Query psy10745
Match_columns 197
No_of_seqs 201 out of 283
Neff 4.0
Searched_HMMs 46136
Date Fri Aug 16 17:27:46 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy10745.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/10745hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3517|consensus 100.0 2.3E-34 4.9E-39 253.8 2.7 84 2-85 43-130 (334)
2 PF00292 PAX: 'Paired box' dom 100.0 2.7E-34 5.8E-39 229.2 -0.1 82 2-83 40-125 (125)
3 PF00292 PAX: 'Paired box' dom 100.0 2.6E-30 5.6E-35 206.4 3.5 64 118-181 1-64 (125)
4 KOG3517|consensus 99.9 8E-29 1.7E-33 218.7 4.2 62 118-179 4-65 (334)
5 KOG3862|consensus 99.9 2.4E-28 5.2E-33 216.8 1.6 85 2-86 48-136 (327)
6 KOG3862|consensus 99.9 1E-27 2.2E-32 212.9 4.3 66 117-182 8-73 (327)
7 KOG0849|consensus 99.8 1.1E-21 2.3E-26 178.0 3.2 172 2-175 38-235 (354)
8 KOG0849|consensus 99.7 1.7E-18 3.7E-23 157.2 1.3 62 120-181 1-62 (354)
9 cd00131 PAX Paired Box domain 99.7 4.8E-17 1E-21 128.7 3.2 81 5-85 43-127 (128)
10 smart00351 PAX Paired Box doma 99.6 7.6E-16 1.7E-20 120.9 3.9 71 13-83 55-125 (125)
11 cd00131 PAX Paired Box domain 99.6 1.6E-15 3.5E-20 120.0 5.0 65 118-182 1-65 (128)
12 smart00351 PAX Paired Box doma 99.5 2.5E-14 5.4E-19 112.4 5.0 65 118-182 1-65 (125)
13 PF13565 HTH_32: Homeodomain-l 97.9 1.7E-05 3.6E-10 55.9 3.9 65 13-82 7-77 (77)
14 PF13384 HTH_23: Homeodomain-l 97.8 5.6E-06 1.2E-10 54.4 1.0 43 136-178 3-45 (50)
15 PF13936 HTH_38: Helix-turn-he 97.4 6.2E-05 1.3E-09 49.7 1.3 41 133-173 3-43 (44)
16 PF04218 CENP-B_N: CENP-B N-te 97.0 0.00063 1.4E-08 46.7 3.2 41 133-173 5-45 (53)
17 PF13518 HTH_28: Helix-turn-he 97.0 0.00065 1.4E-08 44.2 2.8 39 140-178 2-40 (52)
18 PF13551 HTH_29: Winged helix- 96.7 0.0017 3.7E-08 47.6 3.3 68 13-83 34-109 (112)
19 PF13551 HTH_29: Winged helix- 96.7 0.0011 2.3E-08 48.7 2.0 39 140-178 1-40 (112)
20 PF02796 HTH_7: Helix-turn-hel 96.6 0.00096 2.1E-08 43.9 1.3 38 135-172 6-43 (45)
21 COG3415 Transposase and inacti 96.4 0.0022 4.8E-08 52.4 2.6 66 13-84 43-109 (138)
22 cd00569 HTH_Hin_like Helix-tur 96.4 0.0029 6.2E-08 35.6 2.3 38 134-171 5-42 (42)
23 smart00421 HTH_LUXR helix_turn 96.1 0.0068 1.5E-07 38.7 3.2 41 135-176 4-44 (58)
24 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 96.1 0.0047 1E-07 42.7 2.5 41 132-172 2-42 (50)
25 PF12759 HTH_Tnp_IS1: InsA C-t 95.8 0.0069 1.5E-07 41.6 2.4 35 138-172 9-43 (46)
26 PF06056 Terminase_5: Putative 95.4 0.012 2.5E-07 41.4 2.3 44 138-181 1-44 (58)
27 PF01710 HTH_Tnp_IS630: Transp 95.3 0.012 2.6E-07 45.7 2.4 54 15-84 41-94 (119)
28 PF04545 Sigma70_r4: Sigma-70, 95.0 0.023 5E-07 37.4 2.7 41 135-175 5-45 (50)
29 PF13542 HTH_Tnp_ISL3: Helix-t 94.7 0.032 6.9E-07 36.6 2.7 43 132-174 9-51 (52)
30 cd06171 Sigma70_r4 Sigma70, re 94.5 0.047 1E-06 33.9 3.1 42 135-176 11-52 (55)
31 PF13011 LZ_Tnp_IS481: leucine 93.6 0.082 1.8E-06 40.3 3.3 45 134-178 8-53 (85)
32 cd06170 LuxR_C_like C-terminal 93.0 0.13 2.8E-06 33.0 3.2 42 135-177 1-42 (57)
33 PF01022 HTH_5: Bacterial regu 92.9 0.069 1.5E-06 35.1 1.8 40 137-176 1-41 (47)
34 TIGR02531 yecD_yerC TrpR-relat 92.3 0.11 2.5E-06 39.3 2.5 35 137-171 37-71 (88)
35 smart00550 Zalpha Z-DNA-bindin 92.2 0.15 3.3E-06 36.2 2.9 43 136-178 4-50 (68)
36 PF01710 HTH_Tnp_IS630: Transp 91.9 0.14 3E-06 39.8 2.7 45 136-181 4-48 (119)
37 PF01325 Fe_dep_repress: Iron 91.8 0.1 2.2E-06 36.6 1.6 36 143-178 13-50 (60)
38 PF00356 LacI: Bacterial regul 90.9 0.087 1.9E-06 35.5 0.5 21 154-174 3-23 (46)
39 KOG0400|consensus 90.7 0.14 3E-06 42.5 1.6 32 135-166 29-60 (151)
40 TIGR00721 tfx DNA-binding prot 90.1 0.29 6.3E-06 40.0 3.0 39 138-176 9-47 (137)
41 PF12802 MarR_2: MarR family; 89.8 0.31 6.7E-06 32.5 2.5 40 139-178 7-49 (62)
42 cd00090 HTH_ARSR Arsenical Res 89.8 0.41 8.9E-06 31.4 3.1 44 134-177 3-47 (78)
43 PRK03975 tfx putative transcri 89.8 0.3 6.5E-06 40.1 2.8 39 138-176 9-47 (141)
44 PF00196 GerE: Bacterial regul 89.5 0.28 6.1E-06 33.1 2.2 33 141-173 9-41 (58)
45 PF13565 HTH_32: Homeodomain-l 89.1 0.4 8.7E-06 33.5 2.7 41 131-171 26-77 (77)
46 PF08281 Sigma70_r4_2: Sigma-7 88.9 0.37 8E-06 31.7 2.3 43 134-176 10-52 (54)
47 PRK06759 RNA polymerase factor 88.7 0.44 9.6E-06 36.7 3.0 43 134-176 106-148 (154)
48 TIGR02937 sigma70-ECF RNA poly 88.7 0.48 1E-05 34.7 3.0 41 134-175 110-151 (158)
49 COG3415 Transposase and inacti 88.7 0.38 8.2E-06 39.4 2.7 48 132-179 2-50 (138)
50 PRK04217 hypothetical protein; 88.4 0.55 1.2E-05 37.1 3.3 41 135-176 43-84 (110)
51 PRK13413 mpi multiple promoter 88.1 0.4 8.6E-06 39.7 2.5 36 139-174 161-196 (200)
52 PF01527 HTH_Tnp_1: Transposas 88.0 0.27 5.9E-06 34.1 1.3 43 133-175 5-48 (76)
53 PRK00118 putative DNA-binding 87.6 0.6 1.3E-05 36.5 3.1 45 132-176 15-59 (104)
54 PRK09642 RNA polymerase sigma 87.5 0.64 1.4E-05 36.2 3.2 41 135-176 107-148 (160)
55 PF13412 HTH_24: Winged helix- 87.4 0.62 1.3E-05 30.1 2.6 40 138-177 3-44 (48)
56 cd01392 HTH_LacI Helix-turn-he 86.6 0.28 6E-06 31.8 0.6 19 155-173 2-20 (52)
57 PRK13919 putative RNA polymera 86.3 0.84 1.8E-05 36.4 3.4 42 135-176 136-177 (186)
58 PRK11924 RNA polymerase sigma 86.3 0.78 1.7E-05 35.5 3.1 42 135-176 126-167 (179)
59 PRK09639 RNA polymerase sigma 86.0 0.83 1.8E-05 35.6 3.1 41 135-176 113-153 (166)
60 TIGR02985 Sig70_bacteroi1 RNA 85.7 0.88 1.9E-05 34.5 3.1 42 134-176 113-155 (161)
61 PRK15418 transcriptional regul 85.6 0.77 1.7E-05 41.5 3.2 41 139-179 17-58 (318)
62 PRK12534 RNA polymerase sigma 85.6 1 2.2E-05 36.0 3.6 43 134-176 137-179 (187)
63 PHA02591 hypothetical protein; 85.6 0.68 1.5E-05 35.3 2.3 36 137-172 46-81 (83)
64 TIGR02859 spore_sigH RNA polym 85.6 0.77 1.7E-05 36.8 2.8 42 135-176 150-191 (198)
65 PRK12514 RNA polymerase sigma 85.5 1 2.2E-05 35.7 3.5 42 135-176 130-171 (179)
66 PRK09047 RNA polymerase factor 85.3 0.98 2.1E-05 34.9 3.2 42 134-176 106-148 (161)
67 TIGR01529 argR_whole arginine 85.1 0.69 1.5E-05 37.6 2.4 41 40-85 5-45 (146)
68 PHA00738 putative HTH transcri 85.0 0.65 1.4E-05 37.0 2.1 38 135-172 9-48 (108)
69 PF12840 HTH_20: Helix-turn-he 84.7 0.58 1.3E-05 31.9 1.5 42 135-176 7-50 (61)
70 PRK07037 extracytoplasmic-func 84.2 1.1 2.3E-05 34.9 3.0 42 134-176 109-151 (163)
71 TIGR02952 Sig70_famx2 RNA poly 84.1 1.2 2.6E-05 34.6 3.3 42 134-176 122-164 (170)
72 PRK12536 RNA polymerase sigma 84.0 1 2.3E-05 36.1 3.0 42 134-176 129-171 (181)
73 PRK12537 RNA polymerase sigma 83.6 1.4 3E-05 35.4 3.5 42 134-176 133-175 (182)
74 PRK09652 RNA polymerase sigma 83.5 1.3 2.8E-05 34.4 3.2 41 135-176 129-170 (182)
75 PRK10141 DNA-binding transcrip 83.5 1.1 2.5E-05 35.4 2.9 39 134-172 12-52 (117)
76 PF08069 Ribosomal_S13_N: Ribo 83.3 0.33 7.2E-06 34.9 -0.2 30 136-165 30-59 (60)
77 PF13443 HTH_26: Cro/C1-type H 83.2 0.5 1.1E-05 31.8 0.7 29 145-173 5-33 (63)
78 PRK06986 fliA flagellar biosyn 82.8 1.1 2.4E-05 37.8 2.8 42 135-176 185-226 (236)
79 TIGR02479 FliA_WhiG RNA polyme 82.8 1.2 2.6E-05 37.2 3.0 42 135-176 176-217 (224)
80 PRK09645 RNA polymerase sigma 82.7 1.6 3.4E-05 34.4 3.4 41 135-176 119-160 (173)
81 TIGR02989 Sig-70_gvs1 RNA poly 81.9 1.7 3.6E-05 33.5 3.3 42 134-176 111-153 (159)
82 TIGR02983 SigE-fam_strep RNA p 81.3 1.6 3.5E-05 33.9 3.0 42 134-176 110-152 (162)
83 PRK12532 RNA polymerase sigma 81.2 1.6 3.4E-05 35.3 3.0 40 135-175 137-177 (195)
84 PRK10840 transcriptional regul 81.1 1.8 3.8E-05 35.1 3.3 41 134-175 150-190 (216)
85 PRK12542 RNA polymerase sigma 80.6 1.9 4E-05 34.6 3.2 41 135-176 123-164 (185)
86 TIGR02999 Sig-70_X6 RNA polyme 80.6 1.9 4.2E-05 34.1 3.3 41 135-176 135-176 (183)
87 PRK11923 algU RNA polymerase s 80.4 1.6 3.4E-05 35.1 2.7 41 135-176 139-180 (193)
88 PRK12515 RNA polymerase sigma 80.3 2 4.4E-05 34.5 3.4 43 134-176 131-173 (189)
89 TIGR03879 near_KaiC_dom probab 80.2 1.5 3.2E-05 32.6 2.3 36 138-173 18-55 (73)
90 TIGR02984 Sig-70_plancto1 RNA 80.2 2.1 4.5E-05 33.9 3.3 43 134-176 140-182 (189)
91 PRK02277 orotate phosphoribosy 80.1 1.8 3.8E-05 36.5 3.0 41 137-177 5-45 (200)
92 PRK09483 response regulator; P 79.9 1.5 3.3E-05 34.4 2.5 42 135-177 149-190 (217)
93 PRK10651 transcriptional regul 79.9 2.4 5.2E-05 32.7 3.5 45 134-179 155-199 (216)
94 TIGR02948 SigW_bacill RNA poly 79.7 1.8 4E-05 34.2 2.9 41 135-176 137-178 (187)
95 PRK09637 RNA polymerase sigma 79.5 2.1 4.5E-05 34.8 3.2 42 134-176 106-148 (181)
96 COG2826 Tra8 Transposase and i 79.4 1.7 3.6E-05 40.3 2.9 41 134-174 7-47 (318)
97 PRK06474 hypothetical protein; 79.2 2 4.4E-05 35.8 3.1 45 134-178 7-55 (178)
98 PRK08301 sporulation sigma fac 79.2 2 4.3E-05 36.1 3.0 41 135-176 179-224 (234)
99 TIGR02947 SigH_actino RNA poly 79.1 1 2.3E-05 36.3 1.3 58 134-192 131-191 (193)
100 PRK08583 RNA polymerase sigma 79.0 1.9 4.2E-05 36.8 3.0 41 135-176 206-247 (257)
101 TIGR02980 SigBFG RNA polymeras 79.0 2 4.3E-05 35.8 3.0 43 134-176 178-220 (227)
102 COG1595 RpoE DNA-directed RNA 78.9 1.7 3.7E-05 34.9 2.5 43 134-176 127-169 (182)
103 PRK05602 RNA polymerase sigma 78.6 2.2 4.7E-05 34.2 3.0 41 135-176 129-170 (186)
104 TIGR02941 Sigma_B RNA polymera 78.3 2.2 4.9E-05 36.3 3.2 42 134-176 205-247 (255)
105 PRK12547 RNA polymerase sigma 78.2 2.5 5.5E-05 33.3 3.3 42 134-176 112-154 (164)
106 TIGR02607 antidote_HigA addict 77.6 2.4 5.1E-05 29.5 2.6 28 146-173 14-41 (78)
107 PRK12529 RNA polymerase sigma 77.2 2.5 5.5E-05 33.9 3.0 40 135-175 128-168 (178)
108 PRK12540 RNA polymerase sigma 77.1 2.7 5.8E-05 34.2 3.2 42 135-177 112-154 (182)
109 PRK06811 RNA polymerase factor 77.1 2.9 6.3E-05 33.8 3.4 43 134-177 131-174 (189)
110 PRK05911 RNA polymerase sigma 77.0 2.4 5.2E-05 36.7 3.0 43 134-176 205-247 (257)
111 PRK09647 RNA polymerase sigma 76.9 2.8 6.1E-05 34.9 3.3 43 134-176 138-180 (203)
112 PRK12524 RNA polymerase sigma 76.8 2.9 6.3E-05 34.0 3.3 41 134-175 136-177 (196)
113 PRK12538 RNA polymerase sigma 75.9 2.5 5.4E-05 36.2 2.8 41 135-176 172-213 (233)
114 TIGR03209 P21_Cbot clostridium 75.8 1.6 3.5E-05 33.4 1.5 34 135-169 108-142 (142)
115 PRK12539 RNA polymerase sigma 75.7 2.7 5.9E-05 33.7 2.9 41 135-176 132-173 (184)
116 cd00092 HTH_CRP helix_turn_hel 75.6 3.7 7.9E-05 27.4 3.0 28 150-177 25-52 (67)
117 PHA00675 hypothetical protein 75.4 2.5 5.5E-05 32.0 2.4 42 133-174 21-63 (78)
118 TIGR02885 spore_sigF RNA polym 75.4 2.9 6.3E-05 35.0 3.0 43 134-176 183-225 (231)
119 PRK13719 conjugal transfer tra 75.1 2.4 5.1E-05 37.4 2.5 41 134-175 143-183 (217)
120 PRK12527 RNA polymerase sigma 75.1 3.6 7.8E-05 32.0 3.3 41 135-176 106-147 (159)
121 TIGR02954 Sig70_famx3 RNA poly 75.0 3.1 6.6E-05 32.7 2.9 42 134-176 119-161 (169)
122 PRK15411 rcsA colanic acid cap 75.0 2.5 5.4E-05 35.3 2.5 41 134-175 137-177 (207)
123 PRK09644 RNA polymerase sigma 74.9 3.2 6.9E-05 32.6 3.0 42 134-176 108-150 (165)
124 PHA02943 hypothetical protein; 74.7 2 4.3E-05 36.6 1.8 35 140-174 13-48 (165)
125 TIGR02960 SigX5 RNA polymerase 74.6 2.9 6.3E-05 36.4 2.9 43 134-177 142-185 (324)
126 PRK09638 RNA polymerase sigma 74.3 1.6 3.6E-05 34.3 1.2 41 135-176 127-168 (176)
127 PRK12530 RNA polymerase sigma 74.2 3.6 7.7E-05 33.4 3.2 41 135-176 135-176 (189)
128 PRK12516 RNA polymerase sigma 74.1 3.7 8E-05 33.5 3.3 41 135-176 117-158 (187)
129 COG2197 CitB Response regulato 74.1 3 6.4E-05 35.2 2.8 34 139-172 151-185 (211)
130 PRK08561 rps15p 30S ribosomal 74.0 2.1 4.6E-05 35.9 1.8 30 136-165 30-59 (151)
131 PRK12522 RNA polymerase sigma 73.8 3.8 8.2E-05 32.4 3.2 42 134-176 119-161 (173)
132 PF13545 HTH_Crp_2: Crp-like h 73.8 1.3 2.8E-05 30.6 0.4 43 151-195 29-71 (76)
133 PRK12523 RNA polymerase sigma 73.7 3.6 7.7E-05 32.6 3.0 40 135-175 120-160 (172)
134 PRK12517 RNA polymerase sigma 73.7 3.8 8.2E-05 33.4 3.2 42 134-176 128-170 (188)
135 TIGR02846 spore_sigmaK RNA pol 73.5 3.2 6.9E-05 34.9 2.8 40 135-175 175-219 (227)
136 PRK09415 RNA polymerase factor 73.4 3.4 7.4E-05 33.1 2.9 41 135-176 128-169 (179)
137 PRK12531 RNA polymerase sigma 73.3 4.2 9E-05 33.0 3.4 42 134-176 141-183 (194)
138 smart00347 HTH_MARR helix_turn 73.1 5.6 0.00012 27.9 3.6 37 141-177 13-51 (101)
139 TIGR02943 Sig70_famx1 RNA poly 73.1 4 8.7E-05 33.2 3.2 42 134-176 131-173 (188)
140 PRK09413 IS2 repressor TnpA; R 73.1 3.8 8.3E-05 31.8 3.0 45 133-177 11-56 (121)
141 PRK12520 RNA polymerase sigma 73.0 4.1 8.8E-05 32.8 3.2 41 135-176 132-173 (191)
142 cd07377 WHTH_GntR Winged helix 72.8 5.1 0.00011 26.2 3.2 26 153-178 28-53 (66)
143 smart00354 HTH_LACI helix_turn 72.6 1.4 3.1E-05 31.0 0.4 19 154-172 4-22 (70)
144 PRK12512 RNA polymerase sigma 72.4 4.4 9.6E-05 32.3 3.3 42 134-176 131-173 (184)
145 PRK12545 RNA polymerase sigma 72.4 4.3 9.3E-05 33.4 3.3 41 135-176 140-181 (201)
146 PRK09641 RNA polymerase sigma 72.1 4 8.7E-05 32.2 3.0 41 135-176 137-178 (187)
147 PRK12525 RNA polymerase sigma 72.0 4.1 9E-05 32.2 3.0 41 135-176 119-160 (168)
148 PRK09191 two-component respons 72.0 4.3 9.3E-05 33.4 3.2 43 135-178 89-132 (261)
149 smart00418 HTH_ARSR helix_turn 71.8 2.5 5.3E-05 26.9 1.4 30 148-177 8-37 (66)
150 PRK12528 RNA polymerase sigma 71.6 4.9 0.00011 31.3 3.3 41 135-176 114-155 (161)
151 TIGR02835 spore_sigmaE RNA pol 71.5 3.3 7.2E-05 35.0 2.5 40 135-175 179-223 (234)
152 smart00420 HTH_DEOR helix_turn 71.5 4.3 9.2E-05 25.4 2.5 30 148-177 12-41 (53)
153 PRK08215 sporulation sigma fac 71.5 3.9 8.5E-05 35.1 3.0 41 134-175 209-250 (258)
154 PRK07408 RNA polymerase sigma 71.4 4 8.6E-05 35.3 3.0 43 134-176 203-245 (256)
155 smart00346 HTH_ICLR helix_turn 71.3 3.8 8.2E-05 29.0 2.4 37 141-177 8-47 (91)
156 PRK09649 RNA polymerase sigma 71.3 4.3 9.4E-05 32.8 3.0 42 134-176 130-172 (185)
157 TIGR02394 rpoS_proteo RNA poly 71.1 3.3 7.2E-05 36.2 2.5 41 135-176 223-268 (285)
158 PRK12543 RNA polymerase sigma 71.1 4.3 9.4E-05 32.4 3.0 40 135-175 118-158 (179)
159 PRK12533 RNA polymerase sigma 70.9 3.6 7.8E-05 34.9 2.6 41 135-176 135-176 (216)
160 PF13072 DUF3936: Protein of u 70.7 2.7 5.8E-05 27.9 1.4 11 54-64 16-26 (38)
161 PRK09643 RNA polymerase sigma 70.6 5 0.00011 32.7 3.3 40 135-175 135-175 (192)
162 PRK12427 flagellar biosynthesi 70.6 4.8 0.0001 34.4 3.3 43 134-176 183-225 (231)
163 PRK15201 fimbriae regulatory p 70.4 3.6 7.9E-05 35.9 2.5 45 134-179 133-177 (198)
164 COG2771 CsgD DNA-binding HTH d 70.4 4.5 9.9E-05 26.6 2.5 36 139-174 7-43 (65)
165 PTZ00072 40S ribosomal protein 70.3 3 6.4E-05 35.0 1.9 30 136-165 27-56 (148)
166 TIGR02950 SigM_subfam RNA poly 70.3 1.6 3.5E-05 33.4 0.3 42 135-176 106-147 (154)
167 PRK12511 RNA polymerase sigma 70.2 4.6 9.9E-05 32.9 3.0 42 134-176 111-153 (182)
168 PRK06288 RNA polymerase sigma 70.2 5 0.00011 34.7 3.3 41 135-175 213-253 (268)
169 TIGR01610 phage_O_Nterm phage 70.1 5.7 0.00012 29.7 3.3 47 133-179 21-76 (95)
170 PF08279 HTH_11: HTH domain; 70.0 3.2 7E-05 27.3 1.7 44 141-185 3-49 (55)
171 PF13744 HTH_37: Helix-turn-he 69.7 1.6 3.6E-05 31.5 0.2 30 146-175 27-57 (80)
172 PRK12519 RNA polymerase sigma 69.7 4.3 9.2E-05 32.6 2.6 41 135-176 142-183 (194)
173 PRK08295 RNA polymerase factor 69.6 5.1 0.00011 32.4 3.1 41 135-176 156-196 (208)
174 TIGR02959 SigZ RNA polymerase 69.5 5.8 0.00012 31.6 3.4 42 134-176 100-142 (170)
175 PRK06930 positive control sigm 69.1 5.7 0.00012 33.0 3.3 42 134-176 114-156 (170)
176 PF10668 Phage_terminase: Phag 69.0 3 6.6E-05 29.9 1.5 35 138-172 7-44 (60)
177 COG0640 ArsR Predicted transcr 68.8 5.9 0.00013 26.8 2.9 44 135-178 22-67 (110)
178 PRK09648 RNA polymerase sigma 68.8 5.9 0.00013 31.8 3.3 42 134-176 139-181 (189)
179 PRK09636 RNA polymerase sigma 68.7 5.3 0.00011 34.8 3.2 42 135-177 116-158 (293)
180 PRK12526 RNA polymerase sigma 68.6 5.3 0.00011 33.0 3.1 41 135-176 154-195 (206)
181 PRK05572 sporulation sigma fac 68.5 5 0.00011 34.3 3.0 42 134-175 202-243 (252)
182 PRK04841 transcriptional regul 68.4 3.9 8.5E-05 40.1 2.6 42 134-176 838-880 (903)
183 PRK07122 RNA polymerase sigma 68.3 4.6 0.0001 35.2 2.8 36 141-176 221-257 (264)
184 PF01381 HTH_3: Helix-turn-hel 67.8 2.5 5.5E-05 27.5 0.8 27 147-173 6-32 (55)
185 PRK12544 RNA polymerase sigma 67.5 6.3 0.00014 32.9 3.3 42 134-176 148-190 (206)
186 PHA00542 putative Cro-like pro 67.3 4 8.6E-05 29.9 1.8 31 143-173 24-54 (82)
187 PRK11475 DNA-binding transcrip 67.2 4.6 0.0001 34.1 2.5 39 134-173 134-172 (207)
188 PRK09646 RNA polymerase sigma 66.5 6.6 0.00014 31.9 3.2 42 134-176 142-184 (194)
189 TIGR02957 SigX4 RNA polymerase 66.4 6.3 0.00014 34.4 3.2 42 135-177 109-151 (281)
190 PRK07670 RNA polymerase sigma 66.4 6.4 0.00014 33.6 3.2 41 135-176 202-243 (251)
191 PRK08241 RNA polymerase factor 66.4 5 0.00011 35.4 2.6 42 135-177 154-196 (339)
192 TIGR02850 spore_sigG RNA polym 65.9 5.8 0.00012 34.0 2.8 41 134-175 206-247 (254)
193 PRK10100 DNA-binding transcrip 65.6 5.2 0.00011 34.0 2.5 44 134-178 155-198 (216)
194 PRK10430 DNA-binding transcrip 65.4 7.2 0.00016 32.3 3.3 40 135-174 159-202 (239)
195 PF00325 Crp: Bacterial regula 65.4 3.8 8.3E-05 25.9 1.2 26 153-178 5-30 (32)
196 PF01498 HTH_Tnp_Tc3_2: Transp 65.2 1.6 3.5E-05 30.4 -0.6 39 41-84 3-41 (72)
197 PHA01976 helix-turn-helix prot 65.0 4.8 0.0001 27.2 1.8 33 142-174 6-39 (67)
198 TIGR00180 parB_part ParB-like 64.7 5.3 0.00012 33.0 2.3 40 134-173 102-143 (187)
199 smart00419 HTH_CRP helix_turn_ 64.2 3.7 8E-05 25.6 1.1 28 151-178 9-36 (48)
200 TIGR02392 rpoH_proteo alternat 63.8 6.2 0.00013 34.3 2.7 40 134-174 218-260 (270)
201 PF08535 KorB: KorB domain; I 63.5 2.9 6.3E-05 30.9 0.5 27 148-174 1-27 (93)
202 TIGR02702 SufR_cyano iron-sulf 63.3 6.6 0.00014 32.8 2.7 39 139-177 2-42 (203)
203 PRK12513 RNA polymerase sigma 63.3 3.6 7.7E-05 33.2 1.0 41 135-176 140-181 (194)
204 COG2963 Transposase and inacti 63.0 11 0.00025 28.4 3.7 49 133-181 6-56 (116)
205 TIGR02939 RpoE_Sigma70 RNA pol 62.8 6.7 0.00015 31.0 2.5 41 135-176 139-180 (190)
206 PRK15369 two component system 62.3 7.8 0.00017 29.3 2.7 42 135-177 150-191 (211)
207 PRK09954 putative kinase; Prov 61.8 6.9 0.00015 34.9 2.7 42 137-178 2-45 (362)
208 PRK05803 sporulation sigma fac 61.7 8.3 0.00018 32.5 3.0 42 134-176 175-221 (233)
209 TIGR03001 Sig-70_gmx1 RNA poly 61.5 9.3 0.0002 33.1 3.3 41 135-176 162-203 (244)
210 PF00126 HTH_1: Bacterial regu 61.2 6.1 0.00013 26.8 1.7 43 142-185 6-48 (60)
211 PRK09640 RNA polymerase sigma 61.1 3.2 7E-05 33.4 0.4 42 134-176 134-176 (188)
212 PRK12541 RNA polymerase sigma 60.3 9.7 0.00021 29.6 3.0 41 135-176 113-154 (161)
213 PRK11512 DNA-binding transcrip 60.3 7.3 0.00016 30.5 2.3 44 135-178 38-82 (144)
214 PRK12546 RNA polymerase sigma 60.2 9.2 0.0002 31.4 3.0 43 134-177 113-156 (188)
215 TIGR02393 RpoD_Cterm RNA polym 59.7 8.2 0.00018 32.7 2.7 42 134-176 176-222 (238)
216 PF07638 Sigma70_ECF: ECF sigm 59.6 11 0.00023 30.9 3.2 37 139-175 139-176 (185)
217 PRK11050 manganese transport r 59.3 7.6 0.00017 31.3 2.3 30 149-178 50-79 (152)
218 TIGR03020 EpsA transcriptional 58.8 7.9 0.00017 34.1 2.5 42 134-176 190-231 (247)
219 PRK09651 RNA polymerase sigma 58.7 8 0.00017 30.7 2.3 40 135-175 120-160 (172)
220 COG1321 TroR Mn-dependent tran 58.5 8.4 0.00018 31.7 2.4 29 150-178 24-52 (154)
221 PRK11922 RNA polymerase sigma 58.5 5.8 0.00013 33.4 1.5 40 135-175 150-190 (231)
222 PRK09726 antitoxin HipB; Provi 58.3 7.7 0.00017 28.4 2.0 27 147-173 22-48 (88)
223 PRK10046 dpiA two-component re 57.9 9.1 0.0002 31.5 2.6 34 141-174 165-201 (225)
224 PRK03573 transcriptional regul 57.8 9.2 0.0002 29.7 2.5 36 143-178 37-74 (144)
225 PRK06704 RNA polymerase factor 57.7 9.6 0.00021 33.0 2.8 43 134-176 116-158 (228)
226 PRK10727 DNA-binding transcrip 57.4 9.6 0.00021 32.9 2.7 33 129-161 21-55 (343)
227 TIGR02997 Sig70-cyanoRpoD RNA 57.2 9.4 0.0002 33.7 2.7 41 135-176 250-295 (298)
228 PF07750 GcrA: GcrA cell cycle 57.1 8.5 0.00019 32.0 2.3 39 136-174 4-43 (162)
229 PRK11303 DNA-binding transcrip 57.0 10 0.00022 32.2 2.8 33 129-161 20-57 (328)
230 TIGR02417 fruct_sucro_rep D-fr 56.9 11 0.00023 32.2 2.9 56 129-184 19-95 (327)
231 PRK15320 transcriptional activ 56.8 10 0.00022 34.0 2.7 40 135-175 165-204 (251)
232 PRK12535 RNA polymerase sigma 56.5 12 0.00025 30.9 3.0 41 135-176 134-175 (196)
233 PF13613 HTH_Tnp_4: Helix-turn 56.4 19 0.00042 24.1 3.6 42 135-176 3-45 (53)
234 cd00093 HTH_XRE Helix-turn-hel 56.3 6.1 0.00013 23.6 1.0 28 146-173 8-35 (58)
235 smart00530 HTH_XRE Helix-turn- 55.9 6 0.00013 23.4 0.9 29 146-174 6-34 (56)
236 PRK11233 nitrogen assimilation 55.7 9.4 0.0002 32.7 2.4 45 142-187 8-52 (305)
237 TIGR02844 spore_III_D sporulat 55.6 8.1 0.00018 28.9 1.7 34 139-172 7-41 (80)
238 PF01371 Trp_repressor: Trp re 55.5 11 0.00023 28.7 2.4 34 137-170 35-69 (87)
239 PRK12518 RNA polymerase sigma 54.9 5.5 0.00012 31.3 0.8 41 135-176 121-162 (175)
240 PF07508 Recombinase: Recombin 54.9 18 0.00039 26.1 3.5 49 37-87 5-54 (102)
241 PRK09635 sigI RNA polymerase s 54.3 12 0.00027 33.1 3.0 44 134-177 118-161 (290)
242 PRK07500 rpoH2 RNA polymerase 54.3 11 0.00025 33.3 2.8 41 135-176 228-271 (289)
243 smart00529 HTH_DTXR Helix-turn 54.3 7.4 0.00016 27.9 1.3 26 152-177 1-26 (96)
244 cd06571 Bac_DnaA_C C-terminal 53.7 13 0.00029 27.4 2.6 40 138-177 30-72 (90)
245 COG2522 Predicted transcriptio 53.6 6.8 0.00015 31.6 1.1 38 138-175 9-47 (119)
246 TIGR02944 suf_reg_Xantho FeS a 53.5 10 0.00023 29.2 2.1 36 143-178 15-53 (130)
247 PF01978 TrmB: Sugar-specific 53.4 4.7 0.0001 27.8 0.1 32 147-178 19-50 (68)
248 PHA02535 P terminase ATPase su 53.3 9.9 0.00021 37.9 2.4 41 135-175 3-43 (581)
249 TIGR03070 couple_hipB transcri 52.9 7.1 0.00015 24.9 0.9 28 147-174 12-39 (58)
250 PRK10423 transcriptional repre 52.8 14 0.0003 31.4 2.9 32 130-161 19-52 (327)
251 PRK10360 DNA-binding transcrip 52.6 13 0.00028 28.6 2.5 42 134-176 137-178 (196)
252 TIGR02337 HpaR homoprotocatech 52.0 9.2 0.0002 28.8 1.6 31 148-178 40-70 (118)
253 smart00345 HTH_GNTR helix_turn 51.7 10 0.00022 24.3 1.5 42 137-178 3-48 (60)
254 COG2390 DeoR Transcriptional r 51.2 8.4 0.00018 35.4 1.5 32 147-178 23-54 (321)
255 PF01047 MarR: MarR family; I 51.0 6.7 0.00014 25.9 0.6 30 147-176 14-43 (59)
256 PRK10403 transcriptional regul 50.8 14 0.00031 28.2 2.5 41 135-176 154-194 (215)
257 PRK12682 transcriptional regul 50.0 21 0.00045 30.6 3.6 46 142-187 8-53 (309)
258 cd07498 Peptidases_S8_15 Pepti 48.6 16 0.00036 30.2 2.7 33 31-63 209-241 (242)
259 PF04967 HTH_10: HTH DNA bindi 48.0 10 0.00023 26.3 1.2 27 150-176 23-49 (53)
260 PRK09958 DNA-binding transcrip 47.6 16 0.00034 28.3 2.3 39 134-173 143-181 (204)
261 PF12298 Bot1p: Eukaryotic mit 47.6 23 0.00049 30.0 3.4 53 128-180 10-63 (172)
262 TIGR01884 cas_HTH CRISPR locus 47.4 19 0.00041 30.0 2.9 39 139-177 144-184 (203)
263 COG0856 Orotate phosphoribosyl 46.8 23 0.0005 31.0 3.3 42 137-178 5-46 (203)
264 PRK10188 DNA-binding transcrip 46.5 17 0.00036 31.4 2.5 41 134-175 179-219 (240)
265 PRK10703 DNA-binding transcrip 46.3 19 0.00041 30.9 2.8 32 130-161 22-55 (341)
266 PRK09943 DNA-binding transcrip 45.9 15 0.00032 30.0 2.0 41 131-172 2-42 (185)
267 PRK11179 DNA-binding transcrip 45.8 20 0.00043 28.6 2.7 42 137-178 8-51 (153)
268 PRK05657 RNA polymerase sigma 45.8 20 0.00044 32.4 3.0 42 134-176 262-308 (325)
269 COG1961 PinR Site-specific rec 45.7 16 0.00035 30.5 2.2 49 129-177 155-204 (222)
270 PF01316 Arg_repressor: Argini 45.4 15 0.00033 26.7 1.8 41 39-84 7-47 (70)
271 PRK01905 DNA-binding protein F 45.4 13 0.00028 26.9 1.4 40 136-175 35-75 (77)
272 TIGR03643 conserved hypothetic 45.2 9.6 0.00021 28.5 0.7 45 140-184 2-47 (72)
273 PRK03341 arginine repressor; P 45.2 17 0.00038 30.5 2.3 43 37-84 15-57 (168)
274 PF06530 Phage_antitermQ: Phag 45.1 15 0.00034 28.9 1.9 38 138-175 66-103 (125)
275 smart00344 HTH_ASNC helix_turn 45.0 21 0.00046 26.2 2.6 40 139-178 4-45 (108)
276 PF02954 HTH_8: Bacterial regu 45.0 12 0.00025 24.1 1.0 36 139-174 6-42 (42)
277 PF14493 HTH_40: Helix-turn-he 44.9 19 0.00042 26.4 2.3 39 141-179 4-42 (91)
278 PRK06596 RNA polymerase factor 44.8 20 0.00044 31.6 2.8 40 135-175 231-273 (284)
279 PRK10870 transcriptional repre 44.6 16 0.00034 30.1 2.0 29 150-178 71-99 (176)
280 cd04059 Peptidases_S8_Protein_ 44.4 25 0.00054 30.1 3.2 34 30-63 261-294 (297)
281 TIGR01889 Staph_reg_Sar staphy 44.0 21 0.00045 26.9 2.4 30 149-178 42-71 (109)
282 COG2512 Predicted membrane-ass 43.5 23 0.00049 31.7 2.9 50 129-178 187-238 (258)
283 PF13463 HTH_27: Winged helix 43.2 19 0.00041 24.1 1.9 30 148-177 16-45 (68)
284 PRK14987 gluconate operon tran 42.6 24 0.00053 30.1 2.9 32 130-161 26-59 (331)
285 PRK13348 chromosome replicatio 42.1 26 0.00056 29.6 2.9 50 143-193 10-59 (294)
286 PRK13870 transcriptional regul 41.8 22 0.00048 30.6 2.5 41 134-175 173-213 (234)
287 TIGR03541 reg_near_HchA LuxR f 41.5 22 0.00049 30.2 2.5 42 134-176 171-212 (232)
288 PRK07405 RNA polymerase sigma 41.2 22 0.00048 32.0 2.5 41 135-176 257-302 (317)
289 PF09339 HTH_IclR: IclR helix- 41.1 9 0.0002 25.3 0.0 36 142-177 7-45 (52)
290 PRK09526 lacI lac repressor; R 41.0 26 0.00056 30.0 2.8 54 130-183 26-97 (342)
291 CHL00180 rbcR LysR transcripti 40.9 39 0.00085 28.8 3.9 59 134-193 4-63 (305)
292 COG1522 Lrp Transcriptional re 40.8 27 0.00059 27.0 2.7 42 137-178 7-50 (154)
293 PRK11013 DNA-binding transcrip 40.8 23 0.00049 30.4 2.4 45 141-186 10-54 (309)
294 PRK10401 DNA-binding transcrip 40.8 26 0.00056 30.3 2.8 54 130-183 22-93 (346)
295 PRK09791 putative DNA-binding 40.6 34 0.00074 29.0 3.5 52 135-187 5-56 (302)
296 COG1609 PurR Transcriptional r 40.5 26 0.00056 31.3 2.8 34 129-162 20-55 (333)
297 PF01475 FUR: Ferric uptake re 40.2 24 0.00051 26.7 2.2 39 41-84 12-51 (120)
298 PRK10339 DNA-binding transcrip 39.8 29 0.00064 29.7 3.0 31 129-160 21-55 (327)
299 PRK11242 DNA-binding transcrip 39.8 25 0.00054 29.4 2.5 43 143-186 9-51 (296)
300 PF14947 HTH_45: Winged helix- 39.5 28 0.0006 25.0 2.4 41 137-177 5-46 (77)
301 TIGR01481 ccpA catabolite cont 39.4 29 0.00062 29.5 2.8 33 129-161 21-55 (329)
302 PRK11753 DNA-binding transcrip 39.3 16 0.00035 29.3 1.2 28 151-178 169-196 (211)
303 TIGR00637 ModE_repress ModE mo 39.0 30 0.00064 26.3 2.6 46 141-186 7-52 (99)
304 PRK05949 RNA polymerase sigma 38.8 27 0.00059 31.7 2.7 41 135-176 267-312 (327)
305 PRK09986 DNA-binding transcrip 38.8 40 0.00087 28.1 3.6 46 141-187 13-58 (294)
306 COG2826 Tra8 Transposase and i 38.6 25 0.00055 32.8 2.5 37 135-171 75-111 (318)
307 cd07493 Peptidases_S8_9 Peptid 38.5 35 0.00075 28.9 3.2 33 31-63 226-258 (261)
308 PF07453 NUMOD1: NUMOD1 domain 38.3 11 0.00024 23.3 0.1 18 154-171 20-37 (37)
309 PRK03902 manganese transport t 38.3 30 0.00066 27.1 2.6 38 141-178 11-50 (142)
310 PHA02517 putative transposase 38.1 32 0.00069 29.4 2.9 45 35-84 28-73 (277)
311 PF10985 DUF2805: Protein of u 38.0 13 0.00029 27.8 0.5 44 141-184 2-46 (73)
312 PF00392 GntR: Bacterial regul 37.4 19 0.0004 24.6 1.1 36 154-189 28-63 (64)
313 PRK07598 RNA polymerase sigma 37.4 34 0.00074 32.7 3.2 41 135-176 351-396 (415)
314 PLN00061 photosystem II protei 37.0 11 0.00024 31.7 -0.0 27 120-146 116-145 (150)
315 PF02082 Rrf2: Transcriptional 36.4 20 0.00043 25.7 1.2 50 143-192 14-68 (83)
316 PRK00441 argR arginine repress 35.8 33 0.00071 28.1 2.5 43 38-85 5-47 (149)
317 PRK00430 fis global DNA-bindin 35.8 22 0.00047 27.1 1.4 37 139-175 56-93 (95)
318 COG1710 Uncharacterized protei 35.6 35 0.00076 28.2 2.6 42 131-172 88-131 (139)
319 TIGR00738 rrf2_super rrf2 fami 35.4 29 0.00062 26.4 2.0 29 150-178 25-53 (132)
320 PRK12679 cbl transcriptional r 35.3 31 0.00068 29.8 2.5 47 141-187 7-53 (316)
321 COG1846 MarR Transcriptional r 35.3 62 0.0014 23.0 3.7 43 135-177 20-63 (126)
322 TIGR02424 TF_pcaQ pca operon t 35.1 30 0.00066 29.1 2.3 45 142-187 10-54 (300)
323 PRK13918 CRP/FNR family transc 35.0 21 0.00046 28.5 1.3 41 152-194 151-191 (202)
324 PRK11161 fumarate/nitrate redu 34.9 20 0.00044 29.4 1.2 28 152-179 186-213 (235)
325 PRK00215 LexA repressor; Valid 34.4 44 0.00095 27.5 3.1 31 148-178 19-52 (205)
326 PRK09906 DNA-binding transcrip 34.2 37 0.00081 28.5 2.7 44 142-186 8-51 (296)
327 PRK14388 hypothetical protein; 34.1 25 0.00054 26.8 1.4 34 74-107 47-80 (82)
328 PF04297 UPF0122: Putative hel 34.1 32 0.00068 27.0 2.1 38 138-175 20-58 (101)
329 cd00283 GIY-YIG_Cterm GIYX(10- 33.8 66 0.0014 25.3 3.9 64 101-171 18-101 (113)
330 PRK04280 arginine repressor; P 33.8 37 0.0008 27.8 2.5 42 39-85 6-47 (148)
331 PRK11169 leucine-responsive tr 33.7 53 0.0012 26.5 3.4 42 137-178 13-56 (164)
332 cd07483 Peptidases_S8_Subtilis 33.4 39 0.00085 29.5 2.8 35 31-65 256-290 (291)
333 PRK09390 fixJ response regulat 33.3 43 0.00094 25.1 2.7 35 139-173 145-179 (202)
334 PRK05066 arginine repressor; P 32.9 47 0.001 27.5 3.0 44 37-85 9-53 (156)
335 PRK09935 transcriptional regul 32.2 38 0.00082 26.0 2.2 46 134-180 149-194 (210)
336 PRK13890 conjugal transfer pro 32.2 22 0.00048 27.8 1.0 27 146-172 14-40 (120)
337 smart00497 IENR1 Intron encode 32.0 22 0.00047 22.9 0.7 20 154-173 21-40 (53)
338 TIGR03830 CxxCG_CxxCG_HTH puta 31.9 36 0.00077 25.6 2.0 40 132-174 63-102 (127)
339 TIGR01321 TrpR trp operon repr 31.8 39 0.00083 26.3 2.2 34 137-170 41-75 (94)
340 cd07492 Peptidases_S8_8 Peptid 31.8 51 0.0011 27.0 3.0 33 31-63 187-219 (222)
341 cd04848 Peptidases_S8_Autotran 31.3 60 0.0013 26.6 3.4 33 31-63 232-264 (267)
342 PRK01381 Trp operon repressor; 30.9 33 0.00072 26.9 1.7 34 137-170 41-75 (99)
343 TIGR00122 birA_repr_reg BirA b 30.4 51 0.0011 22.6 2.4 36 142-177 4-40 (69)
344 PRK05638 threonine synthase; V 30.4 45 0.00097 31.3 2.8 43 136-178 369-414 (442)
345 cd05562 Peptidases_S53_like Pe 30.4 60 0.0013 28.5 3.4 34 31-64 216-249 (275)
346 TIGR01636 phage_rinA phage tra 30.3 57 0.0012 25.8 3.0 39 135-174 83-124 (134)
347 cd07474 Peptidases_S8_subtilis 30.2 50 0.0011 28.1 2.9 37 31-67 235-271 (295)
348 TIGR03697 NtcA_cyano global ni 29.9 27 0.00058 27.5 1.1 28 151-178 144-171 (193)
349 PRK10014 DNA-binding transcrip 29.6 52 0.0011 28.1 2.9 32 130-161 27-60 (342)
350 PF05344 DUF746: Domain of Unk 29.4 39 0.00084 24.8 1.7 34 143-176 6-39 (65)
351 PF04703 FaeA: FaeA-like prote 29.2 23 0.0005 25.3 0.5 31 148-178 13-43 (62)
352 PF00600 Flu_NS1: Influenza no 29.0 24 0.00052 30.9 0.7 18 51-68 12-29 (217)
353 PRK11139 DNA-binding transcrip 28.9 79 0.0017 26.7 3.8 46 141-187 12-57 (297)
354 PF13560 HTH_31: Helix-turn-he 28.8 18 0.00038 24.5 -0.1 25 148-172 12-36 (64)
355 cd04852 Peptidases_S8_3 Peptid 28.5 51 0.0011 28.7 2.7 33 31-63 272-304 (307)
356 cd07473 Peptidases_S8_Subtilis 28.4 63 0.0014 26.9 3.1 33 31-63 224-256 (259)
357 PRK11151 DNA-binding transcrip 28.2 77 0.0017 26.9 3.6 44 142-186 8-51 (305)
358 PRK09492 treR trehalose repres 28.1 56 0.0012 27.6 2.7 32 130-161 25-58 (315)
359 COG1510 Predicted transcriptio 27.9 32 0.00069 29.7 1.2 48 123-186 30-77 (177)
360 PRK12684 transcriptional regul 27.6 55 0.0012 28.3 2.7 45 143-187 9-53 (313)
361 TIGR00498 lexA SOS regulatory 27.4 81 0.0018 25.8 3.6 41 138-178 6-54 (199)
362 PRK15421 DNA-binding transcrip 27.3 46 0.00099 29.0 2.1 45 141-186 8-52 (317)
363 PF03734 YkuD: L,D-transpeptid 27.1 15 0.00032 27.7 -0.9 10 160-169 115-124 (144)
364 COG1438 ArgR Arginine represso 26.8 54 0.0012 27.4 2.4 42 38-84 7-48 (150)
365 PRK13509 transcriptional repre 26.7 61 0.0013 28.1 2.8 41 137-177 4-46 (251)
366 PRK09706 transcriptional repre 26.5 56 0.0012 25.4 2.3 32 142-173 9-41 (135)
367 cd07496 Peptidases_S8_13 Pepti 26.3 60 0.0013 27.9 2.7 33 31-63 252-284 (285)
368 cd07494 Peptidases_S8_10 Pepti 26.3 80 0.0017 28.0 3.5 36 30-65 247-282 (298)
369 TIGR03613 RutR pyrimidine util 26.3 45 0.00097 26.6 1.8 31 137-167 7-45 (202)
370 TIGR03418 chol_sulf_TF putativ 26.2 47 0.001 27.8 2.0 44 142-186 8-51 (291)
371 TIGR02804 ExbD_2 TonB system t 25.7 1.2E+02 0.0026 23.3 4.0 56 122-178 56-111 (121)
372 PRK10676 DNA-binding transcrip 25.6 70 0.0015 28.2 3.0 57 129-185 10-66 (263)
373 PF11985 DUF3486: Protein of u 25.5 77 0.0017 26.1 3.1 47 35-83 11-57 (180)
374 PRK10411 DNA-binding transcrip 25.5 58 0.0013 28.2 2.5 39 139-177 5-45 (240)
375 cd07489 Peptidases_S8_5 Peptid 25.4 94 0.002 27.1 3.7 63 30-93 229-292 (312)
376 COG1356 tfx Transcriptional re 25.2 26 0.00056 29.2 0.2 37 138-174 11-47 (143)
377 cd07477 Peptidases_S8_Subtilis 25.0 76 0.0016 25.8 2.9 33 31-63 196-228 (229)
378 TIGR03454 partition_RepB plasm 24.9 74 0.0016 29.4 3.1 43 134-176 160-203 (325)
379 PRK10434 srlR DNA-bindng trans 24.6 56 0.0012 28.4 2.2 42 136-177 3-46 (256)
380 cd07482 Peptidases_S8_Lantibio 24.6 83 0.0018 26.6 3.2 34 30-63 259-293 (294)
381 PRK15481 transcriptional regul 24.6 55 0.0012 29.7 2.2 54 137-190 12-69 (431)
382 PRK10837 putative DNA-binding 24.2 72 0.0016 26.5 2.7 45 141-186 9-53 (290)
383 COG1376 ErfK Uncharacterized p 23.9 21 0.00046 30.1 -0.5 8 161-168 200-207 (232)
384 PRK14165 winged helix-turn-hel 23.9 40 0.00087 29.4 1.2 27 151-177 22-48 (217)
385 cd07487 Peptidases_S8_1 Peptid 23.8 1E+02 0.0023 25.5 3.6 34 30-63 228-261 (264)
386 PRK12683 transcriptional regul 23.5 71 0.0015 27.6 2.6 44 143-186 9-52 (309)
387 PRK10072 putative transcriptio 23.4 54 0.0012 25.1 1.7 28 147-174 43-70 (96)
388 TIGR02010 IscR iron-sulfur clu 23.4 84 0.0018 24.5 2.8 38 141-178 12-53 (135)
389 PRK13832 plasmid partitioning 23.3 55 0.0012 32.5 2.0 36 136-171 104-139 (520)
390 cd04077 Peptidases_S8_PCSK9_Pr 23.3 79 0.0017 26.5 2.8 33 31-63 219-251 (255)
391 PRK09462 fur ferric uptake reg 23.3 1E+02 0.0022 24.4 3.3 46 34-84 15-61 (148)
392 PRK12680 transcriptional regul 23.1 70 0.0015 28.1 2.5 44 143-186 9-52 (327)
393 PF12844 HTH_19: Helix-turn-he 23.1 57 0.0012 21.7 1.6 26 148-173 10-35 (64)
394 PRK04140 hypothetical protein; 23.0 48 0.001 30.6 1.5 98 41-172 63-161 (317)
395 PF02001 DUF134: Protein of un 23.0 91 0.002 24.6 2.9 43 135-177 42-84 (106)
396 COG1349 GlpR Transcriptional r 22.9 44 0.00095 29.1 1.2 37 135-171 2-40 (253)
397 cd00782 MutL_Trans MutL_Trans: 22.8 44 0.00096 25.1 1.1 21 127-147 47-67 (122)
398 cd07484 Peptidases_S8_Thermita 22.5 94 0.002 26.0 3.1 33 31-64 223-255 (260)
399 PF07506 RepB: RepB plasmid pa 22.5 56 0.0012 27.0 1.7 32 141-172 12-43 (185)
400 PRK10082 cell density-dependen 22.3 57 0.0012 27.8 1.8 43 143-186 19-61 (303)
401 smart00342 HTH_ARAC helix_turn 22.0 90 0.002 20.6 2.4 38 140-177 39-78 (84)
402 COG1191 FliA DNA-directed RNA 22.0 89 0.0019 27.8 3.0 41 134-174 196-236 (247)
403 PF04552 Sigma54_DBD: Sigma-54 21.9 31 0.00068 28.7 0.1 36 152-194 51-87 (160)
404 PF08765 Mor: Mor transcriptio 21.8 67 0.0015 24.5 1.9 42 135-177 57-99 (108)
405 PRK10341 DNA-binding transcrip 21.5 58 0.0013 27.9 1.7 44 143-187 15-58 (312)
406 PF06413 Neugrin: Neugrin; In 21.5 1E+02 0.0022 27.2 3.2 48 28-84 5-52 (225)
407 cd03482 MutL_Trans_MutL MutL_T 21.4 51 0.0011 25.6 1.2 23 127-149 47-69 (123)
408 COG0735 Fur Fe2+/Zn2+ uptake r 21.4 1.2E+02 0.0026 24.4 3.4 47 33-84 18-64 (145)
409 cd07153 Fur_like Ferric uptake 21.1 1E+02 0.0022 22.8 2.7 38 42-84 6-44 (116)
410 PF06163 DUF977: Bacterial pro 21.0 1.2E+02 0.0027 24.9 3.3 53 138-190 12-66 (127)
411 PRK11639 zinc uptake transcrip 20.9 1.4E+02 0.0031 24.5 3.8 45 34-84 24-69 (169)
412 cd07490 Peptidases_S8_6 Peptid 20.8 1E+02 0.0022 25.6 3.0 32 32-63 220-251 (254)
413 PRK10260 L,D-transpeptidase; P 20.7 32 0.00069 31.8 -0.1 21 35-55 53-77 (306)
414 PRK07122 RNA polymerase sigma 20.4 1.5E+02 0.0032 25.9 3.9 140 23-173 3-166 (264)
415 PF01119 DNA_mis_repair: DNA m 20.3 47 0.001 25.3 0.8 21 125-145 41-61 (119)
416 PRK10094 DNA-binding transcrip 20.2 81 0.0017 27.2 2.3 44 142-186 9-52 (308)
417 cd07481 Peptidases_S8_Bacillop 20.0 1.1E+02 0.0025 25.9 3.1 33 31-63 227-261 (264)
No 1
>KOG3517|consensus
Probab=100.00 E-value=2.3e-34 Score=253.76 Aligned_cols=84 Identities=55% Similarity=0.871 Sum_probs=82.7
Q ss_pred CCCcccccccc----cceeeeccCcccCCCCCCCCcCCHHHHHHHHHHHHhCCCcchHHhHHHHHhcCCCCCCCCCCccc
Q psy10745 2 TPQLLTPFLCP----RRYYETGSFKAGVIGGSKPKVATAPVVDAIASYKRENPTMFAWEIRDRLLAEGICSQDNVPSVSS 77 (197)
Q Consensus 2 ~~~~~~~ilc~----~Ry~ETGSIrPG~IGGSKpk~~tp~v~~~I~~~k~e~P~iFaWEIRdrLl~~GvC~~~~vPSvSS 77 (197)
||||.|+|+|| .||.|||||.||+|||||||++||.|++.|.+||+..|+||||||||||+.+||||+.|||||||
T Consensus 43 SRQLrvSHGCVSKILaRy~EtGsIlPGaIGGSkPRVTTP~VV~~IR~~Kq~DPGIFAWEIRDRLlsdgiCDk~NvPSVSS 122 (334)
T KOG3517|consen 43 SRQLRVSHGCVSKILARYNETGSILPGAIGGSKPRVTTPKVVKYIRSLKQRDPGIFAWEIRDRLLSDGICDKYNVPSVSS 122 (334)
T ss_pred hhhhhhccchHHHHHHHhccCCcccccccCCCCCccCChhHHHHHHHhhccCCceeeehhhhhhhhcccccccCCcchHH
Confidence 79999999999 89999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccccc
Q psy10745 78 INRYITYV 85 (197)
Q Consensus 78 I~Rilr~~ 85 (197)
|+|||||+
T Consensus 123 ISRILRNK 130 (334)
T KOG3517|consen 123 ISRILRNK 130 (334)
T ss_pred HHHHHHhh
Confidence 99999985
No 2
>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=99.98 E-value=2.7e-34 Score=229.21 Aligned_cols=82 Identities=62% Similarity=1.036 Sum_probs=62.6
Q ss_pred CCCcccccccc----cceeeeccCcccCCCCCCCCcCCHHHHHHHHHHHHhCCCcchHHhHHHHHhcCCCCCCCCCCccc
Q psy10745 2 TPQLLTPFLCP----RRYYETGSFKAGVIGGSKPKVATAPVVDAIASYKRENPTMFAWEIRDRLLAEGICSQDNVPSVSS 77 (197)
Q Consensus 2 ~~~~~~~ilc~----~Ry~ETGSIrPG~IGGSKpk~~tp~v~~~I~~~k~e~P~iFaWEIRdrLl~~GvC~~~~vPSvSS 77 (197)
++||.|++.|| +||+|||||+||+|||||||++||+++++|++|++++|+||||||||+|+++|||+++++|||||
T Consensus 40 sr~l~Vs~gcVsKIl~Ry~eTGsi~Pg~iGGskprv~tp~v~~~I~~~k~enP~ifawEiR~~L~~~gvc~~~~~Psvss 119 (125)
T PF00292_consen 40 SRQLRVSHGCVSKILSRYRETGSIRPGPIGGSKPRVATPEVVEKIEQYKRENPTIFAWEIRDRLIADGVCDRSNVPSVSS 119 (125)
T ss_dssp HHHHT--HHHHHHHHHHHHHHS-SS----S----SSS-HCHHHHHHHHHHH-TTS-HHHHHHHHHHTTSS-TTTS--HHH
T ss_pred HHHHccchhHHHHHHHHHHHhcccCcccccCCCCCCCChHHHHHHHHHHhcCCCcchHHHHHHHHHcCCCCCCCCCCHHH
Confidence 46888999998 89999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccc
Q psy10745 78 INRYIT 83 (197)
Q Consensus 78 I~Rilr 83 (197)
|||+||
T Consensus 120 InRilr 125 (125)
T PF00292_consen 120 INRILR 125 (125)
T ss_dssp HHHHHH
T ss_pred HHHhhC
Confidence 999986
No 3
>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=99.96 E-value=2.6e-30 Score=206.35 Aligned_cols=64 Identities=75% Similarity=1.194 Sum_probs=53.1
Q ss_pred CCCccccCCccccCCCCCChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHhhhhcCcc
Q psy10745 118 SHGGVNQLGGVFVNGRPLPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESNLHNYR 181 (197)
Q Consensus 118 ~~~~~nqlg~~~~ngrplp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~~~n~~ 181 (197)
||+++|||||+|+||||||+++|+||||||+.|+|||||||+|+||||||||||+||++|+...
T Consensus 1 g~~~~NqlGg~~~nGrPLp~~~R~rIvela~~G~rp~~Isr~l~Vs~gcVsKIl~Ry~eTGsi~ 64 (125)
T PF00292_consen 1 GQGRVNQLGGVFINGRPLPNELRQRIVELAKEGVRPCDISRQLRVSHGCVSKILSRYRETGSIR 64 (125)
T ss_dssp S-EEE-TTS-EEETTSSS-HHHHHHHHHHHHTT--HHHHHHHHT--HHHHHHHHHHHHHHS-SS
T ss_pred CCccccccCceeeCCccCcHHHHHHHHHHhhhcCCHHHHHHHHccchhHHHHHHHHHHHhcccC
Confidence 6899999999999999999999999999999999999999999999999999999999998753
No 4
>KOG3517|consensus
Probab=99.95 E-value=8e-29 Score=218.69 Aligned_cols=62 Identities=74% Similarity=1.178 Sum_probs=58.9
Q ss_pred CCCccccCCccccCCCCCChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHhhhhcC
Q psy10745 118 SHGGVNQLGGVFVNGRPLPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESNLHN 179 (197)
Q Consensus 118 ~~~~~nqlg~~~~ngrplp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~~~n 179 (197)
.-|.+|||||+|+||||||..+|.||||||..|+|||||||||+||||||||||.||.+|+-
T Consensus 4 ~~GEVNQLGGVFVNGRPLPna~RlrIVELarlGiRPCDISRQLrvSHGCVSKILaRy~EtGs 65 (334)
T KOG3517|consen 4 SYGEVNQLGGVFVNGRPLPNAIRLRIVELARLGIRPCDISRQLRVSHGCVSKILARYNETGS 65 (334)
T ss_pred cccchhhccceeEcCccCcchhhhhHHHHHHcCCCccchhhhhhhccchHHHHHHHhccCCc
Confidence 45799999999999999999999999999999999999999999999999999999977764
No 5
>KOG3862|consensus
Probab=99.94 E-value=2.4e-28 Score=216.85 Aligned_cols=85 Identities=68% Similarity=1.010 Sum_probs=82.8
Q ss_pred CCCcccccccc----cceeeeccCcccCCCCCCCCcCCHHHHHHHHHHHHhCCCcchHHhHHHHHhcCCCCCCCCCCccc
Q psy10745 2 TPQLLTPFLCP----RRYYETGSFKAGVIGGSKPKVATAPVVDAIASYKRENPTMFAWEIRDRLLAEGICSQDNVPSVSS 77 (197)
Q Consensus 2 ~~~~~~~ilc~----~Ry~ETGSIrPG~IGGSKpk~~tp~v~~~I~~~k~e~P~iFaWEIRdrLl~~GvC~~~~vPSvSS 77 (197)
+|||+|+++|| .||+|||||+||.|||+|||++||.|+++|..||++||.||+|||||+|+.++||+.++||||||
T Consensus 48 srQl~vShGcvSkil~r~yEtgS~~pg~iggsk~KvAtp~Vvk~i~~~k~~n~~mfaweiR~~l~~~~ic~~d~vpsVss 127 (327)
T KOG3862|consen 48 SRQLRVSHGCVSKILGRYYETGSIRPGVIGGSKPKVATPKVVKKIALYKRQNPTMFAWEIRDRLLAEPICDNDTVPSVSS 127 (327)
T ss_pred HHHHhhccCCchhHHHHHHHhcCcccCCCCCCccccccchHHHHHHHHhhcCcchhhhhhhhhhhcccccCCCCCchHHH
Confidence 58999999999 89999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccccccc
Q psy10745 78 INRYITYVP 86 (197)
Q Consensus 78 I~Rilr~~~ 86 (197)
|||++|+..
T Consensus 128 inri~r~~~ 136 (327)
T KOG3862|consen 128 INRIIRTKV 136 (327)
T ss_pred HHHHHHHhh
Confidence 999999854
No 6
>KOG3862|consensus
Probab=99.94 E-value=1e-27 Score=212.89 Aligned_cols=66 Identities=82% Similarity=1.257 Sum_probs=63.1
Q ss_pred cCCCccccCCccccCCCCCChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHhhhhcCccc
Q psy10745 117 RSHGGVNQLGGVFVNGRPLPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESNLHNYRL 182 (197)
Q Consensus 117 ~~~~~~nqlg~~~~ngrplp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~~~n~~~ 182 (197)
.||+++|||||+||||||||+.+|++|++|+++|+|||||||||+||||||||||.||++|+-.+.
T Consensus 8 ~ghgGvNQLGGvFVNGRPlpd~Vr~rIv~La~~gvrpcdisrQl~vShGcvSkil~r~yEtgS~~p 73 (327)
T KOG3862|consen 8 SGHGGVNQLGGVFVNGRPLPDVVRQRIVELAQNGVRPCDISRQLRVSHGCVSKILGRYYETGSIRP 73 (327)
T ss_pred CCccchhhccceeecCccCchHHHHHHHHHHHcCCcchhHHHHHhhccCCchhHHHHHHHhcCccc
Confidence 489999999999999999999999999999999999999999999999999999999999886554
No 7
>KOG0849|consensus
Probab=99.83 E-value=1.1e-21 Score=178.01 Aligned_cols=172 Identities=34% Similarity=0.429 Sum_probs=118.5
Q ss_pred CCCcccccccc----cceeeeccCcccCCCCCCCC-cCCHHHHHHHHHHHHhCCCcchHHhHHHHHhcCCCCCCCCCCcc
Q psy10745 2 TPQLLTPFLCP----RRYYETGSFKAGVIGGSKPK-VATAPVVDAIASYKRENPTMFAWEIRDRLLAEGICSQDNVPSVS 76 (197)
Q Consensus 2 ~~~~~~~ilc~----~Ry~ETGSIrPG~IGGSKpk-~~tp~v~~~I~~~k~e~P~iFaWEIRdrLl~~GvC~~~~vPSvS 76 (197)
++||-|+++|| +||++||+|+||.|||+||+ +++++++.+|++||+++|+||+||||++|+.+++|+..++||++
T Consensus 38 ~~~l~vs~~~~~~il~r~~~~~~i~p~~i~~~~~~~~~t~~~~~~i~~~k~~~P~~~~~~ir~~l~~~~~~~~~t~Ps~s 117 (354)
T KOG0849|consen 38 SRQLKVSHGCVSKILNRYYRTGSIRPGGIGGSKPRIVATPEVEAKIEQYKRENPAMFAWEIRDQLLHEGLCTQATLPSVS 117 (354)
T ss_pred hhhhhhhhHHHHhhhcccccccccccccccccccCCCCCchhHHHHHHHHhcCCcccchhhhhcccCcccccCCCCCChh
Confidence 46788888888 79999999999999999999 99999999999999999999999999999999999999999999
Q ss_pred ccccccccccCCC---------------CCCccccCc---cccCC---CCCccccchhhcccCCCccccCCccccCCCCC
Q psy10745 77 SINRYITYVPIGH---------------GGVNQLGGV---FVNGR---PLPDVVRQRIVASRSHGGVNQLGGVFVNGRPL 135 (197)
Q Consensus 77 SI~Rilr~~~iGh---------------G~vnqlGg~---fingr---PLPd~~RqRIVaS~~~~~~nqlg~~~~ngrpl 135 (197)
+|+|.+++..++- ....++|.. ..... ..|.....|-....-....+..+-.+..+-..
T Consensus 118 si~r~~r~~~~~~d~~~~~~~~~~~~~~~~~~~~gs~~~~s~~~~~~~~~p~~~~~~~~rr~rtsft~~Q~~~le~~f~r 197 (354)
T KOG0849|consen 118 SINRVLRNGALGKDQGLPSQQVTKEKSPSISGALGSQAGASLLSADDEEPPGYALQRGGRRNRTSFSPSQLEALEECFQR 197 (354)
T ss_pred hhhHHhhccccccccccccccccccccCCcccccCCccccccccCCccccccccccccccccccccccchHHHHHHHhcC
Confidence 9999999854332 222233321 11111 11111111100000001122222222222222
Q ss_pred ChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHhh
Q psy10745 136 PDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRES 175 (197)
Q Consensus 136 p~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~ 175 (197)
.. .-.|+...+..-+..+.+-+++|.+.|.++...|+.
T Consensus 198 t~--yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~ 235 (354)
T KOG0849|consen 198 TP--YPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQH 235 (354)
T ss_pred CC--CCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcc
Confidence 22 234555566666777788999999999999988886
No 8
>KOG0849|consensus
Probab=99.71 E-value=1.7e-18 Score=157.16 Aligned_cols=62 Identities=69% Similarity=1.153 Sum_probs=59.6
Q ss_pred CccccCCccccCCCCCChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHhhhhcCcc
Q psy10745 120 GGVNQLGGVFVNGRPLPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESNLHNYR 181 (197)
Q Consensus 120 ~~~nqlg~~~~ngrplp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~~~n~~ 181 (197)
+++||+|++|+||||||.++|++|++||.+|+|||+|||+|.||||||||||+||+++++-.
T Consensus 1 ~~~n~~~~~f~~~~~~~~~~r~~~~~~a~~~~~~~~~~~~l~vs~~~~~~il~r~~~~~~i~ 62 (354)
T KOG0849|consen 1 GRVNQLGGVFINGRPLPNHTRQKIVEMAHKGIRPCVISRQLKVSHGCVSKILNRYYRTGSIR 62 (354)
T ss_pred CCcccCCcccccCCCCCCchhhccccccccccCcccchhhhhhhhHHHHhhhcccccccccc
Confidence 47899999999999999999999999999999999999999999999999999999998854
No 9
>cd00131 PAX Paired Box domain
Probab=99.65 E-value=4.8e-17 Score=128.68 Aligned_cols=81 Identities=63% Similarity=1.032 Sum_probs=73.6
Q ss_pred cccccccc----cceeeeccCcccCCCCCCCCcCCHHHHHHHHHHHHhCCCcchHHhHHHHHhcCCCCCCCCCCcccccc
Q psy10745 5 LLTPFLCP----RRYYETGSFKAGVIGGSKPKVATAPVVDAIASYKRENPTMFAWEIRDRLLAEGICSQDNVPSVSSINR 80 (197)
Q Consensus 5 ~~~~ilc~----~Ry~ETGSIrPG~IGGSKpk~~tp~v~~~I~~~k~e~P~iFaWEIRdrLl~~GvC~~~~vPSvSSI~R 80 (197)
+-++..|| .||.|||++.|++.||.+|+..+++++..|..+.+++|++|+|||+++|.++|+|.+++.||+|+|+|
T Consensus 43 ~~Vs~~tV~r~i~r~~e~G~v~pk~~gg~rpr~~~~~~~~~i~~~v~~~p~~Tl~El~~~L~~~gv~~~~~~~s~stI~R 122 (128)
T cd00131 43 LRVSHGCVSKILNRYYETGSIRPGAIGGSKPRVATPEVVKKIEIYKQENPGMFAWEIRDRLLQEGVCDKSNVPSVSSINR 122 (128)
T ss_pred HCcCHHHHHHHHHHHHHcCCcCCCCCCCCCCCcCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCCcccCCCCCHHHHHH
Confidence 34444444 79999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccc
Q psy10745 81 YITYV 85 (197)
Q Consensus 81 ilr~~ 85 (197)
||+.+
T Consensus 123 ~L~~~ 127 (128)
T cd00131 123 ILRNK 127 (128)
T ss_pred HHHhc
Confidence 99864
No 10
>smart00351 PAX Paired Box domain.
Probab=99.59 E-value=7.6e-16 Score=120.93 Aligned_cols=71 Identities=72% Similarity=1.191 Sum_probs=69.0
Q ss_pred cceeeeccCcccCCCCCCCCcCCHHHHHHHHHHHHhCCCcchHHhHHHHHhcCCCCCCCCCCccccccccc
Q psy10745 13 RRYYETGSFKAGVIGGSKPKVATAPVVDAIASYKRENPTMFAWEIRDRLLAEGICSQDNVPSVSSINRYIT 83 (197)
Q Consensus 13 ~Ry~ETGSIrPG~IGGSKpk~~tp~v~~~I~~~k~e~P~iFaWEIRdrLl~~GvC~~~~vPSvSSI~Rilr 83 (197)
.||.|||++.|++.||.+|++.+++++..|.++.+++|++++|||++.|.++|||...++||.|+|+|+|+
T Consensus 55 ~r~~~~G~~~pk~~gg~rp~~~~~~~~~~I~~~~~~~p~~t~~el~~~L~~~gv~~~~~~Ps~sti~~~l~ 125 (125)
T smart00351 55 GRYYETGSIRPGAIGGSKPKVATPKVVKKIADYKQENPGIFAWEIRDRLLSEGVCDKDNVPSVSSINRILR 125 (125)
T ss_pred HHHHHcCCcCCcCCCCCCCCccCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCCCcCCCCCChhhHHHhhC
Confidence 79999999999999999999999999999999999999999999999999999999999999999999985
No 11
>cd00131 PAX Paired Box domain
Probab=99.58 E-value=1.6e-15 Score=119.98 Aligned_cols=65 Identities=75% Similarity=1.215 Sum_probs=61.9
Q ss_pred CCCccccCCccccCCCCCChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHhhhhcCccc
Q psy10745 118 SHGGVNQLGGVFVNGRPLPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESNLHNYRL 182 (197)
Q Consensus 118 ~~~~~nqlg~~~~ngrplp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~~~n~~~ 182 (197)
|++.+||+||.|++|+||+.+.|.+||+|++.|+...+||++++||.+||++++.||.++++..-
T Consensus 1 ~~~~~~~~~~~~~m~~~lS~d~R~rIv~~~~~G~s~~~iA~~~~Vs~~tV~r~i~r~~e~G~v~p 65 (128)
T cd00131 1 GQGGVNQLGGVFVNGRPLPDSIRQRIVELAQSGIRPCDISRQLRVSHGCVSKILNRYYETGSIRP 65 (128)
T ss_pred CCccccCCCccccCCCcCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCC
Confidence 46799999999999999999999999999999999999999999999999999999999988654
No 12
>smart00351 PAX Paired Box domain.
Probab=99.49 E-value=2.5e-14 Score=112.35 Aligned_cols=65 Identities=78% Similarity=1.188 Sum_probs=61.2
Q ss_pred CCCccccCCccccCCCCCChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHhhhhcCccc
Q psy10745 118 SHGGVNQLGGVFVNGRPLPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESNLHNYRL 182 (197)
Q Consensus 118 ~~~~~nqlg~~~~ngrplp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~~~n~~~ 182 (197)
+|.++||+||+|++|+|++.+.|.+||.|++.|....+||++++||..||+|++.||.++++..-
T Consensus 1 ~~~~~~~~~~~~~~~~~~s~~~R~riv~~~~~G~s~~~iA~~~gvs~~tV~kwi~r~~~~G~~~p 65 (125)
T smart00351 1 GHGGVNQLGGVFVNGRPLPDEERQRIVELAQNGVRPCDISRQLCVSHGCVSKILGRYYETGSIRP 65 (125)
T ss_pred CCCccccCCCeecCCCCCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCC
Confidence 36799999999999999999999999999999999999999999999999999999999887543
No 13
>PF13565 HTH_32: Homeodomain-like domain
Probab=97.87 E-value=1.7e-05 Score=55.92 Aligned_cols=65 Identities=29% Similarity=0.332 Sum_probs=53.6
Q ss_pred cceeeec-----cCcccCCCCCCCCcCCHHHHHHHHHHHHhCCCcchHHhHHHHHhc-CCCCCCCCCCcccccccc
Q psy10745 13 RRYYETG-----SFKAGVIGGSKPKVATAPVVDAIASYKRENPTMFAWEIRDRLLAE-GICSQDNVPSVSSINRYI 82 (197)
Q Consensus 13 ~Ry~ETG-----SIrPG~IGGSKpk~~tp~v~~~I~~~k~e~P~iFaWEIRdrLl~~-GvC~~~~vPSvSSI~Ril 82 (197)
.||.++| +..+++-.|-.++ ++++++.|.++..++|.....+|.+.|.++ |+-. -||.++|+|+|
T Consensus 7 ~ry~~~G~~gL~~~~~~~~~Grp~~--~~e~~~~i~~~~~~~p~wt~~~i~~~L~~~~g~~~---~~S~~tv~R~L 77 (77)
T PF13565_consen 7 KRYREEGLEGLKDRKRRPRPGRPRK--DPEQRERIIALIEEHPRWTPREIAEYLEEEFGISV---RVSRSTVYRIL 77 (77)
T ss_pred HHHHhhCchhhhcccccCCCCCCCC--cHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCC---CccHhHHHHhC
Confidence 5899999 7656665665555 888989999999999999999999999998 5433 46999999986
No 14
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=97.84 E-value=5.6e-06 Score=54.36 Aligned_cols=43 Identities=23% Similarity=0.319 Sum_probs=26.9
Q ss_pred ChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHhhhhc
Q psy10745 136 PDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESNLH 178 (197)
Q Consensus 136 p~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~~~ 178 (197)
....|.+||.|..+|....+||+.|+||...|++++.||.+.+
T Consensus 3 ~~~~R~~ii~l~~~G~s~~~ia~~lgvs~~Tv~~w~kr~~~~G 45 (50)
T PF13384_consen 3 SEERRAQIIRLLREGWSIREIAKRLGVSRSTVYRWIKRYREEG 45 (50)
T ss_dssp -------HHHHHHHT--HHHHHHHHTS-HHHHHHHHT------
T ss_pred chhHHHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHHHccccc
Confidence 4578999999999999999999999999999999999997654
No 15
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=97.41 E-value=6.2e-05 Score=49.69 Aligned_cols=41 Identities=29% Similarity=0.387 Sum_probs=26.3
Q ss_pred CCCChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHH
Q psy10745 133 RPLPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSR 173 (197)
Q Consensus 133 rplp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~r 173 (197)
..|.+++|..|-.|.+.|+..-+||++|++|+..|++.|.|
T Consensus 3 ~~Lt~~eR~~I~~l~~~G~s~~~IA~~lg~s~sTV~relkR 43 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQGMSIREIAKRLGRSRSTVSRELKR 43 (44)
T ss_dssp ---------HHHHHHCS---HHHHHHHTT--HHHHHHHHHH
T ss_pred cchhhhHHHHHHHHHHcCCCHHHHHHHHCcCcHHHHHHHhc
Confidence 46889999999999999999999999999999999999987
No 16
>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=97.05 E-value=0.00063 Score=46.65 Aligned_cols=41 Identities=29% Similarity=0.377 Sum_probs=33.7
Q ss_pred CCCChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHH
Q psy10745 133 RPLPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSR 173 (197)
Q Consensus 133 rplp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~r 173 (197)
+.|..++..+||++++.|.+..+||+.++|+...||+|+..
T Consensus 5 ~~LTl~eK~~iI~~~e~g~s~~~ia~~fgv~~sTv~~I~K~ 45 (53)
T PF04218_consen 5 KSLTLEEKLEIIKRLEEGESKRDIAREFGVSRSTVSTILKN 45 (53)
T ss_dssp SS--HHHHHHHHHHHHCTT-HHHHHHHHT--CCHHHHHHHC
T ss_pred ccCCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHh
Confidence 36889999999999999999999999999999999999864
No 17
>PF13518 HTH_28: Helix-turn-helix domain
Probab=97.00 E-value=0.00065 Score=44.25 Aligned_cols=39 Identities=28% Similarity=0.344 Sum_probs=36.9
Q ss_pred HHHHHHHHhcCCCcccchhhhhcccchHHHHHHHhhhhc
Q psy10745 140 RQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESNLH 178 (197)
Q Consensus 140 r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~~~ 178 (197)
|.+||+++.+|...-+||++++||+..|...+.+|.+.+
T Consensus 2 r~~iv~~~~~g~s~~~~a~~~gis~~tv~~w~~~y~~~G 40 (52)
T PF13518_consen 2 RLQIVELYLEGESVREIAREFGISRSTVYRWIKRYREGG 40 (52)
T ss_pred HHHHHHHHHcCCCHHHHHHHHCCCHhHHHHHHHHHHhcC
Confidence 789999999999999999999999999999999998765
No 18
>PF13551 HTH_29: Winged helix-turn helix
Probab=96.68 E-value=0.0017 Score=47.57 Aligned_cols=68 Identities=26% Similarity=0.303 Sum_probs=52.0
Q ss_pred cceeeec--cCcc-cCCCCCCCCcCCHHHHHHHHHHHHhCC-----CcchHHhHHHHHhcCCCCCCCCCCccccccccc
Q psy10745 13 RRYYETG--SFKA-GVIGGSKPKVATAPVVDAIASYKRENP-----TMFAWEIRDRLLAEGICSQDNVPSVSSINRYIT 83 (197)
Q Consensus 13 ~Ry~ETG--SIrP-G~IGGSKpk~~tp~v~~~I~~~k~e~P-----~iFaWEIRdrLl~~GvC~~~~vPSvSSI~Rilr 83 (197)
.+|.++| .+.+ +.-+|..++..++++.+.|.++..++| ..+.-+|++.|+++..-. -+|.++|+|+|+
T Consensus 34 ~~~~~~G~~~l~~~~~~~g~~~~~l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~---~~s~~ti~r~L~ 109 (112)
T PF13551_consen 34 KRYREGGIEGLLPRKPRGGRPRKRLSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGI---DVSPSTIRRILK 109 (112)
T ss_pred HHHHcccHHHHHhccccCCCCCCCCCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCc---cCCHHHHHHHHH
Confidence 4899999 8888 555565555589999999999999988 366778888885544222 259999999986
No 19
>PF13551 HTH_29: Winged helix-turn helix
Probab=96.66 E-value=0.0011 Score=48.66 Aligned_cols=39 Identities=31% Similarity=0.381 Sum_probs=36.9
Q ss_pred HHHHHHHHhcCCC-cccchhhhhcccchHHHHHHHhhhhc
Q psy10745 140 RQRIVELAHNGVR-PCDISRQLRVSHGCVSKILSRESNLH 178 (197)
Q Consensus 140 r~~iv~l~~~g~r-~~~isr~l~vshgcVskil~ry~~~~ 178 (197)
|.+|+.|+.+|+. +.+||+.|+||...|.+++.+|.+.+
T Consensus 1 R~~~l~l~~~g~~~~~~ia~~lg~s~~Tv~r~~~~~~~~G 40 (112)
T PF13551_consen 1 RAQILLLLAEGVSTIAEIARRLGISRRTVYRWLKRYREGG 40 (112)
T ss_pred CHHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHccc
Confidence 6789999999996 99999999999999999999998777
No 20
>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=96.61 E-value=0.00096 Score=43.94 Aligned_cols=38 Identities=29% Similarity=0.384 Sum_probs=30.5
Q ss_pred CChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHH
Q psy10745 135 LPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILS 172 (197)
Q Consensus 135 lp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ 172 (197)
+.++...+|++|++.|+...+||++++||...|-++|.
T Consensus 6 ~~~~~~~~i~~l~~~G~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 6 LSKEQIEEIKELYAEGMSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp SSHCCHHHHHHHHHTT--HHHHHHHTTS-HHHHHHHHC
T ss_pred CCHHHHHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHh
Confidence 44456799999999999999999999999999988874
No 21
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=96.41 E-value=0.0022 Score=52.37 Aligned_cols=66 Identities=21% Similarity=0.229 Sum_probs=54.6
Q ss_pred cceeeeccCcccCCCCCCCCcCCHHHHHHHHHHHHhCCCcchHHhHHHHH-hcCCCCCCCCCCcccccccccc
Q psy10745 13 RRYYETGSFKAGVIGGSKPKVATAPVVDAIASYKRENPTMFAWEIRDRLL-AEGICSQDNVPSVSSINRYITY 84 (197)
Q Consensus 13 ~Ry~ETGSIrPG~IGGSKpk~~tp~v~~~I~~~k~e~P~iFaWEIRdrLl-~~GvC~~~~vPSvSSI~Rilr~ 84 (197)
+||.|||+..|...||.+|+..+++..+.+++..++.. .++-|+++.|. +.||-- +.++++|+|+.
T Consensus 43 ~r~~e~G~~l~~~~~~GrP~kl~~~q~~~l~e~~~~k~-wTl~~~~~~l~~e~gv~y-----~~~~v~~~l~~ 109 (138)
T COG3415 43 RRYRETGLDLPPKPRKGRPRKLSEEQLEILLERLREKD-WTLKELVEELGLEFGVWY-----HASAVRRLLHE 109 (138)
T ss_pred HHhccccccccCccCCCCCcccCHHHHHHHHHHHhccc-chHHHHHHHHhhhcCeEE-----eHHHHHHHHHH
Confidence 79999999999999999999999988887777665544 66777788866 889876 67799999984
No 22
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=96.38 E-value=0.0029 Score=35.64 Aligned_cols=38 Identities=24% Similarity=0.270 Sum_probs=34.1
Q ss_pred CCChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHH
Q psy10745 134 PLPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKIL 171 (197)
Q Consensus 134 plp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil 171 (197)
-++++.+..|+++...|....+||+++++|..+|++++
T Consensus 5 ~~~~~~~~~i~~~~~~~~s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 5 KLTPEQIEEARRLLAAGESVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred cCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHhC
Confidence 36778899999999999999999999999999999864
No 23
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=96.10 E-value=0.0068 Score=38.72 Aligned_cols=41 Identities=24% Similarity=0.323 Sum_probs=36.0
Q ss_pred CChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 135 LPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 135 lp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
|++..+. |+.|...|+...+||++++||.+.|.+.+.|...
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 6766665 9999999999999999999999999998888644
No 24
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=96.10 E-value=0.0047 Score=42.74 Aligned_cols=41 Identities=27% Similarity=0.482 Sum_probs=30.8
Q ss_pred CCCCChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHH
Q psy10745 132 GRPLPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILS 172 (197)
Q Consensus 132 grplp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ 172 (197)
|.+|.+.++-+|.-|.+.|++-.+|||+++=|+-||.+-|+
T Consensus 2 G~~Lt~~Eqaqid~m~qlG~s~~~isr~i~RSr~~Ir~yl~ 42 (50)
T PF11427_consen 2 GKTLTDAEQAQIDVMHQLGMSLREISRRIGRSRTCIRRYLK 42 (50)
T ss_dssp S----HHHHHHHHHHHHTT--HHHHHHHHT--HHHHHHHHH
T ss_pred CCcCCHHHHHHHHHHHHhchhHHHHHHHhCccHHHHHHHhc
Confidence 78999999999999999999999999999999999987653
No 25
>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=95.85 E-value=0.0069 Score=41.56 Aligned_cols=35 Identities=34% Similarity=0.487 Sum_probs=31.6
Q ss_pred HHHHHHHHHHhcCCCcccchhhhhcccchHHHHHH
Q psy10745 138 VVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILS 172 (197)
Q Consensus 138 ~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ 172 (197)
.+.++||||+..|.-.-|+||-|+||...|-+-|.
T Consensus 9 gikeqIvema~nG~GiRdtaRvL~I~~nTVlrtLK 43 (46)
T PF12759_consen 9 GIKEQIVEMAFNGSGIRDTARVLKISINTVLRTLK 43 (46)
T ss_pred cHHHHHHHHHhcCCcchhhHhHhcchHHHHHHHHh
Confidence 57889999999999999999999999999877653
No 26
>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=95.40 E-value=0.012 Score=41.43 Aligned_cols=44 Identities=18% Similarity=0.080 Sum_probs=38.1
Q ss_pred HHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHhhhhcCcc
Q psy10745 138 VVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESNLHNYR 181 (197)
Q Consensus 138 ~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~~~n~~ 181 (197)
+.|.+...|+.+|.++.+||+.|+|+...|..=..||.-..=.+
T Consensus 1 e~k~~A~~LY~~G~~~~eIA~~Lg~~~~TV~~W~~r~~W~~~~~ 44 (58)
T PF06056_consen 1 EVKEQARSLYLQGWSIKEIAEELGVPRSTVYSWKDRYKWDELLP 44 (58)
T ss_pred CHHHHHHHHHHcCCCHHHHHHHHCCChHHHHHHHHhhCccccCc
Confidence 46889999999999999999999999999999999987544333
No 27
>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=95.32 E-value=0.012 Score=45.74 Aligned_cols=54 Identities=31% Similarity=0.423 Sum_probs=43.2
Q ss_pred eeeeccCcccCCCCCCCCcCCHHHHHHHHHHHHhCCCcchHHhHHHHHhcCCCCCCCCCCcccccccccc
Q psy10745 15 YYETGSFKAGVIGGSKPKVATAPVVDAIASYKRENPTMFAWEIRDRLLAEGICSQDNVPSVSSINRYITY 84 (197)
Q Consensus 15 y~ETGSIrPG~IGGSKpk~~tp~v~~~I~~~k~e~P~iFaWEIRdrLl~~GvC~~~~vPSvSSI~Rilr~ 84 (197)
..+||++.|++-|+. +. . .+.+.++..++|+++.+||.++| || |.++|+++|.-
T Consensus 41 ~~~~G~~~~k~r~~~--Ki--d--~~~L~~~v~~~pd~tl~Ela~~l---~V-------s~~ti~~~Lkr 94 (119)
T PF01710_consen 41 RKETGDLEPKPRGRK--KI--D--RDELKALVEENPDATLRELAERL---GV-------SPSTIWRALKR 94 (119)
T ss_pred hcccccccccccccc--cc--c--HHHHHHHHHHCCCcCHHHHHHHc---CC-------CHHHHHHHHHH
Confidence 578999999987665 33 2 45678888899999999998877 44 88999999963
No 28
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=95.02 E-value=0.023 Score=37.38 Aligned_cols=41 Identities=29% Similarity=0.367 Sum_probs=34.8
Q ss_pred CChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHhh
Q psy10745 135 LPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRES 175 (197)
Q Consensus 135 lp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~ 175 (197)
||+..|.=|...+-.|..-.+||+.|++|.+.|++++.|.-
T Consensus 5 L~~~er~vi~~~y~~~~t~~eIa~~lg~s~~~V~~~~~~al 45 (50)
T PF04545_consen 5 LPPREREVIRLRYFEGLTLEEIAERLGISRSTVRRILKRAL 45 (50)
T ss_dssp S-HHHHHHHHHHHTST-SHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHhcCCCCHHHHHHHHCCcHHHHHHHHHHHH
Confidence 78888887777888999999999999999999999998754
No 29
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=94.69 E-value=0.032 Score=36.64 Aligned_cols=43 Identities=26% Similarity=0.294 Sum_probs=39.2
Q ss_pred CCCCChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHh
Q psy10745 132 GRPLPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRE 174 (197)
Q Consensus 132 grplp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry 174 (197)
+..+....++.|++++.....--+||++++||...|..|+.+|
T Consensus 9 ~~r~T~~~~~~i~~~~~~~~s~~~vA~~~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 9 YCRITKRLEQYILKLLRESRSFKDVARELGVSWSTVRRIFDRY 51 (52)
T ss_pred CCcHHHHHHHHHHHHHhhcCCHHHHHHHHCCCHHHHHHHHHhh
Confidence 4467778899999999999899999999999999999999987
No 30
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=94.53 E-value=0.047 Score=33.90 Aligned_cols=42 Identities=26% Similarity=0.315 Sum_probs=35.2
Q ss_pred CChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 135 LPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 135 lp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
||+..|.-+..++..|...-+||..+++|.+.|.+.+.|...
T Consensus 11 l~~~~~~~~~~~~~~~~~~~~ia~~~~~s~~~i~~~~~~~~~ 52 (55)
T cd06171 11 LPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALK 52 (55)
T ss_pred CCHHHHHHHHHHHhcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 677776655555679999999999999999999999988754
No 31
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=93.60 E-value=0.082 Score=40.29 Aligned_cols=45 Identities=22% Similarity=0.164 Sum_probs=40.3
Q ss_pred CCChHHHHHHHHHH-hcCCCcccchhhhhcccchHHHHHHHhhhhc
Q psy10745 134 PLPDVVRQRIVELA-HNGVRPCDISRQLRVSHGCVSKILSRESNLH 178 (197)
Q Consensus 134 plp~~~r~~iv~l~-~~g~r~~~isr~l~vshgcVskil~ry~~~~ 178 (197)
+|...-|..++... ..|..+.+.|++.+||.-|++|-+.||...+
T Consensus 8 ~Lt~~gR~~lv~~vv~~g~~~a~aA~~~gVS~~Ta~kW~~Ryra~G 53 (85)
T PF13011_consen 8 RLTPRGRLRLVRRVVEQGWPVAHAAAEFGVSRRTAYKWLARYRAEG 53 (85)
T ss_pred CCCHHHHHHHHHHHHHcCCcHHHHHHHhCCCHHHHHHHHHHHHHcC
Confidence 67888999999866 7899999999999999999999999996554
No 32
>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=92.99 E-value=0.13 Score=32.98 Aligned_cols=42 Identities=21% Similarity=0.219 Sum_probs=34.8
Q ss_pred CChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHhhhh
Q psy10745 135 LPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESNL 177 (197)
Q Consensus 135 lp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~~ 177 (197)
|++..++ |+.|...|+...+||..+++|.+.|.+.+.|..+.
T Consensus 1 l~~~e~~-i~~~~~~~~s~~eia~~l~~s~~tv~~~~~~~~~~ 42 (57)
T cd06170 1 LTPRERE-VLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRK 42 (57)
T ss_pred CCHHHHH-HHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 3444444 88999999999999999999999999988886553
No 33
>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=92.91 E-value=0.069 Score=35.07 Aligned_cols=40 Identities=28% Similarity=0.444 Sum_probs=31.9
Q ss_pred hHHHHHHHHHHhcC-CCcccchhhhhcccchHHHHHHHhhh
Q psy10745 137 DVVRQRIVELAHNG-VRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 137 ~~~r~~iv~l~~~g-~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
++.|.+|+.+...| ...||||+.+++|.+.||+=|..-.+
T Consensus 1 d~~R~~Il~~L~~~~~~~~el~~~l~~s~~~vs~hL~~L~~ 41 (47)
T PF01022_consen 1 DPTRLRILKLLSEGPLTVSELAEELGLSQSTVSHHLKKLRE 41 (47)
T ss_dssp SHHHHHHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHhCCCchhhHHHhccccchHHHHHHHHHHH
Confidence 46899999877654 56789999999999999998776544
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=92.29 E-value=0.11 Score=39.34 Aligned_cols=35 Identities=17% Similarity=0.258 Sum_probs=32.2
Q ss_pred hHHHHHHHHHHhcCCCcccchhhhhcccchHHHHH
Q psy10745 137 DVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKIL 171 (197)
Q Consensus 137 ~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil 171 (197)
...|.+|++|...|....+||++++||...|+++.
T Consensus 37 Ls~R~~I~~ll~~G~S~~eIA~~LgISrsTIyRi~ 71 (88)
T TIGR02531 37 LAQRLQVAKMLKQGKTYSDIEAETGASTATISRVK 71 (88)
T ss_pred hhHHHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHH
Confidence 45689999999999999999999999999999955
No 35
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=92.20 E-value=0.15 Score=36.18 Aligned_cols=43 Identities=16% Similarity=0.302 Sum_probs=37.2
Q ss_pred ChHHHHHHHHHHhc--C--CCcccchhhhhcccchHHHHHHHhhhhc
Q psy10745 136 PDVVRQRIVELAHN--G--VRPCDISRQLRVSHGCVSKILSRESNLH 178 (197)
Q Consensus 136 p~~~r~~iv~l~~~--g--~r~~~isr~l~vshgcVskil~ry~~~~ 178 (197)
++..+++|+++... + +...|||++|+|+...|.++|.+-.+.+
T Consensus 4 ~~~~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~G 50 (68)
T smart00550 4 QDSLEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKKG 50 (68)
T ss_pred chHHHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCC
Confidence 56788999998765 4 8999999999999999999999887665
No 36
>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=91.89 E-value=0.14 Score=39.78 Aligned_cols=45 Identities=18% Similarity=0.259 Sum_probs=39.7
Q ss_pred ChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHhhhhcCcc
Q psy10745 136 PDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESNLHNYR 181 (197)
Q Consensus 136 p~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~~~n~~ 181 (197)
+.+.|++||...+.|....++|++.+||-..|-..+. ..+++...
T Consensus 4 S~DlR~rVl~~~~~g~s~~eaa~~F~VS~~Tv~~W~k-~~~~G~~~ 48 (119)
T PF01710_consen 4 SLDLRQRVLAYIEKGKSIREAAKRFGVSRNTVYRWLK-RKETGDLE 48 (119)
T ss_pred CHHHHHHHHHHHHccchHHHHHHHhCcHHHHHHHHHH-hccccccc
Confidence 5789999999999999999999999999999999999 55565543
No 37
>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=91.84 E-value=0.1 Score=36.59 Aligned_cols=36 Identities=36% Similarity=0.414 Sum_probs=29.1
Q ss_pred HHHHH--hcCCCcccchhhhhcccchHHHHHHHhhhhc
Q psy10745 143 IVELA--HNGVRPCDISRQLRVSHGCVSKILSRESNLH 178 (197)
Q Consensus 143 iv~l~--~~g~r~~~isr~l~vshgcVskil~ry~~~~ 178 (197)
|.+|. ...+++.|||+.|+||...||+.|.|-.+.+
T Consensus 13 Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~~G 50 (60)
T PF01325_consen 13 IYELSEEGGPVRTKDIAERLGVSPPTVTEMLKRLAEKG 50 (60)
T ss_dssp HHHHHHCTSSBBHHHHHHHHTS-HHHHHHHHHHHHHTT
T ss_pred HHHHHcCCCCccHHHHHHHHCCChHHHHHHHHHHHHCC
Confidence 44444 5678999999999999999999999987654
No 38
>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=90.93 E-value=0.087 Score=35.46 Aligned_cols=21 Identities=38% Similarity=0.510 Sum_probs=18.7
Q ss_pred ccchhhhhcccchHHHHHHHh
Q psy10745 154 CDISRQLRVSHGCVSKILSRE 174 (197)
Q Consensus 154 ~~isr~l~vshgcVskil~ry 174 (197)
-|||+.++||...||++|+-.
T Consensus 3 ~dIA~~agvS~~TVSr~ln~~ 23 (46)
T PF00356_consen 3 KDIAREAGVSKSTVSRVLNGP 23 (46)
T ss_dssp HHHHHHHTSSHHHHHHHHTTC
T ss_pred HHHHHHHCcCHHHHHHHHhCC
Confidence 489999999999999999753
No 39
>KOG0400|consensus
Probab=90.69 E-value=0.14 Score=42.52 Aligned_cols=32 Identities=41% Similarity=0.613 Sum_probs=29.5
Q ss_pred CChHHHHHHHHHHhcCCCcccchhhhhcccch
Q psy10745 135 LPDVVRQRIVELAHNGVRPCDISRQLRVSHGC 166 (197)
Q Consensus 135 lp~~~r~~iv~l~~~g~r~~~isr~l~vshgc 166 (197)
-++++..+|++|+++|+.|++|+=.|+=|||-
T Consensus 29 ~~ddvkeqI~K~akKGltpsqIGviLRDshGi 60 (151)
T KOG0400|consen 29 TADDVKEQIYKLAKKGLTPSQIGVILRDSHGI 60 (151)
T ss_pred CHHHHHHHHHHHHHcCCChhHceeeeecccCc
Confidence 46889999999999999999999999999983
No 40
>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=90.14 E-value=0.29 Score=39.97 Aligned_cols=39 Identities=23% Similarity=0.404 Sum_probs=34.5
Q ss_pred HHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 138 VVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 138 ~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
+..++|++|..+|+.-.+||.+|++|..-|++++.|..+
T Consensus 9 e~qr~VL~Lr~~GlTq~EIAe~LgiS~stV~~~e~ra~k 47 (137)
T TIGR00721 9 ERQIKVLELREKGLSQKEIAKELKTTRANVSAIEKRAME 47 (137)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHhHHH
Confidence 556688999999999999999999999999998887543
No 41
>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=89.85 E-value=0.31 Score=32.46 Aligned_cols=40 Identities=20% Similarity=0.320 Sum_probs=30.6
Q ss_pred HHHHHHHHHhcC---CCcccchhhhhcccchHHHHHHHhhhhc
Q psy10745 139 VRQRIVELAHNG---VRPCDISRQLRVSHGCVSKILSRESNLH 178 (197)
Q Consensus 139 ~r~~iv~l~~~g---~r~~~isr~l~vshgcVskil~ry~~~~ 178 (197)
...=+..|+..+ +.+.|||+.+++|...||+++.+..+.+
T Consensus 7 q~~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~~G 49 (62)
T PF12802_consen 7 QFRVLMALARHPGEELTQSELAERLGISKSTVSRIVKRLEKKG 49 (62)
T ss_dssp HHHHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence 334445566655 7999999999999999999999986644
No 42
>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=89.81 E-value=0.41 Score=31.37 Aligned_cols=44 Identities=25% Similarity=0.381 Sum_probs=35.6
Q ss_pred CCChHHHHHHHHHH-hcCCCcccchhhhhcccchHHHHHHHhhhh
Q psy10745 134 PLPDVVRQRIVELA-HNGVRPCDISRQLRVSHGCVSKILSRESNL 177 (197)
Q Consensus 134 plp~~~r~~iv~l~-~~g~r~~~isr~l~vshgcVskil~ry~~~ 177 (197)
++....+.+|++.. ..++...+|++.+++|...|++.|.+-.+.
T Consensus 3 ~~~~~~~~~il~~l~~~~~~~~ei~~~~~i~~~~i~~~l~~L~~~ 47 (78)
T cd00090 3 ALSDPTRLRILRLLLEGPLTVSELAERLGLSQSTVSRHLKKLEEA 47 (78)
T ss_pred cccChHHHHHHHHHHHCCcCHHHHHHHHCcCHhHHHHHHHHHHHC
Confidence 45556778888864 444889999999999999999999997553
No 43
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=89.78 E-value=0.3 Score=40.10 Aligned_cols=39 Identities=23% Similarity=0.289 Sum_probs=34.0
Q ss_pred HHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 138 VVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 138 ~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
.-.++|++|..+|+.-.+||++|++|.+-||+++.|..+
T Consensus 9 ~rqreVL~lr~~GlTq~EIAe~LGiS~~tVs~ie~ra~k 47 (141)
T PRK03975 9 ERQIEVLRLRERGLTQQEIADILGTSRANVSSIEKRARE 47 (141)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 455678899999999999999999999999999887543
No 44
>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=89.54 E-value=0.28 Score=33.09 Aligned_cols=33 Identities=21% Similarity=0.323 Sum_probs=28.4
Q ss_pred HHHHHHHhcCCCcccchhhhhcccchHHHHHHH
Q psy10745 141 QRIVELAHNGVRPCDISRQLRVSHGCVSKILSR 173 (197)
Q Consensus 141 ~~iv~l~~~g~r~~~isr~l~vshgcVskil~r 173 (197)
.+|+.+...|..+.+||+.|+||...|..-+.+
T Consensus 9 ~~vl~~l~~G~~~~eIA~~l~is~~tV~~~~~~ 41 (58)
T PF00196_consen 9 LEVLRLLAQGMSNKEIAEELGISEKTVKSHRRR 41 (58)
T ss_dssp HHHHHHHHTTS-HHHHHHHHTSHHHHHHHHHHH
T ss_pred HHHHHHHHhcCCcchhHHhcCcchhhHHHHHHH
Confidence 459999999999999999999999999885544
No 45
>PF13565 HTH_32: Homeodomain-like domain
Probab=89.10 E-value=0.4 Score=33.46 Aligned_cols=41 Identities=37% Similarity=0.522 Sum_probs=33.2
Q ss_pred CCCCC-ChHHHHHHHHHHhcC--CCcccchhhhh------c--ccchHHHHH
Q psy10745 131 NGRPL-PDVVRQRIVELAHNG--VRPCDISRQLR------V--SHGCVSKIL 171 (197)
Q Consensus 131 ngrpl-p~~~r~~iv~l~~~g--~r~~~isr~l~------v--shgcVskil 171 (197)
.|||- +++++..|+++.... +.+-+|+..|. | |+..|.+||
T Consensus 26 ~Grp~~~~e~~~~i~~~~~~~p~wt~~~i~~~L~~~~g~~~~~S~~tv~R~L 77 (77)
T PF13565_consen 26 PGRPRKDPEQRERIIALIEEHPRWTPREIAEYLEEEFGISVRVSRSTVYRIL 77 (77)
T ss_pred CCCCCCcHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCCCccHhHHHHhC
Confidence 56665 488889999998776 89999988874 4 999998886
No 46
>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=88.85 E-value=0.37 Score=31.74 Aligned_cols=43 Identities=23% Similarity=0.342 Sum_probs=31.6
Q ss_pred CCChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 134 PLPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 134 plp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
-||+..|.-+.--+-.|....|||+.+++|-+-|-+.|.|-.+
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 3677777766666899999999999999999999999988643
No 47
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=88.73 E-value=0.44 Score=36.66 Aligned_cols=43 Identities=16% Similarity=0.042 Sum_probs=35.7
Q ss_pred CCChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 134 PLPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 134 plp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
-||+..|.=|+-.+-.|....+||..|++|-+.|.+.|.|-.+
T Consensus 106 ~L~~~~r~ii~l~~~~~~s~~EIA~~l~is~~tV~~~~~ra~~ 148 (154)
T PRK06759 106 VLDEKEKYIIFERFFVGKTMGEIALETEMTYYQVRWIYRQALE 148 (154)
T ss_pred hCCHHHHHHHHHHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4676666655556789999999999999999999999988643
No 48
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=88.69 E-value=0.48 Score=34.75 Aligned_cols=41 Identities=29% Similarity=0.448 Sum_probs=33.0
Q ss_pred CCChHHHHHHHHHH-hcCCCcccchhhhhcccchHHHHHHHhh
Q psy10745 134 PLPDVVRQRIVELA-HNGVRPCDISRQLRVSHGCVSKILSRES 175 (197)
Q Consensus 134 plp~~~r~~iv~l~-~~g~r~~~isr~l~vshgcVskil~ry~ 175 (197)
-||+..|+ |+.|. -.|....+||+.++||...|++.+.|-.
T Consensus 110 ~L~~~~~~-ii~~~~~~g~s~~eIA~~l~~s~~~v~~~~~~~~ 151 (158)
T TIGR02937 110 KLPERERE-VLVLRYLEGLSYKEIAEILGISVGTVKRRLKRAR 151 (158)
T ss_pred hCCHHHHH-HHhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 45555554 55554 7999999999999999999999988864
No 49
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=88.66 E-value=0.38 Score=39.43 Aligned_cols=48 Identities=19% Similarity=0.338 Sum_probs=42.7
Q ss_pred CCCCChHHHHHHHHHH-hcCCCcccchhhhhcccchHHHHHHHhhhhcC
Q psy10745 132 GRPLPDVVRQRIVELA-HNGVRPCDISRQLRVSHGCVSKILSRESNLHN 179 (197)
Q Consensus 132 grplp~~~r~~iv~l~-~~g~r~~~isr~l~vshgcVskil~ry~~~~n 179 (197)
.+|-....|.+++... ..|++.-+||..++||-+.|=+-++||.+++=
T Consensus 2 ~k~~s~~~R~~~~~~~~~~G~S~re~Ak~~gvs~sTvy~wv~r~~e~G~ 50 (138)
T COG3415 2 AKPFSNDLRERVVDAVVGEGLSCREAAKRFGVSISTVYRWVRRYRETGL 50 (138)
T ss_pred CchhhHHHHHHHHHHHHHcCccHHHHHHHhCccHHHHHHHHHHhccccc
Confidence 3577888999998887 89999999999999999999999999987653
No 50
>PRK04217 hypothetical protein; Provisional
Probab=88.38 E-value=0.55 Score=37.09 Aligned_cols=41 Identities=17% Similarity=0.276 Sum_probs=34.0
Q ss_pred CChHHHHHHHHHHh-cCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 135 LPDVVRQRIVELAH-NGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 135 lp~~~r~~iv~l~~-~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
|+++.+ .++.|.. +|+...+||+.|+||.+.|.++|.|..+
T Consensus 43 Lt~eer-eai~l~~~eGlS~~EIAk~LGIS~sTV~r~L~RArk 84 (110)
T PRK04217 43 MTYEEF-EALRLVDYEGLTQEEAGKRMGVSRGTVWRALTSARK 84 (110)
T ss_pred CCHHHH-HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 556666 6666665 9999999999999999999999988654
No 51
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=88.10 E-value=0.4 Score=39.71 Aligned_cols=36 Identities=25% Similarity=0.455 Sum_probs=32.5
Q ss_pred HHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHh
Q psy10745 139 VRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRE 174 (197)
Q Consensus 139 ~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry 174 (197)
.+.+|.+|...|....+||+.|+||...|-+++..+
T Consensus 161 ~~~~i~~~~~~g~s~~~iak~lgis~~Tv~r~~k~~ 196 (200)
T PRK13413 161 KEEKIKKLLDKGTSKSEIARKLGVSRTTLARFLKTR 196 (200)
T ss_pred hHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHhc
Confidence 457899999999999999999999999999988753
No 52
>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=87.98 E-value=0.27 Score=34.15 Aligned_cols=43 Identities=12% Similarity=0.143 Sum_probs=36.6
Q ss_pred CCCChHHHHHHHHHH-hcCCCcccchhhhhcccchHHHHHHHhh
Q psy10745 133 RPLPDVVRQRIVELA-HNGVRPCDISRQLRVSHGCVSKILSRES 175 (197)
Q Consensus 133 rplp~~~r~~iv~l~-~~g~r~~~isr~l~vshgcVskil~ry~ 175 (197)
+.-+++.+.+||.++ ..|....++|++++|+..++++=+..|.
T Consensus 5 ~~ys~e~K~~~v~~~~~~g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 5 RRYSPEFKLQAVREYLESGESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp ----HHHHHHHHHHHHHHHCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHHCCCceEeeecccccccccccHHHHHHh
Confidence 356789999999999 9999999999999999999999999996
No 53
>PRK00118 putative DNA-binding protein; Validated
Probab=87.55 E-value=0.6 Score=36.53 Aligned_cols=45 Identities=18% Similarity=0.204 Sum_probs=37.6
Q ss_pred CCCCChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 132 GRPLPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 132 grplp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
|--||+..|+-++-....|....+||++++||.+.|++.|.|-..
T Consensus 15 ~~~L~ekqRevl~L~y~eg~S~~EIAe~lGIS~~TV~r~L~RArk 59 (104)
T PRK00118 15 GSLLTEKQRNYMELYYLDDYSLGEIAEEFNVSRQAVYDNIKRTEK 59 (104)
T ss_pred hccCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 445777777777666899999999999999999999999987543
No 54
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=87.50 E-value=0.64 Score=36.17 Aligned_cols=41 Identities=22% Similarity=0.190 Sum_probs=34.1
Q ss_pred CChHHHHHHHHH-HhcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 135 LPDVVRQRIVEL-AHNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 135 lp~~~r~~iv~l-~~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
||+..|. |+.| .-+|+...+||..|++|.+.|.+.|.|...
T Consensus 107 Lp~~~r~-v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Rar~ 148 (160)
T PRK09642 107 LPENYRD-VVLAHYLEEKSYQEIALQEKIEVKTVEMKLYRARK 148 (160)
T ss_pred CCHHHHH-HHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 7766555 5555 679999999999999999999998888754
No 55
>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=87.36 E-value=0.62 Score=30.15 Aligned_cols=40 Identities=13% Similarity=0.289 Sum_probs=30.1
Q ss_pred HHHHHHHHHHh--cCCCcccchhhhhcccchHHHHHHHhhhh
Q psy10745 138 VVRQRIVELAH--NGVRPCDISRQLRVSHGCVSKILSRESNL 177 (197)
Q Consensus 138 ~~r~~iv~l~~--~g~r~~~isr~l~vshgcVskil~ry~~~ 177 (197)
..+.+|+.+-. .++...+||+.+++|.+-|+++|.+..+.
T Consensus 3 ~~~~~Il~~l~~~~~~t~~ela~~~~is~~tv~~~l~~L~~~ 44 (48)
T PF13412_consen 3 ETQRKILNYLRENPRITQKELAEKLGISRSTVNRYLKKLEEK 44 (48)
T ss_dssp HHHHHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence 45677776653 34788899999999999999999987654
No 56
>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=86.57 E-value=0.28 Score=31.84 Aligned_cols=19 Identities=42% Similarity=0.545 Sum_probs=17.3
Q ss_pred cchhhhhcccchHHHHHHH
Q psy10745 155 DISRQLRVSHGCVSKILSR 173 (197)
Q Consensus 155 ~isr~l~vshgcVskil~r 173 (197)
|||+.++||..+||++|+-
T Consensus 2 ~lA~~~gvs~~tvs~~l~g 20 (52)
T cd01392 2 DIARAAGVSVATVSRVLNG 20 (52)
T ss_pred cHHHHHCcCHHHHHHHHcC
Confidence 7899999999999999863
No 57
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=86.28 E-value=0.84 Score=36.39 Aligned_cols=42 Identities=19% Similarity=0.165 Sum_probs=34.6
Q ss_pred CChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 135 LPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 135 lp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
||+..|.=|+-..-.|.+..+||..|++|.+-|.+.|.|..+
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 676666555555689999999999999999999999988653
No 58
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=86.26 E-value=0.78 Score=35.55 Aligned_cols=42 Identities=26% Similarity=0.277 Sum_probs=35.0
Q ss_pred CChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 135 LPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 135 lp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
||+..|.-++-....|.+..+||..|++|..-|.+.+.|..+
T Consensus 126 L~~~~r~i~~l~~~~~~~~~eIA~~lgis~~tv~~~~~ra~~ 167 (179)
T PRK11924 126 LPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRARQ 167 (179)
T ss_pred CCHHHHHHhhHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 777666655555689999999999999999999999988654
No 59
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=85.98 E-value=0.83 Score=35.57 Aligned_cols=41 Identities=20% Similarity=0.327 Sum_probs=33.5
Q ss_pred CChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 135 LPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 135 lp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
||+..| .|+.|.-.|....+||..|+||.+-|.+.+.|..+
T Consensus 113 L~~~~r-~il~l~~~g~s~~eIA~~lgis~~tV~~~i~ra~~ 153 (166)
T PRK09639 113 MTERDR-TVLLLRFSGYSYKEIAEALGIKESSVGTTLARAKK 153 (166)
T ss_pred CCHHHH-HHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 666554 56666669999999999999999999998887654
No 60
>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=85.74 E-value=0.88 Score=34.54 Aligned_cols=42 Identities=24% Similarity=0.328 Sum_probs=34.1
Q ss_pred CCChHHHHHHHHH-HhcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 134 PLPDVVRQRIVEL-AHNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 134 plp~~~r~~iv~l-~~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
-||+.. ++|+.| .-.|....+||..|+||.+-|.+.+.|-.+
T Consensus 113 ~L~~~~-r~il~l~~~~~~~~~eIA~~lgis~~tv~~~~~ra~~ 155 (161)
T TIGR02985 113 KLPEQC-RKIFILSRFEGKSYKEIAEELGISVKTVEYHISKALK 155 (161)
T ss_pred HCCHHH-HHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 356544 456666 789999999999999999999999988643
No 61
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=85.63 E-value=0.77 Score=41.50 Aligned_cols=41 Identities=22% Similarity=0.329 Sum_probs=35.4
Q ss_pred HHHHHHHHH-hcCCCcccchhhhhcccchHHHHHHHhhhhcC
Q psy10745 139 VRQRIVELA-HNGVRPCDISRQLRVSHGCVSKILSRESNLHN 179 (197)
Q Consensus 139 ~r~~iv~l~-~~g~r~~~isr~l~vshgcVskil~ry~~~~n 179 (197)
.-.++-.|+ ..|+.-.|||++|+||..-||++|.+..+++=
T Consensus 17 l~~~vA~lYY~~g~tQ~eIA~~lgiSR~~VsRlL~~Ar~~Gi 58 (318)
T PRK15418 17 LVARIAWFYYHDGLTQSEIGERLGLTRLKVSRLLEKGRQSGI 58 (318)
T ss_pred HHHHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHHcCc
Confidence 345666775 89999999999999999999999999988763
No 62
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=85.61 E-value=1 Score=36.02 Aligned_cols=43 Identities=14% Similarity=0.130 Sum_probs=35.5
Q ss_pred CCChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 134 PLPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 134 plp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
-||+..|.-+.-..-.|....+||..|++|-+-|.+.|.|-.+
T Consensus 137 ~L~~~~r~i~~l~~~~g~s~~eIA~~lgis~~~v~~~l~Rar~ 179 (187)
T PRK12534 137 ELEPPRSELIRTAFFEGITYEELAARTDTPIGTVKSWIRRGLA 179 (187)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHHhCCChhHHHHHHHHHHH
Confidence 4676666655555579999999999999999999999998754
No 63
>PHA02591 hypothetical protein; Provisional
Probab=85.58 E-value=0.68 Score=35.34 Aligned_cols=36 Identities=31% Similarity=0.242 Sum_probs=32.2
Q ss_pred hHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHH
Q psy10745 137 DVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILS 172 (197)
Q Consensus 137 ~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ 172 (197)
|..+.=-=+|++.|....+||+.|+||.--|||.|.
T Consensus 46 dd~~~vA~eL~eqGlSqeqIA~~LGVsqetVrKYL~ 81 (83)
T PHA02591 46 DDLISVTHELARKGFTVEKIASLLGVSVRKVRRYLE 81 (83)
T ss_pred chHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHh
Confidence 466777779999999999999999999999999875
No 64
>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=85.58 E-value=0.77 Score=36.79 Aligned_cols=42 Identities=14% Similarity=0.160 Sum_probs=36.0
Q ss_pred CChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 135 LPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 135 lp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
||+..++.|+.+.-.|.+-.+||..|++|.+.|..-|.|-.+
T Consensus 150 Ll~~~~~~i~~~~~~~~s~~eIA~~l~~s~~tV~~~l~r~r~ 191 (198)
T TIGR02859 150 LLSDLEWKVLQSYLDGKSYQEIACDLNRHVKSIDNALQRVKR 191 (198)
T ss_pred hcCHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 456677888888999999999999999999999988877543
No 65
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=85.50 E-value=1 Score=35.74 Aligned_cols=42 Identities=12% Similarity=0.070 Sum_probs=36.2
Q ss_pred CChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 135 LPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 135 lp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
||+..|.-|+-.+-.|....+||..|++|-+-|.+-|.|..+
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 787776666666689999999999999999999999988754
No 66
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=85.28 E-value=0.98 Score=34.88 Aligned_cols=42 Identities=21% Similarity=0.280 Sum_probs=34.1
Q ss_pred CCChHHHHHHHHH-HhcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 134 PLPDVVRQRIVEL-AHNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 134 plp~~~r~~iv~l-~~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
-||+..|+ |+.| +-.|..-.+||.+|++|-|.|.+.|.|-.+
T Consensus 106 ~Lp~~~r~-v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~ra~~ 148 (161)
T PRK09047 106 KLPARQRE-AFLLRYWEDMDVAETAAAMGCSEGSVKTHCSRATH 148 (161)
T ss_pred hCCHHHHH-HHHHHHHhcCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 46755554 5555 789999999999999999999998888654
No 67
>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=85.14 E-value=0.69 Score=37.64 Aligned_cols=41 Identities=22% Similarity=0.203 Sum_probs=36.7
Q ss_pred HHHHHHHHhCCCcchHHhHHHHHhcCCCCCCCCCCccccccccccc
Q psy10745 40 DAIASYKRENPTMFAWEIRDRLLAEGICSQDNVPSVSSINRYITYV 85 (197)
Q Consensus 40 ~~I~~~k~e~P~iFaWEIRdrLl~~GvC~~~~vPSvSSI~Rilr~~ 85 (197)
+.|.++-++++-..++||.++|.++|+.. |.++|||.|+..
T Consensus 5 ~~i~~Li~~~~i~tqeeL~~~L~~~G~~v-----sqaTIsRdL~el 45 (146)
T TIGR01529 5 ERIKEIITEEKISTQEELVALLKAEGIEV-----TQATVSRDLREL 45 (146)
T ss_pred HHHHHHHHcCCCCCHHHHHHHHHHhCCCc-----CHHHHHHHHHHc
Confidence 46778888999999999999999999988 999999999854
No 68
>PHA00738 putative HTH transcription regulator
Probab=85.05 E-value=0.65 Score=36.96 Aligned_cols=38 Identities=26% Similarity=0.336 Sum_probs=32.0
Q ss_pred CChHHHHHHHHHHhcC--CCcccchhhhhcccchHHHHHH
Q psy10745 135 LPDVVRQRIVELAHNG--VRPCDISRQLRVSHGCVSKILS 172 (197)
Q Consensus 135 lp~~~r~~iv~l~~~g--~r~~~isr~l~vshgcVskil~ 172 (197)
..+..|.+|+++-..| +-.||||..+.+|...||+=|.
T Consensus 9 ~~dptRr~IL~lL~~~e~~~V~eLae~l~lSQptVS~HLK 48 (108)
T PHA00738 9 RAKILRRKILELIAENYILSASLISHTLLLSYTTVLRHLK 48 (108)
T ss_pred cCCHHHHHHHHHHHHcCCccHHHHHHhhCCCHHHHHHHHH
Confidence 4578999999966664 7889999999999999999443
No 69
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=84.71 E-value=0.58 Score=31.92 Aligned_cols=42 Identities=26% Similarity=0.385 Sum_probs=35.0
Q ss_pred CChHHHHHHHHHH--hcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 135 LPDVVRQRIVELA--HNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 135 lp~~~r~~iv~l~--~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
|.+..|.+|+++. ..++...+||+.++++.+.||+=|..-.+
T Consensus 7 L~~p~R~~Il~~L~~~~~~t~~ela~~l~~~~~t~s~hL~~L~~ 50 (61)
T PF12840_consen 7 LSDPTRLRILRLLASNGPMTVSELAEELGISQSTVSYHLKKLEE 50 (61)
T ss_dssp HTSHHHHHHHHHHHHCSTBEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 5678999999987 78889999999999999999996665544
No 70
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=84.23 E-value=1.1 Score=34.92 Aligned_cols=42 Identities=29% Similarity=0.321 Sum_probs=33.8
Q ss_pred CCChHHHHHHHHH-HhcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 134 PLPDVVRQRIVEL-AHNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 134 plp~~~r~~iv~l-~~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
-||+..|. |+.| .-.|....+||..|++|.+.|.+.|.|-.+
T Consensus 109 ~L~~~~r~-v~~l~~~~~~s~~EIA~~lgis~~tV~~~l~ra~~ 151 (163)
T PRK07037 109 ELPARTRY-AFEMYRLHGETQKDIARELGVSPTLVNFMIRDALV 151 (163)
T ss_pred hCCHHHHH-HHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 46765555 6655 579999999999999999999998877543
No 71
>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=84.09 E-value=1.2 Score=34.57 Aligned_cols=42 Identities=19% Similarity=0.246 Sum_probs=34.5
Q ss_pred CCChHHHHHHHHH-HhcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 134 PLPDVVRQRIVEL-AHNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 134 plp~~~r~~iv~l-~~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
-||+.. +.|+.| .-.|.+..+||..|++|-+.|-+.|.|-.+
T Consensus 122 ~L~~~~-r~vl~l~~~~g~s~~eIA~~l~is~~tv~~~l~ra~~ 164 (170)
T TIGR02952 122 ILTPKQ-QHVIALRFGQNLPIAEVARILGKTEGAVKILQFRAIK 164 (170)
T ss_pred hCCHHH-HHHHHHHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 567554 456666 689999999999999999999999988654
No 72
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=83.98 E-value=1 Score=36.05 Aligned_cols=42 Identities=19% Similarity=0.212 Sum_probs=33.2
Q ss_pred CCChHHHHHHHHH-HhcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 134 PLPDVVRQRIVEL-AHNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 134 plp~~~r~~iv~l-~~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
-||...|. |+.| +-.|++..+||..|++|.+.|-+.|.|-..
T Consensus 129 ~L~~~~r~-v~~l~~~~g~s~~EIA~~l~is~~tV~~~l~rar~ 171 (181)
T PRK12536 129 QLPDRQRL-PIVHVKLEGLSVAETAQLTGLSESAVKVGIHRGLK 171 (181)
T ss_pred HCCHHHHH-HHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 35654444 5555 589999999999999999999999988643
No 73
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=83.56 E-value=1.4 Score=35.35 Aligned_cols=42 Identities=19% Similarity=0.264 Sum_probs=34.1
Q ss_pred CCChHHHHHHHHH-HhcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 134 PLPDVVRQRIVEL-AHNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 134 plp~~~r~~iv~l-~~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
-||+..| .|+.| .-.|..-.|||..|+||.|.|.+-|.|-.+
T Consensus 133 ~L~~~~r-~i~~l~~~~~~s~~eIA~~lgis~~tV~~~l~ra~~ 175 (182)
T PRK12537 133 QLEPARR-NCILHAYVDGCSHAEIAQRLGAPLGTVKAWIKRSLK 175 (182)
T ss_pred hCCHHHH-HHHHHHHHcCCCHHHHHHHHCCChhhHHHHHHHHHH
Confidence 3665555 56666 469999999999999999999999988654
No 74
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=83.47 E-value=1.3 Score=34.42 Aligned_cols=41 Identities=22% Similarity=0.359 Sum_probs=32.8
Q ss_pred CChHHHHHHHHHH-hcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 135 LPDVVRQRIVELA-HNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 135 lp~~~r~~iv~l~-~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
||+..|. |+.|+ -.|....+||..|++|.+.|++.|.|-.+
T Consensus 129 L~~~~r~-vl~l~~~~~~s~~eIA~~lgis~~tV~~~l~ra~~ 170 (182)
T PRK09652 129 LPEELRT-AITLREIEGLSYEEIAEIMGCPIGTVRSRIFRARE 170 (182)
T ss_pred CCHHHHH-HHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 6655555 66664 79999999999999999999998777543
No 75
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=83.45 E-value=1.1 Score=35.41 Aligned_cols=39 Identities=31% Similarity=0.372 Sum_probs=32.9
Q ss_pred CCChHHHHHHHHHHhc--CCCcccchhhhhcccchHHHHHH
Q psy10745 134 PLPDVVRQRIVELAHN--GVRPCDISRQLRVSHGCVSKILS 172 (197)
Q Consensus 134 plp~~~r~~iv~l~~~--g~r~~~isr~l~vshgcVskil~ 172 (197)
-|.+..|.+|+.+-.. .+..+||+.++++|...||+=|.
T Consensus 12 aLadptRl~IL~~L~~~~~~~v~ela~~l~lsqstvS~HL~ 52 (117)
T PRK10141 12 ILSDETRLGIVLLLRESGELCVCDLCTALDQSQPKISRHLA 52 (117)
T ss_pred HhCCHHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHH
Confidence 3788999999997743 46789999999999999999444
No 76
>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=83.33 E-value=0.33 Score=34.90 Aligned_cols=30 Identities=40% Similarity=0.620 Sum_probs=27.4
Q ss_pred ChHHHHHHHHHHhcCCCcccchhhhhcccc
Q psy10745 136 PDVVRQRIVELAHNGVRPCDISRQLRVSHG 165 (197)
Q Consensus 136 p~~~r~~iv~l~~~g~r~~~isr~l~vshg 165 (197)
++++-..|++||++|+.|++|--.|+=+||
T Consensus 30 ~~eVe~~I~klakkG~tpSqIG~iLRD~~G 59 (60)
T PF08069_consen 30 PEEVEELIVKLAKKGLTPSQIGVILRDQYG 59 (60)
T ss_dssp HHHHHHHHHHHCCTTHCHHHHHHHHHHSCT
T ss_pred HHHHHHHHHHHHHcCCCHHHhhhhhhhccC
Confidence 478899999999999999999999987776
No 77
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=83.22 E-value=0.5 Score=31.82 Aligned_cols=29 Identities=28% Similarity=0.489 Sum_probs=22.6
Q ss_pred HHHhcCCCcccchhhhhcccchHHHHHHH
Q psy10745 145 ELAHNGVRPCDISRQLRVSHGCVSKILSR 173 (197)
Q Consensus 145 ~l~~~g~r~~~isr~l~vshgcVskil~r 173 (197)
-|+++|+...++|+..+||..-||++++.
T Consensus 5 ~m~~~~it~~~La~~~gis~~tl~~~~~~ 33 (63)
T PF13443_consen 5 LMAERGITQKDLARKTGISRSTLSRILNG 33 (63)
T ss_dssp HHHHTT--HHHHHHHHT--HHHHHHHHTT
T ss_pred HHHHcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 36899999999999999999999999884
No 78
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=82.85 E-value=1.1 Score=37.78 Aligned_cols=42 Identities=24% Similarity=0.220 Sum_probs=34.7
Q ss_pred CChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 135 LPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 135 lp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
||+..|.=|+-.+-.|+.-.+||+.|+||.+-|++.+.|-.+
T Consensus 185 L~~~~r~vl~l~~~~g~s~~EIA~~lgis~~tV~~~~~ra~~ 226 (236)
T PRK06986 185 LPEREQLVLSLYYQEELNLKEIGAVLGVSESRVSQIHSQAIK 226 (236)
T ss_pred CCHHHHHHHHhHhccCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 676666555555689999999999999999999999887654
No 79
>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=82.82 E-value=1.2 Score=37.16 Aligned_cols=42 Identities=17% Similarity=0.124 Sum_probs=35.6
Q ss_pred CChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 135 LPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 135 lp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
||+..|+=|.-.+-.|+.-.+||..++||.+.|.+.+.|-.+
T Consensus 176 L~~~~r~il~l~y~~~~s~~eIA~~lgis~~tV~~~~~ra~~ 217 (224)
T TIGR02479 176 LSEREQLVLSLYYYEELNLKEIGEVLGLTESRVSQIHSQALK 217 (224)
T ss_pred CCHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 777777666666789999999999999999999999887643
No 80
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=82.75 E-value=1.6 Score=34.45 Aligned_cols=41 Identities=20% Similarity=0.214 Sum_probs=34.0
Q ss_pred CChHHHHHHHHH-HhcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 135 LPDVVRQRIVEL-AHNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 135 lp~~~r~~iv~l-~~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
||+..|. |+.| +-+|....+||..|++|.+.|.+.|.|-.+
T Consensus 119 L~~~~r~-vl~L~~~~g~s~~EIA~~lgis~~tV~~~l~ra~~ 160 (173)
T PRK09645 119 LSPEHRA-VLVRSYYRGWSTAQIAADLGIPEGTVKSRLHYALR 160 (173)
T ss_pred CCHHHHH-HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 7766665 6666 579999999999999999999988877643
No 81
>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=81.92 E-value=1.7 Score=33.49 Aligned_cols=42 Identities=29% Similarity=0.370 Sum_probs=34.0
Q ss_pred CCChHHHHHHHHH-HhcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 134 PLPDVVRQRIVEL-AHNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 134 plp~~~r~~iv~l-~~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
-||+.. ++|+.| .-.|.+..+||..|++|.+-|.+-|.|-.+
T Consensus 111 ~L~~~~-r~v~~l~~~~g~~~~eIA~~l~is~~tv~~~l~Rar~ 153 (159)
T TIGR02989 111 KLPERQ-RELLQLRYQRGVSLTALAEQLGRTVNAVYKALSRLRV 153 (159)
T ss_pred HCCHHH-HHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 466544 455566 889999999999999999999998888653
No 82
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=81.27 E-value=1.6 Score=33.90 Aligned_cols=42 Identities=29% Similarity=0.360 Sum_probs=33.6
Q ss_pred CCChHHHHHHHHH-HhcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 134 PLPDVVRQRIVEL-AHNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 134 plp~~~r~~iv~l-~~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
-||+..| .|+.| .-.|+...+||..|++|.+.|.+.|.|-.+
T Consensus 110 ~L~~~~r-~i~~l~~~~g~s~~eIA~~lgis~~tV~~~l~ra~~ 152 (162)
T TIGR02983 110 RLPARQR-AVVVLRYYEDLSEAQVAEALGISVGTVKSRLSRALA 152 (162)
T ss_pred hCCHHHH-HHhhhHHHhcCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 3565544 45555 579999999999999999999999888654
No 83
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=81.16 E-value=1.6 Score=35.33 Aligned_cols=40 Identities=23% Similarity=0.336 Sum_probs=32.8
Q ss_pred CChHHHHHHHHH-HhcCCCcccchhhhhcccchHHHHHHHhh
Q psy10745 135 LPDVVRQRIVEL-AHNGVRPCDISRQLRVSHGCVSKILSRES 175 (197)
Q Consensus 135 lp~~~r~~iv~l-~~~g~r~~~isr~l~vshgcVskil~ry~ 175 (197)
||+..| .|+.| +-.|+...+||..|++|-+.|.+.|.|..
T Consensus 137 L~~~~r-~i~~L~~~~g~s~~EIA~~lgis~~tVk~~l~Rar 177 (195)
T PRK12532 137 LPENTA-RVFTLKEILGFSSDEIQQMCGISTSNYHTIMHRAR 177 (195)
T ss_pred CCHHHH-HHhhhHHHhCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 665544 56666 68999999999999999999999887753
No 84
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=81.15 E-value=1.8 Score=35.07 Aligned_cols=41 Identities=17% Similarity=0.175 Sum_probs=35.1
Q ss_pred CCChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHhh
Q psy10745 134 PLPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRES 175 (197)
Q Consensus 134 plp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~ 175 (197)
+|..-++ +|+.|..+|..--+||+.|.+|...|+.-+.+-+
T Consensus 150 ~Lt~rE~-evl~~~~~G~s~~eIA~~l~iS~~TV~~h~~~i~ 190 (216)
T PRK10840 150 RLSPKES-EVLRLFAEGFLVTEIAKKLNRSIKTISSQKKSAM 190 (216)
T ss_pred cCCHHHH-HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 5776664 8999999999999999999999999998555543
No 85
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=80.56 E-value=1.9 Score=34.64 Aligned_cols=41 Identities=15% Similarity=0.264 Sum_probs=34.2
Q ss_pred CChHHHHHHHHH-HhcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 135 LPDVVRQRIVEL-AHNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 135 lp~~~r~~iv~l-~~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
||+. .++|+.| .-.|.+..+||..|++|.|.|.+-|.|-.+
T Consensus 123 L~~~-~r~i~~l~~~~g~s~~EIA~~lgis~~tVk~~l~Rar~ 164 (185)
T PRK12542 123 LNES-NRQVFKYKVFYNLTYQEISSVMGITEANVRKQFERARK 164 (185)
T ss_pred CCHH-HHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 6654 5667777 689999999999999999999998887654
No 86
>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=80.56 E-value=1.9 Score=34.10 Aligned_cols=41 Identities=22% Similarity=0.198 Sum_probs=34.3
Q ss_pred CChHHHHHHHHHH-hcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 135 LPDVVRQRIVELA-HNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 135 lp~~~r~~iv~l~-~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
||+..|. |+.|. -.|+.-.|||..|++|-|.|.+.|.|-.+
T Consensus 135 Lp~~~r~-v~~l~~~~g~s~~EIA~~lgis~~tVk~~l~Rar~ 176 (183)
T TIGR02999 135 VDPRQAE-VVELRFFAGLTVEEIAELLGVSVRTVERDWRFARA 176 (183)
T ss_pred CCHHHHH-HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 7766554 66665 69999999999999999999999988654
No 87
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=80.41 E-value=1.6 Score=35.13 Aligned_cols=41 Identities=22% Similarity=0.382 Sum_probs=33.5
Q ss_pred CChHHHHHHHHH-HhcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 135 LPDVVRQRIVEL-AHNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 135 lp~~~r~~iv~l-~~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
||+.. ++|+.| +-.|....+||.+|++|.+-|.+.+.|-..
T Consensus 139 L~~~~-r~v~~l~~~~g~s~~eIA~~lgis~~tv~~~l~Rar~ 180 (193)
T PRK11923 139 LPEDL-RTALTLREFDGLSYEDIASVMQCPVGTVRSRIFRARE 180 (193)
T ss_pred CCHHH-hHHHhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 56655 446666 799999999999999999999998877643
No 88
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=80.32 E-value=2 Score=34.53 Aligned_cols=43 Identities=9% Similarity=0.033 Sum_probs=34.1
Q ss_pred CCChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 134 PLPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 134 plp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
-||+..|.=|+--+-.|....+||+.|++|-+-|.+.|.|-.+
T Consensus 131 ~L~~~~r~vl~l~~~~~~s~~eIA~~lgis~~tV~~~l~Rar~ 173 (189)
T PRK12515 131 KLSPAHREIIDLVYYHEKSVEEVGEIVGIPESTVKTRMFYARK 173 (189)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4676655444444679999999999999999999999888653
No 89
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=80.18 E-value=1.5 Score=32.57 Aligned_cols=36 Identities=19% Similarity=0.265 Sum_probs=30.7
Q ss_pred HHHHHHHHHH--hcCCCcccchhhhhcccchHHHHHHH
Q psy10745 138 VVRQRIVELA--HNGVRPCDISRQLRVSHGCVSKILSR 173 (197)
Q Consensus 138 ~~r~~iv~l~--~~g~r~~~isr~l~vshgcVskil~r 173 (197)
+..+++..|+ .+|+.-.+||+.|+||.+.|++.+.+
T Consensus 18 ~~~r~af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 18 SLAEAAAALAREEAGKTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 4556677775 49999999999999999999999885
No 90
>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=80.17 E-value=2.1 Score=33.86 Aligned_cols=43 Identities=23% Similarity=0.341 Sum_probs=35.0
Q ss_pred CCChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 134 PLPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 134 plp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
-||+..|.=|+--+-.|..-.+||..|+||-+-|.+.|.|..+
T Consensus 140 ~L~~~~r~vi~l~~~~g~s~~eIA~~lgis~~~v~~~l~Ra~~ 182 (189)
T TIGR02984 140 KLPEDYREVILLRHLEGLSFAEVAERMDRSEGAVSMLWVRGLA 182 (189)
T ss_pred cCCHHHHHHHHHHHhcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 3777655555444789999999999999999999999988653
No 91
>PRK02277 orotate phosphoribosyltransferase-like protein; Provisional
Probab=80.10 E-value=1.8 Score=36.54 Aligned_cols=41 Identities=24% Similarity=0.439 Sum_probs=37.6
Q ss_pred hHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHhhhh
Q psy10745 137 DVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESNL 177 (197)
Q Consensus 137 ~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~~ 177 (197)
+++.+|-.||+.+|....+||..|.||.=|++-++.|-...
T Consensus 5 ~~l~~~a~~l~~~~~~~~~ia~el~vs~~t~~~l~~~~~~~ 45 (200)
T PRK02277 5 EELIEKAAELKNKGLSTGEIADELNVSRETATWLLTRAKKL 45 (200)
T ss_pred HHHHHHHHHHHHcCCChhhhhhhhcchHHHHHHHHhcccCC
Confidence 57788999999999999999999999999999999997743
No 92
>PRK09483 response regulator; Provisional
Probab=79.93 E-value=1.5 Score=34.36 Aligned_cols=42 Identities=24% Similarity=0.223 Sum_probs=34.2
Q ss_pred CChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHhhhh
Q psy10745 135 LPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESNL 177 (197)
Q Consensus 135 lp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~~ 177 (197)
|...++ +|++|...|..-.+||+.|.||...|.+.+.+-++-
T Consensus 149 Lt~rE~-~vl~~~~~G~~~~~Ia~~l~is~~TV~~~~~~i~~K 190 (217)
T PRK09483 149 LSEREL-QIMLMITKGQKVNEISEQLNLSPKTVNSYRYRMFSK 190 (217)
T ss_pred cCHHHH-HHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 665554 678999999999999999999999999866655443
No 93
>PRK10651 transcriptional regulator NarL; Provisional
Probab=79.89 E-value=2.4 Score=32.66 Aligned_cols=45 Identities=18% Similarity=0.206 Sum_probs=37.5
Q ss_pred CCChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHhhhhcC
Q psy10745 134 PLPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESNLHN 179 (197)
Q Consensus 134 plp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~~~n 179 (197)
+|+..+ .+|++|..+|..-.+||+.|.+|-..|++-+.+-++--|
T Consensus 155 ~Lt~rE-~~vl~~l~~g~~~~~ia~~l~is~~tV~~~~~~l~~Kl~ 199 (216)
T PRK10651 155 QLTPRE-RDILKLIAQGLPNKMIARRLDITESTVKVHVKHMLKKMK 199 (216)
T ss_pred cCCHHH-HHHHHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHHHHcC
Confidence 376655 599999999999999999999999999997777655444
No 94
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=79.69 E-value=1.8 Score=34.18 Aligned_cols=41 Identities=22% Similarity=0.294 Sum_probs=33.4
Q ss_pred CChHHHHHHHHH-HhcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 135 LPDVVRQRIVEL-AHNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 135 lp~~~r~~iv~l-~~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
||+.. +.|+.| +-.|....+||..|++|.+-|.+.|.|-.+
T Consensus 137 L~~~~-r~v~~l~~~~g~s~~eIA~~lgis~~~v~~~l~Rar~ 178 (187)
T TIGR02948 137 LPPKY-RMVIVLKYMEDLSLKEISEILDLPVGTVKTRIHRGRE 178 (187)
T ss_pred CCHHH-hHHhhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 55443 456666 789999999999999999999999988653
No 95
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=79.54 E-value=2.1 Score=34.76 Aligned_cols=42 Identities=19% Similarity=0.283 Sum_probs=33.7
Q ss_pred CCChHHHHHHHHH-HhcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 134 PLPDVVRQRIVEL-AHNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 134 plp~~~r~~iv~l-~~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
-||+. .+.|+.| .-.|++..+||..|++|.+-|-+.|.|-.+
T Consensus 106 ~L~~~-~r~i~~l~~~~g~~~~EIA~~lgis~~tV~~~l~Rar~ 148 (181)
T PRK09637 106 ALPEK-YAEALRLTELEGLSQKEIAEKLGLSLSGAKSRVQRGRV 148 (181)
T ss_pred hCCHH-HHHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 46654 4556666 479999999999999999999998887643
No 96
>COG2826 Tra8 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]
Probab=79.37 E-value=1.7 Score=40.32 Aligned_cols=41 Identities=27% Similarity=0.310 Sum_probs=38.0
Q ss_pred CCChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHh
Q psy10745 134 PLPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRE 174 (197)
Q Consensus 134 plp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry 174 (197)
-|...+|..|=.|...|+..-+||++|+..|+.||.=|.|=
T Consensus 7 hLT~~eR~~I~~l~~~~~S~reIA~~LgRh~sTIsRElkRn 47 (318)
T COG2826 7 HLTLFERYEIERLLKAKMSIREIAKQLNRHHSTISRELKRN 47 (318)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHHhCCCcchhhHHHhcC
Confidence 47889999999999999999999999999999999988763
No 97
>PRK06474 hypothetical protein; Provisional
Probab=79.23 E-value=2 Score=35.79 Aligned_cols=45 Identities=20% Similarity=0.289 Sum_probs=36.6
Q ss_pred CCChHHHHHHHHHH-hcC--CCcccchhhh-hcccchHHHHHHHhhhhc
Q psy10745 134 PLPDVVRQRIVELA-HNG--VRPCDISRQL-RVSHGCVSKILSRESNLH 178 (197)
Q Consensus 134 plp~~~r~~iv~l~-~~g--~r~~~isr~l-~vshgcVskil~ry~~~~ 178 (197)
-|....|.+|+++. ..+ +..++|+..+ .||..+|+..|....+.+
T Consensus 7 ~La~p~R~~Il~~L~~~~~~~ta~el~~~l~~is~aTvYrhL~~L~e~G 55 (178)
T PRK06474 7 ILMHPVRMKICQVLMRNKEGLTPLELVKILKDVPQATLYRHLQTMVDSG 55 (178)
T ss_pred hhCCHHHHHHHHHHHhCCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHCC
Confidence 36778999999865 433 7899999999 799999999888776554
No 98
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=79.16 E-value=2 Score=36.05 Aligned_cols=41 Identities=22% Similarity=0.345 Sum_probs=33.6
Q ss_pred CChHHHHHHHHHHh-----cCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 135 LPDVVRQRIVELAH-----NGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 135 lp~~~r~~iv~l~~-----~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
||+. .+.|+.|.. +|....+||.+|+||-|.|++.+.|-.+
T Consensus 179 Lp~~-~R~v~~L~y~l~~~eg~s~~EIA~~lgis~~tVk~~~~rA~~ 224 (234)
T PRK08301 179 LSDR-EKQIMELRFGLNGGEEKTQKEVADMLGISQSYISRLEKRIIK 224 (234)
T ss_pred CCHH-HHHHHHHHhccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 5544 567777764 8999999999999999999998887643
No 99
>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=79.07 E-value=1 Score=36.34 Aligned_cols=58 Identities=26% Similarity=0.270 Sum_probs=39.8
Q ss_pred CCChHHHHHHHHH-HhcCCCcccchhhhhcccchHHHHHHHhhhhcCccc--cccccccccc
Q psy10745 134 PLPDVVRQRIVEL-AHNGVRPCDISRQLRVSHGCVSKILSRESNLHNYRL--VREEGCFELS 192 (197)
Q Consensus 134 plp~~~r~~iv~l-~~~g~r~~~isr~l~vshgcVskil~ry~~~~n~~~--~~~~~~~~~~ 192 (197)
-||+..| .|+.| .-.|+...+||..|++|.+.|.+.|.|-.+.--=.+ ..+..+|+|+
T Consensus 131 ~Lp~~~r-~i~~L~~~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~~~~~~~~~~~ 191 (193)
T TIGR02947 131 GLPEEFR-QAVYLADVEGFAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQLVDVAGERGFGPR 191 (193)
T ss_pred hCCHHHh-hheeehhhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHhccccccc
Confidence 3565544 45555 579999999999999999999998888755321111 1234566665
No 100
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=79.03 E-value=1.9 Score=36.75 Aligned_cols=41 Identities=17% Similarity=0.243 Sum_probs=33.6
Q ss_pred CChHHHHHHHHH-HhcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 135 LPDVVRQRIVEL-AHNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 135 lp~~~r~~iv~l-~~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
||+..|+ |+.| +-.|..-.+||..|+||.+.|++++.|..+
T Consensus 206 L~~~~r~-vl~l~~~~g~s~~eIA~~l~is~~tV~~~~~ra~~ 247 (257)
T PRK08583 206 LSDREKS-IIQCTFIENLSQKETGERLGISQMHVSRLQRQAIK 247 (257)
T ss_pred CCHHHHH-HHHHHHhCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 6655554 5556 579999999999999999999999887643
No 101
>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=79.03 E-value=2 Score=35.77 Aligned_cols=43 Identities=23% Similarity=0.338 Sum_probs=35.6
Q ss_pred CCChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 134 PLPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 134 plp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
-||+..|+=|+-.+-.|....+||+.|+||.+.|++++.|-.+
T Consensus 178 ~L~~~~r~vl~l~y~~~~s~~eIA~~lgis~~~v~~~~~ra~~ 220 (227)
T TIGR02980 178 ALPERERRILLLRFFEDKTQSEIAERLGISQMHVSRLLRRALK 220 (227)
T ss_pred cCCHHHHHHHHHHHhcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4777776655555679999999999999999999999988643
No 102
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=78.88 E-value=1.7 Score=34.91 Aligned_cols=43 Identities=26% Similarity=0.296 Sum_probs=38.7
Q ss_pred CCChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 134 PLPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 134 plp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
.||+..|.-|+--.-.|....|||..|+||-|.|-+-|.|-..
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 4888999888888899999999999999999999998888654
No 103
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=78.61 E-value=2.2 Score=34.18 Aligned_cols=41 Identities=20% Similarity=0.360 Sum_probs=33.4
Q ss_pred CChHHHHHHHHH-HhcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 135 LPDVVRQRIVEL-AHNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 135 lp~~~r~~iv~l-~~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
||+..| .|+.| .-.|....+||..|++|-+.|.+.|.|-..
T Consensus 129 L~~~~r-~i~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Rar~ 170 (186)
T PRK05602 129 LPERQR-EAIVLQYYQGLSNIEAAAVMDISVDALESLLARGRR 170 (186)
T ss_pred CCHHHH-HHhhHHHhcCCCHHHHHHHhCcCHHHHHHHHHHHHH
Confidence 465444 45555 679999999999999999999999988754
No 104
>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=78.26 E-value=2.2 Score=36.33 Aligned_cols=42 Identities=14% Similarity=0.235 Sum_probs=34.2
Q ss_pred CCChHHHHHHHHHH-hcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 134 PLPDVVRQRIVELA-HNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 134 plp~~~r~~iv~l~-~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
-||+..|. |+.|. -.|..-.+||..|+||.+.|++++.|..+
T Consensus 205 ~L~~~~r~-ii~l~~~~g~s~~eIA~~lgis~~~V~~~~~ra~~ 247 (255)
T TIGR02941 205 ILSEREKS-IIHCTFEENLSQKETGERLGISQMHVSRLQRQAIS 247 (255)
T ss_pred cCCHHHHH-HHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 47766665 55554 79999999999999999999999887643
No 105
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=78.24 E-value=2.5 Score=33.28 Aligned_cols=42 Identities=21% Similarity=0.204 Sum_probs=33.8
Q ss_pred CCChHHHHHHHHH-HhcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 134 PLPDVVRQRIVEL-AHNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 134 plp~~~r~~iv~l-~~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
-||+..| .|+.| +-.|..-.+||+.|++|-|.|-+-|.|-..
T Consensus 112 ~L~~~~r-~v~~l~~~~g~s~~eIA~~lgis~~tV~~~l~Rar~ 154 (164)
T PRK12547 112 LLSADQR-EAIILIGASGFSYEDAAAICGCAVGTIKSRVSRARN 154 (164)
T ss_pred hCCHHHH-HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 3554444 55556 689999999999999999999999988754
No 106
>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=77.63 E-value=2.4 Score=29.49 Aligned_cols=28 Identities=25% Similarity=0.369 Sum_probs=25.8
Q ss_pred HHhcCCCcccchhhhhcccchHHHHHHH
Q psy10745 146 LAHNGVRPCDISRQLRVSHGCVSKILSR 173 (197)
Q Consensus 146 l~~~g~r~~~isr~l~vshgcVskil~r 173 (197)
|.+.|+...++|+.++||..-||++++-
T Consensus 14 ~~~~~~t~~~lA~~~gis~~tis~~~~g 41 (78)
T TIGR02607 14 LEPLGLSIRALAKALGVSRSTLSRIVNG 41 (78)
T ss_pred HHHcCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 6789999999999999999999998863
No 107
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=77.24 E-value=2.5 Score=33.92 Aligned_cols=40 Identities=20% Similarity=0.319 Sum_probs=33.0
Q ss_pred CChHHHHHHHHH-HhcCCCcccchhhhhcccchHHHHHHHhh
Q psy10745 135 LPDVVRQRIVEL-AHNGVRPCDISRQLRVSHGCVSKILSRES 175 (197)
Q Consensus 135 lp~~~r~~iv~l-~~~g~r~~~isr~l~vshgcVskil~ry~ 175 (197)
||+.. +.|+.| .-.|..-.|||.+|++|-|.|.+-|.|-.
T Consensus 128 Lp~~~-R~v~~L~~~~g~s~~EIA~~lgis~~tVk~~l~rAl 168 (178)
T PRK12529 128 LRPRV-KQAFLMATLDGMKQKDIAQALDIALPTVKKYIHQAY 168 (178)
T ss_pred CCHHH-HHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 66555 456666 68999999999999999999999887753
No 108
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=77.09 E-value=2.7 Score=34.19 Aligned_cols=42 Identities=19% Similarity=0.229 Sum_probs=33.9
Q ss_pred CChHHHHHHHHH-HhcCCCcccchhhhhcccchHHHHHHHhhhh
Q psy10745 135 LPDVVRQRIVEL-AHNGVRPCDISRQLRVSHGCVSKILSRESNL 177 (197)
Q Consensus 135 lp~~~r~~iv~l-~~~g~r~~~isr~l~vshgcVskil~ry~~~ 177 (197)
||+..| .|+.| +-.|....+||..|++|.+.|-+.|.|..+.
T Consensus 112 Lp~~~R-~v~~L~~~~g~s~~EIA~~Lgis~~tV~~~l~RAr~~ 154 (182)
T PRK12540 112 LPQDQR-EALILVGASGFSYEDAAAICGCAVGTIKSRVNRARSK 154 (182)
T ss_pred CCHHHH-HHhhHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 454444 45555 6899999999999999999999998887653
No 109
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=77.06 E-value=2.9 Score=33.81 Aligned_cols=43 Identities=19% Similarity=0.242 Sum_probs=35.4
Q ss_pred CCChHHHHHHHHH-HhcCCCcccchhhhhcccchHHHHHHHhhhh
Q psy10745 134 PLPDVVRQRIVEL-AHNGVRPCDISRQLRVSHGCVSKILSRESNL 177 (197)
Q Consensus 134 plp~~~r~~iv~l-~~~g~r~~~isr~l~vshgcVskil~ry~~~ 177 (197)
-||+. .++|+.| +-.|....+||.+|++|.+-|...|.|-.+.
T Consensus 131 ~L~~~-~r~i~~l~~~~g~s~~EIAe~lgis~~~V~~~l~Ra~~~ 174 (189)
T PRK06811 131 DLEKL-DREIFIRRYLLGEKIEEIAKKLGLTRSAIDNRLSRGRKK 174 (189)
T ss_pred hCCHH-HHHHHHHHHHccCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 56654 5567777 5799999999999999999999999887653
No 110
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=76.97 E-value=2.4 Score=36.72 Aligned_cols=43 Identities=23% Similarity=0.168 Sum_probs=34.4
Q ss_pred CCChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 134 PLPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 134 plp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
-||+..|+=|.-.+-.|..-.+||..|+||.+.|++++.|..+
T Consensus 205 ~L~~~er~vi~l~y~e~~t~~EIA~~lgis~~~V~~~~~ral~ 247 (257)
T PRK05911 205 ALEEKERKVMALYYYEELVLKEIGKILGVSESRVSQIHSKALL 247 (257)
T ss_pred cCCHHHHHHHHHHHhcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4777766544444579999999999999999999999887643
No 111
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=76.94 E-value=2.8 Score=34.88 Aligned_cols=43 Identities=26% Similarity=0.326 Sum_probs=34.4
Q ss_pred CCChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 134 PLPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 134 plp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
-||+..|.-|+-..-.|....+||..|++|.+-|.+-|.|-.+
T Consensus 138 ~L~~~~r~v~~L~~~~g~s~~EIA~~Lgis~~tV~~~l~RArk 180 (203)
T PRK09647 138 SLPPEFRAAVVLCDIEGLSYEEIAATLGVKLGTVRSRIHRGRQ 180 (203)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4676555555555689999999999999999999998887643
No 112
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=76.77 E-value=2.9 Score=34.01 Aligned_cols=41 Identities=20% Similarity=0.370 Sum_probs=33.2
Q ss_pred CCChHHHHHHHHH-HhcCCCcccchhhhhcccchHHHHHHHhh
Q psy10745 134 PLPDVVRQRIVEL-AHNGVRPCDISRQLRVSHGCVSKILSRES 175 (197)
Q Consensus 134 plp~~~r~~iv~l-~~~g~r~~~isr~l~vshgcVskil~ry~ 175 (197)
-||+. -++|+.| +-+|....+||++|+||-+.|.+.|.|..
T Consensus 136 ~L~~~-~r~i~~L~~~~g~s~~eIA~~lgis~~tV~~~l~Ra~ 177 (196)
T PRK12524 136 ALPER-QRQAVVLRHIEGLSNPEIAEVMEIGVEAVESLTARGK 177 (196)
T ss_pred hCCHH-HHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 35543 4456777 57999999999999999999999888854
No 113
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=75.94 E-value=2.5 Score=36.17 Aligned_cols=41 Identities=24% Similarity=0.378 Sum_probs=33.1
Q ss_pred CChHHHHHHHHH-HhcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 135 LPDVVRQRIVEL-AHNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 135 lp~~~r~~iv~l-~~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
||+..|. |+.| +-.|+...+||..|++|-|.|.+.|.|-.+
T Consensus 172 Lp~~~R~-v~~L~~~eg~s~~EIA~~Lgis~~tVk~~l~RAr~ 213 (233)
T PRK12538 172 LPEQQRI-AVILSYHENMSNGEIAEVMDTTVAAVESLLKRGRQ 213 (233)
T ss_pred CCHHHHH-HhhhHHhcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4655554 6666 479999999999999999999998887654
No 114
>TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR. Similarly, tetanus toxin production of Clostridium tetani is regulated by TetR which is a very close relative of BotR. Both BotR and TetR are members of the TIGR02937 subfamily of sigma-70 RNA polymerase sigma factors. Functional complementation experiments have been done for botR and tetR in highly transformable strain of Clostridium perfringens host cells to assess functional interchangeability of sigma factors and it has been confirmed that they are interchangeable in vivo.
Probab=75.79 E-value=1.6 Score=33.39 Aligned_cols=34 Identities=26% Similarity=0.536 Sum_probs=27.9
Q ss_pred CChHHHHHHHHH-HhcCCCcccchhhhhcccchHHH
Q psy10745 135 LPDVVRQRIVEL-AHNGVRPCDISRQLRVSHGCVSK 169 (197)
Q Consensus 135 lp~~~r~~iv~l-~~~g~r~~~isr~l~vshgcVsk 169 (197)
||+ ..+.|+.| .-+|.+-.|||..|++|-|.|.|
T Consensus 108 Lp~-~~r~v~~l~~~~~~s~~EIA~~l~is~~tV~~ 142 (142)
T TIGR03209 108 LPN-KQKKIIYMKFFEDMKEIDIAKKLHISRQSVYK 142 (142)
T ss_pred CCH-HHHHHHHHHHHcCCCHHHHHHHHCcCHHhhcC
Confidence 564 45566677 47999999999999999999875
No 115
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=75.70 E-value=2.7 Score=33.72 Aligned_cols=41 Identities=15% Similarity=0.264 Sum_probs=32.9
Q ss_pred CChHHHHHHHHH-HhcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 135 LPDVVRQRIVEL-AHNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 135 lp~~~r~~iv~l-~~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
||+.. +.|+.| +-.|....+||..|++|.+.|..-|.|-.+
T Consensus 132 L~~~~-r~v~~l~~~~g~s~~eIA~~lgis~~tV~~~l~ra~~ 173 (184)
T PRK12539 132 LPEKM-RLAIQAVKLEGLSVAEAATRSGMSESAVKVSVHRGLK 173 (184)
T ss_pred CCHHH-HHHHHHHHHcCCcHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 55444 456666 579999999999999999999998887644
No 116
>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=75.56 E-value=3.7 Score=27.37 Aligned_cols=28 Identities=18% Similarity=0.190 Sum_probs=24.9
Q ss_pred CCCcccchhhhhcccchHHHHHHHhhhh
Q psy10745 150 GVRPCDISRQLRVSHGCVSKILSRESNL 177 (197)
Q Consensus 150 g~r~~~isr~l~vshgcVskil~ry~~~ 177 (197)
.+...|||..+++|..-|+++|++..+.
T Consensus 25 ~~s~~ela~~~g~s~~tv~r~l~~L~~~ 52 (67)
T cd00092 25 PLTRQEIADYLGLTRETVSRTLKELEEE 52 (67)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 3677789999999999999999999775
No 117
>PHA00675 hypothetical protein
Probab=75.37 E-value=2.5 Score=31.98 Aligned_cols=42 Identities=29% Similarity=0.386 Sum_probs=38.0
Q ss_pred CCCChHHHHHHHHHH-hcCCCcccchhhhhcccchHHHHHHHh
Q psy10745 133 RPLPDVVRQRIVELA-HNGVRPCDISRQLRVSHGCVSKILSRE 174 (197)
Q Consensus 133 rplp~~~r~~iv~l~-~~g~r~~~isr~l~vshgcVskil~ry 174 (197)
--|-+..=+.|-.|. ..|..--+||++++||.+.|++|.++.
T Consensus 21 AKLt~~qV~~IR~l~~r~G~s~~~IA~~fGVsrstV~~I~~gk 63 (78)
T PHA00675 21 AKLTDAEVERIRELHEVEGMSYAVLAEKFEQSKGAIAKICRYE 63 (78)
T ss_pred cccCHHHHHHHHHHHHhcCccHHHHHHHhCCCHHHHHHHHccc
Confidence 368888889999999 899999999999999999999998754
No 118
>TIGR02885 spore_sigF RNA polymerase sigma-F factor. Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore.
Probab=75.37 E-value=2.9 Score=34.96 Aligned_cols=43 Identities=19% Similarity=0.165 Sum_probs=33.4
Q ss_pred CCChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 134 PLPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 134 plp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
-||+..|.=+.-.+..|....+||..|+||.+.|+++..|..+
T Consensus 183 ~L~~~e~~i~~~~~~~~~t~~eIA~~lgis~~~V~~~~~~al~ 225 (231)
T TIGR02885 183 KLDERERQIIMLRYFKDKTQTEVANMLGISQVQVSRLEKKVLK 225 (231)
T ss_pred cCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4665555444444568999999999999999999999887643
No 119
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=75.13 E-value=2.4 Score=37.35 Aligned_cols=41 Identities=15% Similarity=0.150 Sum_probs=33.6
Q ss_pred CCChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHhh
Q psy10745 134 PLPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRES 175 (197)
Q Consensus 134 plp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~ 175 (197)
+|.+. -.+|++|..+|..--+||++|.+|.+.|.+-+.+-+
T Consensus 143 ~LS~R-E~eVL~Lia~G~SnkEIA~~L~IS~~TVk~hvs~I~ 183 (217)
T PRK13719 143 KVTKY-QNDVFILYSFGFSHEYIAQLLNITVGSSKNKISEIL 183 (217)
T ss_pred CCCHH-HHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 45533 357999999999999999999999999998555543
No 120
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=75.06 E-value=3.6 Score=32.00 Aligned_cols=41 Identities=24% Similarity=0.323 Sum_probs=33.9
Q ss_pred CChHHHHHHHHHH-hcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 135 LPDVVRQRIVELA-HNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 135 lp~~~r~~iv~l~-~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
||+..| +|+.|. -.|+.-.|||..|++|-+.|.+-|.|-.+
T Consensus 106 L~~~~r-~v~~l~~~~~~s~~eIA~~lgis~~tv~~~l~ra~~ 147 (159)
T PRK12527 106 LPPACR-DSFLLRKLEGLSHQQIAEHLGISRSLVEKHIVNAMK 147 (159)
T ss_pred CCHHHH-HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 776644 566665 69999999999999999999998887654
No 121
>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=75.04 E-value=3.1 Score=32.72 Aligned_cols=42 Identities=19% Similarity=0.238 Sum_probs=34.4
Q ss_pred CCChHHHHHHHHHH-hcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 134 PLPDVVRQRIVELA-HNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 134 plp~~~r~~iv~l~-~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
-||+..| +|+.|. -.|.+.-+||+.|+||-+-|.+.|.|-.+
T Consensus 119 ~L~~~~r-~i~~l~~~~g~s~~eiA~~lgis~~tv~~~l~Ra~~ 161 (169)
T TIGR02954 119 TLNDKYQ-TAIILRYYHDLTIKEIAEVMNKPEGTVKTYLHRALK 161 (169)
T ss_pred hCCHHHh-HHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3666655 666664 79999999999999999999999888654
No 122
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=74.99 E-value=2.5 Score=35.30 Aligned_cols=41 Identities=17% Similarity=0.169 Sum_probs=34.2
Q ss_pred CCChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHhh
Q psy10745 134 PLPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRES 175 (197)
Q Consensus 134 plp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~ 175 (197)
.|.+-++ +|+.|..+|..--+||++|+||...|++-+++-+
T Consensus 137 ~LT~RE~-eVL~lla~G~snkeIA~~L~iS~~TVk~h~~~I~ 177 (207)
T PRK15411 137 SLSRTES-SMLRMWMAGQGTIQISDQMNIKAKTVSSHKGNIK 177 (207)
T ss_pred cCCHHHH-HHHHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHH
Confidence 3665554 7999999999999999999999999999555543
No 123
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=74.85 E-value=3.2 Score=32.60 Aligned_cols=42 Identities=14% Similarity=0.125 Sum_probs=33.9
Q ss_pred CCChHHHHHHHHH-HhcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 134 PLPDVVRQRIVEL-AHNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 134 plp~~~r~~iv~l-~~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
-||+..| +|+.| +-+|....+||..|++|-+.|.+.|.|..+
T Consensus 108 ~L~~~~r-~v~~l~~~~g~s~~eIA~~lgis~~tv~~~l~Rar~ 150 (165)
T PRK09644 108 TLPVIEA-QAILLCDVHELTYEEAASVLDLKLNTYKSHLFRGRK 150 (165)
T ss_pred hCCHHHH-HHHHhHHHhcCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4565444 45555 589999999999999999999998888754
No 124
>PHA02943 hypothetical protein; Provisional
Probab=74.72 E-value=2 Score=36.55 Aligned_cols=35 Identities=23% Similarity=0.342 Sum_probs=29.4
Q ss_pred HHHHHHHHhcCCC-cccchhhhhcccchHHHHHHHh
Q psy10745 140 RQRIVELAHNGVR-PCDISRQLRVSHGCVSKILSRE 174 (197)
Q Consensus 140 r~~iv~l~~~g~r-~~~isr~l~vshgcVskil~ry 174 (197)
-.+|+|+-+.|.+ ..+||+.|++|||=|.-+|-=-
T Consensus 13 ~~eILE~Lk~G~~TtseIAkaLGlS~~qa~~~LyvL 48 (165)
T PHA02943 13 MIKTLRLLADGCKTTSRIANKLGVSHSMARNALYQL 48 (165)
T ss_pred HHHHHHHHhcCCccHHHHHHHHCCCHHHHHHHHHHH
Confidence 3578999999988 7799999999999999866433
No 125
>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=74.59 E-value=2.9 Score=36.43 Aligned_cols=43 Identities=26% Similarity=0.291 Sum_probs=34.9
Q ss_pred CCChHHHHHHHHH-HhcCCCcccchhhhhcccchHHHHHHHhhhh
Q psy10745 134 PLPDVVRQRIVEL-AHNGVRPCDISRQLRVSHGCVSKILSRESNL 177 (197)
Q Consensus 134 plp~~~r~~iv~l-~~~g~r~~~isr~l~vshgcVskil~ry~~~ 177 (197)
-||+..|. |+.| +-.|..-.+||..|++|-+.|.+.|.|-.+.
T Consensus 142 ~Lp~~~R~-v~~L~~~~g~s~~EIA~~lgis~~tV~~~l~Rar~~ 185 (324)
T TIGR02960 142 YLPPRQRA-VLLLRDVLGWRAAETAELLGTSTASVNSALQRARAT 185 (324)
T ss_pred hCCHHHhh-HhhhHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 46665555 5666 5799999999999999999999999887653
No 126
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=74.30 E-value=1.6 Score=34.30 Aligned_cols=41 Identities=22% Similarity=0.223 Sum_probs=33.2
Q ss_pred CChHHHHHHHHH-HhcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 135 LPDVVRQRIVEL-AHNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 135 lp~~~r~~iv~l-~~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
||+..| .|+.| +-.|..+.+||..|++|.+-|.+.|.|..+
T Consensus 127 L~~~~r-~v~~l~~~~g~s~~eIA~~l~is~~~V~~~l~ra~~ 168 (176)
T PRK09638 127 LDPEFR-APVILKHYYGYTYEEIAKMLNIPEGTVKSRVHHGIK 168 (176)
T ss_pred CCHHHh-heeeehhhcCCCHHHHHHHHCCChhHHHHHHHHHHH
Confidence 665444 45555 689999999999999999999998888654
No 127
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=74.21 E-value=3.6 Score=33.44 Aligned_cols=41 Identities=17% Similarity=0.233 Sum_probs=33.2
Q ss_pred CChHHHHHHHHHH-hcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 135 LPDVVRQRIVELA-HNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 135 lp~~~r~~iv~l~-~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
||+. .+.|+.|. -.|.+-.+||..|++|-|.|.+-|.|..+
T Consensus 135 Lp~~-~R~v~~L~~~~g~s~~EIA~~lgis~~tVk~~l~RAr~ 176 (189)
T PRK12530 135 LPAQ-QARVFMMREYLELSSEQICQECDISTSNLHVLLYRARL 176 (189)
T ss_pred CCHH-HHHHHhHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 5654 45566665 68999999999999999999998888654
No 128
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=74.14 E-value=3.7 Score=33.53 Aligned_cols=41 Identities=17% Similarity=0.278 Sum_probs=33.1
Q ss_pred CChHHHHHHHHH-HhcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 135 LPDVVRQRIVEL-AHNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 135 lp~~~r~~iv~l-~~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
||+. .+.|+.| .-.|+.-.+||.+|++|-+.|-+-|.|-.+
T Consensus 117 Lp~~-~r~i~~L~~~~g~s~~EIA~~Lgis~~tVk~~l~Rar~ 158 (187)
T PRK12516 117 LPDD-QREAIILVGASGFAYEEAAEICGCAVGTIKSRVNRARQ 158 (187)
T ss_pred CCHH-HHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 5654 4556666 579999999999999999999998877654
No 129
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=74.09 E-value=3 Score=35.17 Aligned_cols=34 Identities=24% Similarity=0.394 Sum_probs=28.8
Q ss_pred HHH-HHHHHHhcCCCcccchhhhhcccchHHHHHH
Q psy10745 139 VRQ-RIVELAHNGVRPCDISRQLRVSHGCVSKILS 172 (197)
Q Consensus 139 ~r~-~iv~l~~~g~r~~~isr~l~vshgcVskil~ 172 (197)
.|+ .|+.|..+|..--+||++|.+|.+.|+.=..
T Consensus 151 ~RE~eVL~lla~G~snkeIA~~L~iS~~TVk~h~~ 185 (211)
T COG2197 151 PRELEVLRLLAEGLSNKEIAEELNLSEKTVKTHVS 185 (211)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCHhHHHHHHH
Confidence 444 4669999999999999999999999988433
No 130
>PRK08561 rps15p 30S ribosomal protein S15P; Reviewed
Probab=73.96 E-value=2.1 Score=35.89 Aligned_cols=30 Identities=37% Similarity=0.553 Sum_probs=27.6
Q ss_pred ChHHHHHHHHHHhcCCCcccchhhhhcccc
Q psy10745 136 PDVVRQRIVELAHNGVRPCDISRQLRVSHG 165 (197)
Q Consensus 136 p~~~r~~iv~l~~~g~r~~~isr~l~vshg 165 (197)
++++-..|++||++|+.|+.|-=.|+=+||
T Consensus 30 ~eeve~~I~~lakkG~~pSqIG~~LRD~~g 59 (151)
T PRK08561 30 PEEIEELVVELAKQGYSPSMIGIILRDQYG 59 (151)
T ss_pred HHHHHHHHHHHHHCCCCHHHhhhhHhhccC
Confidence 578899999999999999999999998885
No 131
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=73.84 E-value=3.8 Score=32.41 Aligned_cols=42 Identities=17% Similarity=0.154 Sum_probs=34.7
Q ss_pred CCChHHHHHHHHHH-hcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 134 PLPDVVRQRIVELA-HNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 134 plp~~~r~~iv~l~-~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
-||+..| +|+.|. -.|....+||..|++|-+-|-+-|.|-.+
T Consensus 119 ~L~~~~r-~i~~l~~~~~~s~~EIA~~lgis~~tV~~~l~Ra~~ 161 (173)
T PRK12522 119 LLNEKYK-TVLVLYYYEQYSYKEMSEILNIPIGTVKYRLNYAKK 161 (173)
T ss_pred hCCHHHH-HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 4776666 566665 69999999999999999999998887654
No 132
>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=73.80 E-value=1.3 Score=30.62 Aligned_cols=43 Identities=28% Similarity=0.269 Sum_probs=34.0
Q ss_pred CCcccchhhhhcccchHHHHHHHhhhhcCcccccccccccccCCc
Q psy10745 151 VRPCDISRQLRVSHGCVSKILSRESNLHNYRLVREEGCFELSDLE 195 (197)
Q Consensus 151 ~r~~~isr~l~vshgcVskil~ry~~~~n~~~~~~~~~~~~~~~~ 195 (197)
+...+||..+++|.--||++|.++.+.+=.. .+.+++.+.|.+
T Consensus 29 lt~~~iA~~~g~sr~tv~r~l~~l~~~g~I~--~~~~~i~I~d~~ 71 (76)
T PF13545_consen 29 LTQEEIADMLGVSRETVSRILKRLKDEGIIE--VKRGKIIILDPE 71 (76)
T ss_dssp SSHHHHHHHHTSCHHHHHHHHHHHHHTTSEE--EETTEEEESSHH
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE--EcCCEEEECCHH
Confidence 4567899999999999999999999887333 456677766654
No 133
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=73.69 E-value=3.6 Score=32.61 Aligned_cols=40 Identities=20% Similarity=0.242 Sum_probs=33.0
Q ss_pred CChHHHHHHHHHH-hcCCCcccchhhhhcccchHHHHHHHhh
Q psy10745 135 LPDVVRQRIVELA-HNGVRPCDISRQLRVSHGCVSKILSRES 175 (197)
Q Consensus 135 lp~~~r~~iv~l~-~~g~r~~~isr~l~vshgcVskil~ry~ 175 (197)
||+. .++|+.|. -+|+.-.+||..|++|-|.|.+.|.|-.
T Consensus 120 Lp~~-~r~v~~L~~~~g~s~~EIA~~lgis~~tV~~~l~ra~ 160 (172)
T PRK12523 120 LSSK-ARAAFLYNRLDGMGHAEIAERLGVSVSRVRQYLAQGL 160 (172)
T ss_pred CCHH-HHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 5544 45577775 6999999999999999999999988864
No 134
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=73.66 E-value=3.8 Score=33.41 Aligned_cols=42 Identities=24% Similarity=0.225 Sum_probs=34.5
Q ss_pred CCChHHHHHHHHHH-hcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 134 PLPDVVRQRIVELA-HNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 134 plp~~~r~~iv~l~-~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
-||+..|. |+.|. -.|..-.+||..|++|.+.|.+.|.|..+
T Consensus 128 ~Lp~~~r~-v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Rar~ 170 (188)
T PRK12517 128 KLDPEYRE-PLLLQVIGGFSGEEIAEILDLNKNTVMTRLFRARN 170 (188)
T ss_pred hCCHHHHH-HHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 47766665 55564 79999999999999999999999888754
No 135
>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=73.48 E-value=3.2 Score=34.92 Aligned_cols=40 Identities=23% Similarity=0.319 Sum_probs=33.1
Q ss_pred CChHHHHHHHHHHh-----cCCCcccchhhhhcccchHHHHHHHhh
Q psy10745 135 LPDVVRQRIVELAH-----NGVRPCDISRQLRVSHGCVSKILSRES 175 (197)
Q Consensus 135 lp~~~r~~iv~l~~-----~g~r~~~isr~l~vshgcVskil~ry~ 175 (197)
||+. .+.|+.|.- +|..-.+||..+++|-+.|++++.|..
T Consensus 175 L~~~-~r~il~l~y~~~~~e~~S~~EIAe~lgis~~tV~~~~~rAl 219 (227)
T TIGR02846 175 LDGR-EREVIEMRYGLGDGRRKTQREIAKILGISRSYVSRIEKRAL 219 (227)
T ss_pred CCHH-HHHHHHHHHcCCCCCCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 4544 447888865 899999999999999999999998854
No 136
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=73.37 E-value=3.4 Score=33.11 Aligned_cols=41 Identities=20% Similarity=0.225 Sum_probs=33.3
Q ss_pred CChHHHHHHHHH-HhcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 135 LPDVVRQRIVEL-AHNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 135 lp~~~r~~iv~l-~~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
||...| .|+.| +-.|.+..+||..|++|.|.|.+-|.|..+
T Consensus 128 L~~~~r-~v~~l~~~~g~s~~EIA~~l~is~~tv~~~l~Ra~~ 169 (179)
T PRK09415 128 LPIKYR-EVIYLFYYEELSIKEIAEVTGVNENTVKTRLKKAKE 169 (179)
T ss_pred CCHHHh-hHhHhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 665444 45556 579999999999999999999999988754
No 137
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=73.31 E-value=4.2 Score=33.02 Aligned_cols=42 Identities=14% Similarity=0.246 Sum_probs=33.8
Q ss_pred CCChHHHHHHHHH-HhcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 134 PLPDVVRQRIVEL-AHNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 134 plp~~~r~~iv~l-~~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
-||...|. |+.| +-.|....+||.+|+||-+.|.+-|.|-.+
T Consensus 141 ~Lp~~~r~-v~~l~~~eg~s~~EIA~~lgis~~tVk~rl~ra~~ 183 (194)
T PRK12531 141 RLPKAQRD-VLQAVYLEELPHQQVAEMFDIPLGTVKSRLRLAVE 183 (194)
T ss_pred hCCHHHHH-HHHHHHHcCCCHHHHHHHhCcCHHHHHHHHHHHHH
Confidence 36655555 6666 689999999999999999999988877643
No 138
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=73.13 E-value=5.6 Score=27.85 Aligned_cols=37 Identities=16% Similarity=0.311 Sum_probs=28.9
Q ss_pred HHHHHH-Hh-cCCCcccchhhhhcccchHHHHHHHhhhh
Q psy10745 141 QRIVEL-AH-NGVRPCDISRQLRVSHGCVSKILSRESNL 177 (197)
Q Consensus 141 ~~iv~l-~~-~g~r~~~isr~l~vshgcVskil~ry~~~ 177 (197)
.+|+.+ +. .++...+||+.+.+|++.||++|.+..+.
T Consensus 13 ~~il~~l~~~~~~~~~~la~~~~~s~~~i~~~l~~L~~~ 51 (101)
T smart00347 13 FLVLRILYEEGPLSVSELAKRLGVSPSTVTRVLDRLEKK 51 (101)
T ss_pred HHHHHHHHHcCCcCHHHHHHHHCCCchhHHHHHHHHHHC
Confidence 344443 33 34899999999999999999999987664
No 139
>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=73.06 E-value=4 Score=33.20 Aligned_cols=42 Identities=19% Similarity=0.306 Sum_probs=34.3
Q ss_pred CCChHHHHHHHHH-HhcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 134 PLPDVVRQRIVEL-AHNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 134 plp~~~r~~iv~l-~~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
-||+..|. |+.| +-.|....+||..|++|-|.|.+.|.|-.+
T Consensus 131 ~L~~~~r~-v~~l~~~~g~s~~EIA~~lgis~~tvk~rl~Rar~ 173 (188)
T TIGR02943 131 HLPEQTAR-VFMMREVLGFESDEICQELEISTSNCHVLLYRARL 173 (188)
T ss_pred hCCHHHHH-HHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 47766665 5555 579999999999999999999988887643
No 140
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=73.06 E-value=3.8 Score=31.76 Aligned_cols=45 Identities=16% Similarity=0.035 Sum_probs=38.6
Q ss_pred CCCChHHHHHHHHH-HhcCCCcccchhhhhcccchHHHHHHHhhhh
Q psy10745 133 RPLPDVVRQRIVEL-AHNGVRPCDISRQLRVSHGCVSKILSRESNL 177 (197)
Q Consensus 133 rplp~~~r~~iv~l-~~~g~r~~~isr~l~vshgcVskil~ry~~~ 177 (197)
+--+.+.+..||.+ ...|....+||+.++||++-+++=...|...
T Consensus 11 r~ys~EfK~~aV~~~~~~g~sv~evA~e~gIs~~tl~~W~r~y~~~ 56 (121)
T PRK09413 11 RRRTTQEKIAIVQQSFEPGMTVSLVARQHGVAASQLFLWRKQYQEG 56 (121)
T ss_pred CCCCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHhhc
Confidence 45667888888875 6789999999999999999999999999763
No 141
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=73.00 E-value=4.1 Score=32.83 Aligned_cols=41 Identities=15% Similarity=0.215 Sum_probs=33.6
Q ss_pred CChHHHHHHHHHH-hcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 135 LPDVVRQRIVELA-HNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 135 lp~~~r~~iv~l~-~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
||+..|. |+.|. -.|....+||..|++|-|.|.+-|.|-.+
T Consensus 132 Lp~~~r~-v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Rar~ 173 (191)
T PRK12520 132 LPPRTGR-VFMMREWLELETEEICQELQITATNAWVLLYRARM 173 (191)
T ss_pred CCHHHHH-HHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 6766665 55564 69999999999999999999998887654
No 142
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=72.79 E-value=5.1 Score=26.21 Aligned_cols=26 Identities=19% Similarity=0.185 Sum_probs=23.2
Q ss_pred cccchhhhhcccchHHHHHHHhhhhc
Q psy10745 153 PCDISRQLRVSHGCVSKILSRESNLH 178 (197)
Q Consensus 153 ~~~isr~l~vshgcVskil~ry~~~~ 178 (197)
..+||+.++||-.-|++.|.+..+.+
T Consensus 28 ~~~la~~~~is~~~v~~~l~~L~~~G 53 (66)
T cd07377 28 ERELAEELGVSRTTVREALRELEAEG 53 (66)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHCC
Confidence 45899999999999999999998765
No 143
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=72.64 E-value=1.4 Score=31.03 Aligned_cols=19 Identities=37% Similarity=0.518 Sum_probs=17.1
Q ss_pred ccchhhhhcccchHHHHHH
Q psy10745 154 CDISRQLRVSHGCVSKILS 172 (197)
Q Consensus 154 ~~isr~l~vshgcVskil~ 172 (197)
-|||++++||-+.||++|+
T Consensus 4 ~~iA~~~gvS~~TVSr~ln 22 (70)
T smart00354 4 KDVARLAGVSKATVSRVLN 22 (70)
T ss_pred HHHHHHHCCCHHHHHHHHC
Confidence 4899999999999999885
No 144
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=72.38 E-value=4.4 Score=32.25 Aligned_cols=42 Identities=24% Similarity=0.351 Sum_probs=33.7
Q ss_pred CCChHHHHHHHHH-HhcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 134 PLPDVVRQRIVEL-AHNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 134 plp~~~r~~iv~l-~~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
-||+. .+.|+.| +-.|....+||..|++|.+.|-+-|.|-.+
T Consensus 131 ~L~~~-~r~v~~l~~~~g~s~~eIA~~l~is~~tV~~~l~ra~~ 173 (184)
T PRK12512 131 TLPPR-QRDVVQSISVEGASIKETAAKLSMSEGAVRVALHRGLA 173 (184)
T ss_pred hCCHH-HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 46654 4456666 479999999999999999999998887654
No 145
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=72.36 E-value=4.3 Score=33.38 Aligned_cols=41 Identities=22% Similarity=0.338 Sum_probs=32.7
Q ss_pred CChHHHHHHHHH-HhcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 135 LPDVVRQRIVEL-AHNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 135 lp~~~r~~iv~l-~~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
||+..| .|+.| .-.|..-.+||..|++|-|.|.+-|.|-.+
T Consensus 140 Lp~~~r-~v~~L~~~eg~s~~EIA~~lgis~~tVk~~l~RAr~ 181 (201)
T PRK12545 140 LPEQIG-RVFMMREFLDFEIDDICTELTLTANHCSVLLYRART 181 (201)
T ss_pred CCHHHH-HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 564444 55566 579999999999999999999998887654
No 146
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=72.12 E-value=4 Score=32.23 Aligned_cols=41 Identities=22% Similarity=0.327 Sum_probs=33.0
Q ss_pred CChHHHHHHHHH-HhcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 135 LPDVVRQRIVEL-AHNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 135 lp~~~r~~iv~l-~~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
||+.. +.|+.| +-.|....+||..|+||-+-|.+.|.|-.+
T Consensus 137 L~~~~-r~il~l~~~~~~s~~eIA~~lgis~~~v~~~l~Rar~ 178 (187)
T PRK09641 137 LPEKY-RTVIVLKYIEDLSLKEISEILDLPVGTVKTRIHRGRE 178 (187)
T ss_pred CCHHH-HHHhhhHHhhCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 55544 455566 469999999999999999999999988654
No 147
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=72.03 E-value=4.1 Score=32.19 Aligned_cols=41 Identities=17% Similarity=0.233 Sum_probs=34.0
Q ss_pred CChHHHHHHHHH-HhcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 135 LPDVVRQRIVEL-AHNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 135 lp~~~r~~iv~l-~~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
||+..|. |+.| +-+|..-.+||..|++|-+.|.+-|.|..+
T Consensus 119 L~~~~r~-v~~L~~~eg~s~~EIA~~l~is~~tV~~~l~ra~~ 160 (168)
T PRK12525 119 LSGKARA-AFLMSQLEGLTYVEIGERLGVSLSRIHQYMVEAFK 160 (168)
T ss_pred CCHHHHH-HHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 6666554 6666 699999999999999999999998887643
No 148
>PRK09191 two-component response regulator; Provisional
Probab=71.98 E-value=4.3 Score=33.36 Aligned_cols=43 Identities=16% Similarity=0.135 Sum_probs=35.3
Q ss_pred CChHHHHHHHHH-HhcCCCcccchhhhhcccchHHHHHHHhhhhc
Q psy10745 135 LPDVVRQRIVEL-AHNGVRPCDISRQLRVSHGCVSKILSRESNLH 178 (197)
Q Consensus 135 lp~~~r~~iv~l-~~~g~r~~~isr~l~vshgcVskil~ry~~~~ 178 (197)
||+. .++|+.| .-.|+.-.+||..|++|.|.|-+.+.|..+.-
T Consensus 89 L~~~-~r~v~~l~~~~~~s~~eIA~~l~~s~~tV~~~l~ra~~~l 132 (261)
T PRK09191 89 LTPL-PRQAFLLTALEGFSVEEAAEILGVDPAEAEALLDDARAEI 132 (261)
T ss_pred CCHH-HhHHHHHHHHhcCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 6655 4556666 57999999999999999999999999887643
No 149
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=71.84 E-value=2.5 Score=26.95 Aligned_cols=30 Identities=20% Similarity=0.335 Sum_probs=26.0
Q ss_pred hcCCCcccchhhhhcccchHHHHHHHhhhh
Q psy10745 148 HNGVRPCDISRQLRVSHGCVSKILSRESNL 177 (197)
Q Consensus 148 ~~g~r~~~isr~l~vshgcVskil~ry~~~ 177 (197)
...+...||++.++||.+-|+++|.+..+.
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~~ 37 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLREA 37 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 455778899999999999999999998764
No 150
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=71.60 E-value=4.9 Score=31.29 Aligned_cols=41 Identities=29% Similarity=0.451 Sum_probs=33.4
Q ss_pred CChHHHHHHHHHH-hcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 135 LPDVVRQRIVELA-HNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 135 lp~~~r~~iv~l~-~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
||+.. +.|+.|. -.|+.-.+||..|++|-+.|.+-|.|..+
T Consensus 114 L~~~~-r~v~~L~~~~g~s~~EIA~~l~is~~tV~~~l~ra~~ 155 (161)
T PRK12528 114 LPPLV-KRAFLLAQVDGLGYGEIATELGISLATVKRYLNKAAM 155 (161)
T ss_pred CCHHH-HHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 56554 4577775 69999999999999999999998888643
No 151
>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=71.55 E-value=3.3 Score=34.98 Aligned_cols=40 Identities=20% Similarity=0.277 Sum_probs=32.6
Q ss_pred CChHHHHHHHHHHh-----cCCCcccchhhhhcccchHHHHHHHhh
Q psy10745 135 LPDVVRQRIVELAH-----NGVRPCDISRQLRVSHGCVSKILSRES 175 (197)
Q Consensus 135 lp~~~r~~iv~l~~-----~g~r~~~isr~l~vshgcVskil~ry~ 175 (197)
|| ...++|+.|+. .|..-.+||..|+||-|.|.+.+.|-.
T Consensus 179 Lp-~~~R~ii~L~~~l~~~eg~s~~EIA~~Lgis~~tV~~~l~ra~ 223 (234)
T TIGR02835 179 LN-DREKKIMELRFGLVGGTEKTQKEVADMLGISQSYISRLEKRIL 223 (234)
T ss_pred CC-HHHHHHHHHHHccCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 44 34456777875 799999999999999999999887753
No 152
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=71.54 E-value=4.3 Score=25.42 Aligned_cols=30 Identities=17% Similarity=0.173 Sum_probs=26.3
Q ss_pred hcCCCcccchhhhhcccchHHHHHHHhhhh
Q psy10745 148 HNGVRPCDISRQLRVSHGCVSKILSRESNL 177 (197)
Q Consensus 148 ~~g~r~~~isr~l~vshgcVskil~ry~~~ 177 (197)
+.++...+|++.++||...|++.|.+..+.
T Consensus 12 ~~~~s~~~l~~~l~~s~~tv~~~l~~L~~~ 41 (53)
T smart00420 12 QGKVSVEELAELLGVSEMTIRRDLNKLEEQ 41 (53)
T ss_pred cCCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 457899999999999999999999987654
No 153
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=71.48 E-value=3.9 Score=35.06 Aligned_cols=41 Identities=20% Similarity=0.320 Sum_probs=33.4
Q ss_pred CCChHHHHHHHHHH-hcCCCcccchhhhhcccchHHHHHHHhh
Q psy10745 134 PLPDVVRQRIVELA-HNGVRPCDISRQLRVSHGCVSKILSRES 175 (197)
Q Consensus 134 plp~~~r~~iv~l~-~~g~r~~~isr~l~vshgcVskil~ry~ 175 (197)
-||+..| +|++|. ..|....+||..|+||.+.|+++..|-.
T Consensus 209 ~L~~~er-~vi~~~~~~~~t~~eIA~~lgis~~~V~~~~~~al 250 (258)
T PRK08215 209 KLNDREK-LILNLRFFQGKTQMEVAEEIGISQAQVSRLEKAAL 250 (258)
T ss_pred cCCHHHH-HHHHHHHhcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 4666554 566766 5899999999999999999999987753
No 154
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=71.42 E-value=4 Score=35.27 Aligned_cols=43 Identities=14% Similarity=0.165 Sum_probs=35.6
Q ss_pred CCChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 134 PLPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 134 plp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
-||+..|.=|.-.+-.|....+||..|+||-+-|++++.|-.+
T Consensus 203 ~L~~~~r~vl~l~y~~~~s~~eIA~~lgvs~~~V~~~~~ra~~ 245 (256)
T PRK07408 203 QLEERTREVLEFVFLHDLTQKEAAERLGISPVTVSRRVKKGLD 245 (256)
T ss_pred cCCHHHHHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4776666655555689999999999999999999999888654
No 155
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=71.30 E-value=3.8 Score=29.04 Aligned_cols=37 Identities=14% Similarity=0.322 Sum_probs=30.3
Q ss_pred HHHHHHHhc---CCCcccchhhhhcccchHHHHHHHhhhh
Q psy10745 141 QRIVELAHN---GVRPCDISRQLRVSHGCVSKILSRESNL 177 (197)
Q Consensus 141 ~~iv~l~~~---g~r~~~isr~l~vshgcVskil~ry~~~ 177 (197)
.+|+++... ++...|||+.+++|...|+++|....+.
T Consensus 8 ~~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~~~ 47 (91)
T smart00346 8 LAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQEL 47 (91)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence 457776543 5899999999999999999999887554
No 156
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=71.28 E-value=4.3 Score=32.84 Aligned_cols=42 Identities=14% Similarity=0.180 Sum_probs=33.8
Q ss_pred CCChHHHHHHHHHH-hcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 134 PLPDVVRQRIVELA-HNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 134 plp~~~r~~iv~l~-~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
-||+. .++|+.|. -.|....+||..|++|-|.|.+-|.|..+
T Consensus 130 ~Lp~~-~r~v~~L~~~~g~s~~EIA~~lgis~~tVk~~l~Rar~ 172 (185)
T PRK09649 130 DLTTD-QREALLLTQLLGLSYADAAAVCGCPVGTIRSRVARARD 172 (185)
T ss_pred hCCHH-HhHHhhhHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 35544 55677775 59999999999999999999998887654
No 157
>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=71.14 E-value=3.3 Score=36.18 Aligned_cols=41 Identities=7% Similarity=0.107 Sum_probs=33.7
Q ss_pred CChHHHHHHHHHH-----hcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 135 LPDVVRQRIVELA-----HNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 135 lp~~~r~~iv~l~-----~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
||+.. +.||.|. .+|..-.+||..|+||.+-|++++.|..+
T Consensus 223 Lp~~~-R~Vl~l~ygL~~~e~~s~~EIA~~Lgis~~tVk~~l~rAlk 268 (285)
T TIGR02394 223 LNERQ-REVLARRFGLLGYEPATLEEVAAEVGLTRERVRQIQVEALK 268 (285)
T ss_pred CCHHH-HHHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 55444 4577775 78999999999999999999999988654
No 158
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=71.11 E-value=4.3 Score=32.41 Aligned_cols=40 Identities=18% Similarity=0.283 Sum_probs=32.3
Q ss_pred CChHHHHHHHHH-HhcCCCcccchhhhhcccchHHHHHHHhh
Q psy10745 135 LPDVVRQRIVEL-AHNGVRPCDISRQLRVSHGCVSKILSRES 175 (197)
Q Consensus 135 lp~~~r~~iv~l-~~~g~r~~~isr~l~vshgcVskil~ry~ 175 (197)
||+.. +.|+.| +-.|.+.-+||..|++|.+-|-+-|.|..
T Consensus 118 Lp~~~-r~i~~l~~~e~~s~~EIA~~lgis~~tV~~~l~ra~ 158 (179)
T PRK12543 118 LPYKL-RQVIILRYLHDYSQEEIAQLLQIPIGTVKSRIHAAL 158 (179)
T ss_pred CCHHH-HHHHHHHHHccCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 66544 467777 56999999999999999999988776654
No 159
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=70.94 E-value=3.6 Score=34.86 Aligned_cols=41 Identities=22% Similarity=0.249 Sum_probs=33.8
Q ss_pred CChHHHHHHHHH-HhcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 135 LPDVVRQRIVEL-AHNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 135 lp~~~r~~iv~l-~~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
||+. .+.|+.| +-.|+.-.+||..|+||.+.|.+.|.|-.+
T Consensus 135 Lp~~-~R~v~~L~y~eg~s~~EIAe~LgiS~~tVk~~L~RAr~ 176 (216)
T PRK12533 135 LPVE-YREVLVLRELEDMSYREIAAIADVPVGTVMSRLARARR 176 (216)
T ss_pred CCHH-HHhHhhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 5544 4566677 679999999999999999999999988654
No 160
>PF13072 DUF3936: Protein of unknown function (DUF3936)
Probab=70.65 E-value=2.7 Score=27.91 Aligned_cols=11 Identities=55% Similarity=0.924 Sum_probs=9.5
Q ss_pred hHHhHHHHHhc
Q psy10745 54 AWEIRDRLLAE 64 (197)
Q Consensus 54 aWEIRdrLl~~ 64 (197)
|||||+.|.+=
T Consensus 16 AWeIr~~Lkey 26 (38)
T PF13072_consen 16 AWEIRAKLKEY 26 (38)
T ss_pred HHHHHHHHHHH
Confidence 89999999763
No 161
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=70.64 E-value=5 Score=32.67 Aligned_cols=40 Identities=25% Similarity=0.288 Sum_probs=33.0
Q ss_pred CChHHHHHHHHH-HhcCCCcccchhhhhcccchHHHHHHHhh
Q psy10745 135 LPDVVRQRIVEL-AHNGVRPCDISRQLRVSHGCVSKILSRES 175 (197)
Q Consensus 135 lp~~~r~~iv~l-~~~g~r~~~isr~l~vshgcVskil~ry~ 175 (197)
||+.. +.|++| .-+|....+||..|+||.+.|-+-|.|-.
T Consensus 135 Lp~~~-r~i~~l~~~~g~s~~EIA~~lg~s~~tV~~rl~rar 175 (192)
T PRK09643 135 LPVEQ-RAALVAVDMQGYSVADAARMLGVAEGTVKSRCARGR 175 (192)
T ss_pred CCHHH-HHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 67555 578888 57999999999999999999988776643
No 162
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=70.55 E-value=4.8 Score=34.36 Aligned_cols=43 Identities=7% Similarity=0.074 Sum_probs=35.2
Q ss_pred CCChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 134 PLPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 134 plp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
-||+..|.=|.-.+..|....+||..|+||.+=||+|..+..+
T Consensus 183 ~L~~~er~vi~l~~~~~~t~~EIA~~lgis~~~V~q~~~~~~~ 225 (231)
T PRK12427 183 QLDEREQLILHLYYQHEMSLKEIALVLDLTEARICQLNKKIAQ 225 (231)
T ss_pred cCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4776666666655678999999999999999999998887654
No 163
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=70.38 E-value=3.6 Score=35.87 Aligned_cols=45 Identities=11% Similarity=0.110 Sum_probs=37.1
Q ss_pred CCChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHhhhhcC
Q psy10745 134 PLPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESNLHN 179 (197)
Q Consensus 134 plp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~~~n 179 (197)
.|++.++ +|+.|..+|..--+||..|.+|...|++-+.+-++--|
T Consensus 133 ~LSpREr-EVLrLLAqGkTnKEIAe~L~IS~rTVkth~srImkKLg 177 (198)
T PRK15201 133 HFSVTER-HLLKLIASGYHLSETAALLSLSEEQTKSLRRSIMRKLH 177 (198)
T ss_pred CCCHHHH-HHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 3665444 79999999999999999999999999997777655443
No 164
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=70.38 E-value=4.5 Score=26.57 Aligned_cols=36 Identities=28% Similarity=0.344 Sum_probs=30.2
Q ss_pred HHH-HHHHHHhcCCCcccchhhhhcccchHHHHHHHh
Q psy10745 139 VRQ-RIVELAHNGVRPCDISRQLRVSHGCVSKILSRE 174 (197)
Q Consensus 139 ~r~-~iv~l~~~g~r~~~isr~l~vshgcVskil~ry 174 (197)
.|+ .++.|...|...-+||+.|++|...|..-+.+-
T Consensus 7 ~rE~~v~~l~~~G~s~~eia~~l~is~~tV~~h~~~i 43 (65)
T COG2771 7 PREREILRLVAQGKSNKEIARILGISEETVKTHLRNI 43 (65)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 344 677799999999999999999999999855554
No 165
>PTZ00072 40S ribosomal protein S13; Provisional
Probab=70.30 E-value=3 Score=34.98 Aligned_cols=30 Identities=37% Similarity=0.543 Sum_probs=27.6
Q ss_pred ChHHHHHHHHHHhcCCCcccchhhhhcccc
Q psy10745 136 PDVVRQRIVELAHNGVRPCDISRQLRVSHG 165 (197)
Q Consensus 136 p~~~r~~iv~l~~~g~r~~~isr~l~vshg 165 (197)
++++-..|++||++|+.|++|-=.|+=+||
T Consensus 27 ~eeVe~~I~klaKkG~~pSqIG~iLRD~~g 56 (148)
T PTZ00072 27 SSEVEDQICKLAKKGLTPSQIGVILRDSMG 56 (148)
T ss_pred HHHHHHHHHHHHHCCCCHhHhhhhhhhccC
Confidence 578899999999999999999999999993
No 166
>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=70.25 E-value=1.6 Score=33.43 Aligned_cols=42 Identities=21% Similarity=0.212 Sum_probs=33.3
Q ss_pred CChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 135 LPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 135 lp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
||+..|.-|+-..-.|....+||..|++|.+.|-+.|.|..+
T Consensus 106 L~~~~r~i~~l~~~~g~s~~eIA~~lgis~~tv~~~l~Ra~~ 147 (154)
T TIGR02950 106 LPENYRTVLILREFKEFSYKEIAELLNLSLAKVKSNLFRARK 147 (154)
T ss_pred CCHhheeeeeehhhccCcHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 666555544434579999999999999999999999888754
No 167
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=70.19 E-value=4.6 Score=32.92 Aligned_cols=42 Identities=21% Similarity=0.325 Sum_probs=34.1
Q ss_pred CCChHHHHHHHHH-HhcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 134 PLPDVVRQRIVEL-AHNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 134 plp~~~r~~iv~l-~~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
-||+..|. |+.| +-.|..-.+||..|+||-+.|.+.|.|-..
T Consensus 111 ~Lp~~~R~-v~~L~~~eg~s~~EIA~~lgis~~tV~~~l~Rar~ 153 (182)
T PRK12511 111 DLPEEQRA-ALHLVAIEGLSYQEAAAVLGIPIGTLMSRIGRARA 153 (182)
T ss_pred hCCHHHHH-HHHHHHHcCCCHHHHHHHhCcCHHHHHHHHHHHHH
Confidence 37766665 6666 679999999999999999999998877543
No 168
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=70.16 E-value=5 Score=34.69 Aligned_cols=41 Identities=15% Similarity=0.282 Sum_probs=32.9
Q ss_pred CChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHhh
Q psy10745 135 LPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRES 175 (197)
Q Consensus 135 lp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~ 175 (197)
||+..|.=|.-.+-.|..-.+||..|+||.+-|.+++.|..
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 66665554444468999999999999999999998887754
No 169
>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=70.13 E-value=5.7 Score=29.69 Aligned_cols=47 Identities=13% Similarity=0.078 Sum_probs=36.2
Q ss_pred CCCChHHHHHHHHHH---------hcCCCcccchhhhhcccchHHHHHHHhhhhcC
Q psy10745 133 RPLPDVVRQRIVELA---------HNGVRPCDISRQLRVSHGCVSKILSRESNLHN 179 (197)
Q Consensus 133 rplp~~~r~~iv~l~---------~~g~r~~~isr~l~vshgcVskil~ry~~~~n 179 (197)
.+++.....-++.|+ ...+...+||..+++|.-.||++|.+..+.+=
T Consensus 21 ~~l~~r~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~g~sr~tVsr~L~~Le~~Gl 76 (95)
T TIGR01610 21 ADLSGREFRVLLAIIRLTYGWNKKQDRVTATVIAELTGLSRTHVSDAIKSLARRRI 76 (95)
T ss_pred CCCCHHHHHHHHHHHHHHhCccccCCccCHHHHHHHHCcCHHHHHHHHHHHHHCCC
Confidence 355566666666676 45667788999999999999999999876653
No 170
>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=69.98 E-value=3.2 Score=27.28 Aligned_cols=44 Identities=11% Similarity=0.228 Sum_probs=29.9
Q ss_pred HHHHHHH--hc-CCCcccchhhhhcccchHHHHHHHhhhhcCcccccc
Q psy10745 141 QRIVELA--HN-GVRPCDISRQLRVSHGCVSKILSRESNLHNYRLVRE 185 (197)
Q Consensus 141 ~~iv~l~--~~-g~r~~~isr~l~vshgcVskil~ry~~~~n~~~~~~ 185 (197)
.+|+++. +. .+...+||.+|+||.-.|.+-|.--.+.+ +++..+
T Consensus 3 ~~il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i~~L~~~~-~~I~~~ 49 (55)
T PF08279_consen 3 KQILKLLLESKEPITAKELAEELGVSRRTIRRDIKELREWG-IPIESK 49 (55)
T ss_dssp HHHHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHHHHHHHTT--EEEEE
T ss_pred HHHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCC-CeEEee
Confidence 4566655 23 37888999999999999999777665555 444433
No 171
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=69.70 E-value=1.6 Score=31.53 Aligned_cols=30 Identities=17% Similarity=0.345 Sum_probs=22.9
Q ss_pred HHhcCCCcccchhhhhcccchHHHHHH-Hhh
Q psy10745 146 LAHNGVRPCDISRQLRVSHGCVSKILS-RES 175 (197)
Q Consensus 146 l~~~g~r~~~isr~l~vshgcVskil~-ry~ 175 (197)
+.+.|+...|+|+.++||..=||+|++ ++.
T Consensus 27 ~~~~~ltQ~e~A~~lgisq~~vS~l~~g~~~ 57 (80)
T PF13744_consen 27 REERGLTQAELAERLGISQPRVSRLENGKID 57 (80)
T ss_dssp HHCCT--HHHHHHHHTS-HHHHHHHHTT-GC
T ss_pred HHHcCCCHHHHHHHHCCChhHHHHHHcCccc
Confidence 357899999999999999999999996 554
No 172
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=69.66 E-value=4.3 Score=32.63 Aligned_cols=41 Identities=24% Similarity=0.465 Sum_probs=34.2
Q ss_pred CChHHHHHHHHHH-hcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 135 LPDVVRQRIVELA-HNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 135 lp~~~r~~iv~l~-~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
||+ ..++|+.|. -.|....|||..|++|-+.|...|.|..+
T Consensus 142 L~~-~~~~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~ 183 (194)
T PRK12519 142 LPE-SQRQVLELAYYEGLSQSEIAKRLGIPLGTVKARARQGLL 183 (194)
T ss_pred CCH-HHhhhhhhhhhcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 453 566777775 69999999999999999999999888654
No 173
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=69.65 E-value=5.1 Score=32.37 Aligned_cols=41 Identities=20% Similarity=0.335 Sum_probs=33.5
Q ss_pred CChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 135 LPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 135 lp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
||+. ...|+.|+-.|.+..+||..|++|.+.|...|.|-.+
T Consensus 156 L~~~-~r~vl~l~~e~~s~~EIA~~lgis~~tV~~~l~rar~ 196 (208)
T PRK08295 156 LSEL-EKEVLELYLDGKSYQEIAEELNRHVKSIDNALQRVKR 196 (208)
T ss_pred CCHH-HHHHHHHHHccCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4544 4555666999999999999999999999998888654
No 174
>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=69.54 E-value=5.8 Score=31.60 Aligned_cols=42 Identities=21% Similarity=0.342 Sum_probs=33.8
Q ss_pred CCChHHHHHHHHH-HhcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 134 PLPDVVRQRIVEL-AHNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 134 plp~~~r~~iv~l-~~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
-||+. .+.|+.| .-.|....+||+.|++|-+-|-..|.|-.+
T Consensus 100 ~L~~~-~r~v~~l~~~~g~s~~eIA~~lgis~~tV~~~l~Rar~ 142 (170)
T TIGR02959 100 ELPDE-YREAIRLTELEGLSQQEIAEKLGLSLSGAKSRVQRGRK 142 (170)
T ss_pred hCCHH-HHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 46654 4667777 579999999999999999999888777543
No 175
>PRK06930 positive control sigma-like factor; Validated
Probab=69.09 E-value=5.7 Score=32.99 Aligned_cols=42 Identities=14% Similarity=0.293 Sum_probs=34.2
Q ss_pred CCChHHHHHHHHH-HhcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 134 PLPDVVRQRIVEL-AHNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 134 plp~~~r~~iv~l-~~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
-||+..| +|+.| ...|..-.+||..|++|.+.|.+.+.|..+
T Consensus 114 ~L~~rer-~V~~L~~~eg~s~~EIA~~lgiS~~tVk~~l~Ra~~ 156 (170)
T PRK06930 114 VLTEREK-EVYLMHRGYGLSYSEIADYLNIKKSTVQSMIERAEK 156 (170)
T ss_pred hCCHHHH-HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 3665544 45556 689999999999999999999999888754
No 176
>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=69.01 E-value=3 Score=29.87 Aligned_cols=35 Identities=26% Similarity=0.324 Sum_probs=29.3
Q ss_pred HHHHHHHHHHhc---CCCcccchhhhhcccchHHHHHH
Q psy10745 138 VVRQRIVELAHN---GVRPCDISRQLRVSHGCVSKILS 172 (197)
Q Consensus 138 ~~r~~iv~l~~~---g~r~~~isr~l~vshgcVskil~ 172 (197)
..|.+.-||+.. .++--|||.+|+||.+.|++==+
T Consensus 7 p~rdkA~e~y~~~~g~i~lkdIA~~Lgvs~~tIr~WK~ 44 (60)
T PF10668_consen 7 PNRDKAFEIYKESNGKIKLKDIAEKLGVSESTIRKWKS 44 (60)
T ss_pred cCHHHHHHHHHHhCCCccHHHHHHHHCCCHHHHHHHhh
Confidence 468888899875 68999999999999999987433
No 177
>COG0640 ArsR Predicted transcriptional regulators [Transcription]
Probab=68.83 E-value=5.9 Score=26.80 Aligned_cols=44 Identities=23% Similarity=0.251 Sum_probs=35.9
Q ss_pred CChHHHHHHHHHHhc--CCCcccchhhhhcccchHHHHHHHhhhhc
Q psy10745 135 LPDVVRQRIVELAHN--GVRPCDISRQLRVSHGCVSKILSRESNLH 178 (197)
Q Consensus 135 lp~~~r~~iv~l~~~--g~r~~~isr~l~vshgcVskil~ry~~~~ 178 (197)
|.+..|.+|+.+... ..-.|+|++.+.+|+.-||.=|....+.+
T Consensus 22 l~~~~r~~il~~l~~~~~~~~~~l~~~~~~~~~~v~~hL~~L~~~g 67 (110)
T COG0640 22 LADPTRLEILSLLAEGGELTVGELAEALGLSQSTVSHHLKVLREAG 67 (110)
T ss_pred hCCHHHHHHHHHHHhcCCccHHHHHHHHCCChhHHHHHHHHHHHCC
Confidence 455689999988877 36689999999999999999888765544
No 178
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=68.78 E-value=5.9 Score=31.77 Aligned_cols=42 Identities=19% Similarity=0.291 Sum_probs=34.0
Q ss_pred CCChHHHHHHHHH-HhcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 134 PLPDVVRQRIVEL-AHNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 134 plp~~~r~~iv~l-~~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
-||+. .++|+.| +-.|..-.+||..|++|.+.|-+.+.|..+
T Consensus 139 ~L~~~-~r~i~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~ 181 (189)
T PRK09648 139 TLPEK-QREILILRVVVGLSAEETAEAVGSTPGAVRVAQHRALA 181 (189)
T ss_pred hCCHH-HHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 36654 4667777 579999999999999999999998887643
No 179
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=68.74 E-value=5.3 Score=34.84 Aligned_cols=42 Identities=24% Similarity=0.196 Sum_probs=35.1
Q ss_pred CChHHHHHHHHH-HhcCCCcccchhhhhcccchHHHHHHHhhhh
Q psy10745 135 LPDVVRQRIVEL-AHNGVRPCDISRQLRVSHGCVSKILSRESNL 177 (197)
Q Consensus 135 lp~~~r~~iv~l-~~~g~r~~~isr~l~vshgcVskil~ry~~~ 177 (197)
||+..|. |+.| .-.|....|||+.|++|-+-|.+.|.|..+.
T Consensus 116 L~~~~R~-v~~L~~~~g~s~~EIA~~lg~s~~tVk~~l~RAr~~ 158 (293)
T PRK09636 116 LSPLERA-AFLLHDVFGVPFDEIASTLGRSPAACRQLASRARKH 158 (293)
T ss_pred CCHHHHH-HHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 7766665 5555 4699999999999999999999999987653
No 180
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=68.65 E-value=5.3 Score=32.97 Aligned_cols=41 Identities=22% Similarity=0.289 Sum_probs=32.8
Q ss_pred CChHHHHHHHHH-HhcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 135 LPDVVRQRIVEL-AHNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 135 lp~~~r~~iv~l-~~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
||+..|. |+.| +-.|..-.+||.+|+||-+-|.+.|.|-.+
T Consensus 154 L~~~~r~-vl~l~~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~ 195 (206)
T PRK12526 154 LPEAQQT-VVKGVYFQELSQEQLAQQLNVPLGTVKSRLRLALA 195 (206)
T ss_pred CCHHHHH-HHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 6655554 4555 679999999999999999999998887644
No 181
>PRK05572 sporulation sigma factor SigF; Validated
Probab=68.49 E-value=5 Score=34.31 Aligned_cols=42 Identities=14% Similarity=0.138 Sum_probs=33.4
Q ss_pred CCChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHhh
Q psy10745 134 PLPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRES 175 (197)
Q Consensus 134 plp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~ 175 (197)
-||+..|+=+...+..|+...+||..++||.+-|+++..|-.
T Consensus 202 ~L~~~~~~v~~l~~~~~~s~~eIA~~lgis~~~V~~~~~ral 243 (252)
T PRK05572 202 ELDERERLIVYLRYFKDKTQSEVAKRLGISQVQVSRLEKKIL 243 (252)
T ss_pred cCCHHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 367665554444456999999999999999999999888754
No 182
>PRK04841 transcriptional regulator MalT; Provisional
Probab=68.39 E-value=3.9 Score=40.10 Aligned_cols=42 Identities=17% Similarity=0.237 Sum_probs=35.1
Q ss_pred CCChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHH-hhh
Q psy10745 134 PLPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSR-ESN 176 (197)
Q Consensus 134 plp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~r-y~~ 176 (197)
+|+ .--.+|++|..+|..-.+||..|.||.+.|.+=|.+ |.+
T Consensus 838 ~lt-~~e~~v~~~~~~g~~~~~ia~~l~~s~~tv~~h~~~~~~k 880 (903)
T PRK04841 838 PLT-QREWQVLGLIYSGYSNEQIAGELDVAATTIKTHIRNLYQK 880 (903)
T ss_pred CCC-HHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 455 444689999999999999999999999999987766 443
No 183
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=68.33 E-value=4.6 Score=35.24 Aligned_cols=36 Identities=17% Similarity=0.338 Sum_probs=30.2
Q ss_pred HHHHHHH-hcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 141 QRIVELA-HNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 141 ~~iv~l~-~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
++|+.|. -.|+.-.+||..|+||.+.|++++.|..+
T Consensus 221 r~vl~l~y~~~~t~~EIA~~lgis~~~V~~~~~ral~ 257 (264)
T PRK07122 221 RTVLVLRFFESMTQTQIAERVGISQMHVSRLLAKTLA 257 (264)
T ss_pred HHHHHHHhcCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 3466665 58999999999999999999999887643
No 184
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=67.81 E-value=2.5 Score=27.47 Aligned_cols=27 Identities=19% Similarity=0.401 Sum_probs=22.7
Q ss_pred HhcCCCcccchhhhhcccchHHHHHHH
Q psy10745 147 AHNGVRPCDISRQLRVSHGCVSKILSR 173 (197)
Q Consensus 147 ~~~g~r~~~isr~l~vshgcVskil~r 173 (197)
-+.|+...|+|+.++||..-||++++-
T Consensus 6 ~~~gls~~~la~~~gis~~~i~~~~~g 32 (55)
T PF01381_consen 6 KEKGLSQKELAEKLGISRSTISRIENG 32 (55)
T ss_dssp HHTTS-HHHHHHHHTS-HHHHHHHHTT
T ss_pred HHcCCCHHHHHHHhCCCcchhHHHhcC
Confidence 488999999999999999999998865
No 185
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=67.47 E-value=6.3 Score=32.88 Aligned_cols=42 Identities=14% Similarity=0.203 Sum_probs=33.8
Q ss_pred CCChHHHHHHHHH-HhcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 134 PLPDVVRQRIVEL-AHNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 134 plp~~~r~~iv~l-~~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
-||+..|. |+.| +-.|+...+||..|++|.+.|.+-|.|-.+
T Consensus 148 ~L~~~~r~-v~~L~~~~g~s~~EIAe~lgis~~tV~~~l~RAr~ 190 (206)
T PRK12544 148 GLPAKYAR-VFMMREFIELETNEICHAVDLSVSNLNVLLYRARL 190 (206)
T ss_pred hCCHHHHH-HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 36666655 5555 569999999999999999999998888654
No 186
>PHA00542 putative Cro-like protein
Probab=67.28 E-value=4 Score=29.90 Aligned_cols=31 Identities=23% Similarity=0.291 Sum_probs=26.6
Q ss_pred HHHHHhcCCCcccchhhhhcccchHHHHHHH
Q psy10745 143 IVELAHNGVRPCDISRQLRVSHGCVSKILSR 173 (197)
Q Consensus 143 iv~l~~~g~r~~~isr~l~vshgcVskil~r 173 (197)
+..|...|+...++|+.++||..-||++++-
T Consensus 24 ~~~l~~~glTq~elA~~lgIs~~tIsr~e~g 54 (82)
T PHA00542 24 VCALIRAGWSQEQIADATDVSQPTICRIYSG 54 (82)
T ss_pred HHHHHHCCCCHHHHHHHHCcCHHHHHHHHcC
Confidence 3456688999999999999999999998753
No 187
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=67.25 E-value=4.6 Score=34.10 Aligned_cols=39 Identities=18% Similarity=0.140 Sum_probs=33.1
Q ss_pred CCChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHH
Q psy10745 134 PLPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSR 173 (197)
Q Consensus 134 plp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~r 173 (197)
+|.+-++ +|++|..+|..--+||++|.+|...|++=+.+
T Consensus 134 ~LT~RE~-eVL~ll~~G~snkeIA~~L~iS~~TV~~h~~~ 172 (207)
T PRK11475 134 MLSPTER-EILRFMSRGYSMPQIAEQLERNIKTIRAHKFN 172 (207)
T ss_pred CCCHHHH-HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 4665554 79999999999999999999999999984444
No 188
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=66.48 E-value=6.6 Score=31.87 Aligned_cols=42 Identities=24% Similarity=0.291 Sum_probs=34.5
Q ss_pred CCChHHHHHHHHHH-hcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 134 PLPDVVRQRIVELA-HNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 134 plp~~~r~~iv~l~-~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
-||... ++|+.|. -.|....+||..|+||-+-|.+.|.|-..
T Consensus 142 ~L~~~~-r~vl~l~~~~~~s~~EIA~~Lgis~~tVk~~l~ra~~ 184 (194)
T PRK09646 142 ALTDTQ-RESVTLAYYGGLTYREVAERLAVPLGTVKTRMRDGLI 184 (194)
T ss_pred hCCHHH-HHHHHHHHHcCCCHHHHHHHhCCChHhHHHHHHHHHH
Confidence 477544 4577775 79999999999999999999999888653
No 189
>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=66.44 E-value=6.3 Score=34.39 Aligned_cols=42 Identities=17% Similarity=0.140 Sum_probs=34.2
Q ss_pred CChHHHHHHHHH-HhcCCCcccchhhhhcccchHHHHHHHhhhh
Q psy10745 135 LPDVVRQRIVEL-AHNGVRPCDISRQLRVSHGCVSKILSRESNL 177 (197)
Q Consensus 135 lp~~~r~~iv~l-~~~g~r~~~isr~l~vshgcVskil~ry~~~ 177 (197)
||+..|. |+.| .-.|....|||..|++|-+-|.+.|.|-.+.
T Consensus 109 L~~~~R~-v~~L~~~~g~s~~EIA~~lg~s~~tVr~~l~RAr~~ 151 (281)
T TIGR02957 109 LSPLERA-VFVLREVFDYPYEEIASIVGKSEANCRQLVSRARRH 151 (281)
T ss_pred CCHHHHH-HHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 5655554 4555 5799999999999999999999999988653
No 190
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=66.43 E-value=6.4 Score=33.61 Aligned_cols=41 Identities=20% Similarity=0.265 Sum_probs=33.3
Q ss_pred CChHHHHHHHHH-HhcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 135 LPDVVRQRIVEL-AHNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 135 lp~~~r~~iv~l-~~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
||+..| +|+.| +-.|..-.+||..|+||.+-|++.+.|..+
T Consensus 202 L~~~~r-~vl~l~~~~~~s~~EIA~~lgis~~tV~~~~~ra~~ 243 (251)
T PRK07670 202 LSEKEQ-LVISLFYKEELTLTEIGQVLNLSTSRISQIHSKALF 243 (251)
T ss_pred CCHHHH-HHHHHHHhcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 665554 45555 688999999999999999999999888654
No 191
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=66.39 E-value=5 Score=35.43 Aligned_cols=42 Identities=24% Similarity=0.303 Sum_probs=34.2
Q ss_pred CChHHHHHHHHHH-hcCCCcccchhhhhcccchHHHHHHHhhhh
Q psy10745 135 LPDVVRQRIVELA-HNGVRPCDISRQLRVSHGCVSKILSRESNL 177 (197)
Q Consensus 135 lp~~~r~~iv~l~-~~g~r~~~isr~l~vshgcVskil~ry~~~ 177 (197)
||+..| .|+.|. -.|++..+||..|++|-+.|.+.|.|-.+.
T Consensus 154 Lp~~~R-~v~~L~~~~g~s~~EIA~~lgis~~tVk~~l~RAr~~ 196 (339)
T PRK08241 154 LPPRQR-AVLILRDVLGWSAAEVAELLDTSVAAVNSALQRARAT 196 (339)
T ss_pred CCHHHh-hhhhhHHhhCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 665544 466665 799999999999999999999999887653
No 192
>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=65.89 E-value=5.8 Score=34.03 Aligned_cols=41 Identities=15% Similarity=0.297 Sum_probs=33.1
Q ss_pred CCChHHHHHHHHHH-hcCCCcccchhhhhcccchHHHHHHHhh
Q psy10745 134 PLPDVVRQRIVELA-HNGVRPCDISRQLRVSHGCVSKILSRES 175 (197)
Q Consensus 134 plp~~~r~~iv~l~-~~g~r~~~isr~l~vshgcVskil~ry~ 175 (197)
-||+..| .|+.|. -.|..-.+||..|+||.+-|+++..|..
T Consensus 206 ~L~~rer-~vi~~~~~~~~t~~eIA~~lgis~~~V~~~~~ral 247 (254)
T TIGR02850 206 RLNEREK-MILNMRFFEGKTQMEVAEEIGISQAQVSRLEKAAL 247 (254)
T ss_pred cCCHHHH-HHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 4665554 566665 4899999999999999999999988864
No 193
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=65.61 E-value=5.2 Score=33.96 Aligned_cols=44 Identities=20% Similarity=0.163 Sum_probs=36.2
Q ss_pred CCChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHhhhhc
Q psy10745 134 PLPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESNLH 178 (197)
Q Consensus 134 plp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~~~ 178 (197)
.|++ --.+|++|...|..--+||+.|.+|.+.|++-+.+-++.-
T Consensus 155 ~Lt~-rE~~Vl~l~~~G~s~~eIA~~L~iS~~TVk~~~~~i~~Kl 198 (216)
T PRK10100 155 LLTH-REKEILNKLRIGASNNEIARSLFISENTVKTHLYNLFKKI 198 (216)
T ss_pred CCCH-HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence 4664 5567999999999999999999999999999776655443
No 194
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=65.44 E-value=7.2 Score=32.28 Aligned_cols=40 Identities=10% Similarity=0.091 Sum_probs=33.1
Q ss_pred CChHHHHHHHHHHh----cCCCcccchhhhhcccchHHHHHHHh
Q psy10745 135 LPDVVRQRIVELAH----NGVRPCDISRQLRVSHGCVSKILSRE 174 (197)
Q Consensus 135 lp~~~r~~iv~l~~----~g~r~~~isr~l~vshgcVskil~ry 174 (197)
|....++.++.+.. .|..-.+||++|.+|.+.|.+-+.+-
T Consensus 159 Lt~re~~~l~~~i~~~~~~g~s~~eIA~~l~iS~~Tv~~~~~~~ 202 (239)
T PRK10430 159 LTPQTLRTLCQWIDAHQDYEFSTDELANAVNISRVSCRKYLIWL 202 (239)
T ss_pred CCHHHHHHHHHHHHhCCCCCcCHHHHHHHhCchHHHHHHHHHHH
Confidence 55555566677774 89999999999999999999988865
No 195
>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=65.41 E-value=3.8 Score=25.91 Aligned_cols=26 Identities=27% Similarity=0.308 Sum_probs=21.9
Q ss_pred cccchhhhhcccchHHHHHHHhhhhc
Q psy10745 153 PCDISRQLRVSHGCVSKILSRESNLH 178 (197)
Q Consensus 153 ~~~isr~l~vshgcVskil~ry~~~~ 178 (197)
-.|||..|+.|.=.||.+|.++.+.+
T Consensus 5 r~diA~~lG~t~ETVSR~l~~l~~~g 30 (32)
T PF00325_consen 5 RQDIADYLGLTRETVSRILKKLERQG 30 (32)
T ss_dssp HHHHHHHHTS-HHHHHHHHHHHHHTT
T ss_pred HHHHHHHhCCcHHHHHHHHHHHHHcC
Confidence 45899999999999999999997653
No 196
>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=65.20 E-value=1.6 Score=30.37 Aligned_cols=39 Identities=36% Similarity=0.428 Sum_probs=18.5
Q ss_pred HHHHHHHhCCCcchHHhHHHHHhcCCCCCCCCCCcccccccccc
Q psy10745 41 AIASYKRENPTMFAWEIRDRLLAEGICSQDNVPSVSSINRYITY 84 (197)
Q Consensus 41 ~I~~~k~e~P~iFaWEIRdrLl~~GvC~~~~vPSvSSI~Rilr~ 84 (197)
.|..+.+++|.+.+-||...|.+.|+-. |.++|.|+|+.
T Consensus 3 ~I~~~v~~~p~~s~~~i~~~l~~~~~~v-----S~~TI~r~L~~ 41 (72)
T PF01498_consen 3 RIVRMVRRNPRISAREIAQELQEAGISV-----SKSTIRRRLRE 41 (72)
T ss_dssp -------------HHHHHHHT---T--S------HHHHHHHHHH
T ss_pred HHHHHHHHCCCCCHHHHHHHHHHccCCc-----CHHHHHHHHHH
Confidence 4666778899999999999999998877 99999999984
No 197
>PHA01976 helix-turn-helix protein
Probab=65.04 E-value=4.8 Score=27.25 Aligned_cols=33 Identities=12% Similarity=0.236 Sum_probs=26.6
Q ss_pred HHHHH-HhcCCCcccchhhhhcccchHHHHHHHh
Q psy10745 142 RIVEL-AHNGVRPCDISRQLRVSHGCVSKILSRE 174 (197)
Q Consensus 142 ~iv~l-~~~g~r~~~isr~l~vshgcVskil~ry 174 (197)
+|-++ .+.|+...++|+.++||...||++.+.-
T Consensus 6 rl~~~R~~~glt~~~lA~~~gvs~~~v~~~e~g~ 39 (67)
T PHA01976 6 QLIKARNARAWSAPELSRRAGVRHSLIYDFEADK 39 (67)
T ss_pred HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCC
Confidence 33343 3689999999999999999999987643
No 198
>TIGR00180 parB_part ParB-like partition proteins. This model represents the most well-conserved core of a set of chromosomal and plasmid partition proteins related to ParB, including Spo0J, RepB, and SopB. Spo0J has been shown to bind a specific DNA sequence that, when introduced into a plasmid, can serve as partition site. Study of RepB, which has nicking-closing activity, suggests that it forms a transient protein-DNA covalent intermediate during the strand transfer reaction.
Probab=64.70 E-value=5.3 Score=33.03 Aligned_cols=40 Identities=13% Similarity=0.235 Sum_probs=31.3
Q ss_pred CCChHHHHHHH-HHH-hcCCCcccchhhhhcccchHHHHHHH
Q psy10745 134 PLPDVVRQRIV-ELA-HNGVRPCDISRQLRVSHGCVSKILSR 173 (197)
Q Consensus 134 plp~~~r~~iv-~l~-~~g~r~~~isr~l~vshgcVskil~r 173 (197)
+|.+.++-..+ +|. ..|..+.+||+.+++|...||+.|.-
T Consensus 102 ~lt~~e~a~~~~~l~~~~g~s~~~iA~~lg~s~~~V~r~l~l 143 (187)
T TIGR00180 102 DLSPIEEAQAYKRLLEKFSMTQEDLAKKIGKSRAHITNLLRL 143 (187)
T ss_pred CCCHHHHHHHHHHHHHHhCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 66666655544 544 46999999999999999999998764
No 199
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=64.25 E-value=3.7 Score=25.59 Aligned_cols=28 Identities=21% Similarity=0.252 Sum_probs=24.1
Q ss_pred CCcccchhhhhcccchHHHHHHHhhhhc
Q psy10745 151 VRPCDISRQLRVSHGCVSKILSRESNLH 178 (197)
Q Consensus 151 ~r~~~isr~l~vshgcVskil~ry~~~~ 178 (197)
+...|||+.+++|..-|+++|.+..+.+
T Consensus 9 ~s~~~la~~l~~s~~tv~~~l~~L~~~g 36 (48)
T smart00419 9 LTRQEIAELLGLTRETVSRTLKRLEKEG 36 (48)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHHHHCC
Confidence 4557899999999999999999987654
No 200
>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=63.75 E-value=6.2 Score=34.29 Aligned_cols=40 Identities=18% Similarity=0.229 Sum_probs=30.9
Q ss_pred CCChHHHHHHHHHHh---cCCCcccchhhhhcccchHHHHHHHh
Q psy10745 134 PLPDVVRQRIVELAH---NGVRPCDISRQLRVSHGCVSKILSRE 174 (197)
Q Consensus 134 plp~~~r~~iv~l~~---~g~r~~~isr~l~vshgcVskil~ry 174 (197)
-||+..|. ||.|.- .|+.-.+||+.|+||.+-|++|+.+.
T Consensus 218 ~L~~rer~-vl~l~y~~~~~~t~~eIA~~lgvS~~~V~q~~~~A 260 (270)
T TIGR02392 218 SLDARSRR-IIEARWLDDDKLTLQELAAEYGVSAERIRQIEKNA 260 (270)
T ss_pred cCCHHHHH-HHHHHhcCCCCcCHHHHHHHHCCCHHHHHHHHHHH
Confidence 36666655 555543 47888999999999999999887664
No 201
>PF08535 KorB: KorB domain; InterPro: IPR013741 This entry contains several KorB transcriptional repressor proteins. The korB gene is a major regulatory element in the replication and maintenance of broad host-range plasmid RK2. It negatively controls the replication gene trfA, the host-lethal determinants kilA and kilB, and the korA-korB operon []. This domain includes the DNA-binding HTH motif []. ; PDB: 1R71_C.
Probab=63.52 E-value=2.9 Score=30.94 Aligned_cols=27 Identities=26% Similarity=0.220 Sum_probs=20.0
Q ss_pred hcCCCcccchhhhhcccchHHHHHHHh
Q psy10745 148 HNGVRPCDISRQLRVSHGCVSKILSRE 174 (197)
Q Consensus 148 ~~g~r~~~isr~l~vshgcVskil~ry 174 (197)
+.|+.+.+||+.|+-|..=||+.|.-.
T Consensus 1 ~~G~tq~eIA~~lGks~s~Vs~~l~Ll 27 (93)
T PF08535_consen 1 EFGWTQEEIAKRLGKSRSWVSNHLALL 27 (93)
T ss_dssp HTT--HHHHHHHTT--HHHHHHHHGGG
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 469999999999999999999988643
No 202
>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=63.32 E-value=6.6 Score=32.77 Aligned_cols=39 Identities=13% Similarity=0.204 Sum_probs=32.8
Q ss_pred HHHHHHHHH--hcCCCcccchhhhhcccchHHHHHHHhhhh
Q psy10745 139 VRQRIVELA--HNGVRPCDISRQLRVSHGCVSKILSRESNL 177 (197)
Q Consensus 139 ~r~~iv~l~--~~g~r~~~isr~l~vshgcVskil~ry~~~ 177 (197)
+|.+|+.+. +.+++..+||+.|+||...|++.|.+..+.
T Consensus 2 tr~~IL~~L~~~~~~t~~eLA~~lgis~~tV~~~L~~Le~~ 42 (203)
T TIGR02702 2 TKEDILSYLLKQGQATAAALAEALAISPQAVRRHLKDLETE 42 (203)
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 688899865 456888999999999999999999987543
No 203
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=63.30 E-value=3.6 Score=33.17 Aligned_cols=41 Identities=22% Similarity=0.254 Sum_probs=33.0
Q ss_pred CChHHHHHHHHHH-hcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 135 LPDVVRQRIVELA-HNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 135 lp~~~r~~iv~l~-~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
||+.. ++|+.|. -.|....+||..|++|-+-|.+.|.|..+
T Consensus 140 L~~~~-r~i~~l~~~~g~s~~EIA~~lgis~~tV~~~l~ra~~ 181 (194)
T PRK12513 140 LPDEQ-REVFLLREHGDLELEEIAELTGVPEETVKSRLRYALQ 181 (194)
T ss_pred CCHhH-hhheeeehccCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 55444 4577775 69999999999999999999988887653
No 204
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=63.04 E-value=11 Score=28.36 Aligned_cols=49 Identities=12% Similarity=0.087 Sum_probs=40.9
Q ss_pred CCCChHHHHHHHHHHh-cCCCcccchhhhhc-ccchHHHHHHHhhhhcCcc
Q psy10745 133 RPLPDVVRQRIVELAH-NGVRPCDISRQLRV-SHGCVSKILSRESNLHNYR 181 (197)
Q Consensus 133 rplp~~~r~~iv~l~~-~g~r~~~isr~l~v-shgcVskil~ry~~~~n~~ 181 (197)
|..+++.+.+||+++. .|....+|||+++| +-.-+.|=...|.+.+..-
T Consensus 6 r~~s~EfK~~iv~~~~~~g~sv~~vAr~~gv~~~~~l~~W~~~~~~~~~~~ 56 (116)
T COG2963 6 KKYSPEFKLEAVALYLRGGDTVSEVAREFGIVSATQLYKWRIQLQKGGGLA 56 (116)
T ss_pred ccCCHHHHHHHHHHHHhcCccHHHHHHHhCCCChHHHHHHHHHHHHccccc
Confidence 5678999999999998 58889999999995 9888888777777766443
No 205
>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=62.85 E-value=6.7 Score=31.03 Aligned_cols=41 Identities=24% Similarity=0.352 Sum_probs=33.0
Q ss_pred CChHHHHHHHHHH-hcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 135 LPDVVRQRIVELA-HNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 135 lp~~~r~~iv~l~-~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
||+ ..++|+.|. -.|..-.+||..|++|.+-|.+-|.|-.+
T Consensus 139 L~~-~~r~v~~l~~~~~~s~~EIA~~lgis~~tv~~~l~rar~ 180 (190)
T TIGR02939 139 LPE-DLRTAITLRELEGLSYEDIARIMDCPVGTVRSRIFRARE 180 (190)
T ss_pred CCH-HHhhhhhhhhhcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 444 444577775 79999999999999999999998888654
No 206
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=62.35 E-value=7.8 Score=29.27 Aligned_cols=42 Identities=24% Similarity=0.218 Sum_probs=34.2
Q ss_pred CChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHhhhh
Q psy10745 135 LPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESNL 177 (197)
Q Consensus 135 lp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~~ 177 (197)
|+ ..-.+|+.|..+|..--+||+.|.+|...|+.-+.|-++.
T Consensus 150 lt-~~e~~vl~l~~~g~~~~~Ia~~l~~s~~tv~~~~~~~~~k 191 (211)
T PRK15369 150 LT-PRERQILKLITEGYTNRDIAEQLSISIKTVETHRLNMMRK 191 (211)
T ss_pred CC-HHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 54 3457889999999999999999999999998866665443
No 207
>PRK09954 putative kinase; Provisional
Probab=61.79 E-value=6.9 Score=34.87 Aligned_cols=42 Identities=12% Similarity=0.180 Sum_probs=35.3
Q ss_pred hHHHHHHHHHHhcC--CCcccchhhhhcccchHHHHHHHhhhhc
Q psy10745 137 DVVRQRIVELAHNG--VRPCDISRQLRVSHGCVSKILSRESNLH 178 (197)
Q Consensus 137 ~~~r~~iv~l~~~g--~r~~~isr~l~vshgcVskil~ry~~~~ 178 (197)
++..++|+++.++. +.-.+||++|+||...|.+.|+|-.+.+
T Consensus 2 ~~~~~~il~~l~~~~~~s~~~la~~l~~s~~~v~~~i~~L~~~g 45 (362)
T PRK09954 2 NNREKEILAILRRNPLIQQNEIADILQISRSRVAAHIMDLMRKG 45 (362)
T ss_pred ChHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCC
Confidence 45678899998776 6778899999999999999999887643
No 208
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=61.69 E-value=8.3 Score=32.48 Aligned_cols=42 Identities=21% Similarity=0.329 Sum_probs=33.6
Q ss_pred CCChHHHHHHHHHHh-----cCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 134 PLPDVVRQRIVELAH-----NGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 134 plp~~~r~~iv~l~~-----~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
-||+ .-++|+.|.- .|....+||..|++|.+-|++.+.|..+
T Consensus 175 ~Lp~-~~R~i~~l~y~~~~~e~~S~~EIA~~lgis~~tV~~~~~rA~~ 221 (233)
T PRK05803 175 ILDE-REKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRALK 221 (233)
T ss_pred hCCH-HHHHHHHHHhCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4554 4456777765 8999999999999999999999887654
No 209
>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=61.54 E-value=9.3 Score=33.09 Aligned_cols=41 Identities=20% Similarity=0.317 Sum_probs=32.3
Q ss_pred CChHHHHHHHHHH-hcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 135 LPDVVRQRIVELA-HNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 135 lp~~~r~~iv~l~-~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
||...| .|+.|. -+|..-.|||.+|+||-+.|.+-|.|-.+
T Consensus 162 Lp~~~R-~v~~L~~~eg~S~~EIA~~Lgis~~TVk~rl~RAr~ 203 (244)
T TIGR03001 162 LSERER-HLLRLHFVDGLSMDRIGAMYQVHRSTVSRWVAQARE 203 (244)
T ss_pred CCHHHH-HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 554444 455554 69999999999999999999998877654
No 210
>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=61.15 E-value=6.1 Score=26.80 Aligned_cols=43 Identities=16% Similarity=0.236 Sum_probs=35.3
Q ss_pred HHHHHHhcCCCcccchhhhhcccchHHHHHHHhhhhcCcccccc
Q psy10745 142 RIVELAHNGVRPCDISRQLRVSHGCVSKILSRESNLHNYRLVRE 185 (197)
Q Consensus 142 ~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~~~n~~~~~~ 185 (197)
-++.+++.| .....|+.|+||..-||+-|.+..+.-+.+|+.-
T Consensus 6 ~f~~v~~~g-s~~~AA~~l~is~~~vs~~i~~LE~~lg~~Lf~r 48 (60)
T PF00126_consen 6 YFLAVAETG-SISAAAEELGISQSAVSRQIKQLEEELGVPLFER 48 (60)
T ss_dssp HHHHHHHHS-SHHHHHHHCTSSHHHHHHHHHHHHHHHTS-SEEE
T ss_pred HHHHHHHhC-CHHHHHHHhhccchHHHHHHHHHHHHhCCeEEEE
Confidence 355667777 7788899999999999999999999988888654
No 211
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=61.12 E-value=3.2 Score=33.42 Aligned_cols=42 Identities=10% Similarity=0.109 Sum_probs=33.3
Q ss_pred CCChHHHHHHHHH-HhcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 134 PLPDVVRQRIVEL-AHNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 134 plp~~~r~~iv~l-~~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
-||+. .++|+.| +-.|....+||.+|+||-+.|.+-|.|-.+
T Consensus 134 ~L~~~-~r~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~ 176 (188)
T PRK09640 134 HVNPI-DREILVLRFVAELEFQEIADIMHMGLSATKMRYKRALD 176 (188)
T ss_pred hcChh-heeeeeeHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 45655 3457776 478999999999999999999998877643
No 212
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=60.31 E-value=9.7 Score=29.63 Aligned_cols=41 Identities=24% Similarity=0.216 Sum_probs=33.9
Q ss_pred CChHHHHHHHHHH-hcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 135 LPDVVRQRIVELA-HNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 135 lp~~~r~~iv~l~-~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
||+. .+.|+.|. -.|....+||..|++|-|-|.+-|.|-.+
T Consensus 113 L~~~-~r~v~~l~~~~~~s~~eIA~~lgis~~tv~~~l~Rar~ 154 (161)
T PRK12541 113 LPLE-RRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRK 154 (161)
T ss_pred CCHH-HHHHhhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 5544 45588886 59999999999999999999999988654
No 213
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=60.29 E-value=7.3 Score=30.46 Aligned_cols=44 Identities=14% Similarity=0.292 Sum_probs=31.9
Q ss_pred CChHHHHHHHHHH-hcCCCcccchhhhhcccchHHHHHHHhhhhc
Q psy10745 135 LPDVVRQRIVELA-HNGVRPCDISRQLRVSHGCVSKILSRESNLH 178 (197)
Q Consensus 135 lp~~~r~~iv~l~-~~g~r~~~isr~l~vshgcVskil~ry~~~~ 178 (197)
|....-.=+..|+ +.|+.+.+||+.++++.+-||+++.|--+.+
T Consensus 38 lt~~q~~vL~~l~~~~~~t~~eLa~~l~i~~~tvsr~l~~Le~~G 82 (144)
T PRK11512 38 ITAAQFKVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLVCKG 82 (144)
T ss_pred CCHHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCC
Confidence 4433333333444 4568999999999999999999999875543
No 214
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=60.19 E-value=9.2 Score=31.36 Aligned_cols=43 Identities=23% Similarity=0.254 Sum_probs=34.2
Q ss_pred CCChHHHHHHHHH-HhcCCCcccchhhhhcccchHHHHHHHhhhh
Q psy10745 134 PLPDVVRQRIVEL-AHNGVRPCDISRQLRVSHGCVSKILSRESNL 177 (197)
Q Consensus 134 plp~~~r~~iv~l-~~~g~r~~~isr~l~vshgcVskil~ry~~~ 177 (197)
-||+..| +|+.| +-.|..-.+||..|++|-+-|-+.|.|-.+.
T Consensus 113 ~Lp~~~r-~v~~L~~~~g~s~~EIA~~LgiS~~tVk~~l~Rar~~ 156 (188)
T PRK12546 113 QLPDEQR-EALILVGASGFSYEEAAEMCGVAVGTVKSRANRARAR 156 (188)
T ss_pred hCCHHHh-HHhhhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 3565555 45555 5899999999999999999999988887653
No 215
>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=59.67 E-value=8.2 Score=32.69 Aligned_cols=42 Identities=12% Similarity=0.254 Sum_probs=33.0
Q ss_pred CCChHHHHHHHHHH-----hcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 134 PLPDVVRQRIVELA-----HNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 134 plp~~~r~~iv~l~-----~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
-||+..| .|+.|. ..|..-.+||..|+||.+-|++|+.|.-+
T Consensus 176 ~L~~~er-~vl~l~ygl~~~~~~t~~EIA~~lgis~~~V~q~~~~al~ 222 (238)
T TIGR02393 176 TLTERER-KVLRMRYGLLDGRPHTLEEVGKEFNVTRERIRQIESKALR 222 (238)
T ss_pred hCCHHHH-HHHHHHhCCCCCCCccHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3565544 466665 48899999999999999999999877644
No 216
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=59.65 E-value=11 Score=30.91 Aligned_cols=37 Identities=30% Similarity=0.470 Sum_probs=31.0
Q ss_pred HHHHHHHHH-hcCCCcccchhhhhcccchHHHHHHHhh
Q psy10745 139 VRQRIVELA-HNGVRPCDISRQLRVSHGCVSKILSRES 175 (197)
Q Consensus 139 ~r~~iv~l~-~~g~r~~~isr~l~vshgcVskil~ry~ 175 (197)
...++|+|. -.|....+||..|+||-..|++-|.+..
T Consensus 139 ~~~~~v~l~~~~Gls~~EIA~~lgiS~~tV~r~l~~aR 176 (185)
T PF07638_consen 139 RQRRVVELRFFEGLSVEEIAERLGISERTVRRRLRRAR 176 (185)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 345677775 5999999999999999999999887654
No 217
>PRK11050 manganese transport regulator MntR; Provisional
Probab=59.33 E-value=7.6 Score=31.31 Aligned_cols=30 Identities=33% Similarity=0.388 Sum_probs=27.7
Q ss_pred cCCCcccchhhhhcccchHHHHHHHhhhhc
Q psy10745 149 NGVRPCDISRQLRVSHGCVSKILSRESNLH 178 (197)
Q Consensus 149 ~g~r~~~isr~l~vshgcVskil~ry~~~~ 178 (197)
.++++.+||+.|+||..-||+.|.+..+.+
T Consensus 50 ~~~t~~eLA~~l~is~stVsr~l~~Le~~G 79 (152)
T PRK11050 50 GEARQVDIAARLGVSQPTVAKMLKRLARDG 79 (152)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHCC
Confidence 678999999999999999999999998864
No 218
>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=58.79 E-value=7.9 Score=34.12 Aligned_cols=42 Identities=17% Similarity=0.130 Sum_probs=34.8
Q ss_pred CCChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 134 PLPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 134 plp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
.|++.+ .+|++|...|..-.+||+.|+||...|.+-+.+-++
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 566533 678889999999999999999999999996666543
No 219
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=58.74 E-value=8 Score=30.75 Aligned_cols=40 Identities=23% Similarity=0.338 Sum_probs=33.3
Q ss_pred CChHHHHHHHHHH-hcCCCcccchhhhhcccchHHHHHHHhh
Q psy10745 135 LPDVVRQRIVELA-HNGVRPCDISRQLRVSHGCVSKILSRES 175 (197)
Q Consensus 135 lp~~~r~~iv~l~-~~g~r~~~isr~l~vshgcVskil~ry~ 175 (197)
||+. .++|+.|. -.|..-.+||..|++|-+.|-+-|.|-.
T Consensus 120 L~~~-~r~i~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Ra~ 160 (172)
T PRK09651 120 LNGK-TREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKAT 160 (172)
T ss_pred CCHH-HhHHhhhhhccCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 5554 45777785 6999999999999999999999888864
No 220
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=58.51 E-value=8.4 Score=31.69 Aligned_cols=29 Identities=34% Similarity=0.415 Sum_probs=26.3
Q ss_pred CCCcccchhhhhcccchHHHHHHHhhhhc
Q psy10745 150 GVRPCDISRQLRVSHGCVSKILSRESNLH 178 (197)
Q Consensus 150 g~r~~~isr~l~vshgcVskil~ry~~~~ 178 (197)
-++..|||+.|+||-..||++|+|-.+.+
T Consensus 24 ~~~~~diA~~L~Vsp~sVt~ml~rL~~~G 52 (154)
T COG1321 24 FARTKDIAERLKVSPPSVTEMLKRLERLG 52 (154)
T ss_pred cccHHHHHHHhCCCcHHHHHHHHHHHHCC
Confidence 38999999999999999999999987765
No 221
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=58.47 E-value=5.8 Score=33.38 Aligned_cols=40 Identities=20% Similarity=0.274 Sum_probs=32.3
Q ss_pred CChHHHHHHHHH-HhcCCCcccchhhhhcccchHHHHHHHhh
Q psy10745 135 LPDVVRQRIVEL-AHNGVRPCDISRQLRVSHGCVSKILSRES 175 (197)
Q Consensus 135 lp~~~r~~iv~l-~~~g~r~~~isr~l~vshgcVskil~ry~ 175 (197)
||+. -+.|+.| +-.|....+||..|+||.+-|.+.|.|..
T Consensus 150 L~~~-~r~i~~l~~~~g~s~~EIAe~lgis~~tVk~~l~Rar 190 (231)
T PRK11922 150 LPDA-FRAVFVLRVVEELSVEETAQALGLPEETVKTRLHRAR 190 (231)
T ss_pred CCHH-HhhhheeehhcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 5544 4557777 57999999999999999999998777654
No 222
>PRK09726 antitoxin HipB; Provisional
Probab=58.26 E-value=7.7 Score=28.36 Aligned_cols=27 Identities=11% Similarity=0.384 Sum_probs=24.6
Q ss_pred HhcCCCcccchhhhhcccchHHHHHHH
Q psy10745 147 AHNGVRPCDISRQLRVSHGCVSKILSR 173 (197)
Q Consensus 147 ~~~g~r~~~isr~l~vshgcVskil~r 173 (197)
.+.|+...++|+.++||..-||++.+.
T Consensus 22 ~~~gltq~elA~~~gvs~~tis~~e~g 48 (88)
T PRK09726 22 QQNGWTQSELAKKIGIKQATISNFENN 48 (88)
T ss_pred HHcCCCHHHHHHHHCcCHHHHHHHHCC
Confidence 478999999999999999999999874
No 223
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=57.91 E-value=9.1 Score=31.46 Aligned_cols=34 Identities=12% Similarity=0.139 Sum_probs=29.6
Q ss_pred HHHHHHHhcC---CCcccchhhhhcccchHHHHHHHh
Q psy10745 141 QRIVELAHNG---VRPCDISRQLRVSHGCVSKILSRE 174 (197)
Q Consensus 141 ~~iv~l~~~g---~r~~~isr~l~vshgcVskil~ry 174 (197)
++|++|...| ..--+||++|++|...|.+=+.+-
T Consensus 165 r~Vl~~~~~g~~g~s~~eIa~~l~iS~~Tv~~~~~~~ 201 (225)
T PRK10046 165 NAVRKLFKEPGVQHTAETVAQALTISRTTARRYLEYC 201 (225)
T ss_pred HHHHHHHHcCCCCcCHHHHHHHhCccHHHHHHHHHHH
Confidence 3899999885 788999999999999999977643
No 224
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=57.76 E-value=9.2 Score=29.67 Aligned_cols=36 Identities=3% Similarity=0.150 Sum_probs=29.0
Q ss_pred HHHHHh--cCCCcccchhhhhcccchHHHHHHHhhhhc
Q psy10745 143 IVELAH--NGVRPCDISRQLRVSHGCVSKILSRESNLH 178 (197)
Q Consensus 143 iv~l~~--~g~r~~~isr~l~vshgcVskil~ry~~~~ 178 (197)
+..+.. .|+.+.|||+.++++.+.||+++.|.-+.+
T Consensus 37 L~~l~~~~~~~t~~eLa~~l~~~~~tvt~~v~~Le~~G 74 (144)
T PRK03573 37 LHNIHQLPPEQSQIQLAKAIGIEQPSLVRTLDQLEEKG 74 (144)
T ss_pred HHHHHHcCCCCCHHHHHHHhCCChhhHHHHHHHHHHCC
Confidence 445554 357889999999999999999999986544
No 225
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=57.72 E-value=9.6 Score=33.00 Aligned_cols=43 Identities=23% Similarity=0.142 Sum_probs=33.9
Q ss_pred CCChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 134 PLPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 134 plp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
-||+..|.-++-.+-.|..-.|||..|++|-|.|.+-|.|-.+
T Consensus 116 ~Lp~~~R~v~lL~~~eg~S~~EIAe~LgiS~~tVksrL~Rark 158 (228)
T PRK06704 116 SLNVQQSAILLLKDVFQYSIADIAKVCSVSEGAVKASLFRSRN 158 (228)
T ss_pred hCCHHHhhHhhhHHhhCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4676665544443678999999999999999999998887654
No 226
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=57.38 E-value=9.6 Score=32.89 Aligned_cols=33 Identities=18% Similarity=0.265 Sum_probs=28.2
Q ss_pred ccCCCC-CChHHHHHHHHHH-hcCCCcccchhhhh
Q psy10745 129 FVNGRP-LPDVVRQRIVELA-HNGVRPCDISRQLR 161 (197)
Q Consensus 129 ~~ngrp-lp~~~r~~iv~l~-~~g~r~~~isr~l~ 161 (197)
.+||++ +++++|+||.+.+ +.|-+|...||.|+
T Consensus 21 vLn~~~~Vs~~tr~rV~~~a~elgY~pn~~ar~l~ 55 (343)
T PRK10727 21 VINNSPKASEASRLAVHSAMESLSYHPNANARALA 55 (343)
T ss_pred HhCCCCCCCHHHHHHHHHHHHHHCCCCCHHHHhhh
Confidence 346664 9999999999988 67999999999885
No 227
>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=57.20 E-value=9.4 Score=33.69 Aligned_cols=41 Identities=20% Similarity=0.305 Sum_probs=33.8
Q ss_pred CChHHHHHHHHHHh-----cCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 135 LPDVVRQRIVELAH-----NGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 135 lp~~~r~~iv~l~~-----~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
||+.. ++|+.|.- .+..-.+||..|+||.+-|++|+.|..+
T Consensus 250 L~~re-r~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVrq~~~rAl~ 295 (298)
T TIGR02997 250 LTPRE-RQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKALR 295 (298)
T ss_pred CCHHH-HHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 66555 45777765 7889999999999999999999998643
No 228
>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=57.12 E-value=8.5 Score=32.00 Aligned_cols=39 Identities=31% Similarity=0.333 Sum_probs=33.0
Q ss_pred ChHHHHHHHHHHhcCCCcccchhhhh-cccchHHHHHHHh
Q psy10745 136 PDVVRQRIVELAHNGVRPCDISRQLR-VSHGCVSKILSRE 174 (197)
Q Consensus 136 p~~~r~~iv~l~~~g~r~~~isr~l~-vshgcVskil~ry 174 (197)
.++...++-+|-.+|+.-.+||++|+ ||..-|.=...|-
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 46777889999999999999999999 9998887655553
No 229
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=57.05 E-value=10 Score=32.24 Aligned_cols=33 Identities=18% Similarity=0.497 Sum_probs=28.6
Q ss_pred ccCCCC----CChHHHHHHHHHH-hcCCCcccchhhhh
Q psy10745 129 FVNGRP----LPDVVRQRIVELA-HNGVRPCDISRQLR 161 (197)
Q Consensus 129 ~~ngrp----lp~~~r~~iv~l~-~~g~r~~~isr~l~ 161 (197)
.+||+| +++++|+||.+.+ +.|-+|..+||.|.
T Consensus 20 vLn~~~~~~~Vs~~tr~rV~~~a~elgY~pn~~a~~l~ 57 (328)
T PRK11303 20 VINGKAKQYRVSDKTVEKVMAVVREHNYHPNAVAAGLR 57 (328)
T ss_pred HHcCCCCCCCcCHHHHHHHHHHHHHhCCCCCHHHHHhh
Confidence 357775 9999999999988 67999999999886
No 230
>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=56.88 E-value=11 Score=32.23 Aligned_cols=56 Identities=18% Similarity=0.370 Sum_probs=39.5
Q ss_pred ccCCCC----CChHHHHHHHHHH-hcCCCcccchhhhhc-------------ccchHHH---HHHHhhhhcCccccc
Q psy10745 129 FVNGRP----LPDVVRQRIVELA-HNGVRPCDISRQLRV-------------SHGCVSK---ILSRESNLHNYRLVR 184 (197)
Q Consensus 129 ~~ngrp----lp~~~r~~iv~l~-~~g~r~~~isr~l~v-------------shgcVsk---il~ry~~~~n~~~~~ 184 (197)
.+||++ +++++|+||.+.+ +.|-+|...||.|+- ++--.+. -+..+.+..+|.++-
T Consensus 19 vLn~~~~~~~vs~~tr~rV~~~a~~lgY~pn~~a~~l~~~~~~~Igvi~~~~~~~~~~~~~~~i~~~~~~~gy~~~i 95 (327)
T TIGR02417 19 VINGKAKEYRISQETVERVMAVVREQGYQPNIHAASLRAGRSRTIGLVIPDLENYSYARIAKELEQQCREAGYQLLI 95 (327)
T ss_pred HHcCCCCCCccCHHHHHHHHHHHHHhCCCCCHHHHHhhcCCCceEEEEeCCCCCccHHHHHHHHHHHHHHCCCEEEE
Confidence 457776 9999999999988 679999999988752 1212222 344555667787654
No 231
>PRK15320 transcriptional activator SprB; Provisional
Probab=56.79 E-value=10 Score=34.03 Aligned_cols=40 Identities=10% Similarity=0.163 Sum_probs=32.9
Q ss_pred CChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHhh
Q psy10745 135 LPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRES 175 (197)
Q Consensus 135 lp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~ 175 (197)
|.+.++ .|+.|..+|..--+||.+|.+|...|||=++|-.
T Consensus 165 LSdREI-EVL~LLAkG~SNKEIAekL~LS~KTVSTYKnRLL 204 (251)
T PRK15320 165 VTQAKY-ALLILLSSGHPAIELAKKFGLGTKTVSIYRKKVM 204 (251)
T ss_pred CCHHHH-HHHHHHHcCCCHHHHHHHhccchhhHHHHHHHHH
Confidence 444443 7999999999999999999999999999655543
No 232
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=56.53 E-value=12 Score=30.90 Aligned_cols=41 Identities=20% Similarity=0.217 Sum_probs=32.9
Q ss_pred CChHHHHHHHHHH-hcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 135 LPDVVRQRIVELA-HNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 135 lp~~~r~~iv~l~-~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
||+..| +|+.|. -.|..-.+||..|++|-+.|-+-|.|..+
T Consensus 134 Lp~~~r-~v~~l~~~~g~s~~EIAe~lgis~~tV~~~l~Rar~ 175 (196)
T PRK12535 134 LPPERR-EALILTQVLGYTYEEAAKIADVRVGTIRSRVARARA 175 (196)
T ss_pred CCHHHH-HHhhhHHHhCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 565554 555555 59999999999999999999998887654
No 233
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=56.38 E-value=19 Score=24.05 Aligned_cols=42 Identities=14% Similarity=0.086 Sum_probs=31.6
Q ss_pred CChHHHHHHHHHH-hcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 135 LPDVVRQRIVELA-HNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 135 lp~~~r~~iv~l~-~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
|+.+++.=++=++ .+|..=.++|-..+||.++||+|....-+
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 4445554444443 67888999999999999999999877544
No 234
>cd00093 HTH_XRE Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.
Probab=56.32 E-value=6.1 Score=23.59 Aligned_cols=28 Identities=21% Similarity=0.362 Sum_probs=24.0
Q ss_pred HHhcCCCcccchhhhhcccchHHHHHHH
Q psy10745 146 LAHNGVRPCDISRQLRVSHGCVSKILSR 173 (197)
Q Consensus 146 l~~~g~r~~~isr~l~vshgcVskil~r 173 (197)
+...|+..-++|+.+++|.+-|+++++-
T Consensus 8 ~~~~~~s~~~~a~~~~~~~~~v~~~~~g 35 (58)
T cd00093 8 RKEKGLTQEELAEKLGVSRSTISRIENG 35 (58)
T ss_pred HHHcCCCHHHHHHHHCCCHHHHHHHHcC
Confidence 4467999999999999999999997664
No 235
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=55.91 E-value=6 Score=23.45 Aligned_cols=29 Identities=21% Similarity=0.353 Sum_probs=24.7
Q ss_pred HHhcCCCcccchhhhhcccchHHHHHHHh
Q psy10745 146 LAHNGVRPCDISRQLRVSHGCVSKILSRE 174 (197)
Q Consensus 146 l~~~g~r~~~isr~l~vshgcVskil~ry 174 (197)
+...|+...++|+.+++|..-||++++..
T Consensus 6 ~~~~~~s~~~la~~~~i~~~~i~~~~~~~ 34 (56)
T smart00530 6 REEKGLTQEELAEKLGVSRSTLSRIENGK 34 (56)
T ss_pred HHHcCCCHHHHHHHhCCCHHHHHHHHCCC
Confidence 45678999999999999999999987643
No 236
>PRK11233 nitrogen assimilation transcriptional regulator; Provisional
Probab=55.75 E-value=9.4 Score=32.72 Aligned_cols=45 Identities=13% Similarity=0.169 Sum_probs=38.6
Q ss_pred HHHHHHhcCCCcccchhhhhcccchHHHHHHHhhhhcCcccccccc
Q psy10745 142 RIVELAHNGVRPCDISRQLRVSHGCVSKILSRESNLHNYRLVREEG 187 (197)
Q Consensus 142 ~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~~~n~~~~~~~~ 187 (197)
-.+.++++| .-...|+.|+||+.-||+-+.+..+.-+.+|+.-+|
T Consensus 8 ~F~~v~~~~-S~s~AA~~L~isQ~avS~~I~~LE~~lg~~LF~R~~ 52 (305)
T PRK11233 8 YFVKIVDIG-SLTQAAEVLHIAQPALSQQVATLEGELNQQLLIRTK 52 (305)
T ss_pred HHHHHHHcC-CHHHHHHHhCCCchHHHHHHHHHHHHhCCceEEeCC
Confidence 356778887 778889999999999999999999999999976544
No 237
>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=55.62 E-value=8.1 Score=28.92 Aligned_cols=34 Identities=15% Similarity=0.071 Sum_probs=27.0
Q ss_pred HHHHHHHHHhc-CCCcccchhhhhcccchHHHHHH
Q psy10745 139 VRQRIVELAHN-GVRPCDISRQLRVSHGCVSKILS 172 (197)
Q Consensus 139 ~r~~iv~l~~~-g~r~~~isr~l~vshgcVskil~ 172 (197)
=+++|+|+... -+..-|||+.++||-..||..|+
T Consensus 7 R~~~I~e~l~~~~~ti~dvA~~~gvS~~TVsr~L~ 41 (80)
T TIGR02844 7 RVLEIGKYIVETKATVRETAKVFGVSKSTVHKDVT 41 (80)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHhc
Confidence 35678887765 34556899999999999999884
No 238
>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=55.50 E-value=11 Score=28.75 Aligned_cols=34 Identities=18% Similarity=0.270 Sum_probs=30.7
Q ss_pred hHHHHHHHH-HHhcCCCcccchhhhhcccchHHHH
Q psy10745 137 DVVRQRIVE-LAHNGVRPCDISRQLRVSHGCVSKI 170 (197)
Q Consensus 137 ~~~r~~iv~-l~~~g~r~~~isr~l~vshgcVski 170 (197)
+..|-+|+. |-..|+.--+||..++||-..||.+
T Consensus 35 l~~R~~va~~lL~~g~syreIa~~tgvS~aTItRv 69 (87)
T PF01371_consen 35 LAQRWQVAKELLDEGKSYREIAEETGVSIATITRV 69 (87)
T ss_dssp HHHHHHHHHHHHHTTSSHHHHHHHHTSTHHHHHHH
T ss_pred HHHHHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHH
Confidence 467899998 9999999999999999999988874
No 239
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=54.94 E-value=5.5 Score=31.29 Aligned_cols=41 Identities=20% Similarity=0.191 Sum_probs=33.7
Q ss_pred CChHHHHHHHHH-HhcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 135 LPDVVRQRIVEL-AHNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 135 lp~~~r~~iv~l-~~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
||+..| .|+.| +-.|.+..+||..|++|.+-|.+.|.|-.+
T Consensus 121 L~~~~r-~vl~l~~~~g~s~~eIA~~lg~s~~tv~~~l~Rar~ 162 (175)
T PRK12518 121 LSLEHR-AVLVLHDLEDLPQKEIAEILNIPVGTVKSRLFYARR 162 (175)
T ss_pred CCHHHe-eeeeehHhcCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 564444 67777 579999999999999999999998888643
No 240
>PF07508 Recombinase: Recombinase; InterPro: IPR011109 This domain is usually found associated with IPR006119 from INTERPRO in putative integrases/recombinases of mobile genetic elements of diverse bacteria and phages.
Probab=54.92 E-value=18 Score=26.06 Aligned_cols=49 Identities=20% Similarity=0.144 Sum_probs=38.7
Q ss_pred HHHHHHHHHHHhCCCcchHHhHHHHHhcCCCCCCCCC-CccccccccccccC
Q psy10745 37 PVVDAIASYKRENPTMFAWEIRDRLLAEGICSQDNVP-SVSSINRYITYVPI 87 (197)
Q Consensus 37 ~v~~~I~~~k~e~P~iFaWEIRdrLl~~GvC~~~~vP-SvSSI~Rilr~~~i 87 (197)
+++..|-++.. -+....+|-..|-++|+-.+...+ +.++|+++|+|..+
T Consensus 5 ~vVr~if~~~~--~g~s~~~I~~~ln~~gi~~~~~~~W~~~~v~~iL~np~y 54 (102)
T PF07508_consen 5 EVVREIFELYL--EGYSLRQIARELNEKGIPTPRGKKWSKSTVRRILRNPAY 54 (102)
T ss_pred HHHHHHHHHHH--cCCCHHHHHHHHHhcCCccccCCcccHHHHHHHHhhhhc
Confidence 45666666555 456779999999999998777777 89999999998653
No 241
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=54.28 E-value=12 Score=33.13 Aligned_cols=44 Identities=14% Similarity=0.062 Sum_probs=35.4
Q ss_pred CCChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHhhhh
Q psy10745 134 PLPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESNL 177 (197)
Q Consensus 134 plp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~~ 177 (197)
-||+..|.=++=-.-.|+.-.|||..|++|-+-|.+.|.|-.+.
T Consensus 118 ~L~p~~R~vf~L~~~~g~s~~EIA~~Lgis~~tVr~~l~RAr~~ 161 (290)
T PRK09635 118 RLGPAERVVFVLHEIFGLPYQQIATTIGSQASTCRQLAHRARRK 161 (290)
T ss_pred hCCHHHHHHhhHHHHhCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 36666555444445799999999999999999999999988654
No 242
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=54.27 E-value=11 Score=33.26 Aligned_cols=41 Identities=22% Similarity=0.301 Sum_probs=32.2
Q ss_pred CChHHHHHHHHHHh---cCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 135 LPDVVRQRIVELAH---NGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 135 lp~~~r~~iv~l~~---~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
||+. -++|+.|.- .|..-.+||+.|+||.+-|++|+.|.-+
T Consensus 228 L~~r-er~vl~lr~~~~~~~t~~EIa~~lgvs~~~V~q~~~~Al~ 271 (289)
T PRK07500 228 LNER-ELRIIRERRLREDGATLEALGEELGISKERVRQIEARALE 271 (289)
T ss_pred CCHH-HHHHHHHHhcCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4433 345777753 7999999999999999999999887644
No 243
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=54.26 E-value=7.4 Score=27.95 Aligned_cols=26 Identities=27% Similarity=0.401 Sum_probs=23.2
Q ss_pred CcccchhhhhcccchHHHHHHHhhhh
Q psy10745 152 RPCDISRQLRVSHGCVSKILSRESNL 177 (197)
Q Consensus 152 r~~~isr~l~vshgcVskil~ry~~~ 177 (197)
|+-+||+.++||.+-||++|.+-.+.
T Consensus 1 ~~~ela~~l~is~stvs~~l~~L~~~ 26 (96)
T smart00529 1 RTSEIAERLNVSPPTVTQMLKKLEKD 26 (96)
T ss_pred CHHHHHHHhCCChHHHHHHHHHHHHC
Confidence 45689999999999999999998775
No 244
>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=53.67 E-value=13 Score=27.35 Aligned_cols=40 Identities=25% Similarity=0.336 Sum_probs=32.1
Q ss_pred HHHHHHHHHHh--cCCCcccchhhhh-cccchHHHHHHHhhhh
Q psy10745 138 VVRQRIVELAH--NGVRPCDISRQLR-VSHGCVSKILSRESNL 177 (197)
Q Consensus 138 ~~r~~iv~l~~--~g~r~~~isr~l~-vshgcVskil~ry~~~ 177 (197)
.-|+=.+-|++ .|+.-.+|++.++ .+|.+|++-+.|..+.
T Consensus 30 ~aR~ia~yl~~~~~~~s~~~Ig~~fg~r~hStV~~a~~ri~~~ 72 (90)
T cd06571 30 LARQIAMYLARELTGLSLPEIGRAFGGRDHSTVLHAVRKIEEL 72 (90)
T ss_pred hHHHHHHHHHHHHhCCCHHHHHHHhCCCCHhHHHHHHHHHHHH
Confidence 34555566664 4899999999999 9999999999888763
No 245
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=53.63 E-value=6.8 Score=31.55 Aligned_cols=38 Identities=26% Similarity=0.433 Sum_probs=31.7
Q ss_pred HHHHHH-HHHHhcCCCcccchhhhhcccchHHHHHHHhh
Q psy10745 138 VVRQRI-VELAHNGVRPCDISRQLRVSHGCVSKILSRES 175 (197)
Q Consensus 138 ~~r~~i-v~l~~~g~r~~~isr~l~vshgcVskil~ry~ 175 (197)
.+|-++ -+|...|.+--+||..|+||..-||+=|.-+.
T Consensus 9 aiRa~lA~~L~eeG~Sq~~iA~LLGltqaAVS~Yls~kr 47 (119)
T COG2522 9 AIRALLAKELIEEGLSQYRIAKLLGLTQAAVSQYLSGKR 47 (119)
T ss_pred HHHHHHHHHHHHcCCcHHHHHHHhCCCHHHHHHHHccCC
Confidence 456555 47899999999999999999999999776553
No 246
>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=53.46 E-value=10 Score=29.15 Aligned_cols=36 Identities=31% Similarity=0.319 Sum_probs=29.3
Q ss_pred HHHHHhcC---CCcccchhhhhcccchHHHHHHHhhhhc
Q psy10745 143 IVELAHNG---VRPCDISRQLRVSHGCVSKILSRESNLH 178 (197)
Q Consensus 143 iv~l~~~g---~r~~~isr~l~vshgcVskil~ry~~~~ 178 (197)
++.|++.+ +...+||++++||..-|+|+|.+-.+.+
T Consensus 15 l~~la~~~~~~~s~~eia~~l~is~~~v~~~l~~L~~~G 53 (130)
T TIGR02944 15 LTTLAQNDSQPYSAAEIAEQTGLNAPTVSKILKQLSLAG 53 (130)
T ss_pred HHHHHhCCCCCccHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence 44566543 6778999999999999999999887765
No 247
>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=53.37 E-value=4.7 Score=27.76 Aligned_cols=32 Identities=16% Similarity=0.185 Sum_probs=28.2
Q ss_pred HhcCCCcccchhhhhcccchHHHHHHHhhhhc
Q psy10745 147 AHNGVRPCDISRQLRVSHGCVSKILSRESNLH 178 (197)
Q Consensus 147 ~~~g~r~~~isr~l~vshgcVskil~ry~~~~ 178 (197)
.+.++...|||+.+++|..-|+++|.+-.+.+
T Consensus 19 ~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~G 50 (68)
T PF01978_consen 19 KNGPATAEEIAEELGISRSTVYRALKSLEEKG 50 (68)
T ss_dssp HHCHEEHHHHHHHHTSSHHHHHHHHHHHHHTT
T ss_pred HcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence 47788999999999999999999999886654
No 248
>PHA02535 P terminase ATPase subunit; Provisional
Probab=53.34 E-value=9.9 Score=37.90 Aligned_cols=41 Identities=20% Similarity=0.217 Sum_probs=35.2
Q ss_pred CChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHhh
Q psy10745 135 LPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRES 175 (197)
Q Consensus 135 lp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~ 175 (197)
.+++.|...+.|+.+|.++.+||++|+|+...|.+=-.||.
T Consensus 3 yt~EfK~~Av~Ly~~G~sv~eIA~~LGv~~~Tl~~W~kr~~ 43 (581)
T PHA02535 3 YDDDVRRAAKFLYWQGWTVAEIAEELGLKSRTIYSWKERDG 43 (581)
T ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHhCCChhHHHHHhcccc
Confidence 46788999999999999999999999999887777655554
No 249
>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=52.87 E-value=7.1 Score=24.94 Aligned_cols=28 Identities=11% Similarity=0.165 Sum_probs=24.7
Q ss_pred HhcCCCcccchhhhhcccchHHHHHHHh
Q psy10745 147 AHNGVRPCDISRQLRVSHGCVSKILSRE 174 (197)
Q Consensus 147 ~~~g~r~~~isr~l~vshgcVskil~ry 174 (197)
.+.|+...|.|+.++||..-||++.+.-
T Consensus 12 ~~~gltq~~lA~~~gvs~~~vs~~e~g~ 39 (58)
T TIGR03070 12 KALGLTQADLADLAGVGLRFIRDVENGK 39 (58)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHCCC
Confidence 3679999999999999999999998653
No 250
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=52.79 E-value=14 Score=31.37 Aligned_cols=32 Identities=13% Similarity=0.347 Sum_probs=27.6
Q ss_pred cCCCC-CChHHHHHHHHHH-hcCCCcccchhhhh
Q psy10745 130 VNGRP-LPDVVRQRIVELA-HNGVRPCDISRQLR 161 (197)
Q Consensus 130 ~ngrp-lp~~~r~~iv~l~-~~g~r~~~isr~l~ 161 (197)
+||++ +++++|+||.+.+ +.|-+|..+||.|+
T Consensus 19 Ln~~~~vs~~tr~rV~~~a~~lgY~pn~~a~~l~ 52 (327)
T PRK10423 19 INKDRFVSEAITAKVEAAIKELNYAPSALARSLK 52 (327)
T ss_pred hCCCCCCCHHHHHHHHHHHHHHCCCccHHHHHHh
Confidence 46664 9999999999998 78999999999875
No 251
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=52.55 E-value=13 Score=28.59 Aligned_cols=42 Identities=19% Similarity=0.209 Sum_probs=33.4
Q ss_pred CCChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 134 PLPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 134 plp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
+|...+ ..|++|...|+.-.+||++|.+|-.+|.+-+.|-++
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 455433 478999999999999999999999999886666443
No 252
>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=52.01 E-value=9.2 Score=28.82 Aligned_cols=31 Identities=13% Similarity=0.137 Sum_probs=27.0
Q ss_pred hcCCCcccchhhhhcccchHHHHHHHhhhhc
Q psy10745 148 HNGVRPCDISRQLRVSHGCVSKILSRESNLH 178 (197)
Q Consensus 148 ~~g~r~~~isr~l~vshgcVskil~ry~~~~ 178 (197)
+.++.+.+||+.++++..-||++|.+..+.+
T Consensus 40 ~~~~t~~ela~~~~~~~~tvs~~l~~Le~~G 70 (118)
T TIGR02337 40 QGSMEFTQLANQACILRPSLTGILARLERDG 70 (118)
T ss_pred cCCcCHHHHHHHhCCCchhHHHHHHHHHHCC
Confidence 4577899999999999999999999986653
No 253
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=51.68 E-value=10 Score=24.30 Aligned_cols=42 Identities=29% Similarity=0.315 Sum_probs=29.9
Q ss_pred hHHHHHHHHH-HhcC--C-CcccchhhhhcccchHHHHHHHhhhhc
Q psy10745 137 DVVRQRIVEL-AHNG--V-RPCDISRQLRVSHGCVSKILSRESNLH 178 (197)
Q Consensus 137 ~~~r~~iv~l-~~~g--~-r~~~isr~l~vshgcVskil~ry~~~~ 178 (197)
++++++|+.- ...| + ..-+||+.++||..-|++.|.+-.+.+
T Consensus 3 ~~l~~~i~~~~~~~~~~l~s~~~la~~~~vs~~tv~~~l~~L~~~g 48 (60)
T smart00345 3 ERLREDIVSGELRPGDKLPSERELAAQLGVSRTTVREALSRLEAEG 48 (60)
T ss_pred HHHHHHHHcCCCCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCC
Confidence 4555665553 1223 2 455789999999999999999987764
No 254
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=51.19 E-value=8.4 Score=35.42 Aligned_cols=32 Identities=22% Similarity=0.405 Sum_probs=29.8
Q ss_pred HhcCCCcccchhhhhcccchHHHHHHHhhhhc
Q psy10745 147 AHNGVRPCDISRQLRVSHGCVSKILSRESNLH 178 (197)
Q Consensus 147 ~~~g~r~~~isr~l~vshgcVskil~ry~~~~ 178 (197)
+.+|+.-.+||++|+||+--||+.|.+..+.+
T Consensus 23 Y~~gltQ~eIA~~LgiSR~~v~rlL~~Ar~~G 54 (321)
T COG2390 23 YVEGLTQSEIAERLGISRATVSRLLAKAREEG 54 (321)
T ss_pred HhcCCCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence 48999999999999999999999999998765
No 255
>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=50.96 E-value=6.7 Score=25.88 Aligned_cols=30 Identities=20% Similarity=0.509 Sum_probs=24.9
Q ss_pred HhcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 147 AHNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 147 ~~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
.+.++...+||+.++++++-||+++.+-.+
T Consensus 14 ~~~~~~~~~la~~~~~~~~~~t~~i~~L~~ 43 (59)
T PF01047_consen 14 ENGGITQSELAEKLGISRSTVTRIIKRLEK 43 (59)
T ss_dssp HHSSEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HcCCCCHHHHHHHHCCChhHHHHHHHHHHH
Confidence 366789999999999999999999987644
No 256
>PRK10403 transcriptional regulator NarP; Provisional
Probab=50.83 E-value=14 Score=28.22 Aligned_cols=41 Identities=15% Similarity=0.139 Sum_probs=33.4
Q ss_pred CChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 135 LPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 135 lp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
|...+. +|+++...|+...+||+.|++|-..|..-+.|-++
T Consensus 154 Lt~~e~-~vl~~~~~g~s~~~ia~~l~~s~~tv~~~~~~i~~ 194 (215)
T PRK10403 154 LTEREL-DVLHELAQGLSNKQIASVLNISEQTVKVHIRNLLR 194 (215)
T ss_pred CCHHHH-HHHHHHHCCCCHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 554444 68999999999999999999999998886666544
No 257
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=49.98 E-value=21 Score=30.59 Aligned_cols=46 Identities=15% Similarity=0.161 Sum_probs=40.3
Q ss_pred HHHHHHhcCCCcccchhhhhcccchHHHHHHHhhhhcCcccccccc
Q psy10745 142 RIVELAHNGVRPCDISRQLRVSHGCVSKILSRESNLHNYRLVREEG 187 (197)
Q Consensus 142 ~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~~~n~~~~~~~~ 187 (197)
-.+++++.|-.-...|++|.||...||+-+.+..+.-+.+|+.-+|
T Consensus 8 ~F~~v~~~~~s~s~AA~~L~isq~avSr~I~~LE~~lg~~LF~R~~ 53 (309)
T PRK12682 8 FVREAVRRNLNLTEAAKALHTSQPGVSKAIIELEEELGIEIFIRHG 53 (309)
T ss_pred HHHHHHHccCCHHHHHHHhcCccHHHHHHHHHHHHHhCCeeEEECC
Confidence 3557888888889999999999999999999999999999986543
No 258
>cd07498 Peptidases_S8_15 Peptidase S8 family domain, uncharacterized subfamily 15. This family is a member of the Peptidases S8 or Subtilases serine endo- and exo-peptidase clan. They have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The stability of subtilases may be enhanced by calcium, some members have been shown to bind up to 4 ions via binding sites with different affinity. Some members of this clan contain disulfide bonds. These enzymes can be intra- and extracellular, some function at extreme temperatures and pH values.
Probab=48.65 E-value=16 Score=30.21 Aligned_cols=33 Identities=21% Similarity=0.224 Sum_probs=28.4
Q ss_pred CCcCCHHHHHHHHHHHHhCCCcchHHhHHHHHh
Q psy10745 31 PKVATAPVVDAIASYKRENPTMFAWEIRDRLLA 63 (197)
Q Consensus 31 pk~~tp~v~~~I~~~k~e~P~iFaWEIRdrLl~ 63 (197)
.+.++|-|+..+.-+++++|++...|||+.|..
T Consensus 209 TS~Aap~vaG~~All~~~~p~l~~~~i~~~L~~ 241 (242)
T cd07498 209 TSFASPVAAGVAALILSANPNLTPAEVEDILTS 241 (242)
T ss_pred HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHh
Confidence 346788888888888999999999999999874
No 259
>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=48.04 E-value=10 Score=26.28 Aligned_cols=27 Identities=22% Similarity=0.343 Sum_probs=23.4
Q ss_pred CCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 150 GVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 150 g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
++.-.|+|+.|+||...||..|.|-.+
T Consensus 23 ~~tl~elA~~lgis~st~~~~LRrae~ 49 (53)
T PF04967_consen 23 RITLEELAEELGISKSTVSEHLRRAER 49 (53)
T ss_pred cCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 466778999999999999999998754
No 260
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=47.65 E-value=16 Score=28.29 Aligned_cols=39 Identities=23% Similarity=0.273 Sum_probs=32.8
Q ss_pred CCChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHH
Q psy10745 134 PLPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSR 173 (197)
Q Consensus 134 plp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~r 173 (197)
+|...++ +|+++...|....+||+.+.+|...|.+-+.|
T Consensus 143 ~lt~~E~-~vl~~l~~g~~~~~I~~~l~~s~~tv~~~~~~ 181 (204)
T PRK09958 143 SLSKQEI-SVMRYILDGKDNNDIAEKMFISNKTVSTYKSR 181 (204)
T ss_pred cCCHHHH-HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 4666554 69999999999999999999999999885554
No 261
>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=47.61 E-value=23 Score=30.01 Aligned_cols=53 Identities=17% Similarity=0.250 Sum_probs=46.2
Q ss_pred cccCCCCCChHHHHHHHHHH-hcCCCcccchhhhhcccchHHHHHHHhhhhcCc
Q psy10745 128 VFVNGRPLPDVVRQRIVELA-HNGVRPCDISRQLRVSHGCVSKILSRESNLHNY 180 (197)
Q Consensus 128 ~~~ngrplp~~~r~~iv~l~-~~g~r~~~isr~l~vshgcVskil~ry~~~~n~ 180 (197)
.|..-.+|++++|.+|.++. ..|...-++|.+.+|+--=|--||.-+.-+..+
T Consensus 10 ~f~~~~~lse~~r~~Iy~~~~~~~~sv~~vS~~ygi~~~RV~AIvrLkeiE~~~ 63 (172)
T PF12298_consen 10 SFRSNPVLSEELREQIYEDVMQDGKSVREVSQKYGIKIQRVEAIVRLKEIEKRW 63 (172)
T ss_pred CCCCCCcCCHHHHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 47778899999999999998 778899999999999999999999887766554
No 262
>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=47.39 E-value=19 Score=29.99 Aligned_cols=39 Identities=15% Similarity=0.180 Sum_probs=31.6
Q ss_pred HHHHHHHHHhc--CCCcccchhhhhcccchHHHHHHHhhhh
Q psy10745 139 VRQRIVELAHN--GVRPCDISRQLRVSHGCVSKILSRESNL 177 (197)
Q Consensus 139 ~r~~iv~l~~~--g~r~~~isr~l~vshgcVskil~ry~~~ 177 (197)
...+|+.+..+ +++..+||+.+++|...|++.|.+-.+.
T Consensus 144 ~~~~IL~~l~~~g~~s~~eia~~l~is~stv~r~L~~Le~~ 184 (203)
T TIGR01884 144 EELKVLEVLKAEGEKSVKNIAKKLGKSLSTISRHLRELEKK 184 (203)
T ss_pred HHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 34577776654 5789999999999999999999986554
No 263
>COG0856 Orotate phosphoribosyltransferase homologs [Nucleotide transport and metabolism]
Probab=46.77 E-value=23 Score=31.04 Aligned_cols=42 Identities=21% Similarity=0.331 Sum_probs=37.5
Q ss_pred hHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHhhhhc
Q psy10745 137 DVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESNLH 178 (197)
Q Consensus 137 ~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~~~ 178 (197)
+++-+|-+||...|+.--+||..|.||.-.++-+|.|.+...
T Consensus 5 eeLi~kA~eLk~~Glt~gEIAdELNvSreTa~WL~~r~~~~~ 46 (203)
T COG0856 5 EELIKKARELKSKGLTTGEIADELNVSRETATWLLTRAFKKE 46 (203)
T ss_pred HHHHHHHHHHHHCCCcHHHhhhhhhhhHHHHHHHHhhhhhcc
Confidence 367789999999999999999999999999999999966543
No 264
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=46.45 E-value=17 Score=31.38 Aligned_cols=41 Identities=15% Similarity=0.181 Sum_probs=32.9
Q ss_pred CCChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHhh
Q psy10745 134 PLPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRES 175 (197)
Q Consensus 134 plp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~ 175 (197)
.|.+-+ .+|+.+...|..--|||..|+||...|.+-|.+-+
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 354333 46999999999999999999999999988555544
No 265
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=46.30 E-value=19 Score=30.91 Aligned_cols=32 Identities=16% Similarity=0.271 Sum_probs=27.7
Q ss_pred cCCC-CCChHHHHHHHHHH-hcCCCcccchhhhh
Q psy10745 130 VNGR-PLPDVVRQRIVELA-HNGVRPCDISRQLR 161 (197)
Q Consensus 130 ~ngr-plp~~~r~~iv~l~-~~g~r~~~isr~l~ 161 (197)
+||+ .++++.|+||.+.+ +.|-.|..+||.|.
T Consensus 22 Ln~~~~vs~~tr~~V~~~a~elgY~pn~~a~~l~ 55 (341)
T PRK10703 22 INKTRFVAEETRNAVWAAIKELHYSPSAVARSLK 55 (341)
T ss_pred HcCCCCCCHHHHHHHHHHHHHHCCCcCHHHHHHh
Confidence 3555 59999999999999 78999999999885
No 266
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=45.86 E-value=15 Score=30.00 Aligned_cols=41 Identities=15% Similarity=0.162 Sum_probs=30.1
Q ss_pred CCCCCChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHH
Q psy10745 131 NGRPLPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILS 172 (197)
Q Consensus 131 ngrplp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ 172 (197)
|++++....|.|-+ ..+.|+...++|++++||.+-||+|.+
T Consensus 2 ~~~~~~~g~~l~~~-R~~~glt~~elA~~~gis~~~is~~E~ 42 (185)
T PRK09943 2 SDEGLAPGKRLSEI-RQQQGLSQRRAAELSGLTHSAISTIEQ 42 (185)
T ss_pred cchhhHHHHHHHHH-HHHcCCCHHHHHHHHCCCHHHHHHHHc
Confidence 34444434444433 347899999999999999999999875
No 267
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=45.84 E-value=20 Score=28.61 Aligned_cols=42 Identities=17% Similarity=0.250 Sum_probs=31.9
Q ss_pred hHHHHHHHHHHhcC--CCcccchhhhhcccchHHHHHHHhhhhc
Q psy10745 137 DVVRQRIVELAHNG--VRPCDISRQLRVSHGCVSKILSRESNLH 178 (197)
Q Consensus 137 ~~~r~~iv~l~~~g--~r~~~isr~l~vshgcVskil~ry~~~~ 178 (197)
++.=.+|+++.+.. ....+||++|++|...|..=+.|-.+.+
T Consensus 8 D~~D~~Il~~Lq~d~R~s~~eiA~~lglS~~tV~~Ri~rL~~~G 51 (153)
T PRK11179 8 DNLDRGILEALMENARTPYAELAKQFGVSPGTIHVRVEKMKQAG 51 (153)
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence 34566787777766 4557899999999999998777765544
No 268
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=45.79 E-value=20 Score=32.43 Aligned_cols=42 Identities=17% Similarity=0.233 Sum_probs=32.2
Q ss_pred CCChHHHHHHHHHH-----hcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 134 PLPDVVRQRIVELA-----HNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 134 plp~~~r~~iv~l~-----~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
-||+..|. +|.|. ..|..-.+||..|+||-+-|++++.|..+
T Consensus 262 ~L~~~~R~-vl~lrygL~~~e~~s~~EIA~~Lgis~~tV~~~~~rAl~ 308 (325)
T PRK05657 262 ELNDKQRE-VLARRFGLLGYEAATLEDVAREIGLTRERVRQIQVEALR 308 (325)
T ss_pred cCCHHHHH-HHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 35655554 44432 68999999999999999999999887643
No 269
>COG1961 PinR Site-specific recombinases, DNA invertase Pin homologs [DNA replication, recombination, and repair]
Probab=45.66 E-value=16 Score=30.51 Aligned_cols=49 Identities=22% Similarity=0.311 Sum_probs=42.9
Q ss_pred ccCCCCCChHHHHHHHHHHhcC-CCcccchhhhhcccchHHHHHHHhhhh
Q psy10745 129 FVNGRPLPDVVRQRIVELAHNG-VRPCDISRQLRVSHGCVSKILSRESNL 177 (197)
Q Consensus 129 ~~ngrplp~~~r~~iv~l~~~g-~r~~~isr~l~vshgcVskil~ry~~~ 177 (197)
...+++...+.+..|.+|...| .....|++.+.+|...|.++++.+...
T Consensus 155 ~~~~~~~~~~~~~~v~~l~~~~~~~~~~~a~~~~i~~~t~~r~~~~~~~~ 204 (222)
T COG1961 155 IKKGRKKAEEQAAAVRRLLADGLGSYSEIARALGISRSTVYRILNKLKKR 204 (222)
T ss_pred ccccccccchhHHHHHHHHHhccchHHHHHHHcCccHHHHHHhhhhhhcc
Confidence 3456788889999999999999 799999999999999999999886543
No 270
>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=45.41 E-value=15 Score=26.73 Aligned_cols=41 Identities=22% Similarity=0.184 Sum_probs=30.4
Q ss_pred HHHHHHHHHhCCCcchHHhHHHHHhcCCCCCCCCCCcccccccccc
Q psy10745 39 VDAIASYKRENPTMFAWEIRDRLLAEGICSQDNVPSVSSINRYITY 84 (197)
Q Consensus 39 ~~~I~~~k~e~P~iFaWEIRdrLl~~GvC~~~~vPSvSSI~Rilr~ 84 (197)
.++|.++-.+++=-.--||.+.|.+.|+.. +-++|||-|+.
T Consensus 7 ~~~I~~li~~~~i~sQ~eL~~~L~~~Gi~v-----TQaTiSRDLke 47 (70)
T PF01316_consen 7 QELIKELISEHEISSQEELVELLEEEGIEV-----TQATISRDLKE 47 (70)
T ss_dssp HHHHHHHHHHS---SHHHHHHHHHHTT-T-------HHHHHHHHHH
T ss_pred HHHHHHHHHHCCcCCHHHHHHHHHHcCCCc-----chhHHHHHHHH
Confidence 457788878888778889999999999988 89999999975
No 271
>PRK01905 DNA-binding protein Fis; Provisional
Probab=45.39 E-value=13 Score=26.91 Aligned_cols=40 Identities=13% Similarity=0.129 Sum_probs=31.0
Q ss_pred ChHHHHHHHHHH-hcCCCcccchhhhhcccchHHHHHHHhh
Q psy10745 136 PDVVRQRIVELA-HNGVRPCDISRQLRVSHGCVSKILSRES 175 (197)
Q Consensus 136 p~~~r~~iv~l~-~~g~r~~~isr~l~vshgcVskil~ry~ 175 (197)
....+.-|.++. ..|-.....|++|+||..++.+.|.+|.
T Consensus 35 ~~~E~~~i~~aL~~~~gn~s~aAr~LGIsrstL~rklkk~g 75 (77)
T PRK01905 35 SCVEKPLLEVVMEQAGGNQSLAAEYLGINRNTLRKKLQQHG 75 (77)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHhC
Confidence 334555666654 5677788899999999999999999973
No 272
>TIGR03643 conserved hypothetical protein TIGR03643. This model describes an uncharacterized bacterial protein family. Members average about 90 amino acids in length with several well-conserved uncommon amino acids (Trp, Met). The majority of species are marine bacteria. Few species have more than one copy, but Vibrio cholerae El Tor N16961 has three identical copies.
Probab=45.23 E-value=9.6 Score=28.51 Aligned_cols=45 Identities=27% Similarity=0.406 Sum_probs=37.2
Q ss_pred HHHHHHHHhcCCCc-ccchhhhhcccchHHHHHHHhhhhcCccccc
Q psy10745 140 RQRIVELAHNGVRP-CDISRQLRVSHGCVSKILSRESNLHNYRLVR 184 (197)
Q Consensus 140 r~~iv~l~~~g~r~-~~isr~l~vshgcVskil~ry~~~~n~~~~~ 184 (197)
..+|||||-+--.| ..|-.|.++|+.=|=+|+.+--+...|.+-+
T Consensus 2 ~~riIeMAweDRtpFeaI~~~fGL~E~eVi~lMR~~lk~~Sfk~WR 47 (72)
T TIGR03643 2 IDRIIEMAWEDRTPFEAIEQQFGLSEKEVIKLMRQNLKPSSFKLWR 47 (72)
T ss_pred HHHHHHHHHccCCCHHHHHHHHCCCHHHHHHHHHhhcChhHHHHHH
Confidence 35899999766555 6679999999999999999988888777654
No 273
>PRK03341 arginine repressor; Provisional
Probab=45.17 E-value=17 Score=30.53 Aligned_cols=43 Identities=16% Similarity=0.123 Sum_probs=38.6
Q ss_pred HHHHHHHHHHHhCCCcchHHhHHHHHhcCCCCCCCCCCcccccccccc
Q psy10745 37 PVVDAIASYKRENPTMFAWEIRDRLLAEGICSQDNVPSVSSINRYITY 84 (197)
Q Consensus 37 ~v~~~I~~~k~e~P~iFaWEIRdrLl~~GvC~~~~vPSvSSI~Rilr~ 84 (197)
+--++|.++-++++-..--||.+.|.++|+.. |-++|+|-|+.
T Consensus 15 ~R~~~I~~li~~~~i~tQ~eL~~~L~~~Gi~v-----TQaTiSRDl~e 57 (168)
T PRK03341 15 ARQARIVAILSRQSVRSQAELAALLADEGIEV-----TQATLSRDLDE 57 (168)
T ss_pred HHHHHHHHHHHHCCCccHHHHHHHHHHcCCcc-----cHHHHHHHHHH
Confidence 45567889989999999999999999999998 99999999975
No 274
>PF06530 Phage_antitermQ: Phage antitermination protein Q; InterPro: IPR010534 This entry is represented by Bacteriophage 933W, GpQ. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several phage antitermination protein Q and related bacterial sequences. Phage 993W gene Q encodes a phage-specific positive regulator of late gene expression, thought, by analogy to the corresponding gene of phage lambda, to be a transcription antiterminator. GpQ positively regulates expression of the phage late gene operons. Bacterial host RNA polymerase modified by antitermination proteins transcribes through termination sites that otherwise prevent expression of the regulated genes [, ].; GO: 0003677 DNA binding, 0060567 negative regulation of transcription termination, DNA-dependent
Probab=45.08 E-value=15 Score=28.87 Aligned_cols=38 Identities=24% Similarity=0.262 Sum_probs=31.2
Q ss_pred HHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHhh
Q psy10745 138 VVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRES 175 (197)
Q Consensus 138 ~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~ 175 (197)
+.-+=|+.-+-.|+..-.||+.+++|++.|.|.|.+..
T Consensus 66 ~~~~ll~~~Yv~g~s~r~IA~~~~~s~~~ir~~l~~ae 103 (125)
T PF06530_consen 66 EEYDLLILYYVYGWSKRQIARKLKCSEGKIRKRLQRAE 103 (125)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHhh
Confidence 33344555678999999999999999999999998863
No 275
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=45.04 E-value=21 Score=26.17 Aligned_cols=40 Identities=13% Similarity=0.271 Sum_probs=30.3
Q ss_pred HHHHHHHHHhcC--CCcccchhhhhcccchHHHHHHHhhhhc
Q psy10745 139 VRQRIVELAHNG--VRPCDISRQLRVSHGCVSKILSRESNLH 178 (197)
Q Consensus 139 ~r~~iv~l~~~g--~r~~~isr~l~vshgcVskil~ry~~~~ 178 (197)
.-.+|+++.+.+ +...+||+++++|..-|++.|.+-.+.+
T Consensus 4 ~D~~il~~L~~~~~~~~~~la~~l~~s~~tv~~~l~~L~~~g 45 (108)
T smart00344 4 IDRKILEELQKDARISLAELAKKVGLSPSTVHNRVKRLEEEG 45 (108)
T ss_pred HHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence 345677666553 5667999999999999999888876643
No 276
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=44.98 E-value=12 Score=24.09 Aligned_cols=36 Identities=22% Similarity=0.239 Sum_probs=26.6
Q ss_pred HHHHHHH-HHhcCCCcccchhhhhcccchHHHHHHHh
Q psy10745 139 VRQRIVE-LAHNGVRPCDISRQLRVSHGCVSKILSRE 174 (197)
Q Consensus 139 ~r~~iv~-l~~~g~r~~~isr~l~vshgcVskil~ry 174 (197)
+++-|.+ |...|-.....|+.|+||.-.+.+-|.+|
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 4444444 55788889999999999999998888776
No 277
>PF14493 HTH_40: Helix-turn-helix domain
Probab=44.86 E-value=19 Score=26.38 Aligned_cols=39 Identities=15% Similarity=0.115 Sum_probs=34.8
Q ss_pred HHHHHHHhcCCCcccchhhhhcccchHHHHHHHhhhhcC
Q psy10745 141 QRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESNLHN 179 (197)
Q Consensus 141 ~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~~~n 179 (197)
+.=.+|.++|..+.+||.+-+++-+.|-.=|..|...+.
T Consensus 4 ~~T~~l~~~G~si~eIA~~R~L~~sTI~~HL~~~~~~g~ 42 (91)
T PF14493_consen 4 QITYELFQKGLSIEEIAKIRGLKESTIYGHLAELIESGE 42 (91)
T ss_pred HHHHHHHHcCCCHHHHHHHcCCCHHHHHHHHHHHHHhCC
Confidence 345789999999999999999999999999999988776
No 278
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=44.78 E-value=20 Score=31.58 Aligned_cols=40 Identities=20% Similarity=0.213 Sum_probs=30.9
Q ss_pred CChHHHHHHHHHHh---cCCCcccchhhhhcccchHHHHHHHhh
Q psy10745 135 LPDVVRQRIVELAH---NGVRPCDISRQLRVSHGCVSKILSRES 175 (197)
Q Consensus 135 lp~~~r~~iv~l~~---~g~r~~~isr~l~vshgcVskil~ry~ 175 (197)
||+..|. ||.|.- .+..-.+||..|+||.+-||+|..+.-
T Consensus 231 L~~rEr~-VL~lry~~~~~~Tl~EIA~~lgvS~~rVrqi~~~Al 273 (284)
T PRK06596 231 LDERSRD-IIEARWLDDDKSTLQELAAEYGVSAERVRQIEKNAM 273 (284)
T ss_pred CCHHHHH-HHHHHhcCCCCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 5544444 666654 478889999999999999999988753
No 279
>PRK10870 transcriptional repressor MprA; Provisional
Probab=44.57 E-value=16 Score=30.12 Aligned_cols=29 Identities=17% Similarity=0.260 Sum_probs=25.4
Q ss_pred CCCcccchhhhhcccchHHHHHHHhhhhc
Q psy10745 150 GVRPCDISRQLRVSHGCVSKILSRESNLH 178 (197)
Q Consensus 150 g~r~~~isr~l~vshgcVskil~ry~~~~ 178 (197)
++.+.|||+.++++.+.||+++.|..+.+
T Consensus 71 ~it~~eLa~~l~l~~~tvsr~v~rLe~kG 99 (176)
T PRK10870 71 SIQPSELSCALGSSRTNATRIADELEKRG 99 (176)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHHHCC
Confidence 57888999999999999999999986543
No 280
>cd04059 Peptidases_S8_Protein_convertases_Kexins_Furin-like Peptidase S8 family domain in Protein convertases. Protein convertases, whose members include furins and kexins, are members of the peptidase S8 or Subtilase clan of proteases. They have an Asp/His/Ser catalytic triad that is not homologous to trypsin. Kexins are involved in the activation of peptide hormones, growth factors, and viral proteins. Furin cleaves cell surface vasoactive peptides and proteins involved in cardiovascular tissue remodeling in the TGN, at cell surface, or in endosomes but rarely in the ER. Furin also plays a key role in blood pressure regulation though the activation of transforming growth factor (TGF)-beta. High specificity is seen for cleavage after dibasic (Lys-Arg or Arg-Arg) or multiple basic residues in protein convertases. There is also strong sequence conservation.
Probab=44.41 E-value=25 Score=30.07 Aligned_cols=34 Identities=18% Similarity=0.171 Sum_probs=30.0
Q ss_pred CCCcCCHHHHHHHHHHHHhCCCcchHHhHHHHHh
Q psy10745 30 KPKVATAPVVDAIASYKRENPTMFAWEIRDRLLA 63 (197)
Q Consensus 30 Kpk~~tp~v~~~I~~~k~e~P~iFaWEIRdrLl~ 63 (197)
-.+-++|-|+..+.-+++++|++..-|||+.|++
T Consensus 261 GTS~AaP~VAG~aAll~~~~p~lt~~~v~~~L~~ 294 (297)
T cd04059 261 GTSAAAPLAAGVIALMLEANPNLTWRDVQHILAL 294 (297)
T ss_pred CcchhhhhhHhHHHHhhccCCCCCHHHHHHHHHH
Confidence 3668889888888888999999999999999975
No 281
>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=44.02 E-value=21 Score=26.91 Aligned_cols=30 Identities=13% Similarity=0.238 Sum_probs=26.3
Q ss_pred cCCCcccchhhhhcccchHHHHHHHhhhhc
Q psy10745 149 NGVRPCDISRQLRVSHGCVSKILSRESNLH 178 (197)
Q Consensus 149 ~g~r~~~isr~l~vshgcVskil~ry~~~~ 178 (197)
.++...+||..+.++.+.||+++.+-.+-+
T Consensus 42 ~~~t~~eL~~~l~~~~stvs~~i~~Le~kg 71 (109)
T TIGR01889 42 GKLTLKEIIKEILIKQSALVKIIKKLSKKG 71 (109)
T ss_pred CcCcHHHHHHHHCCCHHHHHHHHHHHHHCC
Confidence 469999999999999999999999876543
No 282
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=43.54 E-value=23 Score=31.68 Aligned_cols=50 Identities=24% Similarity=0.334 Sum_probs=40.9
Q ss_pred ccCCCCCChHHHHHHHHHHhcC--CCcccchhhhhcccchHHHHHHHhhhhc
Q psy10745 129 FVNGRPLPDVVRQRIVELAHNG--VRPCDISRQLRVSHGCVSKILSRESNLH 178 (197)
Q Consensus 129 ~~ngrplp~~~r~~iv~l~~~g--~r~~~isr~l~vshgcVskil~ry~~~~ 178 (197)
-.+--+|++.++.=|-=++.+| ++-.||.|.|+.|...||+||.|--+-+
T Consensus 187 ~~~~~~L~~~e~~il~~i~~~GGri~Q~eL~r~lglsktTvsR~L~~LEk~G 238 (258)
T COG2512 187 LVNEYDLNEDEKEILDLIRERGGRITQAELRRALGLSKTTVSRILRRLEKRG 238 (258)
T ss_pred ccccCCCCHHHHHHHHHHHHhCCEEeHHHHHHhhCCChHHHHHHHHHHHhCC
Confidence 3445689988888777777666 6788999999999999999999876544
No 283
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=43.16 E-value=19 Score=24.06 Aligned_cols=30 Identities=20% Similarity=0.378 Sum_probs=23.8
Q ss_pred hcCCCcccchhhhhcccchHHHHHHHhhhh
Q psy10745 148 HNGVRPCDISRQLRVSHGCVSKILSRESNL 177 (197)
Q Consensus 148 ~~g~r~~~isr~l~vshgcVskil~ry~~~ 177 (197)
...+.+.+||+.++++..-||++|.+..+-
T Consensus 16 ~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~ 45 (68)
T PF13463_consen 16 DGPMTQSDLAERLGISKSTVSRIIKKLEEK 45 (68)
T ss_dssp TS-BEHHHHHHHTT--HHHHHHHHHHHHHT
T ss_pred CCCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 577888999999999999999999987654
No 284
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=42.55 E-value=24 Score=30.14 Aligned_cols=32 Identities=16% Similarity=0.185 Sum_probs=27.3
Q ss_pred cCCCC-CChHHHHHHHHHH-hcCCCcccchhhhh
Q psy10745 130 VNGRP-LPDVVRQRIVELA-HNGVRPCDISRQLR 161 (197)
Q Consensus 130 ~ngrp-lp~~~r~~iv~l~-~~g~r~~~isr~l~ 161 (197)
+||.+ +++++|+||.+.+ +.|-+|...||.|+
T Consensus 26 Ln~~~~vs~~tr~rV~~~a~elgY~pn~~a~~l~ 59 (331)
T PRK14987 26 LRNPEQVSVALRGKIAAALDELGYIPNRAPDILS 59 (331)
T ss_pred hCCCCCCCHHHHHHHHHHHHHhCCCccHHHHHHh
Confidence 45664 9999999999988 67899999999875
No 285
>PRK13348 chromosome replication initiation inhibitor protein; Provisional
Probab=42.13 E-value=26 Score=29.55 Aligned_cols=50 Identities=14% Similarity=0.117 Sum_probs=40.7
Q ss_pred HHHHHhcCCCcccchhhhhcccchHHHHHHHhhhhcCcccccccccccccC
Q psy10745 143 IVELAHNGVRPCDISRQLRVSHGCVSKILSRESNLHNYRLVREEGCFELSD 193 (197)
Q Consensus 143 iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~~~n~~~~~~~~~~~~~~ 193 (197)
.+.++++| .-...|++|.||...||+-+.+-.+.-+.+|+.-.+-.+|.+
T Consensus 10 f~~v~~~g-s~t~AA~~L~iSQ~avS~~i~~LE~~lg~~Lf~R~r~i~lT~ 59 (294)
T PRK13348 10 LAAVVETG-SFERAARRLHVTPSAVSQRIKALEESLGQPLLVRGRPCRPTP 59 (294)
T ss_pred HHHHHHcC-CHHHHHHHhCCCchHHHHHHHHHHHHhCceeeecCCCCccCh
Confidence 45566666 677789999999999999999999999999987766555543
No 286
>PRK13870 transcriptional regulator TraR; Provisional
Probab=41.79 E-value=22 Score=30.58 Aligned_cols=41 Identities=15% Similarity=-0.029 Sum_probs=32.7
Q ss_pred CCChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHhh
Q psy10745 134 PLPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRES 175 (197)
Q Consensus 134 plp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~ 175 (197)
+|..-+ ..++..+..|-...|||..|+||...|-.=|+.-.
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 444333 36999999999999999999999999988665443
No 287
>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=41.54 E-value=22 Score=30.19 Aligned_cols=42 Identities=21% Similarity=0.292 Sum_probs=34.8
Q ss_pred CCChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 134 PLPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 134 plp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
.|++ --+.|+.++..|..--|||+.|+||...|.+-|.+-.+
T Consensus 171 ~Lt~-re~evl~~~a~G~t~~eIa~~l~is~~Tv~~~l~~~~~ 212 (232)
T TIGR03541 171 VLSE-REREVLAWTALGRRQADIAAILGISERTVENHLRSARR 212 (232)
T ss_pred cCCH-HHHHHHHHHHCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 5664 45678899999999999999999999999987666543
No 288
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=41.16 E-value=22 Score=32.02 Aligned_cols=41 Identities=17% Similarity=0.267 Sum_probs=32.5
Q ss_pred CChHHHHHHHHHHh-----cCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 135 LPDVVRQRIVELAH-----NGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 135 lp~~~r~~iv~l~~-----~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
||+ --+.||.|.- .+..-.+||..|+||.+-|++|+.|.-+
T Consensus 257 L~~-rer~Vi~lr~gl~~~~~~Tl~EIa~~lgiS~erVRqi~~rAl~ 302 (317)
T PRK07405 257 LTP-QQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALS 302 (317)
T ss_pred CCH-HHHHHHHHHhhcCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 553 3345788875 6788899999999999999999887643
No 289
>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=41.11 E-value=9 Score=25.28 Aligned_cols=36 Identities=22% Similarity=0.317 Sum_probs=26.4
Q ss_pred HHHHHHh---cCCCcccchhhhhcccchHHHHHHHhhhh
Q psy10745 142 RIVELAH---NGVRPCDISRQLRVSHGCVSKILSRESNL 177 (197)
Q Consensus 142 ~iv~l~~---~g~r~~~isr~l~vshgcVskil~ry~~~ 177 (197)
+|++... .++...|||++++++.+.|..+|.-..+.
T Consensus 7 ~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~~~ 45 (52)
T PF09339_consen 7 RILEALAESGGPLTLSEIARALGLPKSTVHRLLQTLVEE 45 (52)
T ss_dssp HHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred HHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 4555433 34567899999999999999999877554
No 290
>PRK09526 lacI lac repressor; Reviewed
Probab=41.04 E-value=26 Score=29.98 Aligned_cols=54 Identities=17% Similarity=0.265 Sum_probs=37.6
Q ss_pred cCCC-CCChHHHHHHHHHH-hcCCCcccchhhhhccc-------------chHHHH---HHHhhhhcCcccc
Q psy10745 130 VNGR-PLPDVVRQRIVELA-HNGVRPCDISRQLRVSH-------------GCVSKI---LSRESNLHNYRLV 183 (197)
Q Consensus 130 ~ngr-plp~~~r~~iv~l~-~~g~r~~~isr~l~vsh-------------gcVski---l~ry~~~~n~~~~ 183 (197)
+||+ .+++++|+||.+.+ +.|-.|..+||.|+-.+ .--+.+ +.++.+..+|.++
T Consensus 26 Ln~~~~vs~~tr~rV~~~a~elgY~pn~~a~~l~~~~~~~Igvv~~~~~~~~~~~~~~gi~~~a~~~g~~~~ 97 (342)
T PRK09526 26 LNQASHVSAKTREKVEAAMAELNYVPNRVAQQLAGKQSLTIGLATTSLALHAPSQIAAAIKSRADQLGYSVV 97 (342)
T ss_pred hcCCCCCCHHHHHHHHHHHHHHCCCcCHHHHHhhcCCCceEEEEeCCCCcccHHHHHHHHHHHHHHCCCEEE
Confidence 3555 49999999999988 77999999999875322 112343 3355666777764
No 291
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=40.87 E-value=39 Score=28.82 Aligned_cols=59 Identities=17% Similarity=0.128 Sum_probs=45.0
Q ss_pred CCChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHhhhhcCcccccccc-cccccC
Q psy10745 134 PLPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESNLHNYRLVREEG-CFELSD 193 (197)
Q Consensus 134 plp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~~~n~~~~~~~~-~~~~~~ 193 (197)
++....=+-.++++++| .-...|++|.||..-||+-|.+..+.-+.+|+.-+| -++|.+
T Consensus 4 ~~~l~~L~~f~~v~e~g-s~s~AA~~L~isqpavS~~i~~LE~~lg~~Lf~R~~r~~~lT~ 63 (305)
T CHL00180 4 PFTLDQLRILKAIATEG-SFKKAAESLYISQPAVSLQIKNLEKQLNIPLFDRSKNKASLTE 63 (305)
T ss_pred cccHHHHHHHHHHHHcC-CHHHHHHHhcCCChHHHHHHHHHHHHhCCEEEEecCCCceECH
Confidence 34333334556777777 788889999999999999999999999999985544 555543
No 292
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=40.82 E-value=27 Score=26.97 Aligned_cols=42 Identities=19% Similarity=0.333 Sum_probs=34.4
Q ss_pred hHHHHHHHHHHhcCCC--cccchhhhhcccchHHHHHHHhhhhc
Q psy10745 137 DVVRQRIVELAHNGVR--PCDISRQLRVSHGCVSKILSRESNLH 178 (197)
Q Consensus 137 ~~~r~~iv~l~~~g~r--~~~isr~l~vshgcVskil~ry~~~~ 178 (197)
+..-.+|+++.+.+.| -.+||+.+++|-.-|++.+.|-.+.+
T Consensus 7 D~~D~~IL~~L~~d~r~~~~eia~~lglS~~~v~~Ri~~L~~~G 50 (154)
T COG1522 7 DDIDRRILRLLQEDARISNAELAERVGLSPSTVLRRIKRLEEEG 50 (154)
T ss_pred cHHHHHHHHHHHHhCCCCHHHHHHHHCCCHHHHHHHHHHHHHCC
Confidence 4667789998888877 56889999999999999887766554
No 293
>PRK11013 DNA-binding transcriptional regulator LysR; Provisional
Probab=40.80 E-value=23 Score=30.43 Aligned_cols=45 Identities=20% Similarity=0.243 Sum_probs=37.8
Q ss_pred HHHHHHHhcCCCcccchhhhhcccchHHHHHHHhhhhcCccccccc
Q psy10745 141 QRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESNLHNYRLVREE 186 (197)
Q Consensus 141 ~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~~~n~~~~~~~ 186 (197)
+-.+.++++| .-...|+.|.||+..||+-|.+..+.-+.+|+.-+
T Consensus 10 ~~f~av~~~g-S~s~AAe~L~isqsavS~~Ik~LE~~lg~~Lf~R~ 54 (309)
T PRK11013 10 EIFHAVMTAG-SLTEAARLLHTSQPTVSRELARFEKVIGLKLFERV 54 (309)
T ss_pred HHHHHHHHhC-cHHHHHHHHCCCcHHHHHHHHHHHHHhCceeeeec
Confidence 3456677777 78888999999999999999999999999998443
No 294
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=40.77 E-value=26 Score=30.26 Aligned_cols=54 Identities=17% Similarity=0.244 Sum_probs=37.7
Q ss_pred cCCC-CCChHHHHHHHHHH-hcCCCcccchhhhhc-------------ccchHH---HHHHHhhhhcCcccc
Q psy10745 130 VNGR-PLPDVVRQRIVELA-HNGVRPCDISRQLRV-------------SHGCVS---KILSRESNLHNYRLV 183 (197)
Q Consensus 130 ~ngr-plp~~~r~~iv~l~-~~g~r~~~isr~l~v-------------shgcVs---kil~ry~~~~n~~~~ 183 (197)
+||+ .+++++|+||++.+ +.|-.|..+||.|+- ++.=-+ +-+..+.+..+|.++
T Consensus 22 Ln~~~~Vs~~tr~kV~~~a~elgY~pn~~a~~l~~~~~~~Igvi~~~~~~~f~~~l~~gi~~~~~~~gy~~~ 93 (346)
T PRK10401 22 LNNSALVSADTREAVMKAVSELGYRPNANAQALATQVSDTIGVVVMDVSDAFFGALVKAVDLVAQQHQKYVL 93 (346)
T ss_pred HCCCCCCCHHHHHHHHHHHHHHCCCCCHHHHHhhcCCCCEEEEEeCCCCCccHHHHHHHHHHHHHHCCCEEE
Confidence 3555 49999999999999 569999999998751 111122 234566677788765
No 295
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=40.59 E-value=34 Score=28.98 Aligned_cols=52 Identities=19% Similarity=0.144 Sum_probs=41.6
Q ss_pred CChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHhhhhcCcccccccc
Q psy10745 135 LPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESNLHNYRLVREEG 187 (197)
Q Consensus 135 lp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~~~n~~~~~~~~ 187 (197)
+....=+-.+.+++.| .-...|++|.||+.-||+-|....+.-+-+|+.-++
T Consensus 5 ~~l~~L~~f~~v~~~g-s~s~AA~~L~isQ~avS~~i~~LE~~lG~~LF~R~~ 56 (302)
T PRK09791 5 VKIHQIRAFVEVARQG-SIRGASRMLNMSQPALTKSIQELEEGLAAQLFFRRS 56 (302)
T ss_pred ccHHHHHHHHHHHHcC-CHHHHHHHhCCChHHHHHHHHHHHHHhCCeEEEEcC
Confidence 3333444566778888 888889999999999999999999998888876543
No 296
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=40.46 E-value=26 Score=31.34 Aligned_cols=34 Identities=29% Similarity=0.643 Sum_probs=29.0
Q ss_pred ccCCCC-CChHHHHHHHHHH-hcCCCcccchhhhhc
Q psy10745 129 FVNGRP-LPDVVRQRIVELA-HNGVRPCDISRQLRV 162 (197)
Q Consensus 129 ~~ngrp-lp~~~r~~iv~l~-~~g~r~~~isr~l~v 162 (197)
.+||.| +++++|+||.+.+ +.|-+|...||.|+-
T Consensus 20 vln~~~~Vs~eTr~kV~~a~~elgY~pN~~Ar~L~~ 55 (333)
T COG1609 20 VLNGSPYVSEETREKVLAAIKELGYRPNAVARSLRT 55 (333)
T ss_pred HHcCCCCCCHHHHHHHHHHHHHHCCCCCHHHHHHHh
Confidence 456664 9999999999987 679999999999983
No 297
>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=40.22 E-value=24 Score=26.71 Aligned_cols=39 Identities=28% Similarity=0.308 Sum_probs=28.2
Q ss_pred HHHH-HHHhCCCcchHHhHHHHHhcCCCCCCCCCCcccccccccc
Q psy10745 41 AIAS-YKRENPTMFAWEIRDRLLAEGICSQDNVPSVSSINRYITY 84 (197)
Q Consensus 41 ~I~~-~k~e~P~iFaWEIRdrLl~~GvC~~~~vPSvSSI~Rilr~ 84 (197)
.|.+ +++...-+.+-||-+.|.+++... |.++|+|.|..
T Consensus 12 ~Il~~l~~~~~~~ta~ei~~~l~~~~~~i-----s~~TVYR~L~~ 51 (120)
T PF01475_consen 12 AILELLKESPEHLTAEEIYDKLRKKGPRI-----SLATVYRTLDL 51 (120)
T ss_dssp HHHHHHHHHSSSEEHHHHHHHHHHTTTT-------HHHHHHHHHH
T ss_pred HHHHHHHcCCCCCCHHHHHHHhhhccCCc-----CHHHHHHHHHH
Confidence 3444 344444788999999999988766 89999999964
No 298
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=39.84 E-value=29 Score=29.67 Aligned_cols=31 Identities=26% Similarity=0.524 Sum_probs=25.2
Q ss_pred ccCCCC---CChHHHHHHHHHH-hcCCCcccchhhh
Q psy10745 129 FVNGRP---LPDVVRQRIVELA-HNGVRPCDISRQL 160 (197)
Q Consensus 129 ~~ngrp---lp~~~r~~iv~l~-~~g~r~~~isr~l 160 (197)
.+||+| +++++|+||.+.+ +.|-+|.. ++++
T Consensus 21 vln~~~~~~vs~~tr~rV~~~a~~lgY~pn~-~~~~ 55 (327)
T PRK10339 21 VLNDDPTLNVKEETKHRILEIAEKLEYKTSS-ARKL 55 (327)
T ss_pred hhcCCCCCCcCHHHHHHHHHHHHHhCCCCch-hhhh
Confidence 457887 8999999999977 78999998 4444
No 299
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=39.82 E-value=25 Score=29.39 Aligned_cols=43 Identities=16% Similarity=0.218 Sum_probs=35.9
Q ss_pred HHHHHhcCCCcccchhhhhcccchHHHHHHHhhhhcCccccccc
Q psy10745 143 IVELAHNGVRPCDISRQLRVSHGCVSKILSRESNLHNYRLVREE 186 (197)
Q Consensus 143 iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~~~n~~~~~~~ 186 (197)
.+.++++| .-...|++|+||..-||+-|.+-.+.-+.+|+.-+
T Consensus 9 f~~v~~~g-s~s~AA~~L~isqsavS~~i~~LE~~lg~~Lf~R~ 51 (296)
T PRK11242 9 FLAVAEHG-NFTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRS 51 (296)
T ss_pred HHHHHHhC-CHHHHHHHcCCCchHHHHHHHHHHHHhCCeeEeEc
Confidence 34566666 67778999999999999999999999999987654
No 300
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=39.49 E-value=28 Score=25.00 Aligned_cols=41 Identities=12% Similarity=0.160 Sum_probs=30.7
Q ss_pred hHHHHHHHHHH-hcCCCcccchhhhhcccchHHHHHHHhhhh
Q psy10745 137 DVVRQRIVELA-HNGVRPCDISRQLRVSHGCVSKILSRESNL 177 (197)
Q Consensus 137 ~~~r~~iv~l~-~~g~r~~~isr~l~vshgcVskil~ry~~~ 177 (197)
.++-..|++.. +.+.++.+|+...++|+..++++|.--.+.
T Consensus 5 ~~Ii~~IL~~l~~~~~~~t~i~~~~~L~~~~~~~yL~~L~~~ 46 (77)
T PF14947_consen 5 LEIIFDILKILSKGGAKKTEIMYKANLNYSTLKKYLKELEEK 46 (77)
T ss_dssp THHHHHHHHHH-TT-B-HHHHHTTST--HHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHhCcCHHHHHHHHHHHHHC
Confidence 45667888877 899999999999999999999999865443
No 301
>TIGR01481 ccpA catabolite control protein A. Catabolite control protein A is a LacI family global transcriptional regulator found in Gram-positive bacteria. CcpA is involved in repressing carbohydrate utilization genes [ex: alpha-amylase (amyE), acetyl-coenzyme A synthase (acsA)] and in activating genes involved in transporting excess carbon from the cell [ex: acetate kinase (ackA), alpha-acetolactate synthase (alsS)]. Additionally, disruption of CcpA in Bacillus megaterium, Staphylococcus xylosus, Lactobacillus casei and Lactocacillus pentosus also decreases growth rate, which suggests CcpA is involved in the regulation of other metabolic pathways.
Probab=39.38 E-value=29 Score=29.53 Aligned_cols=33 Identities=30% Similarity=0.595 Sum_probs=27.8
Q ss_pred ccCCCC-CChHHHHHHHHHH-hcCCCcccchhhhh
Q psy10745 129 FVNGRP-LPDVVRQRIVELA-HNGVRPCDISRQLR 161 (197)
Q Consensus 129 ~~ngrp-lp~~~r~~iv~l~-~~g~r~~~isr~l~ 161 (197)
.+||++ +++++|+||.+.| +.|-+|...||.|+
T Consensus 21 vLn~~~~vs~~tr~rV~~~a~~lgY~pn~~a~~l~ 55 (329)
T TIGR01481 21 VVNGNPNVKPATRKKVLEVIKRLDYRPNAVARGLA 55 (329)
T ss_pred HhCCCCCCCHHHHHHHHHHHHHHCCCCCHHHHHHh
Confidence 346664 9999999999988 67999999999885
No 302
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=39.31 E-value=16 Score=29.30 Aligned_cols=28 Identities=18% Similarity=0.240 Sum_probs=24.6
Q ss_pred CCcccchhhhhcccchHHHHHHHhhhhc
Q psy10745 151 VRPCDISRQLRVSHGCVSKILSRESNLH 178 (197)
Q Consensus 151 ~r~~~isr~l~vshgcVskil~ry~~~~ 178 (197)
+...+||..|++|.-+||++|+...+.+
T Consensus 169 ~t~~~lA~~lG~tr~tvsR~l~~l~~~g 196 (211)
T PRK11753 169 ITRQEIGRIVGCSREMVGRVLKMLEDQG 196 (211)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence 3456799999999999999999998876
No 303
>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=38.99 E-value=30 Score=26.29 Aligned_cols=46 Identities=11% Similarity=0.049 Sum_probs=36.6
Q ss_pred HHHHHHHhcCCCcccchhhhhcccchHHHHHHHhhhhcCccccccc
Q psy10745 141 QRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESNLHNYRLVREE 186 (197)
Q Consensus 141 ~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~~~n~~~~~~~ 186 (197)
.+++....+-=.....|++|+||+.-||+-+.+..+.-+.+|+.-+
T Consensus 7 l~~~~av~~~gSis~AA~~L~iS~stvs~~I~~LE~~lg~~Lf~R~ 52 (99)
T TIGR00637 7 VALLKAIARMGSISQAAKDAGISYKSAWDYIRAMNNLSGEPLVERA 52 (99)
T ss_pred HHHHHHHHHhCCHHHHHHHHCCCHHHHHHHHHHHHHHhCCCeEEec
Confidence 3444444444566778999999999999999999999999988764
No 304
>PRK05949 RNA polymerase sigma factor; Validated
Probab=38.83 E-value=27 Score=31.72 Aligned_cols=41 Identities=12% Similarity=0.234 Sum_probs=32.4
Q ss_pred CChHHHHHHHHHHh-----cCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 135 LPDVVRQRIVELAH-----NGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 135 lp~~~r~~iv~l~~-----~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
||+. -+.||.|.- .+..-.+||..|+||.+-|.+|+.|..+
T Consensus 267 L~~r-er~Vi~lr~gl~~~e~~Tl~EIa~~lgiS~erVrq~~~rAl~ 312 (327)
T PRK05949 267 LTPQ-QREVLTLRFGLEDGKELSLAKVGERLNLSRERVRQLEHQALA 312 (327)
T ss_pred CCHH-HHHHHHHHhccCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 5533 446777764 6788899999999999999999888643
No 305
>PRK09986 DNA-binding transcriptional activator XapR; Provisional
Probab=38.82 E-value=40 Score=28.12 Aligned_cols=46 Identities=11% Similarity=0.039 Sum_probs=38.2
Q ss_pred HHHHHHHhcCCCcccchhhhhcccchHHHHHHHhhhhcCcccccccc
Q psy10745 141 QRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESNLHNYRLVREEG 187 (197)
Q Consensus 141 ~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~~~n~~~~~~~~ 187 (197)
+-.+.++++| .-...|+.|+||...|||-|.+..+.-|.+|+.-+|
T Consensus 13 ~~f~~v~~~g-s~t~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~ 58 (294)
T PRK09986 13 RYFLAVAEEL-HFGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHS 58 (294)
T ss_pred HHHHHHHHhc-CHHHHHHHhCCCCCHHHHHHHHHHHHhCCeeEeeCC
Confidence 3455667776 777789999999999999999999999999976553
No 306
>COG2826 Tra8 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]
Probab=38.56 E-value=25 Score=32.77 Aligned_cols=37 Identities=22% Similarity=0.230 Sum_probs=33.5
Q ss_pred CChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHH
Q psy10745 135 LPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKIL 171 (197)
Q Consensus 135 lp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil 171 (197)
+..+++..|+|..+.-+.|.+|+..|+.++=|-++|-
T Consensus 75 ~~~eL~~~V~e~L~~~wSPEQI~g~l~~~~i~~eTIY 111 (318)
T COG2826 75 LNPELRELVLEKLKSKWSPEQIIGRLKKSKISFETIY 111 (318)
T ss_pred CCHHHHHHHHHHHHhhCCHHHHHHHHHhcccCHHHHH
Confidence 5579999999999999999999999998878888885
No 307
>cd07493 Peptidases_S8_9 Peptidase S8 family domain, uncharacterized subfamily 9. This family is a member of the Peptidases S8 or Subtilases serine endo- and exo-peptidase clan. They have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The stability of subtilases may be enhanced by calcium, some members have been shown to bind up to 4 ions via binding sites with different affinity. Some members of this clan contain disulfide bonds. These enzymes can be intra- and extracellular, some function at extreme temperatures and pH values.
Probab=38.54 E-value=35 Score=28.89 Aligned_cols=33 Identities=15% Similarity=0.279 Sum_probs=28.9
Q ss_pred CCcCCHHHHHHHHHHHHhCCCcchHHhHHHHHh
Q psy10745 31 PKVATAPVVDAIASYKRENPTMFAWEIRDRLLA 63 (197)
Q Consensus 31 pk~~tp~v~~~I~~~k~e~P~iFaWEIRdrLl~ 63 (197)
.+-++|-|...+..++.++|++...|||+.|+.
T Consensus 226 TS~AaP~vaG~aAll~~~~p~lt~~~i~~~l~~ 258 (261)
T cd07493 226 TSFSCPLIAGLIACLWQAHPNWTNLQIKEAILK 258 (261)
T ss_pred HHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHH
Confidence 446778888889999999999999999999875
No 308
>PF07453 NUMOD1: NUMOD1 domain; InterPro: IPR010896 This helix-turn-helix-containing DNA-binding domain is found associated in homing nucleases [].
Probab=38.32 E-value=11 Score=23.32 Aligned_cols=18 Identities=39% Similarity=0.552 Sum_probs=15.1
Q ss_pred ccchhhhhcccchHHHHH
Q psy10745 154 CDISRQLRVSHGCVSKIL 171 (197)
Q Consensus 154 ~~isr~l~vshgcVskil 171 (197)
.|.||-|+++|+.+|+.|
T Consensus 20 ~eAa~~l~i~~~~I~~~l 37 (37)
T PF07453_consen 20 REAARYLGISHSTISKYL 37 (37)
T ss_pred HHHHHHhCCCHHHHHHhC
Confidence 467999999999999854
No 309
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=38.32 E-value=30 Score=27.07 Aligned_cols=38 Identities=24% Similarity=0.291 Sum_probs=29.7
Q ss_pred HHHHHHHh--cCCCcccchhhhhcccchHHHHHHHhhhhc
Q psy10745 141 QRIVELAH--NGVRPCDISRQLRVSHGCVSKILSRESNLH 178 (197)
Q Consensus 141 ~~iv~l~~--~g~r~~~isr~l~vshgcVskil~ry~~~~ 178 (197)
..|..+.. ..++..+||+.|.||.+-||+.|.+-.+.+
T Consensus 11 ~~I~~l~~~~~~~~~~ela~~l~vs~~svs~~l~~L~~~G 50 (142)
T PRK03902 11 EQIYLLIEEKGYARVSDIAEALSVHPSSVTKMVQKLDKDE 50 (142)
T ss_pred HHHHHHHhcCCCcCHHHHHHHhCCChhHHHHHHHHHHHCC
Confidence 34455543 457888999999999999999999877664
No 310
>PHA02517 putative transposase OrfB; Reviewed
Probab=38.13 E-value=32 Score=29.38 Aligned_cols=45 Identities=16% Similarity=0.122 Sum_probs=36.5
Q ss_pred CHHHHHHHHHHHHh-CCCcchHHhHHHHHhcCCCCCCCCCCcccccccccc
Q psy10745 35 TAPVVDAIASYKRE-NPTMFAWEIRDRLLAEGICSQDNVPSVSSINRYITY 84 (197)
Q Consensus 35 tp~v~~~I~~~k~e-~P~iFaWEIRdrLl~~GvC~~~~vPSvSSI~Rilr~ 84 (197)
.+++.+.|.++..+ +|..-...|.+.|.++|+.. |.++|.|+++.
T Consensus 28 ~~~l~~~I~~i~~~~~~~~G~r~I~~~L~~~g~~v-----s~~tV~Rim~~ 73 (277)
T PHA02517 28 DDWLKSEILRVYDENHQVYGVRKVWRQLNREGIRV-----ARCTVGRLMKE 73 (277)
T ss_pred hHHHHHHHHHHHHHhCCCCCHHHHHHHHHhcCccc-----CHHHHHHHHHH
Confidence 34677888888655 57888899999999999854 88999999975
No 311
>PF10985 DUF2805: Protein of unknown function (DUF2805); InterPro: IPR019882 This entry represents an uncharacterised bacterial protein family. Members average about 90 amino acids in length with several well-conserved uncommon amino acids (Trp, Met). The majority of species are marine bacteria. Few species have more than one copy, but Vibrio cholerae O1 biovar eltor str. N16961 has three identical copies.
Probab=38.05 E-value=13 Score=27.82 Aligned_cols=44 Identities=32% Similarity=0.482 Sum_probs=36.4
Q ss_pred HHHHHHHhcCCCc-ccchhhhhcccchHHHHHHHhhhhcCccccc
Q psy10745 141 QRIVELAHNGVRP-CDISRQLRVSHGCVSKILSRESNLHNYRLVR 184 (197)
Q Consensus 141 ~~iv~l~~~g~r~-~~isr~l~vshgcVskil~ry~~~~n~~~~~ 184 (197)
.+|||||-+--.| .+|-.|.++|+.=|=+|+.+--+...|.+-+
T Consensus 2 ~riIeMAweDRtpFeaI~~qfGl~E~eVi~lMR~~Lk~~sfk~WR 46 (73)
T PF10985_consen 2 SRIIEMAWEDRTPFEAIERQFGLSEKEVIKLMRKELKPSSFKLWR 46 (73)
T ss_pred HHHHHHHHccCCCHHHHHHHHCCCHHHHHHHHHhhcChhHHHHHH
Confidence 4899999766655 5679999999999999999988877776644
No 312
>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=37.43 E-value=19 Score=24.57 Aligned_cols=36 Identities=19% Similarity=0.180 Sum_probs=25.9
Q ss_pred ccchhhhhcccchHHHHHHHhhhhcCcccccccccc
Q psy10745 154 CDISRQLRVSHGCVSKILSRESNLHNYRLVREEGCF 189 (197)
Q Consensus 154 ~~isr~l~vshgcVskil~ry~~~~n~~~~~~~~~~ 189 (197)
-+||++++||..-|.+.|.+-.+.+=-.....-|+|
T Consensus 28 ~~la~~~~vsr~tvr~al~~L~~~g~i~~~~~~G~~ 63 (64)
T PF00392_consen 28 RELAERYGVSRTTVREALRRLEAEGLIERRPGRGTF 63 (64)
T ss_dssp HHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTTEEE
T ss_pred HHHHHHhccCCcHHHHHHHHHHHCCcEEEECCceEE
Confidence 468999999999999999998776644444444443
No 313
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=37.40 E-value=34 Score=32.66 Aligned_cols=41 Identities=22% Similarity=0.303 Sum_probs=32.7
Q ss_pred CChHHHHHHHHHHh-----cCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 135 LPDVVRQRIVELAH-----NGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 135 lp~~~r~~iv~l~~-----~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
||+..| .||.|.- .++.-.+||+.|+||.+-|++++.|..+
T Consensus 351 L~~reR-~VI~LRygl~d~~~~Tl~EIA~~LGvS~erVRqie~rAl~ 396 (415)
T PRK07598 351 LTSRER-DVIRMRFGLADGHTYSLAEIGRALDLSRERVRQIESKALQ 396 (415)
T ss_pred CCHHHH-HHHHHHHhcCCCCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 664444 4667764 6789999999999999999999988754
No 314
>PLN00061 photosystem II protein Psb27; Provisional
Probab=37.01 E-value=11 Score=31.67 Aligned_cols=27 Identities=22% Similarity=0.532 Sum_probs=21.8
Q ss_pred CccccCCccccCC---CCCChHHHHHHHHH
Q psy10745 120 GGVNQLGGVFVNG---RPLPDVVRQRIVEL 146 (197)
Q Consensus 120 ~~~nqlg~~~~ng---rplp~~~r~~iv~l 146 (197)
.-+|.|+|-|.+= ||||+.+|.||.+-
T Consensus 116 tALnsLAghYssyGpnrPLPe~lK~Rll~E 145 (150)
T PLN00061 116 KAIRSLASFYSKAGPSAPLPEDVKSEILDD 145 (150)
T ss_pred HHHHHHHHHHHhcCCCCCCCHHHHHHHHHH
Confidence 4578888877754 89999999999864
No 315
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=36.39 E-value=20 Score=25.75 Aligned_cols=50 Identities=24% Similarity=0.329 Sum_probs=33.6
Q ss_pred HHHHHhcC----CCcccchhhhhcccchHHHHHHHhhhhcCcccccc-ccccccc
Q psy10745 143 IVELAHNG----VRPCDISRQLRVSHGCVSKILSRESNLHNYRLVRE-EGCFELS 192 (197)
Q Consensus 143 iv~l~~~g----~r~~~isr~l~vshgcVskil~ry~~~~n~~~~~~-~~~~~~~ 192 (197)
++.||.++ +...+||.++++|..=|+|||.+-.+.+=-.-.+. .|.|.+.
T Consensus 14 l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~~Gli~s~~G~~GGy~L~ 68 (83)
T PF02082_consen 14 LLYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLKKAGLIESSRGRGGGYRLA 68 (83)
T ss_dssp HHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETSTTSEEEES
T ss_pred HHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhhCCeeEecCCCCCceeec
Confidence 45566544 56678999999999999999999988652222222 3666553
No 316
>PRK00441 argR arginine repressor; Provisional
Probab=35.85 E-value=33 Score=28.10 Aligned_cols=43 Identities=14% Similarity=0.084 Sum_probs=38.1
Q ss_pred HHHHHHHHHHhCCCcchHHhHHHHHhcCCCCCCCCCCccccccccccc
Q psy10745 38 VVDAIASYKRENPTMFAWEIRDRLLAEGICSQDNVPSVSSINRYITYV 85 (197)
Q Consensus 38 v~~~I~~~k~e~P~iFaWEIRdrLl~~GvC~~~~vPSvSSI~Rilr~~ 85 (197)
-.+.|.++-+++.-...-||.+.|.++|+-. |-++|+|=|+..
T Consensus 5 R~~~I~~ll~~~~~~~q~eL~~~L~~~G~~v-----SqaTisRDl~~L 47 (149)
T PRK00441 5 RHAKILEIINSKEIETQEELAEELKKMGFDV-----TQATVSRDIKEL 47 (149)
T ss_pred HHHHHHHHHHHcCCCcHHHHHHHHHhcCCCc-----CHHHHHHHHHHc
Confidence 4567888888999999999999999999988 999999999854
No 317
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=35.81 E-value=22 Score=27.09 Aligned_cols=37 Identities=11% Similarity=0.065 Sum_probs=28.9
Q ss_pred HHHHHHH-HHhcCCCcccchhhhhcccchHHHHHHHhh
Q psy10745 139 VRQRIVE-LAHNGVRPCDISRQLRVSHGCVSKILSRES 175 (197)
Q Consensus 139 ~r~~iv~-l~~~g~r~~~isr~l~vshgcVskil~ry~ 175 (197)
++.-|.+ |...|-.....|+.|+||...+.+-|.+|.
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 4444444 445777888999999999999999999973
No 318
>COG1710 Uncharacterized protein conserved in archaea [Function unknown]
Probab=35.59 E-value=35 Score=28.21 Aligned_cols=42 Identities=33% Similarity=0.479 Sum_probs=32.9
Q ss_pred CCCC--CChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHH
Q psy10745 131 NGRP--LPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILS 172 (197)
Q Consensus 131 ngrp--lp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ 172 (197)
.||| ..-.++..|=||+..|..|-+||+.|++---.|--+|.
T Consensus 88 rGrprkyd~~t~~~i~emlr~gk~preIsk~lGIpirTvyY~l~ 131 (139)
T COG1710 88 RGRPRKYDRNTLLRIREMLRNGKTPREISKDLGIPIRTVYYLLK 131 (139)
T ss_pred CCCCcccchhHHHHHHHHHHcCCCHHHHHHhhCCchhhhHHHHH
Confidence 4665 34556789999999999999999999997666655443
No 319
>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator). This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.
Probab=35.41 E-value=29 Score=26.41 Aligned_cols=29 Identities=21% Similarity=0.202 Sum_probs=25.6
Q ss_pred CCCcccchhhhhcccchHHHHHHHhhhhc
Q psy10745 150 GVRPCDISRQLRVSHGCVSKILSRESNLH 178 (197)
Q Consensus 150 g~r~~~isr~l~vshgcVskil~ry~~~~ 178 (197)
.+...+||+.++++..-|+|||..-.+.+
T Consensus 25 ~~s~~eia~~~~i~~~~v~~il~~L~~~g 53 (132)
T TIGR00738 25 PVSVKEIAERQGISRSYLEKILRTLRRAG 53 (132)
T ss_pred cCcHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence 57788999999999999999999887754
No 320
>PRK12679 cbl transcriptional regulator Cbl; Reviewed
Probab=35.34 E-value=31 Score=29.82 Aligned_cols=47 Identities=17% Similarity=0.176 Sum_probs=40.5
Q ss_pred HHHHHHHhcCCCcccchhhhhcccchHHHHHHHhhhhcCcccccccc
Q psy10745 141 QRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESNLHNYRLVREEG 187 (197)
Q Consensus 141 ~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~~~n~~~~~~~~ 187 (197)
+-+++++++|-.-...|++|.||..-||+-|.+..+.-+.+|+.-+|
T Consensus 7 ~~f~~v~~~~~s~s~AA~~L~iSQ~avSr~I~~LE~~lg~~LF~R~~ 53 (316)
T PRK12679 7 KIIREAARQDYNLTEVANMLFTSQSGVSRHIRELEDELGIEIFIRRG 53 (316)
T ss_pred HHHHHHHHcCCCHHHHHHHhcCCchHHHHHHHHHHHHhCCEEEEECC
Confidence 44677888888889999999999999999999999999999975443
No 321
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=35.27 E-value=62 Score=22.98 Aligned_cols=43 Identities=19% Similarity=0.271 Sum_probs=33.2
Q ss_pred CChHHHHHHHHHHhcCCCc-ccchhhhhcccchHHHHHHHhhhh
Q psy10745 135 LPDVVRQRIVELAHNGVRP-CDISRQLRVSHGCVSKILSRESNL 177 (197)
Q Consensus 135 lp~~~r~~iv~l~~~g~r~-~~isr~l~vshgcVskil~ry~~~ 177 (197)
|....-.=+..++..+--- .+||+.+.|+.+-||++|.|--+-
T Consensus 20 lt~~q~~~L~~l~~~~~~~~~~la~~l~i~~~~vt~~l~~Le~~ 63 (126)
T COG1846 20 LTPPQYQVLLALYEAGGITVKELAERLGLDRSTVTRLLKRLEDK 63 (126)
T ss_pred CCHHHHHHHHHHHHhCCCcHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 5545555556677777666 999999999999999999887543
No 322
>TIGR02424 TF_pcaQ pca operon transcription factor PcaQ. Members of this family are LysR-family transcription factors associated with operons for catabolism of protocatechuate. Members occur only in Proteobacteria.
Probab=35.07 E-value=30 Score=29.13 Aligned_cols=45 Identities=22% Similarity=0.286 Sum_probs=37.8
Q ss_pred HHHHHHhcCCCcccchhhhhcccchHHHHHHHhhhhcCcccccccc
Q psy10745 142 RIVELAHNGVRPCDISRQLRVSHGCVSKILSRESNLHNYRLVREEG 187 (197)
Q Consensus 142 ~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~~~n~~~~~~~~ 187 (197)
-.+.++++| .-...|+.|+||..-||+-|.+..+.-|.+|..-+|
T Consensus 10 ~f~~v~~~g-S~s~AA~~L~isq~avS~~I~~LE~~lg~~LF~R~~ 54 (300)
T TIGR02424 10 CFVEVARQG-SVKRAAEALHITQPAVSKTLRELEEILGTPLFERDR 54 (300)
T ss_pred HHHHHHHhC-CHHHHHHHhCCChHHHHHHHHHHHHHhCCeEEEEcC
Confidence 456677777 777889999999999999999999999999876543
No 323
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=35.03 E-value=21 Score=28.47 Aligned_cols=41 Identities=20% Similarity=0.211 Sum_probs=31.4
Q ss_pred CcccchhhhhcccchHHHHHHHhhhhcCcccccccccccccCC
Q psy10745 152 RPCDISRQLRVSHGCVSKILSRESNLHNYRLVREEGCFELSDL 194 (197)
Q Consensus 152 r~~~isr~l~vshgcVskil~ry~~~~n~~~~~~~~~~~~~~~ 194 (197)
.-.|||..|++|.-.||++|.++.+.+=.. .+.+.+++.|.
T Consensus 151 t~~~iA~~lG~tretvsR~l~~l~~~g~I~--~~~~~i~I~d~ 191 (202)
T PRK13918 151 THDELAAAVGSVRETVTKVIGELSREGYIR--SGYGKIQLLDL 191 (202)
T ss_pred CHHHHHHHhCccHHHHHHHHHHHHHCCCEE--cCCCEEEEECH
Confidence 346899999999999999999998876443 24456666554
No 324
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=34.88 E-value=20 Score=29.42 Aligned_cols=28 Identities=21% Similarity=0.227 Sum_probs=23.9
Q ss_pred CcccchhhhhcccchHHHHHHHhhhhcC
Q psy10745 152 RPCDISRQLRVSHGCVSKILSRESNLHN 179 (197)
Q Consensus 152 r~~~isr~l~vshgcVskil~ry~~~~n 179 (197)
.-.+||..|++|.-.||++|.+..+.+=
T Consensus 186 t~~~iA~~lG~sr~tvsR~l~~l~~~g~ 213 (235)
T PRK11161 186 TRGDIGNYLGLTVETISRLLGRFQKSGM 213 (235)
T ss_pred cHHHHHHHhCCcHHHHHHHHHHHHHCCC
Confidence 3458999999999999999999976653
No 325
>PRK00215 LexA repressor; Validated
Probab=34.41 E-value=44 Score=27.54 Aligned_cols=31 Identities=23% Similarity=0.294 Sum_probs=25.3
Q ss_pred hcCCCcc--cchhhhhc-ccchHHHHHHHhhhhc
Q psy10745 148 HNGVRPC--DISRQLRV-SHGCVSKILSRESNLH 178 (197)
Q Consensus 148 ~~g~r~~--~isr~l~v-shgcVskil~ry~~~~ 178 (197)
++|..+. |||+.+++ |.+.|+.+|.+-.+.+
T Consensus 19 ~~~~~~s~~ela~~~~~~~~~tv~~~l~~L~~~g 52 (205)
T PRK00215 19 ETGYPPSRREIADALGLRSPSAVHEHLKALERKG 52 (205)
T ss_pred HhCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCC
Confidence 3466454 99999999 9999999999887653
No 326
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=34.18 E-value=37 Score=28.50 Aligned_cols=44 Identities=14% Similarity=0.131 Sum_probs=37.3
Q ss_pred HHHHHHhcCCCcccchhhhhcccchHHHHHHHhhhhcCccccccc
Q psy10745 142 RIVELAHNGVRPCDISRQLRVSHGCVSKILSRESNLHNYRLVREE 186 (197)
Q Consensus 142 ~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~~~n~~~~~~~ 186 (197)
-.+.+++.| .-...|++|.||..-||+-|.+-.+.-+.+|+.-+
T Consensus 8 ~f~~v~~~g-s~s~AA~~L~isQ~avSr~i~~LE~~lg~~Lf~R~ 51 (296)
T PRK09906 8 YFVAVAEEL-NFTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRD 51 (296)
T ss_pred HHHHHHhhC-CHHHHHHHhCCCCcHHHHHHHHHHHHhCCeeeeeC
Confidence 456777777 78888999999999999999999999888887433
No 327
>PRK14388 hypothetical protein; Provisional
Probab=34.09 E-value=25 Score=26.78 Aligned_cols=34 Identities=24% Similarity=0.347 Sum_probs=24.3
Q ss_pred CccccccccccccCCCCCCccccCccccCCCCCc
Q psy10745 74 SVSSINRYITYVPIGHGGVNQLGGVFVNGRPLPD 107 (197)
Q Consensus 74 SvSSI~Rilr~~~iGhG~vnqlGg~fingrPLPd 107 (197)
+.-+++||+|.-+++.||.+.+=...=|.+||++
T Consensus 47 ~~l~~~RilRC~P~~~gG~DpVP~~~~~~~~~~~ 80 (82)
T PRK14388 47 LWFTFKRIIKCQPFCDGGYDTVPISIKNSKPLNK 80 (82)
T ss_pred HHHHHHHHhcCCCCCCCCcCCCCCcccCCCCccc
Confidence 4567799999999999999865444444455443
No 328
>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=34.05 E-value=32 Score=26.97 Aligned_cols=38 Identities=21% Similarity=0.336 Sum_probs=27.5
Q ss_pred HHHHHHHHHH-hcCCCcccchhhhhcccchHHHHHHHhh
Q psy10745 138 VVRQRIVELA-HNGVRPCDISRQLRVSHGCVSKILSRES 175 (197)
Q Consensus 138 ~~r~~iv~l~-~~g~r~~~isr~l~vshgcVskil~ry~ 175 (197)
+--.++++|+ .......+||..++||.--|+..+.|-.
T Consensus 20 ~kQ~~~l~lyy~eDlSlsEIAe~~~iSRqaV~d~ikr~~ 58 (101)
T PF04297_consen 20 EKQREILELYYEEDLSLSEIAEELGISRQAVYDSIKRAE 58 (101)
T ss_dssp HHHHHHHHHHCTS---HHHHHHHCTS-HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHccCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 4445666666 8899999999999999999999888754
No 329
>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=33.84 E-value=66 Score=25.27 Aligned_cols=64 Identities=27% Similarity=0.453 Sum_probs=44.2
Q ss_pred cCCCCCccccchhhcccCCCccccCCccccCCCCCChHHHHHHHHHHhcCC--------------------Ccccchhhh
Q psy10745 101 NGRPLPDVVRQRIVASRSHGGVNQLGGVFVNGRPLPDVVRQRIVELAHNGV--------------------RPCDISRQL 160 (197)
Q Consensus 101 ngrPLPd~~RqRIVaS~~~~~~nqlg~~~~ngrplp~~~r~~iv~l~~~g~--------------------r~~~isr~l 160 (197)
=|+...+++++.+..++. |..|. +| |+..+++.+.+|-+-.. |. .--+.||.|
T Consensus 18 ~Gk~hseetk~kms~~~~-G~~n~---~y--Gk~~s~Etk~k~s~~~~-g~kn~~~k~~~~~~ng~i~~F~S~~EAar~l 90 (113)
T cd00283 18 FGKTHSEETKAKISKNRS-GENNP---MF--GKKHSDETKAKISAKKK-GRKNLNAKKKQSDTDGYIGIFDSTTEAARFL 90 (113)
T ss_pred cCccCCHHHHHHHHHHhc-CCCCc---cc--CccCCHHHHHHHHHHHc-CCCCCCcceEEEeCCCCeEEeCCHHHHHHHH
Confidence 378888988888765443 33443 22 78999999999988543 22 112568999
Q ss_pred hcccchHHHHH
Q psy10745 161 RVSHGCVSKIL 171 (197)
Q Consensus 161 ~vshgcVskil 171 (197)
++++..||+.+
T Consensus 91 gi~~~tIs~~~ 101 (113)
T cd00283 91 KVHSGTISKNI 101 (113)
T ss_pred CCCcchhHHHH
Confidence 99888888763
No 330
>PRK04280 arginine repressor; Provisional
Probab=33.80 E-value=37 Score=27.83 Aligned_cols=42 Identities=24% Similarity=0.193 Sum_probs=36.9
Q ss_pred HHHHHHHHHhCCCcchHHhHHHHHhcCCCCCCCCCCccccccccccc
Q psy10745 39 VDAIASYKRENPTMFAWEIRDRLLAEGICSQDNVPSVSSINRYITYV 85 (197)
Q Consensus 39 ~~~I~~~k~e~P~iFaWEIRdrLl~~GvC~~~~vPSvSSI~Rilr~~ 85 (197)
-++|.++-++++=-.--||.+.|.++|+.. +-++|||=++..
T Consensus 6 ~~~I~~iI~~~~I~tQeeL~~~L~~~Gi~v-----TQATiSRDikeL 47 (148)
T PRK04280 6 HIKIREIITNNEIETQDELVDRLREEGFNV-----TQATVSRDIKEL 47 (148)
T ss_pred HHHHHHHHHhCCCCCHHHHHHHHHHcCCCe-----ehHHHHHHHHHc
Confidence 357888888999888999999999999998 899999999863
No 331
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=33.71 E-value=53 Score=26.50 Aligned_cols=42 Identities=14% Similarity=0.174 Sum_probs=32.0
Q ss_pred hHHHHHHHHHHhcCCC--cccchhhhhcccchHHHHHHHhhhhc
Q psy10745 137 DVVRQRIVELAHNGVR--PCDISRQLRVSHGCVSKILSRESNLH 178 (197)
Q Consensus 137 ~~~r~~iv~l~~~g~r--~~~isr~l~vshgcVskil~ry~~~~ 178 (197)
|+.=.+|+.+-+..-| ..+||+++++|...|.+=+.|-.+.+
T Consensus 13 D~~D~~IL~~Lq~d~R~s~~eiA~~lglS~~tv~~Ri~rL~~~G 56 (164)
T PRK11169 13 DRIDRNILNELQKDGRISNVELSKRVGLSPTPCLERVRRLERQG 56 (164)
T ss_pred HHHHHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence 5667788877766544 45899999999999998777665544
No 332
>cd07483 Peptidases_S8_Subtilisin_Novo-like Peptidase S8 family domain in Subtilisin_Novo-like proteins. Subtilisins are a group of alkaline proteinases originating from different strains of Bacillus subtilis. Novo is one of the strains that produced enzymes belonging to this group. The enzymes obtained from the Novo and BPN' strains are identical. The Carlsburg and Novo subtilisins are thought to have arisen from a common ancestral protein. They have similar peptidase and esterase activities, pH profiles, catalyze transesterification reactions, and are both inhibited by diispropyl fluorophosphate, though they differ in 85 positions in the amino acid sequence. Members of the peptidases S8 and S35 clan include endopeptidases, exopeptidases and also a tripeptidyl-peptidase. The S8 family has an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The S53 family contains a cat
Probab=33.43 E-value=39 Score=29.52 Aligned_cols=35 Identities=23% Similarity=0.249 Sum_probs=30.0
Q ss_pred CCcCCHHHHHHHHHHHHhCCCcchHHhHHHHHhcC
Q psy10745 31 PKVATAPVVDAIASYKRENPTMFAWEIRDRLLAEG 65 (197)
Q Consensus 31 pk~~tp~v~~~I~~~k~e~P~iFaWEIRdrLl~~G 65 (197)
.+.++|-|+..+.-+++.+|.+..-|||+.|++-+
T Consensus 256 TS~AaP~vaG~aAl~~s~~p~lt~~~v~~~L~~ta 290 (291)
T cd07483 256 TSMAAPVVSGVAALIWSYYPNLTAKEVKQIILESG 290 (291)
T ss_pred HHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHhC
Confidence 45778888888888899999999999999998754
No 333
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=33.26 E-value=43 Score=25.07 Aligned_cols=35 Identities=17% Similarity=0.192 Sum_probs=29.3
Q ss_pred HHHHHHHHHhcCCCcccchhhhhcccchHHHHHHH
Q psy10745 139 VRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSR 173 (197)
Q Consensus 139 ~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~r 173 (197)
...+|+++...|..-.+||+.+++|...|...+.|
T Consensus 145 ~e~~vl~~~~~~~~~~~ia~~l~~s~~tv~~~~~~ 179 (202)
T PRK09390 145 RERQVMDGLVAGLSNKVIARDLDISPRTVEVYRAN 179 (202)
T ss_pred hHHHHHHHHHccCchHHHHHHcCCCHHHHHHHHHH
Confidence 44578888888999999999999999998875554
No 334
>PRK05066 arginine repressor; Provisional
Probab=32.95 E-value=47 Score=27.54 Aligned_cols=44 Identities=23% Similarity=0.201 Sum_probs=37.8
Q ss_pred HHHHHHHHHHHhCCCcchHHhHHHHHhcCCC-CCCCCCCccccccccccc
Q psy10745 37 PVVDAIASYKRENPTMFAWEIRDRLLAEGIC-SQDNVPSVSSINRYITYV 85 (197)
Q Consensus 37 ~v~~~I~~~k~e~P~iFaWEIRdrLl~~GvC-~~~~vPSvSSI~Rilr~~ 85 (197)
+.-+.|.++-++++=-+--||.+.|.++|+. . +-++|||=++..
T Consensus 9 ~r~~~I~~iI~~~~I~tQeeL~~~L~~~Gi~~v-----TQATiSRDikeL 53 (156)
T PRK05066 9 ELVKAFKALLKEEKFGSQGEIVTALQEQGFDNI-----NQSKVSRMLTKF 53 (156)
T ss_pred HHHHHHHHHHhhCCCCCHHHHHHHHHHCCCCee-----cHHHHHHHHHHc
Confidence 3456788888899988899999999999999 7 889999999853
No 335
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=32.16 E-value=38 Score=26.01 Aligned_cols=46 Identities=22% Similarity=0.155 Sum_probs=35.4
Q ss_pred CCChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHhhhhcCc
Q psy10745 134 PLPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESNLHNY 180 (197)
Q Consensus 134 plp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~~~n~ 180 (197)
||.. .-..++.+..+|+.-.+||+.|.+|-..|.+-+.|-++.=+.
T Consensus 149 ~lt~-re~~vl~~l~~g~s~~eIa~~l~~s~~tv~~~~~~~~~kl~~ 194 (210)
T PRK09935 149 VLSN-REVTILRYLVSGLSNKEIADQLLLSNKTVSAHKSNIYGKLGL 194 (210)
T ss_pred cCCH-HHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHcCC
Confidence 4543 334577888899999999999999999999977776655443
No 336
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=32.15 E-value=22 Score=27.83 Aligned_cols=27 Identities=19% Similarity=0.224 Sum_probs=23.9
Q ss_pred HHhcCCCcccchhhhhcccchHHHHHH
Q psy10745 146 LAHNGVRPCDISRQLRVSHGCVSKILS 172 (197)
Q Consensus 146 l~~~g~r~~~isr~l~vshgcVskil~ 172 (197)
|.+.|++..|+|+.++||.+.+|+|.+
T Consensus 14 l~~~Glsq~eLA~~~Gis~~~is~iE~ 40 (120)
T PRK13890 14 LDERHMTKKELSERSGVSISFLSDLTT 40 (120)
T ss_pred HHHcCCCHHHHHHHHCcCHHHHHHHHc
Confidence 348899999999999999999998764
No 337
>smart00497 IENR1 Intron encoded nuclease repeat motif. Repeat of unknown function, but possibly DNA-binding via helix-turn-helix motif (Ponting, unpublished).
Probab=31.97 E-value=22 Score=22.90 Aligned_cols=20 Identities=30% Similarity=0.486 Sum_probs=17.5
Q ss_pred ccchhhhhcccchHHHHHHH
Q psy10745 154 CDISRQLRVSHGCVSKILSR 173 (197)
Q Consensus 154 ~~isr~l~vshgcVskil~r 173 (197)
.|.||.|+++|+-||+-|..
T Consensus 21 ~eAa~~lg~~~~~I~~~~~~ 40 (53)
T smart00497 21 REAAKYLGISHSSISKYLNT 40 (53)
T ss_pred HHHHHHhCCCHHHHHHHHhC
Confidence 47799999999999998775
No 338
>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=31.86 E-value=36 Score=25.64 Aligned_cols=40 Identities=18% Similarity=0.154 Sum_probs=29.4
Q ss_pred CCCCChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHh
Q psy10745 132 GRPLPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRE 174 (197)
Q Consensus 132 grplp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry 174 (197)
|...|.+++.. ..+.|+...++|+.+++|..-||++.+.-
T Consensus 63 ~~~~~~~i~~~---r~~~gltq~~lA~~lg~~~~tis~~e~g~ 102 (127)
T TIGR03830 63 GLLTPPEIRRI---RKKLGLSQREAAELLGGGVNAFSRYERGE 102 (127)
T ss_pred CCcCHHHHHHH---HHHcCCCHHHHHHHhCCCHHHHHHHHCCC
Confidence 44555555433 34569999999999999999999876543
No 339
>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=31.85 E-value=39 Score=26.26 Aligned_cols=34 Identities=26% Similarity=0.273 Sum_probs=28.6
Q ss_pred hHHHHHHHH-HHhcCCCcccchhhhhcccchHHHH
Q psy10745 137 DVVRQRIVE-LAHNGVRPCDISRQLRVSHGCVSKI 170 (197)
Q Consensus 137 ~~~r~~iv~-l~~~g~r~~~isr~l~vshgcVski 170 (197)
...|-+|+. |.+.|+.--+||..|+||-..||..
T Consensus 41 l~~R~~i~~~Ll~~~~tQrEIa~~lGiS~atIsR~ 75 (94)
T TIGR01321 41 LGDRIRIVNELLNGNMSQREIASKLGVSIATITRG 75 (94)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHhCCChhhhhHH
Confidence 456888887 6678899999999999999988864
No 340
>cd07492 Peptidases_S8_8 Peptidase S8 family domain, uncharacterized subfamily 8. This family is a member of the Peptidases S8 or Subtilases serine endo- and exo-peptidase clan. They have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The stability of subtilases may be enhanced by calcium, some members have been shown to bind up to 4 ions via binding sites with different affinity. Some members of this clan contain disulfide bonds. These enzymes can be intra- and extracellular, some function at extreme temperatures and pH values.
Probab=31.76 E-value=51 Score=27.05 Aligned_cols=33 Identities=21% Similarity=0.221 Sum_probs=28.8
Q ss_pred CCcCCHHHHHHHHHHHHhCCCcchHHhHHHHHh
Q psy10745 31 PKVATAPVVDAIASYKRENPTMFAWEIRDRLLA 63 (197)
Q Consensus 31 pk~~tp~v~~~I~~~k~e~P~iFaWEIRdrLl~ 63 (197)
.+.++|-|...+.-++.++|++..-|||+.|.+
T Consensus 187 TS~Aap~vaG~~All~~~~p~l~~~~v~~~L~~ 219 (222)
T cd07492 187 NSFAAPHVTGMVALLLSEKPDIDANDLKRLLQR 219 (222)
T ss_pred HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHH
Confidence 457788888888888999999999999999975
No 341
>cd04848 Peptidases_S8_Autotransporter_serine_protease_like Peptidase S8 family domain in Autotransporter serine proteases. Autotransporter serine proteases belong to Peptidase S8 or Subtilase family. Subtilases, or subtilisin-like serine proteases, have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure (an example of convergent evolution). Autotransporters are a superfamily of outer membrane/secreted proteins of gram-negative bacteria. The presence of these subtilisin-like domains in these autotransporters are may enable them to be auto-catalytic and may also serve to allow them to act as a maturation protease cleaving other outer membrane proteins at the cell surface.
Probab=31.32 E-value=60 Score=26.58 Aligned_cols=33 Identities=27% Similarity=0.272 Sum_probs=29.1
Q ss_pred CCcCCHHHHHHHHHHHHhCCCcchHHhHHHHHh
Q psy10745 31 PKVATAPVVDAIASYKRENPTMFAWEIRDRLLA 63 (197)
Q Consensus 31 pk~~tp~v~~~I~~~k~e~P~iFaWEIRdrLl~ 63 (197)
.+.+||-|...+.-+++.+|.+..-+||+.|+.
T Consensus 232 TS~Aap~vaG~~Al~~~~~p~l~~~~v~~~l~~ 264 (267)
T cd04848 232 TSFAAPHVSGAAALLAQKFPWLTADQVRQTLLT 264 (267)
T ss_pred eEchHHHHHHHHHHHHHHCCCCCHHHHHHHHHh
Confidence 457889888899999999999999999998864
No 342
>PRK01381 Trp operon repressor; Provisional
Probab=30.87 E-value=33 Score=26.94 Aligned_cols=34 Identities=26% Similarity=0.288 Sum_probs=28.5
Q ss_pred hHHHHHHHHHHhcC-CCcccchhhhhcccchHHHH
Q psy10745 137 DVVRQRIVELAHNG-VRPCDISRQLRVSHGCVSKI 170 (197)
Q Consensus 137 ~~~r~~iv~l~~~g-~r~~~isr~l~vshgcVski 170 (197)
...|-+|+++-..| +.--+||.+|+||-..||.-
T Consensus 41 l~~R~~I~~~L~~g~~sQREIa~~lGvSiaTITRg 75 (99)
T PRK01381 41 LGTRVRIVEELLRGELSQREIKQELGVGIATITRG 75 (99)
T ss_pred HHHHHHHHHHHHcCCcCHHHHHHHhCCceeeehhh
Confidence 45788999877776 88899999999999988763
No 343
>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=30.44 E-value=51 Score=22.64 Aligned_cols=36 Identities=17% Similarity=0.235 Sum_probs=27.3
Q ss_pred HHHHHHhcC-CCcccchhhhhcccchHHHHHHHhhhh
Q psy10745 142 RIVELAHNG-VRPCDISRQLRVSHGCVSKILSRESNL 177 (197)
Q Consensus 142 ~iv~l~~~g-~r~~~isr~l~vshgcVskil~ry~~~ 177 (197)
+|+++-..+ ..-.+||.+++||..-|++-|.+..+.
T Consensus 4 ~il~~L~~~~~~~~eLa~~l~vS~~tv~~~l~~L~~~ 40 (69)
T TIGR00122 4 RLLALLADNPFSGEKLGEALGMSRTAVNKHIQTLREW 40 (69)
T ss_pred HHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 455554444 335678999999999999999998664
No 344
>PRK05638 threonine synthase; Validated
Probab=30.39 E-value=45 Score=31.27 Aligned_cols=43 Identities=12% Similarity=0.117 Sum_probs=35.3
Q ss_pred ChHHHHHHHHHHhcC-CCcccchhhhh--cccchHHHHHHHhhhhc
Q psy10745 136 PDVVRQRIVELAHNG-VRPCDISRQLR--VSHGCVSKILSRESNLH 178 (197)
Q Consensus 136 p~~~r~~iv~l~~~g-~r~~~isr~l~--vshgcVskil~ry~~~~ 178 (197)
....|.+|+.+..++ +..+||++.|+ +|.+-||+.|.+-.+.+
T Consensus 369 ~~~~r~~IL~~L~~~~~~~~el~~~l~~~~s~~~v~~hL~~Le~~G 414 (442)
T PRK05638 369 IGGTKLEILKILSEREMYGYEIWKALGKPLKYQAVYQHIKELEELG 414 (442)
T ss_pred ccchHHHHHHHHhhCCccHHHHHHHHcccCCcchHHHHHHHHHHCC
Confidence 446699999877654 56899999998 99999999999886654
No 345
>cd05562 Peptidases_S53_like Peptidase domain in the S53 family. Members of the peptidase S53 (sedolisin) family include endopeptidases and exopeptidases. The S53 family contains a catalytic triad Glu/Asp/Ser with an additional acidic residue Asp in the oxyanion hole, similar to that of Asn in subtilisin. The stability of these enzymes may be enhanced by calcium, some members have been shown to bind up to 4 ions via binding sites with different affinity. Some members of this clan contain disulfide bonds. These enzymes can be intra- and extracellular, some function at extreme temperatures and pH values. Characterized sedolisins include Kumamolisin, an extracellular calcium-dependent thermostable endopeptidase from Bacillus. The enzyme is synthesized with a 188 amino acid N-terminal preprotein region which is cleaved after the extraction into the extracellular space with low pH. One kumamolysin paralog, kumamolisin-As, is believed to be a collagenase. TPP1 is a serine protease that functi
Probab=30.38 E-value=60 Score=28.50 Aligned_cols=34 Identities=24% Similarity=0.246 Sum_probs=27.8
Q ss_pred CCcCCHHHHHHHHHHHHhCCCcchHHhHHHHHhc
Q psy10745 31 PKVATAPVVDAIASYKRENPTMFAWEIRDRLLAE 64 (197)
Q Consensus 31 pk~~tp~v~~~I~~~k~e~P~iFaWEIRdrLl~~ 64 (197)
.+.++|-|...+.-+++.+|.+...+||+.|.+-
T Consensus 216 TS~AaP~VaG~aALl~~~~p~lt~~~v~~~L~~t 249 (275)
T cd05562 216 TSAAAPHAAGVAALVLSANPGLTPADIRDALRST 249 (275)
T ss_pred chHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHh
Confidence 4566777777777788899999999999999763
No 346
>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=30.26 E-value=57 Score=25.82 Aligned_cols=39 Identities=13% Similarity=0.129 Sum_probs=29.0
Q ss_pred CChHHHHHHHHH-HhcCC--CcccchhhhhcccchHHHHHHHh
Q psy10745 135 LPDVVRQRIVEL-AHNGV--RPCDISRQLRVSHGCVSKILSRE 174 (197)
Q Consensus 135 lp~~~r~~iv~l-~~~g~--r~~~isr~l~vshgcVskil~ry 174 (197)
|++..| +||++ +-.+. .-.+||..|+||..-|+++.+++
T Consensus 83 Ld~~er-~II~~rY~~~~~~t~~~Ia~~l~iS~~t~~r~r~~~ 124 (134)
T TIGR01636 83 ADEQTR-VIIQELYMKKRPLTLVGLAQQLFISKSTAYRLRNHI 124 (134)
T ss_pred CCHHHH-HHHHHHHccCCCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 666776 56665 44444 66899999999999999866554
No 347
>cd07474 Peptidases_S8_subtilisin_Vpr-like Peptidase S8 family domain in Vpr-like proteins. The maturation of the peptide antibiotic (lantibiotic) subtilin in Bacillus subtilis ATCC 6633 includes posttranslational modifications of the propeptide and proteolytic cleavage of the leader peptide. Vpr was identified as one of the proteases, along with WprA, that are capable of processing subtilin. Asp, Ser, His triadPeptidases S8 or Subtilases are a serine endo- and exo-peptidase clan. They have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The stability of subtilases may be enhanced by calcium, some members have been shown to bind up to 4 ions via binding sites with different affinity. Some members of this clan contain disulfide bonds. These enzymes can be intra- and extracellular, some function at extreme temperatures and pH values.
Probab=30.20 E-value=50 Score=28.11 Aligned_cols=37 Identities=22% Similarity=0.228 Sum_probs=31.4
Q ss_pred CCcCCHHHHHHHHHHHHhCCCcchHHhHHHHHhcCCC
Q psy10745 31 PKVATAPVVDAIASYKRENPTMFAWEIRDRLLAEGIC 67 (197)
Q Consensus 31 pk~~tp~v~~~I~~~k~e~P~iFaWEIRdrLl~~GvC 67 (197)
.+.++|-|...+.-+++++|.+...++|+.|+.-..-
T Consensus 235 TS~AaP~vaG~aAll~~~~p~l~~~~v~~~L~~tA~~ 271 (295)
T cd07474 235 TSMAAPHVAGAAALLKQAHPDWSPAQIKAALMNTAKP 271 (295)
T ss_pred HHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHhhCcc
Confidence 5577888888888889999999999999999976543
No 348
>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=29.92 E-value=27 Score=27.51 Aligned_cols=28 Identities=7% Similarity=0.153 Sum_probs=24.6
Q ss_pred CCcccchhhhhcccchHHHHHHHhhhhc
Q psy10745 151 VRPCDISRQLRVSHGCVSKILSRESNLH 178 (197)
Q Consensus 151 ~r~~~isr~l~vshgcVskil~ry~~~~ 178 (197)
+.-.|||..|++|.=.||++|++..+.+
T Consensus 144 ~t~~~iA~~lG~tretvsR~l~~l~~~g 171 (193)
T TIGR03697 144 LSHQAIAEAIGSTRVTITRLLGDLRKKK 171 (193)
T ss_pred CCHHHHHHHhCCcHHHHHHHHHHHHHCC
Confidence 4457999999999999999999997765
No 349
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=29.64 E-value=52 Score=28.12 Aligned_cols=32 Identities=16% Similarity=0.283 Sum_probs=26.7
Q ss_pred cCCC-CCChHHHHHHHHHH-hcCCCcccchhhhh
Q psy10745 130 VNGR-PLPDVVRQRIVELA-HNGVRPCDISRQLR 161 (197)
Q Consensus 130 ~ngr-plp~~~r~~iv~l~-~~g~r~~~isr~l~ 161 (197)
+||+ -+++++|+||.+.+ +.|-.|...||.|+
T Consensus 27 Ln~~~~vs~~tr~~V~~~a~elgY~p~~~a~~l~ 60 (342)
T PRK10014 27 LSGKGRISTATGERVNQAIEELGFVRNRQASALR 60 (342)
T ss_pred HCCCCCCCHHHHHHHHHHHHHhCCCcCHHHHhhc
Confidence 3454 49999999999988 67999999998875
No 350
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=29.39 E-value=39 Score=24.79 Aligned_cols=34 Identities=12% Similarity=0.197 Sum_probs=26.5
Q ss_pred HHHHHhcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 143 IVELAHNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 143 iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
.|.|...-+.--+.|++|+++|++|.+-+..|..
T Consensus 6 fIrlLs~~~s~~~Aa~~lG~~~~~v~~wv~~fR~ 39 (65)
T PF05344_consen 6 FIRLLSQQISVAQAADRLGTDPGTVRRWVRMFRQ 39 (65)
T ss_pred HHHHhcccccHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 3555556666778899999999999998777653
No 351
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=29.21 E-value=23 Score=25.26 Aligned_cols=31 Identities=13% Similarity=0.068 Sum_probs=25.5
Q ss_pred hcCCCcccchhhhhcccchHHHHHHHhhhhc
Q psy10745 148 HNGVRPCDISRQLRVSHGCVSKILSRESNLH 178 (197)
Q Consensus 148 ~~g~r~~~isr~l~vshgcVskil~ry~~~~ 178 (197)
+.+++-.|||..+++|+--|.++|..-.+++
T Consensus 13 ~~p~~T~eiA~~~gls~~~aR~yL~~Le~eG 43 (62)
T PF04703_consen 13 NGPLKTREIADALGLSIYQARYYLEKLEKEG 43 (62)
T ss_dssp TS-EEHHHHHHHHTS-HHHHHHHHHHHHHCT
T ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence 5678888999999999999999999877665
No 352
>PF00600 Flu_NS1: Influenza non-structural protein (NS1); InterPro: IPR000256 NS1 is a homodimeric RNA-binding protein found in influenza virus that is required for viral replication. NS1 binds polyA tails of mRNA keeping them in the nucleus. NS1 inhibits pre-mRNA splicing by tightly binding to a specific stem-bulge of U6 snRNA [].; GO: 0003723 RNA binding; PDB: 2Z0A_C 3P39_E 3P38_C 3P31_C 3M8A_H 3M5R_D 3EE9_B 3KWI_A 3KWG_B 2RHK_A ....
Probab=28.96 E-value=24 Score=30.87 Aligned_cols=18 Identities=22% Similarity=0.652 Sum_probs=14.3
Q ss_pred CcchHHhHHHHHhcCCCC
Q psy10745 51 TMFAWEIRDRLLAEGICS 68 (197)
Q Consensus 51 ~iFaWEIRdrLl~~GvC~ 68 (197)
++|+|-+|.+++.+++++
T Consensus 12 dCfLWHvrKr~ad~~lgD 29 (217)
T PF00600_consen 12 DCFLWHVRKRFADQELGD 29 (217)
T ss_dssp HHHHHHHHHHHHHTT---
T ss_pred eehhhHHHHHhhhccccc
Confidence 589999999999999997
No 353
>PRK11139 DNA-binding transcriptional activator GcvA; Provisional
Probab=28.86 E-value=79 Score=26.71 Aligned_cols=46 Identities=15% Similarity=0.172 Sum_probs=36.7
Q ss_pred HHHHHHHhcCCCcccchhhhhcccchHHHHHHHhhhhcCcccccccc
Q psy10745 141 QRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESNLHNYRLVREEG 187 (197)
Q Consensus 141 ~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~~~n~~~~~~~~ 187 (197)
+-.+++++.| .-...|++|.||...||+-|.+..+.-+.+|+.-+|
T Consensus 12 ~~f~~v~~~g-s~s~AA~~L~isq~avS~~i~~LE~~lg~~Lf~R~~ 57 (297)
T PRK11139 12 RAFEAAARHL-SFTRAAEELFVTQAAVSHQIKALEDFLGLKLFRRRN 57 (297)
T ss_pred HHHHHHHHhC-CHHHHHHHhCCChHHHHHHHHHHHHHhCchheEecC
Confidence 3445566654 456679999999999999999999999999886554
No 354
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=28.75 E-value=18 Score=24.55 Aligned_cols=25 Identities=28% Similarity=0.452 Sum_probs=20.7
Q ss_pred hcCCCcccchhhhhcccchHHHHHH
Q psy10745 148 HNGVRPCDISRQLRVSHGCVSKILS 172 (197)
Q Consensus 148 ~~g~r~~~isr~l~vshgcVskil~ 172 (197)
..|+.-.++|++++||..-||+|.+
T Consensus 12 ~~gls~~~lA~~~g~s~s~v~~iE~ 36 (64)
T PF13560_consen 12 RAGLSQAQLADRLGVSQSTVSRIER 36 (64)
T ss_dssp CHTS-HHHHHHHHTS-HHHHHHHHT
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHC
Confidence 5699999999999999999999865
No 355
>cd04852 Peptidases_S8_3 Peptidase S8 family domain, uncharacterized subfamily 3. This family is a member of the Peptidases S8 or Subtilases serine endo- and exo-peptidase clan. They have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The stability of subtilases may be enhanced by calcium, some members have been shown to bind up to 4 ions via binding sites with different affinity. Some members of this clan contain disulfide bonds. These enzymes can be intra- and extracellular, some function at extreme temperatures and pH values.
Probab=28.51 E-value=51 Score=28.70 Aligned_cols=33 Identities=21% Similarity=0.272 Sum_probs=27.9
Q ss_pred CCcCCHHHHHHHHHHHHhCCCcchHHhHHHHHh
Q psy10745 31 PKVATAPVVDAIASYKRENPTMFAWEIRDRLLA 63 (197)
Q Consensus 31 pk~~tp~v~~~I~~~k~e~P~iFaWEIRdrLl~ 63 (197)
.+.++|-|...+.-+++.+|.+..-|||+.|+.
T Consensus 272 TS~AaP~vaG~aALl~~~~p~~t~~~v~~~L~~ 304 (307)
T cd04852 272 TSMASPHVAGVAALLKSAHPDWSPAAIKSALMT 304 (307)
T ss_pred HHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHH
Confidence 446688888888888889999999999999975
No 356
>cd07473 Peptidases_S8_Subtilisin_like Peptidase S8 family domain in Subtilisin-like proteins. This family is a member of the Peptidases S8 or Subtilases serine endo- and exo-peptidase clan. They have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The stability of subtilases may be enhanced by calcium, some members have been shown to bind up to 4 ions via binding sites with different affinity. Some members of this clan contain disulfide bonds. These enzymes can be intra- and extracellular, some function at extreme temperatures and pH values.
Probab=28.45 E-value=63 Score=26.93 Aligned_cols=33 Identities=33% Similarity=0.385 Sum_probs=29.2
Q ss_pred CCcCCHHHHHHHHHHHHhCCCcchHHhHHHHHh
Q psy10745 31 PKVATAPVVDAIASYKRENPTMFAWEIRDRLLA 63 (197)
Q Consensus 31 pk~~tp~v~~~I~~~k~e~P~iFaWEIRdrLl~ 63 (197)
.+.++|-|...+.-+.+++|.+...|+|+.|+.
T Consensus 224 TS~AaP~vaG~~All~~~~~~~t~~~v~~~L~~ 256 (259)
T cd07473 224 TSMATPHVAGAAALLLSLNPNLTAAQIKDAILS 256 (259)
T ss_pred HhHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHH
Confidence 467888888888899999999999999999975
No 357
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=28.22 E-value=77 Score=26.89 Aligned_cols=44 Identities=16% Similarity=0.116 Sum_probs=37.8
Q ss_pred HHHHHHhcCCCcccchhhhhcccchHHHHHHHhhhhcCccccccc
Q psy10745 142 RIVELAHNGVRPCDISRQLRVSHGCVSKILSRESNLHNYRLVREE 186 (197)
Q Consensus 142 ~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~~~n~~~~~~~ 186 (197)
-.+.++++| .-...|++|.||..-||+-|..-.+.-|.+|+.-+
T Consensus 8 ~f~~v~~~g-S~s~AA~~L~itQpavS~~i~~LE~~lg~~LF~R~ 51 (305)
T PRK11151 8 YLVALAEHR-HFRRAADSCHVSQPTLSGQIRKLEDELGVMLLERT 51 (305)
T ss_pred HHHHHHHhC-CHHHHHHHhCCCchHHHHHHHHHHHHhCchheeeC
Confidence 356677787 88888999999999999999999999999987544
No 358
>PRK09492 treR trehalose repressor; Provisional
Probab=28.07 E-value=56 Score=27.58 Aligned_cols=32 Identities=22% Similarity=0.516 Sum_probs=26.3
Q ss_pred cCCC-CCChHHHHHHHHHH-hcCCCcccchhhhh
Q psy10745 130 VNGR-PLPDVVRQRIVELA-HNGVRPCDISRQLR 161 (197)
Q Consensus 130 ~ngr-plp~~~r~~iv~l~-~~g~r~~~isr~l~ 161 (197)
+||+ .+++++|+||.+.+ +.|-+|...||.|+
T Consensus 25 Ln~~~~vs~~tr~rV~~~a~elgY~pn~~a~~l~ 58 (315)
T PRK09492 25 LNNESGVSEETRERVEAVINQHGFSPSKSARAMR 58 (315)
T ss_pred hCCCCCCCHHHHHHHHHHHHHHCCCcCHHHHHhh
Confidence 3444 59999999999988 67899999988775
No 359
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=27.94 E-value=32 Score=29.69 Aligned_cols=48 Identities=23% Similarity=0.283 Sum_probs=35.4
Q ss_pred ccCCccccCCCCCChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHhhhhcCccccccc
Q psy10745 123 NQLGGVFVNGRPLPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESNLHNYRLVREE 186 (197)
Q Consensus 123 nqlg~~~~ngrplp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~~~n~~~~~~~ 186 (197)
+-||-+|.|..||. -.||+..|++|.+-||.-|.--+..+=-+.+-+.
T Consensus 30 ~iYgilyls~~Pmt----------------l~Ei~E~lg~Sks~vS~~lkkL~~~~lV~~~~~~ 77 (177)
T COG1510 30 QIYGILYLSRKPLT----------------LDEIAEALGMSKSNVSMGLKKLQDWNLVKKVFEK 77 (177)
T ss_pred HHhhhheecCCCcc----------------HHHHHHHHCCCcchHHHHHHHHHhcchHHhhhcc
Confidence 44678899999987 4678999999999999877766655544444443
No 360
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=27.56 E-value=55 Score=28.27 Aligned_cols=45 Identities=16% Similarity=0.183 Sum_probs=39.0
Q ss_pred HHHHHhcCCCcccchhhhhcccchHHHHHHHhhhhcCcccccccc
Q psy10745 143 IVELAHNGVRPCDISRQLRVSHGCVSKILSRESNLHNYRLVREEG 187 (197)
Q Consensus 143 iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~~~n~~~~~~~~ 187 (197)
.++++++|-.-...|+.|+||..-||+-|.+..+.-+.+|+.-+|
T Consensus 9 f~~v~~~g~S~s~AA~~L~isQpavS~~ik~LE~~lg~~Lf~R~~ 53 (313)
T PRK12684 9 VREAVRQNFNLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHG 53 (313)
T ss_pred HHHHHHcCCCHHHHHHHhcCCChHHHHHHHHHHHHhCCeeEEEcC
Confidence 455777777778889999999999999999999999999987664
No 361
>TIGR00498 lexA SOS regulatory protein LexA. LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.
Probab=27.45 E-value=81 Score=25.83 Aligned_cols=41 Identities=17% Similarity=0.314 Sum_probs=31.1
Q ss_pred HHHHHHHHHHh-----cCCCcc--cchhhhhcc-cchHHHHHHHhhhhc
Q psy10745 138 VVRQRIVELAH-----NGVRPC--DISRQLRVS-HGCVSKILSRESNLH 178 (197)
Q Consensus 138 ~~r~~iv~l~~-----~g~r~~--~isr~l~vs-hgcVskil~ry~~~~ 178 (197)
....+|+++.. .|..|. |||+.+++| ...|+..|.+-.+.+
T Consensus 6 ~~q~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~~L~~~g 54 (199)
T TIGR00498 6 ARQQEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLKALERKG 54 (199)
T ss_pred HHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHHHHHHCC
Confidence 44556666655 355576 999999998 999999998876654
No 362
>PRK15421 DNA-binding transcriptional regulator MetR; Provisional
Probab=27.32 E-value=46 Score=29.03 Aligned_cols=45 Identities=16% Similarity=0.228 Sum_probs=38.0
Q ss_pred HHHHHHHhcCCCcccchhhhhcccchHHHHHHHhhhhcCccccccc
Q psy10745 141 QRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESNLHNYRLVREE 186 (197)
Q Consensus 141 ~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~~~n~~~~~~~ 186 (197)
+-++.++++| .-...|++|.||+.-||+=+.+..+.-+.+|+.-.
T Consensus 8 ~~f~av~~~g-s~s~AA~~L~iSqpaVS~~Ik~LE~~lg~~LF~R~ 52 (317)
T PRK15421 8 KTLQALRNCG-SLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVRK 52 (317)
T ss_pred HHHHHHHHcC-CHHHHHHHhCCCHHHHHHHHHHHHHHhCCEEEEec
Confidence 3456777777 77888999999999999999999999999887544
No 363
>PF03734 YkuD: L,D-transpeptidase catalytic domain; InterPro: IPR005490 This family of proteins are found in a range of bacteria. The conserved region contains a conserved histidine and cysteine, suggesting that these proteins have an enzymatic activity. Several members of this family contain peptidoglycan binding domains. So these proteins may use peptidoglycan or a precursor as a substrate. The molecular structure of YkuD protein shows this domain has a novel tertiary fold consisting of a beta-sandwich with two mixed sheets, one containing five strands and the other, six strands. The two beta-sheets form a cradle capped by an alpha-helix. This domain contains a putative catalytic site with a tetrad of invariant His123, Gly124, Cys139, and Arg141. The stereochemistry of this active site shows similarities to peptidotransferases and sortases, and suggests that the enzymes of this family may play an important role in cell wall biology. This family was formerly called the ErfK/YbiS/YcfS/YnhG family, but is now named after the first protein of known structure.; GO: 0016740 transferase activity; PDB: 3ZQD_A 1Y7M_B 4A52_A 2HKL_C 1ZAT_A.
Probab=27.14 E-value=15 Score=27.68 Aligned_cols=10 Identities=40% Similarity=0.730 Sum_probs=7.5
Q ss_pred hhcccchHHH
Q psy10745 160 LRVSHGCVSK 169 (197)
Q Consensus 160 l~vshgcVsk 169 (197)
...|||||.=
T Consensus 115 ~~~S~GCIrl 124 (144)
T PF03734_consen 115 GPASHGCIRL 124 (144)
T ss_dssp HCEESSSEEE
T ss_pred CCCCCCEecc
Confidence 3469999963
No 364
>COG1438 ArgR Arginine repressor [Transcription]
Probab=26.85 E-value=54 Score=27.40 Aligned_cols=42 Identities=19% Similarity=0.189 Sum_probs=35.8
Q ss_pred HHHHHHHHHHhCCCcchHHhHHHHHhcCCCCCCCCCCcccccccccc
Q psy10745 38 VVDAIASYKRENPTMFAWEIRDRLLAEGICSQDNVPSVSSINRYITY 84 (197)
Q Consensus 38 v~~~I~~~k~e~P~iFaWEIRdrLl~~GvC~~~~vPSvSSI~Rilr~ 84 (197)
--++|.++-.+++=-+--||.+.|.++|++. +-+++||=++.
T Consensus 7 R~~~Ik~iI~~~~i~TQ~Elv~~L~~~Gi~v-----TQaTvSRDlke 48 (150)
T COG1438 7 RLELIKEIITEEKISTQEELVELLQEEGIEV-----TQATVSRDLKE 48 (150)
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHHHHcCCeE-----ehHHHHHHHHH
Confidence 3456778777888778899999999999998 88999999985
No 365
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=26.73 E-value=61 Score=28.11 Aligned_cols=41 Identities=15% Similarity=0.114 Sum_probs=32.7
Q ss_pred hHHHHHHHHHHhc--CCCcccchhhhhcccchHHHHHHHhhhh
Q psy10745 137 DVVRQRIVELAHN--GVRPCDISRQLRVSHGCVSKILSRESNL 177 (197)
Q Consensus 137 ~~~r~~iv~l~~~--g~r~~~isr~l~vshgcVskil~ry~~~ 177 (197)
.+-+++|+++-++ -++..|+|+.|+||.-+|.+-|....+.
T Consensus 4 ~~R~~~Il~~l~~~~~~~~~ela~~l~vS~~TirRdL~~Le~~ 46 (251)
T PRK13509 4 AQRHQILLELLAQLGFVTVEKVIERLGISPATARRDINKLDES 46 (251)
T ss_pred HHHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 4567788887543 5899999999999999999988766543
No 366
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=26.48 E-value=56 Score=25.41 Aligned_cols=32 Identities=19% Similarity=0.202 Sum_probs=25.5
Q ss_pred HHHHH-HhcCCCcccchhhhhcccchHHHHHHH
Q psy10745 142 RIVEL-AHNGVRPCDISRQLRVSHGCVSKILSR 173 (197)
Q Consensus 142 ~iv~l-~~~g~r~~~isr~l~vshgcVskil~r 173 (197)
+|-++ ...|+.-.++|+.++||.+-||++.+.
T Consensus 9 rlk~~R~~~gltq~~lA~~~gvs~~~is~~E~g 41 (135)
T PRK09706 9 RIRYRRKQLKLSQRSLAKAVKVSHVSISQWERD 41 (135)
T ss_pred HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 34333 467999999999999999999997644
No 367
>cd07496 Peptidases_S8_13 Peptidase S8 family domain, uncharacterized subfamily 13. This family is a member of the Peptidases S8 or Subtilases serine endo- and exo-peptidase clan. They have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The stability of subtilases may be enhanced by calcium, some members have been shown to bind up to 4 ions via binding sites with different affinity. Some members of this clan contain disulfide bonds. These enzymes can be intra- and extracellular, some function at extreme temperatures and pH values.
Probab=26.32 E-value=60 Score=27.88 Aligned_cols=33 Identities=24% Similarity=0.266 Sum_probs=27.9
Q ss_pred CCcCCHHHHHHHHHHHHhCCCcchHHhHHHHHh
Q psy10745 31 PKVATAPVVDAIASYKRENPTMFAWEIRDRLLA 63 (197)
Q Consensus 31 pk~~tp~v~~~I~~~k~e~P~iFaWEIRdrLl~ 63 (197)
.+.++|-|...+.-+.+++|.+...|||+.|..
T Consensus 252 TS~AaP~vaG~aAlv~~~~p~lt~~~v~~~L~~ 284 (285)
T cd07496 252 TSMAAPHVAGVAALMKSVNPSLTPAQIESLLQS 284 (285)
T ss_pred HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHh
Confidence 445788888888888889999999999999864
No 368
>cd07494 Peptidases_S8_10 Peptidase S8 family domain, uncharacterized subfamily 10. This family is a member of the Peptidases S8 or Subtilases serine endo- and exo-peptidase clan. They have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The stability of subtilases may be enhanced by calcium, some members have been shown to bind up to 4 ions via binding sites with different affinity. Some members of this clan contain disulfide bonds. These enzymes can be intra- and extracellular, some function at extreme temperatures and pH values.
Probab=26.32 E-value=80 Score=27.97 Aligned_cols=36 Identities=19% Similarity=0.135 Sum_probs=29.6
Q ss_pred CCCcCCHHHHHHHHHHHHhCCCcchHHhHHHHHhcC
Q psy10745 30 KPKVATAPVVDAIASYKRENPTMFAWEIRDRLLAEG 65 (197)
Q Consensus 30 Kpk~~tp~v~~~I~~~k~e~P~iFaWEIRdrLl~~G 65 (197)
-.+.++|-|...+.-+++.+|.+...+||+.|.+--
T Consensus 247 GTS~Aap~vaG~aAll~~~~p~~~~~~v~~~l~~ta 282 (298)
T cd07494 247 GTSAAAPQVAGVCALMLQANPGLSPERARSLLNKTA 282 (298)
T ss_pred cchHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHhC
Confidence 345777888888888889999999999999987644
No 369
>TIGR03613 RutR pyrimidine utilization regulatory protein R. This protein is observed in operons extremely similar to that characterized in E. coli K-12 responsible for the import and catabolism of pyrimidines, primarily uracil. This protein is a member of the TetR family of transcriptional regulators defined by the N-teminal model pfam00440 and the C-terminal model pfam08362 (YcdC-like protein, C-terminal region).
Probab=26.26 E-value=45 Score=26.57 Aligned_cols=31 Identities=23% Similarity=0.238 Sum_probs=24.9
Q ss_pred hHHHHHHHHHHh--------cCCCcccchhhhhcccchH
Q psy10745 137 DVVRQRIVELAH--------NGVRPCDISRQLRVSHGCV 167 (197)
Q Consensus 137 ~~~r~~iv~l~~--------~g~r~~~isr~l~vshgcV 167 (197)
...|.+|++=|. .++...|||+..+||+|-+
T Consensus 7 ~~~r~~Il~aA~~lf~e~G~~~~s~~~IA~~agvs~~~l 45 (202)
T TIGR03613 7 EAKRKAILSAALDTFSRFGFHGTSLEQIAELAGVSKTNL 45 (202)
T ss_pred HHHHHHHHHHHHHHHHHhCcccCCHHHHHHHhCCCHHHH
Confidence 467888887554 3577889999999999986
No 370
>TIGR03418 chol_sulf_TF putative choline sulfate-utilization transcription factor. Members of this protein family are transcription factors of the LysR family. Their genes typically are divergently transcribed from choline-sulfatase genes. That enzyme makes choline, a precursor to the osmoprotectant glycine-betaine, available by hydrolysis of choline sulfate.
Probab=26.22 E-value=47 Score=27.84 Aligned_cols=44 Identities=16% Similarity=0.072 Sum_probs=36.6
Q ss_pred HHHHHHhcCCCcccchhhhhcccchHHHHHHHhhhhcCccccccc
Q psy10745 142 RIVELAHNGVRPCDISRQLRVSHGCVSKILSRESNLHNYRLVREE 186 (197)
Q Consensus 142 ~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~~~n~~~~~~~ 186 (197)
-.+.+++.| .-...|++|.||..-||+-+.+-.+.-+.+|..-+
T Consensus 8 ~f~~v~~~g-s~s~AA~~L~itqpavS~~Ik~LE~~lg~~LF~R~ 51 (291)
T TIGR03418 8 VFESAARLA-SFTAAARELGSTQPAVSQQVKRLEEELGTPLFERG 51 (291)
T ss_pred HHHHHHHhC-CHHHHHHHhCCCHHHHHHHHHHHHHHhCcHHhhcC
Confidence 356777777 78888999999999999999998888888877543
No 371
>TIGR02804 ExbD_2 TonB system transport protein ExbD, group 2. Members of this family are Gram-negative bacterial inner membrane proteins, generally designated ExbD, related to the TolR family modeled by TIGRFAMs TIGR02801. Members always are encoded next to a protein designated ExbB (TIGR02797), related to the TolQ family modeled by TIGRFAMs TIGR02796. ExbD and ExbB together form a proton channel through which they can harness the proton-motive force to energize TonB, which in turn energizes TonB-dependent receptors in the outer membrane. TonB-dependent receptors with known specificity tend to import siderophores or vitamin B12. A TonB system and Tol-Pal system often will co-exist in a single bacterial genome.
Probab=25.72 E-value=1.2e+02 Score=23.31 Aligned_cols=56 Identities=5% Similarity=0.036 Sum_probs=37.7
Q ss_pred cccCCccccCCCCCChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHhhhhc
Q psy10745 122 VNQLGGVFVNGRPLPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESNLH 178 (197)
Q Consensus 122 ~nqlg~~~~ngrplp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~~~ 178 (197)
++.-|..|+||+|++.+.-...++-+.. -.+--|.-.-.++++.|-++|..-++.+
T Consensus 56 i~~~g~~~~~~~~v~~~~L~~~l~~~~~-~~~v~i~aD~~~~~~~vv~v~d~~~~~G 111 (121)
T TIGR02804 56 ITADNQLYFNDKPISLEELEAEIAQLNK-DQKVTLKSDKEAKFQDFVTITDMLKAKE 111 (121)
T ss_pred EECCCCEEECCcccCHHHHHHHHHhhCC-CCeEEEEeCCCCCHhHHHHHHHHHHHcC
Confidence 4555788999999987665544443322 2233455556689999999998877654
No 372
>PRK10676 DNA-binding transcriptional regulator ModE; Provisional
Probab=25.58 E-value=70 Score=28.21 Aligned_cols=57 Identities=12% Similarity=0.037 Sum_probs=50.4
Q ss_pred ccCCCCCChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHhhhhcCcccccc
Q psy10745 129 FVNGRPLPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESNLHNYRLVRE 185 (197)
Q Consensus 129 ~~ngrplp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~~~n~~~~~~ 185 (197)
..+++|.-+..+.++++...+-=.....|+.|++|..-||+.+..-.+.-.++|+.-
T Consensus 10 ~~~~~~~~~~~~l~~l~~v~~~gS~s~AA~~l~~s~~a~s~~i~~le~~lg~~L~~r 66 (263)
T PRK10676 10 KLQQRLFADPRRISLLKQIALTGSISQGAKLAGISYKSAWDAINEMNQLSEHILVER 66 (263)
T ss_pred EeCCccccCHHHHHHHHHHHHHCCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCeEEE
Confidence 457788888888899888877778899999999999999999999999999999754
No 373
>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=25.50 E-value=77 Score=26.13 Aligned_cols=47 Identities=19% Similarity=0.194 Sum_probs=33.3
Q ss_pred CHHHHHHHHHHHHhCCCcchHHhHHHHHhcCCCCCCCCCCccccccccc
Q psy10745 35 TAPVVDAIASYKRENPTMFAWEIRDRLLAEGICSQDNVPSVSSINRYIT 83 (197)
Q Consensus 35 tp~v~~~I~~~k~e~P~iFaWEIRdrLl~~GvC~~~~vPSvSSI~Rilr 83 (197)
-|++.+++.+.-++ .+.+..||.+.+.+...- ..-.+|-|+|+|+-.
T Consensus 11 P~eir~~l~~~L~~-~~~t~~ei~~~~~~~~~~-~g~~iSrSav~RY~~ 57 (180)
T PF11985_consen 11 PPEIREWLDQMLRD-GGFTQYEILAEWLEELAE-EGYDISRSAVHRYAQ 57 (180)
T ss_pred CHHHHHHHHHHHHh-CCCChHHHHHHHHHhhhc-cCCCcCHHHHHHHHH
Confidence 45788888886655 567778888887777311 122469999999874
No 374
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=25.50 E-value=58 Score=28.16 Aligned_cols=39 Identities=26% Similarity=0.338 Sum_probs=31.3
Q ss_pred HHHHHHHHH--hcCCCcccchhhhhcccchHHHHHHHhhhh
Q psy10745 139 VRQRIVELA--HNGVRPCDISRQLRVSHGCVSKILSRESNL 177 (197)
Q Consensus 139 ~r~~iv~l~--~~g~r~~~isr~l~vshgcVskil~ry~~~ 177 (197)
-+++|+++. +..++..|||+.|+||.-.|++-|..-.+.
T Consensus 5 R~~~Il~~l~~~~~~~~~eLa~~l~VS~~TiRRdL~~L~~~ 45 (240)
T PRK10411 5 RQQAIVDLLLNHTSLTTEALAEQLNVSKETIRRDLNELQTQ 45 (240)
T ss_pred HHHHHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 456677774 457888999999999999999988876553
No 375
>cd07489 Peptidases_S8_5 Peptidase S8 family domain, uncharacterized subfamily 5. gap in seq This family is a member of the Peptidases S8 or Subtilases serine endo- and exo-peptidase clan. They have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The stability of subtilases may be enhanced by calcium, some members have been shown to bind up to 4 ions via binding sites with different affinity. Some members of this clan contain disulfide bonds. These enzymes can be intra- and extracellular, some function at extreme temperatures and pH values.
Probab=25.38 E-value=94 Score=27.07 Aligned_cols=63 Identities=22% Similarity=0.126 Sum_probs=40.5
Q ss_pred CCCcCCHHHHHHHHHHHHhC-CCcchHHhHHHHHhcCCCCCCCCCCccccccccccccCCCCCCc
Q psy10745 30 KPKVATAPVVDAIASYKREN-PTMFAWEIRDRLLAEGICSQDNVPSVSSINRYITYVPIGHGGVN 93 (197)
Q Consensus 30 Kpk~~tp~v~~~I~~~k~e~-P~iFaWEIRdrLl~~GvC~~~~vPSvSSI~Rilr~~~iGhG~vn 93 (197)
-.+.++|-|...+.-+.+.+ |.++.-|||+.|+.-..-... ..+-..++.+..+..+|+|-+|
T Consensus 229 GTS~Aap~vaG~~Al~~~~~~~~~~~~~v~~~l~~ta~~~~~-~~~~~~~~~~~~~~~~G~G~vn 292 (312)
T cd07489 229 GTSMATPYVAGAAALLIQARHGKLSPAELRDLLASTAKPLPW-SDGTSALPDLAPVAQQGAGLVN 292 (312)
T ss_pred cHHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCccccc-cCCCccccCCCCHhhcCcceee
Confidence 35678888888888888888 999999999999875442211 0112222222233446888777
No 376
>COG1356 tfx Transcriptional regulator [DNA replication, recombination and repair]
Probab=25.18 E-value=26 Score=29.19 Aligned_cols=37 Identities=24% Similarity=0.397 Sum_probs=31.5
Q ss_pred HHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHh
Q psy10745 138 VVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRE 174 (197)
Q Consensus 138 ~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry 174 (197)
+..-+.+-|.++|..-.+|||.|+-|..=||-|=.|.
T Consensus 11 e~qikvl~lRekG~tQ~eIA~~L~TTraNvSaIEkrA 47 (143)
T COG1356 11 EQQIKVLVLREKGLTQSEIARILKTTRANVSAIEKRA 47 (143)
T ss_pred hhheeeeehhhccccHHHHHHHHccchhhHHHHHHHH
Confidence 3345678899999999999999999999999886654
No 377
>cd07477 Peptidases_S8_Subtilisin_subset Peptidase S8 family domain in Subtilisin proteins. This group is composed of many different subtilisins: Pro-TK-subtilisin, subtilisin Carlsberg, serine protease Pb92 subtilisin, and BPN subtilisins just to name a few. Pro-TK-subtilisin is a serine protease from the hyperthermophilic archaeon Thermococcus kodakaraensis and consists of a signal peptide, a propeptide, and a mature domain. TK-subtilisin is matured from pro-TK-subtilisin upon autoprocessing and degradation of the propeptide. Unlike other subtilisins though, the folding of the unprocessed form of pro-TK-subtilisin is induced by Ca2+ binding which is almost completed prior to autoprocessing. Ca2+ is required for activity unlike the bacterial subtilisins. The propeptide is not required for folding of the mature domain unlike the bacterial subtilases because of the stability produced from Ca2+ binding. Subtilisin Carlsberg is extremely similar in structure to subtilisin BPN'/Novo thoug
Probab=24.97 E-value=76 Score=25.78 Aligned_cols=33 Identities=21% Similarity=0.208 Sum_probs=29.0
Q ss_pred CCcCCHHHHHHHHHHHHhCCCcchHHhHHHHHh
Q psy10745 31 PKVATAPVVDAIASYKRENPTMFAWEIRDRLLA 63 (197)
Q Consensus 31 pk~~tp~v~~~I~~~k~e~P~iFaWEIRdrLl~ 63 (197)
.+.++|-|...+.-+++.+|.+..-|||+.|+.
T Consensus 196 TS~Aap~vag~~All~~~~~~~~~~~i~~~l~~ 228 (229)
T cd07477 196 TSMATPHVAGVAALVWSKRPELTNAQVRQALNK 228 (229)
T ss_pred HHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHh
Confidence 557888888899999999999999999999874
No 378
>TIGR03454 partition_RepB plasmid partitioning protein RepB. Members of this family are the RepB protein involved in replicon partitioning. RepB is found, in general, as part of a repABC operon in plasmids and small chromosomes, separate from the main chromosome, in various bacteria. This model describes a rather narrow clade of proteins; it should be noted that additional homologs scoring below the trusted cutoff have very similar functions, although they may be named differently.
Probab=24.91 E-value=74 Score=29.45 Aligned_cols=43 Identities=21% Similarity=0.196 Sum_probs=34.9
Q ss_pred CCChHHHH-HHHHHHhcCCCcccchhhhhcccchHHHHHHHhhh
Q psy10745 134 PLPDVVRQ-RIVELAHNGVRPCDISRQLRVSHGCVSKILSRESN 176 (197)
Q Consensus 134 plp~~~r~-~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~ 176 (197)
.|+..++- -+.+|...|....+|+..|++|..-||++|.-+..
T Consensus 160 dLS~iE~A~~~~~L~~~G~~~~~ia~~Lg~~ks~vSr~lsl~~~ 203 (325)
T TIGR03454 160 DLSFIERALFAQRLEDRGFDRDTIMAALSVDKTELSRMISVARR 203 (325)
T ss_pred CCCHHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHHh
Confidence 56666665 35667789999999999999999999999987643
No 379
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=24.60 E-value=56 Score=28.43 Aligned_cols=42 Identities=14% Similarity=0.186 Sum_probs=32.5
Q ss_pred ChHHHHHHHHHHhc-C-CCcccchhhhhcccchHHHHHHHhhhh
Q psy10745 136 PDVVRQRIVELAHN-G-VRPCDISRQLRVSHGCVSKILSRESNL 177 (197)
Q Consensus 136 p~~~r~~iv~l~~~-g-~r~~~isr~l~vshgcVskil~ry~~~ 177 (197)
+.+=|++|+++.++ | ++..|+|++|+||.-.|.+=|..-.+.
T Consensus 3 ~~eR~~~Il~~L~~~~~v~v~eLa~~l~VS~~TIRRDL~~Le~~ 46 (256)
T PRK10434 3 PRQRQAAILEYLQKQGKTSVEELAQYFDTTGTTIRKDLVILEHA 46 (256)
T ss_pred HHHHHHHHHHHHHHcCCEEHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 34567889998764 4 789999999999999999866554433
No 380
>cd07482 Peptidases_S8_Lantibiotic_specific_protease Peptidase S8 family domain in Lantiobiotic (lanthionine-containing antibiotics) specific proteases. Lantiobiotic (lanthionine-containing antibiotics) specific proteases are very similar in structure to serine proteases. Lantibiotics are ribosomally synthesised antimicrobial agents derived from ribosomally synthesised peptides with antimicrobial activities against Gram-positive bacteria. The proteases that cleave the N-terminal leader peptides from lantiobiotics include: epiP, nsuP, mutP, and nisP. EpiP, from Staphylococcus, is thought to cleave matured epidermin. NsuP, a dehydratase from Streptococcus and NisP, a membrane-anchored subtilisin-like serine protease from Lactococcus cleave nisin. MutP is highly similar to epiP and nisP and is thought to process the prepeptide mutacin III of S. mutans. Members of the peptidases S8 (subtilisin and kexin) and S53 (sedolisin) clan include endopeptidases and exopeptidases. The S8 family h
Probab=24.60 E-value=83 Score=26.61 Aligned_cols=34 Identities=24% Similarity=0.116 Sum_probs=29.3
Q ss_pred CCCcCCHHHHHHHHHHHHhCCCcch-HHhHHHHHh
Q psy10745 30 KPKVATAPVVDAIASYKRENPTMFA-WEIRDRLLA 63 (197)
Q Consensus 30 Kpk~~tp~v~~~I~~~k~e~P~iFa-WEIRdrLl~ 63 (197)
-.+.++|-|...+.-+.+++|.+.. -|||+.|.+
T Consensus 259 GTS~AaP~VaG~aAll~~~~p~~~~~~~v~~~L~~ 293 (294)
T cd07482 259 GTSLAAPKVSGALALIIDKNPLKKPPDEAIRILYN 293 (294)
T ss_pred chhhhhHHHHHHHHHHHHHCCCCCcHHHHHHHHhh
Confidence 4567889888888888999999999 899999874
No 381
>PRK15481 transcriptional regulatory protein PtsJ; Provisional
Probab=24.55 E-value=55 Score=29.75 Aligned_cols=54 Identities=20% Similarity=0.198 Sum_probs=36.6
Q ss_pred hHHHHHHHHHH-hcCCC-cc--cchhhhhcccchHHHHHHHhhhhcCccccccccccc
Q psy10745 137 DVVRQRIVELA-HNGVR-PC--DISRQLRVSHGCVSKILSRESNLHNYRLVREEGCFE 190 (197)
Q Consensus 137 ~~~r~~iv~l~-~~g~r-~~--~isr~l~vshgcVskil~ry~~~~n~~~~~~~~~~~ 190 (197)
+.++.+|.+-. ..|-| |. ++|++|+||.+.|.+-+.+-..++--......|+|-
T Consensus 12 ~~i~~~i~~g~l~~g~~lps~r~la~~~~vsr~tv~~a~~~L~~~g~i~~~~~~G~~v 69 (431)
T PRK15481 12 DSIRQLIQAGRLRPGDSLPPVRELASELGVNRNTVAAAYKRLVTAGLAQSQGRNGTVI 69 (431)
T ss_pred HHHHHHHHcCCCCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCCCceEE
Confidence 34445554431 23344 33 679999999999999999888887666555666654
No 382
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=24.18 E-value=72 Score=26.55 Aligned_cols=45 Identities=20% Similarity=0.211 Sum_probs=37.5
Q ss_pred HHHHHHHhcCCCcccchhhhhcccchHHHHHHHhhhhcCccccccc
Q psy10745 141 QRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESNLHNYRLVREE 186 (197)
Q Consensus 141 ~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~~~n~~~~~~~ 186 (197)
+-++.++++| .-...|++|.||..-||+-+.+..+.-|.+|+.-+
T Consensus 9 ~~f~~v~e~~-s~t~AA~~L~isqpavS~~I~~LE~~lg~~Lf~R~ 53 (290)
T PRK10837 9 EVFAEVLKSG-STTQASVMLALSQSAVSAALTDLEGQLGVQLFDRV 53 (290)
T ss_pred HHHHHHHHcC-CHHHHHHHhCCCccHHHHHHHHHHHHhCCccEeec
Confidence 3456677777 77788999999999999999999999999887543
No 383
>COG1376 ErfK Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.94 E-value=21 Score=30.06 Aligned_cols=8 Identities=63% Similarity=1.331 Sum_probs=6.8
Q ss_pred hcccchHH
Q psy10745 161 RVSHGCVS 168 (197)
Q Consensus 161 ~vshgcVs 168 (197)
.||||||.
T Consensus 200 ~~ShGCIR 207 (232)
T COG1376 200 AVSHGCIR 207 (232)
T ss_pred ccCCceEe
Confidence 48999996
No 384
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=23.88 E-value=40 Score=29.41 Aligned_cols=27 Identities=11% Similarity=0.225 Sum_probs=23.9
Q ss_pred CCcccchhhhhcccchHHHHHHHhhhh
Q psy10745 151 VRPCDISRQLRVSHGCVSKILSRESNL 177 (197)
Q Consensus 151 ~r~~~isr~l~vshgcVskil~ry~~~ 177 (197)
+...+||+.|++|...||++|.+-.+.
T Consensus 22 IS~~eLA~~L~iS~~Tvsr~Lk~LEe~ 48 (217)
T PRK14165 22 ISSSEFANHTGTSSKTAARILKQLEDE 48 (217)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 567799999999999999999998654
No 385
>cd07487 Peptidases_S8_1 Peptidase S8 family domain, uncharacterized subfamily 1. This family is a member of the Peptidases S8 or Subtilases serine endo- and exo-peptidase clan. They have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The stability of subtilases may be enhanced by calcium, some members have been shown to bind up to 4 ions via binding sites with different affinity. Some members of this clan contain disulfide bonds. These enzymes can be intra- and extracellular, some function at extreme temperatures and pH values.
Probab=23.81 E-value=1e+02 Score=25.47 Aligned_cols=34 Identities=29% Similarity=0.249 Sum_probs=29.3
Q ss_pred CCCcCCHHHHHHHHHHHHhCCCcchHHhHHHHHh
Q psy10745 30 KPKVATAPVVDAIASYKRENPTMFAWEIRDRLLA 63 (197)
Q Consensus 30 Kpk~~tp~v~~~I~~~k~e~P~iFaWEIRdrLl~ 63 (197)
-.+.++|-|...+..+.+.+|.+..-|||+.|+.
T Consensus 228 GTS~Aap~vaG~~All~~~~p~~~~~~ik~~L~~ 261 (264)
T cd07487 228 GTSMATPHVSGAIALLLQANPILTPDEVKCILRD 261 (264)
T ss_pred ccchHHHHHHHHHHHHHHHCcCCCHHHHHHHHHh
Confidence 3567888888888888999999999999999874
No 386
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=23.54 E-value=71 Score=27.59 Aligned_cols=44 Identities=16% Similarity=0.155 Sum_probs=37.9
Q ss_pred HHHHHhcCCCcccchhhhhcccchHHHHHHHhhhhcCccccccc
Q psy10745 143 IVELAHNGVRPCDISRQLRVSHGCVSKILSRESNLHNYRLVREE 186 (197)
Q Consensus 143 iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~~~n~~~~~~~ 186 (197)
.+.++++|-.-...|++|+||..-||+-+.+-.+.-+.+|+.-+
T Consensus 9 F~~v~~~~~S~s~AA~~L~isQpavS~~I~~LE~~lg~~Lf~R~ 52 (309)
T PRK12683 9 IREAVRQNFNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIRR 52 (309)
T ss_pred HHHHHHccCCHHHHHHHhcCCcHHHHHHHHHHHHHhCCeeEeeC
Confidence 45677788788889999999999999999999999998887554
No 387
>PRK10072 putative transcriptional regulator; Provisional
Probab=23.37 E-value=54 Score=25.14 Aligned_cols=28 Identities=32% Similarity=0.330 Sum_probs=24.9
Q ss_pred HhcCCCcccchhhhhcccchHHHHHHHh
Q psy10745 147 AHNGVRPCDISRQLRVSHGCVSKILSRE 174 (197)
Q Consensus 147 ~~~g~r~~~isr~l~vshgcVskil~ry 174 (197)
.+.|+.-.++|+.++||.+.||+..+.-
T Consensus 43 ~~~glTQ~elA~~lGvS~~TVs~WE~G~ 70 (96)
T PRK10072 43 KGTGLKIDDFARVLGVSVAMVKEWESRR 70 (96)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHcCC
Confidence 5789999999999999999999987643
No 388
>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR. This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system.
Probab=23.36 E-value=84 Score=24.52 Aligned_cols=38 Identities=21% Similarity=0.311 Sum_probs=30.2
Q ss_pred HHHHHHHhc----CCCcccchhhhhcccchHHHHHHHhhhhc
Q psy10745 141 QRIVELAHN----GVRPCDISRQLRVSHGCVSKILSRESNLH 178 (197)
Q Consensus 141 ~~iv~l~~~----g~r~~~isr~l~vshgcVskil~ry~~~~ 178 (197)
+-.+.||.+ -+...+||++++|+..-|.|||..-.+.+
T Consensus 12 ~~l~~La~~~~~~~~s~~~ia~~~~ip~~~l~kil~~L~~~g 53 (135)
T TIGR02010 12 TAMLDLALNAETGPVTLADISERQGISLSYLEQLFAKLRKAG 53 (135)
T ss_pred HHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCC
Confidence 445677743 25668999999999999999999887765
No 389
>PRK13832 plasmid partitioning protein; Provisional
Probab=23.31 E-value=55 Score=32.49 Aligned_cols=36 Identities=19% Similarity=0.115 Sum_probs=29.9
Q ss_pred ChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHH
Q psy10745 136 PDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKIL 171 (197)
Q Consensus 136 p~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil 171 (197)
|.+.=.-+-.|.+.|+.+.+||+.+++|...|+++|
T Consensus 104 PiEea~AfkrLie~G~T~EeIA~~lG~S~~~V~rll 139 (520)
T PRK13832 104 PVDQWRAIERLVALGWTEEAIAVALALPVRQIRKLR 139 (520)
T ss_pred HHHHHHHHHHHHhcCCCHHHHHHHHCCCHHHHHHHH
Confidence 344455677788999999999999999999999843
No 390
>cd04077 Peptidases_S8_PCSK9_ProteinaseK_like Peptidase S8 family domain in ProteinaseK-like proteins. The peptidase S8 or Subtilase clan of proteases have a Asp/His/Ser catalytic triad that is not homologous to trypsin. This CD contains several members of this clan including: PCSK9 (Proprotein convertase subtilisin/kexin type 9), Proteinase_K, Proteinase_T, and other subtilisin-like serine proteases. PCSK9 posttranslationally regulates hepatic low-density lipoprotein receptors (LDLRs) by binding to LDLRs on the cell surface, leading to their degradation. The binding site of PCSK9 has been localized to the epidermal growth factor-like repeat A (EGF-A) domain of the LDLR. Characterized Proteinases K are secreted endopeptidases with a high degree of sequence conservation. Proteinases K are not substrate-specific and function in a wide variety of species in different pathways. It can hydrolyze keratin and other proteins with subtilisin-like specificity. The number of calcium-binding moti
Probab=23.28 E-value=79 Score=26.50 Aligned_cols=33 Identities=24% Similarity=0.276 Sum_probs=29.3
Q ss_pred CCcCCHHHHHHHHHHHHhCCCcchHHhHHHHHh
Q psy10745 31 PKVATAPVVDAIASYKRENPTMFAWEIRDRLLA 63 (197)
Q Consensus 31 pk~~tp~v~~~I~~~k~e~P~iFaWEIRdrLl~ 63 (197)
.+.++|-|...+.-+.+.+|.+..-|||+.|+.
T Consensus 219 TS~Aap~vaG~~All~~~~p~~~~~~v~~~L~~ 251 (255)
T cd04077 219 TSMAAPHVAGLAAYLLSLGPDLSPAEVKARLLN 251 (255)
T ss_pred HHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHh
Confidence 457888888899999999999999999999985
No 391
>PRK09462 fur ferric uptake regulator; Provisional
Probab=23.28 E-value=1e+02 Score=24.42 Aligned_cols=46 Identities=15% Similarity=0.245 Sum_probs=31.3
Q ss_pred CCHHHHHHHHHHHHhC-CCcchHHhHHHHHhcCCCCCCCCCCcccccccccc
Q psy10745 34 ATAPVVDAIASYKREN-PTMFAWEIRDRLLAEGICSQDNVPSVSSINRYITY 84 (197)
Q Consensus 34 ~tp~v~~~I~~~k~e~-P~iFaWEIRdrLl~~GvC~~~~vPSvSSI~Rilr~ 84 (197)
.|+.-...+..+.... --+.|-||-++|.+++.-. |.++|+|.|.-
T Consensus 15 ~T~qR~~Il~~l~~~~~~h~sa~eI~~~l~~~~~~i-----~~aTVYR~L~~ 61 (148)
T PRK09462 15 VTLPRLKILEVLQEPDNHHVSAEDLYKRLIDMGEEI-----GLATVYRVLNQ 61 (148)
T ss_pred CCHHHHHHHHHHHhCCCCCCCHHHHHHHHHhhCCCC-----CHHHHHHHHHH
Confidence 4554333333333332 3689999999999988544 88999999964
No 392
>PRK12680 transcriptional regulator CysB-like protein; Reviewed
Probab=23.12 E-value=70 Score=28.14 Aligned_cols=44 Identities=14% Similarity=0.163 Sum_probs=37.1
Q ss_pred HHHHHhcCCCcccchhhhhcccchHHHHHHHhhhhcCccccccc
Q psy10745 143 IVELAHNGVRPCDISRQLRVSHGCVSKILSRESNLHNYRLVREE 186 (197)
Q Consensus 143 iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~~~n~~~~~~~ 186 (197)
.+.+++++-.-...|+.|.||+.-||+-|.+-.+.-+.+|+.-+
T Consensus 9 F~~vae~~gS~s~AA~~L~isQpavS~~I~~LE~~lG~~LF~R~ 52 (327)
T PRK12680 9 LVAIADAELNITLAAARVHATQPGLSKQLKQLEDELGFLLFVRK 52 (327)
T ss_pred HHHHHHccCCHHHHHHHhcCCchHHHHHHHHHHHHhCCeEEEEC
Confidence 45567665667889999999999999999999999999988544
No 393
>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=23.08 E-value=57 Score=21.65 Aligned_cols=26 Identities=27% Similarity=0.454 Sum_probs=20.3
Q ss_pred hcCCCcccchhhhhcccchHHHHHHH
Q psy10745 148 HNGVRPCDISRQLRVSHGCVSKILSR 173 (197)
Q Consensus 148 ~~g~r~~~isr~l~vshgcVskil~r 173 (197)
+.|+.-.++|..+++|.+-+|+|.+-
T Consensus 10 ~~~lt~~~~a~~~~i~~~~i~~~e~g 35 (64)
T PF12844_consen 10 EKGLTQKDLAEKLGISRSTISKIENG 35 (64)
T ss_dssp HCT--HHHHHHHHTS-HHHHHHHHTT
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHCC
Confidence 57999999999999999999998754
No 394
>PRK04140 hypothetical protein; Provisional
Probab=23.00 E-value=48 Score=30.57 Aligned_cols=98 Identities=27% Similarity=0.455 Sum_probs=61.5
Q ss_pred HHHHHHHhCCCcchHHhHHHHHhcCCC-CCCCCCCccccccccccccCCCCCCccccCccccCCCCCccccchhhcccCC
Q psy10745 41 AIASYKRENPTMFAWEIRDRLLAEGIC-SQDNVPSVSSINRYITYVPIGHGGVNQLGGVFVNGRPLPDVVRQRIVASRSH 119 (197)
Q Consensus 41 ~I~~~k~e~P~iFaWEIRdrLl~~GvC-~~~~vPSvSSI~Rilr~~~iGhG~vnqlGg~fingrPLPd~~RqRIVaS~~~ 119 (197)
+|..+-.+.|=+-.---|+.-+++||. .+..+|.++- +-|...|++|.|+--. +.
T Consensus 63 ~~~~~~~a~p~ivg~~~~~~~le~gvvy~r~gi~~~~~---------------~tl~~~~~~g~~p~v~------~~--- 118 (317)
T PRK04140 63 RLAKYLKASPLIIGLRTRNEELEDGVVYERHGIPALSP---------------DTLYDDFVEGEPPLIY------AA--- 118 (317)
T ss_pred HHHHHhCCccEEEEEecCCCccCCCcEEEecCceeecH---------------HHHHHHHhCCCCceEE------Ec---
Confidence 466666666766665557777777774 4555554432 2334457777754221 11
Q ss_pred CccccCCccccCCCCCChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHH
Q psy10745 120 GGVNQLGGVFVNGRPLPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILS 172 (197)
Q Consensus 120 ~~~nqlg~~~~ngrplp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ 172 (197)
-||.|++=- ...+|. + ..+.|+...++|+.++||.+-||++.+
T Consensus 119 -----~Gg~~v~i~--GerLk~--l-Re~~GlSq~eLA~~lGVSr~tIskyE~ 161 (317)
T PRK04140 119 -----PGGFYVKID--GDVLRE--A-REELGLSLGELASELGVSRRTISKYEN 161 (317)
T ss_pred -----CCCeeehhh--HHHHHH--H-HHHcCCCHHHHHHHhCCCHHHHHHHHc
Confidence 267777432 122222 2 357899999999999999999999766
No 395
>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function.
Probab=22.99 E-value=91 Score=24.60 Aligned_cols=43 Identities=16% Similarity=0.157 Sum_probs=32.8
Q ss_pred CChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHhhhh
Q psy10745 135 LPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRESNL 177 (197)
Q Consensus 135 lp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~~ 177 (197)
|..++=.-|-=.-.+|+.-.+.|.+.+||...|..||....+.
T Consensus 42 L~~dElEAiRL~D~egl~QeeaA~~MgVSR~T~~ril~~ARkK 84 (106)
T PF02001_consen 42 LTVDELEAIRLVDYEGLSQEEAAERMGVSRPTFQRILESARKK 84 (106)
T ss_pred eeHHHHHHHHHHHHcCCCHHHHHHHcCCcHHHHHHHHHHHHHH
Confidence 3444444333344789999999999999999999999987663
No 396
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=22.92 E-value=44 Score=29.13 Aligned_cols=37 Identities=24% Similarity=0.302 Sum_probs=30.6
Q ss_pred CChHHHHHHHHHHhc--CCCcccchhhhhcccchHHHHH
Q psy10745 135 LPDVVRQRIVELAHN--GVRPCDISRQLRVSHGCVSKIL 171 (197)
Q Consensus 135 lp~~~r~~iv~l~~~--g~r~~~isr~l~vshgcVskil 171 (197)
++.+=+++|++|.++ -++..|+|+.++||.-+|.+=|
T Consensus 2 ~~~eR~~~Il~~l~~~g~v~v~eLa~~~~VS~~TIRRDL 40 (253)
T COG1349 2 LKEERHQKILELLKEKGKVSVEELAELFGVSEMTIRRDL 40 (253)
T ss_pred ChHHHHHHHHHHHHHcCcEEHHHHHHHhCCCHHHHHHhH
Confidence 345667899999866 6899999999999999998843
No 397
>cd00782 MutL_Trans MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the C-terminal domain of DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. Included in this group are proteins similar to human MLH1, hPMS2, hPMS1, hMLH3 and E. coli MutL, MLH1 forms heterodimers with PMS2, PMS1 and MLH3. These three complexes have distinct functions in meiosis. hMLH1-hPMS2 also participates in the repair of all DNA mismatch repair (MMR) substrates. Roles for hMLH1-hPMS1 or hMLH1-hMLH3 in MMR have not been established. Cells lacking either hMLH1 or hPMS2 have a strong mutator phenotype and display microsatellite instability (MSI). Mutation in hMLH1 causes predisposition to HNPCC, Muir-Torre syndrome and Turcot synd
Probab=22.76 E-value=44 Score=25.13 Aligned_cols=21 Identities=38% Similarity=0.618 Sum_probs=14.4
Q ss_pred ccccCCCCCChHHHHHHHHHH
Q psy10745 127 GVFVNGRPLPDVVRQRIVELA 147 (197)
Q Consensus 127 ~~~~ngrplp~~~r~~iv~l~ 147 (197)
=.|+||||+.+..-.+.|.=+
T Consensus 47 ~~fVN~R~v~~~~l~~ai~~~ 67 (122)
T cd00782 47 FLFVNGRPVRDKLLSKAINEA 67 (122)
T ss_pred EEEECCeEecCHHHHHHHHHH
Confidence 579999998765555554433
No 398
>cd07484 Peptidases_S8_Thermitase_like Peptidase S8 family domain in Thermitase-like proteins. Thermitase is a non-specific, trypsin-related serine protease with a very high specific activity. It contains a subtilisin like domain. The tertiary structure of thermitase is similar to that of subtilisin BPN'. It contains a Asp/His/Ser catalytic triad. Members of the peptidases S8 (subtilisin and kexin) and S53 (sedolisin) clan include endopeptidases and exopeptidases. The S8 family has an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. Serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base. The S53 family contains a catalytic triad Glu/Asp/Ser with an additional acidic residue Asp in the oxyanion hole, similar to that of subtilisin. The serine residue here is the nucleophilic equivalent of the serine residue in the S8 family, while glutamic acid
Probab=22.53 E-value=94 Score=26.04 Aligned_cols=33 Identities=30% Similarity=0.330 Sum_probs=28.2
Q ss_pred CCcCCHHHHHHHHHHHHhCCCcchHHhHHHHHhc
Q psy10745 31 PKVATAPVVDAIASYKRENPTMFAWEIRDRLLAE 64 (197)
Q Consensus 31 pk~~tp~v~~~I~~~k~e~P~iFaWEIRdrLl~~ 64 (197)
.+-++|-|...+.-++.++| +...+||+.|+.-
T Consensus 223 TS~Aap~vag~~Al~~~~~p-~t~~~i~~~L~~t 255 (260)
T cd07484 223 TSMATPHVAGVAALLYSQGP-LSASEVRDALKKT 255 (260)
T ss_pred HHHHHHHHHHHHHHHHhcCC-CCHHHHHHHHHHh
Confidence 45778888888888999999 9999999999863
No 399
>PF07506 RepB: RepB plasmid partitioning protein; InterPro: IPR011111 This family includes proteins with sequence similarity to the RepB partitioning protein of the large Ti (tumour-inducing) plasmids of Agrobacterium tumefaciens [, ].
Probab=22.46 E-value=56 Score=27.03 Aligned_cols=32 Identities=22% Similarity=0.342 Sum_probs=29.2
Q ss_pred HHHHHHHhcCCCcccchhhhhcccchHHHHHH
Q psy10745 141 QRIVELAHNGVRPCDISRQLRVSHGCVSKILS 172 (197)
Q Consensus 141 ~~iv~l~~~g~r~~~isr~l~vshgcVskil~ 172 (197)
.-|.+|...|+...+|+.-|.|+-.-||+.|+
T Consensus 12 ~fa~~l~~~G~~~~~I~~aL~id~~~ls~~~~ 43 (185)
T PF07506_consen 12 RFARRLEERGFSREEIAAALGIDKSYLSRMLS 43 (185)
T ss_pred HHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 34678999999999999999999999999887
No 400
>PRK10082 cell density-dependent motility repressor; Provisional
Probab=22.27 E-value=57 Score=27.80 Aligned_cols=43 Identities=12% Similarity=0.078 Sum_probs=35.9
Q ss_pred HHHHHhcCCCcccchhhhhcccchHHHHHHHhhhhcCccccccc
Q psy10745 143 IVELAHNGVRPCDISRQLRVSHGCVSKILSRESNLHNYRLVREE 186 (197)
Q Consensus 143 iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~~~n~~~~~~~ 186 (197)
.+.++++| .-...|+.|.||..-||+-|.+..+.-+.+|+.-+
T Consensus 19 F~av~e~g-S~t~AA~~L~iSQpavS~~I~~LE~~lG~~Lf~R~ 61 (303)
T PRK10082 19 FLTLEKCR-NFSQAAVSRNVSQPAFSRRIRALEQAIGVELFNRQ 61 (303)
T ss_pred HHHHHhcC-CHHHHHHHhCCChHHHHHHHHHHHHHcCCEEEEec
Confidence 45556555 56677999999999999999999999999998654
No 401
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=22.04 E-value=90 Score=20.56 Aligned_cols=38 Identities=13% Similarity=0.199 Sum_probs=29.5
Q ss_pred HHHHHHHHhcC-CCcccchhhhhc-ccchHHHHHHHhhhh
Q psy10745 140 RQRIVELAHNG-VRPCDISRQLRV-SHGCVSKILSRESNL 177 (197)
Q Consensus 140 r~~iv~l~~~g-~r~~~isr~l~v-shgcVskil~ry~~~ 177 (197)
-++++++...+ +...|||..+++ |..-.++...++...
T Consensus 39 ~~~a~~~l~~~~~~~~~ia~~~g~~s~~~f~r~Fk~~~g~ 78 (84)
T smart00342 39 LERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKKLFGV 78 (84)
T ss_pred HHHHHHHHHcCCCCHHHHHHHhCCCChHHHHHHHHHHHCc
Confidence 34566666665 889999999999 888888888777543
No 402
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=22.03 E-value=89 Score=27.84 Aligned_cols=41 Identities=22% Similarity=0.335 Sum_probs=33.9
Q ss_pred CCChHHHHHHHHHHhcCCCcccchhhhhcccchHHHHHHHh
Q psy10745 134 PLPDVVRQRIVELAHNGVRPCDISRQLRVSHGCVSKILSRE 174 (197)
Q Consensus 134 plp~~~r~~iv~l~~~g~r~~~isr~l~vshgcVskil~ry 174 (197)
+|++-.++=|.--+.++..--+|+..|+||-+=||.|..++
T Consensus 196 ~L~EREk~Vl~l~y~eelt~kEI~~~LgISes~VSql~kka 236 (247)
T COG1191 196 PLPEREKLVLVLRYKEELTQKEIAEVLGISESRVSRLHKKA 236 (247)
T ss_pred ccCHHHHHHHHHHHHhccCHHHHHHHhCccHHHHHHHHHHH
Confidence 77776666555556788999999999999999999988775
No 403
>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=21.88 E-value=31 Score=28.68 Aligned_cols=36 Identities=25% Similarity=0.377 Sum_probs=0.6
Q ss_pred CcccchhhhhcccchHHH-HHHHhhhhcCcccccccccccccCC
Q psy10745 152 RPCDISRQLRVSHGCVSK-ILSRESNLHNYRLVREEGCFELSDL 194 (197)
Q Consensus 152 r~~~isr~l~vshgcVsk-il~ry~~~~n~~~~~~~~~~~~~~~ 194 (197)
.-.|||..|+|+-+.||. |=+.|..+. -|.|+++++
T Consensus 51 t~~~iA~~lgl~~STVSRav~~Ky~~t~-------~Gi~plk~f 87 (160)
T PF04552_consen 51 TMKDIADELGLHESTVSRAVKNKYIQTP-------RGIFPLKDF 87 (160)
T ss_dssp -----------------------------------------S--
T ss_pred CHHHHHHHhCCCHhHHHHHHcCceeecC-------CeeeeHHHh
Confidence 346899999999999999 456666554 466666654
No 404
>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=21.78 E-value=67 Score=24.45 Aligned_cols=42 Identities=19% Similarity=0.290 Sum_probs=29.6
Q ss_pred CChHHHH-HHHHHHhcCCCcccchhhhhcccchHHHHHHHhhhh
Q psy10745 135 LPDVVRQ-RIVELAHNGVRPCDISRQLRVSHGCVSKILSRESNL 177 (197)
Q Consensus 135 lp~~~r~-~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~~ 177 (197)
+-...|+ .|.+.+. |....++|+..++|---|.+|+.+..+.
T Consensus 57 ~~~~~R~~~I~~~f~-G~n~~eLA~kyglS~r~I~~Ii~~~~~~ 99 (108)
T PF08765_consen 57 LLRALRNREIRREFN-GMNVRELARKYGLSERQIYRIIKRVRRR 99 (108)
T ss_dssp HHHHHHHHHHHHH---SS-HHHHHHHHT--HHHHHHHHHHHHH-
T ss_pred HHHHHHHHHHHHHhC-CCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 3345565 6666666 9999999999999999999999998764
No 405
>PRK10341 DNA-binding transcriptional activator TdcA; Provisional
Probab=21.55 E-value=58 Score=27.94 Aligned_cols=44 Identities=18% Similarity=0.317 Sum_probs=35.3
Q ss_pred HHHHHhcCCCcccchhhhhcccchHHHHHHHhhhhcCcccccccc
Q psy10745 143 IVELAHNGVRPCDISRQLRVSHGCVSKILSRESNLHNYRLVREEG 187 (197)
Q Consensus 143 iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~~~n~~~~~~~~ 187 (197)
.+.++++| .-...|++|.||..-||+-|.+..+.-|.+|+.-+|
T Consensus 15 F~av~e~g-s~s~AA~~L~iSQpavS~~I~~LE~~lg~~LF~R~~ 58 (312)
T PRK10341 15 FQEVIRSG-SIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKN 58 (312)
T ss_pred HHHHHHcC-CHHHHHHHhCCChHHHHHHHHHHHHHhCCeEEEEcC
Confidence 34445444 566789999999999999999999999999876553
No 406
>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=21.53 E-value=1e+02 Score=27.18 Aligned_cols=48 Identities=27% Similarity=0.439 Sum_probs=36.0
Q ss_pred CCCCCcCCHHHHHHHHHHHHhCCCcchHHhHHHHHhcCCCCCCCCCCcccccccccc
Q psy10745 28 GSKPKVATAPVVDAIASYKRENPTMFAWEIRDRLLAEGICSQDNVPSVSSINRYITY 84 (197)
Q Consensus 28 GSKpk~~tp~v~~~I~~~k~e~P~iFaWEIRdrLl~~GvC~~~~vPSvSSI~Rilr~ 84 (197)
|.-+|..+.+..+.|..++.++|..+.- ++| +++.-. |..+|.|||+.
T Consensus 5 ~~p~k~Ls~~~~~~ir~L~~~~p~~~t~---~~L-ae~F~v-----spe~irrILks 52 (225)
T PF06413_consen 5 GNPPKKLSREAMEQIRYLHKEDPEEWTV---ERL-AESFKV-----SPEAIRRILKS 52 (225)
T ss_pred CCCCCCCCHHHHHHHHHHHHhCccccCH---HHH-HhhCCC-----CHHHHHHHHhc
Confidence 5678888999999999999999998554 233 333433 77888888875
No 407
>cd03482 MutL_Trans_MutL MutL_Trans_MutL: transducer domain, having a ribosomal S5 domain 2-like fold, found in proteins similar to Escherichia coli MutL. EcMutL belongs to the DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from the ATP-binding site to the DNA breakage/reunion regions of the enzymes. It has been suggested that during initiation of DNA mismatch repair in E. coli, the mismatch recognition protein MutS recruits MutL in the presence of ATP. The MutS(ATP)-MutL ternary complex formed, then recruits the latent endonuclease MutH. Prokaryotic MutS and MutL are homodimers.
Probab=21.43 E-value=51 Score=25.61 Aligned_cols=23 Identities=30% Similarity=0.348 Sum_probs=16.4
Q ss_pred ccccCCCCCChHHHHHHHHHHhc
Q psy10745 127 GVFVNGRPLPDVVRQRIVELAHN 149 (197)
Q Consensus 127 ~~~~ngrplp~~~r~~iv~l~~~ 149 (197)
=.|+||||+.+..-.+.|.-+-+
T Consensus 47 ~ifVN~R~V~~~~l~~ai~~~y~ 69 (123)
T cd03482 47 YFYVNGRMVRDKLISHAVRQAYS 69 (123)
T ss_pred EEEEcCcEECChHHHHHHHHHHH
Confidence 47999999877766666655543
No 408
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=21.39 E-value=1.2e+02 Score=24.36 Aligned_cols=47 Identities=17% Similarity=0.170 Sum_probs=32.4
Q ss_pred cCCHHHHHHHHHHHHhCCCcchHHhHHHHHhcCCCCCCCCCCcccccccccc
Q psy10745 33 VATAPVVDAIASYKRENPTMFAWEIRDRLLAEGICSQDNVPSVSSINRYITY 84 (197)
Q Consensus 33 ~~tp~v~~~I~~~k~e~P~iFaWEIRdrLl~~GvC~~~~vPSvSSI~Rilr~ 84 (197)
..|+.-...+.-+.+....+.|.||=++|.+++--. |.++++|.|.-
T Consensus 18 r~T~qR~~vl~~L~~~~~~~sAeei~~~l~~~~p~i-----slaTVYr~L~~ 64 (145)
T COG0735 18 RLTPQRLAVLELLLEADGHLSAEELYEELREEGPGI-----SLATVYRTLKL 64 (145)
T ss_pred CcCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCC-----CHhHHHHHHHH
Confidence 345644443333333333399999999999988766 89999999963
No 409
>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=21.07 E-value=1e+02 Score=22.84 Aligned_cols=38 Identities=24% Similarity=0.269 Sum_probs=27.4
Q ss_pred HHHHH-HhCCCcchHHhHHHHHhcCCCCCCCCCCcccccccccc
Q psy10745 42 IASYK-RENPTMFAWEIRDRLLAEGICSQDNVPSVSSINRYITY 84 (197)
Q Consensus 42 I~~~k-~e~P~iFaWEIRdrLl~~GvC~~~~vPSvSSI~Rilr~ 84 (197)
|.++- +...-+.+-||-++|.+++-- .|.++++|.|..
T Consensus 6 Il~~l~~~~~~~sa~ei~~~l~~~~~~-----i~~~TVYR~L~~ 44 (116)
T cd07153 6 ILEVLLESDGHLTAEEIYERLRKKGPS-----ISLATVYRTLEL 44 (116)
T ss_pred HHHHHHhCCCCCCHHHHHHHHHhcCCC-----CCHHHHHHHHHH
Confidence 44433 334568999999999988643 388999998864
No 410
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=20.99 E-value=1.2e+02 Score=24.87 Aligned_cols=53 Identities=19% Similarity=0.221 Sum_probs=41.9
Q ss_pred HHHHHHHHHHhcC--CCcccchhhhhcccchHHHHHHHhhhhcCccccccccccc
Q psy10745 138 VVRQRIVELAHNG--VRPCDISRQLRVSHGCVSKILSRESNLHNYRLVREEGCFE 190 (197)
Q Consensus 138 ~~r~~iv~l~~~g--~r~~~isr~l~vshgcVskil~ry~~~~n~~~~~~~~~~~ 190 (197)
++-.+||||+.+. +.--|++..+++|+-.|.+.|.---.++..-....-|+|-
T Consensus 12 eLk~rIvElVRe~GRiTi~ql~~~TGasR~Tvk~~lreLVa~G~l~~~G~~GvF~ 66 (127)
T PF06163_consen 12 ELKARIVELVREHGRITIKQLVAKTGASRNTVKRYLRELVARGDLYRHGRSGVFP 66 (127)
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHHCCCHHHHHHHHHHHHHcCCeEeCCCccccc
Confidence 3446899999765 4567899999999999999988887777766666668884
No 411
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=20.87 E-value=1.4e+02 Score=24.46 Aligned_cols=45 Identities=11% Similarity=0.169 Sum_probs=30.4
Q ss_pred CCHHHHHHHHHHHH-hCCCcchHHhHHHHHhcCCCCCCCCCCcccccccccc
Q psy10745 34 ATAPVVDAIASYKR-ENPTMFAWEIRDRLLAEGICSQDNVPSVSSINRYITY 84 (197)
Q Consensus 34 ~tp~v~~~I~~~k~-e~P~iFaWEIRdrLl~~GvC~~~~vPSvSSI~Rilr~ 84 (197)
.|+.-. .|+++-. ..--+.|-||=++|.+++.-. |.++|+|.|.-
T Consensus 24 ~T~qR~-~IL~~l~~~~~hlSa~eI~~~L~~~~~~i-----s~aTVYRtL~~ 69 (169)
T PRK11639 24 LTPQRL-EVLRLMSLQPGAISAYDLLDLLREAEPQA-----KPPTVYRALDF 69 (169)
T ss_pred CCHHHH-HHHHHHHhcCCCCCHHHHHHHHHhhCCCC-----CcchHHHHHHH
Confidence 345333 3333333 333578899999999998544 88999999964
No 412
>cd07490 Peptidases_S8_6 Peptidase S8 family domain, uncharacterized subfamily 6. This family is a member of the Peptidases S8 or Subtilases serine endo- and exo-peptidase clan. They have an Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The stability of subtilases may be enhanced by calcium, some members have been shown to bind up to 4 ions via binding sites with different affinity. Some members of this clan contain disulfide bonds. These enzymes can be intra- and extracellular, some function at extreme temperatures and pH values.
Probab=20.81 E-value=1e+02 Score=25.56 Aligned_cols=32 Identities=22% Similarity=0.274 Sum_probs=27.5
Q ss_pred CcCCHHHHHHHHHHHHhCCCcchHHhHHHHHh
Q psy10745 32 KVATAPVVDAIASYKRENPTMFAWEIRDRLLA 63 (197)
Q Consensus 32 k~~tp~v~~~I~~~k~e~P~iFaWEIRdrLl~ 63 (197)
+.++|-|...+.-+++++|++..-|||+.|+.
T Consensus 220 S~AaP~vaG~aAl~~~~~p~~~~~~i~~~L~~ 251 (254)
T cd07490 220 SMAAPHVAGVAALLAAAHPDLSPEQIKDALTE 251 (254)
T ss_pred HHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHH
Confidence 45678888888888999999999999999875
No 413
>PRK10260 L,D-transpeptidase; Provisional
Probab=20.69 E-value=32 Score=31.83 Aligned_cols=21 Identities=10% Similarity=0.172 Sum_probs=15.7
Q ss_pred CHHHHHH----HHHHHHhCCCcchH
Q psy10745 35 TAPVVDA----IASYKRENPTMFAW 55 (197)
Q Consensus 35 tp~v~~~----I~~~k~e~P~iFaW 55 (197)
.++++++ ...++++||++-.|
T Consensus 53 le~iA~~f~~g~~~l~~aNPgvdp~ 77 (306)
T PRK10260 53 LEYFAAEYQMGLSNMMEANPGVDTF 77 (306)
T ss_pred HHHHHHHhCCCHHHHHHhCcCCCCC
Confidence 3455554 67789999999888
No 414
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=20.39 E-value=1.5e+02 Score=25.91 Aligned_cols=140 Identities=17% Similarity=0.191 Sum_probs=75.0
Q ss_pred ccCCCCCCCCcCCHH---HHHHHHHHHHh-CCCcchHHhHHHHHhcCCCCCCCCCCccccccccccccCCCCCCccccCc
Q psy10745 23 AGVIGGSKPKVATAP---VVDAIASYKRE-NPTMFAWEIRDRLLAEGICSQDNVPSVSSINRYITYVPIGHGGVNQLGGV 98 (197)
Q Consensus 23 PG~IGGSKpk~~tp~---v~~~I~~~k~e-~P~iFaWEIRdrLl~~GvC~~~~vPSvSSI~Rilr~~~iGhG~vnqlGg~ 98 (197)
..+-|||+|+..+.. +.+.+..|... -.+--.++.|++|+...+ |=|-+|-+-+.+..+.....-|-|.+
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~Lv~~~l------~LV~~iA~~y~~~g~~~~DLiQeG~i 76 (264)
T PRK07122 3 ARAAGGSRPRASTDEYADVPEMFRELAGLPAGSPEFQRQRDRIVTRCL------PLADHIARRFDGRGEPRDDLVQVARV 76 (264)
T ss_pred cccCCCCCCCCchhhhhhHHHHHHHHHhccCCCHHHHHHHHHHHHHhH------HHHHHHHHHHHhCCCCHHHHHHHHHH
Confidence 346799999988763 34456777422 134555678999988655 44545444444332222233344432
Q ss_pred -------c---ccCCCCCccccchhhcccCCCccccCCccccCCCCCChHHHHHHHHH-------H-hcCCCc--ccchh
Q psy10745 99 -------F---VNGRPLPDVVRQRIVASRSHGGVNQLGGVFVNGRPLPDVVRQRIVEL-------A-HNGVRP--CDISR 158 (197)
Q Consensus 99 -------f---ingrPLPd~~RqRIVaS~~~~~~nqlg~~~~ngrplp~~~r~~iv~l-------~-~~g~r~--~~isr 158 (197)
- -.|-+.......+|-.+-.+ .+...+.+ --+|...+.++-++ . ..|-.| .+||.
T Consensus 77 GLi~AierFDp~~G~~FsTYA~~~Irg~I~~-~lr~~~~~----ir~Pr~~~~~~~~i~~~~~~l~~~lg~~pt~~eiA~ 151 (264)
T PRK07122 77 GLVNAVNRFDVETGSDFVSFAVPTIMGEVRR-HFRDNSWS----VKVPRRLKELHLRLGRATAELSQRLGRAPTASELAA 151 (264)
T ss_pred HHHHHHHHcCCCCCCChHHHHHHHHHHHHHH-HHHHcCCc----cccCHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHH
Confidence 1 22444444444444321111 11111111 13677766655433 2 346555 57999
Q ss_pred hhhcccchHHHHHHH
Q psy10745 159 QLRVSHGCVSKILSR 173 (197)
Q Consensus 159 ~l~vshgcVskil~r 173 (197)
.|+|+--=|.+++..
T Consensus 152 ~lg~~~~~v~~~~~~ 166 (264)
T PRK07122 152 ELGMDREEVVEGLVA 166 (264)
T ss_pred HhCCCHHHHHHHHHH
Confidence 999998777777654
No 415
>PF01119 DNA_mis_repair: DNA mismatch repair protein, C-terminal domain; InterPro: IPR013507 This entry represents the C-terminal domain of DNA mismatch repair proteins, such as MutL. This domain functions in promoting dimerisation []. The dimeric MutL protein has a key function in communicating mismatch recognition by MutS to downstream repair processes. Mismatch repair contributes to the overall fidelity of DNA replication by targeting mispaired bases that arise through replication errors during homologous recombination and as a result of DNA damage. It involves the correction of mismatched base pairs that have been missed by the proofreading element of the DNA polymerase complex [].; GO: 0005524 ATP binding, 0030983 mismatched DNA binding, 0006298 mismatch repair; PDB: 1B62_A 1NHJ_A 1BKN_B 1NHH_A 1B63_A 1NHI_A 3NA3_A 1EA6_A 1H7U_A 1H7S_B ....
Probab=20.28 E-value=47 Score=25.34 Aligned_cols=21 Identities=29% Similarity=0.534 Sum_probs=12.6
Q ss_pred CCccccCCCCCChHHHHHHHH
Q psy10745 125 LGGVFVNGRPLPDVVRQRIVE 145 (197)
Q Consensus 125 lg~~~~ngrplp~~~r~~iv~ 145 (197)
.--+|+||||+....-.+.|.
T Consensus 41 ~q~ifVN~R~V~~~~l~~~I~ 61 (119)
T PF01119_consen 41 RQFIFVNGRPVENKALSKAIN 61 (119)
T ss_dssp CEEEEETTEEE--HHHHHHHH
T ss_pred cEEEEeCCCeEeChHHHHHHH
Confidence 345799999987665444443
No 416
>PRK10094 DNA-binding transcriptional activator AllS; Provisional
Probab=20.22 E-value=81 Score=27.22 Aligned_cols=44 Identities=11% Similarity=0.094 Sum_probs=36.6
Q ss_pred HHHHHHhcCCCcccchhhhhcccchHHHHHHHhhhhcCccccccc
Q psy10745 142 RIVELAHNGVRPCDISRQLRVSHGCVSKILSRESNLHNYRLVREE 186 (197)
Q Consensus 142 ~iv~l~~~g~r~~~isr~l~vshgcVskil~ry~~~~n~~~~~~~ 186 (197)
-++.++++| .-...|++|.||..-||+-|.+..+.-+.+|+.-+
T Consensus 9 ~f~~v~e~g-s~s~AA~~L~iSQpavS~~I~~LE~~lg~~Lf~R~ 52 (308)
T PRK10094 9 TFIAVAETG-SFSKAAERLCKTTATISYRIKLLEENTGVALFFRT 52 (308)
T ss_pred HHHHHHHhC-CHHHHHHHhcCCHHHHHHHHHHHHHHhCCEEEeeC
Confidence 345666666 77888999999999999999999998888887554
No 417
>cd07481 Peptidases_S8_BacillopeptidaseF-like Peptidase S8 family domain in BacillopeptidaseF-like proteins. Bacillus subtilis produces and secretes proteases and other types of exoenzymes at the end of the exponential phase of growth. The ones that make up this group is known as bacillopeptidase F, encoded by bpr, a serine protease with high esterolytic activity which is inhibited by PMSF. Like other members of the peptidases S8 family these have a Asp/His/Ser catalytic triad similar to that found in trypsin-like proteases, but do not share their three-dimensional structure and are not homologous to trypsin. The stability of these enzymes may be enhanced by calcium, some members have been shown to bind up to 4 ions via binding sites with different affinity.
Probab=20.05 E-value=1.1e+02 Score=25.88 Aligned_cols=33 Identities=18% Similarity=0.034 Sum_probs=28.1
Q ss_pred CCcCCHHHHHHHHHHHHhCCC--cchHHhHHHHHh
Q psy10745 31 PKVATAPVVDAIASYKRENPT--MFAWEIRDRLLA 63 (197)
Q Consensus 31 pk~~tp~v~~~I~~~k~e~P~--iFaWEIRdrLl~ 63 (197)
.+-++|-|...+.-+++++|. +..-|||+.|..
T Consensus 227 TS~AaP~vaG~aAll~~~~p~~~l~~~~v~~~L~~ 261 (264)
T cd07481 227 TSMAAPHVAGVAALLWSANPSLIGDVDATEAILTE 261 (264)
T ss_pred HHHHHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHH
Confidence 456778888888888999999 999999998875
Done!