Query psy4300
Match_columns 307
No_of_seqs 159 out of 1507
Neff 8.8
Searched_HMMs 46136
Date Fri Aug 16 22:03:13 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4300.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4300hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF13359 DDE_Tnp_4: DDE superf 100.0 5.2E-40 1.1E-44 270.2 5.9 152 112-269 1-158 (158)
2 KOG4585|consensus 100.0 1.1E-36 2.3E-41 274.5 12.9 264 1-279 10-280 (326)
3 PF04827 Plant_tran: Plant tra 100.0 2.4E-36 5.1E-41 245.8 9.0 193 82-277 2-203 (205)
4 PF13612 DDE_Tnp_1_3: Transpos 99.2 5.1E-12 1.1E-16 102.5 4.3 126 106-247 4-149 (155)
5 PF13613 HTH_Tnp_4: Helix-turn 99.2 1.5E-11 3.3E-16 81.5 5.6 50 29-78 2-51 (53)
6 PF01609 DDE_Tnp_1: Transposas 98.2 2E-08 4.3E-13 85.2 -6.5 150 108-270 5-213 (213)
7 PF13586 DDE_Tnp_1_2: Transpos 98.0 3.9E-06 8.5E-11 61.7 2.1 48 217-266 35-84 (88)
8 PF13936 HTH_38: Helix-turn-he 97.2 0.00053 1.1E-08 43.3 3.8 41 28-69 3-43 (44)
9 PF02796 HTH_7: Helix-turn-hel 97.2 0.00057 1.2E-08 43.4 3.8 40 28-68 4-43 (45)
10 PF04545 Sigma70_r4: Sigma-70, 97.1 0.0024 5.3E-08 41.3 6.1 45 29-74 4-48 (50)
11 PF04218 CENP-B_N: CENP-B N-te 96.9 0.0023 5E-08 42.1 4.6 42 27-69 4-45 (53)
12 PF13384 HTH_23: Homeodomain-l 96.7 0.0022 4.7E-08 41.5 3.3 38 33-71 5-42 (50)
13 PF13518 HTH_28: Helix-turn-he 96.5 0.0055 1.2E-07 39.7 4.5 37 35-72 2-38 (52)
14 PF13011 LZ_Tnp_IS481: leucine 96.4 0.011 2.5E-07 42.5 6.0 51 27-77 6-60 (85)
15 PF13340 DUF4096: Putative tra 96.4 0.0044 9.6E-08 43.9 3.7 65 1-71 1-65 (75)
16 PF05225 HTH_psq: helix-turn-h 96.3 0.011 2.4E-07 37.4 4.9 37 33-69 2-39 (45)
17 smart00351 PAX Paired Box doma 96.2 0.016 3.5E-07 45.3 6.4 45 27-72 15-59 (125)
18 PF08281 Sigma70_r4_2: Sigma-7 96.0 0.023 5E-07 37.2 5.3 44 29-73 10-53 (54)
19 PF01527 HTH_Tnp_1: Transposas 95.9 0.014 3.1E-07 41.1 4.3 49 27-75 4-52 (76)
20 PRK09413 IS2 repressor TnpA; R 95.9 0.03 6.5E-07 43.6 6.4 46 27-72 10-55 (121)
21 cd00131 PAX Paired Box domain 95.8 0.028 6.2E-07 44.2 6.2 46 27-73 15-60 (128)
22 cd00569 HTH_Hin_like Helix-tur 95.7 0.032 7E-07 32.6 4.9 39 28-67 4-42 (42)
23 COG3415 Transposase and inacti 95.6 0.024 5.2E-07 45.0 4.9 44 29-72 4-47 (138)
24 PF12116 SpoIIID: Stage III sp 95.3 0.018 3.9E-07 40.6 3.0 44 35-78 8-51 (82)
25 cd06171 Sigma70_r4 Sigma70, re 95.2 0.077 1.7E-06 33.9 5.7 44 29-73 10-53 (55)
26 smart00421 HTH_LUXR helix_turn 95.2 0.088 1.9E-06 34.3 6.0 47 29-77 3-49 (58)
27 cd06571 Bac_DnaA_C C-terminal 94.9 0.11 2.4E-06 38.0 6.4 50 27-76 25-75 (90)
28 PF13542 HTH_Tnp_ISL3: Helix-t 94.8 0.063 1.4E-06 34.8 4.3 33 38-70 19-51 (52)
29 TIGR02531 yecD_yerC TrpR-relat 94.7 0.062 1.3E-06 39.3 4.6 36 32-68 37-72 (88)
30 TIGR03879 near_KaiC_dom probab 94.7 0.084 1.8E-06 37.0 5.0 42 28-69 14-55 (73)
31 PRK00118 putative DNA-binding 94.5 0.12 2.7E-06 38.9 5.9 50 28-78 16-65 (104)
32 TIGR01321 TrpR trp operon repr 94.5 0.076 1.6E-06 39.1 4.6 65 4-68 7-77 (94)
33 PRK04217 hypothetical protein; 94.5 0.11 2.3E-06 39.7 5.5 50 28-78 41-90 (110)
34 PRK06030 hypothetical protein; 93.9 0.39 8.4E-06 37.5 7.7 70 5-74 24-97 (124)
35 cd06170 LuxR_C_like C-terminal 93.9 0.24 5.1E-06 32.2 5.8 44 31-76 2-45 (57)
36 TIGR00721 tfx DNA-binding prot 93.8 0.35 7.5E-06 38.4 7.3 73 27-101 4-85 (137)
37 PHA00675 hypothetical protein 93.7 0.2 4.3E-06 35.1 5.1 43 27-69 20-62 (78)
38 TIGR02844 spore_III_D sporulat 93.5 0.15 3.3E-06 36.5 4.4 37 32-68 4-41 (80)
39 PRK12529 RNA polymerase sigma 93.4 0.22 4.8E-06 41.3 6.0 49 28-77 126-174 (178)
40 PF04967 HTH_10: HTH DNA bindi 93.3 0.53 1.2E-05 30.8 6.3 29 47-75 24-52 (53)
41 PRK09639 RNA polymerase sigma 93.2 0.23 5E-06 40.4 5.8 48 28-77 111-158 (166)
42 PF07374 DUF1492: Protein of u 93.1 0.3 6.6E-06 36.5 5.8 43 31-74 57-99 (100)
43 PF01047 MarR: MarR family; I 93.1 0.34 7.4E-06 32.1 5.5 41 32-72 3-43 (59)
44 PF00356 LacI: Bacterial regul 93.1 0.085 1.8E-06 33.5 2.3 22 48-69 1-22 (46)
45 PRK03975 tfx putative transcri 93.1 0.44 9.5E-06 38.0 6.9 73 27-101 4-85 (141)
46 PF12802 MarR_2: MarR family; 93.0 0.36 7.9E-06 32.2 5.6 26 47-72 22-47 (62)
47 COG2963 Transposase and inacti 92.8 0.36 7.7E-06 37.0 6.0 51 27-77 5-56 (116)
48 PF13730 HTH_36: Helix-turn-he 92.8 0.35 7.6E-06 31.6 5.1 43 30-72 3-51 (55)
49 TIGR02985 Sig70_bacteroi1 RNA 92.6 0.33 7.3E-06 38.9 5.9 48 28-76 112-159 (161)
50 PRK12515 RNA polymerase sigma 92.5 0.27 6E-06 41.0 5.5 50 28-78 130-179 (189)
51 PF01371 Trp_repressor: Trp re 92.2 0.37 8E-06 35.1 5.0 38 32-69 35-72 (87)
52 PHA00542 putative Cro-like pro 92.2 0.27 5.7E-06 35.4 4.3 53 37-102 22-74 (82)
53 TIGR02937 sigma70-ECF RNA poly 92.2 0.35 7.6E-06 38.0 5.5 47 29-76 110-156 (158)
54 TIGR02952 Sig70_famx2 RNA poly 92.1 0.4 8.7E-06 39.0 5.9 48 28-76 121-168 (170)
55 PRK07037 extracytoplasmic-func 92.0 0.36 7.8E-06 39.1 5.4 48 29-77 109-156 (163)
56 PF13412 HTH_24: Winged helix- 91.9 0.73 1.6E-05 29.1 5.7 29 44-72 15-43 (48)
57 PF01022 HTH_5: Bacterial regu 91.9 0.46 1E-05 30.1 4.6 38 35-72 4-41 (47)
58 PRK09652 RNA polymerase sigma 91.8 0.44 9.5E-06 39.1 5.8 48 29-77 128-175 (182)
59 PRK15320 transcriptional activ 91.8 0.49 1.1E-05 39.7 5.8 48 28-77 163-210 (251)
60 COG2739 Uncharacterized protei 91.8 0.43 9.3E-06 35.4 4.8 47 30-77 18-64 (105)
61 TIGR02989 Sig-70_gvs1 RNA poly 91.7 0.49 1.1E-05 38.0 5.9 48 28-76 110-157 (159)
62 PF13551 HTH_29: Winged helix- 91.5 0.35 7.6E-06 36.4 4.5 37 38-74 3-40 (112)
63 PRK12514 RNA polymerase sigma 91.4 0.53 1.1E-05 38.8 5.9 49 28-77 128-176 (179)
64 TIGR02392 rpoH_proteo alternat 91.3 0.44 9.5E-06 42.4 5.6 50 28-77 217-267 (270)
65 PF08299 Bac_DnaA_C: Bacterial 91.3 0.37 8E-06 33.5 4.0 43 28-70 27-70 (70)
66 COG3316 Transposase and inacti 91.2 1.1 2.3E-05 38.3 7.5 187 29-273 8-200 (215)
67 PRK11924 RNA polymerase sigma 91.2 0.53 1.2E-05 38.5 5.6 49 28-77 124-172 (179)
68 PRK09047 RNA polymerase factor 91.1 0.53 1.2E-05 37.9 5.5 50 28-78 105-154 (161)
69 PF13610 DDE_Tnp_IS240: DDE do 91.1 0.92 2E-05 36.1 6.7 132 110-273 4-138 (140)
70 TIGR01636 phage_rinA phage tra 91.0 0.97 2.1E-05 35.7 6.7 50 28-77 81-131 (134)
71 PRK12530 RNA polymerase sigma 91.0 0.58 1.2E-05 39.2 5.7 49 28-77 133-181 (189)
72 PRK05803 sporulation sigma fac 91.0 0.5 1.1E-05 41.0 5.5 50 28-77 174-226 (233)
73 PRK12547 RNA polymerase sigma 90.9 0.56 1.2E-05 38.2 5.5 50 28-78 111-160 (164)
74 PRK08301 sporulation sigma fac 90.9 0.54 1.2E-05 40.8 5.7 50 28-77 177-229 (234)
75 PRK05911 RNA polymerase sigma 90.8 0.49 1.1E-05 41.8 5.4 49 28-77 204-252 (257)
76 PRK12511 RNA polymerase sigma 90.8 0.63 1.4E-05 38.8 5.8 49 29-78 111-159 (182)
77 PRK12524 RNA polymerase sigma 90.7 0.64 1.4E-05 39.1 5.8 49 28-77 135-183 (196)
78 PRK06596 RNA polymerase factor 90.7 0.55 1.2E-05 42.2 5.6 50 28-77 229-279 (284)
79 PRK12533 RNA polymerase sigma 90.6 0.5 1.1E-05 40.7 5.1 50 28-78 133-182 (216)
80 PF01325 Fe_dep_repress: Iron 90.6 1.2 2.6E-05 29.9 5.9 41 32-72 5-48 (60)
81 PF08279 HTH_11: HTH domain; 90.6 0.77 1.7E-05 29.9 4.9 29 46-74 15-43 (55)
82 PRK09638 RNA polymerase sigma 90.5 0.31 6.8E-06 40.0 3.7 49 28-77 125-173 (176)
83 PF00196 GerE: Bacterial regul 90.5 0.57 1.2E-05 31.0 4.3 45 30-76 4-48 (58)
84 TIGR02999 Sig-70_X6 RNA polyme 90.5 0.65 1.4E-05 38.4 5.6 47 30-77 135-181 (183)
85 TIGR02846 spore_sigmaK RNA pol 90.4 0.6 1.3E-05 40.4 5.4 50 28-77 173-225 (227)
86 PRK12528 RNA polymerase sigma 90.3 0.78 1.7E-05 37.1 5.8 47 28-75 112-158 (161)
87 PRK01381 Trp operon repressor; 90.2 0.52 1.1E-05 35.0 4.1 40 29-68 32-77 (99)
88 PRK09641 RNA polymerase sigma 90.2 0.68 1.5E-05 38.3 5.5 49 28-77 135-183 (187)
89 TIGR02960 SigX5 RNA polymerase 90.2 1.3 2.8E-05 40.3 7.7 50 28-78 141-190 (324)
90 PRK12537 RNA polymerase sigma 90.1 0.71 1.5E-05 38.3 5.5 49 28-77 132-180 (182)
91 PRK12516 RNA polymerase sigma 90.1 0.8 1.7E-05 38.3 5.8 49 29-78 116-164 (187)
92 PRK07408 RNA polymerase sigma 90.1 0.74 1.6E-05 40.6 5.9 48 29-77 203-250 (256)
93 PF01710 HTH_Tnp_IS630: Transp 90.1 0.34 7.4E-06 37.5 3.3 40 30-72 5-44 (119)
94 TIGR02393 RpoD_Cterm RNA polym 90.0 0.69 1.5E-05 40.3 5.6 49 29-77 176-227 (238)
95 PRK12519 RNA polymerase sigma 90.0 0.61 1.3E-05 39.0 5.1 48 29-77 141-188 (194)
96 PRK06759 RNA polymerase factor 90.0 0.89 1.9E-05 36.3 5.8 47 28-75 105-151 (154)
97 PRK12532 RNA polymerase sigma 89.9 0.55 1.2E-05 39.4 4.8 49 29-78 136-184 (195)
98 PF00126 HTH_1: Bacterial regu 89.9 1 2.2E-05 30.1 5.1 42 36-78 4-45 (60)
99 cd00092 HTH_CRP helix_turn_hel 89.8 0.77 1.7E-05 31.0 4.6 27 46-72 25-51 (67)
100 TIGR02885 spore_sigF RNA polym 89.8 0.85 1.9E-05 39.4 5.9 48 28-76 182-229 (231)
101 TIGR02984 Sig-70_plancto1 RNA 89.8 0.85 1.8E-05 37.7 5.8 49 28-77 139-187 (189)
102 TIGR02980 SigBFG RNA polymeras 89.7 0.89 1.9E-05 39.2 6.0 49 28-77 177-225 (227)
103 PRK05572 sporulation sigma fac 89.7 0.86 1.9E-05 40.1 5.9 49 28-77 201-249 (252)
104 PRK06811 RNA polymerase factor 89.6 0.95 2.1E-05 37.8 5.9 49 28-77 130-178 (189)
105 PRK12512 RNA polymerase sigma 89.4 0.93 2E-05 37.5 5.7 50 28-78 130-179 (184)
106 TIGR02983 SigE-fam_strep RNA p 89.4 0.88 1.9E-05 36.7 5.5 48 29-77 110-157 (162)
107 TIGR03697 NtcA_cyano global ni 89.4 0.7 1.5E-05 38.4 5.0 63 28-92 111-188 (193)
108 PRK05602 RNA polymerase sigma 89.4 0.86 1.9E-05 37.8 5.5 50 28-78 127-176 (186)
109 PRK12531 RNA polymerase sigma 89.3 1 2.2E-05 37.8 5.9 49 29-78 141-189 (194)
110 TIGR02950 SigM_subfam RNA poly 89.3 0.3 6.5E-06 39.1 2.6 48 29-77 105-152 (154)
111 PRK06704 RNA polymerase factor 89.2 1.3 2.8E-05 38.4 6.6 71 28-101 115-186 (228)
112 TIGR03001 Sig-70_gmx1 RNA poly 89.2 0.98 2.1E-05 39.6 5.9 50 28-78 160-209 (244)
113 smart00346 HTH_ICLR helix_turn 89.1 1.2 2.6E-05 32.1 5.5 39 34-72 5-46 (91)
114 COG1191 FliA DNA-directed RNA 89.0 0.97 2.1E-05 39.6 5.7 49 29-78 196-244 (247)
115 PRK09415 RNA polymerase factor 89.0 0.92 2E-05 37.5 5.4 49 28-77 126-174 (179)
116 PF00325 Crp: Bacterial regula 89.0 0.75 1.6E-05 26.7 3.3 25 47-71 3-27 (32)
117 PRK07500 rpoH2 RNA polymerase 88.9 0.92 2E-05 40.8 5.7 51 28-78 226-277 (289)
118 PRK12534 RNA polymerase sigma 88.9 1.1 2.4E-05 37.2 5.9 48 29-77 137-184 (187)
119 PRK08215 sporulation sigma fac 88.9 1 2.2E-05 39.7 5.9 48 29-77 209-256 (258)
120 PRK08583 RNA polymerase sigma 88.9 1 2.3E-05 39.6 6.0 49 28-77 204-252 (257)
121 PRK12525 RNA polymerase sigma 88.9 1.2 2.5E-05 36.4 5.9 49 28-77 117-165 (168)
122 TIGR02835 spore_sigmaE RNA pol 88.8 1 2.2E-05 39.1 5.7 50 28-77 177-229 (234)
123 PRK12520 RNA polymerase sigma 88.6 0.95 2.1E-05 37.8 5.3 50 28-78 130-179 (191)
124 TIGR02997 Sig70-cyanoRpoD RNA 88.6 1 2.2E-05 40.8 5.7 47 28-74 248-297 (298)
125 PF13751 DDE_Tnp_1_6: Transpos 88.5 0.29 6.3E-06 38.0 1.9 49 222-271 73-122 (125)
126 PRK12523 RNA polymerase sigma 88.5 1.1 2.3E-05 36.7 5.4 49 28-77 118-166 (172)
127 PF09339 HTH_IclR: IclR helix- 88.5 0.55 1.2E-05 30.4 2.9 37 36-72 5-44 (52)
128 TIGR02850 spore_sigG RNA polym 88.5 1.1 2.4E-05 39.4 5.8 48 28-76 205-252 (254)
129 TIGR02394 rpoS_proteo RNA poly 88.3 1 2.2E-05 40.4 5.5 51 28-78 221-274 (285)
130 TIGR02954 Sig70_famx3 RNA poly 88.2 1.3 2.8E-05 36.1 5.7 48 29-77 119-166 (169)
131 PRK09645 RNA polymerase sigma 88.2 1.4 3E-05 36.1 5.9 49 29-78 118-166 (173)
132 PRK12540 RNA polymerase sigma 88.2 1.3 2.8E-05 36.8 5.8 50 28-78 110-159 (182)
133 PRK09649 RNA polymerase sigma 88.1 1.2 2.7E-05 37.0 5.6 49 28-77 129-177 (185)
134 PRK12546 RNA polymerase sigma 88.0 1.3 2.7E-05 37.2 5.6 50 28-78 112-161 (188)
135 PRK12544 RNA polymerase sigma 88.0 1.4 3E-05 37.5 5.9 50 28-78 147-196 (206)
136 PF01381 HTH_3: Helix-turn-hel 87.9 0.64 1.4E-05 30.2 3.0 44 42-99 5-48 (55)
137 PRK12539 RNA polymerase sigma 87.8 1.4 3E-05 36.6 5.7 49 28-77 130-178 (184)
138 PRK09643 RNA polymerase sigma 87.8 1.4 3E-05 37.0 5.8 48 29-77 134-181 (192)
139 PRK09642 RNA polymerase sigma 87.8 1.5 3.3E-05 35.3 5.8 49 29-78 106-154 (160)
140 PRK10402 DNA-binding transcrip 87.8 1.7 3.6E-05 37.4 6.4 67 29-97 148-219 (226)
141 TIGR02948 SigW_bacill RNA poly 87.8 1.1 2.4E-05 37.0 5.1 49 28-77 135-183 (187)
142 PRK12536 RNA polymerase sigma 87.7 1.4 3.1E-05 36.4 5.7 48 29-77 129-176 (181)
143 PF13545 HTH_Crp_2: Crp-like h 87.7 1.4 3.1E-05 30.6 4.9 43 47-90 29-71 (76)
144 PRK11512 DNA-binding transcrip 87.7 2 4.3E-05 34.2 6.3 46 27-72 35-80 (144)
145 PRK09637 RNA polymerase sigma 87.6 1.4 3E-05 36.6 5.6 49 29-78 106-154 (181)
146 PRK06930 positive control sigm 87.6 1.6 3.5E-05 36.1 5.9 49 28-77 113-161 (170)
147 PRK13919 putative RNA polymera 87.6 1.5 3.3E-05 36.3 5.9 49 28-77 134-182 (186)
148 PF13560 HTH_31: Helix-turn-he 87.6 0.93 2E-05 30.6 3.8 27 42-68 10-36 (64)
149 PF13463 HTH_27: Winged helix 87.6 1.3 2.8E-05 30.0 4.6 36 38-73 7-45 (68)
150 PRK07405 RNA polymerase sigma 87.3 1.4 3.1E-05 40.2 5.9 50 28-77 255-307 (317)
151 TIGR02941 Sigma_B RNA polymera 87.1 1.5 3.3E-05 38.5 5.8 49 28-77 204-252 (255)
152 TIGR02943 Sig70_famx1 RNA poly 87.1 1.7 3.7E-05 36.3 5.8 49 29-78 131-179 (188)
153 PRK11753 DNA-binding transcrip 86.9 1.3 2.9E-05 37.3 5.2 45 28-72 137-194 (211)
154 PF04297 UPF0122: Putative hel 86.8 1.5 3.2E-05 32.9 4.7 47 30-77 18-64 (101)
155 TIGR02939 RpoE_Sigma70 RNA pol 86.7 1.2 2.7E-05 36.8 4.9 49 28-77 137-185 (190)
156 PHA02591 hypothetical protein; 86.7 1.5 3.2E-05 30.9 4.2 38 32-69 45-82 (83)
157 TIGR02957 SigX4 RNA polymerase 86.7 3.4 7.3E-05 37.0 7.9 67 29-100 108-174 (281)
158 PRK09648 RNA polymerase sigma 86.6 1.9 4.1E-05 35.8 5.9 49 28-77 138-186 (189)
159 COG1595 RpoE DNA-directed RNA 86.5 1.6 3.4E-05 36.2 5.3 49 29-78 127-175 (182)
160 TIGR02959 SigZ RNA polymerase 86.5 2 4.4E-05 35.1 5.9 49 28-77 99-147 (170)
161 PRK12541 RNA polymerase sigma 86.4 1.8 3.9E-05 34.9 5.5 48 29-77 112-159 (161)
162 PRK12545 RNA polymerase sigma 86.4 1.8 4E-05 36.5 5.8 50 28-78 138-187 (201)
163 smart00550 Zalpha Z-DNA-bindin 86.4 2.1 4.5E-05 29.5 5.0 42 31-72 6-48 (68)
164 TIGR01610 phage_O_Nterm phage 86.3 1.6 3.6E-05 32.2 4.7 30 43-72 44-73 (95)
165 PRK06986 fliA flagellar biosyn 86.3 1.7 3.7E-05 37.7 5.6 49 28-77 183-231 (236)
166 PRK15418 transcriptional regul 86.2 0.81 1.8E-05 41.8 3.7 68 38-111 21-89 (318)
167 PRK07670 RNA polymerase sigma 86.2 1.9 4.1E-05 37.9 5.9 49 28-77 200-248 (251)
168 PRK11923 algU RNA polymerase s 86.0 1.8 4E-05 36.0 5.5 49 28-77 137-185 (193)
169 PRK12522 RNA polymerase sigma 85.9 1.5 3.2E-05 35.9 4.8 48 29-77 119-166 (173)
170 PRK12543 RNA polymerase sigma 85.9 2.1 4.6E-05 35.2 5.8 50 28-78 116-165 (179)
171 PRK07122 RNA polymerase sigma 85.9 1.8 3.8E-05 38.5 5.6 49 28-77 214-262 (264)
172 PRK12527 RNA polymerase sigma 85.9 2.2 4.8E-05 34.3 5.8 48 29-77 105-152 (159)
173 PF05344 DUF746: Domain of Unk 85.8 2 4.3E-05 29.3 4.4 43 35-77 2-44 (65)
174 PRK09635 sigI RNA polymerase s 85.7 3.8 8.3E-05 36.9 7.7 67 29-100 118-184 (290)
175 PF13309 HTH_22: HTH domain 85.7 3.1 6.7E-05 28.3 5.5 42 27-68 18-64 (64)
176 PF00165 HTH_AraC: Bacterial r 85.6 1 2.2E-05 27.6 2.8 29 43-71 5-33 (42)
177 PF06056 Terminase_5: Putative 85.6 2.2 4.8E-05 28.5 4.6 32 37-70 6-37 (58)
178 PRK09644 RNA polymerase sigma 85.5 2.2 4.7E-05 34.6 5.6 50 28-78 107-156 (165)
179 TIGR02479 FliA_WhiG RNA polyme 85.5 2.2 4.8E-05 36.6 5.9 49 28-77 174-222 (224)
180 PRK13918 CRP/FNR family transc 85.5 2.4 5.1E-05 35.5 6.0 65 29-95 118-197 (202)
181 smart00419 HTH_CRP helix_turn_ 85.3 1.4 3E-05 27.5 3.5 27 46-72 8-34 (48)
182 PF01978 TrmB: Sugar-specific 85.2 1.9 4.2E-05 29.4 4.4 39 33-72 10-48 (68)
183 PRK12526 RNA polymerase sigma 85.1 2.3 5.1E-05 36.0 5.8 48 29-77 153-200 (206)
184 PRK15201 fimbriae regulatory p 85.0 1.8 4E-05 35.8 4.7 48 28-77 132-179 (198)
185 PF07638 Sigma70_ECF: ECF sigm 84.9 2.3 4.9E-05 35.5 5.5 47 30-77 136-182 (185)
186 PF12840 HTH_20: Helix-turn-he 84.9 2 4.3E-05 28.7 4.2 31 43-73 21-51 (61)
187 cd00090 HTH_ARSR Arsenical Res 84.8 2.8 6E-05 28.4 5.2 29 44-72 18-46 (78)
188 PRK12427 flagellar biosynthesi 84.8 2.5 5.5E-05 36.6 5.9 47 28-75 182-228 (231)
189 PRK12538 RNA polymerase sigma 84.7 2 4.3E-05 37.4 5.3 49 29-78 171-219 (233)
190 PF13744 HTH_37: Helix-turn-he 84.6 2 4.2E-05 30.6 4.3 37 32-68 15-53 (80)
191 PRK07406 RNA polymerase sigma 84.5 2.4 5.1E-05 39.7 5.9 50 28-77 310-362 (373)
192 PRK09646 RNA polymerase sigma 84.4 2.7 5.8E-05 35.2 5.8 49 28-77 141-189 (194)
193 smart00418 HTH_ARSR helix_turn 84.4 1.9 4.1E-05 28.3 4.1 29 44-72 8-36 (66)
194 PF01710 HTH_Tnp_IS630: Transp 84.3 4.9 0.00011 31.0 6.8 65 2-70 31-95 (119)
195 PRK08295 RNA polymerase factor 84.2 2.7 5.8E-05 35.4 5.8 48 28-77 154-201 (208)
196 PRK12542 RNA polymerase sigma 84.2 2.7 5.9E-05 34.8 5.7 50 28-78 121-170 (185)
197 TIGR02337 HpaR homoprotocatech 84.2 6.4 0.00014 30.0 7.4 46 28-73 24-69 (118)
198 PRK09636 RNA polymerase sigma 84.2 5.6 0.00012 35.7 8.1 49 28-77 114-162 (293)
199 PRK08241 RNA polymerase factor 84.0 3.5 7.6E-05 37.8 6.9 48 29-77 153-200 (339)
200 smart00345 HTH_GNTR helix_turn 83.9 1.6 3.4E-05 28.5 3.4 25 48-72 22-46 (60)
201 PF02001 DUF134: Protein of un 83.8 2.8 6.1E-05 31.6 5.0 49 29-78 41-89 (106)
202 TIGR02947 SigH_actino RNA poly 83.5 1.4 3E-05 36.8 3.7 49 29-78 131-179 (193)
203 PRK14086 dnaA chromosomal repl 83.5 4 8.7E-05 40.6 7.3 51 27-77 550-600 (617)
204 PRK03573 transcriptional regul 83.5 2.3 4.9E-05 33.8 4.8 45 28-72 27-72 (144)
205 PF09607 BrkDBD: Brinker DNA-b 83.4 3.8 8.2E-05 27.3 4.8 42 27-68 3-47 (58)
206 PF04703 FaeA: FaeA-like prote 83.4 2.7 5.8E-05 28.5 4.3 38 34-71 3-40 (62)
207 PRK00149 dnaA chromosomal repl 83.3 4.1 8.8E-05 39.1 7.2 72 6-77 359-434 (450)
208 PRK11922 RNA polymerase sigma 83.3 1.5 3.3E-05 37.9 3.9 49 29-78 149-197 (231)
209 TIGR03209 P21_Cbot clostridium 83.1 1.5 3.1E-05 34.7 3.5 36 28-64 106-141 (142)
210 COG2522 Predicted transcriptio 83.1 2.6 5.7E-05 32.5 4.7 27 43-69 19-45 (119)
211 PRK07598 RNA polymerase sigma 83.1 2.9 6.3E-05 39.6 5.9 50 28-77 349-401 (415)
212 COG2390 DeoR Transcriptional r 83.0 5.1 0.00011 36.7 7.3 65 41-111 21-86 (321)
213 PRK13413 mpi multiple promoter 83.0 1.7 3.6E-05 36.8 4.0 30 40-69 166-195 (200)
214 TIGR01889 Staph_reg_Sar staphy 83.0 8 0.00017 29.1 7.4 45 29-73 22-70 (109)
215 PRK09651 RNA polymerase sigma 82.7 2.7 5.9E-05 34.4 5.1 48 29-77 119-166 (172)
216 smart00342 HTH_ARAC helix_turn 82.7 4.9 0.00011 27.8 5.8 40 32-71 35-76 (84)
217 PRK12535 RNA polymerase sigma 82.6 3.1 6.7E-05 35.0 5.5 50 28-78 132-181 (196)
218 PF13404 HTH_AsnC-type: AsnC-t 82.5 6.1 0.00013 24.4 5.4 25 46-70 17-41 (42)
219 PHA00738 putative HTH transcri 82.5 2.2 4.8E-05 32.2 3.9 27 47-73 27-53 (108)
220 PRK14088 dnaA chromosomal repl 82.4 3.7 8E-05 39.3 6.5 71 6-76 344-417 (440)
221 smart00344 HTH_ASNC helix_turn 82.3 4.7 0.0001 30.1 5.9 37 35-72 7-43 (108)
222 PF00292 PAX: 'Paired box' dom 81.9 4.6 9.9E-05 31.5 5.6 46 27-73 15-60 (125)
223 PRK09210 RNA polymerase sigma 81.8 3 6.6E-05 38.9 5.6 50 28-77 304-356 (367)
224 PRK05949 RNA polymerase sigma 81.7 3.3 7E-05 38.1 5.6 50 28-77 265-317 (327)
225 PRK15411 rcsA colanic acid cap 81.7 2.6 5.5E-05 35.9 4.7 47 29-77 137-183 (207)
226 PRK11161 fumarate/nitrate redu 81.5 4.5 9.8E-05 34.7 6.3 64 28-93 152-230 (235)
227 smart00352 POU Found in Pit-Oc 81.5 2 4.3E-05 30.2 3.2 28 41-68 19-52 (75)
228 PRK09391 fixK transcriptional 81.5 3.1 6.8E-05 35.9 5.3 46 28-73 151-206 (230)
229 smart00347 HTH_MARR helix_turn 81.5 5.2 0.00011 28.9 5.8 45 29-73 7-51 (101)
230 PRK05901 RNA polymerase sigma 81.4 5.7 0.00012 38.7 7.4 50 28-77 446-498 (509)
231 TIGR02859 spore_sigH RNA polym 81.3 3.3 7.2E-05 34.5 5.2 43 32-76 153-195 (198)
232 PRK06288 RNA polymerase sigma 81.3 3.8 8.2E-05 36.4 5.8 49 28-77 211-259 (268)
233 PRK05657 RNA polymerase sigma 81.2 3.5 7.5E-05 37.8 5.6 51 28-78 261-314 (325)
234 PRK12517 RNA polymerase sigma 80.5 4.6 0.0001 33.6 5.8 49 29-78 128-176 (188)
235 PRK13870 transcriptional regul 80.4 3 6.4E-05 36.3 4.7 48 28-77 172-219 (234)
236 PF09862 DUF2089: Protein of u 80.3 5.6 0.00012 30.4 5.5 47 29-76 33-79 (113)
237 PF05263 DUF722: Protein of un 80.2 5.2 0.00011 31.4 5.5 47 29-75 81-128 (130)
238 smart00420 HTH_DEOR helix_turn 80.2 6.5 0.00014 24.6 5.2 29 45-73 13-41 (53)
239 PRK09392 ftrB transcriptional 79.8 4.7 0.0001 34.7 5.8 64 28-93 145-218 (236)
240 COG3293 Transposase and inacti 79.6 0.94 2E-05 35.1 1.2 94 139-248 2-101 (124)
241 PF00872 Transposase_mut: Tran 79.6 2.2 4.9E-05 40.0 3.9 131 40-208 108-247 (381)
242 smart00354 HTH_LACI helix_turn 79.2 1.8 3.8E-05 30.0 2.3 21 48-68 2-22 (70)
243 PF05043 Mga: Mga helix-turn-h 79.2 4.6 9.9E-05 29.0 4.7 35 43-77 27-61 (87)
244 PRK14087 dnaA chromosomal repl 79.2 7.6 0.00017 37.3 7.4 73 5-77 357-433 (450)
245 PRK12682 transcriptional regul 79.1 3.9 8.5E-05 36.7 5.3 45 34-78 4-48 (309)
246 TIGR03070 couple_hipB transcri 79.0 3.6 7.7E-05 26.5 3.8 26 43-68 12-37 (58)
247 PRK07921 RNA polymerase sigma 78.9 5 0.00011 36.8 5.9 49 29-77 262-313 (324)
248 PRK09640 RNA polymerase sigma 78.7 2 4.3E-05 35.8 3.0 47 30-77 135-181 (188)
249 PRK12513 RNA polymerase sigma 78.7 2.5 5.5E-05 35.2 3.6 48 29-77 139-186 (194)
250 cd04762 HTH_MerR-trunc Helix-T 78.3 2.4 5.2E-05 26.2 2.6 23 48-70 2-24 (49)
251 TIGR00122 birA_repr_reg BirA b 78.2 4.4 9.5E-05 27.7 4.1 28 46-73 13-40 (69)
252 PRK13719 conjugal transfer tra 78.1 4.2 9.2E-05 34.8 4.7 48 28-77 142-189 (217)
253 PHA01976 helix-turn-helix prot 78.1 3.7 7.9E-05 27.8 3.7 27 42-68 11-37 (67)
254 PF10668 Phage_terminase: Phag 78.0 3.8 8.3E-05 27.5 3.5 27 41-67 15-43 (60)
255 PRK10840 transcriptional regul 77.8 6.5 0.00014 33.2 6.0 48 28-77 149-196 (216)
256 PRK12518 RNA polymerase sigma 77.7 2.4 5.3E-05 34.6 3.2 47 31-78 122-168 (175)
257 PRK12422 chromosomal replicati 77.5 7.6 0.00016 37.3 6.9 71 5-75 353-426 (445)
258 PRK09647 RNA polymerase sigma 77.3 6.4 0.00014 33.3 5.7 49 29-78 138-186 (203)
259 COG5421 Transposase [DNA repli 77.1 3.3 7.3E-05 39.4 4.2 56 136-199 155-210 (480)
260 PF13551 HTH_29: Winged helix- 77.1 19 0.00041 26.7 7.8 69 1-69 24-110 (112)
261 PF14493 HTH_40: Helix-turn-he 76.1 14 0.00031 26.8 6.6 62 36-101 3-64 (91)
262 TIGR01764 excise DNA binding d 75.9 3.2 6.9E-05 25.7 2.7 23 47-69 2-24 (49)
263 TIGR02405 trehalos_R_Ecol treh 75.2 2.1 4.5E-05 38.5 2.3 22 47-68 2-23 (311)
264 COG3355 Predicted transcriptio 75.2 7.4 0.00016 30.4 5.0 31 43-73 39-69 (126)
265 PRK08558 adenine phosphoribosy 75.1 8.8 0.00019 33.5 6.1 40 29-68 6-45 (238)
266 smart00760 Bac_DnaA_C Bacteria 75.1 7.8 0.00017 25.8 4.5 51 7-57 3-56 (60)
267 PF10654 DUF2481: Protein of u 74.9 2.6 5.7E-05 31.9 2.3 39 39-77 72-111 (126)
268 TIGR00637 ModE_repress ModE mo 74.5 6.7 0.00014 29.2 4.5 39 40-78 10-48 (99)
269 PRK12683 transcriptional regul 74.5 6.5 0.00014 35.4 5.3 45 34-78 4-48 (309)
270 PF00392 GntR: Bacterial regul 74.2 4.6 0.0001 27.1 3.3 25 48-72 26-50 (64)
271 PF08220 HTH_DeoR: DeoR-like h 74.1 10 0.00022 25.0 4.8 27 46-72 14-40 (57)
272 PF13443 HTH_26: Cro/C1-type H 73.7 2.9 6.3E-05 27.9 2.2 25 44-68 8-32 (63)
273 PRK11050 manganese transport r 73.7 10 0.00022 30.6 5.7 29 45-73 50-78 (152)
274 PRK00215 LexA repressor; Valid 73.7 9.3 0.0002 32.3 5.8 28 46-73 23-51 (205)
275 PF12728 HTH_17: Helix-turn-he 73.6 3.6 7.8E-05 26.2 2.5 23 47-69 2-24 (51)
276 PF13701 DDE_Tnp_1_4: Transpos 73.5 37 0.0008 32.7 10.4 122 27-164 52-197 (448)
277 PRK09191 two-component respons 73.3 20 0.00043 31.0 8.0 50 28-78 87-136 (261)
278 PRK12679 cbl transcriptional r 73.3 7 0.00015 35.3 5.3 45 34-78 4-48 (316)
279 PRK09492 treR trehalose repres 73.3 2.3 5.1E-05 38.1 2.1 23 47-69 5-27 (315)
280 PF12964 DUF3853: Protein of u 73.2 3.1 6.6E-05 30.6 2.3 30 48-77 47-78 (96)
281 TIGR00180 parB_part ParB-like 73.1 8.7 0.00019 32.1 5.4 43 27-69 100-143 (187)
282 PF03333 PapB: Adhesin biosynt 73.0 24 0.00051 25.9 6.9 37 35-71 41-78 (91)
283 cd07377 WHTH_GntR Winged helix 72.8 5.3 0.00011 26.5 3.4 25 48-72 27-51 (66)
284 PRK11233 nitrogen assimilation 72.6 7.7 0.00017 34.8 5.4 43 35-78 5-47 (305)
285 PRK10188 DNA-binding transcrip 72.5 6.7 0.00014 34.3 4.7 48 28-77 178-225 (240)
286 PRK11475 DNA-binding transcrip 72.3 7.1 0.00015 33.3 4.8 47 29-77 134-180 (207)
287 PRK10163 DNA-binding transcrip 72.2 10 0.00022 33.7 5.9 92 28-119 19-129 (271)
288 COG2771 CsgD DNA-binding HTH d 72.2 10 0.00022 25.0 4.7 39 39-77 12-50 (65)
289 TIGR03541 reg_near_HchA LuxR f 72.1 11 0.00023 32.7 5.9 49 27-77 169-217 (232)
290 PRK11303 DNA-binding transcrip 72.1 2.9 6.2E-05 37.8 2.4 22 48-69 2-23 (328)
291 PRK10141 DNA-binding transcrip 72.1 9.5 0.00021 29.4 4.9 40 34-73 17-57 (117)
292 PRK10100 DNA-binding transcrip 72.0 7 0.00015 33.5 4.7 47 29-77 155-201 (216)
293 PRK10014 DNA-binding transcrip 72.0 3 6.4E-05 37.9 2.5 23 47-69 7-29 (342)
294 PRK09483 response regulator; P 71.9 7.1 0.00015 32.5 4.7 47 28-76 147-193 (217)
295 PRK09526 lacI lac repressor; R 71.7 2.8 6.1E-05 38.0 2.3 23 47-69 6-28 (342)
296 PF02954 HTH_8: Bacterial regu 71.7 6.2 0.00014 24.2 3.2 26 44-69 16-41 (42)
297 PRK10870 transcriptional repre 71.2 15 0.00031 30.5 6.3 45 28-72 51-97 (176)
298 COG2197 CitB Response regulato 71.1 7.5 0.00016 33.2 4.6 47 29-77 148-194 (211)
299 PRK11179 DNA-binding transcrip 70.9 15 0.00032 29.6 6.1 45 29-73 6-50 (153)
300 cd01392 HTH_LacI Helix-turn-he 70.9 2.8 6E-05 26.7 1.5 18 51-68 2-19 (52)
301 TIGR02431 pcaR_pcaU beta-ketoa 70.5 9.4 0.0002 33.3 5.3 91 29-119 4-111 (248)
302 PRK13777 transcriptional regul 70.1 14 0.00031 30.9 5.9 44 28-71 41-84 (185)
303 PRK14987 gluconate operon tran 70.0 2.8 6.1E-05 38.0 1.9 23 47-69 6-28 (331)
304 TIGR03830 CxxCG_CxxCG_HTH puta 69.8 18 0.0004 27.7 6.3 29 40-68 72-100 (127)
305 PF01726 LexA_DNA_bind: LexA D 69.5 18 0.0004 24.6 5.4 27 46-72 25-52 (65)
306 PRK10072 putative transcriptio 69.5 4.9 0.00011 29.8 2.7 27 42-68 42-68 (96)
307 PRK10703 DNA-binding transcrip 69.1 3.4 7.4E-05 37.5 2.3 22 48-69 3-24 (341)
308 PRK12684 transcriptional regul 69.1 9.7 0.00021 34.3 5.2 45 34-78 4-48 (313)
309 TIGR03020 EpsA transcriptional 69.1 14 0.0003 32.5 6.0 49 27-77 188-236 (247)
310 PRK10401 DNA-binding transcrip 69.0 3.4 7.4E-05 37.7 2.2 22 48-69 3-24 (346)
311 TIGR02607 antidote_HigA addict 68.9 14 0.00029 25.7 4.9 27 42-68 14-40 (78)
312 PRK10339 DNA-binding transcrip 67.9 3.2 7E-05 37.5 1.8 22 48-69 3-24 (327)
313 PRK11569 transcriptional repre 67.4 15 0.00033 32.6 6.0 46 28-73 22-70 (274)
314 PRK09834 DNA-binding transcrip 67.3 11 0.00025 33.2 5.1 45 29-73 6-53 (263)
315 TIGR03418 chol_sulf_TF putativ 67.2 12 0.00025 33.2 5.3 43 35-78 5-47 (291)
316 TIGR01884 cas_HTH CRISPR locus 67.2 17 0.00037 30.7 6.0 35 38-72 147-183 (203)
317 TIGR02702 SufR_cyano iron-sulf 67.0 13 0.00028 31.4 5.3 40 32-72 2-41 (203)
318 PRK10094 DNA-binding transcrip 66.8 12 0.00026 33.7 5.3 44 34-78 5-48 (308)
319 PRK11151 DNA-binding transcrip 66.6 12 0.00025 33.5 5.2 44 34-78 4-47 (305)
320 PRK04140 hypothetical protein; 66.5 9.4 0.0002 34.8 4.5 63 1-68 98-161 (317)
321 COG1508 RpoN DNA-directed RNA 66.4 5 0.00011 38.1 2.8 27 42-68 320-352 (444)
322 TIGR02417 fruct_sucro_rep D-fr 66.4 4.1 9E-05 36.7 2.2 22 48-69 1-22 (327)
323 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 66.0 22 0.00047 23.0 4.8 41 28-69 3-43 (50)
324 COG0593 DnaA ATPase involved i 65.9 16 0.00035 34.5 6.0 52 26-77 345-396 (408)
325 COG2512 Predicted membrane-ass 65.9 16 0.00035 32.3 5.7 46 27-72 190-236 (258)
326 PRK12681 cysB transcriptional 65.7 12 0.00027 33.9 5.2 45 34-78 4-48 (324)
327 PRK10651 transcriptional regul 65.7 11 0.00025 30.9 4.7 47 29-77 155-201 (216)
328 PF07453 NUMOD1: NUMOD1 domain 65.5 5.3 0.00011 23.7 1.8 24 44-67 14-37 (37)
329 TIGR01481 ccpA catabolite cont 65.1 4.6 0.0001 36.4 2.3 22 48-69 3-24 (329)
330 PRK10727 DNA-binding transcrip 65.1 4.4 9.5E-05 36.9 2.1 22 48-69 3-24 (343)
331 PRK09791 putative DNA-binding 65.0 14 0.0003 33.0 5.3 44 34-78 8-51 (302)
332 PF05269 Phage_CII: Bacterioph 64.8 7.9 0.00017 28.4 3.0 37 40-77 18-54 (91)
333 smart00529 HTH_DTXR Helix-turn 64.7 8.5 0.00018 27.9 3.3 25 49-73 2-26 (96)
334 PRK13348 chromosome replicatio 64.5 14 0.00031 32.7 5.3 43 35-78 6-48 (294)
335 PRK09726 antitoxin HipB; Provi 64.5 10 0.00022 27.4 3.6 34 35-68 12-47 (88)
336 PRK10423 transcriptional repre 64.3 4.2 9.1E-05 36.6 1.8 19 50-68 2-20 (327)
337 PRK10360 DNA-binding transcrip 64.1 13 0.00029 30.2 4.8 46 29-76 137-182 (196)
338 COG1609 PurR Transcriptional r 63.7 5.3 0.00012 36.6 2.4 22 48-69 2-23 (333)
339 PRK11013 DNA-binding transcrip 63.6 15 0.00032 33.0 5.3 44 34-78 7-50 (309)
340 cd00131 PAX Paired Box domain 63.4 67 0.0015 25.0 8.3 69 1-69 45-126 (128)
341 PF05930 Phage_AlpA: Prophage 63.1 9.4 0.0002 24.5 2.8 22 48-69 5-26 (51)
342 COG3413 Predicted DNA binding 63.0 18 0.00039 30.9 5.4 51 27-77 153-209 (215)
343 PRK11169 leucine-responsive tr 62.9 16 0.00034 29.8 4.8 45 29-73 11-55 (164)
344 PRK15090 DNA-binding transcrip 62.9 18 0.0004 31.7 5.6 46 28-73 8-55 (257)
345 PRK05658 RNA polymerase sigma 62.7 13 0.00028 37.3 5.1 50 28-77 555-607 (619)
346 PRK10403 transcriptional regul 62.6 14 0.00031 30.2 4.7 47 29-77 153-199 (215)
347 PF00440 TetR_N: Bacterial reg 62.4 7.4 0.00016 24.3 2.2 25 45-69 15-39 (47)
348 PRK15092 DNA-binding transcrip 62.4 11 0.00025 33.9 4.3 52 27-78 6-57 (310)
349 PF13556 HTH_30: PucR C-termin 62.4 18 0.0004 23.8 4.3 38 40-77 6-43 (59)
350 PF04552 Sigma54_DBD: Sigma-54 62.0 2.6 5.6E-05 34.5 0.0 23 46-68 49-71 (160)
351 TIGR02424 TF_pcaQ pca operon t 61.8 17 0.00036 32.3 5.3 42 36-78 8-49 (300)
352 PF14549 P22_Cro: DNA-binding 61.7 6.7 0.00014 26.4 2.0 19 48-66 11-29 (60)
353 PF08765 Mor: Mor transcriptio 61.7 9.5 0.00021 28.8 3.1 33 44-76 70-102 (108)
354 COG1654 BirA Biotin operon rep 61.6 24 0.00052 25.1 4.9 46 33-78 5-51 (79)
355 PRK12680 transcriptional regul 61.6 17 0.00036 33.1 5.3 44 35-78 5-48 (327)
356 PRK15421 DNA-binding transcrip 61.5 18 0.00038 32.8 5.4 44 34-78 5-48 (317)
357 PRK09906 DNA-binding transcrip 61.4 14 0.00031 32.6 4.8 41 38-78 7-47 (296)
358 COG1342 Predicted DNA-binding 61.2 23 0.0005 26.1 4.7 46 30-76 34-79 (99)
359 PRK09958 DNA-binding transcrip 61.0 16 0.00035 29.9 4.7 47 29-77 143-189 (204)
360 TIGR03298 argP transcriptional 60.8 18 0.0004 31.9 5.4 43 35-78 5-47 (292)
361 PF01418 HTH_6: Helix-turn-hel 60.7 9.4 0.0002 26.8 2.8 24 46-69 34-57 (77)
362 TIGR02395 rpoN_sigma RNA polym 60.6 5.9 0.00013 37.8 2.1 22 47-68 319-340 (429)
363 PRK11242 DNA-binding transcrip 60.3 17 0.00038 32.0 5.1 42 36-78 6-47 (296)
364 TIGR02944 suf_reg_Xantho FeS a 59.8 21 0.00045 27.7 4.9 26 47-72 26-51 (130)
365 COG1414 IclR Transcriptional r 59.7 24 0.00053 30.8 5.8 39 35-73 5-46 (246)
366 PRK10219 DNA-binding transcrip 59.5 25 0.00055 26.1 5.1 27 45-71 20-46 (107)
367 TIGR01637 phage_arpU phage tra 59.4 23 0.0005 27.6 5.1 50 28-77 78-128 (132)
368 COG1476 Predicted transcriptio 59.2 13 0.00028 25.7 3.0 27 42-68 10-36 (68)
369 PF08280 HTH_Mga: M protein tr 59.1 27 0.00059 23.0 4.7 42 35-77 9-50 (59)
370 PF06530 Phage_antitermQ: Phag 59.1 26 0.00056 27.2 5.2 42 36-77 68-109 (125)
371 COG1846 MarR Transcriptional r 59.0 32 0.0007 25.5 5.8 43 30-72 20-62 (126)
372 PRK09706 transcriptional repre 58.8 14 0.00029 29.1 3.7 27 42-68 14-40 (135)
373 PF05732 RepL: Firmicute plasm 58.7 11 0.00024 31.0 3.1 27 47-73 76-102 (165)
374 PRK09801 transcriptional activ 58.1 24 0.00051 31.8 5.6 48 30-78 5-52 (310)
375 PRK03902 manganese transport t 58.0 28 0.00062 27.4 5.4 41 33-73 7-49 (142)
376 PRK09508 leuO leucine transcri 58.0 21 0.00045 32.1 5.2 43 36-78 26-68 (314)
377 cd04761 HTH_MerR-SF Helix-Turn 57.9 11 0.00024 23.4 2.5 23 48-70 2-24 (49)
378 smart00530 HTH_XRE Helix-turn- 57.7 18 0.00039 21.9 3.5 25 43-67 7-31 (56)
379 CHL00180 rbcR LysR transcripti 57.7 20 0.00044 32.0 5.1 42 36-78 10-51 (305)
380 TIGR02684 dnstrm_HI1420 probab 57.6 16 0.00035 26.6 3.6 34 35-68 32-65 (89)
381 PRK11074 putative DNA-binding 57.5 22 0.00048 31.6 5.3 37 42-78 12-48 (300)
382 PRK10216 DNA-binding transcrip 57.5 23 0.00049 31.9 5.4 42 36-78 13-54 (319)
383 COG5566 Uncharacterized conser 57.4 14 0.00031 28.6 3.3 43 30-72 81-128 (137)
384 PF12844 HTH_19: Helix-turn-he 57.3 13 0.00028 24.7 2.9 28 42-69 8-35 (64)
385 PRK11511 DNA-binding transcrip 57.2 20 0.00043 27.8 4.3 30 42-71 21-50 (127)
386 PRK13509 transcriptional repre 57.2 26 0.00056 30.8 5.5 40 33-72 4-45 (251)
387 cd00093 HTH_XRE Helix-turn-hel 56.9 20 0.00044 21.9 3.7 25 44-68 10-34 (58)
388 PF07037 DUF1323: Putative tra 56.8 12 0.00026 28.8 2.8 22 48-69 2-23 (122)
389 COG4496 Uncharacterized protei 56.6 11 0.00024 27.3 2.4 29 40-68 50-78 (100)
390 PRK15369 two component system 56.5 21 0.00046 28.9 4.7 47 29-77 149-195 (211)
391 PRK12469 RNA polymerase factor 56.1 8.9 0.00019 37.1 2.5 31 47-89 370-400 (481)
392 smart00497 IENR1 Intron encode 56.1 13 0.00029 23.6 2.7 25 45-69 16-40 (53)
393 COG1522 Lrp Transcriptional re 55.8 28 0.00061 27.6 5.2 27 47-73 23-49 (154)
394 TIGR03454 partition_RepB plasm 55.8 28 0.00061 31.9 5.6 44 27-70 158-201 (325)
395 PRK11564 stationary phase indu 55.8 32 0.00068 32.7 6.3 50 27-76 8-60 (426)
396 PRK10341 DNA-binding transcrip 54.8 23 0.0005 31.8 4.9 44 34-78 10-53 (312)
397 cd07153 Fur_like Ferric uptake 54.7 31 0.00067 25.9 5.0 27 46-72 16-47 (116)
398 PRK03635 chromosome replicatio 54.5 27 0.00058 31.0 5.3 42 36-78 7-48 (294)
399 PF08535 KorB: KorB domain; I 54.3 13 0.00028 27.2 2.6 24 45-68 2-25 (93)
400 TIGR02404 trehalos_R_Bsub treh 54.2 15 0.00032 31.7 3.4 25 48-72 26-50 (233)
401 cd01104 HTH_MlrA-CarA Helix-Tu 54.1 15 0.00032 24.7 2.8 23 48-70 2-24 (68)
402 PRK01905 DNA-binding protein F 53.9 38 0.00083 23.8 4.9 29 42-70 46-74 (77)
403 PRK09986 DNA-binding transcrip 53.9 25 0.00054 31.0 5.0 44 34-78 10-53 (294)
404 PRK10411 DNA-binding transcrip 53.3 29 0.00062 30.3 5.1 28 46-73 18-45 (240)
405 PRK10837 putative DNA-binding 53.1 26 0.00057 30.8 5.0 40 39-78 10-49 (290)
406 COG2944 Predicted transcriptio 52.2 15 0.00032 27.7 2.6 25 42-66 53-77 (104)
407 PF12298 Bot1p: Eukaryotic mit 52.1 51 0.0011 27.2 6.1 42 27-68 14-55 (172)
408 TIGR03339 phn_lysR aminoethylp 51.9 21 0.00046 31.0 4.1 38 41-78 6-43 (279)
409 TIGR02612 mob_myst_A mobile my 51.8 18 0.00038 29.3 3.2 31 39-69 31-61 (150)
410 COG3677 Transposase and inacti 51.7 22 0.00047 27.9 3.7 47 31-77 74-120 (129)
411 PRK03601 transcriptional regul 51.6 30 0.00064 30.4 5.1 42 37-78 6-47 (275)
412 PRK04424 fatty acid biosynthes 51.0 33 0.00072 28.6 4.9 40 32-71 5-46 (185)
413 PRK09935 transcriptional regul 50.9 29 0.00063 28.3 4.7 47 29-77 149-195 (210)
414 TIGR00270 conserved hypothetic 50.8 34 0.00073 27.8 4.7 33 36-68 70-104 (154)
415 PF13843 DDE_Tnp_1_7: Transpos 50.4 69 0.0015 29.4 7.5 89 104-199 124-218 (351)
416 PRK13832 plasmid partitioning 50.0 37 0.0008 33.0 5.5 42 27-68 99-140 (520)
417 PRK10086 DNA-binding transcrip 49.9 28 0.00061 31.2 4.7 42 37-78 19-60 (311)
418 PRK10632 transcriptional regul 49.8 26 0.00056 31.4 4.5 38 41-78 11-48 (309)
419 PRK10434 srlR DNA-bindng trans 49.8 35 0.00076 30.0 5.1 42 32-73 3-46 (256)
420 PF02650 HTH_WhiA: WhiA C-term 49.7 69 0.0015 23.1 5.7 45 28-72 36-82 (85)
421 COG3311 AlpA Predicted transcr 49.7 15 0.00032 25.5 2.2 43 47-90 14-56 (70)
422 TIGR02036 dsdC D-serine deamin 49.1 35 0.00076 30.4 5.2 40 39-78 15-54 (302)
423 TIGR02325 C_P_lyase_phnF phosp 49.0 20 0.00044 30.8 3.5 26 47-72 33-58 (238)
424 PRK11482 putative DNA-binding 48.8 33 0.00072 31.0 5.0 43 36-78 33-75 (317)
425 PRK10079 phosphonate metabolis 48.6 21 0.00045 31.0 3.5 26 47-72 36-61 (241)
426 PF09012 FeoC: FeoC like trans 48.4 25 0.00054 24.0 3.2 25 46-70 14-38 (69)
427 PRK06424 transcription factor; 48.3 27 0.00058 28.0 3.7 26 43-68 94-119 (144)
428 TIGR00498 lexA SOS regulatory 48.2 42 0.0009 28.1 5.2 27 46-72 25-52 (199)
429 PF07022 Phage_CI_repr: Bacter 48.2 15 0.00032 25.0 2.0 22 47-68 13-35 (66)
430 COG4565 CitB Response regulato 48.2 50 0.0011 28.4 5.5 28 45-72 172-199 (224)
431 PRK13890 conjugal transfer pro 48.2 17 0.00037 28.0 2.6 25 44-68 16-40 (120)
432 PRK14999 histidine utilization 48.2 21 0.00046 30.9 3.5 26 47-72 37-62 (241)
433 PRK10906 DNA-binding transcrip 47.9 45 0.00097 29.3 5.5 41 33-73 4-46 (252)
434 TIGR02018 his_ut_repres histid 47.9 22 0.00047 30.6 3.5 25 48-72 27-51 (230)
435 PF00376 MerR: MerR family reg 47.7 19 0.00042 21.6 2.2 21 49-69 2-22 (38)
436 PRK09802 DNA-binding transcrip 47.5 38 0.00083 30.1 5.0 46 27-72 10-57 (269)
437 PRK10046 dpiA two-component re 47.4 29 0.00064 29.4 4.2 33 38-70 166-201 (225)
438 PRK11886 bifunctional biotin-- 47.2 36 0.00079 30.9 5.0 35 38-72 8-44 (319)
439 PF13601 HTH_34: Winged helix 47.0 45 0.00097 23.6 4.4 32 44-75 12-43 (80)
440 PRK05932 RNA polymerase factor 46.9 12 0.00025 36.2 1.7 22 47-68 344-365 (455)
441 PRK15243 transcriptional regul 46.8 44 0.00094 30.1 5.4 44 34-78 7-50 (297)
442 PRK10082 cell density-dependen 46.6 41 0.00088 30.0 5.2 41 38-78 17-57 (303)
443 PRK09943 DNA-binding transcrip 46.5 22 0.00047 29.5 3.2 27 42-68 16-42 (185)
444 TIGR03734 PRTRC_parB PRTRC sys 46.4 42 0.00091 33.1 5.4 43 27-69 89-132 (554)
445 PF09182 PuR_N: Bacterial puri 46.2 67 0.0014 22.3 4.9 32 34-65 4-39 (70)
446 PRK06474 hypothetical protein; 46.1 46 0.001 27.6 5.0 41 33-73 11-54 (178)
447 PRK09764 DNA-binding transcrip 45.9 24 0.00052 30.5 3.5 25 48-72 31-55 (240)
448 PRK10430 DNA-binding transcrip 45.8 42 0.00091 28.7 5.0 34 44-77 176-209 (239)
449 PF05584 Sulfolobus_pRN: Sulfo 45.8 84 0.0018 22.0 5.4 41 29-71 3-43 (72)
450 PF03050 DDE_Tnp_IS66: Transpo 45.6 81 0.0018 27.7 6.9 74 29-121 3-81 (271)
451 COG4941 Predicted RNA polymera 45.4 1.3E+02 0.0029 27.8 8.0 63 27-93 118-180 (415)
452 PF07506 RepB: RepB plasmid pa 45.3 58 0.0012 27.1 5.5 42 27-68 2-43 (185)
453 PRK11062 nhaR transcriptional 45.1 45 0.00097 29.6 5.2 38 41-78 13-50 (296)
454 PRK08359 transcription factor; 44.8 24 0.00052 29.3 3.1 43 44-100 96-138 (176)
455 PF07750 GcrA: GcrA cell cycle 44.8 30 0.00066 28.2 3.7 38 33-70 5-43 (162)
456 PRK00430 fis global DNA-bindin 44.5 61 0.0013 23.9 4.9 28 43-70 65-92 (95)
457 PRK11139 DNA-binding transcrip 44.4 43 0.00092 29.7 5.0 44 34-78 9-52 (297)
458 PF13411 MerR_1: MerR HTH fami 44.1 22 0.00047 24.0 2.3 24 48-71 2-25 (69)
459 COG1395 Predicted transcriptio 44.0 18 0.00039 32.7 2.4 64 1-69 98-161 (313)
460 PRK11402 DNA-binding transcrip 43.7 27 0.00059 30.2 3.5 26 47-72 34-59 (241)
461 COG2826 Tra8 Transposase and i 43.5 39 0.00085 30.5 4.3 40 29-69 7-46 (318)
462 PF08769 Spo0A_C: Sporulation 43.3 32 0.0007 25.9 3.3 31 47-77 41-71 (106)
463 smart00342 HTH_ARAC helix_turn 42.7 35 0.00077 23.2 3.4 25 47-71 2-26 (84)
464 PRK14165 winged helix-turn-hel 42.5 43 0.00094 28.8 4.4 27 47-73 22-48 (217)
465 PF13022 HTH_Tnp_1_2: Helix-tu 42.1 45 0.00097 26.5 4.0 31 47-77 35-68 (142)
466 PRK15215 fimbriae biosynthesis 42.0 1.4E+02 0.0031 22.2 7.3 38 34-71 48-86 (100)
467 COG2964 Uncharacterized protei 41.4 1.1E+02 0.0023 26.4 6.4 38 33-70 173-215 (220)
468 PRK14997 LysR family transcrip 41.2 41 0.00089 29.8 4.4 36 43-78 13-48 (301)
469 PRK15183 Vi polysaccharide bio 41.0 68 0.0015 24.1 4.6 51 37-89 89-139 (143)
470 PRK13698 plasmid-partitioning 40.8 48 0.001 30.3 4.6 40 30-69 158-199 (323)
471 TIGR00738 rrf2_super rrf2 fami 40.3 53 0.0011 25.3 4.3 28 46-73 25-52 (132)
472 PF01476 LysM: LysM domain; I 40.1 33 0.00072 20.6 2.5 22 44-65 4-25 (44)
473 PRK13500 transcriptional activ 39.9 70 0.0015 28.9 5.7 38 34-71 206-247 (312)
474 PRK09744 DNA-binding transcrip 39.8 28 0.00061 24.3 2.3 20 47-66 11-30 (75)
475 PRK00441 argR arginine repress 39.6 59 0.0013 26.2 4.5 26 46-71 18-48 (149)
476 PRK13503 transcriptional activ 39.6 63 0.0014 28.2 5.3 29 43-71 184-212 (278)
477 COG2188 PhnF Transcriptional r 39.4 35 0.00075 29.6 3.4 25 48-72 33-57 (236)
478 TIGR02698 CopY_TcrY copper tra 39.3 83 0.0018 24.5 5.3 55 33-88 6-66 (130)
479 PF02082 Rrf2: Transcriptional 39.1 55 0.0012 23.1 3.9 27 47-73 26-52 (83)
480 PF09048 Cro: Cro; InterPro: 38.9 37 0.0008 22.7 2.6 22 49-70 15-36 (59)
481 PRK09390 fixJ response regulat 38.5 67 0.0015 25.7 5.0 46 30-77 142-187 (202)
482 PF08822 DUF1804: Protein of u 38.5 79 0.0017 25.9 5.0 40 31-70 4-43 (165)
483 COG1510 Predicted transcriptio 38.4 37 0.00081 28.0 3.2 40 34-73 29-68 (177)
484 PF13693 HTH_35: Winged helix- 38.1 15 0.00033 26.1 0.8 25 44-68 13-37 (78)
485 PRK04984 fatty acid metabolism 38.0 38 0.00082 29.1 3.5 25 48-72 33-57 (239)
486 PF01316 Arg_repressor: Argini 37.9 90 0.0019 21.6 4.6 24 47-70 20-48 (70)
487 COG3093 VapI Plasmid maintenan 37.9 34 0.00073 25.7 2.6 24 46-69 23-46 (104)
488 COG2973 TrpR Trp operon repres 37.5 47 0.001 24.6 3.2 30 36-65 50-79 (103)
489 PRK09978 DNA-binding transcrip 37.1 95 0.0021 27.8 5.9 27 43-69 155-181 (274)
490 PF01498 HTH_Tnp_Tc3_2: Transp 36.9 39 0.00084 23.0 2.7 24 47-70 14-42 (72)
491 COG0583 LysR Transcriptional r 36.4 65 0.0014 27.9 4.9 39 40-78 9-47 (297)
492 PRK13501 transcriptional activ 36.0 1.3E+02 0.0028 26.7 6.7 30 42-71 188-217 (290)
493 PF14502 HTH_41: Helix-turn-he 35.9 65 0.0014 20.6 3.3 26 47-72 7-32 (48)
494 PF12833 HTH_18: Helix-turn-he 35.1 1.5E+02 0.0032 20.3 6.0 61 1-70 7-70 (81)
495 PRK15340 transcriptional regul 35.0 56 0.0012 28.1 3.9 29 44-72 123-151 (216)
496 PRK09954 putative kinase; Prov 34.9 93 0.002 28.6 5.8 27 46-72 17-43 (362)
497 PRK10681 DNA-binding transcrip 34.8 80 0.0017 27.7 5.0 41 32-72 5-47 (252)
498 TIGR02787 codY_Gpos GTP-sensin 34.7 88 0.0019 27.4 5.0 44 29-72 178-224 (251)
499 cd04764 HTH_MlrA-like_sg1 Heli 34.7 46 0.00099 22.3 2.8 22 48-69 2-23 (67)
500 smart00422 HTH_MERR helix_turn 34.5 38 0.00082 22.7 2.4 22 48-69 2-23 (70)
No 1
>PF13359 DDE_Tnp_4: DDE superfamily endonuclease
Probab=100.00 E-value=5.2e-40 Score=270.21 Aligned_cols=152 Identities=35% Similarity=0.603 Sum_probs=141.2
Q ss_pred ecceeEEeecCCC---CccccccccCCcceeEEeeeCCCcceEeeeeccccccCCCcccccchhhcchhhcCCCCCCCCC
Q psy4300 112 IDGCHIEGKFSKD---IRNDYNNRKCTQSMILQGVCTSNKLLTNIHVGCTGRNHDAKVLSTSQIGRRIDAYGPTSLLYRD 188 (307)
Q Consensus 112 iDgt~i~i~~P~~---~~~~y~~~k~~~s~~~q~v~d~~g~i~~v~~~~~Gs~~D~~i~~~S~l~~~l~~~~~~~~~~~~ 188 (307)
||||||+|++|.+ ....|+++|+.|++|+|++||++|+|++++.++||++||+.+|++|++...+.. .++.
T Consensus 1 iDgt~v~i~~P~~~~~~~~~y~~~k~~~~~~~q~v~d~~g~i~~v~~~~~Gs~~D~~i~~~s~~~~~l~~------~~~~ 74 (158)
T PF13359_consen 1 IDGTHVPIQRPSDKEEQREFYSGKKKNHSLKVQIVCDPDGRIIYVSVGWPGSVHDSTIFRQSGLLDRLEQ------AFPP 74 (158)
T ss_pred CccEEEEEEeCCccccccccccCCCCcceEeEEEEEeccceeEeeecccccccccccccccccccceeec------cccc
Confidence 7999999999998 688999999999999999999999999999999999999999999998887763 1446
Q ss_pred CeEEEecCCCCCCcccccccc--CCCCCCHHHHHHhHHHHhhhhHHHHHHHHHHhhccccc-ccccCChhhHHHHHHHHH
Q psy4300 189 EYHLLGDSAYPLRTWCMVPYK--NFGHMTEEEKKYNTALSKTRVPIENVFGLIKGRWRRLK-YIDVGDPKRMAYIISAAC 265 (307)
Q Consensus 189 ~~~llgD~gY~~~~~l~~P~~--~~~~lt~~q~~fN~~~s~~R~~VE~~fg~LK~rf~iL~-~~~~~~~~~~~~ii~a~~ 265 (307)
++++|||+||++.+++++||+ ...+++++|+.||+.|++.|.+||++||+||+||++|+ +++....+.+..+|.|||
T Consensus 75 ~~~~l~D~gy~~~~~~~~P~~~~~~~~l~~~e~~~N~~~s~~R~~vE~~~~~lK~rf~~l~~~~~~~~~~~~~~ii~~~~ 154 (158)
T PF13359_consen 75 GEYLLGDSGYPLSPYLLTPYKKPKGRELTPEEKEFNRRHSSARIIVERAFGRLKSRFRILRGRLRLSRPEKAPQIILACC 154 (158)
T ss_pred CccccccccccccccccccccccccccccccccchhccccceeeeeHHHHHHHHHhcccCCcccCCCcHhHHHHHHheeE
Confidence 799999999999999999997 44578999999999999999999999999999999999 888834999999999999
Q ss_pred Hhhh
Q psy4300 266 VLHN 269 (307)
Q Consensus 266 ~LhN 269 (307)
+|||
T Consensus 155 ~LhN 158 (158)
T PF13359_consen 155 VLHN 158 (158)
T ss_pred EEEC
Confidence 9999
No 2
>KOG4585|consensus
Probab=100.00 E-value=1.1e-36 Score=274.52 Aligned_cols=264 Identities=29% Similarity=0.423 Sum_probs=219.4
Q ss_pred CCHHHHHHHHHHHhhhcCcccccCCC-CCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccccc
Q psy4300 1 MRKTTFGFLVEALAAINGYETLYERG-VPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQI 79 (307)
Q Consensus 1 ms~~~F~~L~~~l~~~~~~~~~~~~~-~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l~ 79 (307)
+++.+|++++..........+ .... ...++....+++.++.++++.+.+.++..||..++|+ .+.......
T Consensus 10 ~s~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~i~~~fg~~~~~~-----~~~~~~~~~-- 81 (326)
T KOG4585|consen 10 KSYTTFDKICSLVQSLNVVKN-SGFMLSSLLPADTLVAVALWRLKTGESLRTVEKKFGLGQSTC-----KFLEEKEDL-- 81 (326)
T ss_pred HHHHHHHHHhhhhhhhhhhcc-cchhhhccccHHhhhhhhhccccccchHHHHHHHcCCcchhh-----hHHHhhhcc--
Confidence 367889999988766543223 2111 2222289999999999999999999999999999998 555566666
Q ss_pred ccccccCCChHHHHHHHHHHHHhhCCCCcceeecceeEEeecCCCCccccccccCCcceeEEeeeCCCcceEeeeecccc
Q psy4300 80 QCQYIKWPTEEESVIIERNFRALAKFPGVIGAIDGCHIEGKFSKDIRNDYNNRKCTQSMILQGVCTSNKLLTNIHVGCTG 159 (307)
Q Consensus 80 ~~~~i~~P~~~~~~~~~~~f~~~~~~p~~~g~iDgt~i~i~~P~~~~~~y~~~k~~~s~~~q~v~d~~g~i~~v~~~~~G 159 (307)
++.++.||....+..+.+.++. +|+|+|++|+||+++..|+.....|.|+ .++.|+|+|||.+++|+++.+|+||
T Consensus 82 ~~~~~~~p~~~~~~~i~~~~~~---~~~~~g~~d~~hi~~~~~~~~~~~~~n~--~~~~Nvlav~n~d~~f~~v~vg~~G 156 (326)
T KOG4585|consen 82 APHFLKWPSRRILYEIRERFES---LPNCVGAIDTTHIPIRVPPKSGSVYFNK--EQSKNLLAVCNFDMRFIYVDVGWPG 156 (326)
T ss_pred cchhhcCchhhhhhhhcccccc---ccchhccccccccceecCcccccccccc--ccchhhhheecCCceEEEEEccCCC
Confidence 8999999998777788888875 9999999999999999999998888888 8889999999999999999999999
Q ss_pred ccCCCcccccchhhcchhhcCCCCC-----CCCCCeEEEecCCCCCCccccccccCCCCCCHHHHHHhHHHHhhhhHHHH
Q psy4300 160 RNHDAKVLSTSQIGRRIDAYGPTSL-----LYRDEYHLLGDSAYPLRTWCMVPYKNFGHMTEEEKKYNTALSKTRVPIEN 234 (307)
Q Consensus 160 s~~D~~i~~~S~l~~~l~~~~~~~~-----~~~~~~~llgD~gY~~~~~l~~P~~~~~~lt~~q~~fN~~~s~~R~~VE~ 234 (307)
+.||+.+++.+.+......++|..+ ..+...+++|+.+||+.+++++|+..+. .+..++.||.+|+..|.++|+
T Consensus 157 s~~D~kvl~~~~~~~~~~~~~~~k~yl~d~~~~~~~~~~g~~~~~~~~~~~~~~~~~~-~~~~~elFN~rh~~~r~v~e~ 235 (326)
T KOG4585|consen 157 SAHDTKVLQDSLLYKRNFPHPPLKYYLVDSGYPLRPGLLGPIGFPLYSLLMFPYGGPQ-PTNSQELFNKRHSSLRSVAER 235 (326)
T ss_pred CccHHHHHHhhcccccccccCCccccccccCcccccccccccccccchhhhcccCCCC-CCchHHHHhhhhhhHHHHHHH
Confidence 9999999999988776666444211 1124567777777778888888888764 478889999999999999999
Q ss_pred HHHHHHhhccccc-ccccCChhhHHHHHHHHHHhhhhhcccCCcch
Q psy4300 235 VFGLIKGRWRRLK-YIDVGDPKRMAYIISAACVLHNFCYLQDDVVE 279 (307)
Q Consensus 235 ~fg~LK~rf~iL~-~~~~~~~~~~~~ii~a~~~LhN~~~~~~~~~~ 279 (307)
+||++|.||+||. . ...+.++..++|.+||+|||+|++.++...
T Consensus 236 ~fg~lk~rw~il~~~-~~~~~~~~~~iV~a~caLHN~~~~~~~~~~ 280 (326)
T KOG4585|consen 236 AFGVLKAKWRILQRR-EKYDLKKLPKIVTACCALHNIIRDSDEEDP 280 (326)
T ss_pred HHHHhhhhhHHHhhc-ccccccchHHHHHHHHHHHHHHHhhccccc
Confidence 9999999999999 6 555899999999999999999998887443
No 3
>PF04827 Plant_tran: Plant transposon protein; InterPro: IPR006912 This entry represents a putative Harbinger transposase-derived nuclease, which is thought to have nuclease activity. However it does not have transposase activity [, ]. ; GO: 0016788 hydrolase activity, acting on ester bonds
Probab=100.00 E-value=2.4e-36 Score=245.79 Aligned_cols=193 Identities=23% Similarity=0.341 Sum_probs=171.0
Q ss_pred ccccCCChHHHHHHHHHHHHhhCCCCcceeecceeEEee-cCCCCccccc-cccCCcceeEEeeeCCCcceEeeeecccc
Q psy4300 82 QYIKWPTEEESVIIERNFRALAKFPGVIGAIDGCHIEGK-FSKDIRNDYN-NRKCTQSMILQGVCTSNKLLTNIHVGCTG 159 (307)
Q Consensus 82 ~~i~~P~~~~~~~~~~~f~~~~~~p~~~g~iDgt~i~i~-~P~~~~~~y~-~~k~~~s~~~q~v~d~~g~i~~v~~~~~G 159 (307)
+|++-|+.++.+++.+.++. .|||+.+|+|||+|+.++ +|......|. |++|.+++.+++|+++|.+|+++..|.||
T Consensus 2 ~YLr~P~~~d~~rll~~~e~-rGFpGmlGSIDCmHw~WkncP~aw~g~~~~G~~g~pTiiLEaVAs~dlwIWhaffG~~G 80 (205)
T PF04827_consen 2 EYLRRPTNEDLERLLQIGEA-RGFPGMLGSIDCMHWEWKNCPTAWKGQYTRGKEGVPTIILEAVASHDLWIWHAFFGMPG 80 (205)
T ss_pred cccCCCChhHHHHHHHhhhh-cCCCccccceeEEEeehhcchHHhhhcccCCCCCCCeehhhhhhccchhhhheeeccCC
Confidence 67889999999999977776 699999999999999997 5666666676 99999999999999999999999999999
Q ss_pred ccCCCcccccchhhcchhhc-CCCCCCCC-----CCeEEEecCCCCCCccccccccCCCCCCHHHHHHhHHHHhhhhHHH
Q psy4300 160 RNHDAKVLSTSQIGRRIDAY-GPTSLLYR-----DEYHLLGDSAYPLRTWCMVPYKNFGHMTEEEKKYNTALSKTRVPIE 233 (307)
Q Consensus 160 s~~D~~i~~~S~l~~~l~~~-~~~~~~~~-----~~~~llgD~gY~~~~~l~~P~~~~~~lt~~q~~fN~~~s~~R~~VE 233 (307)
|.+|..+++.|+++..+..+ .|..-..- +-.|.|+|..||.+..++.+++.|. +++++.|.+++.++|..||
T Consensus 81 S~NDiNVL~~Splf~~~~~G~ap~v~f~VNg~~Y~~gYYLaDGiYP~watfvktI~~p~--~~k~k~fa~~QE~~RKDVE 158 (205)
T PF04827_consen 81 SNNDINVLDRSPLFDDLLQGQAPRVQFTVNGHEYNMGYYLADGIYPEWATFVKTISLPQ--GEKRKLFAKHQESARKDVE 158 (205)
T ss_pred cccccccccccHHHHHHhcCcCCceEEEecCeecccceeeccCcCcchHhHhhhcchhh--chhhHHHHHhCHHHHHHHH
Confidence 99999999999999877775 23221111 2358889999999999999999864 8899999999999999999
Q ss_pred HHHHHHHhhccccc-ccccCChhhHHHHHHHHHHhhhhhcccCCc
Q psy4300 234 NVFGLIKGRWRRLK-YIDVGDPKRMAYIISAACVLHNFCYLQDDV 277 (307)
Q Consensus 234 ~~fg~LK~rf~iL~-~~~~~~~~~~~~ii~a~~~LhN~~~~~~~~ 277 (307)
++||.|++||+|++ +.+.++.+.+..|+.||++||||+++.+.+
T Consensus 159 rAFGVLQaRfaIi~~p~r~w~~~~l~~Im~aCiILHNMIvEDEr~ 203 (205)
T PF04827_consen 159 RAFGVLQARFAIIRGPARLWDREDLANIMRACIILHNMIVEDERD 203 (205)
T ss_pred HHHHHHHHHHHHhcCchhccCHHHHHHHHHHHHHhhheeEecccc
Confidence 99999999999999 899989999999999999999999987754
No 4
>PF13612 DDE_Tnp_1_3: Transposase DDE domain
Probab=99.25 E-value=5.1e-12 Score=102.50 Aligned_cols=126 Identities=19% Similarity=0.178 Sum_probs=94.2
Q ss_pred CCcceeecceeEEeecCCCC-------ccc---cccccCCcceeEEeeeCCCcceEeeeeccccccCCCcccccchhhcc
Q psy4300 106 PGVIGAIDGCHIEGKFSKDI-------RND---YNNRKCTQSMILQGVCTSNKLLTNIHVGCTGRNHDAKVLSTSQIGRR 175 (307)
Q Consensus 106 p~~~g~iDgt~i~i~~P~~~-------~~~---y~~~k~~~s~~~q~v~d~~g~i~~v~~~~~Gs~~D~~i~~~S~l~~~ 175 (307)
+..+.+||+|.+|++.+... +.. |+..+-+|++|++++|+.+|.++.+.. .||+.||..++..
T Consensus 4 ~~~i~~iDS~Pi~vC~~~R~~r~k~~~~~a~~G~~a~~~fyGfKlHllv~~~G~i~~~~l-T~an~~D~~~~~~------ 76 (155)
T PF13612_consen 4 CTGIYIIDSFPIPVCHNIRIKRHKVFKGLAYRGYCAMGWFYGFKLHLLVNDSGEIVAFTL-TPANVHDRKVLEE------ 76 (155)
T ss_pred ccEEEEEecCChhHhCccchhhhccccCccccceeccceeEeeeeeeEEccCCcEEEEEE-ccccccccccccc------
Confidence 56788999999999876532 122 233344699999999999999999877 7999999988732
Q ss_pred hhhcCCCCCCCCCCeEEEecCCCCCCc----------cccccccCCCCCCHHHHHHhHHHHhhhhHHHHHHHHHHhhccc
Q psy4300 176 IDAYGPTSLLYRDEYHLLGDSAYPLRT----------WCMVPYKNFGHMTEEEKKYNTALSKTRVPIENVFGLIKGRWRR 245 (307)
Q Consensus 176 l~~~~~~~~~~~~~~~llgD~gY~~~~----------~l~~P~~~~~~lt~~q~~fN~~~s~~R~~VE~~fg~LK~rf~i 245 (307)
+.. .....++||+||-... .++||.+++- .......+++.+.+.|.+||.+|+.||..|.+
T Consensus 77 l~~--------~~~g~l~gDkGYis~~L~~~L~~~gI~L~t~~RkNm-k~~~~~~~~~~l~~~R~~IETvfs~Lk~~~~i 147 (155)
T PF13612_consen 77 LSE--------NLKGKLFGDKGYISKELKDELKEQGIKLITPRRKNM-KNKLMPLFDKLLLRKRRIIETVFSQLKNQFNI 147 (155)
T ss_pred ccc--------ccccceecchhhhcchHHhhhhhceEEEeccccccc-cccccchhhhhhhheeeEeehHHHHHHHhhce
Confidence 211 1134799999996433 3799998752 12223457889999999999999999998877
Q ss_pred cc
Q psy4300 246 LK 247 (307)
Q Consensus 246 L~ 247 (307)
=+
T Consensus 148 e~ 149 (155)
T PF13612_consen 148 EH 149 (155)
T ss_pred Ee
Confidence 54
No 5
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=99.24 E-value=1.5e-11 Score=81.52 Aligned_cols=50 Identities=20% Similarity=0.383 Sum_probs=48.1
Q ss_pred CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
+++.+++++++|.||+.|.++.++|..||||+||++++++++++.|+..+
T Consensus 2 kLs~~d~lll~L~~LR~~~~~~~La~~FgIs~stvsri~~~~~~~L~~~l 51 (53)
T PF13613_consen 2 KLSLEDQLLLTLMYLRLNLTFQDLAYRFGISQSTVSRIFHEWIPLLYQVL 51 (53)
T ss_pred CCCHHHHHHHHHHHHHcCCcHhHHhhheeecHHHHHHHHHHHHHHHHHhc
Confidence 68999999999999999999999999999999999999999999999874
No 6
>PF01609 DDE_Tnp_1: Transposase DDE domain; InterPro: IPR002559 Autonomous mobile genetic elements such as transposon or insertion sequences (IS) encode an enzyme, transposase, that is required for excising and inserting the mobile element. Transposases have been grouped into various families [, , ]. This family includes the IS4 transposase. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 3ECP_A 4DM0_A 1MUS_A 1MUH_A 1MM8_A 1B7E_A.
Probab=98.23 E-value=2e-08 Score=85.21 Aligned_cols=150 Identities=23% Similarity=0.234 Sum_probs=88.0
Q ss_pred cceeecceeEEeecCCCC-ccccccccCCcceeEEeee-CCCcceEeeeeccccccCCCcccccchhhcchhhcCCCCCC
Q psy4300 108 VIGAIDGCHIEGKFSKDI-RNDYNNRKCTQSMILQGVC-TSNKLLTNIHVGCTGRNHDAKVLSTSQIGRRIDAYGPTSLL 185 (307)
Q Consensus 108 ~~g~iDgt~i~i~~P~~~-~~~y~~~k~~~s~~~q~v~-d~~g~i~~v~~~~~Gs~~D~~i~~~S~l~~~l~~~~~~~~~ 185 (307)
.+.+||+|.++.. +... ...+.+++...+.++++++ +..|.++.+... +|+.+|...+.. +.+. . .
T Consensus 5 ~~~~iD~T~i~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~d~~~~~~--ll~~--~------~ 72 (213)
T PF01609_consen 5 RVVAIDGTTIRTP-HDKSARRYKKGKKRGFGYKLHLAVDDNSGLPLSVKVT-PGNVHDSKALPE--LLER--K------P 72 (213)
T ss_dssp EEEEEETTT--EE-EEEEE-B-SSGGGHSSHGGHHHHHHHHHGGGGGGEEE-EEEGG-HHHHHH--HHTT----------
T ss_pred eEEEEECcEEEee-cchhhhcccCCCCcCCCEeEEEEEeecccceeeeecc-ccccceeecccc--cccc--c------c
Confidence 4679999999988 1111 3344456667888999999 567788888885 999999988764 2222 1 2
Q ss_pred CCCCeEEEecCCCCCCcc----------ccccccCCCCC---------------------------------CHHHHHHh
Q psy4300 186 YRDEYHLLGDSAYPLRTW----------CMVPYKNFGHM---------------------------------TEEEKKYN 222 (307)
Q Consensus 186 ~~~~~~llgD~gY~~~~~----------l~~P~~~~~~l---------------------------------t~~q~~fN 222 (307)
...+.++++|+||...+. .+.|.+.+... ...++...
T Consensus 73 ~~~~~~vv~D~gy~s~~~~~~l~~~~~~~vi~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 152 (213)
T PF01609_consen 73 GRKPDLVVADRGYDSAENLEALKERGIHFVIRLKKNRKKKIQKIENKFWKSFDRRSARKKPKQKSKRVRVVIRKEQKKKG 152 (213)
T ss_dssp ---EEEEEE-S--BBTTHHHHHHTS---EEEEE--EEEE-TTS-EEEE--EEEEEEEEEEETGGGEEEEEEEEEECS--T
T ss_pred cccccceeecccccceeccccccccccccccccccccccccccchhhccccccccccccccccccccccccccccccccc
Confidence 335789999999974331 24444432111 00111111
Q ss_pred HH--------------HHhhhhHHHHHHHHHHhhcccccccccCChhhHHHHHHHHHHhhhh
Q psy4300 223 TA--------------LSKTRVPIENVFGLIKGRWRRLKYIDVGDPKRMAYIISAACVLHNF 270 (307)
Q Consensus 223 ~~--------------~s~~R~~VE~~fg~LK~rf~iL~~~~~~~~~~~~~ii~a~~~LhN~ 270 (307)
.. +.+.|+.||+.|..||+.|. +.+++....+.+...+.++++-.|+
T Consensus 153 ~~~~~~~~~~~~~~~~~Y~~Rw~IE~~f~~lK~~~~-l~~~~~~~~~~~~~~~~~~~la~nl 213 (213)
T PF01609_consen 153 YFLVTNITTLPRDTAALYRRRWQIERFFRELKQFLG-LERLRVRSPERIEAHLFLTLLAYNL 213 (213)
T ss_dssp TS---EEEEEESS--SHHHCGGHHHHHHHHHTTTTT-GGGS--SSHHHHHHHHHHHHHH---
T ss_pred ccccccccccccccceeecccchhhHHHHHHHhcCC-CchhcccCHHHHHHHHHHHHhhCcC
Confidence 22 89999999999999999644 4566666788888888888877775
No 7
>PF13586 DDE_Tnp_1_2: Transposase DDE domain
Probab=97.97 E-value=3.9e-06 Score=61.69 Aligned_cols=48 Identities=25% Similarity=0.357 Sum_probs=37.5
Q ss_pred HHHHHhHHHHhhhhHHHHHHHHHHhhccccc-ccccCChhhHHHHH-HHHHH
Q psy4300 217 EEKKYNTALSKTRVPIENVFGLIKGRWRRLK-YIDVGDPKRMAYII-SAACV 266 (307)
Q Consensus 217 ~q~~fN~~~s~~R~~VE~~fg~LK~rf~iL~-~~~~~~~~~~~~ii-~a~~~ 266 (307)
.+..+...+.+.|++||++|+.||. |+.|. ++.. .+......+ +||++
T Consensus 35 ~~~~~d~~~~~~Rw~VEr~f~wlk~-~Rrl~~ryek-~~~s~~~~v~la~~~ 84 (88)
T PF13586_consen 35 RPRKFDFRLYKRRWVVERTFAWLKR-FRRLATRYEK-LASSFLAFVHLACIV 84 (88)
T ss_pred ccCccchhhhccceehhhhhHHHHH-cCcccccccc-CHHHHHHHHHHHHHH
Confidence 4667889999999999999999998 88888 8888 555444444 55544
No 8
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=97.21 E-value=0.00053 Score=43.30 Aligned_cols=41 Identities=17% Similarity=0.287 Sum_probs=23.7
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHH
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDS 69 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~ 69 (307)
+.++.+++..+.- ++..|.|.+.||..+|+|+|||++.+++
T Consensus 3 ~~Lt~~eR~~I~~-l~~~G~s~~~IA~~lg~s~sTV~relkR 43 (44)
T PF13936_consen 3 KHLTPEERNQIEA-LLEQGMSIREIAKRLGRSRSTVSRELKR 43 (44)
T ss_dssp ---------HHHH-HHCS---HHHHHHHTT--HHHHHHHHHH
T ss_pred cchhhhHHHHHHH-HHHcCCCHHHHHHHHCcCcHHHHHHHhc
Confidence 4677888877774 4789999999999999999999999875
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=97.19 E-value=0.00057 Score=43.38 Aligned_cols=40 Identities=25% Similarity=0.379 Sum_probs=30.3
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHH
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCID 68 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~ 68 (307)
+.++.+ ++.-++..+..|.+..++|..||||++||+|+++
T Consensus 4 ~~~~~~-~~~~i~~l~~~G~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 4 PKLSKE-QIEEIKELYAEGMSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp SSSSHC-CHHHHHHHHHTT--HHHHHHHTTS-HHHHHHHHC
T ss_pred CCCCHH-HHHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHh
Confidence 334444 5677778889999999999999999999999875
No 10
>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=97.08 E-value=0.0024 Score=41.33 Aligned_cols=45 Identities=20% Similarity=0.437 Sum_probs=38.6
Q ss_pred CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHc
Q psy4300 29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAM 74 (307)
Q Consensus 29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l 74 (307)
.+|++++-.+.++| ..+.++.++|..+|+|.+||+++.++.+.-|
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 68899999999999 6689999999999999999999999877654
No 11
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=96.87 E-value=0.0023 Score=42.10 Aligned_cols=42 Identities=21% Similarity=0.259 Sum_probs=32.0
Q ss_pred CCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHH
Q psy4300 27 VPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDS 69 (307)
Q Consensus 27 ~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~ 69 (307)
+..+++++++-+.-. +..|.+..++|..|||++||++.|+..
T Consensus 4 R~~LTl~eK~~iI~~-~e~g~s~~~ia~~fgv~~sTv~~I~K~ 45 (53)
T PF04218_consen 4 RKSLTLEEKLEIIKR-LEEGESKRDIAREFGVSRSTVSTILKN 45 (53)
T ss_dssp SSS--HHHHHHHHHH-HHCTT-HHHHHHHHT--CCHHHHHHHC
T ss_pred CccCCHHHHHHHHHH-HHcCCCHHHHHHHhCCCHHHHHHHHHh
Confidence 578999999987655 678889999999999999999999874
No 12
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=96.66 E-value=0.0022 Score=41.46 Aligned_cols=38 Identities=21% Similarity=0.378 Sum_probs=22.9
Q ss_pred HHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHH
Q psy4300 33 EKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFL 71 (307)
Q Consensus 33 ~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~ 71 (307)
+.++.+...+.. |.+..++|..+|+|++||+++++++.
T Consensus 5 ~~R~~ii~l~~~-G~s~~~ia~~lgvs~~Tv~~w~kr~~ 42 (50)
T PF13384_consen 5 ERRAQIIRLLRE-GWSIREIAKRLGVSRSTVYRWIKRYR 42 (50)
T ss_dssp -----HHHHHHH-T--HHHHHHHHTS-HHHHHHHHT---
T ss_pred hHHHHHHHHHHC-CCCHHHHHHHHCcCHHHHHHHHHHcc
Confidence 444554444444 99999999999999999999998864
No 13
>PF13518 HTH_28: Helix-turn-helix domain
Probab=96.51 E-value=0.0055 Score=39.75 Aligned_cols=37 Identities=24% Similarity=0.447 Sum_probs=31.6
Q ss_pred HHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300 35 KTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLT 72 (307)
Q Consensus 35 ~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~ 72 (307)
++.+...++ .|.+..++|..||||.+|+++++.++-.
T Consensus 2 r~~iv~~~~-~g~s~~~~a~~~gis~~tv~~w~~~y~~ 38 (52)
T PF13518_consen 2 RLQIVELYL-EGESVREIAREFGISRSTVYRWIKRYRE 38 (52)
T ss_pred HHHHHHHHH-cCCCHHHHHHHHCCCHhHHHHHHHHHHh
Confidence 456677777 6779999999999999999999998765
No 14
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=96.44 E-value=0.011 Score=42.55 Aligned_cols=51 Identities=4% Similarity=0.128 Sum_probs=46.3
Q ss_pred CCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHH----cccc
Q psy4300 27 VPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTA----MSQP 77 (307)
Q Consensus 27 ~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~----l~~~ 77 (307)
+-.+++..++.++-..+..|.+...+|..||||..|+++|+.++-.. |.+.
T Consensus 6 nA~Lt~~gR~~lv~~vv~~g~~~a~aA~~~gVS~~Ta~kW~~Ryra~G~~GL~DR 60 (85)
T PF13011_consen 6 NARLTPRGRLRLVRRVVEQGWPVAHAAAEFGVSRRTAYKWLARYRAEGEAGLQDR 60 (85)
T ss_pred CCCCCHHHHHHHHHHHHHcCCcHHHHHHHhCCCHHHHHHHHHHHHHcCccccccc
Confidence 57899999999999999999999999999999999999999998753 5555
No 15
>PF13340 DUF4096: Putative transposase of IS4/5 family (DUF4096)
Probab=96.39 E-value=0.0044 Score=43.91 Aligned_cols=65 Identities=15% Similarity=0.220 Sum_probs=49.2
Q ss_pred CCHHHHHHHHHHHhhhcCcccccCCCCCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHH
Q psy4300 1 MRKTTFGFLVEALAAINGYETLYERGVPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFL 71 (307)
Q Consensus 1 ms~~~F~~L~~~l~~~~~~~~~~~~~~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~ 71 (307)
||.+++..|-..|.+. .. .++++..+..+.+-..|+.+++|+++++|...|| +.+||++.+++..
T Consensus 1 lsD~~W~~i~p~lp~~----~~-~~~~~~~~~R~v~~ail~~lrtG~~Wr~LP~~fg-~~~tv~~~f~rW~ 65 (75)
T PF13340_consen 1 LSDEEWALIEPLLPPR----KP-RGGRPRIDLREVLNAILYVLRTGCPWRDLPEDFG-PWSTVYRRFRRWS 65 (75)
T ss_pred CCHHHHHHHHhhCCCC----CC-CCCCCccchHHHHhcccccceecceecccchhcc-CcCcHHHHHHHHH
Confidence 3455555555444433 22 3356789999999999999999999999999999 7888888877654
No 16
>PF05225 HTH_psq: helix-turn-helix, Psq domain; InterPro: IPR007889 This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster []. In pipsqueak this domain binds to GAGA sequence []. The pipsqueak family, which includes proteins from fungi, sea urchins, nematodes, insects, and vertebrates appear to be proteins essential for sequence-specific targeting of a polycomb group protein complex [].; GO: 0003677 DNA binding; PDB: 2COB_A.
Probab=96.33 E-value=0.011 Score=37.37 Aligned_cols=37 Identities=19% Similarity=0.311 Sum_probs=29.9
Q ss_pred HHHHHHHHHHHhcC-CcHHHHHhhhCCChhhHHHHHHH
Q psy4300 33 EKKTLVALSYMATQ-LSMRKIGDQFNLADSTVWSCIDS 69 (307)
Q Consensus 33 ~~~l~i~L~~L~~g-~~~~~l~~~fgvs~stv~r~v~~ 69 (307)
++.+..+|..+.+| .|++..|..|||++||+++.++.
T Consensus 2 ee~l~~Ai~~v~~g~~S~r~AA~~ygVp~sTL~~r~~g 39 (45)
T PF05225_consen 2 EEDLQKAIEAVKNGKMSIRKAAKKYGVPRSTLRRRLRG 39 (45)
T ss_dssp HHHHHHHHHHHHTTSS-HHHHHHHHT--HHHHHHHHHH
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHcC
Confidence 57788888888898 99999999999999999987764
No 17
>smart00351 PAX Paired Box domain.
Probab=96.20 E-value=0.016 Score=45.35 Aligned_cols=45 Identities=11% Similarity=0.098 Sum_probs=40.1
Q ss_pred CCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300 27 VPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLT 72 (307)
Q Consensus 27 ~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~ 72 (307)
..+++.+.+.-+.+.+. .|.+..++|..||||++||+++++++-.
T Consensus 15 ~~~~s~~~R~riv~~~~-~G~s~~~iA~~~gvs~~tV~kwi~r~~~ 59 (125)
T smart00351 15 GRPLPDEERQRIVELAQ-NGVRPCDISRQLCVSHGCVSKILGRYYE 59 (125)
T ss_pred CCCCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 45699999998888775 8999999999999999999999999854
No 18
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=95.96 E-value=0.023 Score=37.22 Aligned_cols=44 Identities=18% Similarity=0.323 Sum_probs=33.0
Q ss_pred CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300 29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTA 73 (307)
Q Consensus 29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~ 73 (307)
.+|+.++-++.|.|+. |.++.++|..+|+|.+||...+.+....
T Consensus 10 ~L~~~~r~i~~l~~~~-g~s~~eIa~~l~~s~~~v~~~l~ra~~~ 53 (54)
T PF08281_consen 10 QLPERQREIFLLRYFQ-GMSYAEIAEILGISESTVKRRLRRARKK 53 (54)
T ss_dssp CS-HHHHHHHHHHHTS----HHHHHHHCTS-HHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHH-CcCHHHHHHHHCcCHHHHHHHHHHHHhh
Confidence 5788888888887765 7999999999999999999998876543
No 19
>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=95.87 E-value=0.014 Score=41.08 Aligned_cols=49 Identities=14% Similarity=0.208 Sum_probs=39.3
Q ss_pred CCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcc
Q psy4300 27 VPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMS 75 (307)
Q Consensus 27 ~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~ 75 (307)
+...|++.++-++-.++..|.+..+++..+||+.+|+++|+........
T Consensus 4 r~~ys~e~K~~~v~~~~~~g~sv~~va~~~gi~~~~l~~W~~~~~~~~~ 52 (76)
T PF01527_consen 4 RRRYSPEFKLQAVREYLESGESVSEVAREYGISPSTLYNWRKQYREGQS 52 (76)
T ss_dssp S----HHHHHHHHHHHHHHHCHHHHHHHHHTS-HHHHHHHHHHHH--ST
T ss_pred CCCCCHHHHHHHHHHHHHCCCceEeeecccccccccccHHHHHHhcCCC
Confidence 5789999999999999999999999999999999999999999973333
No 20
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=95.85 E-value=0.03 Score=43.58 Aligned_cols=46 Identities=9% Similarity=0.125 Sum_probs=43.4
Q ss_pred CCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300 27 VPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLT 72 (307)
Q Consensus 27 ~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~ 72 (307)
++..+.+.++-++...+..|.+..++|..||||.+|+++|++.+..
T Consensus 10 rr~ys~EfK~~aV~~~~~~g~sv~evA~e~gIs~~tl~~W~r~y~~ 55 (121)
T PRK09413 10 RRRRTTQEKIAIVQQSFEPGMTVSLVARQHGVAASQLFLWRKQYQE 55 (121)
T ss_pred CCCCCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHhh
Confidence 5789999999999999999999999999999999999999999865
No 21
>cd00131 PAX Paired Box domain
Probab=95.84 E-value=0.028 Score=44.18 Aligned_cols=46 Identities=9% Similarity=0.102 Sum_probs=40.8
Q ss_pred CCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300 27 VPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTA 73 (307)
Q Consensus 27 ~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~ 73 (307)
..++|.+.+.-+.+.+ ..|.+.+++|..||||++||+++++++-+.
T Consensus 15 ~~~lS~d~R~rIv~~~-~~G~s~~~iA~~~~Vs~~tV~r~i~r~~e~ 60 (128)
T cd00131 15 GRPLPDSIRQRIVELA-QSGIRPCDISRQLRVSHGCVSKILNRYYET 60 (128)
T ss_pred CCcCCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHHHHHc
Confidence 4789998888888776 689999999999999999999999998753
No 22
>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=95.71 E-value=0.032 Score=32.58 Aligned_cols=39 Identities=18% Similarity=0.272 Sum_probs=29.5
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHH
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCI 67 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v 67 (307)
..++.++...+.. .+..|.+..+++..||+|++|+++++
T Consensus 4 ~~~~~~~~~~i~~-~~~~~~s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 4 PKLTPEQIEEARR-LLAAGESVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred CcCCHHHHHHHHH-HHHcCCCHHHHHHHHCCCHHHHHHhC
Confidence 4566655554444 45678899999999999999998863
No 23
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=95.60 E-value=0.024 Score=44.97 Aligned_cols=44 Identities=18% Similarity=0.243 Sum_probs=40.2
Q ss_pred CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300 29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLT 72 (307)
Q Consensus 29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~ 72 (307)
+.+...+..++-.++..|.|.+.+|..||||.+|+.+++++.-.
T Consensus 4 ~~s~~~R~~~~~~~~~~G~S~re~Ak~~gvs~sTvy~wv~r~~e 47 (138)
T COG3415 4 PFSNDLRERVVDAVVGEGLSCREAAKRFGVSISTVYRWVRRYRE 47 (138)
T ss_pred hhhHHHHHHHHHHHHHcCccHHHHHHHhCccHHHHHHHHHHhcc
Confidence 45678888999999999999999999999999999999999875
No 24
>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=95.31 E-value=0.018 Score=40.59 Aligned_cols=44 Identities=18% Similarity=0.214 Sum_probs=31.0
Q ss_pred HHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 35 KTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 35 ~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
.+-++-+.+.+..+.+..|..||||+|||++=+.+=+.-+...|
T Consensus 8 ~i~i~~yIi~~~aTVR~~Ak~FGvSKSTVHkDvteRL~~in~~L 51 (82)
T PF12116_consen 8 VIEIANYIIETKATVRQAAKVFGVSKSTVHKDVTERLPKINPEL 51 (82)
T ss_dssp HHHHHHHHHHH---HHHHHHHHTS-HHHHHHHHTTHHHHH-HHH
T ss_pred HHHHHHHHHHcccHHHHHHHHHCCcHHHHHHHHHHHHHhcCHHH
Confidence 45566677899999999999999999999998877666665554
No 25
>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=95.18 E-value=0.077 Score=33.90 Aligned_cols=44 Identities=20% Similarity=0.336 Sum_probs=36.1
Q ss_pred CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300 29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTA 73 (307)
Q Consensus 29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~ 73 (307)
.++..++-++.+.|+ .|.++.++|..+|+|.+|+++++.+...-
T Consensus 10 ~l~~~~~~~~~~~~~-~~~~~~~ia~~~~~s~~~i~~~~~~~~~~ 53 (55)
T cd06171 10 KLPEREREVILLRFG-EGLSYEEIAEILGISRSTVRQRLHRALKK 53 (55)
T ss_pred hCCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 466777777777665 78999999999999999999999887543
No 26
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=95.16 E-value=0.088 Score=34.25 Aligned_cols=47 Identities=11% Similarity=0.319 Sum_probs=36.7
Q ss_pred CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
.++..++-.+ .++..|.++.++|..+|+|.+|+.+.+.+....+-..
T Consensus 3 ~l~~~e~~i~--~~~~~g~s~~eia~~l~is~~tv~~~~~~~~~kl~~~ 49 (58)
T smart00421 3 SLTPREREVL--RLLAEGLTNKEIAERLGISEKTVKTHLSNIMRKLGVR 49 (58)
T ss_pred CCCHHHHHHH--HHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCC
Confidence 4666666543 3357899999999999999999999999887666433
No 27
>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=94.90 E-value=0.11 Score=38.05 Aligned_cols=50 Identities=20% Similarity=0.264 Sum_probs=45.4
Q ss_pred CCCCCHHHHHHHHHHHHhcCCcHHHHHhhhC-CChhhHHHHHHHHHHHccc
Q psy4300 27 VPFVPVEKKTLVALSYMATQLSMRKIGDQFN-LADSTVWSCIDSFLTAMSQ 76 (307)
Q Consensus 27 ~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fg-vs~stv~r~v~~~~~~l~~ 76 (307)
...+...-+++|.|..-..|.|+.++|..|| .+.|||+..++++-..+.+
T Consensus 25 ~~~~~~aR~ia~yl~~~~~~~s~~~Ig~~fg~r~hStV~~a~~ri~~~~~~ 75 (90)
T cd06571 25 KKEIALARQIAMYLARELTGLSLPEIGRAFGGRDHSTVLHAVRKIEELLEE 75 (90)
T ss_pred CcCcchHHHHHHHHHHHHhCCCHHHHHHHhCCCCHhHHHHHHHHHHHHHHh
Confidence 4578889999999999999999999999999 9999999999999887755
No 28
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=94.78 E-value=0.063 Score=34.78 Aligned_cols=33 Identities=18% Similarity=0.307 Sum_probs=26.8
Q ss_pred HHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHH
Q psy4300 38 VALSYMATQLSMRKIGDQFNLADSTVWSCIDSF 70 (307)
Q Consensus 38 i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~ 70 (307)
..+..|....++.++|..+|+|.+||.+++++.
T Consensus 19 ~i~~~~~~~~s~~~vA~~~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 19 YILKLLRESRSFKDVARELGVSWSTVRRIFDRY 51 (52)
T ss_pred HHHHHHhhcCCHHHHHHHHCCCHHHHHHHHHhh
Confidence 334445555799999999999999999999874
No 29
>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=94.74 E-value=0.062 Score=39.26 Aligned_cols=36 Identities=8% Similarity=0.110 Sum_probs=29.8
Q ss_pred HHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHH
Q psy4300 32 VEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCID 68 (307)
Q Consensus 32 ~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~ 68 (307)
..++ ...+.++..|.+..++|..+|+|++|++|+.+
T Consensus 37 Ls~R-~~I~~ll~~G~S~~eIA~~LgISrsTIyRi~R 72 (88)
T TIGR02531 37 LAQR-LQVAKMLKQGKTYSDIEAETGASTATISRVKR 72 (88)
T ss_pred hhHH-HHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 3444 56667799999999999999999999999553
No 30
>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=94.72 E-value=0.084 Score=37.01 Aligned_cols=42 Identities=14% Similarity=0.209 Sum_probs=37.6
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHH
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDS 69 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~ 69 (307)
..+|...+.+..|.+.-.|.|+.+||...|+|.+||...++.
T Consensus 14 ~~l~~~~r~af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 14 TWVDSLAEAAAALAREEAGKTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred hcCCHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 468888888999988889999999999999999999888764
No 31
>PRK00118 putative DNA-binding protein; Validated
Probab=94.54 E-value=0.12 Score=38.88 Aligned_cols=50 Identities=16% Similarity=0.392 Sum_probs=41.9
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
+.++..++-++.|+++ .|.|+.++|..+|+|++||++.+.+....+.+.+
T Consensus 16 ~~L~ekqRevl~L~y~-eg~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~ 65 (104)
T PRK00118 16 SLLTEKQRNYMELYYL-DDYSLGEIAEEFNVSRQAVYDNIKRTEKLLEDYE 65 (104)
T ss_pred ccCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 5677888887766655 4899999999999999999999998887777764
No 32
>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=94.53 E-value=0.076 Score=39.10 Aligned_cols=65 Identities=8% Similarity=0.090 Sum_probs=42.8
Q ss_pred HHHHHHHHHHhhhcCcccccCCCCCCCCHHHHHHHHHHH------HhcCCcHHHHHhhhCCChhhHHHHHH
Q psy4300 4 TTFGFLVEALAAINGYETLYERGVPFVPVEKKTLVALSY------MATQLSMRKIGDQFNLADSTVWSCID 68 (307)
Q Consensus 4 ~~F~~L~~~l~~~~~~~~~~~~~~~~~~~~~~l~i~L~~------L~~g~~~~~l~~~fgvs~stv~r~v~ 68 (307)
+.++.+++++........-...-..-++++++-.+.++| +..+.|++.++...|||++||+|+=+
T Consensus 7 ~~w~~~~~ll~~~~~~~~l~~~l~~lLTp~E~~~l~~R~~i~~~Ll~~~~tQrEIa~~lGiS~atIsR~sn 77 (94)
T TIGR01321 7 QAWEAFLKLLKKADSEDDMQLLLELILTRSEREDLGDRIRIVNELLNGNMSQREIASKLGVSIATITRGSN 77 (94)
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHhCCChhhhhHHHh
Confidence 345666666654421000000012457888888888875 24679999999999999999988644
No 33
>PRK04217 hypothetical protein; Provisional
Probab=94.47 E-value=0.11 Score=39.66 Aligned_cols=50 Identities=20% Similarity=0.295 Sum_probs=40.1
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
..++.+++-++.|+ ...|.++.++|..+|+|.+||++.+.+....|.+.+
T Consensus 41 ~~Lt~eereai~l~-~~eGlS~~EIAk~LGIS~sTV~r~L~RArkkLre~L 90 (110)
T PRK04217 41 IFMTYEEFEALRLV-DYEGLTQEEAGKRMGVSRGTVWRALTSARKKVAQML 90 (110)
T ss_pred ccCCHHHHHHHHHH-HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 56778887544443 447899999999999999999999999887776664
No 34
>PRK06030 hypothetical protein; Provisional
Probab=93.94 E-value=0.39 Score=37.45 Aligned_cols=70 Identities=11% Similarity=0.017 Sum_probs=53.6
Q ss_pred HHHHHHHHHhhhcCccccc---CCC-CCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHc
Q psy4300 5 TFGFLVEALAAINGYETLY---ERG-VPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAM 74 (307)
Q Consensus 5 ~F~~L~~~l~~~~~~~~~~---~~~-~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l 74 (307)
+.+.|.+.+...+...... ..+ +..+...-+++|.|.+--++.|+.++|..||.+.|||...++.+-..+
T Consensus 24 t~d~Ii~~Va~~f~I~~~di~sk~R~rk~i~~aRqIAMYL~r~~~~~sl~~IG~~FGRDHSTV~haikkIe~~~ 97 (124)
T PRK06030 24 LCEAVIDLLALAFGVSGAEIASPLRGRREVSRIRQIAMYVAHVSLGWPMNEVALAFGRDRTTVGHACHTVEDLR 97 (124)
T ss_pred CHHHHHHHHHHHhCCCHHHHhCCCCCCcccchHHHHHHHHHHHHcCCCHHHHHHHHCCChhHHHHHHHHHHHHh
Confidence 3466666666665432111 122 367899999999999999999999999999999999999999776655
No 35
>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=93.90 E-value=0.24 Score=32.17 Aligned_cols=44 Identities=14% Similarity=0.320 Sum_probs=34.1
Q ss_pred CHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccc
Q psy4300 31 PVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQ 76 (307)
Q Consensus 31 ~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~ 76 (307)
+..++-++.+ +..|.++.++|..+++|.+|+.+.+++....+..
T Consensus 2 ~~~e~~i~~~--~~~~~s~~eia~~l~~s~~tv~~~~~~~~~~l~~ 45 (57)
T cd06170 2 TPREREVLRL--LAEGKTNKEIADILGISEKTVKTHLRNIMRKLGV 45 (57)
T ss_pred CHHHHHHHHH--HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHhCC
Confidence 3444444333 4689999999999999999999999988766554
No 36
>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=93.79 E-value=0.35 Score=38.40 Aligned_cols=73 Identities=11% Similarity=0.115 Sum_probs=53.3
Q ss_pred CCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc---------ccccccccCCChHHHHHHHH
Q psy4300 27 VPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP---------QIQCQYIKWPTEEESVIIER 97 (307)
Q Consensus 27 ~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~---------l~~~~~i~~P~~~~~~~~~~ 97 (307)
...++..++-.+.|+ ..|.++.++|..+|+|++||+++.++...-|-.. +-++..+..|...++..+..
T Consensus 4 ~~~Lte~qr~VL~Lr--~~GlTq~EIAe~LgiS~stV~~~e~ra~kkLr~a~~~~~l~~~~~a~~~~~~~~g~~~~~~~~ 81 (137)
T TIGR00721 4 KTFLTERQIKVLELR--EKGLSQKEIAKELKTTRANVSAIEKRAMENIEKARNTLDFVKFIKSPVRILCRRGDDLDEIPK 81 (137)
T ss_pred cCCCCHHHHHHHHHH--HcCCCHHHHHHHHCcCHHHHHHHHHhHHHHHHHHhhHHHHHHHhcCCEEEEecCCCcHHHhHH
Confidence 356888888888883 6999999999999999999998888866666541 12455566666666665555
Q ss_pred HHHH
Q psy4300 98 NFRA 101 (307)
Q Consensus 98 ~f~~ 101 (307)
...+
T Consensus 82 ~v~~ 85 (137)
T TIGR00721 82 RLFK 85 (137)
T ss_pred HHHH
Confidence 5443
No 37
>PHA00675 hypothetical protein
Probab=93.71 E-value=0.2 Score=35.13 Aligned_cols=43 Identities=5% Similarity=-0.017 Sum_probs=34.8
Q ss_pred CCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHH
Q psy4300 27 VPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDS 69 (307)
Q Consensus 27 ~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~ 69 (307)
...|+..+.-.|...+-+.|.|+..||..||||+|||+.|-+.
T Consensus 20 ~AKLt~~qV~~IR~l~~r~G~s~~~IA~~fGVsrstV~~I~~g 62 (78)
T PHA00675 20 NAKLTDAEVERIRELHEVEGMSYAVLAEKFEQSKGAIAKICRY 62 (78)
T ss_pred CcccCHHHHHHHHHHHHhcCccHHHHHHHhCCCHHHHHHHHcc
Confidence 4567777766666666588999999999999999999987653
No 38
>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=93.53 E-value=0.15 Score=36.48 Aligned_cols=37 Identities=22% Similarity=0.386 Sum_probs=29.1
Q ss_pred HHHHHHHHHHHHhcC-CcHHHHHhhhCCChhhHHHHHH
Q psy4300 32 VEKKTLVALSYMATQ-LSMRKIGDQFNLADSTVWSCID 68 (307)
Q Consensus 32 ~~~~l~i~L~~L~~g-~~~~~l~~~fgvs~stv~r~v~ 68 (307)
.++++...+-+|..| .+..++|..||+|.+||++.++
T Consensus 4 ~~~R~~~I~e~l~~~~~ti~dvA~~~gvS~~TVsr~L~ 41 (80)
T TIGR02844 4 IEERVLEIGKYIVETKATVRETAKVFGVSKSTVHKDVT 41 (80)
T ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHhc
Confidence 355666677777654 6788999999999999999764
No 39
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=93.36 E-value=0.22 Score=41.25 Aligned_cols=49 Identities=12% Similarity=0.108 Sum_probs=43.1
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
..+|++++.++.|.++ .|.++.++|..+|+|.+||...+.+-+..+.+.
T Consensus 126 ~~Lp~~~R~v~~L~~~-~g~s~~EIA~~lgis~~tVk~~l~rAl~~~~~~ 174 (178)
T PRK12529 126 DTLRPRVKQAFLMATL-DGMKQKDIAQALDIALPTVKKYIHQAYVTCLSL 174 (178)
T ss_pred HhCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 4688999999999888 789999999999999999999888877777665
No 40
>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=93.28 E-value=0.53 Score=30.82 Aligned_cols=29 Identities=10% Similarity=0.283 Sum_probs=25.2
Q ss_pred CcHHHHHhhhCCChhhHHHHHHHHHHHcc
Q psy4300 47 LSMRKIGDQFNLADSTVWSCIDSFLTAMS 75 (307)
Q Consensus 47 ~~~~~l~~~fgvs~stv~r~v~~~~~~l~ 75 (307)
.+..+||..+|||++|++..+++...-|.
T Consensus 24 ~tl~elA~~lgis~st~~~~LRrae~kli 52 (53)
T PF04967_consen 24 ITLEELAEELGISKSTVSEHLRRAERKLI 52 (53)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHh
Confidence 67899999999999999999998766543
No 41
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=93.25 E-value=0.23 Score=40.37 Aligned_cols=48 Identities=13% Similarity=0.259 Sum_probs=42.9
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
..+|.+++-++.|.+ .|.++.++|..+|+|.+||...+.+....|-..
T Consensus 111 ~~L~~~~r~il~l~~--~g~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~ 158 (166)
T PRK09639 111 AKMTERDRTVLLLRF--SGYSYKEIAEALGIKESSVGTTLARAKKKFRKI 158 (166)
T ss_pred HcCCHHHHHHHHHHH--cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 458889999999988 999999999999999999999999888877665
No 42
>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=93.10 E-value=0.3 Score=36.53 Aligned_cols=43 Identities=14% Similarity=0.415 Sum_probs=37.6
Q ss_pred CHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHc
Q psy4300 31 PVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAM 74 (307)
Q Consensus 31 ~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l 74 (307)
++.++..+.++|+ ++.+|.+++..+++|++|++|+-++.+..|
T Consensus 57 d~~~r~iL~~~Yi-~~~~~~~I~~~l~~S~~t~yr~~~~Al~~L 99 (100)
T PF07374_consen 57 DPDERLILRMRYI-NKLTWEQIAEELNISRRTYYRIHKKALKEL 99 (100)
T ss_pred ChhHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHhc
Confidence 5788999999999 579999999999999999999988776544
No 43
>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=93.09 E-value=0.34 Score=32.07 Aligned_cols=41 Identities=12% Similarity=0.239 Sum_probs=30.3
Q ss_pred HHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300 32 VEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLT 72 (307)
Q Consensus 32 ~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~ 72 (307)
..+-.++...+=..+.+..+|+..++++++++++++++...
T Consensus 3 ~~q~~iL~~l~~~~~~~~~~la~~~~~~~~~~t~~i~~L~~ 43 (59)
T PF01047_consen 3 PSQFRILRILYENGGITQSELAEKLGISRSTVTRIIKRLEK 43 (59)
T ss_dssp HHHHHHHHHHHHHSSEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHHCCChhHHHHHHHHHHH
Confidence 34444444444455689999999999999999999998754
No 44
>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=93.09 E-value=0.085 Score=33.51 Aligned_cols=22 Identities=18% Similarity=0.374 Sum_probs=19.4
Q ss_pred cHHHHHhhhCCChhhHHHHHHH
Q psy4300 48 SMRKIGDQFNLADSTVWSCIDS 69 (307)
Q Consensus 48 ~~~~l~~~fgvs~stv~r~v~~ 69 (307)
+..++|...|+|.+|||++++.
T Consensus 1 Ti~dIA~~agvS~~TVSr~ln~ 22 (46)
T PF00356_consen 1 TIKDIAREAGVSKSTVSRVLNG 22 (46)
T ss_dssp CHHHHHHHHTSSHHHHHHHHTT
T ss_pred CHHHHHHHHCcCHHHHHHHHhC
Confidence 4579999999999999998874
No 45
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=93.09 E-value=0.44 Score=38.02 Aligned_cols=73 Identities=12% Similarity=0.118 Sum_probs=52.5
Q ss_pred CCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccc---------cccccccccCCChHHHHHHHH
Q psy4300 27 VPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQ---------PQIQCQYIKWPTEEESVIIER 97 (307)
Q Consensus 27 ~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~---------~l~~~~~i~~P~~~~~~~~~~ 97 (307)
...+++.++-.+.| ...|.++.++|..+|+|++||+.+.++...-|-. .+-++..+..|...++..+..
T Consensus 4 ~~~Lt~rqreVL~l--r~~GlTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~tl~~~~~l~a~~~v~~~~G~d~~~ip~ 81 (141)
T PRK03975 4 ESFLTERQIEVLRL--RERGLTQQEIADILGTSRANVSSIEKRARENIEKARETLAFAETLNAPVRVTIPAGTDLFDIPK 81 (141)
T ss_pred ccCCCHHHHHHHHH--HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeEEEecCCCcHHHhHH
Confidence 45788888888888 3699999999999999999999988875554332 222444566666666665555
Q ss_pred HHHH
Q psy4300 98 NFRA 101 (307)
Q Consensus 98 ~f~~ 101 (307)
...+
T Consensus 82 ~v~~ 85 (141)
T PRK03975 82 RIYK 85 (141)
T ss_pred HHHH
Confidence 5444
No 46
>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=92.98 E-value=0.36 Score=32.20 Aligned_cols=26 Identities=15% Similarity=0.335 Sum_probs=23.2
Q ss_pred CcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300 47 LSMRKIGDQFNLADSTVWSCIDSFLT 72 (307)
Q Consensus 47 ~~~~~l~~~fgvs~stv~r~v~~~~~ 72 (307)
.+..+|+..++++++|++++++++..
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 69999999999999999999998765
No 47
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=92.83 E-value=0.36 Score=37.03 Aligned_cols=51 Identities=8% Similarity=0.061 Sum_probs=45.5
Q ss_pred CCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCC-ChhhHHHHHHHHHHHcccc
Q psy4300 27 VPFVPVEKKTLVALSYMATQLSMRKIGDQFNL-ADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 27 ~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgv-s~stv~r~v~~~~~~l~~~ 77 (307)
++.+|.+.++-++-.++..|.++..+|..||| +.+++++|+.+....-...
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~sv~~vAr~~gv~~~~~l~~W~~~~~~~~~~~ 56 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGDTVSEVAREFGIVSATQLYKWRIQLQKGGGLA 56 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCccHHHHHHHhCCCChHHHHHHHHHHHHccccc
Confidence 57899999999999999999999999999995 9999999999887755333
No 48
>PF13730 HTH_36: Helix-turn-helix domain
Probab=92.77 E-value=0.35 Score=31.59 Aligned_cols=43 Identities=16% Similarity=0.174 Sum_probs=32.7
Q ss_pred CCH-HHHHHHHHHHHhc--C---CcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300 30 VPV-EKKTLVALSYMAT--Q---LSMRKIGDQFNLADSTVWSCIDSFLT 72 (307)
Q Consensus 30 ~~~-~~~l~i~L~~L~~--g---~~~~~l~~~fgvs~stv~r~v~~~~~ 72 (307)
+++ +..|.+.|..+.+ + .|+..+|...|+|+.||.+.+++..+
T Consensus 3 Ls~~~~~v~~~l~~~~~~~~~~~pS~~~la~~~g~s~~Tv~~~i~~L~~ 51 (55)
T PF13730_consen 3 LSPTAKLVYLYLASYANKNGGCFPSQETLAKDLGVSRRTVQRAIKELEE 51 (55)
T ss_pred CCHHHHHHHHHHHHhcCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 344 4556666766652 2 47899999999999999999998754
No 49
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
Probab=92.63 E-value=0.33 Score=38.85 Aligned_cols=48 Identities=19% Similarity=0.262 Sum_probs=40.2
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccc
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQ 76 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~ 76 (307)
..++..++-++.|+++ .|.++.++|..+|+|.+||...+.+....|-.
T Consensus 112 ~~L~~~~r~il~l~~~-~~~~~~eIA~~lgis~~tv~~~~~ra~~~Lr~ 159 (161)
T TIGR02985 112 EKLPEQCRKIFILSRF-EGKSYKEIAEELGISVKTVEYHISKALKELRK 159 (161)
T ss_pred HHCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 3577888888888777 58999999999999999999998887666543
No 50
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=92.54 E-value=0.27 Score=41.01 Aligned_cols=50 Identities=14% Similarity=0.236 Sum_probs=43.1
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
..+|++++-++.|.++ .|.++.++|..+|+|.+||...+.+....|...+
T Consensus 130 ~~L~~~~r~vl~l~~~-~~~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 179 (189)
T PRK12515 130 AKLSPAHREIIDLVYY-HEKSVEEVGEIVGIPESTVKTRMFYARKKLAELL 179 (189)
T ss_pred HhCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4678888888888887 7899999999999999999999988877776664
No 51
>PF01371 Trp_repressor: Trp repressor protein; InterPro: IPR000831 The Trp repressor (TrpR) binds to at least five operators in the Escherichia coli genome, repressing gene expression. The operators at which it binds vary considerably in DNA sequence and location within the promoter; when bound to the Trp operon it recognises the sequence 5'-ACTAGT-3' and acts to prevent the initiation of transcription. The TrpR controls the trpEDCBA (trpO) operon and the genes for trpR, aroH, mtr and aroL, which are involved in the biosynthesis and uptake of the amino acid tryptophan []. The repressor binds to the operators only in the presence of L-tryptophan, thereby controlling the intracellular level of its effector; the complex also regulates Trp repressor biosynthesis by binding to its own regulatory region. TrpR acts as a dimer that is composed of identical 6-helical subunits, where four of the helices form the core of the protein and intertwine with the corresponding helices from the other subunit.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3FRW_H 3KOR_A 3SSW_N 1P6Z_N 1CO0_B 1JHG_A 1WRT_S 1WRS_R 1WRP_R 1RCS_B ....
Probab=92.25 E-value=0.37 Score=35.07 Aligned_cols=38 Identities=16% Similarity=0.171 Sum_probs=30.6
Q ss_pred HHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHH
Q psy4300 32 VEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDS 69 (307)
Q Consensus 32 ~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~ 69 (307)
..+++.++=..|..|.+|++|+...|+|-.||+|+=+.
T Consensus 35 l~~R~~va~~lL~~g~syreIa~~tgvS~aTItRvsr~ 72 (87)
T PF01371_consen 35 LAQRWQVAKELLDEGKSYREIAEETGVSIATITRVSRC 72 (87)
T ss_dssp HHHHHHHHHHHHHTTSSHHHHHHHHTSTHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 44555555557889999999999999999999886544
No 52
>PHA00542 putative Cro-like protein
Probab=92.22 E-value=0.27 Score=35.41 Aligned_cols=53 Identities=13% Similarity=0.080 Sum_probs=39.0
Q ss_pred HHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccccccccccCCChHHHHHHHHHHHHh
Q psy4300 37 LVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQIQCQYIKWPTEEESVIIERNFRAL 102 (307)
Q Consensus 37 ~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l~~~~~i~~P~~~~~~~~~~~f~~~ 102 (307)
-+...+...|.+..++|...|||++|++++.+.- ..-|+.+.+..+++.+.+.
T Consensus 22 ~l~~~l~~~glTq~elA~~lgIs~~tIsr~e~g~-------------~~~p~~~~l~ki~~~~~~~ 74 (82)
T PHA00542 22 ELVCALIRAGWSQEQIADATDVSQPTICRIYSGR-------------HKDPRYSVVEKLRHLVLNL 74 (82)
T ss_pred HHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHcCC-------------CCCCCHHHHHHHHHHHHHh
Confidence 3445567889999999999999999999976532 1235666667777777654
No 53
>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=92.18 E-value=0.35 Score=38.03 Aligned_cols=47 Identities=17% Similarity=0.335 Sum_probs=39.4
Q ss_pred CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccc
Q psy4300 29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQ 76 (307)
Q Consensus 29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~ 76 (307)
.++..++-++.+.++ .|.++.++|..+|+|.++|++...+....|-.
T Consensus 110 ~L~~~~~~ii~~~~~-~g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 110 KLPEREREVLVLRYL-EGLSYKEIAEILGISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred hCCHHHHHHHhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 577888877777666 68999999999999999999999998776543
No 54
>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=92.12 E-value=0.4 Score=39.00 Aligned_cols=48 Identities=8% Similarity=0.187 Sum_probs=41.4
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccc
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQ 76 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~ 76 (307)
..+|+.++.++.|.|+. |.++.++|..+|+|.+||...+.+....|-.
T Consensus 121 ~~L~~~~r~vl~l~~~~-g~s~~eIA~~l~is~~tv~~~l~ra~~~Lr~ 168 (170)
T TIGR02952 121 KILTPKQQHVIALRFGQ-NLPIAEVARILGKTEGAVKILQFRAIKKLAR 168 (170)
T ss_pred HhCCHHHHHHHHHHHhc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 46889999999998775 8999999999999999999999888776643
No 55
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=91.97 E-value=0.36 Score=39.09 Aligned_cols=48 Identities=10% Similarity=0.113 Sum_probs=39.3
Q ss_pred CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
.++++++-++.|.|+. |.++.++|..+|+|.+||...+.+...-|-..
T Consensus 109 ~L~~~~r~v~~l~~~~-~~s~~EIA~~lgis~~tV~~~l~ra~~~lr~~ 156 (163)
T PRK07037 109 ELPARTRYAFEMYRLH-GETQKDIARELGVSPTLVNFMIRDALVHCRKC 156 (163)
T ss_pred hCCHHHHHHHHHHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 5666777777777665 89999999999999999999888877776655
No 56
>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=91.90 E-value=0.73 Score=29.14 Aligned_cols=29 Identities=10% Similarity=0.327 Sum_probs=23.8
Q ss_pred hcCCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300 44 ATQLSMRKIGDQFNLADSTVWSCIDSFLT 72 (307)
Q Consensus 44 ~~g~~~~~l~~~fgvs~stv~r~v~~~~~ 72 (307)
..+.+..++|..+|+|.+|++++++++.+
T Consensus 15 ~~~~t~~ela~~~~is~~tv~~~l~~L~~ 43 (48)
T PF13412_consen 15 NPRITQKELAEKLGISRSTVNRYLKKLEE 43 (48)
T ss_dssp CTTS-HHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred cCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 44589999999999999999999998764
No 57
>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=91.86 E-value=0.46 Score=30.08 Aligned_cols=38 Identities=13% Similarity=0.219 Sum_probs=27.7
Q ss_pred HHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300 35 KTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLT 72 (307)
Q Consensus 35 ~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~ 72 (307)
++-+.........+..+++..+|+|++|+++.++...+
T Consensus 4 R~~Il~~L~~~~~~~~el~~~l~~s~~~vs~hL~~L~~ 41 (47)
T PF01022_consen 4 RLRILKLLSEGPLTVSELAEELGLSQSTVSHHLKKLRE 41 (47)
T ss_dssp HHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHHHhCCCchhhHHHhccccchHHHHHHHHHHH
Confidence 33443333345588999999999999999999987754
No 58
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=91.80 E-value=0.44 Score=39.08 Aligned_cols=48 Identities=25% Similarity=0.209 Sum_probs=40.9
Q ss_pred CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
.+++.++.++.|.|+ .|.++.++|..+|+|.+||...+.+...-|-..
T Consensus 128 ~L~~~~r~vl~l~~~-~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 175 (182)
T PRK09652 128 SLPEELRTAITLREI-EGLSYEEIAEIMGCPIGTVRSRIFRAREALRAK 175 (182)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 578888888888877 689999999999999999999888877766655
No 59
>PRK15320 transcriptional activator SprB; Provisional
Probab=91.77 E-value=0.49 Score=39.74 Aligned_cols=48 Identities=17% Similarity=0.178 Sum_probs=41.0
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
+.+|..+. -.|.+|+.|.+..+||..+++|.+||+.+..+...-+...
T Consensus 163 ~~LSdREI--EVL~LLAkG~SNKEIAekL~LS~KTVSTYKnRLLeKLgAk 210 (251)
T PRK15320 163 PGVTQAKY--ALLILLSSGHPAIELAKKFGLGTKTVSIYRKKVMYRLGMD 210 (251)
T ss_pred CCCCHHHH--HHHHHHHcCCCHHHHHHHhccchhhHHHHHHHHHHHcCCC
Confidence 44555554 6788999999999999999999999999999998887766
No 60
>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=91.76 E-value=0.43 Score=35.35 Aligned_cols=47 Identities=19% Similarity=0.427 Sum_probs=38.1
Q ss_pred CCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 30 VPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 30 ~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
++-.++--+-|+|+- ..|...+|..|+||+++|+..|+++...+..-
T Consensus 18 LT~KQ~~Y~~lyy~d-DlSl~EIAee~~VSRqAIyDnIKr~~~~L~~Y 64 (105)
T COG2739 18 LTKKQKNYLELYYLD-DLSLSEIAEEFNVSRQAIYDNIKRTEKILEDY 64 (105)
T ss_pred HhHHHHHHHHHHHHh-hccHHHHHHHhCccHHHHHHHHHHHHHHHHHH
Confidence 344556666666654 68999999999999999999999999888764
No 61
>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=91.69 E-value=0.49 Score=38.04 Aligned_cols=48 Identities=15% Similarity=0.358 Sum_probs=42.0
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccc
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQ 76 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~ 76 (307)
..+|+.++-.+.|.++ .|.++.++|..+|+|.+||...+.+....|-+
T Consensus 110 ~~L~~~~r~v~~l~~~-~g~~~~eIA~~l~is~~tv~~~l~Rar~~Lr~ 157 (159)
T TIGR02989 110 EKLPERQRELLQLRYQ-RGVSLTALAEQLGRTVNAVYKALSRLRVRLRD 157 (159)
T ss_pred HHCCHHHHHHHHHHHh-cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Confidence 4688999999999776 68999999999999999999999988777654
No 62
>PF13551 HTH_29: Winged helix-turn helix
Probab=91.52 E-value=0.35 Score=36.40 Aligned_cols=37 Identities=16% Similarity=0.308 Sum_probs=31.4
Q ss_pred HHHHHHhcCCc-HHHHHhhhCCChhhHHHHHHHHHHHc
Q psy4300 38 VALSYMATQLS-MRKIGDQFNLADSTVWSCIDSFLTAM 74 (307)
Q Consensus 38 i~L~~L~~g~~-~~~l~~~fgvs~stv~r~v~~~~~~l 74 (307)
.+|..+..|.+ ..++|..+|+|.+||+++++++...=
T Consensus 3 ~~l~l~~~g~~~~~~ia~~lg~s~~Tv~r~~~~~~~~G 40 (112)
T PF13551_consen 3 QILLLLAEGVSTIAEIARRLGISRRTVYRWLKRYREGG 40 (112)
T ss_pred HHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHccc
Confidence 35667889995 99999999999999999999975433
No 63
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=91.39 E-value=0.53 Score=38.84 Aligned_cols=49 Identities=12% Similarity=0.242 Sum_probs=41.6
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
..+|++++-.+.|.++ .|.|+.++|..+|+|..||...+.+....|-+.
T Consensus 128 ~~L~~~~r~i~~l~~~-~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 176 (179)
T PRK12514 128 EELEKDRAAAVRRAYL-EGLSYKELAERHDVPLNTMRTWLRRSLLKLREC 176 (179)
T ss_pred HhCCHHHHHHHHHHHH-cCCCHHHHHHHHCCChHHHHHHHHHHHHHHHHH
Confidence 3577888888888876 789999999999999999999998887776554
No 64
>TIGR02392 rpoH_proteo alternative sigma factor RpoH. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors.
Probab=91.35 E-value=0.44 Score=42.44 Aligned_cols=50 Identities=2% Similarity=0.260 Sum_probs=43.1
Q ss_pred CCCCHHHHHHHHHHHHh-cCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 28 PFVPVEKKTLVALSYMA-TQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~-~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
..++..++..+.|+|+. .|.|+.++|..+|||+.+|+++..+.+.-|-..
T Consensus 217 ~~L~~rer~vl~l~y~~~~~~t~~eIA~~lgvS~~~V~q~~~~Al~kLr~~ 267 (270)
T TIGR02392 217 GSLDARSRRIIEARWLDDDKLTLQELAAEYGVSAERIRQIEKNAMKKLKAA 267 (270)
T ss_pred HcCCHHHHHHHHHHhcCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 36889999999999974 489999999999999999999988887766544
No 65
>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=91.30 E-value=0.37 Score=33.54 Aligned_cols=43 Identities=26% Similarity=0.269 Sum_probs=34.0
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhC-CChhhHHHHHHHH
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFN-LADSTVWSCIDSF 70 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fg-vs~stv~r~v~~~ 70 (307)
..+...-++++.|..-..+.|+.++|..|| .+.|||...++++
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 346667888998888888999999999999 9999998887764
No 66
>COG3316 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=91.23 E-value=1.1 Score=38.27 Aligned_cols=187 Identities=14% Similarity=0.120 Sum_probs=111.2
Q ss_pred CCCHHHHHHHHHHHHhcCCcHHHHHhh-----hCCChhhHHHHHHHHHHHccccccccccccCCChHHHHHHHHHHHHhh
Q psy4300 29 FVPVEKKTLVALSYMATQLSMRKIGDQ-----FNLADSTVWSCIDSFLTAMSQPQIQCQYIKWPTEEESVIIERNFRALA 103 (307)
Q Consensus 29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~-----fgvs~stv~r~v~~~~~~l~~~l~~~~~i~~P~~~~~~~~~~~f~~~~ 103 (307)
.++-......+=+||+.++|++++... ..++.+|+++++.+.-+.+...+ .. +.
T Consensus 8 ~f~~~vi~~~V~~yl~~~Ls~r~v~e~l~~rgi~v~h~Ti~rwv~k~~~~~~~~~-~~-----r~--------------- 66 (215)
T COG3316 8 QFPRNIIAVAVWLYLRYGLSLRDVEEMLAERGIEVDHETIHRWVQKYGPLLARRL-KR-----RK--------------- 66 (215)
T ss_pred hcchhhHHHHHHHHhhcchhhccHHHHHHHcCcchhHHHHHHHHHHHhHHHHHHh-hh-----hc---------------
Confidence 455556666666778889999988885 35778899999999988777773 11 10
Q ss_pred CCCCcceeecceeEEeecCCCCccccccccCCcceeEEeeeCCCcceEeeeeccccccCCCcccccchhhcchhhcCCCC
Q psy4300 104 KFPGVIGAIDGCHIEGKFSKDIRNDYNNRKCTQSMILQGVCTSNKLLTNIHVGCTGRNHDAKVLSTSQIGRRIDAYGPTS 183 (307)
Q Consensus 104 ~~p~~~g~iDgt~i~i~~P~~~~~~y~~~k~~~s~~~q~v~d~~g~i~~v~~~~~Gs~~D~~i~~~S~l~~~l~~~~~~~ 183 (307)
.-++-.-.||-|.|+|. +.-.+. =..||.+|-.+.+.....-+...+..| +.+.+..
T Consensus 67 ~~~~~~w~vDEt~ikv~-----gkw~yl---------yrAid~~g~~Ld~~L~~rRn~~aAk~F----l~kllk~----- 123 (215)
T COG3316 67 RKAGDSWRVDETYIKVN-----GKWHYL---------YRAIDADGLTLDVWLSKRRNALAAKAF----LKKLLKK----- 123 (215)
T ss_pred cccccceeeeeeEEeec-----cEeeeh---------hhhhccCCCeEEEEEEcccCcHHHHHH----HHHHHHh-----
Confidence 01223447999999984 111111 136788899999988543334444333 3333443
Q ss_pred CCCCCCeEEEecCCCCCCccccccccCCCCCCHHHHHHhHHHHhh-hhHHHHHHHHHHhhcccccccccCChhhHHHHHH
Q psy4300 184 LLYRDEYHLLGDSAYPLRTWCMVPYKNFGHMTEEEKKYNTALSKT-RVPIENVFGLIKGRWRRLKYIDVGDPKRMAYIIS 262 (307)
Q Consensus 184 ~~~~~~~~llgD~gY~~~~~l~~P~~~~~~lt~~q~~fN~~~s~~-R~~VE~~fg~LK~rf~iL~~~~~~~~~~~~~ii~ 262 (307)
...+..++.|++=-....+ .. +.. .+-++-++- ...+|+-+..+|.|=+-+. .+.....+...+.
T Consensus 124 --~g~p~v~vtDka~s~~~A~----~~---l~~---~~ehr~~~ylnN~iE~dh~~iKrr~~~~~--~f~~~~sa~~~~~ 189 (215)
T COG3316 124 --HGEPRVFVTDKAPSYTAAL----RK---LGS---EVEHRTSKYLNNRIEQDHRPIKRRTRPMK--RFKSLSSAASTIS 189 (215)
T ss_pred --cCCCceEEecCccchHHHH----Hh---cCc---chheecccccccchhhcchhHHHHhcccc--cCCChHHHHHHHH
Confidence 2346677788764322111 10 010 122222233 3788999999998665442 2335666677777
Q ss_pred HHHHhhhhhcc
Q psy4300 263 AACVLHNFCYL 273 (307)
Q Consensus 263 a~~~LhN~~~~ 273 (307)
..=.+|++--.
T Consensus 190 gie~i~~~~~~ 200 (215)
T COG3316 190 GIESIHMLYKR 200 (215)
T ss_pred hHHHHHHHHhh
Confidence 77777776443
No 67
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=91.17 E-value=0.53 Score=38.45 Aligned_cols=49 Identities=22% Similarity=0.323 Sum_probs=41.3
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
..+|+.++-++.|.++ .|.++.+||..+|+|.+||.+.+.+....|-..
T Consensus 124 ~~L~~~~r~i~~l~~~-~~~~~~eIA~~lgis~~tv~~~~~ra~~~lr~~ 172 (179)
T PRK11924 124 DALPVKQREVFLLRYV-EGLSYREIAEILGVPVGTVKSRLRRARQLLREC 172 (179)
T ss_pred HhCCHHHHHHhhHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3577777887778777 589999999999999999999999987777655
No 68
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=91.10 E-value=0.53 Score=37.93 Aligned_cols=50 Identities=10% Similarity=0.220 Sum_probs=42.7
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
..+|..++-++.|.|+. |.++.++|..+|+|.+||...+.+....|-..+
T Consensus 105 ~~Lp~~~r~v~~l~~~~-g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 154 (161)
T PRK09047 105 QKLPARQREAFLLRYWE-DMDVAETAAAMGCSEGSVKTHCSRATHALAKAL 154 (161)
T ss_pred HhCCHHHHHHHHHHHHh-cCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 46777888888887765 899999999999999999999999888887764
No 69
>PF13610 DDE_Tnp_IS240: DDE domain
Probab=91.06 E-value=0.92 Score=36.08 Aligned_cols=132 Identities=16% Similarity=0.086 Sum_probs=74.6
Q ss_pred eeecceeEEeecCCCCccccccccCCcceeEEeeeCCCcceEeeeeccccccCCCcccccchhhcchhhcCCCCCCCCCC
Q psy4300 110 GAIDGCHIEGKFSKDIRNDYNNRKCTQSMILQGVCTSNKLLTNIHVGCTGRNHDAKVLSTSQIGRRIDAYGPTSLLYRDE 189 (307)
Q Consensus 110 g~iDgt~i~i~~P~~~~~~y~~~k~~~s~~~q~v~d~~g~i~~v~~~~~Gs~~D~~i~~~S~l~~~l~~~~~~~~~~~~~ 189 (307)
-.||-|.|+|. +.- .=+=.++|++|+++++.+...-...++..| +.+.+... ...+
T Consensus 4 w~~DEt~iki~-----G~~---------~yl~~aiD~~~~~l~~~ls~~Rd~~aA~~F----l~~~l~~~------~~~p 59 (140)
T PF13610_consen 4 WHVDETYIKIK-----GKW---------HYLWRAIDAEGNILDFYLSKRRDTAAAKRF----LKRALKRH------RGEP 59 (140)
T ss_pred EEEeeEEEEEC-----CEE---------EEEEEeecccccchhhhhhhhcccccceee----ccccceee------cccc
Confidence 36899999984 111 112468999999988888533333333222 22223221 1234
Q ss_pred eEEEecCC--CCCCccccccc-cCCCCCCHHHHHHhHHHHhhhhHHHHHHHHHHhhcccccccccCChhhHHHHHHHHHH
Q psy4300 190 YHLLGDSA--YPLRTWCMVPY-KNFGHMTEEEKKYNTALSKTRVPIENVFGLIKGRWRRLKYIDVGDPKRMAYIISAACV 266 (307)
Q Consensus 190 ~~llgD~g--Y~~~~~l~~P~-~~~~~lt~~q~~fN~~~s~~R~~VE~~fg~LK~rf~iL~~~~~~~~~~~~~ii~a~~~ 266 (307)
..++.|+. |+.--.-+.+- ..+..... ....-.++.||+-+..+|.|.+....+ .+.+.+...+.+-.+
T Consensus 60 ~~ivtDk~~aY~~A~~~l~~~~~~~~~v~~------~~~k~~nN~iE~~h~~~K~r~r~~~gF--ks~~~A~~~l~~~~~ 131 (140)
T PF13610_consen 60 RVIVTDKLPAYPAAIKELNPEGRLHDKVEH------RQRKYLNNRIERDHRTIKRRTRPMNGF--KSFRSAQRTLSGFEA 131 (140)
T ss_pred ceeecccCCccchhhhhcccccccccccce------eechhhhChhhHhhhhhhhhcccccCc--CCHHHHHHHHHHHHH
Confidence 56776764 32111111110 00000000 011123678999999999988776655 368888999999999
Q ss_pred hhhhhcc
Q psy4300 267 LHNFCYL 273 (307)
Q Consensus 267 LhN~~~~ 273 (307)
.||+...
T Consensus 132 ~~n~~r~ 138 (140)
T PF13610_consen 132 YHNFRRP 138 (140)
T ss_pred HHHHhCC
Confidence 9999764
No 70
>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=91.04 E-value=0.97 Score=35.75 Aligned_cols=50 Identities=14% Similarity=0.280 Sum_probs=42.5
Q ss_pred CCCCHHHHHHHHHHHHhc-CCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 28 PFVPVEKKTLVALSYMAT-QLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~-g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
..++.+++-.+.++|+.. ..++..+|..+|+|++|+++.-+.++.-+...
T Consensus 81 ~~Ld~~er~II~~rY~~~~~~t~~~Ia~~l~iS~~t~~r~r~~~l~kla~~ 131 (134)
T TIGR01636 81 NEADEQTRVIIQELYMKKRPLTLVGLAQQLFISKSTAYRLRNHIIEAVAEE 131 (134)
T ss_pred HhCCHHHHHHHHHHHccCCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 358899999999999843 35999999999999999999988888777654
No 71
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=90.97 E-value=0.58 Score=39.16 Aligned_cols=49 Identities=10% Similarity=0.164 Sum_probs=42.3
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
..+|...+-++.|+|+. |.++.++|..+|+|.+||...+.+....|-..
T Consensus 133 ~~Lp~~~R~v~~L~~~~-g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~ 181 (189)
T PRK12530 133 NHLPAQQARVFMMREYL-ELSSEQICQECDISTSNLHVLLYRARLQLQAC 181 (189)
T ss_pred HhCCHHHHHHHhHHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 35678888888888877 89999999999999999999888887777665
No 72
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=90.96 E-value=0.5 Score=41.00 Aligned_cols=50 Identities=14% Similarity=0.218 Sum_probs=42.8
Q ss_pred CCCCHHHHHHHHHHHH---hcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 28 PFVPVEKKTLVALSYM---ATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L---~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
..+|+.++.++.|.|+ -.|.|+.++|..+|+|.+||.+..++....|...
T Consensus 174 ~~Lp~~~R~i~~l~y~~~~~e~~S~~EIA~~lgis~~tV~~~~~rA~~kLr~~ 226 (233)
T PRK05803 174 DILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRALKKLFKE 226 (233)
T ss_pred HhCCHHHHHHHHHHhCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 4688899999999886 4789999999999999999999888877666554
No 73
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=90.92 E-value=0.56 Score=38.17 Aligned_cols=50 Identities=10% Similarity=0.078 Sum_probs=42.5
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
..+|+.++-++.|.++ .|.++.++|..+|+|.+||...+.+....|-..+
T Consensus 111 ~~L~~~~r~v~~l~~~-~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 160 (164)
T PRK12547 111 NLLSADQREAIILIGA-SGFSYEDAAAICGCAVGTIKSRVSRARNRLQELL 160 (164)
T ss_pred HhCCHHHHHHHHHHHH-cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 4577788888888888 7899999999999999999999998887776653
No 74
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=90.91 E-value=0.54 Score=40.77 Aligned_cols=50 Identities=8% Similarity=0.216 Sum_probs=42.7
Q ss_pred CCCCHHHHHHHHHHHH---hcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 28 PFVPVEKKTLVALSYM---ATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L---~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
..+|+.++-++.|+|. -.|.|+.++|..+|+|.+||...+.+....|-..
T Consensus 177 ~~Lp~~~R~v~~L~y~l~~~eg~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~~ 229 (234)
T PRK08301 177 KKLSDREKQIMELRFGLNGGEEKTQKEVADMLGISQSYISRLEKRIIKRLKKE 229 (234)
T ss_pred HhCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4578888888888874 6799999999999999999999988887777655
No 75
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=90.81 E-value=0.49 Score=41.83 Aligned_cols=49 Identities=18% Similarity=0.315 Sum_probs=42.8
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
..+++.++..+.|+|+ .|.++.++|..+|+|.++|++...+...-|-..
T Consensus 204 ~~L~~~er~vi~l~y~-e~~t~~EIA~~lgis~~~V~~~~~ral~kLr~~ 252 (257)
T PRK05911 204 LALEEKERKVMALYYY-EELVLKEIGKILGVSESRVSQIHSKALLKLRAT 252 (257)
T ss_pred HcCCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 3688889989999886 689999999999999999999999888777665
No 76
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=90.79 E-value=0.63 Score=38.76 Aligned_cols=49 Identities=18% Similarity=0.193 Sum_probs=42.2
Q ss_pred CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
.+|...+-++.|.|+ .|.++.++|..+|+|.+||...+.+....|-..+
T Consensus 111 ~Lp~~~R~v~~L~~~-eg~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~~ 159 (182)
T PRK12511 111 DLPEEQRAALHLVAI-EGLSYQEAAAVLGIPIGTLMSRIGRARAALRAFE 159 (182)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHH
Confidence 678888888888888 5899999999999999999999888877776663
No 77
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=90.75 E-value=0.64 Score=39.08 Aligned_cols=49 Identities=18% Similarity=0.166 Sum_probs=42.3
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
..+|.+++-++.|.|+ .|.++.++|..+|+|.+||...+.+....|-..
T Consensus 135 ~~L~~~~r~i~~L~~~-~g~s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~ 183 (196)
T PRK12524 135 AALPERQRQAVVLRHI-EGLSNPEIAEVMEIGVEAVESLTARGKRALAAL 183 (196)
T ss_pred HhCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 3577888888888877 789999999999999999999999887777665
No 78
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=90.66 E-value=0.55 Score=42.18 Aligned_cols=50 Identities=2% Similarity=0.201 Sum_probs=43.7
Q ss_pred CCCCHHHHHHHHHHHHh-cCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 28 PFVPVEKKTLVALSYMA-TQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~-~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
..++..++..+.++|+. .+.++.++|..+|||+++|+++..+.+.-|-..
T Consensus 229 ~~L~~rEr~VL~lry~~~~~~Tl~EIA~~lgvS~~rVrqi~~~Al~kLR~~ 279 (284)
T PRK06596 229 EGLDERSRDIIEARWLDDDKSTLQELAAEYGVSAERVRQIEKNAMKKLKAA 279 (284)
T ss_pred hcCCHHHHHHHHHHhcCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 46889999999999975 589999999999999999999999887766554
No 79
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=90.65 E-value=0.5 Score=40.65 Aligned_cols=50 Identities=20% Similarity=0.245 Sum_probs=42.9
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
..+|..++-++.|+|+ .|.++.+||..+|+|.+||...+.+....|...+
T Consensus 133 ~~Lp~~~R~v~~L~y~-eg~s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l 182 (216)
T PRK12533 133 AKLPVEYREVLVLREL-EDMSYREIAAIADVPVGTVMSRLARARRRLAALL 182 (216)
T ss_pred HcCCHHHHhHhhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3567788888888888 5899999999999999999999998887777764
No 80
>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=90.61 E-value=1.2 Score=29.95 Aligned_cols=41 Identities=15% Similarity=0.256 Sum_probs=31.4
Q ss_pred HHHHHHHHHHHHh---cCCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300 32 VEKKTLVALSYMA---TQLSMRKIGDQFNLADSTVWSCIDSFLT 72 (307)
Q Consensus 32 ~~~~l~i~L~~L~---~g~~~~~l~~~fgvs~stv~r~v~~~~~ 72 (307)
..+.-+-+++.|. ...+-.+||..+|+|++||+..+++...
T Consensus 5 ~~e~YL~~Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~ 48 (60)
T PF01325_consen 5 SEEDYLKAIYELSEEGGPVRTKDIAERLGVSPPTVTEMLKRLAE 48 (60)
T ss_dssp HHHHHHHHHHHHHHCTSSBBHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHcCCCCccHHHHHHHHCCChHHHHHHHHHHHH
Confidence 3455556666665 5688899999999999999999998754
No 81
>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=90.56 E-value=0.77 Score=29.91 Aligned_cols=29 Identities=7% Similarity=0.205 Sum_probs=25.0
Q ss_pred CCcHHHHHhhhCCChhhHHHHHHHHHHHc
Q psy4300 46 QLSMRKIGDQFNLADSTVWSCIDSFLTAM 74 (307)
Q Consensus 46 g~~~~~l~~~fgvs~stv~r~v~~~~~~l 74 (307)
+.+-.++|..++||+.||.+.++..-+..
T Consensus 15 ~it~~eLa~~l~vS~rTi~~~i~~L~~~~ 43 (55)
T PF08279_consen 15 PITAKELAEELGVSRRTIRRDIKELREWG 43 (55)
T ss_dssp SBEHHHHHHHCTS-HHHHHHHHHHHHHTT
T ss_pred CcCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence 47899999999999999999999887665
No 82
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=90.55 E-value=0.31 Score=40.02 Aligned_cols=49 Identities=16% Similarity=0.171 Sum_probs=41.9
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
..+|+.++.++.|.++ .|.++.++|..+|+|.+||...+.+....|-..
T Consensus 125 ~~L~~~~r~v~~l~~~-~g~s~~eIA~~l~is~~~V~~~l~ra~~~l~~~ 173 (176)
T PRK09638 125 SKLDPEFRAPVILKHY-YGYTYEEIAKMLNIPEGTVKSRVHHGIKQLRKE 173 (176)
T ss_pred HcCCHHHhheeeehhh-cCCCHHHHHHHHCCChhHHHHHHHHHHHHHHHH
Confidence 4578888888888887 599999999999999999998888887776554
No 83
>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=90.54 E-value=0.57 Score=31.04 Aligned_cols=45 Identities=16% Similarity=0.282 Sum_probs=34.5
Q ss_pred CCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccc
Q psy4300 30 VPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQ 76 (307)
Q Consensus 30 ~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~ 76 (307)
++..+.- +|.+++.|.+..++|...|+|.+||......+..-+--
T Consensus 4 LT~~E~~--vl~~l~~G~~~~eIA~~l~is~~tV~~~~~~i~~Kl~~ 48 (58)
T PF00196_consen 4 LTERELE--VLRLLAQGMSNKEIAEELGISEKTVKSHRRRIMKKLGV 48 (58)
T ss_dssp S-HHHHH--HHHHHHTTS-HHHHHHHHTSHHHHHHHHHHHHHHHHT-
T ss_pred cCHHHHH--HHHHHHhcCCcchhHHhcCcchhhHHHHHHHHHHHhCC
Confidence 4444443 67889999999999999999999999998887765543
No 84
>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=90.51 E-value=0.65 Score=38.37 Aligned_cols=47 Identities=17% Similarity=0.186 Sum_probs=39.7
Q ss_pred CCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 30 VPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 30 ~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
+|+..+-++.|.|+. |.++.++|..+|+|.+||...+.+....|-..
T Consensus 135 Lp~~~r~v~~l~~~~-g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 181 (183)
T TIGR02999 135 VDPRQAEVVELRFFA-GLTVEEIAELLGVSVRTVERDWRFARAWLADE 181 (183)
T ss_pred CCHHHHHHHHHHHHc-CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 778888877777665 79999999999999999999999887776554
No 85
>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=90.35 E-value=0.6 Score=40.35 Aligned_cols=50 Identities=12% Similarity=0.194 Sum_probs=43.4
Q ss_pred CCCCHHHHHHHHHHHH---hcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 28 PFVPVEKKTLVALSYM---ATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L---~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
..+|+.++-++.|+|+ ..|.|+.++|..+|+|.+||.+.+++....|-..
T Consensus 173 ~~L~~~~r~il~l~y~~~~~e~~S~~EIAe~lgis~~tV~~~~~rAl~~Lr~~ 225 (227)
T TIGR02846 173 SVLDGREREVIEMRYGLGDGRRKTQREIAKILGISRSYVSRIEKRALMKLYKE 225 (227)
T ss_pred HhCCHHHHHHHHHHHcCCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4678888889999886 4889999999999999999999999888777655
No 86
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=90.26 E-value=0.78 Score=37.06 Aligned_cols=47 Identities=15% Similarity=0.108 Sum_probs=38.4
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcc
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMS 75 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~ 75 (307)
..+|++++-++.|.++. |.++.++|..+|+|.+||...+.+....+.
T Consensus 112 ~~L~~~~r~v~~L~~~~-g~s~~EIA~~l~is~~tV~~~l~ra~~~~~ 158 (161)
T PRK12528 112 DGLPPLVKRAFLLAQVD-GLGYGEIATELGISLATVKRYLNKAAMRCY 158 (161)
T ss_pred HHCCHHHHHHHHHHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 35777778777777665 799999999999999999998888766554
No 87
>PRK01381 Trp operon repressor; Provisional
Probab=90.22 E-value=0.52 Score=35.02 Aligned_cols=40 Identities=13% Similarity=0.242 Sum_probs=30.8
Q ss_pred CCCHHHHHHHHHHH-----H-hcCCcHHHHHhhhCCChhhHHHHHH
Q psy4300 29 FVPVEKKTLVALSY-----M-ATQLSMRKIGDQFNLADSTVWSCID 68 (307)
Q Consensus 29 ~~~~~~~l~i~L~~-----L-~~g~~~~~l~~~fgvs~stv~r~v~ 68 (307)
-+++.++=++..++ | ..+.||++|+...|||.+||+|.-+
T Consensus 32 llTp~Er~al~~R~~I~~~L~~g~~sQREIa~~lGvSiaTITRgsn 77 (99)
T PRK01381 32 LLTPDEREALGTRVRIVEELLRGELSQREIKQELGVGIATITRGSN 77 (99)
T ss_pred hCCHHHHHHHHHHHHHHHHHHcCCcCHHHHHHHhCCceeeehhhHH
Confidence 36777777777665 2 3459999999999999999887543
No 88
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=90.21 E-value=0.68 Score=38.32 Aligned_cols=49 Identities=24% Similarity=0.382 Sum_probs=41.6
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
..++.+++-++.|.|+ .|.++.++|..+|+|.+||...+.+....|-..
T Consensus 135 ~~L~~~~r~il~l~~~-~~~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T PRK09641 135 LQLPEKYRTVIVLKYI-EDLSLKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred HhCCHHHHHHhhhHHh-hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3577888888888887 699999999999999999999988887766554
No 89
>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=90.15 E-value=1.3 Score=40.32 Aligned_cols=50 Identities=8% Similarity=0.203 Sum_probs=43.3
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
..+|+.++-++.|+|+ .|.++.+||..+|+|.+||...+.+....|-+.+
T Consensus 141 ~~Lp~~~R~v~~L~~~-~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 190 (324)
T TIGR02960 141 QYLPPRQRAVLLLRDV-LGWRAAETAELLGTSTASVNSALQRARATLDEVG 190 (324)
T ss_pred HhCCHHHhhHhhhHHH-hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhc
Confidence 3567777777777776 6899999999999999999999999999998874
No 90
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=90.11 E-value=0.71 Score=38.25 Aligned_cols=49 Identities=14% Similarity=0.120 Sum_probs=39.5
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
..+|+..+.++.|. +-.|.++.++|..+|+|.+||...+.+....|-..
T Consensus 132 ~~L~~~~r~i~~l~-~~~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 180 (182)
T PRK12537 132 EQLEPARRNCILHA-YVDGCSHAEIAQRLGAPLGTVKAWIKRSLKALREC 180 (182)
T ss_pred HhCCHHHHHHHHHH-HHcCCCHHHHHHHHCCChhhHHHHHHHHHHHHHHH
Confidence 35666777666666 45689999999999999999999999888776554
No 91
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=90.08 E-value=0.8 Score=38.29 Aligned_cols=49 Identities=10% Similarity=0.112 Sum_probs=42.5
Q ss_pred CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
.+|+.++-++.|.++ .|.++.++|..+|+|.+||...+.+....|-..+
T Consensus 116 ~Lp~~~r~i~~L~~~-~g~s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l 164 (187)
T PRK12516 116 QLPDDQREAIILVGA-SGFAYEEAAEICGCAVGTIKSRVNRARQRLQEIL 164 (187)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 567788888888877 7899999999999999999999998888877764
No 92
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=90.08 E-value=0.74 Score=40.62 Aligned_cols=48 Identities=8% Similarity=0.241 Sum_probs=42.4
Q ss_pred CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
.++..++..+.|+|+ .|.++.++|..+|+|.++|++...+...-|-..
T Consensus 203 ~L~~~~r~vl~l~y~-~~~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~ 250 (256)
T PRK07408 203 QLEERTREVLEFVFL-HDLTQKEAAERLGISPVTVSRRVKKGLDQLKKL 250 (256)
T ss_pred cCCHHHHHHHHHHHH-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 578888998999886 589999999999999999999999988777665
No 93
>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=90.07 E-value=0.34 Score=37.47 Aligned_cols=40 Identities=20% Similarity=0.429 Sum_probs=31.7
Q ss_pred CCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300 30 VPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLT 72 (307)
Q Consensus 30 ~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~ 72 (307)
++..++++ -++..|.+.+.+|..|+||.+||.+|+.+.-.
T Consensus 5 ~DlR~rVl---~~~~~g~s~~eaa~~F~VS~~Tv~~W~k~~~~ 44 (119)
T PF01710_consen 5 LDLRQRVL---AYIEKGKSIREAAKRFGVSRNTVYRWLKRKET 44 (119)
T ss_pred HHHHHHHH---HHHHccchHHHHHHHhCcHHHHHHHHHHhccc
Confidence 44455544 47788999999999999999999999985433
No 94
>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=90.02 E-value=0.69 Score=40.31 Aligned_cols=49 Identities=12% Similarity=0.355 Sum_probs=43.6
Q ss_pred CCCHHHHHHHHHHHH---hcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 29 FVPVEKKTLVALSYM---ATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 29 ~~~~~~~l~i~L~~L---~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
.++..++..+.|+|. ..+.++.++|..+|+|.++|+++..+.+.-|-..
T Consensus 176 ~L~~~er~vl~l~ygl~~~~~~t~~EIA~~lgis~~~V~q~~~~al~kLr~~ 227 (238)
T TIGR02393 176 TLTERERKVLRMRYGLLDGRPHTLEEVGKEFNVTRERIRQIESKALRKLRHP 227 (238)
T ss_pred hCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHhhh
Confidence 688999999999995 5789999999999999999999999888777665
No 95
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=89.97 E-value=0.61 Score=38.99 Aligned_cols=48 Identities=19% Similarity=0.270 Sum_probs=40.0
Q ss_pred CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
.+|++++-++.|+++. |.++.++|..+|+|.+||...+.+....|-..
T Consensus 141 ~L~~~~~~v~~l~~~~-g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 188 (194)
T PRK12519 141 QLPESQRQVLELAYYE-GLSQSEIAKRLGIPLGTVKARARQGLLKLREL 188 (194)
T ss_pred hCCHHHhhhhhhhhhc-CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 4677777777777766 89999999999999999999988887776655
No 96
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=89.97 E-value=0.89 Score=36.32 Aligned_cols=47 Identities=13% Similarity=0.110 Sum_probs=39.6
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcc
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMS 75 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~ 75 (307)
..+|+.++-++.|.|+. |.++.++|..+|+|.+||...+.+....|-
T Consensus 105 ~~L~~~~r~ii~l~~~~-~~s~~EIA~~l~is~~tV~~~~~ra~~~Lr 151 (154)
T PRK06759 105 SVLDEKEKYIIFERFFV-GKTMGEIALETEMTYYQVRWIYRQALEKMR 151 (154)
T ss_pred HhCCHHHHHHHHHHHhc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHh
Confidence 36778888888888765 799999999999999999999988776653
No 97
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=89.94 E-value=0.55 Score=39.36 Aligned_cols=49 Identities=12% Similarity=0.138 Sum_probs=42.4
Q ss_pred CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
.+|..++-++.|.|+ .|.++.++|..+|+|.+||...+.+....|-..+
T Consensus 136 ~L~~~~r~i~~L~~~-~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 184 (195)
T PRK12532 136 NLPENTARVFTLKEI-LGFSSDEIQQMCGISTSNYHTIMHRARESLRQCL 184 (195)
T ss_pred hCCHHHHHHhhhHHH-hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 577888888888777 6899999999999999999999999888877764
No 98
>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=89.91 E-value=1 Score=30.12 Aligned_cols=42 Identities=17% Similarity=0.201 Sum_probs=32.8
Q ss_pred HHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 36 TLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 36 l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
+-+++....+| ++...|..+++|+|++++.++++-..+-..|
T Consensus 4 l~~f~~v~~~g-s~~~AA~~l~is~~~vs~~i~~LE~~lg~~L 45 (60)
T PF00126_consen 4 LRYFLAVAETG-SISAAAEELGISQSAVSRQIKQLEEELGVPL 45 (60)
T ss_dssp HHHHHHHHHHS-SHHHHHHHCTSSHHHHHHHHHHHHHHHTS-S
T ss_pred HHHHHHHHHhC-CHHHHHHHhhccchHHHHHHHHHHHHhCCeE
Confidence 34444444554 8999999999999999999999988877664
No 99
>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=89.80 E-value=0.77 Score=31.00 Aligned_cols=27 Identities=22% Similarity=0.313 Sum_probs=24.4
Q ss_pred CCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300 46 QLSMRKIGDQFNLADSTVWSCIDSFLT 72 (307)
Q Consensus 46 g~~~~~l~~~fgvs~stv~r~v~~~~~ 72 (307)
..+..++|..+|+|++|+++.++.+..
T Consensus 25 ~~s~~ela~~~g~s~~tv~r~l~~L~~ 51 (67)
T cd00092 25 PLTRQEIADYLGLTRETVSRTLKELEE 51 (67)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 378999999999999999999998866
No 100
>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=89.76 E-value=0.85 Score=39.42 Aligned_cols=48 Identities=10% Similarity=0.256 Sum_probs=41.1
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccc
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQ 76 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~ 76 (307)
..++..++.++.++|+ .|.++.++|..+|+|+++|+++.++.+.-|-.
T Consensus 182 ~~L~~~e~~i~~~~~~-~~~t~~eIA~~lgis~~~V~~~~~~al~~Lr~ 229 (231)
T TIGR02885 182 SKLDERERQIIMLRYF-KDKTQTEVANMLGISQVQVSRLEKKVLKKMKE 229 (231)
T ss_pred HcCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 4678888888888775 68899999999999999999999988876644
No 101
>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=89.75 E-value=0.85 Score=37.75 Aligned_cols=49 Identities=14% Similarity=0.213 Sum_probs=41.2
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
..+++.++-++.|.|+ .|.++.++|..+|+|.+||...+.+....|-..
T Consensus 139 ~~L~~~~r~vi~l~~~-~g~s~~eIA~~lgis~~~v~~~l~Ra~~~Lr~~ 187 (189)
T TIGR02984 139 AKLPEDYREVILLRHL-EGLSFAEVAERMDRSEGAVSMLWVRGLARLRQI 187 (189)
T ss_pred HcCCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 3578888888888776 799999999999999999999998887766543
No 102
>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=89.71 E-value=0.89 Score=39.16 Aligned_cols=49 Identities=10% Similarity=0.301 Sum_probs=42.0
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
..+|..++-++.|+|+ .|.++.++|..+|+|.+||++.+.+....|-..
T Consensus 177 ~~L~~~~r~vl~l~y~-~~~s~~eIA~~lgis~~~v~~~~~ra~~~Lr~~ 225 (227)
T TIGR02980 177 AALPERERRILLLRFF-EDKTQSEIAERLGISQMHVSRLLRRALKKLREQ 225 (227)
T ss_pred HcCCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 3688888888888876 589999999999999999999999988776543
No 103
>PRK05572 sporulation sigma factor SigF; Validated
Probab=89.66 E-value=0.86 Score=40.07 Aligned_cols=49 Identities=12% Similarity=0.230 Sum_probs=43.1
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
..+|..++.++.|+|+ .|.++.++|..+|+|.++|+++.++.+.-|-..
T Consensus 201 ~~L~~~~~~v~~l~~~-~~~s~~eIA~~lgis~~~V~~~~~ral~kLr~~ 249 (252)
T PRK05572 201 RELDERERLIVYLRYF-KDKTQSEVAKRLGISQVQVSRLEKKILKQMKEK 249 (252)
T ss_pred HcCCHHHHHHHHHHHh-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 4688999999999886 579999999999999999999999988777654
No 104
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=89.57 E-value=0.95 Score=37.78 Aligned_cols=49 Identities=8% Similarity=0.108 Sum_probs=42.2
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
..+|++++-++.|+|+ .|.|+.++|..+|+|.+||...+.+....|-..
T Consensus 130 ~~L~~~~r~i~~l~~~-~g~s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~ 178 (189)
T PRK06811 130 NDLEKLDREIFIRRYL-LGEKIEEIAKKLGLTRSAIDNRLSRGRKKLQKN 178 (189)
T ss_pred HhCCHHHHHHHHHHHH-ccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHc
Confidence 4688899999999887 589999999999999999999888887776554
No 105
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=89.42 E-value=0.93 Score=37.51 Aligned_cols=50 Identities=12% Similarity=0.234 Sum_probs=42.7
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
..+|.+++-++.|.|+. |.++.++|..+|+|.+||...+.+....|-..+
T Consensus 130 ~~L~~~~r~v~~l~~~~-g~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l 179 (184)
T PRK12512 130 ETLPPRQRDVVQSISVE-GASIKETAAKLSMSEGAVRVALHRGLAALAAKF 179 (184)
T ss_pred HhCCHHHHHHHHHHHHc-CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 35777888888887777 899999999999999999999999888877664
No 106
>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=89.42 E-value=0.88 Score=36.74 Aligned_cols=48 Identities=21% Similarity=0.357 Sum_probs=40.7
Q ss_pred CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
.+|++++.++.|.+ -.|.++.++|..+|+|.+||...+.+....|-..
T Consensus 110 ~L~~~~r~i~~l~~-~~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 157 (162)
T TIGR02983 110 RLPARQRAVVVLRY-YEDLSEAQVAEALGISVGTVKSRLSRALARLREL 157 (162)
T ss_pred hCCHHHHHHhhhHH-HhcCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 45778888877777 5589999999999999999999999988877665
No 107
>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=89.42 E-value=0.7 Score=38.38 Aligned_cols=63 Identities=10% Similarity=0.058 Sum_probs=48.2
Q ss_pred CCCCHHHHHHHHHHHHhc--------------CCcHHHHHhhhCCChhhHHHHHHHHHHH-ccccccccccccCCChHHH
Q psy4300 28 PFVPVEKKTLVALSYMAT--------------QLSMRKIGDQFNLADSTVWSCIDSFLTA-MSQPQIQCQYIKWPTEEES 92 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~--------------g~~~~~l~~~fgvs~stv~r~v~~~~~~-l~~~l~~~~~i~~P~~~~~ 92 (307)
...+++++|+-+|.+|+. ..+..++|...|+++.|++|+++++... +... ....|..++.+.+
T Consensus 111 ~~~~~~~Rla~~L~~l~~~~~~~~~~~~~~~~~~t~~~iA~~lG~tretvsR~l~~l~~~g~I~~--~~~~i~I~d~~~L 188 (193)
T TIGR03697 111 AHRDMGSRLVSFLLILCRDFGVPGQRGVTIDLRLSHQAIAEAIGSTRVTITRLLGDLRKKKLISI--HKKKITVHDPIAL 188 (193)
T ss_pred HhCCHHHHHHHHHHHHHHHhCCCCCCeEEecCCCCHHHHHHHhCCcHHHHHHHHHHHHHCCCEEe--cCCEEEEeCHHHH
Confidence 356889999999987632 2589999999999999999999998776 4554 5556666655443
No 108
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=89.37 E-value=0.86 Score=37.83 Aligned_cols=50 Identities=14% Similarity=0.169 Sum_probs=43.0
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
..+|++++-++.|.|+. |.++.++|..+|+|..||...+.+....|...+
T Consensus 127 ~~L~~~~r~i~~l~~~~-g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 176 (186)
T PRK05602 127 AALPERQREAIVLQYYQ-GLSNIEAAAVMDISVDALESLLARGRRALRAQL 176 (186)
T ss_pred HhCCHHHHHHhhHHHhc-CCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHH
Confidence 35688888888888876 899999999999999999999998887777663
No 109
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=89.33 E-value=1 Score=37.81 Aligned_cols=49 Identities=14% Similarity=0.322 Sum_probs=40.0
Q ss_pred CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
.+|.+.+-++.|.|+ .|.++.++|..+|+|.+||..-+.+....|-..+
T Consensus 141 ~Lp~~~r~v~~l~~~-eg~s~~EIA~~lgis~~tVk~rl~ra~~~Lr~~l 189 (194)
T PRK12531 141 RLPKAQRDVLQAVYL-EELPHQQVAEMFDIPLGTVKSRLRLAVEKLRHSM 189 (194)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHh
Confidence 466677777777777 6899999999999999999988888877776653
No 110
>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=89.31 E-value=0.3 Score=39.08 Aligned_cols=48 Identities=19% Similarity=0.233 Sum_probs=38.8
Q ss_pred CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
.+|..++-++.|.++ .|.++.++|..+|+|.+||...+.+....|-+.
T Consensus 105 ~L~~~~r~i~~l~~~-~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~~ 152 (154)
T TIGR02950 105 RLPENYRTVLILREF-KEFSYKEIAELLNLSLAKVKSNLFRARKELKKL 152 (154)
T ss_pred hCCHhheeeeeehhh-ccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 466666666777666 699999999999999999999988887766543
No 111
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=89.21 E-value=1.3 Score=38.41 Aligned_cols=71 Identities=11% Similarity=0.141 Sum_probs=51.5
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccccccccccCC-ChHHHHHHHHHHHH
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQIQCQYIKWP-TEEESVIIERNFRA 101 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l~~~~~i~~P-~~~~~~~~~~~f~~ 101 (307)
..++..++.++.|.++- |.++.++|...|+|.+||...+.+....|-..+ .....-+ ...+...+...|..
T Consensus 115 ~~Lp~~~R~v~lL~~~e-g~S~~EIAe~LgiS~~tVksrL~Rark~Lr~~l--~~~~~~~~~~~~~~~~~~~~~~ 186 (228)
T PRK06704 115 SSLNVQQSAILLLKDVF-QYSIADIAKVCSVSEGAVKASLFRSRNRLKTVS--EEGIEIVEFTDDMEVVVTSIRE 186 (228)
T ss_pred HhCCHHHhhHhhhHHhh-CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH--HhcCCCCCccccHHHHHHHHHh
Confidence 35777888877777755 799999999999999999999999888888774 3322222 22344555666653
No 112
>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=89.19 E-value=0.98 Score=39.61 Aligned_cols=50 Identities=20% Similarity=0.325 Sum_probs=42.4
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
..+|..++-++.|.++ .|.++.++|..+|+|.+||...+.+....|-..+
T Consensus 160 ~~Lp~~~R~v~~L~~~-eg~S~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~l 209 (244)
T TIGR03001 160 AALSERERHLLRLHFV-DGLSMDRIGAMYQVHRSTVSRWVAQARERLLERT 209 (244)
T ss_pred HhCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 3567777888888777 7899999999999999999999998888777765
No 113
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=89.05 E-value=1.2 Score=32.13 Aligned_cols=39 Identities=18% Similarity=0.396 Sum_probs=31.3
Q ss_pred HHHHHHHHHHhc---CCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300 34 KKTLVALSYMAT---QLSMRKIGDQFNLADSTVWSCIDSFLT 72 (307)
Q Consensus 34 ~~l~i~L~~L~~---g~~~~~l~~~fgvs~stv~r~v~~~~~ 72 (307)
++..-.|.+|.. +.+..+++..+|++++|+++.+.....
T Consensus 5 ~r~~~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~~ 46 (91)
T smart00346 5 ERGLAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQE 46 (91)
T ss_pred HHHHHHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 445555666643 489999999999999999999998865
No 114
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=89.02 E-value=0.97 Score=39.65 Aligned_cols=49 Identities=16% Similarity=0.320 Sum_probs=43.5
Q ss_pred CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
.++-.+++.+.|+|+- +.+...+|...|||+|.||++..+.+..|-..|
T Consensus 196 ~L~EREk~Vl~l~y~e-elt~kEI~~~LgISes~VSql~kkai~kLr~~l 244 (247)
T COG1191 196 PLPEREKLVLVLRYKE-ELTQKEIAEVLGISESRVSRLHKKAIKKLRKEL 244 (247)
T ss_pred ccCHHHHHHHHHHHHh-ccCHHHHHHHhCccHHHHHHHHHHHHHHHHHHh
Confidence 7889999999999954 689999999999999999999999988776653
No 115
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=89.01 E-value=0.92 Score=37.49 Aligned_cols=49 Identities=16% Similarity=0.314 Sum_probs=42.0
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
..+|..++-++.|.++. |.++.++|..+|+|.+||...+.+....|-..
T Consensus 126 ~~L~~~~r~v~~l~~~~-g~s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~~ 174 (179)
T PRK09415 126 MSLPIKYREVIYLFYYE-ELSIKEIAEVTGVNENTVKTRLKKAKELLKKG 174 (179)
T ss_pred HhCCHHHhhHhHhHHhc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 35788888888888877 89999999999999999999888887776655
No 116
>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=88.98 E-value=0.75 Score=26.71 Aligned_cols=25 Identities=20% Similarity=0.307 Sum_probs=20.2
Q ss_pred CcHHHHHhhhCCChhhHHHHHHHHH
Q psy4300 47 LSMRKIGDQFNLADSTVWSCIDSFL 71 (307)
Q Consensus 47 ~~~~~l~~~fgvs~stv~r~v~~~~ 71 (307)
.+..++|...|++..||+|++.++-
T Consensus 3 mtr~diA~~lG~t~ETVSR~l~~l~ 27 (32)
T PF00325_consen 3 MTRQDIADYLGLTRETVSRILKKLE 27 (32)
T ss_dssp --HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred cCHHHHHHHhCCcHHHHHHHHHHHH
Confidence 4678999999999999999998864
No 117
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=88.95 E-value=0.92 Score=40.84 Aligned_cols=51 Identities=6% Similarity=0.156 Sum_probs=45.0
Q ss_pred CCCCHHHHHHHHHHHH-hcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 28 PFVPVEKKTLVALSYM-ATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L-~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
..++..++..+.|+|+ ..|.++.++|..+|+|+++|+++.++.+.-|-..+
T Consensus 226 ~~L~~rer~vl~lr~~~~~~~t~~EIa~~lgvs~~~V~q~~~~Al~kLr~~l 277 (289)
T PRK07500 226 QTLNERELRIIRERRLREDGATLEALGEELGISKERVRQIEARALEKLRRAL 277 (289)
T ss_pred hcCCHHHHHHHHHHhcCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3689999999999986 36899999999999999999999999888877664
No 118
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=88.94 E-value=1.1 Score=37.15 Aligned_cols=48 Identities=13% Similarity=0.149 Sum_probs=38.7
Q ss_pred CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
.++..++-++.|.|+ .|.++.++|..+|+|.+||...+.+....|-..
T Consensus 137 ~L~~~~r~i~~l~~~-~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 184 (187)
T PRK12534 137 ELEPPRSELIRTAFF-EGITYEELAARTDTPIGTVKSWIRRGLAKLKAC 184 (187)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Confidence 456666666666654 789999999999999999999999887776554
No 119
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=88.94 E-value=1 Score=39.71 Aligned_cols=48 Identities=10% Similarity=0.182 Sum_probs=41.3
Q ss_pred CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
.++..++..+.++|+ .|.++.++|..+|+|.++|+++.++.+.-|-..
T Consensus 209 ~L~~~er~vi~~~~~-~~~t~~eIA~~lgis~~~V~~~~~~al~kLr~~ 256 (258)
T PRK08215 209 KLNDREKLILNLRFF-QGKTQMEVAEEIGISQAQVSRLEKAALKHMRKY 256 (258)
T ss_pred cCCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 688888888888875 689999999999999999999999887766543
No 120
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=88.94 E-value=1 Score=39.62 Aligned_cols=49 Identities=12% Similarity=0.363 Sum_probs=41.8
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
..+|+.++-++.|+|+ .|.++.++|..+|+|.+||.+...+....|-..
T Consensus 204 ~~L~~~~r~vl~l~~~-~g~s~~eIA~~l~is~~tV~~~~~ra~~kLr~~ 252 (257)
T PRK08583 204 PVLSDREKSIIQCTFI-ENLSQKETGERLGISQMHVSRLQRQAIKKLREA 252 (257)
T ss_pred HhCCHHHHHHHHHHHh-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3578888888888776 689999999999999999999999888877655
No 121
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=88.91 E-value=1.2 Score=36.42 Aligned_cols=49 Identities=12% Similarity=0.130 Sum_probs=41.1
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
..+|+..+.++.|.| -.|.++.++|..+|+|.+||...+.+....+...
T Consensus 117 ~~L~~~~r~v~~L~~-~eg~s~~EIA~~l~is~~tV~~~l~ra~~~~~~~ 165 (168)
T PRK12525 117 DGLSGKARAAFLMSQ-LEGLTYVEIGERLGVSLSRIHQYMVEAFKCCYQG 165 (168)
T ss_pred HhCCHHHHHHHHHHH-HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 358888888888876 5589999999999999999999888887776654
No 122
>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=88.81 E-value=1 Score=39.12 Aligned_cols=50 Identities=12% Similarity=0.239 Sum_probs=43.0
Q ss_pred CCCCHHHHHHHHHHHH---hcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 28 PFVPVEKKTLVALSYM---ATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L---~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
..+|+.++..+.|+++ -.|.|+.++|...|+|.+||...+.+....|-..
T Consensus 177 ~~Lp~~~R~ii~L~~~l~~~eg~s~~EIA~~Lgis~~tV~~~l~ra~~~LR~~ 229 (234)
T TIGR02835 177 AKLNDREKKIMELRFGLVGGTEKTQKEVADMLGISQSYISRLEKRILKRLKKE 229 (234)
T ss_pred HhCCHHHHHHHHHHHccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4688999999999986 3789999999999999999999888877766554
No 123
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=88.62 E-value=0.95 Score=37.79 Aligned_cols=50 Identities=8% Similarity=0.179 Sum_probs=42.6
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
..+|+.++-++.|.|+. |.|+.++|..+|+|.+||...+.+....|...+
T Consensus 130 ~~Lp~~~r~v~~l~~~~-g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 179 (191)
T PRK12520 130 DRLPPRTGRVFMMREWL-ELETEEICQELQITATNAWVLLYRARMRLRECL 179 (191)
T ss_pred HhCCHHHHHHHHHHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 35778888888887765 799999999999999999999998888877764
No 124
>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=88.62 E-value=1 Score=40.77 Aligned_cols=47 Identities=17% Similarity=0.304 Sum_probs=41.0
Q ss_pred CCCCHHHHHHHHHHHH---hcCCcHHHHHhhhCCChhhHHHHHHHHHHHc
Q psy4300 28 PFVPVEKKTLVALSYM---ATQLSMRKIGDQFNLADSTVWSCIDSFLTAM 74 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L---~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l 74 (307)
..+|+.++..+.|+|. ..+.++.++|..+|+|+.+|..+..+.+.-|
T Consensus 248 ~~L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVrq~~~rAl~kL 297 (298)
T TIGR02997 248 AELTPRERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKALRKL 297 (298)
T ss_pred HcCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHc
Confidence 3589999999999995 6789999999999999999999988876543
No 125
>PF13751 DDE_Tnp_1_6: Transposase DDE domain
Probab=88.50 E-value=0.29 Score=37.99 Aligned_cols=49 Identities=24% Similarity=0.274 Sum_probs=39.0
Q ss_pred hHHHHhhhh-HHHHHHHHHHhhcccccccccCChhhHHHHHHHHHHhhhhh
Q psy4300 222 NTALSKTRV-PIENVFGLIKGRWRRLKYIDVGDPKRMAYIISAACVLHNFC 271 (307)
Q Consensus 222 N~~~s~~R~-~VE~~fg~LK~rf~iL~~~~~~~~~~~~~ii~a~~~LhN~~ 271 (307)
...+.+.|. .||..||.||. +--|.+++......+..-+...|+-|||-
T Consensus 73 ~k~~y~~R~~~VE~~fg~~K~-~~g~~r~~~rG~~kv~~~~~l~a~a~Nl~ 122 (125)
T PF13751_consen 73 GKELYKQRSIKVEGVFGTIKR-NHGLRRFRYRGLEKVRIEFLLAAIAYNLK 122 (125)
T ss_pred hhhhhheeecccccccccchh-ccCCccccccchhhhHHHHHHHHHHHHHH
Confidence 456677787 99999999998 55666556557888888888888889984
No 126
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=88.49 E-value=1.1 Score=36.74 Aligned_cols=49 Identities=8% Similarity=0.087 Sum_probs=41.0
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
..+|+.++-++.|.++. |.++.++|..+|+|.+||...+.+...-+...
T Consensus 118 ~~Lp~~~r~v~~L~~~~-g~s~~EIA~~lgis~~tV~~~l~ra~~~~~~~ 166 (172)
T PRK12523 118 GKLSSKARAAFLYNRLD-GMGHAEIAERLGVSVSRVRQYLAQGLRQCYIA 166 (172)
T ss_pred HhCCHHHHHHHHHHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 45778888888888775 89999999999999999999888877766554
No 127
>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=88.49 E-value=0.55 Score=30.40 Aligned_cols=37 Identities=24% Similarity=0.395 Sum_probs=27.2
Q ss_pred HHHHHHHHhc---CCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300 36 TLVALSYMAT---QLSMRKIGDQFNLADSTVWSCIDSFLT 72 (307)
Q Consensus 36 l~i~L~~L~~---g~~~~~l~~~fgvs~stv~r~v~~~~~ 72 (307)
.+-.|.+++. +.+..+|+...|+++||++|++.....
T Consensus 5 al~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~~ 44 (52)
T PF09339_consen 5 ALRILEALAESGGPLTLSEIARALGLPKSTVHRLLQTLVE 44 (52)
T ss_dssp HHHHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 3344444433 357999999999999999999988764
No 128
>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=88.48 E-value=1.1 Score=39.42 Aligned_cols=48 Identities=8% Similarity=0.203 Sum_probs=41.5
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccc
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQ 76 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~ 76 (307)
..++..++.++.++|+ .|.++.++|..+|+|+++|+++.++.+.-|..
T Consensus 205 ~~L~~rer~vi~~~~~-~~~t~~eIA~~lgis~~~V~~~~~ral~kLr~ 252 (254)
T TIGR02850 205 KRLNEREKMILNMRFF-EGKTQMEVAEEIGISQAQVSRLEKAALKHMRK 252 (254)
T ss_pred HcCCHHHHHHHHHHHc-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHh
Confidence 4688889999999875 58899999999999999999999988776643
No 129
>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=88.27 E-value=1 Score=40.38 Aligned_cols=51 Identities=8% Similarity=0.139 Sum_probs=45.2
Q ss_pred CCCCHHHHHHHHHHH-H--hcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 28 PFVPVEKKTLVALSY-M--ATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~-L--~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
..+|..++..+.|+| | -.|.|+.++|..+|+|.+||...+.+....|-..|
T Consensus 221 ~~Lp~~~R~Vl~l~ygL~~~e~~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~~l 274 (285)
T TIGR02394 221 AELNERQREVLARRFGLLGYEPATLEEVAAEVGLTRERVRQIQVEALKKLRRIL 274 (285)
T ss_pred HcCCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 468889999999998 4 56899999999999999999999999988887764
No 130
>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=88.19 E-value=1.3 Score=36.11 Aligned_cols=48 Identities=19% Similarity=0.329 Sum_probs=40.4
Q ss_pred CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
.+|..++-++.|.++. |.++.++|..+|+|.+||...+.+....|...
T Consensus 119 ~L~~~~r~i~~l~~~~-g~s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~~ 166 (169)
T TIGR02954 119 TLNDKYQTAIILRYYH-DLTIKEIAEVMNKPEGTVKTYLHRALKKLKKR 166 (169)
T ss_pred hCCHHHhHHHHHHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 5777777777777776 89999999999999999999999888777654
No 131
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=88.19 E-value=1.4 Score=36.06 Aligned_cols=49 Identities=20% Similarity=0.259 Sum_probs=40.1
Q ss_pred CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
.+|+..+-++.|.++. |.++.++|..+|+|.+||...+.+....|-..|
T Consensus 118 ~L~~~~r~vl~L~~~~-g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 166 (173)
T PRK09645 118 QLSPEHRAVLVRSYYR-GWSTAQIAADLGIPEGTVKSRLHYALRALRLAL 166 (173)
T ss_pred hCCHHHHHHHHHHHHc-CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 4667777777777655 899999999999999999888888877776654
No 132
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=88.17 E-value=1.3 Score=36.81 Aligned_cols=50 Identities=14% Similarity=0.098 Sum_probs=43.0
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
..+|...+-++.|.|+ .|.++.++|..+|+|.+||...+.+....|-..+
T Consensus 110 ~~Lp~~~R~v~~L~~~-~g~s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l 159 (182)
T PRK12540 110 DKLPQDQREALILVGA-SGFSYEDAAAICGCAVGTIKSRVNRARSKLSALL 159 (182)
T ss_pred HhCCHHHHHHhhHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3577788888888776 7899999999999999999999999888887775
No 133
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=88.07 E-value=1.2 Score=36.99 Aligned_cols=49 Identities=12% Similarity=0.086 Sum_probs=40.3
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
..+|+.++-++.|.|+. |.++.++|..+|+|.+||...+.+....|-+.
T Consensus 129 ~~Lp~~~r~v~~L~~~~-g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 177 (185)
T PRK09649 129 ADLTTDQREALLLTQLL-GLSYADAAAVCGCPVGTIRSRVARARDALLAD 177 (185)
T ss_pred HhCCHHHhHHhhhHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 35677777777777665 78999999999999999999998887777654
No 134
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=88.03 E-value=1.3 Score=37.17 Aligned_cols=50 Identities=16% Similarity=0.133 Sum_probs=44.0
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
..+|+.++-++.|+++ .|.++.++|..+|+|.+||...+.+....|-..+
T Consensus 112 ~~Lp~~~r~v~~L~~~-~g~s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l 161 (188)
T PRK12546 112 AQLPDEQREALILVGA-SGFSYEEAAEMCGVAVGTVKSRANRARARLAELL 161 (188)
T ss_pred HhCCHHHhHHhhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4678888888889888 7899999999999999999999999888887764
No 135
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=88.00 E-value=1.4 Score=37.51 Aligned_cols=50 Identities=10% Similarity=0.062 Sum_probs=43.0
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
..+|+.++-++.|+|+. |.++.++|..+|+|.+||...+.+....|-..+
T Consensus 147 ~~L~~~~r~v~~L~~~~-g~s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l 196 (206)
T PRK12544 147 DGLPAKYARVFMMREFI-ELETNEICHAVDLSVSNLNVLLYRARLRLRECL 196 (206)
T ss_pred HhCCHHHHHHHHHHHHc-CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 46778888888888766 899999999999999999999999888877764
No 136
>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=87.86 E-value=0.64 Score=30.15 Aligned_cols=44 Identities=14% Similarity=0.229 Sum_probs=30.9
Q ss_pred HHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccccccccccCCChHHHHHHHHHH
Q psy4300 42 YMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQIQCQYIKWPTEEESVIIERNF 99 (307)
Q Consensus 42 ~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l~~~~~i~~P~~~~~~~~~~~f 99 (307)
+...|.++.++|...|+|++|++++.+. -..|+.+.+..++..|
T Consensus 5 r~~~gls~~~la~~~gis~~~i~~~~~g--------------~~~~~~~~~~~ia~~l 48 (55)
T PF01381_consen 5 RKEKGLSQKELAEKLGISRSTISRIENG--------------KRNPSLDTLKKIAKAL 48 (55)
T ss_dssp HHHTTS-HHHHHHHHTS-HHHHHHHHTT--------------SSTSBHHHHHHHHHHH
T ss_pred HHHcCCCHHHHHHHhCCCcchhHHHhcC--------------CCCCCHHHHHHHHHHH
Confidence 3467999999999999999999998765 2235555555655554
No 137
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=87.85 E-value=1.4 Score=36.60 Aligned_cols=49 Identities=14% Similarity=0.183 Sum_probs=42.9
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
..+|+..+-++.|.|+. |.++.++|..+|+|.+||...+.+....|-..
T Consensus 130 ~~L~~~~r~v~~l~~~~-g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 178 (184)
T PRK12539 130 ARLPEKMRLAIQAVKLE-GLSVAEAATRSGMSESAVKVSVHRGLKALAAL 178 (184)
T ss_pred HhCCHHHHHHHHHHHHc-CCcHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 46788888888888885 89999999999999999999999888877665
No 138
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=87.84 E-value=1.4 Score=36.95 Aligned_cols=48 Identities=19% Similarity=0.179 Sum_probs=39.7
Q ss_pred CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
.+|++++-++.|.|+ .|.++.++|..+|+|.+||..-+.+....|-..
T Consensus 134 ~Lp~~~r~i~~l~~~-~g~s~~EIA~~lg~s~~tV~~rl~rar~~Lr~~ 181 (192)
T PRK09643 134 RLPVEQRAALVAVDM-QGYSVADAARMLGVAEGTVKSRCARGRARLAEL 181 (192)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 577888888877777 689999999999999999988887776666555
No 139
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=87.82 E-value=1.5 Score=35.27 Aligned_cols=49 Identities=16% Similarity=0.085 Sum_probs=39.1
Q ss_pred CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
.+|+..+-++.|.++ .|.|+.++|..+|+|.+||...+.+....|-..+
T Consensus 106 ~Lp~~~r~v~~l~~~-~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 154 (160)
T PRK09642 106 ELPENYRDVVLAHYL-EEKSYQEIALQEKIEVKTVEMKLYRARKWIKKHW 154 (160)
T ss_pred hCCHHHHHHHHHHHH-hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 466777777767665 5799999999999999999888888777766653
No 140
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=87.81 E-value=1.7 Score=37.39 Aligned_cols=67 Identities=4% Similarity=0.024 Sum_probs=50.8
Q ss_pred CCCHHHHHHHHHHHHhcC----CcHHHHHhhhCCChhhHHHHHHHHHHH-ccccccccccccCCChHHHHHHHH
Q psy4300 29 FVPVEKKTLVALSYMATQ----LSMRKIGDQFNLADSTVWSCIDSFLTA-MSQPQIQCQYIKWPTEEESVIIER 97 (307)
Q Consensus 29 ~~~~~~~l~i~L~~L~~g----~~~~~l~~~fgvs~stv~r~v~~~~~~-l~~~l~~~~~i~~P~~~~~~~~~~ 97 (307)
..+++++|+-+|..+..+ .+..++|..+|+++.|++|.++++.+. +.+. ....|.-++.+.+.++..
T Consensus 148 ~~~~~~Rla~~L~~~~~~~~~~~t~~~lA~~lG~sretvsR~L~~L~~~G~I~~--~~~~i~I~d~~~L~~~~~ 219 (226)
T PRK10402 148 SFPLENRLAAFILLTQEGDLYHEKHTQAAEYLGVSYRHLLYVLAQFIQDGYLKK--SKRGYLIKNRKQLSGLAL 219 (226)
T ss_pred cChHHHHHHHHHHhcccCCcccchHHHHHHHHCCcHHHHHHHHHHHHHCCCEEe--eCCEEEEeCHHHHHHHHH
Confidence 458999999999876432 467899999999999999999999884 5555 555666666555554433
No 141
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=87.80 E-value=1.1 Score=37.03 Aligned_cols=49 Identities=24% Similarity=0.390 Sum_probs=41.5
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
..+|+.++-++.|.|+ .|.++.++|..+|+|.+||...+.+....|...
T Consensus 135 ~~L~~~~r~v~~l~~~-~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T TIGR02948 135 QALPPKYRMVIVLKYM-EDLSLKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred HhCCHHHhHHhhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4677888888888777 589999999999999999999999887777655
No 142
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=87.68 E-value=1.4 Score=36.38 Aligned_cols=48 Identities=19% Similarity=0.187 Sum_probs=38.7
Q ss_pred CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
.+|+.++.++.|.++ .|.++.++|..+|+|.+||...+.+....|-..
T Consensus 129 ~L~~~~r~v~~l~~~-~g~s~~EIA~~l~is~~tV~~~l~rar~~Lr~~ 176 (181)
T PRK12536 129 QLPDRQRLPIVHVKL-EGLSVAETAQLTGLSESAVKVGIHRGLKALAAK 176 (181)
T ss_pred HCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 466667766666654 589999999999999999999999887777655
No 143
>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=87.67 E-value=1.4 Score=30.62 Aligned_cols=43 Identities=16% Similarity=0.093 Sum_probs=30.2
Q ss_pred CcHHHHHhhhCCChhhHHHHHHHHHHHccccccccccccCCChH
Q psy4300 47 LSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQIQCQYIKWPTEE 90 (307)
Q Consensus 47 ~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l~~~~~i~~P~~~ 90 (307)
.+..++|...|+|+.|++++++++.+.=+-.. ....|.-.+.+
T Consensus 29 lt~~~iA~~~g~sr~tv~r~l~~l~~~g~I~~-~~~~i~I~d~~ 71 (76)
T PF13545_consen 29 LTQEEIADMLGVSRETVSRILKRLKDEGIIEV-KRGKIIILDPE 71 (76)
T ss_dssp SSHHHHHHHHTSCHHHHHHHHHHHHHTTSEEE-ETTEEEESSHH
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE-cCCEEEECCHH
Confidence 67999999999999999999998865422221 34444444433
No 144
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=87.66 E-value=2 Score=34.20 Aligned_cols=46 Identities=4% Similarity=0.018 Sum_probs=36.1
Q ss_pred CCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300 27 VPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLT 72 (307)
Q Consensus 27 ~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~ 72 (307)
...+++.+-.++...+-..+.+..+||..++++++|+++.+++...
T Consensus 35 ~~glt~~q~~vL~~l~~~~~~t~~eLa~~l~i~~~tvsr~l~~Le~ 80 (144)
T PRK11512 35 PLDITAAQFKVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLVC 80 (144)
T ss_pred ccCCCHHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3467776665555445566789999999999999999999998754
No 145
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=87.64 E-value=1.4 Score=36.59 Aligned_cols=49 Identities=16% Similarity=0.165 Sum_probs=40.6
Q ss_pred CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
.+|++++.++.|.++ .|.++.++|..+|+|.+||...+.+....|-..+
T Consensus 106 ~L~~~~r~i~~l~~~-~g~~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 154 (181)
T PRK09637 106 ALPEKYAEALRLTEL-EGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKELL 154 (181)
T ss_pred hCCHHHHHHHHHHHh-cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 577777777777765 4799999999999999999999888877777663
No 146
>PRK06930 positive control sigma-like factor; Validated
Probab=87.63 E-value=1.6 Score=36.05 Aligned_cols=49 Identities=22% Similarity=0.267 Sum_probs=40.6
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
..+|+.++-++.|.+ ..|.++.++|..+|+|.+||...+.+....|-..
T Consensus 113 ~~L~~rer~V~~L~~-~eg~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~ 161 (170)
T PRK06930 113 SVLTEREKEVYLMHR-GYGLSYSEIADYLNIKKSTVQSMIERAEKKIARQ 161 (170)
T ss_pred HhCCHHHHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 367777777777664 6789999999999999999999999887777665
No 147
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=87.61 E-value=1.5 Score=36.26 Aligned_cols=49 Identities=12% Similarity=0.195 Sum_probs=40.7
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
..+|..++-.+.|+|+ .|.++.++|..+|+|.+||...+.+....|-..
T Consensus 134 ~~L~~~~r~vl~l~~~-~~~s~~eIA~~lgis~~~V~~~l~ra~~~Lr~~ 182 (186)
T PRK13919 134 KALSPEERRVIEVLYY-QGYTHREAAQLLGLPLGTLKTRARRALSRLKEV 182 (186)
T ss_pred HhCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 3477777878877775 479999999999999999999998887777655
No 148
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=87.60 E-value=0.93 Score=30.62 Aligned_cols=27 Identities=22% Similarity=0.218 Sum_probs=21.4
Q ss_pred HHhcCCcHHHHHhhhCCChhhHHHHHH
Q psy4300 42 YMATQLSMRKIGDQFNLADSTVWSCID 68 (307)
Q Consensus 42 ~L~~g~~~~~l~~~fgvs~stv~r~v~ 68 (307)
+-+.|.|+.++|...|+|+|+++++-+
T Consensus 10 R~~~gls~~~lA~~~g~s~s~v~~iE~ 36 (64)
T PF13560_consen 10 RERAGLSQAQLADRLGVSQSTVSRIER 36 (64)
T ss_dssp HHCHTS-HHHHHHHHTS-HHHHHHHHT
T ss_pred HHHcCCCHHHHHHHHCcCHHHHHHHHC
Confidence 446689999999999999999998754
No 149
>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=87.57 E-value=1.3 Score=30.00 Aligned_cols=36 Identities=17% Similarity=0.268 Sum_probs=26.8
Q ss_pred HHHHHHh---cCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300 38 VALSYMA---TQLSMRKIGDQFNLADSTVWSCIDSFLTA 73 (307)
Q Consensus 38 i~L~~L~---~g~~~~~l~~~fgvs~stv~r~v~~~~~~ 73 (307)
.+|+++. ...+..+|+..++++++++++.+++.+..
T Consensus 7 ~vL~~l~~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~ 45 (68)
T PF13463_consen 7 QVLRALAHSDGPMTQSDLAERLGISKSTVSRIIKKLEEK 45 (68)
T ss_dssp HHHHHHT--TS-BEHHHHHHHTT--HHHHHHHHHHHHHT
T ss_pred HHHHHHHccCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 3455555 45888999999999999999999988654
No 150
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=87.28 E-value=1.4 Score=40.19 Aligned_cols=50 Identities=20% Similarity=0.359 Sum_probs=43.5
Q ss_pred CCCCHHHHHHHHHHHH---hcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 28 PFVPVEKKTLVALSYM---ATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L---~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
..+++.++..+.|+|. ..+.++.++|..+|+|+.+|..+..+.+.-|-..
T Consensus 255 ~~L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVRqi~~rAl~kLr~~ 307 (317)
T PRK07405 255 EDLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKLRKR 307 (317)
T ss_pred HcCCHHHHHHHHHHhhcCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 3689999999999996 5679999999999999999999998887776553
No 151
>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=87.09 E-value=1.5 Score=38.55 Aligned_cols=49 Identities=12% Similarity=0.353 Sum_probs=41.8
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
..+|+.++-.+.|+|+ .|.++.++|..+|+|.+||++.+.+....|-..
T Consensus 204 ~~L~~~~r~ii~l~~~-~g~s~~eIA~~lgis~~~V~~~~~ra~~~Lr~~ 252 (255)
T TIGR02941 204 PILSEREKSIIHCTFE-ENLSQKETGERLGISQMHVSRLQRQAISKLKEA 252 (255)
T ss_pred HcCCHHHHHHHHHHHc-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 4678888888888875 589999999999999999999998887776554
No 152
>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=87.06 E-value=1.7 Score=36.29 Aligned_cols=49 Identities=6% Similarity=0.100 Sum_probs=40.4
Q ss_pred CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
.+++.++-++.|.|+. |.++.++|..+|+|.+||...+.+....|-..+
T Consensus 131 ~L~~~~r~v~~l~~~~-g~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l 179 (188)
T TIGR02943 131 HLPEQTARVFMMREVL-GFESDEICQELEISTSNCHVLLYRARLSLRACL 179 (188)
T ss_pred hCCHHHHHHHHHHHHh-CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 4666677777777665 899999999999999999999988888777663
No 153
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=86.92 E-value=1.3 Score=37.30 Aligned_cols=45 Identities=16% Similarity=0.223 Sum_probs=37.3
Q ss_pred CCCCHHHHHHHHHHHHhc-------------CCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300 28 PFVPVEKKTLVALSYMAT-------------QLSMRKIGDQFNLADSTVWSCIDSFLT 72 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~-------------g~~~~~l~~~fgvs~stv~r~v~~~~~ 72 (307)
...++.++++-+|..|+. ..+..+||...|+++.|++|+++++..
T Consensus 137 ~~~~~~~Rl~~~L~~l~~~~~~~~~~~~~~~~~t~~~lA~~lG~tr~tvsR~l~~l~~ 194 (211)
T PRK11753 137 AFLDVTGRIAQTLLDLAKQPDAMTHPDGMQIKITRQEIGRIVGCSREMVGRVLKMLED 194 (211)
T ss_pred HhcChhhHHHHHHHHHHHhcCCcCCCCceecCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 567899999999887753 245689999999999999999988754
No 154
>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=86.83 E-value=1.5 Score=32.86 Aligned_cols=47 Identities=13% Similarity=0.359 Sum_probs=33.4
Q ss_pred CCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 30 VPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 30 ~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
++..++=.+- .|+-.+.|...+|..+|||+.+|+..+++....|...
T Consensus 18 LT~kQ~~~l~-lyy~eDlSlsEIAe~~~iSRqaV~d~ikr~~~~L~~y 64 (101)
T PF04297_consen 18 LTEKQREILE-LYYEEDLSLSEIAEELGISRQAVYDSIKRAEKKLEEY 64 (101)
T ss_dssp S-HHHHHHHH-HHCTS---HHHHHHHCTS-HHHHHHHHHHHHHHHHHH
T ss_pred CCHHHHHHHH-HHHccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3444444444 5667789999999999999999999999998888664
No 155
>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=86.75 E-value=1.2 Score=36.81 Aligned_cols=49 Identities=22% Similarity=0.188 Sum_probs=40.5
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
..++.+.+-++.|.|+ .|.++.+||..+|+|.+||...+.+....|-+.
T Consensus 137 ~~L~~~~r~v~~l~~~-~~~s~~EIA~~lgis~~tv~~~l~rar~~Lr~~ 185 (190)
T TIGR02939 137 EALPEDLRTAITLREL-EGLSYEDIARIMDCPVGTVRSRIFRAREAIAIR 185 (190)
T ss_pred HcCCHHHhhhhhhhhh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 3466667776767665 789999999999999999999999888877766
No 156
>PHA02591 hypothetical protein; Provisional
Probab=86.66 E-value=1.5 Score=30.88 Aligned_cols=38 Identities=13% Similarity=0.176 Sum_probs=31.1
Q ss_pred HHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHH
Q psy4300 32 VEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDS 69 (307)
Q Consensus 32 ~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~ 69 (307)
-.+-+.++=...+.|.+...+|...|+++.+|+++++.
T Consensus 45 ~dd~~~vA~eL~eqGlSqeqIA~~LGVsqetVrKYL~~ 82 (83)
T PHA02591 45 EDDLISVTHELARKGFTVEKIASLLGVSVRKVRRYLES 82 (83)
T ss_pred cchHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHhc
Confidence 34455566666788999999999999999999999864
No 157
>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=86.65 E-value=3.4 Score=36.96 Aligned_cols=67 Identities=9% Similarity=0.110 Sum_probs=48.2
Q ss_pred CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccccccccccCCChHHHHHHHHHHH
Q psy4300 29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQIQCQYIKWPTEEESVIIERNFR 100 (307)
Q Consensus 29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l~~~~~i~~P~~~~~~~~~~~f~ 100 (307)
.+|+.++-++.|+++- |.++.++|..+|+|.+||...+.+....|-+. .+.+- +..++...+.+.|-
T Consensus 108 ~L~~~~R~v~~L~~~~-g~s~~EIA~~lg~s~~tVr~~l~RAr~~Lr~~--~~~~~--~~~~~~~~~~~~f~ 174 (281)
T TIGR02957 108 RLSPLERAVFVLREVF-DYPYEEIASIVGKSEANCRQLVSRARRHLDAR--RPRFE--VSREESRQLLERFV 174 (281)
T ss_pred hCCHHHHHHHHHHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhh--CCCCC--CChHHHHHHHHHHH
Confidence 5666767666666554 79999999999999999999999999999887 44332 22233345555553
No 158
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=86.58 E-value=1.9 Score=35.84 Aligned_cols=49 Identities=12% Similarity=0.200 Sum_probs=40.2
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
..+|+.++-++.|.|+. |.++.++|..+|+|.+||...+.+....|-..
T Consensus 138 ~~L~~~~r~i~~l~~~~-g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 186 (189)
T PRK09648 138 DTLPEKQREILILRVVV-GLSAEETAEAVGSTPGAVRVAQHRALARLRAE 186 (189)
T ss_pred HhCCHHHHHHHHHHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 35777777777777776 89999999999999999999888877766544
No 159
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=86.52 E-value=1.6 Score=36.20 Aligned_cols=49 Identities=18% Similarity=0.272 Sum_probs=41.9
Q ss_pred CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
.+|++++-++.|.++. |.|+.++|...|||.+||...+.+....+-..+
T Consensus 127 ~Lp~~~R~~~~l~~~~-gls~~EIA~~l~i~~~tVks~l~ra~~~l~~~l 175 (182)
T COG1595 127 RLPPRQREAFLLRYLE-GLSYEEIAEILGISVGTVKSRLHRARKKLREQL 175 (182)
T ss_pred hCCHHHhHHhhhHhhc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 5778888888887775 799999999999999999999999888777663
No 160
>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=86.51 E-value=2 Score=35.10 Aligned_cols=49 Identities=18% Similarity=0.194 Sum_probs=41.4
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
..+|+.++.++.|.++. |.++.++|..+|+|.+||...+.+....|-..
T Consensus 99 ~~L~~~~r~v~~l~~~~-g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 147 (170)
T TIGR02959 99 KELPDEYREAIRLTELE-GLSQQEIAEKLGLSLSGAKSRVQRGRKKLKEL 147 (170)
T ss_pred HhCCHHHHHHHHHHHHc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 46788888888887764 79999999999999999999988887777666
No 161
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=86.44 E-value=1.8 Score=34.94 Aligned_cols=48 Identities=15% Similarity=0.144 Sum_probs=40.1
Q ss_pred CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
.+|+.++.++.|.++. |.++.++|..+|+|.+||...+.+....|-+.
T Consensus 112 ~L~~~~r~v~~l~~~~-~~s~~eIA~~lgis~~tv~~~l~Rar~~L~~~ 159 (161)
T PRK12541 112 SLPLERRNVLLLRDYY-GFSYKEIAEMTGLSLAKVKIELHRGRKETKSI 159 (161)
T ss_pred HCCHHHHHHhhhHHhc-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 5788888888887765 78999999999999999999998887766543
No 162
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=86.42 E-value=1.8 Score=36.51 Aligned_cols=50 Identities=8% Similarity=0.087 Sum_probs=41.3
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
..+|+..+-++.|.|+. |.++.++|..+|+|.+||...+.+....|-..+
T Consensus 138 ~~Lp~~~r~v~~L~~~e-g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l 187 (201)
T PRK12545 138 DHLPEQIGRVFMMREFL-DFEIDDICTELTLTANHCSVLLYRARTRLRTCL 187 (201)
T ss_pred HhCCHHHHHHHHHHHHc-CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 45777788888887654 789999999999999999988888877776663
No 163
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=86.38 E-value=2.1 Score=29.49 Aligned_cols=42 Identities=17% Similarity=0.177 Sum_probs=32.6
Q ss_pred CHHHHHHHHHHHHhc-CCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300 31 PVEKKTLVALSYMAT-QLSMRKIGDQFNLADSTVWSCIDSFLT 72 (307)
Q Consensus 31 ~~~~~l~i~L~~L~~-g~~~~~l~~~fgvs~stv~r~v~~~~~ 72 (307)
+.+++++-+|.--+. +.+..+||..+|+++++|++.+..+..
T Consensus 6 ~~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~ 48 (68)
T smart00550 6 SLEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEK 48 (68)
T ss_pred HHHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 356666666665544 489999999999999999998887643
No 164
>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=86.29 E-value=1.6 Score=32.19 Aligned_cols=30 Identities=17% Similarity=0.211 Sum_probs=25.8
Q ss_pred HhcCCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300 43 MATQLSMRKIGDQFNLADSTVWSCIDSFLT 72 (307)
Q Consensus 43 L~~g~~~~~l~~~fgvs~stv~r~v~~~~~ 72 (307)
.....+.++||...|+|++||+|.++++..
T Consensus 44 ~~~~is~~eLa~~~g~sr~tVsr~L~~Le~ 73 (95)
T TIGR01610 44 KQDRVTATVIAELTGLSRTHVSDAIKSLAR 73 (95)
T ss_pred cCCccCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 345689999999999999999999988754
No 165
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=86.27 E-value=1.7 Score=37.72 Aligned_cols=49 Identities=16% Similarity=0.347 Sum_probs=41.5
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
..+|+.++-.+.|.|+ .|.++.++|..+|+|.+||...+.+....|-..
T Consensus 183 ~~L~~~~r~vl~l~~~-~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~ 231 (236)
T PRK06986 183 ESLPEREQLVLSLYYQ-EELNLKEIGAVLGVSESRVSQIHSQAIKRLRAR 231 (236)
T ss_pred HhCCHHHHHHHHhHhc-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3567888888888775 689999999999999999999999888777665
No 166
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=86.23 E-value=0.81 Score=41.83 Aligned_cols=68 Identities=16% Similarity=0.173 Sum_probs=46.0
Q ss_pred HHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHH-ccccccccccccCCChHHHHHHHHHHHHhhCCCCccee
Q psy4300 38 VALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTA-MSQPQIQCQYIKWPTEEESVIIERNFRALAKFPGVIGA 111 (307)
Q Consensus 38 i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~-l~~~l~~~~~i~~P~~~~~~~~~~~f~~~~~~p~~~g~ 111 (307)
++=.|+-.|.++.++|..+|+|+++|+|.+.+-.+. +.+. -|.-|.. ....+...+++..++..|+-+
T Consensus 21 vA~lYY~~g~tQ~eIA~~lgiSR~~VsRlL~~Ar~~GiV~I-----~I~~~~~-~~~~Le~~L~~~fgLk~~iVv 89 (318)
T PRK15418 21 IAWFYYHDGLTQSEIGERLGLTRLKVSRLLEKGRQSGIIRV-----QINSRFE-GCLELENALRQHFSLQHIRVL 89 (318)
T ss_pred HHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHcCcEEE-----EEeCCCc-cHHHHHHHHHHHhCCCEEEEE
Confidence 556678889999999999999999999999976442 2222 2333432 223455556665577777543
No 167
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=86.21 E-value=1.9 Score=37.85 Aligned_cols=49 Identities=18% Similarity=0.312 Sum_probs=41.5
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
..+|+.++-++.|.|+ .|.++.++|..+|+|.+||...+.+....|-..
T Consensus 200 ~~L~~~~r~vl~l~~~-~~~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~ 248 (251)
T PRK07670 200 KQLSEKEQLVISLFYK-EELTLTEIGQVLNLSTSRISQIHSKALFKLKKL 248 (251)
T ss_pred hcCCHHHHHHHHHHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 4578888888888875 789999999999999999999998887766544
No 168
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=86.04 E-value=1.8 Score=36.04 Aligned_cols=49 Identities=22% Similarity=0.196 Sum_probs=41.2
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
..++.+++-.+.|.|+ .|.++.++|..+|+|..||...+.+....|-..
T Consensus 137 ~~L~~~~r~v~~l~~~-~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~ 185 (193)
T PRK11923 137 QQLPEDLRTALTLREF-DGLSYEDIASVMQCPVGTVRSRIFRAREAIDKA 185 (193)
T ss_pred HhCCHHHhHHHhhHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3467777777888776 689999999999999999999998887777665
No 169
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=85.94 E-value=1.5 Score=35.93 Aligned_cols=48 Identities=21% Similarity=0.267 Sum_probs=37.0
Q ss_pred CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
.+|+..+-++.| ++-.|.++.++|..+|+|.+||...+.+....|...
T Consensus 119 ~L~~~~r~i~~l-~~~~~~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 166 (173)
T PRK12522 119 LLNEKYKTVLVL-YYYEQYSYKEMSEILNIPIGTVKYRLNYAKKQMREH 166 (173)
T ss_pred hCCHHHHHHHHH-HHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 344555544444 445689999999999999999999999888887766
No 170
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=85.93 E-value=2.1 Score=35.25 Aligned_cols=50 Identities=22% Similarity=0.331 Sum_probs=40.3
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
..+|+.++-++.|.|+ .|.++.++|..+|+|.+||...+.+....|-..|
T Consensus 116 ~~Lp~~~r~i~~l~~~-e~~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 165 (179)
T PRK12543 116 HKLPYKLRQVIILRYL-HDYSQEEIAQLLQIPIGTVKSRIHAALKKLRQKE 165 (179)
T ss_pred HhCCHHHHHHHHHHHH-ccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3577777777777655 4789999999999999999998888877776653
No 171
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=85.90 E-value=1.8 Score=38.48 Aligned_cols=49 Identities=12% Similarity=0.339 Sum_probs=41.1
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
..++..++-++.|+|+ .|.++.++|..+|+|.++|++++.+....|-..
T Consensus 214 ~~L~~rer~vl~l~y~-~~~t~~EIA~~lgis~~~V~~~~~ral~kLr~~ 262 (264)
T PRK07122 214 AALPERERTVLVLRFF-ESMTQTQIAERVGISQMHVSRLLAKTLARLRDQ 262 (264)
T ss_pred HcCCHHHHHHHHHHhc-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 3577888888888885 589999999999999999999999887766543
No 172
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=85.88 E-value=2.2 Score=34.27 Aligned_cols=48 Identities=17% Similarity=0.135 Sum_probs=39.5
Q ss_pred CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
.+|++++-++.|.+ -.|.++.++|..+|+|.+||..-+.+....|-..
T Consensus 105 ~L~~~~r~v~~l~~-~~~~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~ 152 (159)
T PRK12527 105 ELPPACRDSFLLRK-LEGLSHQQIAEHLGISRSLVEKHIVNAMKHCRVR 152 (159)
T ss_pred hCCHHHHHHHHHHH-HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 46777777776765 5689999999999999999999988887777665
No 173
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=85.83 E-value=2 Score=29.26 Aligned_cols=43 Identities=19% Similarity=0.229 Sum_probs=39.1
Q ss_pred HHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 35 KTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 35 ~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
++-.+..+|+...+..+.|...|+...++.+++..+...+.+.
T Consensus 2 ~~~~fIrlLs~~~s~~~Aa~~lG~~~~~v~~wv~~fR~wll~L 44 (65)
T PF05344_consen 2 KARAFIRLLSQQISVAQAADRLGTDPGTVRRWVRMFRQWLLQL 44 (65)
T ss_pred cHHHHHHHhcccccHHHHHHHHCcCHHHHHHHHHHHHHHHHHc
Confidence 4456788999999999999999999999999999999998887
No 174
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=85.71 E-value=3.8 Score=36.88 Aligned_cols=67 Identities=10% Similarity=0.112 Sum_probs=47.3
Q ss_pred CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccccccccccCCChHHHHHHHHHHH
Q psy4300 29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQIQCQYIKWPTEEESVIIERNFR 100 (307)
Q Consensus 29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l~~~~~i~~P~~~~~~~~~~~f~ 100 (307)
.+|+.++-++.|+++ .|.++.++|...|+|.+||...+.+....|-.. .+.+- +...+...+...|-
T Consensus 118 ~L~p~~R~vf~L~~~-~g~s~~EIA~~Lgis~~tVr~~l~RAr~~Lr~~--~~~~~--~~~~~~~~~~~~f~ 184 (290)
T PRK09635 118 RLGPAERVVFVLHEI-FGLPYQQIATTIGSQASTCRQLAHRARRKINES--RIAAS--VEPAQHRVVTRAFI 184 (290)
T ss_pred hCCHHHHHHhhHHHH-hCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHhh--CCCCC--CChHHHHHHHHHHH
Confidence 455555555555544 489999999999999999999999999988886 44332 22333445555554
No 175
>PF13309 HTH_22: HTH domain
Probab=85.66 E-value=3.1 Score=28.30 Aligned_cols=42 Identities=10% Similarity=0.197 Sum_probs=35.0
Q ss_pred CCCCCHHHHHHHHHHHHhcC-----CcHHHHHhhhCCChhhHHHHHH
Q psy4300 27 VPFVPVEKKTLVALSYMATQ-----LSMRKIGDQFNLADSTVWSCID 68 (307)
Q Consensus 27 ~~~~~~~~~l~i~L~~L~~g-----~~~~~l~~~fgvs~stv~r~v~ 68 (307)
...++-++++-+.-.....| .+-..+|..+|||+.||+++++
T Consensus 18 ~~~l~~~~k~~iV~~L~~~G~F~lKgav~~vA~~L~iS~~TVY~YLr 64 (64)
T PF13309_consen 18 PSRLSKEEKKEIVRQLYEKGIFLLKGAVEYVAEKLGISRATVYRYLR 64 (64)
T ss_pred hhhCCHHHHHHHHHHHHHCCCcccCcHHHHHHHHHCCCHHHHHHHcC
Confidence 35688889988887777777 6678999999999999999863
No 176
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=85.60 E-value=1 Score=27.60 Aligned_cols=29 Identities=14% Similarity=0.180 Sum_probs=21.9
Q ss_pred HhcCCcHHHHHhhhCCChhhHHHHHHHHH
Q psy4300 43 MATQLSMRKIGDQFNLADSTVWSCIDSFL 71 (307)
Q Consensus 43 L~~g~~~~~l~~~fgvs~stv~r~v~~~~ 71 (307)
|.++.+..++|..+|+|.+.++|.+++..
T Consensus 5 ~~~~~~l~~iA~~~g~S~~~f~r~Fk~~~ 33 (42)
T PF00165_consen 5 LQQKLTLEDIAEQAGFSPSYFSRLFKKET 33 (42)
T ss_dssp T-SS--HHHHHHHHTS-HHHHHHHHHHHT
T ss_pred ccCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 45678899999999999999999998753
No 177
>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=85.59 E-value=2.2 Score=28.47 Aligned_cols=32 Identities=25% Similarity=0.427 Sum_probs=26.2
Q ss_pred HHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHH
Q psy4300 37 LVALSYMATQLSMRKIGDQFNLADSTVWSCIDSF 70 (307)
Q Consensus 37 ~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~ 70 (307)
+..|++ .|.+..+||..+|++.+||+.+..+.
T Consensus 6 A~~LY~--~G~~~~eIA~~Lg~~~~TV~~W~~r~ 37 (58)
T PF06056_consen 6 ARSLYL--QGWSIKEIAEELGVPRSTVYSWKDRY 37 (58)
T ss_pred HHHHHH--cCCCHHHHHHHHCCChHHHHHHHHhh
Confidence 444443 69999999999999999999988764
No 178
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=85.54 E-value=2.2 Score=34.62 Aligned_cols=50 Identities=14% Similarity=0.074 Sum_probs=40.4
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
..+|+.++-++.|.++ .|.++.++|..+|+|.+||...+.+....|-..+
T Consensus 107 ~~L~~~~r~v~~l~~~-~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l 156 (165)
T PRK09644 107 HTLPVIEAQAILLCDV-HELTYEEAASVLDLKLNTYKSHLFRGRKRLKALL 156 (165)
T ss_pred HhCCHHHHHHHHhHHH-hcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4567777777766655 4799999999999999999999998887776653
No 179
>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=85.51 E-value=2.2 Score=36.64 Aligned_cols=49 Identities=18% Similarity=0.347 Sum_probs=41.0
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
..+++.++-++.|+|+ .|.++.++|..+|+|.+||.+.+.+....|-..
T Consensus 174 ~~L~~~~r~il~l~y~-~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~ 222 (224)
T TIGR02479 174 ESLSEREQLVLSLYYY-EELNLKEIGEVLGLTESRVSQIHSQALKKLRAK 222 (224)
T ss_pred HhCCHHHHHHHHHHHh-CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 3578888888888875 578999999999999999999988887766543
No 180
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=85.48 E-value=2.4 Score=35.49 Aligned_cols=65 Identities=9% Similarity=0.006 Sum_probs=49.0
Q ss_pred CCCHHHHHHHHHHHHhc--------------CCcHHHHHhhhCCChhhHHHHHHHHHH-HccccccccccccCCChHHHH
Q psy4300 29 FVPVEKKTLVALSYMAT--------------QLSMRKIGDQFNLADSTVWSCIDSFLT-AMSQPQIQCQYIKWPTEEESV 93 (307)
Q Consensus 29 ~~~~~~~l~i~L~~L~~--------------g~~~~~l~~~fgvs~stv~r~v~~~~~-~l~~~l~~~~~i~~P~~~~~~ 93 (307)
..+++++|+-+|..|+. ..+..+||...|+++.|++|+++++.. -+... ....|..++.+.+.
T Consensus 118 ~~~~~~Rla~~Ll~l~~~~~~~~~~~~~~~~~~t~~~iA~~lG~tretvsR~l~~l~~~g~I~~--~~~~i~I~d~~~L~ 195 (202)
T PRK13918 118 GQRLKNRIAAALLELSDTPLATQEDSGETMIYATHDELAAAVGSVRETVTKVIGELSREGYIRS--GYGKIQLLDLKGLE 195 (202)
T ss_pred hCchHHHHHHHHHHHHHHhCCCCCCCCeEEecCCHHHHHHHhCccHHHHHHHHHHHHHCCCEEc--CCCEEEEECHHHHH
Confidence 45689999999987653 147899999999999999999999876 34443 55567666665554
Q ss_pred HH
Q psy4300 94 II 95 (307)
Q Consensus 94 ~~ 95 (307)
++
T Consensus 196 ~~ 197 (202)
T PRK13918 196 EL 197 (202)
T ss_pred HH
Confidence 43
No 181
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=85.31 E-value=1.4 Score=27.46 Aligned_cols=27 Identities=19% Similarity=0.287 Sum_probs=23.9
Q ss_pred CCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300 46 QLSMRKIGDQFNLADSTVWSCIDSFLT 72 (307)
Q Consensus 46 g~~~~~l~~~fgvs~stv~r~v~~~~~ 72 (307)
..+..++|..+|+|++|+++.++.+..
T Consensus 8 ~~s~~~la~~l~~s~~tv~~~l~~L~~ 34 (48)
T smart00419 8 PLTRQEIAELLGLTRETVSRTLKRLEK 34 (48)
T ss_pred ccCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 467899999999999999999988765
No 182
>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=85.22 E-value=1.9 Score=29.43 Aligned_cols=39 Identities=23% Similarity=0.366 Sum_probs=30.2
Q ss_pred HHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300 33 EKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLT 72 (307)
Q Consensus 33 ~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~ 72 (307)
+.++...|. -..+.+..+|+...|+++++|+++++...+
T Consensus 10 E~~vy~~Ll-~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~ 48 (68)
T PF01978_consen 10 EAKVYLALL-KNGPATAEEIAEELGISRSTVYRALKSLEE 48 (68)
T ss_dssp HHHHHHHHH-HHCHEEHHHHHHHHTSSHHHHHHHHHHHHH
T ss_pred HHHHHHHHH-HcCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 445555554 244589999999999999999999998764
No 183
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=85.06 E-value=2.3 Score=35.99 Aligned_cols=48 Identities=25% Similarity=0.310 Sum_probs=38.7
Q ss_pred CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
.+|.+++.++.|.|+ .|.++.++|..+|+|.+||...+.+....|...
T Consensus 153 ~L~~~~r~vl~l~~~-~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 200 (206)
T PRK12526 153 KLPEAQQTVVKGVYF-QELSQEQLAQQLNVPLGTVKSRLRLALAKLKVQ 200 (206)
T ss_pred hCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 466677777666665 479999999999999999999888887777655
No 184
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=84.99 E-value=1.8 Score=35.76 Aligned_cols=48 Identities=13% Similarity=0.182 Sum_probs=40.2
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
..+|+.|. =+|.+++.|.+..++|...++|.+||...+.++..-+--.
T Consensus 132 ~~LSpREr--EVLrLLAqGkTnKEIAe~L~IS~rTVkth~srImkKLgV~ 179 (198)
T PRK15201 132 RHFSVTER--HLLKLIASGYHLSETAALLSLSEEQTKSLRRSIMRKLHVK 179 (198)
T ss_pred CCCCHHHH--HHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Confidence 45777665 5677899999999999999999999999998887766554
No 185
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=84.93 E-value=2.3 Score=35.51 Aligned_cols=47 Identities=15% Similarity=0.324 Sum_probs=36.7
Q ss_pred CCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 30 VPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 30 ~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
+++++.=.+.|+++ .|.++.++|...|+|.+||.+-+...-..+...
T Consensus 136 l~~~~~~~v~l~~~-~Gls~~EIA~~lgiS~~tV~r~l~~aR~~l~~~ 182 (185)
T PF07638_consen 136 LDPRQRRVVELRFF-EGLSVEEIAERLGISERTVRRRLRRARAWLRRE 182 (185)
T ss_pred cCHHHHHHHHHHHH-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 55555556666555 789999999999999999999988876665544
No 186
>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=84.86 E-value=2 Score=28.73 Aligned_cols=31 Identities=13% Similarity=0.274 Sum_probs=26.5
Q ss_pred HhcCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300 43 MATQLSMRKIGDQFNLADSTVWSCIDSFLTA 73 (307)
Q Consensus 43 L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~ 73 (307)
-..+.+..+|+..+|++++|+++.++...++
T Consensus 21 ~~~~~t~~ela~~l~~~~~t~s~hL~~L~~a 51 (61)
T PF12840_consen 21 SNGPMTVSELAEELGISQSTVSYHLKKLEEA 51 (61)
T ss_dssp HCSTBEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred cCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 5778999999999999999999999887654
No 187
>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=84.84 E-value=2.8 Score=28.39 Aligned_cols=29 Identities=17% Similarity=0.329 Sum_probs=25.0
Q ss_pred hcCCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300 44 ATQLSMRKIGDQFNLADSTVWSCIDSFLT 72 (307)
Q Consensus 44 ~~g~~~~~l~~~fgvs~stv~r~v~~~~~ 72 (307)
..+.+..+++..+|++.+|+++.++.+..
T Consensus 18 ~~~~~~~ei~~~~~i~~~~i~~~l~~L~~ 46 (78)
T cd00090 18 EGPLTVSELAERLGLSQSTVSRHLKKLEE 46 (78)
T ss_pred HCCcCHHHHHHHHCcCHhHHHHHHHHHHH
Confidence 34489999999999999999999988754
No 188
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=84.75 E-value=2.5 Score=36.65 Aligned_cols=47 Identities=11% Similarity=0.261 Sum_probs=39.8
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcc
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMS 75 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~ 75 (307)
..++..++-.+.|+|+ .|.++.++|..+|+|+++|+++.++...-|-
T Consensus 182 ~~L~~~er~vi~l~~~-~~~t~~EIA~~lgis~~~V~q~~~~~~~kLr 228 (231)
T PRK12427 182 SQLDEREQLILHLYYQ-HEMSLKEIALVLDLTEARICQLNKKIAQKIK 228 (231)
T ss_pred HcCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 3578888888888885 6899999999999999999999888776553
No 189
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=84.73 E-value=2 Score=37.38 Aligned_cols=49 Identities=18% Similarity=0.205 Sum_probs=40.5
Q ss_pred CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
.+|..++-++.|.|+ .|.++.++|..+|+|.+||...+.+....|-..+
T Consensus 171 ~Lp~~~R~v~~L~~~-eg~s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~l 219 (233)
T PRK12538 171 RLPEQQRIAVILSYH-ENMSNGEIAEVMDTTVAAVESLLKRGRQQLRDLL 219 (233)
T ss_pred hCCHHHHHHhhhHHh-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 466777777777665 4799999999999999999999999888877763
No 190
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=84.65 E-value=2 Score=30.63 Aligned_cols=37 Identities=8% Similarity=0.234 Sum_probs=26.8
Q ss_pred HHHHHHHHHHHH--hcCCcHHHHHhhhCCChhhHHHHHH
Q psy4300 32 VEKKTLVALSYM--ATQLSMRKIGDQFNLADSTVWSCID 68 (307)
Q Consensus 32 ~~~~l~i~L~~L--~~g~~~~~l~~~fgvs~stv~r~v~ 68 (307)
....|+..|..+ ..|.++.++|...|+++|+++++.+
T Consensus 15 ~k~~l~~~i~~~~~~~~ltQ~e~A~~lgisq~~vS~l~~ 53 (80)
T PF13744_consen 15 AKAQLMAAIRELREERGLTQAELAERLGISQPRVSRLEN 53 (80)
T ss_dssp HHHHHHHHHHHHHHCCT--HHHHHHHHTS-HHHHHHHHT
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHCCChhHHHHHHc
Confidence 445566666655 5689999999999999999999875
No 191
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=84.48 E-value=2.4 Score=39.70 Aligned_cols=50 Identities=16% Similarity=0.333 Sum_probs=43.5
Q ss_pred CCCCHHHHHHHHHHHH---hcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 28 PFVPVEKKTLVALSYM---ATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L---~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
..++..++..+.|+|+ ..+.++.+||..+|||+.+|+++..+.+.-|-..
T Consensus 310 ~~L~~rEr~IL~lrygl~~~~~~Tl~EIA~~lgiS~eRVRQie~rAL~KLR~~ 362 (373)
T PRK07406 310 ATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHP 362 (373)
T ss_pred HcCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHhch
Confidence 3689999999999986 3468999999999999999999999988777654
No 192
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=84.44 E-value=2.7 Score=35.20 Aligned_cols=49 Identities=16% Similarity=0.234 Sum_probs=39.9
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
..+|..++-++.|.|+ .|.++.++|..+|+|.+||...+.+....|-..
T Consensus 141 ~~L~~~~r~vl~l~~~-~~~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~ 189 (194)
T PRK09646 141 DALTDTQRESVTLAYY-GGLTYREVAERLAVPLGTVKTRMRDGLIRLRDC 189 (194)
T ss_pred HhCCHHHHHHHHHHHH-cCCCHHHHHHHhCCChHhHHHHHHHHHHHHHHH
Confidence 3577777777776665 579999999999999999999998887777665
No 193
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=84.41 E-value=1.9 Score=28.30 Aligned_cols=29 Identities=17% Similarity=0.280 Sum_probs=25.6
Q ss_pred hcCCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300 44 ATQLSMRKIGDQFNLADSTVWSCIDSFLT 72 (307)
Q Consensus 44 ~~g~~~~~l~~~fgvs~stv~r~v~~~~~ 72 (307)
....+..+++..+|+|.+|+++.++++..
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~ 36 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLRE 36 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 45688999999999999999999998765
No 194
>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=84.31 E-value=4.9 Score=30.96 Aligned_cols=65 Identities=17% Similarity=0.285 Sum_probs=38.2
Q ss_pred CHHHHHHHHHHHhhhcCcccccCCCCCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHH
Q psy4300 2 RKTTFGFLVEALAAINGYETLYERGVPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSF 70 (307)
Q Consensus 2 s~~~F~~L~~~l~~~~~~~~~~~~~~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~ 70 (307)
++.|..+.+...+ . +.......++..++.+ . +..+.--....+..++|..||||.+|+++.++++
T Consensus 31 S~~Tv~~W~k~~~-~-G~~~~k~r~~~Kid~~-~-L~~~v~~~pd~tl~Ela~~l~Vs~~ti~~~Lkrl 95 (119)
T PF01710_consen 31 SRNTVYRWLKRKE-T-GDLEPKPRGRKKIDRD-E-LKALVEENPDATLRELAERLGVSPSTIWRALKRL 95 (119)
T ss_pred HHHHHHHHHHhcc-c-ccccccccccccccHH-H-HHHHHHHCCCcCHHHHHHHcCCCHHHHHHHHHHc
Confidence 4566666666222 2 1112212222256532 2 3333333456888999999999999999888775
No 195
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=84.21 E-value=2.7 Score=35.44 Aligned_cols=48 Identities=13% Similarity=0.245 Sum_probs=39.8
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
..++..++-++.| |+ .|.++.++|..+|+|.+||...+.+....|-..
T Consensus 154 ~~L~~~~r~vl~l-~~-e~~s~~EIA~~lgis~~tV~~~l~rar~~Lr~~ 201 (208)
T PRK08295 154 ELLSELEKEVLEL-YL-DGKSYQEIAEELNRHVKSIDNALQRVKRKLEKY 201 (208)
T ss_pred HhCCHHHHHHHHH-HH-ccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3567777777777 65 689999999999999999998888877776665
No 196
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=84.21 E-value=2.7 Score=34.77 Aligned_cols=50 Identities=6% Similarity=0.112 Sum_probs=39.6
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
..+|+..+-++.|.|+ .|.++.++|..+|+|.+||...+.+....|-..+
T Consensus 121 ~~L~~~~r~i~~l~~~-~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 170 (185)
T PRK12542 121 KELNESNRQVFKYKVF-YNLTYQEISSVMGITEANVRKQFERARKRVQNMI 170 (185)
T ss_pred HhCCHHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3466666666666655 4799999999999999999999888887776663
No 197
>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=84.19 E-value=6.4 Score=30.01 Aligned_cols=46 Identities=2% Similarity=0.034 Sum_probs=34.4
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTA 73 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~ 73 (307)
..+++.+-.++....-..+.+..+|+..++++++|+++.+++....
T Consensus 24 ~~lt~~q~~iL~~l~~~~~~t~~ela~~~~~~~~tvs~~l~~Le~~ 69 (118)
T TIGR02337 24 HGLTEQQWRILRILAEQGSMEFTQLANQACILRPSLTGILARLERD 69 (118)
T ss_pred cCCCHHHHHHHHHHHHcCCcCHHHHHHHhCCCchhHHHHHHHHHHC
Confidence 3566666444433344567889999999999999999999987654
No 198
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=84.15 E-value=5.6 Score=35.71 Aligned_cols=49 Identities=4% Similarity=0.005 Sum_probs=41.8
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
..+|+.++-++.|+++- |.++.++|..+|+|.+||...+.+....|-+.
T Consensus 114 ~~L~~~~R~v~~L~~~~-g~s~~EIA~~lg~s~~tVk~~l~RAr~~Lr~~ 162 (293)
T PRK09636 114 ERLSPLERAAFLLHDVF-GVPFDEIASTLGRSPAACRQLASRARKHVRAA 162 (293)
T ss_pred HhCCHHHHHHHHHHHHh-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 35677777777776655 79999999999999999999999999999887
No 199
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=83.96 E-value=3.5 Score=37.79 Aligned_cols=48 Identities=10% Similarity=0.225 Sum_probs=40.4
Q ss_pred CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
.+|..++-++.|+|+ .|.++.+||..+|+|.+||...+.+....|-..
T Consensus 153 ~Lp~~~R~v~~L~~~-~g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~ 200 (339)
T PRK08241 153 HLPPRQRAVLILRDV-LGWSAAEVAELLDTSVAAVNSALQRARATLAER 200 (339)
T ss_pred hCCHHHhhhhhhHHh-hCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhhc
Confidence 466666776666654 579999999999999999999999999999885
No 200
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=83.91 E-value=1.6 Score=28.53 Aligned_cols=25 Identities=20% Similarity=0.351 Sum_probs=22.6
Q ss_pred cHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300 48 SMRKIGDQFNLADSTVWSCIDSFLT 72 (307)
Q Consensus 48 ~~~~l~~~fgvs~stv~r~v~~~~~ 72 (307)
+..+++..||+|++|+.+.+.....
T Consensus 22 s~~~la~~~~vs~~tv~~~l~~L~~ 46 (60)
T smart00345 22 SERELAAQLGVSRTTVREALSRLEA 46 (60)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 7889999999999999999988765
No 201
>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function.
Probab=83.80 E-value=2.8 Score=31.65 Aligned_cols=49 Identities=12% Similarity=0.191 Sum_probs=38.7
Q ss_pred CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
.+++++-=++-|..+- |.++.+.|...|||++|+.++++..-.-+.+.|
T Consensus 41 ~L~~dElEAiRL~D~e-gl~QeeaA~~MgVSR~T~~ril~~ARkKiA~AL 89 (106)
T PF02001_consen 41 VLTVDELEAIRLVDYE-GLSQEEAAERMGVSRPTFQRILESARKKIADAL 89 (106)
T ss_pred EeeHHHHHHHHHHHHc-CCCHHHHHHHcCCcHHHHHHHHHHHHHHHHHHH
Confidence 4677777777777765 699999999999999999999987655554443
No 202
>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=83.55 E-value=1.4 Score=36.84 Aligned_cols=49 Identities=16% Similarity=0.142 Sum_probs=39.3
Q ss_pred CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
.+|...+-++.|.++ .|.++.++|..+|+|.+||...+.+....|-..+
T Consensus 131 ~Lp~~~r~i~~L~~~-~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 179 (193)
T TIGR02947 131 GLPEEFRQAVYLADV-EGFAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQL 179 (193)
T ss_pred hCCHHHhhheeehhh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 456666666666554 5799999999999999999999998887777663
No 203
>PRK14086 dnaA chromosomal replication initiation protein; Provisional
Probab=83.55 E-value=4 Score=40.63 Aligned_cols=51 Identities=24% Similarity=0.266 Sum_probs=46.5
Q ss_pred CCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 27 VPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 27 ~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
...+...-+++|.|.+=-++.|+..|+..||.+.|||...++++-..|.+.
T Consensus 550 ~~~i~~aRqiAMYL~r~lt~~Sl~~IG~~FgRdHSTV~~A~~kI~~~~~~d 600 (617)
T PRK14086 550 SRVLVTARQIAMYLCRELTDLSLPKIGQQFGRDHTTVMHADRKIRALMAER 600 (617)
T ss_pred CcccchHHHHHHHHHHHHcCCCHHHHHHHhCCChhHHHHHHHHHHHHHHhC
Confidence 557889999999999999999999999999999999999999998877654
No 204
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=83.51 E-value=2.3 Score=33.79 Aligned_cols=45 Identities=9% Similarity=0.119 Sum_probs=33.3
Q ss_pred CCCCHHHH-HHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300 28 PFVPVEKK-TLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLT 72 (307)
Q Consensus 28 ~~~~~~~~-l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~ 72 (307)
..+++.+- ++..|.....+.+..+|+..++++++|+++.+++...
T Consensus 27 ~glt~~q~~vL~~l~~~~~~~t~~eLa~~l~~~~~tvt~~v~~Le~ 72 (144)
T PRK03573 27 LELTQTHWVTLHNIHQLPPEQSQIQLAKAIGIEQPSLVRTLDQLEE 72 (144)
T ss_pred cCCCHHHHHHHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHHHHHH
Confidence 45666664 3344443444678999999999999999999998754
No 205
>PF09607 BrkDBD: Brinker DNA-binding domain; InterPro: IPR018586 This DNA-binding domain is the first approx. 100 residues of the N-terminal end of Brinker. The structure of this domain in complex with DNA consists of four alpha-helices that contain a helix-turn-helix DNA recognition motif specific for GC-rich DNA. The Brinker nuclear repressor is a major element of the Drosophila Decapentaplegic morphogen signalling pathway []. ; PDB: 2GLO_A.
Probab=83.38 E-value=3.8 Score=27.27 Aligned_cols=42 Identities=17% Similarity=0.024 Sum_probs=29.7
Q ss_pred CCCCCHHHHHHHHHHHHhcCC---cHHHHHhhhCCChhhHHHHHH
Q psy4300 27 VPFVPVEKKTLVALSYMATQL---SMRKIGDQFNLADSTVWSCID 68 (307)
Q Consensus 27 ~~~~~~~~~l~i~L~~L~~g~---~~~~l~~~fgvs~stv~r~v~ 68 (307)
+...++.-+|-+.-++..++. .++..|..|||++..|.+|..
T Consensus 3 rrsy~~~FKL~Vv~~a~~~~nc~~~~RAaarkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 3 RRSYTAEFKLKVVEYAEKDNNCKGNQRAAARKFNVSRRQVRKWRK 47 (58)
T ss_dssp -----HHHHHHHHHHHHH-TTTTT-HHHHHHHTTS-HHHHHHHHT
T ss_pred ccccChHHHHHHHHHHHHccchhhhHHHHHHHhCccHHHHHHHHH
Confidence 567889999988888888875 679999999999999888764
No 206
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=83.37 E-value=2.7 Score=28.50 Aligned_cols=38 Identities=18% Similarity=0.198 Sum_probs=29.6
Q ss_pred HHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHH
Q psy4300 34 KKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFL 71 (307)
Q Consensus 34 ~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~ 71 (307)
++++-+|.-..++++-+++|..+|+|..++.+++....
T Consensus 3 e~Il~~i~~~~~p~~T~eiA~~~gls~~~aR~yL~~Le 40 (62)
T PF04703_consen 3 EKILEYIKEQNGPLKTREIADALGLSIYQARYYLEKLE 40 (62)
T ss_dssp HCHHHHHHHHTS-EEHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred HHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 45566666677889999999999999999999887764
No 207
>PRK00149 dnaA chromosomal replication initiation protein; Reviewed
Probab=83.29 E-value=4.1 Score=39.12 Aligned_cols=72 Identities=14% Similarity=0.170 Sum_probs=54.7
Q ss_pred HHHHHHHHhhhcCcccc---cCCCCCCCCHHHHHHHHHHHHhcCCcHHHHHhhh-CCChhhHHHHHHHHHHHcccc
Q psy4300 6 FGFLVEALAAINGYETL---YERGVPFVPVEKKTLVALSYMATQLSMRKIGDQF-NLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 6 F~~L~~~l~~~~~~~~~---~~~~~~~~~~~~~l~i~L~~L~~g~~~~~l~~~f-gvs~stv~r~v~~~~~~l~~~ 77 (307)
.+.|.+.+...++.-.. +.++...+...-+++|.|.+--++.|+.++|..| |.++|||...++++-..+..-
T Consensus 359 ~~~i~~~v~~~~~i~~~~l~~~~R~~~~~~aR~iamyl~~~~~~~s~~~Ig~~fg~rdhstV~~a~~~i~~~~~~d 434 (450)
T PRK00149 359 IENIQKVVAEYYNIKVSDLKSKSRTRNIARPRQIAMYLAKELTDLSLPEIGRAFGGRDHTTVLHAVRKIEKLLEED 434 (450)
T ss_pred HHHHHHHHHHHcCCCHHHHhCCCCCcccChHHHHHHHHHHHhcCCCHHHHHHHcCCCCHhHHHHHHHHHHHHHHhC
Confidence 45555665555432111 1233568889999999999999999999999999 599999999999998876543
No 208
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=83.29 E-value=1.5 Score=37.91 Aligned_cols=49 Identities=14% Similarity=0.231 Sum_probs=40.2
Q ss_pred CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
.+|.+++-++.|+++. |.++.++|..+|+|.+||...+.+....|-..+
T Consensus 149 ~L~~~~r~i~~l~~~~-g~s~~EIAe~lgis~~tVk~~l~Rar~kLr~~l 197 (231)
T PRK11922 149 ALPDAFRAVFVLRVVE-ELSVEETAQALGLPEETVKTRLHRARRLLRESL 197 (231)
T ss_pred hCCHHHhhhheeehhc-CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4667777777676655 899999999999999999999888877777764
No 209
>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=83.12 E-value=1.5 Score=34.67 Aligned_cols=36 Identities=11% Similarity=0.467 Sum_probs=30.2
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHH
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVW 64 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~ 64 (307)
..+|+..+-++.|.|+. |.|+.++|..+|+|.+||.
T Consensus 106 ~~Lp~~~r~v~~l~~~~-~~s~~EIA~~l~is~~tV~ 141 (142)
T TIGR03209 106 SILPNKQKKIIYMKFFE-DMKEIDIAKKLHISRQSVY 141 (142)
T ss_pred HhCCHHHHHHHHHHHHc-CCCHHHHHHHHCcCHHhhc
Confidence 46778888888886654 7999999999999999985
No 210
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=83.07 E-value=2.6 Score=32.50 Aligned_cols=27 Identities=19% Similarity=0.298 Sum_probs=23.8
Q ss_pred HhcCCcHHHHHhhhCCChhhHHHHHHH
Q psy4300 43 MATQLSMRKIGDQFNLADSTVWSCIDS 69 (307)
Q Consensus 43 L~~g~~~~~l~~~fgvs~stv~r~v~~ 69 (307)
-.-|.|+..+|...|+|++.||+++..
T Consensus 19 ~eeG~Sq~~iA~LLGltqaAVS~Yls~ 45 (119)
T COG2522 19 IEEGLSQYRIAKLLGLTQAAVSQYLSG 45 (119)
T ss_pred HHcCCcHHHHHHHhCCCHHHHHHHHcc
Confidence 344999999999999999999999863
No 211
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=83.05 E-value=2.9 Score=39.61 Aligned_cols=50 Identities=16% Similarity=0.317 Sum_probs=42.9
Q ss_pred CCCCHHHHHHHHHHHH---hcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 28 PFVPVEKKTLVALSYM---ATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L---~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
..+++.++-.+.|+|. ..+.++.+||..+|+|+++|..+.++....|-..
T Consensus 349 ~~L~~reR~VI~LRygl~d~~~~Tl~EIA~~LGvS~erVRqie~rAl~KLR~~ 401 (415)
T PRK07598 349 ADLTSRERDVIRMRFGLADGHTYSLAEIGRALDLSRERVRQIESKALQKLRQP 401 (415)
T ss_pred HhCCHHHHHHHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHhch
Confidence 3688999999999986 3568999999999999999999999887776643
No 212
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=83.05 E-value=5.1 Score=36.66 Aligned_cols=65 Identities=15% Similarity=0.227 Sum_probs=42.6
Q ss_pred HHHhcCCcHHHHHhhhCCChhhHHHHHHHHHH-HccccccccccccCCChHHHHHHHHHHHHhhCCCCccee
Q psy4300 41 SYMATQLSMRKIGDQFNLADSTVWSCIDSFLT-AMSQPQIQCQYIKWPTEEESVIIERNFRALAKFPGVIGA 111 (307)
Q Consensus 41 ~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~-~l~~~l~~~~~i~~P~~~~~~~~~~~f~~~~~~p~~~g~ 111 (307)
.|+-.|.++.+||..+|+|+.+|+|.+.+-.+ -|.+. .|.-|. ...-++.+..++..+++.|+-+
T Consensus 21 lYY~~gltQ~eIA~~LgiSR~~v~rlL~~Ar~~GiV~I-----~i~~~~-~~~~~Le~~L~~~fgL~~a~VV 86 (321)
T COG2390 21 LYYVEGLTQSEIAERLGISRATVSRLLAKAREEGIVKI-----SINSPV-EGCLELEQQLKERFGLKEAIVV 86 (321)
T ss_pred HHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCeEEE-----EeCCCC-cchHHHHHHHHHhcCCCeEEEE
Confidence 46688999999999999999999999987543 23333 233222 2223345555555577776543
No 213
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=83.02 E-value=1.7 Score=36.79 Aligned_cols=30 Identities=10% Similarity=0.189 Sum_probs=26.5
Q ss_pred HHHHhcCCcHHHHHhhhCCChhhHHHHHHH
Q psy4300 40 LSYMATQLSMRKIGDQFNLADSTVWSCIDS 69 (307)
Q Consensus 40 L~~L~~g~~~~~l~~~fgvs~stv~r~v~~ 69 (307)
..++..|.|+..+|..+|||++|++|+++.
T Consensus 166 ~~~~~~g~s~~~iak~lgis~~Tv~r~~k~ 195 (200)
T PRK13413 166 KKLLDKGTSKSEIARKLGVSRTTLARFLKT 195 (200)
T ss_pred HHHHHCCCCHHHHHHHHCCCHHHHHHHHHh
Confidence 445788999999999999999999999874
No 214
>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=83.02 E-value=8 Score=29.13 Aligned_cols=45 Identities=13% Similarity=0.228 Sum_probs=32.6
Q ss_pred CCCHHHHHHH-HHHHH---hcCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300 29 FVPVEKKTLV-ALSYM---ATQLSMRKIGDQFNLADSTVWSCIDSFLTA 73 (307)
Q Consensus 29 ~~~~~~~l~i-~L~~L---~~g~~~~~l~~~fgvs~stv~r~v~~~~~~ 73 (307)
.+++.+-..+ .|.++ ..+.+..+|+..++++++|+++.+++....
T Consensus 22 ~ls~~q~~vL~~l~~~~~~~~~~t~~eL~~~l~~~~stvs~~i~~Le~k 70 (109)
T TIGR01889 22 NLSLEELLILYYLGKLENNEGKLTLKEIIKEILIKQSALVKIIKKLSKK 70 (109)
T ss_pred CCCHHHHHHHHHHHhhhccCCcCcHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 4566554444 33322 245999999999999999999999987653
No 215
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=82.67 E-value=2.7 Score=34.39 Aligned_cols=48 Identities=13% Similarity=0.062 Sum_probs=37.2
Q ss_pred CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
.+|++++-++.|.++ .|.++.++|..+|+|.+||...+.+....+...
T Consensus 119 ~L~~~~r~i~~l~~~-~g~s~~EIA~~lgis~~tV~~~l~Ra~~~~~~~ 166 (172)
T PRK09651 119 GLNGKTREAFLLSQL-DGLTYSEIAHKLGVSVSSVKKYVAKATEHCLLF 166 (172)
T ss_pred hCCHHHhHHhhhhhc-cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 566777766555555 478999999999999999998888877665543
No 216
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=82.66 E-value=4.9 Score=27.78 Aligned_cols=40 Identities=13% Similarity=0.173 Sum_probs=33.9
Q ss_pred HHHHHHHHHHHHhcC-CcHHHHHhhhCC-ChhhHHHHHHHHH
Q psy4300 32 VEKKTLVALSYMATQ-LSMRKIGDQFNL-ADSTVWSCIDSFL 71 (307)
Q Consensus 32 ~~~~l~i~L~~L~~g-~~~~~l~~~fgv-s~stv~r~v~~~~ 71 (307)
...++.-++.+|..+ .+..++|..+|. |.+++++.+++..
T Consensus 35 ~~~r~~~a~~~l~~~~~~~~~ia~~~g~~s~~~f~r~Fk~~~ 76 (84)
T smart00342 35 RDRRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLF 76 (84)
T ss_pred HHHHHHHHHHHHHcCCCCHHHHHHHhCCCChHHHHHHHHHHH
Confidence 355677788888776 899999999999 9999999998764
No 217
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=82.60 E-value=3.1 Score=35.00 Aligned_cols=50 Identities=10% Similarity=0.134 Sum_probs=41.4
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
..+|+..+-++.|.|+. |.++.++|..+|+|.+||...+.+....|-..+
T Consensus 132 ~~Lp~~~r~v~~l~~~~-g~s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l 181 (196)
T PRK12535 132 DALPPERREALILTQVL-GYTYEEAAKIADVRVGTIRSRVARARADLIAAT 181 (196)
T ss_pred HcCCHHHHHHhhhHHHh-CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 34677777777777665 688999999999999999999998888888774
No 218
>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=82.54 E-value=6.1 Score=24.37 Aligned_cols=25 Identities=24% Similarity=0.393 Sum_probs=19.7
Q ss_pred CCcHHHHHhhhCCChhhHHHHHHHH
Q psy4300 46 QLSMRKIGDQFNLADSTVWSCIDSF 70 (307)
Q Consensus 46 g~~~~~l~~~fgvs~stv~r~v~~~ 70 (307)
-.||.++|...|+|.+||.+=+.+.
T Consensus 17 r~s~~~la~~lglS~~~v~~Ri~rL 41 (42)
T PF13404_consen 17 RRSYAELAEELGLSESTVRRRIRRL 41 (42)
T ss_dssp TS-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred CccHHHHHHHHCcCHHHHHHHHHHh
Confidence 3789999999999999998877653
No 219
>PHA00738 putative HTH transcription regulator
Probab=82.46 E-value=2.2 Score=32.21 Aligned_cols=27 Identities=22% Similarity=0.183 Sum_probs=24.1
Q ss_pred CcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300 47 LSMRKIGDQFNLADSTVWSCIDSFLTA 73 (307)
Q Consensus 47 ~~~~~l~~~fgvs~stv~r~v~~~~~~ 73 (307)
++-.+|+..|++|+++||+.++-.-++
T Consensus 27 ~~V~eLae~l~lSQptVS~HLKvLreA 53 (108)
T PHA00738 27 LSASLISHTLLLSYTTVLRHLKILNEQ 53 (108)
T ss_pred ccHHHHHHhhCCCHHHHHHHHHHHHHC
Confidence 788899999999999999999877655
No 220
>PRK14088 dnaA chromosomal replication initiation protein; Provisional
Probab=82.42 E-value=3.7 Score=39.32 Aligned_cols=71 Identities=14% Similarity=0.164 Sum_probs=54.1
Q ss_pred HHHHHHHHhhhcCcccc---cCCCCCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccc
Q psy4300 6 FGFLVEALAAINGYETL---YERGVPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQ 76 (307)
Q Consensus 6 F~~L~~~l~~~~~~~~~---~~~~~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~ 76 (307)
.+.|.+.+...++.... +.++...+...-+++|.|.+=-++.|+.++|..||.+.|||...++++-..+.+
T Consensus 344 ~~~I~~~V~~~~~i~~~~l~s~~R~~~i~~aR~iamyl~r~~~~~s~~~Ig~~fgr~hstV~~a~~~i~~~~~~ 417 (440)
T PRK14088 344 IDELIEIVAKVTGVSREEILSNSRNVKALLARRIGMYVAKNYLGSSLRTIAEKFNRSHPVVVDSVKKVKDSLLK 417 (440)
T ss_pred HHHHHHHHHHHcCCcHHHHhCCCCCccccHHHHHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Confidence 45555555555432111 122356788999999999999999999999999999999999999999887644
No 221
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=82.28 E-value=4.7 Score=30.13 Aligned_cols=37 Identities=22% Similarity=0.323 Sum_probs=28.6
Q ss_pred HHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300 35 KTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLT 72 (307)
Q Consensus 35 ~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~ 72 (307)
+++..|.. ....++.+++..+|+|++|+.+.++++..
T Consensus 7 ~il~~L~~-~~~~~~~~la~~l~~s~~tv~~~l~~L~~ 43 (108)
T smart00344 7 KILEELQK-DARISLAELAKKVGLSPSTVHNRVKRLEE 43 (108)
T ss_pred HHHHHHHH-hCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 33333333 33589999999999999999999998866
No 222
>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=81.86 E-value=4.6 Score=31.50 Aligned_cols=46 Identities=11% Similarity=0.083 Sum_probs=33.5
Q ss_pred CCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300 27 VPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTA 73 (307)
Q Consensus 27 ~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~ 73 (307)
.+++|.+.+.-+.=.. ..|.+-.+++..+.||+++|++++.++-+.
T Consensus 15 GrPLp~~~R~rIvela-~~G~rp~~Isr~l~Vs~gcVsKIl~Ry~eT 60 (125)
T PF00292_consen 15 GRPLPNELRQRIVELA-KEGVRPCDISRQLRVSHGCVSKILSRYRET 60 (125)
T ss_dssp TSSS-HHHHHHHHHHH-HTT--HHHHHHHHT--HHHHHHHHHHHHHH
T ss_pred CccCcHHHHHHHHHHh-hhcCCHHHHHHHHccchhHHHHHHHHHHHh
Confidence 5788888888776333 469999999999999999999999998543
No 223
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=81.83 E-value=3 Score=38.89 Aligned_cols=50 Identities=10% Similarity=0.264 Sum_probs=42.4
Q ss_pred CCCCHHHHHHHHHHHH-h--cCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 28 PFVPVEKKTLVALSYM-A--TQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L-~--~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
..++..++..+.|+|. . .+.++.+||..||||+..|+++-.+.+.-|-..
T Consensus 304 ~~L~~rEr~Vl~lrygl~~~~~~tl~EIa~~lgvs~erVrQi~~~Al~kLr~~ 356 (367)
T PRK09210 304 DTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHP 356 (367)
T ss_pred HhCCHHHHHHHHHHhccCCCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHhCh
Confidence 3689999999999985 3 458999999999999999999988877766554
No 224
>PRK05949 RNA polymerase sigma factor; Validated
Probab=81.74 E-value=3.3 Score=38.05 Aligned_cols=50 Identities=18% Similarity=0.357 Sum_probs=42.5
Q ss_pred CCCCHHHHHHHHHHHH---hcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 28 PFVPVEKKTLVALSYM---ATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L---~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
..+++.++-.+.|+|. ..+.++.++|..+|+|+++|..+..+.+.-|-..
T Consensus 265 ~~L~~rer~Vi~lr~gl~~~e~~Tl~EIa~~lgiS~erVrq~~~rAl~kLr~~ 317 (327)
T PRK05949 265 AELTPQQREVLTLRFGLEDGKELSLAKVGERLNLSRERVRQLEHQALAHLRRR 317 (327)
T ss_pred HhCCHHHHHHHHHHhccCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 3588999999999984 3569999999999999999999999887776553
No 225
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=81.70 E-value=2.6 Score=35.90 Aligned_cols=47 Identities=17% Similarity=0.125 Sum_probs=40.2
Q ss_pred CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
.+++.|+ =+|.+++.|.+..++|...++|.+||...+.++..-+--.
T Consensus 137 ~LT~RE~--eVL~lla~G~snkeIA~~L~iS~~TVk~h~~~I~~KL~v~ 183 (207)
T PRK15411 137 SLSRTES--SMLRMWMAGQGTIQISDQMNIKAKTVSSHKGNIKRKIKTH 183 (207)
T ss_pred cCCHHHH--HHHHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHHHHhCCC
Confidence 4777666 5678899999999999999999999999999887777655
No 226
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=81.55 E-value=4.5 Score=34.75 Aligned_cols=64 Identities=14% Similarity=0.215 Sum_probs=46.0
Q ss_pred CCCCHHHHHHHHHHHHhc--------------CCcHHHHHhhhCCChhhHHHHHHHHHHH-ccccccccccccCCChHHH
Q psy4300 28 PFVPVEKKTLVALSYMAT--------------QLSMRKIGDQFNLADSTVWSCIDSFLTA-MSQPQIQCQYIKWPTEEES 92 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~--------------g~~~~~l~~~fgvs~stv~r~v~~~~~~-l~~~l~~~~~i~~P~~~~~ 92 (307)
...+++++++-+|..|.. ..+..+||...|+++.|++|+++++-.. +.+. ....|...+...+
T Consensus 152 ~~~~~~~Rla~~L~~l~~~~~~~~~~~~~~~~~lt~~~iA~~lG~sr~tvsR~l~~l~~~g~I~~--~~~~i~i~d~~~L 229 (235)
T PRK11161 152 SKKNAEERLAAFIYNLSRRFAQRGFSPREFRLTMTRGDIGNYLGLTVETISRLLGRFQKSGMLAV--KGKYITIENNDAL 229 (235)
T ss_pred hCCCHHHHHHHHHHHHHHHHhhcCCCCceeEccccHHHHHHHhCCcHHHHHHHHHHHHHCCCEEe--cCCEEEEcCHHHH
Confidence 346899999999998752 2578899999999999999999877543 3333 4445555544443
Q ss_pred H
Q psy4300 93 V 93 (307)
Q Consensus 93 ~ 93 (307)
.
T Consensus 230 ~ 230 (235)
T PRK11161 230 A 230 (235)
T ss_pred H
Confidence 3
No 227
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=81.54 E-value=2 Score=30.21 Aligned_cols=28 Identities=7% Similarity=0.171 Sum_probs=24.1
Q ss_pred HHHhcCCcHHHHHhhhC------CChhhHHHHHH
Q psy4300 41 SYMATQLSMRKIGDQFN------LADSTVWSCID 68 (307)
Q Consensus 41 ~~L~~g~~~~~l~~~fg------vs~stv~r~v~ 68 (307)
.+...|.++.++|...| +|++||+|+-.
T Consensus 19 ~R~~lGLTQ~dvA~~lg~~~g~i~SQstISR~Es 52 (75)
T smart00352 19 RRIKLGFTQADVGLALGALYGPDFSQTTICRFEA 52 (75)
T ss_pred HHHHcCCCHHHHHHHhcccccCcCCHHHHHHHHh
Confidence 35677999999999999 59999999765
No 228
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=81.53 E-value=3.1 Score=35.86 Aligned_cols=46 Identities=20% Similarity=0.152 Sum_probs=38.7
Q ss_pred CCCCHHHHHHHHHHHHhc----------CCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300 28 PFVPVEKKTLVALSYMAT----------QLSMRKIGDQFNLADSTVWSCIDSFLTA 73 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~----------g~~~~~l~~~fgvs~stv~r~v~~~~~~ 73 (307)
...+++++|+-+|..+.. ..+..+||...|+++.|++|+++++.+.
T Consensus 151 ~~~~~~~Rla~~Ll~l~~~~g~~~~i~i~lt~~~IA~~lGisretlsR~L~~L~~~ 206 (230)
T PRK09391 151 GRKTAMERVAAFLLEMDERLGGAGMMALPMSRRDIADYLGLTIETVSRALSQLQDR 206 (230)
T ss_pred cCCCHHHHHHHHHHHHHHHhCCCCEEEecCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 346899999999998743 2567899999999999999999988654
No 229
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=81.52 E-value=5.2 Score=28.94 Aligned_cols=45 Identities=16% Similarity=0.218 Sum_probs=34.1
Q ss_pred CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300 29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTA 73 (307)
Q Consensus 29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~ 73 (307)
.++..+...+.+..-..+.+..+++..+++|++++++.++.+...
T Consensus 7 ~l~~~~~~il~~l~~~~~~~~~~la~~~~~s~~~i~~~l~~L~~~ 51 (101)
T smart00347 7 GLTPTQFLVLRILYEEGPLSVSELAKRLGVSPSTVTRVLDRLEKK 51 (101)
T ss_pred CCCHHHHHHHHHHHHcCCcCHHHHHHHHCCCchhHHHHHHHHHHC
Confidence 455554444444444556899999999999999999999998775
No 230
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=81.39 E-value=5.7 Score=38.69 Aligned_cols=50 Identities=8% Similarity=0.257 Sum_probs=43.8
Q ss_pred CCCCHHHHHHHHHHHH---hcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 28 PFVPVEKKTLVALSYM---ATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L---~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
..++..++..+.++|. ..+.++.+||..||||++.|+++-.+.+.-|-..
T Consensus 446 ~~L~eREr~VI~lRyGL~~~e~~TL~EIa~~lGVSrERVRQIe~kAL~KLR~~ 498 (509)
T PRK05901 446 ETLSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESKTLRKLRHP 498 (509)
T ss_pred hhCCHHHHHHHHHHhhccCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3699999999999995 4679999999999999999999998887776654
No 231
>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=81.32 E-value=3.3 Score=34.51 Aligned_cols=43 Identities=12% Similarity=0.110 Sum_probs=32.7
Q ss_pred HHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccc
Q psy4300 32 VEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQ 76 (307)
Q Consensus 32 ~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~ 76 (307)
...+.+ .+.++ .|.++.++|..+|+|.+||...+++....|-.
T Consensus 153 ~~~~~i-~~~~~-~~~s~~eIA~~l~~s~~tV~~~l~r~r~~L~~ 195 (198)
T TIGR02859 153 DLEWKV-LQSYL-DGKSYQEIACDLNRHVKSIDNALQRVKRKLEK 195 (198)
T ss_pred HHHHHH-HHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 333443 34554 79999999999999999999888887766544
No 232
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=81.30 E-value=3.8 Score=36.35 Aligned_cols=49 Identities=16% Similarity=0.344 Sum_probs=40.8
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
..+|+.++-++.|+|+ .|.++.++|..+|+|.+||.+.+.+....|-..
T Consensus 211 ~~L~~~~r~vl~l~~~-~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~ 259 (268)
T PRK06288 211 KTLPEREKKVLILYYY-EDLTLKEIGKVLGVTESRISQLHTKAVLQLRAK 259 (268)
T ss_pred HhCCHHHHHHHHHHHH-cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 3588888888888875 589999999999999999998888777666554
No 233
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=81.18 E-value=3.5 Score=37.84 Aligned_cols=51 Identities=8% Similarity=0.111 Sum_probs=44.4
Q ss_pred CCCCHHHHHHHHHHH-H--hcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 28 PFVPVEKKTLVALSY-M--ATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~-L--~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
..++..++.++.++| | -.|.++.++|..+|+|.+||..++.+....|-..|
T Consensus 261 ~~L~~~~R~vl~lrygL~~~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l 314 (325)
T PRK05657 261 FELNDKQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQIQVEALRRLREIL 314 (325)
T ss_pred HcCCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 468899999999887 4 46899999999999999999999999888887764
No 234
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=80.53 E-value=4.6 Score=33.63 Aligned_cols=49 Identities=14% Similarity=0.139 Sum_probs=39.0
Q ss_pred CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
.+|...+-++.|.++ .|.++.++|..+|+|.+||...+.+....|...+
T Consensus 128 ~Lp~~~r~v~~l~~~-~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 176 (188)
T PRK12517 128 KLDPEYREPLLLQVI-GGFSGEEIAEILDLNKNTVMTRLFRARNQLKEAL 176 (188)
T ss_pred hCCHHHHHHHHHHHH-hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 456666665555544 5899999999999999999999998888777763
No 235
>PRK13870 transcriptional regulator TraR; Provisional
Probab=80.37 E-value=3 Score=36.32 Aligned_cols=48 Identities=13% Similarity=0.180 Sum_probs=41.3
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
..+|++|+ =+|.|.+.|.+..++|...|||++||...++....-|-..
T Consensus 172 ~~LT~RE~--E~L~W~A~GKT~~EIa~ILgISe~TV~~Hl~na~~KLga~ 219 (234)
T PRK13870 172 AWLDPKEA--TYLRWIAVGKTMEEIADVEGVKYNSVRVKLREAMKRFDVR 219 (234)
T ss_pred CCCCHHHH--HHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCCC
Confidence 45777665 4689999999999999999999999999999988777665
No 236
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=80.29 E-value=5.6 Score=30.40 Aligned_cols=47 Identities=9% Similarity=0.201 Sum_probs=37.9
Q ss_pred CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccc
Q psy4300 29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQ 76 (307)
Q Consensus 29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~ 76 (307)
.++.+++ .....++.+..+..+++..+|||=+||..-+++++..|--
T Consensus 33 ~L~~E~~-~Fi~~Fi~~rGnlKe~e~~lgiSYPTvR~rLd~ii~~lg~ 79 (113)
T PF09862_consen 33 RLSPEQL-EFIKLFIKNRGNLKEMEKELGISYPTVRNRLDKIIEKLGY 79 (113)
T ss_pred cCCHHHH-HHHHHHHHhcCCHHHHHHHHCCCcHHHHHHHHHHHHHhCC
Confidence 4555554 4555566667789999999999999999999999998876
No 237
>PF05263 DUF722: Protein of unknown function (DUF722); InterPro: IPR007927 This entry is represented by Bacteriophage bIL285, Orf38. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=80.19 E-value=5.2 Score=31.43 Aligned_cols=47 Identities=17% Similarity=0.277 Sum_probs=39.4
Q ss_pred CCCHHHHHHHHHHHHhc-CCcHHHHHhhhCCChhhHHHHHHHHHHHcc
Q psy4300 29 FVPVEKKTLVALSYMAT-QLSMRKIGDQFNLADSTVWSCIDSFLTAMS 75 (307)
Q Consensus 29 ~~~~~~~l~i~L~~L~~-g~~~~~l~~~fgvs~stv~r~v~~~~~~l~ 75 (307)
.+..+++-.+-|+|-+. +.+|..+|..+++|.+|+.++..+|-+.+.
T Consensus 81 ~l~de~k~Ii~lry~~r~~~TW~~IA~~l~i~erta~r~~~~fK~~i~ 128 (130)
T PF05263_consen 81 TLIDEEKRIIKLRYDRRSRRTWYQIAQKLHISERTARRWRDRFKNDIY 128 (130)
T ss_pred hhCHHHHHHHHHHHcccccchHHHHHHHhCccHHHHHHHHHHHHHHhc
Confidence 45666777778888866 899999999999999999999998876554
No 238
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=80.16 E-value=6.5 Score=24.64 Aligned_cols=29 Identities=7% Similarity=0.268 Sum_probs=25.0
Q ss_pred cCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300 45 TQLSMRKIGDQFNLADSTVWSCIDSFLTA 73 (307)
Q Consensus 45 ~g~~~~~l~~~fgvs~stv~r~v~~~~~~ 73 (307)
.+.+..+++..|++|++|+++.+..+...
T Consensus 13 ~~~s~~~l~~~l~~s~~tv~~~l~~L~~~ 41 (53)
T smart00420 13 GKVSVEELAELLGVSEMTIRRDLNKLEEQ 41 (53)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 35789999999999999999999887553
No 239
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=79.83 E-value=4.7 Score=34.70 Aligned_cols=64 Identities=3% Similarity=-0.009 Sum_probs=48.6
Q ss_pred CCCCHHHHHHHHHHHHhcC----------CcHHHHHhhhCCChhhHHHHHHHHHHHccccccccccccCCChHHHH
Q psy4300 28 PFVPVEKKTLVALSYMATQ----------LSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQIQCQYIKWPTEEESV 93 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g----------~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l~~~~~i~~P~~~~~~ 93 (307)
...+++++++-+|..+... .+..++|...|+++.|++|+++++...=... ....|..++.+.+.
T Consensus 145 ~~~~~~~Rla~~Ll~~~~~~~~~~~~~i~~t~~~iA~~lG~tretvsR~l~~L~~~gl~~--~~~~i~I~d~~~L~ 218 (236)
T PRK09392 145 KLRSSAERLANYLLKQSLRQGGADVVTLPYEKRVLASYLGMTPENLSRAFAALASHGVHV--DGSAVTITDPAGLA 218 (236)
T ss_pred hcCCHHHHHHHHHHHhccccCCCcEEEeeCCHHHHHHHhCCChhHHHHHHHHHHhCCeEe--eCCEEEEcCHHHHH
Confidence 3568999999999887541 3357899999999999999999877665533 55667777665554
No 240
>COG3293 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=79.61 E-value=0.94 Score=35.10 Aligned_cols=94 Identities=16% Similarity=0.171 Sum_probs=60.6
Q ss_pred eEEeeeCCCcceEeeeeccccccCCCcccccchhhcchhhcCCCCCCCCCCeEEEecCCCCCCccccccccCCC-----C
Q psy4300 139 ILQGVCTSNKLLTNIHVGCTGRNHDAKVLSTSQIGRRIDAYGPTSLLYRDEYHLLGDSAYPLRTWCMVPYKNFG-----H 213 (307)
Q Consensus 139 ~~q~v~d~~g~i~~v~~~~~Gs~~D~~i~~~S~l~~~l~~~~~~~~~~~~~~~llgD~gY~~~~~l~~P~~~~~-----~ 213 (307)
+.++++|..|+++....+ +|..+ ..... . .++. ..-.-+|.|.+|....|...|-..+. .
T Consensus 2 ~~~~l~D~~~~~i~~~lp-~~~~~-~~~~~-~----~~~~--------~~v~~~i~~~~~~g~~wr~~p~~~~~~~~~~~ 66 (124)
T COG3293 2 KLHALVDAEWRPVEPLLP-PAKYG-GPPGV-T----LLRD--------REVLNGIADLLYTGCAWRALPADFPPATTVIP 66 (124)
T ss_pred CcccccccccceeeccCC-CcccC-CCCCC-c----cccc--------HHHHHHHHHHhccchHHHHhHHHhCCCceEeC
Confidence 467899999999999885 33333 21111 0 0110 01134567888887777555543311 1
Q ss_pred CCHHHHHHhHHHHhhhhHHHHHHHHHHhhccccc-c
Q psy4300 214 MTEEEKKYNTALSKTRVPIENVFGLIKGRWRRLK-Y 248 (307)
Q Consensus 214 lt~~q~~fN~~~s~~R~~VE~~fg~LK~rf~iL~-~ 248 (307)
....+.-++..+...|..+|+.|+++|. |+.+. +
T Consensus 67 ~~~~~~~~~~g~~~~~~~~~~~f~~~~~-~r~~~~~ 101 (124)
T COG3293 67 YRRFRRWFKRGLWKRRNLVERTFGRLKQ-FRRTATR 101 (124)
T ss_pred CCcchhhHHHHHHHHHHHHHHHHHHHhc-ccceecc
Confidence 1124678899999999999999999997 88877 5
No 241
>PF00872 Transposase_mut: Transposase, Mutator family; InterPro: IPR001207 Autonomous mobile genetic elements such as transposon or insertion sequences (IS) encode an enzyme, transposase, that is required for excising and inserting the mobile element. Transposases have been grouped into various families [, , ]. The mutator family of transposases consists of a number of elements that include, mutator from maize, IsT2 from Thiobacillus ferrooxidans, Is256 from Staphylococcus aureus, Is1201 from Lactobacillus helveticus, Is1081 from Mycobacterium bovis, IsRm3 from Rhizobium meliloti and others. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=79.55 E-value=2.2 Score=39.98 Aligned_cols=131 Identities=15% Similarity=0.119 Sum_probs=70.2
Q ss_pred HHHHhcCCcHHHHHhh----hC---CChhhHHHHHHHHHHHccccccccccccCCChHHHHHHHHHHHHhhCCCCcceee
Q psy4300 40 LSYMATQLSMRKIGDQ----FN---LADSTVWSCIDSFLTAMSQPQIQCQYIKWPTEEESVIIERNFRALAKFPGVIGAI 112 (307)
Q Consensus 40 L~~L~~g~~~~~l~~~----fg---vs~stv~r~v~~~~~~l~~~l~~~~~i~~P~~~~~~~~~~~f~~~~~~p~~~g~i 112 (307)
+..+..|.|.++++.. +| +|++|||+++..+.+.+... . +. ...+.|-.+-.|
T Consensus 108 ~~ly~~G~Str~i~~~l~~l~g~~~~S~s~vSri~~~~~~~~~~w--~-------~R-----------~L~~~~y~~l~i 167 (381)
T PF00872_consen 108 ISLYLKGVSTRDIEEALEELYGEVAVSKSTVSRITKQLDEEVEAW--R-------NR-----------PLESEPYPYLWI 167 (381)
T ss_pred hhhhccccccccccchhhhhhcccccCchhhhhhhhhhhhhHHHH--h-------hh-----------ccccccccceee
Confidence 3446778888877664 46 99999999888875544433 1 11 011223346789
Q ss_pred cceeEEeecCCCCccccccccCCcceeEEeeeCCCcc--eEeeeeccccccCCCcccccchhhcchhhcCCCCCCCCCCe
Q psy4300 113 DGCHIEGKFSKDIRNDYNNRKCTQSMILQGVCTSNKL--LTNIHVGCTGRNHDAKVLSTSQIGRRIDAYGPTSLLYRDEY 190 (307)
Q Consensus 113 Dgt~i~i~~P~~~~~~y~~~k~~~s~~~q~v~d~~g~--i~~v~~~~~Gs~~D~~i~~~S~l~~~l~~~~~~~~~~~~~~ 190 (307)
||++++++.-. .-...++-+-+-+|.+|+ ++.+..+ ..-....|. .+...|... .+....
T Consensus 168 D~~~~kvr~~~--------~~~~~~~~v~iGi~~dG~r~vLg~~~~---~~Es~~~W~--~~l~~L~~R-----Gl~~~~ 229 (381)
T PF00872_consen 168 DGTYFKVREDG--------RVVKKAVYVAIGIDEDGRREVLGFWVG---DRESAASWR--EFLQDLKER-----GLKDIL 229 (381)
T ss_pred eeeeccccccc--------ccccchhhhhhhhhcccccceeeeecc---cCCccCEee--ecchhhhhc-----cccccc
Confidence 99999986211 111223444445677774 5555543 222333332 233333331 122356
Q ss_pred EEEecCCCCCCccccccc
Q psy4300 191 HLLGDSAYPLRTWCMVPY 208 (307)
Q Consensus 191 ~llgD~gY~~~~~l~~P~ 208 (307)
.+++|..=.+...+-.-|
T Consensus 230 lvv~Dg~~gl~~ai~~~f 247 (381)
T PF00872_consen 230 LVVSDGHKGLKEAIREVF 247 (381)
T ss_pred eeeccccccccccccccc
Confidence 777776554444443333
No 242
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=79.21 E-value=1.8 Score=29.97 Aligned_cols=21 Identities=10% Similarity=0.301 Sum_probs=18.4
Q ss_pred cHHHHHhhhCCChhhHHHHHH
Q psy4300 48 SMRKIGDQFNLADSTVWSCID 68 (307)
Q Consensus 48 ~~~~l~~~fgvs~stv~r~v~ 68 (307)
+..++|...|+|.+|||++++
T Consensus 2 t~~~iA~~~gvS~~TVSr~ln 22 (70)
T smart00354 2 TIKDVARLAGVSKATVSRVLN 22 (70)
T ss_pred CHHHHHHHHCCCHHHHHHHHC
Confidence 567999999999999999764
No 243
>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=79.19 E-value=4.6 Score=29.00 Aligned_cols=35 Identities=11% Similarity=0.236 Sum_probs=28.6
Q ss_pred HhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 43 MATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 43 L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
...+.+..++|..+.+|+||+.+.++.+-..+..-
T Consensus 27 ~~~~~s~~~la~~~~iS~sti~~~i~~l~~~l~~~ 61 (87)
T PF05043_consen 27 NNEYVSIEDLAEELFISRSTIYRDIKKLNKYLKKY 61 (87)
T ss_dssp H-SEEEHHHHHHHHT--HHHHHHHHHHHHHHHHCC
T ss_pred cCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHc
Confidence 57789999999999999999999999998887754
No 244
>PRK14087 dnaA chromosomal replication initiation protein; Provisional
Probab=79.15 E-value=7.6 Score=37.32 Aligned_cols=73 Identities=11% Similarity=0.129 Sum_probs=56.0
Q ss_pred HHHHHHHHHhhhcCccccc---CCCCCCCCHHHHHHHHHHHHhcCCcHHHHHhhhC-CChhhHHHHHHHHHHHcccc
Q psy4300 5 TFGFLVEALAAINGYETLY---ERGVPFVPVEKKTLVALSYMATQLSMRKIGDQFN-LADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 5 ~F~~L~~~l~~~~~~~~~~---~~~~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fg-vs~stv~r~v~~~~~~l~~~ 77 (307)
+.+.|.+.+...++.-... ..+...+...-+++|.|.+=-++.|+.+||..|| .++|||...++++-..+..-
T Consensus 357 t~~~I~~~Va~~~~i~~~dl~s~~R~~~i~~~RqiamyL~r~~t~~sl~~IG~~FggrdHsTV~~a~~ki~~~~~~d 433 (450)
T PRK14087 357 NVKKIKEVVSEKYGISVNAIDGKARSKSIVTARHIAMYLTKEILNHTLAQIGEEFGGRDHTTVINAERKIEKMLKKD 433 (450)
T ss_pred CHHHHHHHHHHHcCCCHHHHhCCCCCccccHHHHHHHHHHHHHcCCCHHHHHHHhCCCChHHHHHHHHHHHHHHHhC
Confidence 4566666666665432111 1235678999999999999999999999999997 99999999999888877543
No 245
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=79.05 E-value=3.9 Score=36.73 Aligned_cols=45 Identities=7% Similarity=0.062 Sum_probs=39.9
Q ss_pred HHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 34 KKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 34 ~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
.+|-.++....+|.+++..|...+||+|+||+.+++.-..+-..|
T Consensus 4 ~~L~~F~~v~~~~~s~s~AA~~L~isq~avSr~I~~LE~~lg~~L 48 (309)
T PRK12682 4 QQLRFVREAVRRNLNLTEAAKALHTSQPGVSKAIIELEEELGIEI 48 (309)
T ss_pred HHHHHHHHHHHccCCHHHHHHHhcCccHHHHHHHHHHHHHhCCee
Confidence 456677777788889999999999999999999999999988876
No 246
>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=78.98 E-value=3.6 Score=26.54 Aligned_cols=26 Identities=12% Similarity=0.066 Sum_probs=22.8
Q ss_pred HhcCCcHHHHHhhhCCChhhHHHHHH
Q psy4300 43 MATQLSMRKIGDQFNLADSTVWSCID 68 (307)
Q Consensus 43 L~~g~~~~~l~~~fgvs~stv~r~v~ 68 (307)
-..|.++.++|...|+|+++++++.+
T Consensus 12 ~~~gltq~~lA~~~gvs~~~vs~~e~ 37 (58)
T TIGR03070 12 KALGLTQADLADLAGVGLRFIRDVEN 37 (58)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHC
Confidence 35689999999999999999999764
No 247
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=78.94 E-value=5 Score=36.80 Aligned_cols=49 Identities=12% Similarity=0.266 Sum_probs=42.1
Q ss_pred CCCHHHHHHHHHHHH---hcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 29 FVPVEKKTLVALSYM---ATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 29 ~~~~~~~l~i~L~~L---~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
.++..++..+.++|. ....++.+||..||||+..|+++-.+.+.-|-..
T Consensus 262 ~L~eREr~Vl~~rygl~~~~~~Tl~eIa~~lgvS~eRVrQIe~~Al~KLr~~ 313 (324)
T PRK07921 262 TLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLRNG 313 (324)
T ss_pred hCCHHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Confidence 588999999999985 2458999999999999999999998887776554
No 248
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=78.72 E-value=2 Score=35.77 Aligned_cols=47 Identities=15% Similarity=0.263 Sum_probs=35.3
Q ss_pred CCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 30 VPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 30 ~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
+|.+++=++.|.|+ .|.++.++|..+|+|.+||...+.+....|-..
T Consensus 135 L~~~~r~v~~l~~~-~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 181 (188)
T PRK09640 135 VNPIDREILVLRFV-AELEFQEIADIMHMGLSATKMRYKRALDKLREK 181 (188)
T ss_pred cChhheeeeeeHHh-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 34444444444444 689999999999999999999988887777665
No 249
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=78.67 E-value=2.5 Score=35.24 Aligned_cols=48 Identities=19% Similarity=0.255 Sum_probs=36.8
Q ss_pred CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
.+|+.++-++.|++ -.|.++.++|..+|+|.+||...+.+....|-..
T Consensus 139 ~L~~~~r~i~~l~~-~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~ 186 (194)
T PRK12513 139 TLPDEQREVFLLRE-HGDLELEEIAELTGVPEETVKSRLRYALQKLREL 186 (194)
T ss_pred hCCHhHhhheeeeh-ccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 45566666555554 4689999999999999999988888777666555
No 250
>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=78.32 E-value=2.4 Score=26.20 Aligned_cols=23 Identities=9% Similarity=0.183 Sum_probs=20.2
Q ss_pred cHHHHHhhhCCChhhHHHHHHHH
Q psy4300 48 SMRKIGDQFNLADSTVWSCIDSF 70 (307)
Q Consensus 48 ~~~~l~~~fgvs~stv~r~v~~~ 70 (307)
+..++|..+|||.+|+.+++.+-
T Consensus 2 s~~e~a~~lgvs~~tl~~~~~~g 24 (49)
T cd04762 2 TTKEAAELLGVSPSTLRRWVKEG 24 (49)
T ss_pred CHHHHHHHHCcCHHHHHHHHHcC
Confidence 56789999999999999998863
No 251
>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=78.24 E-value=4.4 Score=27.72 Aligned_cols=28 Identities=18% Similarity=0.302 Sum_probs=23.9
Q ss_pred CCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300 46 QLSMRKIGDQFNLADSTVWSCIDSFLTA 73 (307)
Q Consensus 46 g~~~~~l~~~fgvs~stv~r~v~~~~~~ 73 (307)
..+..+++..+|+|++|+++.+...-..
T Consensus 13 ~~~~~eLa~~l~vS~~tv~~~l~~L~~~ 40 (69)
T TIGR00122 13 PFSGEKLGEALGMSRTAVNKHIQTLREW 40 (69)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 3568899999999999999999987553
No 252
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=78.09 E-value=4.2 Score=34.82 Aligned_cols=48 Identities=13% Similarity=0.072 Sum_probs=39.3
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
..+++.++= +|..++.|.+..++|..+++|.+||...+.++..-+--.
T Consensus 142 ~~LS~RE~e--VL~Lia~G~SnkEIA~~L~IS~~TVk~hvs~I~~KLgv~ 189 (217)
T PRK13719 142 NKVTKYQND--VFILYSFGFSHEYIAQLLNITVGSSKNKISEILKFFGIS 189 (217)
T ss_pred CCCCHHHHH--HHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Confidence 456766654 566789999999999999999999999999887766654
No 253
>PHA01976 helix-turn-helix protein
Probab=78.07 E-value=3.7 Score=27.75 Aligned_cols=27 Identities=11% Similarity=0.101 Sum_probs=23.3
Q ss_pred HHhcCCcHHHHHhhhCCChhhHHHHHH
Q psy4300 42 YMATQLSMRKIGDQFNLADSTVWSCID 68 (307)
Q Consensus 42 ~L~~g~~~~~l~~~fgvs~stv~r~v~ 68 (307)
+-..|.+..++|...|+|+++++++.+
T Consensus 11 R~~~glt~~~lA~~~gvs~~~v~~~e~ 37 (67)
T PHA01976 11 RNARAWSAPELSRRAGVRHSLIYDFEA 37 (67)
T ss_pred HHHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 445789999999999999999998654
No 254
>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=78.02 E-value=3.8 Score=27.52 Aligned_cols=27 Identities=15% Similarity=0.450 Sum_probs=21.8
Q ss_pred HHHhc--CCcHHHHHhhhCCChhhHHHHH
Q psy4300 41 SYMAT--QLSMRKIGDQFNLADSTVWSCI 67 (307)
Q Consensus 41 ~~L~~--g~~~~~l~~~fgvs~stv~r~v 67 (307)
.|+.+ .....+||..+|||.+||.++=
T Consensus 15 ~y~~~~g~i~lkdIA~~Lgvs~~tIr~WK 43 (60)
T PF10668_consen 15 IYKESNGKIKLKDIAEKLGVSESTIRKWK 43 (60)
T ss_pred HHHHhCCCccHHHHHHHHCCCHHHHHHHh
Confidence 34544 4889999999999999998754
No 255
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=77.76 E-value=6.5 Score=33.18 Aligned_cols=48 Identities=15% Similarity=0.123 Sum_probs=40.7
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
..+++.++ =+|..++.|.+..++|...++|.+||...+.+...-|--.
T Consensus 149 ~~Lt~rE~--evl~~~~~G~s~~eIA~~l~iS~~TV~~h~~~i~~Kl~v~ 196 (216)
T PRK10840 149 KRLSPKES--EVLRLFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVE 196 (216)
T ss_pred ccCCHHHH--HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCCC
Confidence 45888886 6788889999999999999999999999998887666543
No 256
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=77.70 E-value=2.4 Score=34.59 Aligned_cols=47 Identities=17% Similarity=0.183 Sum_probs=35.0
Q ss_pred CHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 31 PVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 31 ~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
|..++-++.|.| -.|.++.++|..+|+|.+||...+.+....|...+
T Consensus 122 ~~~~r~vl~l~~-~~g~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l 168 (175)
T PRK12518 122 SLEHRAVLVLHD-LEDLPQKEIAEILNIPVGTVKSRLFYARRQLRKFL 168 (175)
T ss_pred CHHHeeeeeehH-hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 333333333333 45789999999999999999999998888777664
No 257
>PRK12422 chromosomal replication initiation protein; Provisional
Probab=77.54 E-value=7.6 Score=37.28 Aligned_cols=71 Identities=24% Similarity=0.195 Sum_probs=54.6
Q ss_pred HHHHHHHHHhhhcCcccc---cCCCCCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcc
Q psy4300 5 TFGFLVEALAAINGYETL---YERGVPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMS 75 (307)
Q Consensus 5 ~F~~L~~~l~~~~~~~~~---~~~~~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~ 75 (307)
+.+.|.+.+...++.-.. +..+...+...-+++|.|.+=-++.|+.++|..||-++|||.-.++.+-..+.
T Consensus 353 t~~~I~~~Va~~~~v~~~dl~s~~R~~~i~~~Rqiamyl~r~~t~~s~~~IG~~fgrdHsTV~~a~~ki~~~~~ 426 (445)
T PRK12422 353 TPSKIIRAVAQYYGVSPESILGRSQSREYVLPRQVAMYLCRQKLSLSYVKIGDVFSRDHSTVISSIRAISQKLE 426 (445)
T ss_pred CHHHHHHHHHHHhCCCHHHHhcCCCCcccccHHHHHHHHHHHhcCCCHHHHHHHhCCChHHHHHHHHHHHHHHH
Confidence 345566666555432111 12346788999999999999999999999999999999999999998887773
No 258
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=77.29 E-value=6.4 Score=33.31 Aligned_cols=49 Identities=22% Similarity=0.166 Sum_probs=39.0
Q ss_pred CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
.++...+-.+.|.+ -.|.++.++|..+|+|.+||...+.+....|-..+
T Consensus 138 ~L~~~~r~v~~L~~-~~g~s~~EIA~~Lgis~~tV~~~l~RArk~Lr~~l 186 (203)
T PRK09647 138 SLPPEFRAAVVLCD-IEGLSYEEIAATLGVKLGTVRSRIHRGRQQLRAAL 186 (203)
T ss_pred hCCHHHHHHHHHHH-HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 45566666666665 56899999999999999999999998877777663
No 259
>COG5421 Transposase [DNA replication, recombination, and repair]
Probab=77.15 E-value=3.3 Score=39.44 Aligned_cols=56 Identities=16% Similarity=0.284 Sum_probs=41.2
Q ss_pred cceeEEeeeCCCcceEeeeeccccccCCCcccccchhhcchhhcCCCCCCCCCCeEEEecCCCC
Q psy4300 136 QSMILQGVCTSNKLLTNIHVGCTGRNHDAKVLSTSQIGRRIDAYGPTSLLYRDEYHLLGDSAYP 199 (307)
Q Consensus 136 ~s~~~q~v~d~~g~i~~v~~~~~Gs~~D~~i~~~S~l~~~l~~~~~~~~~~~~~~~llgD~gY~ 199 (307)
.-+++..+++..|-.+.+.+ ++|+++|...+- +....+... ....+.++++|+|+-
T Consensus 155 ~QI~vsMi~~~~gIPl~~~v-~~Gni~D~~~~~--~ti~kl~~~-----l~~~~~~~V~Dkgf~ 210 (480)
T COG5421 155 PQINVSMIVNQKGIPLFVRV-YSGNISDKNTLI--KTIQKLKSV-----LVKDEVYLVADKGFN 210 (480)
T ss_pred ceeEEEEEEcCCCCceEEEc-cCCCccchHHHH--HHHHHHHHh-----cccceEEEEEccccc
Confidence 56889999998898888888 899999997774 333333331 122348999999995
No 260
>PF13551 HTH_29: Winged helix-turn helix
Probab=77.13 E-value=19 Score=26.68 Aligned_cols=69 Identities=10% Similarity=0.142 Sum_probs=40.7
Q ss_pred CCHHHHHHHHHHHhhhc--Cccc-ccCCCCCC--CCHHHHHHHHHHHHhcC------CcHHHHHhhh-------CCChhh
Q psy4300 1 MRKTTFGFLVEALAAIN--GYET-LYERGVPF--VPVEKKTLVALSYMATQ------LSMRKIGDQF-------NLADST 62 (307)
Q Consensus 1 ms~~~F~~L~~~l~~~~--~~~~-~~~~~~~~--~~~~~~l~i~L~~L~~g------~~~~~l~~~f-------gvs~st 62 (307)
+++.|+...+......- ...+ ...++++. ++.++.-.+.=....+. .+...++... .+|.+|
T Consensus 24 ~s~~Tv~r~~~~~~~~G~~~l~~~~~~~g~~~~~l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~t 103 (112)
T PF13551_consen 24 ISRRTVYRWLKRYREGGIEGLLPRKPRGGRPRKRLSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPST 103 (112)
T ss_pred cCHHHHHHHHHHHHcccHHHHHhccccCCCCCCCCCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHHH
Confidence 47888888888876552 1122 11223322 66666554443333332 4556777633 699999
Q ss_pred HHHHHHH
Q psy4300 63 VWSCIDS 69 (307)
Q Consensus 63 v~r~v~~ 69 (307)
+++++++
T Consensus 104 i~r~L~~ 110 (112)
T PF13551_consen 104 IRRILKR 110 (112)
T ss_pred HHHHHHH
Confidence 9999875
No 261
>PF14493 HTH_40: Helix-turn-helix domain
Probab=76.11 E-value=14 Score=26.79 Aligned_cols=62 Identities=18% Similarity=0.236 Sum_probs=45.7
Q ss_pred HHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccccccccccCCChHHHHHHHHHHHH
Q psy4300 36 TLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQIQCQYIKWPTEEESVIIERNFRA 101 (307)
Q Consensus 36 l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l~~~~~i~~P~~~~~~~~~~~f~~ 101 (307)
...|+..+..|.+..++|..-|++.+||...+-+.+..=...- ..+ |-+.++.+.+.+.+.+
T Consensus 3 ~~~T~~l~~~G~si~eIA~~R~L~~sTI~~HL~~~~~~g~~~~-~~~---~l~~e~~~~I~~~~~~ 64 (91)
T PF14493_consen 3 AQITYELFQKGLSIEEIAKIRGLKESTIYGHLAELIESGEPLD-IEE---LLSEEEIKQIEDAIEK 64 (91)
T ss_pred HHHHHHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHHHhCCCCC-HHH---hCCHHHHHHHHHHHHH
Confidence 3568888999999999999999999999998888877755331 233 3344555666666654
No 262
>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=75.94 E-value=3.2 Score=25.72 Aligned_cols=23 Identities=17% Similarity=0.416 Sum_probs=20.1
Q ss_pred CcHHHHHhhhCCChhhHHHHHHH
Q psy4300 47 LSMRKIGDQFNLADSTVWSCIDS 69 (307)
Q Consensus 47 ~~~~~l~~~fgvs~stv~r~v~~ 69 (307)
.+..++|..+|+|++|+.+++++
T Consensus 2 lt~~e~a~~lgis~~ti~~~~~~ 24 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTVYRLIHE 24 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHc
Confidence 46789999999999999998865
No 263
>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=75.24 E-value=2.1 Score=38.52 Aligned_cols=22 Identities=23% Similarity=0.369 Sum_probs=20.0
Q ss_pred CcHHHHHhhhCCChhhHHHHHH
Q psy4300 47 LSMRKIGDQFNLADSTVWSCID 68 (307)
Q Consensus 47 ~~~~~l~~~fgvs~stv~r~v~ 68 (307)
.+..++|..+|||++||||+++
T Consensus 2 ~ti~dIA~~agVS~sTVSr~Ln 23 (311)
T TIGR02405 2 LTIKDIARLAGVGKSTVSRVLN 23 (311)
T ss_pred CcHHHHHHHhCCCHHHHHHHhC
Confidence 3678999999999999999996
No 264
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=75.24 E-value=7.4 Score=30.36 Aligned_cols=31 Identities=23% Similarity=0.409 Sum_probs=27.4
Q ss_pred HhcCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300 43 MATQLSMRKIGDQFNLADSTVWSCIDSFLTA 73 (307)
Q Consensus 43 L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~ 73 (307)
-..+.+-.+||...++++|||+|.++..+.+
T Consensus 39 ~~~~~tvdelae~lnr~rStv~rsl~~L~~~ 69 (126)
T COG3355 39 ENGPLTVDELAEILNRSRSTVYRSLQNLLEA 69 (126)
T ss_pred hcCCcCHHHHHHHHCccHHHHHHHHHHHHHc
Confidence 3566899999999999999999999998765
No 265
>PRK08558 adenine phosphoribosyltransferase; Provisional
Probab=75.14 E-value=8.8 Score=33.52 Aligned_cols=40 Identities=10% Similarity=0.194 Sum_probs=34.8
Q ss_pred CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHH
Q psy4300 29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCID 68 (307)
Q Consensus 29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~ 68 (307)
.+-...++.-.|+-|+...+|++|+..+|++.|.++|+++
T Consensus 6 ~~~~~~~~v~~lr~lk~~~ty~el~~~~g~p~~~l~RYv~ 45 (238)
T PRK08558 6 KVRLQLRAVRVLRSLKKTYTYEELSSITGLPESVLNRYVN 45 (238)
T ss_pred hHHHHHHHHHHHHHHhcccCHHHHHHHHCCCHHHHHHHHc
Confidence 3445667788899999999999999999999999999876
No 266
>smart00760 Bac_DnaA_C Bacterial dnaA protein helix-turn-helix domain. Could be involved in DNA-binding.
Probab=75.06 E-value=7.8 Score=25.79 Aligned_cols=51 Identities=22% Similarity=0.241 Sum_probs=36.2
Q ss_pred HHHHHHHhhhcCccccc---CCCCCCCCHHHHHHHHHHHHhcCCcHHHHHhhhC
Q psy4300 7 GFLVEALAAINGYETLY---ERGVPFVPVEKKTLVALSYMATQLSMRKIGDQFN 57 (307)
Q Consensus 7 ~~L~~~l~~~~~~~~~~---~~~~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fg 57 (307)
+.|++.+...++..... ..+...+...-+++|.|..--.|.|+.++|..||
T Consensus 3 ~~I~~~Va~~~~i~~~~i~s~~R~~~~~~aR~iamyla~~~~~~sl~~Ig~~fg 56 (60)
T smart00760 3 EEIIEAVAEYFGVKPEDLKSKSRKREIVLARQIAMYLARELTDLSLPEIGKIFG 56 (60)
T ss_pred HHHHHHHHHHhCCCHHHHhcCCCCcchhHHHHHHHHHHHHHHCCCHHHHHHHhC
Confidence 45555555554321111 1235778889999999999999999999999998
No 267
>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=74.90 E-value=2.6 Score=31.90 Aligned_cols=39 Identities=18% Similarity=0.217 Sum_probs=29.5
Q ss_pred HHHHHhc-CCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 39 ALSYMAT-QLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 39 ~L~~L~~-g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
-+.-|++ |.++.++|..|+||+||+..++.+.-.--+..
T Consensus 72 Efi~LR~AGlt~~aIAd~F~iS~s~~~nft~~n~~eYyr~ 111 (126)
T PF10654_consen 72 EFIELRHAGLTCYAIADYFKISKSTVFNFTQNNKKEYYRI 111 (126)
T ss_pred HHHHHHhcCCChHHHHHHHhHHHHHHHHHHHHhHHHHHHH
Confidence 3444555 89999999999999999988887665444433
No 268
>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=74.53 E-value=6.7 Score=29.21 Aligned_cols=39 Identities=15% Similarity=0.282 Sum_probs=33.0
Q ss_pred HHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 40 LSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 40 L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
|.-+....|++..|...|+|+||+++.+++.-+.+-..|
T Consensus 10 ~~av~~~gSis~AA~~L~iS~stvs~~I~~LE~~lg~~L 48 (99)
T TIGR00637 10 LKAIARMGSISQAAKDAGISYKSAWDYIRAMNNLSGEPL 48 (99)
T ss_pred HHHHHHhCCHHHHHHHHCCCHHHHHHHHHHHHHHhCCCe
Confidence 333444568999999999999999999999999988875
No 269
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=74.49 E-value=6.5 Score=35.44 Aligned_cols=45 Identities=7% Similarity=0.115 Sum_probs=39.6
Q ss_pred HHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 34 KKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 34 ~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
.+|-.++....+|.|++..|...++|+|++|+.+++.-..+-..|
T Consensus 4 ~~L~~F~~v~~~~~S~s~AA~~L~isQpavS~~I~~LE~~lg~~L 48 (309)
T PRK12683 4 QQLRIIREAVRQNFNLTEVANALYTSQSGVSKQIKDLEDELGVEI 48 (309)
T ss_pred HHHHHHHHHHHccCCHHHHHHHhcCCcHHHHHHHHHHHHHhCCee
Confidence 356667777778889999999999999999999999999988887
No 270
>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=74.15 E-value=4.6 Score=27.15 Aligned_cols=25 Identities=16% Similarity=0.405 Sum_probs=19.9
Q ss_pred cHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300 48 SMRKIGDQFNLADSTVWSCIDSFLT 72 (307)
Q Consensus 48 ~~~~l~~~fgvs~stv~r~v~~~~~ 72 (307)
+..+++..||+|++|+.+.+.....
T Consensus 26 s~~~la~~~~vsr~tvr~al~~L~~ 50 (64)
T PF00392_consen 26 SERELAERYGVSRTTVREALRRLEA 50 (64)
T ss_dssp -HHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CHHHHHHHhccCCcHHHHHHHHHHH
Confidence 6679999999999999998887654
No 271
>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=74.09 E-value=10 Score=25.00 Aligned_cols=27 Identities=11% Similarity=0.437 Sum_probs=22.9
Q ss_pred CCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300 46 QLSMRKIGDQFNLADSTVWSCIDSFLT 72 (307)
Q Consensus 46 g~~~~~l~~~fgvs~stv~r~v~~~~~ 72 (307)
..+..+++..||||..|+.|-+.....
T Consensus 14 ~~s~~ela~~~~VS~~TiRRDl~~L~~ 40 (57)
T PF08220_consen 14 KVSVKELAEEFGVSEMTIRRDLNKLEK 40 (57)
T ss_pred CEEHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 478889999999999999998876543
No 272
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=73.75 E-value=2.9 Score=27.85 Aligned_cols=25 Identities=8% Similarity=0.248 Sum_probs=19.0
Q ss_pred hcCCcHHHHHhhhCCChhhHHHHHH
Q psy4300 44 ATQLSMRKIGDQFNLADSTVWSCID 68 (307)
Q Consensus 44 ~~g~~~~~l~~~fgvs~stv~r~v~ 68 (307)
..|.+..++|...|+|++|++++++
T Consensus 8 ~~~it~~~La~~~gis~~tl~~~~~ 32 (63)
T PF13443_consen 8 ERGITQKDLARKTGISRSTLSRILN 32 (63)
T ss_dssp HTT--HHHHHHHHT--HHHHHHHHT
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHh
Confidence 5678999999999999999999876
No 273
>PRK11050 manganese transport regulator MntR; Provisional
Probab=73.75 E-value=10 Score=30.62 Aligned_cols=29 Identities=10% Similarity=0.162 Sum_probs=26.3
Q ss_pred cCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300 45 TQLSMRKIGDQFNLADSTVWSCIDSFLTA 73 (307)
Q Consensus 45 ~g~~~~~l~~~fgvs~stv~r~v~~~~~~ 73 (307)
.+.+..+++..+++|++++++.+.++...
T Consensus 50 ~~~t~~eLA~~l~is~stVsr~l~~Le~~ 78 (152)
T PRK11050 50 GEARQVDIAARLGVSQPTVAKMLKRLARD 78 (152)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 56899999999999999999999988765
No 274
>PRK00215 LexA repressor; Validated
Probab=73.69 E-value=9.3 Score=32.27 Aligned_cols=28 Identities=25% Similarity=0.323 Sum_probs=24.9
Q ss_pred CCcHHHHHhhhCC-ChhhHHHHHHHHHHH
Q psy4300 46 QLSMRKIGDQFNL-ADSTVWSCIDSFLTA 73 (307)
Q Consensus 46 g~~~~~l~~~fgv-s~stv~r~v~~~~~~ 73 (307)
+.+..+||..+|+ +++|++++++.+...
T Consensus 23 ~~s~~ela~~~~~~~~~tv~~~l~~L~~~ 51 (205)
T PRK00215 23 PPSRREIADALGLRSPSAVHEHLKALERK 51 (205)
T ss_pred CCCHHHHHHHhCCCChHHHHHHHHHHHHC
Confidence 3589999999999 999999999988755
No 275
>PF12728 HTH_17: Helix-turn-helix domain
Probab=73.55 E-value=3.6 Score=26.21 Aligned_cols=23 Identities=22% Similarity=0.475 Sum_probs=20.1
Q ss_pred CcHHHHHhhhCCChhhHHHHHHH
Q psy4300 47 LSMRKIGDQFNLADSTVWSCIDS 69 (307)
Q Consensus 47 ~~~~~l~~~fgvs~stv~r~v~~ 69 (307)
.+..++|..+|||.+|+.+++++
T Consensus 2 lt~~e~a~~l~is~~tv~~~~~~ 24 (51)
T PF12728_consen 2 LTVKEAAELLGISRSTVYRWIRQ 24 (51)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHc
Confidence 46789999999999999998864
No 276
>PF13701 DDE_Tnp_1_4: Transposase DDE domain group 1
Probab=73.49 E-value=37 Score=32.65 Aligned_cols=122 Identities=10% Similarity=-0.054 Sum_probs=68.9
Q ss_pred CCCCCHHHHHHHHHHHHhcC-CcHHHHHh---------hhC----------CChhhHHHHHHHHHHHccccccccccccC
Q psy4300 27 VPFVPVEKKTLVALSYMATQ-LSMRKIGD---------QFN----------LADSTVWSCIDSFLTAMSQPQIQCQYIKW 86 (307)
Q Consensus 27 ~~~~~~~~~l~i~L~~L~~g-~~~~~l~~---------~fg----------vs~stv~r~v~~~~~~l~~~l~~~~~i~~ 86 (307)
.-..+..+.|...++-+..| ....++.. .+| -|++|++|..+.+...-...+ ..
T Consensus 52 ~~~h~~~~ll~q~i~~i~~Gyed~~d~~~LR~Dp~f~~~~g~~~~~~~~~Las~~t~sR~e~~~~~~~~~~~-~~----- 125 (448)
T PF13701_consen 52 YVRHSLEDLLRQRIFQIAAGYEDDNDADRLRHDPVFKLALGRLPEPGSDRLASQPTLSRLENRPDERDLKRL-RR----- 125 (448)
T ss_pred cccCcHHHHHHHHHHHHHccCCChHHHHHhccCHHHHHHhccCCCCccccccchhhHHHHHccccHHHHHHH-HH-----
Confidence 45678888887777655444 44433332 122 567787776655433322221 11
Q ss_pred CChHHHHHHHHHHHHh--hCCCCcceeecceeEEeecCCCC-ccccccccCCcceeEEeeeC-CCcceEeeeeccccccC
Q psy4300 87 PTEEESVIIERNFRAL--AKFPGVIGAIDGCHIEGKFSKDI-RNDYNNRKCTQSMILQGVCT-SNKLLTNIHVGCTGRNH 162 (307)
Q Consensus 87 P~~~~~~~~~~~f~~~--~~~p~~~g~iDgt~i~i~~P~~~-~~~y~~~k~~~s~~~q~v~d-~~g~i~~v~~~~~Gs~~ 162 (307)
.+.+.|-.. ..-..++-=||+|..++. ++. +..|..|++.++..-.++.+ ..|.++.+.. .||+.|
T Consensus 126 -------~~~~~~~~~~~~~~~~i~LDiD~T~~~~~--G~Qe~~~~n~y~g~~gY~PL~~f~g~~G~~l~a~L-RpGn~~ 195 (448)
T PF13701_consen 126 -------ALVDLFLASYKKPPKEIVLDIDSTVDDVH--GEQEGAVFNTYYGEDGYHPLVAFDGQTGYLLAAEL-RPGNVH 195 (448)
T ss_pred -------HHHHHHHHHhccccceEEEecccccccch--hhcccccccccCCCcccccceeccCCCCceEEEEc-cCCCCC
Confidence 122222111 122346677889976653 222 34566677777766666664 5888888755 899998
Q ss_pred CC
Q psy4300 163 DA 164 (307)
Q Consensus 163 D~ 164 (307)
-+
T Consensus 196 sa 197 (448)
T PF13701_consen 196 SA 197 (448)
T ss_pred hH
Confidence 86
No 277
>PRK09191 two-component response regulator; Provisional
Probab=73.30 E-value=20 Score=31.00 Aligned_cols=50 Identities=6% Similarity=0.084 Sum_probs=42.5
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
..+|...+-.+.|.++. |.++.++|...|+|.+||...+.+....+...+
T Consensus 87 ~~L~~~~r~v~~l~~~~-~~s~~eIA~~l~~s~~tV~~~l~ra~~~l~~~~ 136 (261)
T PRK09191 87 AGLTPLPRQAFLLTALE-GFSVEEAAEILGVDPAEAEALLDDARAEIARQV 136 (261)
T ss_pred HhCCHHHhHHHHHHHHh-cCCHHHHHHHHCCCHHHHHHHHHHHHHHHhccC
Confidence 35777777777777665 789999999999999999999999999888775
No 278
>PRK12679 cbl transcriptional regulator Cbl; Reviewed
Probab=73.28 E-value=7 Score=35.31 Aligned_cols=45 Identities=7% Similarity=0.062 Sum_probs=39.5
Q ss_pred HHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 34 KKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 34 ~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
++|-.++....+|.|+...|...++|+||+|+.+++.-..+-..|
T Consensus 4 ~~l~~f~~v~~~~~s~s~AA~~L~iSQ~avSr~I~~LE~~lg~~L 48 (316)
T PRK12679 4 QQLKIIREAARQDYNLTEVANMLFTSQSGVSRHIRELEDELGIEI 48 (316)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHhcCCchHHHHHHHHHHHHhCCEE
Confidence 456667777778889999999999999999999999999988876
No 279
>PRK09492 treR trehalose repressor; Provisional
Probab=73.25 E-value=2.3 Score=38.10 Aligned_cols=23 Identities=22% Similarity=0.359 Sum_probs=21.0
Q ss_pred CcHHHHHhhhCCChhhHHHHHHH
Q psy4300 47 LSMRKIGDQFNLADSTVWSCIDS 69 (307)
Q Consensus 47 ~~~~~l~~~fgvs~stv~r~v~~ 69 (307)
.+..+||..+|||.+||||+++.
T Consensus 5 ~ti~dIA~~agVS~~TVSrvLn~ 27 (315)
T PRK09492 5 LTIKDIARLSGVGKSTVSRVLNN 27 (315)
T ss_pred CcHHHHHHHhCCCHHHHhHHhCC
Confidence 57899999999999999999974
No 280
>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=73.18 E-value=3.1 Score=30.65 Aligned_cols=30 Identities=17% Similarity=0.151 Sum_probs=22.6
Q ss_pred cHHHHHhhhCCChhhHHHHHHH--HHHHcccc
Q psy4300 48 SMRKIGDQFNLADSTVWSCIDS--FLTAMSQP 77 (307)
Q Consensus 48 ~~~~l~~~fgvs~stv~r~v~~--~~~~l~~~ 77 (307)
-+.-||..||+|.||++|+... .-+|+.+.
T Consensus 47 G~~GlAklfgcSv~Ta~RiK~sG~id~AI~Q~ 78 (96)
T PF12964_consen 47 GLKGLAKLFGCSVPTANRIKKSGKIDPAITQI 78 (96)
T ss_pred hHHHHHHHhCCCchhHHHHHhcCCccHHHHHc
Confidence 3678999999999999999874 22444444
No 281
>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=73.10 E-value=8.7 Score=32.08 Aligned_cols=43 Identities=0% Similarity=-0.011 Sum_probs=35.0
Q ss_pred CCCCCHHHHHHHHHHHHh-cCCcHHHHHhhhCCChhhHHHHHHH
Q psy4300 27 VPFVPVEKKTLVALSYMA-TQLSMRKIGDQFNLADSTVWSCIDS 69 (307)
Q Consensus 27 ~~~~~~~~~l~i~L~~L~-~g~~~~~l~~~fgvs~stv~r~v~~ 69 (307)
+..+++.++...+...+. .|.+..++|..+|+|+++|++.+.-
T Consensus 100 r~~lt~~e~a~~~~~l~~~~g~s~~~iA~~lg~s~~~V~r~l~l 143 (187)
T TIGR00180 100 REDLSPIEEAQAYKRLLEKFSMTQEDLAKKIGKSRAHITNLLRL 143 (187)
T ss_pred ccCCCHHHHHHHHHHHHHHhCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 457888887766666664 6899999999999999999998764
No 282
>PF03333 PapB: Adhesin biosynthesis transcription regulatory protein; InterPro: IPR004356 P pili, or fimbriae, are ~68A in diameter and 1 micron in length, the bulk of which is a fibre composed of the main structural protein PapA []. At its tip, the pilus is terminated by a fibrillum consisting of repeating units of the PapE protein. This, in turn, is topped by the adhesins, PapF and PapG, both of which are needed for receptor binding. The tip fibrillum is anchored to the main PapA fibre by the PapK pilus-adaptor protein. PapH, an outer membrane protein, then anchors the entire rod in the bacterial envelope []. A cytoplasmic chaperone (PapD) assists in assembling the monomers of the macromolecule in the membrane. All of the functional pap genes are arranged in a cluster (operon) on the Escherichia coli genome. It is believed that selective pressure exerted by the host's urinal and intestinal tract isoreceptors forced the spread of this operon to other strains via lateral transfer []. PapB, encoded within the cluster, acts as a transcriptional regulator of the functional pap genes and is located in the bacterial cytoplasm []. Its mechanism involves differential binding to separate sites in the cluster, suggesting that this protein is both an activator and repressor of pilus-adhesion transcription. The protein shares similarity with other E. coli fimbrial- adhesion transcription regulators, such as AfaA, DaaA and FanB. ; GO: 0006355 regulation of transcription, DNA-dependent; PDB: 3M8J_A.
Probab=72.97 E-value=24 Score=25.90 Aligned_cols=37 Identities=19% Similarity=0.318 Sum_probs=26.0
Q ss_pred HHHHHHH-HHhcCCcHHHHHhhhCCChhhHHHHHHHHH
Q psy4300 35 KTLVALS-YMATQLSMRKIGDQFNLADSTVWSCIDSFL 71 (307)
Q Consensus 35 ~l~i~L~-~L~~g~~~~~l~~~fgvs~stv~r~v~~~~ 71 (307)
++..+|+ ||-.|.+-.+++..+||+++-+++.+.++-
T Consensus 41 kiI~AL~dyLV~G~srkeac~~~gV~~syfs~~L~rL~ 78 (91)
T PF03333_consen 41 KIIAALRDYLVDGLSRKEACERHGVNQSYFSRALNRLN 78 (91)
T ss_dssp HHHHHHHHHHTT---HHHHHHHTT--HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHcCCcHHHHHHHhCCCHHHHHHHHHHHH
Confidence 3444454 899999999999999999999999888753
No 283
>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=72.82 E-value=5.3 Score=26.46 Aligned_cols=25 Identities=16% Similarity=0.372 Sum_probs=22.3
Q ss_pred cHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300 48 SMRKIGDQFNLADSTVWSCIDSFLT 72 (307)
Q Consensus 48 ~~~~l~~~fgvs~stv~r~v~~~~~ 72 (307)
+..+++..|++|++++++.+.++.+
T Consensus 27 ~~~~la~~~~is~~~v~~~l~~L~~ 51 (66)
T cd07377 27 SERELAEELGVSRTTVREALRELEA 51 (66)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 5889999999999999999888765
No 284
>PRK11233 nitrogen assimilation transcriptional regulator; Provisional
Probab=72.63 E-value=7.7 Score=34.78 Aligned_cols=43 Identities=7% Similarity=0.138 Sum_probs=35.3
Q ss_pred HHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 35 KTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 35 ~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
+|-.++....+| |++..|...++|+||||+.++++-..+-..|
T Consensus 5 ~L~~F~~v~~~~-S~s~AA~~L~isQ~avS~~I~~LE~~lg~~L 47 (305)
T PRK11233 5 RLKYFVKIVDIG-SLTQAAEVLHIAQPALSQQVATLEGELNQQL 47 (305)
T ss_pred HHHHHHHHHHcC-CHHHHHHHhCCCchHHHHHHHHHHHHhCCce
Confidence 444455445554 9999999999999999999999999988876
No 285
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=72.45 E-value=6.7 Score=34.25 Aligned_cols=48 Identities=15% Similarity=0.155 Sum_probs=39.8
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
..+++.++= +|.|++.|.+..++|...+||..||...+..+..-|-..
T Consensus 178 ~~LT~rE~e--vl~~~a~G~t~~eIa~~l~is~~TV~~h~~~~~~KL~~~ 225 (240)
T PRK10188 178 MNFSKREKE--ILKWTAEGKTSAEIAMILSISENTVNFHQKNMQKKFNAP 225 (240)
T ss_pred CCCCHHHHH--HHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Confidence 457776664 566679999999999999999999999999887776654
No 286
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=72.33 E-value=7.1 Score=33.26 Aligned_cols=47 Identities=15% Similarity=0.244 Sum_probs=38.7
Q ss_pred CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
.+++.|+ =+|..++.|.+..++|...++|..||.....++..-+--.
T Consensus 134 ~LT~RE~--eVL~ll~~G~snkeIA~~L~iS~~TV~~h~~~I~~KLgv~ 180 (207)
T PRK11475 134 MLSPTER--EILRFMSRGYSMPQIAEQLERNIKTIRAHKFNVMSKLGVS 180 (207)
T ss_pred CCCHHHH--HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCCC
Confidence 4676665 5677889999999999999999999999998886665543
No 287
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=72.19 E-value=10 Score=33.74 Aligned_cols=92 Identities=13% Similarity=0.021 Sum_probs=59.7
Q ss_pred CCCCHHHHHHHHHHHHhc---CCcHHHHHhhhCCChhhHHHHHHHHHHHccccc--cccccc------c--------CCC
Q psy4300 28 PFVPVEKKTLVALSYMAT---QLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ--IQCQYI------K--------WPT 88 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~---g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l--~~~~~i------~--------~P~ 88 (307)
..++.-++.+-.|..++. +.+..+|+...|+++||++|+++.++..=+-.. ....|. . .+-
T Consensus 19 ~~~~sl~r~l~IL~~~~~~~~~~tl~eIa~~lglpkStv~RlL~tL~~~G~l~~~~~~~~Y~lG~~l~~Lg~~~~~~~~l 98 (271)
T PRK10163 19 KGAQALERGIAILQYLEKSGGSSSVSDISLNLDLPLSTTFRLLKVLQAADFVYQDSQLGWWHIGLGVFNVGAAYIHNRDV 98 (271)
T ss_pred ccchHHHHHHHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcCCCCeEEecHHHHHHHHHHHhcCCH
Confidence 457788888888888864 478999999999999999999998877432210 001110 0 000
Q ss_pred hHHHHHHHHHHHHhhCCCCcceeecceeEEe
Q psy4300 89 EEESVIIERNFRALAKFPGVIGAIDGCHIEG 119 (307)
Q Consensus 89 ~~~~~~~~~~f~~~~~~p~~~g~iDgt~i~i 119 (307)
.+.....+....+..+..-.+++.|+.++-+
T Consensus 99 ~~~a~p~l~~La~~~getv~l~v~~g~~~v~ 129 (271)
T PRK10163 99 LSVAGPFMRRLMLLSGETVNVAIRNGNEAVL 129 (271)
T ss_pred HHHHHHHHHHHHHHHCCeEEEEEEECCEEEE
Confidence 0112234445555567777888999886654
No 288
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=72.17 E-value=10 Score=24.99 Aligned_cols=39 Identities=15% Similarity=0.231 Sum_probs=32.5
Q ss_pred HHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 39 ALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 39 ~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
.+.+++.|.+..++|..+++|..||......+..-+-..
T Consensus 12 v~~l~~~G~s~~eia~~l~is~~tV~~h~~~i~~Kl~~~ 50 (65)
T COG2771 12 ILRLVAQGKSNKEIARILGISEETVKTHLRNIYRKLGVK 50 (65)
T ss_pred HHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCC
Confidence 466788899999999999999999998888876555444
No 289
>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=72.12 E-value=11 Score=32.70 Aligned_cols=49 Identities=12% Similarity=0.127 Sum_probs=41.0
Q ss_pred CCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 27 VPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 27 ~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
...++..++=.+.+ .+.|.++.++|..+|+|.+||...+.+...-+...
T Consensus 169 ~~~Lt~re~evl~~--~a~G~t~~eIa~~l~is~~Tv~~~l~~~~~kl~~~ 217 (232)
T TIGR03541 169 AGVLSEREREVLAW--TALGRRQADIAAILGISERTVENHLRSARRKLGVA 217 (232)
T ss_pred hccCCHHHHHHHHH--HHCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHCCC
Confidence 45788877766666 58999999999999999999999999987776654
No 290
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=72.07 E-value=2.9 Score=37.76 Aligned_cols=22 Identities=14% Similarity=0.193 Sum_probs=19.9
Q ss_pred cHHHHHhhhCCChhhHHHHHHH
Q psy4300 48 SMRKIGDQFNLADSTVWSCIDS 69 (307)
Q Consensus 48 ~~~~l~~~fgvs~stv~r~v~~ 69 (307)
+..++|...|||.+||||+++.
T Consensus 2 ti~dIA~~aGVS~~TVSrvLn~ 23 (328)
T PRK11303 2 KLDEIARLAGVSRTTASYVING 23 (328)
T ss_pred CHHHHHHHhCCCHHHHHHHHcC
Confidence 5789999999999999999874
No 291
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=72.07 E-value=9.5 Score=29.40 Aligned_cols=40 Identities=5% Similarity=0.110 Sum_probs=30.2
Q ss_pred HHHHHHHHHHhc-CCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300 34 KKTLVALSYMAT-QLSMRKIGDQFNLADSTVWSCIDSFLTA 73 (307)
Q Consensus 34 ~~l~i~L~~L~~-g~~~~~l~~~fgvs~stv~r~v~~~~~~ 73 (307)
.++.|....... ..+..+++..++++++|+++.++...++
T Consensus 17 tRl~IL~~L~~~~~~~v~ela~~l~lsqstvS~HL~~L~~A 57 (117)
T PRK10141 17 TRLGIVLLLRESGELCVCDLCTALDQSQPKISRHLALLRES 57 (117)
T ss_pred HHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 344444433333 4688999999999999999999988766
No 292
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=72.05 E-value=7 Score=33.51 Aligned_cols=47 Identities=13% Similarity=0.233 Sum_probs=37.0
Q ss_pred CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
.+++.++=. |.+++.|.+..++|..+++|..||...+.+...-+.-.
T Consensus 155 ~Lt~rE~~V--l~l~~~G~s~~eIA~~L~iS~~TVk~~~~~i~~Kl~v~ 201 (216)
T PRK10100 155 LLTHREKEI--LNKLRIGASNNEIARSLFISENTVKTHLYNLFKKIAVK 201 (216)
T ss_pred CCCHHHHHH--HHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Confidence 467655544 45566699999999999999999999998887666554
No 293
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=71.96 E-value=3 Score=37.91 Aligned_cols=23 Identities=13% Similarity=0.173 Sum_probs=21.0
Q ss_pred CcHHHHHhhhCCChhhHHHHHHH
Q psy4300 47 LSMRKIGDQFNLADSTVWSCIDS 69 (307)
Q Consensus 47 ~~~~~l~~~fgvs~stv~r~v~~ 69 (307)
.+..+||..+|||.+||||+++.
T Consensus 7 ~Ti~dIA~~agVS~~TVSr~Ln~ 29 (342)
T PRK10014 7 ITIHDVALAAGVSVSTVSLVLSG 29 (342)
T ss_pred CcHHHHHHHhCCCHHHHHHHHCC
Confidence 57899999999999999999874
No 294
>PRK09483 response regulator; Provisional
Probab=71.95 E-value=7.1 Score=32.47 Aligned_cols=47 Identities=15% Similarity=0.203 Sum_probs=38.7
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccc
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQ 76 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~ 76 (307)
..++..+.=.+ .++..|.+..++|..+++|.+||..++.+...-+--
T Consensus 147 ~~Lt~rE~~vl--~~~~~G~~~~~Ia~~l~is~~TV~~~~~~i~~Kl~v 193 (217)
T PRK09483 147 ASLSERELQIM--LMITKGQKVNEISEQLNLSPKTVNSYRYRMFSKLNI 193 (217)
T ss_pred cccCHHHHHHH--HHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHcCC
Confidence 45788776654 567899999999999999999999999888776644
No 295
>PRK09526 lacI lac repressor; Reviewed
Probab=71.73 E-value=2.8 Score=38.04 Aligned_cols=23 Identities=9% Similarity=0.181 Sum_probs=20.8
Q ss_pred CcHHHHHhhhCCChhhHHHHHHH
Q psy4300 47 LSMRKIGDQFNLADSTVWSCIDS 69 (307)
Q Consensus 47 ~~~~~l~~~fgvs~stv~r~v~~ 69 (307)
.+..++|...|||.+||||+++.
T Consensus 6 ~ti~dIA~~aGVS~~TVSrvLn~ 28 (342)
T PRK09526 6 VTLYDVARYAGVSYQTVSRVLNQ 28 (342)
T ss_pred CcHHHHHHHhCCCHHHHHHHhcC
Confidence 47889999999999999999974
No 296
>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=71.68 E-value=6.2 Score=24.18 Aligned_cols=26 Identities=8% Similarity=0.148 Sum_probs=20.2
Q ss_pred hcCCcHHHHHhhhCCChhhHHHHHHH
Q psy4300 44 ATQLSMRKIGDQFNLADSTVWSCIDS 69 (307)
Q Consensus 44 ~~g~~~~~l~~~fgvs~stv~r~v~~ 69 (307)
.++......|...|||++|+++-+.+
T Consensus 16 ~~~gn~~~aA~~Lgisr~tL~~klkk 41 (42)
T PF02954_consen 16 RCGGNVSKAARLLGISRRTLYRKLKK 41 (42)
T ss_dssp HTTT-HHHHHHHHTS-HHHHHHHHHH
T ss_pred HhCCCHHHHHHHHCCCHHHHHHHHHh
Confidence 45667899999999999999987764
No 297
>PRK10870 transcriptional repressor MprA; Provisional
Probab=71.16 E-value=15 Score=30.46 Aligned_cols=45 Identities=4% Similarity=-0.023 Sum_probs=30.7
Q ss_pred CCCCHHHHHH-HHHHHHhc-CCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300 28 PFVPVEKKTL-VALSYMAT-QLSMRKIGDQFNLADSTVWSCIDSFLT 72 (307)
Q Consensus 28 ~~~~~~~~l~-i~L~~L~~-g~~~~~l~~~fgvs~stv~r~v~~~~~ 72 (307)
..++..+-.. ..|+.... +.+..+||..++++++|+++++++...
T Consensus 51 ~gLt~~q~~iL~~L~~~~~~~it~~eLa~~l~l~~~tvsr~v~rLe~ 97 (176)
T PRK10870 51 QGINETLFMALITLESQENHSIQPSELSCALGSSRTNATRIADELEK 97 (176)
T ss_pred CCCCHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4566654333 33322222 467899999999999999999988754
No 298
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=71.09 E-value=7.5 Score=33.18 Aligned_cols=47 Identities=21% Similarity=0.360 Sum_probs=39.2
Q ss_pred CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
.++.++. -.|..|+.|.+-.++|...++|.+||...+.+...-|.-.
T Consensus 148 ~LT~RE~--eVL~lla~G~snkeIA~~L~iS~~TVk~h~~~i~~KL~v~ 194 (211)
T COG2197 148 LLTPREL--EVLRLLAEGLSNKEIAEELNLSEKTVKTHVSNILRKLGVR 194 (211)
T ss_pred CCCHHHH--HHHHHHHCCCCHHHHHHHHCCCHhHHHHHHHHHHHHcCCC
Confidence 4666554 4577899999999999999999999999999887776655
No 299
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=70.92 E-value=15 Score=29.60 Aligned_cols=45 Identities=9% Similarity=0.174 Sum_probs=33.3
Q ss_pred CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300 29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTA 73 (307)
Q Consensus 29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~ 73 (307)
.++..++-.+.+..-..-.||.+||...|+|++||.+-++++.+.
T Consensus 6 ~lD~~D~~Il~~Lq~d~R~s~~eiA~~lglS~~tV~~Ri~rL~~~ 50 (153)
T PRK11179 6 QIDNLDRGILEALMENARTPYAELAKQFGVSPGTIHVRVEKMKQA 50 (153)
T ss_pred ccCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 455555544444444455899999999999999999988887654
No 300
>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=70.92 E-value=2.8 Score=26.70 Aligned_cols=18 Identities=17% Similarity=0.207 Sum_probs=16.1
Q ss_pred HHHhhhCCChhhHHHHHH
Q psy4300 51 KIGDQFNLADSTVWSCID 68 (307)
Q Consensus 51 ~l~~~fgvs~stv~r~v~ 68 (307)
++|...|||++||+++++
T Consensus 2 ~lA~~~gvs~~tvs~~l~ 19 (52)
T cd01392 2 DIARAAGVSVATVSRVLN 19 (52)
T ss_pred cHHHHHCcCHHHHHHHHc
Confidence 689999999999999875
No 301
>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=70.47 E-value=9.4 Score=33.33 Aligned_cols=91 Identities=11% Similarity=0.120 Sum_probs=57.0
Q ss_pred CCCHHHHHHHHHHHHhc---CCcHHHHHhhhCCChhhHHHHHHHHHHHccccccccccccCC--------------ChHH
Q psy4300 29 FVPVEKKTLVALSYMAT---QLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQIQCQYIKWP--------------TEEE 91 (307)
Q Consensus 29 ~~~~~~~l~i~L~~L~~---g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l~~~~~i~~P--------------~~~~ 91 (307)
.++.-++.+-.|..++. +.+..+|+...|+++||++|++......=+-.--...|.-=| -.+.
T Consensus 4 ~v~sl~ral~IL~~l~~~~~~~~l~eia~~lglpksT~~RlL~tL~~~G~l~~~~~~Y~lG~~~~~lg~~~~~~~~l~~~ 83 (248)
T TIGR02431 4 FVASLARGLAVIEAFGAERPRLTLTDVAEATGLTRAAARRFLLTLVELGYVTSDGRLFWLTPRVLRLGYAYLSSAPLPKV 83 (248)
T ss_pred hHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeCCCEEEecHHHHHHHHHHHhcCchHHH
Confidence 35556677777777753 579999999999999999999998765422220011121000 0111
Q ss_pred HHHHHHHHHHhhCCCCcceeecceeEEe
Q psy4300 92 SVIIERNFRALAKFPGVIGAIDGCHIEG 119 (307)
Q Consensus 92 ~~~~~~~f~~~~~~p~~~g~iDgt~i~i 119 (307)
....+..+.+..+..-.+++.||.++-+
T Consensus 84 a~p~l~~L~~~~g~tv~L~v~~g~~~v~ 111 (248)
T TIGR02431 84 AQPLLERLSAQTHESCSVAVLDGDEIVY 111 (248)
T ss_pred HHHHHHHHHHHHCCeEEEEEEeCCEEEE
Confidence 2244555555567777888888876533
No 302
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=70.07 E-value=14 Score=30.92 Aligned_cols=44 Identities=11% Similarity=0.102 Sum_probs=34.4
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHH
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFL 71 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~ 71 (307)
..+++.+-..+...+-..|.+..+||...+++++|+++++++..
T Consensus 41 ~gLt~~q~~iL~~L~~~~~itq~eLa~~l~l~~sTvtr~l~rLE 84 (185)
T PRK13777 41 YDLNINEHHILWIAYHLKGASISEIAKFGVMHVSTAFNFSKKLE 84 (185)
T ss_pred CCCCHHHHHHHHHHHhCCCcCHHHHHHHHCCCHhhHHHHHHHHH
Confidence 45777666555555556689999999999999999999888764
No 303
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=69.99 E-value=2.8 Score=37.96 Aligned_cols=23 Identities=13% Similarity=0.267 Sum_probs=20.5
Q ss_pred CcHHHHHhhhCCChhhHHHHHHH
Q psy4300 47 LSMRKIGDQFNLADSTVWSCIDS 69 (307)
Q Consensus 47 ~~~~~l~~~fgvs~stv~r~v~~ 69 (307)
.+..++|...|||.+||||+++.
T Consensus 6 ~ti~dIA~~agVS~~TVSrvLn~ 28 (331)
T PRK14987 6 PVLQDVADRVGVTKMTVSRFLRN 28 (331)
T ss_pred CcHHHHHHHhCCCHHHhhhhhCC
Confidence 47889999999999999999863
No 304
>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=69.82 E-value=18 Score=27.70 Aligned_cols=29 Identities=10% Similarity=-0.087 Sum_probs=24.7
Q ss_pred HHHHhcCCcHHHHHhhhCCChhhHHHHHH
Q psy4300 40 LSYMATQLSMRKIGDQFNLADSTVWSCID 68 (307)
Q Consensus 40 L~~L~~g~~~~~l~~~fgvs~stv~r~v~ 68 (307)
-.+-..|.+..++|..+|+|++|+++|-+
T Consensus 72 ~~r~~~gltq~~lA~~lg~~~~tis~~e~ 100 (127)
T TIGR03830 72 RIRKKLGLSQREAAELLGGGVNAFSRYER 100 (127)
T ss_pred HHHHHcCCCHHHHHHHhCCCHHHHHHHHC
Confidence 33556799999999999999999999754
No 305
>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=69.52 E-value=18 Score=24.59 Aligned_cols=27 Identities=22% Similarity=0.332 Sum_probs=20.5
Q ss_pred CCcHHHHHhhhCCC-hhhHHHHHHHHHH
Q psy4300 46 QLSMRKIGDQFNLA-DSTVWSCIDSFLT 72 (307)
Q Consensus 46 g~~~~~l~~~fgvs-~stv~r~v~~~~~ 72 (307)
..+.++|+..||++ .+||++.+.....
T Consensus 25 ~Pt~rEIa~~~g~~S~~tv~~~L~~Le~ 52 (65)
T PF01726_consen 25 PPTVREIAEALGLKSTSTVQRHLKALER 52 (65)
T ss_dssp ---HHHHHHHHTSSSHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHhCCCChHHHHHHHHHHHH
Confidence 37899999999996 9999888877643
No 306
>PRK10072 putative transcriptional regulator; Provisional
Probab=69.52 E-value=4.9 Score=29.80 Aligned_cols=27 Identities=11% Similarity=0.065 Sum_probs=23.6
Q ss_pred HHhcCCcHHHHHhhhCCChhhHHHHHH
Q psy4300 42 YMATQLSMRKIGDQFNLADSTVWSCID 68 (307)
Q Consensus 42 ~L~~g~~~~~l~~~fgvs~stv~r~v~ 68 (307)
+-..|.++..+|..+|+|.+||++|.+
T Consensus 42 R~~~glTQ~elA~~lGvS~~TVs~WE~ 68 (96)
T PRK10072 42 RKGTGLKIDDFARVLGVSVAMVKEWES 68 (96)
T ss_pred HHHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 346699999999999999999999765
No 307
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=69.14 E-value=3.4 Score=37.52 Aligned_cols=22 Identities=14% Similarity=0.365 Sum_probs=20.2
Q ss_pred cHHHHHhhhCCChhhHHHHHHH
Q psy4300 48 SMRKIGDQFNLADSTVWSCIDS 69 (307)
Q Consensus 48 ~~~~l~~~fgvs~stv~r~v~~ 69 (307)
+..+||...|||++||||+++.
T Consensus 3 Ti~dIA~~agVS~~TVSrvLn~ 24 (341)
T PRK10703 3 TIKDVAKRAGVSTTTVSHVINK 24 (341)
T ss_pred CHHHHHHHhCCCHHHHHHHHcC
Confidence 6789999999999999999874
No 308
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=69.10 E-value=9.7 Score=34.32 Aligned_cols=45 Identities=4% Similarity=0.026 Sum_probs=38.9
Q ss_pred HHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 34 KKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 34 ~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
.+|-+++....+|.|++..|...++|++++|+.+++.-..+-..|
T Consensus 4 ~~L~~f~~v~~~g~S~s~AA~~L~isQpavS~~ik~LE~~lg~~L 48 (313)
T PRK12684 4 HQLRFVREAVRQNFNLTEAAKALYTSQPGVSKAIIELEDELGVEI 48 (313)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHhcCCChHHHHHHHHHHHHhCCee
Confidence 356666666677779999999999999999999999999998887
No 309
>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=69.08 E-value=14 Score=32.49 Aligned_cols=49 Identities=8% Similarity=0.180 Sum_probs=40.3
Q ss_pred CCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 27 VPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 27 ~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
...++..++=.+.| ++.|.+..++|..++||..||...+.+...-+-..
T Consensus 188 ~~~LT~RE~evl~l--~a~G~s~~eIA~~L~IS~~TVk~hl~~i~~KL~v~ 236 (247)
T TIGR03020 188 AGLITAREAEILAW--VRDGKTNEEIAAILGISSLTVKNHLQHIFKKLDVR 236 (247)
T ss_pred ccCCCHHHHHHHHH--HHCCCCHHHHHHHHCcCHHHHHHHHHHHHHHhCCC
Confidence 45788888777775 57999999999999999999999998886655443
No 310
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=68.96 E-value=3.4 Score=37.69 Aligned_cols=22 Identities=18% Similarity=0.345 Sum_probs=20.0
Q ss_pred cHHHHHhhhCCChhhHHHHHHH
Q psy4300 48 SMRKIGDQFNLADSTVWSCIDS 69 (307)
Q Consensus 48 ~~~~l~~~fgvs~stv~r~v~~ 69 (307)
+..+||...|||.+||||+++.
T Consensus 3 ti~dIA~~aGVS~~TVSrvLn~ 24 (346)
T PRK10401 3 TIRDVARQAGVSVATVSRVLNN 24 (346)
T ss_pred CHHHHHHHhCCCHHHHHHHHCC
Confidence 6789999999999999999973
No 311
>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=68.94 E-value=14 Score=25.67 Aligned_cols=27 Identities=19% Similarity=0.308 Sum_probs=23.6
Q ss_pred HHhcCCcHHHHHhhhCCChhhHHHHHH
Q psy4300 42 YMATQLSMRKIGDQFNLADSTVWSCID 68 (307)
Q Consensus 42 ~L~~g~~~~~l~~~fgvs~stv~r~v~ 68 (307)
.-..|.+..++|...|+|++|++++.+
T Consensus 14 ~~~~~~t~~~lA~~~gis~~tis~~~~ 40 (78)
T TIGR02607 14 LEPLGLSIRALAKALGVSRSTLSRIVN 40 (78)
T ss_pred HHHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 356789999999999999999999765
No 312
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=67.89 E-value=3.2 Score=37.54 Aligned_cols=22 Identities=14% Similarity=0.243 Sum_probs=19.9
Q ss_pred cHHHHHhhhCCChhhHHHHHHH
Q psy4300 48 SMRKIGDQFNLADSTVWSCIDS 69 (307)
Q Consensus 48 ~~~~l~~~fgvs~stv~r~v~~ 69 (307)
+..+||...|||++||||+++.
T Consensus 3 ti~dIA~~agVS~~TVSrvln~ 24 (327)
T PRK10339 3 TLKDIAIEAGVSLATVSRVLND 24 (327)
T ss_pred CHHHHHHHhCCCHHhhhhhhcC
Confidence 5789999999999999999864
No 313
>PRK11569 transcriptional repressor IclR; Provisional
Probab=67.44 E-value=15 Score=32.59 Aligned_cols=46 Identities=17% Similarity=0.261 Sum_probs=38.7
Q ss_pred CCCCHHHHHHHHHHHHhc---CCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300 28 PFVPVEKKTLVALSYMAT---QLSMRKIGDQFNLADSTVWSCIDSFLTA 73 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~---g~~~~~l~~~fgvs~stv~r~v~~~~~~ 73 (307)
..+..-++.+-.|.+|+. +.+..+|+...|+++||++|++......
T Consensus 22 ~~v~sl~ral~IL~~l~~~~~~~~lseia~~lglpksTv~RlL~tL~~~ 70 (274)
T PRK11569 22 GQVQSLTRGLKLLEWIAESNGSVALTELAQQAGLPNSTTHRLLTTMQQQ 70 (274)
T ss_pred cCccHHHHHHHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 456778888888888864 4799999999999999999999987654
No 314
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=67.31 E-value=11 Score=33.20 Aligned_cols=45 Identities=13% Similarity=0.152 Sum_probs=36.6
Q ss_pred CCCHHHHHHHHHHHHhc---CCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300 29 FVPVEKKTLVALSYMAT---QLSMRKIGDQFNLADSTVWSCIDSFLTA 73 (307)
Q Consensus 29 ~~~~~~~l~i~L~~L~~---g~~~~~l~~~fgvs~stv~r~v~~~~~~ 73 (307)
.+..-++.+-.|..|+. +.+..+|+..+|+++||++|+++.+...
T Consensus 6 ~v~sl~ral~iL~~l~~~~~~ls~~eia~~lgl~kstv~RlL~tL~~~ 53 (263)
T PRK09834 6 TVRGLSRGLMVLRALNRLDGGATVGLLAELTGLHRTTVRRLLETLQEE 53 (263)
T ss_pred hHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 45566777777888753 3789999999999999999999987654
No 315
>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=67.20 E-value=12 Score=33.16 Aligned_cols=43 Identities=12% Similarity=0.067 Sum_probs=35.2
Q ss_pred HHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 35 KTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 35 ~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
+|-.++....+| +++..|...++|+|++++-+++.-..+-..|
T Consensus 5 ~L~~f~~v~~~g-s~s~AA~~L~itqpavS~~Ik~LE~~lg~~L 47 (291)
T TIGR03418 5 ALRVFESAARLA-SFTAAARELGSTQPAVSQQVKRLEEELGTPL 47 (291)
T ss_pred HHHHHHHHHHhC-CHHHHHHHhCCCHHHHHHHHHHHHHHhCcHH
Confidence 444555555554 8999999999999999999999998887776
No 316
>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=67.19 E-value=17 Score=30.71 Aligned_cols=35 Identities=14% Similarity=0.195 Sum_probs=27.9
Q ss_pred HHHHHHhc--CCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300 38 VALSYMAT--QLSMRKIGDQFNLADSTVWSCIDSFLT 72 (307)
Q Consensus 38 i~L~~L~~--g~~~~~l~~~fgvs~stv~r~v~~~~~ 72 (307)
..|.+|.. +.+..+++..+++|++|+++.+.....
T Consensus 147 ~IL~~l~~~g~~s~~eia~~l~is~stv~r~L~~Le~ 183 (203)
T TIGR01884 147 KVLEVLKAEGEKSVKNIAKKLGKSLSTISRHLRELEK 183 (203)
T ss_pred HHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 44555543 569999999999999999999988654
No 317
>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=67.03 E-value=13 Score=31.43 Aligned_cols=40 Identities=13% Similarity=0.164 Sum_probs=30.8
Q ss_pred HHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300 32 VEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLT 72 (307)
Q Consensus 32 ~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~ 72 (307)
...+++..|..- .+.+..+|+..+|++++||++.++.+..
T Consensus 2 tr~~IL~~L~~~-~~~t~~eLA~~lgis~~tV~~~L~~Le~ 41 (203)
T TIGR02702 2 TKEDILSYLLKQ-GQATAAALAEALAISPQAVRRHLKDLET 41 (203)
T ss_pred HHHHHHHHHHHc-CCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 345555555543 4599999999999999999999888744
No 318
>PRK10094 DNA-binding transcriptional activator AllS; Provisional
Probab=66.83 E-value=12 Score=33.68 Aligned_cols=44 Identities=11% Similarity=0.022 Sum_probs=35.7
Q ss_pred HHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 34 KKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 34 ~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
++|-+++....+ .+++..|...++|+|++|+.+++.-..+-..|
T Consensus 5 ~~L~~f~~v~e~-gs~s~AA~~L~iSQpavS~~I~~LE~~lg~~L 48 (308)
T PRK10094 5 ETLRTFIAVAET-GSFSKAAERLCKTTATISYRIKLLEENTGVAL 48 (308)
T ss_pred HHHHHHHHHHHh-CCHHHHHHHhcCCHHHHHHHHHHHHHHhCCEE
Confidence 344455555555 48999999999999999999999999988776
No 319
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=66.61 E-value=12 Score=33.48 Aligned_cols=44 Identities=9% Similarity=0.138 Sum_probs=36.9
Q ss_pred HHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 34 KKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 34 ~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
.+|-+++....+| |+...|...++|+|++|+.+++.-..+-..|
T Consensus 4 ~~L~~f~~v~~~g-S~s~AA~~L~itQpavS~~i~~LE~~lg~~L 47 (305)
T PRK11151 4 RDLEYLVALAEHR-HFRRAADSCHVSQPTLSGQIRKLEDELGVML 47 (305)
T ss_pred HHHHHHHHHHHhC-CHHHHHHHhCCCchHHHHHHHHHHHHhCchh
Confidence 3455566666666 9999999999999999999999999888776
No 320
>PRK04140 hypothetical protein; Provisional
Probab=66.45 E-value=9.4 Score=34.84 Aligned_cols=63 Identities=13% Similarity=0.162 Sum_probs=42.9
Q ss_pred CCHHH-HHHHHHHHhhhcCcccccCCCCCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHH
Q psy4300 1 MRKTT-FGFLVEALAAINGYETLYERGVPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCID 68 (307)
Q Consensus 1 ms~~~-F~~L~~~l~~~~~~~~~~~~~~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~ 68 (307)
|+.+| |.++++-..|.+ ... .+ .-.+...-..+ --.+-..|.++.++|...|+|++|+++|.+
T Consensus 98 ~~~~tl~~~~~~g~~p~v--~~~-~G-g~~v~i~GerL-k~lRe~~GlSq~eLA~~lGVSr~tIskyE~ 161 (317)
T PRK04140 98 LSPDTLYDDFVEGEPPLI--YAA-PG-GFYVKIDGDVL-REAREELGLSLGELASELGVSRRTISKYEN 161 (317)
T ss_pred ecHHHHHHHHhCCCCceE--EEc-CC-CeeehhhHHHH-HHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 57788 888887777764 122 22 33343332222 233677899999999999999999999765
No 321
>COG1508 RpoN DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription]
Probab=66.42 E-value=5 Score=38.15 Aligned_cols=27 Identities=22% Similarity=0.501 Sum_probs=23.3
Q ss_pred HHhcC------CcHHHHHhhhCCChhhHHHHHH
Q psy4300 42 YMATQ------LSMRKIGDQFNLADSTVWSCID 68 (307)
Q Consensus 42 ~L~~g------~~~~~l~~~fgvs~stv~r~v~ 68 (307)
||.+| ...+++|...|++.|||||++.
T Consensus 320 Ff~~g~~~l~PL~LrdvA~~i~~HESTISRai~ 352 (444)
T COG1508 320 FFEGGEEALKPLVLRDVADEIGMHESTISRAIT 352 (444)
T ss_pred HHhCCcccCCcccHHHHHHHhCccHHHHHHHHh
Confidence 45666 7789999999999999999874
No 322
>TIGR02417 fruct_sucro_rep D-fructose-responsive transcription factor. Members of this family belong the lacI helix-turn-helix family (pfam00356) of DNA-binding transcriptional regulators. All members are from the proteobacteria. Characterized members act as positive and negative transcriptional regulators of fructose and sucrose transport and metabolism. Sucrose is a disaccharide composed of fructose and glucose; D-fructose-1-phosphate rather than an intact sucrose moiety has been shown to act as the inducer.
Probab=66.41 E-value=4.1 Score=36.72 Aligned_cols=22 Identities=14% Similarity=0.229 Sum_probs=19.4
Q ss_pred cHHHHHhhhCCChhhHHHHHHH
Q psy4300 48 SMRKIGDQFNLADSTVWSCIDS 69 (307)
Q Consensus 48 ~~~~l~~~fgvs~stv~r~v~~ 69 (307)
+..++|...|||.+||||+++.
T Consensus 1 ti~dIA~~aGVS~~TVSrvLn~ 22 (327)
T TIGR02417 1 TLSDIAKLAGVSKTTASYVING 22 (327)
T ss_pred CHHHHHHHhCCCHHHHHHHHcC
Confidence 3579999999999999999864
No 323
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=65.97 E-value=22 Score=22.96 Aligned_cols=41 Identities=7% Similarity=0.182 Sum_probs=25.7
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHH
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDS 69 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~ 69 (307)
+.++..||--+-++ ...|.+..+++...|-|+.++.++++.
T Consensus 3 ~~Lt~~Eqaqid~m-~qlG~s~~~isr~i~RSr~~Ir~yl~d 43 (50)
T PF11427_consen 3 KTLTDAEQAQIDVM-HQLGMSLREISRRIGRSRTCIRRYLKD 43 (50)
T ss_dssp ----HHHHHHHHHH-HHTT--HHHHHHHHT--HHHHHHHHHS
T ss_pred CcCCHHHHHHHHHH-HHhchhHHHHHHHhCccHHHHHHHhcC
Confidence 45677676665553 455789999999999999999998763
No 324
>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]
Probab=65.92 E-value=16 Score=34.54 Aligned_cols=52 Identities=17% Similarity=0.226 Sum_probs=46.9
Q ss_pred CCCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 26 GVPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 26 ~~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
+.+.+...-|++|.|.+--+..|+..+|..||-.+|||.-.++.+...+.+-
T Consensus 345 R~~~i~~~RqiamyL~r~lt~~Slp~IG~~FgrdHtTV~~a~~kI~~~~~~d 396 (408)
T COG0593 345 RTRNIVRPRQIAMYLARELTNLSLPEIGKAFGRDHTTVLHAVRKIEQLIEED 396 (408)
T ss_pred cccccchHHHHHHHHHHHHccCcHHHHHHHhCCCccHHHHHHHHHHHHHhcC
Confidence 4677889999999999999999999999999999999999888888777664
No 325
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=65.91 E-value=16 Score=32.33 Aligned_cols=46 Identities=11% Similarity=0.104 Sum_probs=39.2
Q ss_pred CCCCCHHHHHHHHHHHHhcC-CcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300 27 VPFVPVEKKTLVALSYMATQ-LSMRKIGDQFNLADSTVWSCIDSFLT 72 (307)
Q Consensus 27 ~~~~~~~~~l~i~L~~L~~g-~~~~~l~~~fgvs~stv~r~v~~~~~ 72 (307)
...++..++-.+-+..=+.| ..+.+|.+..|.|++|++|++++...
T Consensus 190 ~~~L~~~e~~il~~i~~~GGri~Q~eL~r~lglsktTvsR~L~~LEk 236 (258)
T COG2512 190 EYDLNEDEKEILDLIRERGGRITQAELRRALGLSKTTVSRILRRLEK 236 (258)
T ss_pred cCCCCHHHHHHHHHHHHhCCEEeHHHHHHhhCCChHHHHHHHHHHHh
Confidence 46788888888877777777 88999999999999999999998743
No 326
>PRK12681 cysB transcriptional regulator CysB; Reviewed
Probab=65.67 E-value=12 Score=33.91 Aligned_cols=45 Identities=2% Similarity=0.044 Sum_probs=38.2
Q ss_pred HHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 34 KKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 34 ~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
.+|-.++....+|.|++..|...++|+|++|+.+++.-..+-..|
T Consensus 4 ~~L~~f~avae~g~S~s~AA~~L~iSQpavS~~I~~LE~~lG~~L 48 (324)
T PRK12681 4 QQLRYIVEVVNHNLNVSATAEGLYTSQPGISKQVRMLEDELGIQI 48 (324)
T ss_pred HHHHHHHHHHHccCCHHHHHHHhcCCcHHHHHHHHHHHHHhCCEe
Confidence 345556666667779999999999999999999999999988876
No 327
>PRK10651 transcriptional regulator NarL; Provisional
Probab=65.67 E-value=11 Score=30.91 Aligned_cols=47 Identities=19% Similarity=0.277 Sum_probs=38.7
Q ss_pred CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
.+++.+. =.|.++..|.+..++|..+++|..||..++.+...-|.-.
T Consensus 155 ~Lt~rE~--~vl~~l~~g~~~~~ia~~l~is~~tV~~~~~~l~~Kl~~~ 201 (216)
T PRK10651 155 QLTPRER--DILKLIAQGLPNKMIARRLDITESTVKVHVKHMLKKMKLK 201 (216)
T ss_pred cCCHHHH--HHHHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHHHHcCCC
Confidence 4777665 4556688999999999999999999999999987776544
No 328
>PF07453 NUMOD1: NUMOD1 domain; InterPro: IPR010896 This helix-turn-helix-containing DNA-binding domain is found associated in homing nucleases [].
Probab=65.47 E-value=5.3 Score=23.68 Aligned_cols=24 Identities=17% Similarity=0.229 Sum_probs=20.0
Q ss_pred hcCCcHHHHHhhhCCChhhHHHHH
Q psy4300 44 ATQLSMRKIGDQFNLADSTVWSCI 67 (307)
Q Consensus 44 ~~g~~~~~l~~~fgvs~stv~r~v 67 (307)
..-.|.++.+..+|++++|+++++
T Consensus 14 ~~F~Si~eAa~~l~i~~~~I~~~l 37 (37)
T PF07453_consen 14 KSFDSIREAARYLGISHSTISKYL 37 (37)
T ss_pred EEEcCHHHHHHHhCCCHHHHHHhC
Confidence 345688999999999999998763
No 329
>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=65.14 E-value=4.6 Score=36.42 Aligned_cols=22 Identities=9% Similarity=0.227 Sum_probs=19.9
Q ss_pred cHHHHHhhhCCChhhHHHHHHH
Q psy4300 48 SMRKIGDQFNLADSTVWSCIDS 69 (307)
Q Consensus 48 ~~~~l~~~fgvs~stv~r~v~~ 69 (307)
+..++|...|||.+||||+++.
T Consensus 3 ti~dIA~~agvS~~TVSrvLn~ 24 (329)
T TIGR01481 3 TIYDVAREAGVSMATVSRVVNG 24 (329)
T ss_pred cHHHHHHHhCCCHHHHHHHhCC
Confidence 6789999999999999999864
No 330
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=65.06 E-value=4.4 Score=36.93 Aligned_cols=22 Identities=14% Similarity=0.268 Sum_probs=19.9
Q ss_pred cHHHHHhhhCCChhhHHHHHHH
Q psy4300 48 SMRKIGDQFNLADSTVWSCIDS 69 (307)
Q Consensus 48 ~~~~l~~~fgvs~stv~r~v~~ 69 (307)
+..++|...|||.+||||+++.
T Consensus 3 ti~dIA~~aGVS~~TVSrvLn~ 24 (343)
T PRK10727 3 TIKDVARLAGVSVATVSRVINN 24 (343)
T ss_pred CHHHHHHHhCCCHHHHHHHhCC
Confidence 5789999999999999999863
No 331
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=65.03 E-value=14 Score=32.97 Aligned_cols=44 Identities=9% Similarity=0.146 Sum_probs=36.2
Q ss_pred HHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 34 KKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 34 ~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
.+|-.++....+| +++..|...++|+|++|+.++++-+.+-..|
T Consensus 8 ~~L~~f~~v~~~g-s~s~AA~~L~isQ~avS~~i~~LE~~lG~~L 51 (302)
T PRK09791 8 HQIRAFVEVARQG-SIRGASRMLNMSQPALTKSIQELEEGLAAQL 51 (302)
T ss_pred HHHHHHHHHHHcC-CHHHHHHHhCCChHHHHHHHHHHHHHhCCeE
Confidence 4455555555555 9999999999999999999999999888776
No 332
>PF05269 Phage_CII: Bacteriophage CII protein; InterPro: IPR007933 The CII protein is a transcription activator, conserved in bacteriophage lambda and related phages, that plays a key role in the decision between lytic or lysogenic phage development. CII is regulated at multiple levels including transcription, translation initiation, mRNA stability, and proteolysis []. Conditions that stabilise cII favour lysogenic development. The lambda CII protein activates three specific promoters, binding to direct repeat sequences rather than the more usual inverted repeats. Structurally, CII is a homotetramer where each monomer is composed of four alpha helices and a disordered C terminus [, ]. The alpha helical region is responsible for DNA binding and multimerisation. The homotetramer has an unusual spatial arrangement that allows recognition of the direct repeat sequences.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1ZS4_C 1ZPQ_C 1XWR_A.
Probab=64.83 E-value=7.9 Score=28.38 Aligned_cols=37 Identities=19% Similarity=0.402 Sum_probs=27.5
Q ss_pred HHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 40 LSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 40 L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
|..|+. .++..+|...|++.|||||+-..+++-+...
T Consensus 18 L~rlA~-~gq~~vA~~~Gv~eStISR~k~~~~~~~a~l 54 (91)
T PF05269_consen 18 LNRLAS-VGQKKVAEAMGVDESTISRWKNDFIEKMAML 54 (91)
T ss_dssp HHHHHH-HHHHHHHHHHTSSTTTHHHHHHHHHHHHHHH
T ss_pred HHHHHH-HhhHHHHHHhCCCHHHHHHHHhhHHHHHHHH
Confidence 344443 4688999999999999999987765555544
No 333
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=64.71 E-value=8.5 Score=27.95 Aligned_cols=25 Identities=16% Similarity=0.290 Sum_probs=22.2
Q ss_pred HHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300 49 MRKIGDQFNLADSTVWSCIDSFLTA 73 (307)
Q Consensus 49 ~~~l~~~fgvs~stv~r~v~~~~~~ 73 (307)
..++|..+|++++|+++.+.+....
T Consensus 2 ~~ela~~l~is~stvs~~l~~L~~~ 26 (96)
T smart00529 2 TSEIAERLNVSPPTVTQMLKKLEKD 26 (96)
T ss_pred HHHHHHHhCCChHHHHHHHHHHHHC
Confidence 5689999999999999999987764
No 334
>PRK13348 chromosome replication initiation inhibitor protein; Provisional
Probab=64.48 E-value=14 Score=32.70 Aligned_cols=43 Identities=16% Similarity=0.204 Sum_probs=34.9
Q ss_pred HHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 35 KTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 35 ~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
+|-.++....+ .+++..|...++|+|++|+.+++.-+.+-..|
T Consensus 6 ~L~~f~~v~~~-gs~t~AA~~L~iSQ~avS~~i~~LE~~lg~~L 48 (294)
T PRK13348 6 QLEALAAVVET-GSFERAARRLHVTPSAVSQRIKALEESLGQPL 48 (294)
T ss_pred HHHHHHHHHHc-CCHHHHHHHhCCCchHHHHHHHHHHHHhCcee
Confidence 34444444444 58999999999999999999999999888876
No 335
>PRK09726 antitoxin HipB; Provisional
Probab=64.47 E-value=10 Score=27.38 Aligned_cols=34 Identities=6% Similarity=0.141 Sum_probs=26.5
Q ss_pred HHHHHHHH--HhcCCcHHHHHhhhCCChhhHHHHHH
Q psy4300 35 KTLVALSY--MATQLSMRKIGDQFNLADSTVWSCID 68 (307)
Q Consensus 35 ~l~i~L~~--L~~g~~~~~l~~~fgvs~stv~r~v~ 68 (307)
.+..-|.. -..|.+..++|...|||++|++++.+
T Consensus 12 ~l~~~lk~~R~~~gltq~elA~~~gvs~~tis~~e~ 47 (88)
T PRK09726 12 QLANAMKLVRQQNGWTQSELAKKIGIKQATISNFEN 47 (88)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHC
Confidence 44444433 46789999999999999999998765
No 336
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=64.35 E-value=4.2 Score=36.61 Aligned_cols=19 Identities=21% Similarity=0.294 Sum_probs=17.8
Q ss_pred HHHHhhhCCChhhHHHHHH
Q psy4300 50 RKIGDQFNLADSTVWSCID 68 (307)
Q Consensus 50 ~~l~~~fgvs~stv~r~v~ 68 (307)
.+||...|||.+||||+++
T Consensus 2 ~dIA~~agVS~~TVSrvLn 20 (327)
T PRK10423 2 KDVARLAGVSTSTVSHVIN 20 (327)
T ss_pred hhHHHHhCCcHHHHHHHhC
Confidence 5899999999999999997
No 337
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=64.15 E-value=13 Score=30.21 Aligned_cols=46 Identities=11% Similarity=0.216 Sum_probs=36.5
Q ss_pred CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccc
Q psy4300 29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQ 76 (307)
Q Consensus 29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~ 76 (307)
.+++.+. -.|.+|+.|.+..++|..+++|.+|+...+.++..-+-.
T Consensus 137 ~Lt~~E~--~il~~l~~g~~~~~Ia~~l~~s~~tv~~~~~~l~~Kl~~ 182 (196)
T PRK10360 137 PLTKRER--QVAEKLAQGMAVKEIAAELGLSPKTVHVHRANLMEKLGV 182 (196)
T ss_pred CCCHHHH--HHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 4555554 456668899999999999999999999999988766543
No 338
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=63.72 E-value=5.3 Score=36.64 Aligned_cols=22 Identities=9% Similarity=0.306 Sum_probs=19.9
Q ss_pred cHHHHHhhhCCChhhHHHHHHH
Q psy4300 48 SMRKIGDQFNLADSTVWSCIDS 69 (307)
Q Consensus 48 ~~~~l~~~fgvs~stv~r~v~~ 69 (307)
+..++|...|||.+||||+++.
T Consensus 2 TikDVA~~AGVS~sTVSrvln~ 23 (333)
T COG1609 2 TIKDVAKLAGVSKATVSRVLNG 23 (333)
T ss_pred CHHHHHHHhCCCHHHHHHHHcC
Confidence 5679999999999999999875
No 339
>PRK11013 DNA-binding transcriptional regulator LysR; Provisional
Probab=63.55 E-value=15 Score=33.00 Aligned_cols=44 Identities=11% Similarity=0.102 Sum_probs=36.1
Q ss_pred HHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 34 KKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 34 ~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
.+|-+++....+ .|++..|...++|+|++|+.++++.+.+-..|
T Consensus 7 ~~L~~f~av~~~-gS~s~AAe~L~isqsavS~~Ik~LE~~lg~~L 50 (309)
T PRK11013 7 RHIEIFHAVMTA-GSLTEAARLLHTSQPTVSRELARFEKVIGLKL 50 (309)
T ss_pred HHHHHHHHHHHh-CcHHHHHHHHCCCcHHHHHHHHHHHHHhCcee
Confidence 445555555555 49999999999999999999999999888776
No 340
>cd00131 PAX Paired Box domain
Probab=63.45 E-value=67 Score=25.00 Aligned_cols=69 Identities=10% Similarity=0.070 Sum_probs=40.4
Q ss_pred CCHHHHHHHHHHHhhhcCcccccCCC-CCC-CCHHH-HHHHHHHHHhcCCcHHHHHhhh---CC-------ChhhHHHHH
Q psy4300 1 MRKTTFGFLVEALAAINGYETLYERG-VPF-VPVEK-KTLVALSYMATQLSMRKIGDQF---NL-------ADSTVWSCI 67 (307)
Q Consensus 1 ms~~~F~~L~~~l~~~~~~~~~~~~~-~~~-~~~~~-~l~i~L~~L~~g~~~~~l~~~f---gv-------s~stv~r~v 67 (307)
+++++...++...+..-...+...++ ++. +..+. ..++.+..-....+..+++..+ |+ |.||++|++
T Consensus 45 Vs~~tV~r~i~r~~e~G~v~pk~~gg~rpr~~~~~~~~~i~~~v~~~p~~Tl~El~~~L~~~gv~~~~~~~s~stI~R~L 124 (128)
T cd00131 45 VSHGCVSKILNRYYETGSIRPGAIGGSKPRVATPEVVKKIEIYKQENPGMFAWEIRDRLLQEGVCDKSNVPSVSSINRIL 124 (128)
T ss_pred cCHHHHHHHHHHHHHcCCcCCCCCCCCCCCcCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCCcccCCCCCHHHHHHHH
Confidence 36778888888877664333433332 233 34433 3333333333346677777764 56 999999987
Q ss_pred HH
Q psy4300 68 DS 69 (307)
Q Consensus 68 ~~ 69 (307)
+.
T Consensus 125 ~~ 126 (128)
T cd00131 125 RN 126 (128)
T ss_pred Hh
Confidence 64
No 341
>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=63.11 E-value=9.4 Score=24.47 Aligned_cols=22 Identities=14% Similarity=0.472 Sum_probs=17.9
Q ss_pred cHHHHHhhhCCChhhHHHHHHH
Q psy4300 48 SMRKIGDQFNLADSTVWSCIDS 69 (307)
Q Consensus 48 ~~~~l~~~fgvs~stv~r~v~~ 69 (307)
+..+++..+|+|++|+++.+++
T Consensus 5 ~~~ev~~~~g~s~~ti~~~~k~ 26 (51)
T PF05930_consen 5 RIKEVAELLGVSRSTIYRLIKD 26 (51)
T ss_dssp -HHHHHHHHSS-HHHHHHHHHH
T ss_pred cHHHHHHHHCCCHHHHHHHHhc
Confidence 4678999999999999999884
No 342
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=63.02 E-value=18 Score=30.86 Aligned_cols=51 Identities=10% Similarity=0.197 Sum_probs=38.0
Q ss_pred CCCCCHHHHHHHHHHHHhc------CCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 27 VPFVPVEKKTLVALSYMAT------QLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 27 ~~~~~~~~~l~i~L~~L~~------g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
...++..|.-++.+=|=.. ..+..+||..||||+||++..+++...-|...
T Consensus 153 ~~~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ehLRrAe~Kl~~~ 209 (215)
T COG3413 153 KNDLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEHLRRAERKLIEA 209 (215)
T ss_pred cccCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 3467777766665554322 27889999999999999999999877666554
No 343
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=62.93 E-value=16 Score=29.82 Aligned_cols=45 Identities=4% Similarity=0.035 Sum_probs=33.1
Q ss_pred CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300 29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTA 73 (307)
Q Consensus 29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~ 73 (307)
.++..++-.+.+..-..-.++.+||...|+|++||.+-+++..+.
T Consensus 11 ~lD~~D~~IL~~Lq~d~R~s~~eiA~~lglS~~tv~~Ri~rL~~~ 55 (164)
T PRK11169 11 DLDRIDRNILNELQKDGRISNVELSKRVGLSPTPCLERVRRLERQ 55 (164)
T ss_pred hHHHHHHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 355555555544444445899999999999999999988887654
No 344
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=62.85 E-value=18 Score=31.68 Aligned_cols=46 Identities=15% Similarity=0.256 Sum_probs=37.7
Q ss_pred CCCCHHHHHHHHHHHHhcC--CcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300 28 PFVPVEKKTLVALSYMATQ--LSMRKIGDQFNLADSTVWSCIDSFLTA 73 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g--~~~~~l~~~fgvs~stv~r~v~~~~~~ 73 (307)
..++.-++.+-.|..|+.. .+..+|+...|+++||++|+++..+..
T Consensus 8 ~~v~sl~r~l~IL~~l~~~~~l~l~eia~~lgl~kstv~Rll~tL~~~ 55 (257)
T PRK15090 8 DSVSSVLKVFGILQALGEEREIGITELSQRVMMSKSTVYRFLQTMKTL 55 (257)
T ss_pred cccHHHHHHHHHHHHhhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 4577777888888887543 689999999999999999999987654
No 345
>PRK05658 RNA polymerase sigma factor RpoD; Validated
Probab=62.68 E-value=13 Score=37.32 Aligned_cols=50 Identities=12% Similarity=0.319 Sum_probs=42.7
Q ss_pred CCCCHHHHHHHHHHHH---hcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 28 PFVPVEKKTLVALSYM---ATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L---~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
..++..++..+.++|. ..+.++..+|..||||++.|+++-.+.+.-|-..
T Consensus 555 ~~L~~rE~~Vl~~r~g~~~~~~~tl~ei~~~lgvs~eRVrQie~~al~kLr~~ 607 (619)
T PRK05658 555 ASLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 607 (619)
T ss_pred HcCCHHHHHHHHHhcCCCCCCCccHHHHHHHhCCCHHHHHHHHHHHHHHHhch
Confidence 4689999999999995 4678999999999999999999988877766554
No 346
>PRK10403 transcriptional regulator NarP; Provisional
Probab=62.57 E-value=14 Score=30.23 Aligned_cols=47 Identities=21% Similarity=0.290 Sum_probs=38.4
Q ss_pred CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
.++..+.- .|.++..|.+..+++...++|..||..++.+...-+--.
T Consensus 153 ~Lt~~e~~--vl~~~~~g~s~~~ia~~l~~s~~tv~~~~~~i~~kl~~~ 199 (215)
T PRK10403 153 VLTERELD--VLHELAQGLSNKQIASVLNISEQTVKVHIRNLLRKLNVR 199 (215)
T ss_pred cCCHHHHH--HHHHHHCCCCHHHHHHHcCCCHHHHHHHHHHHHHHcCCC
Confidence 46665554 466788999999999999999999999999987776544
No 347
>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=62.44 E-value=7.4 Score=24.33 Aligned_cols=25 Identities=16% Similarity=0.355 Sum_probs=21.2
Q ss_pred cCCcHHHHHhhhCCChhhHHHHHHH
Q psy4300 45 TQLSMRKIGDQFNLADSTVWSCIDS 69 (307)
Q Consensus 45 ~g~~~~~l~~~fgvs~stv~r~v~~ 69 (307)
.+.+.++|+...|+|++++++.+..
T Consensus 15 ~~~s~~~Ia~~~gvs~~~~y~~f~~ 39 (47)
T PF00440_consen 15 EAVSIRDIARRAGVSKGSFYRYFPS 39 (47)
T ss_dssp TTSSHHHHHHHHTSCHHHHHHHCSS
T ss_pred HhCCHHHHHHHHccchhhHHHHcCC
Confidence 3589999999999999998887653
No 348
>PRK15092 DNA-binding transcriptional repressor LrhA; Provisional
Probab=62.43 E-value=11 Score=33.94 Aligned_cols=52 Identities=10% Similarity=0.088 Sum_probs=42.8
Q ss_pred CCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 27 VPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 27 ~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
++.....-+.+-.+.-++...++...|...+||++|+|+-+++.-..+-..|
T Consensus 6 ~~~~~m~l~~L~~F~~v~e~gs~s~AA~~L~iSQpavS~~I~~LE~~lG~~L 57 (310)
T PRK15092 6 RPIINLDLDLLRTFVAVADLNTFAAAAAAVCRTQSAVSQQMQRLEQLVGKEL 57 (310)
T ss_pred hhhhcCCHHHHHHHHHHHHcCCHHHHHHHhCCChHHHHHHHHHHHHHhCcce
Confidence 3445555566666677777789999999999999999999999999888776
No 349
>PF13556 HTH_30: PucR C-terminal helix-turn-helix domain; PDB: 3ONQ_B.
Probab=62.38 E-value=18 Score=23.85 Aligned_cols=38 Identities=8% Similarity=0.157 Sum_probs=30.2
Q ss_pred HHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 40 LSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 40 L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
-.|+.++.+....|...+|++.|+..-++++.+.+---
T Consensus 6 ~~yl~~~~n~~~tA~~L~iHrNTl~yRl~ki~~l~g~d 43 (59)
T PF13556_consen 6 RAYLENNGNISKTARALHIHRNTLRYRLKKIEELLGLD 43 (59)
T ss_dssp HHHHHTTT-HHHHHHHHTS-HHHHHHHHHHHHHHHS--
T ss_pred HHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCcC
Confidence 35889999999999999999999999888887776555
No 350
>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=62.03 E-value=2.6 Score=34.46 Aligned_cols=23 Identities=35% Similarity=0.590 Sum_probs=0.0
Q ss_pred CCcHHHHHhhhCCChhhHHHHHH
Q psy4300 46 QLSMRKIGDQFNLADSTVWSCID 68 (307)
Q Consensus 46 g~~~~~l~~~fgvs~stv~r~v~ 68 (307)
.++..++|...|++.|||||.+.
T Consensus 49 PLt~~~iA~~lgl~~STVSRav~ 71 (160)
T PF04552_consen 49 PLTMKDIADELGLHESTVSRAVK 71 (160)
T ss_dssp -----------------------
T ss_pred CCCHHHHHHHhCCCHhHHHHHHc
Confidence 37889999999999999999875
No 351
>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=61.84 E-value=17 Score=32.32 Aligned_cols=42 Identities=10% Similarity=0.180 Sum_probs=34.1
Q ss_pred HHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 36 TLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 36 l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
|-+++.... ..|+...|...++|++++|+.+++.-..+-..|
T Consensus 8 l~~f~~v~~-~gS~s~AA~~L~isq~avS~~I~~LE~~lg~~L 49 (300)
T TIGR02424 8 LQCFVEVAR-QGSVKRAAEALHITQPAVSKTLRELEEILGTPL 49 (300)
T ss_pred HHHHHHHHH-hCCHHHHHHHhCCChHHHHHHHHHHHHHhCCeE
Confidence 334444444 458999999999999999999999999988776
No 352
>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B.
Probab=61.70 E-value=6.7 Score=26.36 Aligned_cols=19 Identities=11% Similarity=0.189 Sum_probs=16.8
Q ss_pred cHHHHHhhhCCChhhHHHH
Q psy4300 48 SMRKIGDQFNLADSTVWSC 66 (307)
Q Consensus 48 ~~~~l~~~fgvs~stv~r~ 66 (307)
+...+|..+|||+++|+.|
T Consensus 11 ~~~~lAkalGVs~~aVs~W 29 (60)
T PF14549_consen 11 GQSKLAKALGVSPQAVSQW 29 (60)
T ss_dssp SHHHHHHHHTS-HHHHHHH
T ss_pred CHHHHHHHHCCCHHHHHHh
Confidence 6789999999999999998
No 353
>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=61.66 E-value=9.5 Score=28.81 Aligned_cols=33 Identities=9% Similarity=0.331 Sum_probs=22.4
Q ss_pred hcCCcHHHHHhhhCCChhhHHHHHHHHHHHccc
Q psy4300 44 ATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQ 76 (307)
Q Consensus 44 ~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~ 76 (307)
-.|.+..+||..||+|...|.+|+++.-.....
T Consensus 70 f~G~n~~eLA~kyglS~r~I~~Ii~~~~~~~~~ 102 (108)
T PF08765_consen 70 FNGMNVRELARKYGLSERQIYRIIKRVRRRERR 102 (108)
T ss_dssp --SS-HHHHHHHHT--HHHHHHHHHHHHH----
T ss_pred hCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 358999999999999999999999987654433
No 354
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=61.65 E-value=24 Score=25.11 Aligned_cols=46 Identities=15% Similarity=0.304 Sum_probs=33.0
Q ss_pred HHHHHHHHHHHhc-CCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 33 EKKTLVALSYMAT-QLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 33 ~~~l~i~L~~L~~-g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
.+.+.+.|.-+.. ..|-..||...|+|+++|.+.|...-+.=++.+
T Consensus 5 ~~~~~~ll~~~~~~~~SGe~La~~LgiSRtaVwK~Iq~Lr~~G~~I~ 51 (79)
T COG1654 5 SQMLLLLLLLLTGNFVSGEKLAEELGISRTAVWKHIQQLREEGVDIE 51 (79)
T ss_pred HHHHHHHHHHcCCCcccHHHHHHHHCccHHHHHHHHHHHHHhCCceE
Confidence 3444444444433 388899999999999999999988776555543
No 355
>PRK12680 transcriptional regulator CysB-like protein; Reviewed
Probab=61.64 E-value=17 Score=33.13 Aligned_cols=44 Identities=2% Similarity=0.015 Sum_probs=35.5
Q ss_pred HHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 35 KTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 35 ~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
+|-+++....++.|++..|...++|+||+|+.+++....+-..|
T Consensus 5 ~L~~F~~vae~~gS~s~AA~~L~isQpavS~~I~~LE~~lG~~L 48 (327)
T PRK12680 5 QLRYLVAIADAELNITLAAARVHATQPGLSKQLKQLEDELGFLL 48 (327)
T ss_pred HHHHHHHHHHccCCHHHHHHHhcCCchHHHHHHHHHHHHhCCeE
Confidence 33344434444679999999999999999999999999988876
No 356
>PRK15421 DNA-binding transcriptional regulator MetR; Provisional
Probab=61.48 E-value=18 Score=32.78 Aligned_cols=44 Identities=7% Similarity=-0.004 Sum_probs=36.6
Q ss_pred HHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 34 KKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 34 ~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
.+|-.++....+| +++..|...++|+++||+-+++.-..+-..|
T Consensus 5 ~~L~~f~av~~~g-s~s~AA~~L~iSqpaVS~~Ik~LE~~lg~~L 48 (317)
T PRK15421 5 KHLKTLQALRNCG-SLAAAAATLHQTQSALSHQFSDLEQRLGFRL 48 (317)
T ss_pred HHHHHHHHHHHcC-CHHHHHHHhCCCHHHHHHHHHHHHHHhCCEE
Confidence 3455556666666 9999999999999999999999999888775
No 357
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=61.39 E-value=14 Score=32.64 Aligned_cols=41 Identities=15% Similarity=0.235 Sum_probs=34.5
Q ss_pred HHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 38 VALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 38 i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
-++..++...+++..|...++|+|++|+.+++.-+.+-..|
T Consensus 7 ~~f~~v~~~gs~s~AA~~L~isQ~avSr~i~~LE~~lg~~L 47 (296)
T PRK09906 7 RYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENCVGVPL 47 (296)
T ss_pred HHHHHHHhhCCHHHHHHHhCCCCcHHHHHHHHHHHHhCCee
Confidence 34444555569999999999999999999999999888776
No 358
>COG1342 Predicted DNA-binding proteins [General function prediction only]
Probab=61.16 E-value=23 Score=26.11 Aligned_cols=46 Identities=13% Similarity=0.252 Sum_probs=33.1
Q ss_pred CCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccc
Q psy4300 30 VPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQ 76 (307)
Q Consensus 30 ~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~ 76 (307)
+++++-=++-|.-+- |.++.+.|...|||++|+.+.++.--.-+.+
T Consensus 34 lt~eElEAlRLvD~~-~l~QeeAA~rMgISr~Tfwr~l~sAR~KvA~ 79 (99)
T COG1342 34 LTIEELEALRLVDYE-GLTQEEAALRMGISRQTFWRLLTSARKKVAD 79 (99)
T ss_pred ecHHHHHHHHHHhHh-hccHHHHHHHhcccHHHHHHHHHHHHHHHHH
Confidence 555555555555443 6899999999999999999988764433333
No 359
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=60.95 E-value=16 Score=29.94 Aligned_cols=47 Identities=9% Similarity=0.178 Sum_probs=38.8
Q ss_pred CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
.++..+. -+|..|..|.+..+++..+++|.+||..++.+...-|...
T Consensus 143 ~lt~~E~--~vl~~l~~g~~~~~I~~~l~~s~~tv~~~~~~l~~Kl~~~ 189 (204)
T PRK09958 143 SLSKQEI--SVMRYILDGKDNNDIAEKMFISNKTVSTYKSRLMEKLECK 189 (204)
T ss_pred cCCHHHH--HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHcCCC
Confidence 4777665 4777888999999999999999999999999887776443
No 360
>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=60.84 E-value=18 Score=31.90 Aligned_cols=43 Identities=14% Similarity=0.168 Sum_probs=35.0
Q ss_pred HHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 35 KTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 35 ~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
+|-.++....+ .+++..|...++|++++|+-+++.-..+-..|
T Consensus 5 ~l~~f~~v~~~-~s~t~AA~~L~isQpavS~~I~~LE~~lg~~L 47 (292)
T TIGR03298 5 QLAALAAVVEE-GSFERAAAALSVTPSAVSQRIKALEERLGQPL 47 (292)
T ss_pred HHHHHHHHHHc-CCHHHHHHHhCCCHHHHHHHHHHHHHHhCchh
Confidence 34444444454 49999999999999999999999999888776
No 361
>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=60.75 E-value=9.4 Score=26.81 Aligned_cols=24 Identities=13% Similarity=0.243 Sum_probs=18.6
Q ss_pred CCcHHHHHhhhCCChhhHHHHHHH
Q psy4300 46 QLSMRKIGDQFNLADSTVWSCIDS 69 (307)
Q Consensus 46 g~~~~~l~~~fgvs~stv~r~v~~ 69 (307)
..+-.++|...|||++||.|..+.
T Consensus 34 ~~si~elA~~~~vS~sti~Rf~kk 57 (77)
T PF01418_consen 34 FMSISELAEKAGVSPSTIVRFCKK 57 (77)
T ss_dssp T--HHHHHHHCTS-HHHHHHHHHH
T ss_pred HccHHHHHHHcCCCHHHHHHHHHH
Confidence 588999999999999999987665
No 362
>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=60.56 E-value=5.9 Score=37.83 Aligned_cols=22 Identities=27% Similarity=0.629 Sum_probs=20.2
Q ss_pred CcHHHHHhhhCCChhhHHHHHH
Q psy4300 47 LSMRKIGDQFNLADSTVWSCID 68 (307)
Q Consensus 47 ~~~~~l~~~fgvs~stv~r~v~ 68 (307)
++..++|...|++.|||||+++
T Consensus 319 LtlkdiA~~lglheSTVSRav~ 340 (429)
T TIGR02395 319 LTLREVAEELGLHESTISRAIN 340 (429)
T ss_pred CcHHHHHHHhCCCccchhhhhc
Confidence 7899999999999999999873
No 363
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=60.34 E-value=17 Score=32.02 Aligned_cols=42 Identities=7% Similarity=0.080 Sum_probs=34.0
Q ss_pred HHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 36 TLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 36 l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
|-.++....+ .+++..|...++|+|++|+-++++-..+-..|
T Consensus 6 L~~f~~v~~~-gs~s~AA~~L~isqsavS~~i~~LE~~lg~~L 47 (296)
T PRK11242 6 IRYFLAVAEH-GNFTRAAEALHVSQPTLSQQIRQLEESLGVQL 47 (296)
T ss_pred HHHHHHHHHh-CCHHHHHHHcCCCchHHHHHHHHHHHHhCCee
Confidence 3333334444 58999999999999999999999999888876
No 364
>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=59.77 E-value=21 Score=27.70 Aligned_cols=26 Identities=23% Similarity=0.229 Sum_probs=23.2
Q ss_pred CcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300 47 LSMRKIGDQFNLADSTVWSCIDSFLT 72 (307)
Q Consensus 47 ~~~~~l~~~fgvs~stv~r~v~~~~~ 72 (307)
.+..+|+..+|+|++++++++.....
T Consensus 26 ~s~~eia~~l~is~~~v~~~l~~L~~ 51 (130)
T TIGR02944 26 YSAAEIAEQTGLNAPTVSKILKQLSL 51 (130)
T ss_pred ccHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 68999999999999999998887654
No 365
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=59.72 E-value=24 Score=30.84 Aligned_cols=39 Identities=23% Similarity=0.459 Sum_probs=29.9
Q ss_pred HHHHHHHHHhc-C--CcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300 35 KTLVALSYMAT-Q--LSMRKIGDQFNLADSTVWSCIDSFLTA 73 (307)
Q Consensus 35 ~l~i~L~~L~~-g--~~~~~l~~~fgvs~stv~r~v~~~~~~ 73 (307)
+-+-.|.+|+. + ++..+|+...|+++||++|++......
T Consensus 5 ral~iL~~l~~~~~~l~l~ela~~~glpksT~~RlL~tL~~~ 46 (246)
T COG1414 5 RALAILDLLAEGPGGLSLAELAERLGLPKSTVHRLLQTLVEL 46 (246)
T ss_pred HHHHHHHHHHhCCCCCCHHHHHHHhCcCHHHHHHHHHHHHHC
Confidence 44455555553 2 469999999999999999999987654
No 366
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=59.47 E-value=25 Score=26.05 Aligned_cols=27 Identities=4% Similarity=0.049 Sum_probs=23.4
Q ss_pred cCCcHHHHHhhhCCChhhHHHHHHHHH
Q psy4300 45 TQLSMRKIGDQFNLADSTVWSCIDSFL 71 (307)
Q Consensus 45 ~g~~~~~l~~~fgvs~stv~r~v~~~~ 71 (307)
...+..++|..+|+|.++++|.+++..
T Consensus 20 ~~~~~~~lA~~~~~S~~~l~r~f~~~~ 46 (107)
T PRK10219 20 QPLNIDVVAKKSGYSKWYLQRMFRTVT 46 (107)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 346888999999999999999999863
No 367
>TIGR01637 phage_arpU phage transcriptional regulator, ArpU family. This model represents a family of phage proteins, including ArpU, called a putative autolysin regulatory protein. ArpU was described as a regulator of cellular muramidase-2 of Enterococcus hirae but appears to have been cloned from a prophage. This family appears related to the RinA family of bacteriophage transcriptional activators and to some sporulation-specific sigma factors. We propose that this is a phage transcriptional activator family.
Probab=59.44 E-value=23 Score=27.56 Aligned_cols=50 Identities=8% Similarity=0.024 Sum_probs=41.4
Q ss_pred CCCCHHHHHHHHHHHHh-cCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 28 PFVPVEKKTLVALSYMA-TQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~-~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
..++..++-.+...|+. .+.+...++..+|+|++++++.-++.+..+...
T Consensus 78 ~~l~~~~r~Il~~~Yl~~~~~~~~~I~~~l~~s~~~~y~~k~~Al~~fA~~ 128 (132)
T TIGR01637 78 NQLDEISRQILYDKYLEPDQKYDYQIMMELGYSHRQYYRIKKRALLRFATL 128 (132)
T ss_pred HhCCHHHHHHHHHHHcCccccchHHHHHHhCCcHHHHHHHHHHHHHHHHHH
Confidence 36788888899999997 367888999999999999999888777666655
No 368
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=59.19 E-value=13 Score=25.66 Aligned_cols=27 Identities=7% Similarity=0.106 Sum_probs=22.5
Q ss_pred HHhcCCcHHHHHhhhCCChhhHHHHHH
Q psy4300 42 YMATQLSMRKIGDQFNLADSTVWSCID 68 (307)
Q Consensus 42 ~L~~g~~~~~l~~~fgvs~stv~r~v~ 68 (307)
+-..|.++.++|...|||+.|+..+=+
T Consensus 10 R~~~~ltQ~elA~~vgVsRQTi~~iEk 36 (68)
T COG1476 10 RAELGLTQEELAKLVGVSRQTIIAIEK 36 (68)
T ss_pred HHHhCcCHHHHHHHcCcCHHHHHHHHc
Confidence 446689999999999999999876544
No 369
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [].; PDB: 2WTE_A 3SQN_A.
Probab=59.15 E-value=27 Score=23.03 Aligned_cols=42 Identities=14% Similarity=0.270 Sum_probs=29.9
Q ss_pred HHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 35 KTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 35 ~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
+|+-.|.- ....++.++|...|+|..|+...+.+.-+.+-+.
T Consensus 9 ~Ll~~L~~-~~~~~~~ela~~l~~S~rti~~~i~~L~~~f~~~ 50 (59)
T PF08280_consen 9 KLLELLLK-NKWITLKELAKKLNISERTIKNDINELNEFFPEN 50 (59)
T ss_dssp HHHHHHHH-HTSBBHHHHHHHCTS-HHHHHHHHHHHHTT--TC
T ss_pred HHHHHHHc-CCCCcHHHHHHHHCCCHHHHHHHHHHHHHHhhhh
Confidence 34444444 6678999999999999999999988876555443
No 370
>PF06530 Phage_antitermQ: Phage antitermination protein Q; InterPro: IPR010534 This entry is represented by Bacteriophage 933W, GpQ. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several phage antitermination protein Q and related bacterial sequences. Phage 993W gene Q encodes a phage-specific positive regulator of late gene expression, thought, by analogy to the corresponding gene of phage lambda, to be a transcription antiterminator. GpQ positively regulates expression of the phage late gene operons. Bacterial host RNA polymerase modified by antitermination proteins transcribes through termination sites that otherwise prevent expression of the regulated genes [, ].; GO: 0003677 DNA binding, 0060567 negative regulation of transcription termination, DNA-dependent
Probab=59.14 E-value=26 Score=27.22 Aligned_cols=42 Identities=10% Similarity=0.090 Sum_probs=32.3
Q ss_pred HHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 36 TLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 36 l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
.-+.+.|+..|.|.+.||...++|..++.+.+..-...+.-.
T Consensus 68 ~~ll~~~Yv~g~s~r~IA~~~~~s~~~ir~~l~~ae~~i~g~ 109 (125)
T PF06530_consen 68 YDLLILYYVYGWSKRQIARKLKCSEGKIRKRLQRAEGFIDGC 109 (125)
T ss_pred HHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHhhhhHhhh
Confidence 344555666899999999999999999998887655554444
No 371
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=58.96 E-value=32 Score=25.54 Aligned_cols=43 Identities=14% Similarity=0.254 Sum_probs=29.6
Q ss_pred CCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300 30 VPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLT 72 (307)
Q Consensus 30 ~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~ 72 (307)
+++.+...+...+-..+.+..+++...+++++++++.+++...
T Consensus 20 lt~~q~~~L~~l~~~~~~~~~~la~~l~i~~~~vt~~l~~Le~ 62 (126)
T COG1846 20 LTPPQYQVLLALYEAGGITVKELAERLGLDRSTVTRLLKRLED 62 (126)
T ss_pred CCHHHHHHHHHHHHhCCCcHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 5555444444433333333399999999999999999988754
No 372
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=58.84 E-value=14 Score=29.06 Aligned_cols=27 Identities=11% Similarity=0.139 Sum_probs=23.1
Q ss_pred HHhcCCcHHHHHhhhCCChhhHHHHHH
Q psy4300 42 YMATQLSMRKIGDQFNLADSTVWSCID 68 (307)
Q Consensus 42 ~L~~g~~~~~l~~~fgvs~stv~r~v~ 68 (307)
+-..|.+..++|...|||++|+++|.+
T Consensus 14 R~~~gltq~~lA~~~gvs~~~is~~E~ 40 (135)
T PRK09706 14 RKQLKLSQRSLAKAVKVSHVSISQWER 40 (135)
T ss_pred HHHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 345689999999999999999998754
No 373
>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=58.66 E-value=11 Score=30.96 Aligned_cols=27 Identities=15% Similarity=0.315 Sum_probs=24.5
Q ss_pred CcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300 47 LSMRKIGDQFNLADSTVWSCIDSFLTA 73 (307)
Q Consensus 47 ~~~~~l~~~fgvs~stv~r~v~~~~~~ 73 (307)
+++.++|..+|+|++|++|.+....+.
T Consensus 76 ~t~~~ia~~l~iS~~Tv~r~ik~L~e~ 102 (165)
T PF05732_consen 76 ATQKEIAEKLGISKPTVSRAIKELEEK 102 (165)
T ss_pred eeHHHHHHHhCCCHHHHHHHHHHHHhC
Confidence 789999999999999999999987654
No 374
>PRK09801 transcriptional activator TtdR; Provisional
Probab=58.13 E-value=24 Score=31.79 Aligned_cols=48 Identities=13% Similarity=0.105 Sum_probs=38.5
Q ss_pred CCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 30 VPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 30 ~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
++.-.+|-.++....+ .+++..|..+++|+||+|+-|++.-..+-..|
T Consensus 5 ~~~~~~L~~F~~v~~~-gs~t~AA~~L~iSQpavS~~I~~LE~~LG~~L 52 (310)
T PRK09801 5 WPLAKDLQVLVEIVHS-GSFSAAAATLGQTPAFVTKRIQILENTLATTL 52 (310)
T ss_pred cHHHHHHHHHHHHHHc-CCHHHHHHHhCcCHHHHHHHHHHHHHHhCCEe
Confidence 4445566555555554 57999999999999999999999999988776
No 375
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=58.00 E-value=28 Score=27.43 Aligned_cols=41 Identities=10% Similarity=0.078 Sum_probs=29.8
Q ss_pred HHHHHHHHHHHh--cCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300 33 EKKTLVALSYMA--TQLSMRKIGDQFNLADSTVWSCIDSFLTA 73 (307)
Q Consensus 33 ~~~l~i~L~~L~--~g~~~~~l~~~fgvs~stv~r~v~~~~~~ 73 (307)
++-|-..+.++. ...+..+|+..+++|++||++.+++....
T Consensus 7 edyL~~I~~l~~~~~~~~~~ela~~l~vs~~svs~~l~~L~~~ 49 (142)
T PRK03902 7 EDYIEQIYLLIEEKGYARVSDIAEALSVHPSSVTKMVQKLDKD 49 (142)
T ss_pred HHHHHHHHHHHhcCCCcCHHHHHHHhCCChhHHHHHHHHHHHC
Confidence 444444444443 34677899999999999999999887655
No 376
>PRK09508 leuO leucine transcriptional activator; Reviewed
Probab=57.98 E-value=21 Score=32.10 Aligned_cols=43 Identities=5% Similarity=0.185 Sum_probs=36.3
Q ss_pred HHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 36 TLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 36 l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
.+-++.-++...+++..|...++|++|+|+.+++.-..+-..|
T Consensus 26 ~L~~f~avae~gs~s~AA~~L~isQpavS~~I~~LE~~lg~~L 68 (314)
T PRK09508 26 LLTVFDAVMQEQNITRAAHNLGMSQPAVSNAVARLKVMFNDEL 68 (314)
T ss_pred HHHHHHHHHhcCCHHHHHHHhCCCHHHHHHHHHHHHHhhCCCc
Confidence 3455555566677999999999999999999999999998886
No 377
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=57.94 E-value=11 Score=23.40 Aligned_cols=23 Identities=9% Similarity=-0.008 Sum_probs=19.5
Q ss_pred cHHHHHhhhCCChhhHHHHHHHH
Q psy4300 48 SMRKIGDQFNLADSTVWSCIDSF 70 (307)
Q Consensus 48 ~~~~l~~~fgvs~stv~r~v~~~ 70 (307)
+-.++|..+||+.+|+..+..+-
T Consensus 2 ~~~e~a~~~gv~~~tlr~~~~~g 24 (49)
T cd04761 2 TIGELAKLTGVSPSTLRYYERIG 24 (49)
T ss_pred cHHHHHHHHCcCHHHHHHHHHCC
Confidence 45789999999999999887654
No 378
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=57.74 E-value=18 Score=21.95 Aligned_cols=25 Identities=12% Similarity=0.200 Sum_probs=21.1
Q ss_pred HhcCCcHHHHHhhhCCChhhHHHHH
Q psy4300 43 MATQLSMRKIGDQFNLADSTVWSCI 67 (307)
Q Consensus 43 L~~g~~~~~l~~~fgvs~stv~r~v 67 (307)
-..+.+..+++...|++.++++++.
T Consensus 7 ~~~~~s~~~la~~~~i~~~~i~~~~ 31 (56)
T smart00530 7 EEKGLTQEELAEKLGVSRSTLSRIE 31 (56)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHH
Confidence 3467899999999999999988754
No 379
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=57.70 E-value=20 Score=31.96 Aligned_cols=42 Identities=12% Similarity=0.165 Sum_probs=34.4
Q ss_pred HHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 36 TLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 36 l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
|-+++.... ..+++..|...++|++++|+.++++-..+-..|
T Consensus 10 L~~f~~v~e-~gs~s~AA~~L~isqpavS~~i~~LE~~lg~~L 51 (305)
T CHL00180 10 LRILKAIAT-EGSFKKAAESLYISQPAVSLQIKNLEKQLNIPL 51 (305)
T ss_pred HHHHHHHHH-cCCHHHHHHHhcCCChHHHHHHHHHHHHhCCEE
Confidence 444444444 458999999999999999999999999988876
No 380
>TIGR02684 dnstrm_HI1420 probable addiction module antidote protein. gene pairs, when found on the bacterial chromosome, are located often with prophage regions, but also both in integrated plasmid regions and in housekeeping gene regions. Analysis suggests that the gene pair may serve as an addiction module.
Probab=57.64 E-value=16 Score=26.62 Aligned_cols=34 Identities=18% Similarity=0.354 Sum_probs=25.1
Q ss_pred HHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHH
Q psy4300 35 KTLVALSYMATQLSMRKIGDQFNLADSTVWSCID 68 (307)
Q Consensus 35 ~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~ 68 (307)
.+...|..++.-..+..+|...|||++|++++.+
T Consensus 32 ~~~~~l~~~r~~~glSqLAe~~GIs~stLs~iE~ 65 (89)
T TIGR02684 32 YIAHALGYIARARGMTQLARKTGLSRESLYKALS 65 (89)
T ss_pred HHHHHHHHHHHHCChHHHHHHHCCCHHHHHHHHc
Confidence 3555566665544556799999999999998764
No 381
>PRK11074 putative DNA-binding transcriptional regulator; Provisional
Probab=57.52 E-value=22 Score=31.62 Aligned_cols=37 Identities=14% Similarity=0.097 Sum_probs=32.0
Q ss_pred HHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 42 YMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 42 ~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
-+..-.+++..|...++|++++|+.+++.-..+-..|
T Consensus 12 ~v~e~~s~s~AA~~L~isQpavS~~I~~LE~~lg~~L 48 (300)
T PRK11074 12 AVARTGSFSAAAQELHRVPSAVSYTVRQLEEWLAVPL 48 (300)
T ss_pred HHHHhCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCee
Confidence 3344458999999999999999999999999988876
No 382
>PRK10216 DNA-binding transcriptional regulator YidZ; Provisional
Probab=57.48 E-value=23 Score=31.92 Aligned_cols=42 Identities=19% Similarity=0.214 Sum_probs=33.8
Q ss_pred HHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 36 TLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 36 l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
|-.++....+ .|++..|..+++|+|++|+.+.+.-..+-..|
T Consensus 13 L~~f~av~e~-gs~t~AA~~L~iSQpavS~~I~~LE~~lg~~L 54 (319)
T PRK10216 13 LLCLQLLMQE-RSVTKAAKRMNVTPSAVSKSLAKLRAWFDDPL 54 (319)
T ss_pred HHHHHHHHHh-CCHHHHHHHhCCCHHHHHHHHHHHHHHhCCce
Confidence 3344433444 48999999999999999999999999888776
No 383
>COG5566 Uncharacterized conserved protein [Function unknown]
Probab=57.40 E-value=14 Score=28.61 Aligned_cols=43 Identities=12% Similarity=0.226 Sum_probs=32.3
Q ss_pred CCHHHHHHHHHHHH-----hcCCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300 30 VPVEKKTLVALSYM-----ATQLSMRKIGDQFNLADSTVWSCIDSFLT 72 (307)
Q Consensus 30 ~~~~~~l~i~L~~L-----~~g~~~~~l~~~fgvs~stv~r~v~~~~~ 72 (307)
+|.-+.+.-+++-. -.|.++.+|+..+.+|.++|+++|+++..
T Consensus 81 lP~G~s~r~t~Rn~~ifsd~dG~n~~eLaKkYrlS~~~Iy~VIrr~~t 128 (137)
T COG5566 81 LPKGDSIRATLRNKQIFSDFDGSNYVELAKKYRLSENHIYRVIRRTHT 128 (137)
T ss_pred eeCchHHHHHHHHHHHHHhcCCccHHHHHHHhcccHHHHHHHHHHHHH
Confidence 44445555555422 34899999999999999999999997754
No 384
>PF12844 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_A 2XIU_B 2GZU_B 2XJ3_A 1UTX_A 2XI8_B 3F6W_C 3EUS_B.
Probab=57.33 E-value=13 Score=24.70 Aligned_cols=28 Identities=11% Similarity=0.239 Sum_probs=20.9
Q ss_pred HHhcCCcHHHHHhhhCCChhhHHHHHHH
Q psy4300 42 YMATQLSMRKIGDQFNLADSTVWSCIDS 69 (307)
Q Consensus 42 ~L~~g~~~~~l~~~fgvs~stv~r~v~~ 69 (307)
+-..|.++.++|...|+++++++++.+.
T Consensus 8 r~~~~lt~~~~a~~~~i~~~~i~~~e~g 35 (64)
T PF12844_consen 8 REEKGLTQKDLAEKLGISRSTISKIENG 35 (64)
T ss_dssp HHHCT--HHHHHHHHTS-HHHHHHHHTT
T ss_pred HHHcCCCHHHHHHHHCcCHHHHHHHHCC
Confidence 3456899999999999999999988754
No 385
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=57.23 E-value=20 Score=27.81 Aligned_cols=30 Identities=10% Similarity=0.146 Sum_probs=25.4
Q ss_pred HHhcCCcHHHHHhhhCCChhhHHHHHHHHH
Q psy4300 42 YMATQLSMRKIGDQFNLADSTVWSCIDSFL 71 (307)
Q Consensus 42 ~L~~g~~~~~l~~~fgvs~stv~r~v~~~~ 71 (307)
.+....+..++|..+|+|++++.+.+++..
T Consensus 21 ~~~~~~sl~~lA~~~g~S~~~l~r~Fk~~~ 50 (127)
T PRK11511 21 NLESPLSLEKVSERSGYSKWHLQRMFKKET 50 (127)
T ss_pred hcCCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 344557899999999999999999999874
No 386
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=57.21 E-value=26 Score=30.76 Aligned_cols=40 Identities=13% Similarity=0.258 Sum_probs=31.5
Q ss_pred HHHHHHHHHHHhc--CCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300 33 EKKTLVALSYMAT--QLSMRKIGDQFNLADSTVWSCIDSFLT 72 (307)
Q Consensus 33 ~~~l~i~L~~L~~--g~~~~~l~~~fgvs~stv~r~v~~~~~ 72 (307)
+++....|.+|.. ..+..+++..||||++|+.|.++.+..
T Consensus 4 ~~R~~~Il~~l~~~~~~~~~ela~~l~vS~~TirRdL~~Le~ 45 (251)
T PRK13509 4 AQRHQILLELLAQLGFVTVEKVIERLGISPATARRDINKLDE 45 (251)
T ss_pred HHHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 3455556666654 378889999999999999999998755
No 387
>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=56.86 E-value=20 Score=21.86 Aligned_cols=25 Identities=12% Similarity=0.274 Sum_probs=21.6
Q ss_pred hcCCcHHHHHhhhCCChhhHHHHHH
Q psy4300 44 ATQLSMRKIGDQFNLADSTVWSCID 68 (307)
Q Consensus 44 ~~g~~~~~l~~~fgvs~stv~r~v~ 68 (307)
..|.+..+++...|+++++++++.+
T Consensus 10 ~~~~s~~~~a~~~~~~~~~v~~~~~ 34 (58)
T cd00093 10 EKGLTQEELAEKLGVSRSTISRIEN 34 (58)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHc
Confidence 5688999999999999999887644
No 388
>PF07037 DUF1323: Putative transcription regulator (DUF1323); InterPro: IPR010749 This family consists of several hypothetical Enterobacterial proteins of around 120 residues in length. The function of this family is unknown.
Probab=56.84 E-value=12 Score=28.77 Aligned_cols=22 Identities=5% Similarity=0.123 Sum_probs=19.5
Q ss_pred cHHHHHhhhCCChhhHHHHHHH
Q psy4300 48 SMRKIGDQFNLADSTVWSCIDS 69 (307)
Q Consensus 48 ~~~~l~~~fgvs~stv~r~v~~ 69 (307)
+-.+||...|+|+.||+||+++
T Consensus 2 T~eELA~~tG~srQTINrWvRk 23 (122)
T PF07037_consen 2 TPEELAELTGYSRQTINRWVRK 23 (122)
T ss_pred CHHHHHHHhCccHHHHHHHHHh
Confidence 4578999999999999999875
No 389
>COG4496 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=56.56 E-value=11 Score=27.30 Aligned_cols=29 Identities=14% Similarity=0.149 Sum_probs=25.5
Q ss_pred HHHHhcCCcHHHHHhhhCCChhhHHHHHH
Q psy4300 40 LSYMATQLSMRKIGDQFNLADSTVWSCID 68 (307)
Q Consensus 40 L~~L~~g~~~~~l~~~fgvs~stv~r~v~ 68 (307)
-..|..|-+|+++...-|.|..|++|+-+
T Consensus 50 a~mL~eg~tY~~I~~eTGaStaTIsRVkR 78 (100)
T COG4496 50 AKMLKEGRTYRDIEDETGASTATISRVKR 78 (100)
T ss_pred HHHHHcCCCcchhhhccCcchhhHHHHHH
Confidence 45789999999999999999999998543
No 390
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=56.55 E-value=21 Score=28.89 Aligned_cols=47 Identities=13% Similarity=0.240 Sum_probs=36.7
Q ss_pred CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
.++..+.=. |.++..|.+..++|...++|..||...+.+...-+.-.
T Consensus 149 ~lt~~e~~v--l~l~~~g~~~~~Ia~~l~~s~~tv~~~~~~~~~kl~~~ 195 (211)
T PRK15369 149 LLTPRERQI--LKLITEGYTNRDIAEQLSISIKTVETHRLNMMRKLDVH 195 (211)
T ss_pred CCCHHHHHH--HHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Confidence 366654444 44578999999999999999999999999877666543
No 391
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=56.13 E-value=8.9 Score=37.13 Aligned_cols=31 Identities=23% Similarity=0.465 Sum_probs=25.7
Q ss_pred CcHHHHHhhhCCChhhHHHHHHHHHHHccccccccccccCCCh
Q psy4300 47 LSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQIQCQYIKWPTE 89 (307)
Q Consensus 47 ~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l~~~~~i~~P~~ 89 (307)
++.+++|...|++.|||||++ ...|+.-|..
T Consensus 370 LtlkdVAe~lglHeSTVSRa~------------~~KY~~tp~G 400 (481)
T PRK12469 370 LVLRDVAEELGLHESTISRAT------------GNKYMATPRG 400 (481)
T ss_pred CcHHHHHHHhCCCcchhhHHh------------cCceeecCCc
Confidence 688999999999999999987 4566666654
No 392
>smart00497 IENR1 Intron encoded nuclease repeat motif. Repeat of unknown function, but possibly DNA-binding via helix-turn-helix motif (Ponting, unpublished).
Probab=56.07 E-value=13 Score=23.57 Aligned_cols=25 Identities=12% Similarity=0.276 Sum_probs=21.4
Q ss_pred cCCcHHHHHhhhCCChhhHHHHHHH
Q psy4300 45 TQLSMRKIGDQFNLADSTVWSCIDS 69 (307)
Q Consensus 45 ~g~~~~~l~~~fgvs~stv~r~v~~ 69 (307)
.-.|..+.|..+|+++++++++++.
T Consensus 16 ~f~S~~eAa~~lg~~~~~I~~~~~~ 40 (53)
T smart00497 16 EFSSIREAAKYLGISHSSISKYLNT 40 (53)
T ss_pred EecCHHHHHHHhCCCHHHHHHHHhC
Confidence 3468889999999999999998774
No 393
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=55.84 E-value=28 Score=27.56 Aligned_cols=27 Identities=22% Similarity=0.300 Sum_probs=24.1
Q ss_pred CcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300 47 LSMRKIGDQFNLADSTVWSCIDSFLTA 73 (307)
Q Consensus 47 ~~~~~l~~~fgvs~stv~r~v~~~~~~ 73 (307)
.|+.++|...|+|.+|+.+-+++..+.
T Consensus 23 ~~~~eia~~lglS~~~v~~Ri~~L~~~ 49 (154)
T COG1522 23 ISNAELAERVGLSPSTVLRRIKRLEEE 49 (154)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 789999999999999999988887554
No 394
>TIGR03454 partition_RepB plasmid partitioning protein RepB. Members of this family are the RepB protein involved in replicon partitioning. RepB is found, in general, as part of a repABC operon in plasmids and small chromosomes, separate from the main chromosome, in various bacteria. This model describes a rather narrow clade of proteins; it should be noted that additional homologs scoring below the trusted cutoff have very similar functions, although they may be named differently.
Probab=55.83 E-value=28 Score=31.91 Aligned_cols=44 Identities=9% Similarity=0.028 Sum_probs=37.9
Q ss_pred CCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHH
Q psy4300 27 VPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSF 70 (307)
Q Consensus 27 ~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~ 70 (307)
+..++..++.......+..|.+...++..+|++++++++++.-.
T Consensus 158 R~dLS~iE~A~~~~~L~~~G~~~~~ia~~Lg~~ks~vSr~lsl~ 201 (325)
T TIGR03454 158 RRDLSFIERALFAQRLEDRGFDRDTIMAALSVDKTELSRMISVA 201 (325)
T ss_pred ccCCCHHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 57889988877777777889999999999999999999988743
No 395
>PRK11564 stationary phase inducible protein CsiE; Provisional
Probab=55.77 E-value=32 Score=32.67 Aligned_cols=50 Identities=8% Similarity=0.102 Sum_probs=39.0
Q ss_pred CCCCCHHHHHHHHHHHH---hcCCcHHHHHhhhCCChhhHHHHHHHHHHHccc
Q psy4300 27 VPFVPVEKKTLVALSYM---ATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQ 76 (307)
Q Consensus 27 ~~~~~~~~~l~i~L~~L---~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~ 76 (307)
.+-++.+++....+.+| ..+.+..+++..++||++|+.+-++++-..+..
T Consensus 8 ~~~~s~~ER~~~il~~LL~~~~~v~l~~Lae~l~VSrsTi~~DLk~l~~~L~~ 60 (426)
T PRK11564 8 PSVLSAPQRRCQILLMLFQPGLTVTLETFSQLNGVDDDTARQDIAETGREIQR 60 (426)
T ss_pred CcCCCHHHHHHHHHHHHhcCCCCccHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 45677877766555443 345889999999999999999999998777755
No 396
>PRK10341 DNA-binding transcriptional activator TdcA; Provisional
Probab=54.76 E-value=23 Score=31.79 Aligned_cols=44 Identities=11% Similarity=0.129 Sum_probs=35.4
Q ss_pred HHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 34 KKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 34 ~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
.+|-. +.-+....|++..|...++|+|++|+.+++.-..+-..|
T Consensus 10 ~~L~~-F~av~e~gs~s~AA~~L~iSQpavS~~I~~LE~~lg~~L 53 (312)
T PRK10341 10 QHLVV-FQEVIRSGSIGSAAKELGLTQPAVSKIINDIEDYFGVEL 53 (312)
T ss_pred HHHHH-HHHHHHcCCHHHHHHHhCCChHHHHHHHHHHHHHhCCeE
Confidence 34444 444455678999999999999999999999999988776
No 397
>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=54.74 E-value=31 Score=25.93 Aligned_cols=27 Identities=15% Similarity=0.341 Sum_probs=19.8
Q ss_pred CCcHHHHHhhh-----CCChhhHHHHHHHHHH
Q psy4300 46 QLSMRKIGDQF-----NLADSTVWSCIDSFLT 72 (307)
Q Consensus 46 g~~~~~l~~~f-----gvs~stv~r~v~~~~~ 72 (307)
..+-.+|.... ++|.+||+|.++.+.+
T Consensus 16 ~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~ 47 (116)
T cd07153 16 HLTAEEIYERLRKKGPSISLATVYRTLELLEE 47 (116)
T ss_pred CCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHh
Confidence 35666666655 7999999998887644
No 398
>PRK03635 chromosome replication initiation inhibitor protein; Validated
Probab=54.52 E-value=27 Score=30.98 Aligned_cols=42 Identities=12% Similarity=0.119 Sum_probs=34.3
Q ss_pred HHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 36 TLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 36 l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
|-.++.... ..+++..|...++|++++|+.++++-..+-..|
T Consensus 7 L~~f~~v~e-~gs~s~AA~~L~isq~avS~~I~~LE~~lg~~L 48 (294)
T PRK03635 7 LEALAAVVR-EGSFERAAQKLHITQSAVSQRIKALEERVGQVL 48 (294)
T ss_pred HHHHHHHHH-cCCHHHHHHHhCCChHHHHHHHHHHHHHhCcee
Confidence 334444444 458999999999999999999999999988876
No 399
>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=54.31 E-value=13 Score=27.18 Aligned_cols=24 Identities=13% Similarity=0.095 Sum_probs=18.0
Q ss_pred cCCcHHHHHhhhCCChhhHHHHHH
Q psy4300 45 TQLSMRKIGDQFNLADSTVWSCID 68 (307)
Q Consensus 45 ~g~~~~~l~~~fgvs~stv~r~v~ 68 (307)
.|.+..+||..+|.|++.|++.+.
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 588999999999999999998765
No 400
>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=54.18 E-value=15 Score=31.69 Aligned_cols=25 Identities=20% Similarity=0.300 Sum_probs=20.8
Q ss_pred cHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300 48 SMRKIGDQFNLADSTVWSCIDSFLT 72 (307)
Q Consensus 48 ~~~~l~~~fgvs~stv~r~v~~~~~ 72 (307)
|-.+|+..||||+.||.+.+.....
T Consensus 26 sE~eLa~~~gVSR~TVR~Al~~L~~ 50 (233)
T TIGR02404 26 SEHELMDQYGASRETVRKALNLLTE 50 (233)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 5568899999999999998887543
No 401
>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=54.09 E-value=15 Score=24.73 Aligned_cols=23 Identities=4% Similarity=0.146 Sum_probs=19.9
Q ss_pred cHHHHHhhhCCChhhHHHHHHHH
Q psy4300 48 SMRKIGDQFNLADSTVWSCIDSF 70 (307)
Q Consensus 48 ~~~~l~~~fgvs~stv~r~v~~~ 70 (307)
+..++|..+|||.+|+.++.++.
T Consensus 2 s~~eva~~~gvs~~tlr~w~~~~ 24 (68)
T cd01104 2 TIGAVARLTGVSPDTLRAWERRY 24 (68)
T ss_pred CHHHHHHHHCcCHHHHHHHHHhC
Confidence 46789999999999999998753
No 402
>PRK01905 DNA-binding protein Fis; Provisional
Probab=53.94 E-value=38 Score=23.75 Aligned_cols=29 Identities=3% Similarity=0.007 Sum_probs=24.1
Q ss_pred HHhcCCcHHHHHhhhCCChhhHHHHHHHH
Q psy4300 42 YMATQLSMRKIGDQFNLADSTVWSCIDSF 70 (307)
Q Consensus 42 ~L~~g~~~~~l~~~fgvs~stv~r~v~~~ 70 (307)
+-.++......|...|+|++|+++.+++.
T Consensus 46 L~~~~gn~s~aAr~LGIsrstL~rklkk~ 74 (77)
T PRK01905 46 MEQAGGNQSLAAEYLGINRNTLRKKLQQH 74 (77)
T ss_pred HHHcCCCHHHHHHHHCCCHHHHHHHHHHh
Confidence 34567789999999999999999888763
No 403
>PRK09986 DNA-binding transcriptional activator XapR; Provisional
Probab=53.85 E-value=25 Score=30.98 Aligned_cols=44 Identities=14% Similarity=0.190 Sum_probs=36.1
Q ss_pred HHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 34 KKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 34 ~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
.+|-+++....+ .|+...|...++|+|+||+.+++.-..+-..|
T Consensus 10 ~~l~~f~~v~~~-gs~t~AA~~L~itq~avS~~i~~LE~~lg~~L 53 (294)
T PRK09986 10 KLLRYFLAVAEE-LHFGRAAARLNISQPPLSIHIKELEDQLGTPL 53 (294)
T ss_pred HHHHHHHHHHHh-cCHHHHHHHhCCCCCHHHHHHHHHHHHhCCee
Confidence 345555555555 48999999999999999999999999888776
No 404
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=53.26 E-value=29 Score=30.30 Aligned_cols=28 Identities=18% Similarity=0.379 Sum_probs=25.4
Q ss_pred CCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300 46 QLSMRKIGDQFNLADSTVWSCIDSFLTA 73 (307)
Q Consensus 46 g~~~~~l~~~fgvs~stv~r~v~~~~~~ 73 (307)
..+..+++..||||++|+.|.++.....
T Consensus 18 ~~~~~eLa~~l~VS~~TiRRdL~~L~~~ 45 (240)
T PRK10411 18 SLTTEALAEQLNVSKETIRRDLNELQTQ 45 (240)
T ss_pred CCcHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 5889999999999999999999998763
No 405
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=53.07 E-value=26 Score=30.78 Aligned_cols=40 Identities=10% Similarity=0.075 Sum_probs=33.3
Q ss_pred HHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 39 ALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 39 ~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
++.-+....+++..|...++|++++|+.+++.-..+-..|
T Consensus 10 ~f~~v~e~~s~t~AA~~L~isqpavS~~I~~LE~~lg~~L 49 (290)
T PRK10837 10 VFAEVLKSGSTTQASVMLALSQSAVSAALTDLEGQLGVQL 49 (290)
T ss_pred HHHHHHHcCCHHHHHHHhCCCccHHHHHHHHHHHHhCCcc
Confidence 3444444569999999999999999999999999887765
No 406
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=52.17 E-value=15 Score=27.65 Aligned_cols=25 Identities=20% Similarity=0.050 Sum_probs=21.3
Q ss_pred HHhcCCcHHHHHhhhCCChhhHHHH
Q psy4300 42 YMATQLSMRKIGDQFNLADSTVWSC 66 (307)
Q Consensus 42 ~L~~g~~~~~l~~~fgvs~stv~r~ 66 (307)
+=+.+.|+...|..+|+|.+||..|
T Consensus 53 Re~~~lSQ~vFA~~L~vs~~Tv~~W 77 (104)
T COG2944 53 REKLGLSQPVFARYLGVSVSTVRKW 77 (104)
T ss_pred HHHhCCCHHHHHHHHCCCHHHHHHH
Confidence 4467899999999999999998774
No 407
>PF12298 Bot1p: Eukaryotic mitochondrial regulator protein ; InterPro: IPR021036 This entry represents Ribosomal protein S35, which localises to the mitochondria in live cells and co-fractionates with purified mitochondrial ribosomes. This group of proteins have a novel function in the control of cell respiration by acting on the mitochondrial protein synthesis machinery and a role in mitochondrial integrity. Observations also indicate that in Schizosaccharomyces pombe (Fission yeast), alterations of mitochondrial function are linked to changes in cell cycle and cell morphology control mechanisms [].
Probab=52.12 E-value=51 Score=27.24 Aligned_cols=42 Identities=14% Similarity=0.227 Sum_probs=38.9
Q ss_pred CCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHH
Q psy4300 27 VPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCID 68 (307)
Q Consensus 27 ~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~ 68 (307)
.+.||-+.+-.|.-.+...|.+.+.||..|||+.+.|.-|++
T Consensus 14 ~~~lse~~r~~Iy~~~~~~~~sv~~vS~~ygi~~~RV~AIvr 55 (172)
T PF12298_consen 14 NPVLSEELREQIYEDVMQDGKSVREVSQKYGIKIQRVEAIVR 55 (172)
T ss_pred CCcCCHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 678999999999999999999999999999999999877776
No 408
>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=51.87 E-value=21 Score=31.04 Aligned_cols=38 Identities=13% Similarity=0.108 Sum_probs=32.7
Q ss_pred HHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 41 SYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 41 ~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
.-++...++...|...++|+|++|+.+++.-..+-..|
T Consensus 6 ~~v~~~gs~~~AA~~L~isqsavS~~i~~LE~~lg~~L 43 (279)
T TIGR03339 6 HAVARCGSFTRAAERLGLSQPTVTDQVRKLEERYGVEL 43 (279)
T ss_pred HHHHhcCCHHHHHHHhcCCchHHHHHHHHHHHHhCCcc
Confidence 34455568999999999999999999999999888776
No 409
>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=51.78 E-value=18 Score=29.25 Aligned_cols=31 Identities=13% Similarity=0.039 Sum_probs=26.3
Q ss_pred HHHHHhcCCcHHHHHhhhCCChhhHHHHHHH
Q psy4300 39 ALSYMATQLSMRKIGDQFNLADSTVWSCIDS 69 (307)
Q Consensus 39 ~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~ 69 (307)
--.+-..|.+..++|...|||+++|+++-+.
T Consensus 31 r~~R~~lGmTq~eLAerlGVS~~tIs~iE~G 61 (150)
T TIGR02612 31 RAIRKALGMSGAQLAGRLGVTPQRVEALEKS 61 (150)
T ss_pred HHHHHHcCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 3346677999999999999999999998763
No 410
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=51.66 E-value=22 Score=27.91 Aligned_cols=47 Identities=19% Similarity=0.193 Sum_probs=40.2
Q ss_pred CHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 31 PVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 31 ~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
+..+...-+..++..|.+.++++...||+.+++.++..++...+...
T Consensus 74 ~~~~~~~~~~~~~~~~~~i~~~a~~l~i~~~~~~r~~~r~~~~~~~~ 120 (129)
T COG3677 74 ALYKIKLQAVTLYMLGLGIRDIARTLGISINTVNRWSKRFGSRVEGL 120 (129)
T ss_pred cchHHHHHHHHHHHcCCCcccHHHHhcccHHHHHHHHHhhcchhhcc
Confidence 44667777777888889999999999999999999999998877665
No 411
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=51.62 E-value=30 Score=30.44 Aligned_cols=42 Identities=12% Similarity=0.103 Sum_probs=35.0
Q ss_pred HHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 37 LVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 37 ~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
+-++..++.-.|+...|...++|+|++|+.+.+.-..+-..|
T Consensus 6 l~~f~~v~~~gs~s~AA~~L~isqpavS~~I~~LE~~lG~~L 47 (275)
T PRK03601 6 LKTFLEVSRTRHFGRAAESLYLTQSAVSFRIRQLENQLGVNL 47 (275)
T ss_pred HHHHHHHHHcCCHHHHHHHhCCChHHHHHHHHHHHHHhCCce
Confidence 334555566678999999999999999999999999887766
No 412
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=50.99 E-value=33 Score=28.59 Aligned_cols=40 Identities=5% Similarity=0.086 Sum_probs=29.8
Q ss_pred HHHHHHHHHHHHhcC--CcHHHHHhhhCCChhhHHHHHHHHH
Q psy4300 32 VEKKTLVALSYMATQ--LSMRKIGDQFNLADSTVWSCIDSFL 71 (307)
Q Consensus 32 ~~~~l~i~L~~L~~g--~~~~~l~~~fgvs~stv~r~v~~~~ 71 (307)
.+++....|.+|... .+..+|+..||+|.+|+.|=+....
T Consensus 5 ~~~R~~~Il~~l~~~~~~~~~~La~~~~vS~~TiRRDl~~L~ 46 (185)
T PRK04424 5 KKERQKALQELIEENPFITDEELAEKFGVSIQTIRLDRMELG 46 (185)
T ss_pred HHHHHHHHHHHHHHCCCEEHHHHHHHHCcCHHHHHHHHHHHh
Confidence 345555666666443 6788999999999999998777653
No 413
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=50.91 E-value=29 Score=28.35 Aligned_cols=47 Identities=23% Similarity=0.318 Sum_probs=38.0
Q ss_pred CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
+++..+.. .|.+|..|.+..++|...++|..||...+.+...-+.-.
T Consensus 149 ~lt~re~~--vl~~l~~g~s~~eIa~~l~~s~~tv~~~~~~~~~kl~~~ 195 (210)
T PRK09935 149 VLSNREVT--ILRYLVSGLSNKEIADQLLLSNKTVSAHKSNIYGKLGLH 195 (210)
T ss_pred cCCHHHHH--HHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHcCCC
Confidence 45665554 556799999999999999999999999999887766543
No 414
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=50.81 E-value=34 Score=27.75 Aligned_cols=33 Identities=6% Similarity=0.014 Sum_probs=25.8
Q ss_pred HHHHHHHH--hcCCcHHHHHhhhCCChhhHHHHHH
Q psy4300 36 TLVALSYM--ATQLSMRKIGDQFNLADSTVWSCID 68 (307)
Q Consensus 36 l~i~L~~L--~~g~~~~~l~~~fgvs~stv~r~v~ 68 (307)
+.-.|..+ ..|.|+.+||...|++++++++|-+
T Consensus 70 ~g~~Ir~~Re~~glSqeeLA~~lgvs~s~IsriE~ 104 (154)
T TIGR00270 70 YGIIIRREREKRGWSQEQLAKKIQEKESLIKKIEN 104 (154)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHC
Confidence 33445544 5699999999999999999998653
No 415
>PF13843 DDE_Tnp_1_7: Transposase IS4
Probab=50.36 E-value=69 Score=29.45 Aligned_cols=89 Identities=15% Similarity=0.161 Sum_probs=56.4
Q ss_pred CCCCcceeecceeEEeecCCCCccccccccCCcceeEEeeeC-CCcceEeeeeccccccCCCccccc----chh-hcchh
Q psy4300 104 KFPGVIGAIDGCHIEGKFSKDIRNDYNNRKCTQSMILQGVCT-SNKLLTNIHVGCTGRNHDAKVLST----SQI-GRRID 177 (307)
Q Consensus 104 ~~p~~~g~iDgt~i~i~~P~~~~~~y~~~k~~~s~~~q~v~d-~~g~i~~v~~~~~Gs~~D~~i~~~----S~l-~~~l~ 177 (307)
--|+-..+||-.-++..-.......-.++...+++|+-++|| .+|.++++.. +.|.......-++ ..+ .++++
T Consensus 124 y~P~~~lsvDE~mv~~~gr~~~~~~~~~Kp~k~G~k~~~l~d~~tgy~~~~~~-~~g~~~~~~~~~~~~~~~~vV~~L~~ 202 (351)
T PF13843_consen 124 YSPSQNLSVDESMVPFKGRSPFKQYIPNKPHKWGIKLWVLCDSSTGYILNFEL-YEGKDREVPNPRELGLGQAVVLRLTE 202 (351)
T ss_pred ccccceEEEecccccccccchhhhccccccCCCceeEEEEeccCcceeeeeEE-EccCccccccccccCchhhhHHHhhh
Confidence 458888899999987753333333333666789999999999 7888888777 4555444332111 111 22222
Q ss_pred hcCCCCCCCCCCeEEEecCCCC
Q psy4300 178 AYGPTSLLYRDEYHLLGDSAYP 199 (307)
Q Consensus 178 ~~~~~~~~~~~~~~llgD~gY~ 199 (307)
. ....++.|..|..|-
T Consensus 203 ~------~~~~g~~v~~Dn~ft 218 (351)
T PF13843_consen 203 P------LQGKGHHVYFDNFFT 218 (351)
T ss_pred h------hcccCcEEEEcCccc
Confidence 2 224578999999884
No 416
>PRK13832 plasmid partitioning protein; Provisional
Probab=50.00 E-value=37 Score=33.04 Aligned_cols=42 Identities=7% Similarity=-0.140 Sum_probs=37.9
Q ss_pred CCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHH
Q psy4300 27 VPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCID 68 (307)
Q Consensus 27 ~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~ 68 (307)
+..+++-++...+-.....|.+..+||..||+|+++|.+...
T Consensus 99 RedL~PiEea~AfkrLie~G~T~EeIA~~lG~S~~~V~rlll 140 (520)
T PRK13832 99 REPLNPVDQWRAIERLVALGWTEEAIAVALALPVRQIRKLRL 140 (520)
T ss_pred cCCCCHHHHHHHHHHHHhcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 578999999999988889999999999999999999998544
No 417
>PRK10086 DNA-binding transcriptional regulator DsdC; Provisional
Probab=49.94 E-value=28 Score=31.19 Aligned_cols=42 Identities=19% Similarity=0.192 Sum_probs=35.0
Q ss_pred HHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 37 LVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 37 ~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
+-++.-++...+++..|...++|+||+|+-+++.-..+-..|
T Consensus 19 L~~f~~va~~gs~s~AA~~L~iSQpavS~~I~~LE~~lG~~L 60 (311)
T PRK10086 19 LHTFEVAARHQSFALAADELSLTPSAVSHRINQLEEELGIKL 60 (311)
T ss_pred HHHHHHHHHcCCHHHHHHHHCCCHHHHHHHHHHHHHHhCCee
Confidence 444455566678999999999999999999999999987665
No 418
>PRK10632 transcriptional regulator; Provisional
Probab=49.82 E-value=26 Score=31.41 Aligned_cols=38 Identities=8% Similarity=0.072 Sum_probs=32.8
Q ss_pred HHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 41 SYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 41 ~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
..++...|++..|...++|+|++|+.+++.-..+-..|
T Consensus 11 ~~v~e~gS~t~AA~~L~isQpavS~~I~~LE~~lg~~L 48 (309)
T PRK10632 11 AKVVEFGSFTAAARQLQMSVSSISQTVSKLEDELQVKL 48 (309)
T ss_pred HHHHhcCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCee
Confidence 34455578999999999999999999999999888776
No 419
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=49.76 E-value=35 Score=30.03 Aligned_cols=42 Identities=17% Similarity=0.282 Sum_probs=33.6
Q ss_pred HHHHHHHHHHHHhcC--CcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300 32 VEKKTLVALSYMATQ--LSMRKIGDQFNLADSTVWSCIDSFLTA 73 (307)
Q Consensus 32 ~~~~l~i~L~~L~~g--~~~~~l~~~fgvs~stv~r~v~~~~~~ 73 (307)
.+++....|-+|... .+..+|+..|+||..|+.|-+......
T Consensus 3 ~~eR~~~Il~~L~~~~~v~v~eLa~~l~VS~~TIRRDL~~Le~~ 46 (256)
T PRK10434 3 PRQRQAAILEYLQKQGKTSVEELAQYFDTTGTTIRKDLVILEHA 46 (256)
T ss_pred HHHHHHHHHHHHHHcCCEEHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 356666677777653 689999999999999999999987654
No 420
>PF02650 HTH_WhiA: WhiA C-terminal HTH domain; InterPro: IPR023054 This domain is found at the C terminus of the sporulation regulator WhiA. It is predicted to form a DNA binding helix-turn-helix structure []. ; PDB: 3HYI_A.
Probab=49.68 E-value=69 Score=23.13 Aligned_cols=45 Identities=13% Similarity=0.258 Sum_probs=30.4
Q ss_pred CCCCHHHHHHHHHHHHhcCCcHHHHHhhh--CCChhhHHHHHHHHHH
Q psy4300 28 PFVPVEKKTLVALSYMATQLSMRKIGDQF--NLADSTVWSCIDSFLT 72 (307)
Q Consensus 28 ~~~~~~~~l~i~L~~L~~g~~~~~l~~~f--gvs~stv~r~v~~~~~ 72 (307)
..+|...+-+.-|+.=--..|..+||..+ .||+|++.-.+.++..
T Consensus 36 ~~l~~~l~~~a~lRl~~Pd~SL~EL~~~~~~~iSKSgvnhrlrKl~~ 82 (85)
T PF02650_consen 36 DKLPEKLREFAELRLENPDASLKELGELLEPPISKSGVNHRLRKLKK 82 (85)
T ss_dssp GGS-HHHHHHHHHHHH-TTS-HHHHHHTT--T--HHHHHHHHHHHHH
T ss_pred ccCCHHHHHHHHHHHHCccccHHHHHHHHcCcCcHHHHHHHHHHHHH
Confidence 45666666555555555569999999999 9999999988887654
No 421
>COG3311 AlpA Predicted transcriptional regulator [Transcription]
Probab=49.65 E-value=15 Score=25.51 Aligned_cols=43 Identities=19% Similarity=0.343 Sum_probs=29.2
Q ss_pred CcHHHHHhhhCCChhhHHHHHHHHHHHccccccccccccCCChH
Q psy4300 47 LSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQIQCQYIKWPTEE 90 (307)
Q Consensus 47 ~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l~~~~~i~~P~~~ 90 (307)
....+++...|+|+||+++.++.-.-==-.. +....+.|+..+
T Consensus 14 lrl~ev~~~~GlSrstiYr~i~~~~FPkpvk-lG~r~v~W~~SE 56 (70)
T COG3311 14 LRLPEVAQLTGLSRSTIYRLIKDGTFPKPVK-LGGRSVAWPESE 56 (70)
T ss_pred hhHHHHHHHHCccHHHHHHHHccCCCCCCee-cCcccccccHHH
Confidence 3567899999999999999998751000001 144667788775
No 422
>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=49.09 E-value=35 Score=30.43 Aligned_cols=40 Identities=13% Similarity=0.172 Sum_probs=33.5
Q ss_pred HHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 39 ALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 39 ~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
++.-++...|+...|...++|+||||+-++.....+-..|
T Consensus 15 ~F~~va~~gs~s~AA~~L~isQpavS~~I~~LE~~lg~~L 54 (302)
T TIGR02036 15 TFEVAARHQSFSLAAEELSLTPSAISHRINQLEEELGIQL 54 (302)
T ss_pred HHHHHHHhCCHHHHHHHHCCCHHHHHHHHHHHHHHhCCce
Confidence 3344455568999999999999999999999999888775
No 423
>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=49.02 E-value=20 Score=30.81 Aligned_cols=26 Identities=15% Similarity=0.330 Sum_probs=21.8
Q ss_pred CcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300 47 LSMRKIGDQFNLADSTVWSCIDSFLT 72 (307)
Q Consensus 47 ~~~~~l~~~fgvs~stv~r~v~~~~~ 72 (307)
.|-.+|+..||||+.||.+.+.....
T Consensus 33 PsE~eLa~~~~VSR~TvR~Al~~L~~ 58 (238)
T TIGR02325 33 PAEMQLAERFGVNRHTVRRAIAALVE 58 (238)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 36679999999999999998887543
No 424
>PRK11482 putative DNA-binding transcriptional regulator; Provisional
Probab=48.83 E-value=33 Score=30.96 Aligned_cols=43 Identities=14% Similarity=0.203 Sum_probs=35.1
Q ss_pred HHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 36 TLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 36 l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
.+-++.-+....+++..|...++|++++|+.+++.-..+-..|
T Consensus 33 ~L~~f~av~e~gs~s~AA~~L~isQpavS~~I~~LE~~lG~~L 75 (317)
T PRK11482 33 LLTIFEAVYVHKGIVNAAKILNLTPSAISQSIQKLRVIFPDPL 75 (317)
T ss_pred HHHHHHHHHHcCCHHHHHHHhCCChHHHHHHHHHHHHHhCCcc
Confidence 3444444555569999999999999999999999999887776
No 425
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=48.60 E-value=21 Score=30.98 Aligned_cols=26 Identities=12% Similarity=0.346 Sum_probs=21.8
Q ss_pred CcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300 47 LSMRKIGDQFNLADSTVWSCIDSFLT 72 (307)
Q Consensus 47 ~~~~~l~~~fgvs~stv~r~v~~~~~ 72 (307)
.+-.+|+..||||+.||.+.+.....
T Consensus 36 PsE~eLa~~~~VSR~TVR~Al~~L~~ 61 (241)
T PRK10079 36 PAEQQLAARYEVNRHTLRRAIDQLVE 61 (241)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 36678999999999999998887643
No 426
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=48.35 E-value=25 Score=23.99 Aligned_cols=25 Identities=12% Similarity=0.428 Sum_probs=18.2
Q ss_pred CCcHHHHHhhhCCChhhHHHHHHHH
Q psy4300 46 QLSMRKIGDQFNLADSTVWSCIDSF 70 (307)
Q Consensus 46 g~~~~~l~~~fgvs~stv~r~v~~~ 70 (307)
..+..+||..|++|.+++.-.+..+
T Consensus 14 ~~S~~eLa~~~~~s~~~ve~mL~~l 38 (69)
T PF09012_consen 14 RVSLAELAREFGISPEAVEAMLEQL 38 (69)
T ss_dssp SEEHHHHHHHTT--HHHHHHHHHHH
T ss_pred CcCHHHHHHHHCcCHHHHHHHHHHH
Confidence 4799999999999999966655544
No 427
>PRK06424 transcription factor; Provisional
Probab=48.34 E-value=27 Score=28.01 Aligned_cols=26 Identities=8% Similarity=-0.020 Sum_probs=23.0
Q ss_pred HhcCCcHHHHHhhhCCChhhHHHHHH
Q psy4300 43 MATQLSMRKIGDQFNLADSTVWSCID 68 (307)
Q Consensus 43 L~~g~~~~~l~~~fgvs~stv~r~v~ 68 (307)
-..|.++.+||...|++++++++|-+
T Consensus 94 e~~GLSQ~eLA~~iGvs~stIskiE~ 119 (144)
T PRK06424 94 ERLSMSQADLAAKIFERKNVIASIER 119 (144)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHC
Confidence 36799999999999999999998754
No 428
>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=48.24 E-value=42 Score=28.10 Aligned_cols=27 Identities=19% Similarity=0.202 Sum_probs=23.2
Q ss_pred CCcHHHHHhhhCCC-hhhHHHHHHHHHH
Q psy4300 46 QLSMRKIGDQFNLA-DSTVWSCIDSFLT 72 (307)
Q Consensus 46 g~~~~~l~~~fgvs-~stv~r~v~~~~~ 72 (307)
+.+.++||..+|++ ++|+++.+.....
T Consensus 25 ~~~~~ela~~~~~~s~~tv~~~l~~L~~ 52 (199)
T TIGR00498 25 PPSIREIARAVGLRSPSAAEEHLKALER 52 (199)
T ss_pred CCcHHHHHHHhCCCChHHHHHHHHHHHH
Confidence 37788999999998 9999998887654
No 429
>PF07022 Phage_CI_repr: Bacteriophage CI repressor helix-turn-helix domain; InterPro: IPR010744 This family consists of several phage CI repressor proteins and related bacterial sequences. The CI repressor is known to function as a transcriptional switch, determining whether transcription is lytic or lysogenic [].; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2FJR_B.
Probab=48.22 E-value=15 Score=25.00 Aligned_cols=22 Identities=14% Similarity=0.256 Sum_probs=16.2
Q ss_pred CcHHHHHhhhCCChhhHH-HHHH
Q psy4300 47 LSMRKIGDQFNLADSTVW-SCID 68 (307)
Q Consensus 47 ~~~~~l~~~fgvs~stv~-r~v~ 68 (307)
.+..++|..+|||++|++ .+..
T Consensus 13 ~~~~~lA~~lgis~st~s~~~~~ 35 (66)
T PF07022_consen 13 KSDKELAERLGISKSTLSNNWKK 35 (66)
T ss_dssp SSCHHHHCCTT--HHHHH-HHHH
T ss_pred CCHHHHHHHhCcCHHHhhHHHHh
Confidence 456799999999999998 6554
No 430
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=48.22 E-value=50 Score=28.36 Aligned_cols=28 Identities=7% Similarity=0.315 Sum_probs=24.1
Q ss_pred cCCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300 45 TQLSMRKIGDQFNLADSTVWSCIDSFLT 72 (307)
Q Consensus 45 ~g~~~~~l~~~fgvs~stv~r~v~~~~~ 72 (307)
.+.|-.++|...|+|+.|+.|++.....
T Consensus 172 ~~~Taeela~~~giSRvTaRRYLeyl~~ 199 (224)
T COG4565 172 QELTAEELAQALGISRVTARRYLEYLVS 199 (224)
T ss_pred CccCHHHHHHHhCccHHHHHHHHHHHHh
Confidence 5678889999999999999999887654
No 431
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=48.22 E-value=17 Score=28.02 Aligned_cols=25 Identities=4% Similarity=0.119 Sum_probs=22.2
Q ss_pred hcCCcHHHHHhhhCCChhhHHHHHH
Q psy4300 44 ATQLSMRKIGDQFNLADSTVWSCID 68 (307)
Q Consensus 44 ~~g~~~~~l~~~fgvs~stv~r~v~ 68 (307)
..|.+..++|...|+|+++++++.+
T Consensus 16 ~~Glsq~eLA~~~Gis~~~is~iE~ 40 (120)
T PRK13890 16 ERHMTKKELSERSGVSISFLSDLTT 40 (120)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHc
Confidence 5689999999999999999998764
No 432
>PRK14999 histidine utilization repressor; Provisional
Probab=48.19 E-value=21 Score=30.91 Aligned_cols=26 Identities=12% Similarity=0.169 Sum_probs=22.3
Q ss_pred CcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300 47 LSMRKIGDQFNLADSTVWSCIDSFLT 72 (307)
Q Consensus 47 ~~~~~l~~~fgvs~stv~r~v~~~~~ 72 (307)
.+-.+|+..||||+.||.+.+.....
T Consensus 37 PsE~eLa~~~gVSR~TVR~Al~~L~~ 62 (241)
T PRK14999 37 PSEAELVAQYGFSRMTINRALRELTD 62 (241)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 37789999999999999999887543
No 433
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=47.87 E-value=45 Score=29.31 Aligned_cols=41 Identities=10% Similarity=0.256 Sum_probs=31.2
Q ss_pred HHHHHHHHHHHhcC--CcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300 33 EKKTLVALSYMATQ--LSMRKIGDQFNLADSTVWSCIDSFLTA 73 (307)
Q Consensus 33 ~~~l~i~L~~L~~g--~~~~~l~~~fgvs~stv~r~v~~~~~~ 73 (307)
.++..-.|.+|... .+..+|+..|+||..|+.|-+....+.
T Consensus 4 ~~R~~~Il~~l~~~~~~~~~ela~~l~vS~~TiRRdL~~Le~~ 46 (252)
T PRK10906 4 TQRHDAIIELVKQQGYVSTEELVEHFSVSPQTIRRDLNDLAEQ 46 (252)
T ss_pred HHHHHHHHHHHHHcCCEeHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence 34455555555443 688899999999999999998887764
No 434
>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=47.87 E-value=22 Score=30.58 Aligned_cols=25 Identities=16% Similarity=0.179 Sum_probs=21.1
Q ss_pred cHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300 48 SMRKIGDQFNLADSTVWSCIDSFLT 72 (307)
Q Consensus 48 ~~~~l~~~fgvs~stv~r~v~~~~~ 72 (307)
+-++|+..||||+.||.+.+.....
T Consensus 27 sE~eLa~~~~VSR~TVR~Al~~L~~ 51 (230)
T TIGR02018 27 SEHELVAQYGCSRMTVNRALRELTD 51 (230)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 5668899999999999998887654
No 435
>PF00376 MerR: MerR family regulatory protein; InterPro: IPR000551 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these is the MerR subfamily. MerR, which is found in many bacterial species mediates the mercuric-dependent induction of the mercury resistance operon. In the absence of mercury merR represses transcription by binding tightly, as a dimer, to the 'mer' operator region; when mercury is present the dimeric complex binds a single ion and becomes a potent transcriptional activator, while remaining bound to the mer site. Members of the family include the mercuric resistance operon regulatory protein merR; Bacillus subtilis bltR and bmrR; Bacillus glnR; Streptomyces coelicolor hspR; Bradyrhizobium japonicum nolA; Escherichia coli superoxide response regulator soxR; and Streptomyces lividans transcriptional activator tipA [, , , , , ]. Other members include hypothetical proteins from E. coli, B. subtilis and Haemophilus influenzae. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3HH0_A 2DG6_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q07_A 1Q06_A 1Q05_B ....
Probab=47.73 E-value=19 Score=21.55 Aligned_cols=21 Identities=5% Similarity=0.115 Sum_probs=15.9
Q ss_pred HHHHHhhhCCChhhHHHHHHH
Q psy4300 49 MRKIGDQFNLADSTVWSCIDS 69 (307)
Q Consensus 49 ~~~l~~~fgvs~stv~r~v~~ 69 (307)
..++|..+|||.+|+..+-..
T Consensus 2 i~e~A~~~gvs~~tlR~ye~~ 22 (38)
T PF00376_consen 2 IGEVAKLLGVSPRTLRYYERE 22 (38)
T ss_dssp HHHHHHHHTS-HHHHHHHHHT
T ss_pred HHHHHHHHCCCHHHHHHHHHC
Confidence 468899999999998776543
No 436
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=47.50 E-value=38 Score=30.08 Aligned_cols=46 Identities=4% Similarity=0.108 Sum_probs=37.4
Q ss_pred CCCCCHHHHHHHHHHHHhcC--CcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300 27 VPFVPVEKKTLVALSYMATQ--LSMRKIGDQFNLADSTVWSCIDSFLT 72 (307)
Q Consensus 27 ~~~~~~~~~l~i~L~~L~~g--~~~~~l~~~fgvs~stv~r~v~~~~~ 72 (307)
++.-...++....+.+|... .+..+|+..||||..|+.|=+.....
T Consensus 10 ~~~~~~~eR~~~Il~~L~~~~~vtv~eLa~~l~VS~~TIRRDL~~Le~ 57 (269)
T PRK09802 10 KRVTGTSERREQIIQRLRQQGSVQVNDLSALYGVSTVTIRNDLAFLEK 57 (269)
T ss_pred hhhccHHHHHHHHHHHHHHcCCEeHHHHHHHHCCCHHHHHHHHHHHHh
Confidence 34455578888888888664 68889999999999999999988754
No 437
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=47.40 E-value=29 Score=29.45 Aligned_cols=33 Identities=3% Similarity=0.137 Sum_probs=27.5
Q ss_pred HHHHHHhcC---CcHHHHHhhhCCChhhHHHHHHHH
Q psy4300 38 VALSYMATQ---LSMRKIGDQFNLADSTVWSCIDSF 70 (307)
Q Consensus 38 i~L~~L~~g---~~~~~l~~~fgvs~stv~r~v~~~ 70 (307)
-+|..++.| .+..++|...++|..||.+++...
T Consensus 166 ~Vl~~~~~g~~g~s~~eIa~~l~iS~~Tv~~~~~~~ 201 (225)
T PRK10046 166 AVRKLFKEPGVQHTAETVAQALTISRTTARRYLEYC 201 (225)
T ss_pred HHHHHHHcCCCCcCHHHHHHHhCccHHHHHHHHHHH
Confidence 456677774 799999999999999999988754
No 438
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=47.19 E-value=36 Score=30.90 Aligned_cols=35 Identities=20% Similarity=0.457 Sum_probs=27.6
Q ss_pred HHHHHHhc--CCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300 38 VALSYMAT--QLSMRKIGDQFNLADSTVWSCIDSFLT 72 (307)
Q Consensus 38 i~L~~L~~--g~~~~~l~~~fgvs~stv~r~v~~~~~ 72 (307)
-.|..|.. ..+..+||..+|+|++||++.+.....
T Consensus 8 ~il~~L~~~~~~s~~~LA~~lgvsr~tV~~~l~~L~~ 44 (319)
T PRK11886 8 QLLSLLADGDFHSGEQLGEELGISRAAIWKHIQTLEE 44 (319)
T ss_pred HHHHHHHcCCCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 33444444 367789999999999999999999886
No 439
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=46.95 E-value=45 Score=23.61 Aligned_cols=32 Identities=9% Similarity=0.207 Sum_probs=25.4
Q ss_pred hcCCcHHHHHhhhCCChhhHHHHHHHHHHHcc
Q psy4300 44 ATQLSMRKIGDQFNLADSTVWSCIDSFLTAMS 75 (307)
Q Consensus 44 ~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~ 75 (307)
....+|.+|....|++.+++++.++...++=+
T Consensus 12 ~~~~~f~~L~~~l~lt~g~Ls~hL~~Le~~Gy 43 (80)
T PF13601_consen 12 NEEATFSELKEELGLTDGNLSKHLKKLEEAGY 43 (80)
T ss_dssp HSEEEHHHHHHHTT--HHHHHHHHHHHHHTTS
T ss_pred cCCCCHHHHHHHhCcCHHHHHHHHHHHHHCCC
Confidence 45699999999999999999999988776543
No 440
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=46.87 E-value=12 Score=36.15 Aligned_cols=22 Identities=18% Similarity=0.443 Sum_probs=20.2
Q ss_pred CcHHHHHhhhCCChhhHHHHHH
Q psy4300 47 LSMRKIGDQFNLADSTVWSCID 68 (307)
Q Consensus 47 ~~~~~l~~~fgvs~stv~r~v~ 68 (307)
++..++|...|++.|||||+++
T Consensus 344 LtlkdvAe~lglheSTVSRav~ 365 (455)
T PRK05932 344 LVLKDIAEELGMHESTISRATT 365 (455)
T ss_pred ccHHHHHHHhCCCccchhhhhc
Confidence 6889999999999999999873
No 441
>PRK15243 transcriptional regulator SpvR; Provisional
Probab=46.80 E-value=44 Score=30.13 Aligned_cols=44 Identities=16% Similarity=0.152 Sum_probs=35.2
Q ss_pred HHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 34 KKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 34 ~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
.+|-.++....+ .|++..|...++||||+|+.+++.-..+-..|
T Consensus 7 rqL~~F~aVae~-gSfs~AA~~L~isQpavS~~Ik~LE~eLG~~L 50 (297)
T PRK15243 7 KKLKIFITLMET-GSFSIATSVLYITRTPLSRVISDLERELKQRL 50 (297)
T ss_pred HHHHHHHHHHHc-CCHHHHHHHHCcCHHHHHHHHHHHHHHhCCcc
Confidence 344444444444 58999999999999999999999999887775
No 442
>PRK10082 cell density-dependent motility repressor; Provisional
Probab=46.60 E-value=41 Score=29.97 Aligned_cols=41 Identities=7% Similarity=0.012 Sum_probs=34.3
Q ss_pred HHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 38 VALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 38 i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
-++.-+..-.|++..|...++|++++|+.+++....+-..|
T Consensus 17 ~~F~av~e~gS~t~AA~~L~iSQpavS~~I~~LE~~lG~~L 57 (303)
T PRK10082 17 YDFLTLEKCRNFSQAAVSRNVSQPAFSRRIRALEQAIGVEL 57 (303)
T ss_pred HHHHHHHhcCCHHHHHHHhCCChHHHHHHHHHHHHHcCCEE
Confidence 33444455578999999999999999999999999988776
No 443
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=46.50 E-value=22 Score=29.51 Aligned_cols=27 Identities=19% Similarity=0.165 Sum_probs=23.4
Q ss_pred HHhcCCcHHHHHhhhCCChhhHHHHHH
Q psy4300 42 YMATQLSMRKIGDQFNLADSTVWSCID 68 (307)
Q Consensus 42 ~L~~g~~~~~l~~~fgvs~stv~r~v~ 68 (307)
+...|.+..++|...|+|++|++++-+
T Consensus 16 R~~~glt~~elA~~~gis~~~is~~E~ 42 (185)
T PRK09943 16 RQQQGLSQRRAAELSGLTHSAISTIEQ 42 (185)
T ss_pred HHHcCCCHHHHHHHHCCCHHHHHHHHc
Confidence 346689999999999999999998764
No 444
>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=46.36 E-value=42 Score=33.13 Aligned_cols=43 Identities=5% Similarity=-0.032 Sum_probs=37.4
Q ss_pred CCCCCHHHHHHHHHHHHhcCC-cHHHHHhhhCCChhhHHHHHHH
Q psy4300 27 VPFVPVEKKTLVALSYMATQL-SMRKIGDQFNLADSTVWSCIDS 69 (307)
Q Consensus 27 ~~~~~~~~~l~i~L~~L~~g~-~~~~l~~~fgvs~stv~r~v~~ 69 (307)
+..+++.++...+...+..|. +..+++..||+|+++|++.+.-
T Consensus 89 RedLtP~EeA~A~~rLl~~g~~t~eeIA~~lG~S~~~V~rrLkL 132 (554)
T TIGR03734 89 RADMSPAEEAEAAARLLGRCKGDREEAARRLGWSPATLDRRLAL 132 (554)
T ss_pred cCCCCHHHHHHHHHHHhhhcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 578999999988888887776 8999999999999999998763
No 445
>PF09182 PuR_N: Bacterial purine repressor, N-terminal; InterPro: IPR015265 The N-terminal domain of the bacterial purine repressor PuR is a winged-helix domain, a subdivision of the HTH structural family. It consists of a canonical arrangement of secondary structures: a1-b1-a2-T-a3-b2-W-b3, where a2-T-a3 is the HTH motif, a3 is the recognition helix, and W is the wing. The domain allows for recognition of a conserved CGAA sequence in the centre of a DNA PurBox, resulting in binding to the major groove of DNA []. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1O57_B 1P4A_D.
Probab=46.19 E-value=67 Score=22.29 Aligned_cols=32 Identities=16% Similarity=0.381 Sum_probs=21.2
Q ss_pred HHHHHHHHHHhcC----CcHHHHHhhhCCChhhHHH
Q psy4300 34 KKTLVALSYMATQ----LSMRKIGDQFNLADSTVWS 65 (307)
Q Consensus 34 ~~l~i~L~~L~~g----~~~~~l~~~fgvs~stv~r 65 (307)
++|...-.+|-.+ .+....+..|+.++||+|.
T Consensus 4 eRlv~it~~L~~~P~~lisL~~Fae~f~~AKSsISE 39 (70)
T PF09182_consen 4 ERLVAITKYLLENPNKLISLTYFAERFGAAKSSISE 39 (70)
T ss_dssp HHHHHHHHHHHTSTT--EEHHHHHHHHT--HHHHHH
T ss_pred hHHHHHHHHHHcCCcceEcHHHHHHHhcccccchHH
Confidence 4455555555443 5778999999999999775
No 446
>PRK06474 hypothetical protein; Provisional
Probab=46.12 E-value=46 Score=27.58 Aligned_cols=41 Identities=7% Similarity=0.242 Sum_probs=28.5
Q ss_pred HHHHHHHHHHHhcC--CcHHHHHhhh-CCChhhHHHHHHHHHHH
Q psy4300 33 EKKTLVALSYMATQ--LSMRKIGDQF-NLADSTVWSCIDSFLTA 73 (307)
Q Consensus 33 ~~~l~i~L~~L~~g--~~~~~l~~~f-gvs~stv~r~v~~~~~~ 73 (307)
..++.|.-....++ .+-.+|+..+ ++|++|+++.++.+.++
T Consensus 11 p~R~~Il~~L~~~~~~~ta~el~~~l~~is~aTvYrhL~~L~e~ 54 (178)
T PRK06474 11 PVRMKICQVLMRNKEGLTPLELVKILKDVPQATLYRHLQTMVDS 54 (178)
T ss_pred HHHHHHHHHHHhCCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHC
Confidence 33444443333443 6888999988 79999999998877543
No 447
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=45.93 E-value=24 Score=30.55 Aligned_cols=25 Identities=12% Similarity=0.306 Sum_probs=21.2
Q ss_pred cHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300 48 SMRKIGDQFNLADSTVWSCIDSFLT 72 (307)
Q Consensus 48 ~~~~l~~~fgvs~stv~r~v~~~~~ 72 (307)
+-.+|+..||||+.||.+.+.....
T Consensus 31 sE~eL~~~~~VSR~TvR~Al~~L~~ 55 (240)
T PRK09764 31 TESALQTEFGVSRVTVRQALRQLVE 55 (240)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 5678999999999999998887643
No 448
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=45.82 E-value=42 Score=28.74 Aligned_cols=34 Identities=6% Similarity=0.074 Sum_probs=30.5
Q ss_pred hcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 44 ATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 44 ~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
+.|.+..++|..+++|..||..++.+..+.....
T Consensus 176 ~~g~s~~eIA~~l~iS~~Tv~~~~~~~~~~~~~~ 209 (239)
T PRK10430 176 DYEFSTDELANAVNISRVSCRKYLIWLVNCHILF 209 (239)
T ss_pred CCCcCHHHHHHHhCchHHHHHHHHHHHHhCCEEE
Confidence 5899999999999999999999999987776663
No 449
>PF05584 Sulfolobus_pRN: Sulfolobus plasmid regulatory protein; InterPro: IPR008848 This family consists of several plasmid regulatory proteins from the extreme thermophilic and acidophilic archaea Sulfolobus.
Probab=45.81 E-value=84 Score=21.96 Aligned_cols=41 Identities=15% Similarity=0.265 Sum_probs=31.9
Q ss_pred CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHH
Q psy4300 29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFL 71 (307)
Q Consensus 29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~ 71 (307)
.++..+.+++.|-.= +++...+-...|+++.++..++.++.
T Consensus 3 klt~~~~IL~~ls~~--c~TLeeL~ekTgi~k~~LlV~LsrL~ 43 (72)
T PF05584_consen 3 KLTVTQKILIILSKR--CCTLEELEEKTGISKNTLLVYLSRLA 43 (72)
T ss_pred hhhHHHHHHHHHHhc--cCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 355666666655544 79999999999999999998888764
No 450
>PF03050 DDE_Tnp_IS66: Transposase IS66 family ; InterPro: IPR004291 Transposase proteins are necessary for efficient DNA transposition. This family includes the bacterial insertion sequence (IS) element, IS66, from Agrobacterium tumefaciens []. IS66 may cause genetic and structural variations of the T region and the vir region of the octopine Ti plasmids []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=45.64 E-value=81 Score=27.70 Aligned_cols=74 Identities=12% Similarity=0.061 Sum_probs=52.0
Q ss_pred CCCHHHHHHHHHHHHhcCCcHHHHHhhh-----CCChhhHHHHHHHHHHHccccccccccccCCChHHHHHHHHHHHHhh
Q psy4300 29 FVPVEKKTLVALSYMATQLSMRKIGDQF-----NLADSTVWSCIDSFLTAMSQPQIQCQYIKWPTEEESVIIERNFRALA 103 (307)
Q Consensus 29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~f-----gvs~stv~r~v~~~~~~l~~~l~~~~~i~~P~~~~~~~~~~~f~~~~ 103 (307)
.+++.-.-.+++.....+.|+.-++..| .||.+|+..++.++.+.+... .. .+.....
T Consensus 3 ~~g~~~~a~i~~l~~~~~lp~~r~~~~~~~~G~~is~~ti~~~~~~~~~~l~~~--~~------------~l~~~~~--- 65 (271)
T PF03050_consen 3 RYGPSLLALIAYLKYVYHLPLYRIQQMLEDLGITISRGTIANWIKRVAEALKPL--YE------------ALKEELR--- 65 (271)
T ss_pred cCCHHHHHHHHHHHhcCCCCHHHHhhhhhccceeeccchhHhHhhhhhhhhhhh--hh------------hhhhhcc---
Confidence 4556666666667777789999988887 799999999999998886554 22 1222221
Q ss_pred CCCCcceeecceeEEeec
Q psy4300 104 KFPGVIGAIDGCHIEGKF 121 (307)
Q Consensus 104 ~~p~~~g~iDgt~i~i~~ 121 (307)
..-+--+|-|.+++..
T Consensus 66 --~~~~~~~DET~~~vl~ 81 (271)
T PF03050_consen 66 --SSPVVHADETGWRVLD 81 (271)
T ss_pred --ccceeccCCceEEEec
Confidence 1235578999998765
No 451
>COG4941 Predicted RNA polymerase sigma factor containing a TPR repeat domain [Transcription]
Probab=45.40 E-value=1.3e+02 Score=27.83 Aligned_cols=63 Identities=17% Similarity=0.269 Sum_probs=47.0
Q ss_pred CCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccccccccccCCChHHHH
Q psy4300 27 VPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQIQCQYIKWPTEEESV 93 (307)
Q Consensus 27 ~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l~~~~~i~~P~~~~~~ 93 (307)
.+.++++++++++|+.++ |.|-.+|+..|=|+.+|+-+-|.+--.-|.+. .-.| .-|...++.
T Consensus 118 HPal~~~~riALtLR~v~-GLs~~eIArAFLv~e~am~QRivRAK~ri~~a--giPf-evP~~~e~~ 180 (415)
T COG4941 118 HPALPPEQRIALTLRLVG-GLSTAEIARAFLVPEAAMAQRIVRAKARIREA--GIPF-EVPGPQELP 180 (415)
T ss_pred CCCCChhhHHHHHHHHHc-CCcHHHHHHHHcCCcHHHHHHHHHHHHHHHhc--CCCC-cCCChhhHH
Confidence 578999999999997665 89999999999999999876666665555554 3222 335554443
No 452
>PF07506 RepB: RepB plasmid partitioning protein; InterPro: IPR011111 This family includes proteins with sequence similarity to the RepB partitioning protein of the large Ti (tumour-inducing) plasmids of Agrobacterium tumefaciens [, ].
Probab=45.33 E-value=58 Score=27.08 Aligned_cols=42 Identities=10% Similarity=0.049 Sum_probs=37.7
Q ss_pred CCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHH
Q psy4300 27 VPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCID 68 (307)
Q Consensus 27 ~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~ 68 (307)
+..+|.-++..++......|-+-..|+...|++.+++++.+.
T Consensus 2 R~~Ls~IE~~~fa~~l~~~G~~~~~I~~aL~id~~~ls~~~~ 43 (185)
T PF07506_consen 2 RRDLSFIERARFARRLEERGFSREEIAAALGIDKSYLSRMLS 43 (185)
T ss_pred CccCcHHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 457899999999999999999999999999999999966644
No 453
>PRK11062 nhaR transcriptional activator NhaR; Provisional
Probab=45.12 E-value=45 Score=29.62 Aligned_cols=38 Identities=11% Similarity=0.054 Sum_probs=32.6
Q ss_pred HHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 41 SYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 41 ~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
..++...+++..|...++|+|++|+-+++.-..+-..|
T Consensus 13 ~~v~e~gs~s~AA~~L~isqpavS~~I~~LE~~lg~~L 50 (296)
T PRK11062 13 WMVCKEGSVVGAAEALFLTPQTITGQIKALEERLQGKL 50 (296)
T ss_pred HHHHhcCCHHHHHHHhCCChHHHHHHHHHHHHHcCccc
Confidence 33444578999999999999999999999999888776
No 454
>PRK08359 transcription factor; Validated
Probab=44.84 E-value=24 Score=29.29 Aligned_cols=43 Identities=21% Similarity=0.265 Sum_probs=31.2
Q ss_pred hcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccccccccccCCChHHHHHHHHHHH
Q psy4300 44 ATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQIQCQYIKWPTEEESVIIERNFR 100 (307)
Q Consensus 44 ~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l~~~~~i~~P~~~~~~~~~~~f~ 100 (307)
..|.|+.+||...|+|++|+++|=+ . -.-|+.+.+..+++.|.
T Consensus 96 ~kglSQeeLA~~lgvs~stI~~iE~-----------G---~~~Ps~~~l~kLak~l~ 138 (176)
T PRK08359 96 KSGLSYEELSHEVGLSVNDLRRIAH-----------G---EYEPTIKEAKKLERYFK 138 (176)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHC-----------C---CcCCCHHHHHHHHHHhC
Confidence 6799999999999999999877532 1 12366666666666664
No 455
>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=44.79 E-value=30 Score=28.25 Aligned_cols=38 Identities=16% Similarity=0.174 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHhcCCcHHHHHhhhC-CChhhHHHHHHHH
Q psy4300 33 EKKTLVALSYMATQLSMRKIGDQFN-LADSTVWSCIDSF 70 (307)
Q Consensus 33 ~~~l~i~L~~L~~g~~~~~l~~~fg-vs~stv~r~v~~~ 70 (307)
++++...-.+++.|.|..+||..+| +|+.+|.=.+++.
T Consensus 5 de~~~~L~~lw~~G~SasqIA~~lg~vsRnAViGk~hRl 43 (162)
T PF07750_consen 5 DERVERLRKLWAEGLSASQIARQLGGVSRNAVIGKAHRL 43 (162)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHhCCcchhhhhhhhhcc
Confidence 3455555556689999999999999 9999987766663
No 456
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=44.51 E-value=61 Score=23.86 Aligned_cols=28 Identities=7% Similarity=0.086 Sum_probs=23.4
Q ss_pred HhcCCcHHHHHhhhCCChhhHHHHHHHH
Q psy4300 43 MATQLSMRKIGDQFNLADSTVWSCIDSF 70 (307)
Q Consensus 43 L~~g~~~~~l~~~fgvs~stv~r~v~~~ 70 (307)
-.++......|...|||++|+++.+++.
T Consensus 65 ~~~~gn~s~AAr~LGIsRsTL~rKLkr~ 92 (95)
T PRK00430 65 QYTRGNQTRAALMLGINRGTLRKKLKKY 92 (95)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHHHh
Confidence 3466778999999999999999888763
No 457
>PRK11139 DNA-binding transcriptional activator GcvA; Provisional
Probab=44.44 E-value=43 Score=29.66 Aligned_cols=44 Identities=9% Similarity=0.055 Sum_probs=35.9
Q ss_pred HHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 34 KKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 34 ~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
.+|-+++....+ .+++..|...++|+|++|+.++++-..+-..|
T Consensus 9 ~~l~~f~~v~~~-gs~s~AA~~L~isq~avS~~i~~LE~~lg~~L 52 (297)
T PRK11139 9 NALRAFEAAARH-LSFTRAAEELFVTQAAVSHQIKALEDFLGLKL 52 (297)
T ss_pred HHHHHHHHHHHh-CCHHHHHHHhCCChHHHHHHHHHHHHHhCchh
Confidence 455555555554 68999999999999999999999999888776
No 458
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=44.09 E-value=22 Score=23.96 Aligned_cols=24 Identities=13% Similarity=0.189 Sum_probs=21.1
Q ss_pred cHHHHHhhhCCChhhHHHHHHHHH
Q psy4300 48 SMRKIGDQFNLADSTVWSCIDSFL 71 (307)
Q Consensus 48 ~~~~l~~~fgvs~stv~r~v~~~~ 71 (307)
+..++|..+|||.+|+..+.++..
T Consensus 2 ti~eva~~~gvs~~tlr~y~~~gl 25 (69)
T PF13411_consen 2 TIKEVAKLLGVSPSTLRYYEREGL 25 (69)
T ss_dssp EHHHHHHHTTTTHHHHHHHHHTTS
T ss_pred cHHHHHHHHCcCHHHHHHHHHhcC
Confidence 457899999999999999988776
No 459
>COG1395 Predicted transcriptional regulator [Transcription]
Probab=44.00 E-value=18 Score=32.71 Aligned_cols=64 Identities=19% Similarity=0.196 Sum_probs=42.6
Q ss_pred CCHHHHHHHHHHHhhhcCcccccCCCCCCCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHH
Q psy4300 1 MRKTTFGFLVEALAAINGYETLYERGVPFVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDS 69 (307)
Q Consensus 1 ms~~~F~~L~~~l~~~~~~~~~~~~~~~~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~ 69 (307)
++++||..++.-..|.. .. .+|.-.+...-..+=-+ +...|.|..++|...|+|+.|++++=+.
T Consensus 98 vs~~Tf~~~~~Ge~P~v---~a-~rGG~yV~Idge~Lre~-Ree~glSlG~lA~~lgVSRktV~~YE~G 161 (313)
T COG1395 98 VSPETFYDYVEGEPPYV---YA-ARGGFYVKIDGEKLREK-REEMGLSLGDLATMLGVSRKTVYKYEKG 161 (313)
T ss_pred eCHHHHHHHhCCCCceE---Ee-cCCeEEEEechHHHHHH-HHHcCcCHHHHHHHhCccHHHHHHhccC
Confidence 57899988888444443 22 22223333333322222 7788999999999999999999986554
No 460
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=43.70 E-value=27 Score=30.19 Aligned_cols=26 Identities=15% Similarity=0.334 Sum_probs=21.5
Q ss_pred CcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300 47 LSMRKIGDQFNLADSTVWSCIDSFLT 72 (307)
Q Consensus 47 ~~~~~l~~~fgvs~stv~r~v~~~~~ 72 (307)
.+-.+|+..||||+.||.+.+.....
T Consensus 34 PsE~eLa~~~~VSR~TvR~Al~~L~~ 59 (241)
T PRK11402 34 PTENELCTQYNVSRITIRKAISDLVA 59 (241)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 35668999999999999998887543
No 461
>COG2826 Tra8 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]
Probab=43.46 E-value=39 Score=30.48 Aligned_cols=40 Identities=18% Similarity=0.276 Sum_probs=33.6
Q ss_pred CCCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHH
Q psy4300 29 FVPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDS 69 (307)
Q Consensus 29 ~~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~ 69 (307)
.++..++..|-= +++.|.|-++||...|.++|||+|=+++
T Consensus 7 hLT~~eR~~I~~-l~~~~~S~reIA~~LgRh~sTIsRElkR 46 (318)
T COG2826 7 HLTLFERYEIER-LLKAKMSIREIAKQLNRHHSTISRELKR 46 (318)
T ss_pred hCCHHHHHHHHH-HHHcCCCHHHHHHHhCCCcchhhHHHhc
Confidence 577777776654 4488999999999999999999998875
No 462
>PF08769 Spo0A_C: Sporulation initiation factor Spo0A C terminal; InterPro: IPR014879 The response regulator Spo0A is comprised of a phophoacceptor domain and a transcription activation domain. This domain corresponds to the transcription activation domain and forms an alpha helical structure comprising of 6 alpha helices. The structure contains a helix-turn-helix and binds DNA [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0005509 calcium ion binding, 0006355 regulation of transcription, DNA-dependent, 0042173 regulation of sporulation resulting in formation of a cellular spore, 0005737 cytoplasm; PDB: 1FC3_C 1LQ1_D.
Probab=43.33 E-value=32 Score=25.94 Aligned_cols=31 Identities=13% Similarity=0.063 Sum_probs=28.1
Q ss_pred CcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 47 LSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 47 ~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
.=|.++|..++.+.+.|-|.++..++..+..
T Consensus 41 ~LYp~IA~k~~TT~s~VERaIR~aI~~~w~~ 71 (106)
T PF08769_consen 41 ELYPDIAKKYGTTPSRVERAIRHAIEVAWTR 71 (106)
T ss_dssp THHHHHHHHTTS-HHHHHHHHHHHHHHHHHC
T ss_pred hHHHHHHHHHCCCHHHHHHHHHHHHHHHHHc
Confidence 5589999999999999999999999999996
No 463
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=42.75 E-value=35 Score=23.20 Aligned_cols=25 Identities=4% Similarity=0.187 Sum_probs=21.4
Q ss_pred CcHHHHHhhhCCChhhHHHHHHHHH
Q psy4300 47 LSMRKIGDQFNLADSTVWSCIDSFL 71 (307)
Q Consensus 47 ~~~~~l~~~fgvs~stv~r~v~~~~ 71 (307)
.+..++|..+|+|.+++++.+.+..
T Consensus 2 ~~~~~la~~~~~s~~~l~~~f~~~~ 26 (84)
T smart00342 2 LTLEDLAEALGMSPRHLQRLFKKET 26 (84)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHh
Confidence 4678999999999999999988764
No 464
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=42.53 E-value=43 Score=28.79 Aligned_cols=27 Identities=7% Similarity=0.107 Sum_probs=24.7
Q ss_pred CcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300 47 LSMRKIGDQFNLADSTVWSCIDSFLTA 73 (307)
Q Consensus 47 ~~~~~l~~~fgvs~stv~r~v~~~~~~ 73 (307)
.+..++|..+++|++|+++.++++...
T Consensus 22 IS~~eLA~~L~iS~~Tvsr~Lk~LEe~ 48 (217)
T PRK14165 22 ISSSEFANHTGTSSKTAARILKQLEDE 48 (217)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 689999999999999999999998654
No 465
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=42.05 E-value=45 Score=26.53 Aligned_cols=31 Identities=13% Similarity=0.295 Sum_probs=23.6
Q ss_pred CcHHHHHhhhCCChhhHHHHHH---HHHHHcccc
Q psy4300 47 LSMRKIGDQFNLADSTVWSCID---SFLTAMSQP 77 (307)
Q Consensus 47 ~~~~~l~~~fgvs~stv~r~v~---~~~~~l~~~ 77 (307)
.++.++|...||+++|+++|-+ .|+..+...
T Consensus 35 ~T~~eiAee~Gis~~tLYrWr~~~~~Fiey~n~l 68 (142)
T PF13022_consen 35 RTQAEIAEEVGISRSTLYRWRQQNKAFIEYKNEL 68 (142)
T ss_dssp S-HHHHHHHHTS-HHHHHHHHHH-HHHHHHHHHH
T ss_pred chHHHHHHHhCCCHHHHHHHHhcCHHHHHHHHHH
Confidence 6799999999999999999985 266665554
No 466
>PRK15215 fimbriae biosynthesis regulatory protein; Provisional
Probab=42.04 E-value=1.4e+02 Score=22.18 Aligned_cols=38 Identities=13% Similarity=0.360 Sum_probs=31.7
Q ss_pred HHHHHHHH-HHhcCCcHHHHHhhhCCChhhHHHHHHHHH
Q psy4300 34 KKTLVALS-YMATQLSMRKIGDQFNLADSTVWSCIDSFL 71 (307)
Q Consensus 34 ~~l~i~L~-~L~~g~~~~~l~~~fgvs~stv~r~v~~~~ 71 (307)
+++..+|+ ||-.|.+-.+++...+|+++-++-.++++-
T Consensus 48 ~KvI~AL~dyLV~G~trkevCe~~~Vn~gYfS~~L~rL~ 86 (100)
T PRK15215 48 EKIIQALRDYLVFGVSRKDVCERYEVNNGYFSTSLNRLS 86 (100)
T ss_pred HHHHHHHHHHHHcCccHHHHHHccCCCHHHHHHHHHHHH
Confidence 45556665 899999999999999999999988877654
No 467
>COG2964 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=41.38 E-value=1.1e+02 Score=26.42 Aligned_cols=38 Identities=13% Similarity=0.303 Sum_probs=26.7
Q ss_pred HHHHHHHHHHHhcC-----CcHHHHHhhhCCChhhHHHHHHHH
Q psy4300 33 EKKTLVALSYMATQ-----LSMRKIGDQFNLADSTVWSCIDSF 70 (307)
Q Consensus 33 ~~~l~i~L~~L~~g-----~~~~~l~~~fgvs~stv~r~v~~~ 70 (307)
.+.--+++-....| .-..-+|...|+|++||++++++.
T Consensus 173 ~~~reiV~~L~EkGiF~lK~Ai~~VA~~L~iSr~TVY~YL~~~ 215 (220)
T COG2964 173 AKNREIVKALYEKGIFNLKDAINIVADRLGISRHTVYRYLRKF 215 (220)
T ss_pred HHHHHHHHHHHhcCccchhhHHHHHHHHhCCChHHHHHHHHHh
Confidence 33333555555555 334578889999999999999865
No 468
>PRK14997 LysR family transcriptional regulator; Provisional
Probab=41.20 E-value=41 Score=29.78 Aligned_cols=36 Identities=8% Similarity=0.071 Sum_probs=31.8
Q ss_pred HhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 43 MATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 43 L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
++.-.+++..|...++|+|++|+-+++.-..+-..|
T Consensus 13 va~~gs~s~AA~~L~isQpavS~~I~~LE~~lG~~L 48 (301)
T PRK14997 13 VVEEGGFAAAGRALDEPKSKLSRRIAQLEERLGVRL 48 (301)
T ss_pred HHHcCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCEe
Confidence 344568999999999999999999999999988876
No 469
>PRK15183 Vi polysaccharide biosynthesis protein TviA; Provisional
Probab=40.95 E-value=68 Score=24.09 Aligned_cols=51 Identities=18% Similarity=0.386 Sum_probs=40.5
Q ss_pred HHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccccccccccCCCh
Q psy4300 37 LVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQIQCQYIKWPTE 89 (307)
Q Consensus 37 ~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l~~~~~i~~P~~ 89 (307)
.+-+.|+-+-....+++.+|--|.||.+||-++..--+--+ .++|+-.|..
T Consensus 89 i~kmkyflsesgmeelqdrfmns~st~yrwrke~a~kfgvr--~prylllpds 139 (143)
T PRK15183 89 IVKMKYFLSESGMEELQDRFMNSSSTMYRWRKELAVKFGVR--EPRYLLLPDS 139 (143)
T ss_pred hhHhhhhhhhccHHHHHHHHccChHHHHHHHHHHHHHhcCC--CCceEecCcc
Confidence 45556666667788999999999999999999887777766 7777777764
No 470
>PRK13698 plasmid-partitioning protein; Provisional
Probab=40.83 E-value=48 Score=30.31 Aligned_cols=40 Identities=15% Similarity=0.217 Sum_probs=29.6
Q ss_pred CCHHHHHHHHHH-HH-hcCCcHHHHHhhhCCChhhHHHHHHH
Q psy4300 30 VPVEKKTLVALS-YM-ATQLSMRKIGDQFNLADSTVWSCIDS 69 (307)
Q Consensus 30 ~~~~~~l~i~L~-~L-~~g~~~~~l~~~fgvs~stv~r~v~~ 69 (307)
+++.+.=.-... .. ..|.++..||..+|+|+++|++.++-
T Consensus 158 ls~iE~A~ay~~~L~~~~~~tQeeLA~~lG~SRs~Vsn~Lrl 199 (323)
T PRK13698 158 TSAYERGLRYASRLQNEFAGNISALADAENISRKIITRCINT 199 (323)
T ss_pred CCHHHHHHHHHHHHHHhcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 466554443323 33 55789999999999999999998874
No 471
>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator). This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.
Probab=40.33 E-value=53 Score=25.30 Aligned_cols=28 Identities=14% Similarity=0.266 Sum_probs=25.1
Q ss_pred CCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300 46 QLSMRKIGDQFNLADSTVWSCIDSFLTA 73 (307)
Q Consensus 46 g~~~~~l~~~fgvs~stv~r~v~~~~~~ 73 (307)
..+-.+|+..++++++++.+++.....+
T Consensus 25 ~~s~~eia~~~~i~~~~v~~il~~L~~~ 52 (132)
T TIGR00738 25 PVSVKEIAERQGISRSYLEKILRTLRRA 52 (132)
T ss_pred cCcHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 5789999999999999999999988764
No 472
>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=40.12 E-value=33 Score=20.62 Aligned_cols=22 Identities=5% Similarity=0.185 Sum_probs=15.5
Q ss_pred hcCCcHHHHHhhhCCChhhHHH
Q psy4300 44 ATQLSMRKIGDQFNLADSTVWS 65 (307)
Q Consensus 44 ~~g~~~~~l~~~fgvs~stv~r 65 (307)
..|.+...||..||++.+.+.+
T Consensus 4 ~~gDtl~~IA~~~~~~~~~l~~ 25 (44)
T PF01476_consen 4 QPGDTLWSIAKRYGISVDELME 25 (44)
T ss_dssp -TT--HHHHHHHTTS-HHHHHH
T ss_pred CcCCcHHHHHhhhhhhHhHHHH
Confidence 4688999999999999888655
No 473
>PRK13500 transcriptional activator RhaR; Provisional
Probab=39.89 E-value=70 Score=28.86 Aligned_cols=38 Identities=5% Similarity=0.054 Sum_probs=29.3
Q ss_pred HHHHHHHHHH----hcCCcHHHHHhhhCCChhhHHHHHHHHH
Q psy4300 34 KKTLVALSYM----ATQLSMRKIGDQFNLADSTVWSCIDSFL 71 (307)
Q Consensus 34 ~~l~i~L~~L----~~g~~~~~l~~~fgvs~stv~r~v~~~~ 71 (307)
..+.-++.|+ +...+..++|..+|+|.++++|++++.+
T Consensus 206 ~~l~~i~~yI~~~~~e~isl~~lA~~~~iS~~~L~r~FK~~t 247 (312)
T PRK13500 206 TLLDKLITRLAASLKSPFALDKFCDEASCSERVLRQQFRQQT 247 (312)
T ss_pred HHHHHHHHHHHHcccCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 3444455555 4457889999999999999999999863
No 474
>PRK09744 DNA-binding transcriptional regulator DicC; Provisional
Probab=39.77 E-value=28 Score=24.35 Aligned_cols=20 Identities=15% Similarity=0.044 Sum_probs=17.9
Q ss_pred CcHHHHHhhhCCChhhHHHH
Q psy4300 47 LSMRKIGDQFNLADSTVWSC 66 (307)
Q Consensus 47 ~~~~~l~~~fgvs~stv~r~ 66 (307)
.+.+.+|..+|||.++|++|
T Consensus 11 Gs~~kvA~aLGIs~~AVsQW 30 (75)
T PRK09744 11 GSKTKLANAAGVRLASVAAW 30 (75)
T ss_pred CcHHHHHHHHCCCHHHHHHH
Confidence 46789999999999999997
No 475
>PRK00441 argR arginine repressor; Provisional
Probab=39.65 E-value=59 Score=26.16 Aligned_cols=26 Identities=12% Similarity=0.226 Sum_probs=22.0
Q ss_pred CCcHHHHHhhh-----CCChhhHHHHHHHHH
Q psy4300 46 QLSMRKIGDQF-----NLADSTVWSCIDSFL 71 (307)
Q Consensus 46 g~~~~~l~~~f-----gvs~stv~r~v~~~~ 71 (307)
-.+..+|+..+ ++|++|++|-++++-
T Consensus 18 ~~~q~eL~~~L~~~G~~vSqaTisRDl~~L~ 48 (149)
T PRK00441 18 IETQEELAEELKKMGFDVTQATVSRDIKELK 48 (149)
T ss_pred CCcHHHHHHHHHhcCCCcCHHHHHHHHHHcC
Confidence 36788999985 999999999998753
No 476
>PRK13503 transcriptional activator RhaS; Provisional
Probab=39.56 E-value=63 Score=28.25 Aligned_cols=29 Identities=21% Similarity=0.315 Sum_probs=25.0
Q ss_pred HhcCCcHHHHHhhhCCChhhHHHHHHHHH
Q psy4300 43 MATQLSMRKIGDQFNLADSTVWSCIDSFL 71 (307)
Q Consensus 43 L~~g~~~~~l~~~fgvs~stv~r~v~~~~ 71 (307)
+....+..++|..+|+|+++++|.+++..
T Consensus 184 ~~~~~tl~~lA~~~~lS~~~l~r~Fk~~~ 212 (278)
T PRK13503 184 FAEEVNWEALADQFSLSLRTLHRQLKQQT 212 (278)
T ss_pred hcCCCCHHHHHHHHCCCHHHHHHHHHHHh
Confidence 34567899999999999999999998763
No 477
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=39.43 E-value=35 Score=29.60 Aligned_cols=25 Identities=28% Similarity=0.530 Sum_probs=21.2
Q ss_pred cHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300 48 SMRKIGDQFNLADSTVWSCIDSFLT 72 (307)
Q Consensus 48 ~~~~l~~~fgvs~stv~r~v~~~~~ 72 (307)
+-.+|+..||||+-||.+.+.....
T Consensus 33 sE~eLa~~f~VSR~TvRkAL~~L~~ 57 (236)
T COG2188 33 SERELAEQFGVSRMTVRKALDELVE 57 (236)
T ss_pred CHHHHHHHHCCcHHHHHHHHHHHHH
Confidence 5568999999999999999887654
No 478
>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family. This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferble copper resistance) of an Enterocuccus faecium plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this model are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI.
Probab=39.28 E-value=83 Score=24.53 Aligned_cols=55 Identities=13% Similarity=0.087 Sum_probs=33.3
Q ss_pred HHHHHHHHHHHhcCCcHHHHHh----hhCCChhhHHHHHHHHHHH-cccc-ccccccccCCC
Q psy4300 33 EKKTLVALSYMATQLSMRKIGD----QFNLADSTVWSCIDSFLTA-MSQP-QIQCQYIKWPT 88 (307)
Q Consensus 33 ~~~l~i~L~~L~~g~~~~~l~~----~fgvs~stv~r~v~~~~~~-l~~~-l~~~~~i~~P~ 88 (307)
+..++-.||- ..+.+.++|.. ..+++.+|+..++++...- +..+ -....++..|.
T Consensus 6 E~~VM~vlW~-~~~~t~~eI~~~l~~~~~~~~tTv~T~L~rL~~KG~v~~~k~gr~~~Y~p~ 66 (130)
T TIGR02698 6 EWEVMRVVWT-LGETTSRDIIRILAEKKDWSDSTIKTLLGRLVDKGCLTTEKEGRKFIYTAL 66 (130)
T ss_pred HHHHHHHHHc-CCCCCHHHHHHHHhhccCCcHHHHHHHHHHHHHCCceeeecCCCcEEEEec
Confidence 4455555554 44678888444 4589999999999987652 2221 00344566664
No 479
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=39.11 E-value=55 Score=23.12 Aligned_cols=27 Identities=15% Similarity=0.329 Sum_probs=22.7
Q ss_pred CcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300 47 LSMRKIGDQFNLADSTVWSCIDSFLTA 73 (307)
Q Consensus 47 ~~~~~l~~~fgvs~stv~r~v~~~~~~ 73 (307)
.+-.+||...++|.+.+.+++......
T Consensus 26 ~s~~eiA~~~~i~~~~l~kil~~L~~~ 52 (83)
T PF02082_consen 26 VSSKEIAERLGISPSYLRKILQKLKKA 52 (83)
T ss_dssp BEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHhhC
Confidence 688999999999999999998887553
No 480
>PF09048 Cro: Cro; InterPro: IPR000655 Bacteriophage lambda encodes two repressors: the Cro repressor that acts to turn off early gene transcription during the lytic cycle, and the lambda or cI repressor that is required to maintain lysogenic growth. Together the Cro and cI repressors form a helix-turn-helix (HTH) superfamily. The lambda Cro repressor binds to DNA as a highly flexible dimer. The crystal structure of the lambda Cro repressor [] reveals a HTH DNA-binding protein with an alpha/beta fold that differs from other Cro family members, possibly by an evolutionary fold change []. Most Cro proteins, such as Enterobacteria phage P22 Cro and Bacteriophage 434 Cro, have an all-alpha structure that is thought to be ancestral to lambda Cro, where the fourth and fifth helices are replaced by a beta-sheet, possibly as a result of secondary structure switching rather than by nonhomologous replacement []. This entry represents the lambda-type Cro repressor with an alpha/beta topology.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 5CRO_A 2ECS_A 2OVG_A 6CRO_A 1D1L_A 2ORC_A 1D1M_B 3ORC_A 1ORC_A 2A63_A ....
Probab=38.95 E-value=37 Score=22.66 Aligned_cols=22 Identities=9% Similarity=0.125 Sum_probs=17.9
Q ss_pred HHHHHhhhCCChhhHHHHHHHH
Q psy4300 49 MRKIGDQFNLADSTVWSCIDSF 70 (307)
Q Consensus 49 ~~~l~~~fgvs~stv~r~v~~~ 70 (307)
+...|..+||+++.+|+.++.-
T Consensus 15 Q~kaA~~lGV~Q~AIsKAlr~g 36 (59)
T PF09048_consen 15 QAKAARALGVTQSAISKALRAG 36 (59)
T ss_dssp HHHHHHHHTS-HHHHHHHHHCT
T ss_pred hHHHHHHcCCcHHHHHHHHHcC
Confidence 7789999999999999987643
No 481
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=38.50 E-value=67 Score=25.65 Aligned_cols=46 Identities=15% Similarity=0.221 Sum_probs=34.7
Q ss_pred CCHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHcccc
Q psy4300 30 VPVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQP 77 (307)
Q Consensus 30 ~~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~ 77 (307)
++..++-.+ ..+..|.+...++..+|+|..|+...+.+...-+...
T Consensus 142 l~~~e~~vl--~~~~~~~~~~~ia~~l~~s~~tv~~~~~~~~~kl~~~ 187 (202)
T PRK09390 142 LSERERQVM--DGLVAGLSNKVIARDLDISPRTVEVYRANVMTKMQAG 187 (202)
T ss_pred hhhhHHHHH--HHHHccCchHHHHHHcCCCHHHHHHHHHHHHHHHccc
Confidence 444443333 3466788999999999999999999998887776544
No 482
>PF08822 DUF1804: Protein of unknown function (DUF1804); InterPro: IPR014926 This entry is represented by Bacteriophage D3112, Orf24. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=38.46 E-value=79 Score=25.93 Aligned_cols=40 Identities=18% Similarity=0.248 Sum_probs=30.5
Q ss_pred CHHHHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHH
Q psy4300 31 PVEKKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSF 70 (307)
Q Consensus 31 ~~~~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~ 70 (307)
+.+.+-.+==.|.-.+.++..+|..+|||.+|+.||=.+-
T Consensus 4 ~~e~R~~~R~~YV~~~~sLe~aA~~~gVs~~TarrWK~~A 43 (165)
T PF08822_consen 4 PQETRDAVRRAYVFDRLSLEQAAAKCGVSYATARRWKREA 43 (165)
T ss_pred cHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 3444445555567788999999999999999998876643
No 483
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=38.42 E-value=37 Score=27.97 Aligned_cols=40 Identities=13% Similarity=0.155 Sum_probs=31.8
Q ss_pred HHHHHHHHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHH
Q psy4300 34 KKTLVALSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTA 73 (307)
Q Consensus 34 ~~l~i~L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~ 73 (307)
-++..+|+.=+...+.++++...|+|+|.+|-.++....+
T Consensus 29 G~iYgilyls~~Pmtl~Ei~E~lg~Sks~vS~~lkkL~~~ 68 (177)
T COG1510 29 GQIYGILYLSRKPLTLDEIAEALGMSKSNVSMGLKKLQDW 68 (177)
T ss_pred HHHhhhheecCCCccHHHHHHHHCCCcchHHHHHHHHHhc
Confidence 3455555544788999999999999999999988876554
No 484
>PF13693 HTH_35: Winged helix-turn-helix DNA-binding; PDB: 1NEQ_A 1NER_A.
Probab=38.12 E-value=15 Score=26.05 Aligned_cols=25 Identities=16% Similarity=0.244 Sum_probs=18.1
Q ss_pred hcCCcHHHHHhhhCCChhhHHHHHH
Q psy4300 44 ATQLSMRKIGDQFNLADSTVWSCID 68 (307)
Q Consensus 44 ~~g~~~~~l~~~fgvs~stv~r~v~ 68 (307)
+.|.|+..|+...|++.+|+...+.
T Consensus 13 krG~sL~~lsr~~Gl~~~tl~nal~ 37 (78)
T PF13693_consen 13 KRGTSLAALSREAGLSSSTLRNALR 37 (78)
T ss_dssp TTS--HHHHHHHHSS-HHHHHHTTT
T ss_pred HcCCCHHHHHHHcCCCHHHHHHHHc
Confidence 4689999999999999999776543
No 485
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=38.02 E-value=38 Score=29.15 Aligned_cols=25 Identities=8% Similarity=0.286 Sum_probs=21.0
Q ss_pred cHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300 48 SMRKIGDQFNLADSTVWSCIDSFLT 72 (307)
Q Consensus 48 ~~~~l~~~fgvs~stv~r~v~~~~~ 72 (307)
+-++|+..||||++||...+.....
T Consensus 33 sE~eLae~~gVSRt~VReAL~~L~~ 57 (239)
T PRK04984 33 AERELSELIGVTRTTLREVLQRLAR 57 (239)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4668999999999999988887543
No 486
>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=37.91 E-value=90 Score=21.61 Aligned_cols=24 Identities=8% Similarity=0.169 Sum_probs=14.2
Q ss_pred CcHHHHHhh-----hCCChhhHHHHHHHH
Q psy4300 47 LSMRKIGDQ-----FNLADSTVWSCIDSF 70 (307)
Q Consensus 47 ~~~~~l~~~-----fgvs~stv~r~v~~~ 70 (307)
.++.+|... |.++++|+||-++++
T Consensus 20 ~sQ~eL~~~L~~~Gi~vTQaTiSRDLkeL 48 (70)
T PF01316_consen 20 SSQEELVELLEEEGIEVTQATISRDLKEL 48 (70)
T ss_dssp -SHHHHHHHHHHTT-T--HHHHHHHHHHH
T ss_pred CCHHHHHHHHHHcCCCcchhHHHHHHHHc
Confidence 344444443 679999999988875
No 487
>COG3093 VapI Plasmid maintenance system antidote protein [General function prediction only]
Probab=37.91 E-value=34 Score=25.74 Aligned_cols=24 Identities=13% Similarity=0.325 Sum_probs=22.6
Q ss_pred CCcHHHHHhhhCCChhhHHHHHHH
Q psy4300 46 QLSMRKIGDQFNLADSTVWSCIDS 69 (307)
Q Consensus 46 g~~~~~l~~~fgvs~stv~r~v~~ 69 (307)
|.+...+|...||++.|++.+++.
T Consensus 23 glt~~~lA~~lgV~r~~is~ling 46 (104)
T COG3093 23 GLTQTELAEALGVTRNTISELING 46 (104)
T ss_pred cCCHHHHHHHhCCCHHHHHHHHcC
Confidence 799999999999999999999984
No 488
>COG2973 TrpR Trp operon repressor [Transcription]
Probab=37.45 E-value=47 Score=24.60 Aligned_cols=30 Identities=17% Similarity=0.265 Sum_probs=23.9
Q ss_pred HHHHHHHHhcCCcHHHHHhhhCCChhhHHH
Q psy4300 36 TLVALSYMATQLSMRKIGDQFNLADSTVWS 65 (307)
Q Consensus 36 l~i~L~~L~~g~~~~~l~~~fgvs~stv~r 65 (307)
+-|.=-.|....|+++++..+|+|-.|+-|
T Consensus 50 v~Iv~eLL~ge~sQREi~~~LgvsiAtITR 79 (103)
T COG2973 50 VRIVEELLRGELSQREIAQKLGVSIATITR 79 (103)
T ss_pred HHHHHHHHhccccHHHHHHHhCcchhhhcc
Confidence 333444588899999999999999999654
No 489
>PRK09978 DNA-binding transcriptional regulator GadX; Provisional
Probab=37.14 E-value=95 Score=27.75 Aligned_cols=27 Identities=11% Similarity=0.250 Sum_probs=24.0
Q ss_pred HhcCCcHHHHHhhhCCChhhHHHHHHH
Q psy4300 43 MATQLSMRKIGDQFNLADSTVWSCIDS 69 (307)
Q Consensus 43 L~~g~~~~~l~~~fgvs~stv~r~v~~ 69 (307)
+....+..++|..+|+|+++++|.+++
T Consensus 155 ~~~~lsl~~lA~~~g~S~~~L~R~Fk~ 181 (274)
T PRK09978 155 IAHEWTLARIASELLMSPSLLKKKLRE 181 (274)
T ss_pred ccCCCCHHHHHHHHCcCHHHHHHHHHh
Confidence 455689999999999999999999976
No 490
>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=36.93 E-value=39 Score=23.05 Aligned_cols=24 Identities=21% Similarity=0.387 Sum_probs=17.5
Q ss_pred CcHHHHHhhh-----CCChhhHHHHHHHH
Q psy4300 47 LSMRKIGDQF-----NLADSTVWSCIDSF 70 (307)
Q Consensus 47 ~~~~~l~~~f-----gvs~stv~r~v~~~ 70 (307)
.++.+|+..+ .||.+||.+++++.
T Consensus 14 ~s~~~i~~~l~~~~~~vS~~TI~r~L~~~ 42 (72)
T PF01498_consen 14 ISAREIAQELQEAGISVSKSTIRRRLREA 42 (72)
T ss_dssp --HHHHHHHT---T--S-HHHHHHHHHHT
T ss_pred CCHHHHHHHHHHccCCcCHHHHHHHHHHc
Confidence 6788899877 89999999999875
No 491
>COG0583 LysR Transcriptional regulator [Transcription]
Probab=36.45 E-value=65 Score=27.95 Aligned_cols=39 Identities=18% Similarity=0.258 Sum_probs=33.1
Q ss_pred HHHHhcCCcHHHHHhhhCCChhhHHHHHHHHHHHccccc
Q psy4300 40 LSYMATQLSMRKIGDQFNLADSTVWSCIDSFLTAMSQPQ 78 (307)
Q Consensus 40 L~~L~~g~~~~~l~~~fgvs~stv~r~v~~~~~~l~~~l 78 (307)
+.-++...|+...|...++|+|++|+-+.+.-+.+-..|
T Consensus 9 F~~v~~~~s~t~AA~~L~isqsavS~~I~~LE~~lg~~L 47 (297)
T COG0583 9 FVAVAEEGSFTRAAERLGLSQSAVSRQIKRLEEELGVPL 47 (297)
T ss_pred HHHHHHcCcHHHHHHHhCCCChHHHHHHHHHHHHhCchh
Confidence 333444678999999999999999999999999888776
No 492
>PRK13501 transcriptional activator RhaR; Provisional
Probab=35.97 E-value=1.3e+02 Score=26.66 Aligned_cols=30 Identities=7% Similarity=0.087 Sum_probs=25.6
Q ss_pred HHhcCCcHHHHHhhhCCChhhHHHHHHHHH
Q psy4300 42 YMATQLSMRKIGDQFNLADSTVWSCIDSFL 71 (307)
Q Consensus 42 ~L~~g~~~~~l~~~fgvs~stv~r~v~~~~ 71 (307)
.++...+..++|..+|+|+++++|.+++..
T Consensus 188 ~~~e~~sl~~lA~~~~lS~~~l~r~Fk~~~ 217 (290)
T PRK13501 188 SLGAYFDMADFCHKNQLVERSLKQLFRQQT 217 (290)
T ss_pred hhccCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 345668899999999999999999999754
No 493
>PF14502 HTH_41: Helix-turn-helix domain
Probab=35.91 E-value=65 Score=20.57 Aligned_cols=26 Identities=8% Similarity=0.270 Sum_probs=20.7
Q ss_pred CcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300 47 LSMRKIGDQFNLADSTVWSCIDSFLT 72 (307)
Q Consensus 47 ~~~~~l~~~fgvs~stv~r~v~~~~~ 72 (307)
.+..+++..|++|+.|+...++..-+
T Consensus 7 ~tI~e~~~~~~vs~GtiQ~Alk~Le~ 32 (48)
T PF14502_consen 7 PTISEYSEKFGVSRGTIQNALKFLEE 32 (48)
T ss_pred CCHHHHHHHhCcchhHHHHHHHHHHH
Confidence 35678999999999998887765543
No 494
>PF12833 HTH_18: Helix-turn-helix domain; PDB: 2K9S_A 3LSG_C 3OIO_A 1D5Y_B 3GBG_A 3OOU_A 1BL0_A 1XS9_A 3MN2_B 3MKL_B ....
Probab=35.12 E-value=1.5e+02 Score=20.34 Aligned_cols=61 Identities=13% Similarity=0.182 Sum_probs=38.8
Q ss_pred CCHHHHHHHHHHHhhhcCcccccCCCCCCCCHHHHHHHHHHHH-h-cCCcHHHHHhhhCCC-hhhHHHHHHHH
Q psy4300 1 MRKTTFGFLVEALAAINGYETLYERGVPFVPVEKKTLVALSYM-A-TQLSMRKIGDQFNLA-DSTVWSCIDSF 70 (307)
Q Consensus 1 ms~~~F~~L~~~l~~~~~~~~~~~~~~~~~~~~~~l~i~L~~L-~-~g~~~~~l~~~fgvs-~stv~r~v~~~ 70 (307)
||+.++.+++...... + -..+-...++..++..| . ++.+..++|..+|-+ .+..++.+++.
T Consensus 7 ~s~~~l~~~f~~~~g~----s-----~~~~~~~~R~~~a~~~L~~~~~~~i~~ia~~~Gf~~~~~f~~~fk~~ 70 (81)
T PF12833_consen 7 MSERYLSRIFKKETGM----S-----FKQYLRELRLQRAKELLRQNTDLSIAEIAEECGFSSQSHFSRAFKRY 70 (81)
T ss_dssp S-HHHHHHHHHHHHSS----------HHHHHHHHHHHHHHHHHHHHTT--HHHHHHHTT-SSHHHHHHHHHHH
T ss_pred cCHHHHHHHHHHHHCc----C-----HHHHHHHHHHHHHHHHHHHhhcccHHHHHHHcCCCCHHHHHHHHHHH
Confidence 5667777777764322 1 01233567788888888 3 789999999999966 66777777765
No 495
>PRK15340 transcriptional regulator InvF; Provisional
Probab=35.00 E-value=56 Score=28.10 Aligned_cols=29 Identities=14% Similarity=0.273 Sum_probs=25.4
Q ss_pred hcCCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300 44 ATQLSMRKIGDQFNLADSTVWSCIDSFLT 72 (307)
Q Consensus 44 ~~g~~~~~l~~~fgvs~stv~r~v~~~~~ 72 (307)
....+..++|..+|+|.++++|.+++.+.
T Consensus 123 ~~~~sleeLA~~~gvS~r~f~RlFk~~~G 151 (216)
T PRK15340 123 TSGNTMRMLGEDYGVSYTHFRRLCSRALG 151 (216)
T ss_pred cCCCCHHHHHHHHCcCHHHHHHHHHHHHC
Confidence 55689999999999999999999998643
No 496
>PRK09954 putative kinase; Provisional
Probab=34.91 E-value=93 Score=28.64 Aligned_cols=27 Identities=19% Similarity=0.288 Sum_probs=24.7
Q ss_pred CCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300 46 QLSMRKIGDQFNLADSTVWSCIDSFLT 72 (307)
Q Consensus 46 g~~~~~l~~~fgvs~stv~r~v~~~~~ 72 (307)
..+..+|+..+|+|++||.+.+++...
T Consensus 17 ~~s~~~la~~l~~s~~~v~~~i~~L~~ 43 (362)
T PRK09954 17 LIQQNEIADILQISRSRVAAHIMDLMR 43 (362)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 378999999999999999999998776
No 497
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=34.84 E-value=80 Score=27.67 Aligned_cols=41 Identities=7% Similarity=0.169 Sum_probs=32.0
Q ss_pred HHHHHHHHHHHHhcC--CcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300 32 VEKKTLVALSYMATQ--LSMRKIGDQFNLADSTVWSCIDSFLT 72 (307)
Q Consensus 32 ~~~~l~i~L~~L~~g--~~~~~l~~~fgvs~stv~r~v~~~~~ 72 (307)
.+++....+.+|... .+..+|+..||||..|+.|=+...-.
T Consensus 5 ~~eR~~~I~~~l~~~~~v~v~eLa~~~~VS~~TIRRDL~~Le~ 47 (252)
T PRK10681 5 RDERIGQLLQALKRSDKLHLKDAAALLGVSEMTIRRDLNAHSA 47 (252)
T ss_pred HHHHHHHHHHHHHHcCCCcHHHHHHHhCCCHHHHHHHHHHhhc
Confidence 345666667777443 68889999999999999999998554
No 498
>TIGR02787 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY. This model represents the full length of CodY, a pleiotropic repressor in Bacillus subtilis and other Firmicutes (low-GC Gram-positive bacteria) that responds to intracellular levels of GTP and branched chain amino acids. The C-terminal helix-turn-helix DNA-binding region is modeled by pfam08222 in Pfam.
Probab=34.69 E-value=88 Score=27.40 Aligned_cols=44 Identities=11% Similarity=0.103 Sum_probs=33.6
Q ss_pred CCCHHHHHHHHHHHHhc---CCcHHHHHhhhCCChhhHHHHHHHHHH
Q psy4300 29 FVPVEKKTLVALSYMAT---QLSMRKIGDQFNLADSTVWSCIDSFLT 72 (307)
Q Consensus 29 ~~~~~~~l~i~L~~L~~---g~~~~~l~~~fgvs~stv~r~v~~~~~ 72 (307)
+.|--+.+--.|.-|.. -.+...+|..+|+|++++.+-++++..
T Consensus 178 SySEleAv~~IL~~L~~~egrlse~eLAerlGVSRs~ireAlrkLE~ 224 (251)
T TIGR02787 178 SYSELEAVEHIFEELDGNEGLLVASKIADRVGITRSVIVNALRKLES 224 (251)
T ss_pred cHhHHHHHHHHHHHhccccccccHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 44555666666666655 378999999999999999888887644
No 499
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). 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. 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-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=34.66 E-value=46 Score=22.28 Aligned_cols=22 Identities=5% Similarity=0.190 Sum_probs=18.9
Q ss_pred cHHHHHhhhCCChhhHHHHHHH
Q psy4300 48 SMRKIGDQFNLADSTVWSCIDS 69 (307)
Q Consensus 48 ~~~~l~~~fgvs~stv~r~v~~ 69 (307)
+-.++|..+|||.+|+..+..+
T Consensus 2 ~i~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 2 TIKEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred CHHHHHHHHCcCHHHHHHHHHh
Confidence 4568999999999999988765
No 500
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=34.50 E-value=38 Score=22.72 Aligned_cols=22 Identities=5% Similarity=0.004 Sum_probs=19.0
Q ss_pred cHHHHHhhhCCChhhHHHHHHH
Q psy4300 48 SMRKIGDQFNLADSTVWSCIDS 69 (307)
Q Consensus 48 ~~~~l~~~fgvs~stv~r~v~~ 69 (307)
+..++|..+|||.+|+..+..+
T Consensus 2 s~~eva~~~gvs~~tlr~~~~~ 23 (70)
T smart00422 2 TIGEVAKLAGVSVRTLRYYERI 23 (70)
T ss_pred CHHHHHHHHCcCHHHHHHHHHC
Confidence 4578999999999999998763
Done!