Query 043121
Match_columns 169
No_of_seqs 201 out of 1200
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 13:05:19 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043121.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/043121hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0216 PrfA Protein chain rel 100.0 3.1E-36 6.8E-41 265.4 4.7 97 16-116 217-319 (363)
2 KOG2726 Mitochondrial polypept 100.0 4.9E-32 1.1E-36 241.7 7.3 128 25-161 247-380 (386)
3 PF00472 RF-1: RF-1 domain; I 100.0 2.8E-31 6E-36 201.7 5.2 96 15-114 5-106 (113)
4 PRK08787 peptide chain release 100.0 3.1E-31 6.7E-36 232.0 5.2 103 17-127 171-278 (313)
5 TIGR03072 release_prfH putativ 100.0 4E-31 8.6E-36 219.2 5.4 88 26-113 106-198 (200)
6 PRK05589 peptide chain release 100.0 3.7E-31 7.9E-36 232.6 5.2 96 17-116 191-292 (325)
7 PRK06746 peptide chain release 100.0 7E-31 1.5E-35 230.9 4.5 96 16-116 191-293 (326)
8 PRK08179 prfH peptide chain re 100.0 1.8E-30 3.8E-35 215.4 5.8 91 17-111 102-197 (200)
9 TIGR00019 prfA peptide chain r 100.0 1.3E-30 2.8E-35 231.8 5.2 97 26-126 221-323 (360)
10 PRK07342 peptide chain release 100.0 1.7E-30 3.8E-35 229.4 4.7 90 26-115 199-294 (339)
11 PRK00591 prfA peptide chain re 100.0 3.6E-30 7.9E-35 228.8 5.2 98 25-126 220-323 (359)
12 TIGR00020 prfB peptide chain r 100.0 1.9E-30 4.1E-35 231.0 3.3 92 25-116 234-331 (364)
13 PRK00578 prfB peptide chain re 100.0 9.2E-30 2E-34 226.7 4.3 96 17-116 230-331 (367)
14 COG1186 PrfB Protein chain rel 99.9 2.1E-28 4.5E-33 207.5 0.8 88 26-113 110-202 (239)
15 PRK09256 hypothetical protein; 99.9 2.9E-22 6.3E-27 157.9 6.8 65 15-83 6-94 (138)
16 KOG3429 Predicted peptidyl-tRN 99.6 1.1E-15 2.3E-20 124.0 5.8 55 28-82 42-121 (172)
17 PF02954 HTH_8: Bacterial regu 95.5 0.032 7E-07 35.2 4.3 34 119-152 8-41 (42)
18 PRK01905 DNA-binding protein F 88.4 0.92 2E-05 32.0 4.2 34 120-153 41-74 (77)
19 smart00342 HTH_ARAC helix_turn 87.8 1.1 2.4E-05 29.5 4.2 37 116-152 37-74 (84)
20 PRK00430 fis global DNA-bindin 86.4 1.3 2.9E-05 32.7 4.3 33 121-153 60-92 (95)
21 PF13744 HTH_37: Helix-turn-he 86.0 2.4 5.3E-05 29.8 5.3 35 117-151 19-53 (80)
22 PF12728 HTH_17: Helix-turn-he 82.0 1.8 3.8E-05 27.5 2.9 23 131-153 3-25 (51)
23 PF02796 HTH_7: Helix-turn-hel 81.7 3.2 7E-05 26.2 4.0 34 118-152 11-44 (45)
24 PF13542 HTH_Tnp_ISL3: Helix-t 81.0 5.2 0.00011 25.2 4.8 44 108-152 7-50 (52)
25 PF13384 HTH_23: Homeodomain-l 80.3 3.5 7.6E-05 25.8 3.8 25 129-153 17-41 (50)
26 PF00165 HTH_AraC: Bacterial r 80.1 2 4.4E-05 26.4 2.6 26 128-153 7-32 (42)
27 PF00440 TetR_N: Bacterial reg 79.5 5.5 0.00012 25.0 4.6 43 118-160 2-47 (47)
28 smart00342 HTH_ARAC helix_turn 79.3 2.7 5.9E-05 27.5 3.2 38 130-167 2-41 (84)
29 PF05225 HTH_psq: helix-turn-h 79.2 4.9 0.00011 25.8 4.3 38 118-155 5-42 (45)
30 PRK10371 DNA-binding transcrip 78.9 4.5 9.7E-05 34.8 5.2 51 117-167 192-247 (302)
31 PRK13503 transcriptional activ 77.9 4.8 0.0001 33.1 4.9 52 117-168 172-228 (278)
32 TIGR02974 phageshock_pspF psp 77.3 3.9 8.5E-05 36.0 4.5 33 121-153 297-329 (329)
33 PRK10219 DNA-binding transcrip 76.4 5.7 0.00012 28.6 4.5 50 118-167 7-61 (107)
34 PF00126 HTH_1: Bacterial regu 76.0 3.1 6.8E-05 27.5 2.8 24 129-152 13-36 (60)
35 TIGR01764 excise DNA binding d 75.6 3.8 8.2E-05 24.7 2.9 23 131-153 3-25 (49)
36 COG2522 Predicted transcriptio 75.4 4.8 0.0001 31.4 4.0 44 112-155 5-48 (119)
37 PRK11608 pspF phage shock prot 74.6 4.9 0.00011 35.2 4.4 33 121-153 291-323 (326)
38 PF12802 MarR_2: MarR family; 72.6 10 0.00023 24.3 4.6 39 114-152 3-44 (62)
39 smart00497 IENR1 Intron encode 72.3 4.7 0.0001 25.4 2.8 22 131-152 19-40 (53)
40 PRK15115 response regulator Gl 71.9 6.1 0.00013 35.1 4.4 34 120-153 402-435 (444)
41 TIGR02915 PEP_resp_reg putativ 71.7 6.1 0.00013 35.1 4.3 35 119-153 408-442 (445)
42 PRK13502 transcriptional activ 71.4 7.1 0.00015 32.4 4.4 53 116-168 176-233 (282)
43 PRK11511 DNA-binding transcrip 71.2 7.6 0.00016 29.4 4.2 39 128-166 24-64 (127)
44 cd06171 Sigma70_r4 Sigma70, re 71.0 13 0.00028 22.0 4.5 37 116-152 13-49 (55)
45 PRK11361 acetoacetate metaboli 70.9 6.3 0.00014 35.0 4.2 34 120-153 421-454 (457)
46 PF13936 HTH_38: Helix-turn-he 70.8 6.5 0.00014 24.8 3.2 29 124-152 15-43 (44)
47 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 70.5 9.8 0.00021 25.4 4.1 36 118-154 9-44 (50)
48 PHA00542 putative Cro-like pro 70.3 13 0.00028 26.4 5.0 33 121-153 23-55 (82)
49 TIGR02607 antidote_HigA addict 70.2 14 0.0003 24.9 5.0 39 115-153 4-42 (78)
50 PRK10572 DNA-binding transcrip 70.0 7.6 0.00017 32.4 4.3 52 117-168 184-240 (290)
51 TIGR02297 HpaA 4-hydroxyphenyl 69.0 10 0.00022 31.4 4.9 52 117-168 187-243 (287)
52 PRK10365 transcriptional regul 69.0 7.9 0.00017 34.1 4.4 33 120-152 409-441 (441)
53 TIGR01818 ntrC nitrogen regula 69.0 7.7 0.00017 34.6 4.4 32 121-152 431-462 (463)
54 PF04218 CENP-B_N: CENP-B N-te 68.6 3.1 6.7E-05 27.5 1.3 29 129-157 22-50 (53)
55 COG3284 AcoR Transcriptional a 68.3 7.1 0.00015 38.0 4.2 35 119-153 568-602 (606)
56 PF13518 HTH_28: Helix-turn-he 68.0 11 0.00025 23.3 3.9 26 129-154 12-37 (52)
57 PRK07037 extracytoplasmic-func 67.7 22 0.00047 26.9 6.1 44 115-164 111-154 (163)
58 PRK13500 transcriptional activ 67.2 13 0.00028 32.0 5.2 52 117-168 207-263 (312)
59 PRK05022 anaerobic nitric oxid 66.8 8.6 0.00019 35.7 4.3 35 119-153 471-505 (509)
60 PF01047 MarR: MarR family; I 66.3 11 0.00024 24.1 3.7 32 121-152 8-40 (59)
61 PRK00118 putative DNA-binding 66.1 13 0.00029 28.1 4.6 43 110-152 14-56 (104)
62 PF04545 Sigma70_r4: Sigma-70, 65.5 20 0.00043 22.5 4.7 44 115-164 6-49 (50)
63 PRK10923 glnG nitrogen regulat 65.0 9.9 0.00021 34.1 4.3 32 121-152 434-465 (469)
64 COG2207 AraC AraC-type DNA-bin 64.3 26 0.00057 24.5 5.6 42 125-166 32-75 (127)
65 PRK09685 DNA-binding transcrip 64.0 12 0.00026 31.3 4.3 50 118-167 199-253 (302)
66 PF03374 ANT: Phage antirepres 64.0 13 0.00028 27.1 4.1 38 119-156 12-51 (111)
67 TIGR01817 nifA Nif-specific re 63.2 11 0.00024 34.9 4.4 34 120-153 494-527 (534)
68 PF00356 LacI: Bacterial regul 62.3 8.6 0.00019 24.9 2.5 25 132-156 2-26 (46)
69 PF07453 NUMOD1: NUMOD1 domain 62.2 8.1 0.00018 23.2 2.3 21 130-150 17-37 (37)
70 PRK15424 propionate catabolism 61.9 11 0.00025 35.8 4.3 35 119-153 500-534 (538)
71 PF08281 Sigma70_r4_2: Sigma-7 61.7 19 0.00041 22.8 4.1 37 115-151 12-48 (54)
72 PRK09940 transcriptional regul 61.6 16 0.00034 31.6 4.7 49 119-168 141-190 (253)
73 cd04762 HTH_MerR-trunc Helix-T 61.3 12 0.00025 22.3 2.9 23 131-153 2-24 (49)
74 PF13443 HTH_26: Cro/C1-type H 60.9 19 0.00041 23.3 4.1 33 121-153 2-34 (63)
75 TIGR02329 propionate_PrpR prop 60.4 13 0.00028 35.2 4.4 34 119-152 493-526 (526)
76 PRK11388 DNA-binding transcrip 60.3 13 0.00029 35.2 4.4 35 119-153 594-628 (638)
77 TIGR00637 ModE_repress ModE mo 59.2 10 0.00022 28.0 2.8 24 129-152 16-39 (99)
78 PRK13501 transcriptional activ 58.9 20 0.00044 30.0 4.9 47 122-168 185-233 (290)
79 TIGR02040 PpsR-CrtJ transcript 58.9 15 0.00032 32.6 4.2 33 121-153 408-440 (442)
80 PF02042 RWP-RK: RWP-RK domain 58.7 22 0.00048 23.9 4.1 31 123-153 9-39 (52)
81 TIGR03070 couple_hipB transcri 58.4 26 0.00057 21.6 4.3 34 120-153 6-39 (58)
82 PF01381 HTH_3: Helix-turn-hel 58.0 25 0.00053 22.0 4.1 30 124-153 4-33 (55)
83 PRK09393 ftrA transcriptional 57.8 33 0.00071 29.4 6.1 54 115-168 217-275 (322)
84 PRK09978 DNA-binding transcrip 57.5 17 0.00037 31.8 4.3 51 118-168 144-198 (274)
85 TIGR03613 RutR pyrimidine util 57.3 24 0.00052 27.5 4.8 47 115-161 11-60 (202)
86 PF10213 MRP-S28: Mitochondria 57.3 36 0.00078 26.6 5.7 32 56-87 59-91 (127)
87 PRK15121 right oriC-binding tr 57.3 25 0.00054 29.8 5.2 50 118-167 7-61 (289)
88 PF00325 Crp: Bacterial regula 56.2 13 0.00028 22.7 2.4 22 131-152 4-25 (32)
89 PF13412 HTH_24: Winged helix- 54.9 30 0.00065 21.4 4.1 32 120-151 7-39 (48)
90 PRK09726 antitoxin HipB; Provi 54.7 57 0.0012 23.0 6.0 37 117-153 13-49 (88)
91 cd00093 HTH_XRE Helix-turn-hel 54.4 34 0.00073 19.7 4.1 33 121-153 4-36 (58)
92 PF09339 HTH_IclR: IclR helix- 53.9 19 0.00042 22.9 3.1 32 120-151 7-40 (52)
93 cd00569 HTH_Hin_like Helix-tur 53.9 31 0.00068 17.9 4.4 24 126-149 18-41 (42)
94 COG2204 AtoC Response regulato 53.9 19 0.00041 33.9 4.3 36 118-153 419-454 (464)
95 smart00530 HTH_XRE Helix-turn- 53.4 33 0.00071 19.6 3.9 31 123-153 4-34 (56)
96 PHA02591 hypothetical protein; 51.6 23 0.00049 26.2 3.5 32 121-152 51-82 (83)
97 TIGR03879 near_KaiC_dom probab 50.9 47 0.001 23.8 5.0 44 115-158 17-61 (73)
98 PF12833 HTH_18: Helix-turn-he 50.7 17 0.00037 24.5 2.7 32 136-167 2-35 (81)
99 PRK13890 conjugal transfer pro 50.3 22 0.00047 27.1 3.4 41 110-153 2-42 (120)
100 PF01418 HTH_6: Helix-turn-hel 50.2 25 0.00054 24.4 3.4 26 127-152 32-57 (77)
101 PRK11062 nhaR transcriptional 50.1 20 0.00043 29.9 3.4 25 128-152 17-41 (296)
102 smart00347 HTH_MARR helix_turn 50.0 46 0.00099 22.5 4.8 39 113-151 7-46 (101)
103 PF08535 KorB: KorB domain; I 49.9 19 0.00041 25.8 2.9 35 127-161 1-38 (93)
104 PRK15435 bifunctional DNA-bind 48.4 39 0.00085 30.3 5.2 52 116-167 85-139 (353)
105 PRK04217 hypothetical protein; 48.0 44 0.00096 25.5 4.8 36 118-153 47-82 (110)
106 TIGR02424 TF_pcaQ pca operon t 47.2 19 0.00041 29.7 2.8 25 128-152 16-40 (300)
107 PRK09986 DNA-binding transcrip 46.9 15 0.00033 30.0 2.3 24 129-152 21-44 (294)
108 PRK15092 DNA-binding transcrip 46.6 24 0.00052 30.1 3.5 26 127-152 23-48 (310)
109 PRK10296 DNA-binding transcrip 46.6 32 0.00069 28.5 4.1 51 117-167 172-228 (278)
110 PRK06759 RNA polymerase factor 46.4 71 0.0015 23.7 5.7 36 116-151 109-144 (154)
111 PRK10082 cell density-dependen 46.2 20 0.00044 29.8 2.9 26 127-152 23-48 (303)
112 smart00418 HTH_ARSR helix_turn 46.2 37 0.00081 20.7 3.5 29 123-151 4-32 (66)
113 PRK13501 transcriptional activ 46.0 30 0.00066 28.9 3.9 37 117-153 229-266 (290)
114 PF02815 MIR: MIR domain; Int 45.9 40 0.00087 26.8 4.5 39 30-68 121-159 (190)
115 PF12844 HTH_19: Helix-turn-he 45.6 52 0.0011 21.2 4.3 32 121-152 4-35 (64)
116 PRK09047 RNA polymerase factor 45.6 50 0.0011 24.7 4.7 37 115-151 108-144 (161)
117 PRK06811 RNA polymerase factor 45.5 71 0.0015 25.0 5.8 49 113-167 131-179 (189)
118 smart00421 HTH_LUXR helix_turn 45.2 57 0.0012 19.6 4.2 30 121-151 11-40 (58)
119 PRK10837 putative DNA-binding 45.1 20 0.00043 29.2 2.7 24 129-152 17-40 (290)
120 PRK12515 RNA polymerase sigma 45.0 56 0.0012 25.5 5.1 39 113-151 131-169 (189)
121 smart00550 Zalpha Z-DNA-bindin 44.8 50 0.0011 22.5 4.2 33 119-151 9-44 (68)
122 PRK09508 leuO leucine transcri 44.5 22 0.00048 29.8 2.9 27 126-152 33-59 (314)
123 PRK12523 RNA polymerase sigma 44.2 90 0.002 23.9 6.1 37 114-150 120-156 (172)
124 PRK09652 RNA polymerase sigma 44.0 52 0.0011 24.8 4.6 33 119-151 134-166 (182)
125 PRK09791 putative DNA-binding 43.9 23 0.00051 29.3 2.9 24 129-152 19-42 (302)
126 PRK11013 DNA-binding transcrip 43.9 26 0.00057 29.3 3.3 24 129-152 18-41 (309)
127 TIGR02937 sigma70-ECF RNA poly 43.5 53 0.0012 23.2 4.4 34 119-152 116-149 (158)
128 PRK10341 DNA-binding transcrip 43.2 24 0.00051 29.6 2.9 24 129-152 21-44 (312)
129 PF14549 P22_Cro: DNA-binding 43.2 44 0.00095 22.9 3.7 34 123-158 4-37 (60)
130 PF13011 LZ_Tnp_IS481: leucine 42.9 66 0.0014 23.7 4.8 39 115-153 11-49 (85)
131 PRK10216 DNA-binding transcrip 42.8 24 0.00053 29.7 2.9 25 128-152 21-45 (319)
132 COG3604 FhlA Transcriptional r 42.8 36 0.00079 32.9 4.3 36 118-153 508-543 (550)
133 COG1846 MarR Transcriptional r 42.7 44 0.00095 23.2 3.8 37 116-152 22-59 (126)
134 PF07638 Sigma70_ECF: ECF sigm 42.7 55 0.0012 26.0 4.8 32 121-152 143-174 (185)
135 PF13551 HTH_29: Winged helix- 42.5 38 0.00081 23.8 3.5 27 126-152 8-35 (112)
136 PRK11139 DNA-binding transcrip 42.4 24 0.00051 29.2 2.7 24 129-152 20-43 (297)
137 PRK10572 DNA-binding transcrip 42.1 36 0.00077 28.4 3.8 37 117-153 236-273 (290)
138 PRK12525 RNA polymerase sigma 42.0 1E+02 0.0023 23.5 6.1 38 113-150 118-155 (168)
139 PRK12541 RNA polymerase sigma 42.0 55 0.0012 24.7 4.5 36 114-149 113-148 (161)
140 PRK15185 transcriptional regul 41.7 40 0.00087 30.2 4.2 42 126-167 219-261 (309)
141 PRK11482 putative DNA-binding 41.6 31 0.00068 29.3 3.4 24 129-152 43-66 (317)
142 cd01392 HTH_LacI Helix-turn-he 41.4 21 0.00045 22.2 1.8 21 134-154 2-22 (52)
143 PRK09642 RNA polymerase sigma 41.3 62 0.0013 24.3 4.7 37 115-151 108-144 (160)
144 CHL00180 rbcR LysR transcripti 40.8 23 0.0005 29.5 2.4 24 129-152 19-42 (305)
145 PF13560 HTH_31: Helix-turn-he 40.3 53 0.0011 21.5 3.7 34 121-154 6-39 (64)
146 TIGR02844 spore_III_D sporulat 40.3 1E+02 0.0022 22.3 5.4 36 118-153 8-43 (80)
147 PRK12514 RNA polymerase sigma 40.2 77 0.0017 24.4 5.2 33 117-149 133-165 (179)
148 PF04297 UPF0122: Putative hel 39.7 33 0.00071 26.0 2.9 34 120-153 24-57 (101)
149 PRK11924 RNA polymerase sigma 39.4 61 0.0013 24.3 4.4 35 118-152 130-164 (179)
150 PRK13919 putative RNA polymera 39.0 65 0.0014 24.8 4.6 35 117-151 139-173 (186)
151 PRK09647 RNA polymerase sigma 38.9 89 0.0019 25.2 5.5 35 117-151 142-176 (203)
152 PHA01976 helix-turn-helix prot 38.8 82 0.0018 20.5 4.5 33 121-153 7-39 (67)
153 PRK10086 DNA-binding transcrip 38.8 31 0.00068 29.0 3.0 25 128-152 27-51 (311)
154 PF01527 HTH_Tnp_1: Transposas 38.7 47 0.001 22.1 3.3 34 120-153 14-47 (76)
155 cd04761 HTH_MerR-SF Helix-Turn 38.6 43 0.00092 20.3 2.9 22 131-152 2-23 (49)
156 PRK09801 transcriptional activ 38.1 33 0.00071 29.0 3.0 26 127-152 18-43 (310)
157 smart00419 HTH_CRP helix_turn_ 38.0 43 0.00093 20.0 2.8 23 129-151 8-30 (48)
158 cd00090 HTH_ARSR Arsenical Res 37.7 83 0.0018 19.6 4.3 32 120-151 11-42 (78)
159 PRK15186 AraC family transcrip 37.5 63 0.0014 28.2 4.7 41 127-167 195-236 (291)
160 cd06170 LuxR_C_like C-terminal 37.3 89 0.0019 18.9 4.2 26 126-151 12-37 (57)
161 PF04967 HTH_10: HTH DNA bindi 37.2 39 0.00086 22.6 2.7 23 130-152 24-46 (53)
162 smart00346 HTH_ICLR helix_turn 37.1 71 0.0015 21.8 4.1 32 120-151 9-42 (91)
163 PF06056 Terminase_5: Putative 36.9 54 0.0012 22.1 3.3 29 125-153 9-37 (58)
164 smart00420 HTH_DEOR helix_turn 36.8 94 0.002 18.5 4.3 31 121-151 5-36 (53)
165 TIGR02985 Sig70_bacteroi1 RNA 36.7 85 0.0019 23.0 4.8 34 118-151 118-151 (161)
166 smart00422 HTH_MERR helix_turn 36.7 43 0.00093 21.8 2.8 21 131-151 2-22 (70)
167 PRK12547 RNA polymerase sigma 36.7 79 0.0017 24.1 4.7 36 116-151 115-150 (164)
168 TIGR02036 dsdC D-serine deamin 36.6 43 0.00093 28.0 3.4 26 127-152 20-45 (302)
169 PRK09744 DNA-binding transcrip 36.5 80 0.0017 23.0 4.3 34 123-157 5-38 (75)
170 PF09030 Creb_binding: Creb bi 36.5 32 0.0007 26.5 2.4 25 144-168 73-97 (104)
171 PF02001 DUF134: Protein of un 36.4 64 0.0014 24.7 4.0 32 121-152 49-80 (106)
172 cd04764 HTH_MlrA-like_sg1 Heli 36.2 32 0.0007 22.7 2.2 21 131-151 2-22 (67)
173 TIGR02999 Sig-70_X6 RNA polyme 35.7 86 0.0019 24.0 4.8 38 114-151 135-172 (183)
174 TIGR03384 betaine_BetI transcr 35.6 1.1E+02 0.0023 23.2 5.3 49 115-163 11-62 (189)
175 PRK09641 RNA polymerase sigma 35.4 79 0.0017 24.2 4.5 34 118-151 141-174 (187)
176 TIGR02959 SigZ RNA polymerase 35.4 86 0.0019 24.2 4.8 37 114-150 101-137 (170)
177 PRK09639 RNA polymerase sigma 35.4 86 0.0019 23.6 4.7 36 115-151 114-149 (166)
178 TIGR02954 Sig70_famx3 RNA poly 35.3 81 0.0018 24.0 4.5 34 117-150 123-156 (169)
179 PRK15429 formate hydrogenlyase 35.2 46 0.00099 32.0 3.8 34 119-152 644-680 (686)
180 PRK12522 RNA polymerase sigma 35.1 81 0.0017 24.2 4.5 36 116-151 122-157 (173)
181 TIGR02297 HpaA 4-hydroxyphenyl 35.1 58 0.0013 26.9 4.0 36 118-153 240-276 (287)
182 COG3077 RelB DNA-damage-induci 35.0 32 0.0007 25.6 2.1 24 129-152 12-39 (88)
183 PRK09648 RNA polymerase sigma 34.8 1.3E+02 0.0029 23.3 5.8 37 114-150 140-176 (189)
184 TIGR02989 Sig-70_gvs1 RNA poly 34.8 91 0.002 23.2 4.7 36 114-149 112-147 (159)
185 PRK12537 RNA polymerase sigma 34.8 1.3E+02 0.0028 23.3 5.7 30 121-150 141-170 (182)
186 PRK13756 tetracycline represso 34.3 91 0.002 25.5 4.9 48 115-162 7-57 (205)
187 PRK15008 HTH-type transcriptio 34.3 89 0.0019 24.9 4.8 47 114-160 20-69 (212)
188 PF14338 Mrr_N: Mrr N-terminal 34.2 1.4E+02 0.0031 21.1 5.4 41 114-154 2-48 (92)
189 PRK10219 DNA-binding transcrip 33.9 84 0.0018 22.4 4.2 42 111-152 52-94 (107)
190 PRK12519 RNA polymerase sigma 33.8 1.1E+02 0.0024 23.8 5.2 35 116-150 144-178 (194)
191 PF13556 HTH_30: PucR C-termin 33.7 85 0.0018 20.6 3.9 30 120-149 3-32 (59)
192 PRK09645 RNA polymerase sigma 33.6 95 0.0021 23.6 4.7 36 115-150 120-155 (173)
193 PRK13503 transcriptional activ 33.1 72 0.0016 26.1 4.2 37 117-153 224-261 (278)
194 PF01402 RHH_1: Ribbon-helix-h 33.0 43 0.00094 19.8 2.2 21 132-152 14-34 (39)
195 PF01325 Fe_dep_repress: Iron 32.9 1.1E+02 0.0025 20.4 4.4 34 117-151 9-44 (60)
196 cd02394 vigilin_like_KH K homo 32.7 50 0.0011 21.4 2.6 38 37-79 16-60 (62)
197 TIGR01610 phage_O_Nterm phage 32.3 1.1E+02 0.0024 22.0 4.6 23 129-151 47-69 (95)
198 PF01022 HTH_5: Bacterial regu 32.1 68 0.0015 20.0 3.1 32 120-151 6-37 (47)
199 cd00283 GIY-YIG_Cterm GIYX(10- 31.6 40 0.00087 25.7 2.3 27 130-156 81-107 (113)
200 TIGR02983 SigE-fam_strep RNA p 31.6 1E+02 0.0022 23.2 4.5 36 115-150 112-147 (162)
201 COG1309 AcrR Transcriptional r 31.5 1.1E+02 0.0023 21.6 4.4 45 116-160 16-63 (201)
202 PF09607 BrkDBD: Brinker DNA-b 31.4 65 0.0014 22.3 3.0 34 126-159 22-55 (58)
203 PF00376 MerR: MerR family reg 31.3 42 0.00091 20.7 1.9 17 132-148 2-18 (38)
204 TIGR02952 Sig70_famx2 RNA poly 31.2 1.1E+02 0.0024 22.9 4.7 36 115-150 124-159 (170)
205 PF13309 HTH_22: HTH domain 31.1 32 0.0007 23.4 1.5 27 124-150 37-63 (64)
206 TIGR03209 P21_Cbot clostridium 31.1 85 0.0018 23.2 3.9 32 115-146 109-140 (142)
207 PF08279 HTH_11: HTH domain; 30.9 1.2E+02 0.0025 19.1 4.1 32 120-151 4-37 (55)
208 TIGR02984 Sig-70_plancto1 RNA 30.9 1.2E+02 0.0025 23.2 4.8 37 115-151 142-178 (189)
209 PF12840 HTH_20: Helix-turn-he 30.6 93 0.002 20.3 3.7 35 116-150 10-45 (61)
210 PRK15243 transcriptional regul 30.1 53 0.0011 28.3 3.0 26 127-152 16-41 (297)
211 COG1414 IclR Transcriptional r 30.0 81 0.0018 26.6 4.1 32 120-151 8-41 (246)
212 PRK13502 transcriptional activ 29.9 78 0.0017 26.2 3.9 41 118-158 230-275 (282)
213 PRK12542 RNA polymerase sigma 29.6 1.2E+02 0.0026 23.5 4.7 36 115-150 124-159 (185)
214 PRK10668 DNA-binding transcrip 29.6 1.4E+02 0.003 23.5 5.1 46 116-161 15-63 (215)
215 PRK12534 RNA polymerase sigma 29.6 1.2E+02 0.0025 23.5 4.6 32 120-151 144-175 (187)
216 cd00092 HTH_CRP helix_turn_hel 29.5 63 0.0014 20.6 2.7 23 129-151 25-47 (67)
217 smart00351 PAX Paired Box doma 29.3 1.9E+02 0.0041 21.9 5.6 34 119-153 24-57 (125)
218 PRK12530 RNA polymerase sigma 29.3 1.2E+02 0.0026 23.9 4.7 35 116-150 137-171 (189)
219 PF09048 Cro: Cro; InterPro: 29.1 97 0.0021 21.6 3.6 24 132-155 15-38 (59)
220 PF04255 DUF433: Protein of un 29.1 87 0.0019 20.6 3.3 30 118-148 21-51 (56)
221 cd07377 WHTH_GntR Winged helix 29.1 65 0.0014 20.2 2.7 21 131-151 27-47 (66)
222 PRK00767 transcriptional regul 28.9 1.4E+02 0.0029 22.9 4.9 45 115-159 12-59 (197)
223 PRK12527 RNA polymerase sigma 28.7 1.4E+02 0.003 22.4 4.8 37 115-151 107-143 (159)
224 PRK14996 TetR family transcrip 28.5 1.1E+02 0.0024 23.6 4.4 44 116-159 12-58 (192)
225 PRK12516 RNA polymerase sigma 28.4 1.2E+02 0.0027 23.9 4.7 37 115-151 118-154 (187)
226 KOG3933 Mitochondrial ribosoma 28.2 1.1E+02 0.0023 27.6 4.6 32 56-87 201-233 (296)
227 COG3829 RocR Transcriptional r 28.2 87 0.0019 30.5 4.3 35 118-152 522-556 (560)
228 smart00472 MIR Domain in ryano 28.0 63 0.0014 20.5 2.4 21 47-67 7-27 (57)
229 PRK12512 RNA polymerase sigma 27.9 1.3E+02 0.0029 23.1 4.7 36 115-150 133-168 (184)
230 smart00354 HTH_LACI helix_turn 27.7 73 0.0016 21.5 2.8 24 132-155 3-26 (70)
231 PRK12531 RNA polymerase sigma 27.7 1.3E+02 0.0029 23.6 4.7 33 118-150 146-178 (194)
232 PF04760 IF2_N: Translation in 27.6 58 0.0012 20.9 2.2 20 131-150 5-24 (54)
233 TIGR00122 birA_repr_reg BirA b 27.4 1.3E+02 0.0027 20.0 3.9 31 121-151 5-35 (69)
234 PRK12518 RNA polymerase sigma 27.3 53 0.0012 25.0 2.3 25 126-150 133-157 (175)
235 PRK12543 RNA polymerase sigma 27.2 1.4E+02 0.003 23.1 4.7 34 115-148 119-152 (179)
236 TIGR02337 HpaR homoprotocatech 27.1 1E+02 0.0022 22.5 3.7 31 121-151 33-64 (118)
237 TIGR00721 tfx DNA-binding prot 26.8 1.2E+02 0.0025 24.1 4.2 33 119-152 12-44 (137)
238 smart00345 HTH_GNTR helix_turn 26.8 78 0.0017 19.5 2.7 21 131-151 22-42 (60)
239 PRK10130 transcriptional regul 26.7 1.2E+02 0.0027 27.0 4.8 53 115-167 239-296 (350)
240 PRK09415 RNA polymerase factor 26.6 1.2E+02 0.0027 23.4 4.3 34 117-150 131-164 (179)
241 PRK13413 mpi multiple promoter 26.5 1E+02 0.0022 24.7 3.9 33 119-152 163-195 (200)
242 cd01104 HTH_MlrA-CarA Helix-Tu 26.4 82 0.0018 20.5 2.8 23 130-152 1-23 (68)
243 PF09012 FeoC: FeoC like trans 26.3 71 0.0015 21.5 2.6 33 118-150 2-35 (69)
244 TIGR02980 SigBFG RNA polymeras 26.2 1.4E+02 0.0031 24.0 4.8 36 116-151 181-216 (227)
245 PRK12535 RNA polymerase sigma 26.1 2.3E+02 0.0049 22.6 5.9 37 114-150 134-170 (196)
246 PF07292 NID: Nmi/IFP 35 domai 26.0 67 0.0014 23.7 2.5 23 18-40 63-85 (88)
247 PRK12528 RNA polymerase sigma 26.0 1.6E+02 0.0034 22.2 4.7 36 116-151 116-151 (161)
248 PRK12511 RNA polymerase sigma 25.9 1.4E+02 0.0031 23.5 4.6 34 117-150 115-148 (182)
249 PRK12529 RNA polymerase sigma 25.8 1.5E+02 0.0033 22.9 4.7 36 116-151 130-165 (178)
250 PF13463 HTH_27: Winged helix 25.7 72 0.0016 20.6 2.4 25 128-152 17-41 (68)
251 PRK11050 manganese transport r 25.7 1.4E+02 0.003 23.3 4.5 33 119-151 40-73 (152)
252 PRK10820 DNA-binding transcrip 25.5 1.1E+02 0.0024 28.6 4.4 25 129-153 486-510 (520)
253 TIGR02950 SigM_subfam RNA poly 25.4 67 0.0015 23.8 2.5 31 121-151 113-143 (154)
254 PRK15186 AraC family transcrip 25.3 1E+02 0.0022 26.9 3.9 36 118-153 234-270 (291)
255 PRK09643 RNA polymerase sigma 25.2 1.5E+02 0.0033 23.3 4.6 34 117-150 138-171 (192)
256 PF13411 MerR_1: MerR HTH fami 25.1 43 0.00094 21.9 1.3 22 131-152 2-23 (69)
257 PRK05602 RNA polymerase sigma 25.1 1.4E+02 0.0031 23.0 4.4 34 118-151 133-166 (186)
258 PRK09413 IS2 repressor TnpA; R 25.0 1.3E+02 0.0028 22.5 4.0 32 121-152 21-52 (121)
259 PRK05572 sporulation sigma fac 24.9 1.4E+02 0.0031 24.7 4.7 37 115-151 204-240 (252)
260 PF10078 DUF2316: Uncharacteri 24.9 1.7E+02 0.0036 21.8 4.4 35 120-154 14-48 (89)
261 TIGR02948 SigW_bacill RNA poly 24.7 1.5E+02 0.0032 22.6 4.4 30 121-150 144-173 (187)
262 PRK12539 RNA polymerase sigma 24.2 2.1E+02 0.0045 22.2 5.2 36 115-150 133-168 (184)
263 PRK12532 RNA polymerase sigma 23.9 1.6E+02 0.0035 23.0 4.6 37 115-151 138-174 (195)
264 TIGR02943 Sig70_famx1 RNA poly 23.9 1.7E+02 0.0038 23.0 4.8 32 118-149 136-167 (188)
265 PRK12536 RNA polymerase sigma 23.8 1.8E+02 0.0039 22.5 4.8 33 119-151 135-167 (181)
266 PF01978 TrmB: Sugar-specific 23.8 1.2E+02 0.0026 20.0 3.3 28 124-151 17-44 (68)
267 PF00196 GerE: Bacterial regul 23.7 1E+02 0.0022 19.8 2.9 26 125-150 14-39 (58)
268 PRK09649 RNA polymerase sigma 23.7 1.6E+02 0.0035 23.0 4.5 36 115-150 132-167 (185)
269 TIGR03830 CxxCG_CxxCG_HTH puta 23.6 1.6E+02 0.0036 21.4 4.3 33 121-153 70-102 (127)
270 PF07750 GcrA: GcrA cell cycle 23.6 94 0.002 25.1 3.2 32 120-151 9-41 (162)
271 PRK12546 RNA polymerase sigma 23.5 1.5E+02 0.0033 23.5 4.4 37 114-150 114-150 (188)
272 cd00131 PAX Paired Box domain 23.5 1.9E+02 0.0041 22.1 4.7 35 117-152 22-56 (128)
273 PF01710 HTH_Tnp_IS630: Transp 23.5 1.4E+02 0.0029 22.4 3.9 34 119-153 9-42 (119)
274 TIGR02479 FliA_WhiG RNA polyme 23.3 1.6E+02 0.0035 23.7 4.6 35 117-151 179-213 (224)
275 PRK10676 DNA-binding transcrip 23.3 78 0.0017 27.1 2.8 35 117-152 20-54 (263)
276 PRK12544 RNA polymerase sigma 23.1 2.7E+02 0.0059 22.4 5.9 31 120-150 155-185 (206)
277 PRK12427 flagellar biosynthesi 23.0 1.6E+02 0.0035 24.3 4.6 35 118-152 188-222 (231)
278 smart00542 FYRC "FY-rich" doma 23.0 74 0.0016 22.8 2.3 27 136-162 50-76 (86)
279 PRK12520 RNA polymerase sigma 22.9 1.9E+02 0.004 22.6 4.7 33 118-150 136-168 (191)
280 cd04763 HTH_MlrA-like Helix-Tu 22.8 76 0.0016 21.0 2.1 21 131-151 2-22 (68)
281 COG1191 FliA DNA-directed RNA 22.5 1.3E+02 0.0029 26.0 4.1 32 121-152 204-235 (247)
282 PRK12545 RNA polymerase sigma 22.4 2.3E+02 0.0049 22.5 5.2 33 118-150 144-176 (201)
283 PRK13500 transcriptional activ 22.4 1.3E+02 0.0027 25.8 3.9 44 117-160 259-307 (312)
284 PF03683 UPF0175: Uncharacteri 22.3 2E+02 0.0044 20.0 4.3 37 118-154 23-59 (76)
285 PRK03902 manganese transport t 22.3 1.6E+02 0.0036 22.3 4.2 35 117-151 9-44 (142)
286 TIGR00180 parB_part ParB-like 22.3 1.5E+02 0.0033 23.7 4.2 34 127-160 118-154 (187)
287 TIGR02531 yecD_yerC TrpR-relat 22.1 2.1E+02 0.0046 20.9 4.5 25 127-151 48-72 (88)
288 PRK15340 transcriptional regul 22.0 1.4E+02 0.0031 25.3 4.1 38 129-166 125-164 (216)
289 PRK03975 tfx putative transcri 22.0 2.9E+02 0.0063 22.0 5.6 38 114-152 7-44 (141)
290 PRK12524 RNA polymerase sigma 21.9 1.9E+02 0.0042 22.7 4.7 38 115-152 138-175 (196)
291 PRK09644 RNA polymerase sigma 21.9 1.9E+02 0.0041 21.9 4.5 35 116-150 111-145 (165)
292 PRK08583 RNA polymerase sigma 21.7 1.8E+02 0.004 24.0 4.7 35 117-151 209-243 (257)
293 PRK12513 RNA polymerase sigma 21.7 86 0.0019 24.5 2.6 32 119-150 145-176 (194)
294 TIGR02957 SigX4 RNA polymerase 21.7 1.8E+02 0.0039 24.6 4.7 36 116-151 111-146 (281)
295 PF13730 HTH_36: Helix-turn-he 21.7 1.7E+02 0.0037 18.3 3.6 21 131-151 27-47 (55)
296 PF01710 HTH_Tnp_IS630: Transp 21.5 1.2E+02 0.0026 22.6 3.3 34 119-152 60-94 (119)
297 PRK03573 transcriptional regul 21.4 2.3E+02 0.0049 21.2 4.8 31 121-151 36-68 (144)
298 PRK15044 transcriptional regul 21.3 1.2E+02 0.0026 27.1 3.6 41 127-167 206-247 (295)
299 PF06413 Neugrin: Neugrin; In 21.3 85 0.0019 26.8 2.6 27 127-153 27-53 (225)
300 TIGR01884 cas_HTH CRISPR locus 21.3 1.5E+02 0.0033 23.9 4.1 34 118-151 145-179 (203)
301 PRK11557 putative DNA-binding 20.7 1.4E+02 0.0031 24.8 3.9 40 113-152 9-53 (278)
302 PRK07670 RNA polymerase sigma 20.6 1.9E+02 0.0041 24.0 4.5 37 115-151 203-239 (251)
303 PF05269 Phage_CII: Bacterioph 20.5 1.3E+02 0.0027 22.5 3.1 31 120-152 16-46 (91)
304 PRK09834 DNA-binding transcrip 20.4 1.6E+02 0.0035 24.7 4.1 32 121-152 16-49 (263)
305 PRK15418 transcriptional regul 20.4 84 0.0018 27.7 2.5 35 118-152 18-52 (318)
306 PRK11512 DNA-binding transcrip 20.4 2.6E+02 0.0056 21.1 4.9 32 121-152 45-77 (144)
307 PRK09646 RNA polymerase sigma 20.2 2.2E+02 0.0048 22.3 4.7 34 117-150 146-179 (194)
308 PF13348 Y_phosphatase3C: Tyro 20.1 2.1E+02 0.0045 18.9 3.9 37 113-149 26-63 (68)
309 PF02082 Rrf2: Transcriptional 20.1 1.2E+02 0.0027 20.9 2.9 35 117-151 10-47 (83)
No 1
>COG0216 PrfA Protein chain release factor A [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.1e-36 Score=265.42 Aligned_cols=97 Identities=32% Similarity=0.473 Sum_probs=88.5
Q ss_pred CcccChhhhhcceeEEEEeecCCCCCcCCccCceEEEEeeCCceEEEEcccCCHHHHHHHHHHHH-hCCChhhhhh----
Q 043121 16 YLELTDDELLRECEMDTYKLSGPGSQHRNKRESAVRLKHVPTGVIAHAAEDRSQHKNHASSVNLD-AYSPPPQLLQ---- 90 (169)
Q Consensus 16 ~~~i~~~~l~~dl~i~~~RssGpGGQ~vNk~~saVrl~H~ptGi~v~~~~~RSq~~Nr~~Al~~L-~~L~~~el~~---- 90 (169)
-+.|+++|| +|++|||||+||||||+|+|||||||+||||+|.||++|||++||++||+.| ++|++.+.++
T Consensus 217 ei~I~~~Dl----rIDt~RsSGaGGQhVNtTdSAVRiTHlPTGIvV~cQderSQ~kNk~kAmkvL~ARl~~~~~~~~~~~ 292 (363)
T COG0216 217 EIEINPKDL----RIDTFRSSGAGGQHVNTTDSAVRITHLPTGIVVECQDERSQHKNKAKAMKVLRARLYDAERQKAQAE 292 (363)
T ss_pred ccccChHHc----eeeeeecCCCCCCCcCccchhheeeecCCceEEEecchhhhhhhHHHHHHHHHHHHHHHHHHHHHHH
Confidence 477887755 9999999999999999999999999999999999999999999999999999 7999877654
Q ss_pred -cCCCCCcccCCCCCCCCCCCCCCchh
Q 043121 91 -ILPPKSTITSSEVGPQIGPNNPKFSL 116 (169)
Q Consensus 91 -~~~~ksqir~~~rg~qIRtYn~~f~~ 116 (169)
...+++|+++||||++||||||.-+.
T Consensus 293 ~~~~RksqVGSGDRSErIRTYNfPQnR 319 (363)
T COG0216 293 EASERKSQVGSGDRSERIRTYNFPQNR 319 (363)
T ss_pred HHHHHHHhcCCCchhhhhhccCCCCCc
Confidence 37899999999999999999996654
No 2
>KOG2726 consensus Mitochondrial polypeptide chain release factor [Translation, ribosomal structure and biogenesis]
Probab=99.97 E-value=4.9e-32 Score=241.71 Aligned_cols=128 Identities=30% Similarity=0.345 Sum_probs=105.7
Q ss_pred hcceeEEEEeecCCCCCcCCccCceEEEEeeCCceEEEEcccCCHHHHHHHHHHHH-hCCChhhhhh-----cCCCCCcc
Q 043121 25 LRECEMDTYKLSGPGSQHRNKRESAVRLKHVPTGVIAHAAEDRSQHKNHASSVNLD-AYSPPPQLLQ-----ILPPKSTI 98 (169)
Q Consensus 25 ~~dl~i~~~RssGpGGQ~vNk~~saVrl~H~ptGi~v~~~~~RSq~~Nr~~Al~~L-~~L~~~el~~-----~~~~ksqi 98 (169)
++||+|+|+|+|||||||||||+|||||+|+||||+|+|+++|||++||+.||.+| ++|++.+.++ ...++.++
T Consensus 247 ~~dl~i~~~R~~G~GGQhvNktdsaVrl~HiPTGIvv~cq~eRSq~~Nr~~A~~~L~akL~~~~~~~~~~~~~~~r~~qv 326 (386)
T KOG2726|consen 247 EKDLRIETFRASGPGGQHVNKTDSAVRLTHIPTGIVVECQEERSQHKNRALALKRLRAKLAVIYREEKSEEEKKKRKAQV 326 (386)
T ss_pred chheeEEecccCCCCcccccccccceEEEeecCceEEEeecHHhHHhhHHHHHHHHHHHHHHHHHhhhhHHhhhhhHHhh
Confidence 45779999999999999999999999999999999999999999999999999999 7888877654 36777889
Q ss_pred cCCCCCCCCCCCCCCchhHHHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHHhcChhHHHHHH
Q 043121 99 TSSEVGPQIGPNNPKFSLGMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLILSDDSHQIAVN 161 (169)
Q Consensus 99 r~~~rg~qIRtYn~~f~~~l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~~~~~~~~~~n 161 (169)
.+.+|+++||||||.-.. +.|+... +...+...+|. +.|-.||.++.......+
T Consensus 327 ~s~~rsekiRTy~~~q~r----v~D~r~~--~~~~d~~~~l~---G~Ld~li~~~~~~~~~~~ 380 (386)
T KOG2726|consen 327 GSLKRSEKIRTYNFKQDR----VTDHRIG--LESHDLESFLD---GNLDELIEALLSLRREED 380 (386)
T ss_pred cccCchhceeecccCccc----hhhhhhc--ccccchHHHHh---ccHHHHHHHHHHHhhHHH
Confidence 989999999999998877 7888877 44455555554 267777766655554433
No 3
>PF00472 RF-1: RF-1 domain; InterPro: IPR000352 Peptide chain release factors (RFs) are required for the termination of protein biosynthesis []. At present two classes of RFs can be distinguished. Class I RFs bind to ribosomes that have encountered a stop codon at their decoding site and induce release of the nascent polypeptide. Class II RFs are GTP-binding proteins that interact with class I RFs and enhance class I RF activity. In prokaryotes there are two class I RFs that act in a codon specific manner []: RF-1 (gene prfA) mediates UAA and UAG-dependent termination while RF-2 (gene prfB) mediates UAA and UGA-dependent termination. RF-1 and RF-2 are structurally and evolutionary related proteins which have been shown to be part of a larger family [].; GO: 0003747 translation release factor activity, 0006415 translational termination; PDB: 2JY9_A 1ZBT_A 1GQE_A 3F1G_X 3F1E_X 1RQ0_C 4DH9_Y 2JVA_A 1J26_A 3D5A_X ....
Probab=99.97 E-value=2.8e-31 Score=201.66 Aligned_cols=96 Identities=28% Similarity=0.373 Sum_probs=80.4
Q ss_pred CCcccChhhhhcceeEEEEeecCCCCCcCCccCceEEEEeeCCceEEEEcccCCHHHHHHHHHHHH-hCCChhhhhh---
Q 043121 15 NYLELTDDELLRECEMDTYKLSGPGSQHRNKRESAVRLKHVPTGVIAHAAEDRSQHKNHASSVNLD-AYSPPPQLLQ--- 90 (169)
Q Consensus 15 ~~~~i~~~~l~~dl~i~~~RssGpGGQ~vNk~~saVrl~H~ptGi~v~~~~~RSq~~Nr~~Al~~L-~~L~~~el~~--- 90 (169)
..+.|+++ ||+|+|+|||||||||||||+|+|+|+|.||||+|+|+++|||+.|++.|+++| ++|.+...++
T Consensus 5 ~~~~i~~~----dl~~~~~RssGpGGQ~VNk~~s~V~l~h~ptgi~v~~~~~Rsq~~Nr~~A~~~L~~~l~~~~~~~~~~ 80 (113)
T PF00472_consen 5 KEIDIPEK----DLEISFSRSSGPGGQNVNKTNSKVRLRHIPTGIVVKCQESRSQHQNREDALEKLREKLDEAYREKRRE 80 (113)
T ss_dssp SSSCC-GG----GEEEEEEESSSSSSCHHHSSSEEEEEEETTTTEEEEEESSSSHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred cccccCHH----HeEEEEEecCCCCCCcccccCCEEEEEEecccEEEEEcccCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34677776 559999999999999999999999999999999999999999999999999999 4555443221
Q ss_pred --cCCCCCcccCCCCCCCCCCCCCCc
Q 043121 91 --ILPPKSTITSSEVGPQIGPNNPKF 114 (169)
Q Consensus 91 --~~~~ksqir~~~rg~qIRtYn~~f 114 (169)
...++++.+..+++++||+|+|..
T Consensus 81 ~~~~~~~~~~~~~~~~~~iR~y~~~~ 106 (113)
T PF00472_consen 81 KTREIRKSQVKRLERKKKIRTYNFPR 106 (113)
T ss_dssp HTTTTTTTSCCCSSTTSEEEEEETTT
T ss_pred HHHHHHHHHHhHHhhhcceecccCCh
Confidence 256677777789999999999944
No 4
>PRK08787 peptide chain release factor 2; Provisional
Probab=99.97 E-value=3.1e-31 Score=232.03 Aligned_cols=103 Identities=29% Similarity=0.375 Sum_probs=81.8
Q ss_pred cccChhhhhcceeEEEEeecCCCCCcCCccCceEEEEeeCCceEEEEcccCCHHHHHHHHHHHH-hCCChhhhhhcCCCC
Q 043121 17 LELTDDELLRECEMDTYKLSGPGSQHRNKRESAVRLKHVPTGVIAHAAEDRSQHKNHASSVNLD-AYSPPPQLLQILPPK 95 (169)
Q Consensus 17 ~~i~~~~l~~dl~i~~~RssGpGGQ~vNk~~saVrl~H~ptGi~v~~~~~RSq~~Nr~~Al~~L-~~L~~~el~~~~~~k 95 (169)
+.|++. ||+|+|+|||||||||||||+|||||+|+||||+|+|+++|||++||+.||++| ++|++.+++++.+.+
T Consensus 171 i~i~~~----dl~~~~~RssG~GGQ~VNkt~saVri~H~Ptgi~v~~q~eRSQ~~Nk~~A~~~L~~~L~~~~~e~~~~~~ 246 (313)
T PRK08787 171 IDINPA----DLRTDVYRSSGAGGQHVNKTESAVRITHIPTNTVVACQTGRSQHQNRDNAMKMLAAKLYELEVQKRNAEK 246 (313)
T ss_pred cccChh----HeEEEEEECCCCCCCCcCCEeeEEEEEECCCcEEEEECCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455554 669999999999999999999999999999999999999999999999999999 788888776542221
Q ss_pred Cc----ccCCCCCCCCCCCCCCchhHHHHHHHHHHH
Q 043121 96 ST----ITSSEVGPQIGPNNPKFSLGMQALLDLIFA 127 (169)
Q Consensus 96 sq----ir~~~rg~qIRtYn~~f~~~l~~~lD~l~~ 127 (169)
.. .....||+|||||||.-.. +.|+...
T Consensus 247 ~~~~~~k~~i~~g~qIRtY~f~~~~----V~DhRtg 278 (313)
T PRK08787 247 DALEATKSDIGWGSQIRNYVLDQSR----IKDLRTG 278 (313)
T ss_pred HHHhhhhhhCcccccccceeCCCCc----ceeeccC
Confidence 11 1123599999999886322 5555543
No 5
>TIGR03072 release_prfH putative peptide chain release factor H. Members of this protein family are bacterial proteins homologous to peptide chain release factors 1 (RF-1, product of the prfA gene), and 2 (RF-2, product of the prfB gene). The member from Escherichia coli K-12, designated prfH, appears to be a pseudogene. This class I release factor is always found as the downstream gene of a two-gene operon.
Probab=99.97 E-value=4e-31 Score=219.22 Aligned_cols=88 Identities=31% Similarity=0.360 Sum_probs=78.0
Q ss_pred cceeEEEEeecCCCCCcCCccCceEEEEeeCCceEEEEcccCCHHHHHHHHHHHH-hCCChhhhhhc----CCCCCcccC
Q 043121 26 RECEMDTYKLSGPGSQHRNKRESAVRLKHVPTGVIAHAAEDRSQHKNHASSVNLD-AYSPPPQLLQI----LPPKSTITS 100 (169)
Q Consensus 26 ~dl~i~~~RssGpGGQ~vNk~~saVrl~H~ptGi~v~~~~~RSq~~Nr~~Al~~L-~~L~~~el~~~----~~~ksqir~ 100 (169)
+||+|+|+|||||||||||||+|+|+|+|+||||+|+|+++|||++||+.|+++| ++|++.+.+++ ..++++...
T Consensus 106 ~dl~~~~~RssGpGGQ~vNkt~saVrl~h~ptgi~v~~~~~RSQ~~Nk~~A~~~L~~~l~~~~~~~~~~~~~~~r~~~~~ 185 (200)
T TIGR03072 106 DEIRFETLRSSGPGGQHVNKTESAVRATHLASGISVKVQSERSQHANKRLATLLLAVRLADLQQEQAAALRAERRTAHHQ 185 (200)
T ss_pred hheEEEEEECCCCCcccccccceeEEEEECCCcEEEEECCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccc
Confidence 4679999999999999999999999999999999999999999999999999999 67777665543 455666667
Q ss_pred CCCCCCCCCCCCC
Q 043121 101 SEVGPQIGPNNPK 113 (169)
Q Consensus 101 ~~rg~qIRtYn~~ 113 (169)
.+||++||||||.
T Consensus 186 ~~Rg~~iRty~~~ 198 (200)
T TIGR03072 186 IERGNPVRVFKGE 198 (200)
T ss_pred ccccCceEeeeCC
Confidence 7999999999975
No 6
>PRK05589 peptide chain release factor 2; Provisional
Probab=99.97 E-value=3.7e-31 Score=232.62 Aligned_cols=96 Identities=29% Similarity=0.475 Sum_probs=80.9
Q ss_pred cccChhhhhcceeEEEEeecCCCCCcCCccCceEEEEeeCCceEEEEcccCCHHHHHHHHHHHH-hCCChhhhhhc----
Q 043121 17 LELTDDELLRECEMDTYKLSGPGSQHRNKRESAVRLKHVPTGVIAHAAEDRSQHKNHASSVNLD-AYSPPPQLLQI---- 91 (169)
Q Consensus 17 ~~i~~~~l~~dl~i~~~RssGpGGQ~vNk~~saVrl~H~ptGi~v~~~~~RSq~~Nr~~Al~~L-~~L~~~el~~~---- 91 (169)
+.|+++ |++|+|+|||||||||||||+|||||+|+||||+|+|+++|||++||+.|+++| ++|++.+.++.
T Consensus 191 ~~i~~~----dl~~~~~rssG~GGQ~VNkt~saVrl~H~ptgi~v~~q~eRSQ~~Nk~~A~~~L~~kL~~~~~~~~~~~~ 266 (325)
T PRK05589 191 IEIRSE----DLKIDTYRAGGAGGQHVNKTESAVRITHIPTGIVVQCQNERSQHSNKETAMKMLKSKLVELKERAHKEKI 266 (325)
T ss_pred ccCCch----heEEEEeeCCCCCCCcccceeeEEEEEECCCCEEEEECCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 556655 569999999999999999999999999999999999999999999999999999 68888766442
Q ss_pred CCCCCcccCCCCCCCCCCCCC-Cchh
Q 043121 92 LPPKSTITSSEVGPQIGPNNP-KFSL 116 (169)
Q Consensus 92 ~~~ksqir~~~rg~qIRtYn~-~f~~ 116 (169)
...+++.....||++|||||| .+..
T Consensus 267 ~~~r~~~~~~~~g~~IRtY~~~p~~r 292 (325)
T PRK05589 267 EDLTGELKDMGWGSQIRSYVFHPYNL 292 (325)
T ss_pred HHHhcccccccccCCceeeECCCCce
Confidence 223344445589999999999 6654
No 7
>PRK06746 peptide chain release factor 2; Provisional
Probab=99.96 E-value=7e-31 Score=230.91 Aligned_cols=96 Identities=30% Similarity=0.392 Sum_probs=81.6
Q ss_pred CcccChhhhhcceeEEEEeecCCCCCcCCccCceEEEEeeCCceEEEEcccCCHHHHHHHHHHHH-hCCChhhhhhc---
Q 043121 16 YLELTDDELLRECEMDTYKLSGPGSQHRNKRESAVRLKHVPTGVIAHAAEDRSQHKNHASSVNLD-AYSPPPQLLQI--- 91 (169)
Q Consensus 16 ~~~i~~~~l~~dl~i~~~RssGpGGQ~vNk~~saVrl~H~ptGi~v~~~~~RSq~~Nr~~Al~~L-~~L~~~el~~~--- 91 (169)
-+.|++. ||+|+|+|||||||||||||+|||||+|+||||+|+|+++|||++||+.|+++| ++|++.+++++
T Consensus 191 ~i~i~~~----dl~~~~~rssG~GGQ~vNkt~saVrl~h~ptgi~v~~q~~RSQ~~Nk~~A~~~L~akL~~~~~~~~~~~ 266 (326)
T PRK06746 191 EIEVRTE----DLKIDTYRASGAGGQHVNTTDSAVRITHTPTNTVVTCQSERSQIKNREHAMKMLKAKLYQKKLEEQQAE 266 (326)
T ss_pred ccccChH----HeEEEEEeCCCCCCCCccceeeEEEEEEeCCeEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3555555 569999999999999999999999999999999999999999999999999999 78988887653
Q ss_pred --CCCCCcccCCCCCCCCCCCCC-Cchh
Q 043121 92 --LPPKSTITSSEVGPQIGPNNP-KFSL 116 (169)
Q Consensus 92 --~~~ksqir~~~rg~qIRtYn~-~f~~ 116 (169)
..+++++.. .||++|||||| .+..
T Consensus 267 ~~~~r~~~~~~-~rg~~IRtYnf~p~~r 293 (326)
T PRK06746 267 LDEIRGEQKEI-GWGSQIRSYVFHPYSL 293 (326)
T ss_pred HHHHHhhhccC-ccCCCeEEEECCCCce
Confidence 344455533 79999999999 5543
No 8
>PRK08179 prfH peptide chain release factor-like protein; Reviewed
Probab=99.96 E-value=1.8e-30 Score=215.37 Aligned_cols=91 Identities=31% Similarity=0.297 Sum_probs=78.8
Q ss_pred cccChhhhhcceeEEEEeecCCCCCcCCccCceEEEEeeCCceEEEEcccCCHHHHHHHHHHHH-hCCChhhhhhc----
Q 043121 17 LELTDDELLRECEMDTYKLSGPGSQHRNKRESAVRLKHVPTGVIAHAAEDRSQHKNHASSVNLD-AYSPPPQLLQI---- 91 (169)
Q Consensus 17 ~~i~~~~l~~dl~i~~~RssGpGGQ~vNk~~saVrl~H~ptGi~v~~~~~RSq~~Nr~~Al~~L-~~L~~~el~~~---- 91 (169)
+.|+++ ||+|+|+|||||||||||||+|+|+|+|+||||+|+|+++|||++||+.|+++| ++|++.+++++
T Consensus 102 ~~i~~~----dl~~~~~RssGpGGQ~VNkt~saVrl~h~ptgi~v~~~~~RSQ~~Nk~~A~~~L~~~L~~~~~~~~~~~~ 177 (200)
T PRK08179 102 EEEQSD----EIRFETLRSSGPGGQHVNKTDSAVRATHLASGISVKVQSERSQHANKRLARLLIAWKLEQQQQEQSAALK 177 (200)
T ss_pred CccCHH----HeEEEEEEccCCcccccccccceEEEEEcCCcEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455555 569999999999999999999999999999999999999999999999999999 67877766543
Q ss_pred CCCCCcccCCCCCCCCCCCC
Q 043121 92 LPPKSTITSSEVGPQIGPNN 111 (169)
Q Consensus 92 ~~~ksqir~~~rg~qIRtYn 111 (169)
..++++....+||++||||-
T Consensus 178 ~~~~~~~~~~~Rg~~IRt~~ 197 (200)
T PRK08179 178 SQRRMFHHQIERGNPRRVFT 197 (200)
T ss_pred HHHHhccccccccCceEeee
Confidence 45555666778999999984
No 9
>TIGR00019 prfA peptide chain release factor 1. This model describes peptide chain release factor 1 (PrfA, RF-1), and excludes the related peptide chain release factor 2 (PrfB, RF-2). RF-1 helps recognize and terminate translation at UAA and UAG stop codons. The mitochondrial release factors are prfA-like, although not included above the trusted cutoff for this model. RF-1 does not have a translational frameshift.
Probab=99.96 E-value=1.3e-30 Score=231.77 Aligned_cols=97 Identities=30% Similarity=0.427 Sum_probs=84.0
Q ss_pred cceeEEEEeecCCCCCcCCccCceEEEEeeCCceEEEEcccCCHHHHHHHHHHHH-hCCChhhhhh-----cCCCCCccc
Q 043121 26 RECEMDTYKLSGPGSQHRNKRESAVRLKHVPTGVIAHAAEDRSQHKNHASSVNLD-AYSPPPQLLQ-----ILPPKSTIT 99 (169)
Q Consensus 26 ~dl~i~~~RssGpGGQ~vNk~~saVrl~H~ptGi~v~~~~~RSq~~Nr~~Al~~L-~~L~~~el~~-----~~~~ksqir 99 (169)
.||+|+|+|||||||||||||+|||||+|+||||+|.|+++|||++||+.||++| ++|++.+.++ ...+++++.
T Consensus 221 ~dl~~~~~RssG~GGQ~VNkt~SaVrl~h~ptgi~V~~~~eRSQ~~Nk~~A~~~L~~~L~~~~~~~~~~~~~~~r~~~~~ 300 (360)
T TIGR00019 221 ADLRIDTFRSSGAGGQHVNTTDSAVRITHLPTGIVVECQDERSQHKNKDKAMKVLRARLYEAEQEKQQAAQASTRKSQVG 300 (360)
T ss_pred ccEEEEEEECCCCCCCCcCceeeeEEEEECCCcEEEEECCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcc
Confidence 4679999999999999999999999999999999999999999999999999999 6887776642 256688899
Q ss_pred CCCCCCCCCCCCCCchhHHHHHHHHHH
Q 043121 100 SSEVGPQIGPNNPKFSLGMQALLDLIF 126 (169)
Q Consensus 100 ~~~rg~qIRtYn~~f~~~l~~~lD~l~ 126 (169)
.++||++||||||.... +.|+..
T Consensus 301 ~~~Rs~~IRtY~~~~~r----V~DhRt 323 (360)
T TIGR00019 301 SGDRSERIRTYNFPQNR----VTDHRI 323 (360)
T ss_pred eecccCCeEEEECCCCe----eeeecc
Confidence 99999999999984432 555544
No 10
>PRK07342 peptide chain release factor 2; Provisional
Probab=99.96 E-value=1.7e-30 Score=229.36 Aligned_cols=90 Identities=33% Similarity=0.484 Sum_probs=75.4
Q ss_pred cceeEEEEeecCCCCCcCCccCceEEEEeeCCceEEEEcccCCHHHHHHHHHHHH-hCCChhhhhhcCCCCC----cccC
Q 043121 26 RECEMDTYKLSGPGSQHRNKRESAVRLKHVPTGVIAHAAEDRSQHKNHASSVNLD-AYSPPPQLLQILPPKS----TITS 100 (169)
Q Consensus 26 ~dl~i~~~RssGpGGQ~vNk~~saVrl~H~ptGi~v~~~~~RSq~~Nr~~Al~~L-~~L~~~el~~~~~~ks----qir~ 100 (169)
+||+|+|+|||||||||||||+|||||+|+||||+|+|+++|||++||+.||++| ++|++.+++++..... +...
T Consensus 199 ~dl~~~~~RssG~GGQ~VNkt~saVrl~H~ptgi~v~~~~eRSQ~~Nk~~A~~~L~~~L~~~~~~~~~~~~~~~~~~~~~ 278 (339)
T PRK07342 199 SDVRIDTYRSSGAGGQHVNTTDSAVRITHIPTGIVVQCQQERSQHKNRAKAWSMLRARLYEEELKKREEATNAAAASKTD 278 (339)
T ss_pred ccEEEEEEECCCCCCCCccceeeeEEEEEcCCcEEEEECCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Confidence 4679999999999999999999999999999999999999999999999999999 7888877765422111 1112
Q ss_pred CCCCCCCCCCCC-Cch
Q 043121 101 SEVGPQIGPNNP-KFS 115 (169)
Q Consensus 101 ~~rg~qIRtYn~-~f~ 115 (169)
..||++|||||| .+.
T Consensus 279 i~~g~~IRtY~~~p~~ 294 (339)
T PRK07342 279 IGWGHQIRSYVLQPYQ 294 (339)
T ss_pred ccccCCcCCccCCCCc
Confidence 259999999999 544
No 11
>PRK00591 prfA peptide chain release factor 1; Validated
Probab=99.96 E-value=3.6e-30 Score=228.81 Aligned_cols=98 Identities=31% Similarity=0.438 Sum_probs=84.6
Q ss_pred hcceeEEEEeecCCCCCcCCccCceEEEEeeCCceEEEEcccCCHHHHHHHHHHHH-hCCChhhhhhc-----CCCCCcc
Q 043121 25 LRECEMDTYKLSGPGSQHRNKRESAVRLKHVPTGVIAHAAEDRSQHKNHASSVNLD-AYSPPPQLLQI-----LPPKSTI 98 (169)
Q Consensus 25 ~~dl~i~~~RssGpGGQ~vNk~~saVrl~H~ptGi~v~~~~~RSq~~Nr~~Al~~L-~~L~~~el~~~-----~~~ksqi 98 (169)
++||+|+|+|||||||||||||+|+|||+|+||||+|+|+++|||++||+.|+++| ++|++.+++++ ..+++++
T Consensus 220 ~~dl~~~~~RssG~GGQ~VNkt~saVrl~H~ptGi~v~~~~eRSQ~~Nk~~Al~~L~~~L~~~~~~~~~~~~~~~r~~~~ 299 (359)
T PRK00591 220 PKDLRIDTFRSSGAGGQHVNTTDSAVRITHLPTGIVVECQDERSQHKNKAKAMKVLRARLYDAERQKAQAEEAATRKSQV 299 (359)
T ss_pred cccEEEEEEECCCCCCCCccceeeeEEEEECCCcEEEEECCcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 34779999999999999999999999999999999999999999999999999999 68887776543 3567889
Q ss_pred cCCCCCCCCCCCCCCchhHHHHHHHHHH
Q 043121 99 TSSEVGPQIGPNNPKFSLGMQALLDLIF 126 (169)
Q Consensus 99 r~~~rg~qIRtYn~~f~~~l~~~lD~l~ 126 (169)
..++||++||||||.... +.|+..
T Consensus 300 ~~~~Rse~IRtY~f~~~~----V~DhRt 323 (359)
T PRK00591 300 GSGDRSERIRTYNFPQGR----VTDHRI 323 (359)
T ss_pred ccccccCCeeeEECCCCe----eeeecc
Confidence 999999999999984322 555544
No 12
>TIGR00020 prfB peptide chain release factor 2. In many but not all taxa, there is a conserved real translational frameshift at a TGA codon. RF-2 helps terminate translation at TGA codons and can therefore regulate its own production by readthrough when RF-2 is insufficient. There is a Pfam model called "RF-1" for the superfamily of RF-1, RF-2, mitochondrial, RF-H, etc.
Probab=99.96 E-value=1.9e-30 Score=230.98 Aligned_cols=92 Identities=34% Similarity=0.493 Sum_probs=77.8
Q ss_pred hcceeEEEEeecCCCCCcCCccCceEEEEeeCCceEEEEcccCCHHHHHHHHHHHH-hCCChhhhhhcCCC----CCccc
Q 043121 25 LRECEMDTYKLSGPGSQHRNKRESAVRLKHVPTGVIAHAAEDRSQHKNHASSVNLD-AYSPPPQLLQILPP----KSTIT 99 (169)
Q Consensus 25 ~~dl~i~~~RssGpGGQ~vNk~~saVrl~H~ptGi~v~~~~~RSq~~Nr~~Al~~L-~~L~~~el~~~~~~----ksqir 99 (169)
+.|++|+|+|||||||||||||+|+|||+|+||||+|+|+++|||++||+.||++| ++|++.+++++... +++..
T Consensus 234 ~~d~~~~~~rssG~GGQ~VNkt~saVri~H~ptgi~v~~q~~RSQ~~Nk~~A~~~L~~kL~~~~~~~~~~~~~~~r~~~~ 313 (364)
T TIGR00020 234 PEDLRIDTYRASGAGGQHVNKTDSAVRITHIPTGIVVQCQNDRSQHKNKDSAMKVLKAKLYELEMEKEQAEKDAKEGEKS 313 (364)
T ss_pred cccEEEEEeeCCCCCCccccccceEEEEEECCCcEEEEECCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence 34779999999999999999999999999999999999999999999999999999 78988887664222 22222
Q ss_pred CCCCCCCCCCCCC-Cchh
Q 043121 100 SSEVGPQIGPNNP-KFSL 116 (169)
Q Consensus 100 ~~~rg~qIRtYn~-~f~~ 116 (169)
..+||++|||||| .|..
T Consensus 314 ~~~rg~~IRtY~~~~~~r 331 (364)
T TIGR00020 314 EIGWGSQIRSYVLHPYSM 331 (364)
T ss_pred ccCccCCeEEEECCCCCc
Confidence 3379999999999 5554
No 13
>PRK00578 prfB peptide chain release factor 2; Validated
Probab=99.96 E-value=9.2e-30 Score=226.75 Aligned_cols=96 Identities=33% Similarity=0.513 Sum_probs=80.0
Q ss_pred cccChhhhhcceeEEEEeecCCCCCcCCccCceEEEEeeCCceEEEEcccCCHHHHHHHHHHHH-hCCChhhhhhcCCCC
Q 043121 17 LELTDDELLRECEMDTYKLSGPGSQHRNKRESAVRLKHVPTGVIAHAAEDRSQHKNHASSVNLD-AYSPPPQLLQILPPK 95 (169)
Q Consensus 17 ~~i~~~~l~~dl~i~~~RssGpGGQ~vNk~~saVrl~H~ptGi~v~~~~~RSq~~Nr~~Al~~L-~~L~~~el~~~~~~k 95 (169)
+.|+++ ||+|+|+|||||||||||||+|+|||+|+||||+|+|+++|||++||+.|+++| ++|++.+.+++....
T Consensus 230 ~~i~~~----dl~~~~~rssGpGGQ~vNkt~saVrl~h~ptgi~v~~~~~RSQ~~Nk~~A~~~L~~kL~~~~~~~~~~~~ 305 (367)
T PRK00578 230 IEINPK----DLRIDTYRSSGAGGQHVNKTDSAVRITHIPTGIVVQCQNERSQHQNKASAMKMLKAKLYELELEKRAAEK 305 (367)
T ss_pred cccChh----hEEEEEeeCCCCCCCcccceeeEEEEEECCCcEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455554 669999999999999999999999999999999999999999999999999999 788888776542222
Q ss_pred Cc----ccCCCCCCCCCCCCC-Cchh
Q 043121 96 ST----ITSSEVGPQIGPNNP-KFSL 116 (169)
Q Consensus 96 sq----ir~~~rg~qIRtYn~-~f~~ 116 (169)
+. ....+||++|||||| .+..
T Consensus 306 ~~~r~~~~~~~rg~~IRtYn~~p~~r 331 (367)
T PRK00578 306 DALKGEKKEIGWGSQIRSYVLHPYQM 331 (367)
T ss_pred HHHHhhhccccccCCeEEEECCCCce
Confidence 21 234489999999999 6553
No 14
>COG1186 PrfB Protein chain release factor B [Translation, ribosomal structure and biogenesis]
Probab=99.94 E-value=2.1e-28 Score=207.50 Aligned_cols=88 Identities=33% Similarity=0.377 Sum_probs=76.6
Q ss_pred cceeEEEEeecCCCCCcCCccCceEEEEeeCCceEEEEcccCCHHHHHHHHHHHH-hCCChhhhhhcCCCCCccc----C
Q 043121 26 RECEMDTYKLSGPGSQHRNKRESAVRLKHVPTGVIAHAAEDRSQHKNHASSVNLD-AYSPPPQLLQILPPKSTIT----S 100 (169)
Q Consensus 26 ~dl~i~~~RssGpGGQ~vNk~~saVrl~H~ptGi~v~~~~~RSq~~Nr~~Al~~L-~~L~~~el~~~~~~ksqir----~ 100 (169)
.|++|+|+|||||||||||||+|||||||+||||+|.|+.+|||++|++.|+..| .+|+..+.+++.+.+++.+ .
T Consensus 110 ~dl~idt~RASGaGGQhVNKt~SAVrlth~ptgivv~cq~eRSq~~n~~~a~~~l~~kL~~~~~~~Rsqe~n~~~a~~k~ 189 (239)
T COG1186 110 DDLRIDTYRASGAGGQHVNKTDSAVRLTHLPTGIVVLCQNERSQHLNKALARKMLKGKLYILAQEKRSQEKNRERALKKL 189 (239)
T ss_pred cceEEEEEEcCCCCCCccccccccEEEEEcCCCCEecCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 4679999999999999999999999999999999999999999999999999999 6788777766555555444 3
Q ss_pred CCCCCCCCCCCCC
Q 043121 101 SEVGPQIGPNNPK 113 (169)
Q Consensus 101 ~~rg~qIRtYn~~ 113 (169)
..||.|||+|.|+
T Consensus 190 i~wg~qirsyv~~ 202 (239)
T COG1186 190 IGWGNQIRSYVLD 202 (239)
T ss_pred HHHHHhccccCCC
Confidence 3899999988665
No 15
>PRK09256 hypothetical protein; Provisional
Probab=99.86 E-value=2.9e-22 Score=157.92 Aligned_cols=65 Identities=32% Similarity=0.465 Sum_probs=57.3
Q ss_pred CCcccChhhhhcceeEEEEeecCCCCCcCCccCceEEEEe------eC-----------------Cc-eEEEEcccCCHH
Q 043121 15 NYLELTDDELLRECEMDTYKLSGPGSQHRNKRESAVRLKH------VP-----------------TG-VIAHAAEDRSQH 70 (169)
Q Consensus 15 ~~~~i~~~~l~~dl~i~~~RssGpGGQ~vNk~~saVrl~H------~p-----------------tG-i~v~~~~~RSq~ 70 (169)
..+.|++++ |+++|+|||||||||||||+|+|+|+| +| +| |+|+|+++|||+
T Consensus 6 ~~~~i~~~~----l~~~~~RSSGPGGQ~VNKt~SkV~l~~~~~~~~lp~~~~~~l~~~~~~r~~~~g~l~i~~~~~RSQ~ 81 (138)
T PRK09256 6 RRLVIPENE----LEWRFIRASGPGGQNVNKVSTAVELRFDIAASSLPEFYKERLLALAGHRITKDGVIVIKAQEFRSQE 81 (138)
T ss_pred ccCccCHHH----eEEEEEEcCCCCcccccccceeeEEEechhhccCCHHHHHHHHHHhcCcccCCCcEEEEECCcCCHH
Confidence 446777764 599999999999999999999999996 66 36 999999999999
Q ss_pred HHHHHHHHHHhCC
Q 043121 71 KNHASSVNLDAYS 83 (169)
Q Consensus 71 ~Nr~~Al~~L~~L 83 (169)
+|++.|+++|..+
T Consensus 82 ~Nr~~al~kL~~~ 94 (138)
T PRK09256 82 RNREDALERLVAL 94 (138)
T ss_pred HHHHHHHHHHHHH
Confidence 9999999999543
No 16
>KOG3429 consensus Predicted peptidyl-tRNA hydrolase [Translation, ribosomal structure and biogenesis]
Probab=99.60 E-value=1.1e-15 Score=124.01 Aligned_cols=55 Identities=33% Similarity=0.487 Sum_probs=49.8
Q ss_pred eeEEEEeecCCCCCcCCccCceEEEEe-------eC-----------------Cc-eEEEEcccCCHHHHHHHHHHHHhC
Q 043121 28 CEMDTYKLSGPGSQHRNKRESAVRLKH-------VP-----------------TG-VIAHAAEDRSQHKNHASSVNLDAY 82 (169)
Q Consensus 28 l~i~~~RssGpGGQ~vNk~~saVrl~H-------~p-----------------tG-i~v~~~~~RSq~~Nr~~Al~~L~~ 82 (169)
+++.|.||||||||||||++|+|.|+. || .| |+|.++.+|||+.|.+.||++|..
T Consensus 42 ~~i~y~RSSGPGGQNVNKvNTKv~vrf~vs~a~Wipe~~R~~~~~~~~~rink~gelvI~Sd~TRsq~~NiaDcleKlr~ 121 (172)
T KOG3429|consen 42 LEISYSRSSGPGGQNVNKVNTKVEVRFKVSNAEWIPEFLRNKLLTTEKNRINKDGELVIYSDKTRSQHKNIADCLEKLRD 121 (172)
T ss_pred eEEEEeecCCCCCcccccccceEEEEEecchhhhccHHHHHHHHHHHHHhhccCccEEEecchhHHhhccHHHHHHHHHH
Confidence 699999999999999999999999993 33 34 999999999999999999999953
No 17
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=95.49 E-value=0.032 Score=35.16 Aligned_cols=34 Identities=32% Similarity=0.344 Sum_probs=28.2
Q ss_pred HHHHHHHHHhcCCHHHHHHHhcCChhHHHHHHhc
Q 043121 119 QALLDLIFAVEGSVSEAAKLLWLSTGALSRLILS 152 (169)
Q Consensus 119 ~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~~ 152 (169)
+.+.+.|..++|+++.||+.||+|++.|-+-|++
T Consensus 8 ~~i~~aL~~~~gn~~~aA~~Lgisr~tL~~klkk 41 (42)
T PF02954_consen 8 QLIRQALERCGGNVSKAARLLGISRRTLYRKLKK 41 (42)
T ss_dssp HHHHHHHHHTTT-HHHHHHHHTS-HHHHHHHHHH
T ss_pred HHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHh
Confidence 3467889999999999999999999999988765
No 18
>PRK01905 DNA-binding protein Fis; Provisional
Probab=88.39 E-value=0.92 Score=32.03 Aligned_cols=34 Identities=21% Similarity=0.185 Sum_probs=30.3
Q ss_pred HHHHHHHHhcCCHHHHHHHhcCChhHHHHHHhcC
Q 043121 120 ALLDLIFAVEGSVSEAAKLLWLSTGALSRLILSD 153 (169)
Q Consensus 120 ~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~~~ 153 (169)
.+...+..++|+++.||+.||+|++.|.+.+++.
T Consensus 41 ~i~~aL~~~~gn~s~aAr~LGIsrstL~rklkk~ 74 (77)
T PRK01905 41 LLEVVMEQAGGNQSLAAEYLGINRNTLRKKLQQH 74 (77)
T ss_pred HHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHh
Confidence 4677889999999999999999999999988764
No 19
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=87.83 E-value=1.1 Score=29.46 Aligned_cols=37 Identities=22% Similarity=0.124 Sum_probs=32.5
Q ss_pred hHHHHHHHHHHHhcCCHHHHHHHhcC-ChhHHHHHHhc
Q 043121 116 LGMQALLDLIFAVEGSVSEAAKLLWL-STGALSRLILS 152 (169)
Q Consensus 116 ~~l~~~lD~l~~~~~~~~~aa~~l~~-st~~L~k~l~~ 152 (169)
.-+..+++.|...+.++.+.|..+|+ |++.|.+.+++
T Consensus 37 ~r~~~a~~~l~~~~~~~~~ia~~~g~~s~~~f~r~Fk~ 74 (84)
T smart00342 37 RRLERARRLLRDTDLSVTEIALRVGFSSQSYFSRAFKK 74 (84)
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHhCCCChHHHHHHHHH
Confidence 34777888888888999999999999 99999999875
No 20
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=86.40 E-value=1.3 Score=32.74 Aligned_cols=33 Identities=21% Similarity=0.238 Sum_probs=29.5
Q ss_pred HHHHHHHhcCCHHHHHHHhcCChhHHHHHHhcC
Q 043121 121 LLDLIFAVEGSVSEAAKLLWLSTGALSRLILSD 153 (169)
Q Consensus 121 ~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~~~ 153 (169)
+...+..++|+.+.||+.||+|++.|.+.++..
T Consensus 60 i~~aL~~~~gn~s~AAr~LGIsRsTL~rKLkr~ 92 (95)
T PRK00430 60 LDMVMQYTRGNQTRAALMLGINRGTLRKKLKKY 92 (95)
T ss_pred HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHh
Confidence 667788899999999999999999999888764
No 21
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=86.01 E-value=2.4 Score=29.79 Aligned_cols=35 Identities=29% Similarity=0.103 Sum_probs=30.1
Q ss_pred HHHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHHh
Q 043121 117 GMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLIL 151 (169)
Q Consensus 117 ~l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~ 151 (169)
++..+.+.+.+-+++-+++|+.+|+|.+.+++++.
T Consensus 19 l~~~i~~~~~~~~ltQ~e~A~~lgisq~~vS~l~~ 53 (80)
T PF13744_consen 19 LMAAIRELREERGLTQAELAERLGISQPRVSRLEN 53 (80)
T ss_dssp HHHHHHHHHHCCT--HHHHHHHHTS-HHHHHHHHT
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHCCChhHHHHHHc
Confidence 67889999999999999999999999999999995
No 22
>PF12728 HTH_17: Helix-turn-helix domain
Probab=81.99 E-value=1.8 Score=27.49 Aligned_cols=23 Identities=39% Similarity=0.442 Sum_probs=20.7
Q ss_pred CHHHHHHHhcCChhHHHHHHhcC
Q 043121 131 SVSEAAKLLWLSTGALSRLILSD 153 (169)
Q Consensus 131 ~~~~aa~~l~~st~~L~k~l~~~ 153 (169)
+++++|++||+|++.+-+++...
T Consensus 3 t~~e~a~~l~is~~tv~~~~~~g 25 (51)
T PF12728_consen 3 TVKEAAELLGISRSTVYRWIRQG 25 (51)
T ss_pred CHHHHHHHHCcCHHHHHHHHHcC
Confidence 68899999999999999998765
No 23
>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=81.68 E-value=3.2 Score=26.21 Aligned_cols=34 Identities=21% Similarity=0.245 Sum_probs=24.5
Q ss_pred HHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHHhc
Q 043121 118 MQALLDLIFAVEGSVSEAAKLLWLSTGALSRLILS 152 (169)
Q Consensus 118 l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~~ 152 (169)
+..++.++.. +.+++++|+.||+|.+-+-|.+..
T Consensus 11 ~~~i~~l~~~-G~si~~IA~~~gvsr~TvyR~l~~ 44 (45)
T PF02796_consen 11 IEEIKELYAE-GMSIAEIAKQFGVSRSTVYRYLNK 44 (45)
T ss_dssp HHHHHHHHHT-T--HHHHHHHTTS-HHHHHHHHCC
T ss_pred HHHHHHHHHC-CCCHHHHHHHHCcCHHHHHHHHhc
Confidence 4556665544 499999999999999999998764
No 24
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=80.97 E-value=5.2 Score=25.24 Aligned_cols=44 Identities=18% Similarity=0.052 Sum_probs=33.7
Q ss_pred CCCCCCchhHHHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHHhc
Q 043121 108 GPNNPKFSLGMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLILS 152 (169)
Q Consensus 108 RtYn~~f~~~l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~~ 152 (169)
+.|..--..+-+.++..+... .+.++.|+.+|+|.+-+.+++..
T Consensus 7 ~~~~r~T~~~~~~i~~~~~~~-~s~~~vA~~~~vs~~TV~ri~~~ 50 (52)
T PF13542_consen 7 DRYCRITKRLEQYILKLLRES-RSFKDVARELGVSWSTVRRIFDR 50 (52)
T ss_pred CcCCcHHHHHHHHHHHHHhhc-CCHHHHHHHHCCCHHHHHHHHHh
Confidence 333333345667778877777 89999999999999999998864
No 25
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=80.25 E-value=3.5 Score=25.83 Aligned_cols=25 Identities=32% Similarity=0.190 Sum_probs=19.1
Q ss_pred cCCHHHHHHHhcCChhHHHHHHhcC
Q 043121 129 EGSVSEAAKLLWLSTGALSRLILSD 153 (169)
Q Consensus 129 ~~~~~~aa~~l~~st~~L~k~l~~~ 153 (169)
++++.++|+.||+|.+.+.+.++..
T Consensus 17 G~s~~~ia~~lgvs~~Tv~~w~kr~ 41 (50)
T PF13384_consen 17 GWSIREIAKRLGVSRSTVYRWIKRY 41 (50)
T ss_dssp T--HHHHHHHHTS-HHHHHHHHT--
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHc
Confidence 8999999999999999999988764
No 26
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=80.13 E-value=2 Score=26.35 Aligned_cols=26 Identities=19% Similarity=0.189 Sum_probs=20.3
Q ss_pred hcCCHHHHHHHhcCChhHHHHHHhcC
Q 043121 128 VEGSVSEAAKLLWLSTGALSRLILSD 153 (169)
Q Consensus 128 ~~~~~~~aa~~l~~st~~L~k~l~~~ 153 (169)
.++.+.+.|..+|+|++.|.|+++..
T Consensus 7 ~~~~l~~iA~~~g~S~~~f~r~Fk~~ 32 (42)
T PF00165_consen 7 QKLTLEDIAEQAGFSPSYFSRLFKKE 32 (42)
T ss_dssp SS--HHHHHHHHTS-HHHHHHHHHHH
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 45789999999999999999998864
No 27
>PF00440 TetR_N: Bacterial regulatory proteins, tetR family; InterPro: IPR001647 This entry represents a DNA-binding domain with a helix-turn-helix (HTH) structure that is found in several bacterial and archaeal transcriptional regulators, such as TetR, the tetracycline resistance repressor. Numerous other transcriptional regulatory proteins also contain HTH-type DNA-binding domains, and can be grouped into subfamiles based on sequence similarity. The domain represented by this entry is found in a subfamily of proteins that includes the transcriptional regulators TetR, TetC, AcrR, BetI, Bm3R1, EnvR, QacR, MtrR, TcmR, Ttk, YbiH, and YhgD [, , ]. Many of these proteins function as repressors that control the level of susceptibility to hydrophobic antibiotics and detergents. They all have similar molecular weights, ranging from 21 to 25 kDa. The helix-turn-helix motif is located in the initial third of the protein. The 3D structure of the homodimeric TetR protein complexed with 7-chloro-tetracycline-magnesium has been determined to 2.1 A resolution []. TetR folds into ten alpha-helices with connecting turns and loops. The three N-terminal alpha-helices of the repressor form the DNA-binding domain: this structural motif encompasses an HTH fold with an inverse orientation compared with that of other DNA-binding proteins.; GO: 0003677 DNA binding; PDB: 3NPI_B 3IUV_A 3CCY_A 2JK3_A 2FX0_A 2JJ7_A 2WV1_B 3BTI_D 3BR6_E 3BR5_A ....
Probab=79.52 E-value=5.5 Score=25.02 Aligned_cols=43 Identities=26% Similarity=0.268 Sum_probs=35.7
Q ss_pred HHHHHHHHHHhcCC---HHHHHHHhcCChhHHHHHHhcChhHHHHH
Q 043121 118 MQALLDLIFAVEGS---VSEAAKLLWLSTGALSRLILSDDSHQIAV 160 (169)
Q Consensus 118 l~~~lD~l~~~~~~---~~~aa~~l~~st~~L~k~l~~~~~~~~~~ 160 (169)
|...++++...+++ +.+.|+..|+|++.|-+-+.+-..++.+|
T Consensus 2 l~aa~~l~~~~G~~~~s~~~Ia~~~gvs~~~~y~~f~~k~~l~~a~ 47 (47)
T PF00440_consen 2 LEAALELFAEKGYEAVSIRDIARRAGVSKGSFYRYFPSKDDLLRAV 47 (47)
T ss_dssp HHHHHHHHHHHHTTTSSHHHHHHHHTSCHHHHHHHCSSHHHHHHHH
T ss_pred HHHHHHHHHHhCHHhCCHHHHHHHHccchhhHHHHcCCHHHHHhhC
Confidence 56677777777775 89999999999999999998887777654
No 28
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=79.26 E-value=2.7 Score=27.53 Aligned_cols=38 Identities=18% Similarity=0.244 Sum_probs=29.5
Q ss_pred CCHHHHHHHhcCChhHHHHHHhcC--hhHHHHHHHhhhhc
Q 043121 130 GSVSEAAKLLWLSTGALSRLILSD--DSHQIAVNELRTSK 167 (169)
Q Consensus 130 ~~~~~aa~~l~~st~~L~k~l~~~--~~~~~~~n~~R~~~ 167 (169)
+++++.|+.+|+|.+.|.+++... .+....++..|..+
T Consensus 2 ~~~~~la~~~~~s~~~l~~~f~~~~~~s~~~~~~~~r~~~ 41 (84)
T smart00342 2 LTLEDLAEALGMSPRHLQRLFKKETGTTPKQYLRDRRLER 41 (84)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHhCcCHHHHHHHHHHHH
Confidence 578899999999999999999865 34555667666554
No 29
>PF05225 HTH_psq: helix-turn-helix, Psq domain; InterPro: IPR007889 This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster []. In pipsqueak this domain binds to GAGA sequence []. The pipsqueak family, which includes proteins from fungi, sea urchins, nematodes, insects, and vertebrates appear to be proteins essential for sequence-specific targeting of a polycomb group protein complex [].; GO: 0003677 DNA binding; PDB: 2COB_A.
Probab=79.23 E-value=4.9 Score=25.79 Aligned_cols=38 Identities=21% Similarity=0.200 Sum_probs=27.9
Q ss_pred HHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHHhcChh
Q 043121 118 MQALLDLIFAVEGSVSEAAKLLWLSTGALSRLILSDDS 155 (169)
Q Consensus 118 l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~~~~~ 155 (169)
|+..++.+...+.++..||+.+|++.+-|.+-+...++
T Consensus 5 l~~Ai~~v~~g~~S~r~AA~~ygVp~sTL~~r~~g~~~ 42 (45)
T PF05225_consen 5 LQKAIEAVKNGKMSIRKAAKKYGVPRSTLRRRLRGKPS 42 (45)
T ss_dssp HHHHHHHHHTTSS-HHHHHHHHT--HHHHHHHHHHTTT
T ss_pred HHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHcCCCC
Confidence 56677777766688999999999999999987776543
No 30
>PRK10371 DNA-binding transcriptional regulator MelR; Provisional
Probab=78.90 E-value=4.5 Score=34.79 Aligned_cols=51 Identities=10% Similarity=0.123 Sum_probs=43.3
Q ss_pred HHHHHHHHHHHh---cCCHHHHHHHhcCChhHHHHHHhc--ChhHHHHHHHhhhhc
Q 043121 117 GMQALLDLIFAV---EGSVSEAAKLLWLSTGALSRLILS--DDSHQIAVNELRTSK 167 (169)
Q Consensus 117 ~l~~~lD~l~~~---~~~~~~aa~~l~~st~~L~k~l~~--~~~~~~~~n~~R~~~ 167 (169)
.++.+++.|.+. ..++++.|..+|+|+..|.|++++ .-+....+|++|..+
T Consensus 192 ~i~~~~~~i~~~~~~~~tl~~lA~~~~~S~~~l~r~Fk~~~G~t~~~~l~~~Rl~~ 247 (302)
T PRK10371 192 YVSQMLGFIAENYDQALTINDVAEHVKLNANYAMGIFQRVMQLTMKQYITAMRINH 247 (302)
T ss_pred HHHHHHHHHHHhhcCCCCHHHHHHHHCcCHHHHHHHHHHHhCCCHHHHHHHHHHHH
Confidence 467777777664 678999999999999999999998 568889999999765
No 31
>PRK13503 transcriptional activator RhaS; Provisional
Probab=77.86 E-value=4.8 Score=33.10 Aligned_cols=52 Identities=25% Similarity=0.167 Sum_probs=41.1
Q ss_pred HHHHHHHHHHHh---cCCHHHHHHHhcCChhHHHHHHhcC--hhHHHHHHHhhhhcc
Q 043121 117 GMQALLDLIFAV---EGSVSEAAKLLWLSTGALSRLILSD--DSHQIAVNELRTSKV 168 (169)
Q Consensus 117 ~l~~~lD~l~~~---~~~~~~aa~~l~~st~~L~k~l~~~--~~~~~~~n~~R~~~~ 168 (169)
.+..+++.|... ..++++.|+.+++|++.|.+++++. -+...-+|+.|-.+.
T Consensus 172 ~i~~~~~~I~~~~~~~~tl~~lA~~~~lS~~~l~r~Fk~~~G~S~~~yi~~~Rl~~A 228 (278)
T PRK13503 172 RLNQLLAWLEDHFAEEVNWEALADQFSLSLRTLHRQLKQQTGLTPQRYLNRLRLLKA 228 (278)
T ss_pred HHHHHHHHHHHhhcCCCCHHHHHHHHCCCHHHHHHHHHHHhCcCHHHHHHHHHHHHH
Confidence 456666666554 6779999999999999999999875 677888888886553
No 32
>TIGR02974 phageshock_pspF psp operon transcriptional activator PspF. Members of this protein family are PspF, the sigma-54-dependent transcriptional activator of the phage shock protein (psp) operon, in Escherichia coli and numerous other species. The psp operon is induced by a number of stress conditions, including heat shock, ethanol, and filamentous phage infection. Changed com_name to adhere to TIGR role notes conventions. 09/15/06 - DMH
Probab=77.32 E-value=3.9 Score=36.00 Aligned_cols=33 Identities=24% Similarity=0.199 Sum_probs=28.4
Q ss_pred HHHHHHHhcCCHHHHHHHhcCChhHHHHHHhcC
Q 043121 121 LLDLIFAVEGSVSEAAKLLWLSTGALSRLILSD 153 (169)
Q Consensus 121 ~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~~~ 153 (169)
+...|...+|..+.||+.||+|++.|-+.|+++
T Consensus 297 I~~aL~~~~gn~~~aA~~LGisr~tL~rklkk~ 329 (329)
T TIGR02974 297 LQQALAEAQFNQRKAAELLGLTYHQLRGLLRKH 329 (329)
T ss_pred HHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHhC
Confidence 445677789999999999999999999988763
No 33
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=76.43 E-value=5.7 Score=28.61 Aligned_cols=50 Identities=18% Similarity=0.040 Sum_probs=37.9
Q ss_pred HHHHHHHHHH---hcCCHHHHHHHhcCChhHHHHHHhcC--hhHHHHHHHhhhhc
Q 043121 118 MQALLDLIFA---VEGSVSEAAKLLWLSTGALSRLILSD--DSHQIAVNELRTSK 167 (169)
Q Consensus 118 l~~~lD~l~~---~~~~~~~aa~~l~~st~~L~k~l~~~--~~~~~~~n~~R~~~ 167 (169)
+..+++.+.+ ...++++.|+.+++|+..|.++++.. -+....++++|..+
T Consensus 7 ~~~~~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~f~~~~g~s~~~~i~~~Rl~~ 61 (107)
T PRK10219 7 IQTLIAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRTVTHQTLGDYIRQRRLLL 61 (107)
T ss_pred HHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHHHHCcCHHHHHHHHHHHH
Confidence 4444444443 34789999999999999999999985 56677788888654
No 34
>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=76.05 E-value=3.1 Score=27.46 Aligned_cols=24 Identities=46% Similarity=0.476 Sum_probs=21.2
Q ss_pred cCCHHHHHHHhcCChhHHHHHHhc
Q 043121 129 EGSVSEAAKLLWLSTGALSRLILS 152 (169)
Q Consensus 129 ~~~~~~aa~~l~~st~~L~k~l~~ 152 (169)
.++++.||+.|++|.+.+++-|+.
T Consensus 13 ~gs~~~AA~~l~is~~~vs~~i~~ 36 (60)
T PF00126_consen 13 TGSISAAAEELGISQSAVSRQIKQ 36 (60)
T ss_dssp HSSHHHHHHHCTSSHHHHHHHHHH
T ss_pred hCCHHHHHHHhhccchHHHHHHHH
Confidence 458999999999999999988764
No 35
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=75.64 E-value=3.8 Score=24.74 Aligned_cols=23 Identities=39% Similarity=0.443 Sum_probs=20.6
Q ss_pred CHHHHHHHhcCChhHHHHHHhcC
Q 043121 131 SVSEAAKLLWLSTGALSRLILSD 153 (169)
Q Consensus 131 ~~~~aa~~l~~st~~L~k~l~~~ 153 (169)
+++++|++||+|.+.+-++++..
T Consensus 3 t~~e~a~~lgis~~ti~~~~~~g 25 (49)
T TIGR01764 3 TVEEAAEYLGVSKDTVYRLIHEG 25 (49)
T ss_pred CHHHHHHHHCCCHHHHHHHHHcC
Confidence 57899999999999999998765
No 36
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=75.39 E-value=4.8 Score=31.43 Aligned_cols=44 Identities=20% Similarity=0.095 Sum_probs=34.7
Q ss_pred CCchhHHHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHHhcChh
Q 043121 112 PKFSLGMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLILSDDS 155 (169)
Q Consensus 112 ~~f~~~l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~~~~~ 155 (169)
+.+|+.-+.+--.|-.-+.+..+.|+.||+|++++++-|.+...
T Consensus 5 ~vlPaiRa~lA~~L~eeG~Sq~~iA~LLGltqaAVS~Yls~krg 48 (119)
T COG2522 5 EVLPAIRALLAKELIEEGLSQYRIAKLLGLTQAAVSQYLSGKRG 48 (119)
T ss_pred HHHHHHHHHHHHHHHHcCCcHHHHHHHhCCCHHHHHHHHccCCc
Confidence 34566655554444445999999999999999999999998876
No 37
>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional
Probab=74.62 E-value=4.9 Score=35.16 Aligned_cols=33 Identities=24% Similarity=0.168 Sum_probs=29.6
Q ss_pred HHHHHHHhcCCHHHHHHHhcCChhHHHHHHhcC
Q 043121 121 LLDLIFAVEGSVSEAAKLLWLSTGALSRLILSD 153 (169)
Q Consensus 121 ~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~~~ 153 (169)
+...|...+|+.+.||+.||+|++.|-+-|+++
T Consensus 291 I~~aL~~~~gn~~~aA~~LGIsR~tLyrklk~~ 323 (326)
T PRK11608 291 LQRSLQQAKFNQKRAAELLGLTYHQLRALLKKH 323 (326)
T ss_pred HHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHHc
Confidence 667788899999999999999999999988865
No 38
>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=72.59 E-value=10 Score=24.26 Aligned_cols=39 Identities=23% Similarity=0.236 Sum_probs=29.2
Q ss_pred chhHHHHHHHHHHHhcC---CHHHHHHHhcCChhHHHHHHhc
Q 043121 114 FSLGMQALLDLIFAVEG---SVSEAAKLLWLSTGALSRLILS 152 (169)
Q Consensus 114 f~~~l~~~lD~l~~~~~---~~~~aa~~l~~st~~L~k~l~~ 152 (169)
+.+.-..+|-.|...++ .+++.|+.|+++.+.+++.|+.
T Consensus 3 lt~~q~~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~ 44 (62)
T PF12802_consen 3 LTPSQFRVLMALARHPGEELTQSELAERLGISKSTVSRIVKR 44 (62)
T ss_dssp STHHHHHHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHH
T ss_pred cCHHHHHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 33344557777777776 6899999999999999988753
No 39
>smart00497 IENR1 Intron encoded nuclease repeat motif. Repeat of unknown function, but possibly DNA-binding via helix-turn-helix motif (Ponting, unpublished).
Probab=72.25 E-value=4.7 Score=25.42 Aligned_cols=22 Identities=36% Similarity=0.484 Sum_probs=20.1
Q ss_pred CHHHHHHHhcCChhHHHHHHhc
Q 043121 131 SVSEAAKLLWLSTGALSRLILS 152 (169)
Q Consensus 131 ~~~~aa~~l~~st~~L~k~l~~ 152 (169)
++.+||++||++.+.+++.++.
T Consensus 19 S~~eAa~~lg~~~~~I~~~~~~ 40 (53)
T smart00497 19 SIREAAKYLGISHSSISKYLNT 40 (53)
T ss_pred CHHHHHHHhCCCHHHHHHHHhC
Confidence 6889999999999999998876
No 40
>PRK15115 response regulator GlrR; Provisional
Probab=71.95 E-value=6.1 Score=35.10 Aligned_cols=34 Identities=21% Similarity=0.273 Sum_probs=29.9
Q ss_pred HHHHHHHHhcCCHHHHHHHhcCChhHHHHHHhcC
Q 043121 120 ALLDLIFAVEGSVSEAAKLLWLSTGALSRLILSD 153 (169)
Q Consensus 120 ~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~~~ 153 (169)
.+...|...+|..+.||+.||+|++.|-+-|++.
T Consensus 402 ~i~~al~~~~gn~~~aA~~Lgisr~tL~rkl~~~ 435 (444)
T PRK15115 402 YLRKLLQITKGNVTHAARMAGRNRTEFYKLLSRH 435 (444)
T ss_pred HHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHHh
Confidence 4566788999999999999999999999988864
No 41
>TIGR02915 PEP_resp_reg putative PEP-CTERM system response regulator. Members of this protein family share full-length homology with (but do not include) the acetoacetate metabolism regulatory protein AtoC. These proteins have a Fis family DNA binding sequence (pfam02954), a response regulator receiver domain (pfam00072), and sigma-54 interaction domain (pfam00158).
Probab=71.75 E-value=6.1 Score=35.09 Aligned_cols=35 Identities=29% Similarity=0.402 Sum_probs=30.5
Q ss_pred HHHHHHHHHhcCCHHHHHHHhcCChhHHHHHHhcC
Q 043121 119 QALLDLIFAVEGSVSEAAKLLWLSTGALSRLILSD 153 (169)
Q Consensus 119 ~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~~~ 153 (169)
..+...|...+|..+.||+.||+|++.|-+-|++.
T Consensus 408 ~~i~~al~~~~gn~~~aA~~Lgisr~tl~rkl~~~ 442 (445)
T TIGR02915 408 EAVRKAIARVDGNIARAAELLGITRPTLYDLMKKH 442 (445)
T ss_pred HHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHHh
Confidence 34677889999999999999999999999888753
No 42
>PRK13502 transcriptional activator RhaR; Provisional
Probab=71.36 E-value=7.1 Score=32.39 Aligned_cols=53 Identities=8% Similarity=0.008 Sum_probs=41.9
Q ss_pred hHHHHHHHHHH---HhcCCHHHHHHHhcCChhHHHHHHhc--ChhHHHHHHHhhhhcc
Q 043121 116 LGMQALLDLIF---AVEGSVSEAAKLLWLSTGALSRLILS--DDSHQIAVNELRTSKV 168 (169)
Q Consensus 116 ~~l~~~lD~l~---~~~~~~~~aa~~l~~st~~L~k~l~~--~~~~~~~~n~~R~~~~ 168 (169)
..+..+++.|. .-...+++.|+.+|+|++-|.+++++ .-+.-..+++.|-.+.
T Consensus 176 ~~~~~~~~~I~~~~~~~~~~~~lA~~~~iS~~~L~r~fk~~~G~t~~~yi~~~Rl~~A 233 (282)
T PRK13502 176 TLLDKLITALANSLECPFALDAFCQQEQCSERVLRQQFRAQTGMTINQYLRQVRICHA 233 (282)
T ss_pred HHHHHHHHHHHhcccCCCCHHHHHHHHCcCHHHHHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 34555666543 33567899999999999999999997 7888889999987664
No 43
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=71.21 E-value=7.6 Score=29.36 Aligned_cols=39 Identities=13% Similarity=0.046 Sum_probs=31.6
Q ss_pred hcCCHHHHHHHhcCChhHHHHHHhcC--hhHHHHHHHhhhh
Q 043121 128 VEGSVSEAAKLLWLSTGALSRLILSD--DSHQIAVNELRTS 166 (169)
Q Consensus 128 ~~~~~~~aa~~l~~st~~L~k~l~~~--~~~~~~~n~~R~~ 166 (169)
...++.+.|+.+|+|+..|.++++.. -+....++..|..
T Consensus 24 ~~~sl~~lA~~~g~S~~~l~r~Fk~~~G~s~~~~l~~~Rl~ 64 (127)
T PRK11511 24 SPLSLEKVSERSGYSKWHLQRMFKKETGHSLGQYIRSRKMT 64 (127)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHCcCHHHHHHHHHHH
Confidence 35789999999999999999999986 4556667777654
No 44
>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=71.02 E-value=13 Score=22.01 Aligned_cols=37 Identities=19% Similarity=0.148 Sum_probs=29.5
Q ss_pred hHHHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHHhc
Q 043121 116 LGMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLILS 152 (169)
Q Consensus 116 ~~l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~~ 152 (169)
+-...++..+...+.+..++|+.+|+|.+.+.+.+..
T Consensus 13 ~~~~~~~~~~~~~~~~~~~ia~~~~~s~~~i~~~~~~ 49 (55)
T cd06171 13 EREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHR 49 (55)
T ss_pred HHHHHHHHHHHhcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 3445677777778899999999999999999876643
No 45
>PRK11361 acetoacetate metabolism regulatory protein AtoC; Provisional
Probab=70.86 E-value=6.3 Score=34.98 Aligned_cols=34 Identities=21% Similarity=0.244 Sum_probs=29.0
Q ss_pred HHHHHHHHhcCCHHHHHHHhcCChhHHHHHHhcC
Q 043121 120 ALLDLIFAVEGSVSEAAKLLWLSTGALSRLILSD 153 (169)
Q Consensus 120 ~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~~~ 153 (169)
.+...|...+|+.+.||+.||+|++.|-|-|++.
T Consensus 421 ~i~~al~~~~gn~~~aA~~LGisr~tL~rkl~~~ 454 (457)
T PRK11361 421 IIMEVLEQQEGNRTRTALMLGISRRALMYKLQEY 454 (457)
T ss_pred HHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHh
Confidence 3555688899999999999999999999888753
No 46
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=70.84 E-value=6.5 Score=24.83 Aligned_cols=29 Identities=28% Similarity=0.189 Sum_probs=20.3
Q ss_pred HHHHhcCCHHHHHHHhcCChhHHHHHHhc
Q 043121 124 LIFAVEGSVSEAAKLLWLSTGALSRLILS 152 (169)
Q Consensus 124 ~l~~~~~~~~~aa~~l~~st~~L~k~l~~ 152 (169)
.+...+.++.++|+.||.|++-+.+.|+.
T Consensus 15 ~l~~~G~s~~~IA~~lg~s~sTV~relkR 43 (44)
T PF13936_consen 15 ALLEQGMSIREIAKRLGRSRSTVSRELKR 43 (44)
T ss_dssp HHHCS---HHHHHHHTT--HHHHHHHHHH
T ss_pred HHHHcCCCHHHHHHHHCcCcHHHHHHHhc
Confidence 34568899999999999999999998864
No 47
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=70.49 E-value=9.8 Score=25.42 Aligned_cols=36 Identities=22% Similarity=0.288 Sum_probs=27.1
Q ss_pred HHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHHhcCh
Q 043121 118 MQALLDLIFAVEGSVSEAAKLLWLSTGALSRLILSDD 154 (169)
Q Consensus 118 l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~~~~ 154 (169)
=+.-+|++...+.+..++|.+++-|....-++| +||
T Consensus 9 Eqaqid~m~qlG~s~~~isr~i~RSr~~Ir~yl-~dP 44 (50)
T PF11427_consen 9 EQAQIDVMHQLGMSLREISRRIGRSRTCIRRYL-KDP 44 (50)
T ss_dssp HHHHHHHHHHTT--HHHHHHHHT--HHHHHHHH-HSC
T ss_pred HHHHHHHHHHhchhHHHHHHHhCccHHHHHHHh-cCh
Confidence 367899999999999999999999999887765 455
No 48
>PHA00542 putative Cro-like protein
Probab=70.25 E-value=13 Score=26.35 Aligned_cols=33 Identities=15% Similarity=0.079 Sum_probs=28.2
Q ss_pred HHHHHHHhcCCHHHHHHHhcCChhHHHHHHhcC
Q 043121 121 LLDLIFAVEGSVSEAAKLLWLSTGALSRLILSD 153 (169)
Q Consensus 121 ~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~~~ 153 (169)
+.-.+...+++.+++|+.+|+|.+.+.+++...
T Consensus 23 l~~~l~~~glTq~elA~~lgIs~~tIsr~e~g~ 55 (82)
T PHA00542 23 LVCALIRAGWSQEQIADATDVSQPTICRIYSGR 55 (82)
T ss_pred HHHHHHHCCCCHHHHHHHHCcCHHHHHHHHcCC
Confidence 344567889999999999999999999999654
No 49
>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=70.20 E-value=14 Score=24.90 Aligned_cols=39 Identities=23% Similarity=0.186 Sum_probs=31.3
Q ss_pred hhHHHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHHhcC
Q 043121 115 SLGMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLILSD 153 (169)
Q Consensus 115 ~~~l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~~~ 153 (169)
++|-....+.+...+....+.|+.+|+|.+.+.+++...
T Consensus 4 ~~g~~i~~~~~~~~~~t~~~lA~~~gis~~tis~~~~g~ 42 (78)
T TIGR02607 4 HPGEILREEFLEPLGLSIRALAKALGVSRSTLSRIVNGR 42 (78)
T ss_pred CHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCC
Confidence 444332226789999999999999999999999998765
No 50
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=69.97 E-value=7.6 Score=32.41 Aligned_cols=52 Identities=21% Similarity=0.142 Sum_probs=40.8
Q ss_pred HHHHHHHHHH---HhcCCHHHHHHHhcCChhHHHHHHhcC--hhHHHHHHHhhhhcc
Q 043121 117 GMQALLDLIF---AVEGSVSEAAKLLWLSTGALSRLILSD--DSHQIAVNELRTSKV 168 (169)
Q Consensus 117 ~l~~~lD~l~---~~~~~~~~aa~~l~~st~~L~k~l~~~--~~~~~~~n~~R~~~~ 168 (169)
.+..+++.|. ..+.++++.|+.+++|++.|.|++++. -+....+|+.|-.+.
T Consensus 184 ~i~~~~~~i~~~~~~~isl~~lA~~~~lS~~~l~r~Fk~~~G~tp~~~l~~~Rl~~A 240 (290)
T PRK10572 184 RVREACQYISDHLASEFDIESVAQHVCLSPSRLAHLFRQQLGISVLRWREDQRISRA 240 (290)
T ss_pred HHHHHHHHHHhcccCCCCHHHHHHHHCCCHHHHHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 4555666663 356779999999999999999999985 577788888887653
No 51
>TIGR02297 HpaA 4-hydroxyphenylacetate catabolism regulatory protein HpaA. This putative transcriptional regulator, which contains both the substrate-binding, dimerization domain (pfam02311) and the helix-turn-helix DNA-binding domain (pfam00165) of the AraC famil, is located proximal to genes of the 4-hydroxyphenylacetate catabolism pathway.
Probab=68.99 E-value=10 Score=31.38 Aligned_cols=52 Identities=17% Similarity=-0.010 Sum_probs=39.2
Q ss_pred HHHHHHHHHH---HhcCCHHHHHHHhcCChhHHHHHHhc--ChhHHHHHHHhhhhcc
Q 043121 117 GMQALLDLIF---AVEGSVSEAAKLLWLSTGALSRLILS--DDSHQIAVNELRTSKV 168 (169)
Q Consensus 117 ~l~~~lD~l~---~~~~~~~~aa~~l~~st~~L~k~l~~--~~~~~~~~n~~R~~~~ 168 (169)
.+..+++.|. ...+++++.|+.+++|++-|.|++++ .-+....+++.|-.+.
T Consensus 187 ~~~~~~~~I~~~~~~~~sl~~lA~~~~~S~~~l~r~Fk~~~G~t~~~yi~~~Rl~~A 243 (287)
T TIGR02297 187 LFNRFNFLIEENYKQHLRLPEYADRLGISESRLNDICRRFSALSPKRLIIERVMQEA 243 (287)
T ss_pred HHHHHHHHHHHhhccCCCHHHHHHHHCCCHHHHHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 3444555443 34778999999999999999999998 4567777888886653
No 52
>PRK10365 transcriptional regulatory protein ZraR; Provisional
Probab=68.97 E-value=7.9 Score=34.13 Aligned_cols=33 Identities=21% Similarity=0.236 Sum_probs=28.5
Q ss_pred HHHHHHHHhcCCHHHHHHHhcCChhHHHHHHhc
Q 043121 120 ALLDLIFAVEGSVSEAAKLLWLSTGALSRLILS 152 (169)
Q Consensus 120 ~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~~ 152 (169)
.+...|...+|+.+.||+.||+|++.|-+-|++
T Consensus 409 ~i~~~l~~~~gn~~~aa~~Lgisr~tl~rk~~~ 441 (441)
T PRK10365 409 VILAALEKTGGNKTEAARQLGITRKTLLAKLSR 441 (441)
T ss_pred HHHHHHHHhCCCHHHHHHHhCCCHHHHHHHhhC
Confidence 356678889999999999999999999887753
No 53
>TIGR01818 ntrC nitrogen regulation protein NR(I). This model represents NtrC, a DNA-binding response regulator that is phosphorylated by NtrB and interacts with sigma-54. NtrC usually controls the expression of glutamine synthase, GlnA, and may be called GlnL, GlnG, etc.
Probab=68.96 E-value=7.7 Score=34.59 Aligned_cols=32 Identities=28% Similarity=0.271 Sum_probs=27.8
Q ss_pred HHHHHHHhcCCHHHHHHHhcCChhHHHHHHhc
Q 043121 121 LLDLIFAVEGSVSEAAKLLWLSTGALSRLILS 152 (169)
Q Consensus 121 ~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~~ 152 (169)
+...|..++|+.+.||+.||+|++.|-|-|++
T Consensus 431 i~~al~~~~gn~~~aA~~Lgisr~tL~rkl~~ 462 (463)
T TIGR01818 431 LEAALQHTRGHKQEAAALLGWGRNTLTRKLKE 462 (463)
T ss_pred HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHh
Confidence 55677789999999999999999999887763
No 54
>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=68.59 E-value=3.1 Score=27.49 Aligned_cols=29 Identities=17% Similarity=0.179 Sum_probs=21.6
Q ss_pred cCCHHHHHHHhcCChhHHHHHHhcChhHH
Q 043121 129 EGSVSEAAKLLWLSTGALSRLILSDDSHQ 157 (169)
Q Consensus 129 ~~~~~~aa~~l~~st~~L~k~l~~~~~~~ 157 (169)
+.+..+.|..||++.+++..+++..+...
T Consensus 22 g~s~~~ia~~fgv~~sTv~~I~K~k~~i~ 50 (53)
T PF04218_consen 22 GESKRDIAREFGVSRSTVSTILKNKDKIL 50 (53)
T ss_dssp TT-HHHHHHHHT--CCHHHHHHHCHHHHC
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHhHHHHH
Confidence 34789999999999999999998766543
No 55
>COG3284 AcoR Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]
Probab=68.27 E-value=7.1 Score=38.00 Aligned_cols=35 Identities=40% Similarity=0.491 Sum_probs=32.1
Q ss_pred HHHHHHHHHhcCCHHHHHHHhcCChhHHHHHHhcC
Q 043121 119 QALLDLIFAVEGSVSEAAKLLWLSTGALSRLILSD 153 (169)
Q Consensus 119 ~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~~~ 153 (169)
+.+++.+.+++|.++.||+.||+|++-|-|=+++|
T Consensus 568 ~~l~~al~~~~~~is~aa~~lgi~R~T~yrklk~~ 602 (606)
T COG3284 568 AALLAALQATNGNISEAARLLGISRSTLYRKLKRH 602 (606)
T ss_pred HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHh
Confidence 46889999999999999999999999999988875
No 56
>PF13518 HTH_28: Helix-turn-helix domain
Probab=68.01 E-value=11 Score=23.28 Aligned_cols=26 Identities=27% Similarity=0.197 Sum_probs=22.3
Q ss_pred cCCHHHHHHHhcCChhHHHHHHhcCh
Q 043121 129 EGSVSEAAKLLWLSTGALSRLILSDD 154 (169)
Q Consensus 129 ~~~~~~aa~~l~~st~~L~k~l~~~~ 154 (169)
+.++.++|+.||+|.+++-+.++...
T Consensus 12 g~s~~~~a~~~gis~~tv~~w~~~y~ 37 (52)
T PF13518_consen 12 GESVREIAREFGISRSTVYRWIKRYR 37 (52)
T ss_pred CCCHHHHHHHHCCCHhHHHHHHHHHH
Confidence 55999999999999999998886543
No 57
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=67.73 E-value=22 Score=26.91 Aligned_cols=44 Identities=11% Similarity=0.033 Sum_probs=32.2
Q ss_pred hhHHHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHHhcChhHHHHHHHhh
Q 043121 115 SLGMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLILSDDSHQIAVNELR 164 (169)
Q Consensus 115 ~~~l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~~~~~~~~~~n~~R 164 (169)
|+-.+.++-+....+.+++++|+.||+|.+.+-.. +.++++.+|
T Consensus 111 ~~~~r~v~~l~~~~~~s~~EIA~~lgis~~tV~~~------l~ra~~~lr 154 (163)
T PRK07037 111 PARTRYAFEMYRLHGETQKDIARELGVSPTLVNFM------IRDALVHCR 154 (163)
T ss_pred CHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHH------HHHHHHHHH
Confidence 33445566677778899999999999999988765 445555554
No 58
>PRK13500 transcriptional activator RhaR; Provisional
Probab=67.18 E-value=13 Score=31.96 Aligned_cols=52 Identities=10% Similarity=0.017 Sum_probs=41.9
Q ss_pred HHHHHHHHHHHh---cCCHHHHHHHhcCChhHHHHHHhc--ChhHHHHHHHhhhhcc
Q 043121 117 GMQALLDLIFAV---EGSVSEAAKLLWLSTGALSRLILS--DDSHQIAVNELRTSKV 168 (169)
Q Consensus 117 ~l~~~lD~l~~~---~~~~~~aa~~l~~st~~L~k~l~~--~~~~~~~~n~~R~~~~ 168 (169)
.+..+++.|.+. +.++++.|+.+++|+..|.+++++ ..+....+++.|-.+.
T Consensus 207 ~l~~i~~yI~~~~~e~isl~~lA~~~~iS~~~L~r~FK~~tG~T~~~yi~~~RL~~A 263 (312)
T PRK13500 207 LLDKLITRLAASLKSPFALDKFCDEASCSERVLRQQFRQQTGMTINQYLRQVRVCHA 263 (312)
T ss_pred HHHHHHHHHHHcccCCCCHHHHHHHHCcCHHHHHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 455666666653 578899999999999999999998 4788888888887653
No 59
>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional
Probab=66.75 E-value=8.6 Score=35.68 Aligned_cols=35 Identities=26% Similarity=0.228 Sum_probs=31.0
Q ss_pred HHHHHHHHHhcCCHHHHHHHhcCChhHHHHHHhcC
Q 043121 119 QALLDLIFAVEGSVSEAAKLLWLSTGALSRLILSD 153 (169)
Q Consensus 119 ~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~~~ 153 (169)
+.+.+.|..++|..+.||+.||+|++.|-+-|++.
T Consensus 471 ~~I~~aL~~~~gn~~~aA~~LGisr~tL~rklk~~ 505 (509)
T PRK05022 471 QLIRQALAQHQGNWAAAARALELDRANLHRLAKRL 505 (509)
T ss_pred HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHc
Confidence 45788899999999999999999999999888753
No 60
>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=66.35 E-value=11 Score=24.13 Aligned_cols=32 Identities=28% Similarity=0.472 Sum_probs=24.1
Q ss_pred HHHHHHHhcC-CHHHHHHHhcCChhHHHHHHhc
Q 043121 121 LLDLIFAVEG-SVSEAAKLLWLSTGALSRLILS 152 (169)
Q Consensus 121 ~lD~l~~~~~-~~~~aa~~l~~st~~L~k~l~~ 152 (169)
+|..|...++ ..++.|++++++.+.++++++.
T Consensus 8 iL~~l~~~~~~~~~~la~~~~~~~~~~t~~i~~ 40 (59)
T PF01047_consen 8 ILRILYENGGITQSELAEKLGISRSTVTRIIKR 40 (59)
T ss_dssp HHHHHHHHSSEEHHHHHHHHTS-HHHHHHHHHH
T ss_pred HHHHHHHcCCCCHHHHHHHHCCChhHHHHHHHH
Confidence 4555555555 7899999999999999988753
No 61
>PRK00118 putative DNA-binding protein; Validated
Probab=66.13 E-value=13 Score=28.12 Aligned_cols=43 Identities=16% Similarity=0.122 Sum_probs=35.4
Q ss_pred CCCCchhHHHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHHhc
Q 043121 110 NNPKFSLGMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLILS 152 (169)
Q Consensus 110 Yn~~f~~~l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~~ 152 (169)
|++..+.-...++-.....+.+++++|+.+|+|++.+.+.+..
T Consensus 14 ~~~~L~ekqRevl~L~y~eg~S~~EIAe~lGIS~~TV~r~L~R 56 (104)
T PRK00118 14 YGSLLTEKQRNYMELYYLDDYSLGEIAEEFNVSRQAVYDNIKR 56 (104)
T ss_pred HhccCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 4555666777788777888999999999999999999887764
No 62
>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=65.48 E-value=20 Score=22.54 Aligned_cols=44 Identities=20% Similarity=0.259 Sum_probs=33.3
Q ss_pred hhHHHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHHhcChhHHHHHHHhh
Q 043121 115 SLGMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLILSDDSHQIAVNELR 164 (169)
Q Consensus 115 ~~~l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~~~~~~~~~~n~~R 164 (169)
++--+.++...+..+.+.+++|+.||+|.+.+.+... ++++.+|
T Consensus 6 ~~~er~vi~~~y~~~~t~~eIa~~lg~s~~~V~~~~~------~al~kLR 49 (50)
T PF04545_consen 6 PPREREVIRLRYFEGLTLEEIAERLGISRSTVRRILK------RALKKLR 49 (50)
T ss_dssp -HHHHHHHHHHHTST-SHHHHHHHHTSCHHHHHHHHH------HHHHHHH
T ss_pred CHHHHHHHHHHhcCCCCHHHHHHHHCCcHHHHHHHHH------HHHHHhc
Confidence 4445678888888899999999999999999987653 4555554
No 63
>PRK10923 glnG nitrogen regulation protein NR(I); Provisional
Probab=64.98 E-value=9.9 Score=34.10 Aligned_cols=32 Identities=28% Similarity=0.330 Sum_probs=28.1
Q ss_pred HHHHHHHhcCCHHHHHHHhcCChhHHHHHHhc
Q 043121 121 LLDLIFAVEGSVSEAAKLLWLSTGALSRLILS 152 (169)
Q Consensus 121 ~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~~ 152 (169)
+...|..++|+.+.||+.||+|++.|-|-|++
T Consensus 434 i~~aL~~~~gn~~~aA~~Lgisr~tL~rkl~~ 465 (469)
T PRK10923 434 LTTALRHTQGHKQEAARLLGWGRNTLTRKLKE 465 (469)
T ss_pred HHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 55677889999999999999999999988875
No 64
>COG2207 AraC AraC-type DNA-binding domain-containing proteins [Transcription]
Probab=64.28 E-value=26 Score=24.52 Aligned_cols=42 Identities=26% Similarity=0.258 Sum_probs=31.3
Q ss_pred HHHhcCCHHHHHHHhcCChhHHHHHHhcC--hhHHHHHHHhhhh
Q 043121 125 IFAVEGSVSEAAKLLWLSTGALSRLILSD--DSHQIAVNELRTS 166 (169)
Q Consensus 125 l~~~~~~~~~aa~~l~~st~~L~k~l~~~--~~~~~~~n~~R~~ 166 (169)
....++++.+.|..+|+|.+.|.+.++.. -+....+++.|..
T Consensus 32 ~~~~~~~l~~la~~~g~S~~~l~r~f~~~~g~s~~~~~~~~Rl~ 75 (127)
T COG2207 32 NLAEPLTLEDLARRLGMSRRTLSRLFKKETGTSPSQYLRQLRLE 75 (127)
T ss_pred HhcCCCCHHHHHHHHCCCHHHHHHHHHHHHCCCHHHHHHHHHHH
Confidence 33444789999999999999999999843 3333567777654
No 65
>PRK09685 DNA-binding transcriptional activator FeaR; Provisional
Probab=63.96 E-value=12 Score=31.31 Aligned_cols=50 Identities=20% Similarity=0.084 Sum_probs=37.8
Q ss_pred HHHHHHHHHHh----cCCHHHHHHHhcCChhHHHHHHhcCh-hHHHHHHHhhhhc
Q 043121 118 MQALLDLIFAV----EGSVSEAAKLLWLSTGALSRLILSDD-SHQIAVNELRTSK 167 (169)
Q Consensus 118 l~~~lD~l~~~----~~~~~~aa~~l~~st~~L~k~l~~~~-~~~~~~n~~R~~~ 167 (169)
+..+.+.|.+. +.++.+.|+.+|+|...|.++++..- +....+++.|-.+
T Consensus 199 l~~~~~~I~~~l~~~~ls~~~lA~~~giS~r~L~r~Fk~~G~T~~~yi~~~RL~~ 253 (302)
T PRK09685 199 FQKVVALIDQSIQEEILRPEWIAGELGISVRSLYRLFAEQGLVVAQYIRNRRLDR 253 (302)
T ss_pred HHHHHHHHHHhcCCCCCCHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHHHHH
Confidence 44445544443 47899999999999999999999874 3677788888654
No 66
>PF03374 ANT: Phage antirepressor protein KilAC domain; InterPro: IPR005039 This entry is represented by Bacteriophage P1, Ant1 C-terminal domain, which represents the processed Ant2 chain. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Prophages P1 and P7 exist as unit copy DNA plasmids in the bacterial cell. Maintenance of the prophage state requires the continuous expression of two repressors: (i) C1 is a protein which negatively regulates the expression of lytic genes including the C1 inactivator gene coi, and (ii) C4 is an antisense RNA which specifically inhibits the synthesis of an anti-repressor Ant.; GO: 0003677 DNA binding
Probab=63.95 E-value=13 Score=27.07 Aligned_cols=38 Identities=24% Similarity=0.282 Sum_probs=31.6
Q ss_pred HHHHHHHHHhcCC--HHHHHHHhcCChhHHHHHHhcChhH
Q 043121 119 QALLDLIFAVEGS--VSEAAKLLWLSTGALSRLILSDDSH 156 (169)
Q Consensus 119 ~~~lD~l~~~~~~--~~~aa~~l~~st~~L~k~l~~~~~~ 156 (169)
+..+|.+.+.++. +.++|+.||+++..|.++|..+.=+
T Consensus 12 a~~~d~~~~~~~~~ti~~~AK~L~i~~~~l~~~Lr~~g~l 51 (111)
T PF03374_consen 12 AEFYDAFVDSDGLYTIREAAKLLGIGRNKLFQWLREKGWL 51 (111)
T ss_pred hHHHHHHHcCCCCccHHHHHHHhCCCHHHHHHHHHhCCce
Confidence 5678888888764 7889999999999999999876443
No 67
>TIGR01817 nifA Nif-specific regulatory protein. This model represents NifA, a DNA-binding regulatory protein for nitrogen fixation. The model produces scores between the trusted and noise cutoffs for a well-described NifA homolog in Aquifex aeolicus (which lacks nitrogenase), for transcriptional activators of alternative nitrogenases (VFe or FeFe instead of MoFe), and truncated forms.
Probab=63.19 E-value=11 Score=34.92 Aligned_cols=34 Identities=15% Similarity=0.091 Sum_probs=30.3
Q ss_pred HHHHHHHHhcCCHHHHHHHhcCChhHHHHHHhcC
Q 043121 120 ALLDLIFAVEGSVSEAAKLLWLSTGALSRLILSD 153 (169)
Q Consensus 120 ~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~~~ 153 (169)
.+.+.|..++|+++.||+.||+|++.|-+-|++.
T Consensus 494 ~i~~aL~~~~gn~~~aA~~LGisr~tLy~klk~~ 527 (534)
T TIGR01817 494 RLIAALEQAGWVQAKAARLLGMTPRQVGYALRKL 527 (534)
T ss_pred HHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHc
Confidence 5788899999999999999999999998777654
No 68
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=62.33 E-value=8.6 Score=24.90 Aligned_cols=25 Identities=16% Similarity=0.194 Sum_probs=22.0
Q ss_pred HHHHHHHhcCChhHHHHHHhcChhH
Q 043121 132 VSEAAKLLWLSTGALSRLILSDDSH 156 (169)
Q Consensus 132 ~~~aa~~l~~st~~L~k~l~~~~~~ 156 (169)
+++.|+.+|+|.+-+++.|...+..
T Consensus 2 i~dIA~~agvS~~TVSr~ln~~~~v 26 (46)
T PF00356_consen 2 IKDIAREAGVSKSTVSRVLNGPPRV 26 (46)
T ss_dssp HHHHHHHHTSSHHHHHHHHTTCSSS
T ss_pred HHHHHHHHCcCHHHHHHHHhCCCCC
Confidence 5789999999999999999987643
No 69
>PF07453 NUMOD1: NUMOD1 domain; InterPro: IPR010896 This helix-turn-helix-containing DNA-binding domain is found associated in homing nucleases [].
Probab=62.16 E-value=8.1 Score=23.22 Aligned_cols=21 Identities=33% Similarity=0.517 Sum_probs=17.3
Q ss_pred CCHHHHHHHhcCChhHHHHHH
Q 043121 130 GSVSEAAKLLWLSTGALSRLI 150 (169)
Q Consensus 130 ~~~~~aa~~l~~st~~L~k~l 150 (169)
.++.+||+.||++.+-+.+.|
T Consensus 17 ~Si~eAa~~l~i~~~~I~~~l 37 (37)
T PF07453_consen 17 DSIREAARYLGISHSTISKYL 37 (37)
T ss_pred cCHHHHHHHhCCCHHHHHHhC
Confidence 368899999999999877653
No 70
>PRK15424 propionate catabolism operon regulatory protein PrpR; Provisional
Probab=61.88 E-value=11 Score=35.76 Aligned_cols=35 Identities=23% Similarity=0.252 Sum_probs=31.0
Q ss_pred HHHHHHHHHhcCCHHHHHHHhcCChhHHHHHHhcC
Q 043121 119 QALLDLIFAVEGSVSEAAKLLWLSTGALSRLILSD 153 (169)
Q Consensus 119 ~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~~~ 153 (169)
..+...|..++|+.+.||+.||+|++-|-|-|++.
T Consensus 500 ~~I~~~L~~~~Gn~~~aA~~LGIsRtTL~RkLk~~ 534 (538)
T PRK15424 500 ATLQQALERFNGDKTAAANYLGISRTTLWRRLKAE 534 (538)
T ss_pred HHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHHh
Confidence 45778899999999999999999999999888764
No 71
>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=61.72 E-value=19 Score=22.77 Aligned_cols=37 Identities=19% Similarity=0.171 Sum_probs=26.6
Q ss_pred hhHHHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHHh
Q 043121 115 SLGMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLIL 151 (169)
Q Consensus 115 ~~~l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~ 151 (169)
|+-.+.++-+....+.+.+++|+.||+|.+.+-+.+.
T Consensus 12 ~~~~r~i~~l~~~~g~s~~eIa~~l~~s~~~v~~~l~ 48 (54)
T PF08281_consen 12 PERQREIFLLRYFQGMSYAEIAEILGISESTVKRRLR 48 (54)
T ss_dssp -HHHHHHHHHHHTS---HHHHHHHCTS-HHHHHHHHH
T ss_pred CHHHHHHHHHHHHHCcCHHHHHHHHCcCHHHHHHHHH
Confidence 4556778888889999999999999999998876553
No 72
>PRK09940 transcriptional regulator YdeO; Provisional
Probab=61.56 E-value=16 Score=31.63 Aligned_cols=49 Identities=10% Similarity=0.141 Sum_probs=37.4
Q ss_pred HHHHHHHHHhcCCHHHHHHHhcCChhHHHHHHhcC-hhHHHHHHHhhhhcc
Q 043121 119 QALLDLIFAVEGSVSEAAKLLWLSTGALSRLILSD-DSHQIAVNELRTSKV 168 (169)
Q Consensus 119 ~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~~~-~~~~~~~n~~R~~~~ 168 (169)
+.+.+.+ ...+++++.|+.+|+|++.|.|+++.. -+....+|+.|-.+.
T Consensus 141 ~~I~~~~-~~~~tl~~LA~~~gmS~s~l~R~FK~~G~T~~eyl~~~Rl~~A 190 (253)
T PRK09940 141 NIVNMKL-AHPWKLKDICDCLYISESLLKKKLKQEQTTFSQILLDARMQHA 190 (253)
T ss_pred HHHHHhh-cCCCCHHHHHHHHCcCHHHHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 3333333 457999999999999999999999864 456778888887653
No 73
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=61.27 E-value=12 Score=22.27 Aligned_cols=23 Identities=35% Similarity=0.427 Sum_probs=20.0
Q ss_pred CHHHHHHHhcCChhHHHHHHhcC
Q 043121 131 SVSEAAKLLWLSTGALSRLILSD 153 (169)
Q Consensus 131 ~~~~aa~~l~~st~~L~k~l~~~ 153 (169)
++.++|+.||+|++.|-+.+..-
T Consensus 2 s~~e~a~~lgvs~~tl~~~~~~g 24 (49)
T cd04762 2 TTKEAAELLGVSPSTLRRWVKEG 24 (49)
T ss_pred CHHHHHHHHCcCHHHHHHHHHcC
Confidence 57889999999999999988654
No 74
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=60.86 E-value=19 Score=23.31 Aligned_cols=33 Identities=21% Similarity=0.214 Sum_probs=25.3
Q ss_pred HHHHHHHhcCCHHHHHHHhcCChhHHHHHHhcC
Q 043121 121 LLDLIFAVEGSVSEAAKLLWLSTGALSRLILSD 153 (169)
Q Consensus 121 ~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~~~ 153 (169)
+-..+...+.+..+.|+..|+|.+.|.+++...
T Consensus 2 L~~~m~~~~it~~~La~~~gis~~tl~~~~~~~ 34 (63)
T PF13443_consen 2 LKELMAERGITQKDLARKTGISRSTLSRILNGK 34 (63)
T ss_dssp HHHHHHHTT--HHHHHHHHT--HHHHHHHHTTT
T ss_pred HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhcc
Confidence 345677888899999999999999999999987
No 75
>TIGR02329 propionate_PrpR propionate catabolism operon regulatory protein PrpR. At least five distinct pathways exists for the catabolism of propionate by way of propionyl-CoA. Members of this family represent the transcriptional regulatory protein PrpR, whose gene is found in most cases divergently transcribed from an operon for the methylcitric acid cycle of propionate catabolism. 2-methylcitric acid, a catabolite by this pathway, is a coactivator of PrpR.
Probab=60.39 E-value=13 Score=35.16 Aligned_cols=34 Identities=26% Similarity=0.180 Sum_probs=29.8
Q ss_pred HHHHHHHHHhcCCHHHHHHHhcCChhHHHHHHhc
Q 043121 119 QALLDLIFAVEGSVSEAAKLLWLSTGALSRLILS 152 (169)
Q Consensus 119 ~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~~ 152 (169)
..+...|..++|+.+.||+.||+|++-|-|-|++
T Consensus 493 ~~I~~aL~~~~Gn~~~aA~~LGIsRtTL~Rklk~ 526 (526)
T TIGR02329 493 LAVRAALERFGGDRDAAAKALGISRTTLWRRLKA 526 (526)
T ss_pred HHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHhC
Confidence 4577889999999999999999999999887763
No 76
>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional
Probab=60.32 E-value=13 Score=35.18 Aligned_cols=35 Identities=23% Similarity=0.306 Sum_probs=30.9
Q ss_pred HHHHHHHHHhcCCHHHHHHHhcCChhHHHHHHhcC
Q 043121 119 QALLDLIFAVEGSVSEAAKLLWLSTGALSRLILSD 153 (169)
Q Consensus 119 ~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~~~ 153 (169)
+.+.+.|...+|+++.||+.||+|++-|-|-|++.
T Consensus 594 ~~i~~al~~~~gn~~~aA~~LGisR~TLyrklk~~ 628 (638)
T PRK11388 594 EAIINAAQVCGGRIQEMAALLGIGRTTLWRKMKQH 628 (638)
T ss_pred HHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHc
Confidence 44778889999999999999999999999888763
No 77
>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=59.16 E-value=10 Score=27.99 Aligned_cols=24 Identities=33% Similarity=0.193 Sum_probs=21.6
Q ss_pred cCCHHHHHHHhcCChhHHHHHHhc
Q 043121 129 EGSVSEAAKLLWLSTGALSRLILS 152 (169)
Q Consensus 129 ~~~~~~aa~~l~~st~~L~k~l~~ 152 (169)
.++++.||+.|++|.+.+++-|+.
T Consensus 16 ~gSis~AA~~L~iS~stvs~~I~~ 39 (99)
T TIGR00637 16 MGSISQAAKDAGISYKSAWDYIRA 39 (99)
T ss_pred hCCHHHHHHHHCCCHHHHHHHHHH
Confidence 789999999999999999987764
No 78
>PRK13501 transcriptional activator RhaR; Provisional
Probab=58.87 E-value=20 Score=29.99 Aligned_cols=47 Identities=13% Similarity=0.068 Sum_probs=37.3
Q ss_pred HHHHHHhcCCHHHHHHHhcCChhHHHHHHhcC--hhHHHHHHHhhhhcc
Q 043121 122 LDLIFAVEGSVSEAAKLLWLSTGALSRLILSD--DSHQIAVNELRTSKV 168 (169)
Q Consensus 122 lD~l~~~~~~~~~aa~~l~~st~~L~k~l~~~--~~~~~~~n~~R~~~~ 168 (169)
++...+-..++++.|+.+++|++.|.+++++. -+....+|+.|-.+.
T Consensus 185 I~~~~~e~~sl~~lA~~~~lS~~~l~r~Fk~~~G~T~~qyi~~~Ri~~A 233 (290)
T PRK13501 185 LQQSLGAYFDMADFCHKNQLVERSLKQLFRQQTGMSISHYLRQIRLCHA 233 (290)
T ss_pred HHHhhccCCCHHHHHHHHCcCHHHHHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 33334556889999999999999999999975 567788888887653
No 79
>TIGR02040 PpsR-CrtJ transcriptional regulator PpsR. This model represents the transcriptional regulator PpsR which is strictly associated with photosynthetic proteobacteria and found in photosynthetic operons. PpsR has been reported to be a repressor. These proteins contain a Helix-Turn_Helix motif of the "fis" type (pfam02954).
Probab=58.86 E-value=15 Score=32.55 Aligned_cols=33 Identities=18% Similarity=0.077 Sum_probs=28.4
Q ss_pred HHHHHHHhcCCHHHHHHHhcCChhHHHHHHhcC
Q 043121 121 LLDLIFAVEGSVSEAAKLLWLSTGALSRLILSD 153 (169)
Q Consensus 121 ~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~~~ 153 (169)
+...+..++|+.+.||+.||+|++.|.+.+++.
T Consensus 408 i~~~l~~~~~n~~~aa~~lgi~r~~l~~~l~~~ 440 (442)
T TIGR02040 408 IEAALELTRDNRASAAEILGLSRQSLYVKLRRY 440 (442)
T ss_pred HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHHHh
Confidence 346677789999999999999999999988764
No 80
>PF02042 RWP-RK: RWP-RK domain; InterPro: IPR003035 This domain is named RWP-RK after a conserved motif at the C terminus of the domain. The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development [].
Probab=58.72 E-value=22 Score=23.92 Aligned_cols=31 Identities=32% Similarity=0.144 Sum_probs=24.3
Q ss_pred HHHHHhcCCHHHHHHHhcCChhHHHHHHhcC
Q 043121 123 DLIFAVEGSVSEAAKLLWLSTGALSRLILSD 153 (169)
Q Consensus 123 D~l~~~~~~~~~aa~~l~~st~~L~k~l~~~ 153 (169)
|+-.-......+||+.||+|++.|-|.-+.+
T Consensus 9 ~L~~~fhlp~~eAA~~Lgv~~T~LKr~CR~~ 39 (52)
T PF02042_consen 9 DLSQYFHLPIKEAAKELGVSVTTLKRRCRRL 39 (52)
T ss_pred HHHHHhCCCHHHHHHHhCCCHHHHHHHHHHc
Confidence 4444556778999999999999999876543
No 81
>TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
Probab=58.42 E-value=26 Score=21.59 Aligned_cols=34 Identities=9% Similarity=-0.091 Sum_probs=29.1
Q ss_pred HHHHHHHHhcCCHHHHHHHhcCChhHHHHHHhcC
Q 043121 120 ALLDLIFAVEGSVSEAAKLLWLSTGALSRLILSD 153 (169)
Q Consensus 120 ~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~~~ 153 (169)
.+-+.....+++.++.|+.+|+|++.+.++....
T Consensus 6 ~l~~~r~~~gltq~~lA~~~gvs~~~vs~~e~g~ 39 (58)
T TIGR03070 6 LVRARRKALGLTQADLADLAGVGLRFIRDVENGK 39 (58)
T ss_pred HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCCC
Confidence 3556677889999999999999999999998764
No 82
>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=58.00 E-value=25 Score=22.03 Aligned_cols=30 Identities=27% Similarity=0.109 Sum_probs=24.8
Q ss_pred HHHHhcCCHHHHHHHhcCChhHHHHHHhcC
Q 043121 124 LIFAVEGSVSEAAKLLWLSTGALSRLILSD 153 (169)
Q Consensus 124 ~l~~~~~~~~~aa~~l~~st~~L~k~l~~~ 153 (169)
.+...+.+..+.|+.+|+|.+.+.+++..+
T Consensus 4 ~r~~~gls~~~la~~~gis~~~i~~~~~g~ 33 (55)
T PF01381_consen 4 LRKEKGLSQKELAEKLGISRSTISRIENGK 33 (55)
T ss_dssp HHHHTTS-HHHHHHHHTS-HHHHHHHHTTS
T ss_pred HHHHcCCCHHHHHHHhCCCcchhHHHhcCC
Confidence 456788999999999999999999999874
No 83
>PRK09393 ftrA transcriptional activator FtrA; Provisional
Probab=57.76 E-value=33 Score=29.38 Aligned_cols=54 Identities=17% Similarity=0.055 Sum_probs=42.6
Q ss_pred hhHHHHHHHHHHHh---cCCHHHHHHHhcCChhHHHHHHhcC--hhHHHHHHHhhhhcc
Q 043121 115 SLGMQALLDLIFAV---EGSVSEAAKLLWLSTGALSRLILSD--DSHQIAVNELRTSKV 168 (169)
Q Consensus 115 ~~~l~~~lD~l~~~---~~~~~~aa~~l~~st~~L~k~l~~~--~~~~~~~n~~R~~~~ 168 (169)
...+..+++.+... ..++++.|+.+|+|+..|.++++.. .+....++++|-.+.
T Consensus 217 ~~~~~~~~~~i~~~~~~~~sl~~lA~~~~~S~~~l~r~fk~~~g~s~~~~~~~~Rl~~A 275 (322)
T PRK09393 217 SDRLGPLIDWMRAHLAEPHTVASLAARAAMSPRTFLRRFEAATGMTPAEWLLRERLARA 275 (322)
T ss_pred hHHHHHHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 44566777777664 4679999999999999999999985 666788888887653
No 84
>PRK09978 DNA-binding transcriptional regulator GadX; Provisional
Probab=57.47 E-value=17 Score=31.78 Aligned_cols=51 Identities=18% Similarity=0.173 Sum_probs=38.1
Q ss_pred HHHHHHHHHH---hcCCHHHHHHHhcCChhHHHHHHhcC-hhHHHHHHHhhhhcc
Q 043121 118 MQALLDLIFA---VEGSVSEAAKLLWLSTGALSRLILSD-DSHQIAVNELRTSKV 168 (169)
Q Consensus 118 l~~~lD~l~~---~~~~~~~aa~~l~~st~~L~k~l~~~-~~~~~~~n~~R~~~~ 168 (169)
+..+++.|.. ..+++++.|..+|+|+..|.|+++.. -+....+++.|-.+.
T Consensus 144 ~~~v~~yI~~~~~~~lsl~~lA~~~g~S~~~L~R~Fk~~G~S~~~yl~~~Rl~~A 198 (274)
T PRK09978 144 RTRVCTVINNNIAHEWTLARIASELLMSPSLLKKKLREEETSYSQLLTECRMQRA 198 (274)
T ss_pred HHHHHHHHHhcccCCCCHHHHHHHHCcCHHHHHHHHHhcCCCHHHHHHHHHHHHH
Confidence 3445554443 47889999999999999999999864 456677888876653
No 85
>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=57.30 E-value=24 Score=27.47 Aligned_cols=47 Identities=23% Similarity=0.107 Sum_probs=41.1
Q ss_pred hhHHHHHHHHHHHhcCC---HHHHHHHhcCChhHHHHHHhcChhHHHHHH
Q 043121 115 SLGMQALLDLIFAVEGS---VSEAAKLLWLSTGALSRLILSDDSHQIAVN 161 (169)
Q Consensus 115 ~~~l~~~lD~l~~~~~~---~~~aa~~l~~st~~L~k~l~~~~~~~~~~n 161 (169)
-..++..++++...|++ +.+.|+..|+|++.|-.-+.+-..++.+|=
T Consensus 11 ~~Il~aA~~lf~e~G~~~~s~~~IA~~agvs~~~lY~hF~sKe~L~~av~ 60 (202)
T TIGR03613 11 KAILSAALDTFSRFGFHGTSLEQIAELAGVSKTNLLYYFPSKDALYLAVL 60 (202)
T ss_pred HHHHHHHHHHHHHhCcccCCHHHHHHHhCCCHHHHHHHcCCHHHHHHHHH
Confidence 35788999999999887 889999999999999999998888887763
No 86
>PF10213 MRP-S28: Mitochondrial ribosomal subunit protein ; InterPro: IPR019349 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 entry represents a conserved region of approx. 125 residues of one of the proteins that makes up the small subunit of the mitochondrial ribosome. In Saccharomyces cerevisiae (Baker's yeast) it is mitochondrial ribosomal protein S24 whereas in humans it is S35.
Probab=57.29 E-value=36 Score=26.57 Aligned_cols=32 Identities=9% Similarity=-0.062 Sum_probs=26.7
Q ss_pred CCc-eEEEEcccCCHHHHHHHHHHHHhCCChhh
Q 043121 56 PTG-VIAHAAEDRSQHKNHASSVNLDAYSPPPQ 87 (169)
Q Consensus 56 ptG-i~v~~~~~RSq~~Nr~~Al~~L~~L~~~e 87 (169)
.+| |.+.|...-++.+|+.-+...|..|+...
T Consensus 59 ~~d~l~i~sdr~~~~~qN~~~l~~~l~~L~~EA 91 (127)
T PF10213_consen 59 ETDILKISSDRFPTRAQNKKYLSDLLTRLIHEA 91 (127)
T ss_pred CCCEEEEecccCCCHHHHHHHHHHHHHHHHHHH
Confidence 367 89999999999999999999987665443
No 87
>PRK15121 right oriC-binding transcriptional activator; Provisional
Probab=57.28 E-value=25 Score=29.77 Aligned_cols=50 Identities=20% Similarity=0.075 Sum_probs=38.7
Q ss_pred HHHHHHHHHHh---cCCHHHHHHHhcCChhHHHHHHhcC--hhHHHHHHHhhhhc
Q 043121 118 MQALLDLIFAV---EGSVSEAAKLLWLSTGALSRLILSD--DSHQIAVNELRTSK 167 (169)
Q Consensus 118 l~~~lD~l~~~---~~~~~~aa~~l~~st~~L~k~l~~~--~~~~~~~n~~R~~~ 167 (169)
+..++|.|.+. ..++.+.|+.+|+|+..|.|+++.. -+....++.+|..+
T Consensus 7 i~~~~~~i~~~~~~~~~l~~lA~~~~~S~~~l~r~F~~~~g~s~~~yi~~~Rl~~ 61 (289)
T PRK15121 7 IRDLLIWLEGHLDQPLSLDNVAAKAGYSKWHLQRMFKDVTGHAIGAYIRARRLSK 61 (289)
T ss_pred HHHHHHHHHhcccCCCCHHHHHHHHCcCHHHHHHHHHHHHCcCHHHHHHHHHHHH
Confidence 44455555533 5789999999999999999999984 77778888887664
No 88
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=56.20 E-value=13 Score=22.69 Aligned_cols=22 Identities=23% Similarity=0.333 Sum_probs=17.6
Q ss_pred CHHHHHHHhcCChhHHHHHHhc
Q 043121 131 SVSEAAKLLWLSTGALSRLILS 152 (169)
Q Consensus 131 ~~~~aa~~l~~st~~L~k~l~~ 152 (169)
+-.+.|.++|+++.-++|+|.+
T Consensus 4 tr~diA~~lG~t~ETVSR~l~~ 25 (32)
T PF00325_consen 4 TRQDIADYLGLTRETVSRILKK 25 (32)
T ss_dssp -HHHHHHHHTS-HHHHHHHHHH
T ss_pred CHHHHHHHhCCcHHHHHHHHHH
Confidence 4578999999999999998864
No 89
>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=54.86 E-value=30 Score=21.41 Aligned_cols=32 Identities=19% Similarity=0.199 Sum_probs=23.4
Q ss_pred HHHHHHHHhc-CCHHHHHHHhcCChhHHHHHHh
Q 043121 120 ALLDLIFAVE-GSVSEAAKLLWLSTGALSRLIL 151 (169)
Q Consensus 120 ~~lD~l~~~~-~~~~~aa~~l~~st~~L~k~l~ 151 (169)
.+|+.|...+ -+.++.|+.+|+|.+.+.+.|+
T Consensus 7 ~Il~~l~~~~~~t~~ela~~~~is~~tv~~~l~ 39 (48)
T PF13412_consen 7 KILNYLRENPRITQKELAEKLGISRSTVNRYLK 39 (48)
T ss_dssp HHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 4566666644 5788999999999999887765
No 90
>PRK09726 antitoxin HipB; Provisional
Probab=54.72 E-value=57 Score=23.01 Aligned_cols=37 Identities=16% Similarity=-0.024 Sum_probs=31.3
Q ss_pred HHHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHHhcC
Q 043121 117 GMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLILSD 153 (169)
Q Consensus 117 ~l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~~~ 153 (169)
+-..+-......+++..++|+.+|+|.+.+.++....
T Consensus 13 l~~~lk~~R~~~gltq~elA~~~gvs~~tis~~e~g~ 49 (88)
T PRK09726 13 LANAMKLVRQQNGWTQSELAKKIGIKQATISNFENNP 49 (88)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCC
Confidence 3355666778889999999999999999999998854
No 91
>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=54.40 E-value=34 Score=19.69 Aligned_cols=33 Identities=24% Similarity=0.129 Sum_probs=27.0
Q ss_pred HHHHHHHhcCCHHHHHHHhcCChhHHHHHHhcC
Q 043121 121 LLDLIFAVEGSVSEAAKLLWLSTGALSRLILSD 153 (169)
Q Consensus 121 ~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~~~ 153 (169)
+.+.+...+.+....|..+|+|...+.+++...
T Consensus 4 l~~~~~~~~~s~~~~a~~~~~~~~~v~~~~~g~ 36 (58)
T cd00093 4 LKELRKEKGLTQEELAEKLGVSRSTISRIENGK 36 (58)
T ss_pred HHHHHHHcCCCHHHHHHHHCCCHHHHHHHHcCC
Confidence 344566678889999999999999999988765
No 92
>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=53.92 E-value=19 Score=22.95 Aligned_cols=32 Identities=28% Similarity=0.429 Sum_probs=24.9
Q ss_pred HHHHHHHHhcCC--HHHHHHHhcCChhHHHHHHh
Q 043121 120 ALLDLIFAVEGS--VSEAAKLLWLSTGALSRLIL 151 (169)
Q Consensus 120 ~~lD~l~~~~~~--~~~aa~~l~~st~~L~k~l~ 151 (169)
.+||.+...+.. +++.|+.+|++.+-+-|+|.
T Consensus 7 ~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~ 40 (52)
T PF09339_consen 7 RILEALAESGGPLTLSEIARALGLPKSTVHRLLQ 40 (52)
T ss_dssp HHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 366777777764 89999999999998888765
No 93
>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=53.88 E-value=31 Score=17.93 Aligned_cols=24 Identities=38% Similarity=0.375 Sum_probs=19.8
Q ss_pred HHhcCCHHHHHHHhcCChhHHHHH
Q 043121 126 FAVEGSVSEAAKLLWLSTGALSRL 149 (169)
Q Consensus 126 ~~~~~~~~~aa~~l~~st~~L~k~ 149 (169)
...+.++..+|+.+++|.+.+.+.
T Consensus 18 ~~~~~s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 18 LAAGESVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHh
Confidence 345678999999999999988764
No 94
>COG2204 AtoC Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains [Signal transduction mechanisms]
Probab=53.85 E-value=19 Score=33.95 Aligned_cols=36 Identities=31% Similarity=0.245 Sum_probs=31.6
Q ss_pred HHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHHhcC
Q 043121 118 MQALLDLIFAVEGSVSEAAKLLWLSTGALSRLILSD 153 (169)
Q Consensus 118 l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~~~ 153 (169)
-+.+.+.|...+|+++.+|+.||++++.|-+-|+++
T Consensus 419 r~~I~~aL~~~~g~~~~aA~~LGi~R~tLy~Klk~~ 454 (464)
T COG2204 419 RQLILQALERTGGNKSEAAERLGISRKTLYRKLKEY 454 (464)
T ss_pred HHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHh
Confidence 344778899999999999999999999999888765
No 95
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=53.36 E-value=33 Score=19.59 Aligned_cols=31 Identities=26% Similarity=0.124 Sum_probs=26.2
Q ss_pred HHHHHhcCCHHHHHHHhcCChhHHHHHHhcC
Q 043121 123 DLIFAVEGSVSEAAKLLWLSTGALSRLILSD 153 (169)
Q Consensus 123 D~l~~~~~~~~~aa~~l~~st~~L~k~l~~~ 153 (169)
+.+...+.+.++.|+.+|++.+.+.++....
T Consensus 4 ~~~~~~~~s~~~la~~~~i~~~~i~~~~~~~ 34 (56)
T smart00530 4 ELREEKGLTQEELAEKLGVSRSTLSRIENGK 34 (56)
T ss_pred HHHHHcCCCHHHHHHHhCCCHHHHHHHHCCC
Confidence 4566678899999999999999999988764
No 96
>PHA02591 hypothetical protein; Provisional
Probab=51.55 E-value=23 Score=26.22 Aligned_cols=32 Identities=22% Similarity=0.142 Sum_probs=27.2
Q ss_pred HHHHHHHhcCCHHHHHHHhcCChhHHHHHHhc
Q 043121 121 LLDLIFAVEGSVSEAAKLLWLSTGALSRLILS 152 (169)
Q Consensus 121 ~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~~ 152 (169)
+--.|...+.+++.+|..||+|-.++.+.+.+
T Consensus 51 vA~eL~eqGlSqeqIA~~LGVsqetVrKYL~~ 82 (83)
T PHA02591 51 VTHELARKGFTVEKIASLLGVSVRKVRRYLES 82 (83)
T ss_pred HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHhc
Confidence 34456788999999999999999999998865
No 97
>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=50.86 E-value=47 Score=23.76 Aligned_cols=44 Identities=14% Similarity=-0.022 Sum_probs=33.3
Q ss_pred hhHHHHHHHHHH-HhcCCHHHHHHHhcCChhHHHHHHhcChhHHH
Q 043121 115 SLGMQALLDLIF-AVEGSVSEAAKLLWLSTGALSRLILSDDSHQI 158 (169)
Q Consensus 115 ~~~l~~~lD~l~-~~~~~~~~aa~~l~~st~~L~k~l~~~~~~~~ 158 (169)
|+..+.++.+.. ..+.+++++|+.||+|.+.+-+.+...+..=.
T Consensus 17 ~~~~r~af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~~~~~~~ 61 (73)
T TIGR03879 17 DSLAEAAAALAREEAGKTASEIAEELGRTEQTVRNHLKGETKAGG 61 (73)
T ss_pred CHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhcCcccch
Confidence 445555666653 47889999999999999999998887655433
No 98
>PF12833 HTH_18: Helix-turn-helix domain; PDB: 2K9S_A 3LSG_C 3OIO_A 1D5Y_B 3GBG_A 3OOU_A 1BL0_A 1XS9_A 3MN2_B 3MKL_B ....
Probab=50.75 E-value=17 Score=24.52 Aligned_cols=32 Identities=31% Similarity=0.284 Sum_probs=22.1
Q ss_pred HHHhcCChhHHHHHHhc--ChhHHHHHHHhhhhc
Q 043121 136 AKLLWLSTGALSRLILS--DDSHQIAVNELRTSK 167 (169)
Q Consensus 136 a~~l~~st~~L~k~l~~--~~~~~~~~n~~R~~~ 167 (169)
|+.+|+|...|.++++. ..+....+++.|..+
T Consensus 2 A~~~~~s~~~l~~~f~~~~g~s~~~~~~~~R~~~ 35 (81)
T PF12833_consen 2 ADELGMSERYLSRIFKKETGMSFKQYLRELRLQR 35 (81)
T ss_dssp HHHCTS-HHHHHHHHHHHHSS-HHHHHHHHHHHH
T ss_pred hHHhCcCHHHHHHHHHHHHCcCHHHHHHHHHHHH
Confidence 67888888888888876 456666667666554
No 99
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=50.35 E-value=22 Score=27.11 Aligned_cols=41 Identities=22% Similarity=0.083 Sum_probs=32.6
Q ss_pred CCCCchhHHHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHHhcC
Q 043121 110 NNPKFSLGMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLILSD 153 (169)
Q Consensus 110 Yn~~f~~~l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~~~ 153 (169)
||+.|..- +...+...+.+..+.|+..|+|.+.++++....
T Consensus 2 ~~~i~~~~---l~~ll~~~Glsq~eLA~~~Gis~~~is~iE~g~ 42 (120)
T PRK13890 2 YNYIFFTN---VLRLLDERHMTKKELSERSGVSISFLSDLTTGK 42 (120)
T ss_pred HHHHHHHH---HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCC
Confidence 55555443 556677889999999999999999999998753
No 100
>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []. Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.
Probab=50.21 E-value=25 Score=24.39 Aligned_cols=26 Identities=23% Similarity=0.112 Sum_probs=20.2
Q ss_pred HhcCCHHHHHHHhcCChhHHHHHHhc
Q 043121 127 AVEGSVSEAAKLLWLSTGALSRLILS 152 (169)
Q Consensus 127 ~~~~~~~~aa~~l~~st~~L~k~l~~ 152 (169)
....++.+.|+..++|++.++||.++
T Consensus 32 ~~~~si~elA~~~~vS~sti~Rf~kk 57 (77)
T PF01418_consen 32 IAFMSISELAEKAGVSPSTIVRFCKK 57 (77)
T ss_dssp HCT--HHHHHHHCTS-HHHHHHHHHH
T ss_pred HHHccHHHHHHHcCCCHHHHHHHHHH
Confidence 34678999999999999999999875
No 101
>PRK11062 nhaR transcriptional activator NhaR; Provisional
Probab=50.10 E-value=20 Score=29.87 Aligned_cols=25 Identities=36% Similarity=0.462 Sum_probs=22.2
Q ss_pred hcCCHHHHHHHhcCChhHHHHHHhc
Q 043121 128 VEGSVSEAAKLLWLSTGALSRLILS 152 (169)
Q Consensus 128 ~~~~~~~aa~~l~~st~~L~k~l~~ 152 (169)
-.|+++.||+.|++|.+++++-|+.
T Consensus 17 e~gs~s~AA~~L~isqpavS~~I~~ 41 (296)
T PRK11062 17 KEGSVVGAAEALFLTPQTITGQIKA 41 (296)
T ss_pred hcCCHHHHHHHhCCChHHHHHHHHH
Confidence 4789999999999999999988764
No 102
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=49.97 E-value=46 Score=22.53 Aligned_cols=39 Identities=26% Similarity=0.263 Sum_probs=28.4
Q ss_pred CchhHHHHHHHHHHHhc-CCHHHHHHHhcCChhHHHHHHh
Q 043121 113 KFSLGMQALLDLIFAVE-GSVSEAAKLLWLSTGALSRLIL 151 (169)
Q Consensus 113 ~f~~~l~~~lD~l~~~~-~~~~~aa~~l~~st~~L~k~l~ 151 (169)
....-.-.+|..|...+ ..++++|+.+++|.+.+.+.|+
T Consensus 7 ~l~~~~~~il~~l~~~~~~~~~~la~~~~~s~~~i~~~l~ 46 (101)
T smart00347 7 GLTPTQFLVLRILYEEGPLSVSELAKRLGVSPSTVTRVLD 46 (101)
T ss_pred CCCHHHHHHHHHHHHcCCcCHHHHHHHHCCCchhHHHHHH
Confidence 33444455677777654 5889999999999988887765
No 103
>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=49.91 E-value=19 Score=25.79 Aligned_cols=35 Identities=20% Similarity=0.018 Sum_probs=21.0
Q ss_pred HhcCCHHHHHHHhcCChhHHHHHHh---cChhHHHHHH
Q 043121 127 AVEGSVSEAAKLLWLSTGALSRLIL---SDDSHQIAVN 161 (169)
Q Consensus 127 ~~~~~~~~aa~~l~~st~~L~k~l~---~~~~~~~~~n 161 (169)
+.+|...++|+.||.|.+-++++|. .-+.+..+|.
T Consensus 1 ~~G~tq~eIA~~lGks~s~Vs~~l~Ll~lP~~i~~~v~ 38 (93)
T PF08535_consen 1 EFGWTQEEIAKRLGKSRSWVSNHLALLDLPEEIKELVR 38 (93)
T ss_dssp HTT--HHHHHHHTT--HHHHHHHHGGGS--HHHHHHHH
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHcCCHHHHHHHH
Confidence 4678899999999999988877664 3444444444
No 104
>PRK15435 bifunctional DNA-binding transcriptional dual regulator/O6-methylguanine-DNA methyltransferase; Provisional
Probab=48.35 E-value=39 Score=30.31 Aligned_cols=52 Identities=13% Similarity=0.045 Sum_probs=38.4
Q ss_pred hHHHHHHHHHHH-hcCCHHHHHHHhcCChhHHHHHHhcC--hhHHHHHHHhhhhc
Q 043121 116 LGMQALLDLIFA-VEGSVSEAAKLLWLSTGALSRLILSD--DSHQIAVNELRTSK 167 (169)
Q Consensus 116 ~~l~~~lD~l~~-~~~~~~~aa~~l~~st~~L~k~l~~~--~~~~~~~n~~R~~~ 167 (169)
..+..+++.|.. ...++.+.|+.+|+|+..|.|+++.. -+....++.+|..+
T Consensus 85 ~~i~~a~~~I~~~~~lsl~eLA~~lG~S~~~L~R~Fkk~~G~TP~~yl~~~Rl~~ 139 (353)
T PRK15435 85 DKITHACRLLEQETPVTLEALADQVAMSPFHLHRLFKATTGMTPKAWQQAWRARR 139 (353)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHCCCHHHHHHHHHHHHCcCHHHHHHHHHHHH
Confidence 356777777754 45679999999999999999999884 44555556665543
No 105
>PRK04217 hypothetical protein; Provisional
Probab=48.02 E-value=44 Score=25.52 Aligned_cols=36 Identities=25% Similarity=0.133 Sum_probs=30.4
Q ss_pred HHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHHhcC
Q 043121 118 MQALLDLIFAVEGSVSEAAKLLWLSTGALSRLILSD 153 (169)
Q Consensus 118 l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~~~ 153 (169)
-.+++.++...+.+++++|+.||+|.+.+-+.|..-
T Consensus 47 ereai~l~~~eGlS~~EIAk~LGIS~sTV~r~L~RA 82 (110)
T PRK04217 47 EFEALRLVDYEGLTQEEAGKRMGVSRGTVWRALTSA 82 (110)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 356777777788899999999999999999888753
No 106
>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=47.23 E-value=19 Score=29.69 Aligned_cols=25 Identities=32% Similarity=0.424 Sum_probs=22.3
Q ss_pred hcCCHHHHHHHhcCChhHHHHHHhc
Q 043121 128 VEGSVSEAAKLLWLSTGALSRLILS 152 (169)
Q Consensus 128 ~~~~~~~aa~~l~~st~~L~k~l~~ 152 (169)
-.|+++.||+.|++|.+++++-|++
T Consensus 16 ~~gS~s~AA~~L~isq~avS~~I~~ 40 (300)
T TIGR02424 16 RQGSVKRAAEALHITQPAVSKTLRE 40 (300)
T ss_pred HhCCHHHHHHHhCCChHHHHHHHHH
Confidence 3679999999999999999998864
No 107
>PRK09986 DNA-binding transcriptional activator XapR; Provisional
Probab=46.93 E-value=15 Score=29.96 Aligned_cols=24 Identities=33% Similarity=0.144 Sum_probs=21.7
Q ss_pred cCCHHHHHHHhcCChhHHHHHHhc
Q 043121 129 EGSVSEAAKLLWLSTGALSRLILS 152 (169)
Q Consensus 129 ~~~~~~aa~~l~~st~~L~k~l~~ 152 (169)
.|+++.||+.|++|.+++++-|++
T Consensus 21 ~gs~t~AA~~L~itq~avS~~i~~ 44 (294)
T PRK09986 21 ELHFGRAAARLNISQPPLSIHIKE 44 (294)
T ss_pred hcCHHHHHHHhCCCCCHHHHHHHH
Confidence 379999999999999999998864
No 108
>PRK15092 DNA-binding transcriptional repressor LrhA; Provisional
Probab=46.63 E-value=24 Score=30.05 Aligned_cols=26 Identities=19% Similarity=0.137 Sum_probs=23.0
Q ss_pred HhcCCHHHHHHHhcCChhHHHHHHhc
Q 043121 127 AVEGSVSEAAKLLWLSTGALSRLILS 152 (169)
Q Consensus 127 ~~~~~~~~aa~~l~~st~~L~k~l~~ 152 (169)
+-.++++.||+.|++|.+++++-|+.
T Consensus 23 ~e~gs~s~AA~~L~iSQpavS~~I~~ 48 (310)
T PRK15092 23 ADLNTFAAAAAAVCRTQSAVSQQMQR 48 (310)
T ss_pred HHcCCHHHHHHHhCCChHHHHHHHHH
Confidence 45788999999999999999998864
No 109
>PRK10296 DNA-binding transcriptional regulator ChbR; Provisional
Probab=46.59 E-value=32 Score=28.47 Aligned_cols=51 Identities=18% Similarity=0.163 Sum_probs=37.7
Q ss_pred HHHHHHHHHHHh----cCCHHHHHHHhcCChhHHHHHHhcC--hhHHHHHHHhhhhc
Q 043121 117 GMQALLDLIFAV----EGSVSEAAKLLWLSTGALSRLILSD--DSHQIAVNELRTSK 167 (169)
Q Consensus 117 ~l~~~lD~l~~~----~~~~~~aa~~l~~st~~L~k~l~~~--~~~~~~~n~~R~~~ 167 (169)
-+..+++.+... ..++++.|..+++|+.-|.+++++. -+....+|+.|..+
T Consensus 172 ~~~~~i~~i~~~~~~~~~~l~~lA~~~~~s~~~l~r~fk~~~G~t~~~yi~~~Rl~~ 228 (278)
T PRK10296 172 WLKATVEKMHDKEQFSESALENMVRLSGKSQEYLTRATRRYYGKTPMQIINEIRINF 228 (278)
T ss_pred HHHHHHHHHHhccccChhhHHHHHHHhCCCHHHHHHHHHHHHCcCHHHHHHHHHHHH
Confidence 445566655432 2357788899999999999999987 77778888888654
No 110
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=46.39 E-value=71 Score=23.71 Aligned_cols=36 Identities=11% Similarity=-0.073 Sum_probs=27.7
Q ss_pred hHHHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHHh
Q 043121 116 LGMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLIL 151 (169)
Q Consensus 116 ~~l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~ 151 (169)
+--..++-+..--+.+++++|+.||+|.+.+-..+.
T Consensus 109 ~~~r~ii~l~~~~~~s~~EIA~~l~is~~tV~~~~~ 144 (154)
T PRK06759 109 EKEKYIIFERFFVGKTMGEIALETEMTYYQVRWIYR 144 (154)
T ss_pred HHHHHHHHHHHhcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 344555666667788999999999999999886543
No 111
>PRK10082 cell density-dependent motility repressor; Provisional
Probab=46.23 E-value=20 Score=29.84 Aligned_cols=26 Identities=31% Similarity=0.115 Sum_probs=22.9
Q ss_pred HhcCCHHHHHHHhcCChhHHHHHHhc
Q 043121 127 AVEGSVSEAAKLLWLSTGALSRLILS 152 (169)
Q Consensus 127 ~~~~~~~~aa~~l~~st~~L~k~l~~ 152 (169)
+-.|+++.||+.|++|.+++++-|+.
T Consensus 23 ~e~gS~t~AA~~L~iSQpavS~~I~~ 48 (303)
T PRK10082 23 EKCRNFSQAAVSRNVSQPAFSRRIRA 48 (303)
T ss_pred HhcCCHHHHHHHhCCChHHHHHHHHH
Confidence 44689999999999999999998864
No 112
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=46.17 E-value=37 Score=20.73 Aligned_cols=29 Identities=31% Similarity=0.276 Sum_probs=20.9
Q ss_pred HHHHHhcCCHHHHHHHhcCChhHHHHHHh
Q 043121 123 DLIFAVEGSVSEAAKLLWLSTGALSRLIL 151 (169)
Q Consensus 123 D~l~~~~~~~~~aa~~l~~st~~L~k~l~ 151 (169)
..+..-..+..++++.|++|++.+.+.|.
T Consensus 4 ~~l~~~~~~~~~i~~~l~is~~~v~~~l~ 32 (66)
T smart00418 4 KLLAEGELCVCELAEILGLSQSTVSHHLK 32 (66)
T ss_pred HHhhcCCccHHHHHHHHCCCHHHHHHHHH
Confidence 33444445678899999999988877764
No 113
>PRK13501 transcriptional activator RhaR; Provisional
Probab=46.04 E-value=30 Score=28.94 Aligned_cols=37 Identities=14% Similarity=0.079 Sum_probs=32.2
Q ss_pred HHHHHHHHHHHhcCCHHHHHHHhcC-ChhHHHHHHhcC
Q 043121 117 GMQALLDLIFAVEGSVSEAAKLLWL-STGALSRLILSD 153 (169)
Q Consensus 117 ~l~~~lD~l~~~~~~~~~aa~~l~~-st~~L~k~l~~~ 153 (169)
-|..+.++|..-+.+++++|..+|+ +.+.++|++++.
T Consensus 229 Ri~~A~~LL~~t~~sI~eIA~~~GF~~~s~F~r~FKk~ 266 (290)
T PRK13501 229 RLCHAKCLLRGSEHRISDIAARCGFEDSNYFSAVFTRE 266 (290)
T ss_pred HHHHHHHHHHcCCCCHHHHHHHhCCCCHHHHHHHHHHH
Confidence 4788899999999999999999998 778888888774
No 114
>PF02815 MIR: MIR domain; InterPro: IPR003608 The MIR domain is named after three of the proteins in which it occurs: protein Mannosyltransferase (2.4.1.109 from EC), Inositol 1,4,5-trisphosphate receptor (IP3R) and Ryanodine receptor (RyR). MIR domains have also been found in eukaryotic stromal cell-derived factor 2 (SDF-2) and in Chlamydia trachomatis protein CT153. The MIR domain may have a ligand transferase function. This domain has a closed beta-barrel structure with a hairpin triplet, and has an internal pseudo-threefold symmetry. The MIR motifs that make up the MIR domain consist of ~50 residues and are often found in multiple copies. Inositol 1,4,5-trisphosphate (InsP3) is an intracellular second messenger that transduces growth factor and neurotransmitter signals. InsP3 mediates the release of Ca2+ from intracellular stores by binding to specific Ca2+ channel-coupled receptors. Ryanodine receptors are involved in communication between transverse-tubules and the sarcoplamic reticulum of cardiac and skeletal muscle. The proteins function as a Ca2+-release channels following depolarisation of transverse-tubules []. The function is modulated by Ca2+, Mg2+, ATP and calmodulin. Deficiency in the ryanodine receptor may be the cause of malignant hyperthermia (MH) and of central core disease of muscle (CCD) []. protein O-mannosyltransferases transfer mannose from DOL-P-mannose to ser or thr residues on proteins.; GO: 0016020 membrane; PDB: 1T9F_A 3UJ4_B 3UJ0_B 3T8S_B 3MAL_B 2XOA_A 1N4K_A.
Probab=45.94 E-value=40 Score=26.85 Aligned_cols=39 Identities=26% Similarity=0.402 Sum_probs=30.1
Q ss_pred EEEEeecCCCCCcCCccCceEEEEeeCCceEEEEcccCC
Q 043121 30 MDTYKLSGPGSQHRNKRESAVRLKHVPTGVIAHAAEDRS 68 (169)
Q Consensus 30 i~~~RssGpGGQ~vNk~~saVrl~H~ptGi~v~~~~~RS 68 (169)
++..-..|.++..+-..+|.|||+|..||..+.+++.+.
T Consensus 121 ~~~~~~~~~~~~~~~~~~s~frL~H~~t~~~L~~~~~~l 159 (190)
T PF02815_consen 121 FEEKSSTGMGEDEIKTLDSYFRLRHVATGCWLHSHDVKL 159 (190)
T ss_dssp EEEEESSSCSSSSBBBTTSEEEEEETTTTEEEEEEEEES
T ss_pred EEecccCCccCCcEEecccEEEEEECCcCEEEecCCccc
Confidence 334445577778888889999999999998887776554
No 115
>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=45.64 E-value=52 Score=21.23 Aligned_cols=32 Identities=19% Similarity=0.101 Sum_probs=25.1
Q ss_pred HHHHHHHhcCCHHHHHHHhcCChhHHHHHHhc
Q 043121 121 LLDLIFAVEGSVSEAAKLLWLSTGALSRLILS 152 (169)
Q Consensus 121 ~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~~ 152 (169)
+-..+.+.+.+..+.|+.+|++++++.++...
T Consensus 4 lk~~r~~~~lt~~~~a~~~~i~~~~i~~~e~g 35 (64)
T PF12844_consen 4 LKELREEKGLTQKDLAEKLGISRSTISKIENG 35 (64)
T ss_dssp HHHHHHHCT--HHHHHHHHTS-HHHHHHHHTT
T ss_pred HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCC
Confidence 45667788899999999999999999999965
No 116
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=45.60 E-value=50 Score=24.69 Aligned_cols=37 Identities=16% Similarity=0.089 Sum_probs=28.8
Q ss_pred hhHHHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHHh
Q 043121 115 SLGMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLIL 151 (169)
Q Consensus 115 ~~~l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~ 151 (169)
|+-...++-+..--+.+++++|+.||+|.+.+-..+.
T Consensus 108 p~~~r~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~ 144 (161)
T PRK09047 108 PARQREAFLLRYWEDMDVAETAAAMGCSEGSVKTHCS 144 (161)
T ss_pred CHHHHHHHHHHHHhcCCHHHHHHHHCCCHHHHHHHHH
Confidence 3345566666677889999999999999999876554
No 117
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=45.45 E-value=71 Score=25.05 Aligned_cols=49 Identities=16% Similarity=0.141 Sum_probs=35.0
Q ss_pred CchhHHHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHHhcChhHHHHHHHhhhhc
Q 043121 113 KFSLGMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLILSDDSHQIAVNELRTSK 167 (169)
Q Consensus 113 ~f~~~l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~~~~~~~~~~n~~R~~~ 167 (169)
..|+-...++.+..--+.+++++|+.||+|.+.+-.. +.++.+.+|+.+
T Consensus 131 ~L~~~~r~i~~l~~~~g~s~~EIAe~lgis~~~V~~~------l~Ra~~~Lr~~~ 179 (189)
T PRK06811 131 DLEKLDREIFIRRYLLGEKIEEIAKKLGLTRSAIDNR------LSRGRKKLQKNK 179 (189)
T ss_pred hCCHHHHHHHHHHHHccCCHHHHHHHHCCCHHHHHHH------HHHHHHHHHHcc
Confidence 3445566677776777899999999999999887644 345555555543
No 118
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=45.23 E-value=57 Score=19.60 Aligned_cols=30 Identities=23% Similarity=0.172 Sum_probs=24.2
Q ss_pred HHHHHHHhcCCHHHHHHHhcCChhHHHHHHh
Q 043121 121 LLDLIFAVEGSVSEAAKLLWLSTGALSRLIL 151 (169)
Q Consensus 121 ~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~ 151 (169)
++.. ...+.+.+++|+.|++|.+.+-+.+.
T Consensus 11 i~~~-~~~g~s~~eia~~l~is~~tv~~~~~ 40 (58)
T smart00421 11 VLRL-LAEGLTNKEIAERLGISEKTVKTHLS 40 (58)
T ss_pred HHHH-HHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 4444 46788999999999999999887665
No 119
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=45.06 E-value=20 Score=29.22 Aligned_cols=24 Identities=33% Similarity=0.423 Sum_probs=21.6
Q ss_pred cCCHHHHHHHhcCChhHHHHHHhc
Q 043121 129 EGSVSEAAKLLWLSTGALSRLILS 152 (169)
Q Consensus 129 ~~~~~~aa~~l~~st~~L~k~l~~ 152 (169)
.++++.||+.|++|.+++++-|+.
T Consensus 17 ~~s~t~AA~~L~isqpavS~~I~~ 40 (290)
T PRK10837 17 SGSTTQASVMLALSQSAVSAALTD 40 (290)
T ss_pred cCCHHHHHHHhCCCccHHHHHHHH
Confidence 579999999999999999988764
No 120
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=45.05 E-value=56 Score=25.48 Aligned_cols=39 Identities=21% Similarity=0.399 Sum_probs=31.2
Q ss_pred CchhHHHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHHh
Q 043121 113 KFSLGMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLIL 151 (169)
Q Consensus 113 ~f~~~l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~ 151 (169)
..|+-...++.+....+.+++++|+.||+|.+.+-+.|.
T Consensus 131 ~L~~~~r~vl~l~~~~~~s~~eIA~~lgis~~tV~~~l~ 169 (189)
T PRK12515 131 KLSPAHREIIDLVYYHEKSVEEVGEIVGIPESTVKTRMF 169 (189)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 345556777778888999999999999999998866553
No 121
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=44.81 E-value=50 Score=22.49 Aligned_cols=33 Identities=18% Similarity=0.281 Sum_probs=26.2
Q ss_pred HHHHHHHHHhcC---CHHHHHHHhcCChhHHHHHHh
Q 043121 119 QALLDLIFAVEG---SVSEAAKLLWLSTGALSRLIL 151 (169)
Q Consensus 119 ~~~lD~l~~~~~---~~~~aa~~l~~st~~L~k~l~ 151 (169)
..+|..|...++ ..++.|+.||++++.+-++|.
T Consensus 9 ~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~ 44 (68)
T smart00550 9 EKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLY 44 (68)
T ss_pred HHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHH
Confidence 456777777644 588999999999998887765
No 122
>PRK09508 leuO leucine transcriptional activator; Reviewed
Probab=44.47 E-value=22 Score=29.83 Aligned_cols=27 Identities=26% Similarity=0.241 Sum_probs=23.1
Q ss_pred HHhcCCHHHHHHHhcCChhHHHHHHhc
Q 043121 126 FAVEGSVSEAAKLLWLSTGALSRLILS 152 (169)
Q Consensus 126 ~~~~~~~~~aa~~l~~st~~L~k~l~~ 152 (169)
-+-.|+++.||+.|++|.+++++-|+.
T Consensus 33 vae~gs~s~AA~~L~isQpavS~~I~~ 59 (314)
T PRK09508 33 VMQEQNITRAAHNLGMSQPAVSNAVAR 59 (314)
T ss_pred HHhcCCHHHHHHHhCCCHHHHHHHHHH
Confidence 355788999999999999999987763
No 123
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=44.20 E-value=90 Score=23.92 Aligned_cols=37 Identities=16% Similarity=0.002 Sum_probs=29.3
Q ss_pred chhHHHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHH
Q 043121 114 FSLGMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLI 150 (169)
Q Consensus 114 f~~~l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l 150 (169)
.|+--..++-+....+.+++++|+.||+|.+.+-..|
T Consensus 120 Lp~~~r~v~~L~~~~g~s~~EIA~~lgis~~tV~~~l 156 (172)
T PRK12523 120 LSSKARAAFLYNRLDGMGHAEIAERLGVSVSRVRQYL 156 (172)
T ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHH
Confidence 3445666777777788899999999999999887554
No 124
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=43.96 E-value=52 Score=24.78 Aligned_cols=33 Identities=18% Similarity=0.138 Sum_probs=26.0
Q ss_pred HHHHHHHHHhcCCHHHHHHHhcCChhHHHHHHh
Q 043121 119 QALLDLIFAVEGSVSEAAKLLWLSTGALSRLIL 151 (169)
Q Consensus 119 ~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~ 151 (169)
..++.+....+.+++++|+.||+|.+.+.+.+.
T Consensus 134 r~vl~l~~~~~~s~~eIA~~lgis~~tV~~~l~ 166 (182)
T PRK09652 134 RTAITLREIEGLSYEEIAEIMGCPIGTVRSRIF 166 (182)
T ss_pred HHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 345555556788999999999999999976655
No 125
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=43.86 E-value=23 Score=29.32 Aligned_cols=24 Identities=33% Similarity=0.508 Sum_probs=21.7
Q ss_pred cCCHHHHHHHhcCChhHHHHHHhc
Q 043121 129 EGSVSEAAKLLWLSTGALSRLILS 152 (169)
Q Consensus 129 ~~~~~~aa~~l~~st~~L~k~l~~ 152 (169)
.|+++.||+.|++|.+++++-|+.
T Consensus 19 ~gs~s~AA~~L~isQ~avS~~i~~ 42 (302)
T PRK09791 19 QGSIRGASRMLNMSQPALTKSIQE 42 (302)
T ss_pred cCCHHHHHHHhCCChHHHHHHHHH
Confidence 579999999999999999998764
No 126
>PRK11013 DNA-binding transcriptional regulator LysR; Provisional
Probab=43.85 E-value=26 Score=29.30 Aligned_cols=24 Identities=42% Similarity=0.523 Sum_probs=21.8
Q ss_pred cCCHHHHHHHhcCChhHHHHHHhc
Q 043121 129 EGSVSEAAKLLWLSTGALSRLILS 152 (169)
Q Consensus 129 ~~~~~~aa~~l~~st~~L~k~l~~ 152 (169)
.|+++.||+.|++|.+++++-|++
T Consensus 18 ~gS~s~AAe~L~isqsavS~~Ik~ 41 (309)
T PRK11013 18 AGSLTEAARLLHTSQPTVSRELAR 41 (309)
T ss_pred hCcHHHHHHHHCCCcHHHHHHHHH
Confidence 589999999999999999998764
No 127
>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=43.49 E-value=53 Score=23.24 Aligned_cols=34 Identities=26% Similarity=0.299 Sum_probs=26.5
Q ss_pred HHHHHHHHHhcCCHHHHHHHhcCChhHHHHHHhc
Q 043121 119 QALLDLIFAVEGSVSEAAKLLWLSTGALSRLILS 152 (169)
Q Consensus 119 ~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~~ 152 (169)
..++....-.+.+..++|+.||+|.+.+.+.+..
T Consensus 116 ~~ii~~~~~~g~s~~eIA~~l~~s~~~v~~~~~~ 149 (158)
T TIGR02937 116 REVLVLRYLEGLSYKEIAEILGISVGTVKRRLKR 149 (158)
T ss_pred HHHHhhHHhcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 3444555567889999999999999999877654
No 128
>PRK10341 DNA-binding transcriptional activator TdcA; Provisional
Probab=43.22 E-value=24 Score=29.64 Aligned_cols=24 Identities=42% Similarity=0.490 Sum_probs=22.0
Q ss_pred cCCHHHHHHHhcCChhHHHHHHhc
Q 043121 129 EGSVSEAAKLLWLSTGALSRLILS 152 (169)
Q Consensus 129 ~~~~~~aa~~l~~st~~L~k~l~~ 152 (169)
.|+++.||+.|++|.+++++-|++
T Consensus 21 ~gs~s~AA~~L~iSQpavS~~I~~ 44 (312)
T PRK10341 21 SGSIGSAAKELGLTQPAVSKIIND 44 (312)
T ss_pred cCCHHHHHHHhCCChHHHHHHHHH
Confidence 789999999999999999998764
No 129
>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B.
Probab=43.18 E-value=44 Score=22.86 Aligned_cols=34 Identities=29% Similarity=0.150 Sum_probs=22.1
Q ss_pred HHHHHhcCCHHHHHHHhcCChhHHHHHHhcChhHHH
Q 043121 123 DLIFAVEGSVSEAAKLLWLSTGALSRLILSDDSHQI 158 (169)
Q Consensus 123 D~l~~~~~~~~~aa~~l~~st~~L~k~l~~~~~~~~ 158 (169)
|.+... |+.+..|++||+|+++++.- ....+..+
T Consensus 4 ~aI~~~-G~~~~lAkalGVs~~aVs~W-~~~IP~~r 37 (60)
T PF14549_consen 4 DAIKYF-GGQSKLAKALGVSPQAVSQW-GERIPAER 37 (60)
T ss_dssp HHHHHH-SSHHHHHHHHTS-HHHHHHH-HTS--HHH
T ss_pred HHHHHH-CCHHHHHHHHCCCHHHHHHh-cCccCHHH
Confidence 334444 46889999999999999988 44444433
No 130
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=42.94 E-value=66 Score=23.73 Aligned_cols=39 Identities=15% Similarity=0.061 Sum_probs=32.5
Q ss_pred hhHHHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHHhcC
Q 043121 115 SLGMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLILSD 153 (169)
Q Consensus 115 ~~~l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~~~ 153 (169)
|.|-..+.-.+...++.++.+|+.||+|..-.-|-+...
T Consensus 11 ~~gR~~lv~~vv~~g~~~a~aA~~~gVS~~Ta~kW~~Ry 49 (85)
T PF13011_consen 11 PRGRLRLVRRVVEQGWPVAHAAAEFGVSRRTAYKWLARY 49 (85)
T ss_pred HHHHHHHHHHHHHcCCcHHHHHHHhCCCHHHHHHHHHHH
Confidence 557777777888889999999999999998888877543
No 131
>PRK10216 DNA-binding transcriptional regulator YidZ; Provisional
Probab=42.85 E-value=24 Score=29.66 Aligned_cols=25 Identities=32% Similarity=0.360 Sum_probs=22.2
Q ss_pred hcCCHHHHHHHhcCChhHHHHHHhc
Q 043121 128 VEGSVSEAAKLLWLSTGALSRLILS 152 (169)
Q Consensus 128 ~~~~~~~aa~~l~~st~~L~k~l~~ 152 (169)
-.|+++.||+.|++|.+++++-|+.
T Consensus 21 e~gs~t~AA~~L~iSQpavS~~I~~ 45 (319)
T PRK10216 21 QERSVTKAAKRMNVTPSAVSKSLAK 45 (319)
T ss_pred HhCCHHHHHHHhCCCHHHHHHHHHH
Confidence 4579999999999999999998864
No 132
>COG3604 FhlA Transcriptional regulator containing GAF, AAA-type ATPase, and DNA binding domains [Transcription / Signal transduction mechanisms]
Probab=42.79 E-value=36 Score=32.90 Aligned_cols=36 Identities=19% Similarity=0.124 Sum_probs=31.8
Q ss_pred HHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHHhcC
Q 043121 118 MQALLDLIFAVEGSVSEAAKLLWLSTGALSRLILSD 153 (169)
Q Consensus 118 l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~~~ 153 (169)
-+.+.+.|...+|....||..||+++.+|...+++.
T Consensus 508 R~~I~~aL~~~~~~~a~AAr~LGl~~~~L~~~~kRl 543 (550)
T COG3604 508 RQLIIAALEETNGNWAGAARRLGLTRRTLLYRMKRL 543 (550)
T ss_pred HHHHHHHHHHhCCcHHHHHHHhCCCHHHHHHHHHHc
Confidence 456788899999999999999999999999988753
No 133
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=42.72 E-value=44 Score=23.24 Aligned_cols=37 Identities=22% Similarity=0.249 Sum_probs=30.0
Q ss_pred hHHHHHHHHHHHhcCCH-HHHHHHhcCChhHHHHHHhc
Q 043121 116 LGMQALLDLIFAVEGSV-SEAAKLLWLSTGALSRLILS 152 (169)
Q Consensus 116 ~~l~~~lD~l~~~~~~~-~~aa~~l~~st~~L~k~l~~ 152 (169)
+.--.+|..|...++.. ++.|+.++++.+.+++.|.+
T Consensus 22 ~~q~~~L~~l~~~~~~~~~~la~~l~i~~~~vt~~l~~ 59 (126)
T COG1846 22 PPQYQVLLALYEAGGITVKELAERLGLDRSTVTRLLKR 59 (126)
T ss_pred HHHHHHHHHHHHhCCCcHHHHHHHHCCCHHHHHHHHHH
Confidence 34445777788888877 99999999999999988763
No 134
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=42.68 E-value=55 Score=26.00 Aligned_cols=32 Identities=28% Similarity=0.257 Sum_probs=25.4
Q ss_pred HHHHHHHhcCCHHHHHHHhcCChhHHHHHHhc
Q 043121 121 LLDLIFAVEGSVSEAAKLLWLSTGALSRLILS 152 (169)
Q Consensus 121 ~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~~ 152 (169)
++.+....|.++.++|+.||+|+..+-|-+..
T Consensus 143 ~v~l~~~~Gls~~EIA~~lgiS~~tV~r~l~~ 174 (185)
T PF07638_consen 143 VVELRFFEGLSVEEIAERLGISERTVRRRLRR 174 (185)
T ss_pred HHHHHHHCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 34455678888999999999999998876653
No 135
>PF13551 HTH_29: Winged helix-turn helix
Probab=42.55 E-value=38 Score=23.80 Aligned_cols=27 Identities=26% Similarity=0.240 Sum_probs=22.6
Q ss_pred HHhcCC-HHHHHHHhcCChhHHHHHHhc
Q 043121 126 FAVEGS-VSEAAKLLWLSTGALSRLILS 152 (169)
Q Consensus 126 ~~~~~~-~~~aa~~l~~st~~L~k~l~~ 152 (169)
.+-+.+ ++++|+.||+|..-+-+.++.
T Consensus 8 ~~~g~~~~~~ia~~lg~s~~Tv~r~~~~ 35 (112)
T PF13551_consen 8 LAEGVSTIAEIARRLGISRRTVYRWLKR 35 (112)
T ss_pred HHcCCCcHHHHHHHHCcCHHHHHHHHHH
Confidence 445664 999999999999999988876
No 136
>PRK11139 DNA-binding transcriptional activator GcvA; Provisional
Probab=42.43 E-value=24 Score=29.21 Aligned_cols=24 Identities=29% Similarity=0.324 Sum_probs=21.6
Q ss_pred cCCHHHHHHHhcCChhHHHHHHhc
Q 043121 129 EGSVSEAAKLLWLSTGALSRLILS 152 (169)
Q Consensus 129 ~~~~~~aa~~l~~st~~L~k~l~~ 152 (169)
.|+++.||+.|++|.+++++-|+.
T Consensus 20 ~gs~s~AA~~L~isq~avS~~i~~ 43 (297)
T PRK11139 20 HLSFTRAAEELFVTQAAVSHQIKA 43 (297)
T ss_pred hCCHHHHHHHhCCChHHHHHHHHH
Confidence 589999999999999999988764
No 137
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=42.09 E-value=36 Score=28.38 Aligned_cols=37 Identities=8% Similarity=-0.019 Sum_probs=32.0
Q ss_pred HHHHHHHHHHHhcCCHHHHHHHhcCC-hhHHHHHHhcC
Q 043121 117 GMQALLDLIFAVEGSVSEAAKLLWLS-TGALSRLILSD 153 (169)
Q Consensus 117 ~l~~~lD~l~~~~~~~~~aa~~l~~s-t~~L~k~l~~~ 153 (169)
-|+.+.++|..-+.+++++|..+|++ ++-++|+++++
T Consensus 236 Rl~~A~~lL~~t~~sI~eIA~~~GF~d~s~Fsr~FKk~ 273 (290)
T PRK10572 236 RISRAKLLLQTTRMPIATIGRNVGYDDQLYFSRVFKKC 273 (290)
T ss_pred HHHHHHHHHHcCCCCHHHHHHHhCCCCHHHHHHHHHHH
Confidence 37788888888889999999999988 88899998874
No 138
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=41.97 E-value=1e+02 Score=23.53 Aligned_cols=38 Identities=13% Similarity=-0.011 Sum_probs=31.2
Q ss_pred CchhHHHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHH
Q 043121 113 KFSLGMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLI 150 (169)
Q Consensus 113 ~f~~~l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l 150 (169)
..|+-.+.++.+....+.+++++|+.||+|.+.+-.-+
T Consensus 118 ~L~~~~r~v~~L~~~eg~s~~EIA~~l~is~~tV~~~l 155 (168)
T PRK12525 118 GLSGKARAAFLMSQLEGLTYVEIGERLGVSLSRIHQYM 155 (168)
T ss_pred hCCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHH
Confidence 35566777888888889999999999999998876544
No 139
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=41.97 E-value=55 Score=24.73 Aligned_cols=36 Identities=22% Similarity=0.016 Sum_probs=28.6
Q ss_pred chhHHHHHHHHHHHhcCCHHHHHHHhcCChhHHHHH
Q 043121 114 FSLGMQALLDLIFAVEGSVSEAAKLLWLSTGALSRL 149 (169)
Q Consensus 114 f~~~l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~ 149 (169)
.|+-...++.+-...+.++.++|+.||+|.+.+-.-
T Consensus 113 L~~~~r~v~~l~~~~~~s~~eIA~~lgis~~tv~~~ 148 (161)
T PRK12541 113 LPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIE 148 (161)
T ss_pred CCHHHHHHhhhHHhcCCCHHHHHHHHCCCHHHHHHH
Confidence 344556677777788999999999999999986643
No 140
>PRK15185 transcriptional regulator HilD; Provisional
Probab=41.69 E-value=40 Score=30.18 Aligned_cols=42 Identities=17% Similarity=0.203 Sum_probs=31.8
Q ss_pred HHhcCCHHHHHHHhcCChhHHHHHHhcC-hhHHHHHHHhhhhc
Q 043121 126 FAVEGSVSEAAKLLWLSTGALSRLILSD-DSHQIAVNELRTSK 167 (169)
Q Consensus 126 ~~~~~~~~~aa~~l~~st~~L~k~l~~~-~~~~~~~n~~R~~~ 167 (169)
....+++.+.|+.+++|+..|.|.++.. -+....+++.|..+
T Consensus 219 ~~~~~SledLA~~lgmS~~tL~R~FK~~G~S~~~yl~~~Ri~~ 261 (309)
T PRK15185 219 PSRQWKLTDVADHIFMSTSTLKRKLAEEGTSFSDIYLSARMNQ 261 (309)
T ss_pred ccCCCCHHHHHHHHCcCHHHHHHHHHHcCCCHHHHHHHHHHHH
Confidence 3456889999999999999999998763 33444467776554
No 141
>PRK11482 putative DNA-binding transcriptional regulator; Provisional
Probab=41.64 E-value=31 Score=29.30 Aligned_cols=24 Identities=33% Similarity=0.407 Sum_probs=21.6
Q ss_pred cCCHHHHHHHhcCChhHHHHHHhc
Q 043121 129 EGSVSEAAKLLWLSTGALSRLILS 152 (169)
Q Consensus 129 ~~~~~~aa~~l~~st~~L~k~l~~ 152 (169)
.|+++.||+.|++|.+++++-|+.
T Consensus 43 ~gs~s~AA~~L~isQpavS~~I~~ 66 (317)
T PRK11482 43 HKGIVNAAKILNLTPSAISQSIQK 66 (317)
T ss_pred cCCHHHHHHHhCCChHHHHHHHHH
Confidence 679999999999999999987764
No 142
>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=41.36 E-value=21 Score=22.16 Aligned_cols=21 Identities=19% Similarity=0.259 Sum_probs=18.7
Q ss_pred HHHHHhcCChhHHHHHHhcCh
Q 043121 134 EAAKLLWLSTGALSRLILSDD 154 (169)
Q Consensus 134 ~aa~~l~~st~~L~k~l~~~~ 154 (169)
+.|+.+|+|.+.+++++...+
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~ 22 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKP 22 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCC
Confidence 578999999999999999874
No 143
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=41.30 E-value=62 Score=24.33 Aligned_cols=37 Identities=11% Similarity=-0.000 Sum_probs=28.9
Q ss_pred hhHHHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHHh
Q 043121 115 SLGMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLIL 151 (169)
Q Consensus 115 ~~~l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~ 151 (169)
|+-...++-+...-+.+++++|+.||+|.+.+-..|.
T Consensus 108 p~~~r~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~ 144 (160)
T PRK09642 108 PENYRDVVLAHYLEEKSYQEIALQEKIEVKTVEMKLY 144 (160)
T ss_pred CHHHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHH
Confidence 4445666767777889999999999999999865443
No 144
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=40.75 E-value=23 Score=29.53 Aligned_cols=24 Identities=42% Similarity=0.481 Sum_probs=21.7
Q ss_pred cCCHHHHHHHhcCChhHHHHHHhc
Q 043121 129 EGSVSEAAKLLWLSTGALSRLILS 152 (169)
Q Consensus 129 ~~~~~~aa~~l~~st~~L~k~l~~ 152 (169)
.|+++.||+.|++|.+++++-|++
T Consensus 19 ~gs~s~AA~~L~isqpavS~~i~~ 42 (305)
T CHL00180 19 EGSFKKAAESLYISQPAVSLQIKN 42 (305)
T ss_pred cCCHHHHHHHhcCCChHHHHHHHH
Confidence 578999999999999999998864
No 145
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=40.33 E-value=53 Score=21.50 Aligned_cols=34 Identities=24% Similarity=0.080 Sum_probs=27.3
Q ss_pred HHHHHHHhcCCHHHHHHHhcCChhHHHHHHhcCh
Q 043121 121 LLDLIFAVEGSVSEAAKLLWLSTGALSRLILSDD 154 (169)
Q Consensus 121 ~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~~~~ 154 (169)
+-......+.+..++|+.+|+|.+.+.++-..+.
T Consensus 6 lr~~R~~~gls~~~lA~~~g~s~s~v~~iE~G~~ 39 (64)
T PF13560_consen 6 LRRLRERAGLSQAQLADRLGVSQSTVSRIERGRR 39 (64)
T ss_dssp HHHHHHCHTS-HHHHHHHHTS-HHHHHHHHTTSS
T ss_pred HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCC
Confidence 4456677899999999999999999999988766
No 146
>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=40.25 E-value=1e+02 Score=22.27 Aligned_cols=36 Identities=17% Similarity=0.243 Sum_probs=29.0
Q ss_pred HHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHHhcC
Q 043121 118 MQALLDLIFAVEGSVSEAAKLLWLSTGALSRLILSD 153 (169)
Q Consensus 118 l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~~~ 153 (169)
...+++.|....-.+++.|+.+|+|.+-+++.|...
T Consensus 8 ~~~I~e~l~~~~~ti~dvA~~~gvS~~TVsr~L~~~ 43 (80)
T TIGR02844 8 VLEIGKYIVETKATVRETAKVFGVSKSTVHKDVTER 43 (80)
T ss_pred HHHHHHHHHHCCCCHHHHHHHhCCCHHHHHHHhcCC
Confidence 345677777755568999999999999999988764
No 147
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=40.17 E-value=77 Score=24.35 Aligned_cols=33 Identities=12% Similarity=-0.036 Sum_probs=24.4
Q ss_pred HHHHHHHHHHHhcCCHHHHHHHhcCChhHHHHH
Q 043121 117 GMQALLDLIFAVEGSVSEAAKLLWLSTGALSRL 149 (169)
Q Consensus 117 ~l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~ 149 (169)
-...++=+....+.+++++|+.||+|.+.+-+-
T Consensus 133 ~~r~i~~l~~~~g~s~~eIA~~lgis~~tV~~~ 165 (179)
T PRK12514 133 DRAAAVRRAYLEGLSYKELAERHDVPLNTMRTW 165 (179)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHCCChHHHHHH
Confidence 344444445556789999999999999998543
No 148
>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT). Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway [].; PDB: 1S7O_A 1XSV_B.
Probab=39.69 E-value=33 Score=26.02 Aligned_cols=34 Identities=29% Similarity=0.288 Sum_probs=24.5
Q ss_pred HHHHHHHHhcCCHHHHHHHhcCChhHHHHHHhcC
Q 043121 120 ALLDLIFAVEGSVSEAAKLLWLSTGALSRLILSD 153 (169)
Q Consensus 120 ~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~~~ 153 (169)
..+.....-+.+++++|+.+|+|+.++...|+.-
T Consensus 24 ~~l~lyy~eDlSlsEIAe~~~iSRqaV~d~ikr~ 57 (101)
T PF04297_consen 24 EILELYYEEDLSLSEIAEELGISRQAVYDSIKRA 57 (101)
T ss_dssp HHHHHHCTS---HHHHHHHCTS-HHHHHHHHHHH
T ss_pred HHHHHHHccCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 4566666778899999999999999999887753
No 149
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=39.40 E-value=61 Score=24.30 Aligned_cols=35 Identities=17% Similarity=0.187 Sum_probs=27.4
Q ss_pred HHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHHhc
Q 043121 118 MQALLDLIFAVEGSVSEAAKLLWLSTGALSRLILS 152 (169)
Q Consensus 118 l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~~ 152 (169)
-+.++......+.++.++|+.||+|++.+-+.+..
T Consensus 130 ~r~i~~l~~~~~~~~~eIA~~lgis~~tv~~~~~r 164 (179)
T PRK11924 130 QREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRR 164 (179)
T ss_pred HHHHhhHHHHcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 34455566667889999999999999998877654
No 150
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=39.01 E-value=65 Score=24.85 Aligned_cols=35 Identities=23% Similarity=0.276 Sum_probs=27.1
Q ss_pred HHHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHHh
Q 043121 117 GMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLIL 151 (169)
Q Consensus 117 ~l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~ 151 (169)
--+.++-+..-.+.+++++|+.||+|.+.+-+.+.
T Consensus 139 ~~r~vl~l~~~~~~s~~eIA~~lgis~~~V~~~l~ 173 (186)
T PRK13919 139 EERRVIEVLYYQGYTHREAAQLLGLPLGTLKTRAR 173 (186)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 34455555667889999999999999998876554
No 151
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=38.89 E-value=89 Score=25.22 Aligned_cols=35 Identities=23% Similarity=0.067 Sum_probs=27.0
Q ss_pred HHHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHHh
Q 043121 117 GMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLIL 151 (169)
Q Consensus 117 ~l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~ 151 (169)
-.+.++-+....+.+++++|+.||+|.+.+-..|.
T Consensus 142 ~~r~v~~L~~~~g~s~~EIA~~Lgis~~tV~~~l~ 176 (203)
T PRK09647 142 EFRAAVVLCDIEGLSYEEIAATLGVKLGTVRSRIH 176 (203)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 34455666667889999999999999988765554
No 152
>PHA01976 helix-turn-helix protein
Probab=38.85 E-value=82 Score=20.47 Aligned_cols=33 Identities=12% Similarity=-0.011 Sum_probs=27.5
Q ss_pred HHHHHHHhcCCHHHHHHHhcCChhHHHHHHhcC
Q 043121 121 LLDLIFAVEGSVSEAAKLLWLSTGALSRLILSD 153 (169)
Q Consensus 121 ~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~~~ 153 (169)
+.......+.+..+.|+.+|+|.+.+.+.....
T Consensus 7 l~~~R~~~glt~~~lA~~~gvs~~~v~~~e~g~ 39 (67)
T PHA01976 7 LIKARNARAWSAPELSRRAGVRHSLIYDFEADK 39 (67)
T ss_pred HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCC
Confidence 445567788899999999999999999988643
No 153
>PRK10086 DNA-binding transcriptional regulator DsdC; Provisional
Probab=38.84 E-value=31 Score=28.97 Aligned_cols=25 Identities=32% Similarity=0.178 Sum_probs=22.0
Q ss_pred hcCCHHHHHHHhcCChhHHHHHHhc
Q 043121 128 VEGSVSEAAKLLWLSTGALSRLILS 152 (169)
Q Consensus 128 ~~~~~~~aa~~l~~st~~L~k~l~~ 152 (169)
-.|+++.||+.|++|.+++++-|+.
T Consensus 27 ~~gs~s~AA~~L~iSQpavS~~I~~ 51 (311)
T PRK10086 27 RHQSFALAADELSLTPSAVSHRINQ 51 (311)
T ss_pred HcCCHHHHHHHHCCCHHHHHHHHHH
Confidence 3688999999999999999987753
No 154
>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=38.72 E-value=47 Score=22.08 Aligned_cols=34 Identities=21% Similarity=0.066 Sum_probs=26.7
Q ss_pred HHHHHHHHhcCCHHHHHHHhcCChhHHHHHHhcC
Q 043121 120 ALLDLIFAVEGSVSEAAKLLWLSTGALSRLILSD 153 (169)
Q Consensus 120 ~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~~~ 153 (169)
.++.....-+.++.+.|..+|++++.|.+-++..
T Consensus 14 ~~v~~~~~~g~sv~~va~~~gi~~~~l~~W~~~~ 47 (76)
T PF01527_consen 14 QAVREYLESGESVSEVAREYGISPSTLYNWRKQY 47 (76)
T ss_dssp HHHHHHHHHHCHHHHHHHHHTS-HHHHHHHHHHH
T ss_pred HHHHHHHHCCCceEeeecccccccccccHHHHHH
Confidence 3455555668899999999999999999988765
No 155
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=38.57 E-value=43 Score=20.31 Aligned_cols=22 Identities=27% Similarity=0.185 Sum_probs=18.0
Q ss_pred CHHHHHHHhcCChhHHHHHHhc
Q 043121 131 SVSEAAKLLWLSTGALSRLILS 152 (169)
Q Consensus 131 ~~~~aa~~l~~st~~L~k~l~~ 152 (169)
+++++|+.||+|+..|-+....
T Consensus 2 ~~~e~a~~~gv~~~tlr~~~~~ 23 (49)
T cd04761 2 TIGELAKLTGVSPSTLRYYERI 23 (49)
T ss_pred cHHHHHHHHCcCHHHHHHHHHC
Confidence 5789999999999988776543
No 156
>PRK09801 transcriptional activator TtdR; Provisional
Probab=38.15 E-value=33 Score=29.05 Aligned_cols=26 Identities=27% Similarity=0.195 Sum_probs=22.7
Q ss_pred HhcCCHHHHHHHhcCChhHHHHHHhc
Q 043121 127 AVEGSVSEAAKLLWLSTGALSRLILS 152 (169)
Q Consensus 127 ~~~~~~~~aa~~l~~st~~L~k~l~~ 152 (169)
+-.|+++.||+.|++|.+++++-|+.
T Consensus 18 ~~~gs~t~AA~~L~iSQpavS~~I~~ 43 (310)
T PRK09801 18 VHSGSFSAAAATLGQTPAFVTKRIQI 43 (310)
T ss_pred HHcCCHHHHHHHhCcCHHHHHHHHHH
Confidence 45688999999999999999988763
No 157
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=37.96 E-value=43 Score=20.01 Aligned_cols=23 Identities=30% Similarity=0.268 Sum_probs=18.5
Q ss_pred cCCHHHHHHHhcCChhHHHHHHh
Q 043121 129 EGSVSEAAKLLWLSTGALSRLIL 151 (169)
Q Consensus 129 ~~~~~~aa~~l~~st~~L~k~l~ 151 (169)
..+.++.|+.+|+|.+.+.+.|.
T Consensus 8 ~~s~~~la~~l~~s~~tv~~~l~ 30 (48)
T smart00419 8 PLTRQEIAELLGLTRETVSRTLK 30 (48)
T ss_pred ccCHHHHHHHHCCCHHHHHHHHH
Confidence 34678899999999988887664
No 158
>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=37.65 E-value=83 Score=19.58 Aligned_cols=32 Identities=34% Similarity=0.336 Sum_probs=23.6
Q ss_pred HHHHHHHHhcCCHHHHHHHhcCChhHHHHHHh
Q 043121 120 ALLDLIFAVEGSVSEAAKLLWLSTGALSRLIL 151 (169)
Q Consensus 120 ~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~ 151 (169)
.+++.+...+.+.+++++.++++.+.+.+.|.
T Consensus 11 ~il~~l~~~~~~~~ei~~~~~i~~~~i~~~l~ 42 (78)
T cd00090 11 RILRLLLEGPLTVSELAERLGLSQSTVSRHLK 42 (78)
T ss_pred HHHHHHHHCCcCHHHHHHHHCcCHhHHHHHHH
Confidence 45555555557788999999999888776654
No 159
>PRK15186 AraC family transcriptional regulator; Provisional
Probab=37.52 E-value=63 Score=28.20 Aligned_cols=41 Identities=17% Similarity=0.230 Sum_probs=32.0
Q ss_pred HhcCCHHHHHHHhcCChhHHHHHHhcC-hhHHHHHHHhhhhc
Q 043121 127 AVEGSVSEAAKLLWLSTGALSRLILSD-DSHQIAVNELRTSK 167 (169)
Q Consensus 127 ~~~~~~~~aa~~l~~st~~L~k~l~~~-~~~~~~~n~~R~~~ 167 (169)
+..|++.+.|+.+|+|.+.|.|.++.. -+....+++.|..+
T Consensus 195 ~~~~sl~~lA~~~gmS~stl~R~Fk~~g~s~~~~~~~~Rl~~ 236 (291)
T PRK15186 195 SRKWALKDISDSLYMSCSTLKRKLKQENTSFSEVYLNARMNK 236 (291)
T ss_pred cCCCCHHHHHHHHCcCHHHHHHHHHHcCCCHHHHHHHHHHHH
Confidence 358999999999999999999999986 33444456666543
No 160
>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=37.29 E-value=89 Score=18.89 Aligned_cols=26 Identities=19% Similarity=0.172 Sum_probs=22.0
Q ss_pred HHhcCCHHHHHHHhcCChhHHHHHHh
Q 043121 126 FAVEGSVSEAAKLLWLSTGALSRLIL 151 (169)
Q Consensus 126 ~~~~~~~~~aa~~l~~st~~L~k~l~ 151 (169)
...+.+.+++|+.+++|++.+-+.+.
T Consensus 12 ~~~~~s~~eia~~l~~s~~tv~~~~~ 37 (57)
T cd06170 12 LAEGKTNKEIADILGISEKTVKTHLR 37 (57)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 35788999999999999998877665
No 161
>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=37.16 E-value=39 Score=22.61 Aligned_cols=23 Identities=22% Similarity=0.164 Sum_probs=19.0
Q ss_pred CCHHHHHHHhcCChhHHHHHHhc
Q 043121 130 GSVSEAAKLLWLSTGALSRLILS 152 (169)
Q Consensus 130 ~~~~~aa~~l~~st~~L~k~l~~ 152 (169)
-+.++.|+.||+|++.++.-|+.
T Consensus 24 ~tl~elA~~lgis~st~~~~LRr 46 (53)
T PF04967_consen 24 ITLEELAEELGISKSTVSEHLRR 46 (53)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHH
Confidence 45788999999999999976653
No 162
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=37.12 E-value=71 Score=21.78 Aligned_cols=32 Identities=28% Similarity=0.238 Sum_probs=25.0
Q ss_pred HHHHHHHHh--cCCHHHHHHHhcCChhHHHHHHh
Q 043121 120 ALLDLIFAV--EGSVSEAAKLLWLSTGALSRLIL 151 (169)
Q Consensus 120 ~~lD~l~~~--~~~~~~aa~~l~~st~~L~k~l~ 151 (169)
.+++.+... ...+++.|+.+|++.+.+.+.|.
T Consensus 9 ~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~ 42 (91)
T smart00346 9 AVLRALAEEPGGLTLAELAERLGLSKSTAHRLLN 42 (91)
T ss_pred HHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHH
Confidence 356667664 46789999999999999887764
No 163
>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=36.89 E-value=54 Score=22.10 Aligned_cols=29 Identities=14% Similarity=0.029 Sum_probs=23.2
Q ss_pred HHHhcCCHHHHHHHhcCChhHHHHHHhcC
Q 043121 125 IFAVEGSVSEAAKLLWLSTGALSRLILSD 153 (169)
Q Consensus 125 l~~~~~~~~~aa~~l~~st~~L~k~l~~~ 153 (169)
|.-.++.++++|+.||++.+-+-.-...+
T Consensus 9 LY~~G~~~~eIA~~Lg~~~~TV~~W~~r~ 37 (58)
T PF06056_consen 9 LYLQGWSIKEIAEELGVPRSTVYSWKDRY 37 (58)
T ss_pred HHHcCCCHHHHHHHHCCChHHHHHHHHhh
Confidence 44579999999999999988877665543
No 164
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=36.82 E-value=94 Score=18.53 Aligned_cols=31 Identities=32% Similarity=0.306 Sum_probs=22.1
Q ss_pred HHHHHHH-hcCCHHHHHHHhcCChhHHHHHHh
Q 043121 121 LLDLIFA-VEGSVSEAAKLLWLSTGALSRLIL 151 (169)
Q Consensus 121 ~lD~l~~-~~~~~~~aa~~l~~st~~L~k~l~ 151 (169)
+++.+.. ...++.+.++.|++|++.+.+.|.
T Consensus 5 il~~l~~~~~~s~~~l~~~l~~s~~tv~~~l~ 36 (53)
T smart00420 5 ILELLAQQGKVSVEELAELLGVSEMTIRRDLN 36 (53)
T ss_pred HHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHH
Confidence 4555543 235688899999999988877663
No 165
>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=36.74 E-value=85 Score=22.97 Aligned_cols=34 Identities=21% Similarity=0.038 Sum_probs=26.3
Q ss_pred HHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHHh
Q 043121 118 MQALLDLIFAVEGSVSEAAKLLWLSTGALSRLIL 151 (169)
Q Consensus 118 l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~ 151 (169)
-+.++-+....+.+++++|+.||+|.+.+-+.+.
T Consensus 118 ~r~il~l~~~~~~~~~eIA~~lgis~~tv~~~~~ 151 (161)
T TIGR02985 118 CRKIFILSRFEGKSYKEIAEELGISVKTVEYHIS 151 (161)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3455555566788999999999999999876654
No 166
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=36.73 E-value=43 Score=21.84 Aligned_cols=21 Identities=29% Similarity=0.221 Sum_probs=18.1
Q ss_pred CHHHHHHHhcCChhHHHHHHh
Q 043121 131 SVSEAAKLLWLSTGALSRLIL 151 (169)
Q Consensus 131 ~~~~aa~~l~~st~~L~k~l~ 151 (169)
.++++|+.+|+|++.|-+...
T Consensus 2 s~~eva~~~gvs~~tlr~~~~ 22 (70)
T smart00422 2 TIGEVAKLAGVSVRTLRYYER 22 (70)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 578999999999999987754
No 167
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=36.72 E-value=79 Score=24.11 Aligned_cols=36 Identities=19% Similarity=0.089 Sum_probs=27.2
Q ss_pred hHHHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHHh
Q 043121 116 LGMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLIL 151 (169)
Q Consensus 116 ~~l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~ 151 (169)
+--..++-+...-+.+++++|+.||+|++.+-..|.
T Consensus 115 ~~~r~v~~l~~~~g~s~~eIA~~lgis~~tV~~~l~ 150 (164)
T PRK12547 115 ADQREAIILIGASGFSYEDAAAICGCAVGTIKSRVS 150 (164)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHH
Confidence 344555666666788999999999999988775553
No 168
>TIGR02036 dsdC D-serine deaminase transcriptional activator. This family, part of the LysR family of transcriptional regulators, activates transcription of the gene for D-serine deaminase, dsdA. Trusted members of this family so far are found adjacent to dsdA and only in Gammaproteobacteria, including E. coli, Vibrio cholerae, and Colwellia psychrerythraea.
Probab=36.57 E-value=43 Score=28.00 Aligned_cols=26 Identities=38% Similarity=0.238 Sum_probs=22.6
Q ss_pred HhcCCHHHHHHHhcCChhHHHHHHhc
Q 043121 127 AVEGSVSEAAKLLWLSTGALSRLILS 152 (169)
Q Consensus 127 ~~~~~~~~aa~~l~~st~~L~k~l~~ 152 (169)
+-.|+++.||+.|++|.+++++-|+.
T Consensus 20 a~~gs~s~AA~~L~isQpavS~~I~~ 45 (302)
T TIGR02036 20 ARHQSFSLAAEELSLTPSAISHRINQ 45 (302)
T ss_pred HHhCCHHHHHHHHCCCHHHHHHHHHH
Confidence 45688999999999999999987763
No 169
>PRK09744 DNA-binding transcriptional regulator DicC; Provisional
Probab=36.54 E-value=80 Score=23.00 Aligned_cols=34 Identities=15% Similarity=-0.005 Sum_probs=24.5
Q ss_pred HHHHHhcCCHHHHHHHhcCChhHHHHHHhcChhHH
Q 043121 123 DLIFAVEGSVSEAAKLLWLSTGALSRLILSDDSHQ 157 (169)
Q Consensus 123 D~l~~~~~~~~~aa~~l~~st~~L~k~l~~~~~~~ 157 (169)
|++.-. |+....|++||+|+++++.-=..=|..+
T Consensus 5 Dvi~yF-Gs~~kvA~aLGIs~~AVsQWGe~VPe~r 38 (75)
T PRK09744 5 DAIAFF-GSKTKLANAAGVRLASVAAWGELVPEGR 38 (75)
T ss_pred HHHHHh-CcHHHHHHHHCCCHHHHHHHhccCcHHH
Confidence 455555 7789999999999999987633334433
No 170
>PF09030 Creb_binding: Creb binding; InterPro: IPR014744 This entry represents the interlocking domain of the eukaryotic nuclear receptor coactivators CREBP and p300. The interlocking domain forms a 3-helical non-globular array that forms interlocked heterodimers with its target. Nuclear receptors are ligand-activated transcription factors involved in the regulation of many processes, including development, reproduction and homeostasis. Nuclear receptor coactivators act to modulate the function of nuclear receptors. Coactivators associate with promoters and enhancers primarily through protein-protein contacts to facilitate the interaction between DNA-bound transcription factors and the transcription machinery. Many of these coactivators are structurally related, including CBP (CREB-binding protein) and p300 []. CBP and p300 both have histone acetyltransferase activity (2.3.1.48 from EC). CBP/p300 proteins function synergistically to activate transcription, acting to remodel chromatin and to recruit RNA polymerase II and the basal transcription machinery. CBP is required for proper cell cycle control, differentiation and apoptosis. The interaction of CBP/p300 with transcription factors involves several small domains. The IBiD domain in the C-terminal of CBP is responsible for CBP interaction with IRF-3, as well as with the adenoviral oncoprotein E1A, TIF-2 coactivator, and the IRF homologue KSHV IRF-1 []. ; GO: 0003713 transcription coactivator activity, 0004402 histone acetyltransferase activity, 0006355 regulation of transcription, DNA-dependent, 0016573 histone acetylation, 0000123 histone acetyltransferase complex, 0005634 nucleus; PDB: 2KKJ_A 2C52_A 1JJS_A 2L14_A 1KBH_B 1ZOQ_C.
Probab=36.50 E-value=32 Score=26.46 Aligned_cols=25 Identities=16% Similarity=0.139 Sum_probs=22.8
Q ss_pred hHHHHHHhcChhHHHHHHHhhhhcc
Q 043121 144 GALSRLILSDDSHQIAVNELRTSKV 168 (169)
Q Consensus 144 ~~L~k~l~~~~~~~~~~n~~R~~~~ 168 (169)
-++.++|+|+|.|-++|=..|++|.
T Consensus 73 QQVLnILkSNPqLMAAFIKQR~aky 97 (104)
T PF09030_consen 73 QQVLNILKSNPQLMAAFIKQRAAKY 97 (104)
T ss_dssp HHHHHHHHTSHHHHHHHHHHCCTTC
T ss_pred HHHHHHHhhCHHHHHHHHHHHHHHh
Confidence 4799999999999999999999874
No 171
>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function.
Probab=36.44 E-value=64 Score=24.66 Aligned_cols=32 Identities=25% Similarity=0.173 Sum_probs=26.4
Q ss_pred HHHHHHHhcCCHHHHHHHhcCChhHHHHHHhc
Q 043121 121 LLDLIFAVEGSVSEAAKLLWLSTGALSRLILS 152 (169)
Q Consensus 121 ~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~~ 152 (169)
.+=++.-.+.+-.+||+.+|+|.+-+-++|.+
T Consensus 49 AiRL~D~egl~QeeaA~~MgVSR~T~~ril~~ 80 (106)
T PF02001_consen 49 AIRLVDYEGLSQEEAAERMGVSRPTFQRILES 80 (106)
T ss_pred HHHHHHHcCCCHHHHHHHcCCcHHHHHHHHHH
Confidence 44455666788999999999999999998874
No 172
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=36.20 E-value=32 Score=22.70 Aligned_cols=21 Identities=10% Similarity=0.172 Sum_probs=17.4
Q ss_pred CHHHHHHHhcCChhHHHHHHh
Q 043121 131 SVSEAAKLLWLSTGALSRLIL 151 (169)
Q Consensus 131 ~~~~aa~~l~~st~~L~k~l~ 151 (169)
.++++|+.+|+|++.|-..-.
T Consensus 2 ~i~evA~~~gvs~~tlR~~~~ 22 (67)
T cd04764 2 TIKEVSEIIGVKPHTLRYYEK 22 (67)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 578999999999998876543
No 173
>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=35.72 E-value=86 Score=24.04 Aligned_cols=38 Identities=24% Similarity=0.190 Sum_probs=30.0
Q ss_pred chhHHHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHHh
Q 043121 114 FSLGMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLIL 151 (169)
Q Consensus 114 f~~~l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~ 151 (169)
.|+-...++-+....+.+.+++|+.||+|.+.+-..|.
T Consensus 135 Lp~~~r~v~~l~~~~g~s~~EIA~~lgis~~tVk~~l~ 172 (183)
T TIGR02999 135 VDPRQAEVVELRFFAGLTVEEIAELLGVSVRTVERDWR 172 (183)
T ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHH
Confidence 45555667777778889999999999999998875543
No 174
>TIGR03384 betaine_BetI transcriptional repressor BetI. BetI is a DNA-binding transcriptional repressor of the bet (betaine) regulon. In sequence, it is related to TetR (pfam00440). Choline, through BetI, induces the expression of the betaine biosynthesis genes betA and betB by derepression. The choline porter gene betT is also part of this regulon in Escherichia coli. Note that a different transcriptional regulator, ArcA, controls the expression of bet regulon genes in response to oxygen, as BetA is an oxygen-dependent enzyme.
Probab=35.59 E-value=1.1e+02 Score=23.22 Aligned_cols=49 Identities=14% Similarity=0.051 Sum_probs=41.4
Q ss_pred hhHHHHHHHHHHHhcCC---HHHHHHHhcCChhHHHHHHhcChhHHHHHHHh
Q 043121 115 SLGMQALLDLIFAVEGS---VSEAAKLLWLSTGALSRLILSDDSHQIAVNEL 163 (169)
Q Consensus 115 ~~~l~~~lD~l~~~~~~---~~~aa~~l~~st~~L~k~l~~~~~~~~~~n~~ 163 (169)
...+....+++...|+. +.+.|+..|+|.+.|-.-+.+-..++.++-+.
T Consensus 11 ~~Il~aA~~lf~~~G~~~~s~~~IA~~agvsk~~ly~~F~sK~~L~~~~~~~ 62 (189)
T TIGR03384 11 AELIDATIESIGERGSLDVTIAQIARRAGVSSGIISHYFGGKQGLLEATMRH 62 (189)
T ss_pred HHHHHHHHHHHHhcCcccCCHHHHHHHhCCCHHHHHHHcCCHHHHHHHHHHH
Confidence 45788999999998875 88999999999999999998888887775543
No 175
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=35.40 E-value=79 Score=24.22 Aligned_cols=34 Identities=21% Similarity=0.298 Sum_probs=25.6
Q ss_pred HHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHHh
Q 043121 118 MQALLDLIFAVEGSVSEAAKLLWLSTGALSRLIL 151 (169)
Q Consensus 118 l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~ 151 (169)
-+.++.+....+.+++++|+.||+|.+.+-+.+.
T Consensus 141 ~r~il~l~~~~~~s~~eIA~~lgis~~~v~~~l~ 174 (187)
T PRK09641 141 YRTVIVLKYIEDLSLKEISEILDLPVGTVKTRIH 174 (187)
T ss_pred HHHHhhhHHhhCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3444545556788899999999999999876553
No 176
>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=35.36 E-value=86 Score=24.17 Aligned_cols=37 Identities=19% Similarity=0.020 Sum_probs=29.9
Q ss_pred chhHHHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHH
Q 043121 114 FSLGMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLI 150 (169)
Q Consensus 114 f~~~l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l 150 (169)
.|+-...++.+....+.+++++|+.||+|.+.+-..|
T Consensus 101 L~~~~r~v~~l~~~~g~s~~eIA~~lgis~~tV~~~l 137 (170)
T TIGR02959 101 LPDEYREAIRLTELEGLSQQEIAEKLGLSLSGAKSRV 137 (170)
T ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHH
Confidence 3445667788888899999999999999998876554
No 177
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=35.35 E-value=86 Score=23.55 Aligned_cols=36 Identities=19% Similarity=0.135 Sum_probs=29.1
Q ss_pred hhHHHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHHh
Q 043121 115 SLGMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLIL 151 (169)
Q Consensus 115 ~~~l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~ 151 (169)
|+--+.++-+.. .+.+++++|+.||+|.+.+-+.+.
T Consensus 114 ~~~~r~il~l~~-~g~s~~eIA~~lgis~~tV~~~i~ 149 (166)
T PRK09639 114 TERDRTVLLLRF-SGYSYKEIAEALGIKESSVGTTLA 149 (166)
T ss_pred CHHHHHHHHHHH-cCCCHHHHHHHHCCCHHHHHHHHH
Confidence 344566777777 899999999999999999887664
No 178
>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=35.26 E-value=81 Score=23.99 Aligned_cols=34 Identities=15% Similarity=0.223 Sum_probs=26.8
Q ss_pred HHHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHH
Q 043121 117 GMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLI 150 (169)
Q Consensus 117 ~l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l 150 (169)
--..++-.....+.+++++|+.||+|.+.+-+.+
T Consensus 123 ~~r~i~~l~~~~g~s~~eiA~~lgis~~tv~~~l 156 (169)
T TIGR02954 123 KYQTAIILRYYHDLTIKEIAEVMNKPEGTVKTYL 156 (169)
T ss_pred HHhHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHH
Confidence 3445666666778899999999999999887554
No 179
>PRK15429 formate hydrogenlyase transcriptional activator FhlA; Provisional
Probab=35.16 E-value=46 Score=32.05 Aligned_cols=34 Identities=24% Similarity=0.242 Sum_probs=29.6
Q ss_pred HHHHHHHHHhcCCHH---HHHHHhcCChhHHHHHHhc
Q 043121 119 QALLDLIFAVEGSVS---EAAKLLWLSTGALSRLILS 152 (169)
Q Consensus 119 ~~~lD~l~~~~~~~~---~aa~~l~~st~~L~k~l~~ 152 (169)
..+.+.|...+|.++ .||+.||+|++.|-+-+++
T Consensus 644 ~~I~~aL~~~~gn~~~~~~aA~~LGi~R~tL~rklk~ 680 (686)
T PRK15429 644 QLIVRVLKETNGVVAGPKGAAQRLGLKRTTLLSRMKR 680 (686)
T ss_pred HHHHHHHHHcCCCcccHHHHHHHhCCCHHHHHHHHHH
Confidence 457888899999986 9999999999999887765
No 180
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=35.13 E-value=81 Score=24.16 Aligned_cols=36 Identities=17% Similarity=0.187 Sum_probs=28.3
Q ss_pred hHHHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHHh
Q 043121 116 LGMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLIL 151 (169)
Q Consensus 116 ~~l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~ 151 (169)
+-...++.+..--+.+.+++|+.||+|.+.+-+-|.
T Consensus 122 ~~~r~i~~l~~~~~~s~~EIA~~lgis~~tV~~~l~ 157 (173)
T PRK12522 122 EKYKTVLVLYYYEQYSYKEMSEILNIPIGTVKYRLN 157 (173)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHH
Confidence 345566777777889999999999999998875543
No 181
>TIGR02297 HpaA 4-hydroxyphenylacetate catabolism regulatory protein HpaA. This putative transcriptional regulator, which contains both the substrate-binding, dimerization domain (pfam02311) and the helix-turn-helix DNA-binding domain (pfam00165) of the AraC famil, is located proximal to genes of the 4-hydroxyphenylacetate catabolism pathway.
Probab=35.08 E-value=58 Score=26.85 Aligned_cols=36 Identities=19% Similarity=0.224 Sum_probs=29.7
Q ss_pred HHHHHHHHHHhcCCHHHHHHHhcCC-hhHHHHHHhcC
Q 043121 118 MQALLDLIFAVEGSVSEAAKLLWLS-TGALSRLILSD 153 (169)
Q Consensus 118 l~~~lD~l~~~~~~~~~aa~~l~~s-t~~L~k~l~~~ 153 (169)
|..+.++|...+.+++++|..+|++ .+.++|++++.
T Consensus 240 l~~A~~lL~~t~~sI~eIA~~~GF~s~s~Fsr~FKk~ 276 (287)
T TIGR02297 240 MQEARRLLLFTQHSINQIAYDLGYKDPAYFARFFQKE 276 (287)
T ss_pred HHHHHHHHHcCCCCHHHHHHHhCCCCHHHHHHHHHHH
Confidence 7777888888889999999999986 77888888764
No 182
>COG3077 RelB DNA-damage-inducible protein J [DNA replication, recombination, and repair]
Probab=34.95 E-value=32 Score=25.62 Aligned_cols=24 Identities=25% Similarity=0.358 Sum_probs=17.4
Q ss_pred cCCHHHHH----HHhcCChhHHHHHHhc
Q 043121 129 EGSVSEAA----KLLWLSTGALSRLILS 152 (169)
Q Consensus 129 ~~~~~~aa----~~l~~st~~L~k~l~~ 152 (169)
+.+++..| +.+|+++|+.+|+++.
T Consensus 12 D~~vK~eA~~Vl~~mGlt~S~airm~L~ 39 (88)
T COG3077 12 DDEVKEEATAVLEEMGLTISDAIRMFLT 39 (88)
T ss_pred cHHHHHHHHHHHHHhCCCHHHHHHHHHH
Confidence 44455544 7899999999998764
No 183
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=34.82 E-value=1.3e+02 Score=23.26 Aligned_cols=37 Identities=22% Similarity=0.127 Sum_probs=28.0
Q ss_pred chhHHHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHH
Q 043121 114 FSLGMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLI 150 (169)
Q Consensus 114 f~~~l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l 150 (169)
.|+.-..++-...-.+.+++++|+.||+|.+.+-..+
T Consensus 140 L~~~~r~i~~l~~~~g~s~~EIA~~lgis~~tV~~~l 176 (189)
T PRK09648 140 LPEKQREILILRVVVGLSAEETAEAVGSTPGAVRVAQ 176 (189)
T ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHH
Confidence 3444566666666778899999999999998876544
No 184
>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=34.80 E-value=91 Score=23.19 Aligned_cols=36 Identities=19% Similarity=0.170 Sum_probs=27.7
Q ss_pred chhHHHHHHHHHHHhcCCHHHHHHHhcCChhHHHHH
Q 043121 114 FSLGMQALLDLIFAVEGSVSEAAKLLWLSTGALSRL 149 (169)
Q Consensus 114 f~~~l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~ 149 (169)
.|+--+.++-+...-+.+++++|+.||+|.+.+-.-
T Consensus 112 L~~~~r~v~~l~~~~g~~~~eIA~~l~is~~tv~~~ 147 (159)
T TIGR02989 112 LPERQRELLQLRYQRGVSLTALAEQLGRTVNAVYKA 147 (159)
T ss_pred CCHHHHHHHHHHHhcCCCHHHHHHHhCCCHHHHHHH
Confidence 344455566666778899999999999999887644
No 185
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=34.77 E-value=1.3e+02 Score=23.29 Aligned_cols=30 Identities=20% Similarity=0.109 Sum_probs=23.7
Q ss_pred HHHHHHHhcCCHHHHHHHhcCChhHHHHHH
Q 043121 121 LLDLIFAVEGSVSEAAKLLWLSTGALSRLI 150 (169)
Q Consensus 121 ~lD~l~~~~~~~~~aa~~l~~st~~L~k~l 150 (169)
++-+....+.+++++|+.||+|.+.+-+.+
T Consensus 141 i~~l~~~~~~s~~eIA~~lgis~~tV~~~l 170 (182)
T PRK12537 141 CILHAYVDGCSHAEIAQRLGAPLGTVKAWI 170 (182)
T ss_pred HHHHHHHcCCCHHHHHHHHCCChhhHHHHH
Confidence 444445678899999999999999887544
No 186
>PRK13756 tetracycline repressor protein TetR; Provisional
Probab=34.34 E-value=91 Score=25.53 Aligned_cols=48 Identities=15% Similarity=0.047 Sum_probs=39.6
Q ss_pred hhHHHHHHHHHHHhcC---CHHHHHHHhcCChhHHHHHHhcChhHHHHHHH
Q 043121 115 SLGMQALLDLIFAVEG---SVSEAAKLLWLSTGALSRLILSDDSHQIAVNE 162 (169)
Q Consensus 115 ~~~l~~~lD~l~~~~~---~~~~aa~~l~~st~~L~k~l~~~~~~~~~~n~ 162 (169)
-..+...++++.+.+. ++...|+.+|++++.|-+-+.+-..+..++-+
T Consensus 7 e~Il~aA~~l~~e~G~~~lsmr~lA~~lgv~~~slY~hf~~K~~Ll~~~~~ 57 (205)
T PRK13756 7 EKVIDSALELLNEVGIEGLTTRKLAQKLGVEQPTLYWHVKNKRALLDALAI 57 (205)
T ss_pred HHHHHHHHHHHHHcCcccCCHHHHHHHhCCCchHHHHHcCCHHHHHHHHHH
Confidence 3467888898888876 48899999999999999999888887666643
No 187
>PRK15008 HTH-type transcriptional regulator RutR; Provisional
Probab=34.29 E-value=89 Score=24.88 Aligned_cols=47 Identities=23% Similarity=0.102 Sum_probs=40.4
Q ss_pred chhHHHHHHHHHHHhcCC---HHHHHHHhcCChhHHHHHHhcChhHHHHH
Q 043121 114 FSLGMQALLDLIFAVEGS---VSEAAKLLWLSTGALSRLILSDDSHQIAV 160 (169)
Q Consensus 114 f~~~l~~~lD~l~~~~~~---~~~aa~~l~~st~~L~k~l~~~~~~~~~~ 160 (169)
....+..+++++...|++ +.+.|+..|+|.+.|-.-+.+-..++.++
T Consensus 20 r~~IL~AA~~lf~e~Gy~~~s~~dIA~~aGvs~gtiY~hF~sKe~L~~a~ 69 (212)
T PRK15008 20 KKAILSAALDTFSQFGFHGTRLEQIAELAGVSKTNLLYYFPSKEALYIAV 69 (212)
T ss_pred HHHHHHHHHHHHHHhCcccCCHHHHHHHhCcCHHHHHHHCCCHHHHHHHH
Confidence 456899999999999976 88999999999999999888877777654
No 188
>PF14338 Mrr_N: Mrr N-terminal domain
Probab=34.15 E-value=1.4e+02 Score=21.15 Aligned_cols=41 Identities=20% Similarity=0.206 Sum_probs=31.2
Q ss_pred chhHHHHHHHHHHHhcCC------HHHHHHHhcCChhHHHHHHhcCh
Q 043121 114 FSLGMQALLDLIFAVEGS------VSEAAKLLWLSTGALSRLILSDD 154 (169)
Q Consensus 114 f~~~l~~~lD~l~~~~~~------~~~aa~~l~~st~~L~k~l~~~~ 154 (169)
|.-+|..+|..|.+.+++ ...+++.+++|..++-..+.+-+
T Consensus 2 ~~~~~~piL~~L~~~g~~~~~~ei~~~v~~~~~ls~e~~~~~~~sg~ 48 (92)
T PF14338_consen 2 YDELMPPILEALKDLGGSASRKEIYERVAERFGLSDEERNERLPSGQ 48 (92)
T ss_pred HHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHhCCCHHHHHHHcccCC
Confidence 455777789999887777 44578999999998887665444
No 189
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=33.93 E-value=84 Score=22.41 Aligned_cols=42 Identities=12% Similarity=-0.053 Sum_probs=31.6
Q ss_pred CCCchhHHHHHHHHHHHhcCCHHHHHHHhcCC-hhHHHHHHhc
Q 043121 111 NPKFSLGMQALLDLIFAVEGSVSEAAKLLWLS-TGALSRLILS 152 (169)
Q Consensus 111 n~~f~~~l~~~lD~l~~~~~~~~~aa~~l~~s-t~~L~k~l~~ 152 (169)
.|....-|..+...|..-+.++.++|..+|++ ++.|.+.+++
T Consensus 52 ~~i~~~Rl~~a~~~L~~~~~~i~~iA~~~Gf~~~s~f~~~Fk~ 94 (107)
T PRK10219 52 DYIRQRRLLLAAVELRTTERPIFDIAMDLGYVSQQTFSRVFRR 94 (107)
T ss_pred HHHHHHHHHHHHHHHHccCCCHHHHHHHHCCCCHHHHHHHHHH
Confidence 33444567888888888778899999999965 6677777754
No 190
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=33.83 E-value=1.1e+02 Score=23.81 Aligned_cols=35 Identities=26% Similarity=0.210 Sum_probs=26.3
Q ss_pred hHHHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHH
Q 043121 116 LGMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLI 150 (169)
Q Consensus 116 ~~l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l 150 (169)
+--+.++.+..-.+.+++++|+.||+|.+.+-.-+
T Consensus 144 ~~~~~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l 178 (194)
T PRK12519 144 ESQRQVLELAYYEGLSQSEIAKRLGIPLGTVKARA 178 (194)
T ss_pred HHHhhhhhhhhhcCCCHHHHHHHhCCCHHHHHHHH
Confidence 33445555556678889999999999999887554
No 191
>PF13556 HTH_30: PucR C-terminal helix-turn-helix domain; PDB: 3ONQ_B.
Probab=33.68 E-value=85 Score=20.62 Aligned_cols=30 Identities=20% Similarity=0.292 Sum_probs=22.4
Q ss_pred HHHHHHHHhcCCHHHHHHHhcCChhHHHHH
Q 043121 120 ALLDLIFAVEGSVSEAAKLLWLSTGALSRL 149 (169)
Q Consensus 120 ~~lD~l~~~~~~~~~aa~~l~~st~~L~k~ 149 (169)
+.|+.....+++++.+|+.|++.+.-+..=
T Consensus 3 ~TL~~yl~~~~n~~~tA~~L~iHrNTl~yR 32 (59)
T PF13556_consen 3 ETLRAYLENNGNISKTARALHIHRNTLRYR 32 (59)
T ss_dssp -HHHHHHHTTT-HHHHHHHHTS-HHHHHHH
T ss_pred hHHHHHHHcCCCHHHHHHHHCCCHHHHHHH
Confidence 567888899999999999999988766543
No 192
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=33.61 E-value=95 Score=23.62 Aligned_cols=36 Identities=19% Similarity=0.109 Sum_probs=27.6
Q ss_pred hhHHHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHH
Q 043121 115 SLGMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLI 150 (169)
Q Consensus 115 ~~~l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l 150 (169)
|+--..++-+....+.+++++|+.||+|.+.+-..+
T Consensus 120 ~~~~r~vl~L~~~~g~s~~EIA~~lgis~~tV~~~l 155 (173)
T PRK09645 120 SPEHRAVLVRSYYRGWSTAQIAADLGIPEGTVKSRL 155 (173)
T ss_pred CHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHH
Confidence 334555666667779999999999999998886443
No 193
>PRK13503 transcriptional activator RhaS; Provisional
Probab=33.06 E-value=72 Score=26.10 Aligned_cols=37 Identities=16% Similarity=0.148 Sum_probs=30.1
Q ss_pred HHHHHHHHHHHhcCCHHHHHHHhcCC-hhHHHHHHhcC
Q 043121 117 GMQALLDLIFAVEGSVSEAAKLLWLS-TGALSRLILSD 153 (169)
Q Consensus 117 ~l~~~lD~l~~~~~~~~~aa~~l~~s-t~~L~k~l~~~ 153 (169)
-|..+..+|...+++++++|..+|++ .+.++|++++.
T Consensus 224 Rl~~A~~LL~~~~~sI~eIA~~~GF~~~s~F~r~FKk~ 261 (278)
T PRK13503 224 RLLKARHLLRHSDASVTDIAYRCGFGDSNHFSTLFRRE 261 (278)
T ss_pred HHHHHHHHHHcCCCCHHHHHHHhCCCCHHHHHHHHHHH
Confidence 37778888888889999999999975 67788887764
No 194
>PF01402 RHH_1: Ribbon-helix-helix protein, copG family; InterPro: IPR002145 CopG, also known as RepA, is responsible for the regulation of plasmid copy number. It binds to the repAB promoter and controls synthesis of the plasmid replication initiator protein RepB. Many bacterial transcription regulation proteins bind DNA through a 'helix-turn-helix' motif, nevertheless CopG displays a fully defined HTH-motif structure that is involved not in DNA-binding, but in the maintenance of the intrinsic dimeric functional structure and cooperativity [, ].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2BJ3_B 2BJ8_A 2BJ1_A 2BJ9_A 2BJ7_B 1EA4_L 2CPG_C 1B01_B 2BA3_A 2K9I_B ....
Probab=33.04 E-value=43 Score=19.84 Aligned_cols=21 Identities=33% Similarity=0.218 Sum_probs=16.6
Q ss_pred HHHHHHHhcCChhHHHHHHhc
Q 043121 132 VSEAAKLLWLSTGALSRLILS 152 (169)
Q Consensus 132 ~~~aa~~l~~st~~L~k~l~~ 152 (169)
+...|+..|.|.+++++.+..
T Consensus 14 l~~~a~~~g~s~s~~ir~ai~ 34 (39)
T PF01402_consen 14 LDELAKELGRSRSELIREAIR 34 (39)
T ss_dssp HHHHHHHHTSSHHHHHHHHHH
T ss_pred HHHHHHHHCcCHHHHHHHHHH
Confidence 356788899999999987653
No 195
>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=32.94 E-value=1.1e+02 Score=20.39 Aligned_cols=34 Identities=18% Similarity=0.242 Sum_probs=22.8
Q ss_pred HHHHHHHHHHHhcCC--HHHHHHHhcCChhHHHHHHh
Q 043121 117 GMQALLDLIFAVEGS--VSEAAKLLWLSTGALSRLIL 151 (169)
Q Consensus 117 ~l~~~lD~l~~~~~~--~~~aa~~l~~st~~L~k~l~ 151 (169)
+|..++++.. -++. .++.|+.|++|++-.+..|+
T Consensus 9 YL~~Iy~l~~-~~~~v~~~~iA~~L~vs~~tvt~ml~ 44 (60)
T PF01325_consen 9 YLKAIYELSE-EGGPVRTKDIAERLGVSPPTVTEMLK 44 (60)
T ss_dssp HHHHHHHHHH-CTSSBBHHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHHHc-CCCCccHHHHHHHHCCChHHHHHHHH
Confidence 4556666664 2222 78899999999988877664
No 196
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=32.71 E-value=50 Score=21.37 Aligned_cols=38 Identities=13% Similarity=0.246 Sum_probs=23.3
Q ss_pred CCCCCcCCc--cCceEEEEeeC----Cc-eEEEEcccCCHHHHHHHHHHH
Q 043121 37 GPGSQHRNK--RESAVRLKHVP----TG-VIAHAAEDRSQHKNHASSVNL 79 (169)
Q Consensus 37 GpGGQ~vNk--~~saVrl~H~p----tG-i~v~~~~~RSq~~Nr~~Al~~ 79 (169)
|+||.++++ .++.|.|.--+ .+ +++... ..+-..|..+
T Consensus 16 G~~G~~i~~i~~~~g~~I~i~~~~~~~~~v~I~G~-----~~~v~~A~~~ 60 (62)
T cd02394 16 GKKGSNIRKIMEETGVKIRFPDPGSKSDTITITGP-----KENVEKAKEE 60 (62)
T ss_pred CCCCCcHHHHHHHhCCEEEcCCCCCCCCEEEEEcC-----HHHHHHHHHH
Confidence 899999995 44777776544 34 555554 2344555543
No 197
>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=32.27 E-value=1.1e+02 Score=22.03 Aligned_cols=23 Identities=26% Similarity=0.122 Sum_probs=17.0
Q ss_pred cCCHHHHHHHhcCChhHHHHHHh
Q 043121 129 EGSVSEAAKLLWLSTGALSRLIL 151 (169)
Q Consensus 129 ~~~~~~aa~~l~~st~~L~k~l~ 151 (169)
.-+.++.|+.+|+|++.++|.|.
T Consensus 47 ~is~~eLa~~~g~sr~tVsr~L~ 69 (95)
T TIGR01610 47 RVTATVIAELTGLSRTHVSDAIK 69 (95)
T ss_pred ccCHHHHHHHHCcCHHHHHHHHH
Confidence 34467788888888888877654
No 198
>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=32.14 E-value=68 Score=19.98 Aligned_cols=32 Identities=31% Similarity=0.245 Sum_probs=24.2
Q ss_pred HHHHHHHHhcCCHHHHHHHhcCChhHHHHHHh
Q 043121 120 ALLDLIFAVEGSVSEAAKLLWLSTGALSRLIL 151 (169)
Q Consensus 120 ~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~ 151 (169)
.++..|....-.+.+.|+.||+|.+.+++-|+
T Consensus 6 ~Il~~L~~~~~~~~el~~~l~~s~~~vs~hL~ 37 (47)
T PF01022_consen 6 RILKLLSEGPLTVSELAEELGLSQSTVSHHLK 37 (47)
T ss_dssp HHHHHHTTSSEEHHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHhCCCchhhHHHhccccchHHHHHHH
Confidence 45666666677799999999999999986553
No 199
>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=31.61 E-value=40 Score=25.69 Aligned_cols=27 Identities=33% Similarity=0.410 Sum_probs=22.8
Q ss_pred CCHHHHHHHhcCChhHHHHHHhcChhH
Q 043121 130 GSVSEAAKLLWLSTGALSRLILSDDSH 156 (169)
Q Consensus 130 ~~~~~aa~~l~~st~~L~k~l~~~~~~ 156 (169)
.++.+||+.||++.+.+++.+.+...+
T Consensus 81 ~S~~EAar~lgi~~~tIs~~~~~~k~~ 107 (113)
T cd00283 81 DSTTEAARFLKVHSGTISKNIKSGKLL 107 (113)
T ss_pred CCHHHHHHHHCCCcchhHHHHCCCccc
Confidence 468899999999999999998776644
No 200
>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=31.60 E-value=1e+02 Score=23.16 Aligned_cols=36 Identities=19% Similarity=0.213 Sum_probs=28.1
Q ss_pred hhHHHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHH
Q 043121 115 SLGMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLI 150 (169)
Q Consensus 115 ~~~l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l 150 (169)
|+--..++-+....+.+.+++|+.||+|.+.+-+.+
T Consensus 112 ~~~~r~i~~l~~~~g~s~~eIA~~lgis~~tV~~~l 147 (162)
T TIGR02983 112 PARQRAVVVLRYYEDLSEAQVAEALGISVGTVKSRL 147 (162)
T ss_pred CHHHHHHhhhHHHhcCCHHHHHHHhCCCHHHHHHHH
Confidence 344556666667778999999999999999887654
No 201
>COG1309 AcrR Transcriptional regulator [Transcription]
Probab=31.45 E-value=1.1e+02 Score=21.63 Aligned_cols=45 Identities=29% Similarity=0.220 Sum_probs=35.1
Q ss_pred hHHHHHHHHHHHhcCC---HHHHHHHhcCChhHHHHHHhcChhHHHHH
Q 043121 116 LGMQALLDLIFAVEGS---VSEAAKLLWLSTGALSRLILSDDSHQIAV 160 (169)
Q Consensus 116 ~~l~~~lD~l~~~~~~---~~~aa~~l~~st~~L~k~l~~~~~~~~~~ 160 (169)
..+...++++...+.+ +.+.|+.+|+|++.+-+-+.+-..++.++
T Consensus 16 ~ii~aa~~l~~~~G~~~~t~~~Ia~~agvs~~~~Y~~f~~K~~l~~~~ 63 (201)
T COG1309 16 RILDAALRLFAEKGYAATTVDEIAKAAGVSKGTLYRHFPSKEDLLLAL 63 (201)
T ss_pred HHHHHHHHHHHHcCcCCCCHHHHHHHhCCCcchhHHHcCCHHHHHHHH
Confidence 3677788888876665 88999999999999999888765555443
No 202
>PF09607 BrkDBD: Brinker DNA-binding domain; InterPro: IPR018586 This DNA-binding domain is the first approx. 100 residues of the N-terminal end of Brinker. The structure of this domain in complex with DNA consists of four alpha-helices that contain a helix-turn-helix DNA recognition motif specific for GC-rich DNA. The Brinker nuclear repressor is a major element of the Drosophila Decapentaplegic morphogen signalling pathway []. ; PDB: 2GLO_A.
Probab=31.38 E-value=65 Score=22.29 Aligned_cols=34 Identities=12% Similarity=0.118 Sum_probs=26.5
Q ss_pred HHhcCCHHHHHHHhcCChhHHHHHHhcChhHHHH
Q 043121 126 FAVEGSVSEAAKLLWLSTGALSRLILSDDSHQIA 159 (169)
Q Consensus 126 ~~~~~~~~~aa~~l~~st~~L~k~l~~~~~~~~~ 159 (169)
..|.|+.-+||..|+++..++-+-++..+.|...
T Consensus 22 ~nc~~~~RAaarkf~V~r~~Vr~W~kqe~~L~~~ 55 (58)
T PF09607_consen 22 NNCKGNQRAAARKFNVSRRQVRKWRKQEEELREE 55 (58)
T ss_dssp TTTTT-HHHHHHHTTS-HHHHHHHHTTHHHHHHH
T ss_pred cchhhhHHHHHHHhCccHHHHHHHHHHHHHHHhh
Confidence 3456677889999999999999999998888654
No 203
>PF00376 MerR: MerR family regulatory protein; InterPro: IPR000551 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these is the MerR subfamily. MerR, which is found in many bacterial species mediates the mercuric-dependent induction of the mercury resistance operon. In the absence of mercury merR represses transcription by binding tightly, as a dimer, to the 'mer' operator region; when mercury is present the dimeric complex binds a single ion and becomes a potent transcriptional activator, while remaining bound to the mer site. Members of the family include the mercuric resistance operon regulatory protein merR; Bacillus subtilis bltR and bmrR; Bacillus glnR; Streptomyces coelicolor hspR; Bradyrhizobium japonicum nolA; Escherichia coli superoxide response regulator soxR; and Streptomyces lividans transcriptional activator tipA [, , , , , ]. Other members include hypothetical proteins from E. coli, B. subtilis and Haemophilus influenzae. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3HH0_A 2DG6_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q07_A 1Q06_A 1Q05_B ....
Probab=31.28 E-value=42 Score=20.69 Aligned_cols=17 Identities=41% Similarity=0.442 Sum_probs=13.5
Q ss_pred HHHHHHHhcCChhHHHH
Q 043121 132 VSEAAKLLWLSTGALSR 148 (169)
Q Consensus 132 ~~~aa~~l~~st~~L~k 148 (169)
+.++|+.+|+|+..|-.
T Consensus 2 i~e~A~~~gvs~~tlR~ 18 (38)
T PF00376_consen 2 IGEVAKLLGVSPRTLRY 18 (38)
T ss_dssp HHHHHHHHTS-HHHHHH
T ss_pred HHHHHHHHCCCHHHHHH
Confidence 67899999999988754
No 204
>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=31.17 E-value=1.1e+02 Score=22.89 Aligned_cols=36 Identities=25% Similarity=0.312 Sum_probs=28.1
Q ss_pred hhHHHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHH
Q 043121 115 SLGMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLI 150 (169)
Q Consensus 115 ~~~l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l 150 (169)
|+--..++.+..-.+.+++++|+.||+|.+.+-..+
T Consensus 124 ~~~~r~vl~l~~~~g~s~~eIA~~l~is~~tv~~~l 159 (170)
T TIGR02952 124 TPKQQHVIALRFGQNLPIAEVARILGKTEGAVKILQ 159 (170)
T ss_pred CHHHHHHHHHHHhcCCCHHHHHHHHCCCHHHHHHHH
Confidence 344556777777789999999999999998876544
No 205
>PF13309 HTH_22: HTH domain
Probab=31.11 E-value=32 Score=23.41 Aligned_cols=27 Identities=30% Similarity=0.395 Sum_probs=22.5
Q ss_pred HHHHhcCCHHHHHHHhcCChhHHHHHH
Q 043121 124 LIFAVEGSVSEAAKLLWLSTGALSRLI 150 (169)
Q Consensus 124 ~l~~~~~~~~~aa~~l~~st~~L~k~l 150 (169)
.++...|.+...|+.||+|..-+-+-|
T Consensus 37 G~F~lKgav~~vA~~L~iS~~TVY~YL 63 (64)
T PF13309_consen 37 GIFLLKGAVEYVAEKLGISRATVYRYL 63 (64)
T ss_pred CCcccCcHHHHHHHHHCCCHHHHHHHc
Confidence 567788889999999999988776654
No 206
>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=31.10 E-value=85 Score=23.21 Aligned_cols=32 Identities=16% Similarity=0.144 Sum_probs=24.6
Q ss_pred hhHHHHHHHHHHHhcCCHHHHHHHhcCChhHH
Q 043121 115 SLGMQALLDLIFAVEGSVSEAAKLLWLSTGAL 146 (169)
Q Consensus 115 ~~~l~~~lD~l~~~~~~~~~aa~~l~~st~~L 146 (169)
|+-...++-+..--+.+.+++|+.||+|.+.+
T Consensus 109 p~~~r~v~~l~~~~~~s~~EIA~~l~is~~tV 140 (142)
T TIGR03209 109 PNKQKKIIYMKFFEDMKEIDIAKKLHISRQSV 140 (142)
T ss_pred CHHHHHHHHHHHHcCCCHHHHHHHHCcCHHhh
Confidence 44455666666667789999999999998865
No 207
>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=30.92 E-value=1.2e+02 Score=19.07 Aligned_cols=32 Identities=25% Similarity=0.302 Sum_probs=22.4
Q ss_pred HHHHHHHHhcC--CHHHHHHHhcCChhHHHHHHh
Q 043121 120 ALLDLIFAVEG--SVSEAAKLLWLSTGALSRLIL 151 (169)
Q Consensus 120 ~~lD~l~~~~~--~~~~aa~~l~~st~~L~k~l~ 151 (169)
.++..|...++ +.++.|+.|++|...+.+-|.
T Consensus 4 ~il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i~ 37 (55)
T PF08279_consen 4 QILKLLLESKEPITAKELAEELGVSRRTIRRDIK 37 (55)
T ss_dssp HHHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHHH
T ss_pred HHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHH
Confidence 45666754444 678899999999988776554
No 208
>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=30.85 E-value=1.2e+02 Score=23.21 Aligned_cols=37 Identities=24% Similarity=0.129 Sum_probs=28.3
Q ss_pred hhHHHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHHh
Q 043121 115 SLGMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLIL 151 (169)
Q Consensus 115 ~~~l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~ 151 (169)
|+.-..++-.....+.+.+++|+.||+|.+.+-+.+.
T Consensus 142 ~~~~r~vi~l~~~~g~s~~eIA~~lgis~~~v~~~l~ 178 (189)
T TIGR02984 142 PEDYREVILLRHLEGLSFAEVAERMDRSEGAVSMLWV 178 (189)
T ss_pred CHHHHHHHHHHHhcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 4445556666666888999999999999999886543
No 209
>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=30.60 E-value=93 Score=20.26 Aligned_cols=35 Identities=26% Similarity=0.145 Sum_probs=25.9
Q ss_pred hHHHHHHHHH-HHhcCCHHHHHHHhcCChhHHHHHH
Q 043121 116 LGMQALLDLI-FAVEGSVSEAAKLLWLSTGALSRLI 150 (169)
Q Consensus 116 ~~l~~~lD~l-~~~~~~~~~aa~~l~~st~~L~k~l 150 (169)
+.-..+|+.| ..-+..+++.|+.||++.+.+.+=|
T Consensus 10 p~R~~Il~~L~~~~~~t~~ela~~l~~~~~t~s~hL 45 (61)
T PF12840_consen 10 PTRLRILRLLASNGPMTVSELAEELGISQSTVSYHL 45 (61)
T ss_dssp HHHHHHHHHHHHCSTBEHHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHH
Confidence 3345677788 6667779999999999999887543
No 210
>PRK15243 transcriptional regulator SpvR; Provisional
Probab=30.09 E-value=53 Score=28.34 Aligned_cols=26 Identities=35% Similarity=0.477 Sum_probs=22.6
Q ss_pred HhcCCHHHHHHHhcCChhHHHHHHhc
Q 043121 127 AVEGSVSEAAKLLWLSTGALSRLILS 152 (169)
Q Consensus 127 ~~~~~~~~aa~~l~~st~~L~k~l~~ 152 (169)
+-.|+++.||+.|++|.++|++-|+.
T Consensus 16 ae~gSfs~AA~~L~isQpavS~~Ik~ 41 (297)
T PRK15243 16 METGSFSIATSVLYITRTPLSRVISD 41 (297)
T ss_pred HHcCCHHHHHHHHCcCHHHHHHHHHH
Confidence 44689999999999999999987763
No 211
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=29.96 E-value=81 Score=26.57 Aligned_cols=32 Identities=34% Similarity=0.473 Sum_probs=28.4
Q ss_pred HHHHHHHHhcCC--HHHHHHHhcCChhHHHHHHh
Q 043121 120 ALLDLIFAVEGS--VSEAAKLLWLSTGALSRLIL 151 (169)
Q Consensus 120 ~~lD~l~~~~~~--~~~aa~~l~~st~~L~k~l~ 151 (169)
.+||.+...... +++.|+.+|++.+-+-|+|.
T Consensus 8 ~iL~~l~~~~~~l~l~ela~~~glpksT~~RlL~ 41 (246)
T COG1414 8 AILDLLAEGPGGLSLAELAERLGLPKSTVHRLLQ 41 (246)
T ss_pred HHHHHHHhCCCCCCHHHHHHHhCcCHHHHHHHHH
Confidence 488999987777 99999999999999998875
No 212
>PRK13502 transcriptional activator RhaR; Provisional
Probab=29.92 E-value=78 Score=26.16 Aligned_cols=41 Identities=12% Similarity=-0.028 Sum_probs=32.2
Q ss_pred HHHHHHHHHHhcCCHHHHHHHhcCC-hhHHHHHHhcC----hhHHH
Q 043121 118 MQALLDLIFAVEGSVSEAAKLLWLS-TGALSRLILSD----DSHQI 158 (169)
Q Consensus 118 l~~~lD~l~~~~~~~~~aa~~l~~s-t~~L~k~l~~~----~~~~~ 158 (169)
|..+..+|..-+.+++++|..+|++ .+-++|++++. |..++
T Consensus 230 l~~A~~lL~~t~~sI~eIA~~~GF~d~s~F~r~FKk~~G~tP~~yR 275 (282)
T PRK13502 230 ICHAQYLLQHSPLMISEISMQCGFEDSNYFSVVFTRETGMTPSQWR 275 (282)
T ss_pred HHHHHHHHHcCCCCHHHHHHHcCCCCHHHHHHHHHHHHCcCHHHHH
Confidence 6677888888888899999999986 77788888875 55555
No 213
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=29.62 E-value=1.2e+02 Score=23.55 Aligned_cols=36 Identities=3% Similarity=0.061 Sum_probs=27.5
Q ss_pred hhHHHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHH
Q 043121 115 SLGMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLI 150 (169)
Q Consensus 115 ~~~l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l 150 (169)
|+--..++-+..--+.+++++|+.||+|.+.+-..+
T Consensus 124 ~~~~r~i~~l~~~~g~s~~EIA~~lgis~~tVk~~l 159 (185)
T PRK12542 124 NESNRQVFKYKVFYNLTYQEISSVMGITEANVRKQF 159 (185)
T ss_pred CHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHH
Confidence 334455666666788899999999999999887544
No 214
>PRK10668 DNA-binding transcriptional repressor AcrR; Provisional
Probab=29.60 E-value=1.4e+02 Score=23.45 Aligned_cols=46 Identities=17% Similarity=0.066 Sum_probs=39.6
Q ss_pred hHHHHHHHHHHHhcCC---HHHHHHHhcCChhHHHHHHhcChhHHHHHH
Q 043121 116 LGMQALLDLIFAVEGS---VSEAAKLLWLSTGALSRLILSDDSHQIAVN 161 (169)
Q Consensus 116 ~~l~~~lD~l~~~~~~---~~~aa~~l~~st~~L~k~l~~~~~~~~~~n 161 (169)
..+...++++...|++ +.++|+..|+|.+.|-+-+.+-..++.+|-
T Consensus 15 ~Il~AA~~lf~e~G~~~~t~~~Ia~~agvs~~tlY~~F~sKe~Ll~~v~ 63 (215)
T PRK10668 15 HILDAALRLFSQQGVSATSLADIAKAAGVTRGAIYWHFKNKSDLFSEIW 63 (215)
T ss_pred HHHHHHHHHHHHcCcccCCHHHHHHHhCCChHHHHHHCCCHHHHHHHHH
Confidence 3788899999999886 899999999999999999888888776664
No 215
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=29.57 E-value=1.2e+02 Score=23.54 Aligned_cols=32 Identities=19% Similarity=0.072 Sum_probs=24.3
Q ss_pred HHHHHHHHhcCCHHHHHHHhcCChhHHHHHHh
Q 043121 120 ALLDLIFAVEGSVSEAAKLLWLSTGALSRLIL 151 (169)
Q Consensus 120 ~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~ 151 (169)
.++-.....+.+++++|+.||+|.+.+-+.|.
T Consensus 144 ~i~~l~~~~g~s~~eIA~~lgis~~~v~~~l~ 175 (187)
T PRK12534 144 ELIRTAFFEGITYEELAARTDTPIGTVKSWIR 175 (187)
T ss_pred HHHHHHHHcCCCHHHHHHHhCCChhHHHHHHH
Confidence 33444456788999999999999999876543
No 216
>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=29.48 E-value=63 Score=20.64 Aligned_cols=23 Identities=26% Similarity=0.200 Sum_probs=18.5
Q ss_pred cCCHHHHHHHhcCChhHHHHHHh
Q 043121 129 EGSVSEAAKLLWLSTGALSRLIL 151 (169)
Q Consensus 129 ~~~~~~aa~~l~~st~~L~k~l~ 151 (169)
..+.++.|+.+|+|++.+.+.|.
T Consensus 25 ~~s~~ela~~~g~s~~tv~r~l~ 47 (67)
T cd00092 25 PLTRQEIADYLGLTRETVSRTLK 47 (67)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHH
Confidence 35678899999999988887664
No 217
>smart00351 PAX Paired Box domain.
Probab=29.35 E-value=1.9e+02 Score=21.89 Aligned_cols=34 Identities=18% Similarity=0.266 Sum_probs=26.3
Q ss_pred HHHHHHHHHhcCCHHHHHHHhcCChhHHHHHHhcC
Q 043121 119 QALLDLIFAVEGSVSEAAKLLWLSTGALSRLILSD 153 (169)
Q Consensus 119 ~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~~~ 153 (169)
+.+++.. .-+.+..++|+.||+|.+-+.|.++..
T Consensus 24 ~riv~~~-~~G~s~~~iA~~~gvs~~tV~kwi~r~ 57 (125)
T smart00351 24 QRIVELA-QNGVRPCDISRQLCVSHGCVSKILGRY 57 (125)
T ss_pred HHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 3344443 356689999999999999999998864
No 218
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=29.27 E-value=1.2e+02 Score=23.88 Aligned_cols=35 Identities=17% Similarity=0.032 Sum_probs=26.5
Q ss_pred hHHHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHH
Q 043121 116 LGMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLI 150 (169)
Q Consensus 116 ~~l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l 150 (169)
+-...++-+....+.+++++|+.||+|.+.+-..|
T Consensus 137 ~~~R~v~~L~~~~g~s~~EIA~~lgis~~tVk~~l 171 (189)
T PRK12530 137 AQQARVFMMREYLELSSEQICQECDISTSNLHVLL 171 (189)
T ss_pred HHHHHHHhHHHHcCCCHHHHHHHHCCCHHHHHHHH
Confidence 34455555666678999999999999999986443
No 219
>PF09048 Cro: Cro; InterPro: IPR000655 Bacteriophage lambda encodes two repressors: the Cro repressor that acts to turn off early gene transcription during the lytic cycle, and the lambda or cI repressor that is required to maintain lysogenic growth. Together the Cro and cI repressors form a helix-turn-helix (HTH) superfamily. The lambda Cro repressor binds to DNA as a highly flexible dimer. The crystal structure of the lambda Cro repressor [] reveals a HTH DNA-binding protein with an alpha/beta fold that differs from other Cro family members, possibly by an evolutionary fold change []. Most Cro proteins, such as Enterobacteria phage P22 Cro and Bacteriophage 434 Cro, have an all-alpha structure that is thought to be ancestral to lambda Cro, where the fourth and fifth helices are replaced by a beta-sheet, possibly as a result of secondary structure switching rather than by nonhomologous replacement []. This entry represents the lambda-type Cro repressor with an alpha/beta topology.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 5CRO_A 2ECS_A 2OVG_A 6CRO_A 1D1L_A 2ORC_A 1D1M_B 3ORC_A 1ORC_A 2A63_A ....
Probab=29.13 E-value=97 Score=21.58 Aligned_cols=24 Identities=21% Similarity=0.308 Sum_probs=18.8
Q ss_pred HHHHHHHhcCChhHHHHHHhcChh
Q 043121 132 VSEAAKLLWLSTGALSRLILSDDS 155 (169)
Q Consensus 132 ~~~aa~~l~~st~~L~k~l~~~~~ 155 (169)
-..+|+.||++.++++|-|+....
T Consensus 15 Q~kaA~~lGV~Q~AIsKAlr~gR~ 38 (59)
T PF09048_consen 15 QAKAARALGVTQSAISKALRAGRN 38 (59)
T ss_dssp HHHHHHHHTS-HHHHHHHHHCT-E
T ss_pred hHHHHHHcCCcHHHHHHHHHcCCc
Confidence 467899999999999999987543
No 220
>PF04255 DUF433: Protein of unknown function (DUF433); InterPro: IPR007367 This is a family of uncharacterised proteins.; PDB: 2GA1_B.
Probab=29.13 E-value=87 Score=20.59 Aligned_cols=30 Identities=27% Similarity=0.281 Sum_probs=21.8
Q ss_pred HHHHHHHHHHhcCCHHHHHHHhc-CChhHHHH
Q 043121 118 MQALLDLIFAVEGSVSEAAKLLW-LSTGALSR 148 (169)
Q Consensus 118 l~~~lD~l~~~~~~~~~aa~~l~-~st~~L~k 148 (169)
...+++.+ +.++++.+.++.+. |+..++--
T Consensus 21 v~~i~~~~-~~G~s~eeI~~~yp~Lt~~~i~a 51 (56)
T PF04255_consen 21 VRDILDLL-AAGESPEEIAEDYPSLTLEDIRA 51 (56)
T ss_dssp HHHHHHHH-HTT--HHHHHHHSTT--HHHHHH
T ss_pred HHHHHHHH-HcCCCHHHHHHHCCCCCHHHHHH
Confidence 56788888 99999999999998 89888753
No 221
>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=29.09 E-value=65 Score=20.23 Aligned_cols=21 Identities=24% Similarity=0.129 Sum_probs=16.9
Q ss_pred CHHHHHHHhcCChhHHHHHHh
Q 043121 131 SVSEAAKLLWLSTGALSRLIL 151 (169)
Q Consensus 131 ~~~~aa~~l~~st~~L~k~l~ 151 (169)
+..+.|..+++|+..+.+.|.
T Consensus 27 ~~~~la~~~~is~~~v~~~l~ 47 (66)
T cd07377 27 SERELAEELGVSRTTVREALR 47 (66)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 377899999999988876654
No 222
>PRK00767 transcriptional regulator BetI; Validated
Probab=28.91 E-value=1.4e+02 Score=22.90 Aligned_cols=45 Identities=24% Similarity=0.118 Sum_probs=38.1
Q ss_pred hhHHHHHHHHHHHhcCC---HHHHHHHhcCChhHHHHHHhcChhHHHH
Q 043121 115 SLGMQALLDLIFAVEGS---VSEAAKLLWLSTGALSRLILSDDSHQIA 159 (169)
Q Consensus 115 ~~~l~~~lD~l~~~~~~---~~~aa~~l~~st~~L~k~l~~~~~~~~~ 159 (169)
-..+...++++...|++ +.+.|+..|+|.+.|-.-+.+-..++..
T Consensus 12 ~~Il~aA~~lf~~~G~~~~s~~~Ia~~aGvs~gslY~~F~~Ke~L~~~ 59 (197)
T PRK00767 12 QQLIDATLRAIGEVGLLDATIAQIARRAGVSTGIISHYFGGKDGLLEA 59 (197)
T ss_pred HHHHHHHHHHHHHcCcccCCHHHHHHHhCCCHHHHHHHhCCHHHHHHH
Confidence 34788899999998886 8899999999999999999877766654
No 223
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=28.69 E-value=1.4e+02 Score=22.43 Aligned_cols=37 Identities=16% Similarity=0.006 Sum_probs=28.4
Q ss_pred hhHHHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHHh
Q 043121 115 SLGMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLIL 151 (169)
Q Consensus 115 ~~~l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~ 151 (169)
|+-...++-+..-.+.+.+++|+.||+|.+.+-.-|.
T Consensus 107 ~~~~r~v~~l~~~~~~s~~eIA~~lgis~~tv~~~l~ 143 (159)
T PRK12527 107 PPACRDSFLLRKLEGLSHQQIAEHLGISRSLVEKHIV 143 (159)
T ss_pred CHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHH
Confidence 3344556666677888999999999999998875544
No 224
>PRK14996 TetR family transcriptional regulator; Provisional
Probab=28.45 E-value=1.1e+02 Score=23.64 Aligned_cols=44 Identities=16% Similarity=0.098 Sum_probs=36.6
Q ss_pred hHHHHHHHHHHHhcCC---HHHHHHHhcCChhHHHHHHhcChhHHHH
Q 043121 116 LGMQALLDLIFAVEGS---VSEAAKLLWLSTGALSRLILSDDSHQIA 159 (169)
Q Consensus 116 ~~l~~~lD~l~~~~~~---~~~aa~~l~~st~~L~k~l~~~~~~~~~ 159 (169)
..+..++.++...|+. +.+.|+..|+|.+.|-.-+.+-..++..
T Consensus 12 ~Il~aA~~lf~e~G~~~tSi~~Ia~~aGvsk~~lY~~F~sK~~L~~~ 58 (192)
T PRK14996 12 VILQAAMRVALAEGFAAMTVRRIASEAQVAAGQVHHHFSSAGELKAL 58 (192)
T ss_pred HHHHHHHHHHHhcChhhccHHHHHHHhCCCcHHHHHHcCCHHHHHHH
Confidence 3677888888887765 7889999999999999999887776554
No 225
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=28.40 E-value=1.2e+02 Score=23.89 Aligned_cols=37 Identities=16% Similarity=0.062 Sum_probs=28.8
Q ss_pred hhHHHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHHh
Q 043121 115 SLGMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLIL 151 (169)
Q Consensus 115 ~~~l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~ 151 (169)
|+-...++-+..--+.+.+++|+.||+|.+.+-..|.
T Consensus 118 p~~~r~i~~L~~~~g~s~~EIA~~Lgis~~tVk~~l~ 154 (187)
T PRK12516 118 PDDQREAIILVGASGFAYEEAAEICGCAVGTIKSRVN 154 (187)
T ss_pred CHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 4445667777777899999999999999988765543
No 226
>KOG3933 consensus Mitochondrial ribosomal protein S28 [Translation, ribosomal structure and biogenesis]
Probab=28.20 E-value=1.1e+02 Score=27.64 Aligned_cols=32 Identities=9% Similarity=-0.015 Sum_probs=26.0
Q ss_pred CCc-eEEEEcccCCHHHHHHHHHHHHhCCChhh
Q 043121 56 PTG-VIAHAAEDRSQHKNHASSVNLDAYSPPPQ 87 (169)
Q Consensus 56 ptG-i~v~~~~~RSq~~Nr~~Al~~L~~L~~~e 87 (169)
-|+ ++|.|+.--+..+|+..|+.+|..||+..
T Consensus 201 ~tD~~tissDR~~~r~QN~~y~~~lLt~L~~ES 233 (296)
T KOG3933|consen 201 TTDLLTISSDRCEHREQNYDYALYLLTVLYHES 233 (296)
T ss_pred CCCeEEEeccccchhhHhHHHHHHHHHHHHHHh
Confidence 355 88999888899999999999997665443
No 227
>COG3829 RocR Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains [Transcription / Signal transduction mechanisms]
Probab=28.15 E-value=87 Score=30.49 Aligned_cols=35 Identities=26% Similarity=0.196 Sum_probs=30.2
Q ss_pred HHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHHhc
Q 043121 118 MQALLDLIFAVEGSVSEAAKLLWLSTGALSRLILS 152 (169)
Q Consensus 118 l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~~ 152 (169)
...+.+.|...+|+.+.||+.||+|.+-|.+=+++
T Consensus 522 k~~I~~aL~~~~gn~~~aAk~LgIsrttL~rKlkk 556 (560)
T COG3829 522 KHLIREALERHGGNKSKAAKELGISRTTLYRKLKK 556 (560)
T ss_pred HHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 34578899999999999999999999999876664
No 228
>smart00472 MIR Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases.
Probab=27.96 E-value=63 Score=20.51 Aligned_cols=21 Identities=43% Similarity=0.700 Sum_probs=17.2
Q ss_pred CceEEEEeeCCceEEEEcccC
Q 043121 47 ESAVRLKHVPTGVIAHAAEDR 67 (169)
Q Consensus 47 ~saVrl~H~ptGi~v~~~~~R 67 (169)
.+.|||+|..||--+.+++.+
T Consensus 7 g~~vrL~H~~tg~yL~s~~~~ 27 (57)
T smart00472 7 GDVVRLRHVTTGRYLHSHENK 27 (57)
T ss_pred CCEEEEEEhhhCcEeecCCCC
Confidence 579999999999777777665
No 229
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=27.85 E-value=1.3e+02 Score=23.12 Aligned_cols=36 Identities=22% Similarity=0.225 Sum_probs=28.3
Q ss_pred hhHHHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHH
Q 043121 115 SLGMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLI 150 (169)
Q Consensus 115 ~~~l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l 150 (169)
|+-...++-+....+.++.++|+.||+|.+.+-+.+
T Consensus 133 ~~~~r~v~~l~~~~g~s~~eIA~~l~is~~tV~~~l 168 (184)
T PRK12512 133 PPRQRDVVQSISVEGASIKETAAKLSMSEGAVRVAL 168 (184)
T ss_pred CHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHH
Confidence 344566677777789999999999999999887544
No 230
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=27.74 E-value=73 Score=21.53 Aligned_cols=24 Identities=21% Similarity=0.389 Sum_probs=20.8
Q ss_pred HHHHHHHhcCChhHHHHHHhcChh
Q 043121 132 VSEAAKLLWLSTGALSRLILSDDS 155 (169)
Q Consensus 132 ~~~aa~~l~~st~~L~k~l~~~~~ 155 (169)
..+.|+.+|+|.+.++++|...+.
T Consensus 3 ~~~iA~~~gvS~~TVSr~ln~~~~ 26 (70)
T smart00354 3 IKDVARLAGVSKATVSRVLNGNGR 26 (70)
T ss_pred HHHHHHHHCCCHHHHHHHHCCCCC
Confidence 568899999999999999987764
No 231
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=27.66 E-value=1.3e+02 Score=23.56 Aligned_cols=33 Identities=12% Similarity=0.254 Sum_probs=25.6
Q ss_pred HHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHH
Q 043121 118 MQALLDLIFAVEGSVSEAAKLLWLSTGALSRLI 150 (169)
Q Consensus 118 l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l 150 (169)
...++-+....+.+++++|+.||+|.+.+-+-|
T Consensus 146 ~r~v~~l~~~eg~s~~EIA~~lgis~~tVk~rl 178 (194)
T PRK12531 146 QRDVLQAVYLEELPHQQVAEMFDIPLGTVKSRL 178 (194)
T ss_pred HHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHH
Confidence 344566666778899999999999999885443
No 232
>PF04760 IF2_N: Translation initiation factor IF-2, N-terminal region; InterPro: IPR006847 This region is found in the N-terminal half of translation initiation factor IF-2. It is found in two copies in IF-2 alpha isoforms, and in only one copy in the N-terminally truncated beta and gamma isoforms []. Its function is unknown.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1ND9_A.
Probab=27.55 E-value=58 Score=20.95 Aligned_cols=20 Identities=30% Similarity=0.295 Sum_probs=17.7
Q ss_pred CHHHHHHHhcCChhHHHHHH
Q 043121 131 SVSEAAKLLWLSTGALSRLI 150 (169)
Q Consensus 131 ~~~~aa~~l~~st~~L~k~l 150 (169)
.+.+.|+.||+++..|++.|
T Consensus 5 ~V~elAk~l~v~~~~ii~~l 24 (54)
T PF04760_consen 5 RVSELAKELGVPSKEIIKKL 24 (54)
T ss_dssp -TTHHHHHHSSSHHHHHHHH
T ss_pred EHHHHHHHHCcCHHHHHHHH
Confidence 46789999999999999998
No 233
>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=27.36 E-value=1.3e+02 Score=20.00 Aligned_cols=31 Identities=26% Similarity=0.170 Sum_probs=22.6
Q ss_pred HHHHHHHhcCCHHHHHHHhcCChhHHHHHHh
Q 043121 121 LLDLIFAVEGSVSEAAKLLWLSTGALSRLIL 151 (169)
Q Consensus 121 ~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~ 151 (169)
++..+.......++.|+.||+|.+.+.+-|.
T Consensus 5 il~~L~~~~~~~~eLa~~l~vS~~tv~~~l~ 35 (69)
T TIGR00122 5 LLALLADNPFSGEKLGEALGMSRTAVNKHIQ 35 (69)
T ss_pred HHHHHHcCCcCHHHHHHHHCCCHHHHHHHHH
Confidence 4555666666788999999999877665443
No 234
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=27.31 E-value=53 Score=25.03 Aligned_cols=25 Identities=16% Similarity=0.162 Sum_probs=20.4
Q ss_pred HHhcCCHHHHHHHhcCChhHHHHHH
Q 043121 126 FAVEGSVSEAAKLLWLSTGALSRLI 150 (169)
Q Consensus 126 ~~~~~~~~~aa~~l~~st~~L~k~l 150 (169)
...+.+++++|+.||+|++.+-..+
T Consensus 133 ~~~g~s~~eIA~~lg~s~~tv~~~l 157 (175)
T PRK12518 133 DLEDLPQKEIAEILNIPVGTVKSRL 157 (175)
T ss_pred HhcCCCHHHHHHHHCCCHHHHHHHH
Confidence 4567789999999999998876544
No 235
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=27.22 E-value=1.4e+02 Score=23.08 Aligned_cols=34 Identities=21% Similarity=0.303 Sum_probs=25.7
Q ss_pred hhHHHHHHHHHHHhcCCHHHHHHHhcCChhHHHH
Q 043121 115 SLGMQALLDLIFAVEGSVSEAAKLLWLSTGALSR 148 (169)
Q Consensus 115 ~~~l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k 148 (169)
|+--..++-+..-.+.+++++|+.||+|.+.+-.
T Consensus 119 p~~~r~i~~l~~~e~~s~~EIA~~lgis~~tV~~ 152 (179)
T PRK12543 119 PYKLRQVIILRYLHDYSQEEIAQLLQIPIGTVKS 152 (179)
T ss_pred CHHHHHHHHHHHHccCCHHHHHHHHCCCHHHHHH
Confidence 3445556666667788999999999999887543
No 236
>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=27.06 E-value=1e+02 Score=22.45 Aligned_cols=31 Identities=10% Similarity=0.150 Sum_probs=23.2
Q ss_pred HHHHHHH-hcCCHHHHHHHhcCChhHHHHHHh
Q 043121 121 LLDLIFA-VEGSVSEAAKLLWLSTGALSRLIL 151 (169)
Q Consensus 121 ~lD~l~~-~~~~~~~aa~~l~~st~~L~k~l~ 151 (169)
+|..|.. .+.++++.|+.++++++.+++.|.
T Consensus 33 iL~~l~~~~~~t~~ela~~~~~~~~tvs~~l~ 64 (118)
T TIGR02337 33 ILRILAEQGSMEFTQLANQACILRPSLTGILA 64 (118)
T ss_pred HHHHHHHcCCcCHHHHHHHhCCCchhHHHHHH
Confidence 4444444 344689999999999999988775
No 237
>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=26.79 E-value=1.2e+02 Score=24.12 Aligned_cols=33 Identities=24% Similarity=0.095 Sum_probs=27.0
Q ss_pred HHHHHHHHHhcCCHHHHHHHhcCChhHHHHHHhc
Q 043121 119 QALLDLIFAVEGSVSEAAKLLWLSTGALSRLILS 152 (169)
Q Consensus 119 ~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~~ 152 (169)
..++.+. ..+.+.+++|+.||+|.+.+.+.+..
T Consensus 12 r~VL~Lr-~~GlTq~EIAe~LgiS~stV~~~e~r 44 (137)
T TIGR00721 12 IKVLELR-EKGLSQKEIAKELKTTRANVSAIEKR 44 (137)
T ss_pred HHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHh
Confidence 4456664 68899999999999999999977654
No 238
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=26.78 E-value=78 Score=19.45 Aligned_cols=21 Identities=24% Similarity=0.124 Sum_probs=16.2
Q ss_pred CHHHHHHHhcCChhHHHHHHh
Q 043121 131 SVSEAAKLLWLSTGALSRLIL 151 (169)
Q Consensus 131 ~~~~aa~~l~~st~~L~k~l~ 151 (169)
+..+.|+.|++|++.+.+.|.
T Consensus 22 s~~~la~~~~vs~~tv~~~l~ 42 (60)
T smart00345 22 SERELAAQLGVSRTTVREALS 42 (60)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 567789999999887766553
No 239
>PRK10130 transcriptional regulator EutR; Provisional
Probab=26.67 E-value=1.2e+02 Score=27.03 Aligned_cols=53 Identities=9% Similarity=0.041 Sum_probs=37.8
Q ss_pred hhHHHHHHHHHHH---hcCCHHHHHHHhcCChhHHHHHHhcC--hhHHHHHHHhhhhc
Q 043121 115 SLGMQALLDLIFA---VEGSVSEAAKLLWLSTGALSRLILSD--DSHQIAVNELRTSK 167 (169)
Q Consensus 115 ~~~l~~~lD~l~~---~~~~~~~aa~~l~~st~~L~k~l~~~--~~~~~~~n~~R~~~ 167 (169)
...+..+.|.|.+ -..++.+.|+.+++|+..|.+.+++. -+....+..+|-.+
T Consensus 239 ~~~v~~~~~~i~~~~~~~ltv~~lA~~~gvS~r~L~r~Fk~~~G~sp~~ylr~~RL~~ 296 (350)
T PRK10130 239 RRLLSRAREYVLENMSEPVTVLDLCNQLHVSRRTLQNAFHAILGIGPNAWLKRIRLNA 296 (350)
T ss_pred HHHHHHHHHHHHhhhcCCCCHHHHHHHHCCCHHHHHHHHHHHHCcCHHHHHHHHHHHH
Confidence 4456666666543 34679999999999999999999873 45556666666544
No 240
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=26.64 E-value=1.2e+02 Score=23.44 Aligned_cols=34 Identities=15% Similarity=0.212 Sum_probs=26.3
Q ss_pred HHHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHH
Q 043121 117 GMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLI 150 (169)
Q Consensus 117 ~l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l 150 (169)
--+.++.+..-.+.+++++|+.||+|.+.+-..+
T Consensus 131 ~~r~v~~l~~~~g~s~~EIA~~l~is~~tv~~~l 164 (179)
T PRK09415 131 KYREVIYLFYYEELSIKEIAEVTGVNENTVKTRL 164 (179)
T ss_pred HHhhHhHhHHhcCCCHHHHHHHHCCCHHHHHHHH
Confidence 3445666666778899999999999998876544
No 241
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=26.46 E-value=1e+02 Score=24.68 Aligned_cols=33 Identities=27% Similarity=0.309 Sum_probs=26.0
Q ss_pred HHHHHHHHHhcCCHHHHHHHhcCChhHHHHHHhc
Q 043121 119 QALLDLIFAVEGSVSEAAKLLWLSTGALSRLILS 152 (169)
Q Consensus 119 ~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~~ 152 (169)
..+.+. ...+.++.++|+.||+|++-+-|+++.
T Consensus 163 ~~i~~~-~~~g~s~~~iak~lgis~~Tv~r~~k~ 195 (200)
T PRK13413 163 EKIKKL-LDKGTSKSEIARKLGVSRTTLARFLKT 195 (200)
T ss_pred HHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHh
Confidence 334444 345779999999999999999998874
No 242
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=26.39 E-value=82 Score=20.47 Aligned_cols=23 Identities=17% Similarity=0.105 Sum_probs=19.5
Q ss_pred CCHHHHHHHhcCChhHHHHHHhc
Q 043121 130 GSVSEAAKLLWLSTGALSRLILS 152 (169)
Q Consensus 130 ~~~~~aa~~l~~st~~L~k~l~~ 152 (169)
++++++|+.+|+|++.|-+..+.
T Consensus 1 ~s~~eva~~~gvs~~tlr~w~~~ 23 (68)
T cd01104 1 YTIGAVARLTGVSPDTLRAWERR 23 (68)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHh
Confidence 36789999999999999987753
No 243
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=26.33 E-value=71 Score=21.53 Aligned_cols=33 Identities=21% Similarity=0.262 Sum_probs=21.9
Q ss_pred HHHHHHHHHHhc-CCHHHHHHHhcCChhHHHHHH
Q 043121 118 MQALLDLIFAVE-GSVSEAAKLLWLSTGALSRLI 150 (169)
Q Consensus 118 l~~~lD~l~~~~-~~~~~aa~~l~~st~~L~k~l 150 (169)
|..+.|.|..-+ -+..+.|..|++|++++--+|
T Consensus 2 L~~i~~~l~~~~~~S~~eLa~~~~~s~~~ve~mL 35 (69)
T PF09012_consen 2 LQEIRDYLRERGRVSLAELAREFGISPEAVEAML 35 (69)
T ss_dssp CHHHHHHHHHS-SEEHHHHHHHTT--HHHHHHHH
T ss_pred HHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHH
Confidence 345677665554 478899999999999886554
No 244
>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=26.16 E-value=1.4e+02 Score=24.01 Aligned_cols=36 Identities=31% Similarity=0.227 Sum_probs=27.4
Q ss_pred hHHHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHHh
Q 043121 116 LGMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLIL 151 (169)
Q Consensus 116 ~~l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~ 151 (169)
+--+.++......+.+++++|+.||+|++.+-+.+.
T Consensus 181 ~~~r~vl~l~y~~~~s~~eIA~~lgis~~~v~~~~~ 216 (227)
T TIGR02980 181 ERERRILLLRFFEDKTQSEIAERLGISQMHVSRLLR 216 (227)
T ss_pred HHHHHHHHHHHhcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 334455555556678999999999999999987654
No 245
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=26.13 E-value=2.3e+02 Score=22.61 Aligned_cols=37 Identities=19% Similarity=0.153 Sum_probs=28.7
Q ss_pred chhHHHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHH
Q 043121 114 FSLGMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLI 150 (169)
Q Consensus 114 f~~~l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l 150 (169)
.|+--..++-+....+.+++++|+.||+|.+.+-..|
T Consensus 134 Lp~~~r~v~~l~~~~g~s~~EIAe~lgis~~tV~~~l 170 (196)
T PRK12535 134 LPPERREALILTQVLGYTYEEAAKIADVRVGTIRSRV 170 (196)
T ss_pred CCHHHHHHhhhHHHhCCCHHHHHHHhCCCHHHHHHHH
Confidence 3444566666777788999999999999999876544
No 246
>PF07292 NID: Nmi/IFP 35 domain (NID); InterPro: IPR009909 This entry represents a domain of approximately 90 residues that is tandemly repeated within interferon-induced 35 kDa protein (IFP 35) and the homologous N-myc-interactor (Nmi). This domain mediates Nmi-Nmi protein interactions and subcellular localisation [].
Probab=26.00 E-value=67 Score=23.73 Aligned_cols=23 Identities=30% Similarity=0.346 Sum_probs=20.1
Q ss_pred ccChhhhhcceeEEEEeecCCCC
Q 043121 18 ELTDDELLRECEMDTYKLSGPGS 40 (169)
Q Consensus 18 ~i~~~~l~~dl~i~~~RssGpGG 40 (169)
.+++++|..-|+|.|.|++--||
T Consensus 63 ~l~ee~l~D~LeIhFqK~snGGG 85 (88)
T PF07292_consen 63 VLDEEELRDKLEIHFQKPSNGGG 85 (88)
T ss_pred CCChhhheeeEEEEEecCCCCCc
Confidence 68889998889999999988776
No 247
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=25.98 E-value=1.6e+02 Score=22.20 Aligned_cols=36 Identities=17% Similarity=-0.010 Sum_probs=28.0
Q ss_pred hHHHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHHh
Q 043121 116 LGMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLIL 151 (169)
Q Consensus 116 ~~l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~ 151 (169)
+--+.++-+....|.+.+++|+.||+|.+.+-.-|.
T Consensus 116 ~~~r~v~~L~~~~g~s~~EIA~~l~is~~tV~~~l~ 151 (161)
T PRK12528 116 PLVKRAFLLAQVDGLGYGEIATELGISLATVKRYLN 151 (161)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 345556666777899999999999999988775543
No 248
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=25.89 E-value=1.4e+02 Score=23.47 Aligned_cols=34 Identities=32% Similarity=0.269 Sum_probs=26.1
Q ss_pred HHHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHH
Q 043121 117 GMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLI 150 (169)
Q Consensus 117 ~l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l 150 (169)
--..++-+...-+.+.+++|+.||+|.+.+-..+
T Consensus 115 ~~R~v~~L~~~eg~s~~EIA~~lgis~~tV~~~l 148 (182)
T PRK12511 115 EQRAALHLVAIEGLSYQEAAAVLGIPIGTLMSRI 148 (182)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHhCcCHHHHHHHH
Confidence 3445555556678899999999999999876554
No 249
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=25.77 E-value=1.5e+02 Score=22.92 Aligned_cols=36 Identities=8% Similarity=-0.014 Sum_probs=27.1
Q ss_pred hHHHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHHh
Q 043121 116 LGMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLIL 151 (169)
Q Consensus 116 ~~l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~ 151 (169)
+--..++=+....+.+++++|+.||+|.+.+-..+.
T Consensus 130 ~~~R~v~~L~~~~g~s~~EIA~~lgis~~tVk~~l~ 165 (178)
T PRK12529 130 PRVKQAFLMATLDGMKQKDIAQALDIALPTVKKYIH 165 (178)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 334455555566788999999999999998876554
No 250
>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=25.72 E-value=72 Score=20.56 Aligned_cols=25 Identities=28% Similarity=0.234 Sum_probs=17.8
Q ss_pred hcCCHHHHHHHhcCChhHHHHHHhc
Q 043121 128 VEGSVSEAAKLLWLSTGALSRLILS 152 (169)
Q Consensus 128 ~~~~~~~aa~~l~~st~~L~k~l~~ 152 (169)
....+++.|+.|+++.+.+++.|++
T Consensus 17 ~~~t~~~l~~~~~~~~~~vs~~i~~ 41 (68)
T PF13463_consen 17 GPMTQSDLAERLGISKSTVSRIIKK 41 (68)
T ss_dssp S-BEHHHHHHHTT--HHHHHHHHHH
T ss_pred CCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 3344788999999999999988764
No 251
>PRK11050 manganese transport regulator MntR; Provisional
Probab=25.70 E-value=1.4e+02 Score=23.27 Aligned_cols=33 Identities=24% Similarity=0.316 Sum_probs=24.5
Q ss_pred HHHHHHHHHh-cCCHHHHHHHhcCChhHHHHHHh
Q 043121 119 QALLDLIFAV-EGSVSEAAKLLWLSTGALSRLIL 151 (169)
Q Consensus 119 ~~~lD~l~~~-~~~~~~aa~~l~~st~~L~k~l~ 151 (169)
..+++.+... +..++++|+.|++|.+.+++.|.
T Consensus 40 ~~I~~~l~~~~~~t~~eLA~~l~is~stVsr~l~ 73 (152)
T PRK11050 40 ELIADLIAEVGEARQVDIAARLGVSQPTVAKMLK 73 (152)
T ss_pred HHHHHHHHhcCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3455555543 34789999999999999998774
No 252
>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional
Probab=25.47 E-value=1.1e+02 Score=28.64 Aligned_cols=25 Identities=24% Similarity=0.085 Sum_probs=21.9
Q ss_pred cCCHHHHHHHhcCChhHHHHHHhcC
Q 043121 129 EGSVSEAAKLLWLSTGALSRLILSD 153 (169)
Q Consensus 129 ~~~~~~aa~~l~~st~~L~k~l~~~ 153 (169)
.++...||+.||+|.+.|-+-|++.
T Consensus 486 ~~~~~~aA~~LGisr~tL~rkl~~~ 510 (520)
T PRK10820 486 YPSTRKLAKRLGVSHTAIANKLREY 510 (520)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHc
Confidence 5688999999999999999888764
No 253
>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=25.43 E-value=67 Score=23.78 Aligned_cols=31 Identities=32% Similarity=0.159 Sum_probs=22.8
Q ss_pred HHHHHHHhcCCHHHHHHHhcCChhHHHHHHh
Q 043121 121 LLDLIFAVEGSVSEAAKLLWLSTGALSRLIL 151 (169)
Q Consensus 121 ~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~ 151 (169)
++.+..-.+.+++++|+.||+|.+.+-..+.
T Consensus 113 i~~l~~~~g~s~~eIA~~lgis~~tv~~~l~ 143 (154)
T TIGR02950 113 VLILREFKEFSYKEIAELLNLSLAKVKSNLF 143 (154)
T ss_pred eeeehhhccCcHHHHHHHHCCCHHHHHHHHH
Confidence 3333344577899999999999998875543
No 254
>PRK15186 AraC family transcriptional regulator; Provisional
Probab=25.30 E-value=1e+02 Score=26.93 Aligned_cols=36 Identities=14% Similarity=0.110 Sum_probs=30.0
Q ss_pred HHHHHHHHHHhcCCHHHHHHHhcC-ChhHHHHHHhcC
Q 043121 118 MQALLDLIFAVEGSVSEAAKLLWL-STGALSRLILSD 153 (169)
Q Consensus 118 l~~~lD~l~~~~~~~~~aa~~l~~-st~~L~k~l~~~ 153 (169)
|..+..+|...+.+++++|..+|. |++++++.+++.
T Consensus 234 l~~A~~lL~~~~~sI~~IA~~~GY~s~S~Fsr~FK~~ 270 (291)
T PRK15186 234 MNKATKLLRNSEYNITRVAYMCGYDSASYFTCVFKKH 270 (291)
T ss_pred HHHHHHHHHcCCCCHHHHHHHhCCCCHHHHHHHHHHH
Confidence 677788888877899999999998 588888888764
No 255
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=25.16 E-value=1.5e+02 Score=23.33 Aligned_cols=34 Identities=24% Similarity=0.203 Sum_probs=27.0
Q ss_pred HHHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHH
Q 043121 117 GMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLI 150 (169)
Q Consensus 117 ~l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l 150 (169)
--..++.+....+.+++++|+.||+|.+.+-+-|
T Consensus 138 ~~r~i~~l~~~~g~s~~EIA~~lg~s~~tV~~rl 171 (192)
T PRK09643 138 EQRAALVAVDMQGYSVADAARMLGVAEGTVKSRC 171 (192)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHH
Confidence 3455666667788999999999999999986554
No 256
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=25.14 E-value=43 Score=21.90 Aligned_cols=22 Identities=32% Similarity=0.310 Sum_probs=17.6
Q ss_pred CHHHHHHHhcCChhHHHHHHhc
Q 043121 131 SVSEAAKLLWLSTGALSRLILS 152 (169)
Q Consensus 131 ~~~~aa~~l~~st~~L~k~l~~ 152 (169)
.++++|+.+|+|++.|=.....
T Consensus 2 ti~eva~~~gvs~~tlr~y~~~ 23 (69)
T PF13411_consen 2 TIKEVAKLLGVSPSTLRYYERE 23 (69)
T ss_dssp EHHHHHHHTTTTHHHHHHHHHT
T ss_pred cHHHHHHHHCcCHHHHHHHHHh
Confidence 4689999999999998765543
No 257
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=25.09 E-value=1.4e+02 Score=23.03 Aligned_cols=34 Identities=26% Similarity=0.200 Sum_probs=25.7
Q ss_pred HHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHHh
Q 043121 118 MQALLDLIFAVEGSVSEAAKLLWLSTGALSRLIL 151 (169)
Q Consensus 118 l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~ 151 (169)
-+.++-+....+.+++++|+.||+|++.+-..+.
T Consensus 133 ~r~i~~l~~~~g~s~~EIA~~lgis~~tV~~~l~ 166 (186)
T PRK05602 133 QREAIVLQYYQGLSNIEAAAVMDISVDALESLLA 166 (186)
T ss_pred HHHHhhHHHhcCCCHHHHHHHhCcCHHHHHHHHH
Confidence 3444555556788899999999999999876653
No 258
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=25.00 E-value=1.3e+02 Score=22.53 Aligned_cols=32 Identities=16% Similarity=0.031 Sum_probs=26.0
Q ss_pred HHHHHHHhcCCHHHHHHHhcCChhHHHHHHhc
Q 043121 121 LLDLIFAVEGSVSEAAKLLWLSTGALSRLILS 152 (169)
Q Consensus 121 ~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~~ 152 (169)
++-.....+.+++++|+.||+|++.|.+-++.
T Consensus 21 aV~~~~~~g~sv~evA~e~gIs~~tl~~W~r~ 52 (121)
T PRK09413 21 IVQQSFEPGMTVSLVARQHGVAASQLFLWRKQ 52 (121)
T ss_pred HHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 33344556889999999999999999998776
No 259
>PRK05572 sporulation sigma factor SigF; Validated
Probab=24.94 E-value=1.4e+02 Score=24.68 Aligned_cols=37 Identities=27% Similarity=0.180 Sum_probs=28.6
Q ss_pred hhHHHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHHh
Q 043121 115 SLGMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLIL 151 (169)
Q Consensus 115 ~~~l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~ 151 (169)
++--+.++.....-+.+.+++|+.||+|++.+.+...
T Consensus 204 ~~~~~~v~~l~~~~~~s~~eIA~~lgis~~~V~~~~~ 240 (252)
T PRK05572 204 DERERLIVYLRYFKDKTQSEVAKRLGISQVQVSRLEK 240 (252)
T ss_pred CHHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 3345556666666778999999999999999987654
No 260
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=24.87 E-value=1.7e+02 Score=21.82 Aligned_cols=35 Identities=17% Similarity=-0.017 Sum_probs=28.4
Q ss_pred HHHHHHHHhcCCHHHHHHHhcCChhHHHHHHhcCh
Q 043121 120 ALLDLIFAVEGSVSEAAKLLWLSTGALSRLILSDD 154 (169)
Q Consensus 120 ~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~~~~ 154 (169)
++-.-+.-.+-+++.+|+-|++|++.|-++|.-+.
T Consensus 14 ELq~nf~~~~ls~~~ia~dL~~s~~~le~vL~l~~ 48 (89)
T PF10078_consen 14 ELQANFELSGLSLEQIAADLGTSPEHLEQVLNLKQ 48 (89)
T ss_pred HHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCC
Confidence 34444556788899999999999999999998773
No 261
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=24.71 E-value=1.5e+02 Score=22.65 Aligned_cols=30 Identities=23% Similarity=0.338 Sum_probs=23.6
Q ss_pred HHHHHHHhcCCHHHHHHHhcCChhHHHHHH
Q 043121 121 LLDLIFAVEGSVSEAAKLLWLSTGALSRLI 150 (169)
Q Consensus 121 ~lD~l~~~~~~~~~aa~~l~~st~~L~k~l 150 (169)
++-+....+.+++++|+.||+|.+.+-+.|
T Consensus 144 v~~l~~~~g~s~~eIA~~lgis~~~v~~~l 173 (187)
T TIGR02948 144 VIVLKYMEDLSLKEISEILDLPVGTVKTRI 173 (187)
T ss_pred HhhhHHhcCCCHHHHHHHHCCCHHHHHHHH
Confidence 444445678889999999999998887655
No 262
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=24.18 E-value=2.1e+02 Score=22.21 Aligned_cols=36 Identities=22% Similarity=0.089 Sum_probs=27.9
Q ss_pred hhHHHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHH
Q 043121 115 SLGMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLI 150 (169)
Q Consensus 115 ~~~l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l 150 (169)
|+-.+.++-+..-.+.+++++|+.||+|.+.+-..+
T Consensus 133 ~~~~r~v~~l~~~~g~s~~eIA~~lgis~~tV~~~l 168 (184)
T PRK12539 133 PEKMRLAIQAVKLEGLSVAEAATRSGMSESAVKVSV 168 (184)
T ss_pred CHHHHHHHHHHHHcCCcHHHHHHHHCcCHHHHHHHH
Confidence 444555666666678999999999999999887554
No 263
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=23.95 E-value=1.6e+02 Score=22.99 Aligned_cols=37 Identities=14% Similarity=0.066 Sum_probs=27.7
Q ss_pred hhHHHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHHh
Q 043121 115 SLGMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLIL 151 (169)
Q Consensus 115 ~~~l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~ 151 (169)
|+--..++-+....+.+.+++|+.||+|.+.+-..+.
T Consensus 138 ~~~~r~i~~L~~~~g~s~~EIA~~lgis~~tVk~~l~ 174 (195)
T PRK12532 138 PENTARVFTLKEILGFSSDEIQQMCGISTSNYHTIMH 174 (195)
T ss_pred CHHHHHHhhhHHHhCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3344555666667789999999999999998875543
No 264
>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=23.91 E-value=1.7e+02 Score=22.95 Aligned_cols=32 Identities=16% Similarity=0.014 Sum_probs=24.8
Q ss_pred HHHHHHHHHHhcCCHHHHHHHhcCChhHHHHH
Q 043121 118 MQALLDLIFAVEGSVSEAAKLLWLSTGALSRL 149 (169)
Q Consensus 118 l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~ 149 (169)
...++-+..--+.+++++|+.||+|.+.+-..
T Consensus 136 ~r~v~~l~~~~g~s~~EIA~~lgis~~tvk~r 167 (188)
T TIGR02943 136 TARVFMMREVLGFESDEICQELEISTSNCHVL 167 (188)
T ss_pred HHHHHHHHHHhCCCHHHHHHHhCCCHHHHHHH
Confidence 34455566677889999999999999988533
No 265
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=23.80 E-value=1.8e+02 Score=22.51 Aligned_cols=33 Identities=27% Similarity=0.078 Sum_probs=24.9
Q ss_pred HHHHHHHHHhcCCHHHHHHHhcCChhHHHHHHh
Q 043121 119 QALLDLIFAVEGSVSEAAKLLWLSTGALSRLIL 151 (169)
Q Consensus 119 ~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~ 151 (169)
+.++=+..-.+.+++++|+.||+|.+.+-+.|.
T Consensus 135 r~v~~l~~~~g~s~~EIA~~l~is~~tV~~~l~ 167 (181)
T PRK12536 135 RLPIVHVKLEGLSVAETAQLTGLSESAVKVGIH 167 (181)
T ss_pred HHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 334444456778899999999999999876653
No 266
>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=23.75 E-value=1.2e+02 Score=20.02 Aligned_cols=28 Identities=21% Similarity=0.183 Sum_probs=22.8
Q ss_pred HHHHhcCCHHHHHHHhcCChhHHHHHHh
Q 043121 124 LIFAVEGSVSEAAKLLWLSTGALSRLIL 151 (169)
Q Consensus 124 ~l~~~~~~~~~aa~~l~~st~~L~k~l~ 151 (169)
++..-...+++.|+.+|++.+.+.+.|.
T Consensus 17 Ll~~~~~t~~eIa~~l~i~~~~v~~~L~ 44 (68)
T PF01978_consen 17 LLKNGPATAEEIAEELGISRSTVYRALK 44 (68)
T ss_dssp HHHHCHEEHHHHHHHHTSSHHHHHHHHH
T ss_pred HHHcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 3456666789999999999999988775
No 267
>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=23.73 E-value=1e+02 Score=19.77 Aligned_cols=26 Identities=23% Similarity=0.091 Sum_probs=20.0
Q ss_pred HHHhcCCHHHHHHHhcCChhHHHHHH
Q 043121 125 IFAVEGSVSEAAKLLWLSTGALSRLI 150 (169)
Q Consensus 125 l~~~~~~~~~aa~~l~~st~~L~k~l 150 (169)
+.+.+.+.+++|..|++|+..+..-+
T Consensus 14 ~l~~G~~~~eIA~~l~is~~tV~~~~ 39 (58)
T PF00196_consen 14 LLAQGMSNKEIAEELGISEKTVKSHR 39 (58)
T ss_dssp HHHTTS-HHHHHHHHTSHHHHHHHHH
T ss_pred HHHhcCCcchhHHhcCcchhhHHHHH
Confidence 34678889999999999998876543
No 268
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=23.65 E-value=1.6e+02 Score=23.03 Aligned_cols=36 Identities=17% Similarity=0.102 Sum_probs=27.7
Q ss_pred hhHHHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHH
Q 043121 115 SLGMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLI 150 (169)
Q Consensus 115 ~~~l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l 150 (169)
|+--..++-+....+.+++++|+.||+|.+.+-..|
T Consensus 132 p~~~r~v~~L~~~~g~s~~EIA~~lgis~~tVk~~l 167 (185)
T PRK09649 132 TTDQREALLLTQLLGLSYADAAAVCGCPVGTIRSRV 167 (185)
T ss_pred CHHHhHHhhhHHHcCCCHHHHHHHHCCCHHHHHHHH
Confidence 344555666667788899999999999999876544
No 269
>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=23.62 E-value=1.6e+02 Score=21.36 Aligned_cols=33 Identities=27% Similarity=0.139 Sum_probs=27.3
Q ss_pred HHHHHHHhcCCHHHHHHHhcCChhHHHHHHhcC
Q 043121 121 LLDLIFAVEGSVSEAAKLLWLSTGALSRLILSD 153 (169)
Q Consensus 121 ~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~~~ 153 (169)
+.......+.+-.++|+.+|+|.+.+.+.....
T Consensus 70 i~~~r~~~gltq~~lA~~lg~~~~tis~~e~g~ 102 (127)
T TIGR03830 70 IRRIRKKLGLSQREAAELLGGGVNAFSRYERGE 102 (127)
T ss_pred HHHHHHHcCCCHHHHHHHhCCCHHHHHHHHCCC
Confidence 445567778899999999999999999987754
No 270
>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=23.57 E-value=94 Score=25.07 Aligned_cols=32 Identities=25% Similarity=0.115 Sum_probs=26.8
Q ss_pred HHHHHHHHhcCCHHHHHHHhc-CChhHHHHHHh
Q 043121 120 ALLDLIFAVEGSVSEAAKLLW-LSTGALSRLIL 151 (169)
Q Consensus 120 ~~lD~l~~~~~~~~~aa~~l~-~st~~L~k~l~ 151 (169)
+.|--|+..+.+.+.+|..|| +|..+++=.++
T Consensus 9 ~~L~~lw~~G~SasqIA~~lg~vsRnAViGk~h 41 (162)
T PF07750_consen 9 ERLRKLWAEGLSASQIARQLGGVSRNAVIGKAH 41 (162)
T ss_pred HHHHHHHHcCCCHHHHHHHhCCcchhhhhhhhh
Confidence 356678899999999999999 99999885544
No 271
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=23.54 E-value=1.5e+02 Score=23.49 Aligned_cols=37 Identities=22% Similarity=0.105 Sum_probs=28.7
Q ss_pred chhHHHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHH
Q 043121 114 FSLGMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLI 150 (169)
Q Consensus 114 f~~~l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l 150 (169)
.|+--+.++-+....+.+.+++|+.||+|.+.+-.-|
T Consensus 114 Lp~~~r~v~~L~~~~g~s~~EIA~~LgiS~~tVk~~l 150 (188)
T PRK12546 114 LPDEQREALILVGASGFSYEEAAEMCGVAVGTVKSRA 150 (188)
T ss_pred CCHHHhHHhhhHHhcCCCHHHHHHHHCCCHHHHHHHH
Confidence 3455566777777788999999999999998876544
No 272
>cd00131 PAX Paired Box domain
Probab=23.52 E-value=1.9e+02 Score=22.12 Aligned_cols=35 Identities=17% Similarity=0.234 Sum_probs=27.6
Q ss_pred HHHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHHhc
Q 043121 117 GMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLILS 152 (169)
Q Consensus 117 ~l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~~ 152 (169)
.-+.+++.. +.+.+..++|+.|++|.+-+.+.++.
T Consensus 22 ~R~rIv~~~-~~G~s~~~iA~~~~Vs~~tV~r~i~r 56 (128)
T cd00131 22 IRQRIVELA-QSGIRPCDISRQLRVSHGCVSKILNR 56 (128)
T ss_pred HHHHHHHHH-HcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 344556544 56779999999999999999998875
No 273
>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=23.50 E-value=1.4e+02 Score=22.38 Aligned_cols=34 Identities=29% Similarity=0.272 Sum_probs=27.6
Q ss_pred HHHHHHHHHhcCCHHHHHHHhcCChhHHHHHHhcC
Q 043121 119 QALLDLIFAVEGSVSEAAKLLWLSTGALSRLILSD 153 (169)
Q Consensus 119 ~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~~~ 153 (169)
+-+++.+.. ++++..||+.|++|..-+.+.++..
T Consensus 9 ~rVl~~~~~-g~s~~eaa~~F~VS~~Tv~~W~k~~ 42 (119)
T PF01710_consen 9 QRVLAYIEK-GKSIREAAKRFGVSRNTVYRWLKRK 42 (119)
T ss_pred HHHHHHHHc-cchHHHHHHHhCcHHHHHHHHHHhc
Confidence 446775555 7799999999999999999998843
No 274
>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=23.30 E-value=1.6e+02 Score=23.75 Aligned_cols=35 Identities=23% Similarity=0.255 Sum_probs=27.2
Q ss_pred HHHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHHh
Q 043121 117 GMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLIL 151 (169)
Q Consensus 117 ~l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~ 151 (169)
--..++......+.+.+++|+.||+|.+.+-+.+.
T Consensus 179 ~~r~il~l~y~~~~s~~eIA~~lgis~~tV~~~~~ 213 (224)
T TIGR02479 179 REQLVLSLYYYEELNLKEIGEVLGLTESRVSQIHS 213 (224)
T ss_pred HHHHHHHHHHhCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 34556666677788999999999999999765543
No 275
>PRK10676 DNA-binding transcriptional regulator ModE; Provisional
Probab=23.28 E-value=78 Score=27.13 Aligned_cols=35 Identities=31% Similarity=0.219 Sum_probs=25.6
Q ss_pred HHHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHHhc
Q 043121 117 GMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLILS 152 (169)
Q Consensus 117 ~l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~~ 152 (169)
..-.+|..+.. .|+++.||+.|++|.+++++.|+.
T Consensus 20 ~~l~~l~~v~~-~gS~s~AA~~l~~s~~a~s~~i~~ 54 (263)
T PRK10676 20 RRISLLKQIAL-TGSISQGAKLAGISYKSAWDAINE 54 (263)
T ss_pred HHHHHHHHHHH-HCCHHHHHHHhCCCHHHHHHHHHH
Confidence 33344444443 468999999999999999887753
No 276
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=23.11 E-value=2.7e+02 Score=22.42 Aligned_cols=31 Identities=19% Similarity=0.143 Sum_probs=23.6
Q ss_pred HHHHHHHHhcCCHHHHHHHhcCChhHHHHHH
Q 043121 120 ALLDLIFAVEGSVSEAAKLLWLSTGALSRLI 150 (169)
Q Consensus 120 ~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l 150 (169)
.++=+..-.+.+++++|+.||+|.+.+-.-|
T Consensus 155 ~v~~L~~~~g~s~~EIAe~lgis~~tV~~~l 185 (206)
T PRK12544 155 RVFMMREFIELETNEICHAVDLSVSNLNVLL 185 (206)
T ss_pred HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHH
Confidence 3444445678899999999999999886443
No 277
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=23.03 E-value=1.6e+02 Score=24.33 Aligned_cols=35 Identities=29% Similarity=0.284 Sum_probs=27.0
Q ss_pred HHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHHhc
Q 043121 118 MQALLDLIFAVEGSVSEAAKLLWLSTGALSRLILS 152 (169)
Q Consensus 118 l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~~ 152 (169)
-+.++.....-+.+.+++|+.||+|.+.+.++.+.
T Consensus 188 er~vi~l~~~~~~t~~EIA~~lgis~~~V~q~~~~ 222 (231)
T PRK12427 188 EQLILHLYYQHEMSLKEIALVLDLTEARICQLNKK 222 (231)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 34556666666788999999999999988876543
No 278
>smart00542 FYRC "FY-rich" domain, C-terminal region. is sometimes closely juxtaposed with the N-terminal region (FYRN), but sometimes is far distant. Unknown function, but occurs frequently in chromatin-associated proteins.
Probab=23.03 E-value=74 Score=22.82 Aligned_cols=27 Identities=22% Similarity=0.166 Sum_probs=23.7
Q ss_pred HHHhcCChhHHHHHHhcChhHHHHHHH
Q 043121 136 AKLLWLSTGALSRLILSDDSHQIAVNE 162 (169)
Q Consensus 136 a~~l~~st~~L~k~l~~~~~~~~~~n~ 162 (169)
..+||||..+++++|.+-|.+..-.|=
T Consensus 50 ~~mFGls~p~V~~lie~Lpga~~C~~Y 76 (86)
T smart00542 50 EDMFGLSSPAVVKLIEQLPGVHQCTNY 76 (86)
T ss_pred HHHhCCCcHHHHHHHHhCCCchhhhhh
Confidence 578999999999999999998877664
No 279
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=22.94 E-value=1.9e+02 Score=22.57 Aligned_cols=33 Identities=12% Similarity=0.002 Sum_probs=24.8
Q ss_pred HHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHH
Q 043121 118 MQALLDLIFAVEGSVSEAAKLLWLSTGALSRLI 150 (169)
Q Consensus 118 l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l 150 (169)
...++-+....+.+++++|+.||+|.+.+-..|
T Consensus 136 ~r~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l 168 (191)
T PRK12520 136 TGRVFMMREWLELETEEICQELQITATNAWVLL 168 (191)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHH
Confidence 344454555668899999999999999887544
No 280
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=22.78 E-value=76 Score=20.99 Aligned_cols=21 Identities=19% Similarity=0.113 Sum_probs=17.5
Q ss_pred CHHHHHHHhcCChhHHHHHHh
Q 043121 131 SVSEAAKLLWLSTGALSRLIL 151 (169)
Q Consensus 131 ~~~~aa~~l~~st~~L~k~l~ 151 (169)
.++++|+.+|+|++.|-..-.
T Consensus 2 ~i~e~A~~~gVs~~tlr~ye~ 22 (68)
T cd04763 2 TIGEVALLTGIKPHVLRAWER 22 (68)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 578999999999999876643
No 281
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=22.54 E-value=1.3e+02 Score=25.98 Aligned_cols=32 Identities=31% Similarity=0.293 Sum_probs=25.2
Q ss_pred HHHHHHHhcCCHHHHHHHhcCChhHHHHHHhc
Q 043121 121 LLDLIFAVEGSVSEAAKLLWLSTGALSRLILS 152 (169)
Q Consensus 121 ~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~~ 152 (169)
++-+...-+-.-+++|+.||+|.+..+++.++
T Consensus 204 Vl~l~y~eelt~kEI~~~LgISes~VSql~kk 235 (247)
T COG1191 204 VLVLRYKEELTQKEIAEVLGISESRVSRLHKK 235 (247)
T ss_pred HHHHHHHhccCHHHHHHHhCccHHHHHHHHHH
Confidence 34444555677889999999999999998764
No 282
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=22.44 E-value=2.3e+02 Score=22.52 Aligned_cols=33 Identities=12% Similarity=0.107 Sum_probs=24.4
Q ss_pred HHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHH
Q 043121 118 MQALLDLIFAVEGSVSEAAKLLWLSTGALSRLI 150 (169)
Q Consensus 118 l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l 150 (169)
-..++-+....+.+++++|+.||+|.+.+-..|
T Consensus 144 ~r~v~~L~~~eg~s~~EIA~~lgis~~tVk~~l 176 (201)
T PRK12545 144 IGRVFMMREFLDFEIDDICTELTLTANHCSVLL 176 (201)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHH
Confidence 334444555677899999999999998876443
No 283
>PRK13500 transcriptional activator RhaR; Provisional
Probab=22.37 E-value=1.3e+02 Score=25.84 Aligned_cols=44 Identities=9% Similarity=-0.034 Sum_probs=34.9
Q ss_pred HHHHHHHHHHHhcCCHHHHHHHhcC-ChhHHHHHHhcC----hhHHHHH
Q 043121 117 GMQALLDLIFAVEGSVSEAAKLLWL-STGALSRLILSD----DSHQIAV 160 (169)
Q Consensus 117 ~l~~~lD~l~~~~~~~~~aa~~l~~-st~~L~k~l~~~----~~~~~~~ 160 (169)
-|.++..+|...+.+++++|..+|+ +.+-++|+++++ |+-++.-
T Consensus 259 RL~~A~~LL~~t~~sI~eIA~~~GF~d~s~Fsr~FKk~~G~TP~~yRk~ 307 (312)
T PRK13500 259 RVCHAQYLLQHSRLLISDISTECGFEDSNYFSVVFTRETGMTPSQWRHL 307 (312)
T ss_pred HHHHHHHHHHcCCCCHHHHHHHhCCCCHHHHHHHHHHHHCcCHHHHHHH
Confidence 3777888898889999999999998 667788888775 5555543
No 284
>PF03683 UPF0175: Uncharacterised protein family (UPF0175); InterPro: IPR005368 This entry contains small proteins of unknown function.
Probab=22.32 E-value=2e+02 Score=19.99 Aligned_cols=37 Identities=19% Similarity=0.089 Sum_probs=29.6
Q ss_pred HHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHHhcCh
Q 043121 118 MQALLDLIFAVEGSVSEAAKLLWLSTGALSRLILSDD 154 (169)
Q Consensus 118 l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~~~~ 154 (169)
...++.+.....-+...||+..|+|.-.+..+|..+.
T Consensus 23 ~~~Ai~lY~~g~iS~gkAAelag~s~~eF~~~L~~~g 59 (76)
T PF03683_consen 23 EELAIKLYEEGKISLGKAAELAGMSRWEFLELLKERG 59 (76)
T ss_pred HHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHCC
Confidence 3455666666777888899999999999999988764
No 285
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=22.30 E-value=1.6e+02 Score=22.26 Aligned_cols=35 Identities=17% Similarity=0.238 Sum_probs=24.0
Q ss_pred HHHHHHHHHHHhc-CCHHHHHHHhcCChhHHHHHHh
Q 043121 117 GMQALLDLIFAVE-GSVSEAAKLLWLSTGALSRLIL 151 (169)
Q Consensus 117 ~l~~~lD~l~~~~-~~~~~aa~~l~~st~~L~k~l~ 151 (169)
++..++.++...+ ..++++|+.|++|++.+++.|.
T Consensus 9 yL~~I~~l~~~~~~~~~~ela~~l~vs~~svs~~l~ 44 (142)
T PRK03902 9 YIEQIYLLIEEKGYARVSDIAEALSVHPSSVTKMVQ 44 (142)
T ss_pred HHHHHHHHHhcCCCcCHHHHHHHhCCChhHHHHHHH
Confidence 3445555544322 3467899999999999998874
No 286
>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=22.29 E-value=1.5e+02 Score=23.69 Aligned_cols=34 Identities=18% Similarity=0.113 Sum_probs=24.6
Q ss_pred HhcCCHHHHHHHhcCChhHHHHHHh---cChhHHHHH
Q 043121 127 AVEGSVSEAAKLLWLSTGALSRLIL---SDDSHQIAV 160 (169)
Q Consensus 127 ~~~~~~~~aa~~l~~st~~L~k~l~---~~~~~~~~~ 160 (169)
..+++.++.|+.||+|.+.+.+.+. ..+.+..++
T Consensus 118 ~~g~s~~~iA~~lg~s~~~V~r~l~l~~lp~~v~~~~ 154 (187)
T TIGR00180 118 KFSMTQEDLAKKIGKSRAHITNLLRLLKLPSEIQSAI 154 (187)
T ss_pred HhCCCHHHHHHHHCcCHHHHHHHHHHHcCCHHHHHHH
Confidence 3688999999999999987766554 444444444
No 287
>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=22.14 E-value=2.1e+02 Score=20.89 Aligned_cols=25 Identities=20% Similarity=0.056 Sum_probs=21.7
Q ss_pred HhcCCHHHHHHHhcCChhHHHHHHh
Q 043121 127 AVEGSVSEAAKLLWLSTGALSRLIL 151 (169)
Q Consensus 127 ~~~~~~~~aa~~l~~st~~L~k~l~ 151 (169)
+.+.+++++|+.||+|.+-+.|+.+
T Consensus 48 ~~G~S~~eIA~~LgISrsTIyRi~R 72 (88)
T TIGR02531 48 KQGKTYSDIEAETGASTATISRVKR 72 (88)
T ss_pred HCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 3567999999999999999999665
No 288
>PRK15340 transcriptional regulator InvF; Provisional
Probab=22.03 E-value=1.4e+02 Score=25.26 Aligned_cols=38 Identities=11% Similarity=0.060 Sum_probs=30.1
Q ss_pred cCCHHHHHHHhcCChhHHHHHHhcC--hhHHHHHHHhhhh
Q 043121 129 EGSVSEAAKLLWLSTGALSRLILSD--DSHQIAVNELRTS 166 (169)
Q Consensus 129 ~~~~~~aa~~l~~st~~L~k~l~~~--~~~~~~~n~~R~~ 166 (169)
..++++.|+.+|+|+..|.|+++.. -+....+++.|..
T Consensus 125 ~~sleeLA~~~gvS~r~f~RlFk~~~G~tpk~yl~~~Rl~ 164 (216)
T PRK15340 125 GNTMRMLGEDYGVSYTHFRRLCSRALGGKAKSELRNWRMA 164 (216)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHCcCHHHHHHHHHHH
Confidence 4579999999999999999999985 4445566666654
No 289
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=21.98 E-value=2.9e+02 Score=21.96 Aligned_cols=38 Identities=18% Similarity=0.065 Sum_probs=30.1
Q ss_pred chhHHHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHHhc
Q 043121 114 FSLGMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLILS 152 (169)
Q Consensus 114 f~~~l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~~ 152 (169)
.++--..++.+ ...+++.+++|+.||+|.+.+.++...
T Consensus 7 Lt~rqreVL~l-r~~GlTq~EIAe~LGiS~~tVs~ie~r 44 (141)
T PRK03975 7 LTERQIEVLRL-RERGLTQQEIADILGTSRANVSSIEKR 44 (141)
T ss_pred CCHHHHHHHHH-HHcCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 34445667766 479999999999999999888877764
No 290
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=21.94 E-value=1.9e+02 Score=22.66 Aligned_cols=38 Identities=16% Similarity=0.037 Sum_probs=29.1
Q ss_pred hhHHHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHHhc
Q 043121 115 SLGMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLILS 152 (169)
Q Consensus 115 ~~~l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~~ 152 (169)
|+--+.++-+...-+.+++++|+.||+|.+.+-..|..
T Consensus 138 ~~~~r~i~~L~~~~g~s~~eIA~~lgis~~tV~~~l~R 175 (196)
T PRK12524 138 PERQRQAVVLRHIEGLSNPEIAEVMEIGVEAVESLTAR 175 (196)
T ss_pred CHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 33445566666778899999999999999988766543
No 291
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=21.88 E-value=1.9e+02 Score=21.86 Aligned_cols=35 Identities=20% Similarity=0.026 Sum_probs=27.0
Q ss_pred hHHHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHH
Q 043121 116 LGMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLI 150 (169)
Q Consensus 116 ~~l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l 150 (169)
+-...++-+....+.+..++|+.||+|.+.+-..|
T Consensus 111 ~~~r~v~~l~~~~g~s~~eIA~~lgis~~tv~~~l 145 (165)
T PRK09644 111 VIEAQAILLCDVHELTYEEAASVLDLKLNTYKSHL 145 (165)
T ss_pred HHHHHHHHhHHHhcCCHHHHHHHHCCCHHHHHHHH
Confidence 33445666667788999999999999998886544
No 292
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=21.70 E-value=1.8e+02 Score=24.01 Aligned_cols=35 Identities=23% Similarity=0.179 Sum_probs=26.8
Q ss_pred HHHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHHh
Q 043121 117 GMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLIL 151 (169)
Q Consensus 117 ~l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~ 151 (169)
--+.++-+....+.+.+++|+.||+|.+.+.+.+.
T Consensus 209 ~~r~vl~l~~~~g~s~~eIA~~l~is~~tV~~~~~ 243 (257)
T PRK08583 209 REKSIIQCTFIENLSQKETGERLGISQMHVSRLQR 243 (257)
T ss_pred HHHHHHHHHHhCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 34445555666788999999999999999976553
No 293
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=21.68 E-value=86 Score=24.48 Aligned_cols=32 Identities=13% Similarity=0.051 Sum_probs=23.5
Q ss_pred HHHHHHHHHhcCCHHHHHHHhcCChhHHHHHH
Q 043121 119 QALLDLIFAVEGSVSEAAKLLWLSTGALSRLI 150 (169)
Q Consensus 119 ~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l 150 (169)
+.++.+....+.+++++|+.||+|.+.+-..+
T Consensus 145 r~i~~l~~~~g~s~~EIA~~lgis~~tV~~~l 176 (194)
T PRK12513 145 REVFLLREHGDLELEEIAELTGVPEETVKSRL 176 (194)
T ss_pred hhheeeehccCCCHHHHHHHHCCCHHHHHHHH
Confidence 33444445667889999999999999886443
No 294
>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=21.68 E-value=1.8e+02 Score=24.64 Aligned_cols=36 Identities=17% Similarity=0.031 Sum_probs=28.3
Q ss_pred hHHHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHHh
Q 043121 116 LGMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLIL 151 (169)
Q Consensus 116 ~~l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~ 151 (169)
+--..++-+....+.+++++|+.||+|.+.+-..+.
T Consensus 111 ~~~R~v~~L~~~~g~s~~EIA~~lg~s~~tVr~~l~ 146 (281)
T TIGR02957 111 PLERAVFVLREVFDYPYEEIASIVGKSEANCRQLVS 146 (281)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 344556667778899999999999999998776554
No 295
>PF13730 HTH_36: Helix-turn-helix domain
Probab=21.65 E-value=1.7e+02 Score=18.28 Aligned_cols=21 Identities=33% Similarity=0.192 Sum_probs=17.5
Q ss_pred CHHHHHHHhcCChhHHHHHHh
Q 043121 131 SVSEAAKLLWLSTGALSRLIL 151 (169)
Q Consensus 131 ~~~~aa~~l~~st~~L~k~l~ 151 (169)
+.+..|+.+|+|...+.+.|+
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~ 47 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIK 47 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 678899999999888887664
No 296
>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=21.48 E-value=1.2e+02 Score=22.63 Aligned_cols=34 Identities=21% Similarity=0.219 Sum_probs=24.5
Q ss_pred HHHHHHHHHh-cCCHHHHHHHhcCChhHHHHHHhc
Q 043121 119 QALLDLIFAV-EGSVSEAAKLLWLSTGALSRLILS 152 (169)
Q Consensus 119 ~~~lD~l~~~-~~~~~~aa~~l~~st~~L~k~l~~ 152 (169)
..+...+.+. +-...+.|+.||+|++.+.+.|++
T Consensus 60 ~~L~~~v~~~pd~tl~Ela~~l~Vs~~ti~~~Lkr 94 (119)
T PF01710_consen 60 DELKALVEENPDATLRELAERLGVSPSTIWRALKR 94 (119)
T ss_pred HHHHHHHHHCCCcCHHHHHHHcCCCHHHHHHHHHH
Confidence 4445555443 334678999999999999999864
No 297
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=21.45 E-value=2.3e+02 Score=21.19 Aligned_cols=31 Identities=23% Similarity=0.157 Sum_probs=23.9
Q ss_pred HHHHHHHhc--CCHHHHHHHhcCChhHHHHHHh
Q 043121 121 LLDLIFAVE--GSVSEAAKLLWLSTGALSRLIL 151 (169)
Q Consensus 121 ~lD~l~~~~--~~~~~aa~~l~~st~~L~k~l~ 151 (169)
+|-.|...+ -..++.|+.++++.+.++++|.
T Consensus 36 vL~~l~~~~~~~t~~eLa~~l~~~~~tvt~~v~ 68 (144)
T PRK03573 36 TLHNIHQLPPEQSQIQLAKAIGIEQPSLVRTLD 68 (144)
T ss_pred HHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHH
Confidence 455555443 3689999999999999998875
No 298
>PRK15044 transcriptional regulator SirC; Provisional
Probab=21.34 E-value=1.2e+02 Score=27.14 Aligned_cols=41 Identities=22% Similarity=0.267 Sum_probs=30.9
Q ss_pred HhcCCHHHHHHHhcCChhHHHHHHhcCh-hHHHHHHHhhhhc
Q 043121 127 AVEGSVSEAAKLLWLSTGALSRLILSDD-SHQIAVNELRTSK 167 (169)
Q Consensus 127 ~~~~~~~~aa~~l~~st~~L~k~l~~~~-~~~~~~n~~R~~~ 167 (169)
+-.+++.+.|+.+|+|+..|.|.++..- +....+++.|-.+
T Consensus 206 ~~~~SLeeLA~~lgmS~~tL~R~Fk~eg~T~~~y~~~~RL~~ 247 (295)
T PRK15044 206 TRKWSQAEVAGKLFMSVSSLKRKLAAEEVSFSKIYLDARMNQ 247 (295)
T ss_pred ccCCCHHHHHHHhCCCHHHHHHHHHHcCCCHHHHHHHHHHHH
Confidence 3468899999999999999999998642 2335566777544
No 299
>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=21.33 E-value=85 Score=26.80 Aligned_cols=27 Identities=26% Similarity=0.267 Sum_probs=23.7
Q ss_pred HhcCCHHHHHHHhcCChhHHHHHHhcC
Q 043121 127 AVEGSVSEAAKLLWLSTGALSRLILSD 153 (169)
Q Consensus 127 ~~~~~~~~aa~~l~~st~~L~k~l~~~ 153 (169)
-..|.+...|+.|++||.++-|+|++-
T Consensus 27 p~~~t~~~Lae~F~vspe~irrILksk 53 (225)
T PF06413_consen 27 PEEWTVERLAESFKVSPEAIRRILKSK 53 (225)
T ss_pred ccccCHHHHHhhCCCCHHHHHHHHhcC
Confidence 346889999999999999999999873
No 300
>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=21.27 E-value=1.5e+02 Score=23.87 Aligned_cols=34 Identities=29% Similarity=0.219 Sum_probs=26.4
Q ss_pred HHHHHHHHHHhcC-CHHHHHHHhcCChhHHHHHHh
Q 043121 118 MQALLDLIFAVEG-SVSEAAKLLWLSTGALSRLIL 151 (169)
Q Consensus 118 l~~~lD~l~~~~~-~~~~aa~~l~~st~~L~k~l~ 151 (169)
...+|..+...+. ++++.|+.+++|++.+.+.|.
T Consensus 145 ~~~IL~~l~~~g~~s~~eia~~l~is~stv~r~L~ 179 (203)
T TIGR01884 145 ELKVLEVLKAEGEKSVKNIAKKLGKSLSTISRHLR 179 (203)
T ss_pred HHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHH
Confidence 4467777877444 899999999999988777664
No 301
>PRK11557 putative DNA-binding transcriptional regulator; Provisional
Probab=20.66 E-value=1.4e+02 Score=24.79 Aligned_cols=40 Identities=13% Similarity=0.084 Sum_probs=28.7
Q ss_pred CchhHHHHHHHHHHH-----hcCCHHHHHHHhcCChhHHHHHHhc
Q 043121 113 KFSLGMQALLDLIFA-----VEGSVSEAAKLLWLSTGALSRLILS 152 (169)
Q Consensus 113 ~f~~~l~~~lD~l~~-----~~~~~~~aa~~l~~st~~L~k~l~~ 152 (169)
.+.+.-+.+.|.+.. ...++.+.|+..++|++-++||.++
T Consensus 9 ~Lt~~e~~ia~yil~n~~~v~~~si~elA~~~~vS~aTv~Rf~kk 53 (278)
T PRK11557 9 GLAQSDRKLADYLLLQPDTARHLSSQQLANEAGVSQSSVVKFAQK 53 (278)
T ss_pred hCCHHHHHHHHHHHhCHHHHHhcCHHHHHHHhCCCHHHHHHHHHH
Confidence 345544555555433 3477899999999999999999764
No 302
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=20.61 E-value=1.9e+02 Score=23.97 Aligned_cols=37 Identities=27% Similarity=0.319 Sum_probs=28.7
Q ss_pred hhHHHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHHh
Q 043121 115 SLGMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLIL 151 (169)
Q Consensus 115 ~~~l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~ 151 (169)
|+-...++-+....+.+.+++|+.||+|.+.+-..+.
T Consensus 203 ~~~~r~vl~l~~~~~~s~~EIA~~lgis~~tV~~~~~ 239 (251)
T PRK07670 203 SEKEQLVISLFYKEELTLTEIGQVLNLSTSRISQIHS 239 (251)
T ss_pred CHHHHHHHHHHHhcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 3345666666677788999999999999999876553
No 303
>PF05269 Phage_CII: Bacteriophage CII protein; InterPro: IPR007933 The CII protein is a transcription activator, conserved in bacteriophage lambda and related phages, that plays a key role in the decision between lytic or lysogenic phage development. CII is regulated at multiple levels including transcription, translation initiation, mRNA stability, and proteolysis []. Conditions that stabilise cII favour lysogenic development. The lambda CII protein activates three specific promoters, binding to direct repeat sequences rather than the more usual inverted repeats. Structurally, CII is a homotetramer where each monomer is composed of four alpha helices and a disordered C terminus [, ]. The alpha helical region is responsible for DNA binding and multimerisation. The homotetramer has an unusual spatial arrangement that allows recognition of the direct repeat sequences.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1ZS4_C 1ZPQ_C 1XWR_A.
Probab=20.47 E-value=1.3e+02 Score=22.50 Aligned_cols=31 Identities=16% Similarity=0.219 Sum_probs=24.1
Q ss_pred HHHHHHHHhcCCHHHHHHHhcCChhHHHHHHhc
Q 043121 120 ALLDLIFAVEGSVSEAAKLLWLSTGALSRLILS 152 (169)
Q Consensus 120 ~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~~ 152 (169)
.+|--|+.++. ...|+..|++.|+++|+-..
T Consensus 16 ~iL~rlA~~gq--~~vA~~~Gv~eStISR~k~~ 46 (91)
T PF05269_consen 16 EILNRLASVGQ--KKVAEAMGVDESTISRWKND 46 (91)
T ss_dssp HHHHHHHHHHH--HHHHHHHTSSTTTHHHHHHH
T ss_pred HHHHHHHHHhh--HHHHHHhCCCHHHHHHHHhh
Confidence 45666666665 78999999999999998544
No 304
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=20.42 E-value=1.6e+02 Score=24.68 Aligned_cols=32 Identities=22% Similarity=0.282 Sum_probs=24.0
Q ss_pred HHHHHHHhc--CCHHHHHHHhcCChhHHHHHHhc
Q 043121 121 LLDLIFAVE--GSVSEAAKLLWLSTGALSRLILS 152 (169)
Q Consensus 121 ~lD~l~~~~--~~~~~aa~~l~~st~~L~k~l~~ 152 (169)
+|+.+...+ ...++.|+.+|++.+-+.|+|..
T Consensus 16 iL~~l~~~~~~ls~~eia~~lgl~kstv~RlL~t 49 (263)
T PRK09834 16 VLRALNRLDGGATVGLLAELTGLHRTTVRRLLET 49 (263)
T ss_pred HHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 344444433 37999999999999999998753
No 305
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=20.40 E-value=84 Score=27.69 Aligned_cols=35 Identities=20% Similarity=0.121 Sum_probs=26.6
Q ss_pred HHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHHhc
Q 043121 118 MQALLDLIFAVEGSVSEAAKLLWLSTGALSRLILS 152 (169)
Q Consensus 118 l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l~~ 152 (169)
|..+=-+--.-+..-+++|+.||+|+...+|+|..
T Consensus 18 ~~~vA~lYY~~g~tQ~eIA~~lgiSR~~VsRlL~~ 52 (318)
T PRK15418 18 VARIAWFYYHDGLTQSEIGERLGLTRLKVSRLLEK 52 (318)
T ss_pred HHHHHHHHHhcCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 33344444556677899999999999999999864
No 306
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=20.39 E-value=2.6e+02 Score=21.07 Aligned_cols=32 Identities=28% Similarity=0.266 Sum_probs=23.6
Q ss_pred HHHHHHHhc-CCHHHHHHHhcCChhHHHHHHhc
Q 043121 121 LLDLIFAVE-GSVSEAAKLLWLSTGALSRLILS 152 (169)
Q Consensus 121 ~lD~l~~~~-~~~~~aa~~l~~st~~L~k~l~~ 152 (169)
+|-.|...+ -..++.|+.++++.+.++++|..
T Consensus 45 vL~~l~~~~~~t~~eLa~~l~i~~~tvsr~l~~ 77 (144)
T PRK11512 45 VLCSIRCAACITPVELKKVLSVDLGALTRMLDR 77 (144)
T ss_pred HHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 333444433 36899999999999999998753
No 307
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=20.18 E-value=2.2e+02 Score=22.27 Aligned_cols=34 Identities=15% Similarity=0.125 Sum_probs=25.6
Q ss_pred HHHHHHHHHHHhcCCHHHHHHHhcCChhHHHHHH
Q 043121 117 GMQALLDLIFAVEGSVSEAAKLLWLSTGALSRLI 150 (169)
Q Consensus 117 ~l~~~lD~l~~~~~~~~~aa~~l~~st~~L~k~l 150 (169)
--+.++-+-...+.+++++|+.||+|.+.+-+.+
T Consensus 146 ~~r~vl~l~~~~~~s~~EIA~~Lgis~~tVk~~l 179 (194)
T PRK09646 146 TQRESVTLAYYGGLTYREVAERLAVPLGTVKTRM 179 (194)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHhCCChHhHHHHH
Confidence 3444555556678899999999999999886544
No 308
>PF13348 Y_phosphatase3C: Tyrosine phosphatase family C-terminal region; PDB: 1YWF_A 2OZ5_B.
Probab=20.11 E-value=2.1e+02 Score=18.92 Aligned_cols=37 Identities=32% Similarity=0.197 Sum_probs=27.3
Q ss_pred CchhHHHHHHHHHHHhcCCHHHHH-HHhcCChhHHHHH
Q 043121 113 KFSLGMQALLDLIFAVEGSVSEAA-KLLWLSTGALSRL 149 (169)
Q Consensus 113 ~f~~~l~~~lD~l~~~~~~~~~aa-~~l~~st~~L~k~ 149 (169)
..+..|...+|.+...=|++..=- +.||+|...+-+|
T Consensus 26 ~~~e~l~~~l~~i~~~yGs~e~Yl~~~lgl~~~~i~~L 63 (68)
T PF13348_consen 26 VRPEYLEAALDAIDERYGSVENYLREELGLSEEDIERL 63 (68)
T ss_dssp --HHHHHHHHHHHHHHHSSHHHHHHHT-T--HHHHHHH
T ss_pred ccHHHHHHHHHHHHHHcCCHHHHHHHcCCCCHHHHHHH
Confidence 346689999999999999998855 8889999887665
No 309
>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=20.10 E-value=1.2e+02 Score=20.90 Aligned_cols=35 Identities=26% Similarity=0.243 Sum_probs=24.1
Q ss_pred HHHHHHHHHHHhc---CCHHHHHHHhcCChhHHHHHHh
Q 043121 117 GMQALLDLIFAVE---GSVSEAAKLLWLSTGALSRLIL 151 (169)
Q Consensus 117 ~l~~~lD~l~~~~---~~~~~aa~~l~~st~~L~k~l~ 151 (169)
.+..++.+-...+ .+.++.|+.+++++..|.+++.
T Consensus 10 Al~~l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~ 47 (83)
T PF02082_consen 10 ALRILLYLARHPDGKPVSSKEIAERLGISPSYLRKILQ 47 (83)
T ss_dssp HHHHHHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 3444555543333 4688999999999999998875
Done!