Query psy1898
Match_columns 230
No_of_seqs 250 out of 1182
Neff 6.8
Searched_HMMs 46136
Date Fri Aug 16 19:03:16 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1898.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1898hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00292 PAX: 'Paired box' dom 100.0 2.7E-35 5.8E-40 230.7 10.5 125 39-208 1-125 (125)
2 KOG3517|consensus 100.0 9E-34 2E-38 242.1 8.6 126 40-210 5-130 (334)
3 KOG3862|consensus 100.0 9.2E-29 2E-33 213.3 11.4 132 38-214 8-139 (327)
4 cd00131 PAX Paired Box domain 100.0 1.6E-27 3.4E-32 189.1 14.5 125 85-210 3-127 (128)
5 smart00351 PAX Paired Box doma 99.9 2.9E-26 6.3E-31 181.1 13.6 124 84-208 2-125 (125)
6 KOG0849|consensus 99.7 1.6E-18 3.5E-23 158.5 6.4 143 41-228 1-153 (354)
7 COG3415 Transposase and inacti 99.7 3.2E-17 7E-22 131.1 11.5 117 97-219 2-119 (138)
8 PF13551 HTH_29: Winged helix- 99.7 4.9E-17 1.1E-21 123.8 10.1 101 105-211 1-112 (112)
9 PF01710 HTH_Tnp_IS630: Transp 99.7 2.5E-16 5.3E-21 123.3 9.7 100 99-216 2-101 (119)
10 PF13565 HTH_32: Homeodomain-l 99.3 8E-12 1.7E-16 89.7 8.1 72 131-207 1-77 (77)
11 PF00292 PAX: 'Paired box' dom 99.3 1.3E-12 2.9E-17 102.7 3.0 35 2-36 1-35 (125)
12 cd00131 PAX Paired Box domain 99.2 7.6E-11 1.6E-15 93.5 9.8 100 39-138 1-126 (128)
13 KOG3862|consensus 99.1 6.1E-11 1.3E-15 103.3 5.1 122 2-138 9-154 (327)
14 smart00351 PAX Paired Box doma 99.1 3E-10 6.6E-15 89.7 8.3 98 40-137 2-125 (125)
15 KOG3517|consensus 99.0 1.3E-10 2.7E-15 100.4 2.6 33 3-35 5-37 (334)
16 PF13011 LZ_Tnp_IS481: leucine 99.0 3.7E-09 8.1E-14 77.8 8.1 74 97-170 6-83 (85)
17 PF13384 HTH_23: Homeodomain-l 98.9 4.2E-10 9.2E-15 74.4 2.1 44 101-144 3-46 (50)
18 PF13518 HTH_28: Helix-turn-he 98.8 5.5E-09 1.2E-13 69.2 3.8 41 104-144 1-41 (52)
19 PF13936 HTH_38: Helix-turn-he 98.4 9.8E-08 2.1E-12 61.9 2.1 42 97-138 2-43 (44)
20 PRK09413 IS2 repressor TnpA; R 98.4 7.5E-07 1.6E-11 69.8 7.4 49 97-145 10-59 (121)
21 PF01527 HTH_Tnp_1: Transposas 98.4 3.9E-07 8.4E-12 64.9 4.0 46 95-140 2-48 (76)
22 PF02796 HTH_7: Helix-turn-hel 98.2 1.1E-06 2.3E-11 57.2 2.7 40 98-137 4-43 (45)
23 COG2826 Tra8 Transposase and i 98.2 1.1E-05 2.4E-10 72.0 9.6 105 98-212 6-119 (318)
24 PF04218 CENP-B_N: CENP-B N-te 98.1 3.8E-06 8.2E-11 56.6 4.4 42 97-138 4-45 (53)
25 PF06056 Terminase_5: Putative 98.1 2.6E-06 5.6E-11 58.6 3.4 41 103-143 1-41 (58)
26 KOG0849|consensus 98.0 1.1E-06 2.5E-11 80.7 0.7 35 4-38 1-35 (354)
27 PRK09409 IS2 transposase TnpB; 97.9 4.6E-05 9.9E-10 68.6 8.9 97 110-216 6-105 (301)
28 COG2963 Transposase and inacti 97.9 6.2E-05 1.3E-09 58.1 7.8 51 97-147 5-57 (116)
29 cd00569 HTH_Hin_like Helix-tur 97.7 6.3E-05 1.4E-09 44.3 3.7 39 98-136 4-42 (42)
30 PHA02517 putative transposase 97.5 0.00019 4E-09 63.2 6.3 77 125-214 1-78 (277)
31 smart00421 HTH_LUXR helix_turn 97.4 0.00039 8.6E-09 45.6 4.9 41 100-141 4-44 (58)
32 PF13542 HTH_Tnp_ISL3: Helix-t 97.2 0.00058 1.2E-08 45.0 4.4 45 95-139 7-51 (52)
33 cd01104 HTH_MlrA-CarA Helix-Tu 97.2 0.0012 2.6E-08 45.7 6.2 66 116-185 1-67 (68)
34 TIGR02531 yecD_yerC TrpR-relat 97.2 0.00038 8.2E-09 51.8 3.7 35 103-137 38-72 (88)
35 PHA02535 P terminase ATPase su 97.1 0.00096 2.1E-08 64.9 6.5 68 99-177 2-71 (581)
36 PF01498 HTH_Tnp_Tc3_2: Transp 97.1 0.00029 6.3E-09 49.7 2.2 45 164-214 2-46 (72)
37 PF08281 Sigma70_r4_2: Sigma-7 97.1 0.00067 1.5E-08 45.1 3.9 43 99-141 10-52 (54)
38 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 97.1 0.00073 1.6E-08 45.0 3.8 42 97-138 2-43 (50)
39 cd06171 Sigma70_r4 Sigma70, re 97.0 0.0013 2.7E-08 42.2 4.5 42 100-141 11-52 (55)
40 PF04545 Sigma70_r4: Sigma-70, 97.0 0.0012 2.6E-08 43.3 4.0 42 99-140 4-45 (50)
41 PRK00118 putative DNA-binding 96.9 0.0016 3.5E-08 49.9 4.8 44 97-140 15-58 (104)
42 PF01710 HTH_Tnp_IS630: Transp 96.9 0.0029 6.2E-08 49.3 6.3 83 58-140 5-96 (119)
43 PF13592 HTH_33: Winged helix- 96.9 0.0019 4.1E-08 44.4 4.5 41 173-218 2-42 (60)
44 cd06170 LuxR_C_like C-terminal 96.9 0.0022 4.7E-08 42.1 4.6 39 102-141 3-41 (57)
45 PRK10141 DNA-binding transcrip 96.8 0.0013 2.8E-08 51.5 3.7 73 98-170 11-85 (117)
46 PF01022 HTH_5: Bacterial regu 96.7 0.0017 3.7E-08 42.2 3.0 43 103-145 2-45 (47)
47 PF12759 HTH_Tnp_IS1: InsA C-t 96.7 0.0016 3.5E-08 42.5 2.8 40 98-137 4-43 (46)
48 PF04552 Sigma54_DBD: Sigma-54 96.7 0.0021 4.5E-08 53.0 4.2 96 115-216 49-156 (160)
49 PF02796 HTH_7: Helix-turn-hel 96.7 0.0033 7.2E-08 40.6 4.1 44 153-209 1-44 (45)
50 PF10668 Phage_terminase: Phag 96.5 0.0029 6.3E-08 43.7 3.2 37 104-140 8-47 (60)
51 cd01105 HTH_GlnR-like Helix-Tu 96.5 0.023 4.9E-07 41.9 8.2 68 116-187 2-70 (88)
52 PF13411 MerR_1: MerR HTH fami 96.5 0.0029 6.2E-08 43.9 3.2 66 117-187 2-68 (69)
53 PF09607 BrkDBD: Brinker DNA-b 96.5 0.0033 7.1E-08 43.1 3.3 43 97-139 3-49 (58)
54 PF13613 HTH_Tnp_4: Helix-turn 96.4 0.006 1.3E-07 40.7 4.4 42 100-141 3-45 (53)
55 cd04763 HTH_MlrA-like Helix-Tu 96.4 0.015 3.2E-07 40.5 6.4 66 116-185 1-67 (68)
56 PRK04217 hypothetical protein; 96.3 0.0083 1.8E-07 46.5 5.1 44 97-140 40-83 (110)
57 PF14493 HTH_40: Helix-turn-he 96.3 0.029 6.2E-07 41.5 7.8 83 107-204 5-87 (91)
58 TIGR01529 argR_whole arginine 96.3 0.011 2.4E-07 47.9 6.0 45 163-213 4-48 (146)
59 COG2826 Tra8 Transposase and i 96.3 0.011 2.5E-07 53.0 6.5 84 55-138 7-116 (318)
60 PF13551 HTH_29: Winged helix- 96.3 0.015 3.2E-07 43.6 6.4 78 61-138 1-110 (112)
61 PF13412 HTH_24: Winged helix- 96.3 0.0085 1.9E-07 38.8 4.3 43 103-145 3-47 (48)
62 PF07037 DUF1323: Putative tra 96.2 0.0053 1.1E-07 47.9 3.6 55 116-170 1-56 (122)
63 cd04764 HTH_MlrA-like_sg1 Heli 96.2 0.021 4.6E-07 39.5 6.2 65 116-185 1-66 (67)
64 smart00422 HTH_MERR helix_turn 96.1 0.032 6.9E-07 38.5 6.8 50 116-169 1-50 (70)
65 cd04762 HTH_MerR-trunc Helix-T 96.1 0.008 1.7E-07 38.0 3.4 23 116-138 1-23 (49)
66 PRK13413 mpi multiple promoter 96.1 0.0065 1.4E-07 51.2 3.7 36 104-139 161-196 (200)
67 TIGR01321 TrpR trp operon repr 96.1 0.0086 1.9E-07 45.0 3.9 35 103-137 42-77 (94)
68 cd04765 HTH_MlrA-like_sg2 Heli 96.0 0.058 1.3E-06 40.7 8.3 68 116-187 1-70 (99)
69 PF00356 LacI: Bacterial regul 95.9 0.015 3.3E-07 38.0 4.2 40 117-172 1-40 (46)
70 PF05225 HTH_psq: helix-turn-h 95.9 0.015 3.3E-07 37.7 4.0 35 103-137 3-38 (45)
71 PF01371 Trp_repressor: Trp re 95.8 0.016 3.5E-07 43.0 4.5 39 102-140 35-74 (87)
72 TIGR02395 rpoN_sigma RNA polym 95.8 0.036 7.9E-07 52.4 7.9 95 116-216 319-426 (429)
73 TIGR03879 near_KaiC_dom probab 95.8 0.013 2.8E-07 42.1 3.6 44 100-143 16-60 (73)
74 PF13309 HTH_22: HTH domain 95.7 0.009 1.9E-07 41.7 2.6 41 97-137 18-64 (64)
75 PRK05932 RNA polymerase factor 95.7 0.039 8.5E-07 52.6 7.6 93 116-216 344-450 (455)
76 PRK06759 RNA polymerase factor 95.6 0.02 4.3E-07 45.4 4.7 42 99-140 106-147 (154)
77 PF12840 HTH_20: Helix-turn-he 95.6 0.0085 1.8E-07 40.9 2.2 48 100-147 7-56 (61)
78 PF01316 Arg_repressor: Argini 95.6 0.032 6.9E-07 39.7 5.2 46 162-213 6-51 (70)
79 PRK12537 RNA polymerase sigma 95.6 0.022 4.8E-07 46.8 5.0 42 100-141 134-175 (182)
80 TIGR00721 tfx DNA-binding prot 95.5 0.02 4.3E-07 46.0 4.3 42 99-141 6-47 (137)
81 PF00196 GerE: Bacterial regul 95.5 0.018 3.9E-07 38.8 3.5 35 106-140 9-43 (58)
82 cd01106 HTH_TipAL-Mta Helix-Tu 95.5 0.062 1.4E-06 40.5 6.9 68 116-187 1-69 (103)
83 PRK09642 RNA polymerase sigma 95.5 0.025 5.3E-07 45.3 4.8 42 100-141 107-148 (160)
84 cd04782 HTH_BltR Helix-Turn-He 95.5 0.13 2.8E-06 38.5 8.4 68 116-187 1-69 (97)
85 cd04773 HTH_TioE_rpt2 Second H 95.5 0.062 1.3E-06 41.1 6.7 68 116-187 1-69 (108)
86 COG1725 Predicted transcriptio 95.4 0.048 1E-06 43.2 6.1 55 94-148 6-68 (125)
87 TIGR02844 spore_III_D sporulat 95.4 0.056 1.2E-06 39.5 6.0 55 102-171 5-60 (80)
88 PF00325 Crp: Bacterial regula 95.4 0.013 2.8E-07 35.4 2.2 29 116-144 3-31 (32)
89 cd04761 HTH_MerR-SF Helix-Turn 95.4 0.028 6.2E-07 36.0 4.1 47 116-167 1-47 (49)
90 PF02954 HTH_8: Bacterial regu 95.4 0.022 4.8E-07 36.1 3.4 36 104-139 6-42 (42)
91 cd01109 HTH_YyaN Helix-Turn-He 95.4 0.086 1.9E-06 40.4 7.4 68 116-187 1-69 (113)
92 PHA00675 hypothetical protein 95.4 0.02 4.3E-07 41.3 3.5 39 100-138 23-62 (78)
93 PRK03975 tfx putative transcri 95.4 0.025 5.4E-07 45.7 4.4 42 99-141 6-47 (141)
94 TIGR02989 Sig-70_gvs1 RNA poly 95.4 0.028 6.2E-07 44.6 4.7 43 99-141 111-153 (159)
95 PRK09652 RNA polymerase sigma 95.3 0.027 5.9E-07 45.4 4.7 41 100-140 129-169 (182)
96 PF11198 DUF2857: Protein of u 95.3 0.25 5.4E-06 41.4 10.5 92 105-210 77-177 (180)
97 PRK09047 RNA polymerase factor 95.3 0.031 6.6E-07 44.6 4.8 42 99-140 106-147 (161)
98 PHA02591 hypothetical protein; 95.3 0.023 5.1E-07 41.1 3.5 36 102-137 46-81 (83)
99 cd00090 HTH_ARSR Arsenical Res 95.3 0.034 7.3E-07 37.8 4.4 48 100-147 4-52 (78)
100 PRK11924 RNA polymerase sigma 95.3 0.029 6.2E-07 45.1 4.6 41 100-140 126-166 (179)
101 PRK01381 Trp operon repressor; 95.2 0.022 4.8E-07 43.2 3.4 35 103-137 42-77 (99)
102 COG1595 RpoE DNA-directed RNA 95.2 0.027 5.8E-07 46.4 4.3 43 99-141 127-169 (182)
103 PRK12514 RNA polymerase sigma 95.2 0.037 8E-07 45.2 5.0 42 100-141 130-171 (179)
104 TIGR02960 SigX5 RNA polymerase 95.1 0.1 2.2E-06 46.7 8.2 89 99-187 142-231 (324)
105 PRK12528 RNA polymerase sigma 95.1 0.038 8.2E-07 44.3 4.8 42 100-141 114-155 (161)
106 PRK13919 putative RNA polymera 95.1 0.037 8.1E-07 45.3 4.8 42 100-141 136-177 (186)
107 PF08822 DUF1804: Protein of u 95.1 0.043 9.2E-07 45.4 5.0 47 99-145 2-49 (165)
108 cd01108 HTH_CueR Helix-Turn-He 95.1 0.22 4.7E-06 39.1 8.9 68 116-187 1-69 (127)
109 PRK09639 RNA polymerase sigma 95.1 0.036 7.9E-07 44.4 4.6 40 100-140 113-152 (166)
110 PRK11050 manganese transport r 95.1 0.17 3.7E-06 41.0 8.5 34 114-147 50-83 (152)
111 cd04788 HTH_NolA-AlbR Helix-Tu 95.1 0.1 2.2E-06 39.0 6.7 68 116-187 1-69 (96)
112 PRK15418 transcriptional regul 95.1 0.019 4E-07 52.2 3.1 41 105-145 18-59 (318)
113 TIGR03209 P21_Cbot clostridium 95.0 0.026 5.6E-07 44.4 3.5 36 99-134 107-142 (142)
114 TIGR02999 Sig-70_X6 RNA polyme 95.0 0.039 8.5E-07 45.0 4.7 42 100-141 135-176 (183)
115 cd01111 HTH_MerD Helix-Turn-He 95.0 0.11 2.5E-06 39.7 6.9 68 116-187 1-69 (107)
116 PRK12469 RNA polymerase factor 95.0 0.073 1.6E-06 51.1 7.1 95 116-216 370-476 (481)
117 PHA00738 putative HTH transcri 95.0 0.033 7.2E-07 42.8 3.8 50 102-151 11-62 (108)
118 PRK15201 fimbriae regulatory p 94.9 0.052 1.1E-06 45.6 5.2 48 93-141 127-174 (198)
119 PF07638 Sigma70_ECF: ECF sigm 94.9 0.041 8.9E-07 45.7 4.7 36 105-140 140-176 (185)
120 TIGR02937 sigma70-ECF RNA poly 94.9 0.043 9.3E-07 42.2 4.5 41 100-140 111-151 (158)
121 PRK09644 RNA polymerase sigma 94.9 0.041 8.9E-07 44.3 4.5 43 99-141 108-150 (165)
122 PRK12547 RNA polymerase sigma 94.9 0.046 1E-06 44.1 4.7 42 100-141 113-154 (164)
123 smart00550 Zalpha Z-DNA-bindin 94.9 0.055 1.2E-06 38.0 4.5 46 102-147 5-54 (68)
124 TIGR02985 Sig70_bacteroi1 RNA 94.8 0.051 1.1E-06 42.8 4.8 41 100-140 114-154 (161)
125 PRK12530 RNA polymerase sigma 94.8 0.046 1E-06 45.3 4.7 41 100-140 135-175 (189)
126 PF13276 HTH_21: HTH-like doma 94.8 0.13 2.8E-06 34.8 6.1 54 160-218 4-58 (60)
127 PRK07037 extracytoplasmic-func 94.8 0.053 1.2E-06 43.4 4.8 41 100-140 110-150 (163)
128 TIGR02952 Sig70_famx2 RNA poly 94.8 0.052 1.1E-06 43.5 4.7 43 99-141 122-164 (170)
129 cd04783 HTH_MerR1 Helix-Turn-H 94.8 0.15 3.1E-06 40.0 7.1 68 116-187 1-69 (126)
130 TIGR02983 SigE-fam_strep RNA p 94.8 0.048 1E-06 43.6 4.5 42 100-141 111-152 (162)
131 PF12728 HTH_17: Helix-turn-he 94.8 0.017 3.8E-07 37.7 1.6 23 116-138 2-24 (51)
132 PF12298 Bot1p: Eukaryotic mit 94.7 0.071 1.5E-06 44.4 5.5 56 90-145 7-63 (172)
133 cd01279 HTH_HspR-like Helix-Tu 94.7 0.1 2.2E-06 39.3 5.9 67 116-187 2-70 (98)
134 COG5484 Uncharacterized conser 94.7 0.028 6.1E-07 49.4 3.2 37 104-140 8-44 (279)
135 TIGR02044 CueR Cu(I)-responsiv 94.7 0.31 6.8E-06 38.2 8.9 68 116-187 1-69 (127)
136 PRK12529 RNA polymerase sigma 94.7 0.049 1.1E-06 44.7 4.5 42 99-140 127-168 (178)
137 PRK04280 arginine repressor; P 94.7 0.078 1.7E-06 43.1 5.5 45 163-213 6-50 (148)
138 PRK12525 RNA polymerase sigma 94.7 0.06 1.3E-06 43.6 4.9 41 100-140 119-159 (168)
139 cd04768 HTH_BmrR-like Helix-Tu 94.7 0.17 3.6E-06 37.8 7.0 68 116-187 1-69 (96)
140 cd04770 HTH_HMRTR Helix-Turn-H 94.7 0.19 4.1E-06 39.0 7.5 68 116-187 1-69 (123)
141 PF04297 UPF0122: Putative hel 94.6 0.03 6.5E-07 42.7 2.8 44 97-140 15-58 (101)
142 PRK08241 RNA polymerase factor 94.6 0.18 3.9E-06 45.6 8.4 109 100-210 154-267 (339)
143 PRK12519 RNA polymerase sigma 94.6 0.044 9.6E-07 45.3 4.1 41 100-140 142-182 (194)
144 cd04774 HTH_YfmP Helix-Turn-He 94.6 0.11 2.4E-06 38.9 5.9 67 116-187 1-69 (96)
145 PF09339 HTH_IclR: IclR helix- 94.6 0.028 6E-07 37.2 2.3 41 106-146 6-49 (52)
146 cd04775 HTH_Cfa-like Helix-Tur 94.6 0.15 3.3E-06 38.5 6.6 66 116-186 2-68 (102)
147 COG1438 ArgR Arginine represso 94.6 0.087 1.9E-06 42.9 5.6 47 161-213 6-52 (150)
148 cd04780 HTH_MerR-like_sg5 Heli 94.6 0.15 3.2E-06 38.2 6.4 68 116-187 1-70 (95)
149 PRK09645 RNA polymerase sigma 94.6 0.065 1.4E-06 43.4 4.9 41 100-140 119-159 (173)
150 TIGR02957 SigX4 RNA polymerase 94.5 0.19 4.1E-06 44.5 8.2 84 99-187 108-191 (281)
151 PF12116 SpoIIID: Stage III sp 94.5 0.034 7.4E-07 40.5 2.7 26 111-136 15-40 (82)
152 TIGR02047 CadR-PbrR Cd(II)/Pb( 94.5 0.41 8.8E-06 37.6 9.2 68 116-187 1-69 (127)
153 PRK12511 RNA polymerase sigma 94.5 0.063 1.4E-06 44.5 4.7 42 99-140 111-152 (182)
154 cd04772 HTH_TioE_rpt1 First He 94.5 0.21 4.6E-06 37.5 7.2 67 117-187 2-68 (99)
155 PRK09649 RNA polymerase sigma 94.5 0.06 1.3E-06 44.5 4.6 43 99-141 130-172 (185)
156 TIGR02954 Sig70_famx3 RNA poly 94.5 0.066 1.4E-06 43.2 4.7 42 100-141 120-161 (169)
157 cd04767 HTH_HspR-like_MBC Heli 94.5 0.093 2E-06 41.2 5.3 66 116-187 2-69 (120)
158 PRK12516 RNA polymerase sigma 94.4 0.066 1.4E-06 44.5 4.8 41 100-140 117-157 (187)
159 PRK09648 RNA polymerase sigma 94.4 0.069 1.5E-06 44.0 4.8 41 100-140 140-180 (189)
160 PRK09415 RNA polymerase factor 94.4 0.059 1.3E-06 44.2 4.3 42 100-141 128-169 (179)
161 PRK13749 transcriptional regul 94.4 0.22 4.8E-06 39.1 7.3 68 116-187 4-72 (121)
162 PF07900 DUF1670: Protein of u 94.4 0.29 6.3E-06 42.2 8.5 88 111-212 99-189 (220)
163 cd04787 HTH_HMRTR_unk Helix-Tu 94.4 0.18 3.9E-06 39.9 6.9 68 116-187 1-69 (133)
164 PRK12523 RNA polymerase sigma 94.3 0.075 1.6E-06 43.2 4.8 41 100-140 120-160 (172)
165 PRK12522 RNA polymerase sigma 94.3 0.071 1.5E-06 43.3 4.7 42 100-141 120-161 (173)
166 cd04789 HTH_Cfa Helix-Turn-Hel 94.3 0.19 4E-06 38.0 6.6 65 116-185 2-67 (102)
167 PRK12532 RNA polymerase sigma 94.3 0.068 1.5E-06 44.3 4.5 41 100-140 137-177 (195)
168 TIGR03001 Sig-70_gmx1 RNA poly 94.3 0.071 1.5E-06 46.5 4.8 43 99-141 161-203 (244)
169 PF08279 HTH_11: HTH domain; 94.3 0.061 1.3E-06 35.6 3.5 38 106-143 3-43 (55)
170 PF01325 Fe_dep_repress: Iron 94.3 0.043 9.3E-07 37.7 2.7 32 115-146 22-53 (60)
171 TIGR02947 SigH_actino RNA poly 94.3 0.036 7.7E-07 45.9 2.7 41 100-140 132-172 (193)
172 PHA00542 putative Cro-like pro 94.2 0.05 1.1E-06 39.6 3.2 27 111-137 27-53 (82)
173 PRK06930 positive control sigm 94.2 0.08 1.7E-06 43.9 4.8 42 99-140 114-155 (170)
174 PRK03341 arginine repressor; P 94.2 0.13 2.7E-06 42.8 5.9 48 160-213 14-61 (168)
175 TIGR01764 excise DNA binding d 94.2 0.028 6.1E-07 35.6 1.6 22 116-137 2-23 (49)
176 PRK12517 RNA polymerase sigma 94.2 0.079 1.7E-06 44.0 4.8 43 99-141 128-170 (188)
177 PRK09647 RNA polymerase sigma 94.2 0.08 1.7E-06 44.7 4.8 41 100-140 139-179 (203)
178 PRK05066 arginine repressor; P 94.2 0.15 3.2E-06 41.9 6.2 48 161-213 9-56 (156)
179 PRK06811 RNA polymerase factor 94.2 0.084 1.8E-06 43.7 4.9 43 99-141 131-173 (189)
180 TIGR02959 SigZ RNA polymerase 94.2 0.086 1.9E-06 42.9 4.8 42 99-140 100-141 (170)
181 PRK12520 RNA polymerase sigma 94.2 0.083 1.8E-06 43.7 4.7 41 100-140 132-172 (191)
182 smart00345 HTH_GNTR helix_turn 94.1 0.043 9.4E-07 36.2 2.5 45 103-147 4-52 (60)
183 PRK12524 RNA polymerase sigma 94.1 0.085 1.8E-06 43.9 4.7 41 100-140 137-177 (196)
184 TIGR02043 ZntR Zn(II)-responsi 94.1 0.24 5.2E-06 39.1 7.1 68 116-187 2-70 (131)
185 cd01107 HTH_BmrR Helix-Turn-He 94.1 0.41 8.8E-06 36.5 8.1 68 116-187 1-70 (108)
186 PRK08301 sporulation sigma fac 94.1 0.068 1.5E-06 45.8 4.2 41 100-140 179-223 (234)
187 PRK12534 RNA polymerase sigma 94.1 0.1 2.2E-06 42.9 5.0 42 100-141 138-179 (187)
188 PF13022 HTH_Tnp_1_2: Helix-tu 94.0 0.15 3.2E-06 41.1 5.7 76 116-215 35-110 (142)
189 PRK05602 RNA polymerase sigma 94.0 0.082 1.8E-06 43.4 4.5 41 100-140 129-169 (186)
190 cd04784 HTH_CadR-PbrR Helix-Tu 94.0 0.51 1.1E-05 36.9 8.8 68 116-187 1-69 (127)
191 PRK12540 RNA polymerase sigma 94.0 0.089 1.9E-06 43.5 4.7 42 100-141 112-153 (182)
192 PRK12542 RNA polymerase sigma 94.0 0.09 2E-06 43.2 4.7 41 100-140 123-163 (185)
193 cd01282 HTH_MerR-like_sg3 Heli 94.0 0.27 5.8E-06 37.8 7.0 67 116-187 1-68 (112)
194 cd04785 HTH_CadR-PbrR-like Hel 94.0 0.57 1.2E-05 36.7 9.0 68 116-187 1-69 (126)
195 PRK12536 RNA polymerase sigma 94.0 0.094 2E-06 43.0 4.7 41 100-140 130-170 (181)
196 PRK12533 RNA polymerase sigma 94.0 0.078 1.7E-06 45.4 4.4 41 100-140 135-175 (216)
197 PRK12512 RNA polymerase sigma 94.0 0.097 2.1E-06 42.8 4.8 42 99-140 131-172 (184)
198 PRK09514 zntR zinc-responsive 94.0 0.24 5.2E-06 39.6 6.9 68 116-187 2-70 (140)
199 PRK09646 RNA polymerase sigma 93.9 0.1 2.2E-06 43.3 4.9 41 100-140 143-183 (194)
200 PRK12526 RNA polymerase sigma 93.9 0.098 2.1E-06 44.0 4.8 42 99-140 153-194 (206)
201 cd01110 HTH_SoxR Helix-Turn-He 93.9 0.2 4.4E-06 40.0 6.4 66 116-186 2-68 (139)
202 TIGR02054 MerD mercuric resist 93.9 0.27 5.9E-06 38.5 6.9 69 115-187 3-72 (120)
203 PRK09637 RNA polymerase sigma 93.9 0.098 2.1E-06 43.2 4.7 42 99-140 106-147 (181)
204 PRK08583 RNA polymerase sigma 93.9 0.094 2E-06 45.7 4.8 41 100-140 206-246 (257)
205 TIGR02980 SigBFG RNA polymeras 93.9 0.097 2.1E-06 44.6 4.7 42 99-140 178-219 (227)
206 PRK12543 RNA polymerase sigma 93.8 0.11 2.3E-06 42.6 4.8 41 100-140 118-158 (179)
207 PRK12539 RNA polymerase sigma 93.8 0.1 2.2E-06 43.0 4.6 42 99-140 131-172 (184)
208 TIGR02948 SigW_bacill RNA poly 93.8 0.091 2E-06 42.8 4.4 42 100-141 137-178 (187)
209 PF01978 TrmB: Sugar-specific 93.8 0.057 1.2E-06 37.4 2.7 37 111-147 17-54 (68)
210 smart00346 HTH_ICLR helix_turn 93.8 0.34 7.3E-06 34.9 6.9 67 105-173 7-76 (91)
211 cd04766 HTH_HspR Helix-Turn-He 93.8 0.21 4.5E-06 36.8 5.8 66 116-186 2-69 (91)
212 PRK12545 RNA polymerase sigma 93.7 0.11 2.4E-06 43.5 4.8 41 100-140 140-180 (201)
213 cd04786 HTH_MerR-like_sg7 Heli 93.7 0.5 1.1E-05 37.5 8.2 68 116-187 1-69 (131)
214 TIGR00122 birA_repr_reg BirA b 93.7 0.11 2.3E-06 36.2 3.9 39 107-145 4-43 (69)
215 PF04967 HTH_10: HTH DNA bindi 93.7 0.19 4E-06 33.9 4.9 38 103-140 4-48 (53)
216 PRK06986 fliA flagellar biosyn 93.7 0.097 2.1E-06 45.0 4.4 41 100-140 185-225 (236)
217 PRK09636 RNA polymerase sigma 93.7 0.34 7.4E-06 43.0 8.0 43 100-142 116-158 (293)
218 PRK12541 RNA polymerase sigma 93.6 0.11 2.4E-06 41.6 4.4 43 99-141 112-154 (161)
219 PF13936 HTH_38: Helix-turn-he 93.6 0.056 1.2E-06 34.7 2.2 41 156-209 3-43 (44)
220 PRK09638 RNA polymerase sigma 93.6 0.054 1.2E-06 43.9 2.6 42 100-141 127-168 (176)
221 smart00420 HTH_DEOR helix_turn 93.6 0.12 2.7E-06 33.0 3.9 34 114-147 13-46 (53)
222 PRK12544 RNA polymerase sigma 93.6 0.12 2.6E-06 43.7 4.8 42 99-140 148-189 (206)
223 PRK00441 argR arginine repress 93.6 0.23 4.9E-06 40.4 6.2 46 162-213 5-50 (149)
224 COG1508 RpoN DNA-directed RNA 93.5 0.26 5.5E-06 46.8 7.3 94 116-216 331-438 (444)
225 PRK09651 RNA polymerase sigma 93.5 0.1 2.2E-06 42.5 4.0 41 100-140 120-160 (172)
226 PRK11923 algU RNA polymerase s 93.5 0.12 2.5E-06 42.7 4.5 41 100-140 139-179 (193)
227 PRK09635 sigI RNA polymerase s 93.5 0.32 7E-06 43.5 7.6 107 99-210 118-228 (290)
228 PF04703 FaeA: FaeA-like prote 93.5 0.062 1.3E-06 37.3 2.4 43 106-148 3-48 (62)
229 PRK12527 RNA polymerase sigma 93.5 0.14 3.1E-06 40.8 4.8 41 100-140 106-146 (159)
230 PRK12535 RNA polymerase sigma 93.5 0.12 2.6E-06 43.3 4.5 42 100-141 134-175 (196)
231 TIGR02479 FliA_WhiG RNA polyme 93.5 0.12 2.7E-06 43.9 4.7 41 100-140 176-216 (224)
232 TIGR02950 SigM_subfam RNA poly 93.5 0.043 9.3E-07 43.4 1.7 41 100-140 106-146 (154)
233 TIGR02051 MerR Hg(II)-responsi 93.4 0.28 6.2E-06 38.3 6.4 67 117-187 1-68 (124)
234 COG3677 Transposase and inacti 93.4 0.13 2.9E-06 40.8 4.4 45 101-145 75-119 (129)
235 PRK10227 DNA-binding transcrip 93.4 0.39 8.5E-06 38.3 7.2 68 116-187 1-69 (135)
236 PRK12546 RNA polymerase sigma 93.4 0.12 2.7E-06 43.0 4.4 42 99-140 113-154 (188)
237 TIGR02939 RpoE_Sigma70 RNA pol 93.3 0.11 2.3E-06 42.6 4.0 42 100-141 139-180 (190)
238 PRK12531 RNA polymerase sigma 93.3 0.15 3.2E-06 42.4 4.9 42 99-140 141-182 (194)
239 PRK12515 RNA polymerase sigma 93.3 0.15 3.3E-06 42.0 4.9 42 99-140 131-172 (189)
240 TIGR02943 Sig70_famx1 RNA poly 93.2 0.15 3.3E-06 42.3 4.8 41 100-140 132-172 (188)
241 COG3355 Predicted transcriptio 93.2 0.21 4.5E-06 39.6 5.1 74 114-187 41-117 (126)
242 PRK09640 RNA polymerase sigma 93.2 0.051 1.1E-06 44.8 1.8 41 100-140 135-175 (188)
243 PHA01976 helix-turn-helix prot 93.1 0.083 1.8E-06 36.2 2.6 31 107-137 6-37 (67)
244 PF08765 Mor: Mor transcriptio 93.1 0.074 1.6E-06 40.7 2.5 50 93-142 50-99 (108)
245 cd04777 HTH_MerR-like_sg1 Heli 93.1 0.48 1.1E-05 35.9 7.0 66 116-187 1-67 (107)
246 PRK12513 RNA polymerase sigma 93.1 0.067 1.4E-06 44.3 2.4 41 100-140 140-180 (194)
247 PRK15411 rcsA colanic acid cap 93.1 0.1 2.2E-06 44.2 3.5 40 100-140 138-177 (207)
248 PRK12538 RNA polymerase sigma 93.1 0.13 2.8E-06 44.5 4.3 41 100-140 172-212 (233)
249 PF08220 HTH_DeoR: DeoR-like h 93.0 0.13 2.8E-06 34.8 3.3 41 106-146 3-45 (57)
250 TIGR02835 spore_sigmaE RNA pol 93.0 0.15 3.2E-06 43.9 4.5 41 100-140 179-223 (234)
251 TIGR02984 Sig-70_plancto1 RNA 93.0 0.18 3.9E-06 41.1 4.8 42 99-140 140-181 (189)
252 COG2197 CitB Response regulato 92.9 0.41 8.8E-06 40.7 7.1 86 50-139 100-187 (211)
253 cd00592 HTH_MerR-like Helix-Tu 92.9 0.45 9.8E-06 35.3 6.5 67 116-187 1-68 (100)
254 COG0789 SoxR Predicted transcr 92.9 0.5 1.1E-05 36.2 7.0 68 116-187 1-69 (124)
255 PF01381 HTH_3: Helix-turn-hel 92.9 0.075 1.6E-06 34.9 2.0 25 113-137 7-31 (55)
256 TIGR02859 spore_sigH RNA polym 92.9 0.14 3E-06 42.2 4.0 38 103-140 153-190 (198)
257 PRK06704 RNA polymerase factor 92.8 0.15 3.2E-06 44.3 4.3 75 99-176 116-191 (228)
258 PRK10840 transcriptional regul 92.8 0.17 3.6E-06 42.3 4.5 41 98-139 149-189 (216)
259 COG0735 Fur Fe2+/Zn2+ uptake r 92.8 0.43 9.4E-06 38.4 6.7 47 157-210 18-65 (145)
260 PRK09641 RNA polymerase sigma 92.8 0.18 3.8E-06 41.1 4.5 41 100-140 137-177 (187)
261 PF06163 DUF977: Bacterial pro 92.7 0.27 5.8E-06 38.9 5.1 51 97-147 2-58 (127)
262 PF02001 DUF134: Protein of un 92.6 0.22 4.7E-06 38.3 4.4 42 99-140 41-82 (106)
263 PRK10046 dpiA two-component re 92.6 0.24 5.3E-06 41.8 5.3 41 106-146 165-208 (225)
264 PRK13182 racA polar chromosome 92.5 0.38 8.3E-06 40.2 6.1 63 116-183 1-64 (175)
265 PRK05803 sporulation sigma fac 92.5 0.17 3.6E-06 43.5 4.1 42 99-140 175-220 (233)
266 PF05263 DUF722: Protein of un 92.4 0.36 7.8E-06 38.5 5.6 105 19-142 17-126 (130)
267 cd04769 HTH_MerR2 Helix-Turn-H 92.4 0.57 1.2E-05 36.1 6.7 67 116-187 1-68 (116)
268 PF12802 MarR_2: MarR family; 92.4 0.12 2.5E-06 34.8 2.4 31 116-146 22-52 (62)
269 PRK05572 sporulation sigma fac 92.3 0.19 4.2E-06 43.7 4.3 41 100-140 203-243 (252)
270 TIGR03070 couple_hipB transcri 92.2 0.18 3.9E-06 32.9 3.2 25 113-137 13-37 (58)
271 TIGR02941 Sigma_B RNA polymera 92.2 0.21 4.6E-06 43.4 4.5 42 99-140 205-246 (255)
272 COG2390 DeoR Transcriptional r 92.2 0.13 2.8E-06 47.0 3.2 35 111-145 22-56 (321)
273 TIGR02885 spore_sigF RNA polym 92.2 0.24 5.2E-06 42.3 4.8 42 99-140 183-224 (231)
274 COG1710 Uncharacterized protei 92.1 0.3 6.5E-06 38.3 4.7 44 97-140 91-134 (139)
275 smart00354 HTH_LACI helix_turn 92.1 0.27 5.9E-06 34.4 4.2 41 117-173 2-42 (70)
276 PF13730 HTH_36: Helix-turn-he 92.1 0.14 3.1E-06 33.7 2.5 28 117-144 27-54 (55)
277 smart00418 HTH_ARSR helix_turn 92.1 0.25 5.5E-06 32.4 3.8 34 113-146 8-41 (66)
278 PRK07408 RNA polymerase sigma 92.1 0.25 5.3E-06 43.3 4.7 41 100-140 204-244 (256)
279 cd04790 HTH_Cfa-like_unk Helix 92.0 0.71 1.5E-05 38.2 7.2 67 116-186 2-69 (172)
280 PF07750 GcrA: GcrA cell cycle 92.0 0.19 4.1E-06 41.5 3.7 39 101-139 4-43 (162)
281 PF05344 DUF746: Domain of Unk 92.0 0.2 4.4E-06 35.1 3.2 36 107-142 5-40 (65)
282 PRK08295 RNA polymerase factor 91.9 0.27 5.8E-06 40.9 4.6 40 100-140 156-195 (208)
283 cd04776 HTH_GnyR Helix-Turn-He 91.8 0.8 1.7E-05 35.5 6.9 66 116-187 1-67 (118)
284 PF13404 HTH_AsnC-type: AsnC-t 91.8 0.26 5.6E-06 31.4 3.4 34 106-139 6-41 (42)
285 PRK15002 redox-sensitivie tran 91.8 0.63 1.4E-05 38.0 6.5 67 116-187 12-79 (154)
286 PF05930 Phage_AlpA: Prophage 91.8 0.079 1.7E-06 35.0 1.0 22 116-137 4-25 (51)
287 TIGR01950 SoxR redox-sensitive 91.7 0.63 1.4E-05 37.4 6.4 67 116-187 2-69 (142)
288 PRK13509 transcriptional repre 91.6 0.25 5.5E-06 43.2 4.3 43 103-145 5-49 (251)
289 PRK07670 RNA polymerase sigma 91.6 0.29 6.3E-06 42.5 4.6 41 100-140 202-242 (251)
290 PF13443 HTH_26: Cro/C1-type H 91.6 0.12 2.6E-06 34.9 1.8 27 111-137 6-32 (63)
291 TIGR02702 SufR_cyano iron-sulf 91.6 0.28 6.2E-06 41.4 4.4 43 104-146 2-46 (203)
292 PRK05911 RNA polymerase sigma 91.5 0.31 6.6E-06 42.7 4.8 41 100-140 206-246 (257)
293 smart00419 HTH_CRP helix_turn_ 91.5 0.17 3.8E-06 31.9 2.4 32 115-146 8-39 (48)
294 COG2522 Predicted transcriptio 91.5 0.2 4.4E-06 39.3 3.2 36 103-138 9-45 (119)
295 PRK09191 two-component respons 91.5 0.32 7E-06 41.4 4.8 44 99-142 88-131 (261)
296 cd04779 HTH_MerR-like_sg4 Heli 91.4 0.79 1.7E-05 36.6 6.6 67 116-187 1-68 (134)
297 smart00344 HTH_ASNC helix_turn 91.4 0.34 7.3E-06 36.3 4.3 41 106-146 6-48 (108)
298 PF03444 HrcA_DNA-bdg: Winged 91.4 0.75 1.6E-05 33.4 5.8 52 105-156 10-66 (78)
299 COG4496 Uncharacterized protei 91.3 0.22 4.7E-06 37.1 3.0 43 100-143 41-83 (100)
300 PRK12518 RNA polymerase sigma 91.3 0.14 3.1E-06 41.4 2.2 41 100-140 121-161 (175)
301 PF13412 HTH_24: Winged helix- 91.2 0.67 1.4E-05 29.7 5.0 39 161-210 3-41 (48)
302 cd00092 HTH_CRP helix_turn_hel 91.1 0.19 4.2E-06 34.0 2.5 33 115-147 25-57 (67)
303 PRK11179 DNA-binding transcrip 91.1 0.51 1.1E-05 38.0 5.4 42 104-145 10-53 (153)
304 PF10654 DUF2481: Protein of u 91.1 0.21 4.6E-06 38.8 2.9 36 106-141 71-106 (126)
305 PRK07122 RNA polymerase sigma 91.1 0.31 6.7E-06 43.0 4.4 41 100-140 216-256 (264)
306 TIGR02846 spore_sigmaK RNA pol 91.1 0.33 7.1E-06 41.5 4.4 41 100-140 175-219 (227)
307 PRK06288 RNA polymerase sigma 91.1 0.36 7.9E-06 42.4 4.8 41 100-140 213-253 (268)
308 PF13404 HTH_AsnC-type: AsnC-t 91.1 0.87 1.9E-05 28.9 5.3 38 161-209 3-40 (42)
309 TIGR03338 phnR_burk phosphonat 91.1 0.71 1.5E-05 38.7 6.4 60 103-162 19-81 (212)
310 PF07374 DUF1492: Protein of u 91.0 0.45 9.7E-06 35.9 4.6 38 103-140 59-96 (100)
311 PF00392 GntR: Bacterial regul 91.0 0.21 4.5E-06 34.2 2.5 32 117-148 26-57 (64)
312 PRK10100 DNA-binding transcrip 91.0 0.25 5.4E-06 42.3 3.5 88 50-141 107-196 (216)
313 PRK01905 DNA-binding protein F 91.0 0.36 7.9E-06 34.6 3.9 37 104-140 38-75 (77)
314 TIGR02607 antidote_HigA addict 90.9 0.37 8E-06 33.9 3.9 27 111-137 14-40 (78)
315 PRK11475 DNA-binding transcrip 90.9 0.26 5.6E-06 41.9 3.5 78 50-140 95-174 (207)
316 COG2345 Predicted transcriptio 90.8 0.39 8.4E-06 41.5 4.6 56 101-156 9-68 (218)
317 PRK09643 RNA polymerase sigma 90.8 0.43 9.3E-06 39.6 4.7 41 100-140 135-175 (192)
318 cd01392 HTH_LacI Helix-turn-he 90.7 0.34 7.4E-06 31.3 3.3 38 119-172 1-38 (52)
319 PRK11169 leucine-responsive tr 90.7 0.38 8.2E-06 39.3 4.3 43 103-145 14-58 (164)
320 PF02650 HTH_WhiA: WhiA C-term 90.7 0.43 9.4E-06 35.2 4.1 41 160-209 39-79 (85)
321 COG2944 Predicted transcriptio 90.7 0.63 1.4E-05 35.7 5.1 24 114-137 56-79 (104)
322 PRK06474 hypothetical protein; 90.7 0.34 7.5E-06 40.3 4.0 50 97-146 5-58 (178)
323 cd07377 WHTH_GntR Winged helix 90.6 0.23 5E-06 33.2 2.5 30 117-146 27-56 (66)
324 PRK09954 putative kinase; Prov 90.6 0.36 7.9E-06 44.0 4.5 43 103-145 3-47 (362)
325 cd07153 Fur_like Ferric uptake 90.5 0.77 1.7E-05 34.8 5.6 42 163-210 3-45 (116)
326 cd04781 HTH_MerR-like_sg6 Heli 90.5 1.2 2.6E-05 34.5 6.7 67 116-187 1-68 (120)
327 PRK11608 pspF phage shock prot 90.4 0.3 6.5E-06 44.3 3.8 37 104-140 287-324 (326)
328 PRK12427 flagellar biosynthesi 90.4 0.47 1E-05 41.0 4.8 42 100-141 184-225 (231)
329 PF13545 HTH_Crp_2: Crp-like h 90.4 0.24 5.3E-06 34.6 2.5 32 115-146 28-59 (76)
330 PRK10906 DNA-binding transcrip 90.4 0.33 7.1E-06 42.6 3.9 44 102-145 4-49 (252)
331 PF06413 Neugrin: Neugrin; In 90.4 0.62 1.4E-05 40.4 5.5 52 152-215 5-57 (225)
332 PRK08215 sporulation sigma fac 90.3 0.4 8.6E-06 41.8 4.3 40 100-139 210-249 (258)
333 PRK13719 conjugal transfer tra 90.3 0.36 7.8E-06 41.7 3.9 43 97-140 141-183 (217)
334 PRK09492 treR trehalose repres 90.3 0.37 8.1E-06 42.2 4.2 41 116-172 5-45 (315)
335 PF01047 MarR: MarR family; I 90.2 0.45 9.8E-06 31.6 3.6 34 113-146 15-48 (59)
336 PRK10072 putative transcriptio 90.2 0.23 5.1E-06 37.4 2.4 26 112-137 43-68 (96)
337 PF13565 HTH_32: Homeodomain-l 90.2 0.47 1E-05 33.3 3.9 40 97-136 27-77 (77)
338 PRK09863 putative frv operon r 90.2 1.7 3.7E-05 42.4 9.1 94 105-211 6-117 (584)
339 cd07153 Fur_like Ferric uptake 90.2 0.48 1E-05 35.9 4.2 43 104-146 2-52 (116)
340 PF04218 CENP-B_N: CENP-B N-te 90.2 0.35 7.6E-06 32.3 3.0 35 54-88 5-39 (53)
341 PRK13752 putative transcriptio 90.1 1.2 2.6E-05 35.9 6.6 67 116-186 8-75 (144)
342 PRK15043 transcriptional regul 90.1 1 2.2E-05 39.6 6.6 68 116-187 4-72 (243)
343 PRK15320 transcriptional activ 90.1 0.5 1.1E-05 40.5 4.5 40 105-144 169-208 (251)
344 COG2964 Uncharacterized protei 89.9 0.4 8.7E-06 41.4 3.8 41 103-143 173-219 (220)
345 PF07141 Phage_term_sma: Putat 89.9 0.39 8.4E-06 38.4 3.5 44 96-139 12-55 (174)
346 PRK09462 fur ferric uptake reg 89.9 1.2 2.5E-05 35.7 6.4 45 159-210 16-62 (148)
347 PRK11303 DNA-binding transcrip 89.8 0.46 1E-05 41.9 4.4 42 116-172 1-44 (328)
348 PRK00430 fis global DNA-bindin 89.8 0.5 1.1E-05 35.5 3.9 37 104-140 56-93 (95)
349 PRK11414 colanic acid/biofilm 89.7 0.81 1.7E-05 38.7 5.7 46 116-161 35-80 (221)
350 PF01475 FUR: Ferric uptake re 89.7 0.49 1.1E-05 36.3 3.9 43 162-210 9-52 (120)
351 PRK11922 RNA polymerase sigma 89.6 0.3 6.5E-06 41.8 2.9 41 100-140 150-190 (231)
352 PRK09483 response regulator; P 89.6 0.45 9.7E-06 38.9 3.9 41 99-140 148-188 (217)
353 PRK10430 DNA-binding transcrip 89.6 0.7 1.5E-05 39.3 5.2 46 100-145 159-208 (239)
354 COG3415 Transposase and inacti 89.5 2 4.3E-05 34.5 7.4 84 55-138 4-109 (138)
355 TIGR02405 trehalos_R_Ecol treh 89.5 0.46 1E-05 41.8 4.1 41 116-172 2-42 (311)
356 TIGR02394 rpoS_proteo RNA poly 89.4 0.46 9.9E-06 42.2 4.0 41 100-140 223-267 (285)
357 COG2771 CsgD DNA-binding HTH d 89.3 0.55 1.2E-05 31.4 3.5 33 107-139 11-43 (65)
358 PRK10651 transcriptional regul 89.3 0.65 1.4E-05 37.4 4.6 41 100-141 156-196 (216)
359 PRK09726 antitoxin HipB; Provi 89.3 0.42 9E-06 35.0 3.1 25 113-137 23-47 (88)
360 TIGR02787 codY_Gpos GTP-sensin 89.3 1.1 2.3E-05 39.4 6.1 45 105-149 185-232 (251)
361 PF14549 P22_Cro: DNA-binding 89.3 0.21 4.5E-06 34.5 1.3 19 117-135 11-29 (60)
362 PRK09526 lacI lac repressor; R 89.2 0.51 1.1E-05 41.9 4.2 41 116-172 6-46 (342)
363 cd06571 Bac_DnaA_C C-terminal 89.1 2.7 5.9E-05 30.8 7.4 39 103-141 30-71 (90)
364 TIGR01636 phage_rinA phage tra 89.1 0.66 1.4E-05 36.8 4.3 41 100-140 83-125 (134)
365 PF07900 DUF1670: Protein of u 88.9 0.66 1.4E-05 40.1 4.4 68 58-135 150-217 (220)
366 PF00126 HTH_1: Bacterial regu 88.9 0.57 1.2E-05 31.6 3.3 36 107-142 5-40 (60)
367 PRK10703 DNA-binding transcrip 88.9 0.56 1.2E-05 41.6 4.2 41 116-172 2-42 (341)
368 COG1191 FliA DNA-directed RNA 88.9 0.62 1.4E-05 41.0 4.4 42 99-140 196-237 (247)
369 COG1522 Lrp Transcriptional re 88.8 0.63 1.4E-05 36.9 4.1 43 103-145 8-52 (154)
370 COG1321 TroR Mn-dependent tran 88.7 9.1 0.0002 31.2 10.9 98 106-212 12-122 (154)
371 PRK14987 gluconate operon tran 88.7 0.53 1.2E-05 41.7 4.0 41 116-172 6-46 (331)
372 PRK11534 DNA-binding transcrip 88.7 0.85 1.8E-05 38.6 5.0 59 103-161 15-76 (224)
373 PRK10014 DNA-binding transcrip 88.6 0.57 1.2E-05 41.5 4.1 41 116-172 7-47 (342)
374 TIGR03020 EpsA transcriptional 88.6 0.55 1.2E-05 41.3 3.9 42 99-141 190-231 (247)
375 PRK11639 zinc uptake transcrip 88.6 1.3 2.8E-05 36.5 6.0 42 163-210 28-70 (169)
376 PF09862 DUF2089: Protein of u 88.6 5.2 0.00011 31.1 8.8 79 100-185 34-112 (113)
377 PRK10727 DNA-binding transcrip 88.4 0.61 1.3E-05 41.6 4.1 40 117-172 3-42 (343)
378 PRK14702 insertion element IS2 88.3 2.2 4.8E-05 37.5 7.6 53 159-215 10-65 (262)
379 TIGR02850 spore_sigG RNA polym 88.3 0.72 1.6E-05 40.2 4.4 41 100-140 207-247 (254)
380 smart00342 HTH_ARAC helix_turn 88.3 1.7 3.7E-05 29.8 5.6 79 116-215 2-81 (84)
381 TIGR02392 rpoH_proteo alternat 88.2 0.57 1.2E-05 41.3 3.7 40 100-139 219-260 (270)
382 PF12759 HTH_Tnp_IS1: InsA C-t 88.1 0.38 8.3E-06 31.4 1.9 31 58-88 8-38 (46)
383 TIGR02393 RpoD_Cterm RNA polym 88.0 0.59 1.3E-05 40.2 3.7 41 100-140 177-221 (238)
384 smart00550 Zalpha Z-DNA-bindin 88.0 1.7 3.6E-05 30.4 5.3 46 159-215 4-54 (68)
385 smart00529 HTH_DTXR Helix-turn 88.0 3.8 8.2E-05 29.7 7.6 31 118-148 2-32 (96)
386 PF13518 HTH_28: Helix-turn-he 88.0 0.4 8.7E-06 30.9 2.0 29 60-88 1-29 (52)
387 COG1349 GlpR Transcriptional r 87.9 1.7 3.8E-05 38.0 6.6 45 102-146 4-50 (253)
388 PRK15369 two component system 87.8 0.87 1.9E-05 36.2 4.4 41 100-141 150-190 (211)
389 COG1802 GntR Transcriptional r 87.8 1.4 3.1E-05 37.5 5.9 63 103-165 24-89 (230)
390 COG2512 Predicted membrane-ass 87.8 0.74 1.6E-05 40.8 4.2 53 98-150 191-245 (258)
391 PRK10401 DNA-binding transcrip 87.6 0.73 1.6E-05 41.1 4.2 41 116-172 2-42 (346)
392 PF00376 MerR: MerR family reg 87.6 0.31 6.7E-06 30.4 1.2 25 117-145 1-25 (38)
393 TIGR02337 HpaR homoprotocatech 87.5 2.3 5E-05 32.4 6.4 56 114-169 41-99 (118)
394 smart00352 POU Found in Pit-Oc 87.5 0.95 2E-05 32.7 3.8 33 105-137 13-52 (75)
395 PRK09706 transcriptional repre 87.5 0.68 1.5E-05 36.5 3.4 33 106-138 8-41 (135)
396 TIGR01481 ccpA catabolite cont 87.4 0.77 1.7E-05 40.5 4.1 41 116-172 2-42 (329)
397 PF13560 HTH_31: Helix-turn-he 87.4 0.75 1.6E-05 31.3 3.2 24 114-137 13-36 (64)
398 PRK10411 DNA-binding transcrip 87.1 0.91 2E-05 39.5 4.3 44 103-146 4-49 (240)
399 TIGR03541 reg_near_HchA LuxR f 87.1 0.94 2E-05 39.0 4.4 42 98-140 170-211 (232)
400 PRK11361 acetoacetate metaboli 87.1 0.7 1.5E-05 43.1 3.9 38 103-140 417-455 (457)
401 PRK10339 DNA-binding transcrip 87.1 0.82 1.8E-05 40.5 4.1 42 116-172 2-44 (327)
402 cd04778 HTH_MerR-like_sg2 Heli 87.0 2.5 5.3E-05 36.5 6.9 67 116-187 2-69 (219)
403 smart00347 HTH_MARR helix_turn 86.8 4.9 0.00011 28.7 7.6 42 105-146 12-55 (101)
404 COG3355 Predicted transcriptio 86.8 1.2 2.7E-05 35.2 4.5 42 158-210 25-66 (126)
405 TIGR01610 phage_O_Nterm phage 86.6 1.4 3E-05 32.8 4.5 33 114-146 46-78 (95)
406 PRK11014 transcriptional repre 86.6 1 2.2E-05 35.7 4.1 47 103-149 10-59 (141)
407 PRK11511 DNA-binding transcrip 86.5 3.9 8.4E-05 31.8 7.2 82 112-215 22-105 (127)
408 COG3311 AlpA Predicted transcr 86.4 1.2 2.6E-05 31.7 3.8 23 116-138 14-36 (70)
409 COG3413 Predicted DNA binding 86.3 1.3 2.9E-05 37.6 4.9 42 99-140 155-203 (215)
410 smart00530 HTH_XRE Helix-turn- 86.3 0.63 1.4E-05 28.6 2.2 26 112-137 7-32 (56)
411 COG1609 PurR Transcriptional r 86.3 1.1 2.5E-05 40.6 4.7 40 117-172 2-41 (333)
412 cd00093 HTH_XRE Helix-turn-hel 86.2 0.64 1.4E-05 28.9 2.2 25 113-137 10-34 (58)
413 cd00569 HTH_Hin_like Helix-tur 86.1 2.6 5.7E-05 23.5 4.8 41 154-207 2-42 (42)
414 COG2973 TrpR Trp operon repres 86.1 0.8 1.7E-05 34.7 2.9 33 103-135 47-80 (103)
415 TIGR02417 fruct_sucro_rep D-fr 86.0 1 2.2E-05 39.7 4.1 41 117-172 1-43 (327)
416 PF13601 HTH_34: Winged helix 85.9 0.92 2E-05 32.8 3.1 67 104-170 1-73 (80)
417 COG1476 Predicted transcriptio 85.9 0.87 1.9E-05 32.2 2.9 31 107-137 5-36 (68)
418 PF12844 HTH_19: Helix-turn-he 85.8 0.74 1.6E-05 31.1 2.5 25 113-137 10-34 (64)
419 PRK10434 srlR DNA-bindng trans 85.7 0.94 2E-05 39.7 3.7 44 102-145 4-49 (256)
420 PF08220 HTH_DeoR: DeoR-like h 85.6 1.2 2.6E-05 30.0 3.4 36 164-210 3-38 (57)
421 COG1654 BirA Biotin operon rep 85.6 1.6 3.4E-05 31.8 4.2 29 116-144 20-48 (79)
422 PRK09480 slmA division inhibit 85.5 1.3 2.7E-05 36.0 4.2 44 95-138 2-53 (194)
423 PF13384 HTH_23: Homeodomain-l 85.5 0.39 8.5E-06 30.9 0.9 32 57-88 3-34 (50)
424 TIGR02915 PEP_resp_reg putativ 85.3 0.96 2.1E-05 42.2 3.8 37 104-140 406-443 (445)
425 TIGR02997 Sig70-cyanoRpoD RNA 85.3 1.1 2.5E-05 40.0 4.1 41 100-140 250-294 (298)
426 PRK10219 DNA-binding transcrip 85.3 5.4 0.00012 29.7 7.3 81 113-215 19-101 (107)
427 PRK07500 rpoH2 RNA polymerase 85.2 1.3 2.7E-05 39.6 4.4 41 100-140 228-270 (289)
428 PF01418 HTH_6: Helix-turn-hel 85.2 0.61 1.3E-05 33.3 1.9 40 163-213 18-61 (77)
429 PRK05657 RNA polymerase sigma 85.0 1.2 2.5E-05 40.6 4.1 41 100-140 263-307 (325)
430 PF13309 HTH_22: HTH domain 85.0 2.2 4.8E-05 29.5 4.6 48 154-208 17-64 (64)
431 TIGR01453 grpIintron_endo grou 85.0 5 0.00011 34.3 7.8 41 97-137 145-201 (214)
432 COG5352 Uncharacterized protei 84.9 0.92 2E-05 36.6 2.9 43 103-145 5-49 (169)
433 PF13744 HTH_37: Helix-turn-he 84.8 0.86 1.9E-05 32.7 2.6 30 108-137 23-53 (80)
434 PRK15090 DNA-binding transcrip 84.6 3.9 8.4E-05 35.6 7.1 45 103-147 14-60 (257)
435 PRK15424 propionate catabolism 84.6 1.2 2.5E-05 43.6 4.1 40 102-141 496-536 (538)
436 PRK10423 transcriptional repre 84.6 1.1 2.4E-05 39.4 3.7 38 119-172 2-39 (327)
437 PRK09834 DNA-binding transcrip 84.5 3.1 6.6E-05 36.4 6.4 45 102-146 10-57 (263)
438 PRK13890 conjugal transfer pro 84.5 1.1 2.3E-05 35.0 3.1 31 107-137 9-40 (120)
439 PRK10360 DNA-binding transcrip 84.5 1.4 2.9E-05 35.3 3.9 42 99-141 137-178 (196)
440 PF07022 Phage_CI_repr: Bacter 84.3 0.74 1.6E-05 31.9 1.9 22 116-137 13-35 (66)
441 TIGR02974 phageshock_pspF psp 84.3 1.1 2.3E-05 40.8 3.5 35 105-139 294-329 (329)
442 PRK00215 LexA repressor; Valid 84.2 1.7 3.7E-05 36.4 4.5 32 116-147 24-56 (205)
443 PF11985 DUF3486: Protein of u 84.2 3.1 6.8E-05 34.5 6.0 48 157-210 9-59 (180)
444 TIGR02431 pcaR_pcaU beta-ketoa 84.1 1.3 2.8E-05 38.3 3.8 42 105-146 11-55 (248)
445 PRK11512 DNA-binding transcrip 84.0 3.7 7.9E-05 32.4 6.2 55 113-167 52-109 (144)
446 TIGR02404 trehalos_R_Bsub treh 84.0 1.1 2.3E-05 38.3 3.2 33 117-149 26-58 (233)
447 TIGR02844 spore_III_D sporulat 84.0 1.8 3.9E-05 31.5 3.9 68 61-134 8-77 (80)
448 PRK11169 leucine-responsive tr 83.9 1.9 4.1E-05 35.1 4.6 41 159-210 12-52 (164)
449 COG3398 Uncharacterized protei 83.7 8.3 0.00018 33.6 8.4 104 102-216 100-221 (240)
450 PRK10820 DNA-binding transcrip 83.5 1.2 2.6E-05 43.1 3.7 37 104-140 475-511 (520)
451 cd00283 GIY-YIG_Cterm GIYX(10- 83.3 4.7 0.0001 31.2 6.2 67 51-137 17-102 (113)
452 TIGR00647 MG103 conserved hypo 83.2 2 4.4E-05 38.5 4.7 46 160-210 229-274 (279)
453 PRK10403 transcriptional regul 83.2 1.6 3.5E-05 35.0 3.8 40 100-140 154-193 (215)
454 PRK10188 DNA-binding transcrip 83.2 1.5 3.3E-05 38.0 3.9 41 99-140 179-219 (240)
455 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 83.1 1 2.2E-05 30.0 2.1 36 53-88 2-37 (50)
456 PRK06424 transcription factor; 83.1 1.5 3.2E-05 35.5 3.5 31 107-137 88-119 (144)
457 TIGR00637 ModE_repress ModE mo 83.0 5.2 0.00011 30.0 6.3 62 105-166 6-71 (99)
458 TIGR03697 NtcA_cyano global ni 82.8 0.97 2.1E-05 36.8 2.4 32 116-147 144-175 (193)
459 PF09012 FeoC: FeoC like trans 82.5 1.2 2.6E-05 31.0 2.5 39 108-146 5-45 (69)
460 PRK11388 DNA-binding transcrip 82.5 1.4 3E-05 43.5 3.7 39 102-140 590-629 (638)
461 PRK09464 pdhR transcriptional 82.3 2.2 4.9E-05 36.8 4.6 50 103-152 18-71 (254)
462 COG2739 Uncharacterized protei 82.3 1.9 4.1E-05 32.9 3.5 40 100-139 18-57 (105)
463 PRK13870 transcriptional regul 82.3 1.7 3.8E-05 37.6 3.9 41 99-140 173-213 (234)
464 PRK04984 fatty acid metabolism 82.2 2.3 5.1E-05 36.3 4.6 35 116-150 31-66 (239)
465 PRK12682 transcriptional regul 82.2 3.7 8.1E-05 36.1 6.1 36 107-142 7-43 (309)
466 PRK14165 winged helix-turn-hel 82.1 1.7 3.6E-05 37.6 3.6 52 115-166 21-72 (217)
467 PRK10163 DNA-binding transcrip 82.0 6.6 0.00014 34.5 7.6 44 103-146 25-71 (271)
468 TIGR02293 TAS_TIGR02293 putati 81.9 6.5 0.00014 31.1 6.7 24 114-137 35-58 (133)
469 TIGR03830 CxxCG_CxxCG_HTH puta 81.9 1.1 2.4E-05 34.4 2.3 25 113-137 76-100 (127)
470 COG3829 RocR Transcriptional r 81.8 1.9 4.1E-05 42.1 4.2 38 103-140 520-558 (560)
471 PRK11569 transcriptional repre 81.7 2.1 4.5E-05 37.8 4.2 44 103-146 28-74 (274)
472 PF01726 LexA_DNA_bind: LexA D 81.7 1.5 3.1E-05 30.6 2.6 34 113-146 21-57 (65)
473 PRK03902 manganese transport t 81.6 2.9 6.3E-05 33.1 4.7 31 116-146 23-53 (142)
474 PRK15115 response regulator Gl 81.5 1.7 3.7E-05 40.5 3.8 37 104-140 399-436 (444)
475 PF08461 HTH_12: Ribonuclease 81.5 3.1 6.8E-05 28.9 4.3 40 165-210 2-42 (66)
476 COG1961 PinR Site-specific rec 81.5 1.7 3.7E-05 36.9 3.5 47 98-144 159-206 (222)
477 PRK09990 DNA-binding transcrip 81.4 3.2 6.9E-05 35.7 5.2 37 116-152 31-68 (251)
478 TIGR02325 C_P_lyase_phnF phosp 81.3 2.1 4.6E-05 36.3 4.1 33 117-149 34-66 (238)
479 COG5566 Uncharacterized conser 81.2 2 4.2E-05 34.1 3.4 50 93-142 80-129 (137)
480 PRK09935 transcriptional regul 81.2 2.1 4.7E-05 34.3 3.9 34 107-140 156-189 (210)
481 PF06056 Terminase_5: Putative 81.2 1.3 2.9E-05 30.2 2.2 30 59-88 1-30 (58)
482 PRK14999 histidine utilization 81.0 2.3 5E-05 36.5 4.2 33 117-149 38-70 (241)
483 PF08279 HTH_11: HTH domain; 81.0 2.7 5.9E-05 27.4 3.7 35 165-210 4-39 (55)
484 PRK10923 glnG nitrogen regulat 81.0 1.9 4E-05 40.6 3.9 37 104-140 430-467 (469)
485 PRK04841 transcriptional regul 80.8 1.9 4E-05 43.7 4.1 44 99-143 838-882 (903)
486 PF04645 DUF603: Protein of un 80.7 1.8 3.8E-05 36.0 3.1 36 109-144 12-48 (181)
487 PF05269 Phage_CII: Bacterioph 80.7 1.2 2.6E-05 33.3 2.0 26 115-140 23-48 (91)
488 PRK11179 DNA-binding transcrip 80.6 3.3 7.2E-05 33.2 4.7 40 160-210 8-47 (153)
489 PRK12423 LexA repressor; Provi 80.4 2.8 6.1E-05 35.3 4.5 45 103-147 6-58 (202)
490 COG1356 tfx Transcriptional re 80.4 0.97 2.1E-05 35.9 1.5 40 103-142 11-50 (143)
491 PF08069 Ribosomal_S13_N: Ribo 80.4 0.79 1.7E-05 31.6 0.9 31 57-87 30-60 (60)
492 TIGR01889 Staph_reg_Sar staphy 80.4 7.3 0.00016 29.4 6.4 33 114-146 42-74 (109)
493 PRK03837 transcriptional regul 80.3 1.6 3.4E-05 37.3 2.9 34 117-150 39-72 (241)
494 PRK09906 DNA-binding transcrip 80.1 4.9 0.00011 34.9 6.0 36 107-142 7-42 (296)
495 PRK09943 DNA-binding transcrip 80.0 2.1 4.5E-05 35.4 3.5 25 113-137 18-42 (185)
496 COG1497 Predicted transcriptio 79.9 5.4 0.00012 35.1 6.0 96 103-215 10-108 (260)
497 PRK09764 DNA-binding transcrip 79.8 2.8 6E-05 36.0 4.3 33 117-149 31-63 (240)
498 TIGR00498 lexA SOS regulatory 79.8 2.6 5.6E-05 35.2 4.0 32 116-147 26-58 (199)
499 TIGR01884 cas_HTH CRISPR locus 79.7 3 6.6E-05 35.1 4.4 43 105-147 145-189 (203)
500 TIGR02944 suf_reg_Xantho FeS a 79.6 3.9 8.5E-05 31.7 4.8 32 116-147 26-57 (130)
No 1
>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=100.00 E-value=2.7e-35 Score=230.73 Aligned_cols=125 Identities=74% Similarity=1.263 Sum_probs=95.1
Q ss_pred CCCCccccCccccCCCCCChhHHHHHHHHHhcCCChhhhhhhhcccccccccCCcccCCCcCCHHHHHHHHHHHHcCCCH
Q psy1898 39 CQGRMNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGVNQLGGVFINGRPLPNHIRLKIVEMAAAGVRP 118 (230)
Q Consensus 39 ~~~~~~~~g~~~~~g~plp~~~r~~I~e~~~~g~~~~~isr~lrvshg~~~l~~~~~~g~~~s~~~R~rIV~l~~~G~s~ 118 (230)
||+++|||||+|+||+|||.++|.+||||+.+|++||+||++|+|+|||
T Consensus 1 g~~~~NqlGg~~~nGrPLp~~~R~rIvela~~G~rp~~Isr~l~Vs~gc------------------------------- 49 (125)
T PF00292_consen 1 GQGRVNQLGGVFINGRPLPNELRQRIVELAKEGVRPCDISRQLRVSHGC------------------------------- 49 (125)
T ss_dssp S-EEE-TTS-EEETTSSS-HHHHHHHHHHHHTT--HHHHHHHHT--HHH-------------------------------
T ss_pred CCccccccCceeeCCccCcHHHHHHHHHHhhhcCCHHHHHHHHccchhH-------------------------------
Confidence 5788999999999999999999999999998888888888888877777
Q ss_pred HHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCC
Q psy1898 119 CVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAP 198 (230)
Q Consensus 119 ~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~v 198 (230)
|+||++||++||++.|...+|.+|++.++++.++|.++..++|.+++|||++.|.+ .|+|+..++|
T Consensus 50 -------------VsKIl~Ry~eTGsi~Pg~iGGskprv~tp~v~~~I~~~k~enP~ifawEiR~~L~~-~gvc~~~~~P 115 (125)
T PF00292_consen 50 -------------VSKILSRYRETGSIRPGPIGGSKPRVATPEVVEKIEQYKRENPTIFAWEIRDRLIA-DGVCDRSNVP 115 (125)
T ss_dssp -------------HHHHHHHHHHHS-SS----S----SSS-HCHHHHHHHHHHH-TTS-HHHHHHHHHH-TTSS-TTTS-
T ss_pred -------------HHHHHHHHHHhcccCcccccCCCCCCCChHHHHHHHHHHhcCCCcchHHHHHHHHH-cCCCCCCCCC
Confidence 67999999999999999998889999999999999999999999999999999998 9999999999
Q ss_pred CHhHHHHHHH
Q psy1898 199 SVSSISRLLR 208 (230)
Q Consensus 199 S~sTV~R~Lr 208 (230)
|.|+|+|+|+
T Consensus 116 svssInRilr 125 (125)
T PF00292_consen 116 SVSSINRILR 125 (125)
T ss_dssp -HHHHHHHHH
T ss_pred CHHHHHHhhC
Confidence 9999999996
No 2
>KOG3517|consensus
Probab=100.00 E-value=9e-34 Score=242.06 Aligned_cols=126 Identities=72% Similarity=1.185 Sum_probs=121.4
Q ss_pred CCCccccCccccCCCCCChhHHHHHHHHHhcCCChhhhhhhhcccccccccCCcccCCCcCCHHHHHHHHHHHHcCCCHH
Q psy1898 40 QGRMNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGVNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPC 119 (230)
Q Consensus 40 ~~~~~~~g~~~~~g~plp~~~r~~I~e~~~~g~~~~~isr~lrvshg~~~l~~~~~~g~~~s~~~R~rIV~l~~~G~s~~ 119 (230)
.+.||||||+||||||||.++|++|||++..|.+||||||||||||||
T Consensus 5 ~GEVNQLGGVFVNGRPLPna~RlrIVELarlGiRPCDISRQLrvSHGC-------------------------------- 52 (334)
T KOG3517|consen 5 YGEVNQLGGVFVNGRPLPNAIRLRIVELARLGIRPCDISRQLRVSHGC-------------------------------- 52 (334)
T ss_pred ccchhhccceeEcCccCcchhhhhHHHHHHcCCCccchhhhhhhccch--------------------------------
Confidence 368999999999999999999999999999999999999999999999
Q ss_pred HHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCC
Q psy1898 120 VISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPS 199 (230)
Q Consensus 120 ~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS 199 (230)
|+|++.||.|+|++-|.-++|.+|+++|+.+.++|+.+.+.+|.+++|||+++|.. .|||+...++|
T Consensus 53 ------------VSKILaRy~EtGsIlPGaIGGSkPRVTTP~VV~~IR~~Kq~DPGIFAWEIRDRLls-dgiCDk~NvPS 119 (334)
T KOG3517|consen 53 ------------VSKILARYNETGSILPGAIGGSKPRVTTPKVVKYIRSLKQRDPGIFAWEIRDRLLS-DGICDKYNVPS 119 (334)
T ss_pred ------------HHHHHHHhccCCcccccccCCCCCccCChhHHHHHHHhhccCCceeeehhhhhhhh-cccccccCCcc
Confidence 46888999999999999999999999999999999999999999999999999999 99999999999
Q ss_pred HhHHHHHHHcC
Q psy1898 200 VSSISRLLRGG 210 (230)
Q Consensus 200 ~sTV~R~Lr~~ 210 (230)
+|+|.|+|+++
T Consensus 120 VSSISRILRNK 130 (334)
T KOG3517|consen 120 VSSISRILRNK 130 (334)
T ss_pred hHHHHHHHHhh
Confidence 99999999987
No 3
>KOG3862|consensus
Probab=99.96 E-value=9.2e-29 Score=213.31 Aligned_cols=132 Identities=65% Similarity=1.099 Sum_probs=124.4
Q ss_pred CCCCCccccCccccCCCCCChhHHHHHHHHHhcCCChhhhhhhhcccccccccCCcccCCCcCCHHHHHHHHHHHHcCCC
Q psy1898 38 SCQGRMNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGVNQLGGVFINGRPLPNHIRLKIVEMAAAGVR 117 (230)
Q Consensus 38 ~~~~~~~~~g~~~~~g~plp~~~r~~I~e~~~~g~~~~~isr~lrvshg~~~l~~~~~~g~~~s~~~R~rIV~l~~~G~s 117 (230)
.|+++||||||+||||||||+.+|+.|+||+++|++||+|+||++|||||+
T Consensus 8 ~ghgGvNQLGGvFVNGRPlpd~Vr~rIv~La~~gvrpcdisrQl~vShGcv----------------------------- 58 (327)
T KOG3862|consen 8 SGHGGVNQLGGVFVNGRPLPDVVRQRIVELAQNGVRPCDISRQLRVSHGCV----------------------------- 58 (327)
T ss_pred CCccchhhccceeecCccCchHHHHHHHHHHHcCCcchhHHHHHhhccCCc-----------------------------
Confidence 478999999999999999999999999999999999999999999999995
Q ss_pred HHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCC
Q psy1898 118 PCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSA 197 (230)
Q Consensus 118 ~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~ 197 (230)
++++-||-|+|+++++.+++..|+..++.+.+.|..+.+++|.+++|||++.|.. .++|+.+++
T Consensus 59 ---------------Skil~r~yEtgS~~pg~iggsk~KvAtp~Vvk~i~~~k~~n~~mfaweiR~~l~~-~~ic~~d~v 122 (327)
T KOG3862|consen 59 ---------------SKILGRYYETGSIRPGVIGGSKPKVATPKVVKKIALYKRQNPTMFAWEIRDRLLA-EPICDNDTV 122 (327)
T ss_pred ---------------hhHHHHHHHhcCcccCCCCCCccccccchHHHHHHHHhhcCcchhhhhhhhhhhc-ccccCCCCC
Confidence 4667899999999999999999999999999999999999999999999999988 899999999
Q ss_pred CCHhHHHHHHHcCCCCC
Q psy1898 198 PSVSSISRLLRGGRRDD 214 (230)
Q Consensus 198 vS~sTV~R~Lr~~g~~~ 214 (230)
+|++.|.|+++...+.+
T Consensus 123 psVssinri~r~~~~~~ 139 (327)
T KOG3862|consen 123 PSVSSINRIIRTKVQQK 139 (327)
T ss_pred chHHHHHHHHHHhhhhc
Confidence 99999999999886553
No 4
>cd00131 PAX Paired Box domain
Probab=99.95 E-value=1.6e-27 Score=189.07 Aligned_cols=125 Identities=74% Similarity=1.285 Sum_probs=115.8
Q ss_pred ccccccCCcccCCCcCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHH
Q psy1898 85 HGVNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEK 164 (230)
Q Consensus 85 hg~~~l~~~~~~g~~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~ 164 (230)
.++|+||+.|.++++||.+.|.+||+++++|+|.++||++|+||++||++|+++|+++|++.|++.+|.+|++++++..+
T Consensus 3 ~~~~~~~~~~~m~~~lS~d~R~rIv~~~~~G~s~~~iA~~~~Vs~~tV~r~i~r~~e~G~v~pk~~gg~rpr~~~~~~~~ 82 (128)
T cd00131 3 GGVNQLGGVFVNGRPLPDSIRQRIVELAQSGIRPCDISRQLRVSHGCVSKILNRYYETGSIRPGAIGGSKPRVATPEVVK 82 (128)
T ss_pred ccccCCCccccCCCcCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCCCCCCCCCCcCCHHHHH
Confidence 35889999999999999999999999999999999999999999999999999999999999988877678988998888
Q ss_pred HHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcC
Q psy1898 165 RIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGG 210 (230)
Q Consensus 165 ~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~ 210 (230)
+|..+++++|++|++||+++|.. .|++..+..||.|||+|+|+++
T Consensus 83 ~i~~~v~~~p~~Tl~El~~~L~~-~gv~~~~~~~s~stI~R~L~~~ 127 (128)
T cd00131 83 KIEIYKQENPGMFAWEIRDRLLQ-EGVCDKSNVPSVSSINRILRNK 127 (128)
T ss_pred HHHHHHHHCCCCCHHHHHHHHHH-cCCcccCCCCCHHHHHHHHHhc
Confidence 99999999999999999999876 7887666678999999999875
No 5
>smart00351 PAX Paired Box domain.
Probab=99.94 E-value=2.9e-26 Score=181.10 Aligned_cols=124 Identities=73% Similarity=1.247 Sum_probs=116.3
Q ss_pred cccccccCCcccCCCcCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHH
Q psy1898 84 SHGVNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVE 163 (230)
Q Consensus 84 shg~~~l~~~~~~g~~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~ 163 (230)
+.|+|++|+-|.++++||.++|.+||.++++|.+.++||++|+||++||++|+++|+++|.+.|++.++.+|+++++++.
T Consensus 2 ~~~~~~~~~~~~~~~~~s~~~R~riv~~~~~G~s~~~iA~~~gvs~~tV~kwi~r~~~~G~~~pk~~gg~rp~~~~~~~~ 81 (125)
T smart00351 2 HGGVNQLGGVFVNGRPLPDEERQRIVELAQNGVRPCDISRQLCVSHGCVSKILGRYYETGSIRPGAIGGSKPKVATPKVV 81 (125)
T ss_pred CCccccCCCeecCCCCCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCcCCCCCCCCccCHHHH
Confidence 35789999999999999999999999999999999999999999999999999999999999998887778999999999
Q ss_pred HHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHH
Q psy1898 164 KRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLR 208 (230)
Q Consensus 164 ~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr 208 (230)
++|.++++++|++|++||+++|.+ .|++.....||.|||+++|+
T Consensus 82 ~~I~~~~~~~p~~t~~el~~~L~~-~gv~~~~~~Ps~sti~~~l~ 125 (125)
T smart00351 82 KKIADYKQENPGIFAWEIRDRLLS-EGVCDKDNVPSVSSINRILR 125 (125)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHHH-cCCCcCCCCCChhhHHHhhC
Confidence 999999999999999999999986 89887778899999999985
No 6
>KOG0849|consensus
Probab=99.74 E-value=1.6e-18 Score=158.49 Aligned_cols=143 Identities=68% Similarity=1.135 Sum_probs=120.7
Q ss_pred CCccccCccccCCCCCChhHHHHHHHHHhcCCChhhhhhhhcccccccccCCcccCCCcCCHHHHHHHHHHHHcCCCHHH
Q psy1898 41 GRMNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGVNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCV 120 (230)
Q Consensus 41 ~~~~~~g~~~~~g~plp~~~r~~I~e~~~~g~~~~~isr~lrvshg~~~l~~~~~~g~~~s~~~R~rIV~l~~~G~s~~~ 120 (230)
+++||+||+|+||+|+|.++|..|++|+..|.++|.|++++.|+|||
T Consensus 1 ~~~n~~~~~f~~~~~~~~~~r~~~~~~a~~~~~~~~~~~~l~vs~~~--------------------------------- 47 (354)
T KOG0849|consen 1 GRVNQLGGVFINGRPLPNHTRQKIVEMAHKGIRPCVISRQLKVSHGC--------------------------------- 47 (354)
T ss_pred CCcccCCcccccCCCCCCchhhccccccccccCcccchhhhhhhhHH---------------------------------
Confidence 35677777777777777777778888888888889999999866666
Q ss_pred HhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCC-CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCC
Q psy1898 121 ISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR-VATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPS 199 (230)
Q Consensus 121 IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr-~lt~~~~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS 199 (230)
|.+++++|.++|++.|.-.++.+|+ +.+++++.+|..+..++|.+++|+|.+.|.. .++|+..+.+|
T Consensus 48 -----------~~~il~r~~~~~~i~p~~i~~~~~~~~~t~~~~~~i~~~k~~~P~~~~~~ir~~l~~-~~~~~~~t~Ps 115 (354)
T KOG0849|consen 48 -----------VSKILNRYYRTGSIRPGGIGGSKPRIVATPEVEAKIEQYKRENPAMFAWEIRDQLLH-EGLCTQATLPS 115 (354)
T ss_pred -----------HHhhhcccccccccccccccccccCCCCCchhHHHHHHHHhcCCcccchhhhhcccC-cccccCCCCCC
Confidence 5678899999999999888777777 8889999999999999999999999999988 89998888999
Q ss_pred HhHHHHHHHcCCCCCCC---------CCCcCccccccc
Q psy1898 200 VSSISRLLRGGRRDDCD---------RKNHSIDGILEQ 228 (230)
Q Consensus 200 ~sTV~R~Lr~~g~~~~~---------~~~~s~~~~~~~ 228 (230)
.+++.|.|+...+.... .+.+++++++|.
T Consensus 116 ~ssi~r~~r~~~~~~d~~~~~~~~~~~~~~~~~~~~gs 153 (354)
T KOG0849|consen 116 VSSINRVLRNGALGKDQGLPSQQVTKEKSPSISGALGS 153 (354)
T ss_pred hhhhhHHhhccccccccccccccccccccCCcccccCC
Confidence 99999999976654432 367899999986
No 7
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=99.73 E-value=3.2e-17 Score=131.15 Aligned_cols=117 Identities=21% Similarity=0.239 Sum_probs=103.4
Q ss_pred CCcCCHHHHHHHHHHH-HcCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHhCCC
Q psy1898 97 GRPLPNHIRLKIVEMA-AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPG 175 (230)
Q Consensus 97 g~~~s~~~R~rIV~l~-~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~~P~ 175 (230)
.++++.++|..++..+ .+|+|.++||++||||.+||++|++||+++|...+...++++|++++++..+.|...+++..
T Consensus 2 ~k~~s~~~R~~~~~~~~~~G~S~re~Ak~~gvs~sTvy~wv~r~~e~G~~l~~~~~~GrP~kl~~~q~~~l~e~~~~k~- 80 (138)
T COG3415 2 AKPFSNDLRERVVDAVVGEGLSCREAAKRFGVSISTVYRWVRRYRETGLDLPPKPRKGRPRKLSEEQLEILLERLREKD- 80 (138)
T ss_pred CchhhHHHHHHHHHHHHHcCccHHHHHHHhCccHHHHHHHHHHhccccccccCccCCCCCcccCHHHHHHHHHHHhccc-
Confidence 5788999999999877 57999999999999999999999999999998855555677999999999999988887665
Q ss_pred CCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcCCCCCCCCCC
Q psy1898 176 IFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGGRRDDCDRKN 219 (230)
Q Consensus 176 ~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~g~~~~~~~~ 219 (230)
+|+.++...|..++|+. .+.++|+++|++.|++...+..
T Consensus 81 wTl~~~~~~l~~e~gv~-----y~~~~v~~~l~~~GlsykK~~~ 119 (138)
T COG3415 81 WTLKELVEELGLEFGVW-----YHASAVRRLLHELGLSYKKPRW 119 (138)
T ss_pred chHHHHHHHHhhhcCeE-----EeHHHHHHHHHHcCCCcCCCCC
Confidence 99999999998889995 8999999999999999776443
No 8
>PF13551 HTH_29: Winged helix-turn helix
Probab=99.72 E-value=4.9e-17 Score=123.83 Aligned_cols=101 Identities=31% Similarity=0.432 Sum_probs=87.3
Q ss_pred HHHHHHHHHcCCC-HHHHhhhhccccchhhhHHHHHhhhC--CCCc-CCCCCCCCCC-CCHHHHHHHHHHHHhCC-----
Q psy1898 105 RLKIVEMAAAGVR-PCVISRQLRVSHGCVSKILNRYQETG--SIRP-GVIGGSKPRV-ATPDVEKRIEEYKKTNP----- 174 (230)
Q Consensus 105 R~rIV~l~~~G~s-~~~IAr~lgVS~sTV~kwikRy~e~G--~v~p-~~~gg~rpr~-lt~~~~~~I~~l~~~~P----- 174 (230)
|.+|+.++.+|.+ ..+||+.+|||+.||++|+++|+++| .+.+ .++ +++|+. +++++.+.|.+++.++|
T Consensus 1 R~~~l~l~~~g~~~~~~ia~~lg~s~~Tv~r~~~~~~~~G~~~l~~~~~~-~g~~~~~l~~~~~~~l~~~~~~~p~~g~~ 79 (112)
T PF13551_consen 1 RAQILLLLAEGVSTIAEIARRLGISRRTVYRWLKRYREGGIEGLLPRKPR-GGRPRKRLSEEQRAQLIELLRENPPEGRS 79 (112)
T ss_pred CHHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHcccHHHHHhcccc-CCCCCCCCCHHHHHHHHHHHHHCCCCCCC
Confidence 5789999999995 99999999999999999999999999 4445 333 346665 89999999999999988
Q ss_pred CCCHHHHHHHH-HHhhCCCCCCCCCCHhHHHHHHHcCC
Q psy1898 175 GIFSWEIRDRL-VKQDGICDKNSAPSVSSISRLLRGGR 211 (230)
Q Consensus 175 ~~t~~eI~~~L-~~~~Gi~~~~~~vS~sTV~R~Lr~~g 211 (230)
.++..+++++| ++.+|+. +|.+||+|+|+++|
T Consensus 80 ~~t~~~l~~~l~~~~~~~~-----~s~~ti~r~L~~~G 112 (112)
T PF13551_consen 80 RWTLEELAEWLIEEEFGID-----VSPSTIRRILKRAG 112 (112)
T ss_pred cccHHHHHHHHHHhccCcc-----CCHHHHHHHHHHCc
Confidence 58899999987 6667775 89999999999987
No 9
>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=99.68 E-value=2.5e-16 Score=123.35 Aligned_cols=100 Identities=22% Similarity=0.278 Sum_probs=86.7
Q ss_pred cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCH
Q psy1898 99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPGIFS 178 (230)
Q Consensus 99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~~P~~t~ 178 (230)
.||.|+|.+||..++.|.|.+++|+.|+||.+||++|++ ..++|.+.+.++++ + +++ .+.|..++.++|+.|+
T Consensus 2 aYS~DlR~rVl~~~~~g~s~~eaa~~F~VS~~Tv~~W~k-~~~~G~~~~k~r~~--~-Kid---~~~L~~~v~~~pd~tl 74 (119)
T PF01710_consen 2 AYSLDLRQRVLAYIEKGKSIREAAKRFGVSRNTVYRWLK-RKETGDLEPKPRGR--K-KID---RDELKALVEENPDATL 74 (119)
T ss_pred CCCHHHHHHHHHHHHccchHHHHHHHhCcHHHHHHHHHH-hccccccccccccc--c-ccc---HHHHHHHHHHCCCcCH
Confidence 599999999999999999999999999999999999999 67789888776533 2 553 4678999999999999
Q ss_pred HHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcCCCCCCC
Q psy1898 179 WEIRDRLVKQDGICDKNSAPSVSSISRLLRGGRRDDCD 216 (230)
Q Consensus 179 ~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~g~~~~~ 216 (230)
.|+++.| | ||.+||+++|++.|+.-..
T Consensus 75 ~Ela~~l----~-------Vs~~ti~~~Lkrlg~t~KK 101 (119)
T PF01710_consen 75 RELAERL----G-------VSPSTIWRALKRLGITRKK 101 (119)
T ss_pred HHHHHHc----C-------CCHHHHHHHHHHcCchhcc
Confidence 9998754 4 4999999999999998554
No 10
>PF13565 HTH_32: Homeodomain-like domain
Probab=99.32 E-value=8e-12 Score=89.70 Aligned_cols=72 Identities=29% Similarity=0.399 Sum_probs=59.7
Q ss_pred hhhhHHHHHhhhC-----CCCcCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHH
Q psy1898 131 CVSKILNRYQETG-----SIRPGVIGGSKPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISR 205 (230)
Q Consensus 131 TV~kwikRy~e~G-----~v~p~~~gg~rpr~lt~~~~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R 205 (230)
||++|+++|++.| ...+++++ ++|++ ++++.+.|.+++.++|.++..+|++.|..++|+.. .||.+||+|
T Consensus 1 Tv~rw~~ry~~~G~~gL~~~~~~~~~-Grp~~-~~e~~~~i~~~~~~~p~wt~~~i~~~L~~~~g~~~---~~S~~tv~R 75 (77)
T PF13565_consen 1 TVYRWLKRYREEGLEGLKDRKRRPRP-GRPRK-DPEQRERIIALIEEHPRWTPREIAEYLEEEFGISV---RVSRSTVYR 75 (77)
T ss_pred CHHHHHHHHHhhCchhhhcccccCCC-CCCCC-cHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCC---CccHhHHHH
Confidence 8999999999999 32233443 46777 88888999999999999999999999999888740 259999999
Q ss_pred HH
Q psy1898 206 LL 207 (230)
Q Consensus 206 ~L 207 (230)
+|
T Consensus 76 ~L 77 (77)
T PF13565_consen 76 IL 77 (77)
T ss_pred hC
Confidence 86
No 11
>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=99.29 E-value=1.3e-12 Score=102.69 Aligned_cols=35 Identities=71% Similarity=1.206 Sum_probs=27.8
Q ss_pred CCcccccccceeecCccCChhHHHHHHHHHhcCCC
Q psy1898 2 GQGRMNQLGGVFINGRPLPNHIRLKIVEMAAAGRG 36 (230)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 36 (230)
|||++|||||||+||||||+++|++|+|||..|-.
T Consensus 1 g~~~~NqlGg~~~nGrPLp~~~R~rIvela~~G~r 35 (125)
T PF00292_consen 1 GQGRVNQLGGVFINGRPLPNELRQRIVELAKEGVR 35 (125)
T ss_dssp S-EEE-TTS-EEETTSSS-HHHHHHHHHHHHTT--
T ss_pred CCccccccCceeeCCccCcHHHHHHHHHHhhhcCC
Confidence 89999999999999999999999999999986543
No 12
>cd00131 PAX Paired Box domain
Probab=99.22 E-value=7.6e-11 Score=93.52 Aligned_cols=100 Identities=46% Similarity=0.686 Sum_probs=74.9
Q ss_pred CCCCccccCccccCCCCCChhHHHHHHHHHhcCCChhhhhhhhcccccccc--cCCc-----cc---C----CCcCCHHH
Q psy1898 39 CQGRMNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGVNQ--LGGV-----FI---N----GRPLPNHI 104 (230)
Q Consensus 39 ~~~~~~~~g~~~~~g~plp~~~r~~I~e~~~~g~~~~~isr~lrvshg~~~--l~~~-----~~---~----g~~~s~~~ 104 (230)
||+.+||+||+|.+++|++.+.|..|++++.+|.+..+|+++|+|++.++. +.++ +. . .+..+.+.
T Consensus 1 ~~~~~~~~~~~~~m~~~lS~d~R~rIv~~~~~G~s~~~iA~~~~Vs~~tV~r~i~r~~e~G~v~pk~~gg~rpr~~~~~~ 80 (128)
T cd00131 1 GQGGVNQLGGVFVNGRPLPDSIRQRIVELAQSGIRPCDISRQLRVSHGCVSKILNRYYETGSIRPGAIGGSKPRVATPEV 80 (128)
T ss_pred CCccccCCCccccCCCcCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCCCCCCCCCCcCCHHH
Confidence 578899999999999999999999999999999999999999999888751 1111 11 0 11233444
Q ss_pred HHHHHHHHHc--CCCHHHHhhhh---cc-------ccchhhhHHHH
Q psy1898 105 RLKIVEMAAA--GVRPCVISRQL---RV-------SHGCVSKILNR 138 (230)
Q Consensus 105 R~rIV~l~~~--G~s~~~IAr~l---gV-------S~sTV~kwikR 138 (230)
...|+.+..+ ..+..++++.| +| |.+||.+|+++
T Consensus 81 ~~~i~~~v~~~p~~Tl~El~~~L~~~gv~~~~~~~s~stI~R~L~~ 126 (128)
T cd00131 81 VKKIEIYKQENPGMFAWEIRDRLLQEGVCDKSNVPSVSSINRILRN 126 (128)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHcCCcccCCCCCHHHHHHHHHh
Confidence 4455554444 48999999886 55 99999999875
No 13
>KOG3862|consensus
Probab=99.12 E-value=6.1e-11 Score=103.26 Aligned_cols=122 Identities=34% Similarity=0.439 Sum_probs=73.6
Q ss_pred CCcccccccceeecCccCChhHHHHHHHHHhcCCCCCCCCCccccCccccCCCCCChhHHHHHHHHHhcCCChhhhhhhh
Q psy1898 2 GQGRMNQLGGVFINGRPLPNHIRLKIVEMAAAGRGSSCQGRMNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQL 81 (230)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~g~plp~~~r~~I~e~~~~g~~~~~isr~l 81 (230)
|+|-|||||||||||||||+.+|+-|||||--|---..-+. ||- .-+|-+ . +|.-.|. +..|...
T Consensus 9 ghgGvNQLGGvFVNGRPlpd~Vr~rIv~La~~gvrpcdisr--Ql~--vShGcv--S----kil~r~y-----EtgS~~p 73 (327)
T KOG3862|consen 9 GHGGVNQLGGVFVNGRPLPDVVRQRIVELAQNGVRPCDISR--QLR--VSHGCV--S----KILGRYY-----ETGSIRP 73 (327)
T ss_pred CccchhhccceeecCccCchHHHHHHHHHHHcCCcchhHHH--HHh--hccCCc--h----hHHHHHH-----HhcCccc
Confidence 78999999999999999999999999999987743111000 110 011111 0 0111110 1111111
Q ss_pred cc--------cccc----------------cccCCcccCCCcCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHH
Q psy1898 82 RV--------SHGV----------------NQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILN 137 (230)
Q Consensus 82 rv--------shg~----------------~~l~~~~~~g~~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwik 137 (230)
++ ..-| +--.+.+..++++-...++.+|..++.++....++++++++.++|.+-+.
T Consensus 74 g~iggsk~KvAtp~Vvk~i~~~k~~n~~mfaweiR~~l~~~~ic~~d~vpsVssinri~r~~~~~~~~~~~~s~vsk~l~ 153 (327)
T KOG3862|consen 74 GVIGGSKPKVATPKVVKKIALYKRQNPTMFAWEIRDRLLAEPICDNDTVPSVSSINRIIRTKVQQKQLGITHSCVTKVLA 153 (327)
T ss_pred CCCCCCccccccchHHHHHHHHhhcCcchhhhhhhhhhhcccccCCCCCchHHHHHHHHHHhhhhcccCCccchhhcccc
Confidence 11 0001 01112233355555566777888899999999999999999999998877
Q ss_pred H
Q psy1898 138 R 138 (230)
Q Consensus 138 R 138 (230)
+
T Consensus 154 ~ 154 (327)
T KOG3862|consen 154 R 154 (327)
T ss_pred C
Confidence 5
No 14
>smart00351 PAX Paired Box domain.
Probab=99.11 E-value=3e-10 Score=89.65 Aligned_cols=98 Identities=44% Similarity=0.678 Sum_probs=75.3
Q ss_pred CCCccccCccccCCCCCChhHHHHHHHHHhcCCChhhhhhhhccccccc--ccCCc-----cc-------CCCcCCHHHH
Q psy1898 40 QGRMNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGVN--QLGGV-----FI-------NGRPLPNHIR 105 (230)
Q Consensus 40 ~~~~~~~g~~~~~g~plp~~~r~~I~e~~~~g~~~~~isr~lrvshg~~--~l~~~-----~~-------~g~~~s~~~R 105 (230)
+.++||+||+|++++|++.+.|.+|+.++.+|.+..+|+++|+|++.++ .+.++ .. ..+..+....
T Consensus 2 ~~~~~~~~~~~~~~~~~s~~~R~riv~~~~~G~s~~~iA~~~gvs~~tV~kwi~r~~~~G~~~pk~~gg~rp~~~~~~~~ 81 (125)
T smart00351 2 HGGVNQLGGVFVNGRPLPDEERQRIVELAQNGVRPCDISRQLCVSHGCVSKILGRYYETGSIRPGAIGGSKPKVATPKVV 81 (125)
T ss_pred CCccccCCCeecCCCCCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCcCCCCCCCCccCHHHH
Confidence 5789999999999999999999999999999999999999999988876 11111 11 1222444555
Q ss_pred HHHHHHHHc--CCCHHHHhhhhc-----c-----ccchhhhHHH
Q psy1898 106 LKIVEMAAA--GVRPCVISRQLR-----V-----SHGCVSKILN 137 (230)
Q Consensus 106 ~rIV~l~~~--G~s~~~IAr~lg-----V-----S~sTV~kwik 137 (230)
..|+.+..+ .++..+|+..|. + |.+||.+|++
T Consensus 82 ~~I~~~~~~~p~~t~~el~~~L~~~gv~~~~~~Ps~sti~~~l~ 125 (125)
T smart00351 82 KKIADYKQENPGIFAWEIRDRLLSEGVCDKDNVPSVSSINRILR 125 (125)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHHHcCCCcCCCCCChhhHHHhhC
Confidence 666766554 499999998773 3 8899998863
No 15
>KOG3517|consensus
Probab=99.01 E-value=1.3e-10 Score=100.36 Aligned_cols=33 Identities=70% Similarity=1.164 Sum_probs=30.7
Q ss_pred CcccccccceeecCccCChhHHHHHHHHHhcCC
Q psy1898 3 QGRMNQLGGVFINGRPLPNHIRLKIVEMAAAGR 35 (230)
Q Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 35 (230)
-|.|||||||||||||||+.+|.+|||||--|-
T Consensus 5 ~GEVNQLGGVFVNGRPLPna~RlrIVELarlGi 37 (334)
T KOG3517|consen 5 YGEVNQLGGVFVNGRPLPNAIRLRIVELARLGI 37 (334)
T ss_pred ccchhhccceeEcCccCcchhhhhHHHHHHcCC
Confidence 478999999999999999999999999998774
No 16
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=98.96 E-value=3.7e-09 Score=77.85 Aligned_cols=74 Identities=27% Similarity=0.373 Sum_probs=60.3
Q ss_pred CCcCCHHHHHHHHHHH-HcCCCHHHHhhhhccccchhhhHHHHHhhhCCC--Cc-CCCCCCCCCCCCHHHHHHHHHHH
Q psy1898 97 GRPLPNHIRLKIVEMA-AAGVRPCVISRQLRVSHGCVSKILNRYQETGSI--RP-GVIGGSKPRVATPDVEKRIEEYK 170 (230)
Q Consensus 97 g~~~s~~~R~rIV~l~-~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v--~p-~~~gg~rpr~lt~~~~~~I~~l~ 170 (230)
..+++..-|..++..+ .+|++..++|+.||||+.|++||+.||++.|.. .+ .+++...|..+++++++.|.++.
T Consensus 6 nA~Lt~~gR~~lv~~vv~~g~~~a~aA~~~gVS~~Ta~kW~~Ryra~G~~GL~DRSSRP~~sP~~t~~~~~~~I~~lR 83 (85)
T PF13011_consen 6 NARLTPRGRLRLVRRVVEQGWPVAHAAAEFGVSRRTAYKWLARYRAEGEAGLQDRSSRPHRSPRRTPPEVERRIIELR 83 (85)
T ss_pred CCCCCHHHHHHHHHHHHHcCCcHHHHHHHhCCCHHHHHHHHHHHHHcCcccccccCCCCCCCCccCCHHHHHHHHHHh
Confidence 3467888999999866 568999999999999999999999999998743 22 23445578888888888888765
No 17
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=98.93 E-value=4.2e-10 Score=74.36 Aligned_cols=44 Identities=27% Similarity=0.428 Sum_probs=26.7
Q ss_pred CHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhhhCC
Q psy1898 101 PNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGS 144 (230)
Q Consensus 101 s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~ 144 (230)
+.+.|.+|+.++.+|.|.++||+.||||++||++|+++|++.|.
T Consensus 3 ~~~~R~~ii~l~~~G~s~~~ia~~lgvs~~Tv~~w~kr~~~~G~ 46 (50)
T PF13384_consen 3 SEERRAQIIRLLREGWSIREIAKRLGVSRSTVYRWIKRYREEGL 46 (50)
T ss_dssp -------HHHHHHHT--HHHHHHHHTS-HHHHHHHHT-------
T ss_pred chhHHHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHHHcccccc
Confidence 45789999999999999999999999999999999999999884
No 18
>PF13518 HTH_28: Helix-turn-helix domain
Probab=98.79 E-value=5.5e-09 Score=69.17 Aligned_cols=41 Identities=34% Similarity=0.536 Sum_probs=38.5
Q ss_pred HHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhhhCC
Q psy1898 104 IRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGS 144 (230)
Q Consensus 104 ~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~ 144 (230)
+|.+||.++.+|.|..+||++||||++||++|+++|++.|.
T Consensus 1 ~r~~iv~~~~~g~s~~~~a~~~gis~~tv~~w~~~y~~~G~ 41 (52)
T PF13518_consen 1 FRLQIVELYLEGESVREIAREFGISRSTVYRWIKRYREGGI 41 (52)
T ss_pred CHHHHHHHHHcCCCHHHHHHHHCCCHhHHHHHHHHHHhcCH
Confidence 37889999999999999999999999999999999999884
No 19
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=98.45 E-value=9.8e-08 Score=61.92 Aligned_cols=42 Identities=26% Similarity=0.276 Sum_probs=26.2
Q ss_pred CCcCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHH
Q psy1898 97 GRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNR 138 (230)
Q Consensus 97 g~~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikR 138 (230)
.+.++.+.|..|..++.+|+|.++||+.||+|++||+++++|
T Consensus 2 ~~~Lt~~eR~~I~~l~~~G~s~~~IA~~lg~s~sTV~relkR 43 (44)
T PF13936_consen 2 YKHLTPEERNQIEALLEQGMSIREIAKRLGRSRSTVSRELKR 43 (44)
T ss_dssp ----------HHHHHHCS---HHHHHHHTT--HHHHHHHHHH
T ss_pred ccchhhhHHHHHHHHHHcCCCHHHHHHHHCcCcHHHHHHHhc
Confidence 467889999999999999999999999999999999999987
No 20
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=98.44 E-value=7.5e-07 Score=69.79 Aligned_cols=49 Identities=20% Similarity=0.242 Sum_probs=44.1
Q ss_pred CCcCCHHHHHHHHHH-HHcCCCHHHHhhhhccccchhhhHHHHHhhhCCC
Q psy1898 97 GRPLPNHIRLKIVEM-AAAGVRPCVISRQLRVSHGCVSKILNRYQETGSI 145 (230)
Q Consensus 97 g~~~s~~~R~rIV~l-~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v 145 (230)
.+.||.+++..+|.. +..|.+..+||+.||||.+|+++|+++|++.+..
T Consensus 10 rr~ys~EfK~~aV~~~~~~g~sv~evA~e~gIs~~tl~~W~r~y~~~~~~ 59 (121)
T PRK09413 10 RRRRTTQEKIAIVQQSFEPGMTVSLVARQHGVAASQLFLWRKQYQEGSLT 59 (121)
T ss_pred CCCCCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHhhcccc
Confidence 578999999999986 5678999999999999999999999999987754
No 21
>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=98.38 E-value=3.9e-07 Score=64.92 Aligned_cols=46 Identities=15% Similarity=0.242 Sum_probs=37.9
Q ss_pred cCCCcCCHHHHHHHHHHH-HcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 95 INGRPLPNHIRLKIVEMA-AAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 95 ~~g~~~s~~~R~rIV~l~-~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
...+.||.+++.++|..+ ..|.|..++|+.+||+++|+++|++.|.
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLESGESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp -SS----HHHHHHHHHHHHHHHCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHCCCceEeeecccccccccccHHHHHHh
Confidence 346789999999999988 7899999999999999999999999998
No 22
>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=98.20 E-value=1.1e-06 Score=57.17 Aligned_cols=40 Identities=30% Similarity=0.335 Sum_probs=32.7
Q ss_pred CcCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHH
Q psy1898 98 RPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILN 137 (230)
Q Consensus 98 ~~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwik 137 (230)
+.++.+....|+.|+.+|+|..+||+.||||++|||++++
T Consensus 4 ~~~~~~~~~~i~~l~~~G~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 4 PKLSKEQIEEIKELYAEGMSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp SSSSHCCHHHHHHHHHTT--HHHHHHHTTS-HHHHHHHHC
T ss_pred CCCCHHHHHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHh
Confidence 3466667789999999999999999999999999999975
No 23
>COG2826 Tra8 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]
Probab=98.18 E-value=1.1e-05 Score=72.04 Aligned_cols=105 Identities=23% Similarity=0.205 Sum_probs=82.7
Q ss_pred CcCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhhhC---------CCCcCCCCCCCCCCCCHHHHHHHHH
Q psy1898 98 RPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETG---------SIRPGVIGGSKPRVATPDVEKRIEE 168 (230)
Q Consensus 98 ~~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G---------~v~p~~~gg~rpr~lt~~~~~~I~~ 168 (230)
+-++.+.|..|-.+.++|+|.++||++||.+++||++=++|=.... ..+...+...++.+.+++.++.|.+
T Consensus 6 ~hLT~~eR~~I~~l~~~~~S~reIA~~LgRh~sTIsRElkRn~~~~~Y~a~~A~~~~~~~rrr~~~k~~~~~eL~~~V~e 85 (318)
T COG2826 6 KHLTLFERYEIERLLKAKMSIREIAKQLNRHHSTISRELKRNRTRDIYSAVKAQERYRMLRRRRIRKLKLNPELRELVLE 85 (318)
T ss_pred hhCCHHHHHHHHHHHHcCCCHHHHHHHhCCCcchhhHHHhcCCccceeeHHHHHHHHHHhhcccCCcccCCHHHHHHHHH
Confidence 3688899999999999999999999999999999999888732222 1111122234677889999999999
Q ss_pred HHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcCCC
Q psy1898 169 YKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGGRR 212 (230)
Q Consensus 169 l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~g~ 212 (230)
.++.. ++..+|..+|.. .. +|.+||+++|.....
T Consensus 86 ~L~~~--wSPEQI~g~l~~-~~-------i~~eTIYr~ly~~~~ 119 (318)
T COG2826 86 KLKSK--WSPEQIIGRLKK-SK-------ISFETIYRWLYQGKS 119 (318)
T ss_pred HHHhh--CCHHHHHHHHHh-cc-------cCHHHHHHHHhhccc
Confidence 98775 999999999986 22 699999999876543
No 24
>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=98.14 E-value=3.8e-06 Score=56.62 Aligned_cols=42 Identities=29% Similarity=0.370 Sum_probs=34.7
Q ss_pred CCcCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHH
Q psy1898 97 GRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNR 138 (230)
Q Consensus 97 g~~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikR 138 (230)
-+.++.+.+..||.++++|.+..+||+.|||+.+||+.|++.
T Consensus 4 R~~LTl~eK~~iI~~~e~g~s~~~ia~~fgv~~sTv~~I~K~ 45 (53)
T PF04218_consen 4 RKSLTLEEKLEIIKRLEEGESKRDIAREFGVSRSTVSTILKN 45 (53)
T ss_dssp SSS--HHHHHHHHHHHHCTT-HHHHHHHHT--CCHHHHHHHC
T ss_pred CccCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHh
Confidence 457899999999999999999999999999999999999985
No 25
>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=98.12 E-value=2.6e-06 Score=58.57 Aligned_cols=41 Identities=17% Similarity=0.175 Sum_probs=37.0
Q ss_pred HHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhhhC
Q psy1898 103 HIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETG 143 (230)
Q Consensus 103 ~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G 143 (230)
|.|.++..|+-.|+++++||+.|||+.+||+.|.++|.-.+
T Consensus 1 e~k~~A~~LY~~G~~~~eIA~~Lg~~~~TV~~W~~r~~W~~ 41 (58)
T PF06056_consen 1 EVKEQARSLYLQGWSIKEIAEELGVPRSTVYSWKDRYKWDE 41 (58)
T ss_pred CHHHHHHHHHHcCCCHHHHHHHHCCChHHHHHHHHhhCccc
Confidence 46788899999999999999999999999999999988544
No 26
>KOG0849|consensus
Probab=98.05 E-value=1.1e-06 Score=80.71 Aligned_cols=35 Identities=74% Similarity=1.151 Sum_probs=32.7
Q ss_pred cccccccceeecCccCChhHHHHHHHHHhcCCCCC
Q psy1898 4 GRMNQLGGVFINGRPLPNHIRLKIVEMAAAGRGSS 38 (230)
Q Consensus 4 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 38 (230)
|++||+||||+||||||+++|++|+|+|..|+...
T Consensus 1 ~~~n~~~~~f~~~~~~~~~~r~~~~~~a~~~~~~~ 35 (354)
T KOG0849|consen 1 GRVNQLGGVFINGRPLPNHTRQKIVEMAHKGIRPC 35 (354)
T ss_pred CCcccCCcccccCCCCCCchhhccccccccccCcc
Confidence 68999999999999999999999999999998744
No 27
>PRK09409 IS2 transposase TnpB; Reviewed
Probab=97.94 E-value=4.6e-05 Score=68.57 Aligned_cols=97 Identities=24% Similarity=0.185 Sum_probs=72.0
Q ss_pred HHHHcCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhh
Q psy1898 110 EMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQD 189 (230)
Q Consensus 110 ~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~~P~~t~~eI~~~L~~~~ 189 (230)
.|++.+.+...+|+.|+||++|.|+|++++..-- ..+. .+.....+....|.++..++|...+..|..+|..+.
T Consensus 6 ~~~~~~~~v~~lC~~l~VsRs~yY~~~~r~~~~~---~~~~---~~~~~~~~l~~~I~~i~~~~~~yG~Rri~~~L~~~g 79 (301)
T PRK09409 6 ALIARGWGVSLVSRCLRVSRAQLHVILRRTDDWM---DGRR---SRHTDDTDVLLRIHHVIGELPTYGYRRVWALLRRQA 79 (301)
T ss_pred HHHhcCCcHHHHHHhcCcChHHhhhhcccccccc---cccc---ccCcchHHHHHHHHHHHHhCccCCHHHHHHHHHhhh
Confidence 4677889999999999999999999999854211 1111 122234456777777777789999999999997631
Q ss_pred ---CCCCCCCCCCHhHHHHHHHcCCCCCCC
Q psy1898 190 ---GICDKNSAPSVSSISRLLRGGRRDDCD 216 (230)
Q Consensus 190 ---Gi~~~~~~vS~sTV~R~Lr~~g~~~~~ 216 (230)
|+. .++..||+|+|++.||...+
T Consensus 80 ~~~g~~----~v~~k~V~RlMr~~Gl~~~~ 105 (301)
T PRK09409 80 ELDGMP----AINAKRVYRIMRQNALLLER 105 (301)
T ss_pred cccCcc----ccCHHHHHHHHHHcCCcccc
Confidence 441 27999999999999998543
No 28
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=97.89 E-value=6.2e-05 Score=58.09 Aligned_cols=51 Identities=16% Similarity=0.197 Sum_probs=45.2
Q ss_pred CCcCCHHHHHHHHHHHHc-CCCHHHHhhhhcc-ccchhhhHHHHHhhhCCCCc
Q psy1898 97 GRPLPNHIRLKIVEMAAA-GVRPCVISRQLRV-SHGCVSKILNRYQETGSIRP 147 (230)
Q Consensus 97 g~~~s~~~R~rIV~l~~~-G~s~~~IAr~lgV-S~sTV~kwikRy~e~G~v~p 147 (230)
-+.||.+++.+||.++.+ |.+.++||+.||| +.+++++|+++|.+.+...+
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~sv~~vAr~~gv~~~~~l~~W~~~~~~~~~~~~ 57 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGDTVSEVAREFGIVSATQLYKWRIQLQKGGGLAF 57 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCccHHHHHHHhCCCChHHHHHHHHHHHHcccccc
Confidence 367999999999998874 7999999999996 99999999999999876543
No 29
>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=97.67 E-value=6.3e-05 Score=44.31 Aligned_cols=39 Identities=26% Similarity=0.239 Sum_probs=34.9
Q ss_pred CcCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHH
Q psy1898 98 RPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKIL 136 (230)
Q Consensus 98 ~~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwi 136 (230)
+.++.+.+..|++++.++.+..+||+.++++++||++|+
T Consensus 4 ~~~~~~~~~~i~~~~~~~~s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 4 PKLTPEQIEEARRLLAAGESVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred CcCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHhC
Confidence 446778888898999999999999999999999999994
No 30
>PHA02517 putative transposase OrfB; Reviewed
Probab=97.54 E-value=0.00019 Score=63.16 Aligned_cols=77 Identities=10% Similarity=0.077 Sum_probs=56.8
Q ss_pred hccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHh-CCCCCHHHHHHHHHHhhCCCCCCCCCCHhHH
Q psy1898 125 LRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKT-NPGIFSWEIRDRLVKQDGICDKNSAPSVSSI 203 (230)
Q Consensus 125 lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~-~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV 203 (230)
|+||++|.|+|+++... |..+ ..+.....+..+.|.++..+ +|...+..|.+.|.. .|+. +|.+||
T Consensus 1 l~vsrs~yY~~~~~~~~-----p~~~--~~~~~~~~~l~~~I~~i~~~~~~~~G~r~I~~~L~~-~g~~-----vs~~tV 67 (277)
T PHA02517 1 LGIAPSTYYRCQQQRHH-----PDKR--RARAQHDDWLKSEILRVYDENHQVYGVRKVWRQLNR-EGIR-----VARCTV 67 (277)
T ss_pred CCCChHHHHHHHhccCC-----cchh--hhhhhhhHHHHHHHHHHHHHhCCCCCHHHHHHHHHh-cCcc-----cCHHHH
Confidence 68999999999876321 1111 01112345667788877655 678899999999987 6885 899999
Q ss_pred HHHHHcCCCCC
Q psy1898 204 SRLLRGGRRDD 214 (230)
Q Consensus 204 ~R~Lr~~g~~~ 214 (230)
+|+|+++|+..
T Consensus 68 ~Rim~~~gl~~ 78 (277)
T PHA02517 68 GRLMKELGLAG 78 (277)
T ss_pred HHHHHHcCCce
Confidence 99999999963
No 31
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=97.37 E-value=0.00039 Score=45.57 Aligned_cols=41 Identities=22% Similarity=0.280 Sum_probs=35.2
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE 141 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e 141 (230)
++.+.+. ++.++..|++..+||+.++||++||++|+++..+
T Consensus 4 l~~~e~~-i~~~~~~g~s~~eia~~l~is~~tv~~~~~~~~~ 44 (58)
T smart00421 4 LTPRERE-VLRLLAEGLTNKEIAERLGISEKTVKTHLSNIMR 44 (58)
T ss_pred CCHHHHH-HHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 5666665 7788889999999999999999999999998643
No 32
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=97.24 E-value=0.00058 Score=45.03 Aligned_cols=45 Identities=20% Similarity=0.259 Sum_probs=40.7
Q ss_pred cCCCcCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHH
Q psy1898 95 INGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRY 139 (230)
Q Consensus 95 ~~g~~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy 139 (230)
..+..++..++..|+.++.+..|.++||+.+|||.+||.++.++|
T Consensus 7 ~~~~r~T~~~~~~i~~~~~~~~s~~~vA~~~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 7 DRYCRITKRLEQYILKLLRESRSFKDVARELGVSWSTVRRIFDRY 51 (52)
T ss_pred CcCCcHHHHHHHHHHHHHhhcCCHHHHHHHHCCCHHHHHHHHHhh
Confidence 446678889999999999888999999999999999999999886
No 33
>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=97.22 E-value=0.0012 Score=45.71 Aligned_cols=66 Identities=17% Similarity=0.137 Sum_probs=44.0
Q ss_pred CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHH
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRL 185 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L 185 (230)
.+..++|+.+|||.+|+++|.+++ |...+.... +..+..++++...+..... .....+..+|++.|
T Consensus 1 ~s~~eva~~~gvs~~tlr~w~~~~---g~~~~~r~~-~~~r~yt~~~v~~l~~i~~l~~~g~~l~~i~~~~ 67 (68)
T cd01104 1 YTIGAVARLTGVSPDTLRAWERRY---GLPAPQRTD-GGHRLYSEADVARLRLIRRLTSEGVRISQAAALA 67 (68)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHhC---CCCCCCcCC-CCCeecCHHHHHHHHHHHHHHHCCCCHHHHHHHh
Confidence 378899999999999999998764 444332222 2346677776666554433 23467888887765
No 34
>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=97.22 E-value=0.00038 Score=51.79 Aligned_cols=35 Identities=20% Similarity=0.264 Sum_probs=31.6
Q ss_pred HHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHH
Q psy1898 103 HIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILN 137 (230)
Q Consensus 103 ~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwik 137 (230)
..|..|..+..+|.|.++||+.+|||++||++|.+
T Consensus 38 s~R~~I~~ll~~G~S~~eIA~~LgISrsTIyRi~R 72 (88)
T TIGR02531 38 AQRLQVAKMLKQGKTYSDIEAETGASTATISRVKR 72 (88)
T ss_pred hHHHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 45688889999999999999999999999999764
No 35
>PHA02535 P terminase ATPase subunit; Provisional
Probab=97.13 E-value=0.00096 Score=64.94 Aligned_cols=68 Identities=10% Similarity=0.041 Sum_probs=51.3
Q ss_pred cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh--hhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHhCCCC
Q psy1898 99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ--ETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPGI 176 (230)
Q Consensus 99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~--e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~~P~~ 176 (230)
.|+.++|..++.++.+|.|+.+||+.|||+.+||++|.++|+ +...+ ..+...+..+|..++.. +..
T Consensus 2 ~yt~EfK~~Av~Ly~~G~sv~eIA~~LGv~~~Tl~~W~kr~~w~~~~~~----------~~v~~~~~~r~~~l~~k-~~k 70 (581)
T PHA02535 2 AYDDDVRRAAKFLYWQGWTVAEIAEELGLKSRTIYSWKERDGWRDLLPE----------ERIEESIEARLIQLIEK-ENK 70 (581)
T ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCChhHHHHHhccccccccCCc----------ccHHHHHHHHHHHHHcc-CCC
Confidence 589999999999999999999999999999999999999876 22211 11233456666666654 544
Q ss_pred C
Q psy1898 177 F 177 (230)
Q Consensus 177 t 177 (230)
+
T Consensus 71 ~ 71 (581)
T PHA02535 71 T 71 (581)
T ss_pred C
Confidence 4
No 36
>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=97.13 E-value=0.00029 Score=49.75 Aligned_cols=45 Identities=36% Similarity=0.438 Sum_probs=22.2
Q ss_pred HHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcCCCCC
Q psy1898 164 KRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGGRRDD 214 (230)
Q Consensus 164 ~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~g~~~ 214 (230)
+.|...+..+|..|+.+|+..|... |+. ||.+||+|+|++.|+..
T Consensus 2 r~I~~~v~~~p~~s~~~i~~~l~~~-~~~-----vS~~TI~r~L~~~g~~~ 46 (72)
T PF01498_consen 2 RRIVRMVRRNPRISAREIAQELQEA-GIS-----VSKSTIRRRLREAGLKK 46 (72)
T ss_dssp --------------HHHHHHHT----T-------S-HHHHHHHHHHT-EEE
T ss_pred cHHHHHHHHCCCCCHHHHHHHHHHc-cCC-----cCHHHHHHHHHHcCccc
Confidence 4677888999999999999999874 875 89999999999999863
No 37
>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=97.12 E-value=0.00067 Score=45.05 Aligned_cols=43 Identities=23% Similarity=0.261 Sum_probs=32.4
Q ss_pred cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898 99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE 141 (230)
Q Consensus 99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e 141 (230)
.+|...|.-+...+.+|+|..+||+.+|+|.+||..|+.+-+.
T Consensus 10 ~L~~~~r~i~~l~~~~g~s~~eIa~~l~~s~~~v~~~l~ra~~ 52 (54)
T PF08281_consen 10 QLPERQREIFLLRYFQGMSYAEIAEILGISESTVKRRLRRARK 52 (54)
T ss_dssp CS-HHHHHHHHHHHTS---HHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHCcCHHHHHHHHCcCHHHHHHHHHHHHh
Confidence 3667777777777889999999999999999999999988653
No 38
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=97.10 E-value=0.00073 Score=45.02 Aligned_cols=42 Identities=26% Similarity=0.411 Sum_probs=32.0
Q ss_pred CCcCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHH
Q psy1898 97 GRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNR 138 (230)
Q Consensus 97 g~~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikR 138 (230)
|+.++..++.+|..|+..|+|..+||++++-|+.+|.++++.
T Consensus 2 G~~Lt~~Eqaqid~m~qlG~s~~~isr~i~RSr~~Ir~yl~d 43 (50)
T PF11427_consen 2 GKTLTDAEQAQIDVMHQLGMSLREISRRIGRSRTCIRRYLKD 43 (50)
T ss_dssp S----HHHHHHHHHHHHTT--HHHHHHHHT--HHHHHHHHHS
T ss_pred CCcCCHHHHHHHHHHHHhchhHHHHHHHhCccHHHHHHHhcC
Confidence 678999999999999999999999999999999999998864
No 39
>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=97.04 E-value=0.0013 Score=42.25 Aligned_cols=42 Identities=26% Similarity=0.258 Sum_probs=35.2
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE 141 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e 141 (230)
++.+.+.-+...+.+|++..+||..++++.+||++|+.+.++
T Consensus 11 l~~~~~~~~~~~~~~~~~~~~ia~~~~~s~~~i~~~~~~~~~ 52 (55)
T cd06171 11 LPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALK 52 (55)
T ss_pred CCHHHHHHHHHHHhcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 566666666666679999999999999999999999998754
No 40
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=96.97 E-value=0.0012 Score=43.28 Aligned_cols=42 Identities=29% Similarity=0.271 Sum_probs=35.0
Q ss_pred cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
.+|...|.-|...+.+++|..+||+.+|+|.+||.++.++..
T Consensus 4 ~L~~~er~vi~~~y~~~~t~~eIa~~lg~s~~~V~~~~~~al 45 (50)
T PF04545_consen 4 QLPPREREVIRLRYFEGLTLEEIAERLGISRSTVRRILKRAL 45 (50)
T ss_dssp TS-HHHHHHHHHHHTST-SHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcCCCCHHHHHHHHCCcHHHHHHHHHHHH
Confidence 467788888888888999999999999999999999988753
No 41
>PRK00118 putative DNA-binding protein; Validated
Probab=96.92 E-value=0.0016 Score=49.89 Aligned_cols=44 Identities=18% Similarity=0.126 Sum_probs=39.3
Q ss_pred CCcCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 97 GRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 97 g~~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
++.++...|.-+...+.+|+|..+||+.+|||++||++|+.|-+
T Consensus 15 ~~~L~ekqRevl~L~y~eg~S~~EIAe~lGIS~~TV~r~L~RAr 58 (104)
T PRK00118 15 GSLLTEKQRNYMELYYLDDYSLGEIAEEFNVSRQAVYDNIKRTE 58 (104)
T ss_pred hccCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 66788888888888888999999999999999999999998754
No 42
>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=96.91 E-value=0.0029 Score=49.33 Aligned_cols=83 Identities=14% Similarity=0.151 Sum_probs=57.5
Q ss_pred hhHHHHHHHHHhcCCChhhhhhhhccccccc-------ccCCcccCCCcCCHHHHHHHHHHHHc--CCCHHHHhhhhccc
Q psy1898 58 NHIRLKIVEMAAAGVRPCVISRQLRVSHGVN-------QLGGVFINGRPLPNHIRLKIVEMAAA--GVRPCVISRQLRVS 128 (230)
Q Consensus 58 ~~~r~~I~e~~~~g~~~~~isr~lrvshg~~-------~l~~~~~~g~~~s~~~R~rIV~l~~~--G~s~~~IAr~lgVS 128 (230)
-++|..|+..+..|.+..++++.|.||-.++ ..|..-...+.-..-....+..++++ ..+..|+|+.|+||
T Consensus 5 ~DlR~rVl~~~~~g~s~~eaa~~F~VS~~Tv~~W~k~~~~G~~~~k~r~~~Kid~~~L~~~v~~~pd~tl~Ela~~l~Vs 84 (119)
T PF01710_consen 5 LDLRQRVLAYIEKGKSIREAAKRFGVSRNTVYRWLKRKETGDLEPKPRGRKKIDRDELKALVEENPDATLRELAERLGVS 84 (119)
T ss_pred HHHHHHHHHHHHccchHHHHHHHhCcHHHHHHHHHHhcccccccccccccccccHHHHHHHHHHCCCcCHHHHHHHcCCC
Confidence 7899999999999999999999999866543 11111111111001112334445444 59999999999999
Q ss_pred cchhhhHHHHHh
Q psy1898 129 HGCVSKILNRYQ 140 (230)
Q Consensus 129 ~sTV~kwikRy~ 140 (230)
.+||++.+++..
T Consensus 85 ~~ti~~~Lkrlg 96 (119)
T PF01710_consen 85 PSTIWRALKRLG 96 (119)
T ss_pred HHHHHHHHHHcC
Confidence 999999998754
No 43
>PF13592 HTH_33: Winged helix-turn helix
Probab=96.89 E-value=0.0019 Score=44.36 Aligned_cols=41 Identities=20% Similarity=0.033 Sum_probs=36.5
Q ss_pred CCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcCCCCCCCCC
Q psy1898 173 NPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGGRRDDCDRK 218 (230)
Q Consensus 173 ~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~g~~~~~~~ 218 (230)
+..+|..+|++.+.+++|+. .|.++|+++|+++|++...+.
T Consensus 2 ~~~wt~~~i~~~I~~~fgv~-----ys~~~v~~lL~r~G~s~~kp~ 42 (60)
T PF13592_consen 2 GGRWTLKEIAAYIEEEFGVK-----YSPSGVYRLLKRLGFSYQKPR 42 (60)
T ss_pred CCcccHHHHHHHHHHHHCCE-----EcHHHHHHHHHHcCCccccCC
Confidence 46789999999999999996 799999999999999977643
No 44
>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=96.87 E-value=0.0022 Score=42.09 Aligned_cols=39 Identities=21% Similarity=0.190 Sum_probs=32.5
Q ss_pred HHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898 102 NHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE 141 (230)
Q Consensus 102 ~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e 141 (230)
...+. ++.++.+|++..+||+.+++|++||++|+++..+
T Consensus 3 ~~e~~-i~~~~~~~~s~~eia~~l~~s~~tv~~~~~~~~~ 41 (57)
T cd06170 3 PRERE-VLRLLAEGKTNKEIADILGISEKTVKTHLRNIMR 41 (57)
T ss_pred HHHHH-HHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 33444 6777889999999999999999999999998653
No 45
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=96.83 E-value=0.0013 Score=51.46 Aligned_cols=73 Identities=19% Similarity=0.206 Sum_probs=55.1
Q ss_pred CcCCHHHHHHHHHHHHc--CCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHH
Q psy1898 98 RPLPNHIRLKIVEMAAA--GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYK 170 (230)
Q Consensus 98 ~~~s~~~R~rIV~l~~~--G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~ 170 (230)
+.++...|.+|+.++.. ..+..+||+.|+++++||++-++..++.|.+...+.|...--.+.+++.+++....
T Consensus 11 kaLadptRl~IL~~L~~~~~~~v~ela~~l~lsqstvS~HL~~L~~AGLV~~~r~Gr~~~Y~l~~~~~~~~~~~~ 85 (117)
T PRK10141 11 KILSDETRLGIVLLLRESGELCVCDLCTALDQSQPKISRHLALLRESGLLLDRKQGKWVHYRLSPHIPAWAAKII 85 (117)
T ss_pred HHhCCHHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEEEcCEEEEEECchHHHHHHHHH
Confidence 35667899999997753 48999999999999999999999999999886555543333445555555555533
No 46
>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=96.70 E-value=0.0017 Score=42.24 Aligned_cols=43 Identities=26% Similarity=0.488 Sum_probs=38.1
Q ss_pred HHHHHHHHHHHcC-CCHHHHhhhhccccchhhhHHHHHhhhCCC
Q psy1898 103 HIRLKIVEMAAAG-VRPCVISRQLRVSHGCVSKILNRYQETGSI 145 (230)
Q Consensus 103 ~~R~rIV~l~~~G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~v 145 (230)
+.|.+|+.++.+| .+.++||+.+++|++||++-++..++.|-+
T Consensus 2 ~~R~~Il~~L~~~~~~~~el~~~l~~s~~~vs~hL~~L~~~glV 45 (47)
T PF01022_consen 2 PTRLRILKLLSEGPLTVSELAEELGLSQSTVSHHLKKLREAGLV 45 (47)
T ss_dssp HHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred HHHHHHHHHHHhCCCchhhHHHhccccchHHHHHHHHHHHCcCe
Confidence 5789999988776 999999999999999999999999998865
No 47
>PF12759 HTH_Tnp_IS1: InsA C-terminal domain; InterPro: IPR024431 This entry represents the helix-turn-helix domain found at the C-terminal of InsA.
Probab=96.70 E-value=0.0016 Score=42.46 Aligned_cols=40 Identities=30% Similarity=0.290 Sum_probs=35.9
Q ss_pred CcCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHH
Q psy1898 98 RPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILN 137 (230)
Q Consensus 98 ~~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwik 137 (230)
..+.+.++.+|++|..+|...+++|+.|+|+..||-+-++
T Consensus 4 ~A~kpgikeqIvema~nG~GiRdtaRvL~I~~nTVlrtLK 43 (46)
T PF12759_consen 4 EARKPGIKEQIVEMAFNGSGIRDTARVLKISINTVLRTLK 43 (46)
T ss_pred cccCccHHHHHHHHHhcCCcchhhHhHhcchHHHHHHHHh
Confidence 4555688999999999999999999999999999988765
No 48
>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=96.70 E-value=0.0021 Score=52.96 Aligned_cols=96 Identities=16% Similarity=0.176 Sum_probs=34.4
Q ss_pred CCCHHHHhhhhccccchhhhHHH-HHhhhC--CC-----CcCCCCCCCCCCC-CHHHHHHHHHHHHh-CC--CCCHHHHH
Q psy1898 115 GVRPCVISRQLRVSHGCVSKILN-RYQETG--SI-----RPGVIGGSKPRVA-TPDVEKRIEEYKKT-NP--GIFSWEIR 182 (230)
Q Consensus 115 G~s~~~IAr~lgVS~sTV~kwik-Ry~e~G--~v-----~p~~~gg~rpr~l-t~~~~~~I~~l~~~-~P--~~t~~eI~ 182 (230)
-++.++||..+|++.+||++.++ +|-++. .+ -+..........+ ...+...|.+++.+ +| ..+=.+|.
T Consensus 49 PLt~~~iA~~lgl~~STVSRav~~Ky~~t~~Gi~plk~fF~~~~~~~~~~~~S~~~ik~~i~~lI~~Ed~~~PlSD~~i~ 128 (160)
T PF04552_consen 49 PLTMKDIADELGLHESTVSRAVKNKYIQTPRGIFPLKDFFSRSVSSGSGEEFSSEAIKARIKELIEEEDKKKPLSDQEIA 128 (160)
T ss_dssp ------------------------------------S-----SS--SS-SS---TTH-HHHHHHHTTS-TTS---HHHHH
T ss_pred CCCHHHHHHHhCCCHhHHHHHHcCceeecCCeeeeHHHhccccccCCCCcccHHHHHHHHHHHHHHhcCCCCCCCHHHHH
Confidence 47899999999999999999665 465554 21 1111111111112 23467788888875 34 46677899
Q ss_pred HHHHHhhCCCCCCCCCCHhHHHHHHHcCCCCCCC
Q psy1898 183 DRLVKQDGICDKNSAPSVSSISRLLRGGRRDDCD 216 (230)
Q Consensus 183 ~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~g~~~~~ 216 (230)
+.|.+ .|+. +|+.||..+=..+||.++.
T Consensus 129 ~~L~~-~gi~-----isRRTVaKYR~~L~Ip~s~ 156 (160)
T PF04552_consen 129 ELLKE-EGIK-----ISRRTVAKYREELGIPSSS 156 (160)
T ss_dssp HHHTT-TTS--------HHHHHHHHHHHT-S-SH
T ss_pred HHHHH-cCCC-----ccHHHHHHHHHHcCCCChh
Confidence 99987 8885 8999999999999988764
No 49
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=96.66 E-value=0.0033 Score=40.60 Aligned_cols=44 Identities=23% Similarity=0.274 Sum_probs=33.0
Q ss_pred CCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHc
Q psy1898 153 SKPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRG 209 (230)
Q Consensus 153 ~rpr~lt~~~~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~ 209 (230)
+||++++++..+.+.++..+. .+..+|++. +|+ |.+||+|+|+.
T Consensus 1 GRp~~~~~~~~~~i~~l~~~G--~si~~IA~~----~gv-------sr~TvyR~l~~ 44 (45)
T PF02796_consen 1 GRPPKLSKEQIEEIKELYAEG--MSIAEIAKQ----FGV-------SRSTVYRYLNK 44 (45)
T ss_dssp SSSSSSSHCCHHHHHHHHHTT----HHHHHHH----TTS--------HHHHHHHHCC
T ss_pred CcCCCCCHHHHHHHHHHHHCC--CCHHHHHHH----HCc-------CHHHHHHHHhc
Confidence 478899998888888888665 788887764 554 99999999975
No 50
>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=96.50 E-value=0.0029 Score=43.71 Aligned_cols=37 Identities=24% Similarity=0.209 Sum_probs=31.0
Q ss_pred HHHHHHHHHHc---CCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 104 IRLKIVEMAAA---GVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 104 ~R~rIV~l~~~---G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
.|.++.+++.+ .+...+||.+||||.+||.+|..+.+
T Consensus 8 ~rdkA~e~y~~~~g~i~lkdIA~~Lgvs~~tIr~WK~~dk 47 (60)
T PF10668_consen 8 NRDKAFEIYKESNGKIKLKDIAEKLGVSESTIRKWKSRDK 47 (60)
T ss_pred CHHHHHHHHHHhCCCccHHHHHHHHCCCHHHHHHHhhhcc
Confidence 56777777764 39999999999999999999988743
No 51
>cd01105 HTH_GlnR-like Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator GlnR and related proteins, N-terminal domain. The GlnR and TnrA (also known as ScgR) proteins have been shown to regulate expression of glutamine synthetase as well as several genes involved in nitrogen metabolism. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription 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 conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=96.49 E-value=0.023 Score=41.90 Aligned_cols=68 Identities=16% Similarity=0.076 Sum_probs=48.0
Q ss_pred CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK 187 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~ 187 (230)
++..++|+.+|||.+|+..|.+ .|.+.|....++..+..++++...|..... .....+..+|++.+..
T Consensus 2 ~ti~evA~~~gvs~~tLR~ye~----~Gll~p~r~~~~g~R~Ys~~dv~~l~~I~~Lr~~G~sl~~i~~~l~~ 70 (88)
T cd01105 2 IGIGEVSKLTGVSPRQLRYWEE----KGLIKSIRSDGGGQRKYSLADVDRLLVIKELLDEGFTLAAAVEKLRR 70 (88)
T ss_pred cCHHHHHHHHCcCHHHHHHHHH----CCCCCCCccCCCCceecCHHHHHHHHHHHHHHHCCCCHHHHHHHHHH
Confidence 5789999999999999999944 476665443322456677776665543322 2357899999998876
No 52
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=96.48 E-value=0.0029 Score=43.90 Aligned_cols=66 Identities=20% Similarity=0.170 Sum_probs=42.6
Q ss_pred CHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898 117 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK 187 (230)
Q Consensus 117 s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~ 187 (230)
+..++|+.+|||++||..|.++ |.+.|....+ ..+..+.++...|..... .+-..+..+|++.|.+
T Consensus 2 ti~eva~~~gvs~~tlr~y~~~----gll~~~~~~~-g~r~y~~~dv~~l~~i~~l~~~G~sl~~I~~~l~~ 68 (69)
T PF13411_consen 2 TIKEVAKLLGVSPSTLRYYERE----GLLPPPRDEN-GYRYYSEEDVERLREIKELRKQGMSLEEIKKLLKQ 68 (69)
T ss_dssp EHHHHHHHTTTTHHHHHHHHHT----TSSTTBESTT-SSEEE-HHHHHHHHHHHHHHHTTTHHHHHHHHH--
T ss_pred cHHHHHHHHCcCHHHHHHHHHh----cCcccccccC-ceeeccHHHHHHHHHHHHHHHCcCCHHHHHHHHcc
Confidence 6789999999999999999774 4455444323 347788887766643332 1245677777776643
No 53
>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=96.47 E-value=0.0033 Score=43.07 Aligned_cols=43 Identities=26% Similarity=0.288 Sum_probs=31.0
Q ss_pred CCcCCHHHHHHHHHHHHc-CC---CHHHHhhhhccccchhhhHHHHH
Q psy1898 97 GRPLPNHIRLKIVEMAAA-GV---RPCVISRQLRVSHGCVSKILNRY 139 (230)
Q Consensus 97 g~~~s~~~R~rIV~l~~~-G~---s~~~IAr~lgVS~sTV~kwikRy 139 (230)
-+.|+..++.+||+.+.. +. +.+++|+.|+|++.+|.+|++.-
T Consensus 3 rrsy~~~FKL~Vv~~a~~~~nc~~~~RAaarkf~V~r~~Vr~W~kqe 49 (58)
T PF09607_consen 3 RRSYTAEFKLKVVEYAEKDNNCKGNQRAAARKFNVSRRQVRKWRKQE 49 (58)
T ss_dssp -----HHHHHHHHHHHHH-TTTTT-HHHHHHHTTS-HHHHHHHHTTH
T ss_pred ccccChHHHHHHHHHHHHccchhhhHHHHHHHhCccHHHHHHHHHHH
Confidence 357899999999998754 44 45889999999999999998753
No 54
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=96.44 E-value=0.006 Score=40.74 Aligned_cols=42 Identities=17% Similarity=0.194 Sum_probs=34.7
Q ss_pred CCHHHHHHHHHH-HHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898 100 LPNHIRLKIVEM-AAAGVRPCVISRQLRVSHGCVSKILNRYQE 141 (230)
Q Consensus 100 ~s~~~R~rIV~l-~~~G~s~~~IAr~lgVS~sTV~kwikRy~e 141 (230)
+|.+.+.-++.+ ++.+.+..++|..||||++||++|.+.+.+
T Consensus 3 Ls~~d~lll~L~~LR~~~~~~~La~~FgIs~stvsri~~~~~~ 45 (53)
T PF13613_consen 3 LSLEDQLLLTLMYLRLNLTFQDLAYRFGISQSTVSRIFHEWIP 45 (53)
T ss_pred CCHHHHHHHHHHHHHcCCcHhHHhhheeecHHHHHHHHHHHHH
Confidence 466666666664 467999999999999999999999998764
No 55
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, 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-like proteins in this group appear to lack the long dimerization helix seen
Probab=96.40 E-value=0.015 Score=40.47 Aligned_cols=66 Identities=15% Similarity=0.188 Sum_probs=42.1
Q ss_pred CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHH
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRL 185 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L 185 (230)
.+..++|+.+|||.+|+..|.+.+ |.+.|....+ ..+..+.++...+..... .+...+..+|+..|
T Consensus 1 ~~i~e~A~~~gVs~~tlr~ye~~~---gl~~~~r~~~-g~R~yt~~di~~l~~i~~l~~~g~~l~~i~~~l 67 (68)
T cd04763 1 YTIGEVALLTGIKPHVLRAWEREF---GLLKPQRSDG-GHRLFNDADIDRILEIKRWIDNGVQVSKVKKLL 67 (68)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHhc---CCCCCCcCCC-CCcccCHHHHHHHHHHHHHHHcCCCHHHHHHHh
Confidence 367899999999999999985533 5554433222 345677776655543322 22567777776654
No 56
>PRK04217 hypothetical protein; Provisional
Probab=96.31 E-value=0.0083 Score=46.45 Aligned_cols=44 Identities=14% Similarity=0.068 Sum_probs=34.9
Q ss_pred CCcCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 97 GRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 97 g~~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
...++.+.+.-+.....+|+|..+||+.++||.+||++.+.+..
T Consensus 40 ~~~Lt~eereai~l~~~eGlS~~EIAk~LGIS~sTV~r~L~RAr 83 (110)
T PRK04217 40 PIFMTYEEFEALRLVDYEGLTQEEAGKRMGVSRGTVWRALTSAR 83 (110)
T ss_pred cccCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 44567788744444555899999999999999999999998754
No 57
>PF14493 HTH_40: Helix-turn-helix domain
Probab=96.30 E-value=0.029 Score=41.51 Aligned_cols=83 Identities=16% Similarity=0.048 Sum_probs=65.0
Q ss_pred HHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHH
Q psy1898 107 KIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLV 186 (230)
Q Consensus 107 rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~~P~~t~~eI~~~L~ 186 (230)
.-+.++.+|+|..+||+.-+++.+||+.-+-.|...|...+- ...++.+..+.|.....+.+...+..+.+.|.
T Consensus 5 ~T~~l~~~G~si~eIA~~R~L~~sTI~~HL~~~~~~g~~~~~------~~~l~~e~~~~I~~~~~~~~~~~lk~i~e~l~ 78 (91)
T PF14493_consen 5 ITYELFQKGLSIEEIAKIRGLKESTIYGHLAELIESGEPLDI------EELLSEEEIKQIEDAIEKLGSEKLKPIKEALP 78 (91)
T ss_pred HHHHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHHHhCCCCCH------HHhCCHHHHHHHHHHHHHcCcccHHHHHHHCC
Confidence 456789999999999999999999999999999999873221 23467888888888888877777888887664
Q ss_pred HhhCCCCCCCCCCHhHHH
Q psy1898 187 KQDGICDKNSAPSVSSIS 204 (230)
Q Consensus 187 ~~~Gi~~~~~~vS~sTV~ 204 (230)
. .+|+..++
T Consensus 79 ~---------~~sy~~iR 87 (91)
T PF14493_consen 79 G---------DYSYFEIR 87 (91)
T ss_pred C---------CCCHHHHH
Confidence 2 25776665
No 58
>TIGR01529 argR_whole arginine repressor. This model includes most members of the arginine-responsive transcriptional regulator family ArgR. This hexameric protein binds DNA at its amino end to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbor-joining tree, some of these paralogous sequences show long branches and differ significantly in an otherwise well-conserved C-terminal region motif GT[VIL][AC]GDDT. These paralogs are excluded from the seed and score in the gray zone of this model, between trusted and noise cutoffs.
Probab=96.29 E-value=0.011 Score=47.89 Aligned_cols=45 Identities=24% Similarity=0.159 Sum_probs=39.8
Q ss_pred HHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcCCCC
Q psy1898 163 EKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGGRRD 213 (230)
Q Consensus 163 ~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~g~~ 213 (230)
.+.|..++.+++..|++||.+.|.+ .|+. +|.+||+|.|++.|+.
T Consensus 4 ~~~i~~Li~~~~i~tqeeL~~~L~~-~G~~-----vsqaTIsRdL~elglv 48 (146)
T TIGR01529 4 QERIKEIITEEKISTQEELVALLKA-EGIE-----VTQATVSRDLRELGAV 48 (146)
T ss_pred HHHHHHHHHcCCCCCHHHHHHHHHH-hCCC-----cCHHHHHHHHHHcCCE
Confidence 3457788889999999999999977 8985 8999999999999984
No 59
>COG2826 Tra8 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]
Probab=96.28 E-value=0.011 Score=53.04 Aligned_cols=84 Identities=20% Similarity=0.224 Sum_probs=67.3
Q ss_pred CCChhHHHHHHHHHhcCCChhhhhhhhccccccc--ccCC-----ccc----------------CCCcCCHHHHHHHHHH
Q psy1898 55 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGVN--QLGG-----VFI----------------NGRPLPNHIRLKIVEM 111 (230)
Q Consensus 55 plp~~~r~~I~e~~~~g~~~~~isr~lrvshg~~--~l~~-----~~~----------------~g~~~s~~~R~rIV~l 111 (230)
-|+...|.+|-.+..+|++..+|+++|+.+|++. .+.+ .|. ..-..+.+++..|++.
T Consensus 7 hLT~~eR~~I~~l~~~~~S~reIA~~LgRh~sTIsRElkRn~~~~~Y~a~~A~~~~~~~rrr~~~k~~~~~eL~~~V~e~ 86 (318)
T COG2826 7 HLTLFERYEIERLLKAKMSIREIAKQLNRHHSTISRELKRNRTRDIYSAVKAQERYRMLRRRRIRKLKLNPELRELVLEK 86 (318)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHHhCCCcchhhHHHhcCCccceeeHHHHHHHHHHhhcccCCcccCCHHHHHHHHHH
Confidence 4778899999999999999999999999988885 1222 111 1112557899999999
Q ss_pred HHcCCCHHHHhhhhc---cccchhhhHHHH
Q psy1898 112 AAAGVRPCVISRQLR---VSHGCVSKILNR 138 (230)
Q Consensus 112 ~~~G~s~~~IAr~lg---VS~sTV~kwikR 138 (230)
+++-+|+.+|+..+. |+..|+|+|+-.
T Consensus 87 L~~~wSPEQI~g~l~~~~i~~eTIYr~ly~ 116 (318)
T COG2826 87 LKSKWSPEQIIGRLKKSKISFETIYRWLYQ 116 (318)
T ss_pred HHhhCCHHHHHHHHHhcccCHHHHHHHHhh
Confidence 999999999998765 789999999864
No 60
>PF13551 HTH_29: Winged helix-turn helix
Probab=96.28 E-value=0.015 Score=43.58 Aligned_cols=78 Identities=26% Similarity=0.280 Sum_probs=57.2
Q ss_pred HHHHHHHHhcCC-Chhhhhhhhccccccc-------------ccCC-ccc--CCCc-CCHHHHHHHHHHHHcC-------
Q psy1898 61 RLKIVEMAAAGV-RPCVISRQLRVSHGVN-------------QLGG-VFI--NGRP-LPNHIRLKIVEMAAAG------- 115 (230)
Q Consensus 61 r~~I~e~~~~g~-~~~~isr~lrvshg~~-------------~l~~-~~~--~g~~-~s~~~R~rIV~l~~~G------- 115 (230)
|..|+.++.+|. +..++++.+++|..++ .+-. ... .++. ++.+.+..|++++.+.
T Consensus 1 R~~~l~l~~~g~~~~~~ia~~lg~s~~Tv~r~~~~~~~~G~~~l~~~~~~~g~~~~~l~~~~~~~l~~~~~~~p~~g~~~ 80 (112)
T PF13551_consen 1 RAQILLLLAEGVSTIAEIARRLGISRRTVYRWLKRYREGGIEGLLPRKPRGGRPRKRLSEEQRAQLIELLRENPPEGRSR 80 (112)
T ss_pred CHHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHcccHHHHHhccccCCCCCCCCCHHHHHHHHHHHHHCCCCCCCc
Confidence 568899999999 5999999999854432 1111 111 1222 7899999999988762
Q ss_pred CCHHHHhhhh-------ccccchhhhHHHH
Q psy1898 116 VRPCVISRQL-------RVSHGCVSKILNR 138 (230)
Q Consensus 116 ~s~~~IAr~l-------gVS~sTV~kwikR 138 (230)
++..+|+..+ .+|.+||++|+++
T Consensus 81 ~t~~~l~~~l~~~~~~~~~s~~ti~r~L~~ 110 (112)
T PF13551_consen 81 WTLEELAEWLIEEEFGIDVSPSTIRRILKR 110 (112)
T ss_pred ccHHHHHHHHHHhccCccCCHHHHHHHHHH
Confidence 6788888855 5799999999986
No 61
>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=96.26 E-value=0.0085 Score=38.78 Aligned_cols=43 Identities=21% Similarity=0.360 Sum_probs=34.0
Q ss_pred HHHHHHHHHHHc--CCCHHHHhhhhccccchhhhHHHHHhhhCCC
Q psy1898 103 HIRLKIVEMAAA--GVRPCVISRQLRVSHGCVSKILNRYQETGSI 145 (230)
Q Consensus 103 ~~R~rIV~l~~~--G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v 145 (230)
+.+.+|+....+ +.|.++||+.+++|.+||++.+++..+.|-+
T Consensus 3 ~~~~~Il~~l~~~~~~t~~ela~~~~is~~tv~~~l~~L~~~g~I 47 (48)
T PF13412_consen 3 ETQRKILNYLRENPRITQKELAEKLGISRSTVNRYLKKLEEKGLI 47 (48)
T ss_dssp HHHHHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHHHCcCc
Confidence 456677775543 4999999999999999999999999988854
No 62
>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=96.23 E-value=0.0053 Score=47.93 Aligned_cols=55 Identities=16% Similarity=0.221 Sum_probs=38.1
Q ss_pred CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCC-CCCCCCCHHHHHHHHHHH
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGG-SKPRVATPDVEKRIEEYK 170 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg-~rpr~lt~~~~~~I~~l~ 170 (230)
+++.|+|..+|+|+.||.||++++.=.-+..|...+| .|--.++.+++++|...-
T Consensus 1 MT~eELA~~tG~srQTINrWvRkegW~T~p~pGVkGGrARLIhId~~V~efi~s~~ 56 (122)
T PF07037_consen 1 MTPEELAELTGYSRQTINRWVRKEGWKTEPKPGVKGGRARLIHIDEQVREFIRSIP 56 (122)
T ss_pred CCHHHHHHHhCccHHHHHHHHHhcCceeccCCccccccceeeeecHHHHHHHHhhH
Confidence 5789999999999999999998754221223444443 133466778888887554
No 63
>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=96.18 E-value=0.021 Score=39.49 Aligned_cols=65 Identities=15% Similarity=0.105 Sum_probs=41.9
Q ss_pred CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHH
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRL 185 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L 185 (230)
++..++|+.+|||++|+..|.+++. ...++.. +..+..+.++...+..... .+...+..+|++.|
T Consensus 1 ~~i~evA~~~gvs~~tlR~~~~~g~---l~~~~~~--~g~R~y~~~~l~~l~~i~~l~~~g~~l~~i~~~l 66 (67)
T cd04764 1 YTIKEVSEIIGVKPHTLRYYEKEFN---LYIPRTE--NGRRYYTDEDIELLKKIKTLLEKGLSIKEIKEIL 66 (67)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHhcC---CCCCCCC--CCceeeCHHHHHHHHHHHHHHHCCCCHHHHHHHh
Confidence 3678999999999999999976533 2223222 2346677776665543332 22567777777654
No 64
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=96.08 E-value=0.032 Score=38.54 Aligned_cols=50 Identities=12% Similarity=0.050 Sum_probs=33.9
Q ss_pred CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHH
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEY 169 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l 169 (230)
++..++|+.+|||++|+..|.+ .|.+.|..+..+..+..+.++...+...
T Consensus 1 ~s~~eva~~~gvs~~tlr~~~~----~gli~~~~~~~~g~r~y~~~dl~~l~~i 50 (70)
T smart00422 1 YTIGEVAKLAGVSVRTLRYYER----IGLLPPPIRTEGGYRLYSDEDLERLRFI 50 (70)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCccCCCCCEecCHHHHHHHHHH
Confidence 4788999999999999999965 6777654121123456677666555433
No 65
>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=96.06 E-value=0.008 Score=38.03 Aligned_cols=23 Identities=13% Similarity=0.133 Sum_probs=20.7
Q ss_pred CCHHHHhhhhccccchhhhHHHH
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNR 138 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikR 138 (230)
++..++|+.|+||++||++|.+.
T Consensus 1 ~s~~e~a~~lgvs~~tl~~~~~~ 23 (49)
T cd04762 1 LTTKEAAELLGVSPSTLRRWVKE 23 (49)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHc
Confidence 46789999999999999999884
No 66
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=96.06 E-value=0.0065 Score=51.18 Aligned_cols=36 Identities=25% Similarity=0.329 Sum_probs=31.6
Q ss_pred HHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHH
Q psy1898 104 IRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRY 139 (230)
Q Consensus 104 ~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy 139 (230)
.+..|..++.+|.|..+||+.||||++||+++++.+
T Consensus 161 ~~~~i~~~~~~g~s~~~iak~lgis~~Tv~r~~k~~ 196 (200)
T PRK13413 161 KEEKIKKLLDKGTSKSEIARKLGVSRTTLARFLKTR 196 (200)
T ss_pred hHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHhc
Confidence 345777888999999999999999999999999853
No 67
>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=96.05 E-value=0.0086 Score=45.04 Aligned_cols=35 Identities=23% Similarity=0.241 Sum_probs=29.7
Q ss_pred HHHHHHHHHH-HcCCCHHHHhhhhccccchhhhHHH
Q psy1898 103 HIRLKIVEMA-AAGVRPCVISRQLRVSHGCVSKILN 137 (230)
Q Consensus 103 ~~R~rIV~l~-~~G~s~~~IAr~lgVS~sTV~kwik 137 (230)
..|..|+..+ +.++|.++||+.+|||++||+||-+
T Consensus 42 ~~R~~i~~~Ll~~~~tQrEIa~~lGiS~atIsR~sn 77 (94)
T TIGR01321 42 GDRIRIVNELLNGNMSQREIASKLGVSIATITRGSN 77 (94)
T ss_pred HHHHHHHHHHHhCCCCHHHHHHHhCCChhhhhHHHh
Confidence 5677777644 5679999999999999999999965
No 68
>cd04765 HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), 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. 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.
Probab=96.00 E-value=0.058 Score=40.72 Aligned_cols=68 Identities=10% Similarity=0.004 Sum_probs=49.9
Q ss_pred CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH--hCCCCCHHHHHHHHHH
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK--TNPGIFSWEIRDRLVK 187 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~--~~P~~t~~eI~~~L~~ 187 (230)
.+..++|+.+|||.+|+..|.+. .|.+.|...+ +.-+..+.++...|..... ..-.++..++++.|..
T Consensus 1 yti~EvA~~~gVs~~tLR~ye~~---~gli~p~r~~-~g~R~Yt~~di~~l~~I~~llr~~G~~l~~i~~~l~~ 70 (99)
T cd04765 1 FSIGEVAEILGLPPHVLRYWETE---FPQLKPVKRA-GGRRYYRPKDVELLLLIKHLLYEKGYTIEGAKQALKE 70 (99)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHH---cCCCCCcCCC-CCCeeeCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHh
Confidence 36789999999999999999654 3444443322 2466788888777766553 5667999999999876
No 69
>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=95.95 E-value=0.015 Score=37.97 Aligned_cols=40 Identities=30% Similarity=0.361 Sum_probs=32.0
Q ss_pred CHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHh
Q psy1898 117 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKT 172 (230)
Q Consensus 117 s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~ 172 (230)
+.++||+..|||.+||++.++. +..++++.+++|.+..++
T Consensus 1 Ti~dIA~~agvS~~TVSr~ln~----------------~~~vs~~tr~rI~~~a~~ 40 (46)
T PF00356_consen 1 TIKDIAREAGVSKSTVSRVLNG----------------PPRVSEETRERILEAAEE 40 (46)
T ss_dssp CHHHHHHHHTSSHHHHHHHHTT----------------CSSSTHHHHHHHHHHHHH
T ss_pred CHHHHHHHHCcCHHHHHHHHhC----------------CCCCCHHHHHHHHHHHHH
Confidence 4689999999999999999851 235688888888877654
No 70
>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=95.86 E-value=0.015 Score=37.69 Aligned_cols=35 Identities=14% Similarity=0.155 Sum_probs=26.6
Q ss_pred HHHHHHHHHHHcC-CCHHHHhhhhccccchhhhHHH
Q psy1898 103 HIRLKIVEMAAAG-VRPCVISRQLRVSHGCVSKILN 137 (230)
Q Consensus 103 ~~R~rIV~l~~~G-~s~~~IAr~lgVS~sTV~kwik 137 (230)
+.=+.+|..+..| +|.+++|+.|||+++|+++.++
T Consensus 3 e~l~~Ai~~v~~g~~S~r~AA~~ygVp~sTL~~r~~ 38 (45)
T PF05225_consen 3 EDLQKAIEAVKNGKMSIRKAAKKYGVPRSTLRRRLR 38 (45)
T ss_dssp HHHHHHHHHHHTTSS-HHHHHHHHT--HHHHHHHHH
T ss_pred HHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHc
Confidence 3446677888888 9999999999999999997665
No 71
>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=95.84 E-value=0.016 Score=43.02 Aligned_cols=39 Identities=13% Similarity=0.166 Sum_probs=34.3
Q ss_pred HHHHHHHHH-HHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 102 NHIRLKIVE-MAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 102 ~~~R~rIV~-l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
...|.+|+. |+.+|+|.++||+.+|+|..||+|.-+-.+
T Consensus 35 l~~R~~va~~lL~~g~syreIa~~tgvS~aTItRvsr~Lk 74 (87)
T PF01371_consen 35 LAQRWQVAKELLDEGKSYREIAEETGVSIATITRVSRCLK 74 (87)
T ss_dssp HHHHHHHHHHHHHTTSSHHHHHHHHTSTHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 367999998 999999999999999999999999865443
No 72
>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=95.81 E-value=0.036 Score=52.42 Aligned_cols=95 Identities=13% Similarity=0.160 Sum_probs=68.6
Q ss_pred CCHHHHhhhhccccchhhhHHHH-HhhhC--CC-----CcCCCCCCC--CCCCCHHHHHHHHHHHHhC-C--CCCHHHHH
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNR-YQETG--SI-----RPGVIGGSK--PRVATPDVEKRIEEYKKTN-P--GIFSWEIR 182 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikR-y~e~G--~v-----~p~~~gg~r--pr~lt~~~~~~I~~l~~~~-P--~~t~~eI~ 182 (230)
++.++||..+|++.|||+|.++. |-++. .+ ......... .-.-+..+...|.+++... + ..+=.+|.
T Consensus 319 LtlkdiA~~lglheSTVSRav~~Kyi~tp~Gi~~lk~FFs~~~~~~~~g~~~S~~~Ik~~I~~lI~~E~~~~PlSD~~I~ 398 (429)
T TIGR02395 319 LTLREVAEELGLHESTISRAINNKYLQTPRGVFELKYFFSRGVQTDSGEGEVSSTAIKALIKELIAAEDKRKPLSDQKIA 398 (429)
T ss_pred CcHHHHHHHhCCCccchhhhhcCceEecCCceEEHHHhcCCccCCCCCCCccCHHHHHHHHHHHHHhcCCCCCCCHHHHH
Confidence 78999999999999999999864 55553 21 111100000 1133556788888888753 3 36677899
Q ss_pred HHHHHhhCCCCCCCCCCHhHHHHHHHcCCCCCCC
Q psy1898 183 DRLVKQDGICDKNSAPSVSSISRLLRGGRRDDCD 216 (230)
Q Consensus 183 ~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~g~~~~~ 216 (230)
+.|.+ .|+. +|+.||..+=...|+.++.
T Consensus 399 ~~L~~-~Gi~-----IaRRTVaKYRe~L~Ip~s~ 426 (429)
T TIGR02395 399 ELLKE-KGIK-----IARRTVAKYREELGIPSSS 426 (429)
T ss_pred HHHHh-cCCC-----eehHHHHHHHHHcCCCccc
Confidence 99988 6995 9999999999999998875
No 73
>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=95.75 E-value=0.013 Score=42.12 Aligned_cols=44 Identities=16% Similarity=0.149 Sum_probs=32.5
Q ss_pred CCHHHHHHHHHH-HHcCCCHHHHhhhhccccchhhhHHHHHhhhC
Q psy1898 100 LPNHIRLKIVEM-AAAGVRPCVISRQLRVSHGCVSKILNRYQETG 143 (230)
Q Consensus 100 ~s~~~R~rIV~l-~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G 143 (230)
++...|+-+... +.+|+|..+||+.++||.+||..|+.+-...|
T Consensus 16 l~~~~r~af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~~~~~~ 60 (73)
T TIGR03879 16 VDSLAEAAAALAREEAGKTASEIAEELGRTEQTVRNHLKGETKAG 60 (73)
T ss_pred CCHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhcCcccc
Confidence 444555444443 35899999999999999999999998633333
No 74
>PF13309 HTH_22: HTH domain
Probab=95.70 E-value=0.009 Score=41.66 Aligned_cols=41 Identities=20% Similarity=0.220 Sum_probs=33.2
Q ss_pred CCcCCHHHHHHHHHHH-HcC-----CCHHHHhhhhccccchhhhHHH
Q psy1898 97 GRPLPNHIRLKIVEMA-AAG-----VRPCVISRQLRVSHGCVSKILN 137 (230)
Q Consensus 97 g~~~s~~~R~rIV~l~-~~G-----~s~~~IAr~lgVS~sTV~kwik 137 (230)
...++.+.|..||..+ +.| -+...+|+.|+||+.|||+.++
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 4556778899999754 567 5788899999999999999863
No 75
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=95.67 E-value=0.039 Score=52.59 Aligned_cols=93 Identities=14% Similarity=0.181 Sum_probs=68.6
Q ss_pred CCHHHHhhhhccccchhhhHHHH-HhhhC--CC-----CcC---CCCCCCCCCCCHHHHHHHHHHHHhC-C--CCCHHHH
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNR-YQETG--SI-----RPG---VIGGSKPRVATPDVEKRIEEYKKTN-P--GIFSWEI 181 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikR-y~e~G--~v-----~p~---~~gg~rpr~lt~~~~~~I~~l~~~~-P--~~t~~eI 181 (230)
++.++||..+|++.|||+|.++- |-++. .+ ... ...| ...-+..+...|.+++... | ..+=.+|
T Consensus 344 LtlkdvAe~lglheSTVSRav~~Kyv~tp~Gi~~lk~FFs~~~~~~~g--~~~S~~~Ik~~Ik~lI~~Ed~~~PlSD~~I 421 (455)
T PRK05932 344 LVLKDIAEELGMHESTISRATTNKYMATPRGIFELKYFFSSAVSTDGG--GEASSTAIRALIKKLIAAENPKKPLSDSKI 421 (455)
T ss_pred ccHHHHHHHhCCCccchhhhhcCceeecCCceEEHHHhcccccCCCCC--ccccHHHHHHHHHHHHHhcCCCCCCCHHHH
Confidence 78999999999999999998864 54443 21 111 0111 1133455788899998754 3 3667789
Q ss_pred HHHHHHhhCCCCCCCCCCHhHHHHHHHcCCCCCCC
Q psy1898 182 RDRLVKQDGICDKNSAPSVSSISRLLRGGRRDDCD 216 (230)
Q Consensus 182 ~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~g~~~~~ 216 (230)
.+.|.+ .|+. +|+.||..+=...||.++.
T Consensus 422 ~~~L~~-~Gi~-----IaRRTVaKYRe~L~Ip~s~ 450 (455)
T PRK05932 422 AELLKE-QGID-----VARRTVAKYREALNIPSSS 450 (455)
T ss_pred HHHHHH-cCCC-----eehHHHHHHHHHcCCCChH
Confidence 999988 6995 9999999999999999875
No 76
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=95.64 E-value=0.02 Score=45.39 Aligned_cols=42 Identities=17% Similarity=0.008 Sum_probs=36.2
Q ss_pred cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
.+|...|.-++..+-+|+|..+||..+|+|.+||..++.|-.
T Consensus 106 ~L~~~~r~ii~l~~~~~~s~~EIA~~l~is~~tV~~~~~ra~ 147 (154)
T PRK06759 106 VLDEKEKYIIFERFFVGKTMGEIALETEMTYYQVRWIYRQAL 147 (154)
T ss_pred hCCHHHHHHHHHHHhcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 356677777777788999999999999999999999998754
No 77
>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=95.64 E-value=0.0085 Score=40.92 Aligned_cols=48 Identities=25% Similarity=0.412 Sum_probs=40.9
Q ss_pred CCHHHHHHHHHHH-H-cCCCHHHHhhhhccccchhhhHHHHHhhhCCCCc
Q psy1898 100 LPNHIRLKIVEMA-A-AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP 147 (230)
Q Consensus 100 ~s~~~R~rIV~l~-~-~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p 147 (230)
++...|.+|+.++ . .+++..+||+.++++.+||+.-++...+.|.+..
T Consensus 7 L~~p~R~~Il~~L~~~~~~t~~ela~~l~~~~~t~s~hL~~L~~aGli~~ 56 (61)
T PF12840_consen 7 LSDPTRLRILRLLASNGPMTVSELAEELGISQSTVSYHLKKLEEAGLIEV 56 (61)
T ss_dssp HTSHHHHHHHHHHHHCSTBEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred hCCHHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEE
Confidence 4557899999988 4 4599999999999999999999999999997743
No 78
>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=95.63 E-value=0.032 Score=39.73 Aligned_cols=46 Identities=22% Similarity=0.119 Sum_probs=34.7
Q ss_pred HHHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcCCCC
Q psy1898 162 VEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGGRRD 213 (230)
Q Consensus 162 ~~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~g~~ 213 (230)
-.+.|..++.+++-.+..||.+.|.. .|+. ++.+||+|-|+..++.
T Consensus 6 R~~~I~~li~~~~i~sQ~eL~~~L~~-~Gi~-----vTQaTiSRDLkeL~~v 51 (70)
T PF01316_consen 6 RQELIKELISEHEISSQEELVELLEE-EGIE-----VTQATISRDLKELGAV 51 (70)
T ss_dssp HHHHHHHHHHHS---SHHHHHHHHHH-TT-T-------HHHHHHHHHHHT-E
T ss_pred HHHHHHHHHHHCCcCCHHHHHHHHHH-cCCC-----cchhHHHHHHHHcCcE
Confidence 35678889999999999999999988 8995 8999999999999875
No 79
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=95.58 E-value=0.022 Score=46.78 Aligned_cols=42 Identities=21% Similarity=0.227 Sum_probs=35.4
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE 141 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e 141 (230)
+|.+.|.-++..+.+|++..+||+.+|||.+||..++.|-.+
T Consensus 134 L~~~~r~i~~l~~~~~~s~~eIA~~lgis~~tV~~~l~ra~~ 175 (182)
T PRK12537 134 LEPARRNCILHAYVDGCSHAEIAQRLGAPLGTVKAWIKRSLK 175 (182)
T ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHHCCChhhHHHHHHHHHH
Confidence 566777666666779999999999999999999999988653
No 80
>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=95.54 E-value=0.02 Score=46.03 Aligned_cols=42 Identities=26% Similarity=0.388 Sum_probs=34.3
Q ss_pred cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898 99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE 141 (230)
Q Consensus 99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e 141 (230)
.++ +...+|+.++.+|+|..+||+.+|+|++||.++.++..+
T Consensus 6 ~Lt-e~qr~VL~Lr~~GlTq~EIAe~LgiS~stV~~~e~ra~k 47 (137)
T TIGR00721 6 FLT-ERQIKVLELREKGLSQKEIAKELKTTRANVSAIEKRAME 47 (137)
T ss_pred CCC-HHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHhHHH
Confidence 344 444567777889999999999999999999999988553
No 81
>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=95.52 E-value=0.018 Score=38.82 Aligned_cols=35 Identities=23% Similarity=0.321 Sum_probs=30.4
Q ss_pred HHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 106 LKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 106 ~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
..|+.++..|.+..+||..++||..||+.++++-.
T Consensus 9 ~~vl~~l~~G~~~~eIA~~l~is~~tV~~~~~~i~ 43 (58)
T PF00196_consen 9 LEVLRLLAQGMSNKEIAEELGISEKTVKSHRRRIM 43 (58)
T ss_dssp HHHHHHHHTTS-HHHHHHHHTSHHHHHHHHHHHHH
T ss_pred HHHHHHHHhcCCcchhHHhcCcchhhHHHHHHHHH
Confidence 45888999999999999999999999999988744
No 82
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=95.52 E-value=0.062 Score=40.52 Aligned_cols=68 Identities=16% Similarity=0.112 Sum_probs=46.2
Q ss_pred CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK 187 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~ 187 (230)
++..++|+.+|||+.|+..|.+ .|.+.|..+..+.-+..++++...+..... ..-..+..+|++.+..
T Consensus 1 ~ti~eva~~~gvs~~tlR~ye~----~Gll~~~~~~~~g~R~y~~~di~~l~~i~~lr~~g~~l~~i~~~~~~ 69 (103)
T cd01106 1 YTVGEVAKLTGVSVRTLHYYDE----IGLLKPSRRTENGYRLYTEEDLERLQQILFLKELGFSLKEIKELLKD 69 (103)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCccCCCCceeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHHc
Confidence 4688999999999999998765 577655333222346678877665532221 2347888888887754
No 83
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=95.47 E-value=0.025 Score=45.28 Aligned_cols=42 Identities=19% Similarity=0.123 Sum_probs=36.0
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE 141 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e 141 (230)
+|...|.-++..+.+|+|..+||+.+|+|.+||...+.|.+.
T Consensus 107 Lp~~~r~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Rar~ 148 (160)
T PRK09642 107 LPENYRDVVLAHYLEEKSYQEIALQEKIEVKTVEMKLYRARK 148 (160)
T ss_pred CCHHHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 677777777777889999999999999999999999887553
No 84
>cd04782 HTH_BltR Helix-Turn-Helix DNA binding domain of the BltR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BltR (BmrR-like transporter) of Bacillus subtilis, and related proteins; N-terminal domain. Blt, like Bmr, is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. These regulators are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=95.47 E-value=0.13 Score=38.48 Aligned_cols=68 Identities=16% Similarity=0.138 Sum_probs=46.5
Q ss_pred CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK 187 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~ 187 (230)
++..++|+.+|||..|+.-|.+ .|.+.|..++.+.-+..+.++...|..... ..-..+..+|++.+..
T Consensus 1 ~~i~eva~~~gvs~~tlR~ye~----~Gll~p~~~~~~gyR~Y~~~~~~~l~~I~~lr~~G~~l~eI~~~l~~ 69 (97)
T cd04782 1 FTTGEFAKLCGISKQTLFHYDK----IGLFKPEIVKENGYRYYTLEQFEQLDIILLLKELGISLKEIKDYLDN 69 (97)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCccCCCCCccCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhc
Confidence 3678999999999999887744 688877543223456677776655543332 3346888888887743
No 85
>cd04773 HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.
Probab=95.45 E-value=0.062 Score=41.10 Aligned_cols=68 Identities=13% Similarity=0.088 Sum_probs=47.6
Q ss_pred CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK 187 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~ 187 (230)
++..++|+.+|||+.|+..|.+ .|.+.|.....+.-+..++++...+..... ..-..+..+|++.|..
T Consensus 1 ~~i~eva~~~gvs~~tlR~ye~----~Gll~p~~~~~~g~R~Y~~~dl~~l~~I~~lr~~G~~l~~I~~~l~~ 69 (108)
T cd04773 1 MTIGELAHLLGVPPSTLRHWEK----EGLLSPDREPETGYRVYDPSDVRDARLIHLLRRGGYLLEQIATVVEQ 69 (108)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCcCCCCCceeeCHHHHHHHHHHHHHHHCCCCHHHHHHHHHH
Confidence 4789999999999999998854 587766443323456678877666654332 2335788888888764
No 86
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=95.43 E-value=0.048 Score=43.17 Aligned_cols=55 Identities=20% Similarity=0.330 Sum_probs=44.4
Q ss_pred ccCCCcCCHHHHHHHHHHHHcC--------CCHHHHhhhhccccchhhhHHHHHhhhCCCCcC
Q psy1898 94 FINGRPLPNHIRLKIVEMAAAG--------VRPCVISRQLRVSHGCVSKILNRYQETGSIRPG 148 (230)
Q Consensus 94 ~~~g~~~s~~~R~rIV~l~~~G--------~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~ 148 (230)
+.+.+|...++..+|......| -|.+++|..++|++.||.|-.+...+.|.+...
T Consensus 6 f~s~~PIY~QI~~qIk~~I~~g~l~pGdkLPSvRelA~~~~VNpnTv~raY~eLE~eG~i~t~ 68 (125)
T COG1725 6 FDSSKPIYEQIANQIKEQIASGELKPGDKLPSVRELAKDLGVNPNTVQRAYQELEREGIVETK 68 (125)
T ss_pred cCCCCCHHHHHHHHHHHHHHhCCcCCCCCCCcHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEe
Confidence 3456677777777777766554 589999999999999999999999999987544
No 87
>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=95.43 E-value=0.056 Score=39.49 Aligned_cols=55 Identities=15% Similarity=0.160 Sum_probs=42.4
Q ss_pred HHHHHHHHHHHHcC-CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH
Q psy1898 102 NHIRLKIVEMAAAG-VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK 171 (230)
Q Consensus 102 ~~~R~rIV~l~~~G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~ 171 (230)
.+.+..|++++..| .+..+||+.+|||.+||++-+. ..+..++++.++.|.+..+
T Consensus 5 ~~R~~~I~e~l~~~~~ti~dvA~~~gvS~~TVsr~L~---------------~~~~~Vs~~Tr~rV~~aa~ 60 (80)
T TIGR02844 5 EERVLEIGKYIVETKATVRETAKVFGVSKSTVHKDVT---------------ERLPEINPELAEEVKEVLD 60 (80)
T ss_pred HHHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHhc---------------CCCCCCCHHHHHHHHHHHc
Confidence 45567777776657 8999999999999999999652 1112368888999888886
No 88
>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=95.43 E-value=0.013 Score=35.45 Aligned_cols=29 Identities=24% Similarity=0.350 Sum_probs=24.5
Q ss_pred CCHHHHhhhhccccchhhhHHHHHhhhCC
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNRYQETGS 144 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~ 144 (230)
++..+||..+|+++-||+|.++++++.|.
T Consensus 3 mtr~diA~~lG~t~ETVSR~l~~l~~~gl 31 (32)
T PF00325_consen 3 MTRQDIADYLGLTRETVSRILKKLERQGL 31 (32)
T ss_dssp --HHHHHHHHTS-HHHHHHHHHHHHHTTS
T ss_pred cCHHHHHHHhCCcHHHHHHHHHHHHHcCC
Confidence 57889999999999999999999998874
No 89
>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=95.41 E-value=0.028 Score=36.00 Aligned_cols=47 Identities=15% Similarity=0.126 Sum_probs=32.3
Q ss_pred CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHH
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIE 167 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~ 167 (230)
++..++|+.+||+++||..|.+ .|.+.+....+ ..+..+.++...+.
T Consensus 1 ~~~~e~a~~~gv~~~tlr~~~~----~g~l~~~~~~~-~~~~y~~~~v~~l~ 47 (49)
T cd04761 1 YTIGELAKLTGVSPSTLRYYER----IGLLSPARTEG-GYRLYSDADLERLR 47 (49)
T ss_pred CcHHHHHHHHCcCHHHHHHHHH----CCCCCCCcCCC-CCEEeCHHHHHHhh
Confidence 4788999999999999999965 45554332222 45566776665543
No 90
>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=95.39 E-value=0.022 Score=36.15 Aligned_cols=36 Identities=19% Similarity=0.237 Sum_probs=27.3
Q ss_pred HHHHHHHHHH-cCCCHHHHhhhhccccchhhhHHHHH
Q psy1898 104 IRLKIVEMAA-AGVRPCVISRQLRVSHGCVSKILNRY 139 (230)
Q Consensus 104 ~R~rIV~l~~-~G~s~~~IAr~lgVS~sTV~kwikRy 139 (230)
++.-|...++ .+....++|+.||||++|+++-+++|
T Consensus 6 E~~~i~~aL~~~~gn~~~aA~~Lgisr~tL~~klkk~ 42 (42)
T PF02954_consen 6 EKQLIRQALERCGGNVSKAARLLGISRRTLYRKLKKY 42 (42)
T ss_dssp HHHHHHHHHHHTTT-HHHHHHHHTS-HHHHHHHHHHC
T ss_pred HHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHhC
Confidence 4455555554 57899999999999999999999886
No 91
>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB. Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of 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=95.39 E-value=0.086 Score=40.42 Aligned_cols=68 Identities=15% Similarity=0.041 Sum_probs=48.4
Q ss_pred CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK 187 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~ 187 (230)
++..++|+.+|||+.|+..|.+ .|.+.|..+.....+..++++.+.|..... ..-+.++.+|++.|..
T Consensus 1 ~~i~e~a~~~gvs~~tlr~ye~----~gll~~~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~ 69 (113)
T cd01109 1 YTIKEVAEKTGLSADTLRYYEK----EGLLPPVKRDENGIRDFTEEDLEWLEFIKCLRNTGMSIKDIKEYAEL 69 (113)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCCcCCCCCccCCHHHHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 4688999999999999988854 577754433333467788887766643332 3457899999988864
No 92
>PHA00675 hypothetical protein
Probab=95.39 E-value=0.02 Score=41.34 Aligned_cols=39 Identities=23% Similarity=0.362 Sum_probs=32.3
Q ss_pred CCHHHHHHHHHHH-HcCCCHHHHhhhhccccchhhhHHHH
Q psy1898 100 LPNHIRLKIVEMA-AAGVRPCVISRQLRVSHGCVSKILNR 138 (230)
Q Consensus 100 ~s~~~R~rIV~l~-~~G~s~~~IAr~lgVS~sTV~kwikR 138 (230)
+....=..|..++ ..|.|..+||+.||||++||+.+.+.
T Consensus 23 Lt~~qV~~IR~l~~r~G~s~~~IA~~fGVsrstV~~I~~g 62 (78)
T PHA00675 23 LTDAEVERIRELHEVEGMSYAVLAEKFEQSKGAIAKICRY 62 (78)
T ss_pred cCHHHHHHHHHHHHhcCccHHHHHHHhCCCHHHHHHHHcc
Confidence 4555556677777 78999999999999999999999653
No 93
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=95.37 E-value=0.025 Score=45.67 Aligned_cols=42 Identities=24% Similarity=0.297 Sum_probs=33.9
Q ss_pred cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898 99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE 141 (230)
Q Consensus 99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e 141 (230)
.+|... .+|+.++..|+|..+||+.||+|++||..|.++..+
T Consensus 6 ~Lt~rq-reVL~lr~~GlTq~EIAe~LGiS~~tVs~ie~ra~k 47 (141)
T PRK03975 6 FLTERQ-IEVLRLRERGLTQQEIADILGTSRANVSSIEKRARE 47 (141)
T ss_pred CCCHHH-HHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 345444 456677889999999999999999999999987543
No 94
>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=95.35 E-value=0.028 Score=44.65 Aligned_cols=43 Identities=26% Similarity=0.256 Sum_probs=36.1
Q ss_pred cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898 99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE 141 (230)
Q Consensus 99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e 141 (230)
.+|...|.-++..+-+|++.++||+.+|+|.+||+.++.|-+.
T Consensus 111 ~L~~~~r~v~~l~~~~g~~~~eIA~~l~is~~tv~~~l~Rar~ 153 (159)
T TIGR02989 111 KLPERQRELLQLRYQRGVSLTALAEQLGRTVNAVYKALSRLRV 153 (159)
T ss_pred HCCHHHHHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 4666777666666889999999999999999999999988653
No 95
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=95.34 E-value=0.027 Score=45.39 Aligned_cols=41 Identities=22% Similarity=0.261 Sum_probs=34.4
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
+|...|.-+...+..|+|.++||+.||+|.+||+.++.|-+
T Consensus 129 L~~~~r~vl~l~~~~~~s~~eIA~~lgis~~tV~~~l~ra~ 169 (182)
T PRK09652 129 LPEELRTAITLREIEGLSYEEIAEIMGCPIGTVRSRIFRAR 169 (182)
T ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 56677766666678999999999999999999999988744
No 96
>PF11198 DUF2857: Protein of unknown function (DUF2857); InterPro: IPR021364 This is a bacterial family of uncharacterised proteins.
Probab=95.33 E-value=0.25 Score=41.35 Aligned_cols=92 Identities=18% Similarity=0.140 Sum_probs=62.5
Q ss_pred HHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHh---CCC------
Q psy1898 105 RLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKT---NPG------ 175 (230)
Q Consensus 105 R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~---~P~------ 175 (230)
.+.|-.++.-|.|..-+.+.||.|..-|..|.+-- |. +. + .+||+.+++++...|-..-++ .+.
T Consensus 77 ~~~idr~L~lGAS~~mm~~~FGls~~ev~~rR~ll---gi--~~-~-~GR~~~~~ee~~~~iW~~W~~~~~~~~~~~~~~ 149 (180)
T PF11198_consen 77 QQLIDRALRLGASIEMMQRLFGLSSAEVAARRRLL---GI--PV-R-KGRPPALSEEEEAAIWRRWQQLMKKRGVDNLDS 149 (180)
T ss_pred HHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHh---CC--CC-C-CCCCCCcCHHHHHHHHHHHHHHHhhcCCCCccc
Confidence 45555688899999999999999999999986531 22 22 2 348888899888887544432 222
Q ss_pred CCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcC
Q psy1898 176 IFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGG 210 (230)
Q Consensus 176 ~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~ 210 (230)
...-++.-.+.++.++ |.++||..++.+
T Consensus 150 ~~~Le~~m~~Ae~~~i-------sL~~iW~~i~~w 177 (180)
T PF11198_consen 150 PDALELMMLLAEETNI-------SLTVIWSLIQEW 177 (180)
T ss_pred hHHHHHHHHHHHHhCC-------CHHHHHHHHHHH
Confidence 2244444444454554 999999998764
No 97
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=95.30 E-value=0.031 Score=44.56 Aligned_cols=42 Identities=17% Similarity=0.127 Sum_probs=35.7
Q ss_pred cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
.+|...|.-++..+-+|+|..+||..+|||.+||...+.|-+
T Consensus 106 ~Lp~~~r~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~ra~ 147 (161)
T PRK09047 106 KLPARQREAFLLRYWEDMDVAETAAAMGCSEGSVKTHCSRAT 147 (161)
T ss_pred hCCHHHHHHHHHHHHhcCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 366677777777788999999999999999999999988754
No 98
>PHA02591 hypothetical protein; Provisional
Probab=95.28 E-value=0.023 Score=41.12 Aligned_cols=36 Identities=25% Similarity=0.193 Sum_probs=32.1
Q ss_pred HHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHH
Q psy1898 102 NHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILN 137 (230)
Q Consensus 102 ~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwik 137 (230)
.|.+.-+-+|++.|+|..+||+.|||+..+|+++++
T Consensus 46 dd~~~vA~eL~eqGlSqeqIA~~LGVsqetVrKYL~ 81 (83)
T PHA02591 46 DDLISVTHELARKGFTVEKIASLLGVSVRKVRRYLE 81 (83)
T ss_pred chHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHh
Confidence 467777778999999999999999999999999875
No 99
>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=95.28 E-value=0.034 Score=37.81 Aligned_cols=48 Identities=23% Similarity=0.425 Sum_probs=38.7
Q ss_pred CCHHHHHHHHHHHHc-CCCHHHHhhhhccccchhhhHHHHHhhhCCCCc
Q psy1898 100 LPNHIRLKIVEMAAA-GVRPCVISRQLRVSHGCVSKILNRYQETGSIRP 147 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~-G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p 147 (230)
++.+.+..|+..+.. +.+..+||+.++++.+||++++++..+.|-+..
T Consensus 4 ~~~~~~~~il~~l~~~~~~~~ei~~~~~i~~~~i~~~l~~L~~~g~i~~ 52 (78)
T cd00090 4 LSDPTRLRILRLLLEGPLTVSELAERLGLSQSTVSRHLKKLEEAGLVES 52 (78)
T ss_pred ccChHHHHHHHHHHHCCcCHHHHHHHHCcCHhHHHHHHHHHHHCCCeEE
Confidence 334566677775544 499999999999999999999999999987643
No 100
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=95.27 E-value=0.029 Score=45.13 Aligned_cols=41 Identities=27% Similarity=0.242 Sum_probs=34.7
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
+|...|.-++..+..|++..+||+.+|+|++||++|+.+.+
T Consensus 126 L~~~~r~i~~l~~~~~~~~~eIA~~lgis~~tv~~~~~ra~ 166 (179)
T PRK11924 126 LPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRAR 166 (179)
T ss_pred CCHHHHHHhhHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 56666666666677899999999999999999999998854
No 101
>PRK01381 Trp operon repressor; Provisional
Probab=95.20 E-value=0.022 Score=43.17 Aligned_cols=35 Identities=26% Similarity=0.321 Sum_probs=30.6
Q ss_pred HHHHHHHHHHHcC-CCHHHHhhhhccccchhhhHHH
Q psy1898 103 HIRLKIVEMAAAG-VRPCVISRQLRVSHGCVSKILN 137 (230)
Q Consensus 103 ~~R~rIV~l~~~G-~s~~~IAr~lgVS~sTV~kwik 137 (230)
..|.+|+.++..| +|.++||..+|||.+||+|--+
T Consensus 42 ~~R~~I~~~L~~g~~sQREIa~~lGvSiaTITRgsn 77 (99)
T PRK01381 42 GTRVRIVEELLRGELSQREIKQELGVGIATITRGSN 77 (99)
T ss_pred HHHHHHHHHHHcCCcCHHHHHHHhCCceeeehhhHH
Confidence 5688889877775 9999999999999999998855
No 102
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=95.20 E-value=0.027 Score=46.37 Aligned_cols=43 Identities=26% Similarity=0.255 Sum_probs=38.6
Q ss_pred cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898 99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE 141 (230)
Q Consensus 99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e 141 (230)
.+|.+.|.-++..+-+|.|..+||..+|||.+||..++.|-+.
T Consensus 127 ~Lp~~~R~~~~l~~~~gls~~EIA~~l~i~~~tVks~l~ra~~ 169 (182)
T COG1595 127 RLPPRQREAFLLRYLEGLSYEEIAEILGISVGTVKSRLHRARK 169 (182)
T ss_pred hCCHHHhHHhhhHhhcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4778889888888899999999999999999999999988653
No 103
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=95.19 E-value=0.037 Score=45.17 Aligned_cols=42 Identities=12% Similarity=0.048 Sum_probs=36.3
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE 141 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e 141 (230)
+|...|.-++..+-+|+|..+||..||+|.+||..++.|.+.
T Consensus 130 L~~~~r~i~~l~~~~g~s~~eIA~~lgis~~tV~~~l~Rar~ 171 (179)
T PRK12514 130 LEKDRAAAVRRAYLEGLSYKELAERHDVPLNTMRTWLRRSLL 171 (179)
T ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHHCCChHHHHHHHHHHHH
Confidence 566777777777789999999999999999999999988653
No 104
>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=95.13 E-value=0.1 Score=46.65 Aligned_cols=89 Identities=18% Similarity=0.177 Sum_probs=54.6
Q ss_pred cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhhhCC-CCcCCCCCCCCCCCCHHHHHHHHHHHHhCCCCC
Q psy1898 99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGS-IRPGVIGGSKPRVATPDVEKRIEEYKKTNPGIF 177 (230)
Q Consensus 99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~-v~p~~~gg~rpr~lt~~~~~~I~~l~~~~P~~t 177 (230)
.+|...|.-++..+.+|+|..+||+.||+|.+||...+.|-+..=. .-...+....+...+.+..+.+..+...--...
T Consensus 142 ~Lp~~~R~v~~L~~~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~~~~~~~~~~~~~~~~v~~~~~a~~~gD 221 (324)
T TIGR02960 142 YLPPRQRAVLLLRDVLGWRAAETAELLGTSTASVNSALQRARATLDEVGPSARDDQLAQPPSPEEQDLLERYIAAFESYD 221 (324)
T ss_pred hCCHHHhhHhhhHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhcccccccccCCCCCHHHHHHHHHHHHHHHcCC
Confidence 3566777777777789999999999999999999999988764321 111111111122334444444554444322334
Q ss_pred HHHHHHHHHH
Q psy1898 178 SWEIRDRLVK 187 (230)
Q Consensus 178 ~~eI~~~L~~ 187 (230)
...+.+.|..
T Consensus 222 ~~~l~~Lla~ 231 (324)
T TIGR02960 222 LDALTALLHE 231 (324)
T ss_pred HHHHHHHhcC
Confidence 5556666654
No 105
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=95.12 E-value=0.038 Score=44.31 Aligned_cols=42 Identities=21% Similarity=0.286 Sum_probs=35.1
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE 141 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e 141 (230)
+|.+.|.-++..+-+|+|..+||+.+|+|.+||..++.|..+
T Consensus 114 L~~~~r~v~~L~~~~g~s~~EIA~~l~is~~tV~~~l~ra~~ 155 (161)
T PRK12528 114 LPPLVKRAFLLAQVDGLGYGEIATELGISLATVKRYLNKAAM 155 (161)
T ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 566666666666779999999999999999999999988653
No 106
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=95.10 E-value=0.037 Score=45.34 Aligned_cols=42 Identities=17% Similarity=0.081 Sum_probs=35.3
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE 141 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e 141 (230)
+|...|.-++..+-+|++..+||..+|+|.+||.+++.|.++
T Consensus 136 L~~~~r~vl~l~~~~~~s~~eIA~~lgis~~~V~~~l~ra~~ 177 (186)
T PRK13919 136 LSPEERRVIEVLYYQGYTHREAAQLLGLPLGTLKTRARRALS 177 (186)
T ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 566666666666789999999999999999999999988653
No 107
>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=95.09 E-value=0.043 Score=45.37 Aligned_cols=47 Identities=11% Similarity=0.025 Sum_probs=42.1
Q ss_pred cCCHHHHHHHHHHHH-cCCCHHHHhhhhccccchhhhHHHHHhhhCCC
Q psy1898 99 PLPNHIRLKIVEMAA-AGVRPCVISRQLRVSHGCVSKILNRYQETGSI 145 (230)
Q Consensus 99 ~~s~~~R~rIV~l~~-~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v 145 (230)
.++.+.|..+-.+|- ++++...+|..+|||.+|+.+|.++-++.|.-
T Consensus 2 Ah~~e~R~~~R~~YV~~~~sLe~aA~~~gVs~~TarrWK~~Ak~~GDD 49 (165)
T PF08822_consen 2 AHPQETRDAVRRAYVFDRLSLEQAAAKCGVSYATARRWKREAKAKGDD 49 (165)
T ss_pred CCcHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHHHHHHcCCc
Confidence 357799999998876 78999999999999999999999999999954
No 108
>cd01108 HTH_CueR Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators. Helix-turn-helix (HTH) transcription regulators CueR and ActP, copper efflux regulators. In Bacillus subtilis, copper induced CueR regulates the copZA operon, preventing copper toxicity. In Rhizobium leguminosarum, ActP controls copper homeostasis; it detects cytoplasmic copper stress and activates transcription in response to increasing copper concentrations. These proteins are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have two conserved cysteines that define a monovalent copper ion binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements
Probab=95.08 E-value=0.22 Score=39.09 Aligned_cols=68 Identities=18% Similarity=0.111 Sum_probs=47.8
Q ss_pred CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK 187 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~ 187 (230)
++..++|+.+|||..|+.-|. +.|.+.|..+..+.-+..+.++.+.+..... .+-..++.+|++.+..
T Consensus 1 m~I~e~a~~~gvs~~tlRyYe----~~GLl~~~~r~~~g~R~Y~~~~~~~l~~I~~lr~~G~sL~eI~~~l~~ 69 (127)
T cd01108 1 MNIGEAAKLTGLSAKMIRYYE----EIGLIPPPSRSDNGYRVYNQRDIEELRFIRRARDLGFSLEEIRELLAL 69 (127)
T ss_pred CCHHHHHHHHCcCHHHHHHHH----HCCCCCCCCcCCCCceecCHHHHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 478899999999999987664 4687765433223467778877666654332 3557899999988754
No 109
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=95.07 E-value=0.036 Score=44.42 Aligned_cols=40 Identities=18% Similarity=0.186 Sum_probs=34.7
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
+|...|.-++..+ +|++..+||..||+|.+||.+++.|-+
T Consensus 113 L~~~~r~il~l~~-~g~s~~eIA~~lgis~~tV~~~i~ra~ 152 (166)
T PRK09639 113 MTERDRTVLLLRF-SGYSYKEIAEALGIKESSVGTTLARAK 152 (166)
T ss_pred CCHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 5667777777777 999999999999999999999998754
No 110
>PRK11050 manganese transport regulator MntR; Provisional
Probab=95.06 E-value=0.17 Score=41.01 Aligned_cols=34 Identities=29% Similarity=0.399 Sum_probs=31.0
Q ss_pred cCCCHHHHhhhhccccchhhhHHHHHhhhCCCCc
Q psy1898 114 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP 147 (230)
Q Consensus 114 ~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p 147 (230)
++.+..+||+.|+|+++||++++++..+.|.+..
T Consensus 50 ~~~t~~eLA~~l~is~stVsr~l~~Le~~GlI~r 83 (152)
T PRK11050 50 GEARQVDIAARLGVSQPTVAKMLKRLARDGLVEM 83 (152)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence 3589999999999999999999999999997754
No 111
>cd04788 HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR. Helix-turn-helix (HTH) transcription regulators NolA and AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp. NC92, NolA is required for efficient nodulation of host plants. In Xanthomonas albilineans, AlbR regulates the expression of the pathotoxin, albicidin. These proteins are putatively comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=95.05 E-value=0.1 Score=38.96 Aligned_cols=68 Identities=15% Similarity=0.094 Sum_probs=46.6
Q ss_pred CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK 187 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~ 187 (230)
++..++|+.+|||..|+.-|.+ .|.+.|..+..+.-+..++++...|..... .+-..+..+|++.+..
T Consensus 1 m~i~eva~~~gvs~~tlR~ye~----~Gll~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~~l~eI~~~l~~ 69 (96)
T cd04788 1 WKIGELARRTGLSVRTLHHYDH----IGLLSPSQRTEGGHRLYDRADIRRLHQIIALRRLGFSLREIGRALDG 69 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCccCCCCceeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHhC
Confidence 4688999999999999988854 687766433223456777777655543322 2346889999887753
No 112
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=95.05 E-value=0.019 Score=52.22 Aligned_cols=41 Identities=22% Similarity=0.311 Sum_probs=35.7
Q ss_pred HHHHHHH-HHcCCCHHHHhhhhccccchhhhHHHHHhhhCCC
Q psy1898 105 RLKIVEM-AAAGVRPCVISRQLRVSHGCVSKILNRYQETGSI 145 (230)
Q Consensus 105 R~rIV~l-~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v 145 (230)
-.++-.+ |.+|++..|||++||||+++|+|.+++.++.|.+
T Consensus 18 ~~~vA~lYY~~g~tQ~eIA~~lgiSR~~VsRlL~~Ar~~GiV 59 (318)
T PRK15418 18 VARIAWFYYHDGLTQSEIGERLGLTRLKVSRLLEKGRQSGII 59 (318)
T ss_pred HHHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHcCcE
Confidence 4455554 4689999999999999999999999999999976
No 113
>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=95.03 E-value=0.026 Score=44.39 Aligned_cols=36 Identities=25% Similarity=0.265 Sum_probs=30.7
Q ss_pred cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhh
Q psy1898 99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSK 134 (230)
Q Consensus 99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~k 134 (230)
.+|.+.|.-++..+-+|+|..+||..+|+|.+||++
T Consensus 107 ~Lp~~~r~v~~l~~~~~~s~~EIA~~l~is~~tV~~ 142 (142)
T TIGR03209 107 ILPNKQKKIIYMKFFEDMKEIDIAKKLHISRQSVYK 142 (142)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHhhcC
Confidence 366677777777778999999999999999999975
No 114
>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=95.03 E-value=0.039 Score=45.03 Aligned_cols=42 Identities=17% Similarity=-0.021 Sum_probs=36.2
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE 141 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e 141 (230)
+|...|.-++..+-+|+|..+||..+|+|.+||...+.|-+.
T Consensus 135 Lp~~~r~v~~l~~~~g~s~~EIA~~lgis~~tVk~~l~Rar~ 176 (183)
T TIGR02999 135 VDPRQAEVVELRFFAGLTVEEIAELLGVSVRTVERDWRFARA 176 (183)
T ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 677777777777789999999999999999999999988653
No 115
>cd01111 HTH_MerD Helix-Turn-Helix DNA binding domain of the MerD transcription regulator. Helix-turn-helix (HTH) transcription regulator MerD. The putative secondary regulator of mercury resistance (mer) operons, MerD, has been shown to down-regulate the expression of this operon in gram-negative bacteria. It binds to the same operator DNA as MerR that activates transcription of the operon in the presence of mercury ions. The MerD protein shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily, which promote transcription 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 conserved and contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules such as metal ions, drugs,
Probab=95.00 E-value=0.11 Score=39.69 Aligned_cols=68 Identities=15% Similarity=-0.001 Sum_probs=49.8
Q ss_pred CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK 187 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~ 187 (230)
.+..++|+.+|||..|+.-|.+ .|.+.|..+..+.-+..++++...+..... ..-..+..+|++.+..
T Consensus 1 y~Ige~A~~~gvs~~tlR~ye~----~GLl~p~~r~~~g~R~Y~~~~l~~l~~I~~lr~~G~~l~~I~~~l~~ 69 (107)
T cd01111 1 YSISQLALDAGVSVHIVRDYLL----RGLLHPVARTEGGYGLFDDCALQRLRFVRAAFEAGIGLDELARLCRA 69 (107)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 3678999999999999877754 588876544333467778887777765443 4457889999888865
No 116
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=94.99 E-value=0.073 Score=51.10 Aligned_cols=95 Identities=11% Similarity=0.167 Sum_probs=68.7
Q ss_pred CCHHHHhhhhccccchhhhHHHH-HhhhC--CC------CcCCCCCCCCCCCCHHHHHHHHHHHHh-CCC--CCHHHHHH
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNR-YQETG--SI------RPGVIGGSKPRVATPDVEKRIEEYKKT-NPG--IFSWEIRD 183 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikR-y~e~G--~v------~p~~~gg~rpr~lt~~~~~~I~~l~~~-~P~--~t~~eI~~ 183 (230)
++.++||..+|++.|||+|..+. |..|. .+ ............-+..++..|++++.. +|. .+=.+|.+
T Consensus 370 LtlkdVAe~lglHeSTVSRa~~~KY~~tp~GifeLK~FFs~~v~~~~g~~~Ss~~Ik~~Ik~lI~~Ed~~kPLSD~~I~~ 449 (481)
T PRK12469 370 LVLRDVAEELGLHESTISRATGNKYMATPRGTFEFKHFFPRKLEAAGGGECSAAAVRALIKEMIAAEQAGDPLSDVALAE 449 (481)
T ss_pred CcHHHHHHHhCCCcchhhHHhcCceeecCCceEeHHHhhccccCCCCCccccHHHHHHHHHHHHHhcCCCCCCCHHHHHH
Confidence 78899999999999999998764 55553 21 111110000112355688889998875 443 66778999
Q ss_pred HHHHhhCCCCCCCCCCHhHHHHHHHcCCCCCCC
Q psy1898 184 RLVKQDGICDKNSAPSVSSISRLLRGGRRDDCD 216 (230)
Q Consensus 184 ~L~~~~Gi~~~~~~vS~sTV~R~Lr~~g~~~~~ 216 (230)
.|.+ .||. ||+.||-.+=...||.++.
T Consensus 450 ~L~~-~GI~-----IARRTVAKYRe~L~IpsS~ 476 (481)
T PRK12469 450 MLAG-RGVL-----IARRTVAKYREAMKIPPAE 476 (481)
T ss_pred HHHh-cCCC-----eechhHHHHHHHcCCCChh
Confidence 9988 7995 9999999999999998875
No 117
>PHA00738 putative HTH transcription regulator
Probab=94.97 E-value=0.033 Score=42.84 Aligned_cols=50 Identities=30% Similarity=0.317 Sum_probs=43.6
Q ss_pred HHHHHHHHHHHHcC--CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCC
Q psy1898 102 NHIRLKIVEMAAAG--VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIG 151 (230)
Q Consensus 102 ~~~R~rIV~l~~~G--~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~g 151 (230)
...|.+|+.++..+ .+.++|+..|++|++||++-++--++.|.+...+.|
T Consensus 11 dptRr~IL~lL~~~e~~~V~eLae~l~lSQptVS~HLKvLreAGLV~srK~G 62 (108)
T PHA00738 11 KILRRKILELIAENYILSASLISHTLLLSYTTVLRHLKILNEQGYIELYKEG 62 (108)
T ss_pred CHHHHHHHHHHHHcCCccHHHHHHhhCCCHHHHHHHHHHHHHCCceEEEEEC
Confidence 47899999977764 899999999999999999999999999988665543
No 118
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=94.94 E-value=0.052 Score=45.58 Aligned_cols=48 Identities=13% Similarity=0.167 Sum_probs=39.8
Q ss_pred cccCCCcCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898 93 VFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE 141 (230)
Q Consensus 93 ~~~~g~~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e 141 (230)
+|.+...+|..++ +|+.++.+|++.++||+.|++|.+||...+.+-.+
T Consensus 127 ~~~~~~~LSpREr-EVLrLLAqGkTnKEIAe~L~IS~rTVkth~srImk 174 (198)
T PRK15201 127 HYCTTRHFSVTER-HLLKLIASGYHLSETAALLSLSEEQTKSLRRSIMR 174 (198)
T ss_pred cccCCCCCCHHHH-HHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 3455677886655 78889999999999999999999999998887543
No 119
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=94.94 E-value=0.041 Score=45.75 Aligned_cols=36 Identities=25% Similarity=0.310 Sum_probs=29.7
Q ss_pred HHHHHH-HHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 105 RLKIVE-MAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 105 R~rIV~-l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
..++|. .+-+|+|..+||+.+|||..||++.++..+
T Consensus 140 ~~~~v~l~~~~Gls~~EIA~~lgiS~~tV~r~l~~aR 176 (185)
T PF07638_consen 140 QRRVVELRFFEGLSVEEIAERLGISERTVRRRLRRAR 176 (185)
T ss_pred HHHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 344554 556999999999999999999999988755
No 120
>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=94.93 E-value=0.043 Score=42.18 Aligned_cols=41 Identities=29% Similarity=0.310 Sum_probs=33.2
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
+|...+.-+...+..|.+..+||+.+|||++||++++++-.
T Consensus 111 L~~~~~~ii~~~~~~g~s~~eIA~~l~~s~~~v~~~~~~~~ 151 (158)
T TIGR02937 111 LPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRAR 151 (158)
T ss_pred CCHHHHHHHhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 45566655555557899999999999999999999998854
No 121
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=94.90 E-value=0.041 Score=44.33 Aligned_cols=43 Identities=14% Similarity=-0.003 Sum_probs=36.2
Q ss_pred cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898 99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE 141 (230)
Q Consensus 99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e 141 (230)
.+|.+.|.-++..+-+|++..+||..||+|.+||+.++.|-++
T Consensus 108 ~L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~tv~~~l~Rar~ 150 (165)
T PRK09644 108 TLPVIEAQAILLCDVHELTYEEAASVLDLKLNTYKSHLFRGRK 150 (165)
T ss_pred hCCHHHHHHHHhHHHhcCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3566777766667789999999999999999999999988653
No 122
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=94.89 E-value=0.046 Score=44.12 Aligned_cols=42 Identities=17% Similarity=0.172 Sum_probs=35.5
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE 141 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e 141 (230)
+|...|.-++..+-+|+|..+||+.+|||.+||..++.|-+.
T Consensus 113 L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~tV~~~l~Rar~ 154 (164)
T PRK12547 113 LSADQREAIILIGASGFSYEDAAAICGCAVGTIKSRVSRARN 154 (164)
T ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 566777666666789999999999999999999999988653
No 123
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=94.86 E-value=0.055 Score=37.99 Aligned_cols=46 Identities=15% Similarity=0.312 Sum_probs=39.3
Q ss_pred HHHHHHHHHHHHc--C--CCHHHHhhhhccccchhhhHHHHHhhhCCCCc
Q psy1898 102 NHIRLKIVEMAAA--G--VRPCVISRQLRVSHGCVSKILNRYQETGSIRP 147 (230)
Q Consensus 102 ~~~R~rIV~l~~~--G--~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p 147 (230)
...+.+|+.++.. + .+..+||+.+|+++.+|++.+.+..+.|.+..
T Consensus 5 ~~~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~~ 54 (68)
T smart00550 5 DSLEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKKGKVCK 54 (68)
T ss_pred hHHHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence 3567788886654 4 89999999999999999999999999998853
No 124
>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=94.84 E-value=0.051 Score=42.79 Aligned_cols=41 Identities=20% Similarity=0.171 Sum_probs=33.2
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
++...|.-+...+.+|.+..+||+.+|+|.+||+.++.|-+
T Consensus 114 L~~~~r~il~l~~~~~~~~~eIA~~lgis~~tv~~~~~ra~ 154 (161)
T TIGR02985 114 LPEQCRKIFILSRFEGKSYKEIAEELGISVKTVEYHISKAL 154 (161)
T ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 45555555555577899999999999999999999998754
No 125
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=94.83 E-value=0.046 Score=45.35 Aligned_cols=41 Identities=15% Similarity=0.138 Sum_probs=34.9
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
+|...|.-++..+-+|+|..+||..+|+|.+||..++.|.+
T Consensus 135 Lp~~~R~v~~L~~~~g~s~~EIA~~lgis~~tVk~~l~RAr 175 (189)
T PRK12530 135 LPAQQARVFMMREYLELSSEQICQECDISTSNLHVLLYRAR 175 (189)
T ss_pred CCHHHHHHHhHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 56677766666777899999999999999999999988755
No 126
>PF13276 HTH_21: HTH-like domain
Probab=94.77 E-value=0.13 Score=34.83 Aligned_cols=54 Identities=24% Similarity=0.239 Sum_probs=42.7
Q ss_pred HHHHHHHHHHHHhC-CCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcCCCCCCCCC
Q psy1898 160 PDVEKRIEEYKKTN-PGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGGRRDDCDRK 218 (230)
Q Consensus 160 ~~~~~~I~~l~~~~-P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~g~~~~~~~ 218 (230)
.+..+.|.+...++ +...+..|...|..+.|+. +|..+|+|+++..||....++
T Consensus 4 ~~l~~~I~~i~~~~~~~yG~rri~~~L~~~~~~~-----v~~krV~RlM~~~gL~~~~rr 58 (60)
T PF13276_consen 4 EALRELIKEIFKESKPTYGYRRIWAELRREGGIR-----VSRKRVRRLMREMGLRSKRRR 58 (60)
T ss_pred HHHHHHHHHHHHHcCCCeehhHHHHHHhccCccc-----ccHHHHHHHHHHcCCcccCCC
Confidence 44566677777666 6788999999998854674 899999999999999876544
No 127
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=94.77 E-value=0.053 Score=43.38 Aligned_cols=41 Identities=24% Similarity=0.225 Sum_probs=33.5
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
+|...|.-++..+-+|+|..+||+.+|+|.+||...+.|-.
T Consensus 110 L~~~~r~v~~l~~~~~~s~~EIA~~lgis~~tV~~~l~ra~ 150 (163)
T PRK07037 110 LPARTRYAFEMYRLHGETQKDIARELGVSPTLVNFMIRDAL 150 (163)
T ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 45566665555677899999999999999999999987654
No 128
>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=94.77 E-value=0.052 Score=43.55 Aligned_cols=43 Identities=16% Similarity=0.085 Sum_probs=35.8
Q ss_pred cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898 99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE 141 (230)
Q Consensus 99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e 141 (230)
.+|...|.-++..+-+|+|..+||+.||||.+||...+.|-++
T Consensus 122 ~L~~~~r~vl~l~~~~g~s~~eIA~~l~is~~tv~~~l~ra~~ 164 (170)
T TIGR02952 122 ILTPKQQHVIALRFGQNLPIAEVARILGKTEGAVKILQFRAIK 164 (170)
T ss_pred hCCHHHHHHHHHHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4666777666666789999999999999999999999987653
No 129
>cd04783 HTH_MerR1 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator. Helix-turn-helix (HTH) transcription regulator MerR1. MerR1 transcription regulators, such as Tn21 MerR and Tn501 MerR, mediate response to mercury exposure in eubacteria. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines that define a mercury binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=94.76 E-value=0.15 Score=39.97 Aligned_cols=68 Identities=16% Similarity=0.105 Sum_probs=46.5
Q ss_pred CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK 187 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~ 187 (230)
++..++|+.+|||..|+ +.|.+.|.+.|..+..+.-+..++++...+..... ..-..+..+|++.+..
T Consensus 1 m~I~e~a~~~gvs~~tl----R~Ye~~GLl~~~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~ 69 (126)
T cd04783 1 LTIGELAKAAGVNVETI----RYYQRRGLLPEPPRPEGGYRRYPEETVTRLRFIKRAQELGFTLDEIAELLEL 69 (126)
T ss_pred CCHHHHHHHHCcCHHHH----HHHHHCCCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHhc
Confidence 46889999999999999 44566788864333223467778877666543322 3446888888887754
No 130
>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=94.76 E-value=0.048 Score=43.62 Aligned_cols=42 Identities=24% Similarity=0.267 Sum_probs=35.0
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE 141 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e 141 (230)
+|...|.-++..+-+|++..+||..+|+|.+||..++.|-++
T Consensus 111 L~~~~r~i~~l~~~~g~s~~eIA~~lgis~~tV~~~l~ra~~ 152 (162)
T TIGR02983 111 LPARQRAVVVLRYYEDLSEAQVAEALGISVGTVKSRLSRALA 152 (162)
T ss_pred CCHHHHHHhhhHHHhcCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 455666666666788999999999999999999999988653
No 131
>PF12728 HTH_17: Helix-turn-helix domain
Probab=94.75 E-value=0.017 Score=37.74 Aligned_cols=23 Identities=13% Similarity=0.147 Sum_probs=20.8
Q ss_pred CCHHHHhhhhccccchhhhHHHH
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNR 138 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikR 138 (230)
+|..|+|+.|+||++||++|+++
T Consensus 2 lt~~e~a~~l~is~~tv~~~~~~ 24 (51)
T PF12728_consen 2 LTVKEAAELLGISRSTVYRWIRQ 24 (51)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHc
Confidence 47899999999999999999963
No 132
>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=94.75 E-value=0.071 Score=44.45 Aligned_cols=56 Identities=18% Similarity=0.146 Sum_probs=48.4
Q ss_pred cCCcccCCCcCCHHHHHHHHHHHH-cCCCHHHHhhhhccccchhhhHHHHHhhhCCC
Q psy1898 90 LGGVFINGRPLPNHIRLKIVEMAA-AGVRPCVISRQLRVSHGCVSKILNRYQETGSI 145 (230)
Q Consensus 90 l~~~~~~g~~~s~~~R~rIV~l~~-~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v 145 (230)
+.++|.+..++|.+.|..|+..+. .|+|.+++|..|||+...|.-+++-+.-.+..
T Consensus 7 ~Np~f~~~~~lse~~r~~Iy~~~~~~~~sv~~vS~~ygi~~~RV~AIvrLkeiE~~~ 63 (172)
T PF12298_consen 7 LNPSFRSNPVLSEELREQIYEDVMQDGKSVREVSQKYGIKIQRVEAIVRLKEIEKRW 63 (172)
T ss_pred CCCCCCCCCcCCHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 456778899999999999999885 57999999999999999999999887755544
No 133
>cd01279 HTH_HspR-like Helix-Turn-Helix DNA binding domain of HspR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator HspR and related proteins, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription 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 conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=94.75 E-value=0.1 Score=39.26 Aligned_cols=67 Identities=10% Similarity=0.070 Sum_probs=48.0
Q ss_pred CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH--hCCCCCHHHHHHHHHH
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK--TNPGIFSWEIRDRLVK 187 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~--~~P~~t~~eI~~~L~~ 187 (230)
++..++|+.+|||.+|+..|.+ .|.+.|.... +..+..+..+...+..... ++-.++..+|...|.-
T Consensus 2 ~~i~eva~~~gVs~~tLR~ye~----~Gli~p~r~~-~g~R~Ys~~dv~~l~~I~~L~~~~G~~l~~i~~~l~l 70 (98)
T cd01279 2 YPISVAAELLGIHPQTLRVYDR----LGLVSPARTN-GGGRRYSNNDLELLRQVQRLSQDEGFNLAGIKRIIEL 70 (98)
T ss_pred cCHHHHHHHHCcCHHHHHHHHH----CCCCCCCcCC-CCCeeECHHHHHHHHHHHHHHHHCCCCHHHHHHHHHh
Confidence 4688999999999999998854 6777663222 2456678887777765442 3367888888877754
No 134
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=94.75 E-value=0.028 Score=49.36 Aligned_cols=37 Identities=19% Similarity=0.120 Sum_probs=32.2
Q ss_pred HHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 104 IRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 104 ~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
-|..+-.++-+|+...+||..||||+.||.+|.+|+.
T Consensus 8 ~r~~Akk~yl~gmk~~dIAeklGvspntiksWKrr~g 44 (279)
T COG5484 8 KRIIAKKDYLKGMKLKDIAEKLGVSPNTIKSWKRRDG 44 (279)
T ss_pred hHHHHHHHHHhhccHHHHHHHhCCChHHHHHHHHhcC
Confidence 3555566899999999999999999999999999863
No 135
>TIGR02044 CueR Cu(I)-responsive transcriptional regulator. This model represents the copper-, silver- and gold- (I) responsive transcriptional activator of the gamma proteobacterial copper efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X7-Cys. This family also lacks a conserved cysteine at the N-terminal end of the dimerization helix which is required for the binding of divalent metals such as zinc; here it is replaced by a serine residue.
Probab=94.69 E-value=0.31 Score=38.16 Aligned_cols=68 Identities=15% Similarity=0.109 Sum_probs=47.7
Q ss_pred CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK 187 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~ 187 (230)
++..++|+.+|||..|+.-| .+.|.+.|..+..+.-+..+.++...+..... ..-.+++.+|++.+..
T Consensus 1 m~I~e~a~~~gvs~~tlRyY----e~~GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~ 69 (127)
T TIGR02044 1 MNIGQVAKLTGLSSKMIRYY----EEKGLIPPPLRSEGGYRTYTQQHLDELRLISRARQVGFSLEECKELLNL 69 (127)
T ss_pred CCHHHHHHHHCcCHHHHHHH----HHCCCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHCCCCHHHHHHHHHh
Confidence 47889999999999998755 45788866444223467778877666653332 3457889999888753
No 136
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=94.68 E-value=0.049 Score=44.70 Aligned_cols=42 Identities=14% Similarity=0.230 Sum_probs=35.4
Q ss_pred cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
.+|.+.|.-++..+-+|+|..+||+.+|||.+||...+.|-.
T Consensus 127 ~Lp~~~R~v~~L~~~~g~s~~EIA~~lgis~~tVk~~l~rAl 168 (178)
T PRK12529 127 TLRPRVKQAFLMATLDGMKQKDIAQALDIALPTVKKYIHQAY 168 (178)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 367777777777778999999999999999999999987643
No 137
>PRK04280 arginine repressor; Provisional
Probab=94.67 E-value=0.078 Score=43.08 Aligned_cols=45 Identities=22% Similarity=0.178 Sum_probs=41.3
Q ss_pred HHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcCCCC
Q psy1898 163 EKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGGRRD 213 (230)
Q Consensus 163 ~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~g~~ 213 (230)
.+.|.+++.+++-.+..|+.+.|.+ .|+. ++.+||+|-|++.++.
T Consensus 6 ~~~I~~iI~~~~I~tQeeL~~~L~~-~Gi~-----vTQATiSRDikeL~lv 50 (148)
T PRK04280 6 HIKIREIITNNEIETQDELVDRLRE-EGFN-----VTQATVSRDIKELHLV 50 (148)
T ss_pred HHHHHHHHHhCCCCCHHHHHHHHHH-cCCC-----eehHHHHHHHHHcCCE
Confidence 5678899999999999999999988 8995 8999999999999976
No 138
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=94.67 E-value=0.06 Score=43.64 Aligned_cols=41 Identities=17% Similarity=0.165 Sum_probs=35.3
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
+|...|.-++..+-+|+|..+||..||+|.+||..++.+-.
T Consensus 119 L~~~~r~v~~L~~~eg~s~~EIA~~l~is~~tV~~~l~ra~ 159 (168)
T PRK12525 119 LSGKARAAFLMSQLEGLTYVEIGERLGVSLSRIHQYMVEAF 159 (168)
T ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 66677776666678999999999999999999999998754
No 139
>cd04768 HTH_BmrR-like Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators. Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=94.67 E-value=0.17 Score=37.81 Aligned_cols=68 Identities=15% Similarity=0.055 Sum_probs=47.6
Q ss_pred CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK 187 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~ 187 (230)
.+..++|+.+|||..|+.-|.+ .|.+.|..+..+.-+..+.++...|..... .+-.++..+|++.+..
T Consensus 1 ~ti~eva~~~gvs~~tLRyye~----~Gll~p~~~~~~gyR~Y~~~~l~~l~~I~~lr~~G~~l~~I~~~l~~ 69 (96)
T cd04768 1 LTIGEFAKLAGVSIRTLRHYDD----IGLFKPAKIAENGYRYYSYAQLYQLQFILFLRELGFSLAEIKELLDT 69 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCccCCCCeeeCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhc
Confidence 3678999999999999987765 588877544223456777776666543332 3446889999887753
No 140
>cd04770 HTH_HMRTR Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators. Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper), CadR (cadmium), PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located 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=94.66 E-value=0.19 Score=39.00 Aligned_cols=68 Identities=18% Similarity=0.179 Sum_probs=48.3
Q ss_pred CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK 187 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~ 187 (230)
++..++|+.+|||..|+.- |.+.|.+.|..+..+.-+..++++...+..... .+-+.+..+|++.+..
T Consensus 1 ~~I~eva~~~gvs~~tLRy----Ye~~GLl~p~~r~~~gyR~Y~~~~i~~l~~I~~lr~~G~sl~eI~~~l~~ 69 (123)
T cd04770 1 MKIGELAKAAGVSPDTIRY----YERIGLLPPPQRSENGYRLYGEADLARLRFIRRAQALGFSLAEIRELLSL 69 (123)
T ss_pred CCHHHHHHHHCcCHHHHHH----HHHCCCCCCCCCCCCCCccCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHh
Confidence 4788999999999999854 566788876444333467778877666543322 4557889999888764
No 141
>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=94.65 E-value=0.03 Score=42.69 Aligned_cols=44 Identities=18% Similarity=0.192 Sum_probs=29.5
Q ss_pred CCcCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 97 GRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 97 g~~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
|.-++...|.-+-..+.+.+|..+||..++||+..|+.|++|-.
T Consensus 15 g~LLT~kQ~~~l~lyy~eDlSlsEIAe~~~iSRqaV~d~ikr~~ 58 (101)
T PF04297_consen 15 GELLTEKQREILELYYEEDLSLSEIAEELGISRQAVYDSIKRAE 58 (101)
T ss_dssp GGGS-HHHHHHHHHHCTS---HHHHHHHCTS-HHHHHHHHHHHH
T ss_pred HHHCCHHHHHHHHHHHccCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 34455555544444556789999999999999999999999854
No 142
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=94.63 E-value=0.18 Score=45.58 Aligned_cols=109 Identities=17% Similarity=0.134 Sum_probs=61.5
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhhhCCC-CcCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCH
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSI-RPGVIGGSKPRVATPDVEKRIEEYKKTNPGIFS 178 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v-~p~~~gg~rpr~lt~~~~~~I~~l~~~~P~~t~ 178 (230)
+|...|.-++..+-+|+|..+||..||+|.+||...+.|-++.=.. .+.-. ...+.....+..+.+.++...--....
T Consensus 154 Lp~~~R~v~~L~~~~g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~~~~~~-~~~~~~~~~~~~~~v~~~~~A~~~gD~ 232 (339)
T PRK08241 154 LPPRQRAVLILRDVLGWSAAEVAELLDTSVAAVNSALQRARATLAERGPSAA-DTLREPDDPEERALLARYVAAFEAYDV 232 (339)
T ss_pred CCHHHhhhhhhHHhhCCCHHHHHHHhCCCHHHHHHHHHHHHHHHhhcCCCcc-cccCCCCChHHHHHHHHHHHHHhcCCH
Confidence 5667777666677899999999999999999999999887643211 11101 112333334444444444443222334
Q ss_pred HHHHHHHHHhhCCC----CCCCCCCHhHHHHHHHcC
Q psy1898 179 WEIRDRLVKQDGIC----DKNSAPSVSSISRLLRGG 210 (230)
Q Consensus 179 ~eI~~~L~~~~Gi~----~~~~~vS~sTV~R~Lr~~ 210 (230)
..+.+.|.. ..+. ......-..-|..++...
T Consensus 233 ~~l~~lla~-Dv~~~~p~~~~~~~G~~~v~~~~~~~ 267 (339)
T PRK08241 233 DALVALLTE-DATWSMPPFPLWYRGRDAIAAFLAGQ 267 (339)
T ss_pred HHHHHHhcC-CEEEEcCCCCCcccCHHHHHHHHHhh
Confidence 555565544 2211 001133455566666663
No 143
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=94.61 E-value=0.044 Score=45.27 Aligned_cols=41 Identities=20% Similarity=0.219 Sum_probs=33.4
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
+|.+.|.-++..+-+|++.++||..+|+|.+||..++.|.+
T Consensus 142 L~~~~~~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Ra~ 182 (194)
T PRK12519 142 LPESQRQVLELAYYEGLSQSEIAKRLGIPLGTVKARARQGL 182 (194)
T ss_pred CCHHHhhhhhhhhhcCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 45555555555567899999999999999999999998755
No 144
>cd04774 HTH_YfmP Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator. Helix-turn-helix (HTH) transcription regulator, YfmP, and related proteins; N-terminal domain. YfmP regulates the multidrug efflux protein, YfmO, and indirectly regulates the expression of the Bacillus subtilis copZA operon encoding a metallochaperone, CopZ, and a CPx-type ATPase efflux protein, CopA. 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 winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=94.61 E-value=0.11 Score=38.91 Aligned_cols=67 Identities=15% Similarity=0.179 Sum_probs=48.3
Q ss_pred CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH--hCCCCCHHHHHHHHHH
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK--TNPGIFSWEIRDRLVK 187 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~--~~P~~t~~eI~~~L~~ 187 (230)
++..++|+.+|||.+|+..|.+ .|.+.|... .+..+..++.+...+..... +.-..+..+++..+..
T Consensus 1 ~~I~e~a~~~gvs~~tLR~ye~----~Gll~p~r~-~~g~R~Y~~~dv~~l~~I~~L~~~~G~~l~ei~~~l~~ 69 (96)
T cd04774 1 YKVDEVAKRLGLTKRTLKYYEE----IGLVSPERS-EGRYRLYSEEDLKRLERILRLREVLGFSLQEVTHFLER 69 (96)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCcC-CCCCEEECHHHHHHHHHHHHHHHHcCCCHHHHHHHHhc
Confidence 3678999999999999999954 477765433 23567788887776654432 3257888888887754
No 145
>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=94.61 E-value=0.028 Score=37.16 Aligned_cols=41 Identities=27% Similarity=0.417 Sum_probs=33.3
Q ss_pred HHHHHHHHc---CCCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898 106 LKIVEMAAA---GVRPCVISRQLRVSHGCVSKILNRYQETGSIR 146 (230)
Q Consensus 106 ~rIV~l~~~---G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~ 146 (230)
.+|++.+.+ +++..+||+.+|++++||++.++...+.|-+.
T Consensus 6 l~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~~~g~v~ 49 (52)
T PF09339_consen 6 LRILEALAESGGPLTLSEIARALGLPKSTVHRLLQTLVEEGYVE 49 (52)
T ss_dssp HHHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCcCee
Confidence 456665543 37899999999999999999999999998764
No 146
>cd04775 HTH_Cfa-like Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulators; the HTH domain of Cfa, a cyclopropane fatty acid synthase, and other related methyltransferases, as well as, the N-terminal domain of a conserved, uncharacterized ~172 a.a. protein. Based on sequence similarity of the N-terminal domain, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of 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 dissimil
Probab=94.60 E-value=0.15 Score=38.49 Aligned_cols=66 Identities=20% Similarity=0.112 Sum_probs=44.4
Q ss_pred CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHH
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLV 186 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~ 186 (230)
.+..++|+.+|||++|+.-|.+ .|.+.|. +..+.-+..++++...|..... .+...+..+|+..+.
T Consensus 2 ~~i~eva~~~gvs~~tLR~ye~----~Gll~~~-r~~~g~R~Y~~~dl~~l~~I~~l~~~G~~l~ei~~~~~ 68 (102)
T cd04775 2 YTIGQMSRKFGVSRSTLLYYES----IGLIPSA-RSEANYRLYSEADLSRLEKIVFLQAGGLPLEEIAGCLA 68 (102)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH----CCCCCCC-CCCCCCeeeCHHHHHHHHHHHHHHHCCCCHHHHHHHHc
Confidence 4789999999999999966654 5877433 3222346677776665543332 345788999887664
No 147
>COG1438 ArgR Arginine repressor [Transcription]
Probab=94.60 E-value=0.087 Score=42.93 Aligned_cols=47 Identities=19% Similarity=0.085 Sum_probs=42.4
Q ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcCCCC
Q psy1898 161 DVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGGRRD 213 (230)
Q Consensus 161 ~~~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~g~~ 213 (230)
+-.+.|++++.++.-.|..||.+.|++ .|+. ++.+||+|-|++.|+.
T Consensus 6 ~R~~~Ik~iI~~~~i~TQ~Elv~~L~~-~Gi~-----vTQaTvSRDlkelglv 52 (150)
T COG1438 6 ERLELIKEIITEEKISTQEELVELLQE-EGIE-----VTQATVSRDLKELGLV 52 (150)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHHH-cCCe-----EehHHHHHHHHHcCCE
Confidence 346788999999999999999999988 9995 8999999999999986
No 148
>cd04780 HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located 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=94.58 E-value=0.15 Score=38.23 Aligned_cols=68 Identities=16% Similarity=0.155 Sum_probs=48.6
Q ss_pred CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH--hCCCCCHHHHHHHHHH
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK--TNPGIFSWEIRDRLVK 187 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~--~~P~~t~~eI~~~L~~ 187 (230)
++..++|+.+|||..|+.-|.+ .|.+.|..+...--+..++++.+.|..... ++-..+..+|++.+..
T Consensus 1 m~I~eva~~~gvs~~tlR~Ye~----~GLl~p~~r~~~g~r~Y~~~dv~~l~~I~~L~~~~G~~l~~I~~~l~~ 70 (95)
T cd04780 1 MRMSELSKRSGVSVATIKYYLR----EGLLPEGRRLAPNQAEYSEAHVERLRLIRALQQEGGLPISQIKEVLDA 70 (95)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCcCCCCCCeecCHHHHHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 4678999999999999877765 687766433222346788888777765443 3357889999988864
No 149
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=94.56 E-value=0.065 Score=43.36 Aligned_cols=41 Identities=22% Similarity=0.212 Sum_probs=34.3
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
+|...|.-++..+-+|+|..+||+.+|+|.+||...+.|-+
T Consensus 119 L~~~~r~vl~L~~~~g~s~~EIA~~lgis~~tV~~~l~ra~ 159 (173)
T PRK09645 119 LSPEHRAVLVRSYYRGWSTAQIAADLGIPEGTVKSRLHYAL 159 (173)
T ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 56677776666678999999999999999999998887754
No 150
>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=94.53 E-value=0.19 Score=44.53 Aligned_cols=84 Identities=11% Similarity=-0.001 Sum_probs=55.6
Q ss_pred cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCH
Q psy1898 99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPGIFS 178 (230)
Q Consensus 99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~~P~~t~ 178 (230)
.+|...|.-++.....|+|..+||+.+|+|.+||...+.|-+..= .... .++...+++..+.+..++..--.-..
T Consensus 108 ~L~~~~R~v~~L~~~~g~s~~EIA~~lg~s~~tVr~~l~RAr~~L--r~~~---~~~~~~~~~~~~~~~~f~~a~~~gD~ 182 (281)
T TIGR02957 108 RLSPLERAVFVLREVFDYPYEEIASIVGKSEANCRQLVSRARRHL--DARR---PRFEVSREESRQLLERFVEAAQTGDL 182 (281)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH--HhhC---CCCCCChHHHHHHHHHHHHHHHhCCH
Confidence 356677777777778999999999999999999999999877542 1111 01222234455555555544333456
Q ss_pred HHHHHHHHH
Q psy1898 179 WEIRDRLVK 187 (230)
Q Consensus 179 ~eI~~~L~~ 187 (230)
..+.+.|..
T Consensus 183 ~~l~~lL~~ 191 (281)
T TIGR02957 183 DGLLELLAE 191 (281)
T ss_pred HHHHHHHhh
Confidence 667777765
No 151
>PF12116 SpoIIID: Stage III sporulation protein D; InterPro: IPR014208 Members of this entry represent the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if, and only if, the species is capable of endospore formation. In Bacillus subtilis SpoIIID is a DNA binding protein that is involved in gene repression as well as activation [].; PDB: 2L0K_A.
Probab=94.51 E-value=0.034 Score=40.49 Aligned_cols=26 Identities=15% Similarity=0.112 Sum_probs=19.2
Q ss_pred HHHcCCCHHHHhhhhccccchhhhHH
Q psy1898 111 MAAAGVRPCVISRQLRVSHGCVSKIL 136 (230)
Q Consensus 111 l~~~G~s~~~IAr~lgVS~sTV~kwi 136 (230)
.++...+.+++|+.||||.|||++=+
T Consensus 15 Ii~~~aTVR~~Ak~FGvSKSTVHkDv 40 (82)
T PF12116_consen 15 IIETKATVRQAAKVFGVSKSTVHKDV 40 (82)
T ss_dssp HHHH---HHHHHHHHTS-HHHHHHHH
T ss_pred HHHcccHHHHHHHHHCCcHHHHHHHH
Confidence 44668999999999999999999876
No 152
>TIGR02047 CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional regulator. This model represents the cadmium(II) and/or lead(II) responsive transcriptional activator of the proteobacterial metal efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(6-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=94.51 E-value=0.41 Score=37.61 Aligned_cols=68 Identities=18% Similarity=0.113 Sum_probs=46.2
Q ss_pred CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK 187 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~ 187 (230)
++..++|+.+|||..|+.-|.+ .|.+.|..+..+.-+..+.++...+..... ..-.+++.+|++.|..
T Consensus 1 m~I~e~a~~~gvs~~tlR~Ye~----~GLl~~~~r~~~gyR~Y~~~~l~~l~~I~~lr~lG~sL~eI~~~l~~ 69 (127)
T TIGR02047 1 MKIGELAQKTGVSVETIRFYEK----QGLLPPPARTDNNYRVYTVGHVERLAFIRNCRTLDMSLAEIRQLLRY 69 (127)
T ss_pred CcHHHHHHHHCcCHHHHHHHHH----CCCCCCCCcCCCCCCcCCHHHHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 4688999999999999877654 687764333223456777777555543332 3446889999888753
No 153
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=94.51 E-value=0.063 Score=44.48 Aligned_cols=42 Identities=19% Similarity=0.234 Sum_probs=35.7
Q ss_pred cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
.+|...|.-++..+-+|+|..+||..||||.+||..++.|-+
T Consensus 111 ~Lp~~~R~v~~L~~~eg~s~~EIA~~lgis~~tV~~~l~Rar 152 (182)
T PRK12511 111 DLPEEQRAALHLVAIEGLSYQEAAAVLGIPIGTLMSRIGRAR 152 (182)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHHHHH
Confidence 366777777777788999999999999999999999987754
No 154
>cd04772 HTH_TioE_rpt1 First Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD contains the N-terminal or first repeat (rpt1) of these tandem MerR-like domain proteins.
Probab=94.51 E-value=0.21 Score=37.55 Aligned_cols=67 Identities=18% Similarity=0.166 Sum_probs=45.3
Q ss_pred CHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHH
Q psy1898 117 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVK 187 (230)
Q Consensus 117 s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~~P~~t~~eI~~~L~~ 187 (230)
+..++|+.+|||..|+..|. +.|.+.|..+....-+..++++...+.....-....+..++++.+..
T Consensus 2 ~i~e~A~~~gvs~~tlR~Ye----~~Gll~~~~r~~~g~R~Y~~~~v~~l~~I~~l~~g~~l~~i~~~~~~ 68 (99)
T cd04772 2 RTVDLARAIGLSPQTVRNYE----SLGLIPPAERTANGYRIYTDKHIAALRAYRALLPGYGYRVAQRIMRA 68 (99)
T ss_pred CHHHHHHHHCcCHHHHHHHH----HcCCCCCCCcCCCCCeecCHHHHHHHHHHHHHhhCCCHHHHHHHHHH
Confidence 67899999999999998774 47877654332234566788877766544332246777777665544
No 155
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=94.49 E-value=0.06 Score=44.51 Aligned_cols=43 Identities=12% Similarity=0.112 Sum_probs=36.7
Q ss_pred cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898 99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE 141 (230)
Q Consensus 99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e 141 (230)
.+|.+.|.-++..+-+|+|..+||..+|+|.+||...+.|-+.
T Consensus 130 ~Lp~~~r~v~~L~~~~g~s~~EIA~~lgis~~tVk~~l~Rar~ 172 (185)
T PRK09649 130 DLTTDQREALLLTQLLGLSYADAAAVCGCPVGTIRSRVARARD 172 (185)
T ss_pred hCCHHHhHHhhhHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3567777777777889999999999999999999999988654
No 156
>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=94.46 E-value=0.066 Score=43.22 Aligned_cols=42 Identities=17% Similarity=0.155 Sum_probs=35.0
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE 141 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e 141 (230)
+|...|.-++..+-+|+|..+||+.+|||.+||+..+.|-+.
T Consensus 120 L~~~~r~i~~l~~~~g~s~~eiA~~lgis~~tv~~~l~Ra~~ 161 (169)
T TIGR02954 120 LNDKYQTAIILRYYHDLTIKEIAEVMNKPEGTVKTYLHRALK 161 (169)
T ss_pred CCHHHhHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 566666666666778999999999999999999999988653
No 157
>cd04767 HTH_HspR-like_MBC Helix-Turn-Helix DNA binding domain of putative HspR-like transcription regulators. Putative helix-turn-helix (HTH) transcription regulator HspR-like proteins. Unlike the characterized HspR, these proteins have a C-terminal domain with putative metal binding cysteines (MBC). Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind spe
Probab=94.46 E-value=0.093 Score=41.22 Aligned_cols=66 Identities=18% Similarity=0.179 Sum_probs=48.2
Q ss_pred CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH--hCCCCCHHHHHHHHHH
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK--TNPGIFSWEIRDRLVK 187 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~--~~P~~t~~eI~~~L~~ 187 (230)
++..++|+.+|||++|+..|.+ .|.+.|... +..+..++++.+.|..... ++..++..+|+..|..
T Consensus 2 ysI~eVA~~~GVs~~TLR~wE~----~GLl~p~r~--~G~R~Ys~~dv~rL~~I~~L~~e~G~~l~eI~~~L~l 69 (120)
T cd04767 2 YPIGVVAELLNIHPETLRIWER----HGLIKPARR--NGQRLYSNNDLKRLRFIKKLINEKGLNIAGVKQILSM 69 (120)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH----CCCCCCcCC--CCcEEECHHHHHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 4788999999999999998866 377766543 2457778887766654432 3467888888887754
No 158
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=94.45 E-value=0.066 Score=44.48 Aligned_cols=41 Identities=22% Similarity=0.276 Sum_probs=34.9
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
+|...|.-++..+-+|++..+||+.||||.+||...+.|-+
T Consensus 117 Lp~~~r~i~~L~~~~g~s~~EIA~~Lgis~~tVk~~l~Rar 157 (187)
T PRK12516 117 LPDDQREAIILVGASGFAYEEAAEICGCAVGTIKSRVNRAR 157 (187)
T ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 56677766666678999999999999999999999988754
No 159
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=94.40 E-value=0.069 Score=43.98 Aligned_cols=41 Identities=17% Similarity=0.209 Sum_probs=34.2
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
+|...|.-++..+-+|+|..+||..+|||.+||..++.|.+
T Consensus 140 L~~~~r~i~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Ra~ 180 (189)
T PRK09648 140 LPEKQREILILRVVVGLSAEETAEAVGSTPGAVRVAQHRAL 180 (189)
T ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 55666666666678899999999999999999999998754
No 160
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=94.40 E-value=0.059 Score=44.18 Aligned_cols=42 Identities=21% Similarity=0.142 Sum_probs=35.8
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE 141 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e 141 (230)
+|...|.-++..+-+|+|..+||+.+|||.+||..++.|.++
T Consensus 128 L~~~~r~v~~l~~~~g~s~~EIA~~l~is~~tv~~~l~Ra~~ 169 (179)
T PRK09415 128 LPIKYREVIYLFYYEELSIKEIAEVTGVNENTVKTRLKKAKE 169 (179)
T ss_pred CCHHHhhHhHhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 566667666677789999999999999999999999988654
No 161
>PRK13749 transcriptional regulator MerD; Provisional
Probab=94.37 E-value=0.22 Score=39.14 Aligned_cols=68 Identities=15% Similarity=0.021 Sum_probs=52.1
Q ss_pred CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK 187 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~ 187 (230)
++..++|+.+|||..||.- |.+.|.+.|..+..+.-+..++++.+.+..... ..-++++.+|++.|.-
T Consensus 4 ~tIgelA~~~gvS~~tiR~----YE~~GLl~p~~r~~~gyR~Y~~~~l~rL~~I~~~r~~G~sL~eI~~ll~l 72 (121)
T PRK13749 4 YTVSRLALDAGVSVHIVRD----YLLRGLLRPVACTTGGYGLFDDAALQRLCFVRAAFEAGIGLDALARLCRA 72 (121)
T ss_pred CcHHHHHHHHCCCHHHHHH----HHHCCCCCCCCcCCCCCccCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhh
Confidence 6899999999999998754 556788876545334567888888887765554 5668999999998875
No 162
>PF07900 DUF1670: Protein of unknown function (DUF1670); InterPro: IPR012872 The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=94.37 E-value=0.29 Score=42.22 Aligned_cols=88 Identities=19% Similarity=0.131 Sum_probs=57.7
Q ss_pred HHHcC--CCHHHHhhhhccccchhhhHHHHHhhh-CCCCcCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHH
Q psy1898 111 MAAAG--VRPCVISRQLRVSHGCVSKILNRYQET-GSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVK 187 (230)
Q Consensus 111 l~~~G--~s~~~IAr~lgVS~sTV~kwikRy~e~-G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~~P~~t~~eI~~~L~~ 187 (230)
++++| ++..++|-.|++|..||++-++.|++. |.+.|... --+-.--+-.+...|.++-.+. .+..||+.+..
T Consensus 99 Ay~QgglLT~~Dla~LL~~S~~TI~~~i~~yq~e~g~vvPtrG-~i~DiGp~~tHK~~ii~~~l~g--~~~~eiar~t~- 174 (220)
T PF07900_consen 99 AYDQGGLLTQEDLAMLLGISPRTISKDIKEYQKEHGVVVPTRG-TIHDIGPGVTHKKIIIRLYLKG--KPTPEIARRTN- 174 (220)
T ss_pred HHHcCCcccHHHHHHHHCCCHHHHHHHHHHHHHHcCceeccCC-cccccCCcchHHHHHHHHHHcC--CCHHHHHHHhc-
Confidence 55666 999999999999999999999999977 87765421 0010000112334444433333 56777776542
Q ss_pred hhCCCCCCCCCCHhHHHHHHHcCCC
Q psy1898 188 QDGICDKNSAPSVSSISRLLRGGRR 212 (230)
Q Consensus 188 ~~Gi~~~~~~vS~sTV~R~Lr~~g~ 212 (230)
-|..+|-|.++....
T Consensus 175 ----------HS~~av~rYi~~F~r 189 (220)
T PF07900_consen 175 ----------HSPEAVDRYIKDFKR 189 (220)
T ss_pred ----------cCHHHHHHHHHhhHH
Confidence 388899998887643
No 163
>cd04787 HTH_HMRTR_unk Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription regulators. Putative helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR), unknown subgroup. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located 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. This subgroup lacks one of the c
Probab=94.36 E-value=0.18 Score=39.87 Aligned_cols=68 Identities=16% Similarity=0.135 Sum_probs=47.5
Q ss_pred CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK 187 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~ 187 (230)
++..++|+.+|||..|+.- |.+.|.+.|.....+.-+..++++...+..... .+-..++.||++.+..
T Consensus 1 m~IgE~A~~~gvs~~TLRy----YE~~GLl~p~r~~~~gyR~Y~~~~~~~l~~I~~lr~~G~sL~eI~~~l~~ 69 (133)
T cd04787 1 MKVKELANAAGVTPDTVRF----YTRIGLLRPTRDPVNGYRLYSEKDLSRLRFILSARQLGFSLKDIKEILSH 69 (133)
T ss_pred CCHHHHHHHHCcCHHHHHH----HHHCCCCCCCcCCCCCeeeCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhh
Confidence 4688999999999999844 466798877543323356778877666543322 3456889999988864
No 164
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=94.35 E-value=0.075 Score=43.17 Aligned_cols=41 Identities=22% Similarity=0.198 Sum_probs=34.2
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
+|.+.|.-++..+-+|++..+||+.+|+|.+||..++.|-.
T Consensus 120 Lp~~~r~v~~L~~~~g~s~~EIA~~lgis~~tV~~~l~ra~ 160 (172)
T PRK12523 120 LSSKARAAFLYNRLDGMGHAEIAERLGVSVSRVRQYLAQGL 160 (172)
T ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 56666666666677999999999999999999999998754
No 165
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=94.34 E-value=0.071 Score=43.27 Aligned_cols=42 Identities=19% Similarity=0.103 Sum_probs=34.7
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE 141 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e 141 (230)
+|...|.-++..+-+|+|..+||..+|+|.+||...+.|-+.
T Consensus 120 L~~~~r~i~~l~~~~~~s~~EIA~~lgis~~tV~~~l~Ra~~ 161 (173)
T PRK12522 120 LNEKYKTVLVLYYYEQYSYKEMSEILNIPIGTVKYRLNYAKK 161 (173)
T ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 555667666666679999999999999999999999987653
No 166
>cd04789 HTH_Cfa Helix-Turn-Helix DNA binding domain of the Cfa transcription regulator. Putative helix-turn-helix (HTH) MerR-like transcription regulator; the N-terminal domain of Cfa, a cyclopropane fatty acid synthase and other related methyltransferases. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of 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=94.33 E-value=0.19 Score=38.03 Aligned_cols=65 Identities=12% Similarity=0.005 Sum_probs=45.3
Q ss_pred CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHH
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRL 185 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L 185 (230)
++..++|+.+|||++|+.-|.+ .|.+.|... ...-+..++++.+.+..... .+..++..+|++.+
T Consensus 2 ~~i~eva~~~gvs~~tlR~ye~----~Gll~~~r~-~~g~R~Y~~~~l~~l~~I~~l~~~G~~l~ei~~~l 67 (102)
T cd04789 2 YTISELAEKAGISRSTLLYYEK----LGLITGTRN-ANGYRLYPDSDLQRLLLIQQLQAGGLSLKECLACL 67 (102)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCcC-CCCCeeCCHHHHHHHHHHHHHHHCCCCHHHHHHHH
Confidence 4788999999999999986654 588766332 23456777777666653322 34568888888766
No 167
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=94.30 E-value=0.068 Score=44.32 Aligned_cols=41 Identities=17% Similarity=0.179 Sum_probs=34.3
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
+|...|.-++..+-+|+|..+||+.+|+|.+||...+.|-+
T Consensus 137 L~~~~r~i~~L~~~~g~s~~EIA~~lgis~~tVk~~l~Rar 177 (195)
T PRK12532 137 LPENTARVFTLKEILGFSSDEIQQMCGISTSNYHTIMHRAR 177 (195)
T ss_pred CCHHHHHHhhhHHHhCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 56666666666678999999999999999999999988754
No 168
>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=94.29 E-value=0.071 Score=46.55 Aligned_cols=43 Identities=19% Similarity=0.152 Sum_probs=37.0
Q ss_pred cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898 99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE 141 (230)
Q Consensus 99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e 141 (230)
.+|...|.-++..+.+|+|.++||..+|||.+||..++.|-+.
T Consensus 161 ~Lp~~~R~v~~L~~~eg~S~~EIA~~Lgis~~TVk~rl~RAr~ 203 (244)
T TIGR03001 161 ALSERERHLLRLHFVDGLSMDRIGAMYQVHRSTVSRWVAQARE 203 (244)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 3666778777777889999999999999999999999988553
No 169
>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=94.29 E-value=0.061 Score=35.55 Aligned_cols=38 Identities=16% Similarity=0.304 Sum_probs=30.9
Q ss_pred HHHHHHH-Hc-C-CCHHHHhhhhccccchhhhHHHHHhhhC
Q psy1898 106 LKIVEMA-AA-G-VRPCVISRQLRVSHGCVSKILNRYQETG 143 (230)
Q Consensus 106 ~rIV~l~-~~-G-~s~~~IAr~lgVS~sTV~kwikRy~e~G 143 (230)
.+|+.++ .. + +|..++|..|+||+.||++-++.-++.|
T Consensus 3 ~~il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i~~L~~~~ 43 (55)
T PF08279_consen 3 KQILKLLLESKEPITAKELAEELGVSRRTIRRDIKELREWG 43 (55)
T ss_dssp HHHHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence 3566655 33 3 8999999999999999999999999888
No 170
>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=94.25 E-value=0.043 Score=37.71 Aligned_cols=32 Identities=34% Similarity=0.448 Sum_probs=28.9
Q ss_pred CCCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898 115 GVRPCVISRQLRVSHGCVSKILNRYQETGSIR 146 (230)
Q Consensus 115 G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~ 146 (230)
..+..+||+.|+||++||+.-+++..+.|.+.
T Consensus 22 ~v~~~~iA~~L~vs~~tvt~ml~~L~~~GlV~ 53 (60)
T PF01325_consen 22 PVRTKDIAERLGVSPPTVTEMLKRLAEKGLVE 53 (60)
T ss_dssp SBBHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred CccHHHHHHHHCCChHHHHHHHHHHHHCCCEE
Confidence 38999999999999999999999999999774
No 171
>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=94.25 E-value=0.036 Score=45.95 Aligned_cols=41 Identities=22% Similarity=0.246 Sum_probs=34.9
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
+|...|.-++..+-+|+|..+||+.+|+|.+||..++.|-+
T Consensus 132 Lp~~~r~i~~L~~~~g~s~~EIA~~lgis~~tVk~~l~Rar 172 (193)
T TIGR02947 132 LPEEFRQAVYLADVEGFAYKEIAEIMGTPIGTVMSRLHRGR 172 (193)
T ss_pred CCHHHhhheeehhhcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 56666766666778999999999999999999999988754
No 172
>PHA00542 putative Cro-like protein
Probab=94.25 E-value=0.05 Score=39.62 Aligned_cols=27 Identities=22% Similarity=0.266 Sum_probs=24.3
Q ss_pred HHHcCCCHHHHhhhhccccchhhhHHH
Q psy1898 111 MAAAGVRPCVISRQLRVSHGCVSKILN 137 (230)
Q Consensus 111 l~~~G~s~~~IAr~lgVS~sTV~kwik 137 (230)
+...|++..++|+.+|||++||++|.+
T Consensus 27 l~~~glTq~elA~~lgIs~~tIsr~e~ 53 (82)
T PHA00542 27 LIRAGWSQEQIADATDVSQPTICRIYS 53 (82)
T ss_pred HHHCCCCHHHHHHHHCcCHHHHHHHHc
Confidence 446689999999999999999999974
No 173
>PRK06930 positive control sigma-like factor; Validated
Probab=94.24 E-value=0.08 Score=43.90 Aligned_cols=42 Identities=14% Similarity=0.187 Sum_probs=35.3
Q ss_pred cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
.+|...|.-++..+.+|++..+||+.||+|.+||..++.|..
T Consensus 114 ~L~~rer~V~~L~~~eg~s~~EIA~~lgiS~~tVk~~l~Ra~ 155 (170)
T PRK06930 114 VLTEREKEVYLMHRGYGLSYSEIADYLNIKKSTVQSMIERAE 155 (170)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 366676766666678999999999999999999999988754
No 174
>PRK03341 arginine repressor; Provisional
Probab=94.23 E-value=0.13 Score=42.76 Aligned_cols=48 Identities=19% Similarity=0.079 Sum_probs=42.8
Q ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcCCCC
Q psy1898 160 PDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGGRRD 213 (230)
Q Consensus 160 ~~~~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~g~~ 213 (230)
.+-.+.|.+++.+++-.+..|+.+.|.+ .|+. +|.+||+|-|+..++.
T Consensus 14 ~~R~~~I~~li~~~~i~tQ~eL~~~L~~-~Gi~-----vTQaTiSRDl~eL~~~ 61 (168)
T PRK03341 14 AARQARIVAILSRQSVRSQAELAALLAD-EGIE-----VTQATLSRDLDELGAV 61 (168)
T ss_pred HHHHHHHHHHHHHCCCccHHHHHHHHHH-cCCc-----ccHHHHHHHHHHhcCE
Confidence 3456788899999999999999999988 8996 8999999999999876
No 175
>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=94.22 E-value=0.028 Score=35.63 Aligned_cols=22 Identities=18% Similarity=0.209 Sum_probs=20.3
Q ss_pred CCHHHHhhhhccccchhhhHHH
Q psy1898 116 VRPCVISRQLRVSHGCVSKILN 137 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwik 137 (230)
++..++|+.||||++||++|++
T Consensus 2 lt~~e~a~~lgis~~ti~~~~~ 23 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTVYRLIH 23 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHHH
Confidence 4789999999999999999986
No 176
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=94.22 E-value=0.079 Score=44.00 Aligned_cols=43 Identities=19% Similarity=0.152 Sum_probs=36.1
Q ss_pred cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898 99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE 141 (230)
Q Consensus 99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e 141 (230)
.+|...|.-++..+.+|++..+||..+|||.+||..++.|.+.
T Consensus 128 ~Lp~~~r~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Rar~ 170 (188)
T PRK12517 128 KLDPEYREPLLLQVIGGFSGEEIAEILDLNKNTVMTRLFRARN 170 (188)
T ss_pred hCCHHHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3666777766666789999999999999999999999988653
No 177
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=94.20 E-value=0.08 Score=44.69 Aligned_cols=41 Identities=27% Similarity=0.322 Sum_probs=34.9
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
+|...|.-++..+.+|++..+||..||+|.+||+.++.|-+
T Consensus 139 L~~~~r~v~~L~~~~g~s~~EIA~~Lgis~~tV~~~l~RAr 179 (203)
T PRK09647 139 LPPEFRAAVVLCDIEGLSYEEIAATLGVKLGTVRSRIHRGR 179 (203)
T ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 55566666666778999999999999999999999998865
No 178
>PRK05066 arginine repressor; Provisional
Probab=94.20 E-value=0.15 Score=41.86 Aligned_cols=48 Identities=21% Similarity=0.079 Sum_probs=42.2
Q ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcCCCC
Q psy1898 161 DVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGGRRD 213 (230)
Q Consensus 161 ~~~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~g~~ 213 (230)
+..+.|.+++.+++-.|..|+.+.|++ .|+. .++.+||+|-|++.|+.
T Consensus 9 ~r~~~I~~iI~~~~I~tQeeL~~~L~~-~Gi~----~vTQATiSRDikeL~lv 56 (156)
T PRK05066 9 ELVKAFKALLKEEKFGSQGEIVTALQE-QGFD----NINQSKVSRMLTKFGAV 56 (156)
T ss_pred HHHHHHHHHHhhCCCCCHHHHHHHHHH-CCCC----eecHHHHHHHHHHcCCE
Confidence 445788999999999999999999988 8993 27999999999999986
No 179
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=94.18 E-value=0.084 Score=43.65 Aligned_cols=43 Identities=16% Similarity=0.182 Sum_probs=35.5
Q ss_pred cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898 99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE 141 (230)
Q Consensus 99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e 141 (230)
.+|.+.|.-++..+-+|+|..+||+.+|+|.+||...+.|-+.
T Consensus 131 ~L~~~~r~i~~l~~~~g~s~~EIAe~lgis~~~V~~~l~Ra~~ 173 (189)
T PRK06811 131 DLEKLDREIFIRRYLLGEKIEEIAKKLGLTRSAIDNRLSRGRK 173 (189)
T ss_pred hCCHHHHHHHHHHHHccCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4666766666656778999999999999999999999988654
No 180
>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=94.18 E-value=0.086 Score=42.90 Aligned_cols=42 Identities=21% Similarity=0.230 Sum_probs=34.6
Q ss_pred cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
.+|...|.-++..+-+|++..+||+.+|+|.+||..++.|-+
T Consensus 100 ~L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~tV~~~l~Rar 141 (170)
T TIGR02959 100 ELPDEYREAIRLTELEGLSQQEIAEKLGLSLSGAKSRVQRGR 141 (170)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 356666666666678999999999999999999999988744
No 181
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=94.15 E-value=0.083 Score=43.66 Aligned_cols=41 Identities=15% Similarity=0.122 Sum_probs=35.2
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
+|...|.-++..+-+|+|..+||..+|+|.+||...+.|-+
T Consensus 132 Lp~~~r~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Rar 172 (191)
T PRK12520 132 LPPRTGRVFMMREWLELETEEICQELQITATNAWVLLYRAR 172 (191)
T ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 66677777777778999999999999999999999988754
No 182
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=94.15 E-value=0.043 Score=36.19 Aligned_cols=45 Identities=27% Similarity=0.361 Sum_probs=34.5
Q ss_pred HHHHHHHHH-HHcC--C-CHHHHhhhhccccchhhhHHHHHhhhCCCCc
Q psy1898 103 HIRLKIVEM-AAAG--V-RPCVISRQLRVSHGCVSKILNRYQETGSIRP 147 (230)
Q Consensus 103 ~~R~rIV~l-~~~G--~-s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p 147 (230)
.++..++.. +..| + |..++|+.|+||++||.+.+++..+.|.+..
T Consensus 4 ~l~~~i~~~~~~~~~~l~s~~~la~~~~vs~~tv~~~l~~L~~~g~i~~ 52 (60)
T smart00345 4 RLREDIVSGELRPGDKLPSERELAAQLGVSRTTVREALSRLEAEGLVQR 52 (60)
T ss_pred HHHHHHHcCCCCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence 344555443 2223 4 8999999999999999999999999998743
No 183
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=94.10 E-value=0.085 Score=43.87 Aligned_cols=41 Identities=20% Similarity=0.263 Sum_probs=34.5
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
+|...|.-++..+.+|.+..+||+.||||.+||..++.|-+
T Consensus 137 L~~~~r~i~~L~~~~g~s~~eIA~~lgis~~tV~~~l~Ra~ 177 (196)
T PRK12524 137 LPERQRQAVVLRHIEGLSNPEIAEVMEIGVEAVESLTARGK 177 (196)
T ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 56566666666677999999999999999999999998854
No 184
>TIGR02043 ZntR Zn(II)-responsive transcriptional regulator. This model represents the zinc and cadmium (II) responsive transcriptional activator of the gamma proteobacterial zinc efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-Cys-X(8-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=94.10 E-value=0.24 Score=39.13 Aligned_cols=68 Identities=21% Similarity=0.160 Sum_probs=48.3
Q ss_pred CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK 187 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~ 187 (230)
++..++|+.+|||..|+.-|.+ .|.+.|..+....-+..++++...+..... .+-..+..+|++.+..
T Consensus 2 ~~I~e~a~~~gvs~~tlR~Ye~----~GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sl~eI~~~l~~ 70 (131)
T TIGR02043 2 FQIGELAKLCGVTSDTLRFYEK----NGLIKPAGRTDSGYRLYTDEDQKRLRFILKAKELGFTLDEIKELLSI 70 (131)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCCcCCCCceecCHHHHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 5789999999999999877754 588876544233456777777666643332 3457889999988864
No 185
>cd01107 HTH_BmrR Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=94.09 E-value=0.41 Score=36.46 Aligned_cols=68 Identities=15% Similarity=0.144 Sum_probs=47.4
Q ss_pred CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCC-CCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIG-GSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK 187 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~g-g~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~ 187 (230)
++..++|+.+|||++|+.-|.+ .|.+.|..+. ....+..++++...|..... .+-+.+..+|...+..
T Consensus 1 ~~i~eva~~~gis~~tlR~ye~----~GLi~p~~~~~~ngyR~Y~~~~i~~l~~I~~lr~~G~sl~~i~~l~~~ 70 (108)
T cd01107 1 FTIGEFAKLSNLSIKALRYYDK----IGLLKPAYVDPDTGYRYYSAEQLERLNRIKYLRDLGFPLEEIKEILDA 70 (108)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH----cCCCCCCcCCCCCCccccCHHHHHHHHHHHHHHHcCCCHHHHHHHHhc
Confidence 3678999999999999987765 5888664432 13467778887766654332 2346888888877643
No 186
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=94.07 E-value=0.068 Score=45.81 Aligned_cols=41 Identities=12% Similarity=0.111 Sum_probs=32.4
Q ss_pred CCHHHHHHHHHHH----HcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 100 LPNHIRLKIVEMA----AAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 100 ~s~~~R~rIV~l~----~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
+|...|.-++..+ .+|+|..+||+.+|||.+||.+++.|-.
T Consensus 179 Lp~~~R~v~~L~y~l~~~eg~s~~EIA~~lgis~~tVk~~~~rA~ 223 (234)
T PRK08301 179 LSDREKQIMELRFGLNGGEEKTQKEVADMLGISQSYISRLEKRII 223 (234)
T ss_pred CCHHHHHHHHHHhccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 5556555555544 4899999999999999999999987754
No 187
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=94.06 E-value=0.1 Score=42.88 Aligned_cols=42 Identities=14% Similarity=0.031 Sum_probs=35.5
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE 141 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e 141 (230)
+|...|.-++..+.+|++..+||..||+|.+||+..+.|-+.
T Consensus 138 L~~~~r~i~~l~~~~g~s~~eIA~~lgis~~~v~~~l~Rar~ 179 (187)
T PRK12534 138 LEPPRSELIRTAFFEGITYEELAARTDTPIGTVKSWIRRGLA 179 (187)
T ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHhCCChhHHHHHHHHHHH
Confidence 566677666667789999999999999999999999988653
No 188
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=94.05 E-value=0.15 Score=41.14 Aligned_cols=76 Identities=14% Similarity=0.073 Sum_probs=40.2
Q ss_pred CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCC
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKN 195 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~ 195 (230)
.|..+||..+||+++|+|+|.+.-+. -.++...+..+.-.-...++...|....-..
T Consensus 35 ~T~~eiAee~Gis~~tLYrWr~~~~~--------------------Fiey~n~la~~~~~~~~~eVy~~L~~~i~~~--- 91 (142)
T PF13022_consen 35 RTQAEIAEEVGISRSTLYRWRQQNKA--------------------FIEYKNELADRFLSSHREEVYTQLMKKIRGG--- 91 (142)
T ss_dssp S-HHHHHHHHTS-HHHHHHHHHH-HH--------------------HHHHHHHHHHHHHHTTHHHHHHHHHHHHHSS---
T ss_pred chHHHHHHHhCCCHHHHHHHHhcCHH--------------------HHHHHHHHHHHHHHHhHHHHHHHHHHHHhCC---
Confidence 78999999999999999999863111 1111111121111223344433333322222
Q ss_pred CCCCHhHHHHHHHcCCCCCC
Q psy1898 196 SAPSVSSISRLLRGGRRDDC 215 (230)
Q Consensus 196 ~~vS~sTV~R~Lr~~g~~~~ 215 (230)
.+|+..|-=+|+++|+-.+
T Consensus 92 -~~svKaieLflk~~GLLtD 110 (142)
T PF13022_consen 92 -QPSVKAIELFLKRHGLLTD 110 (142)
T ss_dssp -S--HHHHHHHHHHTT--EE
T ss_pred -CccHHHHHHHHHHcCcccc
Confidence 2688899999999998755
No 189
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=94.04 E-value=0.082 Score=43.42 Aligned_cols=41 Identities=22% Similarity=0.257 Sum_probs=34.8
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
+|...|.-++..+-+|++..+||+.+|+|.+||..++.|-+
T Consensus 129 L~~~~r~i~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Rar 169 (186)
T PRK05602 129 LPERQREAIVLQYYQGLSNIEAAAVMDISVDALESLLARGR 169 (186)
T ss_pred CCHHHHHHhhHHHhcCCCHHHHHHHhCcCHHHHHHHHHHHH
Confidence 56676766666678999999999999999999999988755
No 190
>cd04784 HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators. Helix-turn-helix (HTH) CadR and PbrR transcription regulators including Pseudomonas aeruginosa CadR and Ralstonia metallidurans PbrR that regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which form a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=94.03 E-value=0.51 Score=36.86 Aligned_cols=68 Identities=12% Similarity=0.088 Sum_probs=47.0
Q ss_pred CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK 187 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~ 187 (230)
++..++|+.+|||..|+.-| .+.|.+.|..+....-+..++++...+..... ..-.+++.||++.+..
T Consensus 1 m~IgevA~~~gvs~~tLRyY----e~~GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~ 69 (127)
T cd04784 1 MKIGELAKKTGCSVETIRYY----EKEGLLPAPARSANNYRLYDEEHLERLLFIRRCRSLDMSLDEIRTLLQL 69 (127)
T ss_pred CCHHHHHHHHCcCHHHHHHH----HHCCCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 46889999999999997655 45788765444223467778887765543322 3446889999988754
No 191
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=94.02 E-value=0.089 Score=43.50 Aligned_cols=42 Identities=19% Similarity=0.237 Sum_probs=35.5
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE 141 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e 141 (230)
+|...|.-++..+.+|+|..+||+.||+|.+||...+.|.++
T Consensus 112 Lp~~~R~v~~L~~~~g~s~~EIA~~Lgis~~tV~~~l~RAr~ 153 (182)
T PRK12540 112 LPQDQREALILVGASGFSYEDAAAICGCAVGTIKSRVNRARS 153 (182)
T ss_pred CCHHHHHHhhHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 466777777777789999999999999999999999887553
No 192
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=94.01 E-value=0.09 Score=43.19 Aligned_cols=41 Identities=17% Similarity=0.077 Sum_probs=34.3
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
+|...|.-++..+-+|+|..+||..+|+|.+||...+.|-+
T Consensus 123 L~~~~r~i~~l~~~~g~s~~EIA~~lgis~~tVk~~l~Rar 163 (185)
T PRK12542 123 LNESNRQVFKYKVFYNLTYQEISSVMGITEANVRKQFERAR 163 (185)
T ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 56666666666678999999999999999999999988754
No 193
>cd01282 HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 3). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located 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=93.99 E-value=0.27 Score=37.75 Aligned_cols=67 Identities=18% Similarity=0.152 Sum_probs=47.8
Q ss_pred CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK 187 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~ 187 (230)
++..++|+.+|||..|+.-|.+ .|.+.|... .+.-+..++++...|..... ..-..+..+|++.+..
T Consensus 1 m~i~eva~~~gvs~~tlR~Ye~----~GLl~p~r~-~~g~R~Y~~~~~~~l~~I~~lr~~G~sl~eI~~~l~~ 68 (112)
T cd01282 1 MRIGELAARTGVSVRSLRYYEE----QGLLVPERS-ANGYRDYDEAAVDRVRQIRRLLAAGLTLEEIREFLPC 68 (112)
T ss_pred CCHHHHHHHHCCCHHHHHHHHH----CCCCCCCcC-CCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 4688999999999999987755 588876432 23457778877666654332 3457889999987764
No 194
>cd04785 HTH_CadR-PbrR-like Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators. Helix-turn-helix (HTH) CadR- and PbrR-like transcription regulators. CadR and PbrR regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which comprise a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=93.99 E-value=0.57 Score=36.65 Aligned_cols=68 Identities=15% Similarity=0.088 Sum_probs=47.0
Q ss_pred CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK 187 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~ 187 (230)
++..++|+.+|||..|+.-|. +.|.+.|..+..+.-+..++++...+..... ..-.+++.+|++.+..
T Consensus 1 ~~I~e~a~~~gvs~~tlR~Ye----~~Gll~~~~r~~~g~R~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~ 69 (126)
T cd04785 1 LSIGELARRTGVNVETIRYYE----SIGLLPEPARTAGGYRLYGAAHVERLRFIRRARDLGFSLEEIRALLAL 69 (126)
T ss_pred CCHHHHHHHHCcCHHHHHHHH----HCCCCCCCCcCCCCccccCHHHHHHHHHHHHHHHCCCCHHHHHHHHhh
Confidence 468899999999999987554 4687765433223456778877666654332 3446889999888754
No 195
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=93.99 E-value=0.094 Score=42.99 Aligned_cols=41 Identities=24% Similarity=0.304 Sum_probs=33.7
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
+|...|.-++..+.+|+|..+||+.||+|.+||...+.|-+
T Consensus 130 L~~~~r~v~~l~~~~g~s~~EIA~~l~is~~tV~~~l~rar 170 (181)
T PRK12536 130 LPDRQRLPIVHVKLEGLSVAETAQLTGLSESAVKVGIHRGL 170 (181)
T ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 45566665556668999999999999999999999988754
No 196
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=93.98 E-value=0.078 Score=45.36 Aligned_cols=41 Identities=24% Similarity=0.169 Sum_probs=34.2
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
+|...|.-++..+-+|+|..+||+.||||.+||..++.|-+
T Consensus 135 Lp~~~R~v~~L~y~eg~s~~EIAe~LgiS~~tVk~~L~RAr 175 (216)
T PRK12533 135 LPVEYREVLVLRELEDMSYREIAAIADVPVGTVMSRLARAR 175 (216)
T ss_pred CCHHHHhHhhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 55566666666677999999999999999999999998754
No 197
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=93.98 E-value=0.097 Score=42.85 Aligned_cols=42 Identities=24% Similarity=0.277 Sum_probs=34.7
Q ss_pred cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
.+|...|.-++..+-+|++..+||..||+|.+||...+.|-+
T Consensus 131 ~L~~~~r~v~~l~~~~g~s~~eIA~~l~is~~tV~~~l~ra~ 172 (184)
T PRK12512 131 TLPPRQRDVVQSISVEGASIKETAAKLSMSEGAVRVALHRGL 172 (184)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 356666666666667899999999999999999999988754
No 198
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=93.96 E-value=0.24 Score=39.65 Aligned_cols=68 Identities=19% Similarity=0.159 Sum_probs=48.0
Q ss_pred CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK 187 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~ 187 (230)
++..++|+.+|||..|+.-|.+ .|.+.|..+....-+..++++...|..... ..-..++.+|++.+..
T Consensus 2 ~~I~e~a~~~gvs~~tlR~Ye~----~GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~ 70 (140)
T PRK09514 2 YRIGELAKLAEVTPDTLRFYEK----QGLMDPEVRTEGGYRLYTEQDLQRLRFIRRAKQLGFTLEEIRELLSI 70 (140)
T ss_pred CcHHHHHHHHCcCHHHHHHHHH----CCCCCCcccCCCCCeeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 4788999999999999988754 587776444233457778877666643322 3457889998887753
No 199
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=93.94 E-value=0.1 Score=43.32 Aligned_cols=41 Identities=17% Similarity=0.154 Sum_probs=34.1
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
+|...|.-++..+.+|++..+||+.+|+|.+||..++.|-+
T Consensus 143 L~~~~r~vl~l~~~~~~s~~EIA~~Lgis~~tVk~~l~ra~ 183 (194)
T PRK09646 143 LTDTQRESVTLAYYGGLTYREVAERLAVPLGTVKTRMRDGL 183 (194)
T ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHhCCChHhHHHHHHHHH
Confidence 56666665555578999999999999999999999998754
No 200
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=93.92 E-value=0.098 Score=44.02 Aligned_cols=42 Identities=19% Similarity=0.170 Sum_probs=34.6
Q ss_pred cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
.+|...|.-+...+-+|+|..+||..+|||.+||..++.|-+
T Consensus 153 ~L~~~~r~vl~l~~~~g~s~~EIA~~lgis~~tV~~~l~Ra~ 194 (206)
T PRK12526 153 KLPEAQQTVVKGVYFQELSQEQLAQQLNVPLGTVKSRLRLAL 194 (206)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 356666666666678999999999999999999999987754
No 201
>cd01110 HTH_SoxR Helix-Turn-Helix DNA binding domain of the SoxR transcription regulator. Helix-turn-helix (HTH) transcriptional regulator SoxR. The global regulator, SoxR, up-regulates gene expression of another transcription activator, SoxS, which directly stimulates the oxidative stress regulon genes in E. coli. The soxRS response renders the bacterial cell resistant to superoxide-generating agents, macrophage-generated nitric oxide, organic solvents, and antibiotics. The SoxR proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the unusually long spacer between the -35 and -10 promoter elements. They also harbor a regulatory C-terminal domain containing an iron-sulfur center.
Probab=93.92 E-value=0.2 Score=40.04 Aligned_cols=66 Identities=20% Similarity=0.136 Sum_probs=47.3
Q ss_pred CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHH
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLV 186 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~ 186 (230)
++..++|+.+|||..|+.-|.+ .|.+.|.... +.-+..++++.+.|..... .+-..+..+|++.|.
T Consensus 2 ~~I~EvA~~~Gvs~~tLRyYE~----~GLl~p~r~~-~g~R~Y~~~dl~~l~~I~~lr~~G~sl~eI~~~l~ 68 (139)
T cd01110 2 LSVGEVAKRSGVAVSALHFYEQ----KGLIASWRNA-GNQRRYPRDVLRRIAFIKVAQRLGLSLAEIAEALA 68 (139)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCcCC-CCCeEECHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 5789999999999999887765 4877664332 3456778877666654332 345688888888775
No 202
>TIGR02054 MerD mercuric resistence transcriptional repressor protein MerD. This model represents a transcriptional repressor protein of the MerR family (pfam00376) whose expression is regulated by the mercury-sensitive transcriptional activator, MerR. MerD has been shown to repress the transcription of the mer operon.
Probab=93.89 E-value=0.27 Score=38.53 Aligned_cols=69 Identities=16% Similarity=0.035 Sum_probs=50.8
Q ss_pred CCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898 115 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK 187 (230)
Q Consensus 115 G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~ 187 (230)
.++..++|+.+|||..||.-|.+ .|.+.|..+..+.-+..++++.+.|..... ..-..+..+|++.+..
T Consensus 3 ~~tI~elA~~~gvs~~tlR~Ye~----~GLL~p~~r~~~gyR~Y~~~~l~rL~~I~~lr~~G~~L~eI~~ll~~ 72 (120)
T TIGR02054 3 AYTISRLAEDAGVSVHVVRDYLL----RGLLHPVRRTTSGYGIFDDASLQRLRFVRAAFEAGIGLGELARLCRA 72 (120)
T ss_pred CCcHHHHHHHHCcCHHHHHHHHH----CCCCCCCccCCCCCeeCCHHHHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 36899999999999999876644 588877655334567778887777765544 4457889999887754
No 203
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=93.88 E-value=0.098 Score=43.15 Aligned_cols=42 Identities=17% Similarity=0.173 Sum_probs=35.1
Q ss_pred cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
.+|...|.-++..+-+|++..+||..+|+|.+||.+.+.|-+
T Consensus 106 ~L~~~~r~i~~l~~~~g~~~~EIA~~lgis~~tV~~~l~Rar 147 (181)
T PRK09637 106 ALPEKYAEALRLTELEGLSQKEIAEKLGLSLSGAKSRVQRGR 147 (181)
T ss_pred hCCHHHHHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 356677766666678999999999999999999999988754
No 204
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=93.88 E-value=0.094 Score=45.68 Aligned_cols=41 Identities=15% Similarity=0.080 Sum_probs=34.5
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
+|...|.-+...+-.|+|..+||+.||||.+||++|+.+..
T Consensus 206 L~~~~r~vl~l~~~~g~s~~eIA~~l~is~~tV~~~~~ra~ 246 (257)
T PRK08583 206 LSDREKSIIQCTFIENLSQKETGERLGISQMHVSRLQRQAI 246 (257)
T ss_pred CCHHHHHHHHHHHhCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 56677766666678999999999999999999999988754
No 205
>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=93.87 E-value=0.097 Score=44.57 Aligned_cols=42 Identities=24% Similarity=0.246 Sum_probs=35.5
Q ss_pred cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
.+|...|.-+...+.+|+|.++||+.+|+|.+||++++++-.
T Consensus 178 ~L~~~~r~vl~l~y~~~~s~~eIA~~lgis~~~v~~~~~ra~ 219 (227)
T TIGR02980 178 ALPERERRILLLRFFEDKTQSEIAERLGISQMHVSRLLRRAL 219 (227)
T ss_pred cCCHHHHHHHHHHHhcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 366677776666677899999999999999999999998754
No 206
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=93.84 E-value=0.11 Score=42.62 Aligned_cols=41 Identities=20% Similarity=0.212 Sum_probs=34.2
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
+|...|.-++..+-+|+|..+||..+|||.+||...+.|-+
T Consensus 118 Lp~~~r~i~~l~~~e~~s~~EIA~~lgis~~tV~~~l~ra~ 158 (179)
T PRK12543 118 LPYKLRQVIILRYLHDYSQEEIAQLLQIPIGTVKSRIHAAL 158 (179)
T ss_pred CCHHHHHHHHHHHHccCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 56666766666677999999999999999999999988754
No 207
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=93.83 E-value=0.1 Score=42.96 Aligned_cols=42 Identities=21% Similarity=0.289 Sum_probs=35.0
Q ss_pred cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
.+|...|.-++..+-+|++..+||+.+|||.+||..++.|-+
T Consensus 131 ~L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~tV~~~l~ra~ 172 (184)
T PRK12539 131 RLPEKMRLAIQAVKLEGLSVAEAATRSGMSESAVKVSVHRGL 172 (184)
T ss_pred hCCHHHHHHHHHHHHcCCcHHHHHHHHCcCHHHHHHHHHHHH
Confidence 356666666666677899999999999999999999998754
No 208
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=93.83 E-value=0.091 Score=42.84 Aligned_cols=42 Identities=29% Similarity=0.296 Sum_probs=33.9
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE 141 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e 141 (230)
+|...|.-+...+-+|+|..+||+.+|+|.+||+.++.|-+.
T Consensus 137 L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~~v~~~l~Rar~ 178 (187)
T TIGR02948 137 LPPKYRMVIVLKYMEDLSLKEISEILDLPVGTVKTRIHRGRE 178 (187)
T ss_pred CCHHHhHHhhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 455555555555778999999999999999999999988653
No 209
>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=93.81 E-value=0.057 Score=37.45 Aligned_cols=37 Identities=19% Similarity=0.282 Sum_probs=32.5
Q ss_pred HHHc-CCCHHHHhhhhccccchhhhHHHHHhhhCCCCc
Q psy1898 111 MAAA-GVRPCVISRQLRVSHGCVSKILNRYQETGSIRP 147 (230)
Q Consensus 111 l~~~-G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p 147 (230)
++.. +.+..+||+.++++++||++.+++..+.|-+..
T Consensus 17 Ll~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~GlV~~ 54 (68)
T PF01978_consen 17 LLKNGPATAEEIAEELGISRSTVYRALKSLEEKGLVER 54 (68)
T ss_dssp HHHHCHEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEE
T ss_pred HHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence 4444 499999999999999999999999999998754
No 210
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=93.80 E-value=0.34 Score=34.95 Aligned_cols=67 Identities=19% Similarity=0.245 Sum_probs=45.3
Q ss_pred HHHHHHHHHc---CCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHhC
Q psy1898 105 RLKIVEMAAA---GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTN 173 (230)
Q Consensus 105 R~rIV~l~~~---G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~~ 173 (230)
-..|++++.. +.+..+||+.++++++||++.++...+.|-+...+.+ ....+.+...+.-..+....
T Consensus 7 ~~~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~~~g~l~~~~~~--~~y~l~~~~~~~~~~~~~~~ 76 (91)
T smart00346 7 GLAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQELGYVEQDGQN--GRYRLGPKVLELGQSYLSSL 76 (91)
T ss_pred HHHHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeeecCCC--CceeecHHHHHHHHHHHhcC
Confidence 3456665542 4999999999999999999999999999987543221 22344555444444444333
No 211
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=93.80 E-value=0.21 Score=36.83 Aligned_cols=66 Identities=12% Similarity=0.095 Sum_probs=46.1
Q ss_pred CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH--hCCCCCHHHHHHHHH
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK--TNPGIFSWEIRDRLV 186 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~--~~P~~t~~eI~~~L~ 186 (230)
.+..++|+.+|||+.|+..|.+ .|.+.|....+ ..+..++.+...+..... ++-.++..+++..+.
T Consensus 2 ~~i~e~A~~~gvs~~tLr~ye~----~Gli~p~r~~~-g~R~y~~~dv~~l~~i~~L~~d~g~~l~~i~~~l~ 69 (91)
T cd04766 2 YVISVAAELSGMHPQTLRLYER----LGLLSPSRTDG-GTRRYSERDIERLRRIQRLTQELGVNLAGVKRILE 69 (91)
T ss_pred cCHHHHHHHHCcCHHHHHHHHH----CCCcCCCcCCC-CCeeECHHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 4688999999999999999964 58887643322 456778887766654442 335677777765553
No 212
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=93.72 E-value=0.11 Score=43.54 Aligned_cols=41 Identities=20% Similarity=0.173 Sum_probs=34.5
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
+|...|.-++..+-+|+|.++||..+|+|.+||...+.|-+
T Consensus 140 Lp~~~r~v~~L~~~eg~s~~EIA~~lgis~~tVk~~l~RAr 180 (201)
T PRK12545 140 LPEQIGRVFMMREFLDFEIDDICTELTLTANHCSVLLYRAR 180 (201)
T ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 56677777777778999999999999999999998887643
No 213
>cd04786 HTH_MerR-like_sg7 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 7) with a conserved cysteine present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located 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 su
Probab=93.70 E-value=0.5 Score=37.46 Aligned_cols=68 Identities=13% Similarity=0.069 Sum_probs=46.7
Q ss_pred CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK 187 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~ 187 (230)
++..++|+.+|||..|+.-|. +.|.+.|..+....-+..++.+...+..... ..-..++.+|++.|..
T Consensus 1 m~Ige~a~~~gvs~~tLRyYE----~~GLl~p~~r~~~gyR~Y~~~~v~~l~~I~~lr~~GfsL~eI~~ll~~ 69 (131)
T cd04786 1 MKIGELAKRSGMAASRIRFYE----AEGLLSSVERSANGYRDYPPETVWVLEIISSAQQAGFSLDEIRQLLPA 69 (131)
T ss_pred CCHHHHHHHHCcCHHHHHHHH----HCCCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHhc
Confidence 468899999999999986664 4687766433233456777776655543322 3346889999988864
No 214
>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=93.69 E-value=0.11 Score=36.23 Aligned_cols=39 Identities=18% Similarity=0.234 Sum_probs=33.0
Q ss_pred HHHHHHHcC-CCHHHHhhhhccccchhhhHHHHHhhhCCC
Q psy1898 107 KIVEMAAAG-VRPCVISRQLRVSHGCVSKILNRYQETGSI 145 (230)
Q Consensus 107 rIV~l~~~G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~v 145 (230)
+|+.+..++ .+..++|+.|+||++||++-+++.++.|-.
T Consensus 4 ~il~~L~~~~~~~~eLa~~l~vS~~tv~~~l~~L~~~g~~ 43 (69)
T TIGR00122 4 RLLALLADNPFSGEKLGEALGMSRTAVNKHIQTLREWGVD 43 (69)
T ss_pred HHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCe
Confidence 456656555 789999999999999999999999988863
No 215
>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=93.68 E-value=0.19 Score=33.85 Aligned_cols=38 Identities=21% Similarity=0.227 Sum_probs=28.6
Q ss_pred HHHHHHHHHHHcC-------CCHHHHhhhhccccchhhhHHHHHh
Q psy1898 103 HIRLKIVEMAAAG-------VRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 103 ~~R~rIV~l~~~G-------~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
..+.-+..+++.| .+..++|+.||||++|++.-+++-.
T Consensus 4 ~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~~LRrae 48 (53)
T PF04967_consen 4 RQREILKAAYELGYFDVPRRITLEELAEELGISKSTVSEHLRRAE 48 (53)
T ss_pred HHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 3444444455555 7889999999999999999888754
No 216
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=93.67 E-value=0.097 Score=44.98 Aligned_cols=41 Identities=24% Similarity=0.180 Sum_probs=34.8
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
+|...|.-++..+.+|+|..+||+.+|||.+||.+++.+-.
T Consensus 185 L~~~~r~vl~l~~~~g~s~~EIA~~lgis~~tV~~~~~ra~ 225 (236)
T PRK06986 185 LPEREQLVLSLYYQEELNLKEIGAVLGVSESRVSQIHSQAI 225 (236)
T ss_pred CCHHHHHHHHhHhccCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 56677766667778999999999999999999999988754
No 217
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=93.65 E-value=0.34 Score=43.03 Aligned_cols=43 Identities=19% Similarity=0.119 Sum_probs=37.3
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhhh
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQET 142 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~ 142 (230)
+|...|.-++..+..|+|..+||+.+|+|.+||.+.+.|-+..
T Consensus 116 L~~~~R~v~~L~~~~g~s~~EIA~~lg~s~~tVk~~l~RAr~~ 158 (293)
T PRK09636 116 LSPLERAAFLLHDVFGVPFDEIASTLGRSPAACRQLASRARKH 158 (293)
T ss_pred CCHHHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 6777777777777899999999999999999999999987654
No 218
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=93.64 E-value=0.11 Score=41.58 Aligned_cols=43 Identities=21% Similarity=0.083 Sum_probs=35.5
Q ss_pred cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898 99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE 141 (230)
Q Consensus 99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e 141 (230)
.+|...|.-++..+-+|++..+||..+|+|.+||..++.|-+.
T Consensus 112 ~L~~~~r~v~~l~~~~~~s~~eIA~~lgis~~tv~~~l~Rar~ 154 (161)
T PRK12541 112 SLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRK 154 (161)
T ss_pred HCCHHHHHHhhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3566667666666779999999999999999999999988653
No 219
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=93.64 E-value=0.056 Score=34.68 Aligned_cols=41 Identities=37% Similarity=0.500 Sum_probs=22.0
Q ss_pred CCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHc
Q psy1898 156 RVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRG 209 (230)
Q Consensus 156 r~lt~~~~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~ 209 (230)
+.++++++..|..+..+ ..+..+|++.| | +|.+||+|.|++
T Consensus 3 ~~Lt~~eR~~I~~l~~~--G~s~~~IA~~l----g-------~s~sTV~relkR 43 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQ--GMSIREIAKRL----G-------RSRSTVSRELKR 43 (44)
T ss_dssp ---------HHHHHHCS-----HHHHHHHT----T---------HHHHHHHHHH
T ss_pred cchhhhHHHHHHHHHHc--CCCHHHHHHHH----C-------cCcHHHHHHHhc
Confidence 35688888888888644 48888888765 4 399999999986
No 220
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=93.62 E-value=0.054 Score=43.92 Aligned_cols=42 Identities=17% Similarity=0.176 Sum_probs=34.9
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE 141 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e 141 (230)
+|...|.-++..+-.|+|..+||+.||+|.+||..++.|.++
T Consensus 127 L~~~~r~v~~l~~~~g~s~~eIA~~l~is~~~V~~~l~ra~~ 168 (176)
T PRK09638 127 LDPEFRAPVILKHYYGYTYEEIAKMLNIPEGTVKSRVHHGIK 168 (176)
T ss_pred CCHHHhheeeehhhcCCCHHHHHHHHCCChhHHHHHHHHHHH
Confidence 566666666666778999999999999999999999987654
No 221
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=93.61 E-value=0.12 Score=32.99 Aligned_cols=34 Identities=24% Similarity=0.270 Sum_probs=30.6
Q ss_pred cCCCHHHHhhhhccccchhhhHHHHHhhhCCCCc
Q psy1898 114 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRP 147 (230)
Q Consensus 114 ~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p 147 (230)
.+.+..+||+.|+++++||++.++.+.+.|.+..
T Consensus 13 ~~~s~~~l~~~l~~s~~tv~~~l~~L~~~g~i~~ 46 (53)
T smart00420 13 GKVSVEELAELLGVSEMTIRRDLNKLEEQGLLTR 46 (53)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence 3599999999999999999999999999987753
No 222
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=93.59 E-value=0.12 Score=43.69 Aligned_cols=42 Identities=14% Similarity=0.127 Sum_probs=36.1
Q ss_pred cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
.+|...|.-++..+-+|++..+||+.+|+|.+||...+.|-+
T Consensus 148 ~L~~~~r~v~~L~~~~g~s~~EIAe~lgis~~tV~~~l~RAr 189 (206)
T PRK12544 148 GLPAKYARVFMMREFIELETNEICHAVDLSVSNLNVLLYRAR 189 (206)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 466777877777788999999999999999999999988754
No 223
>PRK00441 argR arginine repressor; Provisional
Probab=93.58 E-value=0.23 Score=40.42 Aligned_cols=46 Identities=17% Similarity=0.085 Sum_probs=41.3
Q ss_pred HHHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcCCCC
Q psy1898 162 VEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGGRRD 213 (230)
Q Consensus 162 ~~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~g~~ 213 (230)
-.+.|.+++.++...+..|+.+.|++ .|+. ||.+||+|-|+..++.
T Consensus 5 R~~~I~~ll~~~~~~~q~eL~~~L~~-~G~~-----vSqaTisRDl~~L~lv 50 (149)
T PRK00441 5 RHAKILEIINSKEIETQEELAEELKK-MGFD-----VTQATVSRDIKELKLI 50 (149)
T ss_pred HHHHHHHHHHHcCCCcHHHHHHHHHh-cCCC-----cCHHHHHHHHHHcCcE
Confidence 35678889999999999999999988 7995 8999999999999976
No 224
>COG1508 RpoN DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription]
Probab=93.55 E-value=0.26 Score=46.81 Aligned_cols=94 Identities=11% Similarity=0.144 Sum_probs=68.5
Q ss_pred CCHHHHhhhhccccchhhhHHHH-HhhhC--CC-----Cc---CCCCCCCCCCCCHHHHHHHHHHHHh-CC--CCCHHHH
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNR-YQETG--SI-----RP---GVIGGSKPRVATPDVEKRIEEYKKT-NP--GIFSWEI 181 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikR-y~e~G--~v-----~p---~~~gg~rpr~lt~~~~~~I~~l~~~-~P--~~t~~eI 181 (230)
++.++||..+|++.|||+|.+.. |..+. .+ .. ...+|+. ..-+..++..|.+++.. +| ..+=.+|
T Consensus 331 L~LrdvA~~i~~HESTISRai~nKy~~tprG~feLK~FFs~~i~s~~gg~-~~S~~~Ik~~Ik~lI~~E~~~~pLSD~kI 409 (444)
T COG1508 331 LVLRDVADEIGMHESTISRAITNKYLATPRGLFELKYFFSSSLASSEGGE-ASSTEAIKALIKKLIEAEDKKKPLSDSKI 409 (444)
T ss_pred ccHHHHHHHhCccHHHHHHHHhcccccCCcceeeHHHHHHHhccCCCCCc-cccHHHHHHHHHHHHhhccCCCCCCHHHH
Confidence 77899999999999999998764 66554 21 00 1111111 22245788999999864 55 4567789
Q ss_pred HHHHHHhhCCCCCCCCCCHhHHHHHHHcCCCCCCC
Q psy1898 182 RDRLVKQDGICDKNSAPSVSSISRLLRGGRRDDCD 216 (230)
Q Consensus 182 ~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~g~~~~~ 216 (230)
.+.|++ .||. |++.||-.+=...++.++.
T Consensus 410 a~lLke-kGi~-----iARRTVAKYRe~L~I~sS~ 438 (444)
T COG1508 410 AELLKE-KGID-----VARRTVAKYREELNIPSSS 438 (444)
T ss_pred HHHHHH-cCCc-----hhHHhHHHHHHHcCCCchh
Confidence 999987 8885 9999999999999988775
No 225
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=93.51 E-value=0.1 Score=42.54 Aligned_cols=41 Identities=22% Similarity=0.225 Sum_probs=33.6
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
+|.+.|.-++..+-+|+|..+||+.+|+|.+||..++.|-.
T Consensus 120 L~~~~r~i~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Ra~ 160 (172)
T PRK09651 120 LNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKAT 160 (172)
T ss_pred CCHHHhHHhhhhhccCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 45566655555567899999999999999999999998754
No 226
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=93.50 E-value=0.12 Score=42.70 Aligned_cols=41 Identities=20% Similarity=0.249 Sum_probs=34.1
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
+|...|.-+...+-+|++..+||+.||+|..||+..+.|-+
T Consensus 139 L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~tv~~~l~Rar 179 (193)
T PRK11923 139 LPEDLRTALTLREFDGLSYEDIASVMQCPVGTVRSRIFRAR 179 (193)
T ss_pred CCHHHhHHHhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 55566666666688999999999999999999999987754
No 227
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=93.50 E-value=0.32 Score=43.51 Aligned_cols=107 Identities=10% Similarity=0.002 Sum_probs=66.6
Q ss_pred cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCH
Q psy1898 99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPGIFS 178 (230)
Q Consensus 99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~~P~~t~ 178 (230)
.+|...|.-++...-.|+|..+||+.+|+|.+||...+.|-+.. +..... +....+.+..+.+..++..--.-..
T Consensus 118 ~L~p~~R~vf~L~~~~g~s~~EIA~~Lgis~~tVr~~l~RAr~~--Lr~~~~---~~~~~~~~~~~~~~~f~~a~~~gd~ 192 (290)
T PRK09635 118 RLGPAERVVFVLHEIFGLPYQQIATTIGSQASTCRQLAHRARRK--INESRI---AASVEPAQHRVVTRAFIEACSNGDL 192 (290)
T ss_pred hCCHHHHHHhhHHHHhCCCHHHHHHHHCcCHHHHHHHHHHHHHH--HHhhCC---CCCCChHHHHHHHHHHHHHHHhCCH
Confidence 36677787777777889999999999999999999999987753 211100 1122233445555555554334456
Q ss_pred HHHHHHHHHhhC--CC--CCCCCCCHhHHHHHHHcC
Q psy1898 179 WEIRDRLVKQDG--IC--DKNSAPSVSSISRLLRGG 210 (230)
Q Consensus 179 ~eI~~~L~~~~G--i~--~~~~~vS~sTV~R~Lr~~ 210 (230)
..+.+.|....+ .. ..........|.+++...
T Consensus 193 ~~l~~ll~~d~~~~~~~~~~~~~~G~~~v~~~~~~~ 228 (290)
T PRK09635 193 DTLLEVLDPGVAGEIDARKGVVVVGADRVGPTILRH 228 (290)
T ss_pred HHHHHHhhhhhcCCCcCCCCccccCHHHHHHHHHHh
Confidence 667777754322 11 011224667788887654
No 228
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=93.50 E-value=0.062 Score=37.34 Aligned_cols=43 Identities=19% Similarity=0.219 Sum_probs=33.8
Q ss_pred HHHHHHHH---cCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcC
Q psy1898 106 LKIVEMAA---AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG 148 (230)
Q Consensus 106 ~rIV~l~~---~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~ 148 (230)
.+|++.++ .+.+.++||..+++|+.+|.+|+..-...|.+...
T Consensus 3 e~Il~~i~~~~~p~~T~eiA~~~gls~~~aR~yL~~Le~eG~V~~~ 48 (62)
T PF04703_consen 3 EKILEYIKEQNGPLKTREIADALGLSIYQARYYLEKLEKEGKVERS 48 (62)
T ss_dssp HCHHHHHHHHTS-EEHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEE
T ss_pred HHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEe
Confidence 34555443 45999999999999999999999999999988643
No 229
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=93.47 E-value=0.14 Score=40.85 Aligned_cols=41 Identities=22% Similarity=0.216 Sum_probs=33.7
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
+|.+.|.-++..+-+|+|..+||..+|+|.+||...+.|-.
T Consensus 106 L~~~~r~v~~l~~~~~~s~~eIA~~lgis~~tv~~~l~ra~ 146 (159)
T PRK12527 106 LPPACRDSFLLRKLEGLSHQQIAEHLGISRSLVEKHIVNAM 146 (159)
T ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 56666665555667999999999999999999999988754
No 230
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=93.47 E-value=0.12 Score=43.34 Aligned_cols=42 Identities=17% Similarity=0.174 Sum_probs=35.6
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE 141 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e 141 (230)
+|...|.-++..+-+|++..+||..+|+|.+||..++.|.+.
T Consensus 134 Lp~~~r~v~~l~~~~g~s~~EIAe~lgis~~tV~~~l~Rar~ 175 (196)
T PRK12535 134 LPPERREALILTQVLGYTYEEAAKIADVRVGTIRSRVARARA 175 (196)
T ss_pred CCHHHHHHhhhHHHhCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 566777777777789999999999999999999999887553
No 231
>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=93.46 E-value=0.12 Score=43.93 Aligned_cols=41 Identities=17% Similarity=0.097 Sum_probs=35.4
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
+|...|.-+...+.+|+|.++||..+|+|.+||.+++.+-.
T Consensus 176 L~~~~r~il~l~y~~~~s~~eIA~~lgis~~tV~~~~~ra~ 216 (224)
T TIGR02479 176 LSEREQLVLSLYYYEELNLKEIGEVLGLTESRVSQIHSQAL 216 (224)
T ss_pred CCHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 56677777777788999999999999999999999988754
No 232
>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=93.45 E-value=0.043 Score=43.37 Aligned_cols=41 Identities=22% Similarity=0.152 Sum_probs=33.6
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
+|...|.-++..+-+|++..+||+.||+|.+||..++.|.+
T Consensus 106 L~~~~r~i~~l~~~~g~s~~eIA~~lgis~~tv~~~l~Ra~ 146 (154)
T TIGR02950 106 LPENYRTVLILREFKEFSYKEIAELLNLSLAKVKSNLFRAR 146 (154)
T ss_pred CCHhheeeeeehhhccCcHHHHHHHHCCCHHHHHHHHHHHH
Confidence 45555655555667899999999999999999999998865
No 233
>TIGR02051 MerR Hg(II)-responsive transcriptional regulator. This model represents the mercury (II) responsive transcriptional activator of the mer organomercurial resistance operon. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(8)-Cys-Pro, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=93.45 E-value=0.28 Score=38.31 Aligned_cols=67 Identities=15% Similarity=0.037 Sum_probs=45.5
Q ss_pred CHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898 117 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK 187 (230)
Q Consensus 117 s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~ 187 (230)
+..++|+.+|||..|+.-| .+.|.+.|..+..+.-+..++++.+.|..... ..-..+..+|++.+..
T Consensus 1 ~I~e~a~~~gvs~~tlR~Y----e~~GLl~~~~r~~~g~R~Y~~~~l~~l~~I~~l~~~G~sl~eI~~~l~~ 68 (124)
T TIGR02051 1 TIGELAKAAGVNVETIRYY----ERKGLLPEPDRPEGGYRRYPEETVKRLRFIKRAQELGFSLEEIGGLLGL 68 (124)
T ss_pred CHHHHHHHHCcCHHHHHHH----HHCCCCCCCccCCCCCEeECHHHHHHHHHHHHHHHCCCCHHHHHHHHhc
Confidence 4679999999999999555 55687764333223456667777666653332 3456889998887754
No 234
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=93.40 E-value=0.13 Score=40.79 Aligned_cols=45 Identities=22% Similarity=0.231 Sum_probs=40.5
Q ss_pred CHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhhhCCC
Q psy1898 101 PNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSI 145 (230)
Q Consensus 101 s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v 145 (230)
..+.+..++.++..|.+..++|+.++|+.+||.+|.+++.+....
T Consensus 75 ~~~~~~~~~~~~~~~~~i~~~a~~l~i~~~~~~r~~~r~~~~~~~ 119 (129)
T COG3677 75 LYKIKLQAVTLYMLGLGIRDIARTLGISINTVNRWSKRFGSRVEG 119 (129)
T ss_pred chHHHHHHHHHHHcCCCcccHHHHhcccHHHHHHHHHhhcchhhc
Confidence 368899999999999999999999999999999999998876543
No 235
>PRK10227 DNA-binding transcriptional regulator CueR; Provisional
Probab=93.38 E-value=0.39 Score=38.26 Aligned_cols=68 Identities=10% Similarity=0.084 Sum_probs=48.3
Q ss_pred CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK 187 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~ 187 (230)
++..++|+.+|||..|+.-| .+.|.+.|..+....-+..++++...|..... ..-..++.+|++.+..
T Consensus 1 m~Ige~a~~~gvs~~tlRyY----E~~GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sl~eI~~~l~~ 69 (135)
T PRK10227 1 MNISDVAKITGLTSKAIRFY----EEKGLVTPPMRSENGYRTYTQQHLNELTLLRQARQVGFNLEESGELVNL 69 (135)
T ss_pred CCHHHHHHHHCcCHHHHHHH----HHCCCCCCcccCCCCcccCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHh
Confidence 46889999999999998655 45787766444223467778887777654443 3457888998887753
No 236
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=93.36 E-value=0.12 Score=42.97 Aligned_cols=42 Identities=24% Similarity=0.275 Sum_probs=36.0
Q ss_pred cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
.+|...|.-++..+.+|+|..+||..||||.+||..++.|-+
T Consensus 113 ~Lp~~~r~v~~L~~~~g~s~~EIA~~LgiS~~tVk~~l~Rar 154 (188)
T PRK12546 113 QLPDEQREALILVGASGFSYEEAAEMCGVAVGTVKSRANRAR 154 (188)
T ss_pred hCCHHHhHHhhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 356677777777778999999999999999999999998855
No 237
>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=93.34 E-value=0.11 Score=42.59 Aligned_cols=42 Identities=26% Similarity=0.313 Sum_probs=33.6
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE 141 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e 141 (230)
++...|.-+...+-+|.+..+||..+|+|.+||..++.|-++
T Consensus 139 L~~~~r~v~~l~~~~~~s~~EIA~~lgis~~tv~~~l~rar~ 180 (190)
T TIGR02939 139 LPEDLRTAITLRELEGLSYEDIARIMDCPVGTVRSRIFRARE 180 (190)
T ss_pred CCHHHhhhhhhhhhcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 445556555555678999999999999999999999987553
No 238
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=93.33 E-value=0.15 Score=42.35 Aligned_cols=42 Identities=14% Similarity=0.121 Sum_probs=34.2
Q ss_pred cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
.+|...|.-++..+-+|++..+||..+|||.+||..-+.|.+
T Consensus 141 ~Lp~~~r~v~~l~~~eg~s~~EIA~~lgis~~tVk~rl~ra~ 182 (194)
T PRK12531 141 RLPKAQRDVLQAVYLEELPHQQVAEMFDIPLGTVKSRLRLAV 182 (194)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHHHHHH
Confidence 356667766666678999999999999999999988877654
No 239
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=93.31 E-value=0.15 Score=42.02 Aligned_cols=42 Identities=10% Similarity=-0.077 Sum_probs=34.6
Q ss_pred cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
.+|...|.-++..+-+|++..+||+.||+|.+||.+.+.|-+
T Consensus 131 ~L~~~~r~vl~l~~~~~~s~~eIA~~lgis~~tV~~~l~Rar 172 (189)
T PRK12515 131 KLSPAHREIIDLVYYHEKSVEEVGEIVGIPESTVKTRMFYAR 172 (189)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 356676666666678999999999999999999998887744
No 240
>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=93.24 E-value=0.15 Score=42.26 Aligned_cols=41 Identities=20% Similarity=0.259 Sum_probs=34.1
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
++...|.-++..+-+|++..+||..+|+|.+||...+.|-+
T Consensus 132 L~~~~r~v~~l~~~~g~s~~EIA~~lgis~~tvk~rl~Rar 172 (188)
T TIGR02943 132 LPEQTARVFMMREVLGFESDEICQELEISTSNCHVLLYRAR 172 (188)
T ss_pred CCHHHHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 55667776666678999999999999999999999887644
No 241
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=93.18 E-value=0.21 Score=39.60 Aligned_cols=74 Identities=12% Similarity=0.078 Sum_probs=46.0
Q ss_pred cCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcC--CCCCCCCCCCC-HHHHHHHHHHHHhCCCCCHHHHHHHHHH
Q psy1898 114 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG--VIGGSKPRVAT-PDVEKRIEEYKKTNPGIFSWEIRDRLVK 187 (230)
Q Consensus 114 ~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~--~~gg~rpr~lt-~~~~~~I~~l~~~~P~~t~~eI~~~L~~ 187 (230)
...+.-+||..++++++||+|-+++-.+.|.+... +..+++|.-+= +...+.+...+..+-+--+..+.+++.+
T Consensus 41 ~~~tvdelae~lnr~rStv~rsl~~L~~~GlV~Rek~~~~~Ggy~yiY~~i~~ee~k~~i~~~l~~w~~~~~~~i~~ 117 (126)
T COG3355 41 GPLTVDELAEILNRSRSTVYRSLQNLLEAGLVEREKVNLKGGGYYYLYKPIDPEEIKKKILKDLDEWYDKMKQLIEE 117 (126)
T ss_pred CCcCHHHHHHHHCccHHHHHHHHHHHHHcCCeeeeeeccCCCceeEEEecCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35999999999999999999999999999977321 11233443222 3333333333333322245556666655
No 242
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=93.16 E-value=0.051 Score=44.85 Aligned_cols=41 Identities=12% Similarity=-0.044 Sum_probs=32.8
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
+|...|.-++..+.+|+|..+||..+|||.+||..++.|-+
T Consensus 135 L~~~~r~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Ra~ 175 (188)
T PRK09640 135 VNPIDREILVLRFVAELEFQEIADIMHMGLSATKMRYKRAL 175 (188)
T ss_pred cChhheeeeeeHHhcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 44455554445567899999999999999999999998754
No 243
>PHA01976 helix-turn-helix protein
Probab=93.15 E-value=0.083 Score=36.24 Aligned_cols=31 Identities=16% Similarity=0.204 Sum_probs=25.1
Q ss_pred HHHHHH-HcCCCHHHHhhhhccccchhhhHHH
Q psy1898 107 KIVEMA-AAGVRPCVISRQLRVSHGCVSKILN 137 (230)
Q Consensus 107 rIV~l~-~~G~s~~~IAr~lgVS~sTV~kwik 137 (230)
++-.+. ..|+|..++|+.+|||++||++|.+
T Consensus 6 rl~~~R~~~glt~~~lA~~~gvs~~~v~~~e~ 37 (67)
T PHA01976 6 QLIKARNARAWSAPELSRRAGVRHSLIYDFEA 37 (67)
T ss_pred HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 333433 4589999999999999999999964
No 244
>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=93.13 E-value=0.074 Score=40.69 Aligned_cols=50 Identities=14% Similarity=0.197 Sum_probs=32.1
Q ss_pred cccCCCcCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhhh
Q psy1898 93 VFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQET 142 (230)
Q Consensus 93 ~~~~g~~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~ 142 (230)
|++.+..+....|.+-|..-.+|.+..++|+.||+|..+|++++++.+..
T Consensus 50 yiP~~~~~~~~~R~~~I~~~f~G~n~~eLA~kyglS~r~I~~Ii~~~~~~ 99 (108)
T PF08765_consen 50 YIPKCDRLLRALRNREIRREFNGMNVRELARKYGLSERQIYRIIKRVRRR 99 (108)
T ss_dssp ----SHHHHHHHHHHHHHHH--SS-HHHHHHHHT--HHHHHHHHHHHHH-
T ss_pred EeeCccHHHHHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 44455555567776555544459999999999999999999999998753
No 245
>cd04777 HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 1), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located 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=93.12 E-value=0.48 Score=35.85 Aligned_cols=66 Identities=15% Similarity=0.204 Sum_probs=45.3
Q ss_pred CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK 187 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~ 187 (230)
++..++|+.+|||..|+. -|.+.|.+.|...+|. +..++++.+.+..... .+-+.++.||++.+..
T Consensus 1 m~Ige~a~~~gvs~~tlR----yYe~~GLl~p~~~~g~--r~Y~~~~~~~l~~I~~lr~~G~sL~eI~~~l~~ 67 (107)
T cd04777 1 MKIGKFAKKNNITIDTVR----HYIDLGLLIPEKKGGQ--YFFDEKCQDDLEFILELKGLGFSLIEIQKIFSY 67 (107)
T ss_pred CCHHHHHHHHCcCHHHHH----HHHHCCCcCCccCCCc--cccCHHHHHHHHHHHHHHHCCCCHHHHHHHHHh
Confidence 467899999999999874 4566898877543332 3456666555543332 3447999999998854
No 246
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=93.11 E-value=0.067 Score=44.27 Aligned_cols=41 Identities=17% Similarity=0.084 Sum_probs=32.7
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
+|...|.-++..+-+|+|..+||+.+|+|.+||..++.|.+
T Consensus 140 L~~~~r~i~~l~~~~g~s~~EIA~~lgis~~tV~~~l~ra~ 180 (194)
T PRK12513 140 LPDEQREVFLLREHGDLELEEIAELTGVPEETVKSRLRYAL 180 (194)
T ss_pred CCHhHhhheeeehccCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 45555655555567899999999999999999998887654
No 247
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=93.08 E-value=0.1 Score=44.22 Aligned_cols=40 Identities=23% Similarity=0.216 Sum_probs=34.4
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
+|..++ +|+.++.+|+|.++||++++||..||..-+++-.
T Consensus 138 LT~RE~-eVL~lla~G~snkeIA~~L~iS~~TVk~h~~~I~ 177 (207)
T PRK15411 138 LSRTES-SMLRMWMAGQGTIQISDQMNIKAKTVSSHKGNIK 177 (207)
T ss_pred CCHHHH-HHHHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHH
Confidence 665544 7899999999999999999999999999887743
No 248
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=93.05 E-value=0.13 Score=44.46 Aligned_cols=41 Identities=17% Similarity=0.289 Sum_probs=34.2
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
+|...|.-++..+.+|+|..+||+.||+|.+||...+.|-+
T Consensus 172 Lp~~~R~v~~L~~~eg~s~~EIA~~Lgis~~tVk~~l~RAr 212 (233)
T PRK12538 172 LPEQQRIAVILSYHENMSNGEIAEVMDTTVAAVESLLKRGR 212 (233)
T ss_pred CCHHHHHHhhhHHhcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 56666766666678999999999999999999999988744
No 249
>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=93.02 E-value=0.13 Score=34.78 Aligned_cols=41 Identities=24% Similarity=0.401 Sum_probs=34.8
Q ss_pred HHHHHHHHc-C-CCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898 106 LKIVEMAAA-G-VRPCVISRQLRVSHGCVSKILNRYQETGSIR 146 (230)
Q Consensus 106 ~rIV~l~~~-G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~ 146 (230)
.+|++++.+ | .+..++|..|+||..||.+=++...+.|.+.
T Consensus 3 ~~Il~~l~~~~~~s~~ela~~~~VS~~TiRRDl~~L~~~g~i~ 45 (57)
T PF08220_consen 3 QQILELLKEKGKVSVKELAEEFGVSEMTIRRDLNKLEKQGLIK 45 (57)
T ss_pred HHHHHHHHHcCCEEHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 567776654 4 9999999999999999999999998888763
No 250
>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=92.98 E-value=0.15 Score=43.90 Aligned_cols=41 Identities=12% Similarity=0.104 Sum_probs=32.3
Q ss_pred CCHHHHHHHHHHHH----cCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 100 LPNHIRLKIVEMAA----AGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 100 ~s~~~R~rIV~l~~----~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
+|...|.-++..+. +|+|..+||+.+|||.+||.+++.|-.
T Consensus 179 Lp~~~R~ii~L~~~l~~~eg~s~~EIA~~Lgis~~tV~~~l~ra~ 223 (234)
T TIGR02835 179 LNDREKKIMELRFGLVGGTEKTQKEVADMLGISQSYISRLEKRIL 223 (234)
T ss_pred CCHHHHHHHHHHHccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 55566665555442 789999999999999999999987643
No 251
>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=92.95 E-value=0.18 Score=41.11 Aligned_cols=42 Identities=24% Similarity=0.268 Sum_probs=35.4
Q ss_pred cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
.+|...|.-++..+-.|++..+||..+|||.+||++-+.|.+
T Consensus 140 ~L~~~~r~vi~l~~~~g~s~~eIA~~lgis~~~v~~~l~Ra~ 181 (189)
T TIGR02984 140 KLPEDYREVILLRHLEGLSFAEVAERMDRSEGAVSMLWVRGL 181 (189)
T ss_pred cCCHHHHHHHHHHHhcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 367777777766678999999999999999999999887754
No 252
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=92.93 E-value=0.41 Score=40.74 Aligned_cols=86 Identities=17% Similarity=0.178 Sum_probs=53.3
Q ss_pred ccCCCCCChhHHHHHHHHHhcCCC--hhhhhhhhcccccccccCCcccCCCcCCHHHHHHHHHHHHcCCCHHHHhhhhcc
Q psy1898 50 FINGRPLPNHIRLKIVEMAAAGVR--PCVISRQLRVSHGVNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRV 127 (230)
Q Consensus 50 ~~~g~plp~~~r~~I~e~~~~g~~--~~~isr~lrvshg~~~l~~~~~~g~~~s~~~R~rIV~l~~~G~s~~~IAr~lgV 127 (230)
|+.+. .+.+.-.+.++.+..|.+ +.++.+.+.-...-.. .... ....+| +....|+.++..|+|.++||.+|++
T Consensus 100 yl~K~-~~~~~l~~ai~~v~~G~~~~~~~~~~~~~~~~~~~~-~~~~-~~~~LT-~RE~eVL~lla~G~snkeIA~~L~i 175 (211)
T COG2197 100 YLLKD-ASPEELVEAIRAVAAGGTYLPPDIARKLAGLLPSSS-AEAP-LAELLT-PRELEVLRLLAEGLSNKEIAEELNL 175 (211)
T ss_pred EEeCC-CCHHHHHHHHHHHHCCCeEeCHHHHHHHHhhccccc-cccc-ccCCCC-HHHHHHHHHHHCCCCHHHHHHHHCC
Confidence 44444 456667788888888863 4445554432111100 0000 001233 3344666899999999999999999
Q ss_pred ccchhhhHHHHH
Q psy1898 128 SHGCVSKILNRY 139 (230)
Q Consensus 128 S~sTV~kwikRy 139 (230)
|..||..-+.+-
T Consensus 176 S~~TVk~h~~~i 187 (211)
T COG2197 176 SEKTVKTHVSNI 187 (211)
T ss_pred CHhHHHHHHHHH
Confidence 999998887763
No 253
>cd00592 HTH_MerR-like Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators. Helix-turn-helix (HTH) MerR-like transcription regulator, 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=92.92 E-value=0.45 Score=35.28 Aligned_cols=67 Identities=18% Similarity=0.154 Sum_probs=45.9
Q ss_pred CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK 187 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~ 187 (230)
++..++|+.+||+++||..|.+ .|.+.|...++ .-+..+.++...+..... .....+..++...+..
T Consensus 1 ~~~~eva~~~gi~~~tlr~~~~----~Gll~~~~~~~-g~r~y~~~dv~~l~~i~~l~~~g~~~~~i~~~l~~ 68 (100)
T cd00592 1 YTIGEVAKLLGVSVRTLRYYEE----KGLLPPERSEN-GYRLYSEEDLERLRLIRRLRELGLSLKEIRELLDA 68 (100)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH----CCCcCCCcCCC-CCcccCHHHHHHHHHHHHHHHcCCCHHHHHHHHhc
Confidence 4688999999999999999965 47665433222 445677776665544332 2267888888877754
No 254
>COG0789 SoxR Predicted transcriptional regulators [Transcription]
Probab=92.90 E-value=0.5 Score=36.24 Aligned_cols=68 Identities=18% Similarity=0.085 Sum_probs=47.8
Q ss_pred CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK 187 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~ 187 (230)
++..++|+.+|||..|+.-|. +.|.+.|..+..+.-+..++++.+.+..... .+-..+..+|++.|..
T Consensus 1 ~~I~eva~~~gvs~~tLRyYE----~~GLl~p~~~~~~gyR~Ys~~dl~~l~~I~~~r~~G~~L~~I~~~l~~ 69 (124)
T COG0789 1 YTIGEVAKLTGVSVRTLRFYE----RKGLLSPERRDEGGYRYYTPEDLELLQIIKTLRELGFSLAEIKELLDL 69 (124)
T ss_pred CcHHHHHHHhCCCHHHHHHHH----HcCCCCCcccCCCCceecCHHHHHHHHHHHHHHHcCCCHHHHHHHHhc
Confidence 468899999999999986664 5687876655423466778877655543332 2457889999988865
No 255
>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=92.90 E-value=0.075 Score=34.90 Aligned_cols=25 Identities=24% Similarity=0.408 Sum_probs=21.4
Q ss_pred HcCCCHHHHhhhhccccchhhhHHH
Q psy1898 113 AAGVRPCVISRQLRVSHGCVSKILN 137 (230)
Q Consensus 113 ~~G~s~~~IAr~lgVS~sTV~kwik 137 (230)
+.|+|..++|+.+|||++||++|.+
T Consensus 7 ~~gls~~~la~~~gis~~~i~~~~~ 31 (55)
T PF01381_consen 7 EKGLSQKELAEKLGISRSTISRIEN 31 (55)
T ss_dssp HTTS-HHHHHHHHTS-HHHHHHHHT
T ss_pred HcCCCHHHHHHHhCCCcchhHHHhc
Confidence 5699999999999999999999975
No 256
>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=92.89 E-value=0.14 Score=42.24 Aligned_cols=38 Identities=16% Similarity=0.188 Sum_probs=32.4
Q ss_pred HHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 103 HIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 103 ~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
+.+..++..+-+|+|..+||+.+|+|.+||...+.|-+
T Consensus 153 ~~~~~i~~~~~~~~s~~eIA~~l~~s~~tV~~~l~r~r 190 (198)
T TIGR02859 153 DLEWKVLQSYLDGKSYQEIACDLNRHVKSIDNALQRVK 190 (198)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 55666777788999999999999999999998887755
No 257
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=92.85 E-value=0.15 Score=44.27 Aligned_cols=75 Identities=17% Similarity=0.121 Sum_probs=48.4
Q ss_pred cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhhhCC-CCcCCCCCCCCCCCCHHHHHHHHHHHHhCCCC
Q psy1898 99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGS-IRPGVIGGSKPRVATPDVEKRIEEYKKTNPGI 176 (230)
Q Consensus 99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~-v~p~~~gg~rpr~lt~~~~~~I~~l~~~~P~~ 176 (230)
.+|...|.-++..+.+|+|.++||+.+|+|.+||..++.|-++.=. ... .++ .+.-.+......+..+..++|..
T Consensus 116 ~Lp~~~R~v~lL~~~eg~S~~EIAe~LgiS~~tVksrL~Rark~Lr~~l~--~~~-~~~~~~~~~~~~~~~~~~~~~~~ 191 (228)
T PRK06704 116 SLNVQQSAILLLKDVFQYSIADIAKVCSVSEGAVKASLFRSRNRLKTVSE--EGI-EIVEFTDDMEVVVTSIREERPEL 191 (228)
T ss_pred hCCHHHhhHhhhHHhhCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH--hcC-CCCCccccHHHHHHHHHhcCHHH
Confidence 3566667666666778999999999999999999999888654211 111 111 12222334555566666677654
No 258
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=92.79 E-value=0.17 Score=42.26 Aligned_cols=41 Identities=17% Similarity=0.185 Sum_probs=35.2
Q ss_pred CcCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHH
Q psy1898 98 RPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRY 139 (230)
Q Consensus 98 ~~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy 139 (230)
..+|..++ +|+.++.+|.|.++||+.++||..||..-+++-
T Consensus 149 ~~Lt~rE~-evl~~~~~G~s~~eIA~~l~iS~~TV~~h~~~i 189 (216)
T PRK10840 149 KRLSPKES-EVLRLFAEGFLVTEIAKKLNRSIKTISSQKKSA 189 (216)
T ss_pred ccCCHHHH-HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 34776664 888899999999999999999999999888763
No 259
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=92.78 E-value=0.43 Score=38.42 Aligned_cols=47 Identities=19% Similarity=0.127 Sum_probs=33.3
Q ss_pred CCCHHHHHHHHHHHHhC-CCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcC
Q psy1898 157 VATPDVEKRIEEYKKTN-PGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGG 210 (230)
Q Consensus 157 ~lt~~~~~~I~~l~~~~-P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~ 210 (230)
++|+.-. .|.+++.+. ...++.+|.++|.+ .+.. +|.+||||.|+.+
T Consensus 18 r~T~qR~-~vl~~L~~~~~~~sAeei~~~l~~-~~p~-----islaTVYr~L~~l 65 (145)
T COG0735 18 RLTPQRL-AVLELLLEADGHLSAEELYEELRE-EGPG-----ISLATVYRTLKLL 65 (145)
T ss_pred CcCHHHH-HHHHHHHhcCCCCCHHHHHHHHHH-hCCC-----CCHhHHHHHHHHH
Confidence 3455434 455555543 34999999999987 5553 7999999998764
No 260
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=92.76 E-value=0.18 Score=41.13 Aligned_cols=41 Identities=27% Similarity=0.254 Sum_probs=33.2
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
+|...|.-++..+-.|.+..+||..||||.+||...+.|-+
T Consensus 137 L~~~~r~il~l~~~~~~s~~eIA~~lgis~~~v~~~l~Rar 177 (187)
T PRK09641 137 LPEKYRTVIVLKYIEDLSLKEISEILDLPVGTVKTRIHRGR 177 (187)
T ss_pred CCHHHHHHhhhHHhhCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 45555655555567899999999999999999999988755
No 261
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=92.69 E-value=0.27 Score=38.89 Aligned_cols=51 Identities=18% Similarity=0.307 Sum_probs=42.4
Q ss_pred CCcCCHH----HHHHHHHHHHc-C-CCHHHHhhhhccccchhhhHHHHHhhhCCCCc
Q psy1898 97 GRPLPNH----IRLKIVEMAAA-G-VRPCVISRQLRVSHGCVSKILNRYQETGSIRP 147 (230)
Q Consensus 97 g~~~s~~----~R~rIV~l~~~-G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p 147 (230)
+++++.+ +..+||+++.+ | ++..+++..+|+|+.||.+..+...++|.+-.
T Consensus 2 a~~~T~eer~eLk~rIvElVRe~GRiTi~ql~~~TGasR~Tvk~~lreLVa~G~l~~ 58 (127)
T PF06163_consen 2 ARVFTPEEREELKARIVELVREHGRITIKQLVAKTGASRNTVKRYLRELVARGDLYR 58 (127)
T ss_pred CCcCCHHHHHHHHHHHHHHHHHcCCccHHHHHHHHCCCHHHHHHHHHHHHHcCCeEe
Confidence 4566654 45678887764 6 99999999999999999999999999998854
No 262
>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function.
Probab=92.62 E-value=0.22 Score=38.35 Aligned_cols=42 Identities=17% Similarity=0.105 Sum_probs=34.7
Q ss_pred cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
.++.|+-.-|-+...+|++..+.|++.|||++|+++++...+
T Consensus 41 ~L~~dElEAiRL~D~egl~QeeaA~~MgVSR~T~~ril~~AR 82 (106)
T PF02001_consen 41 VLTVDELEAIRLVDYEGLSQEEAAERMGVSRPTFQRILESAR 82 (106)
T ss_pred EeeHHHHHHHHHHHHcCCCHHHHHHHcCCcHHHHHHHHHHHH
Confidence 356676666666667899999999999999999999998654
No 263
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=92.61 E-value=0.24 Score=41.81 Aligned_cols=41 Identities=10% Similarity=0.071 Sum_probs=36.2
Q ss_pred HHHHHHHHcC---CCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898 106 LKIVEMAAAG---VRPCVISRQLRVSHGCVSKILNRYQETGSIR 146 (230)
Q Consensus 106 ~rIV~l~~~G---~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~ 146 (230)
.+|+.++.+| .+.++||+.++||+.||.+.+..-.+.|.+.
T Consensus 165 r~Vl~~~~~g~~g~s~~eIa~~l~iS~~Tv~~~~~~~~~~~~~~ 208 (225)
T PRK10046 165 NAVRKLFKEPGVQHTAETVAQALTISRTTARRYLEYCASRHLII 208 (225)
T ss_pred HHHHHHHHcCCCCcCHHHHHHHhCccHHHHHHHHHHHHhCCeEE
Confidence 3788888885 8999999999999999999999888888663
No 264
>PRK13182 racA polar chromosome segregation protein; Reviewed
Probab=92.50 E-value=0.38 Score=40.18 Aligned_cols=63 Identities=13% Similarity=0.109 Sum_probs=43.1
Q ss_pred CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHH
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRD 183 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~ 183 (230)
++..++|+.+|||..||.+|.+++ .+.+ .+..+..+..++++.+.|..... .+-+++..+|+.
T Consensus 1 mti~evA~~lGVS~~TLRrw~k~g----~L~~-~R~~~G~R~y~~~dl~~L~~I~~l~~~Gm~i~~i~~ 64 (175)
T PRK13182 1 MKTPFVAKKLGVSPKTVQRWVKQL----NLPC-EKNEYGHYIFTEEDLQLLEYVKSQIEEGQNMQDTQK 64 (175)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcC----CCCC-CcCCCCCEEECHHHHHHHHHHHHHHHcCCCHHHHHH
Confidence 468899999999999999998854 3322 22222356777877766655543 344678888865
No 265
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=92.48 E-value=0.17 Score=43.49 Aligned_cols=42 Identities=21% Similarity=0.118 Sum_probs=32.8
Q ss_pred cCCHHHHHHHHHHH----HcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 99 PLPNHIRLKIVEMA----AAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 99 ~~s~~~R~rIV~l~----~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
.+|...|.-++..+ .+|.|.++||..+|||.+||++++.|..
T Consensus 175 ~Lp~~~R~i~~l~y~~~~~e~~S~~EIA~~lgis~~tV~~~~~rA~ 220 (233)
T PRK05803 175 ILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRAL 220 (233)
T ss_pred hCCHHHHHHHHHHhCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 35556665555545 4889999999999999999999977643
No 266
>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=92.43 E-value=0.36 Score=38.45 Aligned_cols=105 Identities=17% Similarity=0.191 Sum_probs=64.4
Q ss_pred CChhHHHHHHHHHhcCCCCCCCCCccccCccccCCCCCChhHHHHH--HHHHhcCCChhhhhhhhcccccccccCCcccC
Q psy1898 19 LPNHIRLKIVEMAAAGRGSSCQGRMNQLGGVFINGRPLPNHIRLKI--VEMAAAGVRPCVISRQLRVSHGVNQLGGVFIN 96 (230)
Q Consensus 19 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~g~plp~~~r~~I--~e~~~~g~~~~~isr~lrvshg~~~l~~~~~~ 96 (230)
|-..+++..-|+-.+ . ...|+=||.=-|+..-|.+.-+.+ +|+- ..|.+..+.-+-.. ..
T Consensus 17 l~~~I~~R~~el~~~--~----~~DNiGGgra~n~~s~p~e~~li~e~~e~D------~~L~~L~~~k~~id---~~--- 78 (130)
T PF05263_consen 17 LDAKIKLRKLELQYR--E----NDDNIGGGRAQNKSSRPEENVLIKERLESD------EELQSLKRQKEAID---RW--- 78 (130)
T ss_pred HHHHHHHHHHHhhcC--C----CCCCcccccccCCCCcHHHHHHHHHHHHhh------HHHHHHHHHHHHHH---HH---
Confidence 344555555566653 2 223887887668888666665554 3444 44444333222121 11
Q ss_pred CCcCCHHHHHHHHHHH-Hc--CCCHHHHhhhhccccchhhhHHHHHhhh
Q psy1898 97 GRPLPNHIRLKIVEMA-AA--GVRPCVISRQLRVSHGCVSKILNRYQET 142 (230)
Q Consensus 97 g~~~s~~~R~rIV~l~-~~--G~s~~~IAr~lgVS~sTV~kwikRy~e~ 142 (230)
-.++..+ ..+||.+. .. +.|.-+||..++|+.+|+++|...|+++
T Consensus 79 ~~~l~de-~k~Ii~lry~~r~~~TW~~IA~~l~i~erta~r~~~~fK~~ 126 (130)
T PF05263_consen 79 LETLIDE-EKRIIKLRYDRRSRRTWYQIAQKLHISERTARRWRDRFKND 126 (130)
T ss_pred HHhhCHH-HHHHHHHHHcccccchHHHHHHHhCccHHHHHHHHHHHHHH
Confidence 1234444 45555544 33 4999999999999999999999999864
No 267
>cd04769 HTH_MerR2 Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MerR2 and related proteins. MerR2 in Bacillus cereus RC607 regulates resistance to organomercurials. 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 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=92.43 E-value=0.57 Score=36.07 Aligned_cols=67 Identities=15% Similarity=0.094 Sum_probs=47.4
Q ss_pred CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK 187 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~ 187 (230)
++..++|+.+|||..|+.-|. +.|.+.|..+.+ .-+..++.+...|..... .+-..+..+|++.+..
T Consensus 1 ~~ige~a~~~gvs~~tLryYe----~~GLi~p~~~~~-~yR~Y~~~d~~~l~~I~~lr~~G~sl~eI~~~l~~ 68 (116)
T cd04769 1 MYIGELAQQTGVTIKAIRLYE----EKGLLPSPKRSG-NYRVYDAQHVECLRFIKEARQLGFTLAELKAIFAG 68 (116)
T ss_pred CCHHHHHHHHCcCHHHHHHHH----HCCCCCCCCCCC-CceeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHhc
Confidence 478899999999999987664 468887755543 456677777666543322 3346889999988765
No 268
>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=92.37 E-value=0.12 Score=34.76 Aligned_cols=31 Identities=23% Similarity=0.483 Sum_probs=28.3
Q ss_pred CCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNRYQETGSIR 146 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~ 146 (230)
.+..+||+.++++++||++.+++..+.|-+.
T Consensus 22 ~t~~~la~~l~~~~~~vs~~v~~L~~~Glv~ 52 (62)
T PF12802_consen 22 LTQSELAERLGISKSTVSRIVKRLEKKGLVE 52 (62)
T ss_dssp EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred cCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 7999999999999999999999999999773
No 269
>PRK05572 sporulation sigma factor SigF; Validated
Probab=92.26 E-value=0.19 Score=43.67 Aligned_cols=41 Identities=17% Similarity=0.158 Sum_probs=33.4
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
+|...|.-+...+.+|+|..+||+.+|||.+||+++.++-.
T Consensus 203 L~~~~~~v~~l~~~~~~s~~eIA~~lgis~~~V~~~~~ral 243 (252)
T PRK05572 203 LDERERLIVYLRYFKDKTQSEVAKRLGISQVQVSRLEKKIL 243 (252)
T ss_pred CCHHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 56566655555666899999999999999999999988743
No 270
>TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
Probab=92.22 E-value=0.18 Score=32.92 Aligned_cols=25 Identities=16% Similarity=0.191 Sum_probs=22.8
Q ss_pred HcCCCHHHHhhhhccccchhhhHHH
Q psy1898 113 AAGVRPCVISRQLRVSHGCVSKILN 137 (230)
Q Consensus 113 ~~G~s~~~IAr~lgVS~sTV~kwik 137 (230)
..|++..++|+.+|||++||++|.+
T Consensus 13 ~~gltq~~lA~~~gvs~~~vs~~e~ 37 (58)
T TIGR03070 13 ALGLTQADLADLAGVGLRFIRDVEN 37 (58)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHC
Confidence 4589999999999999999999973
No 271
>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=92.20 E-value=0.21 Score=43.38 Aligned_cols=42 Identities=14% Similarity=0.049 Sum_probs=34.5
Q ss_pred cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
.+|...|.-+...+.+|+|..+||..+|||.+||.+++.+..
T Consensus 205 ~L~~~~r~ii~l~~~~g~s~~eIA~~lgis~~~V~~~~~ra~ 246 (255)
T TIGR02941 205 ILSEREKSIIHCTFEENLSQKETGERLGISQMHVSRLQRQAI 246 (255)
T ss_pred cCCHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 356677766666667899999999999999999999987644
No 272
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=92.20 E-value=0.13 Score=46.97 Aligned_cols=35 Identities=26% Similarity=0.458 Sum_probs=32.7
Q ss_pred HHHcCCCHHHHhhhhccccchhhhHHHHHhhhCCC
Q psy1898 111 MAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSI 145 (230)
Q Consensus 111 l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v 145 (230)
.|.+|++..+||++||||+.||++.+++.++.|.+
T Consensus 22 YY~~gltQ~eIA~~LgiSR~~v~rlL~~Ar~~GiV 56 (321)
T COG2390 22 YYVEGLTQSEIAERLGISRATVSRLLAKAREEGIV 56 (321)
T ss_pred HHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCeE
Confidence 45689999999999999999999999999999976
No 273
>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=92.19 E-value=0.24 Score=42.28 Aligned_cols=42 Identities=17% Similarity=0.087 Sum_probs=33.5
Q ss_pred cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
.++...+.-+...+.+|++..+||+.||||+.+|+++.++..
T Consensus 183 ~L~~~e~~i~~~~~~~~~t~~eIA~~lgis~~~V~~~~~~al 224 (231)
T TIGR02885 183 KLDERERQIIMLRYFKDKTQTEVANMLGISQVQVSRLEKKVL 224 (231)
T ss_pred cCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 355556555555566899999999999999999999988754
No 274
>COG1710 Uncharacterized protein conserved in archaea [Function unknown]
Probab=92.13 E-value=0.3 Score=38.29 Aligned_cols=44 Identities=27% Similarity=0.357 Sum_probs=39.0
Q ss_pred CCcCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 97 GRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 97 g~~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
.+.|+...+..|-+|+..|+++++||+.+||.-.|||=.++..+
T Consensus 91 prkyd~~t~~~i~emlr~gk~preIsk~lGIpirTvyY~l~k~k 134 (139)
T COG1710 91 PRKYDRNTLLRIREMLRNGKTPREISKDLGIPIRTVYYLLKKLK 134 (139)
T ss_pred CcccchhHHHHHHHHHHcCCCHHHHHHhhCCchhhhHHHHHHHh
Confidence 56688888999999999999999999999999999998877544
No 275
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=92.12 E-value=0.27 Score=34.42 Aligned_cols=41 Identities=20% Similarity=0.235 Sum_probs=30.8
Q ss_pred CHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHhC
Q psy1898 117 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTN 173 (230)
Q Consensus 117 s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~~ 173 (230)
+..+||+..|||.+||+++++ + ++ .++++..+.|.+..++-
T Consensus 2 t~~~iA~~~gvS~~TVSr~ln--------------~-~~-~v~~~t~~~i~~~~~~~ 42 (70)
T smart00354 2 TIKDVARLAGVSKATVSRVLN--------------G-NG-RVSEETREKVLAAMEEL 42 (70)
T ss_pred CHHHHHHHHCCCHHHHHHHHC--------------C-CC-CCCHHHHHHHHHHHHHh
Confidence 578999999999999999873 1 12 23777787777777653
No 276
>PF13730 HTH_36: Helix-turn-helix domain
Probab=92.07 E-value=0.14 Score=33.75 Aligned_cols=28 Identities=21% Similarity=0.373 Sum_probs=25.9
Q ss_pred CHHHHhhhhccccchhhhHHHHHhhhCC
Q psy1898 117 RPCVISRQLRVSHGCVSKILNRYQETGS 144 (230)
Q Consensus 117 s~~~IAr~lgVS~sTV~kwikRy~e~G~ 144 (230)
|...||+.+|+|++||.++++.-.+.|-
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~L~~~G~ 54 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKELEEKGL 54 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHCcC
Confidence 8899999999999999999999888774
No 277
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=92.06 E-value=0.25 Score=32.38 Aligned_cols=34 Identities=24% Similarity=0.421 Sum_probs=30.6
Q ss_pred HcCCCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898 113 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIR 146 (230)
Q Consensus 113 ~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~ 146 (230)
.+..+..+|++.+++|++||++.+++..+.|-+.
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~~g~i~ 41 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLREAGLVE 41 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHHCCCee
Confidence 3458999999999999999999999999999775
No 278
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=92.06 E-value=0.25 Score=43.28 Aligned_cols=41 Identities=15% Similarity=0.058 Sum_probs=34.3
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
++...|.-+...+.+|+|..+||..+|||.+||++++.+-.
T Consensus 204 L~~~~r~vl~l~y~~~~s~~eIA~~lgvs~~~V~~~~~ra~ 244 (256)
T PRK07408 204 LEERTREVLEFVFLHDLTQKEAAERLGISPVTVSRRVKKGL 244 (256)
T ss_pred CCHHHHHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 55566666666778899999999999999999999988754
No 279
>cd04790 HTH_Cfa-like_unk Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulator; conserved, Cfa-like, unknown proteins (~172 a.a.). The N-terminal domain of these proteins appears to be related to the HTH domain of Cfa, a cyclopropane fatty acid synthase. These Cfa-like proteins have a unique C-terminal domain with conserved histidines (motif HXXFX7HXXF). Based on sequence similarity of the N-terminal domains, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domain
Probab=92.01 E-value=0.71 Score=38.24 Aligned_cols=67 Identities=19% Similarity=0.206 Sum_probs=45.0
Q ss_pred CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHH
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLV 186 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~ 186 (230)
++..++|+.+|||+.|+.-|. +.|.+.|..+....-+..++++...+..... ..-..+..+|+..|.
T Consensus 2 ~~I~evA~~~gvs~~tLRyYe----~~GLl~p~~r~~~gyR~Y~~~dl~rL~~I~~lr~~G~sL~eI~~ll~ 69 (172)
T cd04790 2 LTISQLARQFGLSRSTLLYYE----RIGLLSPSARSESNYRLYGERDLERLEQICAYRSAGVSLEDIRSLLQ 69 (172)
T ss_pred CCHHHHHHHHCcCHHHHHHHH----HCCCCCCCccCCCCCccCCHHHHHHHHHHHHHHHcCCCHHHHHHHHh
Confidence 478999999999999986664 4688877544223456677776555543322 334677888777664
No 280
>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=92.00 E-value=0.19 Score=41.45 Aligned_cols=39 Identities=26% Similarity=0.297 Sum_probs=32.6
Q ss_pred CHHHHHHHHHHHHcCCCHHHHhhhhc-cccchhhhHHHHH
Q psy1898 101 PNHIRLKIVEMAAAGVRPCVISRQLR-VSHGCVSKILNRY 139 (230)
Q Consensus 101 s~~~R~rIV~l~~~G~s~~~IAr~lg-VS~sTV~kwikRy 139 (230)
+.+.-.++-+|+.+|+|..+||++|| ||++.|.--+.|.
T Consensus 4 tde~~~~L~~lw~~G~SasqIA~~lg~vsRnAViGk~hRl 43 (162)
T PF07750_consen 4 TDERVERLRKLWAEGLSASQIARQLGGVSRNAVIGKAHRL 43 (162)
T ss_pred CHHHHHHHHHHHHcCCCHHHHHHHhCCcchhhhhhhhhcc
Confidence 34555566679999999999999999 9999998887775
No 281
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=91.96 E-value=0.2 Score=35.08 Aligned_cols=36 Identities=8% Similarity=0.233 Sum_probs=30.6
Q ss_pred HHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhhh
Q psy1898 107 KIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQET 142 (230)
Q Consensus 107 rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~ 142 (230)
.+|.++-.-.|..++|+++|++..||.+|+..|++-
T Consensus 5 ~fIrlLs~~~s~~~Aa~~lG~~~~~v~~wv~~fR~w 40 (65)
T PF05344_consen 5 AFIRLLSQQISVAQAADRLGTDPGTVRRWVRMFRQW 40 (65)
T ss_pred HHHHHhcccccHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 345566667899999999999999999999999753
No 282
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=91.86 E-value=0.27 Score=40.87 Aligned_cols=40 Identities=15% Similarity=0.088 Sum_probs=33.0
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
+|...|.-++. +-+|+|..+||..+|+|.+||...+.|-+
T Consensus 156 L~~~~r~vl~l-~~e~~s~~EIA~~lgis~~tV~~~l~rar 195 (208)
T PRK08295 156 LSELEKEVLEL-YLDGKSYQEIAEELNRHVKSIDNALQRVK 195 (208)
T ss_pred CCHHHHHHHHH-HHccCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 45566666655 88999999999999999999998887654
No 283
>cd04776 HTH_GnyR Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR. Putative helix-turn-helix (HTH) regulatory protein, GnyR, and other related proteins. GnyR belongs to the gnyRDBHAL cluster, which is involved in acyclic isoprenoid degradation in Pseudomonas aeruginosa. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=91.81 E-value=0.8 Score=35.51 Aligned_cols=66 Identities=20% Similarity=0.208 Sum_probs=48.4
Q ss_pred CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK 187 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~ 187 (230)
++..++|+.+|||..|+.-|-+ .|.+.|...+ .-+..++++.+.|..... .+-..++.+|++.+..
T Consensus 1 ~~Igeva~~~gvs~~tlRyYe~----~GLl~p~r~~--gyR~Y~~~~l~~l~~I~~lr~~G~~L~~I~~~l~~ 67 (118)
T cd04776 1 YTISELAREFDVTPRTLRFYED----KGLLSPERRG--QTRVYSRRDRARLKLILRGKRLGFSLEEIRELLDL 67 (118)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH----CCCCCCcCCC--CccccCHHHHHHHHHHHHHHHCCCCHHHHHHHHHh
Confidence 3678999999999999876654 5888775433 467888887777653332 3457889999888864
No 284
>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=91.80 E-value=0.26 Score=31.38 Aligned_cols=34 Identities=21% Similarity=0.326 Sum_probs=25.1
Q ss_pred HHHHHHHHc-C-CCHHHHhhhhccccchhhhHHHHH
Q psy1898 106 LKIVEMAAA-G-VRPCVISRQLRVSHGCVSKILNRY 139 (230)
Q Consensus 106 ~rIV~l~~~-G-~s~~~IAr~lgVS~sTV~kwikRy 139 (230)
.+|+..+.. + .|..+||+.+|+|.+||.+=+++.
T Consensus 6 ~~Il~~Lq~d~r~s~~~la~~lglS~~~v~~Ri~rL 41 (42)
T PF13404_consen 6 RKILRLLQEDGRRSYAELAEELGLSESTVRRRIRRL 41 (42)
T ss_dssp HHHHHHHHH-TTS-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred HHHHHHHHHcCCccHHHHHHHHCcCHHHHHHHHHHh
Confidence 456665543 4 999999999999999998876654
No 285
>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional
Probab=91.77 E-value=0.63 Score=38.01 Aligned_cols=67 Identities=18% Similarity=0.128 Sum_probs=47.4
Q ss_pred CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHH-HhCCCCCHHHHHHHHHH
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYK-KTNPGIFSWEIRDRLVK 187 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~-~~~P~~t~~eI~~~L~~ 187 (230)
++..++|+.+|||..|+.-|. +.|.+.|....+ .-+..++.+.+.+.-.. ...-.+++.+|++.+..
T Consensus 12 ~~IgevAk~~gvs~~TlRyYE----~~GLi~~~r~~~-g~R~Y~~~~i~~L~~I~~lr~lG~sL~eIk~ll~~ 79 (154)
T PRK15002 12 LTPGEVAKRSGVAVSALHFYE----SKGLITSIRNSG-NQRRYKRDVLRYVAIIKIAQRIGIPLATIGEAFGV 79 (154)
T ss_pred ccHHHHHHHHCcCHHHHHHHH----HCCCCCCccCCC-CCEEECHHHHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 789999999999999986664 578887643333 34677777766654332 23456889999888753
No 286
>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=91.75 E-value=0.079 Score=34.98 Aligned_cols=22 Identities=18% Similarity=0.329 Sum_probs=18.5
Q ss_pred CCHHHHhhhhccccchhhhHHH
Q psy1898 116 VRPCVISRQLRVSHGCVSKILN 137 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwik 137 (230)
++..++++.+|+|++|+++|++
T Consensus 4 l~~~ev~~~~g~s~~ti~~~~k 25 (51)
T PF05930_consen 4 LRIKEVAELLGVSRSTIYRLIK 25 (51)
T ss_dssp E-HHHHHHHHSS-HHHHHHHHH
T ss_pred ccHHHHHHHHCCCHHHHHHHHh
Confidence 3678999999999999999988
No 287
>TIGR01950 SoxR redox-sensitive transcriptional activator SoxR. SoxR is a MerR-family homodimeric transcription factor with a 2Fe-2S cluster in each monomer. The motif CIGCGCxxxxxC is conserved. Oxidation of the iron-sulfur cluster activates SoxR. The physiological role in E. coli is response to oxidative stress. It is activated by superoxide, singlet oxygen, nitric oxide (NO), and hydrogen peroxide. In E. coli, SoxR increases expression of transcription factor SoxS; different downstream targets may exist in other species.
Probab=91.72 E-value=0.63 Score=37.41 Aligned_cols=67 Identities=19% Similarity=0.150 Sum_probs=46.2
Q ss_pred CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK 187 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~ 187 (230)
++..++|+.+|||..|+.-|.+ .|.+.|....+ .-+..++++...|..... ..-..++.+|++.+..
T Consensus 2 ~~IgevA~~~Gvs~~tLRyYE~----~GLl~~~r~~~-g~R~Y~~~di~~l~~I~~lr~~G~sL~eI~~~l~~ 69 (142)
T TIGR01950 2 LTVGELAKRSGVAVSALHFYES----KGLITSIRNSG-NQRRYKRDVLRRVAVIKAAQRVGIPLATIGEALAV 69 (142)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH----CCCCCCccCCC-CCEEECHHHHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 5789999999999999877654 58886633323 346777776655543322 3346889998888753
No 288
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=91.62 E-value=0.25 Score=43.20 Aligned_cols=43 Identities=21% Similarity=0.350 Sum_probs=36.9
Q ss_pred HHHHHHHHHHHc-C-CCHHHHhhhhccccchhhhHHHHHhhhCCC
Q psy1898 103 HIRLKIVEMAAA-G-VRPCVISRQLRVSHGCVSKILNRYQETGSI 145 (230)
Q Consensus 103 ~~R~rIV~l~~~-G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~v 145 (230)
+.+.+|++.+.+ | .+..++|+.|+||..||+|.++...+.|.+
T Consensus 5 ~R~~~Il~~l~~~~~~~~~ela~~l~vS~~TirRdL~~Le~~g~i 49 (251)
T PRK13509 5 QRHQILLELLAQLGFVTVEKVIERLGISPATARRDINKLDESGKL 49 (251)
T ss_pred HHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCE
Confidence 556777776654 4 999999999999999999999999988866
No 289
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=91.60 E-value=0.29 Score=42.53 Aligned_cols=41 Identities=20% Similarity=0.178 Sum_probs=34.6
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
+|...|.-+...+.+|+|..+||..+|+|.+||..++.|..
T Consensus 202 L~~~~r~vl~l~~~~~~s~~EIA~~lgis~~tV~~~~~ra~ 242 (251)
T PRK07670 202 LSEKEQLVISLFYKEELTLTEIGQVLNLSTSRISQIHSKAL 242 (251)
T ss_pred CCHHHHHHHHHHHhcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 56666766666778999999999999999999999987754
No 290
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=91.57 E-value=0.12 Score=34.94 Aligned_cols=27 Identities=33% Similarity=0.517 Sum_probs=20.7
Q ss_pred HHHcCCCHHHHhhhhccccchhhhHHH
Q psy1898 111 MAAAGVRPCVISRQLRVSHGCVSKILN 137 (230)
Q Consensus 111 l~~~G~s~~~IAr~lgVS~sTV~kwik 137 (230)
|.+.|++..++|+..||+++|+++|.+
T Consensus 6 m~~~~it~~~La~~~gis~~tl~~~~~ 32 (63)
T PF13443_consen 6 MAERGITQKDLARKTGISRSTLSRILN 32 (63)
T ss_dssp HHHTT--HHHHHHHHT--HHHHHHHHT
T ss_pred HHHcCCCHHHHHHHHCcCHHHHHHHHh
Confidence 556799999999999999999999985
No 291
>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=91.56 E-value=0.28 Score=41.37 Aligned_cols=43 Identities=16% Similarity=0.254 Sum_probs=36.9
Q ss_pred HHHHHHHHHH-c-CCCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898 104 IRLKIVEMAA-A-GVRPCVISRQLRVSHGCVSKILNRYQETGSIR 146 (230)
Q Consensus 104 ~R~rIV~l~~-~-G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~ 146 (230)
.|.+|+.++. . +.|..+||+.++|+++||++.+++..+.|.+.
T Consensus 2 tr~~IL~~L~~~~~~t~~eLA~~lgis~~tV~~~L~~Le~~GlV~ 46 (203)
T TIGR02702 2 TKEDILSYLLKQGQATAAALAEALAISPQAVRRHLKDLETEGLIE 46 (203)
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeE
Confidence 4677887553 3 59999999999999999999999999999774
No 292
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=91.54 E-value=0.31 Score=42.74 Aligned_cols=41 Identities=22% Similarity=0.098 Sum_probs=34.0
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
++...|.-+...+.+++|..+||..||||.+||.++..+..
T Consensus 206 L~~~er~vi~l~y~e~~t~~EIA~~lgis~~~V~~~~~ral 246 (257)
T PRK05911 206 LEEKERKVMALYYYEELVLKEIGKILGVSESRVSQIHSKAL 246 (257)
T ss_pred CCHHHHHHHHHHHhcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 56666665556667899999999999999999999988754
No 293
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=91.53 E-value=0.17 Score=31.89 Aligned_cols=32 Identities=25% Similarity=0.341 Sum_probs=29.4
Q ss_pred CCCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898 115 GVRPCVISRQLRVSHGCVSKILNRYQETGSIR 146 (230)
Q Consensus 115 G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~ 146 (230)
..+..+||+.+++|++||++.++++.+.|.+.
T Consensus 8 ~~s~~~la~~l~~s~~tv~~~l~~L~~~g~l~ 39 (48)
T smart00419 8 PLTRQEIAELLGLTRETVSRTLKRLEKEGLIS 39 (48)
T ss_pred ccCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 36889999999999999999999999999874
No 294
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=91.50 E-value=0.2 Score=39.27 Aligned_cols=36 Identities=22% Similarity=0.383 Sum_probs=30.9
Q ss_pred HHHHHHHH-HHHcCCCHHHHhhhhccccchhhhHHHH
Q psy1898 103 HIRLKIVE-MAAAGVRPCVISRQLRVSHGCVSKILNR 138 (230)
Q Consensus 103 ~~R~rIV~-l~~~G~s~~~IAr~lgVS~sTV~kwikR 138 (230)
.+|..+.. |..+|+|..+||+.||+|++.|+++++-
T Consensus 9 aiRa~lA~~L~eeG~Sq~~iA~LLGltqaAVS~Yls~ 45 (119)
T COG2522 9 AIRALLAKELIEEGLSQYRIAKLLGLTQAAVSQYLSG 45 (119)
T ss_pred HHHHHHHHHHHHcCCcHHHHHHHhCCCHHHHHHHHcc
Confidence 56766664 7788999999999999999999999863
No 295
>PRK09191 two-component response regulator; Provisional
Probab=91.48 E-value=0.32 Score=41.41 Aligned_cols=44 Identities=16% Similarity=0.079 Sum_probs=36.9
Q ss_pred cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhhh
Q psy1898 99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQET 142 (230)
Q Consensus 99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~ 142 (230)
.+|...|.-++..+.+|+|..+||+.+|+|.+||...+.+..+.
T Consensus 88 ~L~~~~r~v~~l~~~~~~s~~eIA~~l~~s~~tV~~~l~ra~~~ 131 (261)
T PRK09191 88 GLTPLPRQAFLLTALEGFSVEEAAEILGVDPAEAEALLDDARAE 131 (261)
T ss_pred hCCHHHhHHHHHHHHhcCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 36667777666677899999999999999999999999887643
No 296
>cd04779 HTH_MerR-like_sg4 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 4). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located 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=91.42 E-value=0.79 Score=36.56 Aligned_cols=67 Identities=16% Similarity=0.151 Sum_probs=46.5
Q ss_pred CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK 187 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~ 187 (230)
++..++|+.+|||+.|+..|. +.|.+.|....+ .-+..+.++.+.|..... .+-..+..+|++.+..
T Consensus 1 y~I~e~a~~~gvs~~TLR~Ye----~~GLl~p~r~~~-g~R~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~ 68 (134)
T cd04779 1 YRIGQLAHLAGVSKRTIDYYT----NLGLLTPERSDS-NYRYYDETALDRLQLIEHLKGQRLSLAEIKDQLEE 68 (134)
T ss_pred CCHHHHHHHHCcCHHHHHHHH----HCCCCCCccCCC-CCeeECHHHHHHHHHHHHHHHCCCCHHHHHHHHHh
Confidence 367899999999999998885 468887654322 345667766555543322 3456889999988865
No 297
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=91.38 E-value=0.34 Score=36.30 Aligned_cols=41 Identities=22% Similarity=0.362 Sum_probs=34.6
Q ss_pred HHHHHHHHc-C-CCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898 106 LKIVEMAAA-G-VRPCVISRQLRVSHGCVSKILNRYQETGSIR 146 (230)
Q Consensus 106 ~rIV~l~~~-G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~ 146 (230)
.+|+.++.. + .+..+||+.+|+|++||++.+++..+.|-+.
T Consensus 6 ~~il~~L~~~~~~~~~~la~~l~~s~~tv~~~l~~L~~~g~i~ 48 (108)
T smart00344 6 RKILEELQKDARISLAELAKKVGLSPSTVHNRVKRLEEEGVIK 48 (108)
T ss_pred HHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCee
Confidence 466665543 3 8999999999999999999999999999663
No 298
>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress. Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=91.36 E-value=0.75 Score=33.45 Aligned_cols=52 Identities=25% Similarity=0.366 Sum_probs=39.9
Q ss_pred HHHHHHHHHc-C--CCHHHHhhhhccccchhhhHHHHHhhhCCCC--cCCCCCCCCC
Q psy1898 105 RLKIVEMAAA-G--VRPCVISRQLRVSHGCVSKILNRYQETGSIR--PGVIGGSKPR 156 (230)
Q Consensus 105 R~rIV~l~~~-G--~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~--p~~~gg~rpr 156 (230)
-..+|+.+.+ | +.-++||+.+++|..||.+-....++-|.+. |.+.+|..|.
T Consensus 10 L~alV~~Y~~~~~PVgSk~ia~~l~~s~aTIRN~M~~Le~lGlve~~p~~s~GriPT 66 (78)
T PF03444_consen 10 LKALVELYIETGEPVGSKTIAEELGRSPATIRNEMADLEELGLVESQPHPSGGRIPT 66 (78)
T ss_pred HHHHHHHHHhcCCCcCHHHHHHHHCCChHHHHHHHHHHHHCCCccCCCCCCCCCCcC
Confidence 3445566643 4 8889999999999999999999999999885 5555554444
No 299
>COG4496 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=91.32 E-value=0.22 Score=37.10 Aligned_cols=43 Identities=21% Similarity=0.227 Sum_probs=36.7
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhhhC
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETG 143 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G 143 (230)
.|...|.+|+.|+++|.+..+|....|.|..|+++.. |--+.|
T Consensus 41 qslaqRlqVa~mL~eg~tY~~I~~eTGaStaTIsRVk-Rcl~yG 83 (100)
T COG4496 41 QSLAQRLQVAKMLKEGRTYRDIEDETGASTATISRVK-RCLNYG 83 (100)
T ss_pred HHHHHHHHHHHHHHcCCCcchhhhccCcchhhHHHHH-HHHHcC
Confidence 4568899999999999999999999999999999984 444444
No 300
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=91.26 E-value=0.14 Score=41.37 Aligned_cols=41 Identities=20% Similarity=0.110 Sum_probs=32.1
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
+|...|.-++..+-+|+|..+||..+|+|.+||...+.|-+
T Consensus 121 L~~~~r~vl~l~~~~g~s~~eIA~~lg~s~~tv~~~l~Rar 161 (175)
T PRK12518 121 LSLEHRAVLVLHDLEDLPQKEIAEILNIPVGTVKSRLFYAR 161 (175)
T ss_pred CCHHHeeeeeehHhcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 44455544444467999999999999999999999988754
No 301
>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=91.22 E-value=0.67 Score=29.68 Aligned_cols=39 Identities=31% Similarity=0.532 Sum_probs=29.5
Q ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcC
Q psy1898 161 DVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGG 210 (230)
Q Consensus 161 ~~~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~ 210 (230)
+....|..++.++|.++..++++.+ | +|.+||++.|++.
T Consensus 3 ~~~~~Il~~l~~~~~~t~~ela~~~----~-------is~~tv~~~l~~L 41 (48)
T PF13412_consen 3 ETQRKILNYLRENPRITQKELAEKL----G-------ISRSTVNRYLKKL 41 (48)
T ss_dssp HHHHHHHHHHHHCTTS-HHHHHHHH----T-------S-HHHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHh----C-------CCHHHHHHHHHHH
Confidence 3456778888899999999998865 4 4999999998753
No 302
>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=91.14 E-value=0.19 Score=34.01 Aligned_cols=33 Identities=24% Similarity=0.294 Sum_probs=30.3
Q ss_pred CCCHHHHhhhhccccchhhhHHHHHhhhCCCCc
Q psy1898 115 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRP 147 (230)
Q Consensus 115 G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p 147 (230)
.++..+||+.+++|++||++.++++.+.|-+..
T Consensus 25 ~~s~~ela~~~g~s~~tv~r~l~~L~~~g~i~~ 57 (67)
T cd00092 25 PLTRQEIADYLGLTRETVSRTLKELEEEGLISR 57 (67)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence 489999999999999999999999999998753
No 303
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=91.14 E-value=0.51 Score=38.03 Aligned_cols=42 Identities=19% Similarity=0.305 Sum_probs=35.4
Q ss_pred HHHHHHHHHH-cC-CCHHHHhhhhccccchhhhHHHHHhhhCCC
Q psy1898 104 IRLKIVEMAA-AG-VRPCVISRQLRVSHGCVSKILNRYQETGSI 145 (230)
Q Consensus 104 ~R~rIV~l~~-~G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~v 145 (230)
+=.+|+.++. +| .|.++||+++|+|++||.+=+++..+.|.+
T Consensus 10 ~D~~Il~~Lq~d~R~s~~eiA~~lglS~~tV~~Ri~rL~~~GvI 53 (153)
T PRK11179 10 LDRGILEALMENARTPYAELAKQFGVSPGTIHVRVEKMKQAGII 53 (153)
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCe
Confidence 4456666554 45 999999999999999999999999999965
No 304
>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=91.14 E-value=0.21 Score=38.78 Aligned_cols=36 Identities=17% Similarity=0.300 Sum_probs=31.3
Q ss_pred HHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898 106 LKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE 141 (230)
Q Consensus 106 ~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e 141 (230)
...+++..+|+|..+||..|+||++||.....++++
T Consensus 71 ~Efi~LR~AGlt~~aIAd~F~iS~s~~~nft~~n~~ 106 (126)
T PF10654_consen 71 REFIELRHAGLTCYAIADYFKISKSTVFNFTQNNKK 106 (126)
T ss_pred HHHHHHHhcCCChHHHHHHHhHHHHHHHHHHHHhHH
Confidence 456778899999999999999999999999876553
No 305
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=91.14 E-value=0.31 Score=42.95 Aligned_cols=41 Identities=22% Similarity=0.264 Sum_probs=33.0
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
++...|.-+...+.+|++..+||..||||..||++++++..
T Consensus 216 L~~rer~vl~l~y~~~~t~~EIA~~lgis~~~V~~~~~ral 256 (264)
T PRK07122 216 LPERERTVLVLRFFESMTQTQIAERVGISQMHVSRLLAKTL 256 (264)
T ss_pred CCHHHHHHHHHHhcCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 45555555555567899999999999999999999988754
No 306
>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=91.11 E-value=0.33 Score=41.53 Aligned_cols=41 Identities=24% Similarity=0.137 Sum_probs=31.0
Q ss_pred CCHHHHHHHHHHHH----cCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 100 LPNHIRLKIVEMAA----AGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 100 ~s~~~R~rIV~l~~----~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
+|...|.-++..+- +|+|..+||+.+|+|.+||.+++.+-.
T Consensus 175 L~~~~r~il~l~y~~~~~e~~S~~EIAe~lgis~~tV~~~~~rAl 219 (227)
T TIGR02846 175 LDGREREVIEMRYGLGDGRRKTQREIAKILGISRSYVSRIEKRAL 219 (227)
T ss_pred CCHHHHHHHHHHHcCCCCCCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 45555544444342 789999999999999999999887644
No 307
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=91.10 E-value=0.36 Score=42.36 Aligned_cols=41 Identities=15% Similarity=0.179 Sum_probs=34.0
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
+|...|.-+...+.+|+|..+||..+|+|.+||.+++.+..
T Consensus 213 L~~~~r~vl~l~~~~~~s~~eIA~~lgis~~tV~~~~~ra~ 253 (268)
T PRK06288 213 LPEREKKVLILYYYEDLTLKEIGKVLGVTESRISQLHTKAV 253 (268)
T ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 66677766666778899999999999999999998876543
No 308
>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=91.06 E-value=0.87 Score=28.94 Aligned_cols=38 Identities=21% Similarity=0.313 Sum_probs=29.1
Q ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHc
Q psy1898 161 DVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRG 209 (230)
Q Consensus 161 ~~~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~ 209 (230)
+....|...+++++..++.+|.+.+ | +|.+||++.+++
T Consensus 3 ~~D~~Il~~Lq~d~r~s~~~la~~l----g-------lS~~~v~~Ri~r 40 (42)
T PF13404_consen 3 ELDRKILRLLQEDGRRSYAELAEEL----G-------LSESTVRRRIRR 40 (42)
T ss_dssp HHHHHHHHHHHH-TTS-HHHHHHHH----T-------S-HHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHH----C-------cCHHHHHHHHHH
Confidence 4567888888999999999998865 4 499999999875
No 309
>TIGR03338 phnR_burk phosphonate utilization associated transcriptional regulator. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Polaromonas, Burkholderia, Ralstonia and Verminephrobacter.
Probab=91.05 E-value=0.71 Score=38.68 Aligned_cols=60 Identities=23% Similarity=0.254 Sum_probs=42.0
Q ss_pred HHHHHHHH-HHHcC--CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHH
Q psy1898 103 HIRLKIVE-MAAAG--VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDV 162 (230)
Q Consensus 103 ~~R~rIV~-l~~~G--~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~ 162 (230)
.++.+|+. .+..| ++..++|+.||||+++|..-+++....|.+...+..|..-..++.+.
T Consensus 19 ~l~~~I~~g~l~pG~~L~e~~La~~lgVSRtpVReAL~~L~~eGlv~~~~~~G~~V~~~~~~~ 81 (212)
T TIGR03338 19 EIERAILSGELPPGAKLNESDIAARLGVSRGPVREAFRALEEAGLVRNEKNRGVFVREISLAE 81 (212)
T ss_pred HHHHHHHcCCCCCCCEecHHHHHHHhCCChHHHHHHHHHHHHCCCEEEecCCCeEEecCCHHH
Confidence 44445544 23334 67789999999999999999999999998865554443333445443
No 310
>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=91.04 E-value=0.45 Score=35.86 Aligned_cols=38 Identities=16% Similarity=0.059 Sum_probs=31.9
Q ss_pred HHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 103 HIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 103 ~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
+.|.-+...+-.+++..+||..+++|++|+|+|.++.-
T Consensus 59 ~~r~iL~~~Yi~~~~~~~I~~~l~~S~~t~yr~~~~Al 96 (100)
T PF07374_consen 59 DERLILRMRYINKLTWEQIAEELNISRRTYYRIHKKAL 96 (100)
T ss_pred hHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 55655556777899999999999999999999988754
No 311
>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=91.02 E-value=0.21 Score=34.23 Aligned_cols=32 Identities=22% Similarity=0.270 Sum_probs=27.4
Q ss_pred CHHHHhhhhccccchhhhHHHHHhhhCCCCcC
Q psy1898 117 RPCVISRQLRVSHGCVSKILNRYQETGSIRPG 148 (230)
Q Consensus 117 s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~ 148 (230)
+..++|+.|+||++||.+-+++..+.|.+...
T Consensus 26 s~~~la~~~~vsr~tvr~al~~L~~~g~i~~~ 57 (64)
T PF00392_consen 26 SERELAERYGVSRTTVREALRRLEAEGLIERR 57 (64)
T ss_dssp -HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred CHHHHHHHhccCCcHHHHHHHHHHHCCcEEEE
Confidence 88999999999999999999999999987544
No 312
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=90.95 E-value=0.25 Score=42.26 Aligned_cols=88 Identities=14% Similarity=0.063 Sum_probs=52.2
Q ss_pred ccCCCCCChhHHHHHHHHHhcCCC--hhhhhhhhcccccccccCCcccCCCcCCHHHHHHHHHHHHcCCCHHHHhhhhcc
Q psy1898 50 FINGRPLPNHIRLKIVEMAAAGVR--PCVISRQLRVSHGVNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRV 127 (230)
Q Consensus 50 ~~~g~plp~~~r~~I~e~~~~g~~--~~~isr~lrvshg~~~l~~~~~~g~~~s~~~R~rIV~l~~~G~s~~~IAr~lgV 127 (230)
|+.+.- +.+.-.+.++.+..|.. +.++...+--.+.... ... .....+|. .-.+|+.++..|+|.++||+.|++
T Consensus 107 ~l~K~~-~~~~L~~aI~~v~~G~~~~~~~~~~~l~~~~~~~~-~~~-~~~~~Lt~-rE~~Vl~l~~~G~s~~eIA~~L~i 182 (216)
T PRK10100 107 VFYAME-DQERVVNGLQGVLRGECYFTQKLASYLITHSGNYR-YNS-TESALLTH-REKEILNKLRIGASNNEIARSLFI 182 (216)
T ss_pred EEECCC-CHHHHHHHHHHHHcCCcccCHHHHHHHHHhhcccc-cCC-CccCCCCH-HHHHHHHHHHcCCCHHHHHHHhCC
Confidence 445533 35555666677777763 2233322211111000 000 00123664 445788888889999999999999
Q ss_pred ccchhhhHHHHHhh
Q psy1898 128 SHGCVSKILNRYQE 141 (230)
Q Consensus 128 S~sTV~kwikRy~e 141 (230)
|..||..++.+-..
T Consensus 183 S~~TVk~~~~~i~~ 196 (216)
T PRK10100 183 SENTVKTHLYNLFK 196 (216)
T ss_pred CHHHHHHHHHHHHH
Confidence 99999999987543
No 313
>PRK01905 DNA-binding protein Fis; Provisional
Probab=90.95 E-value=0.36 Score=34.63 Aligned_cols=37 Identities=14% Similarity=0.141 Sum_probs=29.5
Q ss_pred HHHHHHHHHH-cCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 104 IRLKIVEMAA-AGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 104 ~R~rIV~l~~-~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
.+.-+..+++ .+.+..++|+.+|||++|+++.+++|.
T Consensus 38 E~~~i~~aL~~~~gn~s~aAr~LGIsrstL~rklkk~g 75 (77)
T PRK01905 38 EKPLLEVVMEQAGGNQSLAAEYLGINRNTLRKKLQQHG 75 (77)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHhC
Confidence 3444555554 467899999999999999999999873
No 314
>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=90.90 E-value=0.37 Score=33.85 Aligned_cols=27 Identities=26% Similarity=0.460 Sum_probs=24.0
Q ss_pred HHHcCCCHHHHhhhhccccchhhhHHH
Q psy1898 111 MAAAGVRPCVISRQLRVSHGCVSKILN 137 (230)
Q Consensus 111 l~~~G~s~~~IAr~lgVS~sTV~kwik 137 (230)
+-+.|++..++|+.+|||++||++|.+
T Consensus 14 ~~~~~~t~~~lA~~~gis~~tis~~~~ 40 (78)
T TIGR02607 14 LEPLGLSIRALAKALGVSRSTLSRIVN 40 (78)
T ss_pred HHHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 445689999999999999999999964
No 315
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=90.87 E-value=0.26 Score=41.92 Aligned_cols=78 Identities=17% Similarity=0.094 Sum_probs=50.9
Q ss_pred ccCCCCCChhHHHHHHHHHhcCCCh--hhhhhhhcccccccccCCcccCCCcCCHHHHHHHHHHHHcCCCHHHHhhhhcc
Q psy1898 50 FINGRPLPNHIRLKIVEMAAAGVRP--CVISRQLRVSHGVNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRV 127 (230)
Q Consensus 50 ~~~g~plp~~~r~~I~e~~~~g~~~--~~isr~lrvshg~~~l~~~~~~g~~~s~~~R~rIV~l~~~G~s~~~IAr~lgV 127 (230)
|+.+ |.+.+.-.+.++.+.+|..+ ..+..... ... -..+|..++ +|+.++.+|++.++||+.|+|
T Consensus 95 yl~K-~~~~~eL~~aI~~v~~G~~~~~~~~~~~~~--------~~~---~~~LT~RE~-eVL~ll~~G~snkeIA~~L~i 161 (207)
T PRK11475 95 VLSK-ASTLEILQQELFLSLNGVRQATDRLNNQWY--------INQ---SRMLSPTER-EILRFMSRGYSMPQIAEQLER 161 (207)
T ss_pred EEec-CCCHHHHHHHHHHHHCCCcccCHHHHHHhh--------ccC---cCCCCHHHH-HHHHHHHCCCCHHHHHHHHCC
Confidence 6666 34455566666666666532 22222110 000 123665554 788999999999999999999
Q ss_pred ccchhhhHHHHHh
Q psy1898 128 SHGCVSKILNRYQ 140 (230)
Q Consensus 128 S~sTV~kwikRy~ 140 (230)
|..||..-+.+-.
T Consensus 162 S~~TV~~h~~~I~ 174 (207)
T PRK11475 162 NIKTIRAHKFNVM 174 (207)
T ss_pred CHHHHHHHHHHHH
Confidence 9999998887743
No 316
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=90.81 E-value=0.39 Score=41.52 Aligned_cols=56 Identities=20% Similarity=0.296 Sum_probs=44.1
Q ss_pred CHHHHHHHHHHHH-c-CCCHHHHhhhhccccchhhhHHHHHhhhCCCCc--CCCCCCCCC
Q psy1898 101 PNHIRLKIVEMAA-A-GVRPCVISRQLRVSHGCVSKILNRYQETGSIRP--GVIGGSKPR 156 (230)
Q Consensus 101 s~~~R~rIV~l~~-~-G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p--~~~gg~rpr 156 (230)
+...|.+|+.+.+ . ++|..+||+.||||..+|.+-+....+.|.+.. .+.+.+||.
T Consensus 9 ~~~tr~~il~lL~~~g~~sa~elA~~Lgis~~avR~HL~~Le~~Glv~~~~~~~g~GRP~ 68 (218)
T COG2345 9 SGSTRERILELLKKSGPVSADELAEELGISPMAVRRHLDDLEAEGLVEVERQQGGRGRPA 68 (218)
T ss_pred CccHHHHHHHHHhccCCccHHHHHHHhCCCHHHHHHHHHHHHhCcceeeeeccCCCCCCc
Confidence 4578889998776 3 499999999999999999999999999996532 222335665
No 317
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=90.80 E-value=0.43 Score=39.60 Aligned_cols=41 Identities=27% Similarity=0.313 Sum_probs=32.4
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
+|...|.-++..+.+|++..+||..+|+|.+||..=+.|-+
T Consensus 135 Lp~~~r~i~~l~~~~g~s~~EIA~~lg~s~~tV~~rl~rar 175 (192)
T PRK09643 135 LPVEQRAALVAVDMQGYSVADAARMLGVAEGTVKSRCARGR 175 (192)
T ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 56666655555577999999999999999999987766543
No 318
>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=90.74 E-value=0.34 Score=31.33 Aligned_cols=38 Identities=32% Similarity=0.429 Sum_probs=26.7
Q ss_pred HHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHh
Q psy1898 119 CVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKT 172 (230)
Q Consensus 119 ~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~ 172 (230)
+++|+.+|||++||++|++ | ++ ..+++....|.+...+
T Consensus 1 ~~lA~~~gvs~~tvs~~l~-----g----------~~-~vs~~~~~~i~~~~~~ 38 (52)
T cd01392 1 KDIARAAGVSVATVSRVLN-----G----------KP-RVSEETRERVLAAAEE 38 (52)
T ss_pred CcHHHHHCcCHHHHHHHHc-----C----------CC-CCCHHHHHHHHHHHHH
Confidence 3789999999999999984 1 11 3456666666666544
No 319
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=90.74 E-value=0.38 Score=39.28 Aligned_cols=43 Identities=19% Similarity=0.271 Sum_probs=36.4
Q ss_pred HHHHHHHHHHH-cC-CCHHHHhhhhccccchhhhHHHHHhhhCCC
Q psy1898 103 HIRLKIVEMAA-AG-VRPCVISRQLRVSHGCVSKILNRYQETGSI 145 (230)
Q Consensus 103 ~~R~rIV~l~~-~G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~v 145 (230)
++=.+|+.++. +| .|.++||+.+|+|++||++=+++..+.|.+
T Consensus 14 ~~D~~IL~~Lq~d~R~s~~eiA~~lglS~~tv~~Ri~rL~~~GvI 58 (164)
T PRK11169 14 RIDRNILNELQKDGRISNVELSKRVGLSPTPCLERVRRLERQGFI 58 (164)
T ss_pred HHHHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCe
Confidence 44567777664 44 999999999999999999999999999965
No 320
>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=90.73 E-value=0.43 Score=35.20 Aligned_cols=41 Identities=24% Similarity=0.282 Sum_probs=28.3
Q ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHc
Q psy1898 160 PDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRG 209 (230)
Q Consensus 160 ~~~~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~ 209 (230)
++....+..+..++|++++.|+.+.+.. .+|.|+|+.+|++
T Consensus 39 ~~~l~~~a~lRl~~Pd~SL~EL~~~~~~---------~iSKSgvnhrlrK 79 (85)
T PF02650_consen 39 PEKLREFAELRLENPDASLKELGELLEP---------PISKSGVNHRLRK 79 (85)
T ss_dssp -HHHHHHHHHHHH-TTS-HHHHHHTT-----------T--HHHHHHHHHH
T ss_pred CHHHHHHHHHHHHCccccHHHHHHHHcC---------cCcHHHHHHHHHH
Confidence 3445567777889999999999998854 2799999999986
No 321
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=90.73 E-value=0.63 Score=35.67 Aligned_cols=24 Identities=33% Similarity=0.296 Sum_probs=22.1
Q ss_pred cCCCHHHHhhhhccccchhhhHHH
Q psy1898 114 AGVRPCVISRQLRVSHGCVSKILN 137 (230)
Q Consensus 114 ~G~s~~~IAr~lgVS~sTV~kwik 137 (230)
.++|..+-|+.||||.+||.+|.+
T Consensus 56 ~~lSQ~vFA~~L~vs~~Tv~~WEq 79 (104)
T COG2944 56 LGLSQPVFARYLGVSVSTVRKWEQ 79 (104)
T ss_pred hCCCHHHHHHHHCCCHHHHHHHHc
Confidence 489999999999999999999954
No 322
>PRK06474 hypothetical protein; Provisional
Probab=90.67 E-value=0.34 Score=40.34 Aligned_cols=50 Identities=18% Similarity=0.336 Sum_probs=42.6
Q ss_pred CCcCCHHHHHHHHHHHHc-C--CCHHHHhhhh-ccccchhhhHHHHHhhhCCCC
Q psy1898 97 GRPLPNHIRLKIVEMAAA-G--VRPCVISRQL-RVSHGCVSKILNRYQETGSIR 146 (230)
Q Consensus 97 g~~~s~~~R~rIV~l~~~-G--~s~~~IAr~l-gVS~sTV~kwikRy~e~G~v~ 146 (230)
...++...|.+|+..+.. + .+..+|+..+ +|+.+|||+-++.+.+.|.+.
T Consensus 5 ~~~La~p~R~~Il~~L~~~~~~~ta~el~~~l~~is~aTvYrhL~~L~e~GLI~ 58 (178)
T PRK06474 5 AEILMHPVRMKICQVLMRNKEGLTPLELVKILKDVPQATLYRHLQTMVDSGILH 58 (178)
T ss_pred HHhhCCHHHHHHHHHHHhCCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHCCCEE
Confidence 345677899999986654 3 8999999999 799999999999999999763
No 323
>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=90.60 E-value=0.23 Score=33.25 Aligned_cols=30 Identities=20% Similarity=0.298 Sum_probs=27.9
Q ss_pred CHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898 117 RPCVISRQLRVSHGCVSKILNRYQETGSIR 146 (230)
Q Consensus 117 s~~~IAr~lgVS~sTV~kwikRy~e~G~v~ 146 (230)
+..+||..+++|+.||++.+++..+.|.+.
T Consensus 27 ~~~~la~~~~is~~~v~~~l~~L~~~G~i~ 56 (66)
T cd07377 27 SERELAEELGVSRTTVREALRELEAEGLVE 56 (66)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 488999999999999999999999999774
No 324
>PRK09954 putative kinase; Provisional
Probab=90.58 E-value=0.36 Score=43.96 Aligned_cols=43 Identities=16% Similarity=0.234 Sum_probs=36.7
Q ss_pred HHHHHHHHHHHcC--CCHHHHhhhhccccchhhhHHHHHhhhCCC
Q psy1898 103 HIRLKIVEMAAAG--VRPCVISRQLRVSHGCVSKILNRYQETGSI 145 (230)
Q Consensus 103 ~~R~rIV~l~~~G--~s~~~IAr~lgVS~sTV~kwikRy~e~G~v 145 (230)
+...+|+..+++. .|..+||+.|+||++||++++++.++.|.+
T Consensus 3 ~~~~~il~~l~~~~~~s~~~la~~l~~s~~~v~~~i~~L~~~g~i 47 (362)
T PRK09954 3 NREKEILAILRRNPLIQQNEIADILQISRSRVAAHIMDLMRKGRI 47 (362)
T ss_pred hHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCc
Confidence 4456788877654 999999999999999999999999998844
No 325
>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=90.50 E-value=0.77 Score=34.79 Aligned_cols=42 Identities=26% Similarity=0.176 Sum_probs=30.6
Q ss_pred HHHHHHHHHh-CCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcC
Q psy1898 163 EKRIEEYKKT-NPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGG 210 (230)
Q Consensus 163 ~~~I~~l~~~-~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~ 210 (230)
+..|.+.+.+ +...++.+|.+.|.+ .+. .+|.+||+|.|..+
T Consensus 3 R~~Il~~l~~~~~~~sa~ei~~~l~~-~~~-----~i~~~TVYR~L~~L 45 (116)
T cd07153 3 RLAILEVLLESDGHLTAEEIYERLRK-KGP-----SISLATVYRTLELL 45 (116)
T ss_pred HHHHHHHHHhCCCCCCHHHHHHHHHh-cCC-----CCCHHHHHHHHHHH
Confidence 4456666655 446899999999987 454 37999999977543
No 326
>cd04781 HTH_MerR-like_sg6 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 6) with at least two conserved cysteines present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located 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, an
Probab=90.49 E-value=1.2 Score=34.45 Aligned_cols=67 Identities=19% Similarity=0.127 Sum_probs=46.8
Q ss_pred CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK 187 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~ 187 (230)
++..++|+.+|||..|+.-|.+ .|.+.|..+.+ .-+..++++...|..... ..-+.+..+|++.+..
T Consensus 1 m~IgevA~~~gvs~~tlRyYe~----~GLl~p~~~~~-gyR~Y~~~~l~~l~~I~~lr~~G~~L~eI~~~l~~ 68 (120)
T cd04781 1 LDIAEVARQSGLPASTLRYYEE----KGLIASIGRRG-LRRQYDPQVLDRLALIALGRAAGFSLDEIQAMLSH 68 (120)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH----CCCCCCCcCCC-CceecCHHHHHHHHHHHHHHHcCCCHHHHHHHHhc
Confidence 4788999999999999876654 58776644433 566778877666653221 2346888888887754
No 327
>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional
Probab=90.43 E-value=0.3 Score=44.32 Aligned_cols=37 Identities=11% Similarity=0.021 Sum_probs=31.0
Q ss_pred HHHHHHHHHH-cCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 104 IRLKIVEMAA-AGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 104 ~R~rIV~l~~-~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
.|..|..+++ .+....++|+.||||++|+|+++++|.
T Consensus 287 Er~~I~~aL~~~~gn~~~aA~~LGIsR~tLyrklk~~g 324 (326)
T PRK11608 287 EKELLQRSLQQAKFNQKRAAELLGLTYHQLRALLKKHQ 324 (326)
T ss_pred HHHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHHcC
Confidence 4555666665 478999999999999999999999873
No 328
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=90.41 E-value=0.47 Score=40.96 Aligned_cols=42 Identities=10% Similarity=0.078 Sum_probs=34.2
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE 141 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e 141 (230)
++...|.-+...+.+|+|..+||+.+|||.++|+++.++..+
T Consensus 184 L~~~er~vi~l~~~~~~t~~EIA~~lgis~~~V~q~~~~~~~ 225 (231)
T PRK12427 184 LDEREQLILHLYYQHEMSLKEIALVLDLTEARICQLNKKIAQ 225 (231)
T ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 455666666666778999999999999999999999887653
No 329
>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=90.41 E-value=0.24 Score=34.57 Aligned_cols=32 Identities=34% Similarity=0.435 Sum_probs=29.7
Q ss_pred CCCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898 115 GVRPCVISRQLRVSHGCVSKILNRYQETGSIR 146 (230)
Q Consensus 115 G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~ 146 (230)
..+..+||..+|+|+.||.+.++++++.|-+.
T Consensus 28 ~lt~~~iA~~~g~sr~tv~r~l~~l~~~g~I~ 59 (76)
T PF13545_consen 28 PLTQEEIADMLGVSRETVSRILKRLKDEGIIE 59 (76)
T ss_dssp ESSHHHHHHHHTSCHHHHHHHHHHHHHTTSEE
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 36899999999999999999999999999775
No 330
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=90.40 E-value=0.33 Score=42.59 Aligned_cols=44 Identities=23% Similarity=0.296 Sum_probs=38.2
Q ss_pred HHHHHHHHHHHHc-C-CCHHHHhhhhccccchhhhHHHHHhhhCCC
Q psy1898 102 NHIRLKIVEMAAA-G-VRPCVISRQLRVSHGCVSKILNRYQETGSI 145 (230)
Q Consensus 102 ~~~R~rIV~l~~~-G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~v 145 (230)
.+.+.+|++++++ + .+..++|+.|+||..||+|.+....+.|.+
T Consensus 4 ~~R~~~Il~~l~~~~~~~~~ela~~l~vS~~TiRRdL~~Le~~g~l 49 (252)
T PRK10906 4 TQRHDAIIELVKQQGYVSTEELVEHFSVSPQTIRRDLNDLAEQNKI 49 (252)
T ss_pred HHHHHHHHHHHHHcCCEeHHHHHHHhCCCHHHHHHHHHHHHHCCCE
Confidence 3567788887765 4 899999999999999999999999999976
No 331
>PF06413 Neugrin: Neugrin; InterPro: IPR010487 This family contains mouse and human neugrin proteins. Neugrin and m-neugrin are mainly expressed in neurons in the nervous system, and are thought to play an important role in the process of neuronal differentiation []. Homologues of neugrin are found in fungi suggesting they have a alternative role or more than one function.
Probab=90.35 E-value=0.62 Score=40.44 Aligned_cols=52 Identities=17% Similarity=0.223 Sum_probs=41.7
Q ss_pred CCCCCCCCHHHHHHHHHHHHhCCC-CCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcCCCCCC
Q psy1898 152 GSKPRVATPDVEKRIEEYKKTNPG-IFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGGRRDDC 215 (230)
Q Consensus 152 g~rpr~lt~~~~~~I~~l~~~~P~-~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~g~~~~ 215 (230)
|.++++++++..+.|..+-..+|. +|...|++. +. ||..+|.|||+.. +.|.
T Consensus 5 ~~p~k~Ls~~~~~~ir~L~~~~p~~~t~~~Lae~----F~-------vspe~irrILksk-w~p~ 57 (225)
T PF06413_consen 5 GNPPKKLSREAMEQIRYLHKEDPEEWTVERLAES----FK-------VSPEAIRRILKSK-WVPT 57 (225)
T ss_pred CCCCCCCCHHHHHHHHHHHHhCccccCHHHHHhh----CC-------CCHHHHHHHHhcC-CCCC
Confidence 568899999999999999999996 777666652 43 5999999999973 4443
No 332
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=90.33 E-value=0.4 Score=41.84 Aligned_cols=40 Identities=15% Similarity=0.167 Sum_probs=31.8
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHH
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRY 139 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy 139 (230)
++...|.-+...+.+|+|..+||+.+|||.+||+++.++-
T Consensus 210 L~~~er~vi~~~~~~~~t~~eIA~~lgis~~~V~~~~~~a 249 (258)
T PRK08215 210 LNDREKLILNLRFFQGKTQMEVAEEIGISQAQVSRLEKAA 249 (258)
T ss_pred CCHHHHHHHHHHHhcCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 5556655444455689999999999999999999998764
No 333
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=90.30 E-value=0.36 Score=41.68 Aligned_cols=43 Identities=9% Similarity=0.138 Sum_probs=35.3
Q ss_pred CCcCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 97 GRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 97 g~~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
-.++|.. -..|+.++.+|++.++||+.+++|.+||.+-+.+-.
T Consensus 141 ~~~LS~R-E~eVL~Lia~G~SnkEIA~~L~IS~~TVk~hvs~I~ 183 (217)
T PRK13719 141 KNKVTKY-QNDVFILYSFGFSHEYIAQLLNITVGSSKNKISEIL 183 (217)
T ss_pred cCCCCHH-HHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 3445543 357888999999999999999999999999988754
No 334
>PRK09492 treR trehalose repressor; Provisional
Probab=90.27 E-value=0.37 Score=42.21 Aligned_cols=41 Identities=22% Similarity=0.281 Sum_probs=31.7
Q ss_pred CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHh
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKT 172 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~ 172 (230)
.+.++||+.+|||++||++.++. + ..++++.+++|.+..++
T Consensus 5 ~ti~dIA~~agVS~~TVSrvLn~---------------~-~~vs~~tr~rV~~~a~e 45 (315)
T PRK09492 5 LTIKDIARLSGVGKSTVSRVLNN---------------E-SGVSEETRERVEAVINQ 45 (315)
T ss_pred CcHHHHHHHhCCCHHHHhHHhCC---------------C-CCCCHHHHHHHHHHHHH
Confidence 58899999999999999999852 1 12467777777766655
No 335
>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=90.25 E-value=0.45 Score=31.60 Aligned_cols=34 Identities=24% Similarity=0.531 Sum_probs=29.9
Q ss_pred HcCCCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898 113 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIR 146 (230)
Q Consensus 113 ~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~ 146 (230)
..+.+..+||+.++++++|+.+++++-.+.|-+.
T Consensus 15 ~~~~~~~~la~~~~~~~~~~t~~i~~L~~~g~I~ 48 (59)
T PF01047_consen 15 NGGITQSELAEKLGISRSTVTRIIKRLEKKGLIE 48 (59)
T ss_dssp HSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred cCCCCHHHHHHHHCCChhHHHHHHHHHHHCCCEE
Confidence 4569999999999999999999999999999773
No 336
>PRK10072 putative transcriptional regulator; Provisional
Probab=90.23 E-value=0.23 Score=37.42 Aligned_cols=26 Identities=23% Similarity=0.202 Sum_probs=23.5
Q ss_pred HHcCCCHHHHhhhhccccchhhhHHH
Q psy1898 112 AAAGVRPCVISRQLRVSHGCVSKILN 137 (230)
Q Consensus 112 ~~~G~s~~~IAr~lgVS~sTV~kwik 137 (230)
...|++..++|+.+|||.+||++|.+
T Consensus 43 ~~~glTQ~elA~~lGvS~~TVs~WE~ 68 (96)
T PRK10072 43 KGTGLKIDDFARVLGVSVAMVKEWES 68 (96)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 34699999999999999999999974
No 337
>PF13565 HTH_32: Homeodomain-like domain
Probab=90.23 E-value=0.47 Score=33.28 Aligned_cols=40 Identities=33% Similarity=0.432 Sum_probs=31.5
Q ss_pred CCcC-CHHHHHHHHHHHHcC--CCHHHHhhhh----c--c--ccchhhhHH
Q psy1898 97 GRPL-PNHIRLKIVEMAAAG--VRPCVISRQL----R--V--SHGCVSKIL 136 (230)
Q Consensus 97 g~~~-s~~~R~rIV~l~~~G--~s~~~IAr~l----g--V--S~sTV~kwi 136 (230)
|++. +.+.+..|++++.+. ++..+|+..+ | + |.+||++|+
T Consensus 27 Grp~~~~e~~~~i~~~~~~~p~wt~~~i~~~L~~~~g~~~~~S~~tv~R~L 77 (77)
T PF13565_consen 27 GRPRKDPEQRERIIALIEEHPRWTPREIAEYLEEEFGISVRVSRSTVYRIL 77 (77)
T ss_pred CCCCCcHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCCCccHhHHHHhC
Confidence 4444 478889999998765 9999999865 3 4 999999984
No 338
>PRK09863 putative frv operon regulatory protein; Provisional
Probab=90.23 E-value=1.7 Score=42.40 Aligned_cols=94 Identities=15% Similarity=0.017 Sum_probs=58.2
Q ss_pred HHHHHHHHH-cCCCHHHHhhhhccccchhhhHHHHHhh----hCCC-CcCCCCCCCC-----C-------CCCHHHHHHH
Q psy1898 105 RLKIVEMAA-AGVRPCVISRQLRVSHGCVSKILNRYQE----TGSI-RPGVIGGSKP-----R-------VATPDVEKRI 166 (230)
Q Consensus 105 R~rIV~l~~-~G~s~~~IAr~lgVS~sTV~kwikRy~e----~G~v-~p~~~gg~rp-----r-------~lt~~~~~~I 166 (230)
..+|+.++. +..+..++|+.|+||..||++=++.-.+ .|.. ..... |-+- . ..+++....+
T Consensus 6 ~~~iL~~L~~~~~t~~~LA~~l~VS~RTIr~dI~~in~~l~~~~~~~i~~~~-Gy~l~~~~~~~~~~~~~~~~~e~~~il 84 (584)
T PRK09863 6 ELKIVDLLEQQDRSGGELAQQLGVSRRTIVRDIAYINFTLNGKAIGSISGSA-KYHLEILNRRSLFQLLQKSDNEDRLLL 84 (584)
T ss_pred HHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhcchhheecCC-ceEEEeCCHHHHHHHHhcCCHHHHHHH
Confidence 355666554 4599999999999999999998886533 3321 11111 1110 0 1122333333
Q ss_pred HHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcCC
Q psy1898 167 EEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGGR 211 (230)
Q Consensus 167 ~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~g 211 (230)
..++. +...+..++++.|. ||.+||.+.|++..
T Consensus 85 ~~Ll~-~~~~~~~~La~~l~-----------vS~sTi~~dl~~v~ 117 (584)
T PRK09863 85 LRLLL-NTFTPMAQLASALN-----------LSRTWVAERLPRLN 117 (584)
T ss_pred HHHHH-cCCccHHHHHHHhC-----------CCHHHHHHHHHHHH
Confidence 44554 55677888887762 69999999987764
No 339
>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=90.21 E-value=0.48 Score=35.92 Aligned_cols=43 Identities=28% Similarity=0.360 Sum_probs=35.8
Q ss_pred HHHHHHHHHHc---CCCHHHHhhhh-----ccccchhhhHHHHHhhhCCCC
Q psy1898 104 IRLKIVEMAAA---GVRPCVISRQL-----RVSHGCVSKILNRYQETGSIR 146 (230)
Q Consensus 104 ~R~rIV~l~~~---G~s~~~IAr~l-----gVS~sTV~kwikRy~e~G~v~ 146 (230)
.|..|++.+.+ ..|..+|...+ .++++|||+.++.+.+.|.+.
T Consensus 2 qR~~Il~~l~~~~~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~Gli~ 52 (116)
T cd07153 2 QRLAILEVLLESDGHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVR 52 (116)
T ss_pred HHHHHHHHHHhCCCCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCEE
Confidence 47777776543 38999999988 699999999999999999764
No 340
>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=90.15 E-value=0.35 Score=32.27 Aligned_cols=35 Identities=23% Similarity=0.296 Sum_probs=27.3
Q ss_pred CCCChhHHHHHHHHHhcCCChhhhhhhhccccccc
Q psy1898 54 RPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGVN 88 (230)
Q Consensus 54 ~plp~~~r~~I~e~~~~g~~~~~isr~lrvshg~~ 88 (230)
..|+...+.+|++++..|.+..+|+++|+|+...+
T Consensus 5 ~~LTl~eK~~iI~~~e~g~s~~~ia~~fgv~~sTv 39 (53)
T PF04218_consen 5 KSLTLEEKLEIIKRLEEGESKRDIAREFGVSRSTV 39 (53)
T ss_dssp SS--HHHHHHHHHHHHCTT-HHHHHHHHT--CCHH
T ss_pred ccCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHH
Confidence 46789999999999999999999999999877665
No 341
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=90.10 E-value=1.2 Score=35.87 Aligned_cols=67 Identities=15% Similarity=-0.004 Sum_probs=46.3
Q ss_pred CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHH
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLV 186 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~ 186 (230)
++..++|+.+|||..|+.-|. +.|.+.|..+..+.-+..++++.+.|..... ..-..++.+|++.+.
T Consensus 8 ~~IgevAk~~Gvs~~TLRyYE----~~GLl~p~~r~~~gyR~Y~~~~l~rl~~I~~lr~~G~sL~eI~~ll~ 75 (144)
T PRK13752 8 LTIGVFAKAAGVNVETIRFYQ----RKGLLPEPDKPYGSIRRYGEADVTRVRFVKSAQRLGFSLDEIAELLR 75 (144)
T ss_pred ccHHHHHHHHCcCHHHHHHHH----HCCCCCCCccCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHh
Confidence 789999999999999976554 4687765433223457778877666653332 234578888887774
No 342
>PRK15043 transcriptional regulator MirA; Provisional
Probab=90.07 E-value=1 Score=39.55 Aligned_cols=68 Identities=18% Similarity=0.220 Sum_probs=48.0
Q ss_pred CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK 187 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~ 187 (230)
++..++|+.+|||..|+..|.++| |.+.|....+ .-+..++++.+.|..... .+-..+..+|++.+..
T Consensus 4 ytIgeVA~~~GVs~~TLR~wErr~---GLL~P~Rt~~-G~R~Ys~~dv~rL~~I~~l~~~G~~i~eIk~ll~~ 72 (243)
T PRK15043 4 YTIGEVALLCDINPVTLRAWQRRY---GLLKPQRTDG-GHRLFNDADIDRIREIKRWIDNGVQVSKVKMLLSN 72 (243)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHhc---CCCCCccCCC-CCEEECHHHHHHHHHHHHHHHcCCCHHHHHHHHhc
Confidence 578999999999999999997654 5666643322 456778877666653332 2346888888887764
No 343
>PRK15320 transcriptional activator SprB; Provisional
Probab=90.06 E-value=0.5 Score=40.55 Aligned_cols=40 Identities=8% Similarity=0.115 Sum_probs=34.2
Q ss_pred HHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhhhCC
Q psy1898 105 RLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGS 144 (230)
Q Consensus 105 R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~ 144 (230)
-..|+.++.+|.|.++||..|++|.+||++...+-.+-=.
T Consensus 169 EIEVL~LLAkG~SNKEIAekL~LS~KTVSTYKnRLLeKLg 208 (251)
T PRK15320 169 KYALLILLSSGHPAIELAKKFGLGTKTVSIYRKKVMYRLG 208 (251)
T ss_pred HHHHHHHHHcCCCHHHHHHHhccchhhHHHHHHHHHHHcC
Confidence 3467778899999999999999999999999998775433
No 344
>COG2964 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=89.88 E-value=0.4 Score=41.38 Aligned_cols=41 Identities=20% Similarity=0.343 Sum_probs=31.8
Q ss_pred HHHHHHHH-HHHcC-----CCHHHHhhhhccccchhhhHHHHHhhhC
Q psy1898 103 HIRLKIVE-MAAAG-----VRPCVISRQLRVSHGCVSKILNRYQETG 143 (230)
Q Consensus 103 ~~R~rIV~-l~~~G-----~s~~~IAr~lgVS~sTV~kwikRy~e~G 143 (230)
+.+.+||. +++.| -....+|..|++|+.|||++++.+++.|
T Consensus 173 ~~~reiV~~L~EkGiF~lK~Ai~~VA~~L~iSr~TVY~YL~~~k~~~ 219 (220)
T COG2964 173 AKNREIVKALYEKGIFNLKDAINIVADRLGISRHTVYRYLRKFKAGG 219 (220)
T ss_pred HHHHHHHHHHHhcCccchhhHHHHHHHHhCCChHHHHHHHHHhhcCC
Confidence 55555665 66778 3455689999999999999999988765
No 345
>PF07141 Phage_term_sma: Putative bacteriophage terminase small subunit; InterPro: IPR010789 This entry is represented by Bacteriophage 712, Gp1; it is a family of uncharacterised viral proteins. This family consists of several putative Lactococcus bacteriophage terminase small subunit proteins. The exact function of this family is unknown.
Probab=89.87 E-value=0.39 Score=38.43 Aligned_cols=44 Identities=9% Similarity=0.078 Sum_probs=38.4
Q ss_pred CCCcCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHH
Q psy1898 96 NGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRY 139 (230)
Q Consensus 96 ~g~~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy 139 (230)
-++-|...+-.+||...+++.+.++|+..|.||+-|.+.|.+.-
T Consensus 12 lpkmYtE~Lve~II~~IE~dt~~sEIc~~L~isrKtFyeWrdtk 55 (174)
T PF07141_consen 12 LPKMYTEPLVEQIIDKIESDTNDSEICTSLHISRKTFYEWRDTK 55 (174)
T ss_pred cHHhhhhHHHHHHHHHHHcCCcHHHHHHHHhccHHHHHHHHhhh
Confidence 34557778889999999999999999999999999999998653
No 346
>PRK09462 fur ferric uptake regulator; Provisional
Probab=89.85 E-value=1.2 Score=35.70 Aligned_cols=45 Identities=18% Similarity=0.147 Sum_probs=32.3
Q ss_pred CHHHHHHHHHHHHhC--CCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcC
Q psy1898 159 TPDVEKRIEEYKKTN--PGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGG 210 (230)
Q Consensus 159 t~~~~~~I~~l~~~~--P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~ 210 (230)
|+. +..|.+.+... ...++.||.+.|.+ .+.. +|.+||||.|..+
T Consensus 16 T~q-R~~Il~~l~~~~~~h~sa~eI~~~l~~-~~~~-----i~~aTVYR~L~~L 62 (148)
T PRK09462 16 TLP-RLKILEVLQEPDNHHVSAEDLYKRLID-MGEE-----IGLATVYRVLNQF 62 (148)
T ss_pred CHH-HHHHHHHHHhCCCCCCCHHHHHHHHHh-hCCC-----CCHHHHHHHHHHH
Confidence 444 44555555542 37899999999987 5553 7999999998654
No 347
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=89.79 E-value=0.46 Score=41.88 Aligned_cols=42 Identities=17% Similarity=0.164 Sum_probs=32.2
Q ss_pred CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCC--CCCCHHHHHHHHHHHHh
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKP--RVATPDVEKRIEEYKKT 172 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rp--r~lt~~~~~~I~~l~~~ 172 (230)
++.++||+..|||.+||++.++. ++ ...+++.+++|.+..++
T Consensus 1 ~ti~dIA~~aGVS~~TVSrvLn~---------------~~~~~~Vs~~tr~rV~~~a~e 44 (328)
T PRK11303 1 MKLDEIARLAGVSRTTASYVING---------------KAKQYRVSDKTVEKVMAVVRE 44 (328)
T ss_pred CCHHHHHHHhCCCHHHHHHHHcC---------------CCCCCCcCHHHHHHHHHHHHH
Confidence 47899999999999999999851 11 13577888888777665
No 348
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=89.77 E-value=0.5 Score=35.51 Aligned_cols=37 Identities=14% Similarity=0.116 Sum_probs=29.2
Q ss_pred HHHHHHHHHH-cCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 104 IRLKIVEMAA-AGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 104 ~R~rIV~l~~-~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
.+.-+..+++ .+....++|+.+|||++|+++.+++|.
T Consensus 56 Er~~i~~aL~~~~gn~s~AAr~LGIsRsTL~rKLkr~g 93 (95)
T PRK00430 56 EAPLLDMVMQYTRGNQTRAALMLGINRGTLRKKLKKYG 93 (95)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHhC
Confidence 3444445444 577899999999999999999999874
No 349
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=89.74 E-value=0.81 Score=38.75 Aligned_cols=46 Identities=13% Similarity=0.024 Sum_probs=35.1
Q ss_pred CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHH
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPD 161 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~ 161 (230)
++..++|+.||||+++|..=+++-...|.+.-.+..|-.-..++.+
T Consensus 35 L~e~~La~~lgVSRtpVREAL~~L~~eGLV~~~~~~g~~v~~~~~~ 80 (221)
T PRK11414 35 LITKNLAEQLGMSITPVREALLRLVSVNALSVAPAQAFTVPEVSKR 80 (221)
T ss_pred cCHHHHHHHHCCCchhHHHHHHHHHHCCCEEecCCCceeecCCCHH
Confidence 6788999999999999999999999999875444433333334443
No 350
>PF01475 FUR: Ferric uptake regulator family; InterPro: IPR002481 The Ferric uptake regulator (FUR) family includes metal ion uptake regulator proteins. These are responsible for controlling the intracellular concentration of iron in many bacteria. Although iron is essential for most organisms, high concentrations can be toxic because of the formation of hydroxyl radicals []. FURs can also control zinc homeostasis [] and is the subject of research on the pathogenesis of mycobacteria.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1MZB_A 2RGV_B 2FE3_B 3F8N_B 3EYY_B 2W57_A 2FU4_A 2O03_A 3MWM_B 2XIG_B ....
Probab=89.68 E-value=0.49 Score=36.33 Aligned_cols=43 Identities=30% Similarity=0.240 Sum_probs=30.5
Q ss_pred HHHHHHHHHHhCC-CCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcC
Q psy1898 162 VEKRIEEYKKTNP-GIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGG 210 (230)
Q Consensus 162 ~~~~I~~l~~~~P-~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~ 210 (230)
.+..|..++.+.+ ..|+.+|.+.|.+ .+.. +|.+||+|.|..+
T Consensus 9 ~R~~Il~~l~~~~~~~ta~ei~~~l~~-~~~~-----is~~TVYR~L~~L 52 (120)
T PF01475_consen 9 QRLAILELLKESPEHLTAEEIYDKLRK-KGPR-----ISLATVYRTLDLL 52 (120)
T ss_dssp HHHHHHHHHHHHSSSEEHHHHHHHHHH-TTTT-------HHHHHHHHHHH
T ss_pred HHHHHHHHHHcCCCCCCHHHHHHHhhh-ccCC-----cCHHHHHHHHHHH
Confidence 3455666665544 7889999999987 6653 8999999998754
No 351
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=89.62 E-value=0.3 Score=41.85 Aligned_cols=41 Identities=20% Similarity=0.217 Sum_probs=32.1
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
+|...|.-+...+-+|++..+||+.||+|.+||...+.|.+
T Consensus 150 L~~~~r~i~~l~~~~g~s~~EIAe~lgis~~tVk~~l~Rar 190 (231)
T PRK11922 150 LPDAFRAVFVLRVVEELSVEETAQALGLPEETVKTRLHRAR 190 (231)
T ss_pred CCHHHhhhheeehhcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 44455544444467899999999999999999999887654
No 352
>PRK09483 response regulator; Provisional
Probab=89.61 E-value=0.45 Score=38.87 Aligned_cols=41 Identities=27% Similarity=0.234 Sum_probs=33.7
Q ss_pred cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
.++..++ +|+.++..|.+.++||..+++|..||...+++-.
T Consensus 148 ~Lt~rE~-~vl~~~~~G~~~~~Ia~~l~is~~TV~~~~~~i~ 188 (217)
T PRK09483 148 SLSEREL-QIMLMITKGQKVNEISEQLNLSPKTVNSYRYRMF 188 (217)
T ss_pred ccCHHHH-HHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 3665554 5567889999999999999999999998887744
No 353
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=89.59 E-value=0.7 Score=39.30 Aligned_cols=46 Identities=9% Similarity=0.024 Sum_probs=37.7
Q ss_pred CCHHHHHHHHHHHH----cCCCHHHHhhhhccccchhhhHHHHHhhhCCC
Q psy1898 100 LPNHIRLKIVEMAA----AGVRPCVISRQLRVSHGCVSKILNRYQETGSI 145 (230)
Q Consensus 100 ~s~~~R~rIV~l~~----~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v 145 (230)
++..+...++.+.. .|++.++||+.+++|..||.+.+++-...|.+
T Consensus 159 Lt~re~~~l~~~i~~~~~~g~s~~eIA~~l~iS~~Tv~~~~~~~~~~~~~ 208 (239)
T PRK10430 159 LTPQTLRTLCQWIDAHQDYEFSTDELANAVNISRVSCRKYLIWLVNCHIL 208 (239)
T ss_pred CCHHHHHHHHHHHHhCCCCCcCHHHHHHHhCchHHHHHHHHHHHHhCCEE
Confidence 55555555555554 79999999999999999999999988888855
No 354
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=89.54 E-value=2 Score=34.54 Aligned_cols=84 Identities=18% Similarity=0.209 Sum_probs=58.3
Q ss_pred CCChhHHHHHHHHH-hcCCChhhhhhhhccccccc--c----------cCCcccCCC--cCCHHHHHHHHHHHHcC-CCH
Q psy1898 55 PLPNHIRLKIVEMA-AAGVRPCVISRQLRVSHGVN--Q----------LGGVFINGR--PLPNHIRLKIVEMAAAG-VRP 118 (230)
Q Consensus 55 plp~~~r~~I~e~~-~~g~~~~~isr~lrvshg~~--~----------l~~~~~~g~--~~s~~~R~rIV~l~~~G-~s~ 118 (230)
|-....|..++..+ ..|.+..+++..|+||-++. - |-..+..|+ -++.+....+++...+. ++.
T Consensus 4 ~~s~~~R~~~~~~~~~~G~S~re~Ak~~gvs~sTvy~wv~r~~e~G~~l~~~~~~GrP~kl~~~q~~~l~e~~~~k~wTl 83 (138)
T COG3415 4 PFSNDLRERVVDAVVGEGLSCREAAKRFGVSISTVYRWVRRYRETGLDLPPKPRKGRPRKLSEEQLEILLERLREKDWTL 83 (138)
T ss_pred hhhHHHHHHHHHHHHHcCccHHHHHHHhCccHHHHHHHHHHhccccccccCccCCCCCcccCHHHHHHHHHHHhcccchH
Confidence 44577888888887 59999999999999865553 0 223333333 37778888888877654 777
Q ss_pred HHH----hhhhcc--ccchhhhHHHH
Q psy1898 119 CVI----SRQLRV--SHGCVSKILNR 138 (230)
Q Consensus 119 ~~I----Ar~lgV--S~sTV~kwikR 138 (230)
+++ ...||| +.++|++++++
T Consensus 84 ~~~~~~l~~e~gv~y~~~~v~~~l~~ 109 (138)
T COG3415 84 KELVEELGLEFGVWYHASAVRRLLHE 109 (138)
T ss_pred HHHHHHHhhhcCeEEeHHHHHHHHHH
Confidence 777 446777 55578888765
No 355
>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=89.49 E-value=0.46 Score=41.81 Aligned_cols=41 Identities=22% Similarity=0.284 Sum_probs=30.7
Q ss_pred CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHh
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKT 172 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~ 172 (230)
.+.++||+.+|||++||++.++. ....+++.+++|.+..++
T Consensus 2 ~ti~dIA~~agVS~sTVSr~Ln~----------------~~~vs~~tr~rV~~~a~~ 42 (311)
T TIGR02405 2 LTIKDIARLAGVGKSTVSRVLNN----------------EPKVSIETRERVEQVIQQ 42 (311)
T ss_pred CcHHHHHHHhCCCHHHHHHHhCC----------------CCCCCHHHHHHHHHHHHH
Confidence 47899999999999999999852 112466777777666655
No 356
>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=89.43 E-value=0.46 Score=42.15 Aligned_cols=41 Identities=10% Similarity=-0.001 Sum_probs=31.8
Q ss_pred CCHHHHHHHHHHH----HcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 100 LPNHIRLKIVEMA----AAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 100 ~s~~~R~rIV~l~----~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
+|...|.-+...+ .+|+|.++||..||||.+||..++.+..
T Consensus 223 Lp~~~R~Vl~l~ygL~~~e~~s~~EIA~~Lgis~~tVk~~l~rAl 267 (285)
T TIGR02394 223 LNERQREVLARRFGLLGYEPATLEEVAAEVGLTRERVRQIQVEAL 267 (285)
T ss_pred CCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHH
Confidence 4555554444333 6899999999999999999999988754
No 357
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=89.34 E-value=0.55 Score=31.36 Aligned_cols=33 Identities=27% Similarity=0.327 Sum_probs=28.6
Q ss_pred HHHHHHHcCCCHHHHhhhhccccchhhhHHHHH
Q psy1898 107 KIVEMAAAGVRPCVISRQLRVSHGCVSKILNRY 139 (230)
Q Consensus 107 rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy 139 (230)
.++.+..+|.+..+||..+++|..||..-+.+-
T Consensus 11 ~v~~l~~~G~s~~eia~~l~is~~tV~~h~~~i 43 (65)
T COG2771 11 EILRLVAQGKSNKEIARILGISEETVKTHLRNI 43 (65)
T ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 455688899999999999999999999887764
No 358
>PRK10651 transcriptional regulator NarL; Provisional
Probab=89.32 E-value=0.65 Score=37.43 Aligned_cols=41 Identities=20% Similarity=0.311 Sum_probs=35.2
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE 141 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e 141 (230)
++... .+|+.++.+|.+.++||+.+++|..||...+++-..
T Consensus 156 Lt~rE-~~vl~~l~~g~~~~~ia~~l~is~~tV~~~~~~l~~ 196 (216)
T PRK10651 156 LTPRE-RDILKLIAQGLPNKMIARRLDITESTVKVHVKHMLK 196 (216)
T ss_pred CCHHH-HHHHHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 66555 488889999999999999999999999999987543
No 359
>PRK09726 antitoxin HipB; Provisional
Probab=89.28 E-value=0.42 Score=34.99 Aligned_cols=25 Identities=12% Similarity=0.318 Sum_probs=23.0
Q ss_pred HcCCCHHHHhhhhccccchhhhHHH
Q psy1898 113 AAGVRPCVISRQLRVSHGCVSKILN 137 (230)
Q Consensus 113 ~~G~s~~~IAr~lgVS~sTV~kwik 137 (230)
+.|++..++|+.+|||++||++|.+
T Consensus 23 ~~gltq~elA~~~gvs~~tis~~e~ 47 (88)
T PRK09726 23 QNGWTQSELAKKIGIKQATISNFEN 47 (88)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHC
Confidence 4589999999999999999999975
No 360
>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=89.28 E-value=1.1 Score=39.42 Aligned_cols=45 Identities=16% Similarity=0.285 Sum_probs=37.8
Q ss_pred HHHHHHHHHc--C-CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCC
Q psy1898 105 RLKIVEMAAA--G-VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV 149 (230)
Q Consensus 105 R~rIV~l~~~--G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~ 149 (230)
=.+|+..+.. | .+..++|+++|||+++|..=+++..+.|.+..++
T Consensus 185 v~~IL~~L~~~egrlse~eLAerlGVSRs~ireAlrkLE~aGvIe~r~ 232 (251)
T TIGR02787 185 VEHIFEELDGNEGLLVASKIADRVGITRSVIVNALRKLESAGVIESRS 232 (251)
T ss_pred HHHHHHHhccccccccHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecc
Confidence 3556666554 4 8999999999999999999999999999887655
No 361
>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B.
Probab=89.26 E-value=0.21 Score=34.49 Aligned_cols=19 Identities=26% Similarity=0.281 Sum_probs=17.3
Q ss_pred CHHHHhhhhccccchhhhH
Q psy1898 117 RPCVISRQLRVSHGCVSKI 135 (230)
Q Consensus 117 s~~~IAr~lgVS~sTV~kw 135 (230)
+...+|+.||||+++|+.|
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 7889999999999999999
No 362
>PRK09526 lacI lac repressor; Reviewed
Probab=89.18 E-value=0.51 Score=41.88 Aligned_cols=41 Identities=22% Similarity=0.265 Sum_probs=30.8
Q ss_pred CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHh
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKT 172 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~ 172 (230)
.+.++||++.|||++||++.++. ++ ..+++.+++|.+..++
T Consensus 6 ~ti~dIA~~aGVS~~TVSrvLn~---------------~~-~vs~~tr~rV~~~a~e 46 (342)
T PRK09526 6 VTLYDVARYAGVSYQTVSRVLNQ---------------AS-HVSAKTREKVEAAMAE 46 (342)
T ss_pred CcHHHHHHHhCCCHHHHHHHhcC---------------CC-CCCHHHHHHHHHHHHH
Confidence 58999999999999999999852 11 2466777777666554
No 363
>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=89.11 E-value=2.7 Score=30.80 Aligned_cols=39 Identities=21% Similarity=0.235 Sum_probs=30.9
Q ss_pred HHHHHHHHHHH--cCCCHHHHhhhhc-cccchhhhHHHHHhh
Q psy1898 103 HIRLKIVEMAA--AGVRPCVISRQLR-VSHGCVSKILNRYQE 141 (230)
Q Consensus 103 ~~R~rIV~l~~--~G~s~~~IAr~lg-VS~sTV~kwikRy~e 141 (230)
.-|+-+..+.. .|+|..+|++.|| .+++||..-+++.++
T Consensus 30 ~aR~ia~yl~~~~~~~s~~~Ig~~fg~r~hStV~~a~~ri~~ 71 (90)
T cd06571 30 LARQIAMYLARELTGLSLPEIGRAFGGRDHSTVLHAVRKIEE 71 (90)
T ss_pred hHHHHHHHHHHHHhCCCHHHHHHHhCCCCHhHHHHHHHHHHH
Confidence 44555555444 3899999999999 999999999888764
No 364
>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=89.08 E-value=0.66 Score=36.77 Aligned_cols=41 Identities=17% Similarity=0.154 Sum_probs=32.7
Q ss_pred CCHHHHHHHHHHHHcCC--CHHHHhhhhccccchhhhHHHHHh
Q psy1898 100 LPNHIRLKIVEMAAAGV--RPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~--s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
++.+.|.-|-..+-.+. +..+||..|++|.+||+++.+++-
T Consensus 83 Ld~~er~II~~rY~~~~~~t~~~Ia~~l~iS~~t~~r~r~~~l 125 (134)
T TIGR01636 83 ADEQTRVIIQELYMKKRPLTLVGLAQQLFISKSTAYRLRNHII 125 (134)
T ss_pred CCHHHHHHHHHHHccCCCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 55677765556665554 999999999999999999988764
No 365
>PF07900 DUF1670: Protein of unknown function (DUF1670); InterPro: IPR012872 The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=88.91 E-value=0.66 Score=40.07 Aligned_cols=68 Identities=15% Similarity=0.122 Sum_probs=50.0
Q ss_pred hhHHHHHHHHHhcCCChhhhhhhhcccccccccCCcccCCCcCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhH
Q psy1898 58 NHIRLKIVEMAAAGVRPCVISRQLRVSHGVNQLGGVFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKI 135 (230)
Q Consensus 58 ~~~r~~I~e~~~~g~~~~~isr~lrvshg~~~l~~~~~~g~~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kw 135 (230)
..-|..|+++++.|..+.+|+|... |...+..+|.. .=.+|..++..|++..+||..+|+|.+-|.-.
T Consensus 150 ~tHK~~ii~~~l~g~~~~eiar~t~--HS~~av~rYi~--------~F~rV~~l~~~~~~~~eia~~tg~S~~Lv~eY 217 (220)
T PF07900_consen 150 VTHKKIIIRLYLKGKPTPEIARRTN--HSPEAVDRYIK--------DFKRVLMLYEKGMSPEEIAFITGMSERLVKEY 217 (220)
T ss_pred chHHHHHHHHHHcCCCHHHHHHHhc--cCHHHHHHHHH--------hhHHhHHHHHcCCCHHHHHHHHCCCHHHHHHH
Confidence 4567888999999998889988765 66665555542 22466667888899999999999987766544
No 366
>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=88.88 E-value=0.57 Score=31.65 Aligned_cols=36 Identities=17% Similarity=0.220 Sum_probs=28.7
Q ss_pred HHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhhh
Q psy1898 107 KIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQET 142 (230)
Q Consensus 107 rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~ 142 (230)
+++..+.+-.+...+|+.++||+++|++.+++.++.
T Consensus 5 ~~f~~v~~~gs~~~AA~~l~is~~~vs~~i~~LE~~ 40 (60)
T PF00126_consen 5 RYFLAVAETGSISAAAEELGISQSAVSRQIKQLEEE 40 (60)
T ss_dssp HHHHHHHHHSSHHHHHHHCTSSHHHHHHHHHHHHHH
T ss_pred HHHHHHHHhCCHHHHHHHhhccchHHHHHHHHHHHH
Confidence 344444443499999999999999999999998854
No 367
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=88.87 E-value=0.56 Score=41.64 Aligned_cols=41 Identities=15% Similarity=0.169 Sum_probs=31.2
Q ss_pred CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHh
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKT 172 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~ 172 (230)
.+.++||++.|||++||++.++. ++ .++++.+++|.+..++
T Consensus 2 ~Ti~dIA~~agVS~~TVSrvLn~---------------~~-~vs~~tr~~V~~~a~e 42 (341)
T PRK10703 2 ATIKDVAKRAGVSTTTVSHVINK---------------TR-FVAEETRNAVWAAIKE 42 (341)
T ss_pred CCHHHHHHHhCCCHHHHHHHHcC---------------CC-CCCHHHHHHHHHHHHH
Confidence 37899999999999999999852 11 2467777777776655
No 368
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=88.86 E-value=0.62 Score=40.99 Aligned_cols=42 Identities=24% Similarity=0.299 Sum_probs=33.3
Q ss_pred cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
+++.-.|.-+...+.++++.++||+.+|||.+.|+++.++.-
T Consensus 196 ~L~EREk~Vl~l~y~eelt~kEI~~~LgISes~VSql~kkai 237 (247)
T COG1191 196 PLPEREKLVLVLRYKEELTQKEIAEVLGISESRVSRLHKKAI 237 (247)
T ss_pred ccCHHHHHHHHHHHHhccCHHHHHHHhCccHHHHHHHHHHHH
Confidence 344455555555677899999999999999999999988753
No 369
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=88.84 E-value=0.63 Score=36.87 Aligned_cols=43 Identities=19% Similarity=0.369 Sum_probs=36.1
Q ss_pred HHHHHHHHHHHc-C-CCHHHHhhhhccccchhhhHHHHHhhhCCC
Q psy1898 103 HIRLKIVEMAAA-G-VRPCVISRQLRVSHGCVSKILNRYQETGSI 145 (230)
Q Consensus 103 ~~R~rIV~l~~~-G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~v 145 (230)
+.-.+|+..+.. + .|.++||+.+|+|.+||.+-+++..+.|.+
T Consensus 8 ~~D~~IL~~L~~d~r~~~~eia~~lglS~~~v~~Ri~~L~~~GiI 52 (154)
T COG1522 8 DIDRRILRLLQEDARISNAELAERVGLSPSTVLRRIKRLEEEGVI 52 (154)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCce
Confidence 445567776654 3 999999999999999999999999999954
No 370
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=88.71 E-value=9.1 Score=31.18 Aligned_cols=98 Identities=20% Similarity=0.149 Sum_probs=59.2
Q ss_pred HHHHH-HHH-cC-CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHH----------HHHHHHh
Q psy1898 106 LKIVE-MAA-AG-VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKR----------IEEYKKT 172 (230)
Q Consensus 106 ~rIV~-l~~-~G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~----------I~~l~~~ 172 (230)
.++|. +.. .| ....+||+.|+|+++||..-+++-.+.|-+.-.+.+ .-.+|+.-.+. +..++.+
T Consensus 12 L~~Iy~l~~~~~~~~~~diA~~L~Vsp~sVt~ml~rL~~~GlV~~~~y~---gi~LT~~G~~~a~~~~r~hrlle~fL~~ 88 (154)
T COG1321 12 LETIYELLEEKGFARTKDIAERLKVSPPSVTEMLKRLERLGLVEYEPYG---GVTLTEKGREKAKELLRKHRLLERFLVD 88 (154)
T ss_pred HHHHHHHHhccCcccHHHHHHHhCCCcHHHHHHHHHHHHCCCeEEecCC---CeEEChhhHHHHHHHHHHHHHHHHHHHH
Confidence 34444 443 34 899999999999999999999999999987543332 23344332211 1222222
Q ss_pred CCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcCCC
Q psy1898 173 NPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGGRR 212 (230)
Q Consensus 173 ~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~g~ 212 (230)
--.....+..+.... ... .+|..++.|+.+-.+.
T Consensus 89 ~lg~~~~~~~~ea~~-leh-----~~s~~~~~rl~~~l~~ 122 (154)
T COG1321 89 VLGLDWEEAHEEAEG-LEH-----ALSDETAERLDELLGF 122 (154)
T ss_pred HhCCCHHHHHHHHHH-Hhh-----cCCHHHHHHHHHHhCC
Confidence 223344444322222 222 2699999999888874
No 371
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=88.68 E-value=0.53 Score=41.66 Aligned_cols=41 Identities=12% Similarity=0.099 Sum_probs=31.2
Q ss_pred CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHh
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKT 172 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~ 172 (230)
.+.++||+..|||++||++.++. . ...+++.+++|.+..++
T Consensus 6 ~ti~dIA~~agVS~~TVSrvLn~---------------~-~~vs~~tr~rV~~~a~e 46 (331)
T PRK14987 6 PVLQDVADRVGVTKMTVSRFLRN---------------P-EQVSVALRGKIAAALDE 46 (331)
T ss_pred CcHHHHHHHhCCCHHHhhhhhCC---------------C-CCCCHHHHHHHHHHHHH
Confidence 58899999999999999999841 1 12467777777766655
No 372
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=88.67 E-value=0.85 Score=38.64 Aligned_cols=59 Identities=8% Similarity=0.117 Sum_probs=40.7
Q ss_pred HHHHHHHHH-HHcC--CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHH
Q psy1898 103 HIRLKIVEM-AAAG--VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPD 161 (230)
Q Consensus 103 ~~R~rIV~l-~~~G--~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~ 161 (230)
.+|..|+.. +..| ++..++|++||||+++|.-=+++-...|.+...+..|-.-..++.+
T Consensus 15 ~i~~~I~~g~l~pG~~L~e~eLae~lgVSRtpVREAL~~L~~eGlv~~~~~~G~~V~~~~~~ 76 (224)
T PRK11534 15 WLKNDIIRGNFQPDEKLRMSLLTSRYALGVGPLREALSQLVAERLVTVVNQKGYRVASMSEQ 76 (224)
T ss_pred HHHHHHHhCCCCCCCcCCHHHHHHHHCCChHHHHHHHHHHHHCCCEEEeCCCceEeCCCCHH
Confidence 344445442 2334 6788999999999999999999999999876544434333334444
No 373
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=88.65 E-value=0.57 Score=41.54 Aligned_cols=41 Identities=17% Similarity=0.144 Sum_probs=30.7
Q ss_pred CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHh
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKT 172 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~ 172 (230)
.|.++||+.+|||++||++.++. ++ .++++.+++|.+..++
T Consensus 7 ~Ti~dIA~~agVS~~TVSr~Ln~---------------~~-~vs~~tr~~V~~~a~e 47 (342)
T PRK10014 7 ITIHDVALAAGVSVSTVSLVLSG---------------KG-RISTATGERVNQAIEE 47 (342)
T ss_pred CcHHHHHHHhCCCHHHHHHHHCC---------------CC-CCCHHHHHHHHHHHHH
Confidence 68999999999999999999852 11 2466667776665544
No 374
>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=88.63 E-value=0.55 Score=41.28 Aligned_cols=42 Identities=17% Similarity=0.099 Sum_probs=34.5
Q ss_pred cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898 99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE 141 (230)
Q Consensus 99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e 141 (230)
.+|..+ ..|+.+..+|+|..+||+.|+||..||...+++-.+
T Consensus 190 ~LT~RE-~evl~l~a~G~s~~eIA~~L~IS~~TVk~hl~~i~~ 231 (247)
T TIGR03020 190 LITARE-AEILAWVRDGKTNEEIAAILGISSLTVKNHLQHIFK 231 (247)
T ss_pred CCCHHH-HHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 566644 456667889999999999999999999999987543
No 375
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=88.62 E-value=1.3 Score=36.48 Aligned_cols=42 Identities=14% Similarity=0.115 Sum_probs=31.0
Q ss_pred HHHHHHHHHhCC-CCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcC
Q psy1898 163 EKRIEEYKKTNP-GIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGG 210 (230)
Q Consensus 163 ~~~I~~l~~~~P-~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~ 210 (230)
+..|.+++...+ ..++.+|.+.|.+ .+.. +|.+||||.|..+
T Consensus 28 R~~IL~~l~~~~~hlSa~eI~~~L~~-~~~~-----is~aTVYRtL~~L 70 (169)
T PRK11639 28 RLEVLRLMSLQPGAISAYDLLDLLRE-AEPQ-----AKPPTVYRALDFL 70 (169)
T ss_pred HHHHHHHHHhcCCCCCHHHHHHHHHh-hCCC-----CCcchHHHHHHHH
Confidence 345555555444 6899999999987 5553 8999999999654
No 376
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=88.61 E-value=5.2 Score=31.11 Aligned_cols=79 Identities=16% Similarity=0.024 Sum_probs=49.2
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHH
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPGIFSW 179 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~~P~~t~~ 179 (230)
++.+...=|...+...-+.+++++.||||.+||..=+.+--+.=...+ .+.......+..|...+. +-.+++.
T Consensus 34 L~~E~~~Fi~~Fi~~rGnlKe~e~~lgiSYPTvR~rLd~ii~~lg~~~------~~~~~~~~~~~~IL~~L~-~GeIs~e 106 (113)
T PF09862_consen 34 LSPEQLEFIKLFIKNRGNLKEMEKELGISYPTVRNRLDKIIEKLGYEE------DEEEEEEDERKEILDKLE-KGEISVE 106 (113)
T ss_pred CCHHHHHHHHHHHHhcCCHHHHHHHHCCCcHHHHHHHHHHHHHhCCCC------CcccccchhHHHHHHHHH-cCCCCHH
Confidence 555555555556667779999999999999999988877543311111 111223344556666663 5577777
Q ss_pred HHHHHH
Q psy1898 180 EIRDRL 185 (230)
Q Consensus 180 eI~~~L 185 (230)
|-.+.|
T Consensus 107 eA~~~L 112 (113)
T PF09862_consen 107 EALEIL 112 (113)
T ss_pred HHHHHh
Confidence 655544
No 377
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=88.36 E-value=0.61 Score=41.57 Aligned_cols=40 Identities=20% Similarity=0.228 Sum_probs=31.7
Q ss_pred CHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHh
Q psy1898 117 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKT 172 (230)
Q Consensus 117 s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~ 172 (230)
+.++||+..|||.+||++.++. ++ ..+++.+++|.+..++
T Consensus 3 ti~dIA~~aGVS~~TVSrvLn~---------------~~-~Vs~~tr~rV~~~a~e 42 (343)
T PRK10727 3 TIKDVARLAGVSVATVSRVINN---------------SP-KASEASRLAVHSAMES 42 (343)
T ss_pred CHHHHHHHhCCCHHHHHHHhCC---------------CC-CCCHHHHHHHHHHHHH
Confidence 7899999999999999999851 11 2578888888777765
No 378
>PRK14702 insertion element IS2 transposase InsD; Provisional
Probab=88.35 E-value=2.2 Score=37.53 Aligned_cols=53 Identities=25% Similarity=0.151 Sum_probs=41.3
Q ss_pred CHHHHHHHHHHHHhCCCCCHHHHHHHHHHh---hCCCCCCCCCCHhHHHHHHHcCCCCCC
Q psy1898 159 TPDVEKRIEEYKKTNPGIFSWEIRDRLVKQ---DGICDKNSAPSVSSISRLLRGGRRDDC 215 (230)
Q Consensus 159 t~~~~~~I~~l~~~~P~~t~~eI~~~L~~~---~Gi~~~~~~vS~sTV~R~Lr~~g~~~~ 215 (230)
..+..+.|.++..++|...+..|...|..+ .|+. .++..||+|+|++.||...
T Consensus 10 ~~~l~~~I~~~~~~~~~yG~rri~~~L~~~~~~~g~~----~v~~krV~rlmr~~gL~~~ 65 (262)
T PRK14702 10 DTDVLLRIHHVIGELPTYGYRRVWALLRRQAELDGMP----AINAKRVYRLMRQNALLLE 65 (262)
T ss_pred hHHHHHHHHHHHHhCcccChHHHHHHHHhhhcccCcc----ccCHHHHHHHHHHhCCccc
Confidence 455677777776788999999999999762 1441 2799999999999999844
No 379
>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=88.31 E-value=0.72 Score=40.15 Aligned_cols=41 Identities=12% Similarity=0.138 Sum_probs=32.1
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
++...|.-+...+.+|++..+||..+|||..+|+++.++..
T Consensus 207 L~~rer~vi~~~~~~~~t~~eIA~~lgis~~~V~~~~~ral 247 (254)
T TIGR02850 207 LNEREKMILNMRFFEGKTQMEVAEEIGISQAQVSRLEKAAL 247 (254)
T ss_pred CCHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 55555544444555799999999999999999999988754
No 380
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=88.30 E-value=1.7 Score=29.82 Aligned_cols=79 Identities=16% Similarity=0.146 Sum_probs=51.2
Q ss_pred CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCC
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKN 195 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~ 195 (230)
.+..++|+.+++|..++++..+++. |. .+.. .+.....+.+..++..+ .++..++++. .|+.
T Consensus 2 ~~~~~la~~~~~s~~~l~~~f~~~~--~~-s~~~-------~~~~~r~~~a~~~l~~~-~~~~~~ia~~----~g~~--- 63 (84)
T smart00342 2 LTLEDLAEALGMSPRHLQRLFKKET--GT-TPKQ-------YLRDRRLERARRLLRDT-DLSVTEIALR----VGFS--- 63 (84)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHh--Cc-CHHH-------HHHHHHHHHHHHHHHcC-CCCHHHHHHH----hCCC---
Confidence 5788999999999999988877542 21 1110 11222344455666555 6788777763 5763
Q ss_pred CCCCHhHHHHHHHcC-CCCCC
Q psy1898 196 SAPSVSSISRLLRGG-RRDDC 215 (230)
Q Consensus 196 ~~vS~sTV~R~Lr~~-g~~~~ 215 (230)
|.++.+|.+++. |.+|.
T Consensus 64 ---s~~~f~r~Fk~~~g~sp~ 81 (84)
T smart00342 64 ---SQSYFSRAFKKLFGVTPS 81 (84)
T ss_pred ---ChHHHHHHHHHHHCcChh
Confidence 899999998654 55543
No 381
>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=88.15 E-value=0.57 Score=41.25 Aligned_cols=40 Identities=15% Similarity=0.024 Sum_probs=30.5
Q ss_pred CCHHHHHHHHHHH--HcCCCHHHHhhhhccccchhhhHHHHH
Q psy1898 100 LPNHIRLKIVEMA--AAGVRPCVISRQLRVSHGCVSKILNRY 139 (230)
Q Consensus 100 ~s~~~R~rIV~l~--~~G~s~~~IAr~lgVS~sTV~kwikRy 139 (230)
+|...|.-+...+ ..++|.++||+.||||..+|+++.++.
T Consensus 219 L~~rer~vl~l~y~~~~~~t~~eIA~~lgvS~~~V~q~~~~A 260 (270)
T TIGR02392 219 LDARSRRIIEARWLDDDKLTLQELAAEYGVSAERIRQIEKNA 260 (270)
T ss_pred CCHHHHHHHHHHhcCCCCcCHHHHHHHHCCCHHHHHHHHHHH
Confidence 5555555444444 247999999999999999999988764
No 382
>PF12759 HTH_Tnp_IS1: InsA C-terminal domain; InterPro: IPR024431 This entry represents the helix-turn-helix domain found at the C-terminal of InsA.
Probab=88.14 E-value=0.38 Score=31.40 Aligned_cols=31 Identities=32% Similarity=0.290 Sum_probs=27.6
Q ss_pred hhHHHHHHHHHhcCCChhhhhhhhccccccc
Q psy1898 58 NHIRLKIVEMAAAGVRPCVISRQLRVSHGVN 88 (230)
Q Consensus 58 ~~~r~~I~e~~~~g~~~~~isr~lrvshg~~ 88 (230)
+.++.+|+||+.+|....+.+|-|+|+...+
T Consensus 8 pgikeqIvema~nG~GiRdtaRvL~I~~nTV 38 (46)
T PF12759_consen 8 PGIKEQIVEMAFNGSGIRDTARVLKISINTV 38 (46)
T ss_pred ccHHHHHHHHHhcCCcchhhHhHhcchHHHH
Confidence 5688999999999999999999999887665
No 383
>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=88.04 E-value=0.59 Score=40.23 Aligned_cols=41 Identities=10% Similarity=0.049 Sum_probs=31.9
Q ss_pred CCHHHHHHHHHHH----HcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 100 LPNHIRLKIVEMA----AAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 100 ~s~~~R~rIV~l~----~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
++...|.-+...+ .+++|..+||..+|||..+|.++.++-.
T Consensus 177 L~~~er~vl~l~ygl~~~~~~t~~EIA~~lgis~~~V~q~~~~al 221 (238)
T TIGR02393 177 LTERERKVLRMRYGLLDGRPHTLEEVGKEFNVTRERIRQIESKAL 221 (238)
T ss_pred CCHHHHHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHH
Confidence 4555555554445 4789999999999999999999987644
No 384
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=87.99 E-value=1.7 Score=30.35 Aligned_cols=46 Identities=15% Similarity=0.265 Sum_probs=34.3
Q ss_pred CHHHHHHHHHHHHhCCC--CCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHc---CCCCCC
Q psy1898 159 TPDVEKRIEEYKKTNPG--IFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRG---GRRDDC 215 (230)
Q Consensus 159 t~~~~~~I~~l~~~~P~--~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~---~g~~~~ 215 (230)
..+.++.|..++.+++. +++.+|.+.| |+ +.++|+|.|.. .|+-.+
T Consensus 4 ~~~~~~~IL~~L~~~g~~~~ta~eLa~~l----gl-------~~~~v~r~L~~L~~~G~V~~ 54 (68)
T smart00550 4 QDSLEEKILEFLENSGDETSTALQLAKNL----GL-------PKKEVNRVLYSLEKKGKVCK 54 (68)
T ss_pred chHHHHHHHHHHHHCCCCCcCHHHHHHHH----CC-------CHHHHHHHHHHHHHCCCEEe
Confidence 34567888888888766 9999988865 44 88899999864 465543
No 385
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=87.98 E-value=3.8 Score=29.73 Aligned_cols=31 Identities=23% Similarity=0.382 Sum_probs=27.6
Q ss_pred HHHHhhhhccccchhhhHHHHHhhhCCCCcC
Q psy1898 118 PCVISRQLRVSHGCVSKILNRYQETGSIRPG 148 (230)
Q Consensus 118 ~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~ 148 (230)
..++|+.++|+++||++.+++..+.|-+...
T Consensus 2 ~~ela~~l~is~stvs~~l~~L~~~glI~r~ 32 (96)
T smart00529 2 TSEIAERLNVSPPTVTQMLKKLEKDGLVEYE 32 (96)
T ss_pred HHHHHHHhCCChHHHHHHHHHHHHCCCEEEc
Confidence 5789999999999999999999999977543
No 386
>PF13518 HTH_28: Helix-turn-helix domain
Probab=87.95 E-value=0.4 Score=30.88 Aligned_cols=29 Identities=31% Similarity=0.424 Sum_probs=25.8
Q ss_pred HHHHHHHHHhcCCChhhhhhhhccccccc
Q psy1898 60 IRLKIVEMAAAGVRPCVISRQLRVSHGVN 88 (230)
Q Consensus 60 ~r~~I~e~~~~g~~~~~isr~lrvshg~~ 88 (230)
+|.+||+++.+|.+..+++++++|++..+
T Consensus 1 ~r~~iv~~~~~g~s~~~~a~~~gis~~tv 29 (52)
T PF13518_consen 1 FRLQIVELYLEGESVREIAREFGISRSTV 29 (52)
T ss_pred CHHHHHHHHHcCCCHHHHHHHHCCCHhHH
Confidence 48899999999999999999999877664
No 387
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=87.93 E-value=1.7 Score=38.04 Aligned_cols=45 Identities=24% Similarity=0.304 Sum_probs=39.1
Q ss_pred HHHHHHHHHHHHc-C-CCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898 102 NHIRLKIVEMAAA-G-VRPCVISRQLRVSHGCVSKILNRYQETGSIR 146 (230)
Q Consensus 102 ~~~R~rIV~l~~~-G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~ 146 (230)
.+.+++|++++.+ | .+..++|+.|+||..||+|=++...+.|.+.
T Consensus 4 ~eR~~~Il~~l~~~g~v~v~eLa~~~~VS~~TIRRDL~~Le~~g~l~ 50 (253)
T COG1349 4 EERHQKILELLKEKGKVSVEELAELFGVSEMTIRRDLNELEEQGLLL 50 (253)
T ss_pred HHHHHHHHHHHHHcCcEEHHHHHHHhCCCHHHHHHhHHHHHHCCcEE
Confidence 4567888887765 6 9999999999999999999999999999764
No 388
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=87.81 E-value=0.87 Score=36.17 Aligned_cols=41 Identities=20% Similarity=0.178 Sum_probs=34.1
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE 141 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e 141 (230)
++.. ..+|+.++.+|.+.++||+.+++|..||..++.+-..
T Consensus 150 lt~~-e~~vl~l~~~g~~~~~Ia~~l~~s~~tv~~~~~~~~~ 190 (211)
T PRK15369 150 LTPR-ERQILKLITEGYTNRDIAEQLSISIKTVETHRLNMMR 190 (211)
T ss_pred CCHH-HHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 5544 4566778899999999999999999999999988553
No 389
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=87.77 E-value=1.4 Score=37.48 Aligned_cols=63 Identities=19% Similarity=0.192 Sum_probs=45.9
Q ss_pred HHHHHHHHHH-HcC--CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHH
Q psy1898 103 HIRLKIVEMA-AAG--VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKR 165 (230)
Q Consensus 103 ~~R~rIV~l~-~~G--~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~ 165 (230)
.+|..|+... .-| ++..+||++||||+..|..-+.+....|.+.-.+..|-.-..++.+..+.
T Consensus 24 ~Lr~~Il~g~l~pG~~l~e~~La~~~gvSrtPVReAL~rL~~eGlv~~~p~rG~~V~~~~~~~~~e 89 (230)
T COG1802 24 ELREAILSGELAPGERLSEEELAEELGVSRTPVREALRRLEAEGLVEIEPNRGAFVAPLSLAEARE 89 (230)
T ss_pred HHHHHHHhCCCCCCCCccHHHHHHHhCCCCccHHHHHHHHHHCCCeEecCCCCCeeCCCCHHHHHH
Confidence 5666666532 334 88999999999999999999999999998865555454444555554333
No 390
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=87.77 E-value=0.74 Score=40.79 Aligned_cols=53 Identities=23% Similarity=0.279 Sum_probs=43.2
Q ss_pred CcCCHHHHHHHHHHHHcC--CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCC
Q psy1898 98 RPLPNHIRLKIVEMAAAG--VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI 150 (230)
Q Consensus 98 ~~~s~~~R~rIV~l~~~G--~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~ 150 (230)
.+++.+.+.-+......| ...+++.+.+|.|++||+|.+++-.+.|-++--+.
T Consensus 191 ~~L~~~e~~il~~i~~~GGri~Q~eL~r~lglsktTvsR~L~~LEk~GlIe~~K~ 245 (258)
T COG2512 191 YDLNEDEKEILDLIRERGGRITQAELRRALGLSKTTVSRILRRLEKRGLIEKEKK 245 (258)
T ss_pred CCCCHHHHHHHHHHHHhCCEEeHHHHHHhhCCChHHHHHHHHHHHhCCceEEEEe
Confidence 467777776666665554 89999999999999999999999999998865444
No 391
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=87.60 E-value=0.73 Score=41.11 Aligned_cols=41 Identities=22% Similarity=0.293 Sum_probs=31.2
Q ss_pred CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHh
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKT 172 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~ 172 (230)
.+.++||+..|||++||++.++. ++ .++++.+++|.+..++
T Consensus 2 ~ti~dIA~~aGVS~~TVSrvLn~---------------~~-~Vs~~tr~kV~~~a~e 42 (346)
T PRK10401 2 ITIRDVARQAGVSVATVSRVLNN---------------SA-LVSADTREAVMKAVSE 42 (346)
T ss_pred CCHHHHHHHhCCCHHHHHHHHCC---------------CC-CCCHHHHHHHHHHHHH
Confidence 47899999999999999999852 11 2467777777776655
No 392
>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=87.59 E-value=0.31 Score=30.37 Aligned_cols=25 Identities=16% Similarity=0.110 Sum_probs=19.5
Q ss_pred CHHHHhhhhccccchhhhHHHHHhhhCCC
Q psy1898 117 RPCVISRQLRVSHGCVSKILNRYQETGSI 145 (230)
Q Consensus 117 s~~~IAr~lgVS~sTV~kwikRy~e~G~v 145 (230)
+..++|+.+|||..|+..|.+ .|.+
T Consensus 1 ti~e~A~~~gvs~~tlR~ye~----~Gll 25 (38)
T PF00376_consen 1 TIGEVAKLLGVSPRTLRYYER----EGLL 25 (38)
T ss_dssp EHHHHHHHHTS-HHHHHHHHH----TTSS
T ss_pred CHHHHHHHHCCCHHHHHHHHH----CCCC
Confidence 467999999999999988755 4766
No 393
>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=87.50 E-value=2.3 Score=32.37 Aligned_cols=56 Identities=13% Similarity=0.068 Sum_probs=40.0
Q ss_pred cCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcC--CCCC-CCCCCCCHHHHHHHHHH
Q psy1898 114 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG--VIGG-SKPRVATPDVEKRIEEY 169 (230)
Q Consensus 114 ~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~--~~gg-~rpr~lt~~~~~~I~~l 169 (230)
.+.+..+||+.++++++||++.+++..+.|-+... +..+ ..--.+|++-.+.+...
T Consensus 41 ~~~t~~ela~~~~~~~~tvs~~l~~Le~~GlI~r~~~~~D~R~~~v~LT~~G~~~~~~~ 99 (118)
T TIGR02337 41 GSMEFTQLANQACILRPSLTGILARLERDGLVTRLKASNDQRRVYISLTPKGQALYASL 99 (118)
T ss_pred CCcCHHHHHHHhCCCchhHHHHHHHHHHCCCEEeccCCCCCCeeEEEECHhHHHHHHHh
Confidence 45999999999999999999999999999976422 1111 12235666666554444
No 394
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=87.46 E-value=0.95 Score=32.66 Aligned_cols=33 Identities=9% Similarity=0.085 Sum_probs=25.9
Q ss_pred HHHHHHHH-HcCCCHHHHhhhhc------cccchhhhHHH
Q psy1898 105 RLKIVEMA-AAGVRPCVISRQLR------VSHGCVSKILN 137 (230)
Q Consensus 105 R~rIV~l~-~~G~s~~~IAr~lg------VS~sTV~kwik 137 (230)
-.++..+. +.|+|..++|+.+| +|++||++|.+
T Consensus 13 ~~~lk~~R~~lGLTQ~dvA~~lg~~~g~i~SQstISR~Es 52 (75)
T smart00352 13 AKTFKQRRIKLGFTQADVGLALGALYGPDFSQTTICRFEA 52 (75)
T ss_pred HHHHHHHHHHcCCCHHHHHHHhcccccCcCCHHHHHHHHh
Confidence 34444444 45999999999999 59999999975
No 395
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=87.46 E-value=0.68 Score=36.47 Aligned_cols=33 Identities=15% Similarity=0.157 Sum_probs=26.5
Q ss_pred HHHHHHH-HcCCCHHHHhhhhccccchhhhHHHH
Q psy1898 106 LKIVEMA-AAGVRPCVISRQLRVSHGCVSKILNR 138 (230)
Q Consensus 106 ~rIV~l~-~~G~s~~~IAr~lgVS~sTV~kwikR 138 (230)
.+|-.+. ..|+|..++|..+|||++||++|.+.
T Consensus 8 ~rlk~~R~~~gltq~~lA~~~gvs~~~is~~E~g 41 (135)
T PRK09706 8 QRIRYRRKQLKLSQRSLAKAVKVSHVSISQWERD 41 (135)
T ss_pred HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 4444444 45899999999999999999999754
No 396
>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=87.42 E-value=0.77 Score=40.48 Aligned_cols=41 Identities=29% Similarity=0.404 Sum_probs=31.1
Q ss_pred CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHh
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKT 172 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~ 172 (230)
.+.++||+..|||.+||++.++. ++ .++++.+++|.+..++
T Consensus 2 ~ti~dIA~~agvS~~TVSrvLn~---------------~~-~vs~~tr~rV~~~a~~ 42 (329)
T TIGR01481 2 VTIYDVAREAGVSMATVSRVVNG---------------NP-NVKPATRKKVLEVIKR 42 (329)
T ss_pred CcHHHHHHHhCCCHHHHHHHhCC---------------CC-CCCHHHHHHHHHHHHH
Confidence 47889999999999999999851 11 2567777777766654
No 397
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=87.36 E-value=0.75 Score=31.30 Aligned_cols=24 Identities=33% Similarity=0.473 Sum_probs=20.2
Q ss_pred cCCCHHHHhhhhccccchhhhHHH
Q psy1898 114 AGVRPCVISRQLRVSHGCVSKILN 137 (230)
Q Consensus 114 ~G~s~~~IAr~lgVS~sTV~kwik 137 (230)
.|+|..++|+.+|+|.+||++|.+
T Consensus 13 ~gls~~~lA~~~g~s~s~v~~iE~ 36 (64)
T PF13560_consen 13 AGLSQAQLADRLGVSQSTVSRIER 36 (64)
T ss_dssp HTS-HHHHHHHHTS-HHHHHHHHT
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHC
Confidence 489999999999999999999964
No 398
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=87.14 E-value=0.91 Score=39.50 Aligned_cols=44 Identities=25% Similarity=0.316 Sum_probs=35.5
Q ss_pred HHHHHHHHHHHc-C-CCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898 103 HIRLKIVEMAAA-G-VRPCVISRQLRVSHGCVSKILNRYQETGSIR 146 (230)
Q Consensus 103 ~~R~rIV~l~~~-G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~ 146 (230)
+.+.+|++.+.+ + .+..++|+.|+||..||+|.++...+.|.+.
T Consensus 4 ~R~~~Il~~l~~~~~~~~~eLa~~l~VS~~TiRRdL~~L~~~~~l~ 49 (240)
T PRK10411 4 ARQQAIVDLLLNHTSLTTEALAEQLNVSKETIRRDLNELQTQGKIL 49 (240)
T ss_pred HHHHHHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 344566666543 3 9999999999999999999999998887663
No 399
>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=87.11 E-value=0.94 Score=39.00 Aligned_cols=42 Identities=21% Similarity=0.218 Sum_probs=34.3
Q ss_pred CcCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 98 RPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 98 ~~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
..+|... ..++.+..+|+|..+||..|+||.+||..++++-.
T Consensus 170 ~~Lt~re-~evl~~~a~G~t~~eIa~~l~is~~Tv~~~l~~~~ 211 (232)
T TIGR03541 170 GVLSERE-REVLAWTALGRRQADIAAILGISERTVENHLRSAR 211 (232)
T ss_pred ccCCHHH-HHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 3466544 45666678999999999999999999999998865
No 400
>PRK11361 acetoacetate metabolism regulatory protein AtoC; Provisional
Probab=87.08 E-value=0.7 Score=43.14 Aligned_cols=38 Identities=16% Similarity=0.087 Sum_probs=31.5
Q ss_pred HHHHHHHHHHH-cCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 103 HIRLKIVEMAA-AGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 103 ~~R~rIV~l~~-~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
.+|..|..+++ .+....++|+.||||++|+|+.+++|.
T Consensus 417 ~E~~~i~~al~~~~gn~~~aA~~LGisr~tL~rkl~~~~ 455 (457)
T PRK11361 417 VEKRIIMEVLEQQEGNRTRTALMLGISRRALMYKLQEYG 455 (457)
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHhC
Confidence 35666666665 478999999999999999999999884
No 401
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=87.07 E-value=0.82 Score=40.46 Aligned_cols=42 Identities=26% Similarity=0.290 Sum_probs=32.4
Q ss_pred CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCC-CCCHHHHHHHHHHHHh
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPR-VATPDVEKRIEEYKKT 172 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr-~lt~~~~~~I~~l~~~ 172 (230)
.+.++||+..|||++||++.++. ++. ..+++.+++|.+..++
T Consensus 2 ~ti~dIA~~agVS~~TVSrvln~---------------~~~~~vs~~tr~rV~~~a~~ 44 (327)
T PRK10339 2 ATLKDIAIEAGVSLATVSRVLND---------------DPTLNVKEETKHRILEIAEK 44 (327)
T ss_pred CCHHHHHHHhCCCHHhhhhhhcC---------------CCCCCcCHHHHHHHHHHHHH
Confidence 37899999999999999999851 121 2578888888877765
No 402
>cd04778 HTH_MerR-like_sg2 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 2). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located 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=87.00 E-value=2.5 Score=36.51 Aligned_cols=67 Identities=15% Similarity=0.110 Sum_probs=48.9
Q ss_pred CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHH-hCCCCCHHHHHHHHHH
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKK-TNPGIFSWEIRDRLVK 187 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~-~~P~~t~~eI~~~L~~ 187 (230)
++..++|+..|||..||.-|.+ .|.+.|..+.+ .-+..++++.+.|..... .....++.+|++.|..
T Consensus 2 y~i~elA~~~Gvs~~tIR~Ye~----~GLL~p~r~~~-~~r~Y~~~~v~rL~~I~~l~~~G~~L~~I~~~l~~ 69 (219)
T cd04778 2 YRIDDLARAAGTTVRNVRAYQD----RGLLPPPRRRG-RVAIYNDSHLARLRLINQLLERGYTLAHIAELLAA 69 (219)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH----CCCCCCcccCC-CCcccCHHHHHHHHHHHHHHHCCCCHHHHHHHHHh
Confidence 5788999999999999877654 58876644432 356888988777765554 3456789999888765
No 403
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=86.83 E-value=4.9 Score=28.72 Aligned_cols=42 Identities=21% Similarity=0.442 Sum_probs=34.3
Q ss_pred HHHHHHHHH-c-CCCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898 105 RLKIVEMAA-A-GVRPCVISRQLRVSHGCVSKILNRYQETGSIR 146 (230)
Q Consensus 105 R~rIV~l~~-~-G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~ 146 (230)
...|+..+. . +++..+||+.++++++||++-+++..+.|-+.
T Consensus 12 ~~~il~~l~~~~~~~~~~la~~~~~s~~~i~~~l~~L~~~g~v~ 55 (101)
T smart00347 12 QFLVLRILYEEGPLSVSELAKRLGVSPSTVTRVLDRLEKKGLIR 55 (101)
T ss_pred HHHHHHHHHHcCCcCHHHHHHHHCCCchhHHHHHHHHHHCCCeE
Confidence 344555443 3 48999999999999999999999999999774
No 404
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=86.82 E-value=1.2 Score=35.20 Aligned_cols=42 Identities=17% Similarity=0.010 Sum_probs=35.1
Q ss_pred CCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcC
Q psy1898 158 ATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGG 210 (230)
Q Consensus 158 lt~~~~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~ 210 (230)
++..+.+.+..+++.+...|..+|++.|. .+.|||+|.|+++
T Consensus 25 Ls~~Dv~v~~~LL~~~~~~tvdelae~ln-----------r~rStv~rsl~~L 66 (126)
T COG3355 25 LSELDVEVYKALLEENGPLTVDELAEILN-----------RSRSTVYRSLQNL 66 (126)
T ss_pred CcHHHHHHHHHHHhhcCCcCHHHHHHHHC-----------ccHHHHHHHHHHH
Confidence 56677778888887888899999999884 3999999999875
No 405
>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=86.64 E-value=1.4 Score=32.83 Aligned_cols=33 Identities=21% Similarity=0.160 Sum_probs=30.8
Q ss_pred cCCCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898 114 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIR 146 (230)
Q Consensus 114 ~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~ 146 (230)
...|..+||..+|+++.||++.+++..+.|-+.
T Consensus 46 ~~is~~eLa~~~g~sr~tVsr~L~~Le~~GlI~ 78 (95)
T TIGR01610 46 DRVTATVIAELTGLSRTHVSDAIKSLARRRIIF 78 (95)
T ss_pred CccCHHHHHHHHCcCHHHHHHHHHHHHHCCCee
Confidence 468999999999999999999999999999885
No 406
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=86.63 E-value=1 Score=35.73 Aligned_cols=47 Identities=19% Similarity=0.232 Sum_probs=37.5
Q ss_pred HHHHHHHHHHH-cC--CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCC
Q psy1898 103 HIRLKIVEMAA-AG--VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV 149 (230)
Q Consensus 103 ~~R~rIV~l~~-~G--~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~ 149 (230)
.+|..|..... .| .+..+||+.++||+.+|.+.+++....|-+...+
T Consensus 10 Al~~~i~la~~~~g~~~s~~~ia~~~~is~~~vrk~l~~L~~~Glv~s~~ 59 (141)
T PRK11014 10 GLRALIYMASLPEGRMTSISEVTEVYGVSRNHMVKIINQLSRAGYVTAVR 59 (141)
T ss_pred HHHHHHHHhcCCCCCccCHHHHHHHHCcCHHHHHHHHHHHHhCCEEEEec
Confidence 56666665532 34 6789999999999999999999999999875443
No 407
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=86.50 E-value=3.9 Score=31.83 Aligned_cols=82 Identities=10% Similarity=0.026 Sum_probs=51.2
Q ss_pred HHcCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHH-HHHHHHHHHhCCCCCHHHHHHHHHHhhC
Q psy1898 112 AAAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDV-EKRIEEYKKTNPGIFSWEIRDRLVKQDG 190 (230)
Q Consensus 112 ~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~-~~~I~~l~~~~P~~t~~eI~~~L~~~~G 190 (230)
+.+..+..++|+.+|+|+.++.++.+++- |.. |...-... .+....++ .+.+.+..+|+.. .|
T Consensus 22 ~~~~~sl~~lA~~~g~S~~~l~r~Fk~~~--G~s---------~~~~l~~~Rl~~A~~~L-~~t~~~i~eIA~~----~G 85 (127)
T PRK11511 22 LESPLSLEKVSERSGYSKWHLQRMFKKET--GHS---------LGQYIRSRKMTEIAQKL-KESNEPILYLAER----YG 85 (127)
T ss_pred cCCCCCHHHHHHHHCcCHHHHHHHHHHHH--CcC---------HHHHHHHHHHHHHHHHH-HcCCCCHHHHHHH----hC
Confidence 33458999999999999999999987643 221 11111111 11122333 2446677666653 68
Q ss_pred CCCCCCCCCHhHHHHHHHcC-CCCCC
Q psy1898 191 ICDKNSAPSVSSISRLLRGG-RRDDC 215 (230)
Q Consensus 191 i~~~~~~vS~sTV~R~Lr~~-g~~~~ 215 (230)
.. +.++..|.+++. |..|.
T Consensus 86 f~------s~s~F~r~Fkk~~G~tP~ 105 (127)
T PRK11511 86 FE------SQQTLTRTFKNYFDVPPH 105 (127)
T ss_pred CC------CHHHHHHHHHHHHCcCHH
Confidence 74 899999988665 66665
No 408
>COG3311 AlpA Predicted transcriptional regulator [Transcription]
Probab=86.41 E-value=1.2 Score=31.72 Aligned_cols=23 Identities=9% Similarity=0.226 Sum_probs=20.5
Q ss_pred CCHHHHhhhhccccchhhhHHHH
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNR 138 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikR 138 (230)
+...|++..+|+|++|+|++++.
T Consensus 14 lrl~ev~~~~GlSrstiYr~i~~ 36 (70)
T COG3311 14 LRLPEVAQLTGLSRSTIYRLIKD 36 (70)
T ss_pred hhHHHHHHHHCccHHHHHHHHcc
Confidence 56789999999999999999874
No 409
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=86.28 E-value=1.3 Score=37.59 Aligned_cols=42 Identities=19% Similarity=0.177 Sum_probs=36.5
Q ss_pred cCCHHHHHHHHHHHHcC-------CCHHHHhhhhccccchhhhHHHHHh
Q psy1898 99 PLPNHIRLKIVEMAAAG-------VRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 99 ~~s~~~R~rIV~l~~~G-------~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
.++..++.-+..+++.| .+.++||+.||||++|++.-+++..
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ehLRrAe 203 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEHLRRAE 203 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 68888887777788888 7899999999999999999988754
No 410
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=86.27 E-value=0.63 Score=28.64 Aligned_cols=26 Identities=27% Similarity=0.377 Sum_probs=22.8
Q ss_pred HHcCCCHHHHhhhhccccchhhhHHH
Q psy1898 112 AAAGVRPCVISRQLRVSHGCVSKILN 137 (230)
Q Consensus 112 ~~~G~s~~~IAr~lgVS~sTV~kwik 137 (230)
...++|..++|+.++++..||++|..
T Consensus 7 ~~~~~s~~~la~~~~i~~~~i~~~~~ 32 (56)
T smart00530 7 EEKGLTQEELAEKLGVSRSTLSRIEN 32 (56)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHC
Confidence 34589999999999999999999963
No 411
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=86.26 E-value=1.1 Score=40.55 Aligned_cols=40 Identities=18% Similarity=0.207 Sum_probs=33.3
Q ss_pred CHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHh
Q psy1898 117 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKT 172 (230)
Q Consensus 117 s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~ 172 (230)
+.++||+..|||++||++.++. +...+++.+++|.+..++
T Consensus 2 TikDVA~~AGVS~sTVSrvln~----------------~~~Vs~eTr~kV~~a~~e 41 (333)
T COG1609 2 TIKDVAKLAGVSKATVSRVLNG----------------SPYVSEETREKVLAAIKE 41 (333)
T ss_pred CHHHHHHHhCCCHHHHHHHHcC----------------CCCCCHHHHHHHHHHHHH
Confidence 6789999999999999999851 225688999999888876
No 412
>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=86.23 E-value=0.64 Score=28.87 Aligned_cols=25 Identities=28% Similarity=0.409 Sum_probs=22.6
Q ss_pred HcCCCHHHHhhhhccccchhhhHHH
Q psy1898 113 AAGVRPCVISRQLRVSHGCVSKILN 137 (230)
Q Consensus 113 ~~G~s~~~IAr~lgVS~sTV~kwik 137 (230)
..+++..++|+.+++++.+|++|.+
T Consensus 10 ~~~~s~~~~a~~~~~~~~~v~~~~~ 34 (58)
T cd00093 10 EKGLTQEELAEKLGVSRSTISRIEN 34 (58)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHc
Confidence 4589999999999999999999964
No 413
>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=86.13 E-value=2.6 Score=23.51 Aligned_cols=41 Identities=29% Similarity=0.342 Sum_probs=27.3
Q ss_pred CCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHH
Q psy1898 154 KPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLL 207 (230)
Q Consensus 154 rpr~lt~~~~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~L 207 (230)
+|..++++....+...... ..+..++.+. +++ |.+||++++
T Consensus 2 r~~~~~~~~~~~i~~~~~~--~~s~~~ia~~----~~i-------s~~tv~~~~ 42 (42)
T cd00569 2 RPPKLTPEQIEEARRLLAA--GESVAEIARR----LGV-------SRSTLYRYL 42 (42)
T ss_pred CCCcCCHHHHHHHHHHHHc--CCCHHHHHHH----HCC-------CHHHHHHhC
Confidence 5666777777677666543 3477777653 454 999999864
No 414
>COG2973 TrpR Trp operon repressor [Transcription]
Probab=86.09 E-value=0.8 Score=34.67 Aligned_cols=33 Identities=24% Similarity=0.274 Sum_probs=26.9
Q ss_pred HHHHHHHHHHHc-CCCHHHHhhhhccccchhhhH
Q psy1898 103 HIRLKIVEMAAA-GVRPCVISRQLRVSHGCVSKI 135 (230)
Q Consensus 103 ~~R~rIV~l~~~-G~s~~~IAr~lgVS~sTV~kw 135 (230)
-.|.+||..+-. .+|.++|+..||+|..||.|=
T Consensus 47 ~~Rv~Iv~eLL~ge~sQREi~~~LgvsiAtITRG 80 (103)
T COG2973 47 GTRVRIVEELLRGELSQREIAQKLGVSIATITRG 80 (103)
T ss_pred HHHHHHHHHHHhccccHHHHHHHhCcchhhhccc
Confidence 457888875555 599999999999999998753
No 415
>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=85.99 E-value=1 Score=39.72 Aligned_cols=41 Identities=17% Similarity=0.165 Sum_probs=31.8
Q ss_pred CHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCC--CCCCHHHHHHHHHHHHh
Q psy1898 117 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKP--RVATPDVEKRIEEYKKT 172 (230)
Q Consensus 117 s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rp--r~lt~~~~~~I~~l~~~ 172 (230)
+.++||+..|||.+||++.++. ++ ..++++.+++|.+..++
T Consensus 1 ti~dIA~~aGVS~~TVSrvLn~---------------~~~~~~vs~~tr~rV~~~a~~ 43 (327)
T TIGR02417 1 TLSDIAKLAGVSKTTASYVING---------------KAKEYRISQETVERVMAVVRE 43 (327)
T ss_pred CHHHHHHHhCCCHHHHHHHHcC---------------CCCCCccCHHHHHHHHHHHHH
Confidence 4689999999999999999851 11 13578888888877766
No 416
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=85.89 E-value=0.92 Score=32.79 Aligned_cols=67 Identities=24% Similarity=0.396 Sum_probs=45.8
Q ss_pred HHHHHHHHHH--cCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCC-CCCCCCC---CCCHHHHHHHHHHH
Q psy1898 104 IRLKIVEMAA--AGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGV-IGGSKPR---VATPDVEKRIEEYK 170 (230)
Q Consensus 104 ~R~rIV~l~~--~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~-~gg~rpr---~lt~~~~~~I~~l~ 170 (230)
+|..|+.++. +.++..+|.+.++++.+++++-++.-.+.|-+.-.+ ..+++|+ .+|+.-++.+..++
T Consensus 1 vRl~Il~~L~~~~~~~f~~L~~~l~lt~g~Ls~hL~~Le~~GyV~~~k~~~~~~p~t~~~lT~~Gr~~~~~~~ 73 (80)
T PF13601_consen 1 VRLAILALLYANEEATFSELKEELGLTDGNLSKHLKKLEEAGYVEVEKEFEGRRPRTWYSLTDKGREAFERYV 73 (80)
T ss_dssp HHHHHHHHHHHHSEEEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEEEE-SSS--EEEEEE-HHHHHHHHHHH
T ss_pred CHHHHHHHHhhcCCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEEEeccCCCCeEEEEECHHHHHHHHHHH
Confidence 4677777543 459999999999999999999999999999774322 2234565 67777777766554
No 417
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=85.89 E-value=0.87 Score=32.23 Aligned_cols=31 Identities=23% Similarity=0.300 Sum_probs=25.3
Q ss_pred HHHHHHH-cCCCHHHHhhhhccccchhhhHHH
Q psy1898 107 KIVEMAA-AGVRPCVISRQLRVSHGCVSKILN 137 (230)
Q Consensus 107 rIV~l~~-~G~s~~~IAr~lgVS~sTV~kwik 137 (230)
++-.+.. .|+|..++|+.+|||+.|+..|.+
T Consensus 5 k~k~~R~~~~ltQ~elA~~vgVsRQTi~~iEk 36 (68)
T COG1476 5 KLKELRAELGLTQEELAKLVGVSRQTIIAIEK 36 (68)
T ss_pred HHHHHHHHhCcCHHHHHHHcCcCHHHHHHHHc
Confidence 4444443 489999999999999999999964
No 418
>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=85.78 E-value=0.74 Score=31.07 Aligned_cols=25 Identities=28% Similarity=0.401 Sum_probs=19.9
Q ss_pred HcCCCHHHHhhhhccccchhhhHHH
Q psy1898 113 AAGVRPCVISRQLRVSHGCVSKILN 137 (230)
Q Consensus 113 ~~G~s~~~IAr~lgVS~sTV~kwik 137 (230)
..|+|..++|..++++++++++|.+
T Consensus 10 ~~~lt~~~~a~~~~i~~~~i~~~e~ 34 (64)
T PF12844_consen 10 EKGLTQKDLAEKLGISRSTISKIEN 34 (64)
T ss_dssp HCT--HHHHHHHHTS-HHHHHHHHT
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHC
Confidence 3589999999999999999999974
No 419
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=85.74 E-value=0.94 Score=39.75 Aligned_cols=44 Identities=14% Similarity=0.196 Sum_probs=37.9
Q ss_pred HHHHHHHHHHHHc-C-CCHHHHhhhhccccchhhhHHHHHhhhCCC
Q psy1898 102 NHIRLKIVEMAAA-G-VRPCVISRQLRVSHGCVSKILNRYQETGSI 145 (230)
Q Consensus 102 ~~~R~rIV~l~~~-G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~v 145 (230)
.+.+.+|++++.+ | .+..++|+.|+||..||+|=++...+.|.+
T Consensus 4 ~eR~~~Il~~L~~~~~v~v~eLa~~l~VS~~TIRRDL~~Le~~g~l 49 (256)
T PRK10434 4 RQRQAAILEYLQKQGKTSVEELAQYFDTTGTTIRKDLVILEHAGTV 49 (256)
T ss_pred HHHHHHHHHHHHHcCCEEHHHHHHHHCCCHHHHHHHHHHHHHCCCE
Confidence 3566778887765 5 999999999999999999999999888865
No 420
>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=85.57 E-value=1.2 Score=29.96 Aligned_cols=36 Identities=25% Similarity=0.207 Sum_probs=30.0
Q ss_pred HHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcC
Q psy1898 164 KRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGG 210 (230)
Q Consensus 164 ~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~ 210 (230)
..|.+++.+++..+..++++.+ + ||.+||+|-|..+
T Consensus 3 ~~Il~~l~~~~~~s~~ela~~~----~-------VS~~TiRRDl~~L 38 (57)
T PF08220_consen 3 QQILELLKEKGKVSVKELAEEF----G-------VSEMTIRRDLNKL 38 (57)
T ss_pred HHHHHHHHHcCCEEHHHHHHHH----C-------cCHHHHHHHHHHH
Confidence 5678888899999999998865 3 5999999988764
No 421
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=85.56 E-value=1.6 Score=31.77 Aligned_cols=29 Identities=24% Similarity=0.322 Sum_probs=27.9
Q ss_pred CCHHHHhhhhccccchhhhHHHHHhhhCC
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNRYQETGS 144 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~ 144 (230)
.|-.+||+.||+|+.+|.+-++.-++.|-
T Consensus 20 ~SGe~La~~LgiSRtaVwK~Iq~Lr~~G~ 48 (79)
T COG1654 20 VSGEKLAEELGISRTAVWKHIQQLREEGV 48 (79)
T ss_pred ccHHHHHHHHCccHHHHHHHHHHHHHhCC
Confidence 89999999999999999999999999994
No 422
>PRK09480 slmA division inhibitor protein; Provisional
Probab=85.52 E-value=1.3 Score=36.04 Aligned_cols=44 Identities=14% Similarity=0.221 Sum_probs=34.3
Q ss_pred cCCCcCCHHHHHHHHHH----H-Hc---CCCHHHHhhhhccccchhhhHHHH
Q psy1898 95 INGRPLPNHIRLKIVEM----A-AA---GVRPCVISRQLRVSHGCVSKILNR 138 (230)
Q Consensus 95 ~~g~~~s~~~R~rIV~l----~-~~---G~s~~~IAr~lgVS~sTV~kwikR 138 (230)
++.++-+.+.|.+|++. + +. +.|..+||++.|||++|+|.+-.-
T Consensus 2 ~~~~~~~~~~r~~Il~aa~~l~~~~~G~~~ti~~Ia~~agvs~gt~Y~~F~~ 53 (194)
T PRK09480 2 AMKRPKKGERREQILQALAQMLESPPGERITTAKLAARVGVSEAALYRHFPS 53 (194)
T ss_pred CCcCCCchhHHHHHHHHHHHHHHhcCCCccCHHHHHHHhCCCHhHHHHHCCC
Confidence 45666677888888873 2 33 489999999999999999987543
No 423
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=85.51 E-value=0.39 Score=30.93 Aligned_cols=32 Identities=22% Similarity=0.279 Sum_probs=20.5
Q ss_pred ChhHHHHHHHHHhcCCChhhhhhhhccccccc
Q psy1898 57 PNHIRLKIVEMAAAGVRPCVISRQLRVSHGVN 88 (230)
Q Consensus 57 p~~~r~~I~e~~~~g~~~~~isr~lrvshg~~ 88 (230)
....|.+|++++.+|.+..+|++.++||+.++
T Consensus 3 ~~~~R~~ii~l~~~G~s~~~ia~~lgvs~~Tv 34 (50)
T PF13384_consen 3 SEERRAQIIRLLREGWSIREIAKRLGVSRSTV 34 (50)
T ss_dssp -------HHHHHHHT--HHHHHHHHTS-HHHH
T ss_pred chhHHHHHHHHHHCCCCHHHHHHHHCcCHHHH
Confidence 36789999999999999999999999888775
No 424
>TIGR02915 PEP_resp_reg putative PEP-CTERM system response regulator. Members of this protein family share full-length homology with (but do not include) the acetoacetate metabolism regulatory protein AtoC. These proteins have a Fis family DNA binding sequence (pfam02954), a response regulator receiver domain (pfam00072), and sigma-54 interaction domain (pfam00158).
Probab=85.34 E-value=0.96 Score=42.20 Aligned_cols=37 Identities=8% Similarity=0.062 Sum_probs=30.2
Q ss_pred HHHHHHHHHH-cCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 104 IRLKIVEMAA-AGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 104 ~R~rIV~l~~-~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
+|..|...+. .+....++|+.||||++|+|+.+++|.
T Consensus 406 E~~~i~~al~~~~gn~~~aA~~Lgisr~tl~rkl~~~~ 443 (445)
T TIGR02915 406 EREAVRKAIARVDGNIARAAELLGITRPTLYDLMKKHG 443 (445)
T ss_pred HHHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHHhC
Confidence 4555666554 478999999999999999999999884
No 425
>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=85.32 E-value=1.1 Score=39.98 Aligned_cols=41 Identities=20% Similarity=0.118 Sum_probs=32.4
Q ss_pred CCHHHHHHHHHHH----HcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 100 LPNHIRLKIVEMA----AAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 100 ~s~~~R~rIV~l~----~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
+|...|.-+...+ .+++|..+||+.||||+.||..+..+..
T Consensus 250 L~~rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVrq~~~rAl 294 (298)
T TIGR02997 250 LTPRERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKAL 294 (298)
T ss_pred CCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 5556655555444 3689999999999999999999988754
No 426
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=85.25 E-value=5.4 Score=29.66 Aligned_cols=81 Identities=12% Similarity=0.018 Sum_probs=51.8
Q ss_pred HcCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCC-CHHHHHHHHHHHHhCCCCCHHHHHHHHHHhhCC
Q psy1898 113 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVA-TPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGI 191 (230)
Q Consensus 113 ~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~l-t~~~~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi 191 (230)
.+..+..++|+.+++|+.++.+..+++ +|.. |... ...-.+....++ .+++.+..+|+.. .|.
T Consensus 19 ~~~~~~~~lA~~~~~S~~~l~r~f~~~--~g~s---------~~~~i~~~Rl~~a~~~L-~~~~~~i~~iA~~----~Gf 82 (107)
T PRK10219 19 DQPLNIDVVAKKSGYSKWYLQRMFRTV--THQT---------LGDYIRQRRLLLAAVEL-RTTERPIFDIAMD----LGY 82 (107)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHH--HCcC---------HHHHHHHHHHHHHHHHH-HccCCCHHHHHHH----HCC
Confidence 345899999999999999999888765 2321 1111 111112223333 3456777766653 687
Q ss_pred CCCCCCCCHhHHHHHHHcC-CCCCC
Q psy1898 192 CDKNSAPSVSSISRLLRGG-RRDDC 215 (230)
Q Consensus 192 ~~~~~~vS~sTV~R~Lr~~-g~~~~ 215 (230)
. +.+...+.+++. |..|.
T Consensus 83 ~------~~s~f~~~Fk~~~G~tP~ 101 (107)
T PRK10219 83 V------SQQTFSRVFRRQFDRTPS 101 (107)
T ss_pred C------CHHHHHHHHHHHHCcCHH
Confidence 4 899999999776 66654
No 427
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=85.24 E-value=1.3 Score=39.62 Aligned_cols=41 Identities=22% Similarity=0.134 Sum_probs=30.3
Q ss_pred CCHHHHHHHHHHHH--cCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 100 LPNHIRLKIVEMAA--AGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 100 ~s~~~R~rIV~l~~--~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
++...|.-+...+- +|+|..+||+.||||..||.++..+..
T Consensus 228 L~~rer~vl~lr~~~~~~~t~~EIa~~lgvs~~~V~q~~~~Al 270 (289)
T PRK07500 228 LNERELRIIRERRLREDGATLEALGEELGISKERVRQIEARAL 270 (289)
T ss_pred CCHHHHHHHHHHhcCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 44444443333333 689999999999999999999988744
No 428
>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=85.21 E-value=0.61 Score=33.28 Aligned_cols=40 Identities=30% Similarity=0.351 Sum_probs=26.0
Q ss_pred HHHHHHHHHhCC----CCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcCCCC
Q psy1898 163 EKRIEEYKKTNP----GIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGGRRD 213 (230)
Q Consensus 163 ~~~I~~l~~~~P----~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~g~~ 213 (230)
++.|.+++.++| ..+..||++. .+ ||.+||.|+.++.|++
T Consensus 18 e~~Ia~yil~~~~~~~~~si~elA~~----~~-------vS~sti~Rf~kkLG~~ 61 (77)
T PF01418_consen 18 EKKIADYILENPDEIAFMSISELAEK----AG-------VSPSTIVRFCKKLGFS 61 (77)
T ss_dssp HHHHHHHHHH-HHHHCT--HHHHHHH----CT-------S-HHHHHHHHHHCTTT
T ss_pred HHHHHHHHHhCHHHHHHccHHHHHHH----cC-------CCHHHHHHHHHHhCCC
Confidence 345666666666 4666666653 44 5999999999999986
No 429
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=85.04 E-value=1.2 Score=40.60 Aligned_cols=41 Identities=12% Similarity=0.092 Sum_probs=31.7
Q ss_pred CCHHHHHHHHHH----HHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 100 LPNHIRLKIVEM----AAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 100 ~s~~~R~rIV~l----~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
+|...|.-+... +.+|+|..+||+.+|||.+||..++.+..
T Consensus 263 L~~~~R~vl~lrygL~~~e~~s~~EIA~~Lgis~~tV~~~~~rAl 307 (325)
T PRK05657 263 LNDKQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQIQVEAL 307 (325)
T ss_pred CCHHHHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 555566555432 25789999999999999999999988744
No 430
>PF13309 HTH_22: HTH domain
Probab=84.98 E-value=2.2 Score=29.49 Aligned_cols=48 Identities=19% Similarity=0.173 Sum_probs=30.8
Q ss_pred CCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHH
Q psy1898 154 KPRVATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLR 208 (230)
Q Consensus 154 rpr~lt~~~~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr 208 (230)
.+..++.+++..|.+.+.++--.-...-.+.+.+..|+ |..||++.|+
T Consensus 17 ~~~~l~~~~k~~iV~~L~~~G~F~lKgav~~vA~~L~i-------S~~TVY~YLr 64 (64)
T PF13309_consen 17 PPSRLSKEEKKEIVRQLYEKGIFLLKGAVEYVAEKLGI-------SRATVYRYLR 64 (64)
T ss_pred ChhhCCHHHHHHHHHHHHHCCCcccCcHHHHHHHHHCC-------CHHHHHHHcC
Confidence 45566788888888888665433333333333343565 9999999985
No 431
>TIGR01453 grpIintron_endo group I intron endonuclease. This model represents one subfamily of endonucleases containing the endo/excinuclease amino terminal domain, Pfam:PF01541 at its amino end. A distinct subfamily includes excinuclease abc subunit c (uvrC). Members of pfam01541 are often termed GIY-YIG endonucleases after conserved motifs near the amino end. This subfamily in this model is found in open reading frames of group I introns in both phage and mitochondria. The closely related endonucleases of phage T4: segA, segB, segC, segD and segE, score below the trusted cutoff for the family.
Probab=84.96 E-value=5 Score=34.29 Aligned_cols=41 Identities=24% Similarity=0.351 Sum_probs=31.3
Q ss_pred CCcCCHHHHHHHHHHHHcC----------------CCHHHHhhhhccccchhhhHHH
Q psy1898 97 GRPLPNHIRLKIVEMAAAG----------------VRPCVISRQLRVSHGCVSKILN 137 (230)
Q Consensus 97 g~~~s~~~R~rIV~l~~~G----------------~s~~~IAr~lgVS~sTV~kwik 137 (230)
|+..+.+.+.++-...+.+ -|..++|+.|+|++.||.++++
T Consensus 145 gk~~s~e~k~k~s~~~k~~~~v~vyd~~~~~~~~F~S~~eAa~~l~i~~~tI~~~l~ 201 (214)
T TIGR01453 145 GKKHSEETKKKISEKEKGAKKVNVYDKNNGLLIIFDSIAEAARHLGISRGTISKYIK 201 (214)
T ss_pred cccCCHHHHHHHHHhhcCCceeEEEECCCCcEEEecCHHHHHHHhCCCHHHHHHHHc
Confidence 7778888888875433221 4789999999999999887764
No 432
>COG5352 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=84.95 E-value=0.92 Score=36.61 Aligned_cols=43 Identities=23% Similarity=0.326 Sum_probs=33.4
Q ss_pred HHHHHHH-HHHHcCCCHHHHhhhhc-cccchhhhHHHHHhhhCCC
Q psy1898 103 HIRLKIV-EMAAAGVRPCVISRQLR-VSHGCVSKILNRYQETGSI 145 (230)
Q Consensus 103 ~~R~rIV-~l~~~G~s~~~IAr~lg-VS~sTV~kwikRy~e~G~v 145 (230)
|+|...+ +++.+|+|.++||++|| ||++.|---+.|..-.|.-
T Consensus 5 dERve~LkKLWseGLSASQIAaQLGGVsRnAVIGKVHRL~lsgR~ 49 (169)
T COG5352 5 DERVETLKKLWSEGLSASQIAAQLGGVSRNAVIGKVHRLGLSGRA 49 (169)
T ss_pred HHHHHHHHHHHHcccCHHHHHHHhcCcchhhhheeeeeccccccC
Confidence 5665555 48899999999999998 8999887777776655543
No 433
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=84.85 E-value=0.86 Score=32.74 Aligned_cols=30 Identities=27% Similarity=0.417 Sum_probs=21.8
Q ss_pred HHHHHH-cCCCHHHHhhhhccccchhhhHHH
Q psy1898 108 IVEMAA-AGVRPCVISRQLRVSHGCVSKILN 137 (230)
Q Consensus 108 IV~l~~-~G~s~~~IAr~lgVS~sTV~kwik 137 (230)
|....+ .|+|..++|+.+||++++|++..+
T Consensus 23 i~~~~~~~~ltQ~e~A~~lgisq~~vS~l~~ 53 (80)
T PF13744_consen 23 IRELREERGLTQAELAERLGISQPRVSRLEN 53 (80)
T ss_dssp HHHHHHCCT--HHHHHHHHTS-HHHHHHHHT
T ss_pred HHHHHHHcCCCHHHHHHHHCCChhHHHHHHc
Confidence 334444 489999999999999999999874
No 434
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=84.63 E-value=3.9 Score=35.55 Aligned_cols=45 Identities=13% Similarity=0.197 Sum_probs=37.1
Q ss_pred HHHHHHHHHHHc--CCCHHHHhhhhccccchhhhHHHHHhhhCCCCc
Q psy1898 103 HIRLKIVEMAAA--GVRPCVISRQLRVSHGCVSKILNRYQETGSIRP 147 (230)
Q Consensus 103 ~~R~rIV~l~~~--G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p 147 (230)
+.=.+|++++.. +++.++||+++|++++||++.++-..+.|-+..
T Consensus 14 ~r~l~IL~~l~~~~~l~l~eia~~lgl~kstv~Rll~tL~~~G~l~~ 60 (257)
T PRK15090 14 LKVFGILQALGEEREIGITELSQRVMMSKSTVYRFLQTMKTLGYVAQ 60 (257)
T ss_pred HHHHHHHHHhhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence 333566766643 489999999999999999999999999998753
No 435
>PRK15424 propionate catabolism operon regulatory protein PrpR; Provisional
Probab=84.60 E-value=1.2 Score=43.58 Aligned_cols=40 Identities=8% Similarity=0.016 Sum_probs=32.3
Q ss_pred HHHHHHHHHHHH-cCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898 102 NHIRLKIVEMAA-AGVRPCVISRQLRVSHGCVSKILNRYQE 141 (230)
Q Consensus 102 ~~~R~rIV~l~~-~G~s~~~IAr~lgVS~sTV~kwikRy~e 141 (230)
...|..|...++ .+....++|+.||||++|+|+++++|..
T Consensus 496 ~~Er~~I~~~L~~~~Gn~~~aA~~LGIsRtTL~RkLk~~g~ 536 (538)
T PRK15424 496 RLLAATLQQALERFNGDKTAAANYLGISRTTLWRRLKAEAK 536 (538)
T ss_pred HHHHHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHHhCC
Confidence 345666666554 5788999999999999999999998853
No 436
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=84.57 E-value=1.1 Score=39.37 Aligned_cols=38 Identities=21% Similarity=0.304 Sum_probs=28.1
Q ss_pred HHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHh
Q psy1898 119 CVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKT 172 (230)
Q Consensus 119 ~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~ 172 (230)
++||+..|||.+||++.++. ++ ..+++.+++|.+..++
T Consensus 2 ~dIA~~agVS~~TVSrvLn~---------------~~-~vs~~tr~rV~~~a~~ 39 (327)
T PRK10423 2 KDVARLAGVSTSTVSHVINK---------------DR-FVSEAITAKVEAAIKE 39 (327)
T ss_pred hhHHHHhCCcHHHHHHHhCC---------------CC-CCCHHHHHHHHHHHHH
Confidence 68999999999999999851 11 2467777777666654
No 437
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=84.53 E-value=3.1 Score=36.42 Aligned_cols=45 Identities=18% Similarity=0.269 Sum_probs=37.3
Q ss_pred HHHHHHHHHHHHc---CCCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898 102 NHIRLKIVEMAAA---GVRPCVISRQLRVSHGCVSKILNRYQETGSIR 146 (230)
Q Consensus 102 ~~~R~rIV~l~~~---G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~ 146 (230)
.+.-..|++.+.+ +.+..+||+.++++++||++.++...+.|-+.
T Consensus 10 l~ral~iL~~l~~~~~~ls~~eia~~lgl~kstv~RlL~tL~~~g~v~ 57 (263)
T PRK09834 10 LSRGLMVLRALNRLDGGATVGLLAELTGLHRTTVRRLLETLQEEGYVR 57 (263)
T ss_pred HHHHHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 3444667776643 38999999999999999999999999999875
No 438
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=84.51 E-value=1.1 Score=35.01 Aligned_cols=31 Identities=13% Similarity=0.164 Sum_probs=25.4
Q ss_pred HHHHHH-HcCCCHHHHhhhhccccchhhhHHH
Q psy1898 107 KIVEMA-AAGVRPCVISRQLRVSHGCVSKILN 137 (230)
Q Consensus 107 rIV~l~-~~G~s~~~IAr~lgVS~sTV~kwik 137 (230)
++..+. +.|+|..++|+..|||++|+++|.+
T Consensus 9 ~l~~ll~~~Glsq~eLA~~~Gis~~~is~iE~ 40 (120)
T PRK13890 9 NVLRLLDERHMTKKELSERSGVSISFLSDLTT 40 (120)
T ss_pred HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHc
Confidence 344433 5699999999999999999999974
No 439
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=84.50 E-value=1.4 Score=35.34 Aligned_cols=42 Identities=24% Similarity=0.219 Sum_probs=33.9
Q ss_pred cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhh
Q psy1898 99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQE 141 (230)
Q Consensus 99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e 141 (230)
.++..+ ..++.++.+|.+.++||+.+++|.+||...+.+.++
T Consensus 137 ~Lt~~E-~~il~~l~~g~~~~~Ia~~l~~s~~tv~~~~~~l~~ 178 (196)
T PRK10360 137 PLTKRE-RQVAEKLAQGMAVKEIAAELGLSPKTVHVHRANLME 178 (196)
T ss_pred CCCHHH-HHHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 344433 367778888999999999999999999999888654
No 440
>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=84.32 E-value=0.74 Score=31.91 Aligned_cols=22 Identities=14% Similarity=0.139 Sum_probs=17.7
Q ss_pred CCHHHHhhhhccccchhh-hHHH
Q psy1898 116 VRPCVISRQLRVSHGCVS-KILN 137 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~-kwik 137 (230)
.+..++|+.+|||++||+ .|.+
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 567799999999999999 8876
No 441
>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF. Members of this protein family are PspF, the sigma-54-dependent transcriptional activator of the phage shock protein (psp) operon, in Escherichia coli and numerous other species. The psp operon is induced by a number of stress conditions, including heat shock, ethanol, and filamentous phage infection. Changed com_name to adhere to TIGR role notes conventions. 09/15/06 - DMH
Probab=84.27 E-value=1.1 Score=40.85 Aligned_cols=35 Identities=11% Similarity=0.016 Sum_probs=28.2
Q ss_pred HHHHHHHHH-cCCCHHHHhhhhccccchhhhHHHHH
Q psy1898 105 RLKIVEMAA-AGVRPCVISRQLRVSHGCVSKILNRY 139 (230)
Q Consensus 105 R~rIV~l~~-~G~s~~~IAr~lgVS~sTV~kwikRy 139 (230)
|.-|...++ .+....++|+.||||++|+|+++++|
T Consensus 294 ~~~I~~aL~~~~gn~~~aA~~LGisr~tL~rklkk~ 329 (329)
T TIGR02974 294 IELLQQALAEAQFNQRKAAELLGLTYHQLRGLLRKH 329 (329)
T ss_pred HHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHhC
Confidence 444444444 47899999999999999999999876
No 442
>PRK00215 LexA repressor; Validated
Probab=84.23 E-value=1.7 Score=36.44 Aligned_cols=32 Identities=25% Similarity=0.258 Sum_probs=29.4
Q ss_pred CCHHHHhhhhcc-ccchhhhHHHHHhhhCCCCc
Q psy1898 116 VRPCVISRQLRV-SHGCVSKILNRYQETGSIRP 147 (230)
Q Consensus 116 ~s~~~IAr~lgV-S~sTV~kwikRy~e~G~v~p 147 (230)
.+.++||+.+++ +++||++++++..+.|.+..
T Consensus 24 ~s~~ela~~~~~~~~~tv~~~l~~L~~~g~i~~ 56 (205)
T PRK00215 24 PSRREIADALGLRSPSAVHEHLKALERKGFIRR 56 (205)
T ss_pred CCHHHHHHHhCCCChHHHHHHHHHHHHCCCEEe
Confidence 588899999999 99999999999999998743
No 443
>PF11985 DUF3486: Protein of unknown function (DUF3486); InterPro: IPR021874 This entry is represented by Bacteriophage Mu, Gp27. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=84.21 E-value=3.1 Score=34.48 Aligned_cols=48 Identities=17% Similarity=0.297 Sum_probs=33.8
Q ss_pred CCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhh---CCCCCCCCCCHhHHHHHHHcC
Q psy1898 157 VATPDVEKRIEEYKKTNPGIFSWEIRDRLVKQD---GICDKNSAPSVSSISRLLRGG 210 (230)
Q Consensus 157 ~lt~~~~~~I~~l~~~~P~~t~~eI~~~L~~~~---Gi~~~~~~vS~sTV~R~Lr~~ 210 (230)
.+++++++.+...+.++ ..|..++.+.|.+.. |.. ||+|+|||+-.+.
T Consensus 9 ~LP~eir~~l~~~L~~~-~~t~~ei~~~~~~~~~~~g~~-----iSrSav~RY~~~~ 59 (180)
T PF11985_consen 9 LLPPEIREWLDQMLRDG-GFTQYEILAEWLEELAEEGYD-----ISRSAVHRYAQRF 59 (180)
T ss_pred hCCHHHHHHHHHHHHhC-CCChHHHHHHHHHhhhccCCC-----cCHHHHHHHHHHH
Confidence 56788999998877555 455555555554535 664 8999999987654
No 444
>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=84.12 E-value=1.3 Score=38.32 Aligned_cols=42 Identities=14% Similarity=0.216 Sum_probs=36.0
Q ss_pred HHHHHHHHHc---CCCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898 105 RLKIVEMAAA---GVRPCVISRQLRVSHGCVSKILNRYQETGSIR 146 (230)
Q Consensus 105 R~rIV~l~~~---G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~ 146 (230)
=..|++++.. +++.++||+.+|++++||++.++-..+.|-+.
T Consensus 11 al~IL~~l~~~~~~~~l~eia~~lglpksT~~RlL~tL~~~G~l~ 55 (248)
T TIGR02431 11 GLAVIEAFGAERPRLTLTDVAEATGLTRAAARRFLLTLVELGYVT 55 (248)
T ss_pred HHHHHHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 3566776653 59999999999999999999999999999875
No 445
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=84.03 E-value=3.7 Score=32.43 Aligned_cols=55 Identities=20% Similarity=0.182 Sum_probs=39.0
Q ss_pred HcCCCHHHHhhhhccccchhhhHHHHHhhhCCCCcC--CCCCC-CCCCCCHHHHHHHH
Q psy1898 113 AAGVRPCVISRQLRVSHGCVSKILNRYQETGSIRPG--VIGGS-KPRVATPDVEKRIE 167 (230)
Q Consensus 113 ~~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~--~~gg~-rpr~lt~~~~~~I~ 167 (230)
..+.+..+||+.++++++||++.+++..+.|-+... +..++ .--.+|++-.+.+.
T Consensus 52 ~~~~t~~eLa~~l~i~~~tvsr~l~~Le~~GlI~R~~~~~DrR~~~l~LT~~G~~~~~ 109 (144)
T PRK11512 52 AACITPVELKKVLSVDLGALTRMLDRLVCKGWVERLPNPNDKRGVLVKLTTSGAAICE 109 (144)
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeccCcccCCeeEeEEChhHHHHHH
Confidence 346999999999999999999999999999977322 22221 22355665554443
No 446
>TIGR02404 trehalos_R_Bsub trehalose operon repressor, B. subtilis-type. This family consists of repressors of the GntR family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gram-positive lineages and does not include the TreR from E. coli.
Probab=83.98 E-value=1.1 Score=38.32 Aligned_cols=33 Identities=27% Similarity=0.199 Sum_probs=29.5
Q ss_pred CHHHHhhhhccccchhhhHHHHHhhhCCCCcCC
Q psy1898 117 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGV 149 (230)
Q Consensus 117 s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~ 149 (230)
|-.++|++||||+.||.+=++.-.+.|.+....
T Consensus 26 sE~eLa~~~gVSR~TVR~Al~~L~~eGli~r~~ 58 (233)
T TIGR02404 26 SEHELMDQYGASRETVRKALNLLTEAGYIQKIQ 58 (233)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeC
Confidence 788999999999999999999999999875443
No 447
>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=83.96 E-value=1.8 Score=31.53 Aligned_cols=68 Identities=12% Similarity=0.041 Sum_probs=47.6
Q ss_pred HHHHHHHHhcCC-ChhhhhhhhcccccccccCCcccCC-CcCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhh
Q psy1898 61 RLKIVEMAAAGV-RPCVISRQLRVSHGVNQLGGVFING-RPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSK 134 (230)
Q Consensus 61 r~~I~e~~~~g~-~~~~isr~lrvshg~~~l~~~~~~g-~~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~k 134 (230)
+.+|+|++..|. +..++++.++||-..+.. ....+ ...+.+.|.+|..+++ +...|+.+....+|-.+
T Consensus 8 ~~~I~e~l~~~~~ti~dvA~~~gvS~~TVsr--~L~~~~~~Vs~~Tr~rV~~aa~----~n~~Ar~l~~~~~~~~~ 77 (80)
T TIGR02844 8 VLEIGKYIVETKATVRETAKVFGVSKSTVHK--DVTERLPEINPELAEEVKEVLD----LNKAERHIRGGKATKLK 77 (80)
T ss_pred HHHHHHHHHHCCCCHHHHHHHhCCCHHHHHH--HhcCCCCCCCHHHHHHHHHHHc----cCHHHHHhhccchHHHH
Confidence 567888887765 788899999987777632 11112 3588999999999888 35667766665555433
No 448
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=83.94 E-value=1.9 Score=35.12 Aligned_cols=41 Identities=17% Similarity=0.168 Sum_probs=34.6
Q ss_pred CHHHHHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcC
Q psy1898 159 TPDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGG 210 (230)
Q Consensus 159 t~~~~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~ 210 (230)
-++.+.+|...+++|+.++..+|++.+ | +|.+||++.++++
T Consensus 12 lD~~D~~IL~~Lq~d~R~s~~eiA~~l----g-------lS~~tv~~Ri~rL 52 (164)
T PRK11169 12 LDRIDRNILNELQKDGRISNVELSKRV----G-------LSPTPCLERVRRL 52 (164)
T ss_pred HHHHHHHHHHHhccCCCCCHHHHHHHH----C-------cCHHHHHHHHHHH
Confidence 456788888999999999999998865 4 4999999998876
No 449
>COG3398 Uncharacterized protein conserved in archaea [Function unknown]
Probab=83.68 E-value=8.3 Score=33.56 Aligned_cols=104 Identities=19% Similarity=0.136 Sum_probs=73.2
Q ss_pred HHHHHHHHHHHHc--CCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCC---C----------CCCCHHHHHHH
Q psy1898 102 NHIRLKIVEMAAA--GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSK---P----------RVATPDVEKRI 166 (230)
Q Consensus 102 ~~~R~rIV~l~~~--G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~r---p----------r~lt~~~~~~I 166 (230)
...|.+|....+. |.+..|+.+.+++.++|..=-++.....+.++...-+|.. | ..+..+..+.|
T Consensus 100 ns~R~~Iy~~i~~nPG~~lsEl~~nl~i~R~TlRyhlriLe~~~li~a~~~~g~~~yfpa~~t~~~~e~~~Lkn~~~k~I 179 (240)
T COG3398 100 NSKRDGIYNYIKPNPGFSLSELRANLYINRSTLRYHLRILESNPLIEAGRVGGALRYFPADMTYGEAEVLSLKNETSKAI 179 (240)
T ss_pred hhhHHHHHHHhccCCCccHHHHHHhcCCChHHHHHHHHHHHhCcchhhhccCCceEEccCCCCcccchHHHhhchhHHHH
Confidence 3678999988764 7999999999999999987777776666655433322210 1 12223345677
Q ss_pred HHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHH---cCCCCCCC
Q psy1898 167 EEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLR---GGRRDDCD 216 (230)
Q Consensus 167 ~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr---~~g~~~~~ 216 (230)
...+++++..+..+|+..+ + +|..||.=.++ ..|+.+..
T Consensus 180 ~~eiq~~~~~t~~~ia~~l----~-------ls~aTV~~~lk~l~~~Gii~~~ 221 (240)
T COG3398 180 IYEIQENKCNTNLLIAYEL----N-------LSVATVAYHLKKLEELGIIPED 221 (240)
T ss_pred HHHHhcCCcchHHHHHHHc----C-------ccHHHHHHHHHHHHHcCCCccc
Confidence 7888889999998888755 3 49999986655 45777764
No 450
>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional
Probab=83.52 E-value=1.2 Score=43.09 Aligned_cols=37 Identities=19% Similarity=0.252 Sum_probs=29.9
Q ss_pred HHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 104 IRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 104 ~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
+|.-+..++....+.+++|+.||||++|+|+.+++|.
T Consensus 475 E~~~i~~~l~~~~~~~~aA~~LGisr~tL~rkl~~~g 511 (520)
T PRK10820 475 ERSVLTRLYRNYPSTRKLAKRLGVSHTAIANKLREYG 511 (520)
T ss_pred HHHHHHHHHHHCCCHHHHHHHhCCCHHHHHHHHHHcC
Confidence 4444555666555899999999999999999999885
No 451
>cd00283 GIY-YIG_Cterm GIYX(10-11)YIG family of class I homing endonucleases C-terminus (GIY-YIG_Cterm). Homing endonucleases promote the mobility of intron or intein by recognizing and cleaving a homologous allele that lacks the sequence. They catalyze a double-strand break in the DNA near the insertion site of that element to facilitate homing at that site. Class I homing endonucleases are sorted into four families based on the presence of these motifs in their respective N-termini: LAGLIDADG, His-Cys box, HNH, and GIY-YIG. This CD contains several but not all members of the GIY-YIG family. The C-terminus of GIY-YIG is a DNA-binding domain which is separated from the N-terminus by a long, flexible linker. The DNA-binding domain consists of a minor-groove binding alpha-helix, and a helix-turn-helix. Some also contain a zinc finger (i.e. I-TevI) which is not required for DNA binding or catalysis, but is a component of the linker and directs the catalytic domain to cleave the homing sit
Probab=83.30 E-value=4.7 Score=31.24 Aligned_cols=67 Identities=22% Similarity=0.341 Sum_probs=46.2
Q ss_pred cCCCCCChhHHHHHHHHHhcCCChhhhhhhhcccccccccCCcccCCCcCCHHHHHHHHHHHHc----------------
Q psy1898 51 INGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGVNQLGGVFINGRPLPNHIRLKIVEMAAA---------------- 114 (230)
Q Consensus 51 ~~g~plp~~~r~~I~e~~~~g~~~~~isr~lrvshg~~~l~~~~~~g~~~s~~~R~rIV~l~~~---------------- 114 (230)
+=|+..++++|..|.+.- .|. ...+| |+..|.+.+.+|-+....
T Consensus 17 ~~Gk~hseetk~kms~~~-~G~-----------------~n~~y--Gk~~s~Etk~k~s~~~~g~kn~~~k~~~~~~ng~ 76 (113)
T cd00283 17 MFGKTHSEETKAKISKNR-SGE-----------------NNPMF--GKKHSDETKAKISAKKKGRKNLNAKKKQSDTDGY 76 (113)
T ss_pred ccCccCCHHHHHHHHHHh-cCC-----------------CCccc--CccCCHHHHHHHHHHHcCCCCCCcceEEEeCCCC
Confidence 557888899888877553 221 11222 666777777777665421
Q ss_pred -C--CCHHHHhhhhccccchhhhHHH
Q psy1898 115 -G--VRPCVISRQLRVSHGCVSKILN 137 (230)
Q Consensus 115 -G--~s~~~IAr~lgVS~sTV~kwik 137 (230)
. -|..++|+.|+++.+||.+++.
T Consensus 77 i~~F~S~~EAar~lgi~~~tIs~~~~ 102 (113)
T cd00283 77 IGIFDSTTEAARFLKVHSGTISKNIK 102 (113)
T ss_pred eEEeCCHHHHHHHHCCCcchhHHHHC
Confidence 1 4889999999999999999853
No 452
>TIGR00647 MG103 conserved hypothetical protein.
Probab=83.22 E-value=2 Score=38.47 Aligned_cols=46 Identities=24% Similarity=0.086 Sum_probs=35.8
Q ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcC
Q psy1898 160 PDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGG 210 (230)
Q Consensus 160 ~~~~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~ 210 (230)
|+..+.+..++.++|++++.|+.+.|...++.. +|.|+|+.+|++.
T Consensus 229 p~~L~~~a~lRl~~Pd~SL~ELgell~~~~~~~-----isKSgvnhRlrKl 274 (279)
T TIGR00647 229 PLNFQRICLLKIDHPDWSLEQIAEFFASKYKVK-----ISRSGIQHRLRKL 274 (279)
T ss_pred CHHHHHHHHHHHhCcccCHHHHHHHhccCCCCC-----cCHHHHHHHHHHH
Confidence 344567777888999999999999985323343 7999999999874
No 453
>PRK10403 transcriptional regulator NarP; Provisional
Probab=83.22 E-value=1.6 Score=34.99 Aligned_cols=40 Identities=18% Similarity=0.184 Sum_probs=33.3
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
++.... .|+.++..|.+.++||+.+++|..||...+++-.
T Consensus 154 Lt~~e~-~vl~~~~~g~s~~~ia~~l~~s~~tv~~~~~~i~ 193 (215)
T PRK10403 154 LTEREL-DVLHELAQGLSNKQIASVLNISEQTVKVHIRNLL 193 (215)
T ss_pred CCHHHH-HHHHHHHCCCCHHHHHHHcCCCHHHHHHHHHHHH
Confidence 554444 5778888999999999999999999999888754
No 454
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=83.21 E-value=1.5 Score=38.03 Aligned_cols=41 Identities=20% Similarity=0.195 Sum_probs=33.6
Q ss_pred cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
.+|..+ ..|+.+..+|+|..+||..|+||..||..-++.-.
T Consensus 179 ~LT~rE-~evl~~~a~G~t~~eIa~~l~is~~TV~~h~~~~~ 219 (240)
T PRK10188 179 NFSKRE-KEILKWTAEGKTSAEIAMILSISENTVNFHQKNMQ 219 (240)
T ss_pred CCCHHH-HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 455444 46777889999999999999999999998887754
No 455
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=83.13 E-value=1 Score=29.97 Aligned_cols=36 Identities=25% Similarity=0.261 Sum_probs=26.5
Q ss_pred CCCCChhHHHHHHHHHhcCCChhhhhhhhccccccc
Q psy1898 53 GRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGVN 88 (230)
Q Consensus 53 g~plp~~~r~~I~e~~~~g~~~~~isr~lrvshg~~ 88 (230)
|.+|+++.+-+|.-|.+.|++..+|+++++.|+.|.
T Consensus 2 G~~Lt~~Eqaqid~m~qlG~s~~~isr~i~RSr~~I 37 (50)
T PF11427_consen 2 GKTLTDAEQAQIDVMHQLGMSLREISRRIGRSRTCI 37 (50)
T ss_dssp S----HHHHHHHHHHHHTT--HHHHHHHHT--HHHH
T ss_pred CCcCCHHHHHHHHHHHHhchhHHHHHHHhCccHHHH
Confidence 678999999999999999999999999999999886
No 456
>PRK06424 transcription factor; Provisional
Probab=83.11 E-value=1.5 Score=35.51 Aligned_cols=31 Identities=3% Similarity=0.060 Sum_probs=25.1
Q ss_pred HHHHHH-HcCCCHHHHhhhhccccchhhhHHH
Q psy1898 107 KIVEMA-AAGVRPCVISRQLRVSHGCVSKILN 137 (230)
Q Consensus 107 rIV~l~-~~G~s~~~IAr~lgVS~sTV~kwik 137 (230)
+|-.+. +.|+|..++|+.+|++.+||++|.+
T Consensus 88 ~Ir~lRe~~GLSQ~eLA~~iGvs~stIskiE~ 119 (144)
T PRK06424 88 LVKNARERLSMSQADLAAKIFERKNVIASIER 119 (144)
T ss_pred HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHC
Confidence 333333 3599999999999999999999964
No 457
>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=83.00 E-value=5.2 Score=30.04 Aligned_cols=62 Identities=15% Similarity=0.104 Sum_probs=43.0
Q ss_pred HHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhhh-CCC-CcCCCC--CCCCCCCCHHHHHHH
Q psy1898 105 RLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQET-GSI-RPGVIG--GSKPRVATPDVEKRI 166 (230)
Q Consensus 105 R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~-G~v-~p~~~g--g~rpr~lt~~~~~~I 166 (230)
..+++..+.+-.|.+..|+.++||++||++-+++.++. |.. -.+..+ +++...+|+.-++.+
T Consensus 6 ~l~~~~av~~~gSis~AA~~L~iS~stvs~~I~~LE~~lg~~Lf~R~~~g~~~~g~~lT~~G~~l~ 71 (99)
T TIGR00637 6 RVALLKAIARMGSISQAAKDAGISYKSAWDYIRAMNNLSGEPLVERATGGKGGGGAVLTEYGQRLI 71 (99)
T ss_pred HHHHHHHHHHhCCHHHHHHHHCCCHHHHHHHHHHHHHHhCCCeEEecCCCCCCCCeeECHHHHHHH
Confidence 34566666666799999999999999999999998854 432 222211 134667777766554
No 458
>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=82.85 E-value=0.97 Score=36.76 Aligned_cols=32 Identities=9% Similarity=0.185 Sum_probs=29.7
Q ss_pred CCHHHHhhhhccccchhhhHHHHHhhhCCCCc
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRP 147 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p 147 (230)
++..+||..+|+++.||++.++++++.|.+.-
T Consensus 144 ~t~~~iA~~lG~tretvsR~l~~l~~~g~I~~ 175 (193)
T TIGR03697 144 LSHQAIAEAIGSTRVTITRLLGDLRKKKLISI 175 (193)
T ss_pred CCHHHHHHHhCCcHHHHHHHHHHHHHCCCEEe
Confidence 68999999999999999999999999998753
No 459
>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=82.53 E-value=1.2 Score=30.99 Aligned_cols=39 Identities=26% Similarity=0.407 Sum_probs=30.2
Q ss_pred HHHHHH-cC-CCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898 108 IVEMAA-AG-VRPCVISRQLRVSHGCVSKILNRYQETGSIR 146 (230)
Q Consensus 108 IV~l~~-~G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~ 146 (230)
|.+.++ .| .|..+||++|++++.+|..-+..+..-|.++
T Consensus 5 i~~~l~~~~~~S~~eLa~~~~~s~~~ve~mL~~l~~kG~I~ 45 (69)
T PF09012_consen 5 IRDYLRERGRVSLAELAREFGISPEAVEAMLEQLIRKGYIR 45 (69)
T ss_dssp HHHHHHHS-SEEHHHHHHHTT--HHHHHHHHHHHHCCTSCE
T ss_pred HHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEE
Confidence 444343 34 8999999999999999999999999999773
No 460
>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional
Probab=82.48 E-value=1.4 Score=43.55 Aligned_cols=39 Identities=13% Similarity=0.129 Sum_probs=32.4
Q ss_pred HHHHHHHHHHHH-cCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 102 NHIRLKIVEMAA-AGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 102 ~~~R~rIV~l~~-~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
..+|..|..+++ .+....++|+.||||++|+|+-+++|.
T Consensus 590 ~~E~~~i~~al~~~~gn~~~aA~~LGisR~TLyrklk~~~ 629 (638)
T PRK11388 590 ELEKEAIINAAQVCGGRIQEMAALLGIGRTTLWRKMKQHG 629 (638)
T ss_pred HHHHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHcC
Confidence 445666777665 578899999999999999999999886
No 461
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=82.29 E-value=2.2 Score=36.76 Aligned_cols=50 Identities=20% Similarity=0.333 Sum_probs=37.2
Q ss_pred HHHHHHHHH-HHcC--C-CHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCC
Q psy1898 103 HIRLKIVEM-AAAG--V-RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGG 152 (230)
Q Consensus 103 ~~R~rIV~l-~~~G--~-s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg 152 (230)
.++..|+.. +..| + +-.++|++||||+++|.--+++....|.+...+..|
T Consensus 18 ~l~~~I~~g~l~pG~~LpsE~eLa~~lgVSRtpVREAL~~L~~eGlv~~~~~~G 71 (254)
T PRK09464 18 QLEFLILEGTLRPGEKLPPERELAKQFDVSRPSLREAIQRLEAKGLLLRRQGGG 71 (254)
T ss_pred HHHHHHHcCCCCCCCcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCce
Confidence 445555542 3335 4 678999999999999999999999999876554433
No 462
>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=82.29 E-value=1.9 Score=32.91 Aligned_cols=40 Identities=13% Similarity=0.115 Sum_probs=30.9
Q ss_pred CCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHH
Q psy1898 100 LPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRY 139 (230)
Q Consensus 100 ~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy 139 (230)
++...+.=+-..+....|..+||..|+||++.||.-++|-
T Consensus 18 LT~KQ~~Y~~lyy~dDlSl~EIAee~~VSRqAIyDnIKr~ 57 (105)
T COG2739 18 LTKKQKNYLELYYLDDLSLSEIAEEFNVSRQAIYDNIKRT 57 (105)
T ss_pred HhHHHHHHHHHHHHhhccHHHHHHHhCccHHHHHHHHHHH
Confidence 3334444444456778999999999999999999999873
No 463
>PRK13870 transcriptional regulator TraR; Provisional
Probab=82.28 E-value=1.7 Score=37.55 Aligned_cols=41 Identities=17% Similarity=-0.030 Sum_probs=33.6
Q ss_pred cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
++|.-+ ..++.+..+|+|..|||..|+||..||..-++.-+
T Consensus 173 ~LT~RE-~E~L~W~A~GKT~~EIa~ILgISe~TV~~Hl~na~ 213 (234)
T PRK13870 173 WLDPKE-ATYLRWIAVGKTMEEIADVEGVKYNSVRVKLREAM 213 (234)
T ss_pred CCCHHH-HHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 455443 46777888999999999999999999998887654
No 464
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=82.22 E-value=2.3 Score=36.25 Aligned_cols=35 Identities=14% Similarity=0.168 Sum_probs=30.5
Q ss_pred C-CHHHHhhhhccccchhhhHHHHHhhhCCCCcCCC
Q psy1898 116 V-RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI 150 (230)
Q Consensus 116 ~-s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~ 150 (230)
+ |-.++|++||||++||..=+++-...|.+...+.
T Consensus 31 LPsE~eLae~~gVSRt~VReAL~~L~~eGlv~~~~g 66 (239)
T PRK04984 31 LPAERELSELIGVTRTTLREVLQRLARDGWLTIQHG 66 (239)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCC
Confidence 5 6889999999999999999999999998754443
No 465
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=82.17 E-value=3.7 Score=36.08 Aligned_cols=36 Identities=22% Similarity=0.256 Sum_probs=30.4
Q ss_pred HHH-HHHHcCCCHHHHhhhhccccchhhhHHHHHhhh
Q psy1898 107 KIV-EMAAAGVRPCVISRQLRVSHGCVSKILNRYQET 142 (230)
Q Consensus 107 rIV-~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~ 142 (230)
++. ..++.|.|.+.+|+.++||+++|++.+++.++.
T Consensus 7 ~~F~~v~~~~~s~s~AA~~L~isq~avSr~I~~LE~~ 43 (309)
T PRK12682 7 RFVREAVRRNLNLTEAAKALHTSQPGVSKAIIELEEE 43 (309)
T ss_pred HHHHHHHHccCCHHHHHHHhcCccHHHHHHHHHHHHH
Confidence 344 455667899999999999999999999999855
No 466
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=82.09 E-value=1.7 Score=37.61 Aligned_cols=52 Identities=12% Similarity=0.161 Sum_probs=37.4
Q ss_pred CCCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHH
Q psy1898 115 GVRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRI 166 (230)
Q Consensus 115 G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I 166 (230)
+.|..++|+.+++|++||++++++..+.|-+.....+...--.+|+.-.+.+
T Consensus 21 ~IS~~eLA~~L~iS~~Tvsr~Lk~LEe~GlI~R~~~~r~~~v~LTekG~~ll 72 (217)
T PRK14165 21 KISSSEFANHTGTSSKTAARILKQLEDEGYITRTIVPRGQLITITEKGLDVL 72 (217)
T ss_pred CcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEEcCCceEEEECHHHHHHH
Confidence 3789999999999999999999999999987432211123334555544443
No 467
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=82.03 E-value=6.6 Score=34.54 Aligned_cols=44 Identities=14% Similarity=0.121 Sum_probs=37.1
Q ss_pred HHHHHHHHHHHc---CCCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898 103 HIRLKIVEMAAA---GVRPCVISRQLRVSHGCVSKILNRYQETGSIR 146 (230)
Q Consensus 103 ~~R~rIV~l~~~---G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~ 146 (230)
+.=..|++++.. +++..+||+.++++++||++.++-..+.|-+.
T Consensus 25 ~r~l~IL~~~~~~~~~~tl~eIa~~lglpkStv~RlL~tL~~~G~l~ 71 (271)
T PRK10163 25 ERGIAILQYLEKSGGSSSVSDISLNLDLPLSTTFRLLKVLQAADFVY 71 (271)
T ss_pred HHHHHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 444667777653 48999999999999999999999999999874
No 468
>TIGR02293 TAS_TIGR02293 putative toxin-antitoxin system antitoxin component, TIGR02293 family. Proteins in this family are found almost exclusively in the Proteobacteria, but also in Gloeobacter violaceus PCC 7421, a cyanobacterium. This family was proposed by Makarova, et al. (2009) to be the antitoxin component of a new class of type 2 toxin-antitoxin system, or addiction module.
Probab=81.87 E-value=6.5 Score=31.05 Aligned_cols=24 Identities=4% Similarity=0.043 Sum_probs=21.5
Q ss_pred cCCCHHHHhhhhccccchhhhHHH
Q psy1898 114 AGVRPCVISRQLRVSHGCVSKILN 137 (230)
Q Consensus 114 ~G~s~~~IAr~lgVS~sTV~kwik 137 (230)
-|.+..+++..++||++|+++|.+
T Consensus 35 l~ls~~el~~~lgis~~Tl~R~~~ 58 (133)
T TIGR02293 35 LAIGKAEIFKATGIPKATLQRRKM 58 (133)
T ss_pred HCCCHHHHHHHHCCCHHHHHHHhh
Confidence 378999999999999999999975
No 469
>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=81.86 E-value=1.1 Score=34.44 Aligned_cols=25 Identities=12% Similarity=0.032 Sum_probs=22.6
Q ss_pred HcCCCHHHHhhhhccccchhhhHHH
Q psy1898 113 AAGVRPCVISRQLRVSHGCVSKILN 137 (230)
Q Consensus 113 ~~G~s~~~IAr~lgVS~sTV~kwik 137 (230)
+.|++..++|+.+|++++||++|.+
T Consensus 76 ~~gltq~~lA~~lg~~~~tis~~e~ 100 (127)
T TIGR03830 76 KLGLSQREAAELLGGGVNAFSRYER 100 (127)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHC
Confidence 4599999999999999999999953
No 470
>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]
Probab=81.85 E-value=1.9 Score=42.06 Aligned_cols=38 Identities=18% Similarity=0.220 Sum_probs=29.9
Q ss_pred HHHHHHHHHHH-cCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 103 HIRLKIVEMAA-AGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 103 ~~R~rIV~l~~-~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
.++..|..+++ .+-+...+|+.||||++|+|+|+++|.
T Consensus 520 ~Ek~~I~~aL~~~~gn~~~aAk~LgIsrttL~rKlkk~~ 558 (560)
T COG3829 520 YEKHLIREALERHGGNKSKAAKELGISRTTLYRKLKKYG 558 (560)
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHHhc
Confidence 34444445554 467999999999999999999999985
No 471
>PRK11569 transcriptional repressor IclR; Provisional
Probab=81.70 E-value=2.1 Score=37.77 Aligned_cols=44 Identities=23% Similarity=0.345 Sum_probs=36.9
Q ss_pred HHHHHHHHHHHc---CCCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898 103 HIRLKIVEMAAA---GVRPCVISRQLRVSHGCVSKILNRYQETGSIR 146 (230)
Q Consensus 103 ~~R~rIV~l~~~---G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~ 146 (230)
+.=..|++++.+ +++.++||+.+|++++||++.+.-..+.|-+.
T Consensus 28 ~ral~IL~~l~~~~~~~~lseia~~lglpksTv~RlL~tL~~~G~l~ 74 (274)
T PRK11569 28 TRGLKLLEWIAESNGSVALTELAQQAGLPNSTTHRLLTTMQQQGFVR 74 (274)
T ss_pred HHHHHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 444567776653 48999999999999999999999999999874
No 472
>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=81.67 E-value=1.5 Score=30.61 Aligned_cols=34 Identities=24% Similarity=0.316 Sum_probs=28.3
Q ss_pred HcC--CCHHHHhhhhccc-cchhhhHHHHHhhhCCCC
Q psy1898 113 AAG--VRPCVISRQLRVS-HGCVSKILNRYQETGSIR 146 (230)
Q Consensus 113 ~~G--~s~~~IAr~lgVS-~sTV~kwikRy~e~G~v~ 146 (230)
+.| -|.+|||+.||++ ++||+.-++.-.+-|.+.
T Consensus 21 ~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le~kG~I~ 57 (65)
T PF01726_consen 21 ENGYPPTVREIAEALGLKSTSTVQRHLKALERKGYIR 57 (65)
T ss_dssp HHSS---HHHHHHHHTSSSHHHHHHHHHHHHHTTSEE
T ss_pred HcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCcCcc
Confidence 346 5778999999995 999999999999999875
No 473
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=81.58 E-value=2.9 Score=33.08 Aligned_cols=31 Identities=19% Similarity=0.297 Sum_probs=29.2
Q ss_pred CCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNRYQETGSIR 146 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~ 146 (230)
.+.++||+.++||++||++.+++..+.|.+.
T Consensus 23 ~~~~ela~~l~vs~~svs~~l~~L~~~Gli~ 53 (142)
T PRK03902 23 ARVSDIAEALSVHPSSVTKMVQKLDKDEYLI 53 (142)
T ss_pred cCHHHHHHHhCCChhHHHHHHHHHHHCCCEE
Confidence 8899999999999999999999999999774
No 474
>PRK15115 response regulator GlrR; Provisional
Probab=81.53 E-value=1.7 Score=40.51 Aligned_cols=37 Identities=11% Similarity=-0.033 Sum_probs=30.6
Q ss_pred HHHHHHHHHH-cCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 104 IRLKIVEMAA-AGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 104 ~R~rIV~l~~-~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
+|..|..+++ .+....++|+.||||++|+|+-+++|.
T Consensus 399 E~~~i~~al~~~~gn~~~aA~~Lgisr~tL~rkl~~~~ 436 (444)
T PRK15115 399 ELNYLRKLLQITKGNVTHAARMAGRNRTEFYKLLSRHE 436 (444)
T ss_pred HHHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHHhC
Confidence 4555666554 478999999999999999999999985
No 475
>PF08461 HTH_12: Ribonuclease R winged-helix domain; InterPro: IPR013668 This domain is found at the amino terminus of Ribonuclease R and a number of presumed transcriptional regulatory proteins from archaea.
Probab=81.49 E-value=3.1 Score=28.94 Aligned_cols=40 Identities=18% Similarity=0.051 Sum_probs=30.9
Q ss_pred HHHHHHHhCC-CCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcC
Q psy1898 165 RIEEYKKTNP-GIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGG 210 (230)
Q Consensus 165 ~I~~l~~~~P-~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~ 210 (230)
+|...+.+.. .++.++|++.|.. .|.. +|..||.|.|+..
T Consensus 2 ~IL~~L~~~~~P~g~~~l~~~L~~-~g~~-----~se~avRrrLr~m 42 (66)
T PF08461_consen 2 FILRILAESDKPLGRKQLAEELKL-RGEE-----LSEEAVRRRLRAM 42 (66)
T ss_pred HHHHHHHHcCCCCCHHHHHHHHHh-cChh-----hhHHHHHHHHHHH
Confidence 4555555544 5899999999987 6874 8999999988764
No 476
>COG1961 PinR Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]
Probab=81.45 E-value=1.7 Score=36.88 Aligned_cols=47 Identities=26% Similarity=0.352 Sum_probs=40.2
Q ss_pred CcCCHHHHHHHHHHHHcC-CCHHHHhhhhccccchhhhHHHHHhhhCC
Q psy1898 98 RPLPNHIRLKIVEMAAAG-VRPCVISRQLRVSHGCVSKILNRYQETGS 144 (230)
Q Consensus 98 ~~~s~~~R~rIV~l~~~G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~ 144 (230)
.+...+....|..++..+ .+..++|+.++++..||++|.+.....+.
T Consensus 159 ~~~~~~~~~~v~~l~~~~~~~~~~~a~~~~i~~~t~~r~~~~~~~~~~ 206 (222)
T COG1961 159 RKKAEEQAAAVRRLLADGLGSYSEIARALGISRSTVYRILNKLKKRGG 206 (222)
T ss_pred ccccchhHHHHHHHHHhccchHHHHHHHcCccHHHHHHhhhhhhcccc
Confidence 556667788888899999 79999999999999999999988765554
No 477
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=81.37 E-value=3.2 Score=35.72 Aligned_cols=37 Identities=16% Similarity=0.175 Sum_probs=31.5
Q ss_pred C-CHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCC
Q psy1898 116 V-RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGG 152 (230)
Q Consensus 116 ~-s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg 152 (230)
+ +-.++|+.||||+++|.-=+++-...|.+.-.+..|
T Consensus 31 LPsE~eLa~~~gVSRtpVREAL~~L~~eGlV~~~~~~G 68 (251)
T PRK09990 31 LPSERRLCEKLGFSRSALREGLTVLRGRGIIETAQGRG 68 (251)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCCCe
Confidence 6 678999999999999999999999999875544433
No 478
>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=81.25 E-value=2.1 Score=36.35 Aligned_cols=33 Identities=15% Similarity=0.256 Sum_probs=29.5
Q ss_pred CHHHHhhhhccccchhhhHHHHHhhhCCCCcCC
Q psy1898 117 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGV 149 (230)
Q Consensus 117 s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~ 149 (230)
|-.++|++|+||+.||.+=++.-.+.|.+....
T Consensus 34 sE~eLa~~~~VSR~TvR~Al~~L~~eGli~r~~ 66 (238)
T TIGR02325 34 AEMQLAERFGVNRHTVRRAIAALVERGLLRAEQ 66 (238)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence 788999999999999999999999999875443
No 479
>COG5566 Uncharacterized conserved protein [Function unknown]
Probab=81.23 E-value=2 Score=34.13 Aligned_cols=50 Identities=14% Similarity=0.272 Sum_probs=36.6
Q ss_pred cccCCCcCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhhh
Q psy1898 93 VFINGRPLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQET 142 (230)
Q Consensus 93 ~~~~g~~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~ 142 (230)
|++.|-..-..+|..-+..--+|.+..++|+.+.+|..+||++++|+...
T Consensus 80 YlP~G~s~r~t~Rn~~ifsd~dG~n~~eLaKkYrlS~~~Iy~VIrr~~t~ 129 (137)
T COG5566 80 YLPKGDSIRATLRNKQIFSDFDGSNYVELAKKYRLSENHIYRVIRRTHTS 129 (137)
T ss_pred EeeCchHHHHHHHHHHHHHhcCCccHHHHHHHhcccHHHHHHHHHHHHHH
Confidence 33334333445665555555569999999999999999999999986643
No 480
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=81.20 E-value=2.1 Score=34.33 Aligned_cols=34 Identities=24% Similarity=0.211 Sum_probs=29.4
Q ss_pred HHHHHHHcCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 107 KIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 107 rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
.++.++.+|++..+||+.+++|..||..++.+-+
T Consensus 156 ~vl~~l~~g~s~~eIa~~l~~s~~tv~~~~~~~~ 189 (210)
T PRK09935 156 TILRYLVSGLSNKEIADQLLLSNKTVSAHKSNIY 189 (210)
T ss_pred HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 4455677899999999999999999999998855
No 481
>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=81.15 E-value=1.3 Score=30.15 Aligned_cols=30 Identities=13% Similarity=0.122 Sum_probs=26.2
Q ss_pred hHHHHHHHHHhcCCChhhhhhhhccccccc
Q psy1898 59 HIRLKIVEMAAAGVRPCVISRQLRVSHGVN 88 (230)
Q Consensus 59 ~~r~~I~e~~~~g~~~~~isr~lrvshg~~ 88 (230)
+.|.++..|+..|+++.+|+..|+++..++
T Consensus 1 e~k~~A~~LY~~G~~~~eIA~~Lg~~~~TV 30 (58)
T PF06056_consen 1 EVKEQARSLYLQGWSIKEIAEELGVPRSTV 30 (58)
T ss_pred CHHHHHHHHHHcCCCHHHHHHHHCCChHHH
Confidence 368889999999999999999999876655
No 482
>PRK14999 histidine utilization repressor; Provisional
Probab=81.01 E-value=2.3 Score=36.55 Aligned_cols=33 Identities=12% Similarity=0.105 Sum_probs=29.7
Q ss_pred CHHHHhhhhccccchhhhHHHHHhhhCCCCcCC
Q psy1898 117 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGV 149 (230)
Q Consensus 117 s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~ 149 (230)
|-.++|++||||+.||.+=+..-.+.|.+...+
T Consensus 38 sE~eLa~~~gVSR~TVR~Al~~L~~eGli~r~~ 70 (241)
T PRK14999 38 SEAELVAQYGFSRMTINRALRELTDEGWLVRLQ 70 (241)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence 789999999999999999999999999875443
No 483
>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=80.98 E-value=2.7 Score=27.44 Aligned_cols=35 Identities=23% Similarity=0.255 Sum_probs=24.3
Q ss_pred HHHHHH-HhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcC
Q psy1898 165 RIEEYK-KTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGG 210 (230)
Q Consensus 165 ~I~~l~-~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~ 210 (230)
.|..++ +.++.++..+|++.| + ||..||++.|+..
T Consensus 4 ~il~~L~~~~~~it~~eLa~~l----~-------vS~rTi~~~i~~L 39 (55)
T PF08279_consen 4 QILKLLLESKEPITAKELAEEL----G-------VSRRTIRRDIKEL 39 (55)
T ss_dssp HHHHHHHHTTTSBEHHHHHHHC----T-------S-HHHHHHHHHHH
T ss_pred HHHHHHHHcCCCcCHHHHHHHh----C-------CCHHHHHHHHHHH
Confidence 344444 555569999998865 3 5999999988764
No 484
>PRK10923 glnG nitrogen regulation protein NR(I); Provisional
Probab=80.97 E-value=1.9 Score=40.62 Aligned_cols=37 Identities=11% Similarity=0.035 Sum_probs=30.3
Q ss_pred HHHHHHHHHH-cCCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 104 IRLKIVEMAA-AGVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 104 ~R~rIV~l~~-~G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
.|.-|..+++ .+....++|+.||||++|+|+.+++|.
T Consensus 430 E~~~i~~aL~~~~gn~~~aA~~Lgisr~tL~rkl~~~~ 467 (469)
T PRK10923 430 ERTLLTTALRHTQGHKQEAARLLGWGRNTLTRKLKELG 467 (469)
T ss_pred HHHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHHhC
Confidence 4555666554 478999999999999999999999884
No 485
>PRK04841 transcriptional regulator MalT; Provisional
Probab=80.79 E-value=1.9 Score=43.73 Aligned_cols=44 Identities=20% Similarity=0.397 Sum_probs=36.6
Q ss_pred cCCHHHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHH-HhhhC
Q psy1898 99 PLPNHIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNR-YQETG 143 (230)
Q Consensus 99 ~~s~~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikR-y~e~G 143 (230)
++|.. -.+|+.++.+|+|.++||..++||.+||...+++ |..-|
T Consensus 838 ~lt~~-e~~v~~~~~~g~~~~~ia~~l~~s~~tv~~h~~~~~~kl~ 882 (903)
T PRK04841 838 PLTQR-EWQVLGLIYSGYSNEQIAGELDVAATTIKTHIRNLYQKLG 882 (903)
T ss_pred CCCHH-HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 45533 3578888999999999999999999999999888 66665
No 486
>PF04645 DUF603: Protein of unknown function, DUF603; InterPro: IPR006739 This family includes several uncharacterised proteins from Borrelia species.
Probab=80.73 E-value=1.8 Score=36.04 Aligned_cols=36 Identities=19% Similarity=0.281 Sum_probs=31.9
Q ss_pred HHHHHcC-CCHHHHhhhhccccchhhhHHHHHhhhCC
Q psy1898 109 VEMAAAG-VRPCVISRQLRVSHGCVSKILNRYQETGS 144 (230)
Q Consensus 109 V~l~~~G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~ 144 (230)
|.++.+| ++-.+||..+|||+..|.+..++|.....
T Consensus 12 i~yF~eg~L~d~~Ia~~lgvs~~nV~kmR~Kwes~~~ 48 (181)
T PF04645_consen 12 IFYFKEGRLSDAEIAKELGVSRVNVWKMRQKWESSED 48 (181)
T ss_pred HHHHhcCCccHHHHHHHHCchHHHHHHHHHHHHhcCC
Confidence 4567788 99999999999999999999999987664
No 487
>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=80.67 E-value=1.2 Score=33.32 Aligned_cols=26 Identities=15% Similarity=0.249 Sum_probs=22.1
Q ss_pred CCCHHHHhhhhccccchhhhHHHHHh
Q psy1898 115 GVRPCVISRQLRVSHGCVSKILNRYQ 140 (230)
Q Consensus 115 G~s~~~IAr~lgVS~sTV~kwikRy~ 140 (230)
..+.+.+|+..||+.+||+||..-|.
T Consensus 23 ~~gq~~vA~~~Gv~eStISR~k~~~~ 48 (91)
T PF05269_consen 23 SVGQKKVAEAMGVDESTISRWKNDFI 48 (91)
T ss_dssp HHHHHHHHHHHTSSTTTHHHHHHHHH
T ss_pred HHhhHHHHHHhCCCHHHHHHHHhhHH
Confidence 35788999999999999999976543
No 488
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=80.55 E-value=3.3 Score=33.24 Aligned_cols=40 Identities=18% Similarity=0.119 Sum_probs=33.4
Q ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHHHHhhCCCCCCCCCCHhHHHHHHHcC
Q psy1898 160 PDVEKRIEEYKKTNPGIFSWEIRDRLVKQDGICDKNSAPSVSSISRLLRGG 210 (230)
Q Consensus 160 ~~~~~~I~~l~~~~P~~t~~eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~ 210 (230)
++.+..|...+++|+..+..+|++.| | +|.+||++.++++
T Consensus 8 D~~D~~Il~~Lq~d~R~s~~eiA~~l----g-------lS~~tV~~Ri~rL 47 (153)
T PRK11179 8 DNLDRGILEALMENARTPYAELAKQF----G-------VSPGTIHVRVEKM 47 (153)
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHH----C-------cCHHHHHHHHHHH
Confidence 34677888888899999999999876 4 4999999998876
No 489
>PRK12423 LexA repressor; Provisional
Probab=80.42 E-value=2.8 Score=35.34 Aligned_cols=45 Identities=22% Similarity=0.254 Sum_probs=34.6
Q ss_pred HHHHHHHHHHH-----cCC--CHHHHhhhhc-cccchhhhHHHHHhhhCCCCc
Q psy1898 103 HIRLKIVEMAA-----AGV--RPCVISRQLR-VSHGCVSKILNRYQETGSIRP 147 (230)
Q Consensus 103 ~~R~rIV~l~~-----~G~--s~~~IAr~lg-VS~sTV~kwikRy~e~G~v~p 147 (230)
..|..|++.+. .|. |.++||++|| +|++||++.+++..+.|.+..
T Consensus 6 ~~q~~il~~l~~~i~~~g~~Ps~~eia~~~g~~s~~~v~~~l~~L~~~G~l~~ 58 (202)
T PRK12423 6 PKRAAILAFIRERIAQAGQPPSLAEIAQAFGFASRSVARKHVQALAEAGLIEV 58 (202)
T ss_pred HHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCCCEEe
Confidence 34555555332 344 9999999999 599999999999999997743
No 490
>COG1356 tfx Transcriptional regulator [DNA replication, recombination and repair]
Probab=80.41 E-value=0.97 Score=35.88 Aligned_cols=40 Identities=25% Similarity=0.373 Sum_probs=34.6
Q ss_pred HHHHHHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhhh
Q psy1898 103 HIRLKIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQET 142 (230)
Q Consensus 103 ~~R~rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~ 142 (230)
+..-+++.|.+.|++..+||+.|+-++.-|+-+.++.+++
T Consensus 11 e~qikvl~lRekG~tQ~eIA~~L~TTraNvSaIEkrA~en 50 (143)
T COG1356 11 EQQIKVLVLREKGLTQSEIARILKTTRANVSAIEKRALEN 50 (143)
T ss_pred hhheeeeehhhccccHHHHHHHHccchhhHHHHHHHHHHH
Confidence 4455677789999999999999999999999999987654
No 491
>PF08069 Ribosomal_S13_N: Ribosomal S13/S15 N-terminal domain; InterPro: IPR012606 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This domain is found at the N terminus of ribosomal S13 and S15 proteins. This domain is also identified as NUC021 [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 3U5C_N 3O30_G 3IZB_O 3O2Z_G 3U5G_N 2XZN_O 2XZM_O 3IZ6_O.
Probab=80.40 E-value=0.79 Score=31.64 Aligned_cols=31 Identities=32% Similarity=0.527 Sum_probs=28.4
Q ss_pred ChhHHHHHHHHHhcCCChhhhhhhhcccccc
Q psy1898 57 PNHIRLKIVEMAAAGVRPCVISRQLRVSHGV 87 (230)
Q Consensus 57 p~~~r~~I~e~~~~g~~~~~isr~lrvshg~ 87 (230)
|+++...|++++..|++|++|--.||-+||+
T Consensus 30 ~~eVe~~I~klakkG~tpSqIG~iLRD~~GI 60 (60)
T PF08069_consen 30 PEEVEELIVKLAKKGLTPSQIGVILRDQYGI 60 (60)
T ss_dssp HHHHHHHHHHHCCTTHCHHHHHHHHHHSCTC
T ss_pred HHHHHHHHHHHHHcCCCHHHhhhhhhhccCC
Confidence 4888899999999999999999999988884
No 492
>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=80.38 E-value=7.3 Score=29.35 Aligned_cols=33 Identities=12% Similarity=0.300 Sum_probs=30.3
Q ss_pred cCCCHHHHhhhhccccchhhhHHHHHhhhCCCC
Q psy1898 114 AGVRPCVISRQLRVSHGCVSKILNRYQETGSIR 146 (230)
Q Consensus 114 ~G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~ 146 (230)
++.+..+||..++++++||++.+++..+.|-+.
T Consensus 42 ~~~t~~eL~~~l~~~~stvs~~i~~Le~kg~I~ 74 (109)
T TIGR01889 42 GKLTLKEIIKEILIKQSALVKIIKKLSKKGYLS 74 (109)
T ss_pred CcCcHHHHHHHHCCCHHHHHHHHHHHHHCCCEe
Confidence 359999999999999999999999999999763
No 493
>PRK03837 transcriptional regulator NanR; Provisional
Probab=80.29 E-value=1.6 Score=37.29 Aligned_cols=34 Identities=12% Similarity=0.079 Sum_probs=30.1
Q ss_pred CHHHHhhhhccccchhhhHHHHHhhhCCCCcCCC
Q psy1898 117 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGVI 150 (230)
Q Consensus 117 s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~ 150 (230)
+..++|++||||++||..-+.+....|-+.-.+.
T Consensus 39 ~E~~Lae~~gVSRt~VREAL~~L~~eGlv~~~~~ 72 (241)
T PRK03837 39 SERELMAFFGVGRPAVREALQALKRKGLVQISHG 72 (241)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 7889999999999999999999999998754443
No 494
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=80.13 E-value=4.9 Score=34.86 Aligned_cols=36 Identities=8% Similarity=0.131 Sum_probs=29.5
Q ss_pred HHHHHHHcCCCHHHHhhhhccccchhhhHHHHHhhh
Q psy1898 107 KIVEMAAAGVRPCVISRQLRVSHGCVSKILNRYQET 142 (230)
Q Consensus 107 rIV~l~~~G~s~~~IAr~lgVS~sTV~kwikRy~e~ 142 (230)
+++..+.+-.|.+.+|+.+++|+++|++++++.++.
T Consensus 7 ~~f~~v~~~gs~s~AA~~L~isQ~avSr~i~~LE~~ 42 (296)
T PRK09906 7 RYFVAVAEELNFTKAAEKLHTAQPSLSQQIKDLENC 42 (296)
T ss_pred HHHHHHHhhCCHHHHHHHhCCCCcHHHHHHHHHHHH
Confidence 444444444599999999999999999999999855
No 495
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=80.03 E-value=2.1 Score=35.38 Aligned_cols=25 Identities=16% Similarity=0.227 Sum_probs=23.0
Q ss_pred HcCCCHHHHhhhhccccchhhhHHH
Q psy1898 113 AAGVRPCVISRQLRVSHGCVSKILN 137 (230)
Q Consensus 113 ~~G~s~~~IAr~lgVS~sTV~kwik 137 (230)
+.|+|..++|+.+|||++||++|.+
T Consensus 18 ~~glt~~elA~~~gis~~~is~~E~ 42 (185)
T PRK09943 18 QQGLSQRRAAELSGLTHSAISTIEQ 42 (185)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHc
Confidence 4589999999999999999999974
No 496
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=79.89 E-value=5.4 Score=35.11 Aligned_cols=96 Identities=16% Similarity=0.110 Sum_probs=65.6
Q ss_pred HHHHHHHHH--HHcC-CCHHHHhhhhccccchhhhHHHHHhhhCCCCcCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHH
Q psy1898 103 HIRLKIVEM--AAAG-VRPCVISRQLRVSHGCVSKILNRYQETGSIRPGVIGGSKPRVATPDVEKRIEEYKKTNPGIFSW 179 (230)
Q Consensus 103 ~~R~rIV~l--~~~G-~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~~gg~rpr~lt~~~~~~I~~l~~~~P~~t~~ 179 (230)
.+|.+|+-. ..++ ..+++||+.+||+...|+-.++...+.|.+... |+-.-.+|.+-.+++.+.+.+- ..+..
T Consensus 10 ~t~fqIL~ei~~~qp~v~q~eIA~~lgiT~QaVsehiK~Lv~eG~i~~~---gR~~Y~iTkkG~e~l~~~~~dl-r~f~~ 85 (260)
T COG1497 10 LTRFQILSEIAVRQPRVKQKEIAKKLGITLQAVSEHIKELVKEGLIEKE---GRGEYEITKKGAEWLLEQLSDL-RRFSE 85 (260)
T ss_pred chHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHHHhccceeec---CCeeEEEehhHHHHHHHHHHHH-HHHHH
Confidence 567777753 3444 999999999999999999999999999988653 2224566777777776665321 12233
Q ss_pred HHHHHHHHhhCCCCCCCCCCHhHHHHHHHcCCCCCC
Q psy1898 180 EIRDRLVKQDGICDKNSAPSVSSISRLLRGGRRDDC 215 (230)
Q Consensus 180 eI~~~L~~~~Gi~~~~~~vS~sTV~R~Lr~~g~~~~ 215 (230)
++ .. ...+..||-++...++...
T Consensus 86 ev----~~---------~l~~~~vw~AIA~edI~~G 108 (260)
T COG1497 86 EV----EL---------VLDYVMVWTAIAKEDIKEG 108 (260)
T ss_pred HH----HH---------HHhhHHHHHHhhHhhhccC
Confidence 33 11 1356677888887777654
No 497
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=79.84 E-value=2.8 Score=36.04 Aligned_cols=33 Identities=15% Similarity=0.143 Sum_probs=29.5
Q ss_pred CHHHHhhhhccccchhhhHHHHHhhhCCCCcCC
Q psy1898 117 RPCVISRQLRVSHGCVSKILNRYQETGSIRPGV 149 (230)
Q Consensus 117 s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p~~ 149 (230)
|-.++|++||||+.||.+-+..-.+.|.+....
T Consensus 31 sE~eL~~~~~VSR~TvR~Al~~L~~eGli~r~~ 63 (240)
T PRK09764 31 TESALQTEFGVSRVTVRQALRQLVEQQILESIQ 63 (240)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence 679999999999999999999999999875443
No 498
>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=79.77 E-value=2.6 Score=35.17 Aligned_cols=32 Identities=16% Similarity=0.179 Sum_probs=28.8
Q ss_pred CCHHHHhhhhccc-cchhhhHHHHHhhhCCCCc
Q psy1898 116 VRPCVISRQLRVS-HGCVSKILNRYQETGSIRP 147 (230)
Q Consensus 116 ~s~~~IAr~lgVS-~sTV~kwikRy~e~G~v~p 147 (230)
.+.++||+.++++ ++||++.+++..+.|-+..
T Consensus 26 ~~~~ela~~~~~~s~~tv~~~l~~L~~~g~i~~ 58 (199)
T TIGR00498 26 PSIREIARAVGLRSPSAAEEHLKALERKGYIER 58 (199)
T ss_pred CcHHHHHHHhCCCChHHHHHHHHHHHHCCCEec
Confidence 6677999999998 9999999999999997753
No 499
>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=79.70 E-value=3 Score=35.06 Aligned_cols=43 Identities=23% Similarity=0.320 Sum_probs=35.9
Q ss_pred HHHHHHHHHc--CCCHHHHhhhhccccchhhhHHHHHhhhCCCCc
Q psy1898 105 RLKIVEMAAA--GVRPCVISRQLRVSHGCVSKILNRYQETGSIRP 147 (230)
Q Consensus 105 R~rIV~l~~~--G~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p 147 (230)
..+|+..+.. +.+..+||+.+++|++||++-+++..+.|-+..
T Consensus 145 ~~~IL~~l~~~g~~s~~eia~~l~is~stv~r~L~~Le~~GlI~r 189 (203)
T TIGR01884 145 ELKVLEVLKAEGEKSVKNIAKKLGKSLSTISRHLRELEKKGLVEQ 189 (203)
T ss_pred HHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence 3566666554 479999999999999999999999999998753
No 500
>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=79.62 E-value=3.9 Score=31.71 Aligned_cols=32 Identities=25% Similarity=0.298 Sum_probs=29.9
Q ss_pred CCHHHHhhhhccccchhhhHHHHHhhhCCCCc
Q psy1898 116 VRPCVISRQLRVSHGCVSKILNRYQETGSIRP 147 (230)
Q Consensus 116 ~s~~~IAr~lgVS~sTV~kwikRy~e~G~v~p 147 (230)
++..+||+.+++|+++|++.++...+.|.+..
T Consensus 26 ~s~~eia~~l~is~~~v~~~l~~L~~~Gli~~ 57 (130)
T TIGR02944 26 YSAAEIAEQTGLNAPTVSKILKQLSLAGIVTS 57 (130)
T ss_pred ccHHHHHHHHCcCHHHHHHHHHHHHHCCcEEe
Confidence 89999999999999999999999999997743
Done!