela~~lgk~g~~isrs~Isn~lrll 165 (258)
T TIGR03764 113 LTFIEKALGVQKARALYEKELGESLSQRELARRLSADGYPISQSHISRMGDTV 165 (258)
T ss_pred CCHHHHHHHHHHHHHHHHhhccCCCCHHHHHHHhcccCCCCCHHHHHHHHHHH
Confidence 3568888863 3442 3578999999999988 999999987643
No 346
>PF07453 NUMOD1: NUMOD1 domain; InterPro: IPR010896 This helix-turn-helix-containing DNA-binding domain is found associated in homing nucleases [].
Probab=49.45 E-value=10 Score=19.65 Aligned_cols=20 Identities=30% Similarity=0.232 Sum_probs=17.3
Q ss_pred cchhhhhhccccchhhHHHH
Q 036324 62 VKSRTIHSRFLRSRETISRY 81 (91)
Q Consensus 62 ~~~r~i~~~F~~S~eTisr~ 81 (91)
.|.+.++..++.|..||+++
T Consensus 17 ~Si~eAa~~l~i~~~~I~~~ 36 (37)
T PF07453_consen 17 DSIREAARYLGISHSTISKY 36 (37)
T ss_pred cCHHHHHHHhCCCHHHHHHh
Confidence 46788899999999999986
No 347
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=49.43 E-value=10 Score=27.91 Aligned_cols=21 Identities=24% Similarity=0.139 Sum_probs=18.5
Q ss_pred chhhhhhccccchhhHHHHHH
Q 036324 63 KSRTIHSRFLRSRETISRYFN 83 (91)
Q Consensus 63 ~~r~i~~~F~~S~eTisr~f~ 83 (91)
+-++|+..=|.|..||||.++
T Consensus 3 ti~dIA~~aGVS~~TVSrvLn 23 (343)
T PRK10727 3 TIKDVARLAGVSVATVSRVIN 23 (343)
T ss_pred CHHHHHHHhCCCHHHHHHHhC
Confidence 567889999999999999986
No 348
>COG1508 RpoN DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription]
Probab=49.28 E-value=15 Score=30.00 Aligned_cols=38 Identities=21% Similarity=0.083 Sum_probs=30.8
Q ss_pred cHHHHHHHHHHHhhcCcch--hhhhhccccchhhHHHHHH
Q 036324 46 SIEEQLCMFLHILAHHVKS--RTIHSRFLRSRETISRYFN 83 (91)
Q Consensus 46 ~veE~vamFL~i~~~~~~~--r~i~~~F~~S~eTisr~f~ 83 (91)
=|+.|=+-|.+-.++--.. |+|++..+.+-+||||...
T Consensus 313 Iv~~Q~~Ff~~g~~~l~PL~LrdvA~~i~~HESTISRai~ 352 (444)
T COG1508 313 IVEYQKAFFEGGEEALKPLVLRDVADEIGMHESTISRAIT 352 (444)
T ss_pred HHHHHHHHHhCCcccCCcccHHHHHHHhCccHHHHHHHHh
Confidence 3567778888777776555 9999999999999999865
No 349
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=49.28 E-value=56 Score=23.29 Aligned_cols=45 Identities=20% Similarity=0.220 Sum_probs=33.7
Q ss_pred HHHHHHHHHHh---CCCCCCCCCccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHH
Q 036324 25 TFELLCGLLRI---NGGLKADGTVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLV 85 (91)
Q Consensus 25 ~F~~L~~~L~~---~~~l~~s~~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~V 85 (91)
-+.++.+.|+. .+.+++...++.|..| +..|+.|+.||-+-+.+.
T Consensus 10 ~y~qI~~~i~~~I~~G~~~~g~kLPsE~eL----------------a~~~~VSR~TvR~Al~~L 57 (241)
T PRK11402 10 LYATVRQRLLDDIAQGVYQAGQQIPTENEL----------------CTQYNVSRITIRKAISDL 57 (241)
T ss_pred HHHHHHHHHHHHHHcCCCCCCCcCcCHHHH----------------HHHHCCCHHHHHHHHHHH
Confidence 35566666666 3677888888888776 578999999998877654
No 350
>PF11469 Ribonucleas_3_2: Ribonuclease III; InterPro: IPR021568 This archaeal family of proteins has no known function. ; PDB: 1ZTD_A.
Probab=49.25 E-value=17 Score=24.42 Aligned_cols=42 Identities=24% Similarity=0.453 Sum_probs=30.8
Q ss_pred CccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHHhC
Q 036324 44 TVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAILQ 91 (91)
Q Consensus 44 ~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai~e 91 (91)
.+++||+|-| +..|.+..+. .|.|-+|+|-+.|-++++-|.|
T Consensus 74 ~it~eEavei----l~~nl~~dv~--~fsrkke~ig~Ala~Ll~~i~E 115 (120)
T PF11469_consen 74 KITIEEAVEI----LKANLTEDVL--HFSRKKEAIGKALAELLKVIKE 115 (120)
T ss_dssp SS-HHHHHHH----HHCT--GGGG---TTTHHHHHHHHHHHHHHHHHH
T ss_pred cccHHHHHHH----HHhcCchhhc--chhHHHHHHHHHHHHHHHHHHH
Confidence 6899999876 5677766554 4779999999999999987754
No 351
>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=49.09 E-value=53 Score=21.83 Aligned_cols=32 Identities=16% Similarity=0.113 Sum_probs=26.7
Q ss_pred HhhcCcchhhhhhccccchhhHHHHHHHHHHH
Q 036324 57 ILAHHVKSRTIHSRFLRSRETISRYFNLVLNA 88 (91)
Q Consensus 57 i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~a 88 (91)
...-..|...|++.|++|++.|+-.++.+..-
T Consensus 29 yy~dDlSl~EIAee~~VSRqAIyDnIKr~~~~ 60 (105)
T COG2739 29 YYLDDLSLSEIAEEFNVSRQAIYDNIKRTEKI 60 (105)
T ss_pred HHHhhccHHHHHHHhCccHHHHHHHHHHHHHH
Confidence 34567899999999999999999998876543
No 352
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=48.96 E-value=19 Score=25.18 Aligned_cols=24 Identities=25% Similarity=0.379 Sum_probs=21.8
Q ss_pred CcchhhhhhccccchhhHHHHHHH
Q 036324 61 HVKSRTIHSRFLRSRETISRYFNL 84 (91)
Q Consensus 61 ~~~~r~i~~~F~~S~eTisr~f~~ 84 (91)
|.+++.|+...+.|..||.+|..-
T Consensus 177 g~s~~eIa~~l~iS~~Tv~~~~~~ 200 (225)
T PRK10046 177 QHTAETVAQALTISRTTARRYLEY 200 (225)
T ss_pred CcCHHHHHHHhCccHHHHHHHHHH
Confidence 589999999999999999999753
No 353
>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=48.79 E-value=43 Score=21.72 Aligned_cols=40 Identities=8% Similarity=0.044 Sum_probs=29.1
Q ss_pred HHHHHHHHHHhhcC---cchhhhhhccccchhhHHHHHHHHHH
Q 036324 48 EEQLCMFLHILAHH---VKSRTIHSRFLRSRETISRYFNLVLN 87 (91)
Q Consensus 48 eE~vamFL~i~~~~---~~~r~i~~~F~~S~eTisr~f~~Vl~ 87 (91)
+-.+.+-+|...++ .+...|+..++.|..+|++++...-+
T Consensus 9 ~yal~~l~~la~~~~~~~s~~eia~~l~is~~~v~~~l~~L~~ 51 (130)
T TIGR02944 9 DYATLVLTTLAQNDSQPYSAAEIAEQTGLNAPTVSKILKQLSL 51 (130)
T ss_pred hHHHHHHHHHHhCCCCCccHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 44555555554332 68899999999999999998876544
No 354
>PRK10082 cell density-dependent motility repressor; Provisional
Probab=48.60 E-value=23 Score=25.69 Aligned_cols=41 Identities=17% Similarity=0.092 Sum_probs=30.4
Q ss_pred CCccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHH
Q 036324 43 GTVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLV 85 (91)
Q Consensus 43 ~~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~V 85 (91)
+++++ +++-.|+ .++...++..++...+.|++|||+.+.+.
T Consensus 9 ~~m~~-~~l~~F~-av~e~gS~t~AA~~L~iSQpavS~~I~~L 49 (303)
T PRK10082 9 HNIET-KWLYDFL-TLEKCRNFSQAAVSRNVSQPAFSRRIRAL 49 (303)
T ss_pred cccch-HHHHHHH-HHHhcCCHHHHHHHhCCChHHHHHHHHHH
Confidence 34433 3454555 45566789999999999999999999875
No 355
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=48.50 E-value=42 Score=24.53 Aligned_cols=41 Identities=10% Similarity=0.072 Sum_probs=30.0
Q ss_pred cHHHHHHHHHHHhhcC--cchhhhhhccccchhhHHHHHHHHH
Q 036324 46 SIEEQLCMFLHILAHH--VKSRTIHSRFLRSRETISRYFNLVL 86 (91)
Q Consensus 46 ~veE~vamFL~i~~~~--~~~r~i~~~F~~S~eTisr~f~~Vl 86 (91)
+++..+.+.-..-.++ .+..+|....+.+++|++|..+...
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 4455555544443433 6899999999999999999987654
No 356
>COG5606 Uncharacterized conserved small protein [Function unknown]
Probab=48.48 E-value=8.9 Score=24.86 Aligned_cols=58 Identities=7% Similarity=0.019 Sum_probs=38.0
Q ss_pred HHHHHHHHHHHHhCCCCCCCCCccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHH
Q 036324 23 KRTFELLCGLLRINGGLKADGTVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISR 80 (91)
Q Consensus 23 ~~~F~~L~~~L~~~~~l~~s~~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr 80 (91)
-++|-.+-+....-..-.++-.+-.+=..++-+|+--.+.+++.|..-++.+++-||-
T Consensus 3 ~~vF~s~~~~~~D~~e~a~~m~ir~~l~~~i~~~i~q~~l~Q~qiae~lgV~qprvS~ 60 (91)
T COG5606 3 NEVFTSVWDAIEDTPEAAENMKIRSALMMAIKQWIEQAALSQAQIAELLGVTQPRVSD 60 (91)
T ss_pred CchhhhHHHHHhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCchHHH
Confidence 3456666555544221111112223333467889999999999999999999999874
No 357
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=48.46 E-value=15 Score=23.00 Aligned_cols=26 Identities=15% Similarity=0.112 Sum_probs=21.2
Q ss_pred HhhcCcchhhhhhcccc------chhhHHHHH
Q 036324 57 ILAHHVKSRTIHSRFLR------SRETISRYF 82 (91)
Q Consensus 57 i~~~~~~~r~i~~~F~~------S~eTisr~f 82 (91)
...-|.++.+++...+. |+.||||.-
T Consensus 20 R~~lGLTQ~dvA~~lg~~~g~i~SQstISR~E 51 (75)
T smart00352 20 RIKLGFTQADVGLALGALYGPDFSQTTICRFE 51 (75)
T ss_pred HHHcCCCHHHHHHHhcccccCcCCHHHHHHHH
Confidence 34567888999999995 999999964
No 358
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=48.44 E-value=36 Score=25.06 Aligned_cols=24 Identities=29% Similarity=0.343 Sum_probs=20.3
Q ss_pred cchhhhhhccccchhhHHHHHHHH
Q 036324 62 VKSRTIHSRFLRSRETISRYFNLV 85 (91)
Q Consensus 62 ~~~r~i~~~F~~S~eTisr~f~~V 85 (91)
.+..++++.|+.|.+||.|...+.
T Consensus 20 ~~~~ela~~l~vS~~TiRRdL~~L 43 (252)
T PRK10906 20 VSTEELVEHFSVSPQTIRRDLNDL 43 (252)
T ss_pred EeHHHHHHHhCCCHHHHHHHHHHH
Confidence 566778899999999999987664
No 359
>COG2973 TrpR Trp operon repressor [Transcription]
Probab=47.67 E-value=30 Score=22.89 Aligned_cols=25 Identities=28% Similarity=0.296 Sum_probs=22.3
Q ss_pred HhhcCcchhhhhhccccchhhHHHH
Q 036324 57 ILAHHVKSRTIHSRFLRSRETISRY 81 (91)
Q Consensus 57 i~~~~~~~r~i~~~F~~S~eTisr~ 81 (91)
-+-.+.+.|.|+...|.|..||.|-
T Consensus 56 LL~ge~sQREi~~~LgvsiAtITRG 80 (103)
T COG2973 56 LLRGELSQREIAQKLGVSIATITRG 80 (103)
T ss_pred HHhccccHHHHHHHhCcchhhhccc
Confidence 3668999999999999999999874
No 360
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=47.56 E-value=17 Score=22.04 Aligned_cols=28 Identities=18% Similarity=0.103 Sum_probs=21.1
Q ss_pred HHhhcCcchhhhhhccccchhhHHHHHH
Q 036324 56 HILAHHVKSRTIHSRFLRSRETISRYFN 83 (91)
Q Consensus 56 ~i~~~~~~~r~i~~~F~~S~eTisr~f~ 83 (91)
.+-..+.++++++...|.|+++||+.-+
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 4456789999999999999999999753
No 361
>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=46.77 E-value=66 Score=22.62 Aligned_cols=44 Identities=25% Similarity=0.357 Sum_probs=31.7
Q ss_pred HHHHHHHHHh---CCCCCCCCCccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHH
Q 036324 26 FELLCGLLRI---NGGLKADGTVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLV 85 (91)
Q Consensus 26 F~~L~~~L~~---~~~l~~s~~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~V 85 (91)
+..+.+.|+. .+.+++...++.|..| +..|+.|+.||-+-+.+.
T Consensus 10 y~~i~~~l~~~I~~g~~~~G~~LPsE~eL----------------a~~~~VSR~TvR~Al~~L 56 (238)
T TIGR02325 10 WRQIADKIEQEIAAGHLRAGDYLPAEMQL----------------AERFGVNRHTVRRAIAAL 56 (238)
T ss_pred HHHHHHHHHHHHHcCCCCCCCcCcCHHHH----------------HHHHCCCHHHHHHHHHHH
Confidence 4555555555 2566777778888775 579999999998877654
No 362
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=46.53 E-value=26 Score=25.23 Aligned_cols=36 Identities=8% Similarity=0.004 Sum_probs=28.4
Q ss_pred HHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHH
Q 036324 50 QLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVL 86 (91)
Q Consensus 50 ~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl 86 (91)
++-.| +.++...++..++..-+.|++|||+.+.+.=
T Consensus 5 ~l~~f-~~v~~~gs~s~AA~~L~isqpavS~~I~~LE 40 (275)
T PRK03601 5 LLKTF-LEVSRTRHFGRAAESLYLTQSAVSFRIRQLE 40 (275)
T ss_pred HHHHH-HHHHHcCCHHHHHHHhCCChHHHHHHHHHHH
Confidence 34444 4566677999999999999999999998753
No 363
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=46.42 E-value=22 Score=18.96 Aligned_cols=25 Identities=16% Similarity=-0.012 Sum_probs=19.0
Q ss_pred cCcchhhhhhccccchhhHHHHHHH
Q 036324 60 HHVKSRTIHSRFLRSRETISRYFNL 84 (91)
Q Consensus 60 ~~~~~r~i~~~F~~S~eTisr~f~~ 84 (91)
++.....++...|.|+.|++++..+
T Consensus 17 ~~gn~~~aA~~Lgisr~tL~~klkk 41 (42)
T PF02954_consen 17 CGGNVSKAARLLGISRRTLYRKLKK 41 (42)
T ss_dssp TTT-HHHHHHHHTS-HHHHHHHHHH
T ss_pred hCCCHHHHHHHHCCCHHHHHHHHHh
Confidence 4456678999999999999998764
No 364
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=46.22 E-value=37 Score=24.32 Aligned_cols=42 Identities=21% Similarity=0.192 Sum_probs=30.4
Q ss_pred HHHHHHHHHHHhCCCCCCCCCccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHH
Q 036324 24 RTFELLCGLLRINGGLKADGTVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYF 82 (91)
Q Consensus 24 ~~F~~L~~~L~~~~~l~~s~~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f 82 (91)
.++..|.+.+.. +.+++...++.|..| +..||.|+.||---+
T Consensus 14 ~v~~~l~~~I~~-g~l~pG~~LpsE~eL----------------a~~lgVSRtpVREAL 55 (254)
T PRK09464 14 VIEQQLEFLILE-GTLRPGEKLPPEREL----------------AKQFDVSRPSLREAI 55 (254)
T ss_pred HHHHHHHHHHHc-CCCCCCCcCCCHHHH----------------HHHhCCCHHHHHHHH
Confidence 566677777765 667887777777654 678999999985443
No 365
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=45.95 E-value=40 Score=25.24 Aligned_cols=37 Identities=3% Similarity=-0.044 Sum_probs=30.8
Q ss_pred HHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 53 MFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 53 mFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
+|+..--.+.++..|+..++.|..||....+...+.+
T Consensus 161 v~~L~~~~g~s~~EIA~~lgis~~tVk~~l~RAr~~L 197 (339)
T PRK08241 161 VLILRDVLGWSAAEVAELLDTSVAAVNSALQRARATL 197 (339)
T ss_pred hhhhHHhhCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 4444556789999999999999999999988877655
No 366
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=45.56 E-value=26 Score=23.97 Aligned_cols=37 Identities=19% Similarity=0.129 Sum_probs=27.7
Q ss_pred HHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHH
Q 036324 47 IEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFN 83 (91)
Q Consensus 47 veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~ 83 (91)
++-.+.+|.=.=-++.+.++|...=|.|+.|+++||.
T Consensus 17 l~aa~~lf~~~G~~~~ti~~Ia~~agvsk~t~Y~~F~ 53 (213)
T PRK09975 17 IETAIAQFALRGVSNTTLNDIADAANVTRGAIYWHFE 53 (213)
T ss_pred HHHHHHHHHHcCcccCCHHHHHHHcCCCHHHHHHHcC
Confidence 4444555543333578999999999999999999994
No 367
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=45.47 E-value=55 Score=20.24 Aligned_cols=27 Identities=7% Similarity=0.043 Sum_probs=23.7
Q ss_pred CcchhhhhhccccchhhHHHHHHHHHH
Q 036324 61 HVKSRTIHSRFLRSRETISRYFNLVLN 87 (91)
Q Consensus 61 ~~~~r~i~~~F~~S~eTisr~f~~Vl~ 87 (91)
..++..++..++.|.+||++.+....+
T Consensus 17 ~~~~~~la~~l~~s~~tv~~~l~~L~~ 43 (108)
T smart00344 17 RISLAELAKKVGLSPSTVHNRVKRLEE 43 (108)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 478999999999999999999887644
No 368
>PRK14997 LysR family transcriptional regulator; Provisional
Probab=45.41 E-value=27 Score=25.16 Aligned_cols=36 Identities=8% Similarity=0.088 Sum_probs=28.7
Q ss_pred HHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHH
Q 036324 50 QLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVL 86 (91)
Q Consensus 50 ~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl 86 (91)
+|-+|+ .++...++..++..-+.|++|||+.+++.=
T Consensus 6 ~L~~f~-~va~~gs~s~AA~~L~isQpavS~~I~~LE 41 (301)
T PRK14997 6 DFAWFV-HVVEEGGFAAAGRALDEPKSKLSRRIAQLE 41 (301)
T ss_pred HHHHHH-HHHHcCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 555555 455567899999999999999999998753
No 369
>PRK03341 arginine repressor; Provisional
Probab=45.41 E-value=52 Score=23.26 Aligned_cols=15 Identities=20% Similarity=0.264 Sum_probs=12.9
Q ss_pred cccchhhHHHHHHHH
Q 036324 71 FLRSRETISRYFNLV 85 (91)
Q Consensus 71 F~~S~eTisr~f~~V 85 (91)
|+.|+.||||-+++.
T Consensus 44 i~vTQaTiSRDl~eL 58 (168)
T PRK03341 44 IEVTQATLSRDLDEL 58 (168)
T ss_pred CcccHHHHHHHHHHh
Confidence 489999999998874
No 370
>PRK11482 putative DNA-binding transcriptional regulator; Provisional
Probab=45.38 E-value=26 Score=25.92 Aligned_cols=40 Identities=13% Similarity=0.077 Sum_probs=30.3
Q ss_pred CccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHH
Q 036324 44 TVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLV 85 (91)
Q Consensus 44 ~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~V 85 (91)
++. -.++-.|+ .++...++..++.+-+.|++||||.+++.
T Consensus 28 ~m~-l~~L~~f~-av~e~gs~s~AA~~L~isQpavS~~I~~L 67 (317)
T PRK11482 28 NID-LNLLTIFE-AVYVHKGIVNAAKILNLTPSAISQSIQKL 67 (317)
T ss_pred ccc-hhHHHHHH-HHHHcCCHHHHHHHhCCChHHHHHHHHHH
Confidence 344 34455555 55556699999999999999999999875
No 371
>COG3179 Predicted chitinase [General function prediction only]
Probab=45.09 E-value=35 Score=25.12 Aligned_cols=70 Identities=11% Similarity=0.165 Sum_probs=50.9
Q ss_pred ChhHHHHHhCCCHHHHHHHHHHHHhCCCCCCCCCccHHHHHHHHHHHhhcCcc-hhhhhhccccchhhHHHHHH
Q 036324 11 SDIECVNQLRMDKRTFELLCGLLRINGGLKADGTVSIEEQLCMFLHILAHHVK-SRTIHSRFLRSRETISRYFN 83 (91)
Q Consensus 11 ~~~~c~~~fRM~~~~F~~L~~~L~~~~~l~~s~~v~veE~vamFL~i~~~~~~-~r~i~~~F~~S~eTisr~f~ 83 (91)
+..+...+++..+..|-...-.|.+ --+...|+--.++||||=-++|-.. ++.+.+.|--|-++.++.|-
T Consensus 5 ~e~~~~ki~p~a~k~~~~v~~al~~---~l~~~gi~~p~r~AmFlAQ~~HESggf~rl~EnlnYSaq~L~~tf~ 75 (206)
T COG3179 5 TEVDLRKIFPKARKEFVDVIVALQP---ALDEAGITTPLRQAMFLAQVMHESGGFTRLDENLNYSAQGLLQTFP 75 (206)
T ss_pred hHHHHHHhcchhhhhhHHHHHHHHH---HHHHhcCCCHHHHHHHHHHHhhhcCCceeehhhcchHHHHHHHhcc
Confidence 3445566677666665555544544 2234567778999999999999977 88999999989888887764
No 372
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=44.61 E-value=53 Score=27.14 Aligned_cols=45 Identities=18% Similarity=0.152 Sum_probs=35.0
Q ss_pred ccHHHHHHHHHHH-h--hcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 45 VSIEEQLCMFLHI-L--AHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 45 v~veE~vamFL~i-~--~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
.+--|+.-+-++. + +.+.+...|+..||.|.+.|+++-...|.-+
T Consensus 448 L~eREr~VI~lRyGL~~~e~~TL~EIa~~lGVSrERVRQIe~kAL~KL 495 (509)
T PRK05901 448 LSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESKTLRKL 495 (509)
T ss_pred CCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 4555666666654 3 5689999999999999999999888777644
No 373
>PRK13870 transcriptional regulator TraR; Provisional
Probab=44.55 E-value=35 Score=24.80 Aligned_cols=44 Identities=9% Similarity=0.010 Sum_probs=36.0
Q ss_pred CccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 44 TVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 44 ~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
..|.-|.= -|.-+|.|-++.+|+..-+.|-.||.-|++.+.+.+
T Consensus 173 ~LT~RE~E--~L~W~A~GKT~~EIa~ILgISe~TV~~Hl~na~~KL 216 (234)
T PRK13870 173 WLDPKEAT--YLRWIAVGKTMEEIADVEGVKYNSVRVKLREAMKRF 216 (234)
T ss_pred CCCHHHHH--HHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHc
Confidence 45655554 355688999999999999999999999999887754
No 374
>PF12728 HTH_17: Helix-turn-helix domain
Probab=44.54 E-value=19 Score=19.56 Aligned_cols=21 Identities=19% Similarity=0.227 Sum_probs=17.3
Q ss_pred chhhhhhccccchhhHHHHHH
Q 036324 63 KSRTIHSRFLRSRETISRYFN 83 (91)
Q Consensus 63 ~~r~i~~~F~~S~eTisr~f~ 83 (91)
+..+++..++.|..||.+..+
T Consensus 3 t~~e~a~~l~is~~tv~~~~~ 23 (51)
T PF12728_consen 3 TVKEAAELLGISRSTVYRWIR 23 (51)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 557888899999999988764
No 375
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=44.51 E-value=55 Score=21.62 Aligned_cols=40 Identities=5% Similarity=0.130 Sum_probs=27.7
Q ss_pred HHHHHHHHHHHhhc--CcchhhhhhccccchhhHHHHHHHHH
Q 036324 47 IEEQLCMFLHILAH--HVKSRTIHSRFLRSRETISRYFNLVL 86 (91)
Q Consensus 47 veE~vamFL~i~~~--~~~~r~i~~~F~~S~eTisr~f~~Vl 86 (91)
.|.-+..+...... ..+...|+..++.|.+||++.+...-
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 34445444444433 35667899999999999999987643
No 376
>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=44.03 E-value=28 Score=27.00 Aligned_cols=33 Identities=18% Similarity=0.205 Sum_probs=29.6
Q ss_pred CCCccHHHHHHHHHHHhhcCcchhhhhhccc-cc
Q 036324 42 DGTVSIEEQLCMFLHILAHHVKSRTIHSRFL-RS 74 (91)
Q Consensus 42 s~~v~veE~vamFL~i~~~~~~~r~i~~~F~-~S 74 (91)
++.+..--|+||+|-.--.+.+...|+..|| |.
T Consensus 371 ~~~~~~~R~~amyl~~~~~~~s~~~ig~~fg~rd 404 (405)
T TIGR00362 371 TRNIVRPRQIAMYLAKELTDLSLPEIGRAFGGRD 404 (405)
T ss_pred CcccchHHHHHHHHHHHHcCCCHHHHHHHhCCCC
Confidence 4578889999999999999999999999997 53
No 377
>PRK14999 histidine utilization repressor; Provisional
Probab=43.92 E-value=85 Score=22.41 Aligned_cols=44 Identities=20% Similarity=0.231 Sum_probs=30.5
Q ss_pred HHHHHHHHHh---CCCCCCCCCccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHH
Q 036324 26 FELLCGLLRI---NGGLKADGTVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLV 85 (91)
Q Consensus 26 F~~L~~~L~~---~~~l~~s~~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~V 85 (91)
..++.+.|+. .+.+++...++.|..| +..|+.|+.||-+-+...
T Consensus 14 y~qi~~~i~~~I~~g~~~~G~~LPsE~eL----------------a~~~gVSR~TVR~Al~~L 60 (241)
T PRK14999 14 YETVKQDICKKIAGGVWQPHDRIPSEAEL----------------VAQYGFSRMTINRALREL 60 (241)
T ss_pred HHHHHHHHHHHHHcCCCCCCCcCCCHHHH----------------HHHHCCCHHHHHHHHHHH
Confidence 4445555544 2566777777777665 689999999998877653
No 378
>COG4496 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=43.88 E-value=18 Score=23.71 Aligned_cols=25 Identities=32% Similarity=0.247 Sum_probs=22.2
Q ss_pred HhhcCcchhhhhhccccchhhHHHH
Q 036324 57 ILAHHVKSRTIHSRFLRSRETISRY 81 (91)
Q Consensus 57 i~~~~~~~r~i~~~F~~S~eTisr~ 81 (91)
++-.+.+|++|...=|-|..||||.
T Consensus 52 mL~eg~tY~~I~~eTGaStaTIsRV 76 (100)
T COG4496 52 MLKEGRTYRDIEDETGASTATISRV 76 (100)
T ss_pred HHHcCCCcchhhhccCcchhhHHHH
Confidence 4567899999999999999999985
No 379
>PRK10870 transcriptional repressor MprA; Provisional
Probab=43.70 E-value=35 Score=23.71 Aligned_cols=26 Identities=12% Similarity=0.157 Sum_probs=22.5
Q ss_pred CcchhhhhhccccchhhHHHHHHHHH
Q 036324 61 HVKSRTIHSRFLRSRETISRYFNLVL 86 (91)
Q Consensus 61 ~~~~r~i~~~F~~S~eTisr~f~~Vl 86 (91)
+.+..++++.++.++.||+|.+...-
T Consensus 71 ~it~~eLa~~l~l~~~tvsr~v~rLe 96 (176)
T PRK10870 71 SIQPSELSCALGSSRTNATRIADELE 96 (176)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 36779999999999999999987653
No 380
>COG1309 AcrR Transcriptional regulator [Transcription]
Probab=43.64 E-value=15 Score=23.09 Aligned_cols=30 Identities=23% Similarity=0.148 Sum_probs=24.7
Q ss_pred cCcchhhhhhccccchhhHHHHHHH---HHHHH
Q 036324 60 HHVKSRTIHSRFLRSRETISRYFNL---VLNAI 89 (91)
Q Consensus 60 ~~~~~r~i~~~F~~S~eTisr~f~~---Vl~ai 89 (91)
++.+.+.|...=|.|..|+++||.. ++.++
T Consensus 31 ~~~t~~~Ia~~agvs~~~~Y~~f~~K~~l~~~~ 63 (201)
T COG1309 31 AATTVDEIAKAAGVSKGTLYRHFPSKEDLLLAL 63 (201)
T ss_pred CCCCHHHHHHHhCCCcchhHHHcCCHHHHHHHH
Confidence 4588999999999999999999964 44444
No 381
>TIGR03613 RutR pyrimidine utilization regulatory protein R. This protein is observed in operons extremely similar to that characterized in E. coli K-12 responsible for the import and catabolism of pyrimidines, primarily uracil. This protein is a member of the TetR family of transcriptional regulators defined by the N-teminal model pfam00440 and the C-terminal model pfam08362 (YcdC-like protein, C-terminal region).
Probab=43.49 E-value=32 Score=23.36 Aligned_cols=37 Identities=19% Similarity=0.150 Sum_probs=29.3
Q ss_pred HHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHH
Q 036324 47 IEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFN 83 (91)
Q Consensus 47 veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~ 83 (91)
++-.+.+|.=-=-++.|.+.|+.+=|.|..|++.||.
T Consensus 14 l~aA~~lf~e~G~~~~s~~~IA~~agvs~~~lY~hF~ 50 (202)
T TIGR03613 14 LSAALDTFSRFGFHGTSLEQIAELAGVSKTNLLYYFP 50 (202)
T ss_pred HHHHHHHHHHhCcccCCHHHHHHHhCCCHHHHHHHcC
Confidence 3445556665556778999999999999999999984
No 382
>PF14393 DUF4422: Domain of unknown function (DUF4422)
Probab=43.27 E-value=13 Score=27.52 Aligned_cols=32 Identities=22% Similarity=0.319 Sum_probs=27.8
Q ss_pred hHHhhcCChhHHHHHhCCCHHHHHHHHHHHHh
Q 036324 4 LSRSIIGSDIECVNQLRMDKRTFELLCGLLRI 35 (91)
Q Consensus 4 l~~ll~~~~~~c~~~fRM~~~~F~~L~~~L~~ 35 (91)
..+.++++....++||=|.++.|..-|++|=+
T Consensus 156 ~~~~~~~~~~~~~NMfImkkelF~~Yc~wLF~ 187 (231)
T PF14393_consen 156 FDKVMNGTSAYFYNMFIMKKELFDEYCEWLFD 187 (231)
T ss_pred HHHHHhCCCceeeeeeEcchHHHHHHHHHHHH
Confidence 45678889999999999999999999998643
No 383
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=43.16 E-value=30 Score=17.22 Aligned_cols=25 Identities=20% Similarity=0.189 Sum_probs=18.7
Q ss_pred hhcCcchhhhhhccccchhhHHHHH
Q 036324 58 LAHHVKSRTIHSRFLRSRETISRYF 82 (91)
Q Consensus 58 ~~~~~~~r~i~~~F~~S~eTisr~f 82 (91)
-..+.+..+++...+.|.+||+++-
T Consensus 7 ~~~~~s~~~la~~~~i~~~~i~~~~ 31 (56)
T smart00530 7 EEKGLTQEELAEKLGVSRSTLSRIE 31 (56)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHH
Confidence 3456777888888888888887754
No 384
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=43.11 E-value=80 Score=22.77 Aligned_cols=44 Identities=20% Similarity=0.347 Sum_probs=31.3
Q ss_pred HHHHHHHHHh---CCCCCCCCCccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHH
Q 036324 26 FELLCGLLRI---NGGLKADGTVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLV 85 (91)
Q Consensus 26 F~~L~~~L~~---~~~l~~s~~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~V 85 (91)
+.++.+.|+. .|.+++...++.|-.| +..|+.|+.||-+-+.+.
T Consensus 9 Y~qI~~~i~~~I~~G~~~~G~~LPsE~eL----------------a~~f~VSR~TvRkAL~~L 55 (236)
T COG2188 9 YQQIAEDIRQRIESGELPPGDKLPSEREL----------------AEQFGVSRMTVRKALDEL 55 (236)
T ss_pred HHHHHHHHHHHHHhCCCCCCCCCCCHHHH----------------HHHHCCcHHHHHHHHHHH
Confidence 3444444443 3677888788877654 689999999998877664
No 385
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=43.03 E-value=22 Score=27.59 Aligned_cols=26 Identities=27% Similarity=0.299 Sum_probs=23.4
Q ss_pred hcCcchhhhhhccccchhhHHHHHHH
Q 036324 59 AHHVKSRTIHSRFLRSRETISRYFNL 84 (91)
Q Consensus 59 ~~~~~~r~i~~~F~~S~eTisr~f~~ 84 (91)
-++.++++|+++.+.|+.||||....
T Consensus 24 ~~gltQ~eIA~~LgiSR~~v~rlL~~ 49 (321)
T COG2390 24 VEGLTQSEIAERLGISRATVSRLLAK 49 (321)
T ss_pred hcCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 46799999999999999999998765
No 386
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=42.79 E-value=53 Score=23.11 Aligned_cols=24 Identities=17% Similarity=0.084 Sum_probs=21.0
Q ss_pred cchhhhhhccccchhhHHHHHHHH
Q 036324 62 VKSRTIHSRFLRSRETISRYFNLV 85 (91)
Q Consensus 62 ~~~r~i~~~F~~S~eTisr~f~~V 85 (91)
.+..++.+.|+.|.+||-|-+.+.
T Consensus 22 ~~~~~La~~~~vS~~TiRRDl~~L 45 (185)
T PRK04424 22 ITDEELAEKFGVSIQTIRLDRMEL 45 (185)
T ss_pred EEHHHHHHHHCcCHHHHHHHHHHH
Confidence 678899999999999999987754
No 387
>PRK11139 DNA-binding transcriptional activator GcvA; Provisional
Probab=42.75 E-value=30 Score=24.92 Aligned_cols=36 Identities=11% Similarity=0.184 Sum_probs=29.6
Q ss_pred HHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHH
Q 036324 49 EQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLV 85 (91)
Q Consensus 49 E~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~V 85 (91)
.++-+|+.++ ...+...++...+.|++|||+.++..
T Consensus 9 ~~l~~f~~v~-~~gs~s~AA~~L~isq~avS~~i~~L 44 (297)
T PRK11139 9 NALRAFEAAA-RHLSFTRAAEELFVTQAAVSHQIKAL 44 (297)
T ss_pred HHHHHHHHHH-HhCCHHHHHHHhCCChHHHHHHHHHH
Confidence 5777776554 45899999999999999999998864
No 388
>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=42.57 E-value=25 Score=19.06 Aligned_cols=24 Identities=13% Similarity=0.062 Sum_probs=18.8
Q ss_pred CcchhhhhhccccchhhHHHHHHH
Q 036324 61 HVKSRTIHSRFLRSRETISRYFNL 84 (91)
Q Consensus 61 ~~~~r~i~~~F~~S~eTisr~f~~ 84 (91)
..+++.++..-|.|.+||.+-+..
T Consensus 17 r~s~~~la~~lglS~~~v~~Ri~r 40 (42)
T PF13404_consen 17 RRSYAELAEELGLSESTVRRRIRR 40 (42)
T ss_dssp TS-HHHHHHHHTS-HHHHHHHHHH
T ss_pred CccHHHHHHHHCcCHHHHHHHHHH
Confidence 478999999999999999987654
No 389
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=42.39 E-value=49 Score=21.22 Aligned_cols=32 Identities=19% Similarity=0.224 Sum_probs=26.9
Q ss_pred hhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 58 LAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 58 ~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
...+.+++.|+..++-|..||..+.+.....+
T Consensus 153 ~~~~~~~~~ia~~l~~s~~tv~~~~~~~~~kl 184 (202)
T PRK09390 153 LVAGLSNKVIARDLDISPRTVEVYRANVMTKM 184 (202)
T ss_pred HHccCchHHHHHHcCCCHHHHHHHHHHHHHHH
Confidence 44567899999999999999999988876653
No 390
>cd01197 INT_FimBE_C FimB and FimE and related proteins, DNA breaking-rejoining enzymes, integrase/recombinases, catalytic domain. This CD includes those proteins similar to E.coli FimE and FimB regulatory proteins and Proteus mirabilis MrpI.
Probab=41.79 E-value=1e+02 Score=20.34 Aligned_cols=63 Identities=13% Similarity=0.063 Sum_probs=39.9
Q ss_pred CCCHHHHHHHHHHHHhCCCCCCCCCccHHH-HHHHHHHHhhcCcchhhhhhcccc-chhhHHHHHHH
Q 036324 20 RMDKRTFELLCGLLRINGGLKADGTVSIEE-QLCMFLHILAHHVKSRTIHSRFLR-SRETISRYFNL 84 (91)
Q Consensus 20 RM~~~~F~~L~~~L~~~~~l~~s~~v~veE-~vamFL~i~~~~~~~r~i~~~F~~-S~eTisr~f~~ 84 (91)
.++.+.+.........+.+++.......-- -.|-.| ...|.+-..|+...|| |.+|+-+|++.
T Consensus 107 ~~~~~~~~~~~~~~~~~~g~~~~~~~H~lRht~~t~l--~~~g~~~~~i~~~lGH~~~~~t~~Y~~~ 171 (180)
T cd01197 107 PLSRQQVYKLIRRLGAQAGLSIKVHPHMLRHACGYAL--ANQGADTRLIQDYLGHRNIRHTVIYTAS 171 (180)
T ss_pred cCCHHHHHHHHHHHHHHcCCCCCCCcchhhhHHHHHH--HHcCCCHHHHHHHhCCCCcchhHHHHhh
Confidence 577788888777777777764321111111 122222 3357788999999999 55788888875
No 391
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=41.71 E-value=79 Score=21.11 Aligned_cols=46 Identities=13% Similarity=0.103 Sum_probs=36.4
Q ss_pred CccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHHh
Q 036324 44 TVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAIL 90 (91)
Q Consensus 44 ~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai~ 90 (91)
..+-|++--+-+++.+. .+-..++..+|.|=.||-..+.+++.++.
T Consensus 33 ~L~~E~~~Fi~~Fi~~r-GnlKe~e~~lgiSYPTvR~rLd~ii~~lg 78 (113)
T PF09862_consen 33 RLSPEQLEFIKLFIKNR-GNLKEMEKELGISYPTVRNRLDKIIEKLG 78 (113)
T ss_pred cCCHHHHHHHHHHHHhc-CCHHHHHHHHCCCcHHHHHHHHHHHHHhC
Confidence 56666666666666654 46788999999999999999999999874
No 392
>PRK14996 TetR family transcriptional regulator; Provisional
Probab=41.37 E-value=28 Score=23.60 Aligned_cols=37 Identities=14% Similarity=0.052 Sum_probs=27.3
Q ss_pred HHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHH
Q 036324 48 EEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNL 84 (91)
Q Consensus 48 eE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~ 84 (91)
+-.+.+|.-.--++.+.+.|+..=|.|+.|+++||..
T Consensus 15 ~aA~~lf~e~G~~~tSi~~Ia~~aGvsk~~lY~~F~s 51 (192)
T PRK14996 15 QAAMRVALAEGFAAMTVRRIASEAQVAAGQVHHHFSS 51 (192)
T ss_pred HHHHHHHHhcChhhccHHHHHHHhCCCcHHHHHHcCC
Confidence 3344445443345589999999999999999999953
No 393
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=41.06 E-value=48 Score=24.20 Aligned_cols=27 Identities=22% Similarity=0.314 Sum_probs=22.9
Q ss_pred CcchhhhhhccccchhhHHHHHHHHHH
Q 036324 61 HVKSRTIHSRFLRSRETISRYFNLVLN 87 (91)
Q Consensus 61 ~~~~r~i~~~F~~S~eTisr~f~~Vl~ 87 (91)
..+..+++..|+.|..||.|.+.+.-.
T Consensus 18 ~~~~~eLa~~l~VS~~TiRRdL~~L~~ 44 (240)
T PRK10411 18 SLTTEALAEQLNVSKETIRRDLNELQT 44 (240)
T ss_pred CCcHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 477888999999999999999987543
No 394
>PRK00441 argR arginine repressor; Provisional
Probab=41.01 E-value=54 Score=22.56 Aligned_cols=24 Identities=17% Similarity=0.221 Sum_probs=18.0
Q ss_pred cchhhhhhc-----cccchhhHHHHHHHH
Q 036324 62 VKSRTIHSR-----FLRSRETISRYFNLV 85 (91)
Q Consensus 62 ~~~r~i~~~-----F~~S~eTisr~f~~V 85 (91)
.+...+... |+.|..||||-+++.
T Consensus 19 ~~q~eL~~~L~~~G~~vSqaTisRDl~~L 47 (149)
T PRK00441 19 ETQEELAEELKKMGFDVTQATVSRDIKEL 47 (149)
T ss_pred CcHHHHHHHHHhcCCCcCHHHHHHHHHHc
Confidence 445556666 699999999998863
No 395
>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=40.79 E-value=83 Score=19.06 Aligned_cols=31 Identities=26% Similarity=0.259 Sum_probs=16.9
Q ss_pred CccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHH
Q 036324 44 TVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLV 85 (91)
Q Consensus 44 ~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~V 85 (91)
.|+..|.|.=-|-.- -|..++.||||-+++.
T Consensus 18 ~i~sQ~eL~~~L~~~-----------Gi~vTQaTiSRDLkeL 48 (70)
T PF01316_consen 18 EISSQEELVELLEEE-----------GIEVTQATISRDLKEL 48 (70)
T ss_dssp ---SHHHHHHHHHHT-----------T-T--HHHHHHHHHHH
T ss_pred CcCCHHHHHHHHHHc-----------CCCcchhHHHHHHHHc
Confidence 455666665555333 3667889999998874
No 396
>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=40.42 E-value=25 Score=24.08 Aligned_cols=33 Identities=24% Similarity=0.282 Sum_probs=29.5
Q ss_pred CccHHHHHHHHHHHhhcCcchhhhhhccccchh
Q 036324 44 TVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRE 76 (91)
Q Consensus 44 ~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~e 76 (91)
..|.-|++|-.|||+|....-..+-+.|..+..
T Consensus 65 kLscvEAlAAaLyI~G~~~~A~~lL~~FkWG~~ 97 (127)
T PF04034_consen 65 KLSCVEALAAALYILGFKEQAEELLSKFKWGHT 97 (127)
T ss_pred cccHHHHHHHHHHHcCCHHHHHHHHhcCCCcHH
Confidence 589999999999999999999999999987654
No 397
>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=40.38 E-value=37 Score=22.64 Aligned_cols=37 Identities=22% Similarity=0.258 Sum_probs=24.5
Q ss_pred HHHHHHHHHHHHhCCCCCCCCCccHHHHHHHHHHHhh
Q 036324 23 KRTFELLCGLLRINGGLKADGTVSIEEQLCMFLHILA 59 (91)
Q Consensus 23 ~~~F~~L~~~L~~~~~l~~s~~v~veE~vamFL~i~~ 59 (91)
+..|.+..+.+-+...+.+--..-=||.+..|.||+-
T Consensus 47 ~~qF~KVL~~v~s~l~~~p~~~~qdde~L~v~~wIle 83 (108)
T PF09246_consen 47 PGQFTKVLDLVCSILQQRPYCSPQDDEILCVFMWILE 83 (108)
T ss_dssp HHHHHHHHHHHHHHHHT-TTG-GG-HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHhcccccccchhHHHHHHHHHH
Confidence 3578888888776544343334567899999999974
No 398
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=40.01 E-value=82 Score=19.92 Aligned_cols=43 Identities=14% Similarity=-0.011 Sum_probs=36.5
Q ss_pred CCccHHHHHHHHHHHhhcCcchhhhhhccc-cchhhHHHHHHHH
Q 036324 43 GTVSIEEQLCMFLHILAHHVKSRTIHSRFL-RSRETISRYFNLV 85 (91)
Q Consensus 43 ~~v~veE~vamFL~i~~~~~~~r~i~~~F~-~S~eTisr~f~~V 85 (91)
+.-|-|.++.+---.+-.+.+...|+..|+ .+..++++..++.
T Consensus 6 r~~s~EfK~~iv~~~~~~g~sv~~vAr~~gv~~~~~l~~W~~~~ 49 (116)
T COG2963 6 KKYSPEFKLEAVALYLRGGDTVSEVAREFGIVSATQLYKWRIQL 49 (116)
T ss_pred ccCCHHHHHHHHHHHHhcCccHHHHHHHhCCCChHHHHHHHHHH
Confidence 456788888888888888889999999999 5999999777654
No 399
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=39.29 E-value=80 Score=22.32 Aligned_cols=44 Identities=9% Similarity=0.067 Sum_probs=30.5
Q ss_pred HHHHHHHHHHHhCCCCCCCCCccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHH
Q 036324 24 RTFELLCGLLRINGGLKADGTVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNL 84 (91)
Q Consensus 24 ~~F~~L~~~L~~~~~l~~s~~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~ 84 (91)
.+...|.+.+.. +.+++...++.|.. ++..||.|+.||-.-+..
T Consensus 11 ~~~~~l~~~I~~-g~l~pG~~LPsE~e----------------Lae~~gVSRt~VReAL~~ 54 (239)
T PRK04984 11 FAEEYIIESIWN-NRFPPGSILPAERE----------------LSELIGVTRTTLREVLQR 54 (239)
T ss_pred HHHHHHHHHHHc-CCCCCCCcCCCHHH----------------HHHHHCCCHHHHHHHHHH
Confidence 455666666665 66777777776655 578999999999655543
No 400
>PF03428 RP-C: Replication protein C N-terminal domain; InterPro: IPR005090 Proteins in this group have homology with the RepC protein of Agrobacterium Ri and Ti plasmids []. They may be involved in plasmid replication and stabilisation functions.
Probab=39.25 E-value=28 Score=24.81 Aligned_cols=67 Identities=16% Similarity=0.112 Sum_probs=43.0
Q ss_pred CCHHHHHHHHHHHHhCCCCCCCCCccHHHHHHHHHHHh----h----cCcchhhhhhcc-ccchhhHHHHHHHHHHH
Q 036324 21 MDKRTFELLCGLLRINGGLKADGTVSIEEQLCMFLHIL----A----HHVKSRTIHSRF-LRSRETISRYFNLVLNA 88 (91)
Q Consensus 21 M~~~~F~~L~~~L~~~~~l~~s~~v~veE~vamFL~i~----~----~~~~~r~i~~~F-~~S~eTisr~f~~Vl~a 88 (91)
++|...+.+....++.++|+++. +.+-..+--|.--- + =-.||.+++.+. |.|..||.|+.....+|
T Consensus 23 ~~k~~ll~~l~~a~~~lgl~~~~-l~vL~aLls~~~~~d~~~~~~piVfpSN~~La~r~~G~s~~tlrR~l~~Lvea 98 (177)
T PF03428_consen 23 VTKWQLLRALKEARPALGLSDRA-LAVLDALLSFTPPDDWEPGRRPIVFPSNAQLAERLNGMSERTLRRHLARLVEA 98 (177)
T ss_pred CCHHHHHHHHHHHHHhcCCChhH-HHHHHHHHHhCCcccccCCCCceeecCHHHHHHHHcCCCHHHHHHHHHHHHHC
Confidence 56666666666677777776543 33333333332110 0 015899999999 99999999998876654
No 401
>COG1740 HyaA Ni,Fe-hydrogenase I small subunit [Energy production and conversion]
Probab=39.05 E-value=38 Score=26.94 Aligned_cols=36 Identities=31% Similarity=0.456 Sum_probs=27.1
Q ss_pred HHHhCCCHHHHHHHHHHHHhCCCCCCCCCccHHHHH
Q 036324 16 VNQLRMDKRTFELLCGLLRINGGLKADGTVSIEEQL 51 (91)
Q Consensus 16 ~~~fRM~~~~F~~L~~~L~~~~~l~~s~~v~veE~v 51 (91)
..+..|+|..|.++|..+....+|..+-...+-+++
T Consensus 8 ~~~~g~~Rr~f~k~~~~~~a~l~L~~~~~~~~~~a~ 43 (355)
T COG1740 8 FKRHGITRRDFLKLCGALAASLGLSASYAPEIAKAL 43 (355)
T ss_pred HHHcCCcHHHHHHHHHHHHHHhccCccchHHHHHHH
Confidence 344559999999999999999888886544444433
No 402
>PRK13756 tetracycline repressor protein TetR; Provisional
Probab=38.78 E-value=33 Score=24.41 Aligned_cols=24 Identities=8% Similarity=0.133 Sum_probs=21.8
Q ss_pred cCcchhhhhhccccchhhHHHHHH
Q 036324 60 HHVKSRTIHSRFLRSRETISRYFN 83 (91)
Q Consensus 60 ~~~~~r~i~~~F~~S~eTisr~f~ 83 (91)
.+.+.|.|+.+-|.|..|+++||.
T Consensus 23 ~~lsmr~lA~~lgv~~~slY~hf~ 46 (205)
T PRK13756 23 EGLTTRKLAQKLGVEQPTLYWHVK 46 (205)
T ss_pred ccCCHHHHHHHhCCCchHHHHHcC
Confidence 357999999999999999999985
No 403
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=38.70 E-value=79 Score=24.16 Aligned_cols=31 Identities=10% Similarity=0.057 Sum_probs=27.5
Q ss_pred hcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 59 AHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 59 ~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
-.+.++..|+...+.|.+||....+.-+..+
T Consensus 280 ~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kL 310 (325)
T PRK05657 280 YEAATLEDVAREIGLTRERVRQIQVEALRRL 310 (325)
T ss_pred CCCcCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 4679999999999999999999998877654
No 404
>PRK10072 putative transcriptional regulator; Provisional
Probab=38.52 E-value=26 Score=22.52 Aligned_cols=27 Identities=7% Similarity=-0.058 Sum_probs=23.3
Q ss_pred HhhcCcchhhhhhccccchhhHHHHHH
Q 036324 57 ILAHHVKSRTIHSRFLRSRETISRYFN 83 (91)
Q Consensus 57 i~~~~~~~r~i~~~F~~S~eTisr~f~ 83 (91)
.-..|.++..++..+|.|..||+++..
T Consensus 42 R~~~glTQ~elA~~lGvS~~TVs~WE~ 68 (96)
T PRK10072 42 RKGTGLKIDDFARVLGVSVAMVKEWES 68 (96)
T ss_pred HHHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 456789999999999999999999864
No 405
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=38.12 E-value=31 Score=22.70 Aligned_cols=27 Identities=15% Similarity=0.130 Sum_probs=21.8
Q ss_pred HhhcCcchhhhhhccccchhhHHHHHH
Q 036324 57 ILAHHVKSRTIHSRFLRSRETISRYFN 83 (91)
Q Consensus 57 i~~~~~~~r~i~~~F~~S~eTisr~f~ 83 (91)
.-..|.+..+++...|.|.+|||++.+
T Consensus 14 R~~~gltq~~lA~~~gvs~~~is~~E~ 40 (135)
T PRK09706 14 RKQLKLSQRSLAKAVKVSHVSISQWER 40 (135)
T ss_pred HHHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 345677888999999999999998754
No 406
>PRK09191 two-component response regulator; Provisional
Probab=38.00 E-value=83 Score=21.92 Aligned_cols=40 Identities=8% Similarity=-0.072 Sum_probs=31.7
Q ss_pred HHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 50 QLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 50 ~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
+-.+|+-..-.+.++..|+...+.|.+||....+.-+..+
T Consensus 93 ~r~v~~l~~~~~~s~~eIA~~l~~s~~tV~~~l~ra~~~l 132 (261)
T PRK09191 93 PRQAFLLTALEGFSVEEAAEILGVDPAEAEALLDDARAEI 132 (261)
T ss_pred HhHHHHHHHHhcCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 3345555566789999999999999999998888766544
No 407
>PRK03837 transcriptional regulator NanR; Provisional
Probab=37.99 E-value=98 Score=21.78 Aligned_cols=43 Identities=16% Similarity=0.224 Sum_probs=28.1
Q ss_pred HHHHHHHHHHHhCCCCCCCCCccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHH
Q 036324 24 RTFELLCGLLRINGGLKADGTVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFN 83 (91)
Q Consensus 24 ~~F~~L~~~L~~~~~l~~s~~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~ 83 (91)
.++..|.+.+.. +.+++...++.|.. ++++||.|+.||-..+.
T Consensus 17 ~v~~~l~~~I~~-g~l~pG~~Lp~E~~----------------Lae~~gVSRt~VREAL~ 59 (241)
T PRK03837 17 EVEERLEQMIRS-GEFGPGDQLPSERE----------------LMAFFGVGRPAVREALQ 59 (241)
T ss_pred HHHHHHHHHHHh-CCCCCCCCCCCHHH----------------HHHHhCCCHHHHHHHHH
Confidence 355555555554 55666666665554 57899999999955443
No 408
>PRK15340 transcriptional regulator InvF; Provisional
Probab=37.69 E-value=66 Score=23.65 Aligned_cols=26 Identities=15% Similarity=0.088 Sum_probs=21.1
Q ss_pred CcchhhhhhccccchhhHHHHHHHHH
Q 036324 61 HVKSRTIHSRFLRSRETISRYFNLVL 86 (91)
Q Consensus 61 ~~~~r~i~~~F~~S~eTisr~f~~Vl 86 (91)
..+..+++..++.|..+++|.|++.+
T Consensus 125 ~~sleeLA~~~gvS~r~f~RlFk~~~ 150 (216)
T PRK15340 125 GNTMRMLGEDYGVSYTHFRRLCSRAL 150 (216)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 35667788899999999999998764
No 409
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=37.64 E-value=64 Score=23.60 Aligned_cols=23 Identities=22% Similarity=0.137 Sum_probs=20.5
Q ss_pred cchhhhhhccccchhhHHHHHHH
Q 036324 62 VKSRTIHSRFLRSRETISRYFNL 84 (91)
Q Consensus 62 ~~~r~i~~~F~~S~eTisr~f~~ 84 (91)
.+..++.+.|+.|.+||-|-+.+
T Consensus 22 v~v~eLa~~~~VS~~TIRRDL~~ 44 (252)
T PRK10681 22 LHLKDAAALLGVSEMTIRRDLNA 44 (252)
T ss_pred CcHHHHHHHhCCCHHHHHHHHHH
Confidence 57788999999999999998876
No 410
>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=37.16 E-value=35 Score=22.05 Aligned_cols=28 Identities=14% Similarity=0.185 Sum_probs=23.2
Q ss_pred HHHHHHhhcCcchhhhhhccccchhhHH
Q 036324 52 CMFLHILAHHVKSRTIHSRFLRSRETIS 79 (91)
Q Consensus 52 amFL~i~~~~~~~r~i~~~F~~S~eTis 79 (91)
.+|...--++.++..|+...|.|..||.
T Consensus 114 ~v~~l~~~~~~s~~EIA~~l~is~~tV~ 141 (142)
T TIGR03209 114 KIIYMKFFEDMKEIDIAKKLHISRQSVY 141 (142)
T ss_pred HHHHHHHHcCCCHHHHHHHHCcCHHhhc
Confidence 3455556689999999999999999985
No 411
>cd00093 HTH_XRE Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.
Probab=37.15 E-value=32 Score=17.23 Aligned_cols=25 Identities=28% Similarity=0.292 Sum_probs=19.9
Q ss_pred hcCcchhhhhhccccchhhHHHHHH
Q 036324 59 AHHVKSRTIHSRFLRSRETISRYFN 83 (91)
Q Consensus 59 ~~~~~~r~i~~~F~~S~eTisr~f~ 83 (91)
.++.+..+++...+.|..+|+++.+
T Consensus 10 ~~~~s~~~~a~~~~~~~~~v~~~~~ 34 (58)
T cd00093 10 EKGLTQEELAEKLGVSRSTISRIEN 34 (58)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHc
Confidence 4577888888888999888887654
No 412
>KOG2072 consensus Translation initiation factor 3, subunit a (eIF-3a) [Translation, ribosomal structure and biogenesis]
Probab=36.89 E-value=32 Score=30.51 Aligned_cols=34 Identities=32% Similarity=0.439 Sum_probs=24.0
Q ss_pred chhHHhhcCChhHHHHHhCCCH-----------------------HHHHHHHHHHHhC
Q 036324 2 PHLSRSIIGSDIECVNQLRMDK-----------------------RTFELLCGLLRIN 36 (91)
Q Consensus 2 ~~l~~ll~~~~~~c~~~fRM~~-----------------------~~F~~L~~~L~~~ 36 (91)
+||+++-. +=..|.+.+|-+. .-|.+||+.||.+
T Consensus 150 PWlkFLWe-SYR~vLdlLRNNa~lE~lY~~ia~~aFqFCLkYqRktEFRrLCe~LR~H 206 (988)
T KOG2072|consen 150 PWLKFLWE-SYRTVLDLLRNNARLEALYHDIARKAFQFCLKYQRKTEFRRLCELLRMH 206 (988)
T ss_pred HHHHHHHH-HHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHH
Confidence 46665433 5566777777653 6799999999986
No 413
>PRK15481 transcriptional regulatory protein PtsJ; Provisional
Probab=36.68 E-value=91 Score=24.05 Aligned_cols=47 Identities=17% Similarity=0.361 Sum_probs=31.0
Q ss_pred HHHHHHHHHHHHhCCCCCCCCCccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHH
Q 036324 23 KRTFELLCGLLRINGGLKADGTVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVL 86 (91)
Q Consensus 23 ~~~F~~L~~~L~~~~~l~~s~~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl 86 (91)
+.+...+.+.+.+ +.+++...++. .|.++..|+.|+.||.+.+++..
T Consensus 8 ~~~~~~i~~~i~~-g~l~~g~~lps----------------~r~la~~~~vsr~tv~~a~~~L~ 54 (431)
T PRK15481 8 NEIFDSIRQLIQA-GRLRPGDSLPP----------------VRELASELGVNRNTVAAAYKRLV 54 (431)
T ss_pred HHHHHHHHHHHHc-CCCCCCCcCcC----------------HHHHHHHHCCCHHHHHHHHHHHH
Confidence 3445555555554 44555555543 45677889999999999887754
No 414
>TIGR01636 phage_rinA phage transcriptional activator, RinA family. This model represents a family of phage proteins, including RinA, a transcriptional activator in staphylococcal phage phi 11. This family shows similarity to ArpU, a phage-related putative autolysin regulator, and to some sporulation-specific sigma factors.
Probab=36.42 E-value=94 Score=20.64 Aligned_cols=43 Identities=12% Similarity=0.142 Sum_probs=30.7
Q ss_pred HHHHHHHHH-HHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 47 IEEQLCMFL-HILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 47 veE~vamFL-~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
-+|+--|-+ |.-....+...|+..++.|..|++|.=+..+..+
T Consensus 85 ~~er~II~~rY~~~~~~t~~~Ia~~l~iS~~t~~r~r~~~l~kl 128 (134)
T TIGR01636 85 EQTRVIIQELYMKKRPLTLVGLAQQLFISKSTAYRLRNHIIEAV 128 (134)
T ss_pred HHHHHHHHHHHccCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 334433433 4434445899999999999999999877777654
No 415
>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=36.25 E-value=12 Score=26.25 Aligned_cols=38 Identities=21% Similarity=0.179 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHhh--cCcchhhhhhccccchhhHHHHHHH
Q 036324 47 IEEQLCMFLHILA--HHVKSRTIHSRFLRSRETISRYFNL 84 (91)
Q Consensus 47 veE~vamFL~i~~--~~~~~r~i~~~F~~S~eTisr~f~~ 84 (91)
++.|-+-|+.--+ .+.+.++|++.-+.|.+||||.+..
T Consensus 33 v~~Q~~ff~~g~~~l~PLt~~~iA~~lgl~~STVSRav~~ 72 (160)
T PF04552_consen 33 VERQKDFFLGGPGALKPLTMKDIADELGLHESTVSRAVKN 72 (160)
T ss_dssp ----------------------------------------
T ss_pred HHHHHHHHhcCcccCcCCCHHHHHHHhCCCHhHHHHHHcC
Confidence 4455555553221 3478899999999999999998753
No 416
>PF06413 Neugrin: Neugrin; InterPro: IPR010487 This family contains mouse and human neugrin proteins. Neugrin and m-neugrin are mainly expressed in neurons in the nervous system, and are thought to play an important role in the process of neuronal differentiation []. Homologues of neugrin are found in fungi suggesting they have a alternative role or more than one function.
Probab=36.14 E-value=90 Score=23.08 Aligned_cols=43 Identities=16% Similarity=0.067 Sum_probs=29.8
Q ss_pred CCCCccHHHHHHHHHHHhhcCc--chhhhhhccccchhhHHHHHH
Q 036324 41 ADGTVSIEEQLCMFLHILAHHV--KSRTIHSRFLRSRETISRYFN 83 (91)
Q Consensus 41 ~s~~v~veE~vamFL~i~~~~~--~~r~i~~~F~~S~eTisr~f~ 83 (91)
+.+.+|-+++-.|=.-.--... +.-.+++.|..|.++|.|+.+
T Consensus 7 p~k~Ls~~~~~~ir~L~~~~p~~~t~~~Lae~F~vspe~irrILk 51 (225)
T PF06413_consen 7 PPKKLSREAMEQIRYLHKEDPEEWTVERLAESFKVSPEAIRRILK 51 (225)
T ss_pred CCCCCCHHHHHHHHHHHHhCccccCHHHHHhhCCCCHHHHHHHHh
Confidence 4456666666666444444443 456799999999999999875
No 417
>PRK12302 bssR biofilm formation regulatory protein BssR; Reviewed
Probab=35.96 E-value=41 Score=22.71 Aligned_cols=30 Identities=17% Similarity=0.050 Sum_probs=22.4
Q ss_pred HHHHHHHHHHHHhCCCCCCCCCccHHHHHHH
Q 036324 23 KRTFELLCGLLRINGGLKADGTVSIEEQLCM 53 (91)
Q Consensus 23 ~~~F~~L~~~L~~~~~l~~s~~v~veE~vam 53 (91)
|+.|+.||.+++.+.. .-.-+..-||..|.
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 5889999999998663 33457777877654
No 418
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=35.81 E-value=79 Score=19.08 Aligned_cols=22 Identities=18% Similarity=0.330 Sum_probs=19.8
Q ss_pred hhhhhccccchhhHHHHHHHHH
Q 036324 65 RTIHSRFLRSRETISRYFNLVL 86 (91)
Q Consensus 65 r~i~~~F~~S~eTisr~f~~Vl 86 (91)
..++...+.+++||++.....-
T Consensus 40 ~~la~~l~i~~~~vt~~l~~Le 61 (126)
T COG1846 40 KELAERLGLDRSTVTRLLKRLE 61 (126)
T ss_pred HHHHHHHCCCHHHHHHHHHHHH
Confidence 9999999999999999987654
No 419
>PF03564 DUF1759: Protein of unknown function (DUF1759); InterPro: IPR005312 This is a small family of proteins of unknown function.
Probab=35.30 E-value=45 Score=21.81 Aligned_cols=40 Identities=20% Similarity=0.218 Sum_probs=35.8
Q ss_pred chhHHhhcCChhHHHHHhCCCHHHHHHHHHHHHhCCCCCC
Q 036324 2 PHLSRSIIGSDIECVNQLRMDKRTFELLCGLLRINGGLKA 41 (91)
Q Consensus 2 ~~l~~ll~~~~~~c~~~fRM~~~~F~~L~~~L~~~~~l~~ 41 (91)
-+|+..|.|...++..-+-++.+.+....+.|+.+||-+.
T Consensus 32 ~~L~~~L~G~A~~~i~~~~~~~~~Y~~a~~~L~~~yg~~~ 71 (145)
T PF03564_consen 32 NYLRSCLKGEAKELIRGLPLSEENYEEAWELLEERYGNPR 71 (145)
T ss_pred HHHHHHhcchHHHHHHcccccchhhHHHHHHHHHHhCCch
Confidence 3688889999999999999999999999999999998554
No 420
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=35.28 E-value=86 Score=23.50 Aligned_cols=38 Identities=11% Similarity=0.037 Sum_probs=31.8
Q ss_pred HHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 52 CMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 52 amFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
++|+..-..+.++..|+...+.|..||....+.-...+
T Consensus 125 ~vf~L~~~~g~s~~EIA~~Lgis~~tVr~~l~RAr~~L 162 (290)
T PRK09635 125 VVFVLHEIFGLPYQQIATTIGSQASTCRQLAHRARRKI 162 (290)
T ss_pred HHhhHHHHhCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 56677778899999999999999999998887665543
No 421
>PRK13824 replication initiation protein RepC; Provisional
Probab=35.24 E-value=69 Score=25.60 Aligned_cols=67 Identities=15% Similarity=0.085 Sum_probs=46.5
Q ss_pred CCHHHHHHHHHHHHhCCCCCCCCCccHHHHHHHHHHHhh--c------Ccchhhhhhc-cccchhhHHHHHHHHHHH
Q 036324 21 MDKRTFELLCGLLRINGGLKADGTVSIEEQLCMFLHILA--H------HVKSRTIHSR-FLRSRETISRYFNLVLNA 88 (91)
Q Consensus 21 M~~~~F~~L~~~L~~~~~l~~s~~v~veE~vamFL~i~~--~------~~~~r~i~~~-F~~S~eTisr~f~~Vl~a 88 (91)
++|-..+.+....++.++|+| +.+.|-..|.-|..--- . =.||.++..+ .|.|..|+.|+.....+|
T Consensus 35 v~Kw~l~r~l~~a~~~lGl~~-~~l~vL~aLlsf~p~~~~~~~~~~IVfpSN~~La~r~~Gms~~tlrRhla~Lvea 110 (404)
T PRK13824 35 VDKWKLFRDLCEARALLGVSD-RALAVLNALLSFYPETELSEEAGLVVFPSNAQLSLRAHGMAGATLRRHLAALVEA 110 (404)
T ss_pred CCHHHHHHHHHHHHHhcCCCh-hHHHHHHHHHhhCCcccccCCCCceechhHHHHHHHHcCCCHHHHHHHHHHHHHC
Confidence 466666666677777788877 34566666655543111 1 1589999998 799999999998876554
No 422
>PRK10668 DNA-binding transcriptional repressor AcrR; Provisional
Probab=34.92 E-value=43 Score=22.97 Aligned_cols=34 Identities=18% Similarity=0.069 Sum_probs=25.2
Q ss_pred HHHHHHHHhhcCcchhhhhhccccchhhHHHHHH
Q 036324 50 QLCMFLHILAHHVKSRTIHSRFLRSRETISRYFN 83 (91)
Q Consensus 50 ~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~ 83 (91)
...+|.=.=-.+.+.++|...-|.|..|+++||.
T Consensus 20 A~~lf~e~G~~~~t~~~Ia~~agvs~~tlY~~F~ 53 (215)
T PRK10668 20 ALRLFSQQGVSATSLADIAKAAGVTRGAIYWHFK 53 (215)
T ss_pred HHHHHHHcCcccCCHHHHHHHhCCChHHHHHHCC
Confidence 3444433333457899999999999999999983
No 423
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=34.91 E-value=1.5e+02 Score=21.48 Aligned_cols=29 Identities=17% Similarity=0.241 Sum_probs=25.4
Q ss_pred hhcCcchhhhhhccccchhhHHHHHHHHH
Q 036324 58 LAHHVKSRTIHSRFLRSRETISRYFNLVL 86 (91)
Q Consensus 58 ~~~~~~~r~i~~~F~~S~eTisr~f~~Vl 86 (91)
.+.+.+-..++..++.|.++++|.|++..
T Consensus 196 ~~~~isl~~lA~~~~lS~~~l~r~Fk~~~ 224 (290)
T PRK10572 196 LASEFDIESVAQHVCLSPSRLAHLFRQQL 224 (290)
T ss_pred ccCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 45668889999999999999999999864
No 424
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=34.85 E-value=1.1e+02 Score=21.85 Aligned_cols=43 Identities=19% Similarity=0.166 Sum_probs=29.4
Q ss_pred HHHHHHHHHHHhCCCCCCCCCccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHH
Q 036324 24 RTFELLCGLLRINGGLKADGTVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFN 83 (91)
Q Consensus 24 ~~F~~L~~~L~~~~~l~~s~~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~ 83 (91)
.+...|.+.+.. +.+++...++.|.. ++..||.|+.||---+.
T Consensus 11 ~v~~~i~~~I~~-g~l~pG~~LPsE~e----------------La~~~gVSRtpVREAL~ 53 (251)
T PRK09990 11 VVAERIERLIVD-GVLKVGQALPSERR----------------LCEKLGFSRSALREGLT 53 (251)
T ss_pred HHHHHHHHHHHc-CCCCCCCcCcCHHH----------------HHHHHCCCHHHHHHHHH
Confidence 455666666654 66777766766654 57899999999955443
No 425
>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=34.67 E-value=54 Score=21.45 Aligned_cols=58 Identities=14% Similarity=0.063 Sum_probs=38.3
Q ss_pred HhCCCHHHHHHHHHHHHhCCCCCCCCCccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHH
Q 036324 18 QLRMDKRTFELLCGLLRINGGLKADGTVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFN 83 (91)
Q Consensus 18 ~fRM~~~~F~~L~~~L~~~~~l~~s~~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~ 83 (91)
..-|+-.-|..|.+.......-+.++.....|+- |+- -+.-++..|+-|.+|++|+-.
T Consensus 10 v~qmTg~ell~L~~~~~~~~~~~~~~~~~~~~~~----yvy----G~~GlAklfgcSv~Ta~RiK~ 67 (96)
T PF12964_consen 10 VWQMTGEELLFLLKEGKTNSEKQTSQKAKKDEKK----YVY----GLKGLAKLFGCSVPTANRIKK 67 (96)
T ss_pred HHHhhHHHHHHHHHHHhcCCCccCCccccCcccc----eee----hHHHHHHHhCCCchhHHHHHh
Confidence 5668888888888888655543333333333332 222 356789999999999999753
No 426
>PRK00767 transcriptional regulator BetI; Validated
Probab=34.05 E-value=54 Score=21.92 Aligned_cols=35 Identities=23% Similarity=0.131 Sum_probs=26.9
Q ss_pred HHHHHHHHHhhcCcchhhhhhccccchhhHHHHHH
Q 036324 49 EQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFN 83 (91)
Q Consensus 49 E~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~ 83 (91)
-...+|.-.=-++.+.+.|...=|.|+.|+++||.
T Consensus 17 aA~~lf~~~G~~~~s~~~Ia~~aGvs~gslY~~F~ 51 (197)
T PRK00767 17 ATLRAIGEVGLLDATIAQIARRAGVSTGIISHYFG 51 (197)
T ss_pred HHHHHHHHcCcccCCHHHHHHHhCCCHHHHHHHhC
Confidence 33444444444568999999999999999999994
No 427
>PF11198 DUF2857: Protein of unknown function (DUF2857); InterPro: IPR021364 This is a bacterial family of uncharacterised proteins.
Probab=34.03 E-value=1.5e+02 Score=20.87 Aligned_cols=29 Identities=10% Similarity=0.033 Sum_probs=24.0
Q ss_pred HHHHHHhhcCcchhhhhhccccchhhHHH
Q 036324 52 CMFLHILAHHVKSRTIHSRFLRSRETISR 80 (91)
Q Consensus 52 amFL~i~~~~~~~r~i~~~F~~S~eTisr 80 (91)
..-=+.+.+|+|...++..||-|..-|++
T Consensus 78 ~~idr~L~lGAS~~mm~~~FGls~~ev~~ 106 (180)
T PF11198_consen 78 QLIDRALRLGASIEMMQRLFGLSSAEVAA 106 (180)
T ss_pred HHHHHHHHcCCCHHHHHHHHCCCHHHHHH
Confidence 44446788999999999999999988875
No 428
>TIGR02812 fadR_gamma fatty acid metabolism transcriptional regulator FadR. Members of this family are FadR, a transcriptional regulator of fatty acid metabolism, including both biosynthesis and beta-oxidation. It is found exclusively in a subset of Gammaproteobacteria, with strictly one copy per genome. It has an N-terminal DNA-binding domain and a less well conserved C-terminal long chain acyl-CoA-binding domain. FadR from this family heterologously expressed in Escherichia coli show differences in regulatory response and fatty acid binding profiles. The family is nevertheless designated equivalog, as all member proteins have at least nominally the same function.
Probab=33.71 E-value=77 Score=22.38 Aligned_cols=43 Identities=9% Similarity=0.094 Sum_probs=30.2
Q ss_pred HHHHHHHHHHHhCCCCCCCCCccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHH
Q 036324 24 RTFELLCGLLRINGGLKADGTVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFN 83 (91)
Q Consensus 24 ~~F~~L~~~L~~~~~l~~s~~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~ 83 (91)
.+...|.+.+.. +.+++...++.|.. ++..||.|+.||-.-+.
T Consensus 10 ~v~~~l~~~I~~-g~l~pG~~LpsE~~----------------La~~lgVSRtpVREAL~ 52 (235)
T TIGR02812 10 FAEEYIVESIWN-NRFPPGSILPAERE----------------LSELIGVTRTTLREVLQ 52 (235)
T ss_pred HHHHHHHHHHHc-CCCCCCCcCcCHHH----------------HHHHHCcCHHHHHHHHH
Confidence 456667777764 66788777766655 56789999999854443
No 429
>PRK11552 putative DNA-binding transcriptional regulator; Provisional
Probab=33.27 E-value=54 Score=23.25 Aligned_cols=36 Identities=25% Similarity=0.325 Sum_probs=27.0
Q ss_pred HHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHH
Q 036324 47 IEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFN 83 (91)
Q Consensus 47 veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~ 83 (91)
++-.+..|.-.==+ .|.+.|+.+=|.|..||++||.
T Consensus 19 l~aA~~lF~~~Gy~-~s~~~IA~~AGvsk~tiy~~F~ 54 (225)
T PRK11552 19 IAAALAQFGEYGLH-ATTRDIAAQAGQNIAAITYYFG 54 (225)
T ss_pred HHHHHHHHHHhCcc-CCHHHHHHHhCCCHHHHHHHcC
Confidence 34445555543334 8999999999999999999984
No 430
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=32.93 E-value=97 Score=23.20 Aligned_cols=43 Identities=16% Similarity=0.257 Sum_probs=34.6
Q ss_pred cHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 46 SIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 46 ~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
+=-||+.+-||- -.+.+...|+..-|.|.++|||.-.+.+..+
T Consensus 198 ~EREk~Vl~l~y-~eelt~kEI~~~LgISes~VSql~kkai~kL 240 (247)
T COG1191 198 PEREKLVLVLRY-KEELTQKEIAEVLGISESRVSRLHKKAIKKL 240 (247)
T ss_pred CHHHHHHHHHHH-HhccCHHHHHHHhCccHHHHHHHHHHHHHHH
Confidence 334566666666 5678999999999999999999998887654
No 431
>PRK10130 transcriptional regulator EutR; Provisional
Probab=32.91 E-value=86 Score=24.29 Aligned_cols=31 Identities=19% Similarity=0.304 Sum_probs=26.3
Q ss_pred HHhhcCcchhhhhhccccchhhHHHHHHHHH
Q 036324 56 HILAHHVKSRTIHSRFLRSRETISRYFNLVL 86 (91)
Q Consensus 56 ~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl 86 (91)
-..+.+.+..++...++.|..|++|.|++++
T Consensus 251 ~~~~~~ltv~~lA~~~gvS~r~L~r~Fk~~~ 281 (350)
T PRK10130 251 ENMSEPVTVLDLCNQLHVSRRTLQNAFHAIL 281 (350)
T ss_pred hhhcCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 3355668889999999999999999999875
No 432
>PF00292 PAX: 'Paired box' domain; InterPro: IPR001523 The paired box is a conserved 124 amino acid N-terminal domain of unknown function that usually, but not always, precedes a homeobox domain (see IPR001356 from INTERPRO) [, ]. Paired box genes are expressed in alternate segments of the developing fruit fly, the observed grouping of segments into pairs depending on the position of the segment in the segmental array, and not on the identity of the segment as in the case of homeotic genes. This implies that the genes affect different processes from those altered by homeotic genes.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 6PAX_A 1K78_E 1MDM_A 2K27_A 1PDN_C.
Probab=32.69 E-value=1.1e+02 Score=20.68 Aligned_cols=43 Identities=14% Similarity=0.111 Sum_probs=29.1
Q ss_pred CCCCCccHHHHHHHH-HHHhhcCcchhhhhhccccchhhHHHHHHH
Q 036324 40 KADGTVSIEEQLCMF-LHILAHHVKSRTIHSRFLRSRETISRYFNL 84 (91)
Q Consensus 40 ~~s~~v~veE~vamF-L~i~~~~~~~r~i~~~F~~S~eTisr~f~~ 84 (91)
.+.+..+.+.+..|- |+. .|.+.++|+.+++.|...||+++..
T Consensus 13 ~nGrPLp~~~R~rIvela~--~G~rp~~Isr~l~Vs~gcVsKIl~R 56 (125)
T PF00292_consen 13 INGRPLPNELRQRIVELAK--EGVRPCDISRQLRVSHGCVSKILSR 56 (125)
T ss_dssp ETTSSS-HHHHHHHHHHHH--TT--HHHHHHHHT--HHHHHHHHHH
T ss_pred eCCccCcHHHHHHHHHHhh--hcCCHHHHHHHHccchhHHHHHHHH
Confidence 345667777776665 443 5899999999999999999998764
No 433
>COG2186 FadR Transcriptional regulators [Transcription]
Probab=32.61 E-value=1.4e+02 Score=21.66 Aligned_cols=40 Identities=23% Similarity=0.315 Sum_probs=28.8
Q ss_pred CHHHHHHHHHHHHhCCCCCCCCCccHHHHHHHHHHHhhcCcchhhhhhccccchhhH
Q 036324 22 DKRTFELLCGLLRINGGLKADGTVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETI 78 (91)
Q Consensus 22 ~~~~F~~L~~~L~~~~~l~~s~~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTi 78 (91)
...+..+|-+.+.+ +.+++....|.|.. +.+.||+|+.||
T Consensus 12 ~~~v~~~i~~~I~~-g~~~~G~~LP~Ere----------------Lae~fgVSR~~v 51 (241)
T COG2186 12 ADEVAEQIGALIVS-GELPPGDRLPSERE----------------LAERFGVSRTVV 51 (241)
T ss_pred HHHHHHHHHHHHHc-CCCCCCCCCCCHHH----------------HHHHHCCCcHHH
Confidence 34556666666665 66777777777755 567899999998
No 434
>COG2378 Predicted transcriptional regulator [Transcription]
Probab=32.44 E-value=95 Score=23.66 Aligned_cols=37 Identities=22% Similarity=0.183 Sum_probs=27.4
Q ss_pred HHHHHHHhhcC-cchhhhhhccccchhhHHHHHHHHHH
Q 036324 51 LCMFLHILAHH-VKSRTIHSRFLRSRETISRYFNLVLN 87 (91)
Q Consensus 51 vamFL~i~~~~-~~~r~i~~~F~~S~eTisr~f~~Vl~ 87 (91)
+.|-.+..++. .+-+.+++.|++|..||.|-|.....
T Consensus 11 ~~ii~~L~~~~~vta~~lA~~~~VS~RTi~RDi~~L~~ 48 (311)
T COG2378 11 LQIIQILRAKETVTAAELADEFEVSVRTIYRDIATLRA 48 (311)
T ss_pred HHHHHHHHhCccchHHHHHHhcCCCHHHHHHHHHHHHH
Confidence 34444444544 47788999999999999999987644
No 435
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=32.31 E-value=35 Score=17.90 Aligned_cols=21 Identities=14% Similarity=-0.037 Sum_probs=16.5
Q ss_pred chhhhhhccccchhhHHHHHH
Q 036324 63 KSRTIHSRFLRSRETISRYFN 83 (91)
Q Consensus 63 ~~r~i~~~F~~S~eTisr~f~ 83 (91)
+...++..++.|..||.++..
T Consensus 2 ~~~e~a~~~gv~~~tlr~~~~ 22 (49)
T cd04761 2 TIGELAKLTGVSPSTLRYYER 22 (49)
T ss_pred cHHHHHHHHCcCHHHHHHHHH
Confidence 346788899999999987754
No 436
>PRK11202 DNA-binding transcriptional repressor FabR; Provisional
Probab=32.02 E-value=26 Score=24.31 Aligned_cols=24 Identities=13% Similarity=0.112 Sum_probs=21.8
Q ss_pred cCcchhhhhhccccchhhHHHHHH
Q 036324 60 HHVKSRTIHSRFLRSRETISRYFN 83 (91)
Q Consensus 60 ~~~~~r~i~~~F~~S~eTisr~f~ 83 (91)
++.+.++|...=|.|+.|+++||.
T Consensus 31 ~~~si~~IA~~Agvs~~t~Y~hF~ 54 (203)
T PRK11202 31 SSLSLREVAREAGIAPTSFYRHFR 54 (203)
T ss_pred ccCCHHHHHHHhCCCcchHHHHCC
Confidence 468999999999999999999993
No 437
>COG1342 Predicted DNA-binding proteins [General function prediction only]
Probab=31.59 E-value=61 Score=21.31 Aligned_cols=47 Identities=23% Similarity=0.193 Sum_probs=36.1
Q ss_pred CCccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHH----HHHHHh
Q 036324 43 GTVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNL----VLNAIL 90 (91)
Q Consensus 43 ~~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~----Vl~ai~ 90 (91)
-.+++||-=||=|--. .+.++..++.+.|.|+.|++|-... |-+|++
T Consensus 32 V~lt~eElEAlRLvD~-~~l~QeeAA~rMgISr~Tfwr~l~sAR~KvA~aLv 82 (99)
T COG1342 32 VILTIEELEALRLVDY-EGLTQEEAALRMGISRQTFWRLLTSARKKVADALV 82 (99)
T ss_pred eeecHHHHHHHHHHhH-hhccHHHHHHHhcccHHHHHHHHHHHHHHHHHHHh
Confidence 3678888877766433 5789999999999999999998764 555554
No 438
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=31.44 E-value=1.1e+02 Score=20.92 Aligned_cols=45 Identities=18% Similarity=0.262 Sum_probs=33.2
Q ss_pred CCccHHHHHHHHHHHhh-----cCcchhhhhhccccchhhHHHHHHHHHH
Q 036324 43 GTVSIEEQLCMFLHILA-----HHVKSRTIHSRFLRSRETISRYFNLVLN 87 (91)
Q Consensus 43 ~~v~veE~vamFL~i~~-----~~~~~r~i~~~F~~S~eTisr~f~~Vl~ 87 (91)
+..|-||+=.+...|+. .-.+.+++...+|-|..|+.++|++...
T Consensus 3 ~~~T~eer~eLk~rIvElVRe~GRiTi~ql~~~TGasR~Tvk~~lreLVa 52 (127)
T PF06163_consen 3 RVFTPEEREELKARIVELVREHGRITIKQLVAKTGASRNTVKRYLRELVA 52 (127)
T ss_pred CcCCHHHHHHHHHHHHHHHHHcCCccHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 34566666666666653 2267788888899999999999998653
No 439
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=31.09 E-value=1.2e+02 Score=21.81 Aligned_cols=43 Identities=14% Similarity=0.170 Sum_probs=29.2
Q ss_pred HHHHHHHHHHHhCCCCCCCCCccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHH
Q 036324 24 RTFELLCGLLRINGGLKADGTVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFN 83 (91)
Q Consensus 24 ~~F~~L~~~L~~~~~l~~s~~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~ 83 (91)
.++..|-+.+.. +.+++...++.|. .+++.||.|+.||-.-+.
T Consensus 6 ~v~~~L~~~I~~-g~l~pG~~LpsE~----------------eLae~~gVSRtpVREAL~ 48 (253)
T PRK10421 6 EVADRVRALIEE-KNLEAGMKLPAER----------------QLAMQLGVSRNSLREALA 48 (253)
T ss_pred HHHHHHHHHHHc-CCCCCCCcCCCHH----------------HHHHHhCCCHHHHHHHHH
Confidence 455566666654 6677776666554 457899999999965544
No 440
>PF05930 Phage_AlpA: Prophage CP4-57 regulatory protein (AlpA); InterPro: IPR010260 This entry is represents phage P4, Orf88. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. In Escherichia coli phage P4 Orf 88 is similar to AlpA of the CP4-57 cryptic prophage []. AlpA acts as a positive transcriptional regulator of slpA, a gene linked to alpA and necessary for suppression of lon mutants [, ]. The sequence of slpA suggests that it encodes an integrase gene closely related to phage P4 int and that both alpA and slpA are part of a cryptic P4-like prophage. Increase in alpA expression increases SlpA synthesis. Increased SlpA leads, in turn, to the excision and loss of the cryptic prophage. ; PDB: 1Z4H_A.
Probab=31.08 E-value=45 Score=18.41 Aligned_cols=21 Identities=24% Similarity=0.281 Sum_probs=15.9
Q ss_pred chhhhhhccccchhhHHHHHH
Q 036324 63 KSRTIHSRFLRSRETISRYFN 83 (91)
Q Consensus 63 ~~r~i~~~F~~S~eTisr~f~ 83 (91)
+-.++....+.|..|+.+..+
T Consensus 5 ~~~ev~~~~g~s~~ti~~~~k 25 (51)
T PF05930_consen 5 RIKEVAELLGVSRSTIYRLIK 25 (51)
T ss_dssp -HHHHHHHHSS-HHHHHHHHH
T ss_pred cHHHHHHHHCCCHHHHHHHHh
Confidence 456788899999999998765
No 441
>PF07750 GcrA: GcrA cell cycle regulator; InterPro: IPR011681 GcrA, together with CtrA (see IPR001789 from INTERPRO and IPR001867 from INTERPRO), form a master cell cycle regulator. These bacterial regulators are involved in controlling the progression and asymmetric polar morphogenesis []. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes []. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery [].
Probab=30.82 E-value=64 Score=22.51 Aligned_cols=37 Identities=14% Similarity=0.137 Sum_probs=27.0
Q ss_pred HHHHHHHHHHhhcCcchhhhhhccc-cchhhHHHHHHH
Q 036324 48 EEQLCMFLHILAHHVKSRTIHSRFL-RSRETISRYFNL 84 (91)
Q Consensus 48 eE~vamFL~i~~~~~~~r~i~~~F~-~S~eTisr~f~~ 84 (91)
+|++..---.-+.|.|..+|+..+| +|+..|-=+.|.
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 3444444444578899999999999 999988655553
No 442
>PF04591 DUF596: Protein of unknown function, DUF596; InterPro: IPR007670 This family contains several uncharacterised proteins.; PDB: 2O5H_B.
Probab=30.73 E-value=32 Score=21.26 Aligned_cols=12 Identities=42% Similarity=0.426 Sum_probs=8.1
Q ss_pred CccHHHHHHHHH
Q 036324 44 TVSIEEQLCMFL 55 (91)
Q Consensus 44 ~v~veE~vamFL 55 (91)
.-|++|||.||=
T Consensus 16 ~Gt~eEqve~fr 27 (70)
T PF04591_consen 16 EGTTEEQVEMFR 27 (70)
T ss_dssp ---HHHHHHHHH
T ss_pred cCCHHHHHHHHH
Confidence 468999999984
No 443
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=30.70 E-value=47 Score=25.71 Aligned_cols=28 Identities=21% Similarity=0.209 Sum_probs=23.0
Q ss_pred CChhHHHHHhCCCHHHHHHHHHHHHhCC
Q 036324 10 GSDIECVNQLRMDKRTFELLCGLLRING 37 (91)
Q Consensus 10 ~~~~~c~~~fRM~~~~F~~L~~~L~~~~ 37 (91)
++|++..+-|+|++.+|.+-..-|-..+
T Consensus 247 SsPEdIk~~FgiSKg~FKrAiGgL~K~g 274 (287)
T COG2996 247 SSPEDIKATFGISKGQFKRAIGGLMKAG 274 (287)
T ss_pred CCHHHHHHHhCcCHHHHHHHHHHHHhCC
Confidence 6899999999999999998666654444
No 444
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=30.21 E-value=48 Score=18.71 Aligned_cols=22 Identities=9% Similarity=-0.058 Sum_probs=17.7
Q ss_pred chhhhhhccccchhhHHHHHHH
Q 036324 63 KSRTIHSRFLRSRETISRYFNL 84 (91)
Q Consensus 63 ~~r~i~~~F~~S~eTisr~f~~ 84 (91)
+...++..++.|.+|+.++.++
T Consensus 2 s~~eva~~~gvs~~tlr~w~~~ 23 (68)
T cd01104 2 TIGAVARLTGVSPDTLRAWERR 23 (68)
T ss_pred CHHHHHHHHCcCHHHHHHHHHh
Confidence 3467888999999999888653
No 445
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=30.02 E-value=54 Score=23.43 Aligned_cols=45 Identities=18% Similarity=0.315 Sum_probs=31.0
Q ss_pred HHHHHHHHHhCC--CCCCCCCccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHH
Q 036324 26 FELLCGLLRING--GLKADGTVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVL 86 (91)
Q Consensus 26 F~~L~~~L~~~~--~l~~s~~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl 86 (91)
+.++.+.|+.+. .+++...++.|..| +..|+.|+.||-+-+.+.-
T Consensus 14 Y~qi~~~L~~~I~~~~~~G~~LPsE~eL----------------a~~~~VSR~TVR~Al~~L~ 60 (241)
T PRK10079 14 YQEIAAKLEQELRQHYRCGDYLPAEQQL----------------AARYEVNRHTLRRAIDQLV 60 (241)
T ss_pred HHHHHHHHHHHHhcccCCCCcCCCHHHH----------------HHHHCCCHHHHHHHHHHHH
Confidence 555666665532 45666667776654 6899999999988877643
No 446
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=29.97 E-value=1.3e+02 Score=22.00 Aligned_cols=39 Identities=13% Similarity=0.187 Sum_probs=27.1
Q ss_pred HHHHHHHHHHHhhcCc--chhhhhhccccchhhHHHHHHHH
Q 036324 47 IEEQLCMFLHILAHHV--KSRTIHSRFLRSRETISRYFNLV 85 (91)
Q Consensus 47 veE~vamFL~i~~~~~--~~r~i~~~F~~S~eTisr~f~~V 85 (91)
++..+.+.=+.-.++. +...|+...+-+++|++|+.+..
T Consensus 3 l~ral~iL~~l~~~~~~l~l~ela~~~glpksT~~RlL~tL 43 (246)
T COG1414 3 LERALAILDLLAEGPGGLSLAELAERLGLPKSTVHRLLQTL 43 (246)
T ss_pred HHHHHHHHHHHHhCCCCCCHHHHHHHhCcCHHHHHHHHHHH
Confidence 3344444333333444 49999999999999999988754
No 447
>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=29.90 E-value=38 Score=27.21 Aligned_cols=37 Identities=30% Similarity=0.271 Sum_probs=27.2
Q ss_pred HHHHHHHHHHHhh--cCcchhhhhhccccchhhHHHHHH
Q 036324 47 IEEQLCMFLHILA--HHVKSRTIHSRFLRSRETISRYFN 83 (91)
Q Consensus 47 veE~vamFL~i~~--~~~~~r~i~~~F~~S~eTisr~f~ 83 (91)
++-|=+-|..-.+ .+.+.++|++..|.+-+||||...
T Consensus 302 v~~Q~~Ff~~G~~~LkPLtlkdiA~~lglheSTVSRav~ 340 (429)
T TIGR02395 302 VEHQKDFFLGGPAALKPLTLREVAEELGLHESTISRAIN 340 (429)
T ss_pred HHHHHHHHhcCcccCcCCcHHHHHHHhCCCccchhhhhc
Confidence 3445555554332 468899999999999999999764
No 448
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=29.89 E-value=82 Score=23.15 Aligned_cols=24 Identities=29% Similarity=0.238 Sum_probs=19.7
Q ss_pred cchhhhhhccccchhhHHHHHHHH
Q 036324 62 VKSRTIHSRFLRSRETISRYFNLV 85 (91)
Q Consensus 62 ~~~r~i~~~F~~S~eTisr~f~~V 85 (91)
.+..++.++|++|.+||-|=+++.
T Consensus 20 v~v~eLa~~~~VS~~TIRRDL~~L 43 (253)
T COG1349 20 VSVEELAELFGVSEMTIRRDLNEL 43 (253)
T ss_pred EEHHHHHHHhCCCHHHHHHhHHHH
Confidence 455677899999999999977764
No 449
>TIGR03337 phnR transcriptional regulator protein. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Salmonella, Vibrio Aeromonas hydrophila, Hahella chejuensis and Psychromonas ingrahamii.
Probab=29.58 E-value=1.8e+02 Score=20.24 Aligned_cols=42 Identities=26% Similarity=0.350 Sum_probs=28.3
Q ss_pred HHHHHHHHhCCCCCCCCCccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHH
Q 036324 27 ELLCGLLRINGGLKADGTVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLV 85 (91)
Q Consensus 27 ~~L~~~L~~~~~l~~s~~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~V 85 (91)
..|.+.+++ +.+++...++.|..| +..|+.|+-||-+-+...
T Consensus 8 ~~l~~~I~~-g~~~~g~~lPsE~eL----------------a~~~~Vsr~Tvr~Al~~L 49 (231)
T TIGR03337 8 DHLSYQIRA-GALLPGDKLPSERDL----------------GERFNTTRVTIREALQQL 49 (231)
T ss_pred HHHHHHHHc-CCCCCCCcCcCHHHH----------------HHHHCCCHHHHHHHHHHH
Confidence 344455554 566776677777765 578899999987766543
No 450
>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=29.50 E-value=38 Score=23.15 Aligned_cols=15 Identities=20% Similarity=0.166 Sum_probs=12.0
Q ss_pred ccccchhhHHHHHHH
Q 036324 70 RFLRSRETISRYFNL 84 (91)
Q Consensus 70 ~F~~S~eTisr~f~~ 84 (91)
-|..|+.||||-+++
T Consensus 30 G~~vsqaTIsRdL~e 44 (146)
T TIGR01529 30 GIEVTQATVSRDLRE 44 (146)
T ss_pred CCCcCHHHHHHHHHH
Confidence 456889999997776
No 451
>TIGR03734 PRTRC_parB PRTRC system ParB family protein. A novel genetic system characterized by six major proteins, included a ParB homolog and a ThiF homolog, is designated PRTRC, or ParB-Related,ThiF-Related Cassette. It is often found on plasmids. This protein family the member related to ParB, and is designated PRTRC system ParB family protein.
Probab=29.33 E-value=97 Score=26.05 Aligned_cols=40 Identities=18% Similarity=0.126 Sum_probs=29.2
Q ss_pred CccHHHHHHHHHHHhhcCc-chhhhhhccccchhhHHHHHH
Q 036324 44 TVSIEEQLCMFLHILAHHV-KSRTIHSRFLRSRETISRYFN 83 (91)
Q Consensus 44 ~v~veE~vamFL~i~~~~~-~~r~i~~~F~~S~eTisr~f~ 83 (91)
.++.-|+..-|--.+..+. +...|+.+|+.|..+|+|...
T Consensus 91 dLtP~EeA~A~~rLl~~g~~t~eeIA~~lG~S~~~V~rrLk 131 (554)
T TIGR03734 91 DMSPAEEAEAAARLLGRCKGDREEAARRLGWSPATLDRRLA 131 (554)
T ss_pred CCCHHHHHHHHHHHhhhcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 4555555544555555555 888999999999999999875
No 452
>PRK15008 HTH-type transcriptional regulator RutR; Provisional
Probab=29.24 E-value=67 Score=22.26 Aligned_cols=36 Identities=19% Similarity=0.157 Sum_probs=27.7
Q ss_pred HHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHH
Q 036324 48 EEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFN 83 (91)
Q Consensus 48 eE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~ 83 (91)
+-...+|.-.--++.+.++|...=|.|..||+.||.
T Consensus 25 ~AA~~lf~e~Gy~~~s~~dIA~~aGvs~gtiY~hF~ 60 (212)
T PRK15008 25 SAALDTFSQFGFHGTRLEQIAELAGVSKTNLLYYFP 60 (212)
T ss_pred HHHHHHHHHhCcccCCHHHHHHHhCcCHHHHHHHCC
Confidence 334445544444668999999999999999999995
No 453
>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=29.24 E-value=1.3e+02 Score=19.09 Aligned_cols=39 Identities=18% Similarity=0.250 Sum_probs=31.6
Q ss_pred cHHHHHHHHHHHhhcCcchhhhhhccccc----hhhHHHHHHHH
Q 036324 46 SIEEQLCMFLHILAHHVKSRTIHSRFLRS----RETISRYFNLV 85 (91)
Q Consensus 46 ~veE~vamFL~i~~~~~~~r~i~~~F~~S----~eTisr~f~~V 85 (91)
..|.+|-=.||-.+. .+.+.|.+.+.-+ ..||....+..
T Consensus 3 ~~E~~IM~~lW~~~~-~t~~eI~~~l~~~~~~~~sTv~t~L~rL 45 (115)
T PF03965_consen 3 DLELEIMEILWESGE-ATVREIHEALPEERSWAYSTVQTLLNRL 45 (115)
T ss_dssp HHHHHHHHHHHHHSS-EEHHHHHHHHCTTSS--HHHHHHHHHHH
T ss_pred HHHHHHHHHHHhCCC-CCHHHHHHHHHhccccchhHHHHHHHHH
Confidence 468889999999999 9999999888766 78887666543
No 454
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=29.15 E-value=81 Score=23.15 Aligned_cols=25 Identities=16% Similarity=0.138 Sum_probs=22.1
Q ss_pred cchhhhhhccccchhhHHHHHHHHH
Q 036324 62 VKSRTIHSRFLRSRETISRYFNLVL 86 (91)
Q Consensus 62 ~~~r~i~~~F~~S~eTisr~f~~Vl 86 (91)
.+...++...+.|..|+||...+.-
T Consensus 22 IS~~eLA~~L~iS~~Tvsr~Lk~LE 46 (217)
T PRK14165 22 ISSSEFANHTGTSSKTAARILKQLE 46 (217)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 5788999999999999999988753
No 455
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=29.07 E-value=1.6e+02 Score=21.11 Aligned_cols=41 Identities=10% Similarity=0.063 Sum_probs=26.0
Q ss_pred HHHHHHHHHhCCCCCCCCCccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHH
Q 036324 26 FELLCGLLRINGGLKADGTVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFN 83 (91)
Q Consensus 26 F~~L~~~L~~~~~l~~s~~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~ 83 (91)
...|.+.+.. +.+++...++.|.. ++..||.|+.||-.-+.
T Consensus 15 ~~~l~~~I~~-g~l~pG~~LpsE~e----------------La~~~gVSRtpVREAL~ 55 (257)
T PRK10225 15 GAMIRDLIIK-TPYNPGERLPPERE----------------IAEMLDVTRTVVREALI 55 (257)
T ss_pred HHHHHHHHHh-CCCCCCCcCcCHHH----------------HHHHhCCCHHHHHHHHH
Confidence 3344444443 56677666665554 57899999999955444
No 456
>PF07526 POX: Associated with HOX; InterPro: IPR006563 This domain in found exclusively in plant proteins, associated with HOX domains which may suggest these proteins are homeodomain transcription factors.
Probab=29.00 E-value=55 Score=22.44 Aligned_cols=62 Identities=18% Similarity=0.114 Sum_probs=35.0
Q ss_pred hCCCHHHHHHHHHHHHhCCCC---CCCCCccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHHHh
Q 036324 19 LRMDKRTFELLCGLLRINGGL---KADGTVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNAIL 90 (91)
Q Consensus 19 fRM~~~~F~~L~~~L~~~~~l---~~s~~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai~ 90 (91)
..+.+.-...|.++...+|.. +--.-++.=|+|| =+|....|...+-+ ||||+|+-.=+||.
T Consensus 75 ~q~kK~KLl~mL~eVd~RY~qY~~Qmq~VvssFe~va----G~gaA~~YtalAlq------amSrhFR~LRdaI~ 139 (140)
T PF07526_consen 75 LQRKKAKLLSMLDEVDRRYRQYYDQMQAVVSSFEAVA----GLGAAAPYTALALQ------AMSRHFRCLRDAIS 139 (140)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh----cCCcchhhHHHHHH------HHHHHHHHHHHHhc
Confidence 334455555555555555421 0001233334443 23344677777766 99999999988885
No 457
>PF10654 DUF2481: Protein of unknown function (DUF2481) ; InterPro: IPR018916 This entry is represented by Bacteriophage A500, Gp59. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=28.79 E-value=62 Score=22.03 Aligned_cols=35 Identities=20% Similarity=0.363 Sum_probs=26.2
Q ss_pred CCccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHH
Q 036324 43 GTVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRY 81 (91)
Q Consensus 43 ~~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~ 81 (91)
..+++-| |.-.=-.|.+.-.|++.|..|.+||..+
T Consensus 66 e~iti~E----fi~LR~AGlt~~aIAd~F~iS~s~~~nf 100 (126)
T PF10654_consen 66 EEITIRE----FIELRHAGLTCYAIADYFKISKSTVFNF 100 (126)
T ss_pred hHhhHHH----HHHHHhcCCChHHHHHHHhHHHHHHHHH
Confidence 3455555 4444556899999999999999998654
No 458
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=28.12 E-value=45 Score=22.46 Aligned_cols=23 Identities=13% Similarity=0.238 Sum_probs=20.7
Q ss_pred CcchhhhhhccccchhhHHHHHH
Q 036324 61 HVKSRTIHSRFLRSRETISRYFN 83 (91)
Q Consensus 61 ~~~~r~i~~~F~~S~eTisr~f~ 83 (91)
|.|+-.|++.-|.|+..||+|.+
T Consensus 22 G~Sq~~iA~LLGltqaAVS~Yls 44 (119)
T COG2522 22 GLSQYRIAKLLGLTQAAVSQYLS 44 (119)
T ss_pred CCcHHHHHHHhCCCHHHHHHHHc
Confidence 67888999999999999999975
No 459
>KOG3414 consensus Component of the U4/U6.U5 snRNP/mitosis protein DIM1 [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=28.01 E-value=26 Score=24.35 Aligned_cols=31 Identities=19% Similarity=0.288 Sum_probs=26.5
Q ss_pred CcchhhhhhccccchhhHHHHHHHHHHHHhC
Q 036324 61 HVKSRTIHSRFLRSRETISRYFNLVLNAILQ 91 (91)
Q Consensus 61 ~~~~r~i~~~F~~S~eTisr~f~~Vl~ai~e 91 (91)
+.+-|.+--||||+.+.+|-+..++|..++|
T Consensus 20 ~t~~rlvViRFGr~~Dp~C~~mD~~L~~i~~ 50 (142)
T KOG3414|consen 20 STEERLVVIRFGRDWDPTCMKMDELLSSIAE 50 (142)
T ss_pred cccceEEEEEecCCCCchHhhHHHHHHHHHH
Confidence 3566778889999999999999999988764
No 460
>PRK09393 ftrA transcriptional activator FtrA; Provisional
Probab=27.99 E-value=1.2e+02 Score=22.63 Aligned_cols=29 Identities=24% Similarity=0.206 Sum_probs=24.5
Q ss_pred hhcCcchhhhhhccccchhhHHHHHHHHH
Q 036324 58 LAHHVKSRTIHSRFLRSRETISRYFNLVL 86 (91)
Q Consensus 58 ~~~~~~~r~i~~~F~~S~eTisr~f~~Vl 86 (91)
...+.+-.+++..++.|..+++|.|++.+
T Consensus 231 ~~~~~sl~~lA~~~~~S~~~l~r~fk~~~ 259 (322)
T PRK09393 231 LAEPHTVASLAARAAMSPRTFLRRFEAAT 259 (322)
T ss_pred cCCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 34457889999999999999999999864
No 461
>PRK13503 transcriptional activator RhaS; Provisional
Probab=27.90 E-value=2.2e+02 Score=20.15 Aligned_cols=27 Identities=19% Similarity=0.203 Sum_probs=23.0
Q ss_pred cCcchhhhhhccccchhhHHHHHHHHH
Q 036324 60 HHVKSRTIHSRFLRSRETISRYFNLVL 86 (91)
Q Consensus 60 ~~~~~r~i~~~F~~S~eTisr~f~~Vl 86 (91)
...+-.+++..++-|..+++|.|+++.
T Consensus 186 ~~~tl~~lA~~~~lS~~~l~r~Fk~~~ 212 (278)
T PRK13503 186 EEVNWEALADQFSLSLRTLHRQLKQQT 212 (278)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHh
Confidence 356778899999999999999998864
No 462
>PF06970 RepA_N: Replication initiator protein A (RepA) N-terminus; InterPro: IPR010724 This entry represents the N terminus (approximately 80 residues) of replication initiator protein A (RepA), a DNA replication initiator in plasmids []. Most proteins in this entry are bacterial, but archaeal and eukaryotic members are also included.
Probab=27.63 E-value=47 Score=20.39 Aligned_cols=22 Identities=9% Similarity=-0.013 Sum_probs=18.7
Q ss_pred chhhhhhccccchhhHHHHHHH
Q 036324 63 KSRTIHSRFLRSRETISRYFNL 84 (91)
Q Consensus 63 ~~r~i~~~F~~S~eTisr~f~~ 84 (91)
++..+++.++.|..||.+..+|
T Consensus 54 s~eel~~~L~~s~~tv~~~~ke 75 (76)
T PF06970_consen 54 SIEELMELLNCSKSTVIKAKKE 75 (76)
T ss_pred eHHHHHHHHCCCHHHHHHHHHc
Confidence 5678888999999999988765
No 463
>COG2909 MalT ATP-dependent transcriptional regulator [Transcription]
Probab=27.49 E-value=50 Score=29.31 Aligned_cols=34 Identities=15% Similarity=0.235 Sum_probs=30.0
Q ss_pred HHHhhcCcchhhhhhccccchhhHHHHHHHHHHH
Q 036324 55 LHILAHHVKSRTIHSRFLRSRETISRYFNLVLNA 88 (91)
Q Consensus 55 L~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~a 88 (91)
|=-+++|.||++|+.+-..|..||--|.+++-..
T Consensus 840 L~Lia~G~SN~eIa~~L~isl~TVKtH~rniy~K 873 (894)
T COG2909 840 LGLIAQGLSNEEIAQELFISLTTVKTHIRNIYQK 873 (894)
T ss_pred HHHHHccCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5567899999999999999999999999987654
No 464
>TIGR02612 mob_myst_A mobile mystery protein A. Members of this protein family are found in mobization-related contexts more often than not, including within a CRISPR-associated gene region in Geobacter sulfurreducens PCA, and on plasmids in Agrobacterium tumefaciens and Coxiella burnetii, always together with mobile mystery protein B, a member of the Fic protein family (pfam02661). This protein is encoded by the upstream member of the gene pair and belongs to a family of helix-turn-helix DNA binding proteins (pfam01381).
Probab=27.44 E-value=49 Score=22.90 Aligned_cols=27 Identities=7% Similarity=0.009 Sum_probs=23.8
Q ss_pred HhhcCcchhhhhhccccchhhHHHHHH
Q 036324 57 ILAHHVKSRTIHSRFLRSRETISRYFN 83 (91)
Q Consensus 57 i~~~~~~~r~i~~~F~~S~eTisr~f~ 83 (91)
.-..|.+..+++++.|.|..|||++-+
T Consensus 34 R~~lGmTq~eLAerlGVS~~tIs~iE~ 60 (150)
T TIGR02612 34 RKALGMSGAQLAGRLGVTPQRVEALEK 60 (150)
T ss_pred HHHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 566788999999999999999999875
No 465
>PF09494 Slx4: Slx4 endonuclease; InterPro: IPR018574 The Slx4 protein is a heteromeric structure-specific endonuclease found in fungi. Slx4 with Slx1 acts as a nuclease on branched DNA substrates, particularly simple-Y, 5'-flap, or replication fork structures by cleaving the strand bearing the 5' non-homologous arm at the branch junction and thus generating ligatable nicked products from 5'-flap or replication fork substrates [].
Probab=27.42 E-value=1e+02 Score=17.99 Aligned_cols=44 Identities=20% Similarity=0.197 Sum_probs=34.9
Q ss_pred chhHHhhcCChhHHHHHhCCCHHHHHHHHHHHHhCCCCCCCCCcc
Q 036324 2 PHLSRSIIGSDIECVNQLRMDKRTFELLCGLLRINGGLKADGTVS 46 (91)
Q Consensus 2 ~~l~~ll~~~~~~c~~~fRM~~~~F~~L~~~L~~~~~l~~s~~v~ 46 (91)
+.+.+++..+|.-.-.++..+|=.+..|..+|...+ ..-++.++
T Consensus 3 ~~lt~~I~~~p~l~ekIL~YePI~L~el~~~L~~~g-~~~~~~~~ 46 (64)
T PF09494_consen 3 EALTKLIRSDPELYEKILMYEPINLEELHAWLKASG-IGFDRKVD 46 (64)
T ss_pred HHHHHHHHcCHHHHHHHHcCCCccHHHHHHHHHHcC-CCccceeC
Confidence 467888999999999999999999999999999544 33333343
No 466
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=27.37 E-value=1.3e+02 Score=25.15 Aligned_cols=44 Identities=14% Similarity=0.172 Sum_probs=32.3
Q ss_pred cHHHHHHHHHHH-h--hcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 46 SIEEQLCMFLHI-L--AHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 46 ~veE~vamFL~i-~--~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
+--|+.-+-++. + +.+.+...|+..|+.|.+.|+++=...|+-+
T Consensus 558 ~~rE~~Vl~~r~g~~~~~~~tl~ei~~~lgvs~eRVrQie~~al~kL 604 (619)
T PRK05658 558 TPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 604 (619)
T ss_pred CHHHHHHHHHhcCCCCCCCccHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 444554555544 3 3678999999999999999998877776644
No 467
>PF01476 LysM: LysM domain; InterPro: IPR018392 This domain is about 40 residues long and is found in a variety of enzymes involved in bacterial cell wall degradation []. This domain may have a general peptidoglycan binding function.; GO: 0016998 cell wall macromolecule catabolic process; PDB: 2DJP_A 3ZQD_A 1Y7M_B 4A52_A 2L9Y_A 1E0G_A.
Probab=27.33 E-value=25 Score=18.24 Aligned_cols=24 Identities=13% Similarity=0.064 Sum_probs=14.7
Q ss_pred HhhcCcchhhhhhccccchhhHHH
Q 036324 57 ILAHHVKSRTIHSRFLRSRETISR 80 (91)
Q Consensus 57 i~~~~~~~r~i~~~F~~S~eTisr 80 (91)
.+..|.+...|+.+|+.+.+.+.+
T Consensus 2 ~V~~gDtl~~IA~~~~~~~~~l~~ 25 (44)
T PF01476_consen 2 TVQPGDTLWSIAKRYGISVDELME 25 (44)
T ss_dssp EE-TT--HHHHHHHTTS-HHHHHH
T ss_pred EECcCCcHHHHHhhhhhhHhHHHH
Confidence 455677788888888888777654
No 468
>PRK10336 DNA-binding transcriptional regulator QseB; Provisional
Probab=27.31 E-value=84 Score=20.76 Aligned_cols=37 Identities=8% Similarity=0.244 Sum_probs=28.4
Q ss_pred HHHHHhhcC----cchhhhhhccc-----cchhhHHHHHHHHHHHH
Q 036324 53 MFLHILAHH----VKSRTIHSRFL-----RSRETISRYFNLVLNAI 89 (91)
Q Consensus 53 mFL~i~~~~----~~~r~i~~~F~-----~S~eTisr~f~~Vl~ai 89 (91)
-+|..+++| .++..|..... .|..||..|+..+.+.+
T Consensus 156 ~il~~l~~~~~~~~s~~~i~~~l~~~~~~~~~~tv~~~i~~lr~Kl 201 (219)
T PRK10336 156 ALLELLMRNAGRVLPRKLIEEKLYTWDEEVTSNAVEVHVHHLRRKL 201 (219)
T ss_pred HHHHHHHhCCCccCcHHHHHHHhcCCCCCCCccCHHHHHHHHHHhc
Confidence 345566666 78999988765 89999999998887654
No 469
>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
Probab=27.16 E-value=91 Score=15.38 Aligned_cols=24 Identities=8% Similarity=0.081 Sum_probs=16.9
Q ss_pred cchhhhhhccc-cchhhHHHHHHHH
Q 036324 62 VKSRTIHSRFL-RSRETISRYFNLV 85 (91)
Q Consensus 62 ~~~r~i~~~F~-~S~eTisr~f~~V 85 (91)
.....|+..++ ||..-|.+++..+
T Consensus 20 ~~w~~Ia~~~~~rs~~~~~~~~~~~ 44 (45)
T cd00167 20 NNWEKIAKELPGRTPKQCRERWRNL 44 (45)
T ss_pred CCHHHHHhHcCCCCHHHHHHHHHHh
Confidence 56677777776 8888777776543
No 470
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=26.81 E-value=1.6e+02 Score=21.01 Aligned_cols=43 Identities=14% Similarity=0.013 Sum_probs=27.7
Q ss_pred HHHHHHHHHHHhCCCCCCCCCccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHH
Q 036324 24 RTFELLCGLLRINGGLKADGTVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFN 83 (91)
Q Consensus 24 ~~F~~L~~~L~~~~~l~~s~~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~ 83 (91)
.++..|.+.+.. +.+++...++.|. .++..||.|+.||-.-+.
T Consensus 12 ~v~~~l~~~I~~-g~l~pG~~LpsE~----------------eLae~~gVSRtpVREAL~ 54 (253)
T PRK11523 12 QLAAELKERIEQ-GVYLVGDKLPAER----------------FIADEKNVSRTVVREAII 54 (253)
T ss_pred HHHHHHHHHHHc-CCCCCCCCCCCHH----------------HHHHHHCCCHHHHHHHHH
Confidence 344455555554 5667766666554 457899999999955443
No 471
>PF05944 Phage_term_smal: Phage small terminase subunit; InterPro: IPR010270 This entry is represented by Bacteriophage P2, GpM. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several phage small terminase subunit proteins as well as some related bacterial sequences []. M protein is probably an endonuclease which directs cos cleavage. The Q, P and M proteins are needed to package DNA into proheads and for the conversion of proheads to capsids.; GO: 0003677 DNA binding, 0004519 endonuclease activity, 0019069 viral capsid assembly
Probab=26.79 E-value=71 Score=21.73 Aligned_cols=38 Identities=18% Similarity=0.186 Sum_probs=29.4
Q ss_pred cHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHHHHH
Q 036324 46 SIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLVLNA 88 (91)
Q Consensus 46 ~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~a 88 (91)
..+..+.++-|.+.||.. .-++|.|+..|+ .-.+|+++
T Consensus 63 d~~~AL~~a~yAi~~~l~---~P~~f~R~~~t~--vaeev~~~ 100 (132)
T PF05944_consen 63 DFDGALDIAEYAIEHGLP---MPDRFKRTLPTF--VAEEVADW 100 (132)
T ss_pred CHHHHHHHHHHHHHcCCC---ccccccCcchHH--HHHHHHHH
Confidence 368899999999999976 678999988886 34455443
No 472
>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=26.70 E-value=67 Score=19.18 Aligned_cols=39 Identities=13% Similarity=0.136 Sum_probs=25.5
Q ss_pred cHHHHHHHHHHH---hhcCcchhhhhhccccchhhHHHHHHH
Q 036324 46 SIEEQLCMFLHI---LAHHVKSRTIHSRFLRSRETISRYFNL 84 (91)
Q Consensus 46 ~veE~vamFL~i---~~~~~~~r~i~~~F~~S~eTisr~f~~ 84 (91)
+.|..+|=|+.- -..+.+-+.++..-+.|..||.|-.+.
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 445666655433 223578899999999999999997654
No 473
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=26.66 E-value=91 Score=23.15 Aligned_cols=24 Identities=17% Similarity=0.193 Sum_probs=21.6
Q ss_pred cchhhhhhccccchhhHHHHHHHH
Q 036324 62 VKSRTIHSRFLRSRETISRYFNLV 85 (91)
Q Consensus 62 ~~~r~i~~~F~~S~eTisr~f~~V 85 (91)
.+..++++.|+.|..||-|-+.+.
T Consensus 32 vtv~eLa~~l~VS~~TIRRDL~~L 55 (269)
T PRK09802 32 VQVNDLSALYGVSTVTIRNDLAFL 55 (269)
T ss_pred EeHHHHHHHHCCCHHHHHHHHHHH
Confidence 788899999999999999998764
No 474
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=26.62 E-value=45 Score=27.01 Aligned_cols=37 Identities=24% Similarity=0.182 Sum_probs=28.3
Q ss_pred HHHHHHHHHHHhh--cCcchhhhhhccccchhhHHHHHH
Q 036324 47 IEEQLCMFLHILA--HHVKSRTIHSRFLRSRETISRYFN 83 (91)
Q Consensus 47 veE~vamFL~i~~--~~~~~r~i~~~F~~S~eTisr~f~ 83 (91)
|+-|=+-|+.-.+ .+.+.++|++.-|.+-+||||...
T Consensus 327 v~~Q~~Ff~~G~~~LkPLtlkdvAe~lglheSTVSRav~ 365 (455)
T PRK05932 327 VEQQRDFFEHGEEALKPLVLKDIAEELGMHESTISRATT 365 (455)
T ss_pred HHHHHHHHhCCcccCcCccHHHHHHHhCCCccchhhhhc
Confidence 4556666665433 468899999999999999999764
No 475
>PF13565 HTH_32: Homeodomain-like domain
Probab=26.21 E-value=46 Score=19.31 Aligned_cols=35 Identities=29% Similarity=0.279 Sum_probs=20.0
Q ss_pred HHHHHHHHHHHhhc-Ccchhhhhh----ccc--c--chhhHHHH
Q 036324 47 IEEQLCMFLHILAH-HVKSRTIHS----RFL--R--SRETISRY 81 (91)
Q Consensus 47 veE~vamFL~i~~~-~~~~r~i~~----~F~--~--S~eTisr~ 81 (91)
.|..-.|-=.+..+ ..+.+.|+. .|+ . |.+||+|+
T Consensus 33 ~e~~~~i~~~~~~~p~wt~~~i~~~L~~~~g~~~~~S~~tv~R~ 76 (77)
T PF13565_consen 33 PEQRERIIALIEEHPRWTPREIAEYLEEEFGISVRVSRSTVYRI 76 (77)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCCCccHhHHHHh
Confidence 33334444444555 356655554 444 3 99999986
No 476
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=26.04 E-value=2.9e+02 Score=20.89 Aligned_cols=72 Identities=19% Similarity=0.093 Sum_probs=48.5
Q ss_pred HhCCCHHHHHHHHHHHHhCCCCCCCCCccHHHHHHHHHHHhh----cCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 18 QLRMDKRTFELLCGLLRINGGLKADGTVSIEEQLCMFLHILA----HHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 18 ~fRM~~~~F~~L~~~L~~~~~l~~s~~v~veE~vamFL~i~~----~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
.+++.+.+=..=+.+++.-+.....++-+.+--+|--||+.+ .+-+.+.|..-.+.+...|.+.|+.+++.+
T Consensus 135 ~L~Lp~~v~e~A~~iyk~~~~~~~~rgrs~~~i~AAclYiACR~~~~prtl~eI~~~~~v~~k~i~~~~~~l~k~L 210 (310)
T PRK00423 135 QLGLPRSVREEAAVIYRKAVEKGLIRGRSIEGVVAAALYAACRRCKVPRTLDEIAEVSRVSRKEIGRCYRFLLREL 210 (310)
T ss_pred HcCCCHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence 344444333333333333333344466777877888888854 457788999999999999999999988765
No 477
>COG0583 LysR Transcriptional regulator [Transcription]
Probab=25.83 E-value=80 Score=21.99 Aligned_cols=31 Identities=16% Similarity=0.117 Sum_probs=25.6
Q ss_pred HHHhhcCcchhhhhhccccchhhHHHHHHHH
Q 036324 55 LHILAHHVKSRTIHSRFLRSRETISRYFNLV 85 (91)
Q Consensus 55 L~i~~~~~~~r~i~~~F~~S~eTisr~f~~V 85 (91)
+..++...++..++..-..|+++||+.+.+.
T Consensus 9 F~~v~~~~s~t~AA~~L~isqsavS~~I~~L 39 (297)
T COG0583 9 FVAVAEEGSFTRAAERLGLSQSAVSRQIKRL 39 (297)
T ss_pred HHHHHHcCcHHHHHHHhCCCChHHHHHHHHH
Confidence 3455557889999999999999999998764
No 478
>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=25.54 E-value=1.8e+02 Score=18.21 Aligned_cols=48 Identities=17% Similarity=0.226 Sum_probs=38.0
Q ss_pred HHHHHHHHHHHh-CCCCCCCCCccHHHHHHHHHHHhhcCcchhhhhhcc
Q 036324 24 RTFELLCGLLRI-NGGLKADGTVSIEEQLCMFLHILAHHVKSRTIHSRF 71 (91)
Q Consensus 24 ~~F~~L~~~L~~-~~~l~~s~~v~veE~vamFL~i~~~~~~~r~i~~~F 71 (91)
.+...+++.|.. .+.+++..++...---|..-+-...|.+.++|+++.
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 355666777765 567777788888888888888889999999999885
No 479
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=25.51 E-value=3e+02 Score=20.83 Aligned_cols=76 Identities=9% Similarity=0.137 Sum_probs=49.0
Q ss_pred HHHHHhCCCHHHHHHHHHHHHhC--CCCCCCCCccHHHHHHHHHH--HhhcCcchhhhhhccccchhhHHHHHHHHHHHH
Q 036324 14 ECVNQLRMDKRTFELLCGLLRIN--GGLKADGTVSIEEQLCMFLH--ILAHHVKSRTIHSRFLRSRETISRYFNLVLNAI 89 (91)
Q Consensus 14 ~c~~~fRM~~~~F~~L~~~L~~~--~~l~~s~~v~veE~vamFL~--i~~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ai 89 (91)
+.-+.|.+..++=..-..+++.- .++...+.-..-=.-|+|+- ..|.+-+.+.|+.--+.|..||-+.+++....+
T Consensus 225 r~~~~L~L~~~v~~~A~~i~~~a~~~~l~~Gr~P~sIAAAaIYlA~~~~g~~~t~keIa~v~~Vs~~tI~~~ykel~~~l 304 (310)
T PRK00423 225 RFASELGLSGEVQKKAIEILQKAKEKGLTSGKGPTGLAAAAIYIASLLLGERRTQREVAEVAGVTEVTVRNRYKELAEKL 304 (310)
T ss_pred HHHHHcCCCHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHHHHHh
Confidence 44556666665544333333221 23444454444445555553 366778999999999999999999999988765
No 480
>COG3139 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.50 E-value=1.9e+02 Score=18.56 Aligned_cols=58 Identities=16% Similarity=0.243 Sum_probs=42.1
Q ss_pred CCHHHHHHHHHHHHhCCCCCCCCCccHHHH----HHHHHHHhhcCcc----------------hhhhhhccccchhhHH
Q 036324 21 MDKRTFELLCGLLRINGGLKADGTVSIEEQ----LCMFLHILAHHVK----------------SRTIHSRFLRSRETIS 79 (91)
Q Consensus 21 M~~~~F~~L~~~L~~~~~l~~s~~v~veE~----vamFL~i~~~~~~----------------~r~i~~~F~~S~eTis 79 (91)
|.|+++-+|.-... .|.-+|....+-|.+ =|.-||-.-||.. -......|+-|.++|.
T Consensus 10 mtPEiYQrL~~AvE-lGKWPdG~~LtqeQke~clQaVmlwqarhN~~aqhmti~~~gq~v~ksk~elk~~f~~~~~~i~ 87 (90)
T COG3139 10 MTPEIYQRLSTAVE-LGKWPDGVALTQEQKENCLQAVMLWQARHNTEAQHMTIDTGGQMVMKSKQELKEDFGISSKPIA 87 (90)
T ss_pred cCHHHHHHHHHHHH-hcCCCCCCcCCHHHHHHHHHHHHHHHHhcCChhhhhccccCCeeeecchHhhhhhhCcCccccc
Confidence 78889988887765 477899999998875 3677898888853 2344556666666654
No 481
>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.
Probab=25.32 E-value=1.4e+02 Score=18.56 Aligned_cols=16 Identities=25% Similarity=0.185 Sum_probs=12.5
Q ss_pred ccchhhHHHHHHHHHH
Q 036324 72 LRSRETISRYFNLVLN 87 (91)
Q Consensus 72 ~~S~eTisr~f~~Vl~ 87 (91)
..|..||+|......+
T Consensus 32 ~i~~~TVYR~L~~L~~ 47 (116)
T cd07153 32 SISLATVYRTLELLEE 47 (116)
T ss_pred CCCHHHHHHHHHHHHh
Confidence 5789999998876543
No 482
>TIGR02297 HpaA 4-hydroxyphenylacetate catabolism regulatory protein HpaA. This putative transcriptional regulator, which contains both the substrate-binding, dimerization domain (pfam02311) and the helix-turn-helix DNA-binding domain (pfam00165) of the AraC famil, is located proximal to genes of the 4-hydroxyphenylacetate catabolism pathway.
Probab=25.18 E-value=77 Score=22.75 Aligned_cols=29 Identities=10% Similarity=0.091 Sum_probs=24.9
Q ss_pred hhcCcchhhhhhccccchhhHHHHHHHHH
Q 036324 58 LAHHVKSRTIHSRFLRSRETISRYFNLVL 86 (91)
Q Consensus 58 ~~~~~~~r~i~~~F~~S~eTisr~f~~Vl 86 (91)
.+...+-.+++..++.|..+++|.|++..
T Consensus 199 ~~~~~sl~~lA~~~~~S~~~l~r~Fk~~~ 227 (287)
T TIGR02297 199 YKQHLRLPEYADRLGISESRLNDICRRFS 227 (287)
T ss_pred hccCCCHHHHHHHHCCCHHHHHHHHHHHh
Confidence 45567889999999999999999999853
No 483
>PRK09726 antitoxin HipB; Provisional
Probab=25.17 E-value=71 Score=19.50 Aligned_cols=27 Identities=15% Similarity=0.096 Sum_probs=20.9
Q ss_pred HhhcCcchhhhhhccccchhhHHHHHH
Q 036324 57 ILAHHVKSRTIHSRFLRSRETISRYFN 83 (91)
Q Consensus 57 i~~~~~~~r~i~~~F~~S~eTisr~f~ 83 (91)
.-..|.+...++..-+.|.+||+++.+
T Consensus 21 R~~~gltq~elA~~~gvs~~tis~~e~ 47 (88)
T PRK09726 21 RQQNGWTQSELAKKIGIKQATISNFEN 47 (88)
T ss_pred HHHcCCCHHHHHHHHCcCHHHHHHHHC
Confidence 346677888888888888888888754
No 484
>PF14291 DUF4371: Domain of unknown function (DUF4371)
Probab=24.76 E-value=56 Score=23.61 Aligned_cols=45 Identities=22% Similarity=0.282 Sum_probs=31.8
Q ss_pred CCCCccHHHHHHHHHHHhhcCcchhhhhhcc-------ccchhhHHHHHHHHHHH
Q 036324 41 ADGTVSIEEQLCMFLHILAHHVKSRTIHSRF-------LRSRETISRYFNLVLNA 88 (91)
Q Consensus 41 ~s~~v~veE~vamFL~i~~~~~~~r~i~~~F-------~~S~eTisr~f~~Vl~a 88 (91)
.|..++-.||+++++-.+-.+. .|.++| ..+.+++...+.++|..
T Consensus 159 ettDis~~eQl~i~vRyv~~~~---~i~E~Fl~f~~~~~~ta~~l~~~i~~~L~~ 210 (235)
T PF14291_consen 159 ETTDISNKEQLSICVRYVDKDG---KIKERFLGFVELEDTTAESLFNAIKDVLEK 210 (235)
T ss_pred ccccccccchhhheeeeeccCc---ceeeeeeeeeccCCccHHHHHHHHHHHHHH
Confidence 4568999999999998885332 267676 45666777777766653
No 485
>KOG0946 consensus ER-Golgi vesicle-tethering protein p115 [Intracellular trafficking, secretion, and vesicular transport]
Probab=24.73 E-value=1.7e+02 Score=26.24 Aligned_cols=42 Identities=21% Similarity=0.517 Sum_probs=36.6
Q ss_pred HHHHHHHHHHHhCCCCCCCCCccHHHHHHHHHHHhhcCcchhhh
Q 036324 24 RTFELLCGLLRINGGLKADGTVSIEEQLCMFLHILAHHVKSRTI 67 (91)
Q Consensus 24 ~~F~~L~~~L~~~~~l~~s~~v~veE~vamFL~i~~~~~~~r~i 67 (91)
++|..|.+++++.|++.+ ++-||+.+-.-+..+-.|.+|.+.
T Consensus 208 NaFerLfsIIeeEGg~dG--gIVveDCL~ll~NLLK~N~SNQ~~ 249 (970)
T KOG0946|consen 208 NAFERLFSIIEEEGGLDG--GIVVEDCLILLNNLLKNNISNQNF 249 (970)
T ss_pred HHHHHHHHHHHhcCCCCC--cchHHHHHHHHHHHHhhCcchhhH
Confidence 689999999999998766 588999999999999999888753
No 486
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=24.64 E-value=1.8e+02 Score=21.39 Aligned_cols=43 Identities=9% Similarity=0.087 Sum_probs=31.7
Q ss_pred ccHHHHHHHHHHHhhc--CcchhhhhhccccchhhHHHHHHHHHH
Q 036324 45 VSIEEQLCMFLHILAH--HVKSRTIHSRFLRSRETISRYFNLVLN 87 (91)
Q Consensus 45 v~veE~vamFL~i~~~--~~~~r~i~~~F~~S~eTisr~f~~Vl~ 87 (91)
-+++..+.|.-++-.+ +.+...|...-+-+++|++|..+...+
T Consensus 22 ~sl~r~l~IL~~~~~~~~~~tl~eIa~~lglpkStv~RlL~tL~~ 66 (271)
T PRK10163 22 QALERGIAILQYLEKSGGSSSVSDISLNLDLPLSTTFRLLKVLQA 66 (271)
T ss_pred hHHHHHHHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 3556666665554433 368999999999999999999876543
No 487
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=24.60 E-value=1e+02 Score=20.98 Aligned_cols=26 Identities=8% Similarity=-0.035 Sum_probs=22.9
Q ss_pred cchhhhhhccccchhhHHHHHHHHHH
Q 036324 62 VKSRTIHSRFLRSRETISRYFNLVLN 87 (91)
Q Consensus 62 ~~~r~i~~~F~~S~eTisr~f~~Vl~ 87 (91)
.+++.|+..-+.|..||.+-++...+
T Consensus 29 ~s~~eiA~~lglS~~tv~~Ri~rL~~ 54 (164)
T PRK11169 29 ISNVELSKRVGLSPTPCLERVRRLER 54 (164)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 78899999999999999999887654
No 488
>PRK15185 transcriptional regulator HilD; Provisional
Probab=24.28 E-value=2e+02 Score=22.31 Aligned_cols=44 Identities=11% Similarity=0.225 Sum_probs=31.7
Q ss_pred CCCCccHHHHHHHHHHH-hhcCcchhhhhhccccchhhHHHHHHH
Q 036324 41 ADGTVSIEEQLCMFLHI-LAHHVKSRTIHSRFLRSRETISRYFNL 84 (91)
Q Consensus 41 ~s~~v~veE~vamFL~i-~~~~~~~r~i~~~F~~S~eTisr~f~~ 84 (91)
.+...+..+++--++.. .+.+.+-.+++..++-|..|++|.|++
T Consensus 201 ~s~~~~~~erV~~~I~~n~~~~~SledLA~~lgmS~~tL~R~FK~ 245 (309)
T PRK15185 201 SSAQITLKERVYNIISSSPSRQWKLTDVADHIFMSTSTLKRKLAE 245 (309)
T ss_pred cccchHHHHHHHHHHHhCccCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 33445566665554443 345578899999999999999999975
No 489
>PF06782 UPF0236: Uncharacterised protein family (UPF0236); InterPro: IPR009620 This is a group of proteins of unknown function.
Probab=24.01 E-value=1.4e+02 Score=24.17 Aligned_cols=54 Identities=20% Similarity=0.061 Sum_probs=36.4
Q ss_pred HHHHHHHHhCCCCCCCCCccHHHHHHHHHHHhhcCcchhhhhhcc-------ccchhhHHHHHHHH
Q 036324 27 ELLCGLLRINGGLKADGTVSIEEQLCMFLHILAHHVKSRTIHSRF-------LRSRETISRYFNLV 85 (91)
Q Consensus 27 ~~L~~~L~~~~~l~~s~~v~veE~vamFL~i~~~~~~~r~i~~~F-------~~S~eTisr~f~~V 85 (91)
..|.|.. .++.+-..+|.+-...+ ..+|...|||.++..+ ..|.+||.+..+++
T Consensus 103 ~yllDe~---LGl~~~~R~S~~~~~~i--~~~a~~~sYr~aa~~l~~~~~~~~iS~~tV~~~v~~~ 163 (470)
T PF06782_consen 103 VYLLDEK---LGLKKYQRISPELKEKI--VELATEMSYRKAAEILEELLGNVSISKQTVWNIVKEA 163 (470)
T ss_pred ccchHHH---hCCCcccchhHHHHHHH--HHHHhhcCHHHHHHHHhhccCCCccCHHHHHHHHHhc
Confidence 3444443 44666566666554443 3446669999998876 38999999998875
No 490
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=23.84 E-value=60 Score=22.33 Aligned_cols=27 Identities=11% Similarity=-0.069 Sum_probs=22.0
Q ss_pred HhhcCcchhhhhhccccchhhHHHHHH
Q 036324 57 ILAHHVKSRTIHSRFLRSRETISRYFN 83 (91)
Q Consensus 57 i~~~~~~~r~i~~~F~~S~eTisr~f~ 83 (91)
.-..+.+.+.+++..+.|.+|||++-+
T Consensus 16 R~~~glt~~elA~~~gis~~~is~~E~ 42 (185)
T PRK09943 16 RQQQGLSQRRAAELSGLTHSAISTIEQ 42 (185)
T ss_pred HHHcCCCHHHHHHHHCCCHHHHHHHHc
Confidence 345678888899999999999998754
No 491
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=23.82 E-value=1e+02 Score=20.65 Aligned_cols=26 Identities=15% Similarity=0.042 Sum_probs=22.9
Q ss_pred cchhhhhhccccchhhHHHHHHHHHH
Q 036324 62 VKSRTIHSRFLRSRETISRYFNLVLN 87 (91)
Q Consensus 62 ~~~r~i~~~F~~S~eTisr~f~~Vl~ 87 (91)
.++..|+..-+.|.+||.+-++...+
T Consensus 24 ~s~~eiA~~lglS~~tV~~Ri~rL~~ 49 (153)
T PRK11179 24 TPYAELAKQFGVSPGTIHVRVEKMKQ 49 (153)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 78999999999999999998887654
No 492
>PRK15183 Vi polysaccharide biosynthesis protein TviA; Provisional
Probab=23.78 E-value=70 Score=21.73 Aligned_cols=24 Identities=21% Similarity=0.371 Sum_probs=20.6
Q ss_pred chhhhhhccccchhhHHHHHHHHH
Q 036324 63 KSRTIHSRFLRSRETISRYFNLVL 86 (91)
Q Consensus 63 ~~r~i~~~F~~S~eTisr~f~~Vl 86 (91)
....+|++|.-|.+|.+|+=+|+.
T Consensus 100 gmeelqdrfmns~st~yrwrke~a 123 (143)
T PRK15183 100 GMEELQDRFMNSSSTMYRWRKELA 123 (143)
T ss_pred cHHHHHHHHccChHHHHHHHHHHH
Confidence 457899999999999999987764
No 493
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=23.66 E-value=1.8e+02 Score=17.65 Aligned_cols=36 Identities=14% Similarity=0.344 Sum_probs=30.4
Q ss_pred HHHHHHHHhhcCcchhhhhhccccchhhHHHHHHHH
Q 036324 50 QLCMFLHILAHHVKSRTIHSRFLRSRETISRYFNLV 85 (91)
Q Consensus 50 ~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~f~~V 85 (91)
+.--|.-.+|+..+..+++++-|.+..||.+.....
T Consensus 2 ~~~~fIrlLs~~~s~~~Aa~~lG~~~~~v~~wv~~f 37 (65)
T PF05344_consen 2 KARAFIRLLSQQISVAQAADRLGTDPGTVRRWVRMF 37 (65)
T ss_pred cHHHHHHHhcccccHHHHHHHHCcCHHHHHHHHHHH
Confidence 445577789999999999999999999998877654
No 494
>PRK13832 plasmid partitioning protein; Provisional
Probab=23.63 E-value=1.2e+02 Score=25.45 Aligned_cols=38 Identities=11% Similarity=0.062 Sum_probs=32.7
Q ss_pred CccHHHHHHHHHHHhhcCcchhhhhhccccchhhHHHH
Q 036324 44 TVSIEEQLCMFLHILAHHVKSRTIHSRFLRSRETISRY 81 (91)
Q Consensus 44 ~v~veE~vamFL~i~~~~~~~r~i~~~F~~S~eTisr~ 81 (91)
.++.-|+..-|--.+..+.+...|+.+|+.|..+|++.
T Consensus 101 dL~PiEea~AfkrLie~G~T~EeIA~~lG~S~~~V~rl 138 (520)
T PRK13832 101 PLNPVDQWRAIERLVALGWTEEAIAVALALPVRQIRKL 138 (520)
T ss_pred CCCHHHHHHHHHHHHhcCCCHHHHHHHHCCCHHHHHHH
Confidence 46667777777777899999999999999999999984
No 495
>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family. Member of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.
Probab=23.42 E-value=1.8e+02 Score=20.77 Aligned_cols=41 Identities=12% Similarity=0.132 Sum_probs=30.2
Q ss_pred cHHHHHHHHHHHhh--cCcchhhhhhccccchhhHHHHHHHHH
Q 036324 46 SIEEQLCMFLHILA--HHVKSRTIHSRFLRSRETISRYFNLVL 86 (91)
Q Consensus 46 ~veE~vamFL~i~~--~~~~~r~i~~~F~~S~eTisr~f~~Vl 86 (91)
+++..+.|--+.-. .+.+..+|...-+-+++|++|+.+...
T Consensus 7 sl~ral~IL~~l~~~~~~~~l~eia~~lglpksT~~RlL~tL~ 49 (248)
T TIGR02431 7 SLARGLAVIEAFGAERPRLTLTDVAEATGLTRAAARRFLLTLV 49 (248)
T ss_pred HHHHHHHHHHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 35555555444443 347999999999999999999987654
No 496
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=23.38 E-value=1.6e+02 Score=17.81 Aligned_cols=29 Identities=3% Similarity=0.048 Sum_probs=22.8
Q ss_pred hcCcchhhhhhccccchhhHHHHHHHHHH
Q 036324 59 AHHVKSRTIHSRFLRSRETISRYFNLVLN 87 (91)
Q Consensus 59 ~~~~~~r~i~~~F~~S~eTisr~f~~Vl~ 87 (91)
....++..+++..+-|.+++|++....-+
T Consensus 12 ~~~~~f~~L~~~l~lt~g~Ls~hL~~Le~ 40 (80)
T PF13601_consen 12 NEEATFSELKEELGLTDGNLSKHLKKLEE 40 (80)
T ss_dssp HSEEEHHHHHHHTT--HHHHHHHHHHHHH
T ss_pred cCCCCHHHHHHHhCcCHHHHHHHHHHHHH
Confidence 35689999999999999999999876543
No 497
>PHA03078 transcriptional elongation factor; Provisional
Probab=23.32 E-value=82 Score=23.50 Aligned_cols=25 Identities=12% Similarity=0.313 Sum_probs=21.6
Q ss_pred hhhhccccchhhHHHHHHHHHHHHh
Q 036324 66 TIHSRFLRSRETISRYFNLVLNAIL 90 (91)
Q Consensus 66 ~i~~~F~~S~eTisr~f~~Vl~ai~ 90 (91)
.+++.|.+|..+|+|..++|..++.
T Consensus 189 Ll~~lf~~~~~~inr~Lr~Ifysv~ 213 (219)
T PHA03078 189 LLKNLFDKGSGVINKALRKIFYSVL 213 (219)
T ss_pred HHHHHHhccccHHHHHHHHHHHHHh
Confidence 3567889999999999999998875
No 498
>COG2207 AraC AraC-type DNA-binding domain-containing proteins [Transcription]
Probab=23.13 E-value=1.1e+02 Score=18.54 Aligned_cols=27 Identities=26% Similarity=0.297 Sum_probs=21.4
Q ss_pred cCcchhhhhhccccchhhHHHHHHHHH
Q 036324 60 HHVKSRTIHSRFLRSRETISRYFNLVL 86 (91)
Q Consensus 60 ~~~~~r~i~~~F~~S~eTisr~f~~Vl 86 (91)
++.+-..++..++-|..+++|.|..+.
T Consensus 35 ~~~~l~~la~~~g~S~~~l~r~f~~~~ 61 (127)
T COG2207 35 EPLTLEDLARRLGMSRRTLSRLFKKET 61 (127)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 336788888889999999999888653
No 499
>PF09758 FPL: Uncharacterised conserved protein; InterPro: IPR019155 The proteins in this family are functionally uncharacterised. They contain a highly conserved FPL motif.
Probab=22.96 E-value=1e+02 Score=21.53 Aligned_cols=76 Identities=16% Similarity=0.276 Sum_probs=53.3
Q ss_pred ChhHHHHHhCCCHHHHHHHHHHHHhCCCCCCCCCccHHHHHHHHH----------HHhhcCcchhhhhhccccchhhHHH
Q 036324 11 SDIECVNQLRMDKRTFELLCGLLRINGGLKADGTVSIEEQLCMFL----------HILAHHVKSRTIHSRFLRSRETISR 80 (91)
Q Consensus 11 ~~~~c~~~fRM~~~~F~~L~~~L~~~~~l~~s~~v~veE~vamFL----------~i~~~~~~~r~i~~~F~~S~eTisr 80 (91)
++..+.+ +=|+++++-.+.+.|+. ...++-.+-+-+.+.|.+ |++++|.-|+-|...|.-+.|-+--
T Consensus 14 ~~~~~Fd-~F~E~nil~~f~~il~~--~~~~~V~~QlLQtlsiLiqNi~~~~slyyllSnn~iN~iI~~~~d~~~ee~l~ 90 (149)
T PF09758_consen 14 NDPSFFD-FFMEKNILSTFVRILKQ--SRSSSVKLQLLQTLSILIQNIRSETSLYYLLSNNHINEIITYPFDFSDEEVLS 90 (149)
T ss_pred CCcHHHH-HHHHHHHHHHHHHHHHh--cCChHHHHHHHHHHHHHHHhcCCCcceEEEecchHHHHHHhcCCCCCcchhHH
Confidence 3444444 44899999999999987 223333455666777766 4567777888899999888888777
Q ss_pred HHHHHHHHH
Q 036324 81 YFNLVLNAI 89 (91)
Q Consensus 81 ~f~~Vl~ai 89 (91)
+.=..|+++
T Consensus 91 yYIsfLK~l 99 (149)
T PF09758_consen 91 YYISFLKTL 99 (149)
T ss_pred HHHHHHHHH
Confidence 776666664
No 500
>PF08765 Mor: Mor transcription activator family; InterPro: IPR014875 Mor (Middle operon regulator) is a sequence specific DNA binding protein. It mediates transcription activation through its interactions with the C-terminal domains of the alpha and sigma subunits of bacterial RNA polymerase. The N-terminal region of Mor is the dimerisation region, and the C-terminal contains a helix-turn-helix motif which binds DNA []. ; PDB: 1RR7_A.
Probab=22.86 E-value=82 Score=20.12 Aligned_cols=27 Identities=19% Similarity=0.221 Sum_probs=20.8
Q ss_pred CcchhhhhhccccchhhHHHHHHHHHH
Q 036324 61 HVKSRTIHSRFLRSRETISRYFNLVLN 87 (91)
Q Consensus 61 ~~~~r~i~~~F~~S~eTisr~f~~Vl~ 87 (91)
|.+.+.++..|+-|..+|.++++++-+
T Consensus 72 G~n~~eLA~kyglS~r~I~~Ii~~~~~ 98 (108)
T PF08765_consen 72 GMNVRELARKYGLSERQIYRIIKRVRR 98 (108)
T ss_dssp SS-HHHHHHHHT--HHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 667889999999999999999988644
Done!