Query gi|254781147|ref|YP_003065560.1| transcriptional regulator [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 83
No_of_seqs 109 out of 8897
Neff 7.1
Searched_HMMs 39220
Date Mon May 30 05:28:34 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254781147.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK09943 DNA-binding transcrip 99.7 2.2E-16 5.6E-21 118.1 8.1 63 20-82 6-68 (185)
2 PHA01976 helix-turn-helix prot 99.6 6.3E-15 1.6E-19 109.4 7.9 61 21-81 2-62 (67)
3 PRK13890 conjugal transfer pro 99.6 7.9E-15 2E-19 108.9 7.6 64 19-82 3-66 (119)
4 PRK09706 transcriptional repre 99.5 1.9E-14 4.8E-19 106.6 7.6 64 19-82 3-66 (135)
5 TIGR03070 couple_hipB transcri 99.5 1.7E-13 4.4E-18 100.9 6.8 57 21-77 2-58 (58)
6 PRK08154 anaerobic benzoate ca 99.4 5.2E-12 1.3E-16 92.1 8.9 65 18-82 25-89 (304)
7 smart00530 HTH_XRE Helix-turn- 99.3 3.9E-12 1E-16 92.8 6.5 56 25-80 1-56 (56)
8 pfam01381 HTH_3 Helix-turn-hel 99.3 3.7E-12 9.4E-17 93.0 6.3 55 26-80 1-55 (55)
9 COG1476 Predicted transcriptio 99.3 1.3E-11 3.2E-16 89.8 7.1 59 24-82 4-62 (68)
10 PRK09726 DNA-binding transcrip 99.2 8.8E-11 2.2E-15 84.8 6.6 59 20-78 11-69 (88)
11 PRK06424 transcription factor; 99.1 1.9E-10 4.7E-15 82.9 7.9 69 11-79 74-142 (144)
12 cd00093 HTH_XRE Helix-turn-hel 99.1 1.1E-10 2.9E-15 84.2 6.5 58 23-80 1-58 (58)
13 PRK08359 transcription factor; 99.1 6.2E-10 1.6E-14 79.8 7.7 62 19-80 81-142 (175)
14 COG3620 Predicted transcriptio 99.0 1.4E-09 3.5E-14 77.8 6.2 52 23-74 7-58 (187)
15 COG1813 Predicted transcriptio 99.0 2.6E-09 6.7E-14 76.1 7.6 68 14-81 72-139 (165)
16 PRK04140 hypothetical protein; 98.7 3E-08 7.6E-13 69.8 6.6 56 23-78 127-182 (319)
17 TIGR00270 TIGR00270 conserved 98.6 7E-08 1.8E-12 67.6 6.2 78 4-81 66-143 (169)
18 TIGR02612 mob_myst_A mobile my 98.5 6.6E-08 1.7E-12 67.8 3.3 59 25-83 29-89 (150)
19 COG1395 Predicted transcriptio 98.3 1.3E-06 3.3E-11 60.1 6.2 56 23-78 127-182 (313)
20 TIGR02607 antidote_HigA addict 98.3 1.6E-06 4.1E-11 59.5 5.7 66 6-81 2-67 (81)
21 COG1709 Predicted transcriptio 98.3 1.1E-06 2.8E-11 60.5 4.4 53 21-73 27-80 (241)
22 COG3655 Predicted transcriptio 98.2 2.6E-06 6.7E-11 58.3 5.9 61 22-82 3-64 (73)
23 COG1426 Predicted transcriptio 98.2 4.9E-06 1.2E-10 56.7 7.0 62 21-82 3-70 (284)
24 KOG3398 consensus 98.2 2.6E-06 6.5E-11 58.3 5.6 59 20-78 72-130 (135)
25 PRK13355 bifunctional HTH-doma 98.1 1.5E-05 3.7E-10 53.9 7.1 63 20-82 4-71 (518)
26 COG1396 HipB Predicted transcr 98.0 2.9E-05 7.5E-10 52.0 7.7 61 22-82 2-63 (120)
27 COG3093 VapI Plasmid maintenan 98.0 2.3E-05 5.8E-10 52.7 7.0 52 30-81 19-70 (104)
28 PRK10856 hypothetical protein; 98.0 2.8E-05 7.2E-10 52.2 7.0 64 18-81 11-80 (332)
29 COG2944 Predicted transcriptio 97.9 2E-05 5.1E-10 53.1 4.9 44 23-66 46-89 (104)
30 PRK10072 putative transcriptio 97.7 0.0001 2.6E-09 48.9 5.6 43 25-67 37-79 (96)
31 TIGR02684 dnstrm_HI1420 probab 97.5 0.00017 4.3E-09 47.6 5.3 57 20-78 33-89 (91)
32 COG5499 Predicted transcriptio 97.4 0.00045 1.1E-08 45.0 6.1 58 24-82 63-120 (120)
33 KOG3802 consensus 97.4 0.00029 7.4E-09 46.1 4.9 58 15-74 204-267 (398)
34 COG4800 Predicted transcriptio 97.3 0.00082 2.1E-08 43.5 6.6 55 18-73 13-67 (170)
35 smart00352 POU Found in Pit-Oc 97.3 0.0014 3.6E-08 42.1 7.3 57 16-74 6-68 (75)
36 PHA00542 putative Cro-like pro 97.0 0.0016 4E-08 41.8 5.6 49 24-72 21-70 (82)
37 pfam08667 BetR BetR domain. Th 97.0 0.005 1.3E-07 38.8 7.8 64 19-82 3-70 (146)
38 pfam00157 Pou Pou domain - N-t 97.0 0.0044 1.1E-07 39.2 7.3 57 16-74 6-68 (75)
39 COG5606 Uncharacterized conser 96.9 0.0023 6E-08 40.8 5.6 67 12-78 19-86 (91)
40 pfam07022 Phage_CI_repr Bacter 96.8 0.0054 1.4E-07 38.6 6.7 56 26-82 3-59 (65)
41 PRK10014 DNA-binding transcrip 96.8 0.0021 5.4E-08 41.0 4.4 47 31-77 3-52 (342)
42 PRK09526 lacI lac repressor; R 96.7 0.0023 6E-08 40.8 4.0 47 31-77 2-51 (342)
43 PRK02866 cyanate hydratase; Va 96.6 0.016 4.1E-07 35.8 8.1 62 19-80 3-64 (147)
44 TIGR02846 spore_sigmaK RNA pol 96.6 0.00095 2.4E-08 43.1 1.6 28 30-57 191-218 (228)
45 PRK09492 treR trehalose repres 96.5 0.0045 1.2E-07 39.1 4.9 47 32-78 2-51 (315)
46 COG2522 Predicted transcriptio 96.5 0.005 1.3E-07 38.8 4.6 39 27-66 16-55 (119)
47 PRK11303 DNA-binding transcrip 96.3 0.0083 2.1E-07 37.5 4.8 43 35-77 1-49 (330)
48 pfam00356 LacI Bacterial regul 96.1 0.011 2.8E-07 36.8 4.8 37 36-72 1-37 (46)
49 PRK10401 DNA-binding transcrip 96.1 0.012 3E-07 36.6 4.9 43 35-77 2-47 (346)
50 PRK10727 DNA-binding transcrip 96.0 0.014 3.5E-07 36.2 4.8 42 36-77 3-47 (342)
51 smart00354 HTH_LACI helix_turn 95.9 0.016 4.1E-07 35.8 4.8 42 36-77 2-46 (70)
52 PRK08099 nicotinamide-nucleoti 95.8 0.032 8.2E-07 34.0 6.2 56 24-79 5-61 (411)
53 COG3636 Predicted transcriptio 95.8 0.014 3.5E-07 36.2 4.2 51 26-78 43-93 (100)
54 KOG1168 consensus 95.8 0.0043 1.1E-07 39.2 1.5 46 13-58 213-267 (385)
55 PRK11041 DNA-binding transcrip 95.7 0.019 5E-07 35.3 4.8 44 35-78 10-56 (341)
56 PRK10703 DNA-binding transcrip 95.7 0.021 5.3E-07 35.1 4.7 42 36-77 3-47 (335)
57 COG1609 PurR Transcriptional r 95.6 0.021 5.4E-07 35.1 4.7 42 35-76 1-45 (333)
58 COG2390 DeoR Transcriptional r 95.5 0.028 7.3E-07 34.3 4.9 60 17-76 9-81 (321)
59 PRK10339 DNA-binding transcrip 95.4 0.035 8.8E-07 33.8 5.1 41 36-76 3-48 (327)
60 TIGR02980 SigBFG RNA polymeras 95.4 0.0038 9.7E-08 39.5 0.1 33 25-57 187-219 (229)
61 PRK08558 adenine phosphoribosy 95.1 0.12 2.9E-06 30.7 7.0 50 27-76 15-65 (238)
62 PRK03975 tfx putative transcri 95.1 0.039 9.9E-07 33.5 4.5 29 28-57 14-42 (139)
63 COG3423 Nlp Predicted transcri 94.6 0.13 3.3E-06 30.5 6.2 55 24-81 11-65 (82)
64 COG1191 FliA DNA-directed RNA 94.6 0.043 1.1E-06 33.2 3.8 35 23-57 201-235 (247)
65 TIGR00673 cynS cyanate hydrata 94.5 0.16 4.1E-06 29.8 6.4 63 18-80 10-72 (156)
66 TIGR01321 TrpR trp operon repr 94.4 0.061 1.6E-06 32.3 4.2 38 17-54 37-76 (95)
67 PRK10423 transcriptional repre 94.3 0.074 1.9E-06 31.8 4.4 42 37-78 1-45 (327)
68 pfam01371 Trp_repressor Trp re 94.3 0.098 2.5E-06 31.1 4.9 40 17-56 30-71 (88)
69 pfam04814 HNF-1_N Hepatocyte n 94.2 0.067 1.7E-06 32.1 4.1 40 19-58 113-152 (177)
70 cd01392 HTH_LacI Helix-turn-he 94.0 0.075 1.9E-06 31.8 3.9 39 38-76 1-42 (52)
71 TIGR00721 tfx DNA-binding prot 93.9 0.034 8.6E-07 33.9 1.9 28 31-58 18-45 (142)
72 PRK10344 DNA-binding transcrip 93.7 0.28 7.1E-06 28.4 6.4 55 24-81 11-65 (90)
73 TIGR02885 spore_sigF RNA polym 93.4 0.024 6.1E-07 34.8 0.5 33 25-57 190-222 (231)
74 COG1356 tfx Transcriptional re 93.3 0.042 1.1E-06 33.3 1.7 46 31-77 20-68 (143)
75 TIGR02835 spore_sigmaE RNA pol 92.8 0.07 1.8E-06 32.0 2.2 27 31-57 195-221 (234)
76 pfam04545 Sigma70_r4 Sigma-70, 92.8 0.11 2.9E-06 30.8 3.2 33 25-57 11-43 (50)
77 COG1513 CynS Cyanate lyase [In 92.7 0.74 1.9E-05 25.9 7.3 62 19-80 6-67 (151)
78 PRK08301 sporulation sigma fac 92.0 0.18 4.6E-06 29.6 3.4 32 26-57 191-226 (239)
79 pfam02001 DUF134 Protein of un 91.9 0.11 2.9E-06 30.7 2.4 27 30-56 48-74 (100)
80 PRK12427 flagellar biosynthesi 91.5 0.22 5.6E-06 29.0 3.5 32 26-57 189-220 (229)
81 PRK07122 RNA polymerase sigma 91.4 0.25 6.4E-06 28.7 3.7 34 24-57 220-253 (263)
82 PRK05572 sporulation sigma fac 91.0 0.28 7.1E-06 28.5 3.5 33 25-57 208-240 (251)
83 PRK07408 RNA polymerase sigma 90.9 0.3 7.7E-06 28.2 3.7 31 26-56 211-241 (256)
84 PRK08583 RNA polymerase sigma 90.9 0.3 7.6E-06 28.3 3.6 32 26-57 213-244 (257)
85 COG2973 TrpR Trp operon repres 90.8 0.95 2.4E-05 25.3 6.2 42 18-59 42-85 (103)
86 TIGR02147 Fsuc_second hypothet 90.7 0.16 4E-06 29.9 2.0 46 31-76 24-71 (281)
87 TIGR01950 SoxR redox-sensitive 90.5 0.26 6.7E-06 28.6 3.1 46 35-80 2-63 (142)
88 TIGR02937 sigma70-ECF RNA poly 90.4 0.41 1.1E-05 27.4 4.0 34 23-56 119-152 (162)
89 PRK06288 RNA polymerase sigma 90.4 0.33 8.3E-06 28.0 3.4 33 25-57 215-247 (261)
90 PRK08215 sporulation sigma fac 90.3 0.36 9.1E-06 27.8 3.6 33 25-57 216-248 (257)
91 TIGR02405 trehalos_R_Ecol treh 90.1 0.11 2.9E-06 30.7 0.9 41 34-74 1-41 (311)
92 PRK04217 hypothetical protein; 89.9 0.23 5.9E-06 28.9 2.4 32 26-57 48-81 (110)
93 TIGR02417 fruct_sucro_rep D-fr 89.9 0.21 5.4E-06 29.1 2.2 42 36-77 1-48 (335)
94 PRK13869 plasmid-partitioning 89.8 1.8 4.5E-05 23.7 8.0 70 5-74 9-100 (405)
95 PRK12529 RNA polymerase sigma 89.4 0.56 1.4E-05 26.6 4.0 33 23-55 132-164 (178)
96 PRK07670 RNA polymerase sigma 89.2 0.42 1.1E-05 27.4 3.2 32 26-57 205-236 (250)
97 PRK05911 RNA polymerase sigma 89.0 0.43 1.1E-05 27.3 3.2 32 26-57 213-244 (257)
98 PRK06759 RNA polymerase factor 89.0 0.53 1.4E-05 26.8 3.7 33 25-57 113-145 (154)
99 pfam05339 DUF739 Protein of un 89.0 1.6 4E-05 24.0 6.1 50 31-80 13-62 (69)
100 PRK06986 fliA flagellar biosyn 88.7 0.48 1.2E-05 27.0 3.3 32 26-57 191-222 (234)
101 pfam08965 DUF1870 Domain of un 88.6 1.2 3.2E-05 24.6 5.4 48 24-71 3-52 (117)
102 PRK01381 Trp operon repressor; 88.6 0.85 2.2E-05 25.6 4.5 54 17-70 36-91 (99)
103 cd00569 HTH_Hin_like Helix-tur 88.5 0.52 1.3E-05 26.8 3.4 26 29-54 16-41 (42)
104 COG1342 Predicted DNA-binding 88.4 0.44 1.1E-05 27.2 2.9 38 29-73 44-81 (99)
105 cd01108 HTH_CueR Helix-Turn-He 88.4 1.4 3.6E-05 24.3 5.5 46 35-80 1-63 (127)
106 pfam08535 KorB KorB domain. Th 88.4 0.97 2.5E-05 25.2 4.6 46 32-78 1-60 (93)
107 cd04774 HTH_YfmP Helix-Turn-He 88.3 1.5 3.9E-05 24.0 5.6 46 35-80 1-63 (96)
108 cd04789 HTH_Cfa Helix-Turn-Hel 87.7 1.8 4.7E-05 23.6 5.7 46 35-80 2-63 (102)
109 cd04768 HTH_BmrR-like Helix-Tu 87.6 1.6 4E-05 24.0 5.4 46 35-80 1-63 (96)
110 cd04762 HTH_MerR-trunc Helix-T 87.4 0.79 2E-05 25.8 3.7 23 35-57 1-23 (49)
111 cd04781 HTH_MerR-like_sg6 Heli 87.2 1.2 3E-05 24.7 4.5 46 35-80 1-62 (120)
112 TIGR02959 SigZ RNA polymerase 87.1 0.22 5.7E-06 29.0 0.8 34 26-59 108-142 (170)
113 PRK07500 rpoH2 RNA polymerase 87.1 1.2 3.1E-05 24.6 4.6 45 33-81 244-288 (289)
114 pfam04552 Sigma54_DBD Sigma-54 86.9 0.15 3.8E-06 30.0 -0.2 40 32-71 47-86 (160)
115 cd01111 HTH_MerD Helix-Turn-He 86.8 1.9 4.8E-05 23.5 5.4 46 35-80 1-63 (107)
116 PRK05932 RNA polymerase factor 86.7 0.27 7E-06 28.5 1.1 30 33-62 348-377 (461)
117 COG4197 Uncharacterized protei 86.5 0.69 1.8E-05 26.1 3.0 45 36-80 14-60 (96)
118 cd04785 HTH_CadR-PbrR-like Hel 86.4 2.2 5.7E-05 23.1 5.6 46 35-80 1-63 (126)
119 PHA00675 hypothetical protein 86.4 1.1 2.7E-05 25.0 3.9 34 21-54 26-59 (78)
120 PRK12528 RNA polymerase sigma 86.3 1.1 2.7E-05 24.9 3.9 31 24-54 125-155 (167)
121 PRK12523 RNA polymerase sigma 86.2 1.2 3.1E-05 24.6 4.2 31 25-55 126-156 (172)
122 PRK12469 RNA polymerase factor 86.2 0.23 5.9E-06 28.9 0.4 41 33-73 362-402 (475)
123 COG2842 Uncharacterized ATPase 86.1 1.8 4.5E-05 23.7 4.9 60 19-79 4-64 (297)
124 PRK09954 hypothetical protein; 86.0 1.2 3E-05 24.7 4.0 29 26-54 9-37 (362)
125 PRK12525 RNA polymerase sigma 85.8 1.2 3.1E-05 24.6 4.0 31 24-54 124-154 (168)
126 cd06171 Sigma70_r4 Sigma70, re 85.7 1.3 3.3E-05 24.5 4.1 33 24-56 16-48 (55)
127 PRK13752 putative transcriptio 85.6 1.4 3.6E-05 24.2 4.2 48 33-80 6-70 (144)
128 TIGR02941 Sigma_B RNA polymera 85.6 0.34 8.7E-06 27.9 1.1 33 25-57 213-245 (256)
129 pfam01047 MarR MarR family. Th 85.6 0.88 2.2E-05 25.5 3.2 31 24-54 7-37 (59)
130 PRK05657 RNA polymerase sigma 85.5 1.8 4.7E-05 23.6 4.8 46 32-81 283-328 (328)
131 cd04787 HTH_HMRTR_unk Helix-Tu 85.1 1.9 4.9E-05 23.5 4.7 46 35-80 1-63 (133)
132 cd04783 HTH_MerR1 Helix-Turn-H 85.1 1.9 4.9E-05 23.5 4.7 46 35-80 1-63 (126)
133 cd01110 HTH_SoxR Helix-Turn-He 84.9 1.6 4.1E-05 23.9 4.2 46 35-80 2-63 (139)
134 PRK00767 transcriptional regul 84.8 1.9 4.8E-05 23.5 4.6 63 11-73 4-68 (197)
135 cd04782 HTH_BltR Helix-Turn-He 84.7 3 7.7E-05 22.3 5.6 46 35-80 1-63 (97)
136 pfam07638 Sigma70_ECF ECF sigm 84.7 1.2 3.1E-05 24.6 3.6 29 25-53 142-170 (185)
137 PRK05803 sporulation sigma fac 84.6 1.2 3E-05 24.7 3.4 26 32-57 192-217 (228)
138 PRK10227 DNA-binding transcrip 84.3 2.1 5.3E-05 23.2 4.6 45 35-79 1-62 (135)
139 pfam02376 CUT CUT domain. The 84.3 2.2 5.5E-05 23.2 4.7 59 20-78 6-71 (81)
140 PRK13918 CRP/FNR family transc 84.2 3.5 9E-05 21.9 5.7 42 33-74 144-198 (201)
141 PRK11512 DNA-binding transcrip 83.7 1.3 3.4E-05 24.4 3.4 30 25-54 45-74 (144)
142 cd01106 HTH_TipAL-Mta Helix-Tu 83.6 3.1 7.8E-05 22.2 5.2 46 35-80 1-63 (103)
143 PHA01083 hypothetical protein 83.6 2.9 7.4E-05 22.4 5.1 55 26-80 5-61 (153)
144 TIGR03453 partition_RepA plasm 83.6 4 0.0001 21.6 7.2 61 15-75 4-86 (387)
145 COG2512 Predicted membrane-ass 83.5 1.2 2.9E-05 24.8 3.0 33 22-54 197-230 (258)
146 PRK03573 transcriptional regul 83.0 1.3 3.4E-05 24.4 3.2 29 26-54 37-66 (144)
147 TIGR03384 betaine_BetI transcr 82.8 3.5 9E-05 21.9 5.3 63 11-73 3-67 (189)
148 pfam01527 Transposase_8 Transp 82.7 3.2 8.2E-05 22.1 5.0 33 23-55 12-44 (75)
149 PRK13413 mpi multiple promoter 82.6 1.6 4.1E-05 23.9 3.5 30 26-56 165-194 (200)
150 PRK12527 RNA polymerase sigma 82.4 2 5.1E-05 23.3 3.9 31 24-54 111-141 (159)
151 cd04766 HTH_HspR Helix-Turn-He 82.2 3.9 9.9E-05 21.6 5.3 46 35-80 2-64 (91)
152 PRK07773 replicative DNA helic 82.2 3.1 8E-05 22.2 4.8 52 22-76 712-763 (868)
153 PRK09651 RNA polymerase sigma 82.2 2.2 5.5E-05 23.2 4.0 31 24-54 125-155 (172)
154 cd04769 HTH_MerR2 Helix-Turn-H 82.0 2.8 7.1E-05 22.5 4.5 46 35-80 1-62 (116)
155 TIGR02999 Sig-70_X6 RNA polyme 81.9 1.6 4.1E-05 23.9 3.3 31 23-53 150-180 (194)
156 pfam02796 HTH_7 Helix-turn-hel 81.9 2.5 6.5E-05 22.7 4.3 32 26-57 13-44 (45)
157 smart00419 HTH_CRP helix_turn_ 81.8 1.1 2.9E-05 24.8 2.4 24 32-55 6-29 (48)
158 cd00092 HTH_CRP helix_turn_hel 81.7 3.2 8.3E-05 22.1 4.8 25 31-55 22-46 (67)
159 PRK07037 extracytoplasmic-func 81.7 2.2 5.7E-05 23.1 3.9 31 24-54 129-159 (183)
160 TIGR02395 rpoN_sigma RNA polym 81.6 0.26 6.6E-06 28.6 -0.9 44 30-73 361-404 (477)
161 smart00347 HTH_MARR helix_turn 81.3 1.9 4.7E-05 23.5 3.4 30 25-54 15-44 (101)
162 cd04786 HTH_MerR-like_sg7 Heli 81.1 3.1 7.9E-05 22.2 4.5 46 35-80 1-63 (131)
163 pfam02954 HTH_8 Bacterial regu 80.7 2.5 6.4E-05 22.8 3.9 30 24-53 8-37 (42)
164 cd04775 HTH_Cfa-like Helix-Tur 80.5 3.3 8.4E-05 22.1 4.4 46 35-80 2-63 (102)
165 TIGR02850 spore_sigG RNA polym 80.5 1.5 3.9E-05 24.0 2.7 35 23-57 211-245 (254)
166 cd01104 HTH_MlrA-CarA Helix-Tu 79.9 1.9 4.8E-05 23.5 3.1 22 35-56 1-22 (68)
167 PRK09514 zntR zinc-responsive 79.8 4.2 0.00011 21.4 4.8 46 35-80 2-64 (140)
168 PRK06930 positive control sigm 79.8 2.9 7.3E-05 22.4 3.9 46 25-77 121-166 (170)
169 PRK06596 RNA polymerase factor 79.7 2 5.1E-05 23.4 3.1 32 26-57 238-271 (284)
170 PRK10668 DNA-binding transcrip 79.3 3.2 8.1E-05 22.2 4.1 39 23-61 20-58 (216)
171 cd04761 HTH_MerR-SF Helix-Turn 79.0 1.5 3.9E-05 24.1 2.3 23 35-57 1-23 (49)
172 pfam04967 HTH_10 HTH DNA bindi 78.8 1.7 4.4E-05 23.7 2.6 30 26-55 15-44 (53)
173 smart00342 HTH_ARAC helix_turn 78.7 2.6 6.5E-05 22.7 3.4 31 35-65 2-32 (84)
174 pfam08281 Sigma70_r4_2 Sigma-7 78.4 3.2 8.2E-05 22.1 3.8 31 24-54 16-46 (54)
175 pfam07900 DUF1670 Protein of u 78.2 6.1 0.00016 20.5 5.2 45 22-66 92-143 (220)
176 pfam01418 HTH_6 Helix-turn-hel 78.2 3.4 8.7E-05 22.0 3.9 36 22-57 21-57 (106)
177 PRK11753 cAMP-regulatory prote 78.0 4.9 0.00012 21.1 4.7 22 34-55 168-189 (211)
178 COG1974 LexA SOS-response tran 78.0 1.6 4.2E-05 23.9 2.2 49 29-78 7-55 (201)
179 cd04773 HTH_TioE_rpt2 Second H 77.9 1.8 4.6E-05 23.6 2.4 46 35-80 1-63 (108)
180 TIGR02985 Sig70_bacteroi1 RNA 77.7 2.8 7.1E-05 22.5 3.4 31 23-53 124-154 (167)
181 COG1309 AcrR Transcriptional r 77.6 5.1 0.00013 20.9 4.7 49 23-71 21-69 (201)
182 cd01107 HTH_BmrR Helix-Turn-He 77.4 1.9 4.8E-05 23.5 2.4 46 35-80 1-64 (108)
183 COG1508 RpoN DNA-directed RNA 77.3 1.5 3.8E-05 24.1 1.9 39 35-73 331-369 (444)
184 PRK11922 RNA polymerase sigma 77.0 3.5 9E-05 21.9 3.7 35 24-58 155-190 (231)
185 PRK10430 DNA-binding transcrip 76.8 4.8 0.00012 21.1 4.4 34 21-54 163-198 (239)
186 pfam08279 HTH_11 HTH domain. T 76.7 2.9 7.3E-05 22.4 3.2 30 25-54 5-35 (55)
187 PRK10219 DNA-binding transcrip 76.6 5 0.00013 21.0 4.4 32 32-63 19-50 (107)
188 smart00422 HTH_MERR helix_turn 76.4 2 5.2E-05 23.3 2.4 46 35-80 1-63 (70)
189 COG3415 Transposase and inacti 76.3 6.6 0.00017 20.3 5.0 31 24-54 11-41 (138)
190 pfam00376 MerR MerR family reg 76.2 2 5.1E-05 23.4 2.3 24 36-59 1-24 (38)
191 PRK12516 RNA polymerase sigma 76.1 3.7 9.5E-05 21.8 3.7 29 25-53 126-154 (190)
192 cd04780 HTH_MerR-like_sg5 Heli 76.1 2.1 5.3E-05 23.3 2.3 22 35-56 1-22 (95)
193 TIGR01817 nifA Nif-specific re 76.0 3 7.6E-05 22.3 3.1 31 24-54 533-563 (574)
194 PRK11179 DNA-binding transcrip 75.7 4 0.0001 21.6 3.7 29 24-52 13-41 (153)
195 PRK09637 RNA polymerase sigma 75.7 3.8 9.8E-05 21.7 3.6 30 24-53 112-141 (181)
196 PRK11169 leucine-responsive tr 75.3 4.2 0.00011 21.5 3.7 31 23-53 17-47 (164)
197 PRK11569 transcriptional repre 75.3 6.7 0.00017 20.2 4.8 53 2-54 10-63 (274)
198 PRK12532 RNA polymerase sigma 75.3 4.1 0.0001 21.5 3.7 31 24-54 142-172 (195)
199 PRK10572 DNA-binding transcrip 75.2 5.8 0.00015 20.6 4.4 34 31-64 196-229 (290)
200 cd04770 HTH_HMRTR Helix-Turn-H 75.0 2.4 6E-05 22.9 2.4 23 35-57 1-23 (123)
201 PRK12541 RNA polymerase sigma 74.9 4.2 0.00011 21.4 3.7 30 24-53 118-147 (161)
202 pfam07037 DUF1323 Putative tra 74.8 2.4 6.2E-05 22.9 2.4 22 35-56 1-22 (122)
203 PRK12539 RNA polymerase sigma 74.8 5 0.00013 21.0 4.0 30 24-53 137-166 (184)
204 cd04763 HTH_MlrA-like Helix-Tu 74.7 2.2 5.5E-05 23.1 2.2 22 35-56 1-22 (68)
205 pfam05269 Phage_CII Bacterioph 74.6 1.6 4.2E-05 23.9 1.5 36 33-69 22-57 (91)
206 PRK12547 RNA polymerase sigma 74.6 4.4 0.00011 21.3 3.7 30 24-53 118-147 (164)
207 PRK12543 RNA polymerase sigma 74.5 4.4 0.00011 21.3 3.7 34 24-57 135-169 (190)
208 PRK13919 putative RNA polymera 74.5 4.5 0.00011 21.3 3.7 30 25-54 143-172 (187)
209 cd00592 HTH_MerR-like Helix-Tu 74.5 2.5 6.4E-05 22.8 2.4 46 35-80 1-62 (100)
210 PRK12526 RNA polymerase sigma 74.4 4.4 0.00011 21.3 3.7 29 25-53 160-188 (206)
211 PRK09646 RNA polymerase sigma 74.3 4.5 0.00012 21.3 3.7 45 24-76 148-193 (194)
212 PRK09775 hypothetical protein; 74.1 3.7 9.4E-05 21.8 3.2 31 25-55 3-33 (443)
213 cd04764 HTH_MlrA-like_sg1 Heli 73.8 2.6 6.7E-05 22.7 2.4 22 35-56 1-22 (67)
214 PRK09975 DNA-binding transcrip 73.6 4.8 0.00012 21.1 3.7 39 23-61 20-58 (213)
215 COG0789 SoxR Predicted transcr 73.6 2.6 6.7E-05 22.7 2.3 46 35-80 1-63 (124)
216 cd01109 HTH_YyaN Helix-Turn-He 73.4 2.7 6.9E-05 22.6 2.4 46 35-80 1-63 (113)
217 PRK09641 RNA polymerase sigma 73.2 5.7 0.00014 20.7 4.0 30 25-54 143-172 (187)
218 PRK12524 RNA polymerase sigma 73.0 5 0.00013 21.0 3.7 31 24-54 142-172 (196)
219 smart00344 HTH_ASNC helix_turn 72.9 5.3 0.00013 20.9 3.8 30 24-53 7-36 (108)
220 PRK12546 RNA polymerase sigma 72.9 4.8 0.00012 21.1 3.5 34 24-57 119-153 (188)
221 PRK12531 RNA polymerase sigma 72.8 5.2 0.00013 20.9 3.7 33 25-57 148-181 (194)
222 PRK12542 RNA polymerase sigma 72.8 4.9 0.00012 21.1 3.6 31 24-54 128-158 (185)
223 pfam04218 CENP-B_N CENP-B N-te 72.6 3.9 9.8E-05 21.7 3.0 30 29-58 17-46 (53)
224 PRK09047 RNA polymerase factor 72.5 4.8 0.00012 21.1 3.5 47 25-76 113-160 (161)
225 PRK12519 RNA polymerase sigma 72.4 5 0.00013 21.0 3.5 30 25-54 148-177 (194)
226 PRK12517 RNA polymerase sigma 72.3 5.4 0.00014 20.8 3.7 30 24-53 134-163 (188)
227 PRK09638 RNA polymerase sigma 72.3 6.1 0.00016 20.5 4.0 31 24-54 133-163 (177)
228 PRK11511 DNA-binding transcrip 72.3 4.3 0.00011 21.4 3.2 34 31-64 22-55 (127)
229 pfam00440 TetR_N Bacterial reg 72.2 3.8 9.8E-05 21.7 2.9 37 23-59 5-41 (47)
230 PRK11161 fumarate/nitrate redu 72.2 8.8 0.00022 19.5 4.8 21 34-54 184-204 (235)
231 COG1522 Lrp Transcriptional re 72.1 5.3 0.00013 20.9 3.6 31 24-54 12-42 (154)
232 PRK05949 RNA polymerase sigma 71.8 4.8 0.00012 21.1 3.4 32 26-57 274-309 (327)
233 cd01105 HTH_GlnR-like Helix-Tu 71.8 3.3 8.5E-05 22.0 2.5 22 35-56 2-23 (88)
234 PRK05602 RNA polymerase sigma 71.6 5.5 0.00014 20.7 3.6 31 24-54 134-164 (186)
235 PRK12537 RNA polymerase sigma 71.5 5.5 0.00014 20.7 3.6 28 26-53 143-170 (184)
236 PRK09644 RNA polymerase sigma 71.5 5.4 0.00014 20.8 3.5 30 24-53 114-143 (165)
237 PRK09647 RNA polymerase sigma 71.2 5.6 0.00014 20.7 3.6 34 24-57 163-197 (222)
238 PRK11924 RNA polymerase sigma 71.2 6.8 0.00017 20.2 4.0 30 25-54 132-161 (180)
239 PRK09652 RNA polymerase sigma 71.1 7 0.00018 20.1 4.1 34 24-57 143-177 (192)
240 pfam11268 DUF3071 Protein of u 71.1 4.4 0.00011 21.3 3.0 35 22-56 56-90 (169)
241 PRK10046 dpiA two-component re 70.8 7.7 0.0002 19.9 4.2 29 26-54 168-197 (225)
242 PRK13705 plasmid-partitioning 70.8 9.5 0.00024 19.3 7.7 61 16-76 11-97 (388)
243 cd04790 HTH_Cfa-like_unk Helix 70.5 3.5 8.9E-05 21.9 2.4 46 35-80 2-64 (172)
244 COG1737 RpiR Transcriptional r 70.3 7.5 0.00019 19.9 4.1 39 19-57 21-59 (281)
245 PRK12540 RNA polymerase sigma 70.3 6.1 0.00015 20.5 3.6 35 24-58 117-152 (181)
246 TIGR02989 Sig-70_gvs1 RNA poly 70.3 6.4 0.00016 20.4 3.7 32 23-54 120-151 (163)
247 PRK12536 RNA polymerase sigma 70.2 6.4 0.00016 20.4 3.7 28 26-53 134-161 (178)
248 TIGR02479 FliA_WhiG RNA polyme 69.7 5.8 0.00015 20.6 3.4 31 26-56 186-216 (227)
249 PRK10681 DNA-binding transcrip 69.6 6.5 0.00017 20.3 3.6 34 20-53 7-40 (252)
250 PRK09640 RNA polymerase sigma 69.5 6.8 0.00017 20.2 3.7 30 24-53 140-169 (188)
251 PRK09645 RNA polymerase sigma 69.5 7.6 0.00019 19.9 4.0 48 24-76 122-170 (171)
252 PRK12534 RNA polymerase sigma 69.4 6.8 0.00017 20.2 3.7 34 24-57 143-177 (187)
253 PRK09391 fixK transcriptional 69.4 3.8 9.7E-05 21.7 2.4 23 32-54 171-193 (224)
254 PRK12538 RNA polymerase sigma 69.4 6.9 0.00017 20.2 3.7 29 26-54 179-207 (233)
255 PRK12512 RNA polymerase sigma 69.2 6.7 0.00017 20.2 3.6 31 24-54 137-167 (184)
256 PRK11302 DNA-binding transcrip 69.1 7.8 0.0002 19.8 4.0 37 22-58 21-58 (284)
257 PRK12515 RNA polymerase sigma 69.1 8.1 0.00021 19.8 4.0 48 24-76 137-185 (189)
258 COG4565 CitB Response regulato 69.0 6.7 0.00017 20.2 3.6 23 32-54 171-193 (224)
259 cd01282 HTH_MerR-like_sg3 Heli 69.0 3.9 1E-04 21.6 2.4 22 35-56 1-22 (112)
260 pfam09048 Cro Cro. Members of 68.9 5.1 0.00013 20.9 3.0 35 27-63 6-40 (58)
261 cd04776 HTH_GnyR Helix-Turn-He 68.9 3.9 9.9E-05 21.6 2.4 21 35-55 1-21 (118)
262 PRK11337 DNA-binding transcrip 68.9 7.7 0.0002 19.9 3.9 36 22-57 34-70 (293)
263 PRK11557 putative DNA-binding 68.7 8 0.0002 19.8 3.9 37 21-57 20-57 (282)
264 TIGR00014 arsC arsenate reduct 68.6 7 0.00018 20.1 3.6 39 43-81 8-57 (114)
265 PRK12513 RNA polymerase sigma 68.3 8.5 0.00022 19.6 4.0 31 24-54 145-175 (194)
266 PRK11923 algU RNA polymerase s 68.2 7.5 0.00019 19.9 3.7 33 25-57 145-178 (193)
267 PRK09639 RNA polymerase sigma 68.2 8.1 0.00021 19.7 3.9 28 26-54 120-147 (166)
268 PRK12530 RNA polymerase sigma 68.2 7.5 0.00019 20.0 3.7 28 26-53 144-171 (191)
269 PRK12518 RNA polymerase sigma 67.9 8.6 0.00022 19.6 4.0 30 25-54 127-156 (175)
270 PRK06811 RNA polymerase factor 67.9 7.7 0.0002 19.9 3.7 31 24-54 134-164 (185)
271 pfam04760 IF2_N Translation in 67.8 11 0.00028 19.0 4.9 44 33-76 2-52 (52)
272 PRK12544 RNA polymerase sigma 67.7 7.7 0.0002 19.9 3.7 30 25-54 156-185 (207)
273 PRK12522 RNA polymerase sigma 67.6 7.9 0.0002 19.8 3.7 30 24-53 125-154 (173)
274 PRK12514 RNA polymerase sigma 67.4 7.5 0.00019 20.0 3.6 33 25-57 136-169 (179)
275 PRK13749 transcriptional regul 67.3 8.9 0.00023 19.5 3.9 48 33-80 2-66 (121)
276 PRK07405 RNA polymerase sigma 67.2 7.1 0.00018 20.1 3.4 25 33-57 276-300 (318)
277 cd04788 HTH_NolA-AlbR Helix-Tu 66.9 4.6 0.00012 21.2 2.4 46 35-80 1-63 (96)
278 TIGR01764 excise DNA binding d 66.9 3.7 9.3E-05 21.8 1.9 24 35-58 2-26 (49)
279 pfam07471 Phage_Nu1 Phage DNA 66.8 5 0.00013 21.0 2.6 23 34-56 2-24 (164)
280 PRK12535 RNA polymerase sigma 66.7 8.2 0.00021 19.7 3.7 34 24-57 138-172 (195)
281 cd01279 HTH_HspR-like Helix-Tu 66.5 4.4 0.00011 21.3 2.2 22 35-56 2-23 (98)
282 TIGR00491 aIF-2 translation in 66.2 1.8 4.7E-05 23.6 0.3 49 20-74 413-461 (1145)
283 pfam05225 HTH_psq helix-turn-h 66.0 12 0.0003 18.8 4.6 40 20-60 3-42 (45)
284 cd04784 HTH_CadR-PbrR Helix-Tu 65.8 5 0.00013 21.0 2.4 23 35-57 1-23 (127)
285 smart00420 HTH_DEOR helix_turn 65.7 6.1 0.00015 20.5 2.8 31 24-54 4-34 (53)
286 PRK09392 ftrB transcriptional 65.6 12 0.00031 18.7 4.8 22 33-54 172-193 (236)
287 PRK10371 DNA-binding transcrip 65.5 9.1 0.00023 19.5 3.7 42 23-64 194-237 (302)
288 TIGR00160 MGSA methylglyoxal s 65.5 3.7 9.5E-05 21.7 1.7 23 56-78 85-108 (143)
289 PRK13502 transcriptional activ 65.5 11 0.00027 19.1 4.0 32 31-62 189-220 (282)
290 pfam05930 Phage_AlpA Prophage 65.5 6.6 0.00017 20.3 3.0 29 34-62 3-31 (51)
291 PRK11608 pspF phage shock prot 65.5 10 0.00026 19.2 3.9 31 24-54 289-319 (325)
292 PRK09649 RNA polymerase sigma 65.3 9.1 0.00023 19.5 3.7 34 24-57 136-170 (185)
293 COG3413 Predicted DNA binding 65.2 5.5 0.00014 20.8 2.5 26 31-56 175-200 (215)
294 PRK09643 RNA polymerase sigma 65.2 9.1 0.00023 19.4 3.7 30 25-54 138-167 (197)
295 COG1595 RpoE DNA-directed RNA 65.2 9 0.00023 19.5 3.6 32 24-55 133-164 (182)
296 cd06170 LuxR_C_like C-terminal 65.0 5.8 0.00015 20.6 2.6 27 30-56 11-37 (57)
297 PRK09415 RNA polymerase factor 64.6 11 0.00028 19.0 4.0 31 24-54 133-163 (177)
298 PRK12545 RNA polymerase sigma 64.3 9.4 0.00024 19.4 3.6 31 24-54 145-175 (201)
299 cd04765 HTH_MlrA-like_sg2 Heli 64.2 5.6 0.00014 20.7 2.4 22 35-56 1-22 (99)
300 pfam00165 HTH_AraC Bacterial r 64.1 4.4 0.00011 21.3 1.9 29 32-60 6-35 (43)
301 pfam09339 HTH_IclR IclR helix- 64.1 6.3 0.00016 20.4 2.7 30 27-56 10-40 (52)
302 PRK09642 RNA polymerase sigma 63.8 10 0.00026 19.2 3.7 30 24-53 112-141 (160)
303 TIGR03454 partition_RepB plasm 63.4 8.5 0.00022 19.6 3.2 50 19-72 166-215 (325)
304 COG2826 Tra8 Transposase and i 63.2 6.9 0.00018 20.2 2.7 32 25-57 15-47 (318)
305 PRK11388 DNA-binding transcrip 62.9 12 0.00031 18.7 3.9 32 23-54 593-624 (639)
306 cd00090 HTH_ARSR Arsenical Res 62.7 10 0.00026 19.1 3.5 28 26-54 13-40 (78)
307 PRK09863 putative frv operon r 62.5 8.1 0.00021 19.8 3.0 22 31-52 14-35 (585)
308 cd04772 HTH_TioE_rpt1 First He 62.3 8.2 0.00021 19.7 3.0 24 35-58 1-24 (99)
309 PRK03837 transcriptional regul 62.1 8.6 0.00022 19.6 3.1 51 1-54 5-58 (243)
310 smart00418 HTH_ARSR helix_turn 61.8 8.7 0.00022 19.6 3.0 27 27-54 4-30 (66)
311 PRK09648 RNA polymerase sigma 61.8 12 0.0003 18.8 3.7 30 25-54 144-173 (187)
312 PRK09802 DNA-binding transcrip 61.7 14 0.00037 18.3 4.3 42 9-54 10-51 (269)
313 PRK09480 slmA nucleoid occlusi 61.5 7.1 0.00018 20.1 2.5 42 30-71 26-67 (194)
314 PHA01082 putative transcriptio 61.4 9 0.00023 19.5 3.0 49 24-72 20-69 (133)
315 PRK13182 racA polar chromosome 61.3 8.1 0.00021 19.8 2.8 36 37-72 3-49 (178)
316 PRK07921 RNA polymerase sigma 60.5 10 0.00026 19.2 3.2 24 34-57 278-301 (320)
317 PRK09744 DNA-binding transcrip 60.4 6.5 0.00016 20.3 2.2 25 36-62 12-36 (75)
318 smart00421 HTH_LUXR helix_turn 60.2 7.7 0.0002 19.9 2.5 27 30-56 14-40 (58)
319 cd04779 HTH_MerR-like_sg4 Heli 60.0 7.4 0.00019 20.0 2.4 46 35-80 1-62 (134)
320 PRK10365 transcriptional regul 59.7 15 0.00038 18.2 3.9 31 23-53 407-437 (441)
321 PRK13509 transcriptional repre 59.7 11 0.00029 18.9 3.3 34 21-54 6-39 (251)
322 cd04777 HTH_MerR-like_sg1 Heli 59.6 7.3 0.00019 20.0 2.3 22 35-56 1-22 (107)
323 TIGR02899 spore_safA spore coa 59.5 5.5 0.00014 20.7 1.7 19 64-82 5-23 (44)
324 TIGR02431 pcaR_pcaU beta-ketoa 59.1 5.7 0.00015 20.7 1.7 24 31-54 21-44 (252)
325 PRK12533 RNA polymerase sigma 59.1 13 0.00034 18.4 3.6 33 25-57 144-177 (217)
326 PRK10906 DNA-binding transcrip 59.0 12 0.0003 18.8 3.3 33 22-54 7-39 (252)
327 COG1318 Predicted transcriptio 59.0 11 0.00029 18.9 3.2 32 29-60 56-87 (182)
328 TIGR00651 pta phosphate acetyl 58.9 11 0.00027 19.0 3.1 37 17-54 61-97 (322)
329 TIGR02812 fadR_gamma fatty aci 58.9 4 0.0001 21.6 0.9 17 38-54 34-50 (275)
330 pfam00196 GerE Bacterial regul 58.8 8.6 0.00022 19.6 2.6 27 30-56 14-40 (58)
331 PRK07598 RNA polymerase sigma 58.8 11 0.00029 18.8 3.2 25 33-57 364-388 (410)
332 pfam08220 HTH_DeoR DeoR-like h 58.7 13 0.00033 18.5 3.5 30 24-53 4-33 (57)
333 COG1349 GlpR Transcriptional r 58.6 12 0.0003 18.8 3.3 32 22-53 7-38 (253)
334 cd04767 HTH_HspR-like_MBC Heli 58.4 7.8 0.0002 19.9 2.3 22 35-56 2-23 (120)
335 PRK07406 RNA polymerase sigma 58.0 13 0.00034 18.4 3.5 23 35-57 344-366 (385)
336 pfam01022 HTH_5 Bacterial regu 57.9 14 0.00036 18.3 3.6 28 26-54 8-35 (47)
337 PHA02519 plasmid partition pro 57.9 12 0.0003 18.8 3.1 56 21-76 16-97 (387)
338 PRK10434 srlR DNA-bindng trans 57.8 13 0.00032 18.6 3.3 33 22-54 7-39 (256)
339 PRK12511 RNA polymerase sigma 57.6 4.5 0.00012 21.2 1.0 32 26-57 119-151 (182)
340 PRK08295 RNA polymerase factor 56.9 17 0.00044 17.8 4.4 30 26-56 163-192 (209)
341 TIGR02983 SigE-fam_strep RNA p 56.8 4.1 0.0001 21.5 0.7 27 27-53 122-148 (165)
342 PRK12520 RNA polymerase sigma 56.6 18 0.00045 17.7 4.1 30 25-54 138-167 (191)
343 pfam04645 DUF603 Protein of un 56.5 14 0.00035 18.4 3.3 40 21-61 7-50 (181)
344 smart00346 HTH_ICLR helix_turn 56.4 10 0.00027 19.1 2.7 24 31-54 17-40 (91)
345 TIGR03001 Sig-70_gmx1 RNA poly 56.4 6.9 0.00018 20.2 1.8 26 30-55 178-203 (249)
346 pfam01710 Transposase_14 Trans 56.2 14 0.00036 18.3 3.3 33 21-54 6-38 (120)
347 PRK10840 transcriptional regul 55.7 18 0.00047 17.7 3.9 48 30-77 161-212 (216)
348 TIGR00738 rrf2_super rrf2 fami 55.4 9 0.00023 19.5 2.2 31 26-56 15-47 (133)
349 PRK10923 glnG nitrogen regulat 55.3 19 0.00047 17.6 4.0 31 24-54 432-462 (469)
350 COG3355 Predicted transcriptio 54.3 15 0.00039 18.1 3.2 29 26-54 33-62 (126)
351 PRK01905 DNA-binding protein F 54.1 17 0.00044 17.8 3.5 31 23-53 39-69 (77)
352 PRK05901 RNA polymerase sigma 53.2 15 0.00038 18.1 3.1 25 33-57 354-378 (398)
353 PRK11361 acetoacetate metaboli 52.9 20 0.00052 17.4 4.0 32 23-54 419-450 (457)
354 COG3888 Predicted transcriptio 52.8 15 0.00039 18.1 3.0 24 31-54 17-40 (321)
355 COG4496 Uncharacterized protei 51.6 21 0.00053 17.3 3.6 38 19-56 40-78 (100)
356 pfam10668 Phage_terminase Phag 51.5 9.3 0.00024 19.4 1.8 24 33-56 21-44 (60)
357 TIGR01481 ccpA catabolite cont 51.2 3.2 8.2E-05 22.1 -0.6 40 34-73 2-41 (332)
358 COG3311 AlpA Predicted transcr 50.5 16 0.00042 17.9 2.9 30 33-62 12-41 (70)
359 PRK13501 transcriptional activ 50.1 22 0.00057 17.1 3.7 32 32-63 190-221 (290)
360 PRK10141 DNA-binding transcrip 50.1 22 0.00057 17.1 3.5 29 26-54 20-48 (106)
361 PRK10411 DNA-binding transcrip 49.5 23 0.00059 17.1 3.9 33 22-54 6-38 (240)
362 COG2378 Predicted transcriptio 49.4 23 0.00059 17.0 4.4 36 19-54 7-42 (311)
363 PRK09958 DNA-binding transcrip 49.3 15 0.00039 18.1 2.6 26 31-56 155-180 (204)
364 PRK09834 DNA-binding transcrip 49.3 16 0.0004 18.0 2.7 25 30-54 22-46 (264)
365 COG1510 Predicted transcriptio 49.1 10 0.00026 19.2 1.6 23 32-54 39-61 (177)
366 TIGR02233 Myxo_sigma_rel Myxoc 49.0 11 0.00028 18.9 1.8 34 25-58 31-64 (106)
367 PRK09210 RNA polymerase sigma 48.6 13 0.00034 18.5 2.2 24 34-57 326-349 (368)
368 COG4367 Uncharacterized protei 48.5 24 0.00061 17.0 4.7 53 19-73 8-60 (97)
369 COG1654 BirA Biotin operon rep 47.4 25 0.00063 16.9 3.7 27 28-54 11-39 (79)
370 PRK10360 DNA-binding transcrip 46.9 18 0.00045 17.7 2.6 28 30-57 148-175 (196)
371 PRK13503 transcriptional activ 46.2 26 0.00066 16.7 5.9 38 26-63 177-216 (278)
372 pfam02787 CPSase_L_D3 Carbamoy 46.1 19 0.00049 17.5 2.7 25 32-56 21-45 (122)
373 PRK10403 transcriptional regul 46.1 19 0.00048 17.6 2.6 26 31-56 165-190 (215)
374 COG2207 AraC AraC-type DNA-bin 45.8 26 0.00067 16.7 4.2 41 22-63 25-65 (127)
375 PRK12681 cysB transcriptional 45.7 26 0.00067 16.7 3.9 30 25-54 5-36 (324)
376 pfam09572 RE_XamI XamI restric 45.7 26 0.00067 16.7 3.4 60 11-73 7-74 (251)
377 COG1414 IclR Transcriptional r 45.3 25 0.00065 16.8 3.2 24 31-54 16-39 (246)
378 pfam06056 Terminase_5 Putative 45.3 15 0.00037 18.2 2.0 28 30-57 9-36 (58)
379 PRK09935 transcriptional regul 45.2 19 0.00049 17.5 2.6 44 31-74 161-208 (210)
380 TIGR01405 polC_Gram_pos DNA po 44.5 25 0.00063 16.9 3.0 37 20-56 1210-1248(1264)
381 TIGR02047 CadR-PbrR Cd(II)/Pb( 43.5 13 0.00033 18.6 1.5 28 35-62 1-28 (127)
382 PRK09483 response regulator; P 42.8 22 0.00057 17.1 2.6 45 30-74 159-207 (216)
383 COG2963 Transposase and inacti 42.6 30 0.00075 16.4 5.0 34 21-54 11-45 (116)
384 pfam05732 RepL Firmicute plasm 42.1 18 0.00046 17.7 2.0 22 33-54 74-95 (165)
385 TIGR02043 ZntR Zn(II)-responsi 42.1 18 0.00045 17.7 2.0 23 24-46 46-70 (132)
386 pfam03333 PapB Adhesin biosynt 41.7 18 0.00047 17.6 2.0 29 26-54 43-73 (91)
387 PRK11202 DNA-binding transcrip 41.6 16 0.00042 17.9 1.8 49 21-69 16-67 (203)
388 PRK11050 manganese transport r 41.5 31 0.00078 16.3 3.7 34 21-54 40-74 (155)
389 PRK00430 fis DNA-binding prote 41.2 31 0.00079 16.3 3.5 31 23-53 60-90 (98)
390 PRK09393 ftrA transcriptional 41.1 31 0.00079 16.3 3.8 34 29-62 227-260 (320)
391 PRK05022 anaerobic nitric oxid 40.7 32 0.00081 16.2 4.1 32 23-54 471-502 (510)
392 pfam08822 DUF1804 Protein of u 40.2 32 0.00082 16.2 3.7 34 23-56 8-41 (165)
393 COG2197 CitB Response regulato 40.0 32 0.00083 16.2 3.3 29 29-57 158-186 (211)
394 PRK10651 transcriptional regul 39.9 27 0.00068 16.7 2.6 26 31-56 167-192 (216)
395 TIGR03613 RutR pyrimidine util 38.9 34 0.00086 16.1 4.6 51 23-73 17-67 (202)
396 TIGR02944 suf_reg_Xantho FeS a 38.1 9.2 0.00023 19.4 0.0 35 22-56 13-47 (130)
397 TIGR03541 reg_near_HchA LuxR f 38.0 32 0.00081 16.2 2.8 26 31-56 183-208 (232)
398 TIGR01293 Kv_beta voltage-depe 37.8 20 0.00051 17.4 1.7 50 31-80 234-287 (338)
399 pfam07278 DUF1441 Protein of u 37.3 29 0.00074 16.5 2.5 25 34-58 1-25 (152)
400 PTZ00298 mevalonate kinase; Pr 37.2 36 0.00092 15.9 4.5 37 36-74 238-274 (328)
401 PRK12680 transcriptional regul 37.1 36 0.00092 15.9 3.9 30 25-54 5-36 (327)
402 pfam11985 DUF3486 Protein of u 37.1 36 0.00092 15.9 4.2 47 1-55 1-56 (179)
403 PRK07758 hypothetical protein; 36.7 32 0.00082 16.2 2.6 40 18-57 47-86 (95)
404 pfam10078 DUF2316 Uncharacteri 36.4 37 0.00094 15.8 6.0 56 18-74 7-62 (89)
405 TIGR02952 Sig70_famx2 RNA poly 36.3 23 0.00059 17.0 1.9 32 24-55 129-160 (171)
406 PRK00118 putative DNA-binding 36.3 37 0.00095 15.8 4.0 31 26-56 25-55 (105)
407 pfam00325 Crp Bacterial regula 36.2 30 0.00077 16.4 2.4 22 34-55 2-23 (32)
408 pfam02042 RWP-RK RWP-RK domain 35.5 38 0.00098 15.7 3.7 29 26-54 7-35 (52)
409 PRK10163 DNA-binding transcrip 35.5 38 0.00098 15.7 5.3 29 26-54 31-60 (271)
410 COG2452 Predicted site-specifi 35.3 39 0.00098 15.7 2.9 23 34-56 1-23 (193)
411 pfam00392 GntR Bacterial regul 35.0 27 0.00069 16.6 2.0 22 33-54 22-44 (64)
412 PRK10820 DNA-binding transcrip 34.7 39 0.001 15.7 3.8 29 24-53 471-499 (513)
413 PRK11552 putative DNA-binding 34.3 40 0.001 15.6 5.9 41 33-74 32-72 (224)
414 pfam04297 UPF0122 Putative hel 34.0 41 0.001 15.6 3.9 29 27-55 26-54 (101)
415 pfam05043 Mga Mga helix-turn-h 33.7 41 0.001 15.6 3.1 36 21-56 17-52 (87)
416 pfam09571 RE_XcyI XcyI restric 33.6 19 0.00048 17.6 1.0 56 26-81 77-135 (318)
417 COG1339 Transcriptional regula 33.2 25 0.00064 16.8 1.6 25 29-54 15-39 (214)
418 PRK10402 DNA-binding transcrip 33.1 35 0.00088 16.0 2.3 41 34-74 156-209 (213)
419 TIGR02054 MerD mercuric resist 33.1 20 0.00052 17.4 1.1 16 59-74 59-74 (120)
420 cd07377 WHTH_GntR Winged helix 32.9 33 0.00083 16.2 2.2 34 21-54 9-45 (66)
421 COG1555 ComEA DNA uptake prote 32.4 43 0.0011 15.4 3.0 36 21-56 108-145 (149)
422 smart00345 HTH_GNTR helix_turn 32.3 34 0.00086 16.1 2.2 21 34-54 19-40 (60)
423 pfam07506 RepB RepB plasmid pa 32.1 44 0.0011 15.4 2.8 25 31-55 18-42 (185)
424 cd04778 HTH_MerR-like_sg2 Heli 31.6 37 0.00094 15.9 2.3 14 31-44 54-67 (219)
425 pfam01978 TrmB Sugar-specific 31.6 45 0.0011 15.4 4.0 28 27-54 15-42 (68)
426 pfam07750 GcrA GcrA cell cycle 31.5 38 0.00098 15.7 2.3 20 32-51 16-36 (162)
427 pfam06970 RepA_N Replication i 31.4 35 0.00089 16.0 2.1 22 35-56 53-74 (76)
428 COG4189 Predicted transcriptio 31.2 45 0.0012 15.3 5.5 30 24-53 27-56 (308)
429 TIGR02051 MerR Hg(II)-responsi 31.0 10 0.00026 19.1 -0.6 21 27-47 49-69 (126)
430 PRK12679 cbl transcriptional r 30.9 46 0.0012 15.3 3.7 29 25-53 5-35 (316)
431 PRK11014 transcriptional repre 30.9 37 0.00094 15.9 2.2 21 35-55 26-46 (141)
432 COG5484 Uncharacterized conser 30.7 46 0.0012 15.3 3.6 28 31-58 16-43 (279)
433 pfam07453 NUMOD1 NUMOD1 domain 30.3 28 0.00072 16.5 1.5 19 36-54 18-36 (37)
434 PRK12737 gatY tagatose-bisphos 30.1 33 0.00083 16.1 1.8 39 39-77 162-205 (284)
435 PRK11920 rirA iron-responsive 30.0 44 0.0011 15.4 2.4 25 31-55 21-45 (153)
436 KOG0774 consensus 29.7 20 0.00052 17.4 0.7 36 25-60 185-244 (334)
437 COG4753 Response regulator con 29.6 47 0.0012 15.2 2.5 32 31-62 385-416 (475)
438 PRK04435 hypothetical protein; 29.5 26 0.00067 16.7 1.2 29 29-57 28-56 (146)
439 PRK10870 transcriptional repre 29.4 41 0.001 15.6 2.2 24 31-54 68-91 (176)
440 PRK00423 tfb transcription ini 29.3 49 0.0012 15.1 3.2 20 35-54 183-202 (310)
441 TIGR01529 argR_whole arginine 29.3 49 0.0012 15.1 2.9 32 24-55 5-43 (155)
442 pfam01476 LysM LysM domain. Th 29.3 31 0.00078 16.3 1.5 23 33-55 5-27 (43)
443 COG4977 Transcriptional regula 29.3 49 0.0012 15.1 4.2 37 22-58 222-260 (328)
444 pfam02082 Rrf2 Transcriptional 29.2 39 0.00099 15.7 2.0 23 34-56 24-46 (82)
445 PRK09464 pdhR transcriptional 29.2 49 0.0012 15.1 3.9 50 1-53 1-53 (254)
446 PRK10857 DNA-binding transcrip 29.0 39 0.00099 15.7 2.0 23 34-56 25-47 (164)
447 TIGR02392 rpoH_proteo alternat 28.9 50 0.0013 15.1 3.6 30 27-57 238-268 (279)
448 PRK09940 transcriptional regul 28.8 44 0.0011 15.4 2.3 32 23-54 136-170 (253)
449 smart00257 LysM Lysin motif. 28.7 27 0.00069 16.7 1.2 22 33-54 6-27 (44)
450 PRK13866 plasmid partitioning 28.4 50 0.0013 15.0 3.3 43 30-72 175-217 (336)
451 PRK12683 transcriptional regul 28.3 51 0.0013 15.0 3.9 30 25-54 5-36 (308)
452 pfam00126 HTH_1 Bacterial regu 28.1 44 0.0011 15.4 2.2 19 36-54 15-33 (60)
453 PRK10188 DNA-binding transcrip 28.1 49 0.0012 15.1 2.4 26 31-56 191-216 (240)
454 TIGR02984 Sig-70_plancto1 RNA 28.0 51 0.0013 15.0 3.5 32 23-54 146-177 (190)
455 COG3284 AcoR Transcriptional a 27.9 51 0.0013 15.0 4.1 34 21-54 565-598 (606)
456 COG1725 Predicted transcriptio 27.8 43 0.0011 15.5 2.1 22 33-54 34-55 (125)
457 COG1497 Predicted transcriptio 27.7 52 0.0013 15.0 2.6 27 28-54 19-45 (260)
458 TIGR02702 SufR_cyano iron-sulf 27.3 53 0.0013 14.9 2.7 30 25-54 6-35 (215)
459 PRK11475 DNA-binding transcrip 27.2 50 0.0013 15.0 2.3 28 30-57 145-172 (205)
460 TIGR02997 Sig70-cyanoRpoD RNA 27.0 45 0.0011 15.4 2.0 21 35-55 308-328 (336)
461 COG4294 Uve UV damage repair e 26.9 54 0.0014 14.9 4.1 40 38-77 191-233 (347)
462 PRK06801 hypothetical protein; 26.9 39 0.001 15.7 1.7 40 38-77 162-206 (286)
463 pfam06323 Phage_antiter_Q Phag 26.5 44 0.0011 15.4 1.9 48 23-74 154-203 (230)
464 PRK12682 transcriptional regul 26.3 55 0.0014 14.8 3.9 24 31-54 13-36 (309)
465 PRK09195 gatY tagatose-bisphos 26.1 41 0.001 15.6 1.7 32 46-77 174-205 (284)
466 cd04334 ProRS-INS INS is an am 25.9 42 0.0011 15.5 1.8 24 59-82 31-54 (160)
467 cd00118 LysM Lysin domain, fou 25.7 36 0.00091 15.9 1.3 25 32-56 6-30 (46)
468 PRK10265 chaperone-modulator p 25.5 57 0.0015 14.7 2.5 28 34-61 7-35 (101)
469 COG0856 Orotate phosphoribosyl 25.3 57 0.0015 14.7 3.2 24 31-54 15-38 (203)
470 PRK12738 kbaY tagatose-bisphos 25.1 45 0.0011 15.3 1.8 32 46-77 174-205 (286)
471 TIGR02329 propionate_PrpR prop 25.1 58 0.0015 14.7 3.7 47 10-56 611-657 (658)
472 COG1959 Predicted transcriptio 24.9 59 0.0015 14.7 2.3 44 34-77 25-87 (150)
473 PRK11052 malQ 4-alpha-glucanot 24.9 14 0.00036 18.3 -0.8 16 61-76 29-44 (694)
474 PRK09636 RNA polymerase sigma 24.8 59 0.0015 14.6 3.1 29 26-54 119-147 (289)
475 PRK10026 arsenate reductase; P 24.7 59 0.0015 14.6 4.0 40 43-82 11-60 (141)
476 PRK06806 fructose-bisphosphate 24.7 43 0.0011 15.5 1.6 39 39-77 160-203 (281)
477 COG4695 Phage-related protein 24.7 59 0.0015 14.6 2.4 44 19-62 262-305 (398)
478 PRK12684 transcriptional regul 24.6 59 0.0015 14.6 3.9 24 31-54 13-36 (313)
479 COG2739 Uncharacterized protei 24.4 60 0.0015 14.6 2.3 26 28-53 27-52 (105)
480 PRK07452 DNA polymerase III su 24.3 60 0.0015 14.6 5.8 53 20-72 237-296 (326)
481 TIGR02044 CueR Cu(I)-responsiv 24.1 61 0.0015 14.6 3.3 45 35-79 1-62 (127)
482 PRK13500 transcriptional activ 24.1 61 0.0016 14.6 5.8 43 22-64 208-252 (312)
483 PRK09685 DNA-binding transcrip 24.0 61 0.0016 14.6 4.3 50 24-73 205-259 (303)
484 PRK08241 RNA polymerase factor 24.0 61 0.0016 14.5 3.0 28 26-53 164-191 (341)
485 smart00497 IENR1 Intron encode 23.9 44 0.0011 15.4 1.5 23 36-58 19-41 (53)
486 TIGR03020 EpsA transcriptional 23.8 62 0.0016 14.5 2.8 25 31-55 202-226 (247)
487 PRK13870 transcriptional regul 22.8 64 0.0016 14.4 2.5 24 31-54 185-208 (234)
488 TIGR02111 PQQ_syn_pqqC coenzym 22.7 41 0.001 15.6 1.2 59 22-80 39-106 (239)
489 PRK09390 fixJ response regulat 22.6 65 0.0017 14.4 2.6 44 31-74 153-200 (202)
490 pfam04492 Phage_rep_O Bacterio 22.5 38 0.00096 15.8 1.0 30 26-55 39-75 (100)
491 pfam03932 CutC CutC family. Co 22.2 28 0.00071 16.6 0.2 45 39-83 14-59 (202)
492 PRK13756 tetracycline represso 22.1 52 0.0013 15.0 1.6 41 21-61 9-51 (205)
493 TIGR01884 cas_HTH CRISPR locus 21.9 67 0.0017 14.3 2.6 31 24-54 173-204 (231)
494 PRK08610 fructose-bisphosphate 21.8 57 0.0015 14.7 1.8 39 39-77 163-206 (286)
495 PRK05417 glutathione-dependent 21.5 69 0.0018 14.2 2.2 50 28-83 123-172 (191)
496 COG1321 TroR Mn-dependent tran 21.3 69 0.0018 14.2 3.9 34 21-54 10-44 (154)
497 PRK12857 putative aldolase; Re 21.1 60 0.0015 14.6 1.7 38 40-77 163-205 (284)
498 TIGR02393 RpoD_Cterm RNA polym 21.0 49 0.0012 15.1 1.3 22 36-57 105-126 (240)
499 PRK11534 DNA-binding transcrip 20.8 68 0.0017 14.3 2.0 17 35-51 31-47 (224)
500 PRK10783 mltD membrane-bound l 20.8 71 0.0018 14.2 4.2 53 29-81 346-428 (449)
No 1
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=99.67 E-value=2.2e-16 Score=118.11 Aligned_cols=63 Identities=21% Similarity=0.288 Sum_probs=61.2
Q ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHCC
Q ss_conf 999999999999839949999998634299998875589994489999999992899999608
Q gi|254781147|r 20 MIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLWKLLK 82 (83)
Q Consensus 20 ~~~g~~ir~~R~~~gltq~ela~~~gis~~~is~iE~G~~~~~~~~l~~la~al~i~~~~l~~ 82 (83)
..+|.+||.+|+++|||++|||+++|+|.++||+||||+.+|++.+|.+||++|||++.+||.
T Consensus 6 ~~iG~rIr~lR~~~glTL~eLA~~sGvS~s~LSqIErg~~~PSl~tL~kIa~aL~v~l~~lf~ 68 (185)
T PRK09943 6 LAPGKRLSEIRQQQGLSQRRAAELSGLTHSAISTIEQDKVSPAISTLQKLLKVYGLSLSEFFS 68 (185)
T ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHC
T ss_conf 248899999999859989999988796999999998799999999999999984999999827
No 2
>PHA01976 helix-turn-helix protein
Probab=99.58 E-value=6.3e-15 Score=109.43 Aligned_cols=61 Identities=25% Similarity=0.320 Sum_probs=59.6
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHC
Q ss_conf 9999999999983994999999863429999887558999448999999999289999960
Q gi|254781147|r 21 IFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLWKLL 81 (83)
Q Consensus 21 ~~g~~ir~~R~~~gltq~ela~~~gis~~~is~iE~G~~~~~~~~l~~la~al~i~~~~l~ 81 (83)
.|+.+|+.+|+++||||+|||+++||++++|++||+|++.|++++|.+||++|||+++.|+
T Consensus 2 ~F~~RL~~lR~~~g~sQ~eLA~~lGVs~~~is~wE~g~~~P~~d~L~~la~~~~VS~D~Ll 62 (67)
T PHA01976 2 SFAIQLIKARNARAWSAPELSRRAGVRHSLIYDFEADKRLPNLKTLLRLADALGVTLDWLC 62 (67)
T ss_pred CHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHH
T ss_conf 7899999999986999999999949989999999878989998999999999797899992
No 3
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=99.57 E-value=7.9e-15 Score=108.85 Aligned_cols=64 Identities=36% Similarity=0.559 Sum_probs=61.0
Q ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHCC
Q ss_conf 9999999999999839949999998634299998875589994489999999992899999608
Q gi|254781147|r 19 RMIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLWKLLK 82 (83)
Q Consensus 19 ~~~~g~~ir~~R~~~gltq~ela~~~gis~~~is~iE~G~~~~~~~~l~~la~al~i~~~~l~~ 82 (83)
..+|--||+++|.++||||.|||+++|+|.+++|+||+|+.|||+.+|..||+||+||+..||.
T Consensus 3 n~ifftNv~RLr~ErGmT~~eLAe~AGIS~s~LSqIE~Gk~NPSL~tLe~IA~AL~VPL~~Lle 66 (119)
T PRK13890 3 NYIFFTNVLRLLDERHMTKKELSDRSGVSISFLSDLTTGKANPSLKVMEDIAQALETPLPLLLE 66 (119)
T ss_pred CCHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHH
T ss_conf 3145887999999859979999988298899999997799898799999999998797799876
No 4
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=99.54 E-value=1.9e-14 Score=106.60 Aligned_cols=64 Identities=25% Similarity=0.265 Sum_probs=61.5
Q ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHCC
Q ss_conf 9999999999999839949999998634299998875589994489999999992899999608
Q gi|254781147|r 19 RMIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLWKLLK 82 (83)
Q Consensus 19 ~~~~g~~ir~~R~~~gltq~ela~~~gis~~~is~iE~G~~~~~~~~l~~la~al~i~~~~l~~ 82 (83)
..+||.+|+.+|+++||||.+||+++|||.++||+||+|...|+.++|.+||++|||++++||.
T Consensus 3 ~~tiG~Ri~~~R~~~glTQ~eLA~~~Gvs~~tVs~wE~g~~~P~~~~L~~LA~~L~vs~~wLL~ 66 (135)
T PRK09706 3 NETLGQRIRYRRKQLKLSQRALAKAVGVSHVSISQWERDETEPAGKNLFALAQALQCSPTWLLF 66 (135)
T ss_pred CCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHCC
T ss_conf 1309999999999859999999999698899999998289888999999999998909999848
No 5
>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=99.45 E-value=1.7e-13 Score=100.91 Aligned_cols=57 Identities=26% Similarity=0.415 Sum_probs=55.2
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCH
Q ss_conf 999999999998399499999986342999988755899944899999999928999
Q gi|254781147|r 21 IFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPL 77 (83)
Q Consensus 21 ~~g~~ir~~R~~~gltq~ela~~~gis~~~is~iE~G~~~~~~~~l~~la~al~i~~ 77 (83)
.||..||..|+++||||++||+.+|+|+++|++||+|+.+|+++++.+||++||+++
T Consensus 2 ~lG~~Ir~~Rk~~glTQ~~LA~~aGvs~~~Is~iE~G~~~~~l~~l~~i~~aLGi~l 58 (58)
T TIGR03070 2 QIGALVRARRKALGLTQADLADLAGVGLRFIRDIEKGKPTVRLDKVLRVLEALGLEL 58 (58)
T ss_pred HHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCC
T ss_conf 588999999999499899999881998999999978999888999999999808989
No 6
>PRK08154 anaerobic benzoate catabolism transcriptional regulator; Reviewed
Probab=99.35 E-value=5.2e-12 Score=92.13 Aligned_cols=65 Identities=22% Similarity=0.385 Sum_probs=61.8
Q ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHCC
Q ss_conf 99999999999999839949999998634299998875589994489999999992899999608
Q gi|254781147|r 18 ERMIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLWKLLK 82 (83)
Q Consensus 18 ~~~~~g~~ir~~R~~~gltq~ela~~~gis~~~is~iE~G~~~~~~~~l~~la~al~i~~~~l~~ 82 (83)
.-..+|.+||.+|..+|||+++||+.+|||..|++++|.|+.|||+..|.++|.||++++.+|+.
T Consensus 25 ~l~~lg~rvr~~R~~rg~sr~~la~~sgvS~r~la~lE~G~gN~si~~L~~iA~Al~~~l~~l~~ 89 (304)
T PRK08154 25 FLAALGERVRTLRARRGMSRKVLAQASGVSERYLAQLESGQGNVSILLLRRVARALGCPLADLLG 89 (304)
T ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHC
T ss_conf 99999999999999759989999987299899999882588885199999999995998999817
No 7
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=99.31 E-value=3.9e-12 Score=92.84 Aligned_cols=56 Identities=30% Similarity=0.502 Sum_probs=54.0
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHH
Q ss_conf 99999998399499999986342999988755899944899999999928999996
Q gi|254781147|r 25 NFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLWKL 80 (83)
Q Consensus 25 ~ir~~R~~~gltq~ela~~~gis~~~is~iE~G~~~~~~~~l~~la~al~i~~~~l 80 (83)
+|+.+|+++||||+|||+.+|+|+++|++||+|...|+.+++.+||++||+++.+|
T Consensus 1 rlr~~R~~~glsq~~lA~~~gis~~~is~~E~g~~~p~~~~l~~ia~~l~~~~~~l 56 (56)
T smart00530 1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56 (56)
T ss_pred CHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHC
T ss_conf 98999977299999999998959999999997998999999999999988889879
No 8
>pfam01381 HTH_3 Helix-turn-helix. This large family of DNA binding helix-turn helix proteins includes Cro and CI.
Probab=99.31 E-value=3.7e-12 Score=93.02 Aligned_cols=55 Identities=31% Similarity=0.508 Sum_probs=53.2
Q ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHH
Q ss_conf 9999998399499999986342999988755899944899999999928999996
Q gi|254781147|r 26 FRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLWKL 80 (83)
Q Consensus 26 ir~~R~~~gltq~ela~~~gis~~~is~iE~G~~~~~~~~l~~la~al~i~~~~l 80 (83)
||.+|+++||||+++|+.+|+|+++|++||+|...|+++++.+||++||+++++|
T Consensus 1 ir~~R~~~g~tq~~lA~~~gis~~~is~~E~g~~~p~~~~l~~ia~~l~v~~~~l 55 (55)
T pfam01381 1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55 (55)
T ss_pred CHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHC
T ss_conf 9898978299899999998969999999987999999999999999978979879
No 9
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=99.27 E-value=1.3e-11 Score=89.83 Aligned_cols=59 Identities=22% Similarity=0.401 Sum_probs=57.1
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHCC
Q ss_conf 99999999839949999998634299998875589994489999999992899999608
Q gi|254781147|r 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLWKLLK 82 (83)
Q Consensus 24 ~~ir~~R~~~gltq~ela~~~gis~~~is~iE~G~~~~~~~~l~~la~al~i~~~~l~~ 82 (83)
.+++.+|...|+||++||+.+|||+++|..||+|+.+|++....+||+.|+++++++|.
T Consensus 4 nk~k~~R~~~~ltQ~elA~~vgVsRQTi~~iEkgky~Psl~La~kia~~f~~~iedIF~ 62 (68)
T COG1476 4 NKLKELRAELGLTQEELAKLVGVSRQTIIAIEKGKYNPSLELALKIARVFGKTIEDIFQ 62 (68)
T ss_pred HHHHHHHHHHCCCHHHHHHHCCCCHHHHHHHHCCCCCCHHHHHHHHHHHHCCCHHHHHH
T ss_conf 59999999828589999999195799999999179883099999999993997999986
No 10
>PRK09726 DNA-binding transcriptional regulator HipB; Provisional
Probab=99.15 E-value=8.8e-11 Score=84.84 Aligned_cols=59 Identities=19% Similarity=0.351 Sum_probs=56.2
Q ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHH
Q ss_conf 99999999999983994999999863429999887558999448999999999289999
Q gi|254781147|r 20 MIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLW 78 (83)
Q Consensus 20 ~~~g~~ir~~R~~~gltq~ela~~~gis~~~is~iE~G~~~~~~~~l~~la~al~i~~~ 78 (83)
..+|..||..|+++||||.++|+++|+.+++||.+|++-..+++++|++|+.+||+.+.
T Consensus 11 ~qLa~~Lr~~Rk~~gLsQ~~lA~~vGi~Q~TiS~~E~~p~~~~leTLFkiL~aL~Lel~ 69 (88)
T PRK09726 11 TQLANAMKLVRQQNGWTQSELAKKIGIKQATISNFENNPDNTTLTTFFKILQSLELSMT 69 (88)
T ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHCCCEEE
T ss_conf 99999999999985987999999819749999999759987869999999996787688
No 11
>PRK06424 transcription factor; Provisional
Probab=99.14 E-value=1.9e-10 Score=82.90 Aligned_cols=69 Identities=19% Similarity=0.187 Sum_probs=61.3
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHH
Q ss_conf 898999999999999999999839949999998634299998875589994489999999992899999
Q gi|254781147|r 11 LSDAILRERMIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLWK 79 (83)
Q Consensus 11 ~~~~~~~~~~~~g~~ir~~R~~~gltq~ela~~~gis~~~is~iE~G~~~~~~~~l~~la~al~i~~~~ 79 (83)
..+.....-+.|+..||.+|+.+||||+|||.+++.+.+.|.+||+|+..|+.+...+|-++|||.+.+
T Consensus 74 ~~~~~~elveDy~~~Ir~ARE~~GlsqeeLA~ki~ek~svI~kiE~G~l~P~~~~~kKLEk~L~I~L~E 142 (144)
T PRK06424 74 ASDEDLDIVEDYAELVKNARERLSMSQADLAAKIFERKNVIASIERGDLLPDIKTARKLEKILGITLIE 142 (144)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCEEEE
T ss_conf 303456688779999999999849999999999654499999998389899989999999984967663
No 12
>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=99.13 E-value=1.1e-10 Score=84.19 Aligned_cols=58 Identities=33% Similarity=0.488 Sum_probs=55.5
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHH
Q ss_conf 9999999998399499999986342999988755899944899999999928999996
Q gi|254781147|r 23 VNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLWKL 80 (83)
Q Consensus 23 g~~ir~~R~~~gltq~ela~~~gis~~~is~iE~G~~~~~~~~l~~la~al~i~~~~l 80 (83)
|.+|+.+|+.+|+||.++|+.+|++++++++||+|...|+.+.+.+||+.|++++.+|
T Consensus 1 g~~l~~~r~~~~ls~~~lA~~~gis~~~l~~~e~g~~~p~~~~l~~la~~~~~~~~~l 58 (58)
T cd00093 1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58 (58)
T ss_pred CHHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHC
T ss_conf 9899999997599999995714999999999987998999999999999938989879
No 13
>PRK08359 transcription factor; Validated
Probab=99.06 E-value=6.2e-10 Score=79.79 Aligned_cols=62 Identities=13% Similarity=0.199 Sum_probs=58.3
Q ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHH
Q ss_conf 99999999999998399499999986342999988755899944899999999928999996
Q gi|254781147|r 19 RMIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLWKL 80 (83)
Q Consensus 19 ~~~~g~~ir~~R~~~gltq~ela~~~gis~~~is~iE~G~~~~~~~~l~~la~al~i~~~~l 80 (83)
-+.|+..|+.+|+.+||||+|||.+++++.+.|.+||+|+..|+++...+|-++|||.+.+-
T Consensus 81 veDY~~~Ir~ARE~~GlSqeeLA~ki~ek~nvI~kiE~G~l~P~~~~akKLEk~L~IkL~E~ 142 (175)
T PRK08359 81 VEDYAERVYEAIRKSGLSYEELSHKVGLSVNDLRRIAHGEYTPTIEEARKLERFFKIKLIER 142 (175)
T ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHCCHHHHHHHHHCCCCCCCHHHHHHHHHHHCEEEEEE
T ss_conf 75699999999998599999999997222999999983887999899999999849068851
No 14
>COG3620 Predicted transcriptional regulator with C-terminal CBS domains [Transcription]
Probab=98.96 E-value=1.4e-09 Score=77.78 Aligned_cols=52 Identities=31% Similarity=0.531 Sum_probs=49.2
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHC
Q ss_conf 9999999998399499999986342999988755899944899999999928
Q gi|254781147|r 23 VNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLD 74 (83)
Q Consensus 23 g~~ir~~R~~~gltq~ela~~~gis~~~is~iE~G~~~~~~~~l~~la~al~ 74 (83)
-+.||+.|++.|+||++||+++|+|+++|+++|.|+.+|.++++.+|.++|.
T Consensus 7 pedlrk~Rk~LGitQ~dLA~~aGVSQ~~IArlE~G~vdPrlSt~k~Il~aL~ 58 (187)
T COG3620 7 PEDLRKRRKELGITQKDLARRAGVSQPYIARLEAGKVDPRLSTVKRILEALE 58 (187)
T ss_pred HHHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHH
T ss_conf 7999999987597789999870864888999863887930899999999999
No 15
>COG1813 Predicted transcription factor, homolog of eukaryotic MBF1 [Transcription]
Probab=98.96 E-value=2.6e-09 Score=76.08 Aligned_cols=68 Identities=21% Similarity=0.205 Sum_probs=61.0
Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHC
Q ss_conf 99999999999999999983994999999863429999887558999448999999999289999960
Q gi|254781147|r 14 AILRERMIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLWKLL 81 (83)
Q Consensus 14 ~~~~~~~~~g~~ir~~R~~~gltq~ela~~~gis~~~is~iE~G~~~~~~~~l~~la~al~i~~~~l~ 81 (83)
.....-+.++..|+.+|+++||||++||++++++.+.|.+||+|+..|++....+|.++|+|.+.+..
T Consensus 72 ~~~elvedY~e~Ir~ARE~~G~SqedLA~ki~ek~svI~~iE~g~~~P~~~~akkLEk~LgIkL~e~~ 139 (165)
T COG1813 72 ELPELVEDYGERIREAREKRGLSQEDLAAKLKEKVSVIRRIERGEATPNIKVAKKLEKLLGIKLVEKV 139 (165)
T ss_pred HHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCHHHHHHHHHHHCCEEEEEC
T ss_conf 17888877999999999982888999999965469999999841367558899999998585522003
No 16
>PRK04140 hypothetical protein; Provisional
Probab=98.73 E-value=3e-08 Score=69.80 Aligned_cols=56 Identities=29% Similarity=0.404 Sum_probs=54.3
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHH
Q ss_conf 99999999983994999999863429999887558999448999999999289999
Q gi|254781147|r 23 VNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLW 78 (83)
Q Consensus 23 g~~ir~~R~~~gltq~ela~~~gis~~~is~iE~G~~~~~~~~l~~la~al~i~~~ 78 (83)
|..||.+|++.|||..+||+.+|||+.++++||+|..++|+++..+|.+.||.++.
T Consensus 127 g~~Lr~~Re~~g~SlG~LA~~LGVSRrtv~~YE~g~~~~sievA~kLeeif~~~i~ 182 (319)
T PRK04140 127 GDLLRELREKLGLSLGELASELGVSRRTISKYENGGMNASIEVAIKLEEILDEPLT 182 (319)
T ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCHHHHHHHHHHHCCCCC
T ss_conf 79999999981988889999849869999999706886649999999998387323
No 17
>TIGR00270 TIGR00270 conserved hypothetical protein TIGR00270; InterPro: IPR004451 This family of conserved hypothetical proteins includes proteins of unknown function from archaebacteria..
Probab=98.64 E-value=7e-08 Score=67.60 Aligned_cols=78 Identities=17% Similarity=0.129 Sum_probs=69.4
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHC
Q ss_conf 888888689899999999999999999983994999999863429999887558999448999999999289999960
Q gi|254781147|r 4 RKRDEPHLSDAILRERMIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLWKLL 81 (83)
Q Consensus 4 ~~~~~p~~~~~~~~~~~~~g~~ir~~R~~~gltq~ela~~~gis~~~is~iE~G~~~~~~~~l~~la~al~i~~~~l~ 81 (83)
++++.-+.-|.+....+.||.-||..|+.+|||++|||+++..-.|.|.+||+..-.|....+.+|-+.|+|.|.+-|
T Consensus 66 r~rrGst~~dt~~elvEdyg~iIR~eREKRgwS~E~LAkki~eK~S~i~kiE~~e~eP~~k~~~kLEkllkIkL~E~~ 143 (169)
T TIGR00270 66 RKRRGSTKIDTVEELVEDYGRIIREEREKRGWSREELAKKIKEKASVIKKIEREELEPEEKVVKKLEKLLKIKLLEKV 143 (169)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCCC
T ss_conf 033688621035666643225422000146878789999874106788887540379888999998888350100235
No 18
>TIGR02612 mob_myst_A mobile mystery protein A; InterPro: IPR013435 Proteins in this entry are more often encoded within mobilisation-related contexts than not. This includes a CRISPR-associated gene region in Geobacter sulfurreducens PCA, and plasmids in Agrobacterium tumefaciens and Coxiella burnetii. They are found together with mobile mystery protein B, a member of the Fic protein family (IPR003812 from INTERPRO). Mobile mystery protein A is encoded by the upstream member of the gene pair and contains a helix-turn-helix domain..
Probab=98.52 E-value=6.6e-08 Score=67.76 Aligned_cols=59 Identities=19% Similarity=0.319 Sum_probs=55.5
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCC--CCCHHHHHHHHHHHCCCHHHHCCC
Q ss_conf 99999998399499999986342999988755899--944899999999928999996088
Q gi|254781147|r 25 NFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKS--TINIDNMIILAHTLDTPLWKLLKP 83 (83)
Q Consensus 25 ~ir~~R~~~gltq~ela~~~gis~~~is~iE~G~~--~~~~~~l~~la~al~i~~~~l~~P 83 (83)
.||.+|+..|||..|||.++||.++.|..||+... .+++.+|.+-|+||||.+-.-|.|
T Consensus 29 WvR~~R~ALGms~~QLA~RlGV~p~Rv~~~E~~E~~G~VTL~tlr~aAEAl~C~FVYafVP 89 (150)
T TIGR02612 29 WVRAIRKALGMSGAQLAARLGVTPQRVEAIEKSELSGAVTLKTLRKAAEALDCTFVYAFVP 89 (150)
T ss_pred CHHHHHHHHCCCHHHHHHHCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCEEEEECCC
T ss_conf 1688987725157887665289737799988887555355888999999859844340188
No 19
>COG1395 Predicted transcriptional regulator [Transcription]
Probab=98.34 E-value=1.3e-06 Score=60.06 Aligned_cols=56 Identities=16% Similarity=0.265 Sum_probs=53.7
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHH
Q ss_conf 99999999983994999999863429999887558999448999999999289999
Q gi|254781147|r 23 VNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLW 78 (83)
Q Consensus 23 g~~ir~~R~~~gltq~ela~~~gis~~~is~iE~G~~~~~~~~l~~la~al~i~~~ 78 (83)
|..||..|++.|+|..++|..+|+|+.+|++||+|..++++++..++-+.||.++.
T Consensus 127 ge~Lre~Ree~glSlG~lA~~lgVSRktV~~YE~G~~~~sleva~kLeei~g~~iv 182 (313)
T COG1395 127 GEKLREKREEMGLSLGDLATMLGVSRKTVYKYEKGLSDASLEVALKLEEIFGEDIV 182 (313)
T ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHCCCCCCCCHHHHHHHHHHHCCHHH
T ss_conf 29999999980867878898838468889876247777329999999998562220
No 20
>TIGR02607 antidote_HigA addiction module antidote protein, HigA family; InterPro: IPR013430 Proteins in this entry form a distinct group of helix-turn-helix proteins, which are strictly bacterial and nearly always shorter than 110 amino acids. They include the characterised 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 encoded by the upstream member of the gene pair.; GO: 0003677 DNA binding.
Probab=98.28 E-value=1.6e-06 Score=59.54 Aligned_cols=66 Identities=23% Similarity=0.317 Sum_probs=55.0
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHC
Q ss_conf 8888689899999999999999999983994999999863429999887558999448999999999289999960
Q gi|254781147|r 6 RDEPHLSDAILRERMIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLWKLL 81 (83)
Q Consensus 6 ~~~p~~~~~~~~~~~~~g~~ir~~R~~~gltq~ela~~~gis~~~is~iE~G~~~~~~~~l~~la~al~i~~~~l~ 81 (83)
.+++|++|-+. ..+-+..|+|+.+||+.+|||+++||+|=||++.+|.++..+|+++||.+...-+
T Consensus 2 ~~P~HPGE~L~----------eEfL~PLg~s~~~LA~~LgVsr~~~sriv~~~~~iT~dmALRL~~~lG~sp~~WL 67 (81)
T TIGR02607 2 RNPAHPGEILL----------EEFLEPLGLSVRALAKALGVSRSTLSRIVNGRRGITADMALRLAKALGTSPEFWL 67 (81)
T ss_pred CCCCCCCCHHH----------HHHHHCCCHHHHHHHHHCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHCCCHHHHH
T ss_conf 89778841328----------7752104706899998709997888888744899888899999997389876899
No 21
>COG1709 Predicted transcriptional regulator [Transcription]
Probab=98.26 E-value=1.1e-06 Score=60.50 Aligned_cols=53 Identities=23% Similarity=0.269 Sum_probs=50.0
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCC-CCHHHHHHHHHHH
Q ss_conf 9999999999983994999999863429999887558999-4489999999992
Q gi|254781147|r 21 IFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKST-INIDNMIILAHTL 73 (83)
Q Consensus 21 ~~g~~ir~~R~~~gltq~ela~~~gis~~~is~iE~G~~~-~~~~~l~~la~al 73 (83)
..|.-+|+||+.-+.||.|+|..+|+|+|.||.||+|++. |....+.++-+||
T Consensus 27 ~pge~lrKWR~~F~iSQ~elA~~l~vSpSVISDYE~GRRk~Pg~~~vkk~V~AL 80 (241)
T COG1709 27 DPGETLRKWREIFNVSQTELARELGVSPSVISDYESGRRKSPGIAFVKKFVEAL 80 (241)
T ss_pred CHHHHHHHHHHHCCCCHHHHHHHHCCCCCEEEHHHCCCCCCCCHHHHHHHHHHH
T ss_conf 825899999998182499999872899100312112575686178999999999
No 22
>COG3655 Predicted transcriptional regulator [Transcription]
Probab=98.24 E-value=2.6e-06 Score=58.28 Aligned_cols=61 Identities=20% Similarity=0.358 Sum_probs=55.7
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCC-CCCHHHHHHHHHHHCCCHHHHCC
Q ss_conf 99999999998399499999986342999988755899-94489999999992899999608
Q gi|254781147|r 22 FVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKS-TINIDNMIILAHTLDTPLWKLLK 82 (83)
Q Consensus 22 ~g~~ir~~R~~~gltq~ela~~~gis~~~is~iE~G~~-~~~~~~l~~la~al~i~~~~l~~ 82 (83)
+..++.....+++++..|||+.+|+|.+++|.+.+|+. .+++++|.+||++|++.+.+++.
T Consensus 3 i~~~l~~~l~~r~~~~~eLa~~igis~~~ls~l~~gk~k~I~~~tL~~iC~~LeCqpgDile 64 (73)
T COG3655 3 IAVRLDVMLADRKISLKELAEAIGISEANLSKLKTGKVKAIRLSTLEKICKALECQPGDILE 64 (73)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHCCCCCEEEHHHHHHHHHHCCCCHHHEEE
T ss_conf 13767999999750177899998436989999972886604489999999983898405457
No 23
>COG1426 Predicted transcriptional regulator contains Xre-like HTH domain [Function unknown]
Probab=98.22 E-value=4.9e-06 Score=56.67 Aligned_cols=62 Identities=23% Similarity=0.275 Sum_probs=54.2
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCC--CC----HHHHHHHHHHHCCCHHHHCC
Q ss_conf 9999999999983994999999863429999887558999--44----89999999992899999608
Q gi|254781147|r 21 IFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKST--IN----IDNMIILAHTLDTPLWKLLK 82 (83)
Q Consensus 21 ~~g~~ir~~R~~~gltq~ela~~~gis~~~is~iE~G~~~--~~----~~~l~~la~al~i~~~~l~~ 82 (83)
.+|..+|..|+++|||++|++.+++|..+++-.||.|... |. -.-+..+|++|+++..+|+.
T Consensus 3 ~~Ge~Lr~~Re~~gLsL~dva~~t~I~~~~L~aiEeg~~~~lp~~~y~rG~ir~YA~~l~ld~~~l~~ 70 (284)
T COG1426 3 TLGERLRQAREEKGLSLEDVAARTKIRKSYLRALEEGNFDKLPGPVYIRGYIRSYAKFLGLDEDELLQ 70 (284)
T ss_pred CHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHCCCHHHHHH
T ss_conf 77899999999849999999988577599999986677010641576789999999996899899999
No 24
>KOG3398 consensus
Probab=98.22 E-value=2.6e-06 Score=58.34 Aligned_cols=59 Identities=15% Similarity=0.249 Sum_probs=55.8
Q ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHH
Q ss_conf 99999999999983994999999863429999887558999448999999999289999
Q gi|254781147|r 20 MIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLW 78 (83)
Q Consensus 20 ~~~g~~ir~~R~~~gltq~ela~~~gis~~~is~iE~G~~~~~~~~l~~la~al~i~~~ 78 (83)
..+|.-|...|.++||||++||.+++-.++.|..||+|+..|+-..|.++-++||+.+.
T Consensus 72 ~~Vg~aIq~aR~~KgmsqkDLA~kInekpqVv~dyEsGrAIpNqqil~kmEraLgvKlr 130 (135)
T KOG3398 72 LEVGKAIQQARAQKGMSQKDLAQKINEKPQVIQDYESGRAIPNQQILSKMERALGVKLR 130 (135)
T ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHCCCCCCHHHHHHHHHHHHCEECC
T ss_conf 78999999988863754889999960286136557503567419999999998531124
No 25
>PRK13355 bifunctional HTH-domain containing protein/aminotransferase; Provisional
Probab=98.08 E-value=1.5e-05 Score=53.85 Aligned_cols=63 Identities=21% Similarity=0.208 Sum_probs=58.2
Q ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHH-----HHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHCC
Q ss_conf 99999999999983994999999863-----4299998875589994489999999992899999608
Q gi|254781147|r 20 MIFVNNFRNIRKEAKLTQKEIRNRTG-----FAQSWISELETGKSTINIDNMIILAHTLDTPLWKLLK 82 (83)
Q Consensus 20 ~~~g~~ir~~R~~~gltq~ela~~~g-----is~~~is~iE~G~~~~~~~~l~~la~al~i~~~~l~~ 82 (83)
..++.+|+.++..+|++|.||...+. ++++.+|+|++|+..|.-+.+.-||+.|+|+-.+|+.
T Consensus 4 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 71 (518)
T PRK13355 4 STQAERLVQLMNSRGLKQEDLVHAAEARGVKVGKSHISQYVRGKTGPRSDKLPFLASELGVSEGWLLG 71 (518)
T ss_pred CCHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHCC
T ss_conf 20899999999876996899999999817550478887773388644211799999996889788607
No 26
>COG1396 HipB Predicted transcriptional regulators [Transcription]
Probab=98.02 E-value=2.9e-05 Score=52.05 Aligned_cols=61 Identities=31% Similarity=0.485 Sum_probs=57.3
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCC-CCCHHHHHHHHHHHCCCHHHHCC
Q ss_conf 99999999998399499999986342999988755899-94489999999992899999608
Q gi|254781147|r 22 FVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKS-TINIDNMIILAHTLDTPLWKLLK 82 (83)
Q Consensus 22 ~g~~ir~~R~~~gltq~ela~~~gis~~~is~iE~G~~-~~~~~~l~~la~al~i~~~~l~~ 82 (83)
++.+++..|+..|+||.++|...|++..+++.+|+|.. .|++..+..++..|+++...++.
T Consensus 2 ~~~~~~~~r~~~~~s~~~~a~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 63 (120)
T COG1396 2 IGERLKELRKKKGLSQEELAERLGVSRSTISRIERGRSESPSLELLARLAAALGVSLDELLE 63 (120)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHH
T ss_conf 78999999998699999999893988999999980787784699999999996978998840
No 27
>COG3093 VapI Plasmid maintenance system antidote protein [General function prediction only]
Probab=98.01 E-value=2.3e-05 Score=52.72 Aligned_cols=52 Identities=31% Similarity=0.316 Sum_probs=47.8
Q ss_pred HHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHC
Q ss_conf 9983994999999863429999887558999448999999999289999960
Q gi|254781147|r 30 RKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLWKLL 81 (83)
Q Consensus 30 R~~~gltq~ela~~~gis~~~is~iE~G~~~~~~~~l~~la~al~i~~~~l~ 81 (83)
-+..|+||.++|+.+||++.+|+.+-||++.+|.++..+|+++||.+....+
T Consensus 19 lep~glt~~~lA~~lgV~r~~is~ling~~~iT~dmAlrL~k~fGtspefWl 70 (104)
T COG3093 19 LEPLGLTQTELAEALGVTRNTISELINGRRAITADMALRLAKVFGTSPEFWL 70 (104)
T ss_pred HCCCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHH
T ss_conf 4521698999999939989999999837767899999999999299899999
No 28
>PRK10856 hypothetical protein; Provisional
Probab=97.98 E-value=2.8e-05 Score=52.16 Aligned_cols=64 Identities=20% Similarity=0.236 Sum_probs=55.3
Q ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCC------CCHHHHHHHHHHHCCCHHHHC
Q ss_conf 9999999999999983994999999863429999887558999------448999999999289999960
Q gi|254781147|r 18 ERMIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKST------INIDNMIILAHTLDTPLWKLL 81 (83)
Q Consensus 18 ~~~~~g~~ir~~R~~~gltq~ela~~~gis~~~is~iE~G~~~------~~~~~l~~la~al~i~~~~l~ 81 (83)
+....|..||..|+++|||++|+|.++.++.++|..||++... ..-.-+..+|+.||++...|+
T Consensus 11 ~~~t~G~~Lr~ARE~~GlSi~dvA~~LkL~~~~ieALE~dd~~~Lp~~tF~RGylRsYAr~LglD~~~ll 80 (332)
T PRK10856 11 EALTTGVRLRQAREQLGLSQQAVAERLCLKVSTVRDIEEDKAPADLASTFLRGYIRSYARLVHIPEEELL 80 (332)
T ss_pred CCCCHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCHHCCCCHHHHHHHHHHHHHHHCCCHHHHH
T ss_conf 6568879999999985999999998708989999998578221087036479999999999788979965
No 29
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=97.89 E-value=2e-05 Score=53.06 Aligned_cols=44 Identities=18% Similarity=0.249 Sum_probs=39.9
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHH
Q ss_conf 99999999983994999999863429999887558999448999
Q gi|254781147|r 23 VNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNM 66 (83)
Q Consensus 23 g~~ir~~R~~~gltq~ela~~~gis~~~is~iE~G~~~~~~~~l 66 (83)
+..|+.+|+..|+||.++|..+|+|.+++++||.|...|+=.-+
T Consensus 46 ~~eIk~iRe~~~lSq~vFA~~L~vs~~Tv~~WEqGr~kPsg~Al 89 (104)
T COG2944 46 PTEIKAIREKLGLSQPVFARYLGVSVSTVRKWEQGRKKPSGAAL 89 (104)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHCCCCCCCCHHH
T ss_conf 89999999982888999999988879999999817858997999
No 30
>PRK10072 putative transcriptional regulator; Provisional
Probab=97.67 E-value=0.0001 Score=48.88 Aligned_cols=43 Identities=16% Similarity=0.292 Sum_probs=39.2
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHH
Q ss_conf 9999999839949999998634299998875589994489999
Q gi|254781147|r 25 NFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMI 67 (83)
Q Consensus 25 ~ir~~R~~~gltq~ela~~~gis~~~is~iE~G~~~~~~~~l~ 67 (83)
.++++|+..|++|.++|+.+|+|.+++..||.|+++|+=..+.
T Consensus 37 dvkaIR~~tgl~q~eFA~~lGvSv~tvksWEq~Rr~Ptg~a~k 79 (96)
T PRK10072 37 EFEQLRKGTGLKIDDFARVLGVSVAMVKEWESRRVKPSSAELK 79 (96)
T ss_pred CHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCHHHHH
T ss_conf 3999998809999999999777799999999678789839999
No 31
>TIGR02684 dnstrm_HI1420 probable addiction module antidote protein; InterPro: IPR014057 Members of this strictly bacterial protein family are small, at roughly 100 amino acids. The gene is almost invariably the downstream member of a gene pair. It is a predicted DNA-binding protein from a clade within the helix-turn-helix family IPR001387 from INTERPRO. These gene pairs, when found on the bacterial chromosome, are located often with prophage regions, but also both in integrated plasmid regions and in housekeeping gene regions. Analysis suggests that the gene pair may serve as an addiction module..
Probab=97.54 E-value=0.00017 Score=47.56 Aligned_cols=57 Identities=16% Similarity=0.292 Sum_probs=49.8
Q ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHH
Q ss_conf 99999999999983994999999863429999887558999448999999999289999
Q gi|254781147|r 20 MIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLW 78 (83)
Q Consensus 20 ~~~g~~ir~~R~~~gltq~ela~~~gis~~~is~iE~G~~~~~~~~l~~la~al~i~~~ 78 (83)
..|..-|=.+=+.+|||| +|+.+|+|+=.+.+=-+++.||+++|+.++++|||+.+.
T Consensus 33 ~~~~~ALG~iArArGMtq--lA~~tGlsREsLYkALs~~GnP~f~T~lkV~~ALG~~L~ 89 (91)
T TIGR02684 33 ALIAAALGVIARARGMTQ--LAKKTGLSRESLYKALSGGGNPTFDTILKVTKALGLKLT 89 (91)
T ss_pred HHHHHHHHHHHHHCCHHH--HHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHCCCEEE
T ss_conf 899999889986516578--999828767887887356889566888999984086020
No 32
>COG5499 Predicted transcription regulator containing HTH domain [Transcription]
Probab=97.41 E-value=0.00045 Score=45.03 Aligned_cols=58 Identities=19% Similarity=0.384 Sum_probs=53.5
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHCC
Q ss_conf 99999999839949999998634299998875589994489999999992899999608
Q gi|254781147|r 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLWKLLK 82 (83)
Q Consensus 24 ~~ir~~R~~~gltq~ela~~~gis~~~is~iE~G~~~~~~~~l~~la~al~i~~~~l~~ 82 (83)
.-|+.+..+.|+|+++||..+| |.+.+|+|-+|++..+++.+.++.+-||+|.+-|..
T Consensus 63 e~I~t~Md~~glt~~dLa~~iG-Sks~vS~iL~~rraLTle~ikkL~q~~gIpa~~lIe 120 (120)
T COG5499 63 EVIRTLMDQYGLTLADLANEIG-SKSRVSNILSGRRALTLEHIKKLHQRFGIPADVLIE 120 (120)
T ss_pred HHHHHHHHHHCCCHHHHHHHHC-CHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHCC
T ss_conf 9999999993871888899867-618899997320676699999999986958887539
No 33
>KOG3802 consensus
Probab=97.39 E-value=0.00029 Score=46.15 Aligned_cols=58 Identities=28% Similarity=0.373 Sum_probs=50.5
Q ss_pred HHHHHHHHHHHHHHHHHHCCCCHHHHHHHHH------HHHHHHHHHHCCCCCCCHHHHHHHHHHHC
Q ss_conf 9999999999999999983994999999863------42999988755899944899999999928
Q gi|254781147|r 15 ILRERMIFVNNFRNIRKEAKLTQKEIRNRTG------FAQSWISELETGKSTINIDNMIILAHTLD 74 (83)
Q Consensus 15 ~~~~~~~~g~~ir~~R~~~gltq~ela~~~g------is~~~is~iE~G~~~~~~~~l~~la~al~ 74 (83)
.+.+-+.|++.+|..|...|+||.||+..+| +|+++|+|+|. -+.++.++.||--.|+
T Consensus 204 ~leELEqFAK~FKqRRIkLGfTQaDVGlALG~lyGn~FSQTTIcRFEA--LqLSFKNMCKLKPLL~ 267 (398)
T KOG3802 204 DLEELEQFAKTFKQRRIKLGFTQADVGLALGALYGNVFSQTTICRFEA--LQLSFKNMCKLKPLLE 267 (398)
T ss_pred CHHHHHHHHHHHHHHEECCCCCHHHHHHHHHHHHCCCCCHHHHHHHHH--HCCCHHHHHHHHHHHH
T ss_conf 999999999998765000364426788898765076443026667676--2547787766379999
No 34
>COG4800 Predicted transcriptional regulator with an HTH domain [Transcription]
Probab=97.33 E-value=0.00082 Score=43.47 Aligned_cols=55 Identities=20% Similarity=0.230 Sum_probs=51.3
Q ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHH
Q ss_conf 99999999999999839949999998634299998875589994489999999992
Q gi|254781147|r 18 ERMIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTL 73 (83)
Q Consensus 18 ~~~~~g~~ir~~R~~~gltq~ela~~~gis~~~is~iE~G~~~~~~~~l~~la~al 73 (83)
..+.|+.-++++-.++|||..|+|+++|+..|++.++-.| ..|.+++|.+|.+++
T Consensus 13 s~E~F~~~l~~~l~Elglt~~eFak~anIP~StLYKil~G-~dpr~~tl~~I~kti 67 (170)
T COG4800 13 SGEDFGSCLQKLLDELGLTPSEFAKRANIPLSTLYKILKG-SDPRYDTLTRIFKTI 67 (170)
T ss_pred CHHHHHHHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHHC-CCCCHHHHHHHHHHH
T ss_conf 4007999999999981999899988709989999999817-996577899999999
No 35
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=97.27 E-value=0.0014 Score=42.06 Aligned_cols=57 Identities=28% Similarity=0.397 Sum_probs=47.9
Q ss_pred HHHHHHHHHHHHHHHHHCCCCHHHHHHHHH------HHHHHHHHHHCCCCCCCHHHHHHHHHHHC
Q ss_conf 999999999999999983994999999863------42999988755899944899999999928
Q gi|254781147|r 16 LRERMIFVNNFRNIRKEAKLTQKEIRNRTG------FAQSWISELETGKSTINIDNMIILAHTLD 74 (83)
Q Consensus 16 ~~~~~~~g~~ir~~R~~~gltq~ela~~~g------is~~~is~iE~G~~~~~~~~l~~la~al~ 74 (83)
+.+-+.|+..++..|...|+||.+++..+| .|+++|+++|+ -+.+..++.++--.|.
T Consensus 6 l~Ele~Fa~~fk~rRi~LG~TQ~dVG~aL~~l~g~~~SQttIcRFE~--l~LS~kn~~kLkPiL~ 68 (75)
T smart00352 6 PRELEAFAKTFKQRRIKLGFTQADVGLALGALYGPDFSQTTICRFEA--LQLSFKNMCKLKPLLE 68 (75)
T ss_pred HHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCCHHHHHHHHH--CCCCHHHHHHHHHHHH
T ss_conf 99999999999998987377599999999986186431468889886--0547988998899999
No 36
>PHA00542 putative Cro-like protein
Probab=97.04 E-value=0.0016 Score=41.76 Aligned_cols=49 Identities=18% Similarity=0.195 Sum_probs=42.0
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCC-CCCCHHHHHHHHHH
Q ss_conf 99999999839949999998634299998875589-99448999999999
Q gi|254781147|r 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGK-STINIDNMIILAHT 72 (83)
Q Consensus 24 ~~ir~~R~~~gltq~ela~~~gis~~~is~iE~G~-~~~~~~~l~~la~a 72 (83)
..+...-...||||.++++.+||+++.||+|-+|+ ..|.++++.++-+.
T Consensus 21 ~E~V~aLi~~G~tQ~qI~~~tgv~QpsisRilsGk~kDpR~s~v~~L~~L 70 (82)
T PHA00542 21 DELVCALIRAGWSQEQIADATDVSQPTICRIYSGRHKDPRYSVVEKLRHL 70 (82)
T ss_pred HHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHCCCCCCCCCHHHHHHHHH
T ss_conf 99999999822569999986087703689998088789720699999999
No 37
>pfam08667 BetR BetR domain. This family includes an N-terminal helix-turn-helix domain.
Probab=96.98 E-value=0.005 Score=38.80 Aligned_cols=64 Identities=19% Similarity=0.241 Sum_probs=58.8
Q ss_pred HHHHHHHHHHHHHHCCCCHH----HHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHCC
Q ss_conf 99999999999998399499----99998634299998875589994489999999992899999608
Q gi|254781147|r 19 RMIFVNNFRNIRKEAKLTQK----EIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLWKLLK 82 (83)
Q Consensus 19 ~~~~g~~ir~~R~~~gltq~----ela~~~gis~~~is~iE~G~~~~~~~~l~~la~al~i~~~~l~~ 82 (83)
...++.+||.+....|+.-. .++..+|+|.|.-.+=-+|...=++..|.+++++||+|+.+||.
T Consensus 3 ~~~ia~rvr~lL~r~GI~kRqh~s~is~iL~LSfS~a~RKLkG~spW~l~Ql~kVA~~fg~~~a~L~~ 70 (146)
T pfam08667 3 DLIVAERVRKLLTRTGIAERQHNTTIANILGLSFSQAYRKLKGSIPWNLAQLQKVAQYFGVPAAILLI 70 (146)
T ss_pred CHHHHHHHHHHHHHCCCCHHHHHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHC
T ss_conf 18999999999986399756778899999787489887873589974499999999995979999927
No 38
>pfam00157 Pou Pou domain - N-terminal to homeobox domain.
Probab=96.96 E-value=0.0044 Score=39.16 Aligned_cols=57 Identities=26% Similarity=0.338 Sum_probs=47.6
Q ss_pred HHHHHHHHHHHHHHHHHCCCCHHHHHHHHHH------HHHHHHHHHCCCCCCCHHHHHHHHHHHC
Q ss_conf 9999999999999999839949999998634------2999988755899944899999999928
Q gi|254781147|r 16 LRERMIFVNNFRNIRKEAKLTQKEIRNRTGF------AQSWISELETGKSTINIDNMIILAHTLD 74 (83)
Q Consensus 16 ~~~~~~~g~~ir~~R~~~gltq~ela~~~gi------s~~~is~iE~G~~~~~~~~l~~la~al~ 74 (83)
+.+-+.|+..++..|...|+||.+++..+|. |+++|+++|+ -+.+..++.++--.|.
T Consensus 6 l~Ele~Fa~~fk~rRi~LG~TQ~dVg~al~~l~G~~~SQttIcRFE~--l~Ls~kn~~kLkP~L~ 68 (75)
T pfam00157 6 LEELEQFAKEFKQRRIKLGYTQADVGLALGALYGPVFSQTTICRFEA--LQLSFKNMCKLKPLLE 68 (75)
T ss_pred HHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCCHHHHHHHHH--CCCCHHHHHHHHHHHH
T ss_conf 99999999999998987377599999999987086542358888885--0447998998899999
No 39
>COG5606 Uncharacterized conserved small protein [Function unknown]
Probab=96.92 E-value=0.0023 Score=40.76 Aligned_cols=67 Identities=19% Similarity=0.309 Sum_probs=60.1
Q ss_pred CHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCC-CCHHHHHHHHHHHCCCHH
Q ss_conf 9899999999999999999983994999999863429999887558999-448999999999289999
Q gi|254781147|r 12 SDAILRERMIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKST-INIDNMIILAHTLDTPLW 78 (83)
Q Consensus 12 ~~~~~~~~~~~g~~ir~~R~~~gltq~ela~~~gis~~~is~iE~G~~~-~~~~~l~~la~al~i~~~ 78 (83)
....+.-+..++..|..+-++++++|++.|+.+||+++.+|.+-+|+.. .+++.|.-.....|.++.
T Consensus 19 ~a~~m~ir~~l~~~i~~~i~q~~l~Q~qiae~lgV~qprvS~l~~gk~~~fs~dkLvtml~~~g~ei~ 86 (91)
T COG5606 19 AAENMKIRSALMMAIKQWIEQAALSQAQIAELLGVTQPRVSDLARGKIQDFSIDKLVTMLARAGQEID 86 (91)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHCCHHHHHHHHHHHHHHHCCCCCC
T ss_conf 89989999999999999999978779999998388873188998361457669999999997598552
No 40
>pfam07022 Phage_CI_repr Bacteriophage CI repressor helix-turn-helix domain. This family consists of several phage CI repressor proteins and related bacterial sequences. The CI repressor is known to function as a transcriptional switch, determining whether transcription is lytic or lysogenic.
Probab=96.80 E-value=0.0054 Score=38.59 Aligned_cols=56 Identities=16% Similarity=0.134 Sum_probs=47.5
Q ss_pred HHHHHHHCCCC-HHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHCC
Q ss_conf 99999983994-9999998634299998875589994489999999992899999608
Q gi|254781147|r 26 FRNIRKEAKLT-QKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLWKLLK 82 (83)
Q Consensus 26 ir~~R~~~glt-q~ela~~~gis~~~is~iE~G~~~~~~~~l~~la~al~i~~~~l~~ 82 (83)
|.++.+.-|.+ |.|||+.+||+++++|.+-... ..+.+-+.+++...|+++.+|+.
T Consensus 3 i~Rl~~a~G~~t~~eLA~~LgI~~stis~w~~R~-~~P~e~iv~~~~~tGvsl~WL~~ 59 (65)
T pfam07022 3 IERLMKAYGFKSRSELADHLGVSKSTLSTWYKRD-SFPAEWVIRCALETGVSLDWLAT 59 (65)
T ss_pred HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCC-CCCHHHHHHHHHHHCCCHHHHHC
T ss_conf 9999999688869999999698888899999869-99899999999998829999970
No 41
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=96.76 E-value=0.0021 Score=41.00 Aligned_cols=47 Identities=19% Similarity=0.177 Sum_probs=38.6
Q ss_pred HHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHH---HHHHHHHHCCCH
Q ss_conf 98399499999986342999988755899944899---999999928999
Q gi|254781147|r 31 KEAKLTQKEIRNRTGFAQSWISELETGKSTINIDN---MIILAHTLDTPL 77 (83)
Q Consensus 31 ~~~gltq~ela~~~gis~~~is~iE~G~~~~~~~~---l~~la~al~i~~ 77 (83)
+.+++|..|+|+.+|||.+|+|++-||...++-++ +.+.++.+|..+
T Consensus 3 ~~kkvTi~dIA~~aGVS~aTVSrvLn~~~~Vs~eTr~rV~~aa~elgY~p 52 (342)
T PRK10014 3 TAKKITIHDVALAAGVSVSTVSLVLSGKGRISTATGERVNQAIEELGFVR 52 (342)
T ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCC
T ss_conf 99988799999998969999999977989999999999999999948997
No 42
>PRK09526 lacI lac repressor; Reviewed
Probab=96.66 E-value=0.0023 Score=40.75 Aligned_cols=47 Identities=13% Similarity=0.112 Sum_probs=38.4
Q ss_pred HHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHH---HHHHHHHHCCCH
Q ss_conf 98399499999986342999988755899944899---999999928999
Q gi|254781147|r 31 KEAKLTQKEIRNRTGFAQSWISELETGKSTINIDN---MIILAHTLDTPL 77 (83)
Q Consensus 31 ~~~gltq~ela~~~gis~~~is~iE~G~~~~~~~~---l~~la~al~i~~ 77 (83)
+++..|.+|+|+.+|||.+|+|++-||...++-++ +.+.++-+|..+
T Consensus 2 ~~k~~TikDIA~~agVS~sTVSrvLn~~~~vs~~tr~rV~~~a~elgY~p 51 (342)
T PRK09526 2 KSKPVTLYDVARYAGVSYQTVSRVLNQASHVSAKTREKVEAAMAELNYVP 51 (342)
T ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCC
T ss_conf 98997699999998969999999978979999999999999999839997
No 43
>PRK02866 cyanate hydratase; Validated
Probab=96.63 E-value=0.016 Score=35.79 Aligned_cols=62 Identities=19% Similarity=0.269 Sum_probs=56.8
Q ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHH
Q ss_conf 99999999999998399499999986342999988755899944899999999928999996
Q gi|254781147|r 19 RMIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLWKL 80 (83)
Q Consensus 19 ~~~~g~~ir~~R~~~gltq~ela~~~gis~~~is~iE~G~~~~~~~~l~~la~al~i~~~~l 80 (83)
+..+.+.|..++.++|+|=+++|+.+|.|.-++...--|+...+-+...++++.|+++-+..
T Consensus 3 r~~lte~i~~aK~~kgltw~~ia~~~G~s~v~~aaa~lGQ~~~~~e~A~~l~~~L~L~~~~~ 64 (147)
T PRK02866 3 REELTEKILAAKKEKGLTWADIAEAIGLSEVWVTAALLGQMTLPAEEAEKVAELLGLDEDAV 64 (147)
T ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCHHHHHHHHHHCCCCHHHH
T ss_conf 89999999999998499899999894989999999984677899999999999749999999
No 44
>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor; InterPro: IPR014209 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 recognized by the major sigma factors , . The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homologue sigma-E (sigma-29, see IPR014200 from INTERPRO), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note: that in Bacillus subtilis (and apparently also in Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K .; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=96.58 E-value=0.00095 Score=43.07 Aligned_cols=28 Identities=29% Similarity=0.483 Sum_probs=24.7
Q ss_pred HHHCCCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 9983994999999863429999887558
Q gi|254781147|r 30 RKEAKLTQKEIRNRTGFAQSWISELETG 57 (83)
Q Consensus 30 R~~~gltq~ela~~~gis~~~is~iE~G 57 (83)
......||.|.|+.+|||+||+|+||.-
T Consensus 191 ~~~~~~tQREIA~~LgISRSYVSRIEK~ 218 (228)
T TIGR02846 191 KDGREKTQREIAKILGISRSYVSRIEKK 218 (228)
T ss_pred CCCCCCCHHHHHHHHCCCCHHHHHHHHH
T ss_conf 8889541789987708650045488899
No 45
>PRK09492 treR trehalose repressor; Provisional
Probab=96.55 E-value=0.0045 Score=39.06 Aligned_cols=47 Identities=17% Similarity=0.183 Sum_probs=38.6
Q ss_pred HCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHH---HHHHHHHHCCCHH
Q ss_conf 8399499999986342999988755899944899---9999999289999
Q gi|254781147|r 32 EAKLTQKEIRNRTGFAQSWISELETGKSTINIDN---MIILAHTLDTPLW 78 (83)
Q Consensus 32 ~~gltq~ela~~~gis~~~is~iE~G~~~~~~~~---l~~la~al~i~~~ 78 (83)
.+++|.+|+|+.+|+|.+++|++-||...++-++ +.+.++.||..+.
T Consensus 2 ~kkvTikDIA~~aGVS~aTVSrvLn~~~~vs~eTr~rV~~~a~elgY~Pn 51 (315)
T PRK09492 2 QNKLTIKDIARLSGVGKSTVSRVLNNEPKVSPRTRERVEAVINQHGFSPS 51 (315)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCCC
T ss_conf 89887999999989799999999789899999999999999999699807
No 46
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=96.46 E-value=0.005 Score=38.81 Aligned_cols=39 Identities=23% Similarity=0.413 Sum_probs=31.7
Q ss_pred HHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCC-CCHHHH
Q ss_conf 9999983994999999863429999887558999-448999
Q gi|254781147|r 27 RNIRKEAKLTQKEIRNRTGFAQSWISELETGKST-INIDNM 66 (83)
Q Consensus 27 r~~R~~~gltq~ela~~~gis~~~is~iE~G~~~-~~~~~l 66 (83)
+.++.+ |+||.++|+.+|+|++.+|+|-+|++. ..++.+
T Consensus 16 ~~L~ee-G~Sq~~iA~LLGltqaAVS~Yls~krg~~~~~~~ 55 (119)
T COG2522 16 KELIEE-GLSQYRIAKLLGLTQAAVSQYLSGKRGSARLEDI 55 (119)
T ss_pred HHHHHC-CCCHHHHHHHHCCCHHHHHHHHCCCCCHHHHHHH
T ss_conf 999995-8869999999688899999997367736889999
No 47
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=96.25 E-value=0.0083 Score=37.51 Aligned_cols=43 Identities=16% Similarity=0.210 Sum_probs=34.3
Q ss_pred CCHHHHHHHHHHHHHHHHHHHCCCCC---CCHHH---HHHHHHHHCCCH
Q ss_conf 94999999863429999887558999---44899---999999928999
Q gi|254781147|r 35 LTQKEIRNRTGFAQSWISELETGKST---INIDN---MIILAHTLDTPL 77 (83)
Q Consensus 35 ltq~ela~~~gis~~~is~iE~G~~~---~~~~~---l~~la~al~i~~ 77 (83)
+|.+|+|+.+|||.+|+|++-||+.. ++-++ +.+.++.||..+
T Consensus 1 vTikDVA~~AGVS~aTVSrvLNg~~~~~~Vs~~Tr~rV~~aa~eLgY~P 49 (330)
T PRK11303 1 MKLDEIARLAGVSRTTASYVINGKAKQYRISDKTVEKVMAVVREHNYHP 49 (330)
T ss_pred CCHHHHHHHHCCCHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHCCCC
T ss_conf 9789999997979989988838999888769999999999999968994
No 48
>pfam00356 LacI Bacterial regulatory proteins, lacI family.
Probab=96.09 E-value=0.011 Score=36.75 Aligned_cols=37 Identities=11% Similarity=0.175 Sum_probs=31.9
Q ss_pred CHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHH
Q ss_conf 4999999863429999887558999448999999999
Q gi|254781147|r 36 TQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHT 72 (83)
Q Consensus 36 tq~ela~~~gis~~~is~iE~G~~~~~~~~l~~la~a 72 (83)
|..|+|+.+|+|.+++|++-||...++-++-.++.++
T Consensus 1 Ti~DIA~~agVS~~TVSr~ln~~~~vs~~tr~rI~~~ 37 (46)
T pfam00356 1 TIKDVARLAGVSKATVSRVLNNPERVSEETREKVEAA 37 (46)
T ss_pred CHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHH
T ss_conf 9999999989799999999879798999999999999
No 49
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=96.07 E-value=0.012 Score=36.56 Aligned_cols=43 Identities=12% Similarity=0.229 Sum_probs=35.2
Q ss_pred CCHHHHHHHHHHHHHHHHHHHCCCCCCCHHH---HHHHHHHHCCCH
Q ss_conf 9499999986342999988755899944899---999999928999
Q gi|254781147|r 35 LTQKEIRNRTGFAQSWISELETGKSTINIDN---MIILAHTLDTPL 77 (83)
Q Consensus 35 ltq~ela~~~gis~~~is~iE~G~~~~~~~~---l~~la~al~i~~ 77 (83)
.|.+|+|+.+|||.+++|++-||...++-++ +.+.++.||..+
T Consensus 2 vTi~DVA~~AGVS~aTVSrvLn~~~~Vs~eTr~rV~~aa~eLgY~P 47 (346)
T PRK10401 2 ITIRDVARQAGVSVATVSRVLNNSALVSPDTREAVMKAVSELGYRP 47 (346)
T ss_pred CCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCC
T ss_conf 9789999998979999999977949999999999999999949984
No 50
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=95.96 E-value=0.014 Score=36.19 Aligned_cols=42 Identities=12% Similarity=0.103 Sum_probs=35.0
Q ss_pred CHHHHHHHHHHHHHHHHHHHCCCCCCCHHH---HHHHHHHHCCCH
Q ss_conf 499999986342999988755899944899---999999928999
Q gi|254781147|r 36 TQKEIRNRTGFAQSWISELETGKSTINIDN---MIILAHTLDTPL 77 (83)
Q Consensus 36 tq~ela~~~gis~~~is~iE~G~~~~~~~~---l~~la~al~i~~ 77 (83)
|.+|+|+.+|||.+++|++-||...++-++ +.+.++.||..+
T Consensus 3 TIkDIA~~AGVS~sTVSrvLN~~~~Vs~~Tr~rV~~aa~eLgY~P 47 (342)
T PRK10727 3 TIKDVARLAGVSVATVSRVINNSPKASEASRLAVHSAMESLSYHP 47 (342)
T ss_pred CHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCC
T ss_conf 889999997969999999977979999999999999999939985
No 51
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=95.87 E-value=0.016 Score=35.80 Aligned_cols=42 Identities=14% Similarity=0.249 Sum_probs=34.1
Q ss_pred CHHHHHHHHHHHHHHHHHHHCCCCCCCHHH---HHHHHHHHCCCH
Q ss_conf 499999986342999988755899944899---999999928999
Q gi|254781147|r 36 TQKEIRNRTGFAQSWISELETGKSTINIDN---MIILAHTLDTPL 77 (83)
Q Consensus 36 tq~ela~~~gis~~~is~iE~G~~~~~~~~---l~~la~al~i~~ 77 (83)
|.+|+|+.+|+|.+++|++-||...++-++ +..+++.+|..+
T Consensus 2 Ti~dvA~~aGVS~sTVSr~ln~~~~Vs~~tr~rV~~~a~~lgY~p 46 (70)
T smart00354 2 TIKDVARLAGVSKATVSRVLNGNGRVSEETREKVLAAMEELGYIP 46 (70)
T ss_pred CHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCC
T ss_conf 899999998959999999977999899999999999999978998
No 52
>PRK08099 nicotinamide-nucleotide adenylyltransferase; Provisional
Probab=95.82 E-value=0.032 Score=34.02 Aligned_cols=56 Identities=14% Similarity=0.271 Sum_probs=51.2
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCC-CCCCHHHHHHHHHHHCCCHHH
Q ss_conf 99999999839949999998634299998875589-994489999999992899999
Q gi|254781147|r 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGK-STINIDNMIILAHTLDTPLWK 79 (83)
Q Consensus 24 ~~ir~~R~~~gltq~ela~~~gis~~~is~iE~G~-~~~~~~~l~~la~al~i~~~~ 79 (83)
..++..+++.|++..++++.+|+++.|++++-+|+ .+|+...|..+-+.|++....
T Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 61 (411)
T PRK08099 5 DYLKTAIKQQGCTLQQVADASGMTKGYLSQLLNAKIKSPSAQKLEALHRFLGLEFPR 61 (411)
T ss_pred HHHHHHHHHHCCCHHHHHHHHCCHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCHH
T ss_conf 899999998488298876542340999999862524894378999999995886402
No 53
>COG3636 Predicted transcriptional regulator [Transcription]
Probab=95.78 E-value=0.014 Score=36.19 Aligned_cols=51 Identities=8% Similarity=0.216 Sum_probs=42.7
Q ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHH
Q ss_conf 99999983994999999863429999887558999448999999999289999
Q gi|254781147|r 26 FRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLW 78 (83)
Q Consensus 26 ir~~R~~~gltq~ela~~~gis~~~is~iE~G~~~~~~~~l~~la~al~i~~~ 78 (83)
+-..--.+||| ++|+.+|+++..+.+--+...||+++++.+++++||+.+.
T Consensus 43 lg~var~~GMs--qvA~~aGlsRe~LYkaLS~~GNPtf~Til~V~kAlG~rl~ 93 (100)
T COG3636 43 LGVVARSRGMS--QVARKAGLSREGLYKALSPGGNPTFDTILAVLKALGLRLS 93 (100)
T ss_pred HHHHHHHCCHH--HHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHCCCEEE
T ss_conf 99999865789--9999949669999998478999758999999998086542
No 54
>KOG1168 consensus
Probab=95.78 E-value=0.0043 Score=39.21 Aligned_cols=46 Identities=26% Similarity=0.312 Sum_probs=39.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHH---------HHHHHHHHHHCCC
Q ss_conf 899999999999999999983994999999863---------4299998875589
Q gi|254781147|r 13 DAILRERMIFVNNFRNIRKEAKLTQKEIRNRTG---------FAQSWISELETGK 58 (83)
Q Consensus 13 ~~~~~~~~~~g~~ir~~R~~~gltq~ela~~~g---------is~~~is~iE~G~ 58 (83)
|...++.+.|+++.++.|...|.||+|+++.+. +|+++|.++|.=.
T Consensus 213 dtDPReLEaFAErFKQRRIKLGVTQADVG~ALAnLKiPGVGsLSQSTICRFESLT 267 (385)
T KOG1168 213 DTDPRELEAFAERFKQRRIKLGVTQADVGKALANLKIPGVGSLSQSTICRFESLT 267 (385)
T ss_pred CCCHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCEEEEEEEC
T ss_conf 7888999999999875454306427777889872768875532312133210000
No 55
>PRK11041 DNA-binding transcriptional regulator CytR; Provisional
Probab=95.74 E-value=0.019 Score=35.30 Aligned_cols=44 Identities=9% Similarity=0.034 Sum_probs=35.7
Q ss_pred CCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHH---HHHHHCCCHH
Q ss_conf 9499999986342999988755899944899999---9999289999
Q gi|254781147|r 35 LTQKEIRNRTGFAQSWISELETGKSTINIDNMII---LAHTLDTPLW 78 (83)
Q Consensus 35 ltq~ela~~~gis~~~is~iE~G~~~~~~~~l~~---la~al~i~~~ 78 (83)
-|.+|+|+.+|||.+|+|++-||...++-++-.+ .++.||..+.
T Consensus 10 aTikDIA~~aGVS~sTVSrvLn~~~~Vs~~Tr~rV~~aa~eLgY~pn 56 (341)
T PRK11041 10 ATMKDVALKAGVSTATVSRALMNPEKVSQSTRNRVEQAVLEVGYSPQ 56 (341)
T ss_pred CCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCCC
T ss_conf 88999999979799999999789899999999999999998199838
No 56
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=95.68 E-value=0.021 Score=35.12 Aligned_cols=42 Identities=14% Similarity=0.194 Sum_probs=34.6
Q ss_pred CHHHHHHHHHHHHHHHHHHHCCCCCCCHHH---HHHHHHHHCCCH
Q ss_conf 499999986342999988755899944899---999999928999
Q gi|254781147|r 36 TQKEIRNRTGFAQSWISELETGKSTINIDN---MIILAHTLDTPL 77 (83)
Q Consensus 36 tq~ela~~~gis~~~is~iE~G~~~~~~~~---l~~la~al~i~~ 77 (83)
|.+|+|+.+|||.+|+|++-||...++-++ +.+.++.||..+
T Consensus 3 TikDIA~~AGVS~aTVSrvLn~~~~Vs~~Tr~rV~~aa~eLgY~p 47 (335)
T PRK10703 3 TIKDVAKRAGVSTTTVSHVINKTRFVAEETRNAVWAAIKELHYSP 47 (335)
T ss_pred CHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCC
T ss_conf 889999997989999999968969989999999999999829997
No 57
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=95.64 E-value=0.021 Score=35.07 Aligned_cols=42 Identities=14% Similarity=0.177 Sum_probs=34.2
Q ss_pred CCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHH---HHHHHCCC
Q ss_conf 9499999986342999988755899944899999---99992899
Q gi|254781147|r 35 LTQKEIRNRTGFAQSWISELETGKSTINIDNMII---LAHTLDTP 76 (83)
Q Consensus 35 ltq~ela~~~gis~~~is~iE~G~~~~~~~~l~~---la~al~i~ 76 (83)
.|.+|+|+.+|||.+|+|++-||...++-++-.+ .++.||..
T Consensus 1 ~TikDVA~~AGVS~sTVSrvln~~~~Vs~eTr~rV~~a~~elgY~ 45 (333)
T COG1609 1 ATIKDVAKLAGVSKATVSRVLNGSPYVSEETREKVLAAIKELGYR 45 (333)
T ss_pred CCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCC
T ss_conf 968999999689998988987799987999999999999997899
No 58
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=95.49 E-value=0.028 Score=34.32 Aligned_cols=60 Identities=25% Similarity=0.238 Sum_probs=43.2
Q ss_pred HHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH-----HCCCCCCCHH--------HHHHHHHHHCCC
Q ss_conf 99999999999999983994999999863429999887-----5589994489--------999999992899
Q gi|254781147|r 17 RERMIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISEL-----ETGKSTINID--------NMIILAHTLDTP 76 (83)
Q Consensus 17 ~~~~~~g~~ir~~R~~~gltq~ela~~~gis~~~is~i-----E~G~~~~~~~--------~l~~la~al~i~ 76 (83)
.+...+..++.++....||||.|+|+++|+|+.+++++ +.|-..++++ .-.+|.+.||+.
T Consensus 9 ~~~~~l~~~~A~lYY~~gltQ~eIA~~LgiSR~~v~rlL~~Ar~~GiV~I~i~~~~~~~~~Le~~L~~~fgL~ 81 (321)
T COG2390 9 MEEERLLARAAWLYYVEGLTQSEIAERLGISRATVSRLLAKAREEGIVKISINSPVEGCLELEQQLKERFGLK 81 (321)
T ss_pred HHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEEEECCCCCCHHHHHHHHHHHCCCC
T ss_conf 2689999999999984688799999883988999999999999879389996798765399999999965997
No 59
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=95.39 E-value=0.035 Score=33.82 Aligned_cols=41 Identities=20% Similarity=0.293 Sum_probs=33.8
Q ss_pred CHHHHHHHHHHHHHHHHHHHCCCCC--CC---HHHHHHHHHHHCCC
Q ss_conf 4999999863429999887558999--44---89999999992899
Q gi|254781147|r 36 TQKEIRNRTGFAQSWISELETGKST--IN---IDNMIILAHTLDTP 76 (83)
Q Consensus 36 tq~ela~~~gis~~~is~iE~G~~~--~~---~~~l~~la~al~i~ 76 (83)
|.+|+|+.+|||.+++|++-||+.. ++ -+.+.+.++-+|..
T Consensus 3 TikDVA~~AGVS~sTVSrvLn~~~~~~V~~~Tr~rV~~aa~elgY~ 48 (327)
T PRK10339 3 TLKDIAIEAGVSLATVSRVLNDDPTLNVKEETKHRILEIAEKLEYK 48 (327)
T ss_pred CHHHHHHHHCCCHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHCCC
T ss_conf 6899999978889999999589899996899999999999996899
No 60
>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily; InterPro: IPR014322 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 recognized by the major sigma factors , . This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:IPR014236 from INTERPRO and SigG:IPR014212 from INTERPRO as well as SigB:IPR014288 from INTERPRO), and the high GC Gram-positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=95.35 E-value=0.0038 Score=39.49 Aligned_cols=33 Identities=30% Similarity=0.267 Sum_probs=29.4
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 999999983994999999863429999887558
Q gi|254781147|r 25 NFRNIRKEAKLTQKEIRNRTGFAQSWISELETG 57 (83)
Q Consensus 25 ~ir~~R~~~gltq~ela~~~gis~~~is~iE~G 57 (83)
.|-.+|--.++||.|+|+.+||||=++|+|++-
T Consensus 187 ~il~lRFf~~~TQ~eiA~~lGiSQMhVSRl~~~ 219 (229)
T TIGR02980 187 RILLLRFFEDKTQSEIAERLGISQMHVSRLLRR 219 (229)
T ss_pred EEEEEEEECCCCHHHHHHHCCCCHHHHHHHHHH
T ss_conf 761000106977899997818436788999999
No 61
>PRK08558 adenine phosphoribosyltransferase; Provisional
Probab=95.12 E-value=0.12 Score=30.71 Aligned_cols=50 Identities=18% Similarity=0.252 Sum_probs=41.6
Q ss_pred HHHH-HHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCC
Q ss_conf 9999-9839949999998634299998875589994489999999992899
Q gi|254781147|r 27 RNIR-KEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTP 76 (83)
Q Consensus 27 r~~R-~~~gltq~ela~~~gis~~~is~iE~G~~~~~~~~l~~la~al~i~ 76 (83)
+.+| ...-+|-+||++.+|+..+.+++|=||+..|+.++...|.+.++-.
T Consensus 15 ~~LR~lK~~~tykELs~~~gip~s~L~RYv~g~vlPs~e~A~~i~~~l~~~ 65 (238)
T PRK08558 15 RYLRSLKKTYTYEELSSILGLPESVLSRYVNGHVLPSVERAREIVEKLKPY 65 (238)
T ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHH
T ss_conf 999998502689999988797999985053488787589999999984211
No 62
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=95.05 E-value=0.039 Score=33.52 Aligned_cols=29 Identities=34% Similarity=0.426 Sum_probs=25.9
Q ss_pred HHHHHCCCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 999983994999999863429999887558
Q gi|254781147|r 28 NIRKEAKLTQKEIRNRTGFAQSWISELETG 57 (83)
Q Consensus 28 ~~R~~~gltq~ela~~~gis~~~is~iE~G 57 (83)
++| ++|+||+|.|+.+|.|++.||.||..
T Consensus 14 ~lR-~~G~tQ~eIA~~lgTSraNvs~iEk~ 42 (139)
T PRK03975 14 RLR-KRGLTQQEIADILGTSRANISIIEKR 42 (139)
T ss_pred HHH-HCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 999-82897999999977328899999999
No 63
>COG3423 Nlp Predicted transcriptional regulator [Transcription]
Probab=94.64 E-value=0.13 Score=30.45 Aligned_cols=55 Identities=13% Similarity=0.124 Sum_probs=44.0
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHC
Q ss_conf 9999999983994999999863429999887558999448999999999289999960
Q gi|254781147|r 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLWKLL 81 (83)
Q Consensus 24 ~~ir~~R~~~gltq~ela~~~gis~~~is~iE~G~~~~~~~~l~~la~al~i~~~~l~ 81 (83)
..|...-+.+|+|.+.|+...|+|.+++...-.. .=|.-+ ..||+++|+++.+..
T Consensus 11 adI~A~Lkk~G~Sl~~LS~~agls~~tL~n~L~r-p~pkgE--riIA~algv~P~eIW 65 (82)
T COG3423 11 ADIIAALKKKGTSLAALSREAGLSSSTLANALDR-PWPKGE--RIIADALGVPPEEIW 65 (82)
T ss_pred HHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHCC-CCCHHH--HHHHHHHCCCHHHHC
T ss_conf 9999999985642999998808787899998747-887188--999999589888818
No 64
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=94.63 E-value=0.043 Score=33.24 Aligned_cols=35 Identities=31% Similarity=0.349 Sum_probs=30.8
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 99999999983994999999863429999887558
Q gi|254781147|r 23 VNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETG 57 (83)
Q Consensus 23 g~~ir~~R~~~gltq~ela~~~gis~~~is~iE~G 57 (83)
=+.|-.+|...++||.|+|+.+|||++.+|+++.-
T Consensus 201 Ek~Vl~l~y~eelt~kEI~~~LgISes~VSql~kk 235 (247)
T COG1191 201 EKLVLVLRYKEELTQKEIAEVLGISESRVSRLHKK 235 (247)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 99999999970157999999949149899999999
No 65
>TIGR00673 cynS cyanate hydratase; InterPro: IPR008076 Cyanase, an enzyme found in bacteria and plants, catalyses the reaction of cyanate with bicarbonate to produce ammonia and carbon dioxide, allowing the host organisms to overcome the toxicity of environmental cyanate . The cyanate lyase monomer is composed of two domains: an N-terminal domain that shows structural similarity to the DNA-binding alpha-helix bundle motif, and a C-terminal domain that has an 'open fold' that shows no structural similarity to other proteins . The enzyme is active as a homodecamer of 17kDa subunits, and displays half-site binding of substrates or substrate analogues. The dimer structure reveals the C-terminal domains to be intertwined; the decamer is formed from a pentamer of these dimers. The active site of the enzyme is located between dimers and comprises residues from four adjacent subunits of the homodecamer. Synonym(s): cyanase lyase, cyanase hydrolase ; GO: 0016836 hydro-lyase activity, 0008152 metabolic process.
Probab=94.46 E-value=0.16 Score=29.84 Aligned_cols=63 Identities=17% Similarity=0.275 Sum_probs=57.9
Q ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHH
Q ss_conf 999999999999998399499999986342999988755899944899999999928999996
Q gi|254781147|r 18 ERMIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLWKL 80 (83)
Q Consensus 18 ~~~~~g~~ir~~R~~~gltq~ela~~~gis~~~is~iE~G~~~~~~~~l~~la~al~i~~~~l 80 (83)
.|..++..|-...+.+|+|=+|++..+|-+..|++.+--|....+.+....+++.||.+=..+
T Consensus 10 irldl~~~lle~Kk~kgltfad~~~~lG~~ev~~aa~~ygqa~a~~dea~~v~~~L~L~ed~~ 72 (156)
T TIGR00673 10 IRLDLAKKLLEAKKKKGLTFADVEDKLGKAEVYVAAVLYGQAAADADEAKKVAELLDLEEDEV 72 (156)
T ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHHHHHCCCHHHHHHHHHHCCCCHHHH
T ss_conf 577789999998873599789986531875999999998420688889999998709981134
No 66
>TIGR01321 TrpR trp operon repressor; InterPro: IPR013335 The Trp repressor (TrpR) binds to at least five operators in the Escherichia coli genome, repressing gene expression. The operators at which it binds vary considerably in DNA sequence and location within the promoter; when bound to the Trp operon it recognises the sequence 5'-ACTAGT-3' and acts to prevent the initiation of transcription. The TrpR controls the trpEDCBA (trpO) operon and the genes for trpR, aroH, mtr and aroL, which are involved in the biosynthesis and uptake of the amino acid tryptophan . The repressor binds to the operators only in the presence of L-tryptophan, thereby controlling the intracellular level of its effector; the complex also regulates Trp repressor biosynthesis by binding to its own regulatory region. TrpR acts as a dimer that is composed of identical 6-helical subunits, where four of the helices form the core of the protein and intertwine with the corresponding helices from the other subunit. This entry represents Trp repressors found in proteobacterial and chlamydial species.; GO: 0016564 transcription repressor activity, 0006355 regulation of transcription DNA-dependent.
Probab=94.43 E-value=0.061 Score=32.34 Aligned_cols=38 Identities=24% Similarity=0.307 Sum_probs=32.5
Q ss_pred HHHHHHHHHHHHHH--HHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 99999999999999--983994999999863429999887
Q gi|254781147|r 17 RERMIFVNNFRNIR--KEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 17 ~~~~~~g~~ir~~R--~~~gltq~ela~~~gis~~~is~i 54 (83)
.+++.+|.+++..+ ....+||.|++...|+|.++|.+=
T Consensus 37 ~Er~dl~~R~~I~~~LL~~~~~QREi~~~lG~SiA~ITRG 76 (95)
T TIGR01321 37 DEREDLGSRVRIVEELLEGEMSQREIAEKLGVSIATITRG 76 (95)
T ss_pred HHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 3799998799999999614897478888637616678787
No 67
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=94.30 E-value=0.074 Score=31.85 Aligned_cols=42 Identities=12% Similarity=0.071 Sum_probs=33.5
Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCCHHH---HHHHHHHHCCCHH
Q ss_conf 99999986342999988755899944899---9999999289999
Q gi|254781147|r 37 QKEIRNRTGFAQSWISELETGKSTINIDN---MIILAHTLDTPLW 78 (83)
Q Consensus 37 q~ela~~~gis~~~is~iE~G~~~~~~~~---l~~la~al~i~~~ 78 (83)
.+|+|+.+|||.+|+|++-||...++-++ +.+.++.||..+.
T Consensus 1 ikDIA~~AGVS~sTVSrvLn~~~~Vs~~tr~rV~~aa~elgY~pn 45 (327)
T PRK10423 1 MKDVARLAGVSTSTVSHVINKDRFVSEAITAKVEAAIKELNYAPS 45 (327)
T ss_pred CHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCCC
T ss_conf 968987869899999999789599999999999999998299868
No 68
>pfam01371 Trp_repressor Trp repressor protein. This protein binds to tryptophan and represses transcription of the Trp operon.
Probab=94.26 E-value=0.098 Score=31.12 Aligned_cols=40 Identities=23% Similarity=0.294 Sum_probs=34.5
Q ss_pred HHHHHHHHHHHHHH--HHCCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 99999999999999--98399499999986342999988755
Q gi|254781147|r 17 RERMIFVNNFRNIR--KEAKLTQKEIRNRTGFAQSWISELET 56 (83)
Q Consensus 17 ~~~~~~g~~ir~~R--~~~gltq~ela~~~gis~~~is~iE~ 56 (83)
.+...++.+++.++ ...++||.++++.+|+|..+|++.-+
T Consensus 30 ~E~~ala~R~~va~~LL~~~~syreI~~~~g~S~aTItRvsr 71 (88)
T pfam01371 30 DEREALAQRLRIAKELLRGELSQREIAQELGASIATITRGSN 71 (88)
T ss_pred HHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 999999999999999997899899999985985231478899
No 69
>pfam04814 HNF-1_N Hepatocyte nuclear factor 1 (HNF-1), N terminus. This family consists of the N terminus of homeobox-containing transcription factor HNF-1. This region contains a dimerization sequence and an acidic region that may be involved in transcription activation. Mutations and the common Ala/Val 98 polymorphism in HNF-1 cause the type 3 form of maturity-onset diabetes of the young (MODY3).
Probab=94.25 E-value=0.067 Score=32.09 Aligned_cols=40 Identities=18% Similarity=0.249 Sum_probs=35.5
Q ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf 9999999999999839949999998634299998875589
Q gi|254781147|r 19 RMIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGK 58 (83)
Q Consensus 19 ~~~~g~~ir~~R~~~gltq~ela~~~gis~~~is~iE~G~ 58 (83)
...+++.|+.+..+++++|.+++..+|+++|+||+.-|.-
T Consensus 113 ~~~v~~~Ik~~m~~h~ipQ~~vv~~TGlnQS~lSq~LnkG 152 (177)
T pfam04814 113 PWRVAKMIKSYMQQHNIPQREVVDATGLNQSHLSQHLNKG 152 (177)
T ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHHCC
T ss_conf 4999999999998768846678761065599999999668
No 70
>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=93.97 E-value=0.075 Score=31.83 Aligned_cols=39 Identities=21% Similarity=0.277 Sum_probs=30.9
Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHH---HHHHCCC
Q ss_conf 99999863429999887558999448999999---9992899
Q gi|254781147|r 38 KEIRNRTGFAQSWISELETGKSTINIDNMIIL---AHTLDTP 76 (83)
Q Consensus 38 ~ela~~~gis~~~is~iE~G~~~~~~~~l~~l---a~al~i~ 76 (83)
.|+|+.+|+|.+++|++-||...++-++-.+| ++.+|..
T Consensus 1 ~diA~~~gvS~~TVSr~ln~~~~Vs~~tr~~I~~~~~elgY~ 42 (52)
T cd01392 1 KDIARAAGVSVATVSRVLNGKPRVSEETRERVLAAAEELGYR 42 (52)
T ss_pred CHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCC
T ss_conf 928888785999999998798989999999999999998889
No 71
>TIGR00721 tfx DNA-binding protein, Tfx family; InterPro: IPR004645 This is a family of Tfx DNA-binding proteins, which is restricted to the archaea. Homology among the members is strongest in the helix-turn-helix-containing N-terminal region. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.; GO: 0003677 DNA binding.
Probab=93.86 E-value=0.034 Score=33.89 Aligned_cols=28 Identities=29% Similarity=0.274 Sum_probs=25.5
Q ss_pred HHCCCCHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf 9839949999998634299998875589
Q gi|254781147|r 31 KEAKLTQKEIRNRTGFAQSWISELETGK 58 (83)
Q Consensus 31 ~~~gltq~ela~~~gis~~~is~iE~G~ 58 (83)
-++||+|++.|+.++-|++.+|-||+--
T Consensus 18 R~kGl~Q~eIAk~LkTtRaNvS~iEkrA 45 (142)
T TIGR00721 18 REKGLKQKEIAKILKTTRANVSIIEKRA 45 (142)
T ss_pred HHCCCCHHHHHHHHCCCCHHHHHHHHHH
T ss_conf 6338887889877267201378988874
No 72
>PRK10344 DNA-binding transcriptional regulator Nlp; Provisional
Probab=93.69 E-value=0.28 Score=28.43 Aligned_cols=55 Identities=15% Similarity=0.194 Sum_probs=43.3
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHC
Q ss_conf 9999999983994999999863429999887558999448999999999289999960
Q gi|254781147|r 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLWKLL 81 (83)
Q Consensus 24 ~~ir~~R~~~gltq~ela~~~gis~~~is~iE~G~~~~~~~~l~~la~al~i~~~~l~ 81 (83)
..|...-..+|+|...||...|++.++++..-.. .-|.-+ ..||++||+++.+.-
T Consensus 11 ADIiAAL~KrG~sLa~Lsr~aGls~sTL~nAL~r-pwPKgE--~iIA~aLGv~P~eIW 65 (90)
T PRK10344 11 ADIIAGLRKKGTSMAAESRRNGLSSSTLANALSR-PWPKGE--MIIAKALGTDPWVIW 65 (90)
T ss_pred HHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHCC-CCCHHH--HHHHHHHCCCHHHCC
T ss_conf 9999999986886999999909986889998748-995679--999999787988809
No 73
>TIGR02885 spore_sigF RNA polymerase sigma-F factor; InterPro: IPR014236 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 recognized by the major sigma factors , . Members of this entry represent RNA polymerase sigma factor F. Within the Firmicutes, Sigma-F is specifically, and universally, a component of the endospore formation program, and is expressed in the forespore to turn on the expression of dozens of genes. It is closely related to sigma-G, which is also expressed in the forespore.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=93.37 E-value=0.024 Score=34.77 Aligned_cols=33 Identities=27% Similarity=0.262 Sum_probs=28.8
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 999999983994999999863429999887558
Q gi|254781147|r 25 NFRNIRKEAKLTQKEIRNRTGFAQSWISELETG 57 (83)
Q Consensus 25 ~ir~~R~~~gltq~ela~~~gis~~~is~iE~G 57 (83)
.|--+|.=+-.||-|+|+.+||||=.+||+|+-
T Consensus 190 ~ii~LRYFKDkTQ~eVA~~LGISQVQVSRlEkk 222 (231)
T TIGR02885 190 QIIMLRYFKDKTQTEVAKMLGISQVQVSRLEKK 222 (231)
T ss_pred EEEEEECCCCCHHHHHHHHCCCCCCHHHHHHHH
T ss_conf 897741014001799997718570012278999
No 74
>COG1356 tfx Transcriptional regulator [DNA replication, recombination and repair]
Probab=93.34 E-value=0.042 Score=33.31 Aligned_cols=46 Identities=28% Similarity=0.410 Sum_probs=32.2
Q ss_pred HHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHH---HHHHHHHHHCCCH
Q ss_conf 9839949999998634299998875589994489---9999999928999
Q gi|254781147|r 31 KEAKLTQKEIRNRTGFAQSWISELETGKSTINID---NMIILAHTLDTPL 77 (83)
Q Consensus 31 ~~~gltq~ela~~~gis~~~is~iE~G~~~~~~~---~l~~la~al~i~~ 77 (83)
.++||||++.|+.+|-+++.+|.||+.- .-+++ +-..+.+.++-|+
T Consensus 20 RekG~tQ~eIA~~L~TTraNvSaIEkrA-~enIekarnTL~l~~~i~spv 68 (143)
T COG1356 20 REKGLTQSEIARILKTTRANVSAIEKRA-LENIEKARNTLLLWEQINSPV 68 (143)
T ss_pred HHCCCCHHHHHHHHCCCCCCHHHHHHHH-HHHHHHHHHHHHHHHHHCCCE
T ss_conf 6405648999999754510179999999-998999988999999846975
No 75
>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor; InterPro: IPR014200 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 recognized by the major sigma factors , . Members of this entry represent the endospore formation-specific sigma factor SigE, also called SpoIIGB and sigma-29. In Bacillus subtilis, sigma-29 is synthesized as a precursor (P31), specifically in the mother cell compartment, and is activated by a cleavage that removes the N-terminal 29 amino acids .; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=92.84 E-value=0.07 Score=32.01 Aligned_cols=27 Identities=41% Similarity=0.519 Sum_probs=23.2
Q ss_pred HHCCCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 983994999999863429999887558
Q gi|254781147|r 31 KEAKLTQKEIRNRTGFAQSWISELETG 57 (83)
Q Consensus 31 ~~~gltq~ela~~~gis~~~is~iE~G 57 (83)
....-||+++|..+|+|++|||++|..
T Consensus 195 ~~~e~tqk~vad~lGisqsyisrlek~ 221 (234)
T TIGR02835 195 GGTEKTQKEVADLLGISQSYISRLEKR 221 (234)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 772146788898862468999999999
No 76
>pfam04545 Sigma70_r4 Sigma-70, region 4. Region 4 of sigma-70 like sigma-factors are 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.
Probab=92.81 E-value=0.11 Score=30.77 Aligned_cols=33 Identities=24% Similarity=0.353 Sum_probs=28.4
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 999999983994999999863429999887558
Q gi|254781147|r 25 NFRNIRKEAKLTQKEIRNRTGFAQSWISELETG 57 (83)
Q Consensus 25 ~ir~~R~~~gltq~ela~~~gis~~~is~iE~G 57 (83)
.|-.+|.-.|+|+.|+|+.+|+|.++++++++.
T Consensus 11 ~ii~l~y~~~~t~~EIA~~lgis~~~V~~~~~r 43 (50)
T pfam04545 11 EVLVLRFGEGLTLEEIGERLGISRERVRQIEKR 43 (50)
T ss_pred HHHHHHCCCCCHHHHHHHHHCCCHHHHHHHHHH
T ss_conf 999987068824999999989799999999999
No 77
>COG1513 CynS Cyanate lyase [Inorganic ion transport and metabolism]
Probab=92.67 E-value=0.74 Score=25.91 Aligned_cols=62 Identities=13% Similarity=0.217 Sum_probs=56.0
Q ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHH
Q ss_conf 99999999999998399499999986342999988755899944899999999928999996
Q gi|254781147|r 19 RMIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLWKL 80 (83)
Q Consensus 19 ~~~~g~~ir~~R~~~gltq~ela~~~gis~~~is~iE~G~~~~~~~~l~~la~al~i~~~~l 80 (83)
+..++..|-...+.+|+|-++++..+|.+..++...--|+...+.+....++++||.+=+.+
T Consensus 6 i~~l~~~ll~~Kk~kgLsfaDl~~~lG~~ev~vaa~~ygq~~~~~~ear~v~e~L~L~~~~v 67 (151)
T COG1513 6 ILDLADALLLAKKKKGLSFADLADGLGLAEVFVAAALYGQAALPADEARAVGEALDLDEDAI 67 (151)
T ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHCCCHHHH
T ss_conf 89999999997875499699997550833999999997620289999999999819987889
No 78
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=91.96 E-value=0.18 Score=29.57 Aligned_cols=32 Identities=38% Similarity=0.495 Sum_probs=26.4
Q ss_pred HHHHHH----HCCCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 999999----83994999999863429999887558
Q gi|254781147|r 26 FRNIRK----EAKLTQKEIRNRTGFAQSWISELETG 57 (83)
Q Consensus 26 ir~~R~----~~gltq~ela~~~gis~~~is~iE~G 57 (83)
|-.+|- ...+||+|+|+.+|||+..|++||.-
T Consensus 191 Ii~lRfGL~~~~~~Tl~EIa~~lgISrerVrQIe~~ 226 (239)
T PRK08301 191 IMELRFGLAGGEEKTQKEVADMLGISQSYISRLEKR 226 (239)
T ss_pred HHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 999995788998406999999989789999999999
No 79
>pfam02001 DUF134 Protein of unknown function DUF134. This family of archaeal proteins has no known function.
Probab=91.92 E-value=0.11 Score=30.73 Aligned_cols=27 Identities=22% Similarity=0.166 Sum_probs=23.9
Q ss_pred HHHCCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 998399499999986342999988755
Q gi|254781147|r 30 RKEAKLTQKEIRNRTGFAQSWISELET 56 (83)
Q Consensus 30 R~~~gltq~ela~~~gis~~~is~iE~ 56 (83)
---.|+||+|-|+++|||++|+++|-.
T Consensus 48 ~D~egl~QeeaA~~MgVSR~Tf~ril~ 74 (100)
T pfam02001 48 VDYEDYTQEEAAKLMGISRRTVWRLLT 74 (100)
T ss_pred HHHCCCCHHHHHHHCCCCHHHHHHHHH
T ss_conf 736079899999884976999999999
No 80
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=91.55 E-value=0.22 Score=29.04 Aligned_cols=32 Identities=19% Similarity=0.286 Sum_probs=28.2
Q ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 99999983994999999863429999887558
Q gi|254781147|r 26 FRNIRKEAKLTQKEIRNRTGFAQSWISELETG 57 (83)
Q Consensus 26 ir~~R~~~gltq~ela~~~gis~~~is~iE~G 57 (83)
|-.++-..++|++|+|+.+|||++-||+|++.
T Consensus 189 Vi~l~y~e~ltlkEIa~~LgvS~~RVsQi~~k 220 (229)
T PRK12427 189 ILHLYYQQELSMKEIAQVLDLTEARICQLNKK 220 (229)
T ss_pred HHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 99998058998999999979889999999999
No 81
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=91.40 E-value=0.25 Score=28.70 Aligned_cols=34 Identities=26% Similarity=0.308 Sum_probs=29.2
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 9999999983994999999863429999887558
Q gi|254781147|r 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISELETG 57 (83)
Q Consensus 24 ~~ir~~R~~~gltq~ela~~~gis~~~is~iE~G 57 (83)
+.|-.+|--.++|+.|+|+.+|||+..|++||+.
T Consensus 220 r~Vi~lry~e~~Tl~EIa~~lGiSreRVrQIe~~ 253 (263)
T PRK07122 220 RTVLVLRFFESMTQTQIAERVGISQMHVSRLLAK 253 (263)
T ss_pred HHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 9999999569998999999989799999999999
No 82
>PRK05572 sporulation sigma factor SigF; Validated
Probab=90.97 E-value=0.28 Score=28.46 Aligned_cols=33 Identities=30% Similarity=0.298 Sum_probs=28.5
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 999999983994999999863429999887558
Q gi|254781147|r 25 NFRNIRKEAKLTQKEIRNRTGFAQSWISELETG 57 (83)
Q Consensus 25 ~ir~~R~~~gltq~ela~~~gis~~~is~iE~G 57 (83)
.|-.+|...+.|++|+|+.+|||+..|++||+.
T Consensus 208 ~Vi~~ry~~~~tl~EIa~~lgiS~eRVrQI~~~ 240 (251)
T PRK05572 208 LIIYLRYFKDKTQSEVAKRLGISQVQVSRLEKK 240 (251)
T ss_pred HHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 999998178988999999979799999999999
No 83
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=90.94 E-value=0.3 Score=28.23 Aligned_cols=31 Identities=26% Similarity=0.174 Sum_probs=27.6
Q ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 9999998399499999986342999988755
Q gi|254781147|r 26 FRNIRKEAKLTQKEIRNRTGFAQSWISELET 56 (83)
Q Consensus 26 ir~~R~~~gltq~ela~~~gis~~~is~iE~ 56 (83)
|-.+|.-.++|++|+|+.+|||+..||+++.
T Consensus 211 Il~~ry~~~~tl~EIa~~lgvS~~rVsqi~~ 241 (256)
T PRK07408 211 VLEFVFLHDLTQKEAAERLGISPVTVSRRVK 241 (256)
T ss_pred HHHHHHCCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 9999963799899999897989999999999
No 84
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=90.90 E-value=0.3 Score=28.26 Aligned_cols=32 Identities=28% Similarity=0.313 Sum_probs=27.7
Q ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 99999983994999999863429999887558
Q gi|254781147|r 26 FRNIRKEAKLTQKEIRNRTGFAQSWISELETG 57 (83)
Q Consensus 26 ir~~R~~~gltq~ela~~~gis~~~is~iE~G 57 (83)
|-.+|.-.++|++++|+.+|||+..|++||+.
T Consensus 213 Ii~lry~~~~t~~eIa~~lGiS~eRVrQi~~~ 244 (257)
T PRK08583 213 IIQCTFIENLSQKETGERLGISQMHVSRLQRQ 244 (257)
T ss_pred HHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 99999579999999999989699999999999
No 85
>COG2973 TrpR Trp operon repressor [Transcription]
Probab=90.81 E-value=0.95 Score=25.27 Aligned_cols=42 Identities=21% Similarity=0.276 Sum_probs=33.0
Q ss_pred HHHHHHHHHHHHH--HHCCCCHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf 9999999999999--98399499999986342999988755899
Q gi|254781147|r 18 ERMIFVNNFRNIR--KEAKLTQKEIRNRTGFAQSWISELETGKS 59 (83)
Q Consensus 18 ~~~~~g~~ir~~R--~~~gltq~ela~~~gis~~~is~iE~G~~ 59 (83)
+++.+|.+++..+ .+..+||.|++...|+|..+|.+=-|.-.
T Consensus 42 EReal~~Rv~Iv~eLL~ge~sQREi~~~LgvsiAtITRGSN~LK 85 (103)
T COG2973 42 EREALGTRVRIVEELLRGELSQREIAQKLGVSIATITRGSNSLK 85 (103)
T ss_pred HHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHCCCHHHHC
T ss_conf 89999999999999995635399999985862565504444423
No 86
>TIGR02147 Fsuc_second hypothetical protein, TIGR02147; InterPro: IPR011873 This family consists of the 40 members of a paralogous protein family in the rumen anaerobe Fibrobacter succinogenes S85. Member proteins are about 270 residues long and appear to lack signal sequences and transmembrane helices. The only perfectly conserved residue is a glycine in an otherwise poorly conserved region, suggesting members are not enzymes. The family is not characterised..
Probab=90.70 E-value=0.16 Score=29.94 Aligned_cols=46 Identities=15% Similarity=0.358 Sum_probs=41.6
Q ss_pred HHCCCCHHHHHHHHHHHH--HHHHHHHCCCCCCCHHHHHHHHHHHCCC
Q ss_conf 983994999999863429--9998875589994489999999992899
Q gi|254781147|r 31 KEAKLTQKEIRNRTGFAQ--SWISELETGKSTINIDNMIILAHTLDTP 76 (83)
Q Consensus 31 ~~~gltq~ela~~~gis~--~~is~iE~G~~~~~~~~l~~la~al~i~ 76 (83)
...-+|-..+|+++|.|. +++.+|=.|+.+.|...+.+++++|+..
T Consensus 24 ~~~~FS~R~fa~KaGfsS~r~~~~~~~~GK~~Lt~~~i~k~~~~l~Ld 71 (281)
T TIGR02147 24 TDRAFSWRSFAEKAGFSSKRSYLKRIIKGKKNLTKRMIPKFAEALGLD 71 (281)
T ss_pred CCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf 154330899998648898777888998666753000357666552467
No 87
>TIGR01950 SoxR redox-sensitive transcriptional activator SoxR; InterPro: IPR010211 SoxR is a MerR-family homodimeric transcription factor with a 2Fe-2S cluster in each monomer. The motif CIGCGCxxxxxC is conserved. Oxidation of the iron-sulphur cluster activates SoxR. The physiological role in Escherichia coli is response to oxidative stress. It is activated by superoxide, singlet oxygen, nitric oxide (NO), and hydrogen peroxide. In Escherichia coli, SoxR increases expression of transcription factor SoxS; different downstream targets may exist in other species.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0005506 iron ion binding, 0006118 electron transport, 0006355 regulation of transcription DNA-dependent, 0006979 response to oxidative stress.
Probab=90.52 E-value=0.26 Score=28.60 Aligned_cols=46 Identities=26% Similarity=0.311 Sum_probs=36.7
Q ss_pred CCHHHHHHHHHHHHHHHHHHHCCC-----------CC-----CCHHHHHHHHHHHCCCHHHH
Q ss_conf 949999998634299998875589-----------99-----44899999999928999996
Q gi|254781147|r 35 LTQKEIRNRTGFAQSWISELETGK-----------ST-----INIDNMIILAHTLDTPLWKL 80 (83)
Q Consensus 35 ltq~ela~~~gis~~~is~iE~G~-----------~~-----~~~~~l~~la~al~i~~~~l 80 (83)
||.-+||+++||..|.+.-||.-- +. .---.+.|+|+..|+|+.+.
T Consensus 2 lTvG~lA~R~GVAVSALHFYE~KGLI~S~Rn~GnQRRy~Rd~LRRVa~Ik~AQ~vGipL~~I 63 (142)
T TIGR01950 2 LTVGELAKRAGVAVSALHFYESKGLIHSVRNAGNQRRYKRDVLRRVAVIKVAQRVGIPLAEI 63 (142)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHCCCEECCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCHHHH
T ss_conf 86101655655788877654103561011368883423200111567433233258988899
No 88
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family; InterPro: IPR014284 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 recognized by the major sigma factors , . This entry is found in all varieties of the sigma-70 type sigma factors, including the ECF subfamily. A number of sigma factors have names with a different number than 70 (i.e. sigma-38), but in fact, all except for the Sigma-54 family (IPR000394 from INTERPRO) are included within this entry. ; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=90.38 E-value=0.41 Score=27.43 Aligned_cols=34 Identities=18% Similarity=0.135 Sum_probs=29.3
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 9999999998399499999986342999988755
Q gi|254781147|r 23 VNNFRNIRKEAKLTQKEIRNRTGFAQSWISELET 56 (83)
Q Consensus 23 g~~ir~~R~~~gltq~ela~~~gis~~~is~iE~ 56 (83)
-+.+-.++.-.|+|++|+|+.+|||.++|++..+
T Consensus 119 ~r~~~~l~~~~~~s~~eIA~~lg~s~~~v~~~~~ 152 (162)
T TIGR02937 119 EREVLVLRYLEGLSYKEIAEILGISEGTVKSRLK 152 (162)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 9999999997189988999986899999999999
No 89
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=90.35 E-value=0.33 Score=28.04 Aligned_cols=33 Identities=30% Similarity=0.306 Sum_probs=28.2
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 999999983994999999863429999887558
Q gi|254781147|r 25 NFRNIRKEAKLTQKEIRNRTGFAQSWISELETG 57 (83)
Q Consensus 25 ~ir~~R~~~gltq~ela~~~gis~~~is~iE~G 57 (83)
.|-.+|-..++|++++|+.+|||+..|++||..
T Consensus 215 ~Il~lry~e~~Tl~eIa~~lgiS~eRVrQie~~ 247 (261)
T PRK06288 215 KVITLYYYEDLTLKEIGEVLGVTESRISQIHTK 247 (261)
T ss_pred HHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 999998079988999999979789999999999
No 90
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=90.34 E-value=0.36 Score=27.80 Aligned_cols=33 Identities=30% Similarity=0.334 Sum_probs=27.9
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 999999983994999999863429999887558
Q gi|254781147|r 25 NFRNIRKEAKLTQKEIRNRTGFAQSWISELETG 57 (83)
Q Consensus 25 ~ir~~R~~~gltq~ela~~~gis~~~is~iE~G 57 (83)
.|-..|--.+.|+.|+|+.+|||+..|++||+.
T Consensus 216 ~Ii~~ry~~~~Tl~eIa~~lGvSreRVrQie~~ 248 (257)
T PRK08215 216 MILNLRFFQGKTQMEVADEIGISQAQVSRLEKA 248 (257)
T ss_pred HHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 999999479998999999989699999999999
No 91
>TIGR02405 trehalos_R_Ecol trehalose operon repressor; InterPro: IPR012771 Trehalose is a non-reducing disaccharide which can be used as both a carbon source and an osmoprotectant in bacteria. Trehalose uptake into the cytoplasm occurs via a trehalose-specific phosphotransferase system which phosphorylates trehalase to trehalose-6-phosphate (Tre6P) during transport into the cytoplasm, and a hydrolase which hydrolyses Tre6P to glucose and glucose-6-phophate. This entry represents LacI-type TreR, a transcriptional repressor of trehalose uptake found mainly within the gamma-proteobacteria. It does not include the GntR-type TreR's such as those found in Bacillus species. It is capable of binding both the inducer Tre6P and trehalose. Binding of trehalose does not affect the repressor's affinity for its DNA binding site, while binding Tre6P substantially reduces its affinity. The repression activity of TreR is therefore regulated by the ratio of trehalose to Tre6P within the cell . The protein is composed of two domains, an N-terminal DNA-binding helix-turn-helix domain, and a C-terminal effector-binding domain which is homologous to that of LacI. The effector-binding domain is composed of two subdomains, both of which form an alpha-beta-alpha sandwhich, with the effector binding site located at the interface of these subdomains . Tre6P and trehalose bind competitively to this site, with the affinty for trehalose substantially lower than that for Tre6P.; GO: 0003677 DNA binding, 0016566 specific transcriptional repressor activity, 0005991 trehalose metabolic process, 0016481 negative regulation of transcription.
Probab=90.06 E-value=0.11 Score=30.72 Aligned_cols=41 Identities=24% Similarity=0.338 Sum_probs=33.4
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHC
Q ss_conf 99499999986342999988755899944899999999928
Q gi|254781147|r 34 KLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLD 74 (83)
Q Consensus 34 gltq~ela~~~gis~~~is~iE~G~~~~~~~~l~~la~al~ 74 (83)
+||..|.|+.+||+.||+||+-|....++..+=+++-...+
T Consensus 1 kLTIkDIArLagVgKSTVSRVLnNe~~V~~~tRERVE~viq 41 (311)
T TIGR02405 1 KLTIKDIARLAGVGKSTVSRVLNNESKVSIETRERVEAVIQ 41 (311)
T ss_pred CCHHHHHHHHHCCCCEEEEEEEECCCCCCCHHHHHHHHHHH
T ss_conf 96177769770886202331561688887203368888875
No 92
>PRK04217 hypothetical protein; Provisional
Probab=89.92 E-value=0.23 Score=28.93 Aligned_cols=32 Identities=28% Similarity=0.352 Sum_probs=25.6
Q ss_pred HHHHH--HHCCCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 99999--983994999999863429999887558
Q gi|254781147|r 26 FRNIR--KEAKLTQKEIRNRTGFAQSWISELETG 57 (83)
Q Consensus 26 ir~~R--~~~gltq~ela~~~gis~~~is~iE~G 57 (83)
+-.+| --.|++|+|-|+++|||++++++|-..
T Consensus 48 ~EaiRL~D~egl~qeeaA~~M~VSR~Tf~ril~~ 81 (110)
T PRK04217 48 FEALRLVDYEGLTQEEAGKRMGVSRGTVWRALTS 81 (110)
T ss_pred HHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHHH
T ss_conf 9999987360798999998849769999999999
No 93
>TIGR02417 fruct_sucro_rep D-fructose-responsive transcription factor; InterPro: IPR012781 Members of this family belong the lacI helix-turn-helix family of DNA-binding transcriptional regulators. All members are from the proteobacteria. Characterised members act as positive and negative transcriptional regulators of fructose and sucrose transport and metabolism. Sucrose is a disaccharide composed of fructose and glucose; D-fructose-1-phosphate rather than an intact sucrose moiety has been shown to act as the inducer.; GO: 0003677 DNA binding, 0006355 regulation of transcription DNA-dependent, 0009750 response to fructose stimulus, 0045449 regulation of transcription.
Probab=89.85 E-value=0.21 Score=29.13 Aligned_cols=42 Identities=17% Similarity=0.223 Sum_probs=31.6
Q ss_pred CHHHHHHHHHHHHHHHHHHHCCCCC---CCHHH---HHHHHHHHCCCH
Q ss_conf 4999999863429999887558999---44899---999999928999
Q gi|254781147|r 36 TQKEIRNRTGFAQSWISELETGKST---INIDN---MIILAHTLDTPL 77 (83)
Q Consensus 36 tq~ela~~~gis~~~is~iE~G~~~---~~~~~---l~~la~al~i~~ 77 (83)
|..|.|+.+|||.+|.|-+=||+.. ++-+| +..+++..|..+
T Consensus 1 tL~dIA~LAGVS~TTASyViNGka~~~Ris~~T~erV~Avv~e~~Y~P 48 (335)
T TIGR02417 1 TLDDIAKLAGVSKTTASYVINGKAKEYRISEETVERVMAVVEEQGYKP 48 (335)
T ss_pred CCHHHHHHCCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf 900576660823232212000431110136787889999898737857
No 94
>PRK13869 plasmid-partitioning protein RepA; Provisional
Probab=89.82 E-value=1.8 Score=23.67 Aligned_cols=70 Identities=13% Similarity=0.219 Sum_probs=55.5
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHH----------CCCCHHHHHHHHHHHHHHHHHH------------HCCCCCCC
Q ss_conf 8888868989999999999999999998----------3994999999863429999887------------55899944
Q gi|254781147|r 5 KRDEPHLSDAILRERMIFVNNFRNIRKE----------AKLTQKEIRNRTGFAQSWISEL------------ETGKSTIN 62 (83)
Q Consensus 5 ~~~~p~~~~~~~~~~~~~g~~ir~~R~~----------~gltq~ela~~~gis~~~is~i------------E~G~~~~~ 62 (83)
+.+.|.....+......++..+..+|.+ +.+|-.|+|+.+||+.+++.+. ++|.+.-+
T Consensus 9 ~~~~~~~~~~i~~~a~~ls~~l~~~r~~~~~P~~~K~lr~fs~~e~a~l~gv~~~~lr~~~~~g~~p~p~~~~~grr~yt 88 (405)
T PRK13869 9 RNDRPSVDVTIGEHAEQLSSQLQAMSEALFPPTSHKSLRKFTSGEAARLMKISDSTLRKMTLAGEGPQPELASNGRRFYT 88 (405)
T ss_pred HCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCCEEC
T ss_conf 24897753899999999999999999850899665665878889999996969999999986599999987899854301
Q ss_pred HHHHHHHHHHHC
Q ss_conf 899999999928
Q gi|254781147|r 63 IDNMIILAHTLD 74 (83)
Q Consensus 63 ~~~l~~la~al~ 74 (83)
++.+..+-+.|+
T Consensus 89 l~~i~~lR~~l~ 100 (405)
T PRK13869 89 LGQINEIRGMLA 100 (405)
T ss_pred HHHHHHHHHHHH
T ss_conf 999999999997
No 95
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=89.45 E-value=0.56 Score=26.65 Aligned_cols=33 Identities=15% Similarity=0.087 Sum_probs=27.8
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 999999999839949999998634299998875
Q gi|254781147|r 23 VNNFRNIRKEAKLTQKEIRNRTGFAQSWISELE 55 (83)
Q Consensus 23 g~~ir~~R~~~gltq~ela~~~gis~~~is~iE 55 (83)
-+.+-.++.-.|+|+.|+|+.+|||.+++-++-
T Consensus 132 ~R~vF~L~r~eGls~~EIAe~LgiS~~tV~~~l 164 (178)
T PRK12529 132 VKQAFLMATLDGMKQKDIAQALDIALPTVKKYI 164 (178)
T ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 889987998829999999999895999999999
No 96
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=89.17 E-value=0.42 Score=27.38 Aligned_cols=32 Identities=22% Similarity=0.242 Sum_probs=27.4
Q ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 99999983994999999863429999887558
Q gi|254781147|r 26 FRNIRKEAKLTQKEIRNRTGFAQSWISELETG 57 (83)
Q Consensus 26 ir~~R~~~gltq~ela~~~gis~~~is~iE~G 57 (83)
|-.+|...++|++++|+.+|||+..|++||..
T Consensus 205 Vl~l~y~e~~Tl~eIa~~lgvS~erVrQi~~~ 236 (250)
T PRK07670 205 VISLFYKEELTLTEIGQVLNLSTSRISQIHSK 236 (250)
T ss_pred HHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 99997489868999999989799999999999
No 97
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=89.04 E-value=0.43 Score=27.33 Aligned_cols=32 Identities=22% Similarity=0.267 Sum_probs=28.1
Q ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 99999983994999999863429999887558
Q gi|254781147|r 26 FRNIRKEAKLTQKEIRNRTGFAQSWISELETG 57 (83)
Q Consensus 26 ir~~R~~~gltq~ela~~~gis~~~is~iE~G 57 (83)
|-.+|....+|++|+|+.+|||+..|++||..
T Consensus 213 Ii~lry~e~~Tl~EIg~~lgvS~eRVrQi~~~ 244 (257)
T PRK05911 213 VMALYYYEELVLKEIGKILGVSESRVSQIHSK 244 (257)
T ss_pred HHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 99987489878999998979889999999999
No 98
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=89.01 E-value=0.53 Score=26.78 Aligned_cols=33 Identities=15% Similarity=-0.141 Sum_probs=28.7
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 999999983994999999863429999887558
Q gi|254781147|r 25 NFRNIRKEAKLTQKEIRNRTGFAQSWISELETG 57 (83)
Q Consensus 25 ~ir~~R~~~gltq~ela~~~gis~~~is~iE~G 57 (83)
.+-.++--.|+|+.|+|+.+|+|.+++.++++.
T Consensus 113 ~ii~~~~~~g~t~~EIA~~~gis~~~Vk~~~r~ 145 (154)
T PRK06759 113 YIIFERFFVGKTMGEIALETEMTYYQVRWIYRQ 145 (154)
T ss_pred HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 999999996998999999989899999999999
No 99
>pfam05339 DUF739 Protein of unknown function (DUF739). This family contains several bacteriophage proteins. Some of the proteins in this family have been labeled putative cro repressor proteins.
Probab=88.99 E-value=1.6 Score=23.97 Aligned_cols=50 Identities=16% Similarity=0.044 Sum_probs=45.8
Q ss_pred HHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHH
Q ss_conf 98399499999986342999988755899944899999999928999996
Q gi|254781147|r 31 KEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLWKL 80 (83)
Q Consensus 31 ~~~gltq~ela~~~gis~~~is~iE~G~~~~~~~~l~~la~al~i~~~~l 80 (83)
.++--||..+|..+|+|..++|.=-||+..-..+...+.++.|++|.+++
T Consensus 13 ~Ek~gtq~~Fa~~lg~se~tlslkln~~v~w~q~ei~kai~lL~i~~d~i 62 (69)
T pfam05339 13 LEKYGTQYNFASAIGLSERSLSLKLNDKVIWVANEIEKAIDLLGIPKDDI 62 (69)
T ss_pred HHHHCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHH
T ss_conf 89956798999995811768889876867753999999999968998887
No 100
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=88.71 E-value=0.48 Score=27.03 Aligned_cols=32 Identities=22% Similarity=0.330 Sum_probs=27.1
Q ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 99999983994999999863429999887558
Q gi|254781147|r 26 FRNIRKEAKLTQKEIRNRTGFAQSWISELETG 57 (83)
Q Consensus 26 ir~~R~~~gltq~ela~~~gis~~~is~iE~G 57 (83)
|-.+|-..++|++|+|+.+|||+..|++||+.
T Consensus 191 Ii~l~y~~~~tl~eIa~~lgiS~eRVrQie~~ 222 (234)
T PRK06986 191 VLSLYYDEELNLKEIGAVLGVSESRVSQIHSQ 222 (234)
T ss_pred HHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 99987389989999999979789999999999
No 101
>pfam08965 DUF1870 Domain of unknown function (DUF1870). This domain is found in a set of hypothetical bacterial proteins.
Probab=88.62 E-value=1.2 Score=24.58 Aligned_cols=48 Identities=23% Similarity=0.179 Sum_probs=41.3
Q ss_pred HHHHHHHHHCCCCHHHHHHHHH--HHHHHHHHHHCCCCCCCHHHHHHHHH
Q ss_conf 9999999983994999999863--42999988755899944899999999
Q gi|254781147|r 24 NNFRNIRKEAKLTQKEIRNRTG--FAQSWISELETGKSTINIDNMIILAH 71 (83)
Q Consensus 24 ~~ir~~R~~~gltq~ela~~~g--is~~~is~iE~G~~~~~~~~l~~la~ 71 (83)
..|..+|+-.-||..|-|.-+| .+..+..++|+|...+..+...++..
T Consensus 3 ~ELQAlR~if~mti~EaA~~I~~~~~s~~Wq~WE~G~~~IP~~i~~~~~~ 52 (117)
T pfam08965 3 NELQALRKILFLTIVEAAELIGQSVSSRTWQRWEKGDIAIPDEVEAKLRK 52 (117)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCCCCHHHHHHHHH
T ss_conf 78999999999649999999946888899999975898899999999999
No 102
>PRK01381 Trp operon repressor; Provisional
Probab=88.56 E-value=0.85 Score=25.56 Aligned_cols=54 Identities=20% Similarity=0.150 Sum_probs=37.4
Q ss_pred HHHHHHHHHHHHHH-HHCC-CCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHH
Q ss_conf 99999999999999-9839-949999998634299998875589994489999999
Q gi|254781147|r 17 RERMIFVNNFRNIR-KEAK-LTQKEIRNRTGFAQSWISELETGKSTINIDNMIILA 70 (83)
Q Consensus 17 ~~~~~~g~~ir~~R-~~~g-ltq~ela~~~gis~~~is~iE~G~~~~~~~~l~~la 70 (83)
.++..++.+++..+ ..+| +||.++|+..|+|.++|.+=-|--...+.+.-.-+.
T Consensus 36 ~Er~al~~R~~I~~~Ll~ge~sQReIa~~lgvsiAtITRGSn~LK~~~~~~k~~l~ 91 (99)
T PRK01381 36 DEREALGTRVRIVEELLRGELSQREIKQELGVGIATITRGSNSLKTAPPEFKEWLE 91 (99)
T ss_pred HHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCEECCCCHHHHHCCCHHHHHHHH
T ss_conf 99999999999999999487649999998497402000026988539999999999
No 103
>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=88.50 E-value=0.52 Score=26.82 Aligned_cols=26 Identities=23% Similarity=0.148 Sum_probs=23.0
Q ss_pred HHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 99983994999999863429999887
Q gi|254781147|r 29 IRKEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 29 ~R~~~gltq~ela~~~gis~~~is~i 54 (83)
.+.+.|.|..++|+..|||+++|.++
T Consensus 16 ~l~~~G~~~~~iA~~~GVsr~Tiyr~ 41 (42)
T cd00569 16 RLLAAGESVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred HHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 99997898999999979799999865
No 104
>COG1342 Predicted DNA-binding proteins [General function prediction only]
Probab=88.41 E-value=0.44 Score=27.24 Aligned_cols=38 Identities=26% Similarity=0.206 Sum_probs=28.3
Q ss_pred HHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHH
Q ss_conf 999839949999998634299998875589994489999999992
Q gi|254781147|r 29 IRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTL 73 (83)
Q Consensus 29 ~R~~~gltq~ela~~~gis~~~is~iE~G~~~~~~~~l~~la~al 73 (83)
+.-..++||+|.|.++|||++++.+.-+. --.++|++|
T Consensus 44 LvD~~~l~QeeAA~rMgISr~Tfwr~l~s-------AR~KvA~aL 81 (99)
T COG1342 44 LVDYEGLTQEEAALRMGISRQTFWRLLTS-------ARKKVADAL 81 (99)
T ss_pred HHHHHHCCHHHHHHHHCCCHHHHHHHHHH-------HHHHHHHHH
T ss_conf 88686105789999846429999999999-------999999998
No 105
>cd01108 HTH_CueR Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators. Helix-turn-helix (HTH) transcription regulators CueR and ActP, copper efflux regulators. In Bacillus subtilis, copper induced CueR regulates the copZA operon, preventing copper toxicity. In Rhizobium leguminosarum, ActP controls copper homeostasis; it detects cytoplasmic copper stress and activates transcription in response to increasing copper concentrations. These proteins are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have two conserved cysteines that define a monovalent copper ion binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements
Probab=88.39 E-value=1.4 Score=24.28 Aligned_cols=46 Identities=22% Similarity=0.163 Sum_probs=29.4
Q ss_pred CCHHHHHHHHHHHHHHHHHHHCCC------------CCCCHH-----HHHHHHHHHCCCHHHH
Q ss_conf 949999998634299998875589------------994489-----9999999928999996
Q gi|254781147|r 35 LTQKEIRNRTGFAQSWISELETGK------------STINID-----NMIILAHTLDTPLWKL 80 (83)
Q Consensus 35 ltq~ela~~~gis~~~is~iE~G~------------~~~~~~-----~l~~la~al~i~~~~l 80 (83)
||..|+|+.+|+|..+|.-||.-- +.-+.+ .+.+.++.+|.++.+.
T Consensus 1 M~Ige~Ak~~gvs~~tlRyYe~~GLl~p~~r~~~gyR~Y~~~~~~~l~~I~~~r~~G~sL~eI 63 (127)
T cd01108 1 MNIGEAAKLTGLSAKMIRYYEEIGLIPPPSRSDNGYRVYNQRDIEELRFIRRARDLGFSLEEI 63 (127)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCHHHH
T ss_conf 978999999895999999999858989865199998425199999999999999879989999
No 106
>pfam08535 KorB KorB domain. This family consists of 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.
Probab=88.37 E-value=0.97 Score=25.24 Aligned_cols=46 Identities=20% Similarity=0.294 Sum_probs=32.9
Q ss_pred HCCCCHHHHHHHHHHHHHHHHHH--------------HCCCCCCCHHHHHHHHHHHCCCHH
Q ss_conf 83994999999863429999887--------------558999448999999999289999
Q gi|254781147|r 32 EAKLTQKEIRNRTGFAQSWISEL--------------ETGKSTINIDNMIILAHTLDTPLW 78 (83)
Q Consensus 32 ~~gltq~ela~~~gis~~~is~i--------------E~G~~~~~~~~l~~la~al~i~~~ 78 (83)
..|++|.++|+.+|-|.++||+. .+|. .-++.+|..|..++...+.
T Consensus 1 ~~G~kk~~IAk~LGks~s~VS~hlaL~d~Pd~l~~l~~~g~-~~dv~~l~eL~~~~~k~p~ 60 (93)
T pfam08535 1 AKGVKQAEIAKKLGKSKSFVSQHLALLDMPDCIREAYDSGR-CSDIRALYELRRAARKHPE 60 (93)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHCCCHHHHHHHHCCC-CCCHHHHHHHHHHHHHCHH
T ss_conf 99877999999978898899999998348699999987477-6879999999999997999
No 107
>cd04774 HTH_YfmP Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator. Helix-turn-helix (HTH) transcription regulator, YfmP, and related proteins; N-terminal domain. YfmP regulates the multidrug efflux protein, YfmO, and indirectly regulates the expression of the Bacillus subtilis copZA operon encoding a metallochaperone, CopZ, and a CPx-type ATPase efflux protein, CopA. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=88.29 E-value=1.5 Score=24.03 Aligned_cols=46 Identities=15% Similarity=0.195 Sum_probs=30.1
Q ss_pred CCHHHHHHHHHHHHHHHHHHHC-----------CCCCCCHHHHH------HHHHHHCCCHHHH
Q ss_conf 9499999986342999988755-----------89994489999------9999928999996
Q gi|254781147|r 35 LTQKEIRNRTGFAQSWISELET-----------GKSTINIDNMI------ILAHTLDTPLWKL 80 (83)
Q Consensus 35 ltq~ela~~~gis~~~is~iE~-----------G~~~~~~~~l~------~la~al~i~~~~l 80 (83)
+|..|+|+++|+|.++|.-||. |.+.-+-..+. .+.+.+|.++.+.
T Consensus 1 ytIgevA~~~Gvs~~tlRyYE~~GLl~P~R~~~gyR~Y~~~dl~rL~~I~~l~~~lGfsL~eI 63 (96)
T cd04774 1 YKVDEVAKRLGLTKRTLKYYEEIGLVSPERSEGRYRLYSEEDLKRLERILRLREVLGFSLQEV 63 (96)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCHHHH
T ss_conf 948899999897999999999879989986999982359999999999999999579989999
No 108
>cd04789 HTH_Cfa Helix-Turn-Helix DNA binding domain of the Cfa transcription regulator. Putative helix-turn-helix (HTH) MerR-like transcription regulator; the N-terminal domain of Cfa, a cyclopropane fatty acid synthase and other related methyltransferases. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=87.67 E-value=1.8 Score=23.58 Aligned_cols=46 Identities=17% Similarity=0.154 Sum_probs=33.3
Q ss_pred CCHHHHHHHHHHHHHHHHHHH-----------CCCCCCCHHH-----HHHHHHHHCCCHHHH
Q ss_conf 949999998634299998875-----------5899944899-----999999928999996
Q gi|254781147|r 35 LTQKEIRNRTGFAQSWISELE-----------TGKSTINIDN-----MIILAHTLDTPLWKL 80 (83)
Q Consensus 35 ltq~ela~~~gis~~~is~iE-----------~G~~~~~~~~-----l~~la~al~i~~~~l 80 (83)
||..|+|+++|+|.++|.-|| ||-+.-+.+. ..+.++.+|+++.+.
T Consensus 2 ~~Ige~A~~~gvs~~TlRyYe~~GLl~~~R~~ngyR~Y~~~~l~~l~~I~~lr~~G~sL~eI 63 (102)
T cd04789 2 YTISELAEKAGISRSTLLYYEKLGLITGTRNANGYRLYPDSDLQRLLLIQQLQAGGLSLKEC 63 (102)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCHHHH
T ss_conf 80999999989799999999986998988199999506999999999999999979989999
No 109
>cd04768 HTH_BmrR-like Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators. Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=87.62 E-value=1.6 Score=23.96 Aligned_cols=46 Identities=17% Similarity=0.243 Sum_probs=32.9
Q ss_pred CCHHHHHHHHHHHHHHHHHHHC------------CCCCCCHHH-----HHHHHHHHCCCHHHH
Q ss_conf 9499999986342999988755------------899944899-----999999928999996
Q gi|254781147|r 35 LTQKEIRNRTGFAQSWISELET------------GKSTINIDN-----MIILAHTLDTPLWKL 80 (83)
Q Consensus 35 ltq~ela~~~gis~~~is~iE~------------G~~~~~~~~-----l~~la~al~i~~~~l 80 (83)
||..|+|+.+|+|..+|.-||. |-+.-+.+. ..+.++.+|+|+.+.
T Consensus 1 ~tIge~Ak~~gvs~~tlRyYe~~GLl~p~~~~~ngyR~Y~~~~~~~l~~I~~lr~~G~~L~eI 63 (96)
T cd04768 1 LTIGEFAKLAGVSIRTLRHYDDIGLFKPAKIAENGYRYYSYAQLYQLQFILFLRELGFSLAEI 63 (96)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCEECCHHHHHHHHHHHHHHHCCCCHHHH
T ss_conf 978999999886999999998439979872499998517999999999999999979999999
No 110
>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=87.41 E-value=0.79 Score=25.77 Aligned_cols=23 Identities=26% Similarity=0.224 Sum_probs=20.4
Q ss_pred CCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 94999999863429999887558
Q gi|254781147|r 35 LTQKEIRNRTGFAQSWISELETG 57 (83)
Q Consensus 35 ltq~ela~~~gis~~~is~iE~G 57 (83)
||-.|+|+.+|||.++|.+|+.-
T Consensus 1 lt~~e~A~~lgVs~~TlrrW~~~ 23 (49)
T cd04762 1 LTTKEAAELLGVSPSTLRRWVKE 23 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHC
T ss_conf 98899999979899999999987
No 111
>cd04781 HTH_MerR-like_sg6 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 6) with at least two conserved cysteines present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, an
Probab=87.20 E-value=1.2 Score=24.73 Aligned_cols=46 Identities=17% Similarity=0.251 Sum_probs=30.2
Q ss_pred CCHHHHHHHHHHHHHHHHHHHCC-----------CCCCCHH-----HHHHHHHHHCCCHHHH
Q ss_conf 94999999863429999887558-----------9994489-----9999999928999996
Q gi|254781147|r 35 LTQKEIRNRTGFAQSWISELETG-----------KSTINID-----NMIILAHTLDTPLWKL 80 (83)
Q Consensus 35 ltq~ela~~~gis~~~is~iE~G-----------~~~~~~~-----~l~~la~al~i~~~~l 80 (83)
||..|+|+++|+|.++|.-||.- .+.-+-+ .+.+.++.+|.++.+.
T Consensus 1 mtIgelA~~~gvs~~TiRyYE~~GLl~~~~r~~gyR~Y~~~~l~rl~~I~~~r~lGfsL~EI 62 (120)
T cd04781 1 LDIAEVARQSGLPASTLRYYEEKGLIASIGRRGLRRQYDPQVLDRLALIALGRAAGFSLDEI 62 (120)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCHHHH
T ss_conf 96899999988688989899964980654469984158899999999999999959999999
No 112
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family; InterPro: IPR014304 This entry is a group of RNA polymerase sigma factors where one of the members is designated as SigZ in Bacillus subtilis . This group has a very sporadic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member Dechloromonas aromatica (strain RCB), that appears to have two of these sigma factors. A member of which appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri (strain ATCC 700601 / ES114), where a second one is chromosomally encoded..
Probab=87.11 E-value=0.22 Score=29.03 Aligned_cols=34 Identities=26% Similarity=0.364 Sum_probs=27.4
Q ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHH-HHHHCCCC
Q ss_conf 99999983994999999863429999-88755899
Q gi|254781147|r 26 FRNIRKEAKLTQKEIRNRTGFAQSWI-SELETGKS 59 (83)
Q Consensus 26 ir~~R~~~gltq~ela~~~gis~~~i-s~iE~G~~ 59 (83)
.-.+-.-.|+||+++|+++|+|.|.. |++-+|..
T Consensus 108 a~~L~el~G~sQ~e~A~kLGlSlSGaKSRVQRGR~ 142 (170)
T TIGR02959 108 AIRLTELEGLSQKEIAEKLGLSLSGAKSRVQRGRK 142 (170)
T ss_pred HHHHHHCCCCCHHHHHHHCCCCCCCHHHHHHHHHH
T ss_conf 98887507998279987617533515678899999
No 113
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=87.08 E-value=1.2 Score=24.61 Aligned_cols=45 Identities=9% Similarity=0.147 Sum_probs=32.3
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHC
Q ss_conf 3994999999863429999887558999448999999999289999960
Q gi|254781147|r 33 AKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLWKLL 81 (83)
Q Consensus 33 ~gltq~ela~~~gis~~~is~iE~G~~~~~~~~l~~la~al~i~~~~l~ 81 (83)
.++|++|+|+.+|||+..|++||+. .+..|.+-...-...+..||
T Consensus 244 e~~TL~EIg~~lgvSreRVRQIe~k----AL~KLR~~L~~~~~e~~~~~ 288 (289)
T PRK07500 244 DGATLEALGEELGISKERVRQIEAR----ALEKLRRALLSQSPEAAYFL 288 (289)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH----HHHHHHHHHHHHCHHHHHHH
T ss_conf 9858999999979799999999999----99999999998477988863
No 114
>pfam04552 Sigma54_DBD Sigma-54, DNA binding domain. This DNA binding domain is based on peptide fragmentation data. This domain is proximal to DNA in the promoter/holoenzyme complex. Furthermore this region contains a putative helix-turn-helix motif. At the C-terminus, there is a highly conserved region known as the RpoN box and is the signature of the sigma-54 proteins.
Probab=86.87 E-value=0.15 Score=30.02 Aligned_cols=40 Identities=23% Similarity=0.198 Sum_probs=28.8
Q ss_pred HCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHH
Q ss_conf 8399499999986342999988755899944899999999
Q gi|254781147|r 32 EAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAH 71 (83)
Q Consensus 32 ~~gltq~ela~~~gis~~~is~iE~G~~~~~~~~l~~la~ 71 (83)
-+-||+.|+|+.+|++.||||++-+|+.--+-.-+..+-.
T Consensus 47 l~PLtlk~iA~~l~lh~STVSRav~~Kyi~tp~Gi~~lk~ 86 (160)
T pfam04552 47 LRPLTLREVAEALGMHESTVSRATTNKYLATPRGLFELKY 86 (160)
T ss_pred CCCCCHHHHHHHCCCCCCHHHHHHHHHHHHCCCCEEEHHH
T ss_conf 7576199999880998106999996139767995165999
No 115
>cd01111 HTH_MerD Helix-Turn-Helix DNA binding domain of the MerD transcription regulator. Helix-turn-helix (HTH) transcription regulator MerD. The putative secondary regulator of mercury resistance (mer) operons, MerD, has been shown to down-regulate the expression of this operon in gram-negative bacteria. It binds to the same operator DNA as MerR that activates transcription of the operon in the presence of mercury ions. The MerD protein shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily, which promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are conserved and contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules such as metal ions, drugs,
Probab=86.85 E-value=1.9 Score=23.53 Aligned_cols=46 Identities=9% Similarity=0.029 Sum_probs=31.4
Q ss_pred CCHHHHHHHHHHHHHHHHHHHCCC------------CCCCHHH-----HHHHHHHHCCCHHHH
Q ss_conf 949999998634299998875589------------9944899-----999999928999996
Q gi|254781147|r 35 LTQKEIRNRTGFAQSWISELETGK------------STINIDN-----MIILAHTLDTPLWKL 80 (83)
Q Consensus 35 ltq~ela~~~gis~~~is~iE~G~------------~~~~~~~-----l~~la~al~i~~~~l 80 (83)
+|..|+|+.+|+|..+|.-||+-- +.-+-+. +.+-++.+|.++.+.
T Consensus 1 ytIgelA~~~Gvs~~TiRyYe~~GLl~~~~Rt~~GyR~Y~~~~l~rL~fI~~~r~~G~sl~eI 63 (107)
T cd01111 1 YSISQLALDAGVSVHIVRDYLLRGLLHPVARTEGGYGLFDDCALQRLRFVRAAFEAGIGLDEL 63 (107)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCHHHH
T ss_conf 958899999788948998999878989988899988135999999999999999879999999
No 116
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=86.75 E-value=0.27 Score=28.48 Aligned_cols=30 Identities=30% Similarity=0.292 Sum_probs=25.9
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf 399499999986342999988755899944
Q gi|254781147|r 33 AKLTQKEIRNRTGFAQSWISELETGKSTIN 62 (83)
Q Consensus 33 ~gltq~ela~~~gis~~~is~iE~G~~~~~ 62 (83)
+-||++++|+.+|++.||||++=+|+.--+
T Consensus 348 kPL~lkdiA~~lglheSTVSRav~~Kyi~t 377 (461)
T PRK05932 348 KPLVLKDIAEALGMHESTISRATTNKYMAT 377 (461)
T ss_pred CCCCHHHHHHHCCCCHHHHHHHHHCCEECC
T ss_conf 676399999873998125889871661148
No 117
>COG4197 Uncharacterized protein conserved in bacteria, prophage-related [Function unknown]
Probab=86.46 E-value=0.69 Score=26.11 Aligned_cols=45 Identities=11% Similarity=0.214 Sum_probs=39.4
Q ss_pred CHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHC--CCHHHH
Q ss_conf 499999986342999988755899944899999999928--999996
Q gi|254781147|r 36 TQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLD--TPLWKL 80 (83)
Q Consensus 36 tq~ela~~~gis~~~is~iE~G~~~~~~~~l~~la~al~--i~~~~l 80 (83)
.|..+|.++|+|.++++++-+|.+...-.....|..+.+ |+-.+|
T Consensus 14 ~q~a~a~LLgvsp~~vnQw~~g~r~~~a~r~~aIerAt~g~Vs~~el 60 (96)
T COG4197 14 GQKALARLLGVSPPSVNQWIKGRRQVAAERALAIERATSGQVSREEL 60 (96)
T ss_pred CHHHHHHHHCCCCHHHHHHHHHEEECCCCCCHHHHHHHCCCCCHHHH
T ss_conf 38999999726814788776520104755332899985377159997
No 118
>cd04785 HTH_CadR-PbrR-like Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators. Helix-turn-helix (HTH) CadR- and PbrR-like transcription regulators. CadR and PbrR regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which comprise a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=86.38 E-value=2.2 Score=23.08 Aligned_cols=46 Identities=24% Similarity=0.185 Sum_probs=28.7
Q ss_pred CCHHHHHHHHHHHHHHHHHHHCC------------CCCCCHHH-----HHHHHHHHCCCHHHH
Q ss_conf 94999999863429999887558------------99944899-----999999928999996
Q gi|254781147|r 35 LTQKEIRNRTGFAQSWISELETG------------KSTINIDN-----MIILAHTLDTPLWKL 80 (83)
Q Consensus 35 ltq~ela~~~gis~~~is~iE~G------------~~~~~~~~-----l~~la~al~i~~~~l 80 (83)
||..|+|+.+|+|..+|.-||.- .+.-+.+. +.+.++.+|.++.+.
T Consensus 1 m~IgelA~~~gvs~~tlRyYE~~GLl~~~~r~~~gyR~Y~~~~l~~l~~I~~~r~~GfsL~eI 63 (126)
T cd04785 1 LSIGELARRTGVNVETIRYYESIGLLPEPARTAGGYRLYGAAHVERLRFIRRARDLGFSLEEI 63 (126)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCEECCCCCCCCCHHHHHHHHHHHHHHHCCCCHHHH
T ss_conf 968999999894999999999849989870589998427899999999999999879989999
No 119
>PHA00675 hypothetical protein
Probab=86.37 E-value=1.1 Score=24.97 Aligned_cols=34 Identities=9% Similarity=0.170 Sum_probs=30.8
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999999983994999999863429999887
Q gi|254781147|r 21 IFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 21 ~~g~~ir~~R~~~gltq~ela~~~gis~~~is~i 54 (83)
..-..||.+|+..||+-..||...+++.++|.+|
T Consensus 26 ~~Vd~IR~LrE~~gl~Yg~La~~f~~pkgtIAkI 59 (78)
T PHA00675 26 AEVERIRELHEVEGMSYAVLAEKFEQSKGAIAKI 59 (78)
T ss_pred HHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 9999999999872843899999972756899999
No 120
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=86.29 E-value=1.1 Score=24.95 Aligned_cols=31 Identities=13% Similarity=0.088 Sum_probs=27.1
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999983994999999863429999887
Q gi|254781147|r 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 24 ~~ir~~R~~~gltq~ela~~~gis~~~is~i 54 (83)
+.+-.++...|+|++|+|+.+|||.+++.+.
T Consensus 125 R~vf~L~r~~gls~~EIA~~LgiS~~tVk~~ 155 (167)
T PRK12528 125 KRAFLLAQVDGLGYGEIATELGISLATVKRY 155 (167)
T ss_pred HHHHHHHHHHCCCHHHHHHHHCCCHHHHHHH
T ss_conf 9999999982989999999979799999999
No 121
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=86.20 E-value=1.2 Score=24.63 Aligned_cols=31 Identities=16% Similarity=0.129 Sum_probs=26.4
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999839949999998634299998875
Q gi|254781147|r 25 NFRNIRKEAKLTQKEIRNRTGFAQSWISELE 55 (83)
Q Consensus 25 ~ir~~R~~~gltq~ela~~~gis~~~is~iE 55 (83)
.+-.++.-.|+|++|+|+.+|||.++|.+.-
T Consensus 126 ~v~~L~~~eGls~~EIA~~LgiS~~tVk~~l 156 (172)
T PRK12523 126 AAFLYNRLDGMGHAEIAERLGVSVSRVRQYL 156 (172)
T ss_pred HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 9999999939999999999893999999999
No 122
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=86.18 E-value=0.23 Score=28.92 Aligned_cols=41 Identities=15% Similarity=0.199 Sum_probs=30.7
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHH
Q ss_conf 39949999998634299998875589994489999999992
Q gi|254781147|r 33 AKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTL 73 (83)
Q Consensus 33 ~gltq~ela~~~gis~~~is~iE~G~~~~~~~~l~~la~al 73 (83)
+-||++++|+.+|++.||||++=+|+.--+-.-++.+-..|
T Consensus 362 kPL~lkdiA~~lglheSTVSRav~~Kyi~tp~Gi~~lk~FF 402 (475)
T PRK12469 362 KPLVLRDVAEELGLHESTVSRATGNKYMATPRGTFEFKHFF 402 (475)
T ss_pred CCCCHHHHHHHHCCCCCHHHHHHCCCEECCCCCEEEHHHHH
T ss_conf 67349999998199820376886275023798546699862
No 123
>COG2842 Uncharacterized ATPase, putative transposase [General function prediction only]
Probab=86.11 E-value=1.8 Score=23.67 Aligned_cols=60 Identities=13% Similarity=0.115 Sum_probs=46.3
Q ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHH-HHHHHHCCCHHH
Q ss_conf 9999999999999839949999998634299998875589994489999-999992899999
Q gi|254781147|r 19 RMIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMI-ILAHTLDTPLWK 79 (83)
Q Consensus 19 ~~~~g~~ir~~R~~~gltq~ela~~~gis~~~is~iE~G~~~~~~~~l~-~la~al~i~~~~ 79 (83)
..+.-+.+++.-+-.+++|..+|.-+|+|..++|++-+| ..+...+.+ +++..++.+..+
T Consensus 4 n~~~~k~~k~f~e~~~~~q~~~a~gi~~~~~~vsk~L~g-~~g~~~~~~a~ia~~le~~~~q 64 (297)
T COG2842 4 NFIEIKKLKEFAEFSGMCQKYLARGIGTSAPALSKYLNG-YKGDYATNEAKIAAFLEKKGVQ 64 (297)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHCC-CCCHHHHHHHHHHHHHCCCCCC
T ss_conf 389999999999861666999998736684457878437-6741777899999997277763
No 124
>PRK09954 hypothetical protein; Provisional
Probab=85.96 E-value=1.2 Score=24.70 Aligned_cols=29 Identities=17% Similarity=0.291 Sum_probs=25.5
Q ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 99999983994999999863429999887
Q gi|254781147|r 26 FRNIRKEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 26 ir~~R~~~gltq~ela~~~gis~~~is~i 54 (83)
|..+|+.==.||.|||+++|+|++.++-.
T Consensus 9 l~~i~~~p~i~q~ela~~lgisrs~va~h 37 (362)
T PRK09954 9 LAILRRNPLIQQNEIADILQISRSRVAAH 37 (362)
T ss_pred HHHHHHCCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 99998789958999999979879999999
No 125
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=85.80 E-value=1.2 Score=24.62 Aligned_cols=31 Identities=26% Similarity=0.192 Sum_probs=26.1
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999983994999999863429999887
Q gi|254781147|r 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 24 ~~ir~~R~~~gltq~ela~~~gis~~~is~i 54 (83)
+.+-.++.-.|+|.+|+|+.+|||.+++-+.
T Consensus 124 R~vflL~~~eGlsy~EIAe~LgIS~~tV~~~ 154 (168)
T PRK12525 124 RAAFLMSQLEGLTYVEIGERLGVSLSRIHQY 154 (168)
T ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 9999999992999999999989799999999
No 126
>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=85.74 E-value=1.3 Score=24.49 Aligned_cols=33 Identities=18% Similarity=0.160 Sum_probs=27.3
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 999999998399499999986342999988755
Q gi|254781147|r 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISELET 56 (83)
Q Consensus 24 ~~ir~~R~~~gltq~ela~~~gis~~~is~iE~ 56 (83)
+.+-.++.-.|+|.+|+|+.+|+|.+++....+
T Consensus 16 r~vl~l~y~~~~s~~EIa~~lgis~~tVk~~l~ 48 (55)
T cd06171 16 REVILLRFGEGLSYEEIAEILGISRSTVRQRLH 48 (55)
T ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 898999998099999999998959999999999
No 127
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=85.61 E-value=1.4 Score=24.25 Aligned_cols=48 Identities=15% Similarity=0.020 Sum_probs=34.3
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHCCCCCC------------CH-----HHHHHHHHHHCCCHHHH
Q ss_conf 39949999998634299998875589994------------48-----99999999928999996
Q gi|254781147|r 33 AKLTQKEIRNRTGFAQSWISELETGKSTI------------NI-----DNMIILAHTLDTPLWKL 80 (83)
Q Consensus 33 ~gltq~ela~~~gis~~~is~iE~G~~~~------------~~-----~~l~~la~al~i~~~~l 80 (83)
.+||..++|+++|++..+|.-||+-.-.+ +- -.+.+-|+.+|.++.+.
T Consensus 6 ~~m~IgelAk~~gvs~~tIRyYE~~GLl~~~~R~~~gyR~Y~~~~v~rL~fI~~~r~lGfsL~eI 70 (144)
T PRK13752 6 ENLTIGVFAKAAGVNVETIRFYQRKGLLPEPDKPYGSIRRYGEADVTRVRFVKSAQRLGFSLDEI 70 (144)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCHHHH
T ss_conf 23829999999789845667987259979877799998247999999999999999879989999
No 128
>TIGR02941 Sigma_B RNA polymerase sigma-B factor; InterPro: IPR014288 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 recognized by the major sigma factors , . This entry represents the sigma factor, sigmaB. It is restricted to certain species within the order Bacillales including Staphylococcus aureus , Listeria monocytogenes and Bacillus cereus (strain ATCC 14579 / DSM 31) ..
Probab=85.60 E-value=0.34 Score=27.90 Aligned_cols=33 Identities=27% Similarity=0.315 Sum_probs=28.2
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 999999983994999999863429999887558
Q gi|254781147|r 25 NFRNIRKEAKLTQKEIRNRTGFAQSWISELETG 57 (83)
Q Consensus 25 ~ir~~R~~~gltq~ela~~~gis~~~is~iE~G 57 (83)
.|-..--..||+|+|-++++|+|+=++||+-+-
T Consensus 213 ~ii~c~f~enlsQKeTGErlGiSQMHVSRl~R~ 245 (256)
T TIGR02941 213 EIIECTFIENLSQKETGERLGISQMHVSRLQRR 245 (256)
T ss_pred HHHHHHHHCCCCCCHHHHHCCHHHHHHHHHHHH
T ss_conf 766655314787300232224035567788899
No 129
>pfam01047 MarR MarR family. The Mar proteins are involved in the multiple antibiotic resistance, a non-specific resistance system. The expression of the mar operon is controlled by a repressor, MarR. A large number of compounds induce transcription of the mar operon. This is thought to be due to the compound binding to MarR, and the resulting complex stops MarR binding to the DNA. With the MarR repression lost, transcription of the operon proceeds. The structure of MarR is known and shows MarR as a dimer with each subunit containing a winged-helix DNA binding motif.
Probab=85.60 E-value=0.88 Score=25.48 Aligned_cols=31 Identities=19% Similarity=0.339 Sum_probs=27.0
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999983994999999863429999887
Q gi|254781147|r 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 24 ~~ir~~R~~~gltq~ela~~~gis~~~is~i 54 (83)
.-|..+...-|+||.++|+.++++.++++++
T Consensus 7 ~vL~~l~~~~~~s~~~la~~~~~~~~~vs~~ 37 (59)
T pfam01047 7 HILRILYEHGPLTVSELAEKLGVDRSTVTRV 37 (59)
T ss_pred HHHHHHHHCCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 9999999469929999999988586549999
No 130
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=85.52 E-value=1.8 Score=23.58 Aligned_cols=46 Identities=11% Similarity=0.169 Sum_probs=39.3
Q ss_pred HCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHC
Q ss_conf 83994999999863429999887558999448999999999289999960
Q gi|254781147|r 32 EAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLWKLL 81 (83)
Q Consensus 32 ~~gltq~ela~~~gis~~~is~iE~G~~~~~~~~l~~la~al~i~~~~l~ 81 (83)
...+|++++|+..|||+..|.+||+. .+..|.+..+.-++..+.||
T Consensus 283 ~e~~TL~EIg~~lgvSRERVRQIE~~----AL~KLR~~l~~~~l~~~~~~ 328 (328)
T PRK05657 283 YEAATLEEVAREIGLTRERVRQIQVE----ALRRLREILQTQGLSKDALF 328 (328)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHH----HHHHHHHHHHHCCCCHHHCC
T ss_conf 89605999998969799999999999----99998799998699734249
No 131
>cd04787 HTH_HMRTR_unk Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription regulators. Putative helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR), unknown subgroup. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules, such as, metal ions, drugs, and organic substrates. This subgroup lacks one of the c
Probab=85.11 E-value=1.9 Score=23.47 Aligned_cols=46 Identities=17% Similarity=0.173 Sum_probs=28.9
Q ss_pred CCHHHHHHHHHHHHHHHHHHHCCC------------CCCCHH-----HHHHHHHHHCCCHHHH
Q ss_conf 949999998634299998875589------------994489-----9999999928999996
Q gi|254781147|r 35 LTQKEIRNRTGFAQSWISELETGK------------STINID-----NMIILAHTLDTPLWKL 80 (83)
Q Consensus 35 ltq~ela~~~gis~~~is~iE~G~------------~~~~~~-----~l~~la~al~i~~~~l 80 (83)
|+..|+|+.+|+|..+|.-||.-- +.-+.+ .+.+.++.+|.++.+.
T Consensus 1 M~Ige~A~~~gvs~~TlRyYe~~GLl~p~~r~~~GyR~Y~~~~~~~l~~I~~~r~~G~sL~eI 63 (133)
T cd04787 1 MKVKELANAAGVTPDTVRFYTRIGLLRPTRDPVNGYRLYSEKDLSRLRFILSARQLGFSLKDI 63 (133)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCEECHHHHHHHHHHHHHHHHCCCCHHHH
T ss_conf 968999999897899999999859998862289994513299999999999999869999999
No 132
>cd04783 HTH_MerR1 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator. Helix-turn-helix (HTH) transcription regulator MerR1. MerR1 transcription regulators, such as Tn21 MerR and Tn501 MerR, mediate response to mercury exposure in eubacteria. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines that define a mercury binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=85.07 E-value=1.9 Score=23.46 Aligned_cols=46 Identities=20% Similarity=0.148 Sum_probs=26.6
Q ss_pred CCHHHHHHHHHHHHHHHHHHHCCC------------CCCCHH-----HHHHHHHHHCCCHHHH
Q ss_conf 949999998634299998875589------------994489-----9999999928999996
Q gi|254781147|r 35 LTQKEIRNRTGFAQSWISELETGK------------STINID-----NMIILAHTLDTPLWKL 80 (83)
Q Consensus 35 ltq~ela~~~gis~~~is~iE~G~------------~~~~~~-----~l~~la~al~i~~~~l 80 (83)
||..|+|+++|+|..+|.-||.-- +.-+.+ .+.+.++.+|.++.+.
T Consensus 1 m~IgevA~~~gvs~~TlRyYE~~GLl~~~~R~~~gyR~Y~~~~l~rL~~I~~~r~~G~sL~eI 63 (126)
T cd04783 1 LTIGELAKAAGVNVETIRYYQRRGLLPEPPRPEGGYRRYPEETVTRLRFIKRAQELGFTLDEI 63 (126)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCHHHH
T ss_conf 978999999893989999999869988763189996017799999999999999879989999
No 133
>cd01110 HTH_SoxR Helix-Turn-Helix DNA binding domain of the SoxR transcription regulator. Helix-turn-helix (HTH) transcriptional regulator SoxR. The global regulator, SoxR, up-regulates gene expression of another transcription activator, SoxS, which directly stimulates the oxidative stress regulon genes in E. coli. The soxRS response renders the bacterial cell resistant to superoxide-generating agents, macrophage-generated nitric oxide, organic solvents, and antibiotics. The SoxR proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the unusually long spacer between the -35 and -10 promoter elements. They also harbor a regulatory C-terminal domain containing an iron-sulfur center.
Probab=84.85 E-value=1.6 Score=23.91 Aligned_cols=46 Identities=26% Similarity=0.311 Sum_probs=31.3
Q ss_pred CCHHHHHHHHHHHHHHHHHHHC-----------CCCCCCHH-----HHHHHHHHHCCCHHHH
Q ss_conf 9499999986342999988755-----------89994489-----9999999928999996
Q gi|254781147|r 35 LTQKEIRNRTGFAQSWISELET-----------GKSTINID-----NMIILAHTLDTPLWKL 80 (83)
Q Consensus 35 ltq~ela~~~gis~~~is~iE~-----------G~~~~~~~-----~l~~la~al~i~~~~l 80 (83)
||..|+|+++|+|..+|.-||. |-+.-+-+ .+.+.++.+|.++.+.
T Consensus 2 mtIgelA~~~gvs~~tiRyYE~~GLl~p~R~~~gyR~Y~~~~l~rl~~I~~~r~lGfsL~eI 63 (139)
T cd01110 2 LSVGEVAKRSGVAVSALHFYEQKGLIASWRNAGNQRRYPRDVLRRIAFIKVAQRLGLSLAEI 63 (139)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCEECHHHHHHHHHHHHHHHCCCCHHHH
T ss_conf 97899999988788999999987884666789887704989999999999999859989999
No 134
>PRK00767 transcriptional regulator BetI; Validated
Probab=84.80 E-value=1.9 Score=23.49 Aligned_cols=63 Identities=21% Similarity=0.189 Sum_probs=41.5
Q ss_pred CCHHHHHHHHHHHHHHH--HHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHH
Q ss_conf 89899999999999999--9999839949999998634299998875589994489999999992
Q gi|254781147|r 11 LSDAILRERMIFVNNFR--NIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTL 73 (83)
Q Consensus 11 ~~~~~~~~~~~~g~~ir--~~R~~~gltq~ela~~~gis~~~is~iE~G~~~~~~~~l~~la~al 73 (83)
.++...+...++-.-++ ..+--.|.|..++|+.+|+|.+.+..|..++...-...+..+.+-+
T Consensus 4 ~~~~~~RR~~i~~Aa~~~i~~~G~~~~t~~~IA~~AGvs~g~v~~yF~~k~~Ll~~a~~~~~~~~ 68 (197)
T PRK00767 4 VGMEPIRRQQLIDATLRSIGEVGLLDTTIAQIARRAGVSSGIISHYFGGKDGLLEATMRHLLRQL 68 (197)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 98707899999999999999859352889999999599899999990879999999999999999
No 135
>cd04782 HTH_BltR Helix-Turn-Helix DNA binding domain of the BltR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BltR (BmrR-like transporter) of Bacillus subtilis, and related proteins; N-terminal domain. Blt, like Bmr, is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. These regulators are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=84.71 E-value=3 Score=22.28 Aligned_cols=46 Identities=15% Similarity=0.247 Sum_probs=32.2
Q ss_pred CCHHHHHHHHHHHHHHHHHHHCC------------CCCCCHHH-----HHHHHHHHCCCHHHH
Q ss_conf 94999999863429999887558------------99944899-----999999928999996
Q gi|254781147|r 35 LTQKEIRNRTGFAQSWISELETG------------KSTINIDN-----MIILAHTLDTPLWKL 80 (83)
Q Consensus 35 ltq~ela~~~gis~~~is~iE~G------------~~~~~~~~-----l~~la~al~i~~~~l 80 (83)
+|..|+|+.+|||..+|.-||.- -+.-+.+. ..+.++.+|+|+.+.
T Consensus 1 y~Ige~Ak~~gvs~~TLRyYe~~GLl~p~~~~~ngYR~Y~~~~~~~l~~I~~~r~lG~sL~eI 63 (97)
T cd04782 1 FTTGEFAKLCGISKQTLFHYDKIGLFKPEIVKENGYRYYTLEQFEQLDIILLLKELGISLKEI 63 (97)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCHHHH
T ss_conf 978999999896999999999669989861399998427999999999999999969999999
No 136
>pfam07638 Sigma70_ECF ECF sigma factor. These proteins are probably RNA polymerase sigma factors belonging to the extra-cytoplasmic function (ECF) subfamily and show sequence similarity to pfam04542 and pfam04545.
Probab=84.69 E-value=1.2 Score=24.62 Aligned_cols=29 Identities=24% Similarity=0.350 Sum_probs=25.2
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 99999998399499999986342999988
Q gi|254781147|r 25 NFRNIRKEAKLTQKEIRNRTGFAQSWISE 53 (83)
Q Consensus 25 ~ir~~R~~~gltq~ela~~~gis~~~is~ 53 (83)
.+-.++.-.|+|.+|.|+.+|||.+++-.
T Consensus 142 ~v~~L~~~eglS~~EIAe~Lgis~~TVk~ 170 (185)
T pfam07638 142 RLVELRFFAGLSNDEIAERLGVSERTVER 170 (185)
T ss_pred HHHHHHHHCCCCHHHHHHHHCCCHHHHHH
T ss_conf 89888997599999999997969989999
No 137
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=84.58 E-value=1.2 Score=24.71 Aligned_cols=26 Identities=31% Similarity=0.505 Sum_probs=23.9
Q ss_pred HCCCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 83994999999863429999887558
Q gi|254781147|r 32 EAKLTQKEIRNRTGFAQSWISELETG 57 (83)
Q Consensus 32 ~~gltq~ela~~~gis~~~is~iE~G 57 (83)
...+|++|+|+..|||+..+++||..
T Consensus 192 ~~~~Tl~eIg~~lgiSrERVRQIe~~ 217 (228)
T PRK05803 192 GKEKTQREIAKALGISRSYVSRIEKK 217 (228)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 99715999999989799999999999
No 138
>PRK10227 DNA-binding transcriptional regulator CueR; Provisional
Probab=84.35 E-value=2.1 Score=23.24 Aligned_cols=45 Identities=13% Similarity=0.122 Sum_probs=28.7
Q ss_pred CCHHHHHHHHHHHHHHHHHHHCCCCC------------CCHH-----HHHHHHHHHCCCHHH
Q ss_conf 94999999863429999887558999------------4489-----999999992899999
Q gi|254781147|r 35 LTQKEIRNRTGFAQSWISELETGKST------------INID-----NMIILAHTLDTPLWK 79 (83)
Q Consensus 35 ltq~ela~~~gis~~~is~iE~G~~~------------~~~~-----~l~~la~al~i~~~~ 79 (83)
|+..|+|+++|++..+|.-||.-.-. -+-+ .+.+-|+.+|.++.+
T Consensus 1 M~IgelAk~tGv~~~TIRyYE~~GLl~~~~R~~~GyR~Y~~~~l~rL~fI~~ar~lGfsL~E 62 (135)
T PRK10227 1 MNISDVAKITGLTSKAIRFYEEKGLVTPPMRSENGYRTYTQQHLNELTLLRQARQVGFNLEE 62 (135)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCHHH
T ss_conf 96899999989699999999983897734328999217789999999999999887999999
No 139
>pfam02376 CUT CUT domain. The CUT domain is a DNA-binding motif which can bind independently or in cooperation with the homeodomain, often found downstream of the CUT domain. Multiple copies of the CUT domain can exist in one protein .
Probab=84.28 E-value=2.2 Score=23.17 Aligned_cols=59 Identities=15% Similarity=0.115 Sum_probs=43.6
Q ss_pred HHHHHHHHHHHHHCCCCHHHHHHHH-HHHHHHHHHHHCCCCC------CCHHHHHHHHHHHCCCHH
Q ss_conf 9999999999998399499999986-3429999887558999------448999999999289999
Q gi|254781147|r 20 MIFVNNFRNIRKEAKLTQKEIRNRT-GFAQSWISELETGKST------INIDNMIILAHTLDTPLW 78 (83)
Q Consensus 20 ~~~g~~ir~~R~~~gltq~ela~~~-gis~~~is~iE~G~~~------~~~~~l~~la~al~i~~~ 78 (83)
..++..|+...+..+++|+-+|+.+ |.|++++|.+-+.-.. -.-+...++-.-|+.|-.
T Consensus 6 ~~i~~~i~~eL~~~~I~Q~~Fa~~vL~rsQGtlSdLL~~PKPW~~l~~~gr~~y~RM~~wL~~p~~ 71 (81)
T pfam02376 6 AEIARRIKEELKRANISQALFAEVVLGRSQGSLSDLLRRPKPWNKLLLKGREPFRRMQNFLSLPEA 71 (81)
T ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHHCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCHH
T ss_conf 999999999999949769999999973183789998818997788508506989999999868598
No 140
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=84.19 E-value=3.5 Score=21.91 Aligned_cols=42 Identities=17% Similarity=0.263 Sum_probs=31.6
Q ss_pred CCCCHHHHHHHHHHHHHHHHHH------------HCCC-CCCCHHHHHHHHHHHC
Q ss_conf 3994999999863429999887------------5589-9944899999999928
Q gi|254781147|r 33 AKLTQKEIRNRTGFAQSWISEL------------ETGK-STINIDNMIILAHTLD 74 (83)
Q Consensus 33 ~gltq~ela~~~gis~~~is~i------------E~G~-~~~~~~~l~~la~al~ 74 (83)
..+|++|+|..+|.++.++|++ ..|+ ...+.+.|.++|++=|
T Consensus 144 l~lT~~eLA~~iGttREtVsR~L~~l~~~GlI~~~~~~I~I~D~~~L~~lAe~~g 198 (201)
T PRK13918 144 IYATHDELAAAVGSVRETVTKVVGELSREGVIRSGYGKIQLLDLKALKELAESRG 198 (201)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCEEEEECHHHHHHHHHHCC
T ss_conf 0579999998859868999999999998898896799899928999999987447
No 141
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=83.70 E-value=1.3 Score=24.42 Aligned_cols=30 Identities=17% Similarity=0.190 Sum_probs=26.8
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 999999983994999999863429999887
Q gi|254781147|r 25 NFRNIRKEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 25 ~ir~~R~~~gltq~ela~~~gis~~~is~i 54 (83)
-|..++..-++||.++|+.++++.++++++
T Consensus 45 vL~~L~~~~~~t~~eLa~~l~id~~tvt~~ 74 (144)
T PRK11512 45 VLCSIRCAACITPVELKKVLSVDLGALTRM 74 (144)
T ss_pred HHHHHHHCCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 999999869979999999978888789999
No 142
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=83.63 E-value=3.1 Score=22.25 Aligned_cols=46 Identities=15% Similarity=0.154 Sum_probs=30.2
Q ss_pred CCHHHHHHHHHHHHHHHHHHHCCC------------CCCCHHH-----HHHHHHHHCCCHHHH
Q ss_conf 949999998634299998875589------------9944899-----999999928999996
Q gi|254781147|r 35 LTQKEIRNRTGFAQSWISELETGK------------STINIDN-----MIILAHTLDTPLWKL 80 (83)
Q Consensus 35 ltq~ela~~~gis~~~is~iE~G~------------~~~~~~~-----l~~la~al~i~~~~l 80 (83)
+|..|+|+.+|||.++|.-||.-. +.-+.+. ....++.+|+|+.+.
T Consensus 1 ytIge~a~~~gvs~~tlRyYe~~GLl~p~~~~~~gyR~Y~~~~i~~l~~I~~lr~~G~~l~eI 63 (103)
T cd01106 1 YTVGEVAKLTGVSVRTLHYYDEIGLLKPSRRTENGYRLYTEEDLERLQQILFLKELGFSLKEI 63 (103)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCEECCCCCEECCHHHHHHHHHHHHHHHCCCCHHHH
T ss_conf 978899999896999999998538978861489998656899999999999999979999999
No 143
>PHA01083 hypothetical protein
Probab=83.60 E-value=2.9 Score=22.41 Aligned_cols=55 Identities=24% Similarity=0.261 Sum_probs=45.9
Q ss_pred HHHHHHHCCCCH-HHHHHHHHHHHHHHHHHHCCCC-CCCHHHHHHHHHHHCCCHHHH
Q ss_conf 999999839949-9999986342999988755899-944899999999928999996
Q gi|254781147|r 26 FRNIRKEAKLTQ-KEIRNRTGFAQSWISELETGKS-TINIDNMIILAHTLDTPLWKL 80 (83)
Q Consensus 26 ir~~R~~~gltq-~ela~~~gis~~~is~iE~G~~-~~~~~~l~~la~al~i~~~~l 80 (83)
|..+.+.+++.| +++|--+|++++.||++-+|.+ -.+-+...-||+.-|+..+.-
T Consensus 5 ldAYK~aknYvQdKQIAhDlg~~pq~iS~~RkG~R~Ylsd~eAifLAe~~GiD~E~a 61 (153)
T PHA01083 5 LDAYKKAKNYVQYKQIAHDLGVSPQKISKMRTGVRTYISDEEAIFLAESAGIDPEIA 61 (153)
T ss_pred HHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHCHHHHCCHHHHHHHHHHCCCCHHHH
T ss_conf 999999998888999999809998999999812376435388999898709988888
No 144
>TIGR03453 partition_RepA plasmid partitioning protein RepA. Members of this family are the RepA (or ParA) protein involved in replicon partitioning. All known examples occur in bacterial species with two or more replicons, on a plasmid or the smaller chromosome. Note that an apparent exception may be seen as a pseudomolecule from assembly of an incompletely sequenced genome. Members of this family belong to a larger family that also includes the enzyme cobyrinic acid a,c-diamide synthase, but assignment of that name to members of this family would be in error.
Probab=83.59 E-value=4 Score=21.59 Aligned_cols=61 Identities=18% Similarity=0.377 Sum_probs=43.6
Q ss_pred HHHHHHHHHHHHHHHHHH----------CCCCHHHHHHHHHHHHHHHHHHH------------CCCCCCCHHHHHHHHHH
Q ss_conf 999999999999999998----------39949999998634299998875------------58999448999999999
Q gi|254781147|r 15 ILRERMIFVNNFRNIRKE----------AKLTQKEIRNRTGFAQSWISELE------------TGKSTINIDNMIILAHT 72 (83)
Q Consensus 15 ~~~~~~~~g~~ir~~R~~----------~gltq~ela~~~gis~~~is~iE------------~G~~~~~~~~l~~la~a 72 (83)
+..+...+...|..+|.+ +.+|..|+|+.+||+.+++.+++ +|.+.-|++.+..+-+.
T Consensus 4 i~~~a~~ls~~l~~~r~~~~~P~~~K~lr~f~~~e~a~l~gv~~~~lr~~~~~g~~p~p~~~~~grR~ytl~ei~~lR~~ 83 (387)
T TIGR03453 4 IARQARELSSQLQALRERLFPPNAQKTLRRFTSGEAAKLLGVTDSYLRQLSLEGKGPQPEVLANGRRSYTLEQINELRRH 83 (387)
T ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCEEEEHHHHHHHHHH
T ss_conf 89999999999999999737996556668888899998849699999999866999998758998258439999999999
Q ss_pred HCC
Q ss_conf 289
Q gi|254781147|r 73 LDT 75 (83)
Q Consensus 73 l~i 75 (83)
|+.
T Consensus 84 l~~ 86 (387)
T TIGR03453 84 LAQ 86 (387)
T ss_pred HHH
T ss_conf 986
No 145
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=83.52 E-value=1.2 Score=24.78 Aligned_cols=33 Identities=24% Similarity=0.362 Sum_probs=28.9
Q ss_pred HHHHHHHHHHHCC-CCHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999999839-94999999863429999887
Q gi|254781147|r 22 FVNNFRNIRKEAK-LTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 22 ~g~~ir~~R~~~g-ltq~ela~~~gis~~~is~i 54 (83)
--.-|..++.+-| .+|+|+.+.+|.|++++|++
T Consensus 197 e~~il~~i~~~GGri~Q~eL~r~lglsktTvsR~ 230 (258)
T COG2512 197 EKEILDLIRERGGRITQAELRRALGLSKTTVSRI 230 (258)
T ss_pred HHHHHHHHHHHCCEEEHHHHHHHHCCCHHHHHHH
T ss_conf 9999999998589786999888609976779999
No 146
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=83.02 E-value=1.3 Score=24.39 Aligned_cols=29 Identities=17% Similarity=0.290 Sum_probs=23.7
Q ss_pred HHHHHH-HCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 999999-83994999999863429999887
Q gi|254781147|r 26 FRNIRK-EAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 26 ir~~R~-~~gltq~ela~~~gis~~~is~i 54 (83)
|..+.. .-|+||.+||+.+|+++++++++
T Consensus 37 L~~L~~~~~g~tq~eLa~~l~v~~~t~tr~ 66 (144)
T PRK03573 37 LHNIHQLPPDQSQIQLAKAIGIEQPSLVRT 66 (144)
T ss_pred HHHHHHCCCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 999997398989999999979878369999
No 147
>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=82.75 E-value=3.5 Score=21.90 Aligned_cols=63 Identities=22% Similarity=0.244 Sum_probs=41.4
Q ss_pred CCHHHHHHHHHHHHHHHHH--HHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHH
Q ss_conf 8989999999999999999--99839949999998634299998875589994489999999992
Q gi|254781147|r 11 LSDAILRERMIFVNNFRNI--RKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTL 73 (83)
Q Consensus 11 ~~~~~~~~~~~~g~~ir~~--R~~~gltq~ela~~~gis~~~is~iE~G~~~~~~~~l~~la~al 73 (83)
.+....+...++-.-++-+ +--.+.|..++|+.+|+|.+.+..+...|...=...+..+.+-+
T Consensus 3 ~~~~~~RR~~il~Aa~~~i~~~G~~~~t~~~IA~~AGvS~G~v~~yF~sK~~Ll~~~~~~~~~~~ 67 (189)
T TIGR03384 3 VGMEPIRRAELIDATIESIGERGSLDVTIAQIARRAGVSSGIISHYFGGKQGLLEATMRHLLSEL 67 (189)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 99973799999999999999849352889999999699999999983889999999999999999
No 148
>pfam01527 Transposase_8 Transposase. Transposase proteins are necessary for efficient DNA transposition. This family consists of various E. coli insertion elements and other bacterial transposases some of which are members of the IS3 family.
Probab=82.68 E-value=3.2 Score=22.13 Aligned_cols=33 Identities=9% Similarity=0.050 Sum_probs=25.6
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 999999999839949999998634299998875
Q gi|254781147|r 23 VNNFRNIRKEAKLTQKEIRNRTGFAQSWISELE 55 (83)
Q Consensus 23 g~~ir~~R~~~gltq~ela~~~gis~~~is~iE 55 (83)
-..+...-.+-|.|..++|...||+.++|.+|-
T Consensus 12 K~~~V~~~~~~g~sv~~var~~gi~~~~l~~W~ 44 (75)
T pfam01527 12 KARAVKESLEPGASVSELAREHGVSPATLYKWR 44 (75)
T ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 999999998099849999999895999999999
No 149
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=82.63 E-value=1.6 Score=23.92 Aligned_cols=30 Identities=10% Similarity=0.132 Sum_probs=24.4
Q ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 9999998399499999986342999988755
Q gi|254781147|r 26 FRNIRKEAKLTQKEIRNRTGFAQSWISELET 56 (83)
Q Consensus 26 ir~~R~~~gltq~ela~~~gis~~~is~iE~ 56 (83)
+..+ ...|+|..++|+.+|||++++.+|-.
T Consensus 165 i~~~-~~~g~s~~~iak~~gvsrsTvyR~lK 194 (200)
T PRK13413 165 ITKE-LKKGTTKSEIAKKLKVSRTTLARFLK 194 (200)
T ss_pred HHHH-HHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 9999-98889999999998929999999997
No 150
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=82.44 E-value=2 Score=23.35 Aligned_cols=31 Identities=19% Similarity=0.290 Sum_probs=26.3
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999983994999999863429999887
Q gi|254781147|r 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 24 ~~ir~~R~~~gltq~ela~~~gis~~~is~i 54 (83)
+.+-.++...|+|.+|+|+.+|||.+++..-
T Consensus 111 R~v~~L~~~egls~~EIA~~lgis~~tVk~~ 141 (159)
T PRK12527 111 RESFLLRKLEGLSHQQIAEHLGISRSLVEKH 141 (159)
T ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 8999889873979999999989199999999
No 151
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=82.24 E-value=3.9 Score=21.64 Aligned_cols=46 Identities=13% Similarity=0.070 Sum_probs=31.4
Q ss_pred CCHHHHHHHHHHHHHHHHHHHCCC-CCCC-------------HHHHH---HHHHHHCCCHHHH
Q ss_conf 949999998634299998875589-9944-------------89999---9999928999996
Q gi|254781147|r 35 LTQKEIRNRTGFAQSWISELETGK-STIN-------------IDNMI---ILAHTLDTPLWKL 80 (83)
Q Consensus 35 ltq~ela~~~gis~~~is~iE~G~-~~~~-------------~~~l~---~la~al~i~~~~l 80 (83)
+|..++|+.+|+|..+|..||.-. -.|. +..|. .+++.+|+++.+.
T Consensus 2 YtIgevA~~~Gvs~~tLR~yE~~GLl~P~R~~~g~R~Ys~~di~~l~~I~~L~~~~G~sl~~I 64 (91)
T cd04766 2 YVISVAAELSGMHPQTLRLYERLGLLSPSRTDGGTRRYSERDIERLRRIQRLTQELGVNLAGV 64 (91)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCEECCHHHHHHHHHHHHHHHHCCCCHHHH
T ss_conf 658999999892999999999859979883999997447999999999999999869989999
No 152
>PRK07773 replicative DNA helicase; Validated
Probab=82.18 E-value=3.1 Score=22.19 Aligned_cols=52 Identities=10% Similarity=0.099 Sum_probs=42.8
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCC
Q ss_conf 9999999999839949999998634299998875589994489999999992899
Q gi|254781147|r 22 FVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTP 76 (83)
Q Consensus 22 ~g~~ir~~R~~~gltq~ela~~~gis~~~is~iE~G~~~~~~~~l~~la~al~i~ 76 (83)
+-..++....+.|+|..++++.+|+..+..+-+ +..++-..+.++|.+|+-.
T Consensus 712 vw~~Vr~a~~~~g~t~r~~~~~~g~~~~g~~~~---k~~~SR~Rl~~~A~~l~~~ 763 (868)
T PRK07773 712 VWKQVRPRLQAKQMTTRQLHEPIGTSYCGSTLW---KHSPSRERAHRVAARIQSR 763 (868)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHHCCCCCCCHHH---CCCCCHHHHHHHHHHHCCH
T ss_conf 999999999860654899998725454640132---0342277899999874788
No 153
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=82.15 E-value=2.2 Score=23.16 Aligned_cols=31 Identities=19% Similarity=0.177 Sum_probs=26.6
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999983994999999863429999887
Q gi|254781147|r 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 24 ~~ir~~R~~~gltq~ela~~~gis~~~is~i 54 (83)
+.+-.++.-.|+|.+|+|+.+|||.+++...
T Consensus 125 R~v~~L~~~egls~~EIA~~lgiS~~tVk~~ 155 (172)
T PRK09651 125 REAFLLSQLDGLTYSEIAHKLGVSISSVKKY 155 (172)
T ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 9999999883999999999989399999999
No 154
>cd04769 HTH_MerR2 Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MerR2 and related proteins. MerR2 in Bacillus cereus RC607 regulates resistance to organomercurials. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=81.95 E-value=2.8 Score=22.52 Aligned_cols=46 Identities=22% Similarity=0.151 Sum_probs=26.7
Q ss_pred CCHHHHHHHHHHHHHHHHHHHCCCCCC-----------CHH-----HHHHHHHHHCCCHHHH
Q ss_conf 949999998634299998875589994-----------489-----9999999928999996
Q gi|254781147|r 35 LTQKEIRNRTGFAQSWISELETGKSTI-----------NID-----NMIILAHTLDTPLWKL 80 (83)
Q Consensus 35 ltq~ela~~~gis~~~is~iE~G~~~~-----------~~~-----~l~~la~al~i~~~~l 80 (83)
|...|+|+++|+|..+|.-||.-.--+ +.+ .....++.+|.++.++
T Consensus 1 M~IgevAk~~gvs~~TlRyYE~~GLl~~~~r~~~yR~Y~~~~l~~l~~I~~~r~~GfsL~eI 62 (116)
T cd04769 1 MYIGELAQQTGVTIKAIRLYEEKGLLPSPKRSGNYRVYDAQHVECLRFIKEARQLGFTLAEL 62 (116)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCHHHH
T ss_conf 96899999989699999999986999987577773322899999999999999979999999
No 155
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family; InterPro: IPR011517 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 recognized by the major sigma factors , . This entry represents a group of sigma factors that are able to regulate extra cellular function (ECF) . Eubacteria display considerable genetic diversity between ECF-sigma factors, but all retain two features: the ability to respond to extra-cytoplasmic functions; and regulation by anti-sigma and anti-anti-sigma factors . This family show sequence similarity to IPR007627 from INTERPRO and IPR007630 from INTERPRO.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=81.95 E-value=1.6 Score=23.92 Aligned_cols=31 Identities=23% Similarity=0.181 Sum_probs=28.2
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 9999999998399499999986342999988
Q gi|254781147|r 23 VNNFRNIRKEAKLTQKEIRNRTGFAQSWISE 53 (83)
Q Consensus 23 g~~ir~~R~~~gltq~ela~~~gis~~~is~ 53 (83)
-.+|-.+|.=-|||.+|.|+.+|||.+||-+
T Consensus 150 ~a~~veLr~F~Gl~~~E~A~~L~~S~~Tv~R 180 (194)
T TIGR02999 150 QAEVVELRFFAGLTVEEIAELLGVSVRTVER 180 (194)
T ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHH
T ss_conf 8998853110488989999986888878998
No 156
>pfam02796 HTH_7 Helix-turn-helix domain of resolvase.
Probab=81.90 E-value=2.5 Score=22.73 Aligned_cols=32 Identities=16% Similarity=0.050 Sum_probs=26.6
Q ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 99999983994999999863429999887558
Q gi|254781147|r 26 FRNIRKEAKLTQKEIRNRTGFAQSWISELETG 57 (83)
Q Consensus 26 ir~~R~~~gltq~ela~~~gis~~~is~iE~G 57 (83)
.-..+.+.|.+..++|+..|||+++|-+|-+.
T Consensus 13 ~v~~L~~~G~~i~~IA~~~~vsrsTvYRyl~~ 44 (45)
T pfam02796 13 EVITLLEEGISIKQIAKIFGISRSTVYRYLAA 44 (45)
T ss_pred HHHHHHHCCCCHHHHHHHHCCHHHHHHHHCCC
T ss_conf 99999987994999999986008888764458
No 157
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=81.80 E-value=1.1 Score=24.84 Aligned_cols=24 Identities=25% Similarity=0.300 Sum_probs=21.0
Q ss_pred HCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 839949999998634299998875
Q gi|254781147|r 32 EAKLTQKEIRNRTGFAQSWISELE 55 (83)
Q Consensus 32 ~~gltq~ela~~~gis~~~is~iE 55 (83)
...+|++|+|+.+|.++.++|++-
T Consensus 6 ~l~lt~~~iA~~lG~tretvsR~l 29 (48)
T smart00419 6 RLPLTRQEIAELLGLTRETVSRTL 29 (48)
T ss_pred EECCCHHHHHHHHCCCHHHHHHHH
T ss_conf 833799999999799799999999
No 158
>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=81.74 E-value=3.2 Score=22.11 Aligned_cols=25 Identities=24% Similarity=0.306 Sum_probs=21.6
Q ss_pred HHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 9839949999998634299998875
Q gi|254781147|r 31 KEAKLTQKEIRNRTGFAQSWISELE 55 (83)
Q Consensus 31 ~~~gltq~ela~~~gis~~~is~iE 55 (83)
....+|++|+|+.+|.++.++|+.-
T Consensus 22 ~~l~ltr~eiA~~lG~t~eTVsR~l 46 (67)
T cd00092 22 VQLPLTRQEIADYLGLTRETVSRTL 46 (67)
T ss_pred EECCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 6617799999999789099999999
No 159
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=81.68 E-value=2.2 Score=23.06 Aligned_cols=31 Identities=10% Similarity=0.080 Sum_probs=26.1
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999983994999999863429999887
Q gi|254781147|r 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 24 ~~ir~~R~~~gltq~ela~~~gis~~~is~i 54 (83)
+.+-.++.-.|+|++|+|+.+|||.+++...
T Consensus 129 R~v~~L~~~eg~s~~EIAe~LgiS~~tVk~~ 159 (183)
T PRK07037 129 RAAFEMVRLRGETLQDIARELNVSQTLVNFM 159 (183)
T ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 9998989873989999999989299999999
No 160
>TIGR02395 rpoN_sigma RNA polymerase sigma-54 factor; InterPro: IPR000394 Sigma factors are bacterial transcription initiation factors that promote the attachment of the core RNA polymerase to specific initiation sites and are then released. They alter the specificity of promoter recognition. 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. The sigma-70 family has many different sigma factors (see the relevant entry IPR000943 from INTERPRO). The sigma-54 family consists exclusively of sigma-54 factor , required for the transcription of promoters that have a characteristic -24 and -12 consensus recognition element but which are devoid of the typical -10, -35 sequences recognized by the major sigma factors. The sigma-54 factor is also characterised by its interaction with ATP-dependent positive regulatory proteins that bind to upstream activating sequences. Structurally sigma-54 factors consist of three distinct regions: A relatively well conserved N-terminal glutamine-rich region of about 50 residues that contains a potential leucine zipper motif. A region of variable length which is not well conserved. A well conserved C-terminal region of about 350 residues that contains a second potential leucine zipper, a potential DNA-binding 'helix-turn-helix' motif and a perfectly conserved octapeptide whose function is not known. ; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0003899 DNA-directed RNA polymerase activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=81.64 E-value=0.26 Score=28.62 Aligned_cols=44 Identities=20% Similarity=0.138 Sum_probs=32.9
Q ss_pred HHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHH
Q ss_conf 99839949999998634299998875589994489999999992
Q gi|254781147|r 30 RKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTL 73 (83)
Q Consensus 30 R~~~gltq~ela~~~gis~~~is~iE~G~~~~~~~~l~~la~al 73 (83)
+.-+=||.+++|+.+|+|.|||||+=+||.--|---++.|=..|
T Consensus 361 ~~LkPL~L~~vA~el~~heSTiSRai~~KYl~T~~G~f~Lk~FF 404 (477)
T TIGR02395 361 AALKPLTLREVAEELGLHESTISRAINNKYLQTPRGVFELKYFF 404 (477)
T ss_pred HCCCCCCHHHHHHHHCCCCCCEEEEECCCEEECCCCCHHHHHHC
T ss_conf 00688638999988588987246331773576076403365431
No 161
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=81.31 E-value=1.9 Score=23.54 Aligned_cols=30 Identities=23% Similarity=0.386 Sum_probs=25.5
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 999999983994999999863429999887
Q gi|254781147|r 25 NFRNIRKEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 25 ~ir~~R~~~gltq~ela~~~gis~~~is~i 54 (83)
-|..+...-++||.++|+.++++.+++|++
T Consensus 15 vL~~l~~~~~~t~~~la~~l~~~~~~vs~~ 44 (101)
T smart00347 15 VLRILYEEGPLSVSELAKRLGVSPSTVTRV 44 (101)
T ss_pred HHHHHHHCCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 999999769979999999989688799999
No 162
>cd04786 HTH_MerR-like_sg7 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 7) with a conserved cysteine present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic su
Probab=81.09 E-value=3.1 Score=22.22 Aligned_cols=46 Identities=22% Similarity=0.205 Sum_probs=29.2
Q ss_pred CCHHHHHHHHHHHHHHHHHHHCCCCC------------CCHH-----HHHHHHHHHCCCHHHH
Q ss_conf 94999999863429999887558999------------4489-----9999999928999996
Q gi|254781147|r 35 LTQKEIRNRTGFAQSWISELETGKST------------INID-----NMIILAHTLDTPLWKL 80 (83)
Q Consensus 35 ltq~ela~~~gis~~~is~iE~G~~~------------~~~~-----~l~~la~al~i~~~~l 80 (83)
|+..|+|+++|+|..+|.-||.---. -+-+ .+.+-++.+|.++.+.
T Consensus 1 M~IgelA~~~gvs~~tlR~YE~~GLl~p~~r~~nGyR~Y~~~~i~~l~~I~~~r~lGfsL~eI 63 (131)
T cd04786 1 MKIGELAKRSGMAASRIRFYEAEGLLSSVERSANGYRDYPPETVWVLEIISSAQQAGFSLDEI 63 (131)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCEEECHHHHHHHHHHHHHHHCCCCHHHH
T ss_conf 978999999887889999999779989877699997534999999999999999969999999
No 163
>pfam02954 HTH_8 Bacterial regulatory protein, Fis family.
Probab=80.70 E-value=2.5 Score=22.76 Aligned_cols=30 Identities=3% Similarity=-0.006 Sum_probs=26.4
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 999999998399499999986342999988
Q gi|254781147|r 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISE 53 (83)
Q Consensus 24 ~~ir~~R~~~gltq~ela~~~gis~~~is~ 53 (83)
..|...-+..++.+.+.|+.+|||++++.+
T Consensus 8 ~~I~~aL~~~~gn~~~aA~~LGisr~tL~~ 37 (42)
T pfam02954 8 ELIEAALERTGGNKSKAARLLGISRRTLYR 37 (42)
T ss_pred HHHHHHHHHHCCCHHHHHHHHCCCHHHHHH
T ss_conf 999999999499799999997969999999
No 164
>cd04775 HTH_Cfa-like Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulators; the HTH domain of Cfa, a cyclopropane fatty acid synthase, and other related methyltransferases, as well as, the N-terminal domain of a conserved, uncharacterized ~172 a.a. protein. Based on sequence similarity of the N-terminal domain, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimil
Probab=80.50 E-value=3.3 Score=22.08 Aligned_cols=46 Identities=15% Similarity=0.152 Sum_probs=31.1
Q ss_pred CCHHHHHHHHHHHHHHHHHHHCC-----------CCCCCHHH-----HHHHHHHHCCCHHHH
Q ss_conf 94999999863429999887558-----------99944899-----999999928999996
Q gi|254781147|r 35 LTQKEIRNRTGFAQSWISELETG-----------KSTINIDN-----MIILAHTLDTPLWKL 80 (83)
Q Consensus 35 ltq~ela~~~gis~~~is~iE~G-----------~~~~~~~~-----l~~la~al~i~~~~l 80 (83)
+|..|+|+.+|+|.++|.-||.- -+.-+.+. ....++.+|+|+.+.
T Consensus 2 ~~Ige~a~~~gis~~tlRyYe~~GLl~~~r~~~gyR~Y~~~~i~~l~~I~~lr~~G~sL~eI 63 (102)
T cd04775 2 YTIGQMSRKFGVSRSTLLYYESIGLIPSARSEANYRLYSEADLSRLEKIVFLQAGGLPLEEI 63 (102)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCEECCHHHHHHHHHHHHHHHCCCCHHHH
T ss_conf 87899999989499999999987999987399999637899999999999999969999999
No 165
>TIGR02850 spore_sigG RNA polymerase sigma-G factor; InterPro: IPR014212 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 recognized by the major sigma factors , . Members of this entry comprise the Firmicutes lineage endospore formation-specific sigma factor SigG. It is also designated stage III sporulation protein G (SpoIIIG). Members of this entry are closely related to sigma-F (SpoIIAC), another sporulation sigma factor.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=80.46 E-value=1.5 Score=24.05 Aligned_cols=35 Identities=26% Similarity=0.258 Sum_probs=30.7
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 99999999983994999999863429999887558
Q gi|254781147|r 23 VNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETG 57 (83)
Q Consensus 23 g~~ir~~R~~~gltq~ela~~~gis~~~is~iE~G 57 (83)
-+-|-..|--.|-||-|+|+.+|+|++.+|++|..
T Consensus 211 e~~il~~rff~G~tqmeva~eiGisqaqvsrlek~ 245 (254)
T TIGR02850 211 EKLILKLRFFEGKTQMEVAEEIGISQAQVSRLEKA 245 (254)
T ss_pred HHHHHHHHHHCCCHHHHHHHHHCCHHHHHHHHHHH
T ss_conf 88777755314631334565403016888888899
No 166
>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=79.94 E-value=1.9 Score=23.51 Aligned_cols=22 Identities=18% Similarity=0.191 Sum_probs=20.3
Q ss_pred CCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 9499999986342999988755
Q gi|254781147|r 35 LTQKEIRNRTGFAQSWISELET 56 (83)
Q Consensus 35 ltq~ela~~~gis~~~is~iE~ 56 (83)
+|..|+|+.+||+..+|..||+
T Consensus 1 YtI~eva~~~gv~~~tLR~wE~ 22 (68)
T cd01104 1 YTIGAVARLTGVSPDTLRAWER 22 (68)
T ss_pred CCHHHHHHHHCCCHHHHHHHHH
T ss_conf 9789999998829899999998
No 167
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=79.76 E-value=4.2 Score=21.41 Aligned_cols=46 Identities=13% Similarity=0.008 Sum_probs=28.5
Q ss_pred CCHHHHHHHHHHHHHHHHHHHCCCCCC-----------------CHHHHHHHHHHHCCCHHHH
Q ss_conf 949999998634299998875589994-----------------4899999999928999996
Q gi|254781147|r 35 LTQKEIRNRTGFAQSWISELETGKSTI-----------------NIDNMIILAHTLDTPLWKL 80 (83)
Q Consensus 35 ltq~ela~~~gis~~~is~iE~G~~~~-----------------~~~~l~~la~al~i~~~~l 80 (83)
++..|+|+++|+|..+|.-||.-.-.+ .--.+.+-++.+|.++.+.
T Consensus 2 ~~Ige~A~~~gvs~~tiRyYE~~GLl~~~~R~~~gyR~Y~~~~v~rL~fI~~~r~lGfsL~eI 64 (140)
T PRK09514 2 YRIGELAKLCEVTPDTLRFYEKQGLMDPSVRTESGYRLYTEQDLQRLRFILRAKQLGFTLEEI 64 (140)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCEECCCCCHHHHHHHHHHHHHCCCCHHHH
T ss_conf 869999999896899999999869998651189980206710999999999999939999999
No 168
>PRK06930 positive control sigma-like factor; Validated
Probab=79.76 E-value=2.9 Score=22.44 Aligned_cols=46 Identities=13% Similarity=0.130 Sum_probs=32.1
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCH
Q ss_conf 99999998399499999986342999988755899944899999999928999
Q gi|254781147|r 25 NFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPL 77 (83)
Q Consensus 25 ~ir~~R~~~gltq~ela~~~gis~~~is~iE~G~~~~~~~~l~~la~al~i~~ 77 (83)
.+.-+....|+|+.++|+.+|||.+++...-.. ...+|.+-++-++
T Consensus 121 evfll~~~~glsy~EIA~~L~Is~~tV~~~l~R-------A~~Ki~~~~~~~L 166 (170)
T PRK06930 121 EVYLMHRGYGLSYSEIAAYLNIKKSTVQSMIER-------AEKKIAKQINESL 166 (170)
T ss_pred HHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHH-------HHHHHHHHHCCCC
T ss_conf 999889761888999999979889999999999-------9999999854053
No 169
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=79.72 E-value=2 Score=23.35 Aligned_cols=32 Identities=22% Similarity=0.298 Sum_probs=24.2
Q ss_pred HHHHHH--HCCCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 999999--83994999999863429999887558
Q gi|254781147|r 26 FRNIRK--EAKLTQKEIRNRTGFAQSWISELETG 57 (83)
Q Consensus 26 ir~~R~--~~gltq~ela~~~gis~~~is~iE~G 57 (83)
|-..|- ..++|++|+|+..|||+..|++||+.
T Consensus 238 Il~~Ry~~d~~~TL~EIg~~lgiSrERVRQIe~k 271 (284)
T PRK06596 238 IIEARWLDDDKSTLQELAAEYGVSAERIRQIEKN 271 (284)
T ss_pred HHHHHCCCCCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 9999767999948999999979799999999999
No 170
>PRK10668 DNA-binding transcriptional repressor AcrR; Provisional
Probab=79.28 E-value=3.2 Score=22.15 Aligned_cols=39 Identities=13% Similarity=0.052 Sum_probs=29.7
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf 999999999839949999998634299998875589994
Q gi|254781147|r 23 VNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTI 61 (83)
Q Consensus 23 g~~ir~~R~~~gltq~ela~~~gis~~~is~iE~G~~~~ 61 (83)
+..+-.-+--.|.|..|+|+.+|||+++|..+..+|..+
T Consensus 20 A~~lFaekGy~~ttl~dIA~~AGVS~GaiY~HF~sK~dL 58 (216)
T PRK10668 20 ALRLFSQQGVSATSLADIAKAAGVTRGAIYWHFKNKSDL 58 (216)
T ss_pred HHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHCCCHHHH
T ss_conf 999999849351889999999689857999875999999
No 171
>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=79.00 E-value=1.5 Score=24.07 Aligned_cols=23 Identities=26% Similarity=0.169 Sum_probs=20.7
Q ss_pred CCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 94999999863429999887558
Q gi|254781147|r 35 LTQKEIRNRTGFAQSWISELETG 57 (83)
Q Consensus 35 ltq~ela~~~gis~~~is~iE~G 57 (83)
+|..|+|+.+|++..+|.-||.-
T Consensus 1 ytI~eva~~~gvs~~tlR~ye~~ 23 (49)
T cd04761 1 YTIGELAKLTGVSPSTLRYYERI 23 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHC
T ss_conf 95889999989399999999997
No 172
>pfam04967 HTH_10 HTH DNA binding domain.
Probab=78.81 E-value=1.7 Score=23.72 Aligned_cols=30 Identities=20% Similarity=0.256 Sum_probs=23.4
Q ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 999999839949999998634299998875
Q gi|254781147|r 26 FRNIRKEAKLTQKEIRNRTGFAQSWISELE 55 (83)
Q Consensus 26 ir~~R~~~gltq~ela~~~gis~~~is~iE 55 (83)
.=.+-.-++.|..|+|+.+|||.++++..-
T Consensus 15 ~GYfd~PR~~~l~elA~~lgis~sT~~~hL 44 (53)
T pfam04967 15 MGYFDYPRRVTLKDLAKELGISKSTLSEHL 44 (53)
T ss_pred CCCCCCCCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 689778876889999999698999999999
No 173
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=78.70 E-value=2.6 Score=22.72 Aligned_cols=31 Identities=13% Similarity=0.224 Sum_probs=20.8
Q ss_pred CCHHHHHHHHHHHHHHHHHHHCCCCCCCHHH
Q ss_conf 9499999986342999988755899944899
Q gi|254781147|r 35 LTQKEIRNRTGFAQSWISELETGKSTINIDN 65 (83)
Q Consensus 35 ltq~ela~~~gis~~~is~iE~G~~~~~~~~ 65 (83)
||.+++|+.+|+|.++++++-+-....+...
T Consensus 2 lsl~~lA~~~~~S~~~l~~~f~~~~g~s~~~ 32 (84)
T smart00342 2 LTLEDLAEALGMSPRHLQRLFKKETGTTPKQ 32 (84)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHCCCHHH
T ss_conf 8999999988909999999999988939999
No 174
>pfam08281 Sigma70_r4_2 Sigma-70, region 4. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif.
Probab=78.35 E-value=3.2 Score=22.13 Aligned_cols=31 Identities=16% Similarity=0.141 Sum_probs=26.1
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999983994999999863429999887
Q gi|254781147|r 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 24 ~~ir~~R~~~gltq~ela~~~gis~~~is~i 54 (83)
+.+-.++.-.|+|.+|.|+.+|+|.+++...
T Consensus 16 r~~~~l~~~~~~s~~eIA~~lg~s~~tVk~~ 46 (54)
T pfam08281 16 REVFLLRYLEGLSYAEIAELLGISEGTVKSR 46 (54)
T ss_pred HHHHHHHHHHCCCHHHHHHHHCCCHHHHHHH
T ss_conf 9896879987859999999989499999999
No 175
>pfam07900 DUF1670 Protein of unknown function (DUF1670). The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=78.18 E-value=6.1 Score=20.47 Aligned_cols=45 Identities=22% Similarity=0.234 Sum_probs=30.8
Q ss_pred HHHHHHHHHHHC-CCCHHHHHHHHHHHHHHHHHH------HCCCCCCCHHHH
Q ss_conf 999999999983-994999999863429999887------558999448999
Q gi|254781147|r 22 FVNNFRNIRKEA-KLTQKEIRNRTGFAQSWISEL------ETGKSTINIDNM 66 (83)
Q Consensus 22 ~g~~ir~~R~~~-gltq~ela~~~gis~~~is~i------E~G~~~~~~~~l 66 (83)
+.+-...+..+- =+||+|+|..+|+|.++|++. |+|..-|+-.+.
T Consensus 92 i~Ri~~EA~~QgglLT~~Dla~LL~~S~~TI~~~ik~ye~~~g~vvPtRG~i 143 (220)
T pfam07900 92 IVRIFNEAYEQGALLTHADIAILLGVSTTTISRHVKEYEERTGEVVPTRGII 143 (220)
T ss_pred HHHHHHHHHHCCCEEEHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCCCCCCC
T ss_conf 9999999997388511766999988988899999999999709663578720
No 176
>pfam01418 HTH_6 Helix-turn-helix domain, rpiR family. This domain contains a helix-turn-helix motif. The best characterized member of this family is RpiR, a regulator of the expression of rpiB gene.
Probab=78.18 E-value=3.4 Score=21.97 Aligned_cols=36 Identities=8% Similarity=0.180 Sum_probs=28.1
Q ss_pred HHHH-HHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 9999-99999983994999999863429999887558
Q gi|254781147|r 22 FVNN-FRNIRKEAKLTQKEIRNRTGFAQSWISELETG 57 (83)
Q Consensus 22 ~g~~-ir~~R~~~gltq~ela~~~gis~~~is~iE~G 57 (83)
++.. +.....-..+|..++|+.+|+|.++|.++=+.
T Consensus 21 ia~yil~~~~~~~~~si~~lA~~~~vS~atv~Rf~kk 57 (106)
T pfam01418 21 IADYILASPDNAIHLSIAELAKAAGVSEASVVRFCRK 57 (106)
T ss_pred HHHHHHHCHHHHHHCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 9999992999998833999998969989999999999
No 177
>PRK11753 cAMP-regulatory protein; Provisional
Probab=77.99 E-value=4.9 Score=21.05 Aligned_cols=22 Identities=23% Similarity=0.403 Sum_probs=19.9
Q ss_pred CCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 9949999998634299998875
Q gi|254781147|r 34 KLTQKEIRNRTGFAQSWISELE 55 (83)
Q Consensus 34 gltq~ela~~~gis~~~is~iE 55 (83)
.+||+|+|..+|+|+.++|++-
T Consensus 168 ~lt~~eLA~~lG~sretvsR~L 189 (211)
T PRK11753 168 KITRQEIGRIVGCSREMVGRVL 189 (211)
T ss_pred CCCHHHHHHHHCCCHHHHHHHH
T ss_conf 4699999988699899999999
No 178
>COG1974 LexA SOS-response transcriptional repressors (RecA-mediated autopeptidases) [Transcription / Signal transduction mechanisms]
Probab=77.95 E-value=1.6 Score=23.87 Aligned_cols=49 Identities=14% Similarity=0.116 Sum_probs=44.1
Q ss_pred HHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHH
Q ss_conf 99983994999999863429999887558999448999999999289999
Q gi|254781147|r 29 IRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLW 78 (83)
Q Consensus 29 ~R~~~gltq~ela~~~gis~~~is~iE~G~~~~~~~~l~~la~al~i~~~ 78 (83)
..++.+.+++++++.+|+++ ++..|.++-..++.+.+...+++|+..-.
T Consensus 7 rq~el~~~~~~~~~~~g~~p-s~~e~~~~~~~~s~~~~~~~l~~L~~~g~ 55 (201)
T COG1974 7 RQKELLDFIRSLIKETGYPP-SIREIGDALGLASPSAIHSHLKALERKGY 55 (201)
T ss_pred HHHHHHHHHHHHHHHHCCCC-HHHHHHHHHCCCCHHHHHHHHHHHHCCCC
T ss_conf 89998999999999728993-08999875178984899999999730885
No 179
>cd04773 HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.
Probab=77.94 E-value=1.8 Score=23.65 Aligned_cols=46 Identities=17% Similarity=0.141 Sum_probs=30.5
Q ss_pred CCHHHHHHHHHHHHHHHHHHHCC------------CCCCCHHH-----HHHHHHHHCCCHHHH
Q ss_conf 94999999863429999887558------------99944899-----999999928999996
Q gi|254781147|r 35 LTQKEIRNRTGFAQSWISELETG------------KSTINIDN-----MIILAHTLDTPLWKL 80 (83)
Q Consensus 35 ltq~ela~~~gis~~~is~iE~G------------~~~~~~~~-----l~~la~al~i~~~~l 80 (83)
||..|+|+++|++.++|.-||.- -+.-+... ....++.+|.++.+.
T Consensus 1 mtIgelAk~~gvs~~tlRyYE~~GLl~p~r~~~~gyR~Y~~~~i~~l~~I~~lr~~G~sl~eI 63 (108)
T cd04773 1 MTIGELAHLLGVPPSTLRHWEKEGLLSPDREPETGYRVYDPSDVRDARLIHLLRRGGYLLEQI 63 (108)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCEECCHHHHHHHHHHHHHHHCCCCHHHH
T ss_conf 968999999897999999999779829987799985467999999999999999969999999
No 180
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1; InterPro: IPR014327 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 recognized by the major sigma factors , . This group of sigma factors are members of the sigma-70 family and are found primarily in the genus Bacteroides. This appears to have resulted from a lineage-specific expansion as Bacteroides thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037 (Tannerella forsythensis ATCC 43037), Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currently only two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=77.67 E-value=2.8 Score=22.51 Aligned_cols=31 Identities=16% Similarity=0.188 Sum_probs=26.0
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 9999999998399499999986342999988
Q gi|254781147|r 23 VNNFRNIRKEAKLTQKEIRNRTGFAQSWISE 53 (83)
Q Consensus 23 g~~ir~~R~~~gltq~ela~~~gis~~~is~ 53 (83)
-+.|-.+-...|+|-+|.|+.+|||..||-.
T Consensus 124 ~R~iF~lsr~eg~s~~EIA~~L~iS~~TVe~ 154 (167)
T TIGR02985 124 CREIFILSRFEGLSNKEIAEELGISVKTVEY 154 (167)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHCCCHHHHHH
T ss_conf 9999999886179867899884898889999
No 181
>COG1309 AcrR Transcriptional regulator [Transcription]
Probab=77.64 E-value=5.1 Score=20.94 Aligned_cols=49 Identities=12% Similarity=0.021 Sum_probs=33.6
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHH
Q ss_conf 9999999998399499999986342999988755899944899999999
Q gi|254781147|r 23 VNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAH 71 (83)
Q Consensus 23 g~~ir~~R~~~gltq~ela~~~gis~~~is~iE~G~~~~~~~~l~~la~ 71 (83)
+..+...+--.++|..++|+.+|++++++.++...+...-...+..+..
T Consensus 21 a~~l~~~~G~~~~t~~~Ia~~agvs~~~~Y~~f~~K~~l~~~~~~~~~~ 69 (201)
T COG1309 21 ALRLFAEKGYAATTVDEIAKAAGVSKGTLYRHFPSKEDLLLALLERALE 69 (201)
T ss_pred HHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHCCCHHHHHHHHHHHHHH
T ss_conf 9999986593228999999887949789998878999999999999999
No 182
>cd01107 HTH_BmrR Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=77.41 E-value=1.9 Score=23.53 Aligned_cols=46 Identities=13% Similarity=0.084 Sum_probs=31.2
Q ss_pred CCHHHHHHHHHHHHHHHHHHHCCC-CCCC------------HHH-----HHHHHHHHCCCHHHH
Q ss_conf 949999998634299998875589-9944------------899-----999999928999996
Q gi|254781147|r 35 LTQKEIRNRTGFAQSWISELETGK-STIN------------IDN-----MIILAHTLDTPLWKL 80 (83)
Q Consensus 35 ltq~ela~~~gis~~~is~iE~G~-~~~~------------~~~-----l~~la~al~i~~~~l 80 (83)
+|..|+|+.+|||.++|.-||.-. -.|. .+. ....++.+|+|+.+.
T Consensus 1 ~tIgevAk~~gvs~~TlRyYE~~GLl~P~~~~~~ngyR~Y~~~~i~~l~~I~~lr~~G~sL~eI 64 (108)
T cd01107 1 FTIGEFAKLSNLSIKALRYYDKIGLLKPAYVDPDTGYRYYSAEQLERLNRIKYLRDLGFPLEEI 64 (108)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCEECCCCCCEEECHHHHHHHHHHHHHHHCCCCHHHH
T ss_conf 9789999998959999999998599885415699984437788989999999999979999999
No 183
>COG1508 RpoN DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription]
Probab=77.30 E-value=1.5 Score=24.15 Aligned_cols=39 Identities=21% Similarity=0.217 Sum_probs=30.1
Q ss_pred CCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHH
Q ss_conf 949999998634299998875589994489999999992
Q gi|254781147|r 35 LTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTL 73 (83)
Q Consensus 35 ltq~ela~~~gis~~~is~iE~G~~~~~~~~l~~la~al 73 (83)
|+..++|+.+|++.||||++-+++..-+---++.+-..|
T Consensus 331 L~LrdvA~~i~~HESTISRai~nKy~~tprG~feLk~FF 369 (444)
T COG1508 331 LVLRDVADEIGMHESTISRAITNKYLATPRGLFELKYFF 369 (444)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCEEEHHHHH
T ss_conf 319999988371288899998254104886334489887
No 184
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=76.95 E-value=3.5 Score=21.90 Aligned_cols=35 Identities=14% Similarity=0.235 Sum_probs=28.0
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHH-HHHCCC
Q ss_conf 99999999839949999998634299998-875589
Q gi|254781147|r 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWIS-ELETGK 58 (83)
Q Consensus 24 ~~ir~~R~~~gltq~ela~~~gis~~~is-~iE~G~ 58 (83)
+.+-.++.-.|+|.+|+|+.+|+|.+++. ++-++.
T Consensus 155 R~v~~L~~~eglS~~EIA~~Lgis~~TVKsrL~RAr 190 (231)
T PRK11922 155 RAVFVLRVVEELSVEETAQALGLPEETVKTRLHRAR 190 (231)
T ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf 999999999399999999998939999999999999
No 185
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=76.84 E-value=4.8 Score=21.09 Aligned_cols=34 Identities=9% Similarity=0.123 Sum_probs=24.5
Q ss_pred HHHHHHHHHHHHC--CCCHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999999983--994999999863429999887
Q gi|254781147|r 21 IFVNNFRNIRKEA--KLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 21 ~~g~~ir~~R~~~--gltq~ela~~~gis~~~is~i 54 (83)
++..-+..++... .+|-+|+|+.+|+|+.+..+|
T Consensus 163 TL~~i~~~l~~~~~~~~sa~eva~~~giSRvTaRRY 198 (239)
T PRK10430 163 TLRTLCQWIDAHQDYEFSTDELANEVNISRVSCRKY 198 (239)
T ss_pred HHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 999999999827999846999998858529889999
No 186
>pfam08279 HTH_11 HTH domain. This family includes helix-turn-helix domains in a wide variety of proteins.
Probab=76.75 E-value=2.9 Score=22.42 Aligned_cols=30 Identities=10% Similarity=0.202 Sum_probs=23.6
Q ss_pred HHHHHHHHCC-CCHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999839-94999999863429999887
Q gi|254781147|r 25 NFRNIRKEAK-LTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 25 ~ir~~R~~~g-ltq~ela~~~gis~~~is~i 54 (83)
-+..++...+ +|-.++|+.+|||+++|.+.
T Consensus 5 il~~L~~~~~~vt~~~La~~l~VSr~TV~rd 35 (55)
T pfam08279 5 ILELLLQAREPISGQELAEKLGVSRRTIRRD 35 (55)
T ss_pred HHHHHHHCCCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 9999997699918999999969889999999
No 187
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=76.59 E-value=5 Score=21.01 Aligned_cols=32 Identities=6% Similarity=0.289 Sum_probs=25.5
Q ss_pred HCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCH
Q ss_conf 83994999999863429999887558999448
Q gi|254781147|r 32 EAKLTQKEIRNRTGFAQSWISELETGKSTINI 63 (83)
Q Consensus 32 ~~gltq~ela~~~gis~~~is~iE~G~~~~~~ 63 (83)
...+|.+++|+.+|+|+++++++-+.....++
T Consensus 19 ~~~i~l~~lA~~~~~S~~~l~r~Fk~~~g~t~ 50 (107)
T PRK10219 19 DQPLNIDVVAKKSGYSKWYLQRMFRTVTHQTL 50 (107)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHCCCH
T ss_conf 99999999998989399999999999989099
No 188
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=76.44 E-value=2 Score=23.30 Aligned_cols=46 Identities=15% Similarity=0.068 Sum_probs=30.4
Q ss_pred CCHHHHHHHHHHHHHHHHHHHCCC-CCC-----------CHHH-----HHHHHHHHCCCHHHH
Q ss_conf 949999998634299998875589-994-----------4899-----999999928999996
Q gi|254781147|r 35 LTQKEIRNRTGFAQSWISELETGK-STI-----------NIDN-----MIILAHTLDTPLWKL 80 (83)
Q Consensus 35 ltq~ela~~~gis~~~is~iE~G~-~~~-----------~~~~-----l~~la~al~i~~~~l 80 (83)
+|..|+|+.+|++.++|.-||.-. -.| +... ..+..+.+|+++.+.
T Consensus 1 ytI~e~a~~~gvs~~tlR~ye~~Gll~p~~r~~~g~R~Y~~~di~~l~~I~~lr~~G~~l~~I 63 (70)
T smart00422 1 YTIGEVAKLAGVSVRTLRYYERIGLLPPPIRTEGGYRLYSDEDLERLRFIKRLKELGFSLEEI 63 (70)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCEECCHHHHHHHHHHHHHHHCCCCHHHH
T ss_conf 978899999896999999999858989984489997443999999999999999978999999
No 189
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=76.29 E-value=6.6 Score=20.27 Aligned_cols=31 Identities=16% Similarity=0.130 Sum_probs=25.0
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999983994999999863429999887
Q gi|254781147|r 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 24 ~~ir~~R~~~gltq~ela~~~gis~~~is~i 54 (83)
..+-.+-...|+|..++|++.|+|.+++-++
T Consensus 11 ~~~~~~~~~~G~S~re~Ak~~gvs~sTvy~w 41 (138)
T COG3415 11 ERVVDAVVGEGLSCREAAKRFGVSISTVYRW 41 (138)
T ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 9999999976854999999969229999999
No 190
>pfam00376 MerR MerR family regulatory protein.
Probab=76.24 E-value=2 Score=23.37 Aligned_cols=24 Identities=17% Similarity=0.040 Sum_probs=20.7
Q ss_pred CHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf 499999986342999988755899
Q gi|254781147|r 36 TQKEIRNRTGFAQSWISELETGKS 59 (83)
Q Consensus 36 tq~ela~~~gis~~~is~iE~G~~ 59 (83)
|..|+|+.+|||.++|..||+---
T Consensus 1 ti~e~A~~~gvs~~tlR~ye~~Gl 24 (38)
T pfam00376 1 TIGEVAKLLGVSPRTLRYYEKIGL 24 (38)
T ss_pred CHHHHHHHHCCCHHHHHHHHHCCC
T ss_conf 989999998879999999998689
No 191
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=76.14 E-value=3.7 Score=21.75 Aligned_cols=29 Identities=14% Similarity=0.036 Sum_probs=25.3
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 99999998399499999986342999988
Q gi|254781147|r 25 NFRNIRKEAKLTQKEIRNRTGFAQSWISE 53 (83)
Q Consensus 25 ~ir~~R~~~gltq~ela~~~gis~~~is~ 53 (83)
.+-.++.-.|+|.+|+|+.+|||.+++-.
T Consensus 126 ~vl~L~~~egls~~EIAe~Lgis~~TVks 154 (190)
T PRK12516 126 EAIILIGASGFAYEEAAEICGCAVGTIKS 154 (190)
T ss_pred HHHHHHHHCCCCHHHHHHHHCCCHHHHHH
T ss_conf 99998998299999999998949999999
No 192
>cd04780 HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=76.14 E-value=2.1 Score=23.28 Aligned_cols=22 Identities=18% Similarity=0.262 Sum_probs=17.1
Q ss_pred CCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 9499999986342999988755
Q gi|254781147|r 35 LTQKEIRNRTGFAQSWISELET 56 (83)
Q Consensus 35 ltq~ela~~~gis~~~is~iE~ 56 (83)
|+..|+|+++|++..+|.-||+
T Consensus 1 M~IgelA~~tGvs~~TIRyYe~ 22 (95)
T cd04780 1 MRMSELSKRSGVSVATIKYYLR 22 (95)
T ss_pred CCHHHHHHHHCCCHHHHHHHHH
T ss_conf 9789999998978999999999
No 193
>TIGR01817 nifA Nif-specific regulatory protein; InterPro: IPR010113 This entry represents NifA, a DNA-binding regulatory protein for nitrogen fixation. Not included in this group are: the homologue in Aquifex aeolicus (which lacks nitrogenase), transcriptional activators of alternative nitrogenases (VFe or FeFe instead of MoFe), and truncated forms. In diazotrophic proteobacteria, the sigma54-dependent activator NifA activates transcription of the nif (nitrogen fixation) genes by a conserved mechanism common to members of the enhancer binding protein family. Although NifA proteins have similar domain structures, both transcriptional regulation of nifA expression and posttranslational regulation of NifA activity by oxygen and fixed nitrogen vary significantly from one organism to another. In Klebsiella pneumoniae and Azotobacter vinelandii, nifA is co-ordinately transcribed with a second gene, nifL, whose product inhibits NifA activity in response to oxygen and fixed nitrogen .; GO: 0003677 DNA binding, 0016563 transcription activator activity, 0009399 nitrogen fixation.
Probab=76.02 E-value=3 Score=22.32 Aligned_cols=31 Identities=10% Similarity=0.057 Sum_probs=27.2
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999983994999999863429999887
Q gi|254781147|r 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 24 ~~ir~~R~~~gltq~ela~~~gis~~~is~i 54 (83)
++|-.+.++.||-|+.-|..+|+++..++.=
T Consensus 533 ERli~AlE~aGWVQAKAARlLg~TPRQVgYa 563 (574)
T TIGR01817 533 ERLIAALEKAGWVQAKAARLLGLTPRQVGYA 563 (574)
T ss_pred HHHHHHHHHCCHHHHHHHHHHCCCHHHHHHH
T ss_conf 8999999751537999999737865589999
No 194
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=75.75 E-value=4 Score=21.56 Aligned_cols=29 Identities=14% Similarity=0.219 Sum_probs=26.0
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHH
Q ss_conf 99999999839949999998634299998
Q gi|254781147|r 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWIS 52 (83)
Q Consensus 24 ~~ir~~R~~~gltq~ela~~~gis~~~is 52 (83)
+-|+.+.+...+|-.++|+.+|+|.+++.
T Consensus 13 ~IL~~Lq~d~R~s~~eiA~~lglS~stv~ 41 (153)
T PRK11179 13 GILEALMENARTPYAELAKQFGVSPGTIH 41 (153)
T ss_pred HHHHHHHHCCCCCHHHHHHHHCCCHHHHH
T ss_conf 99999998489999999999892999999
No 195
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=75.72 E-value=3.8 Score=21.67 Aligned_cols=30 Identities=23% Similarity=0.255 Sum_probs=25.7
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 999999998399499999986342999988
Q gi|254781147|r 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISE 53 (83)
Q Consensus 24 ~~ir~~R~~~gltq~ela~~~gis~~~is~ 53 (83)
+.+-.++.-.|+|.+|+|+.+|+|.+++..
T Consensus 112 R~v~~L~~~eg~s~~EIA~~L~is~~tVks 141 (181)
T PRK09637 112 AEALRLTELEGLSQKEIAEKLGLSLSGAKS 141 (181)
T ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHH
T ss_conf 899799988599999999998949999999
No 196
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=75.35 E-value=4.2 Score=21.46 Aligned_cols=31 Identities=19% Similarity=0.399 Sum_probs=26.8
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 9999999998399499999986342999988
Q gi|254781147|r 23 VNNFRNIRKEAKLTQKEIRNRTGFAQSWISE 53 (83)
Q Consensus 23 g~~ir~~R~~~gltq~ela~~~gis~~~is~ 53 (83)
-+-|+.+.....+|..++|+++|+|++++.+
T Consensus 17 ~~IL~~Lq~daR~s~~eLA~~vglS~stv~~ 47 (164)
T PRK11169 17 RNILNELQKDGRISNVELSKRVGLSPTPCLE 47 (164)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHCCCHHHHHH
T ss_conf 9999999984899999999998929999999
No 197
>PRK11569 transcriptional repressor IclR; Provisional
Probab=75.31 E-value=6.7 Score=20.22 Aligned_cols=53 Identities=11% Similarity=0.121 Sum_probs=31.0
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHHHHHHH-HHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 69888888689899999999999999999-983994999999863429999887
Q gi|254781147|r 2 PRRKRDEPHLSDAILRERMIFVNNFRNIR-KEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 2 p~~~~~~p~~~~~~~~~~~~~g~~ir~~R-~~~gltq~ela~~~gis~~~is~i 54 (83)
|+++.+...++....+.-+.--.-|..+- ...++|..|+|+.+|++++++.++
T Consensus 10 ~~~~~~~~~~~~~~Vqsl~Ral~IL~~la~~~~~lsl~eia~~lglpksT~~Rl 63 (274)
T PRK11569 10 GRKPAAATAPATGQVQSLTRGLKLLEWIAESNGSVALTELAQQAGLPNSTTHRL 63 (274)
T ss_pred CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 989998899988877699999999999963899989999999879199999999
No 198
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=75.28 E-value=4.1 Score=21.53 Aligned_cols=31 Identities=13% Similarity=0.217 Sum_probs=26.2
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999983994999999863429999887
Q gi|254781147|r 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 24 ~~ir~~R~~~gltq~ela~~~gis~~~is~i 54 (83)
+.+-.+|.-.|+|.+|+|+.+|+|.+++...
T Consensus 142 R~vl~L~~~egls~~EIA~~lgis~~tVks~ 172 (195)
T PRK12532 142 ARVFTLKEILGFSSDEIQQMCGISTSNYHTI 172 (195)
T ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 8999999981999999999989599999999
No 199
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=75.16 E-value=5.8 Score=20.60 Aligned_cols=34 Identities=12% Similarity=0.135 Sum_probs=27.6
Q ss_pred HHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHH
Q ss_conf 9839949999998634299998875589994489
Q gi|254781147|r 31 KEAKLTQKEIRNRTGFAQSWISELETGKSTINID 64 (83)
Q Consensus 31 ~~~gltq~ela~~~gis~~~is~iE~G~~~~~~~ 64 (83)
....+|.+++|+.+|+|+++++++.+.....|+.
T Consensus 196 ~~~~isl~~lA~~~~lS~s~l~rlFk~~~G~sp~ 229 (290)
T PRK10572 196 LASEFDIESVAQHVCLSPSRLSHLFRQQLGISVL 229 (290)
T ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHHHHHCCCHH
T ss_conf 3799999999989697999999999986498999
No 200
>cd04770 HTH_HMRTR Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators. Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper), CadR (cadmium), PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=75.04 E-value=2.4 Score=22.93 Aligned_cols=23 Identities=17% Similarity=0.163 Sum_probs=15.9
Q ss_pred CCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 94999999863429999887558
Q gi|254781147|r 35 LTQKEIRNRTGFAQSWISELETG 57 (83)
Q Consensus 35 ltq~ela~~~gis~~~is~iE~G 57 (83)
||..|+|+.+|+|.++|.-||.-
T Consensus 1 m~Ige~A~~~gvs~~tlR~Ye~~ 23 (123)
T cd04770 1 MKIGELAKAAGVSPDTIRYYERI 23 (123)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHC
T ss_conf 96899999989599999999981
No 201
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=74.87 E-value=4.2 Score=21.42 Aligned_cols=30 Identities=23% Similarity=0.234 Sum_probs=25.4
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 999999998399499999986342999988
Q gi|254781147|r 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISE 53 (83)
Q Consensus 24 ~~ir~~R~~~gltq~ela~~~gis~~~is~ 53 (83)
+.+-.+|.-.|+|.+|+|+.+|+|.+++..
T Consensus 118 R~v~~L~~~~g~s~~EIA~~lgis~~tVk~ 147 (161)
T PRK12541 118 RNVLLLRDYYGFSYKEIAEMTGLSLAKVKI 147 (161)
T ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHH
T ss_conf 999998997499999999998939999999
No 202
>pfam07037 DUF1323 Putative transcription regulator (DUF1323). This family consists of several hypothetical Enterobacterial proteins of around 120 residues in length. This family appears to have an HTH domain and is therefore likely to act as a transcriptional regulator.
Probab=74.81 E-value=2.4 Score=22.87 Aligned_cols=22 Identities=23% Similarity=0.407 Sum_probs=19.7
Q ss_pred CCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 9499999986342999988755
Q gi|254781147|r 35 LTQKEIRNRTGFAQSWISELET 56 (83)
Q Consensus 35 ltq~ela~~~gis~~~is~iE~ 56 (83)
||-+|||+.+|+|+++|+++-+
T Consensus 1 mT~eELa~~~G~srQtINkwaR 22 (122)
T pfam07037 1 MTPEELAELTGYSRQTINRWVR 22 (122)
T ss_pred CCHHHHHHHHCCHHHHHHHHHH
T ss_conf 9878998874712999999999
No 203
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=74.80 E-value=5 Score=20.99 Aligned_cols=30 Identities=20% Similarity=0.145 Sum_probs=25.7
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 999999998399499999986342999988
Q gi|254781147|r 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISE 53 (83)
Q Consensus 24 ~~ir~~R~~~gltq~ela~~~gis~~~is~ 53 (83)
+.+-.++.-.|+|.+|+|+.+|+|.+++..
T Consensus 137 r~v~~L~~~eg~s~~EIA~~lgis~~tVks 166 (184)
T PRK12539 137 RLAIQAVKLDGLSVAEAATRSGMSESAVKV 166 (184)
T ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHH
T ss_conf 999999999499999999998919999999
No 204
>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=74.73 E-value=2.2 Score=23.15 Aligned_cols=22 Identities=23% Similarity=0.190 Sum_probs=20.3
Q ss_pred CCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 9499999986342999988755
Q gi|254781147|r 35 LTQKEIRNRTGFAQSWISELET 56 (83)
Q Consensus 35 ltq~ela~~~gis~~~is~iE~ 56 (83)
+|..|+|+.+||+..+|.-||+
T Consensus 1 ysI~eva~~~Gv~~~tLR~wE~ 22 (68)
T cd04763 1 YTIGEVALLTGIKPHVLRAWER 22 (68)
T ss_pred CCHHHHHHHHCCCHHHHHHHHH
T ss_conf 9788999998879457589887
No 205
>pfam05269 Phage_CII Bacteriophage CII protein. This family consists of several phage CII regulatory proteins. CII plays a key role in the lysis-lysogeny decision in bacteriophage lambda and related phages.
Probab=74.65 E-value=1.6 Score=23.86 Aligned_cols=36 Identities=19% Similarity=0.226 Sum_probs=27.1
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHH
Q ss_conf 3994999999863429999887558999448999999
Q gi|254781147|r 33 AKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIIL 69 (83)
Q Consensus 33 ~gltq~ela~~~gis~~~is~iE~G~~~~~~~~l~~l 69 (83)
.-++|..+|+.+|++.+.||++.++= .|....|..+
T Consensus 22 a~~gq~~~A~~~Gv~es~ISRwK~~~-~~~~smllAv 57 (91)
T pfam05269 22 AMLGQRKTAEAVGVDESQISRWKRDW-IPKFSMLLAV 57 (91)
T ss_pred HHHHHHHHHHHHCCCHHHHHHHHHHH-HHHHHHHHHH
T ss_conf 99843668999688899863444306-9999999999
No 206
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=74.64 E-value=4.4 Score=21.35 Aligned_cols=30 Identities=13% Similarity=0.048 Sum_probs=25.6
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 999999998399499999986342999988
Q gi|254781147|r 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISE 53 (83)
Q Consensus 24 ~~ir~~R~~~gltq~ela~~~gis~~~is~ 53 (83)
+.+-.++...|+|.+|+|+.+|+|.+++..
T Consensus 118 r~v~~L~~~~g~s~~EIA~~lgis~~tVks 147 (164)
T PRK12547 118 REAIILIGASGFSYEEAAEICGCAVGTIKS 147 (164)
T ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHH
T ss_conf 999998998499999999998939999999
No 207
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=74.55 E-value=4.4 Score=21.30 Aligned_cols=34 Identities=9% Similarity=0.098 Sum_probs=27.7
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHH-HHCC
Q ss_conf 999999998399499999986342999988-7558
Q gi|254781147|r 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISE-LETG 57 (83)
Q Consensus 24 ~~ir~~R~~~gltq~ela~~~gis~~~is~-iE~G 57 (83)
+.+-.+|.-.|+|.+|+|+.+|+|.+++.. +-+|
T Consensus 135 R~vi~L~~~~g~s~~EIA~~l~is~~tVk~rl~rA 169 (190)
T PRK12543 135 KQVIILRYLHDYSQEEVAQILHIPIGTVKSRIHAA 169 (190)
T ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 99999999859999999999893999999999999
No 208
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=74.48 E-value=4.5 Score=21.29 Aligned_cols=30 Identities=10% Similarity=0.062 Sum_probs=25.1
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 999999983994999999863429999887
Q gi|254781147|r 25 NFRNIRKEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 25 ~ir~~R~~~gltq~ela~~~gis~~~is~i 54 (83)
.+-.++.-.|+|.+|+|+.+|+|.+++-..
T Consensus 143 ~vi~L~~~~g~s~~EIA~~L~is~~TVk~~ 172 (187)
T PRK13919 143 RVIEVLYYQGYTHREAARLLGLPLGTLKTW 172 (187)
T ss_pred HHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 999999985999999999989399999999
No 209
>cd00592 HTH_MerR-like Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators. Helix-turn-helix (HTH) MerR-like transcription regulator, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=74.46 E-value=2.5 Score=22.77 Aligned_cols=46 Identities=15% Similarity=0.117 Sum_probs=28.1
Q ss_pred CCHHHHHHHHHHHHHHHHHHHCC-----------CCCCCHHH-----HHHHHHHHCCCHHHH
Q ss_conf 94999999863429999887558-----------99944899-----999999928999996
Q gi|254781147|r 35 LTQKEIRNRTGFAQSWISELETG-----------KSTINIDN-----MIILAHTLDTPLWKL 80 (83)
Q Consensus 35 ltq~ela~~~gis~~~is~iE~G-----------~~~~~~~~-----l~~la~al~i~~~~l 80 (83)
+|..|+|+.+|++.++|.-||+- .+.-+... ..+.++.+|+|+.+.
T Consensus 1 ysI~eva~~~gvs~~tlR~Ye~~GLl~p~r~~~g~R~Y~~~~i~~l~~I~~lr~~G~sl~~I 62 (100)
T cd00592 1 YTIGEVAKLLGVSVRTLRYYEEKGLLPPERSENGYRLYSEEDLERLRLIRRLRELGLSLKEI 62 (100)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCHHHH
T ss_conf 97889999989599999999876999988358997425699999999999999979999999
No 210
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=74.44 E-value=4.4 Score=21.33 Aligned_cols=29 Identities=7% Similarity=0.021 Sum_probs=24.5
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 99999998399499999986342999988
Q gi|254781147|r 25 NFRNIRKEAKLTQKEIRNRTGFAQSWISE 53 (83)
Q Consensus 25 ~ir~~R~~~gltq~ela~~~gis~~~is~ 53 (83)
.+-.++.-.|+|.+|+|+.+|+|.+++-.
T Consensus 160 ~vi~L~~~egls~~EIA~~l~is~~TVks 188 (206)
T PRK12526 160 TVVKGVYFQELSQEQLAQQLNVPLGTVKS 188 (206)
T ss_pred HHHHHHHHCCCCHHHHHHHHCCCHHHHHH
T ss_conf 89899998599999999998939999999
No 211
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=74.33 E-value=4.5 Score=21.26 Aligned_cols=45 Identities=16% Similarity=0.199 Sum_probs=33.8
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHH-HHCCCCCCCHHHHHHHHHHHCCC
Q ss_conf 999999998399499999986342999988-75589994489999999992899
Q gi|254781147|r 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISE-LETGKSTINIDNMIILAHTLDTP 76 (83)
Q Consensus 24 ~~ir~~R~~~gltq~ela~~~gis~~~is~-iE~G~~~~~~~~l~~la~al~i~ 76 (83)
+.+-.++.-.|+|.+|+|+.+|+|.+++-. +-+| +.+|-+.||++
T Consensus 148 R~vi~L~~~~g~s~~EIA~~Lgis~~TVk~rl~rA--------~~~LR~~LG~~ 193 (194)
T PRK09646 148 REAITLAYYGGLTYREVAERLAVPLGTVKTRMRDG--------LRRLRDCLGVS 193 (194)
T ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHH--------HHHHHHHHCCC
T ss_conf 89999999939999999999891999999999999--------99999983789
No 212
>PRK09775 hypothetical protein; Provisional
Probab=74.15 E-value=3.7 Score=21.78 Aligned_cols=31 Identities=23% Similarity=0.322 Sum_probs=27.3
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999839949999998634299998875
Q gi|254781147|r 25 NFRNIRKEAKLTQKEIRNRTGFAQSWISELE 55 (83)
Q Consensus 25 ~ir~~R~~~gltq~ela~~~gis~~~is~iE 55 (83)
.|..++.+--+|-.+|++++|||+.++|+.-
T Consensus 3 ~l~~Ll~~Gp~~a~eLa~~lgvSqpTlSR~l 33 (443)
T PRK09775 3 LLTTLLLQGPLSAAELAQRLGISQATLSRLL 33 (443)
T ss_pred HHHHHHHCCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 6899997399359999998688888899999
No 213
>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=73.85 E-value=2.6 Score=22.65 Aligned_cols=22 Identities=23% Similarity=0.217 Sum_probs=20.2
Q ss_pred CCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 9499999986342999988755
Q gi|254781147|r 35 LTQKEIRNRTGFAQSWISELET 56 (83)
Q Consensus 35 ltq~ela~~~gis~~~is~iE~ 56 (83)
+|..|+|+.+|++..+|.-||.
T Consensus 1 YtI~eva~~~Gv~~~tLRyyEk 22 (67)
T cd04764 1 YTIKEVSEIIGVKPHTLRYYEK 22 (67)
T ss_pred CCHHHHHHHHCCCHHHHHHHHH
T ss_conf 9789999998868789999987
No 214
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=73.58 E-value=4.8 Score=21.09 Aligned_cols=39 Identities=15% Similarity=0.058 Sum_probs=30.0
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf 999999999839949999998634299998875589994
Q gi|254781147|r 23 VNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTI 61 (83)
Q Consensus 23 g~~ir~~R~~~gltq~ela~~~gis~~~is~iE~G~~~~ 61 (83)
+..+-.-+--.+-|.+++|+.+|||+++|..+..+|-..
T Consensus 20 A~~lFae~G~~~tTl~~IA~~AGVt~GaiY~HF~nKe~L 58 (213)
T PRK09975 20 AIAQFALRGVANTTLNDIADAANVTRGAIYWHFENKTQL 58 (213)
T ss_pred HHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHCCCHHHH
T ss_conf 999999859455889999999689848999877999999
No 215
>COG0789 SoxR Predicted transcriptional regulators [Transcription]
Probab=73.56 E-value=2.6 Score=22.66 Aligned_cols=46 Identities=17% Similarity=0.097 Sum_probs=28.3
Q ss_pred CCHHHHHHHHHHHHHHHHHHHCCC------------CCCCHH---H--HHHHHHHHCCCHHHH
Q ss_conf 949999998634299998875589------------994489---9--999999928999996
Q gi|254781147|r 35 LTQKEIRNRTGFAQSWISELETGK------------STINID---N--MIILAHTLDTPLWKL 80 (83)
Q Consensus 35 ltq~ela~~~gis~~~is~iE~G~------------~~~~~~---~--l~~la~al~i~~~~l 80 (83)
||..++|+.+|||..+|.-||.-- +.-+-. . +.+.++.+|+++.+.
T Consensus 1 ~~I~eva~~~gvs~~tLRyYe~~GLl~p~~~~~~gyR~Ys~~dl~~l~~I~~~r~~G~sL~eI 63 (124)
T COG0789 1 YTIGEVAKLTGVSVRTLRFYERKGLLSPERRDEGGYRYYTPEDLELLQIIKTLRELGFSLAEI 63 (124)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCEECCHHHHHHHHHHHHHHHCCCCHHHH
T ss_conf 959999999796999999999908999763589997631999999999999999869989999
No 216
>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB. Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=73.43 E-value=2.7 Score=22.56 Aligned_cols=46 Identities=15% Similarity=0.216 Sum_probs=28.2
Q ss_pred CCHHHHHHHHHHHHHHHHHHHCCC------------CCCCHH-----HHHHHHHHHCCCHHHH
Q ss_conf 949999998634299998875589------------994489-----9999999928999996
Q gi|254781147|r 35 LTQKEIRNRTGFAQSWISELETGK------------STINID-----NMIILAHTLDTPLWKL 80 (83)
Q Consensus 35 ltq~ela~~~gis~~~is~iE~G~------------~~~~~~-----~l~~la~al~i~~~~l 80 (83)
+|..|+|+.+|+|.++|.-||.-. +.-+.+ .....++.+|.++.+.
T Consensus 1 ytIgelA~~~gvs~~tlRyYe~~GLl~~~~r~~~gyR~Y~~~~v~rl~~I~~lr~lG~sL~eI 63 (113)
T cd01109 1 YTIKEVAEKTGLSADTLRYYEKEGLLPPVKRDENGIRDFTEEDLEWLEFIKCLRNTGMSIKDI 63 (113)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCEECCHHHHHHHHHHHHHHHCCCCHHHH
T ss_conf 978899999895999999999838979984089988623498989999797599879989999
No 217
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=73.18 E-value=5.7 Score=20.67 Aligned_cols=30 Identities=13% Similarity=0.095 Sum_probs=25.5
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 999999983994999999863429999887
Q gi|254781147|r 25 NFRNIRKEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 25 ~ir~~R~~~gltq~ela~~~gis~~~is~i 54 (83)
.+-.++.-.|+|.+|+|+.+|+|.+++...
T Consensus 143 ~v~~L~~~~~~s~~EIA~~l~is~~tVk~~ 172 (187)
T PRK09641 143 TVIVLKYIEELSLKEISEILDLPVGTVKTR 172 (187)
T ss_pred HHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 999999982998999999989399999999
No 218
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=73.03 E-value=5 Score=21.01 Aligned_cols=31 Identities=16% Similarity=0.140 Sum_probs=26.1
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999983994999999863429999887
Q gi|254781147|r 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 24 ~~ir~~R~~~gltq~ela~~~gis~~~is~i 54 (83)
+.+-.++.-.|+|.+|+|+.+|+|.+++...
T Consensus 142 R~vi~L~~~eg~s~~EIA~~lgis~~tVk~~ 172 (196)
T PRK12524 142 RQAVVLRHIEGLSNPEIAEVMQIGVEAVESL 172 (196)
T ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 9998999980899999999989299999999
No 219
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=72.92 E-value=5.3 Score=20.86 Aligned_cols=30 Identities=17% Similarity=0.448 Sum_probs=25.8
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 999999998399499999986342999988
Q gi|254781147|r 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISE 53 (83)
Q Consensus 24 ~~ir~~R~~~gltq~ela~~~gis~~~is~ 53 (83)
+-|+.+.+.-.+|-.++|+.+|+|.+++.+
T Consensus 7 ~Il~~L~~n~R~s~~~iA~~lg~S~~tv~~ 36 (108)
T smart00344 7 KILEELQKDARISLAELAKKVGLSPSTVHN 36 (108)
T ss_pred HHHHHHHHCCCCCHHHHHHHHCCCHHHHHH
T ss_conf 999999982899999999998939999999
No 220
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=72.91 E-value=4.8 Score=21.12 Aligned_cols=34 Identities=9% Similarity=0.057 Sum_probs=27.3
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHH-HHHCC
Q ss_conf 99999999839949999998634299998-87558
Q gi|254781147|r 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWIS-ELETG 57 (83)
Q Consensus 24 ~~ir~~R~~~gltq~ela~~~gis~~~is-~iE~G 57 (83)
+.+-.++.-.|+|.+|+|+.+|++.+++- ++-+|
T Consensus 119 R~vl~L~~~egls~~EIAe~Lgis~gTVKsRL~RA 153 (188)
T PRK12546 119 REALILVGASGFSYEEAAEMCGVAVGTVKSRANRA 153 (188)
T ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 88958799829899999999893999999999999
No 221
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=72.79 E-value=5.2 Score=20.91 Aligned_cols=33 Identities=6% Similarity=0.063 Sum_probs=26.6
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHHH-HHCC
Q ss_conf 99999998399499999986342999988-7558
Q gi|254781147|r 25 NFRNIRKEAKLTQKEIRNRTGFAQSWISE-LETG 57 (83)
Q Consensus 25 ~ir~~R~~~gltq~ela~~~gis~~~is~-iE~G 57 (83)
.+-.++.-.|+|.+|+|+.+|+|.+++-. +-+|
T Consensus 148 ~vi~L~~~e~~s~~EIAe~l~is~~TVKsrl~rA 181 (194)
T PRK12531 148 DVLQAVYLEELPHQQVAEMFDIPLGTVKSRLRLA 181 (194)
T ss_pred HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 9999998869999999999892999999999999
No 222
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=72.77 E-value=4.9 Score=21.05 Aligned_cols=31 Identities=16% Similarity=0.170 Sum_probs=26.7
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999983994999999863429999887
Q gi|254781147|r 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 24 ~~ir~~R~~~gltq~ela~~~gis~~~is~i 54 (83)
+.|-.+|.-.|+|.+|+|+.+|+|.+++...
T Consensus 128 R~v~~L~~~~gls~~EIA~~L~is~~tVk~r 158 (185)
T PRK12542 128 RQVFKYKVFYNLTYQEISSVMGITEANVRKQ 158 (185)
T ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 8997679983999999999989299999999
No 223
>pfam04218 CENP-B_N CENP-B N-terminal DNA-binding domain. 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.
Probab=72.59 E-value=3.9 Score=21.66 Aligned_cols=30 Identities=17% Similarity=0.229 Sum_probs=26.4
Q ss_pred HHHHCCCCHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf 999839949999998634299998875589
Q gi|254781147|r 29 IRKEAKLTQKEIRNRTGFAQSWISELETGK 58 (83)
Q Consensus 29 ~R~~~gltq~ela~~~gis~~~is~iE~G~ 58 (83)
-|.+.|.|-.++|...||..|+++.|-..+
T Consensus 17 ~~~e~G~s~~~lar~~gi~~STl~~I~Knk 46 (53)
T pfam04218 17 QRSEEGESKASLARRFNVPRSTLRDILKNK 46 (53)
T ss_pred HHHHCCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 999858968899999698797999999809
No 224
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=72.47 E-value=4.8 Score=21.08 Aligned_cols=47 Identities=6% Similarity=-0.001 Sum_probs=32.1
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHHHH-HCCCCCCCHHHHHHHHHHHCCC
Q ss_conf 999999983994999999863429999887-5589994489999999992899
Q gi|254781147|r 25 NFRNIRKEAKLTQKEIRNRTGFAQSWISEL-ETGKSTINIDNMIILAHTLDTP 76 (83)
Q Consensus 25 ~ir~~R~~~gltq~ela~~~gis~~~is~i-E~G~~~~~~~~l~~la~al~i~ 76 (83)
.+-.+|.-.|||.+|+|+.+|+|.+++... -++ ...|.+..+.-|+.
T Consensus 113 ~vl~L~~~egls~~EIA~~l~is~~tVk~~l~RA-----r~~Lr~~Le~~gi~ 160 (161)
T PRK09047 113 EAFLLRYWEDMDVAETAAAMGCSEGSVKTHCSRA-----THTLAKALEAKGIT 160 (161)
T ss_pred HHHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHH-----HHHHHHHHHHCCCC
T ss_conf 9989999987799999999896999999999999-----99999999986983
No 225
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=72.39 E-value=5 Score=21.00 Aligned_cols=30 Identities=20% Similarity=0.219 Sum_probs=25.1
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 999999983994999999863429999887
Q gi|254781147|r 25 NFRNIRKEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 25 ~ir~~R~~~gltq~ela~~~gis~~~is~i 54 (83)
.+-.++.-.|+|.+|+|+.+|+|.+++...
T Consensus 148 ~v~~L~~~eg~s~~EIA~~lgis~~tVk~r 177 (194)
T PRK12519 148 QVLELAYYEGLSQSEIAKRLGIPLGTVKAR 177 (194)
T ss_pred HHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 688999981999999999989499999999
No 226
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=72.35 E-value=5.4 Score=20.81 Aligned_cols=30 Identities=7% Similarity=0.021 Sum_probs=25.7
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 999999998399499999986342999988
Q gi|254781147|r 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISE 53 (83)
Q Consensus 24 ~~ir~~R~~~gltq~ela~~~gis~~~is~ 53 (83)
+.+-.+|.-.|+|.+|+|+.+|+|.+++..
T Consensus 134 R~vi~L~~~eg~s~~EIA~~Lgis~~tVks 163 (188)
T PRK12517 134 REPLLLQVIGGFSGEEIAEILDLNKNTVMT 163 (188)
T ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHH
T ss_conf 999999998399999999998939999999
No 227
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=72.32 E-value=6.1 Score=20.47 Aligned_cols=31 Identities=13% Similarity=0.054 Sum_probs=25.8
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999983994999999863429999887
Q gi|254781147|r 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 24 ~~ir~~R~~~gltq~ela~~~gis~~~is~i 54 (83)
+.+-.+|.-.|+|.+|+|+.+|+|.+++...
T Consensus 133 r~v~~L~~~eg~s~~EIA~~l~is~~tVk~~ 163 (177)
T PRK09638 133 RAPFILKHYYGYTYEEIAKMLGIPEGTVKSR 163 (177)
T ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 8999999991999999999989399999999
No 228
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=72.28 E-value=4.3 Score=21.36 Aligned_cols=34 Identities=12% Similarity=0.325 Sum_probs=26.9
Q ss_pred HHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHH
Q ss_conf 9839949999998634299998875589994489
Q gi|254781147|r 31 KEAKLTQKEIRNRTGFAQSWISELETGKSTINID 64 (83)
Q Consensus 31 ~~~gltq~ela~~~gis~~~is~iE~G~~~~~~~ 64 (83)
....+|.+++|+.+|+|+++++++.+.....++.
T Consensus 22 ~~~~lsl~~lA~~~~~S~~~l~r~Fk~~~G~s~~ 55 (127)
T PRK11511 22 LESPLSLEKVSERSGYSKWHLQRMFKKETGHSLG 55 (127)
T ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHHHHHCCCHH
T ss_conf 5899999999999895999999999999891999
No 229
>pfam00440 TetR_N Bacterial regulatory proteins, tetR family.
Probab=72.24 E-value=3.8 Score=21.67 Aligned_cols=37 Identities=14% Similarity=0.081 Sum_probs=29.2
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf 9999999998399499999986342999988755899
Q gi|254781147|r 23 VNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKS 59 (83)
Q Consensus 23 g~~ir~~R~~~gltq~ela~~~gis~~~is~iE~G~~ 59 (83)
+..+-..+--.+.|..++|+.+|+|++++..+..++.
T Consensus 5 A~~l~~~~G~~~~s~~~Ia~~agvs~~~iy~~F~~K~ 41 (47)
T pfam00440 5 ALELFAEKGYDATTVREIAKEAGVSKGALYRHFPSKE 41 (47)
T ss_pred HHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHCCCHH
T ss_conf 9999998691507799999997969889998876999
No 230
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=72.24 E-value=8.8 Score=19.54 Aligned_cols=21 Identities=33% Similarity=0.433 Sum_probs=19.6
Q ss_pred CCCHHHHHHHHHHHHHHHHHH
Q ss_conf 994999999863429999887
Q gi|254781147|r 34 KLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 34 gltq~ela~~~gis~~~is~i 54 (83)
.+||+|+|..+|.++-++|++
T Consensus 184 ~lt~~dLA~~lG~trEtVsR~ 204 (235)
T PRK11161 184 TMTRGDIGNYLGLTVETISRL 204 (235)
T ss_pred CCCHHHHHHHHCCCHHHHHHH
T ss_conf 378999998878989999999
No 231
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=72.12 E-value=5.3 Score=20.85 Aligned_cols=31 Identities=19% Similarity=0.409 Sum_probs=25.9
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999983994999999863429999887
Q gi|254781147|r 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 24 ~~ir~~R~~~gltq~ela~~~gis~~~is~i 54 (83)
+-|+.+......++.++|+.+|+|.+++++.
T Consensus 12 ~IL~~L~~d~r~~~~eia~~lglS~~~v~~R 42 (154)
T COG1522 12 RILRLLQEDARISNAELAERVGLSPSTVLRR 42 (154)
T ss_pred HHHHHHHHCCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 9999999727657999999979798999999
No 232
>PRK05949 RNA polymerase sigma factor; Validated
Probab=71.80 E-value=4.8 Score=21.08 Aligned_cols=32 Identities=16% Similarity=0.293 Sum_probs=24.3
Q ss_pred HHHHHH----HCCCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 999999----83994999999863429999887558
Q gi|254781147|r 26 FRNIRK----EAKLTQKEIRNRTGFAQSWISELETG 57 (83)
Q Consensus 26 ir~~R~----~~gltq~ela~~~gis~~~is~iE~G 57 (83)
|-.+|- ...+|++|+|+..|||+..|.+||+.
T Consensus 274 Ii~~RfGl~~~~~~TL~EIg~~lgiSrERVRQIE~r 309 (327)
T PRK05949 274 VLTLRFGLEDGKELSLAKVGQRLNLSRERVRQLEHQ 309 (327)
T ss_pred HHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 999971899969857999999989599999999999
No 233
>cd01105 HTH_GlnR-like Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator GlnR and related proteins, N-terminal domain. The GlnR and TnrA (also known as ScgR) proteins have been shown to regulate expression of glutamine synthetase as well as several genes involved in nitrogen metabolism. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=71.76 E-value=3.3 Score=22.04 Aligned_cols=22 Identities=18% Similarity=0.210 Sum_probs=19.2
Q ss_pred CCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 9499999986342999988755
Q gi|254781147|r 35 LTQKEIRNRTGFAQSWISELET 56 (83)
Q Consensus 35 ltq~ela~~~gis~~~is~iE~ 56 (83)
+|..|+|+.+|++.++|.-||.
T Consensus 2 ~tIgeva~~~gvs~~tLRyye~ 23 (88)
T cd01105 2 IGIGEVSKLTGVSPRQLRYWEE 23 (88)
T ss_pred CCHHHHHHHHCCCHHHHHHHHH
T ss_conf 6789999998959999999999
No 234
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=71.60 E-value=5.5 Score=20.73 Aligned_cols=31 Identities=13% Similarity=0.097 Sum_probs=26.1
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999983994999999863429999887
Q gi|254781147|r 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 24 ~~ir~~R~~~gltq~ela~~~gis~~~is~i 54 (83)
+.+-.++.-.|+|.+|+|+.+|+|.+++...
T Consensus 134 R~v~~L~~~~g~s~~EIA~~l~is~~tVk~~ 164 (186)
T PRK05602 134 REAIVLQYYQGLSNIEAARVMGLSVDALESL 164 (186)
T ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 8999999863899999999989399999999
No 235
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=71.55 E-value=5.5 Score=20.74 Aligned_cols=28 Identities=14% Similarity=0.010 Sum_probs=23.1
Q ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 9999998399499999986342999988
Q gi|254781147|r 26 FRNIRKEAKLTQKEIRNRTGFAQSWISE 53 (83)
Q Consensus 26 ir~~R~~~gltq~ela~~~gis~~~is~ 53 (83)
+-.++.-.|+|.+|+|+.+|+|.+++..
T Consensus 143 ~i~l~~~eg~s~~EIA~~l~is~~TVk~ 170 (184)
T PRK12537 143 CILHAYVDGCSHAEIAQRLGAPLGTVKA 170 (184)
T ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHH
T ss_conf 9999884399999999998929999999
No 236
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=71.50 E-value=5.4 Score=20.81 Aligned_cols=30 Identities=10% Similarity=-0.014 Sum_probs=25.8
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 999999998399499999986342999988
Q gi|254781147|r 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISE 53 (83)
Q Consensus 24 ~~ir~~R~~~gltq~ela~~~gis~~~is~ 53 (83)
+.+-.++.-.|+|.+|+|+.+|+|.+++..
T Consensus 114 r~v~~L~~~~~~s~~EIA~~l~is~~tVk~ 143 (165)
T PRK09644 114 AQAILLCDVHELTYEEAASVLDLKENTYKS 143 (165)
T ss_pred HHHHHHHHHHCCCHHHHHHHHCCCHHHHHH
T ss_conf 999999999888999999998939999999
No 237
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=71.19 E-value=5.6 Score=20.69 Aligned_cols=34 Identities=15% Similarity=0.154 Sum_probs=27.3
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHH-HHHCC
Q ss_conf 99999999839949999998634299998-87558
Q gi|254781147|r 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWIS-ELETG 57 (83)
Q Consensus 24 ~~ir~~R~~~gltq~ela~~~gis~~~is-~iE~G 57 (83)
+.+-.+|.-.|+|.+|+|+.+|+|.+++. ++-++
T Consensus 163 R~vl~Lr~~eglS~~EIAe~Lgis~gTVKsrl~RA 197 (222)
T PRK09647 163 RAAVVLCDIEGLSYEEIAATLGVKLGTVRSRIHRG 197 (222)
T ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 88998799639999999999893999999999999
No 238
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=71.16 E-value=6.8 Score=20.22 Aligned_cols=30 Identities=17% Similarity=0.173 Sum_probs=25.5
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 999999983994999999863429999887
Q gi|254781147|r 25 NFRNIRKEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 25 ~ir~~R~~~gltq~ela~~~gis~~~is~i 54 (83)
.+-.++.-.|+|.+|+|+.+|+|.+++...
T Consensus 132 ~il~l~~~~g~s~~eIA~~lgis~~tv~~~ 161 (180)
T PRK11924 132 EVFLLRYVEGLSYQEIADQLGVPLGTVKSR 161 (180)
T ss_pred HHHHHHHHHCCCHHHHHHHHCCCHHHHHHH
T ss_conf 999999996859999999989499999999
No 239
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=71.11 E-value=7 Score=20.13 Aligned_cols=34 Identities=15% Similarity=0.149 Sum_probs=26.6
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHH-HHHCC
Q ss_conf 99999999839949999998634299998-87558
Q gi|254781147|r 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWIS-ELETG 57 (83)
Q Consensus 24 ~~ir~~R~~~gltq~ela~~~gis~~~is-~iE~G 57 (83)
+.+-.++.-.|+|.+|+|+.+|+|.+++. .+-++
T Consensus 143 r~v~~l~~~~~~s~~EIA~~lgis~~tVk~~l~Ra 177 (192)
T PRK09652 143 RTAITLREIEGLSYEEIAEIMGCPIGTVRSRIFRA 177 (192)
T ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 98888999729999999999893999999999999
No 240
>pfam11268 DUF3071 Protein of unknown function (DUF3071). Some members in this family of proteins are annotated as DNA-binding proteins however this cannot be confirmed. Currently no function is known.
Probab=71.06 E-value=4.4 Score=21.30 Aligned_cols=35 Identities=14% Similarity=0.212 Sum_probs=29.0
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 99999999998399499999986342999988755
Q gi|254781147|r 22 FVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELET 56 (83)
Q Consensus 22 ~g~~ir~~R~~~gltq~ela~~~gis~~~is~iE~ 56 (83)
+.-+=-+.|...|.|.+|+|+.+|++...|-+|+.
T Consensus 56 lspreIQarIRaGas~eevA~~~g~~~~rVerfa~ 90 (169)
T pfam11268 56 LSPREIQARIRAGASAEEVAEAAGVPEERVERFEG 90 (169)
T ss_pred CCHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHCCC
T ss_conf 89899999988799999999995999999874223
No 241
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=70.82 E-value=7.7 Score=19.90 Aligned_cols=29 Identities=3% Similarity=0.038 Sum_probs=22.5
Q ss_pred HHHHH-HHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 99999-983994999999863429999887
Q gi|254781147|r 26 FRNIR-KEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 26 ir~~R-~~~gltq~ela~~~gis~~~is~i 54 (83)
...++ ...++|-+|+|+.+|+|+.+..+|
T Consensus 168 ~~~l~~~~~~~ta~eva~~~giSrvTaRRY 197 (225)
T PRK10046 168 RKLFKEPGVQHTAETVAQALTISRTTARRY 197 (225)
T ss_pred HHHHHCCCCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 999971799868999999858519999999
No 242
>PRK13705 plasmid-partitioning protein SopA; Provisional
Probab=70.80 E-value=9.5 Score=19.35 Aligned_cols=61 Identities=11% Similarity=0.157 Sum_probs=41.9
Q ss_pred HHHHHHHHHHHHHHHHH----------CCCCHHHHHHHHHHHHHHHHHHHC------------CC----CCCCHHHHHHH
Q ss_conf 99999999999999998----------399499999986342999988755------------89----99448999999
Q gi|254781147|r 16 LRERMIFVNNFRNIRKE----------AKLTQKEIRNRTGFAQSWISELET------------GK----STINIDNMIIL 69 (83)
Q Consensus 16 ~~~~~~~g~~ir~~R~~----------~gltq~ela~~~gis~~~is~iE~------------G~----~~~~~~~l~~l 69 (83)
+..-..+...|+.+|.+ +.+|-.|+|+.+|||.+++.+.+- |. +.-+++.+..+
T Consensus 11 ~~~g~~~~~~l~~~~~~~~~P~~~K~lR~Fs~~EvA~l~gvs~~~lr~~~~~g~~P~p~~~~~gr~~~R~~Ytl~~i~~l 90 (388)
T PRK13705 11 IEAGHEMTKAIAIAQFNDDSPEARKITRRWRIGEAADLVGVSSQAIRDAEKAGRLPHPDMEMRGRVEQRVGYTIEQINHM 90 (388)
T ss_pred HHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHH
T ss_conf 99999999999998624799821125588887999999399999999786468999997687776554551069999999
Q ss_pred HHHHCCC
Q ss_conf 9992899
Q gi|254781147|r 70 AHTLDTP 76 (83)
Q Consensus 70 a~al~i~ 76 (83)
-+.|+..
T Consensus 91 R~~~~~~ 97 (388)
T PRK13705 91 RDVFGTR 97 (388)
T ss_pred HHHHCCC
T ss_conf 9996438
No 243
>cd04790 HTH_Cfa-like_unk Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulator; conserved, Cfa-like, unknown proteins (~172 a.a.). The N-terminal domain of these proteins appears to be related to the HTH domain of Cfa, a cyclopropane fatty acid synthase. These Cfa-like proteins have a unique C-terminal domain with conserved histidines (motif HXXFX7HXXF). Based on sequence similarity of the N-terminal domains, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domain
Probab=70.47 E-value=3.5 Score=21.93 Aligned_cols=46 Identities=15% Similarity=0.098 Sum_probs=30.0
Q ss_pred CCHHHHHHHHHHHHHHHHHHHCC------------CCCCCHHH-----HHHHHHHHCCCHHHH
Q ss_conf 94999999863429999887558------------99944899-----999999928999996
Q gi|254781147|r 35 LTQKEIRNRTGFAQSWISELETG------------KSTINIDN-----MIILAHTLDTPLWKL 80 (83)
Q Consensus 35 ltq~ela~~~gis~~~is~iE~G------------~~~~~~~~-----l~~la~al~i~~~~l 80 (83)
+|..++|+.+|+|..+|.-||.- -+.-+.+. .....+.+|+|+.+.
T Consensus 2 ~tI~e~Ak~~gvs~~TLRyYe~~GLl~P~~r~~nGYR~Ys~~dl~rL~~I~~lr~lG~sL~eI 64 (172)
T cd04790 2 LTISQLARQFGLSRSTLLYYERIGLLSPSARSESNYRLYGERDLERLEQICAYRSAGVSLEDI 64 (172)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCHHHH
T ss_conf 978999999894988999999887989988499987077999999999999999879999999
No 244
>COG1737 RpiR Transcriptional regulators [Transcription]
Probab=70.34 E-value=7.5 Score=19.94 Aligned_cols=39 Identities=21% Similarity=0.202 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 999999999999983994999999863429999887558
Q gi|254781147|r 19 RMIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETG 57 (83)
Q Consensus 19 ~~~~g~~ir~~R~~~gltq~ela~~~gis~~~is~iE~G 57 (83)
+.+--.-+....+-..+|..|+|+.+|||+++|.++=+.
T Consensus 21 r~iA~yil~~~~~~~~~si~elA~~a~VS~aTv~Rf~~k 59 (281)
T COG1737 21 RKIADYILANPDEVALLSIAELAERAGVSPATVVRFARK 59 (281)
T ss_pred HHHHHHHHHCHHHHHHCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 999999993967885614999998819988899999998
No 245
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=70.33 E-value=6.1 Score=20.50 Aligned_cols=35 Identities=9% Similarity=0.083 Sum_probs=27.9
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHH-HHHCCC
Q ss_conf 99999999839949999998634299998-875589
Q gi|254781147|r 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWIS-ELETGK 58 (83)
Q Consensus 24 ~~ir~~R~~~gltq~ela~~~gis~~~is-~iE~G~ 58 (83)
+.+-.++.-.|+|.+|+|+.+|++.+++- ++-+|.
T Consensus 117 R~vl~L~~~egls~~EIA~iL~is~gTVKsRL~RAr 152 (181)
T PRK12540 117 REALILVGASGFSYEDAAAICGCAVGTIKSRVNRAR 152 (181)
T ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf 899887998099999999998949999999999999
No 246
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family; InterPro: IPR014331 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 recognized by the major sigma factors , . This entry of sigma factors are members of the sigma-70 family and are abundantly found in the species Rhodopirellula baltica, and Verrucomicrobium spinosum and to a lesser extent in Gemmata obscuriglobus.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=70.30 E-value=6.4 Score=20.35 Aligned_cols=32 Identities=6% Similarity=0.135 Sum_probs=29.1
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 99999999983994999999863429999887
Q gi|254781147|r 23 VNNFRNIRKEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 23 g~~ir~~R~~~gltq~ela~~~gis~~~is~i 54 (83)
.+.|-.+|.+.|++..++|+.+|.+.+.+.+.
T Consensus 120 ~R~Ll~~rY~~G~~~~~~A~~~g~~~~A~~~~ 151 (163)
T TIGR02989 120 QRELLQLRYQRGVSLEALAEQLGRTVNAVYKA 151 (163)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHCCHHHHHHHH
T ss_conf 89999998227978789998847138999999
No 247
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=70.20 E-value=6.4 Score=20.36 Aligned_cols=28 Identities=21% Similarity=0.081 Sum_probs=23.9
Q ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 9999998399499999986342999988
Q gi|254781147|r 26 FRNIRKEAKLTQKEIRNRTGFAQSWISE 53 (83)
Q Consensus 26 ir~~R~~~gltq~ela~~~gis~~~is~ 53 (83)
+-.++.-.|+|.+|+|+.+|+|.+++-.
T Consensus 134 ~~~l~~~eg~s~~EIA~~lgis~~tVk~ 161 (178)
T PRK12536 134 PIVHVKLEGLSVEETAQLTGLSESAVKV 161 (178)
T ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHH
T ss_conf 9999988599999999998929999999
No 248
>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family; InterPro: IPR012845 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 recognized by the major sigma factors , . 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.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0045449 regulation of transcription.
Probab=69.67 E-value=5.8 Score=20.62 Aligned_cols=31 Identities=23% Similarity=0.326 Sum_probs=26.9
Q ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 9999998399499999986342999988755
Q gi|254781147|r 26 FRNIRKEAKLTQKEIRNRTGFAQSWISELET 56 (83)
Q Consensus 26 ir~~R~~~gltq~ela~~~gis~~~is~iE~ 56 (83)
|-.+-...+||++|.|+.+|+|.|=||+|-+
T Consensus 186 Vl~LYY~eELnLKEIg~VL~lsESRvSQiHs 216 (227)
T TIGR02479 186 VLSLYYYEELNLKEIGEVLGLSESRVSQIHS 216 (227)
T ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 8888641276688999883787057999999
No 249
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=69.57 E-value=6.5 Score=20.32 Aligned_cols=34 Identities=15% Similarity=0.170 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 9999999999998399499999986342999988
Q gi|254781147|r 20 MIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISE 53 (83)
Q Consensus 20 ~~~g~~ir~~R~~~gltq~ela~~~gis~~~is~ 53 (83)
+....-+..+++...++..|||+..|+|..||.+
T Consensus 7 eR~~~Il~~L~~~g~v~v~eLa~~~~VS~~TIRR 40 (252)
T PRK10681 7 ERIGQLLQALKRSDKLHLKDAAALLGVSEMTIRR 40 (252)
T ss_pred HHHHHHHHHHHHCCCEEHHHHHHHHCCCHHHHHH
T ss_conf 9999999999986979999999887979989987
No 250
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=69.50 E-value=6.8 Score=20.20 Aligned_cols=30 Identities=20% Similarity=0.090 Sum_probs=26.4
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 999999998399499999986342999988
Q gi|254781147|r 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISE 53 (83)
Q Consensus 24 ~~ir~~R~~~gltq~ela~~~gis~~~is~ 53 (83)
+.+-.+|.-.|+|.+|+|+.+|+|.+++..
T Consensus 140 R~vl~L~~~~~ls~~EIA~~l~is~~tVks 169 (188)
T PRK09640 140 REILVLRFVAELEFQEIADIMHMGLSATKM 169 (188)
T ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHH
T ss_conf 999999999299999999998929999999
No 251
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=69.49 E-value=7.6 Score=19.92 Aligned_cols=48 Identities=6% Similarity=0.075 Sum_probs=34.1
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHH-HHCCCCCCCHHHHHHHHHHHCCC
Q ss_conf 999999998399499999986342999988-75589994489999999992899
Q gi|254781147|r 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISE-LETGKSTINIDNMIILAHTLDTP 76 (83)
Q Consensus 24 ~~ir~~R~~~gltq~ela~~~gis~~~is~-iE~G~~~~~~~~l~~la~al~i~ 76 (83)
+.+-.+|.-.|+|.+|+|+.+|+|.+++.. +-+| ...|.+..+-+||+
T Consensus 122 r~v~~l~~~~g~s~~EIA~~l~is~~tVk~~l~ra-----~~~Lr~~L~~~gi~ 170 (171)
T PRK09645 122 RAVLVRSYYRGWSTAQIAADLGIPEGTVKSRLHYA-----VRALRLTLQEMGVT 170 (171)
T ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHH-----HHHHHHHHHHCCCC
T ss_conf 87989999869999999999892999999999999-----99999999970999
No 252
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=69.43 E-value=6.8 Score=20.18 Aligned_cols=34 Identities=15% Similarity=0.158 Sum_probs=26.4
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHH-HHCC
Q ss_conf 999999998399499999986342999988-7558
Q gi|254781147|r 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISE-LETG 57 (83)
Q Consensus 24 ~~ir~~R~~~gltq~ela~~~gis~~~is~-iE~G 57 (83)
+.+-.++.-.|+|.+|+|+.+|++.+++-. +-+|
T Consensus 143 r~vi~l~~~eg~s~~EIA~~l~i~~gTVksrl~ra 177 (187)
T PRK12534 143 SELIRTAFFEGITYEELAARTDTPIGTVKSWIRRG 177 (187)
T ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 99999999849999999999891999999999999
No 253
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=69.40 E-value=3.8 Score=21.70 Aligned_cols=23 Identities=13% Similarity=0.297 Sum_probs=20.6
Q ss_pred HCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 83994999999863429999887
Q gi|254781147|r 32 EAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 32 ~~gltq~ela~~~gis~~~is~i 54 (83)
...+|++|+|..+|+++.++|++
T Consensus 171 ~l~lT~~dLA~~lG~trETVsR~ 193 (224)
T PRK09391 171 ALPMSRRDIADYLGLTIETVSRA 193 (224)
T ss_pred ECCCCHHHHHHHHCCCHHHHHHH
T ss_conf 71579999998879979999999
No 254
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=69.37 E-value=6.9 Score=20.18 Aligned_cols=29 Identities=10% Similarity=0.069 Sum_probs=25.2
Q ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 99999983994999999863429999887
Q gi|254781147|r 26 FRNIRKEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 26 ir~~R~~~gltq~ela~~~gis~~~is~i 54 (83)
+-.++...|+|.+|+|+.+|+|.+++...
T Consensus 179 vl~L~~~egls~~EIA~~Lgis~~TVKsr 207 (233)
T PRK12538 179 AVILSYHENMSNGEIAEVMDTTVAAVESL 207 (233)
T ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 99999984999999999989299999999
No 255
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=69.25 E-value=6.7 Score=20.23 Aligned_cols=31 Identities=6% Similarity=0.005 Sum_probs=25.9
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999983994999999863429999887
Q gi|254781147|r 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 24 ~~ir~~R~~~gltq~ela~~~gis~~~is~i 54 (83)
+.+-.++.-.|+|.+|+|+.+|+|.+++...
T Consensus 137 R~vi~L~~~~g~s~~EIA~~lgis~~tVk~~ 167 (184)
T PRK12512 137 RDVVQSIAVEGASIKETAAKLSMSEGAVRVA 167 (184)
T ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 9999999855979999999989199999999
No 256
>PRK11302 DNA-binding transcriptional regulator HexR; Provisional
Probab=69.15 E-value=7.8 Score=19.84 Aligned_cols=37 Identities=0% Similarity=0.008 Sum_probs=27.6
Q ss_pred HHHH-HHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf 9999-999999839949999998634299998875589
Q gi|254781147|r 22 FVNN-FRNIRKEAKLTQKEIRNRTGFAQSWISELETGK 58 (83)
Q Consensus 22 ~g~~-ir~~R~~~gltq~ela~~~gis~~~is~iE~G~ 58 (83)
++.. +..--.-..+|..|||+.+|+|.++|.|+=+.-
T Consensus 21 iA~yIl~n~~~v~~~si~eLA~~~~vS~aTV~Rf~kkL 58 (284)
T PRK11302 21 VAEVILASPQTAIHSSIATLAKMANVSEPTVNRFCRSL 58 (284)
T ss_pred HHHHHHCCHHHHHHCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 99999809899976669999989699888999999995
No 257
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=69.07 E-value=8.1 Score=19.77 Aligned_cols=48 Identities=8% Similarity=0.046 Sum_probs=33.9
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH-HCCCCCCCHHHHHHHHHHHCCC
Q ss_conf 9999999983994999999863429999887-5589994489999999992899
Q gi|254781147|r 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISEL-ETGKSTINIDNMIILAHTLDTP 76 (83)
Q Consensus 24 ~~ir~~R~~~gltq~ela~~~gis~~~is~i-E~G~~~~~~~~l~~la~al~i~ 76 (83)
+.+-.++.-.|+|.+|+|+.+|+|.+++... -++ ...|.++.+.-|+.
T Consensus 137 R~vi~l~~~e~~s~~EIA~~lgis~~tV~~~l~RA-----r~~Lr~~L~~~g~~ 185 (189)
T PRK12515 137 REIIDLVYYHEKSVEEVGEIVGIPESTVKTRMFYA-----RKKLAELLKAAGVE 185 (189)
T ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHH-----HHHHHHHHHHHCCC
T ss_conf 99999999849999999999892999999999999-----99999999972833
No 258
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=69.01 E-value=6.7 Score=20.22 Aligned_cols=23 Identities=17% Similarity=0.305 Sum_probs=16.8
Q ss_pred HCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 83994999999863429999887
Q gi|254781147|r 32 EAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 32 ~~gltq~ela~~~gis~~~is~i 54 (83)
...+|-+++|+.+|+|+.+..+|
T Consensus 171 ~~~~Taeela~~~giSRvTaRRY 193 (224)
T COG4565 171 DQELTAEELAQALGISRVTARRY 193 (224)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 77647999998837219999999
No 259
>cd01282 HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 3). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=68.99 E-value=3.9 Score=21.62 Aligned_cols=22 Identities=23% Similarity=0.282 Sum_probs=12.7
Q ss_pred CCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 9499999986342999988755
Q gi|254781147|r 35 LTQKEIRNRTGFAQSWISELET 56 (83)
Q Consensus 35 ltq~ela~~~gis~~~is~iE~ 56 (83)
|+..|+|+.+|+|..+|.-||.
T Consensus 1 M~Ige~a~~~gvs~~tlRyYe~ 22 (112)
T cd01282 1 MRIGELAARTGVSVRSLRYYEE 22 (112)
T ss_pred CCHHHHHHHHCCCHHHHHHHHH
T ss_conf 9689999998979999999998
No 260
>pfam09048 Cro Cro. Members of this family are involved in the repression of transcription by binding as a homodimer to palindromic DNA operator sites in phage lambda: they repress genes expressed in early phage development and are necessary for the late stage of lytic growth. These proteins have a secondary structure consisting of three alpha-helices and three beta-sheets, and dimerize through interactions between the two antiparallel beta-strands.
Probab=68.94 E-value=5.1 Score=20.94 Aligned_cols=35 Identities=23% Similarity=0.212 Sum_probs=27.2
Q ss_pred HHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCH
Q ss_conf 9999983994999999863429999887558999448
Q gi|254781147|r 27 RNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINI 63 (83)
Q Consensus 27 r~~R~~~gltq~ela~~~gis~~~is~iE~G~~~~~~ 63 (83)
-..-++.| |...|+.+|+.++.||+.-+..+++-+
T Consensus 6 ~dyv~~~G--Q~kaA~~lGV~Q~AISKAlragR~I~v 40 (58)
T pfam09048 6 SDYVEEHG--QAKAAKDLGVNQSAISKALRAGRNIEV 40 (58)
T ss_pred HHHHHHHC--HHHHHHHCCCCHHHHHHHHHCCCEEEE
T ss_conf 99999976--598999829758999999964881799
No 261
>cd04776 HTH_GnyR Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR. Putative helix-turn-helix (HTH) regulatory protein, GnyR, and other related proteins. GnyR belongs to the gnyRDBHAL cluster, which is involved in acyclic isoprenoid degradation in Pseudomonas aeruginosa. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=68.93 E-value=3.9 Score=21.63 Aligned_cols=21 Identities=14% Similarity=0.069 Sum_probs=12.4
Q ss_pred CCHHHHHHHHHHHHHHHHHHH
Q ss_conf 949999998634299998875
Q gi|254781147|r 35 LTQKEIRNRTGFAQSWISELE 55 (83)
Q Consensus 35 ltq~ela~~~gis~~~is~iE 55 (83)
+|..|+|+.+|+|..+|.-||
T Consensus 1 ytIge~A~~~gvs~~tlRyYe 21 (118)
T cd04776 1 YTISELAREFDVTPRTLRFYE 21 (118)
T ss_pred CCHHHHHHHHCCCHHHHHHHH
T ss_conf 958899999897999999999
No 262
>PRK11337 DNA-binding transcriptional repressor RpiR; Provisional
Probab=68.85 E-value=7.7 Score=19.87 Aligned_cols=36 Identities=8% Similarity=0.097 Sum_probs=28.3
Q ss_pred HHHH-HHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 9999-99999983994999999863429999887558
Q gi|254781147|r 22 FVNN-FRNIRKEAKLTQKEIRNRTGFAQSWISELETG 57 (83)
Q Consensus 22 ~g~~-ir~~R~~~gltq~ela~~~gis~~~is~iE~G 57 (83)
++.. +.....-..+|..|||+.+|+|.++|.|+=+.
T Consensus 34 IA~yIL~~~~~v~~~si~eLA~~~~vS~aTVvRf~kk 70 (293)
T PRK11337 34 VVDWLLKPGNLSCATALKDVAEALAVSEAMIVKVAKL 70 (293)
T ss_pred HHHHHHCCHHHHHHCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 9999982989997666999998959988899999999
No 263
>PRK11557 putative DNA-binding transcriptional regulator; Provisional
Probab=68.75 E-value=8 Score=19.77 Aligned_cols=37 Identities=14% Similarity=0.254 Sum_probs=27.7
Q ss_pred HHHHHHH-HHHHHCCCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 9999999-999983994999999863429999887558
Q gi|254781147|r 21 IFVNNFR-NIRKEAKLTQKEIRNRTGFAQSWISELETG 57 (83)
Q Consensus 21 ~~g~~ir-~~R~~~gltq~ela~~~gis~~~is~iE~G 57 (83)
.++..|- .--.-..+|..|||+.+|+|.++|.|+=+.
T Consensus 20 ~IA~yIl~n~~~v~~~si~eLA~~~~vS~aTVvRf~kk 57 (282)
T PRK11557 20 KLADYLLLQPDTARHLSSQQLANEAGVSQSSVVKFAQK 57 (282)
T ss_pred HHHHHHHCCHHHHHHCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 99999980989997656999998969998899999999
No 264
>TIGR00014 arsC arsenate reductase; InterPro: IPR006659 This entry describes a distinct clade, including ArsC itself, of the broader family of ArsC and related proteins. This clade is almost completely restricted to the proteobacteria. An anion-translocating ATPase has been identified as the product of the arsenical resistance operon of resistance plasmid R773 . When expressed in Escherichia coli this ATP-driven oxyanion pump catalyses extrusion of the oxyanions arsenite, antimonite and arsenate. The pump is composed of two polypeptides, the products of the arsA and arsB genes. The pump alone produces resistance to arsenite and antimonite. This protein, ArsC, catalyzes the reduction of arsenate to arsenite, and thus extends resistance to include arsenate. ; GO: 0008794 arsenate reductase (glutaredoxin) activity, 0006118 electron transport.
Probab=68.64 E-value=7 Score=20.12 Aligned_cols=39 Identities=15% Similarity=0.161 Sum_probs=32.0
Q ss_pred HHHHHHHHHHHHHCC----------CCCCCHHHHHHHHHHHCCCH-HHHC
Q ss_conf 863429999887558----------99944899999999928999-9960
Q gi|254781147|r 43 RTGFAQSWISELETG----------KSTINIDNMIILAHTLDTPL-WKLL 81 (83)
Q Consensus 43 ~~gis~~~is~iE~G----------~~~~~~~~l~~la~al~i~~-~~l~ 81 (83)
+|+-|+++++-+|.. +..|+-..|..+.+.||++. -+++
T Consensus 8 RCSkSR~tLalL~dkgi~P~vV~YL~~pp~~seL~~~~~~LG~~~ar~~~ 57 (114)
T TIGR00014 8 RCSKSRQTLALLEDKGIEPEVVKYLKNPPTKSELKALLAKLGISSAREMI 57 (114)
T ss_pred CCCHHHHHHHHHHHCCCCCEEEECCCCCCCHHHHHHHHHHCCCCHHHHHC
T ss_conf 87246899999985699954741458974868899999870897036301
No 265
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=68.33 E-value=8.5 Score=19.63 Aligned_cols=31 Identities=19% Similarity=0.234 Sum_probs=25.9
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999983994999999863429999887
Q gi|254781147|r 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 24 ~~ir~~R~~~gltq~ela~~~gis~~~is~i 54 (83)
+.+-.++.-.|+|.+|+|+.+|+|.+++...
T Consensus 145 r~il~L~~~~g~s~~EIA~~l~is~~tVk~~ 175 (194)
T PRK12513 145 REVFLLREHGDLSLEEIAQLTGVPLETVKSR 175 (194)
T ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 9999999984999999999989499999999
No 266
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=68.22 E-value=7.5 Score=19.93 Aligned_cols=33 Identities=9% Similarity=0.058 Sum_probs=26.5
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHHH-HHCC
Q ss_conf 99999998399499999986342999988-7558
Q gi|254781147|r 25 NFRNIRKEAKLTQKEIRNRTGFAQSWISE-LETG 57 (83)
Q Consensus 25 ~ir~~R~~~gltq~ela~~~gis~~~is~-iE~G 57 (83)
.+-.++.-.|+|.+|+|+.+|+|.+++-. +-++
T Consensus 145 ~v~~L~~~egls~~EIA~~l~is~~tVk~rl~RA 178 (193)
T PRK11923 145 TALTLREFDGLSYEDIASVMQCPVGTVRSRIFRA 178 (193)
T ss_pred HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 9999999949999999999892999999999999
No 267
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=68.19 E-value=8.1 Score=19.74 Aligned_cols=28 Identities=21% Similarity=0.215 Sum_probs=22.6
Q ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 99999983994999999863429999887
Q gi|254781147|r 26 FRNIRKEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 26 ir~~R~~~gltq~ela~~~gis~~~is~i 54 (83)
+-.+|. .|+|.+|+|+.+|+|.+++...
T Consensus 120 v~~l~~-~g~s~~EIA~~l~is~~tVk~~ 147 (166)
T PRK09639 120 VLLLRF-SGYSYKEIAQALGIDESSVGTT 147 (166)
T ss_pred HHHHHH-HCCCHHHHHHHHCCCHHHHHHH
T ss_conf 999999-3899999999989199999999
No 268
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=68.17 E-value=7.5 Score=19.95 Aligned_cols=28 Identities=14% Similarity=0.118 Sum_probs=24.4
Q ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 9999998399499999986342999988
Q gi|254781147|r 26 FRNIRKEAKLTQKEIRNRTGFAQSWISE 53 (83)
Q Consensus 26 ir~~R~~~gltq~ela~~~gis~~~is~ 53 (83)
+-.+|.-.|+|.+|+|+.+|+|.+++-.
T Consensus 144 v~~Lr~~~~ls~~EIA~~l~is~~tVks 171 (191)
T PRK12530 144 VFMMREFLELSSEQICQECHITTSNLHV 171 (191)
T ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHH
T ss_conf 9999999299999999998969999999
No 269
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=67.93 E-value=8.6 Score=19.60 Aligned_cols=30 Identities=17% Similarity=0.108 Sum_probs=25.8
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 999999983994999999863429999887
Q gi|254781147|r 25 NFRNIRKEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 25 ~ir~~R~~~gltq~ela~~~gis~~~is~i 54 (83)
.+-.++.-.|+|.+|+|+.+|+|.+++...
T Consensus 127 ~vi~l~~~~~~s~~EIA~~l~is~~tVk~~ 156 (175)
T PRK12518 127 AVLVLHDLEDLPQKEIAEILNIPVGTVKSR 156 (175)
T ss_pred HHHHHHHHHCCCHHHHHHHHCCCHHHHHHH
T ss_conf 999999992999999999989599999999
No 270
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=67.93 E-value=7.7 Score=19.88 Aligned_cols=31 Identities=19% Similarity=0.124 Sum_probs=25.7
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999983994999999863429999887
Q gi|254781147|r 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 24 ~~ir~~R~~~gltq~ela~~~gis~~~is~i 54 (83)
+.+-.+|.-.|+|.+|+|+.+|+|.+++...
T Consensus 134 r~v~~l~~~~~~s~~EIA~~l~is~~tVk~r 164 (185)
T PRK06811 134 REIFIKRYLLGESIEEIAKKLGLTRSAIDNR 164 (185)
T ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 9999999994999999999989299999999
No 271
>pfam04760 IF2_N Translation initiation factor IF-2, N-terminal region. This conserved feature at the N-terminus of bacterial translation initiation factor IF2 has recently had its structure solved. It shows structural similarity to the tRNA anticodon Stem Contact Fold domains of the methionyl-tRNA and glutaminyl-tRNA synthetases, and a similar fold is also found in the B5 domain of the phenylalanine-tRNA synthetase.
Probab=67.77 E-value=11 Score=18.96 Aligned_cols=44 Identities=18% Similarity=0.282 Sum_probs=32.5
Q ss_pred CCCCHHHHHHHHHHHHHHHHHH--HCC-----CCCCCHHHHHHHHHHHCCC
Q ss_conf 3994999999863429999887--558-----9994489999999992899
Q gi|254781147|r 33 AKLTQKEIRNRTGFAQSWISEL--ETG-----KSTINIDNMIILAHTLDTP 76 (83)
Q Consensus 33 ~gltq~ela~~~gis~~~is~i--E~G-----~~~~~~~~l~~la~al~i~ 76 (83)
.++|..|||+.+|++..-|=+. ..| ...++.++...|++.|+..
T Consensus 2 ~~itV~elA~~l~~~~~~vi~~L~~~Gi~~~~n~~ld~e~a~~i~~~~~~~ 52 (52)
T pfam04760 2 EKIRVYELAKELGVSSKELIKKLFKLGIMKTHNSTLDEETAELLAEEFGVE 52 (52)
T ss_pred CCEEHHHHHHHHCCCHHHHHHHHHHCCCEECCCCCCCHHHHHHHHHHHCCC
T ss_conf 817399999998888999999999879855677745999999999981989
No 272
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=67.65 E-value=7.7 Score=19.90 Aligned_cols=30 Identities=17% Similarity=0.162 Sum_probs=25.6
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 999999983994999999863429999887
Q gi|254781147|r 25 NFRNIRKEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 25 ~ir~~R~~~gltq~ela~~~gis~~~is~i 54 (83)
.+-.+|.-.|+|.+|+|+.+|+|.+++-..
T Consensus 156 ~vl~Lr~~eglS~~EIAe~Lgis~~tVks~ 185 (207)
T PRK12544 156 RVFMMREFIELETPEICHNEDLTVSNLNVM 185 (207)
T ss_pred HHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 999999981999999999979799999999
No 273
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=67.56 E-value=7.9 Score=19.83 Aligned_cols=30 Identities=7% Similarity=-0.020 Sum_probs=25.3
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 999999998399499999986342999988
Q gi|254781147|r 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISE 53 (83)
Q Consensus 24 ~~ir~~R~~~gltq~ela~~~gis~~~is~ 53 (83)
+.+-.++.-.|+|.+|+|+.+|+|.+++..
T Consensus 125 R~vi~L~~~~~~s~~EIA~~l~is~~tVks 154 (173)
T PRK12522 125 KTVLVLYYYEQYSYKEMSEILNIPIGTVKY 154 (173)
T ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHH
T ss_conf 999999998399999999998939999999
No 274
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=67.41 E-value=7.5 Score=19.96 Aligned_cols=33 Identities=15% Similarity=0.040 Sum_probs=25.5
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHH-HHHCC
Q ss_conf 9999999839949999998634299998-87558
Q gi|254781147|r 25 NFRNIRKEAKLTQKEIRNRTGFAQSWIS-ELETG 57 (83)
Q Consensus 25 ~ir~~R~~~gltq~ela~~~gis~~~is-~iE~G 57 (83)
.+-.++.-.|+|.+|+|+.+|+|.+++. ++-++
T Consensus 136 ~~~~l~~~eg~s~~EIA~~l~is~~tVk~~l~rA 169 (179)
T PRK12514 136 AAVRRAYLEGLSYKELAERHDVPLNTMRTWLRRS 169 (179)
T ss_pred HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 9999996069989999998890999999999999
No 275
>PRK13749 transcriptional regulator MerD; Provisional
Probab=67.29 E-value=8.9 Score=19.51 Aligned_cols=48 Identities=10% Similarity=0.076 Sum_probs=30.3
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHCCC------------CCCC---HH--HHHHHHHHHCCCHHHH
Q ss_conf 39949999998634299998875589------------9944---89--9999999928999996
Q gi|254781147|r 33 AKLTQKEIRNRTGFAQSWISELETGK------------STIN---ID--NMIILAHTLDTPLWKL 80 (83)
Q Consensus 33 ~gltq~ela~~~gis~~~is~iE~G~------------~~~~---~~--~l~~la~al~i~~~~l 80 (83)
..+|..+||+.+|+|..+|..||.-- +.-+ ++ ...+-|+.+|.+++++
T Consensus 2 ~aytIg~LA~~aGVsv~tIR~Y~~~GLL~p~~Rt~gGyRlyd~~~l~RL~FIR~a~elGf~LdeI 66 (121)
T PRK13749 2 NAYTVSRLALDAGVSVHIVRDYLLRGLLRPVACTTGGYGLFDDAALQRLCFVRAAFEAGIGLDAL 66 (121)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCHHHH
T ss_conf 84209999999599735548898768989988899884367899999999999999908989999
No 276
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=67.17 E-value=7.1 Score=20.09 Aligned_cols=25 Identities=20% Similarity=0.332 Sum_probs=21.1
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 3994999999863429999887558
Q gi|254781147|r 33 AKLTQKEIRNRTGFAQSWISELETG 57 (83)
Q Consensus 33 ~gltq~ela~~~gis~~~is~iE~G 57 (83)
.-+|++|+|+..|||+..|.+||..
T Consensus 276 ~~~TL~EIg~~lgvSrERVRQIE~~ 300 (318)
T PRK07405 276 QPLTLAKIGERLNISRERVRQIERE 300 (318)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 9747999998979599999999999
No 277
>cd04788 HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR. Helix-turn-helix (HTH) transcription regulators NolA and AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp. NC92, NolA is required for efficient nodulation of host plants. In Xanthomonas albilineans, AlbR regulates the expression of the pathotoxin, albicidin. These proteins are putatively comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=66.92 E-value=4.6 Score=21.19 Aligned_cols=46 Identities=17% Similarity=0.192 Sum_probs=29.6
Q ss_pred CCHHHHHHHHHHHHHHHHHHHCCC-CCC-----------CHHH-----HHHHHHHHCCCHHHH
Q ss_conf 949999998634299998875589-994-----------4899-----999999928999996
Q gi|254781147|r 35 LTQKEIRNRTGFAQSWISELETGK-STI-----------NIDN-----MIILAHTLDTPLWKL 80 (83)
Q Consensus 35 ltq~ela~~~gis~~~is~iE~G~-~~~-----------~~~~-----l~~la~al~i~~~~l 80 (83)
|+..|+|+.+|||..+|.-||.-. -.| +.+. ....++.+|+|+.+.
T Consensus 1 y~Ige~Ak~~gvs~~tlRyYe~~GLl~p~~r~~~gyR~Y~~~~i~~l~~I~~lr~~G~sl~eI 63 (96)
T cd04788 1 WKIGELARRTGLSVRTLHHYDHIGLLSPSQRTEGGHRLYDRADIRRLHQIIALRRLGFSLREI 63 (96)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCEECCHHHHHHHHHHHHHHHCCCCHHHH
T ss_conf 948899999895999999999739989888799988218999999999999999979999999
No 278
>TIGR01764 excise DNA binding domain, excisionase family; InterPro: IPR010093 An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This entry 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 entry 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 (IPR000551 from INTERPRO).; GO: 0003677 DNA binding.
Probab=66.88 E-value=3.7 Score=21.80 Aligned_cols=24 Identities=33% Similarity=0.433 Sum_probs=20.8
Q ss_pred CCHHHHHHHHHHHHHHHHHH-HCCC
Q ss_conf 94999999863429999887-5589
Q gi|254781147|r 35 LTQKEIRNRTGFAQSWISEL-ETGK 58 (83)
Q Consensus 35 ltq~ela~~~gis~~~is~i-E~G~ 58 (83)
||-+|+|+.+|||.+++-++ ++|+
T Consensus 2 lTv~EaA~yLgv~~~t~~~l~~~g~ 26 (49)
T TIGR01764 2 LTVEEAAEYLGVSKSTVYRLIEEGE 26 (49)
T ss_pred CCHHHHHHHCCCCHHHHHHHHHCCC
T ss_conf 8778899771999057899997189
No 279
>pfam07471 Phage_Nu1 Phage DNA packaging protein Nu1. Terminase, the DNA packaging enzyme of bacteriophage lambda, is a heteromultimer composed of subunits Nu1 and A. The smaller Nu1 terminase subunit has a low-affinity ATPase stimulated by non-specific DNA.
Probab=66.75 E-value=5 Score=21.01 Aligned_cols=23 Identities=13% Similarity=0.270 Sum_probs=20.3
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 99499999986342999988755
Q gi|254781147|r 34 KLTQKEIRNRTGFAQSWISELET 56 (83)
Q Consensus 34 gltq~ela~~~gis~~~is~iE~ 56 (83)
.+|.++||+..|||..++.+|-.
T Consensus 2 ~vnk~elA~~~gVS~~tv~~W~~ 24 (164)
T pfam07471 2 EVNKKQLAEIFGVSIRTIDNWQS 24 (164)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 67899999996988889999998
No 280
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=66.69 E-value=8.2 Score=19.71 Aligned_cols=34 Identities=9% Similarity=-0.014 Sum_probs=27.1
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHH-HHHCC
Q ss_conf 99999999839949999998634299998-87558
Q gi|254781147|r 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWIS-ELETG 57 (83)
Q Consensus 24 ~~ir~~R~~~gltq~ela~~~gis~~~is-~iE~G 57 (83)
+.+-.++.-.|+|.+|+|+.+|++.+++- ++-++
T Consensus 138 R~~l~L~~~~g~s~~EIA~ilgi~~gTVKsRl~RA 172 (195)
T PRK12535 138 REALILTQVLGYTYEEAAKIADVRVGTIRSRVARA 172 (195)
T ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 79999999829989999999893999999999999
No 281
>cd01279 HTH_HspR-like Helix-Turn-Helix DNA binding domain of HspR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator HspR and related proteins, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=66.50 E-value=4.4 Score=21.31 Aligned_cols=22 Identities=5% Similarity=-0.014 Sum_probs=17.6
Q ss_pred CCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 9499999986342999988755
Q gi|254781147|r 35 LTQKEIRNRTGFAQSWISELET 56 (83)
Q Consensus 35 ltq~ela~~~gis~~~is~iE~ 56 (83)
++..++|+.+|+++++|..||+
T Consensus 2 Y~IgevA~l~Gv~~~tLR~yEr 23 (98)
T cd01279 2 YPISVAAELLGIHPQTLRVYDR 23 (98)
T ss_pred CCHHHHHHHHCCCHHHHHHHHH
T ss_conf 3589999997989999999999
No 282
>TIGR00491 aIF-2 translation initiation factor aIF-2; InterPro: IPR004544 Initiation factor 2 (IF-2) is one of the three factors required for the initiation of protein biosynthesis in bacteria. IF-2 promotes the GTP-dependent binding of the initiator tRNA to the small subunit of the ribosome. IF-2 is a protein of about 70 to 95 Kd which contains a central GTP-binding domain flanked by a highly variable N-terminal domain and a more conserved C-terminal domain. Some members of this family undergo protein self splicing that involves a post-translational excision of the intein followed by peptide ligation.; GO: 0003743 translation initiation factor activity, 0005525 GTP binding, 0006413 translational initiation, 0005622 intracellular.
Probab=66.21 E-value=1.8 Score=23.57 Aligned_cols=49 Identities=16% Similarity=0.251 Sum_probs=42.1
Q ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHC
Q ss_conf 9999999999998399499999986342999988755899944899999999928
Q gi|254781147|r 20 MIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLD 74 (83)
Q Consensus 20 ~~~g~~ir~~R~~~gltq~ela~~~gis~~~is~iE~G~~~~~~~~l~~la~al~ 74 (83)
..+....+++|.--|||..+ +..||+++||||+-.|+.+.+.++...|.
T Consensus 413 yPinkdmkrlrilfGmtrne------vnvsyyakyenGkeiPsyeivkkflnslk 461 (1145)
T TIGR00491 413 YPINKDMKRLRILFGMTRNE------VNVSYYAKYENGKEIPSYEIVKKFLNSLK 461 (1145)
T ss_pred CCCHHHHHHHHHHHCCCCCC------EEEEEEEEECCCCCCCHHHHHHHHHHHCC
T ss_conf 86303445534432121000------34555543047863750899999985227
No 283
>pfam05225 HTH_psq helix-turn-helix, Psq domain. This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster. In pipsqueak this domain binds to GAGA sequence.
Probab=66.04 E-value=12 Score=18.76 Aligned_cols=40 Identities=13% Similarity=0.209 Sum_probs=31.7
Q ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf 99999999999983994999999863429999887558999
Q gi|254781147|r 20 MIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKST 60 (83)
Q Consensus 20 ~~~g~~ir~~R~~~gltq~ela~~~gis~~~is~iE~G~~~ 60 (83)
+.+..-|..+|... +|+.+.|..-||..+++.+.-+|...
T Consensus 3 e~l~~Al~av~~g~-~S~~kAa~~ygIP~sTL~~r~~g~~~ 42 (45)
T pfam05225 3 EDLAEALEAVRNGK-MSLRKAARKYGIPRSTLWRRLRGKYS 42 (45)
T ss_pred HHHHHHHHHHHCCC-CCHHHHHHHHCCCHHHHHHHHCCCCC
T ss_conf 89999999999199-67999999978985899999756343
No 284
>cd04784 HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators. Helix-turn-helix (HTH) CadR and PbrR transcription regulators including Pseudomonas aeruginosa CadR and Ralstonia metallidurans PbrR that regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which form a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=65.79 E-value=5 Score=20.99 Aligned_cols=23 Identities=22% Similarity=0.260 Sum_probs=15.5
Q ss_pred CCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 94999999863429999887558
Q gi|254781147|r 35 LTQKEIRNRTGFAQSWISELETG 57 (83)
Q Consensus 35 ltq~ela~~~gis~~~is~iE~G 57 (83)
|...|+|+++|+|..+|.-||.-
T Consensus 1 M~Ige~a~~~gvs~~tlRyYE~~ 23 (127)
T cd04784 1 MKIGELAKKTGCSVETIRYYEKE 23 (127)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHC
T ss_conf 96899999989499999999985
No 285
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=65.66 E-value=6.1 Score=20.50 Aligned_cols=31 Identities=13% Similarity=0.189 Sum_probs=26.2
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999983994999999863429999887
Q gi|254781147|r 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 24 ~~ir~~R~~~gltq~ela~~~gis~~~is~i 54 (83)
.-+..+.+...+|..|||+..|+|..|+.+=
T Consensus 4 ~Il~~l~~~~~~~i~~La~~~~VS~~TiRRD 34 (53)
T smart00420 4 QILELLAQQGKVSVEELAELLGVSEMTIRRD 34 (53)
T ss_pred HHHHHHHHCCCEEHHHHHHHHCCCHHHHHHH
T ss_conf 9999999869797999999989799999996
No 286
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=65.64 E-value=12 Score=18.71 Aligned_cols=22 Identities=9% Similarity=0.178 Sum_probs=19.8
Q ss_pred CCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 3994999999863429999887
Q gi|254781147|r 33 AKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 33 ~gltq~ela~~~gis~~~is~i 54 (83)
..+|+.++|..+|+++.++|+.
T Consensus 172 l~~t~~~lA~~lG~tretvsR~ 193 (236)
T PRK09392 172 LPYEKRTLASYLGMTPENLSRA 193 (236)
T ss_pred ECCCHHHHHHHHCCCHHHHHHH
T ss_conf 3478999999878989999999
No 287
>PRK10371 DNA-binding transcriptional regulator MelR; Provisional
Probab=65.52 E-value=9.1 Score=19.45 Aligned_cols=42 Identities=7% Similarity=0.143 Sum_probs=29.7
Q ss_pred HHHHHHHHH--HCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHH
Q ss_conf 999999999--839949999998634299998875589994489
Q gi|254781147|r 23 VNNFRNIRK--EAKLTQKEIRNRTGFAQSWISELETGKSTINID 64 (83)
Q Consensus 23 g~~ir~~R~--~~gltq~ela~~~gis~~~is~iE~G~~~~~~~ 64 (83)
-.-+..+.. ...+|.+++|+.+|+|+++.+++-+.....|..
T Consensus 194 ~~il~YI~~hY~e~IsL~diA~~~~lS~~y~sr~FKk~tG~T~~ 237 (302)
T PRK10371 194 SQMLGFIAENYDQALTINDVAEHVKLNANYAMGIFQRVMQLTMK 237 (302)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHCCCHH
T ss_conf 99999999982899999999989795999999999999890999
No 288
>TIGR00160 MGSA methylglyoxal synthase; InterPro: IPR004363 Methylglyoxal synthase (MGS) catalyzes the conversion of dihydroxyacetone phosphate to methylglyoxal and phosphate: Glycerone phosphate = methylglyoxal + phosphate It provides bacteria with an alternative to triosephosphate isomerase for metabolizing dihydroxyacetone phosphate. MGS is a small protein of about 13 to 17 kDa. An aspartate residue is involved in the catalytic mechanism. Methylglyoxal synthase contains a domain shared by other enzymes. Other proteins containing this domain include purine biosynthesis protein PurH and carbamoyl phosphate synthetase.; GO: 0008929 methylglyoxal synthase activity, 0019242 methylglyoxal biosynthetic process, 0005737 cytoplasm.
Probab=65.52 E-value=3.7 Score=21.75 Aligned_cols=23 Identities=13% Similarity=0.332 Sum_probs=19.4
Q ss_pred CCC-CCCCHHHHHHHHHHHCCCHH
Q ss_conf 589-99448999999999289999
Q gi|254781147|r 56 TGK-STINIDNMIILAHTLDTPLW 78 (83)
Q Consensus 56 ~G~-~~~~~~~l~~la~al~i~~~ 78 (83)
+.. ..|.+..|.+||++++||+.
T Consensus 85 ~AqPHEPDV~ALlRLc~V~nIPlA 108 (143)
T TIGR00160 85 NAQPHEPDVKALLRLCDVYNIPLA 108 (143)
T ss_pred CCCCCCCCHHHHHHHHHHCCCHHH
T ss_conf 478888007889878645025034
No 289
>PRK13502 transcriptional activator RhaR; Provisional
Probab=65.51 E-value=11 Score=19.07 Aligned_cols=32 Identities=3% Similarity=0.065 Sum_probs=24.5
Q ss_pred HHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf 98399499999986342999988755899944
Q gi|254781147|r 31 KEAKLTQKEIRNRTGFAQSWISELETGKSTIN 62 (83)
Q Consensus 31 ~~~gltq~ela~~~gis~~~is~iE~G~~~~~ 62 (83)
....+|.+++|+.+|+|+++++++-+-....+
T Consensus 189 ~~~~isl~~lA~~~~~S~~~lsr~FK~~tG~t 220 (282)
T PRK13502 189 LECPFALDAFCQQEQCSERVLRQQFRAQTGMT 220 (282)
T ss_pred HCCCCCHHHHHHHHCCCHHHHHHHHHHHHCCC
T ss_conf 66998899999897979999999999998929
No 290
>pfam05930 Phage_AlpA Prophage CP4-57 regulatory protein (AlpA). This family consists of several short bacterial and phage proteins which are related to the E. coli protein AlpA. AlpA suppress two phenotypes of a delta lon protease mutant, overproduction of capsular polysaccharide and sensitivity to UV light. Several of the sequences in this family are thought to be DNA-binding proteins.
Probab=65.50 E-value=6.6 Score=20.27 Aligned_cols=29 Identities=28% Similarity=0.223 Sum_probs=23.3
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf 99499999986342999988755899944
Q gi|254781147|r 34 KLTQKEIRNRTGFAQSWISELETGKSTIN 62 (83)
Q Consensus 34 gltq~ela~~~gis~~~is~iE~G~~~~~ 62 (83)
=+...|+.+.+|+|+++|.+..+...-|.
T Consensus 3 llr~~eV~~~~glsrstiyr~i~~G~FP~ 31 (51)
T pfam05930 3 FLRLKEVEQLTGLSRSTIYRLIKDGEFPK 31 (51)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHCCCCCC
T ss_conf 13799999998989999999998799999
No 291
>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional
Probab=65.46 E-value=10 Score=19.16 Aligned_cols=31 Identities=19% Similarity=0.224 Sum_probs=25.4
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999983994999999863429999887
Q gi|254781147|r 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 24 ~~ir~~R~~~gltq~ela~~~gis~~~is~i 54 (83)
..|...-.+.++.+.+.|+.+|||++++.+.
T Consensus 289 ~~I~~aL~~~~gn~~~aA~~LGIsR~tL~~k 319 (325)
T PRK11608 289 ELLQRSLQQAKFNQKRAAELLGLTYHQFRAL 319 (325)
T ss_pred HHHHHHHHHHCCCHHHHHHHHCCCHHHHHHH
T ss_conf 9999999993998999999988899999999
No 292
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=65.30 E-value=9.1 Score=19.45 Aligned_cols=34 Identities=9% Similarity=0.026 Sum_probs=27.2
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHH-HHHCC
Q ss_conf 99999999839949999998634299998-87558
Q gi|254781147|r 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWIS-ELETG 57 (83)
Q Consensus 24 ~~ir~~R~~~gltq~ela~~~gis~~~is-~iE~G 57 (83)
+.+-.+|.-.|+|.+|+|+.+|++.+++- ++-++
T Consensus 136 R~vl~L~~~egls~~EIA~~lg~~~gTVKsRl~RA 170 (185)
T PRK09649 136 REALLLTQLLGLSYADAAAVCGCPVGTIRSRVARA 170 (185)
T ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 99999899729999999999893999999999999
No 293
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=65.22 E-value=5.5 Score=20.75 Aligned_cols=26 Identities=19% Similarity=0.281 Sum_probs=21.5
Q ss_pred HHCCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 98399499999986342999988755
Q gi|254781147|r 31 KEAKLTQKEIRNRTGFAQSWISELET 56 (83)
Q Consensus 31 ~~~gltq~ela~~~gis~~~is~iE~ 56 (83)
.-+..|.+|||+.+|||.++++..-+
T Consensus 175 ~PR~~~l~dLA~~lGISkst~~ehLR 200 (215)
T COG3413 175 YPRRVSLKDLAKELGISKSTLSEHLR 200 (215)
T ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 87658999999995998889999999
No 294
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=65.19 E-value=9.1 Score=19.44 Aligned_cols=30 Identities=7% Similarity=-0.056 Sum_probs=25.5
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 999999983994999999863429999887
Q gi|254781147|r 25 NFRNIRKEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 25 ~ir~~R~~~gltq~ela~~~gis~~~is~i 54 (83)
.+-.++.-.|+|.+|+|+.+|+|.+++-..
T Consensus 138 ~vl~L~~~eg~s~~EIA~~lgis~~tVKsr 167 (197)
T PRK09643 138 AALVAVDMQGYSVADTARMLGVAEGTVKSR 167 (197)
T ss_pred HHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 999999981999999999989399999999
No 295
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=65.17 E-value=9 Score=19.47 Aligned_cols=32 Identities=16% Similarity=0.064 Sum_probs=26.4
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 99999999839949999998634299998875
Q gi|254781147|r 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISELE 55 (83)
Q Consensus 24 ~~ir~~R~~~gltq~ela~~~gis~~~is~iE 55 (83)
+.+-.++.-.|+|++|.|+.+|++.+++-..-
T Consensus 133 R~~~~l~~~~gls~~EIA~~l~i~~~tVks~l 164 (182)
T COG1595 133 REAFLLRYLEGLSYEEIAEILGISVGTVKSRL 164 (182)
T ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 99999999859999999989599999999999
No 296
>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=65.04 E-value=5.8 Score=20.63 Aligned_cols=27 Identities=19% Similarity=0.121 Sum_probs=23.2
Q ss_pred HHHCCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 998399499999986342999988755
Q gi|254781147|r 30 RKEAKLTQKEIRNRTGFAQSWISELET 56 (83)
Q Consensus 30 R~~~gltq~ela~~~gis~~~is~iE~ 56 (83)
....|+|-.|.|+.+|+|.+++..+-+
T Consensus 11 ~~~~G~s~~eIA~~L~is~~TV~~~~~ 37 (57)
T cd06170 11 LLAEGKTNKEIADILGISEKTVKTHLR 37 (57)
T ss_pred HHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 998079999999998978999999999
No 297
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=64.57 E-value=11 Score=18.96 Aligned_cols=31 Identities=23% Similarity=0.170 Sum_probs=26.1
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999983994999999863429999887
Q gi|254781147|r 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 24 ~~ir~~R~~~gltq~ela~~~gis~~~is~i 54 (83)
+.+-.+|.-.|+|.+|+|+.+|+|.+++..-
T Consensus 133 r~ii~l~~~~~~s~~EIA~~l~is~~tV~~r 163 (177)
T PRK09415 133 REVIYLFYYEELSIKEIATVTGVNENTIKTR 163 (177)
T ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 9999999980998999999889299999999
No 298
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=64.27 E-value=9.4 Score=19.35 Aligned_cols=31 Identities=13% Similarity=0.093 Sum_probs=26.2
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999983994999999863429999887
Q gi|254781147|r 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 24 ~~ir~~R~~~gltq~ela~~~gis~~~is~i 54 (83)
+.+-.+|.-.|+|.+|+|+.+|+|.+++-..
T Consensus 145 R~v~~Lr~~egls~~EIA~~L~is~~tVksr 175 (201)
T PRK12545 145 GRVFMMREFLDFEIDDICTELTLTANHCSVL 175 (201)
T ss_pred HHHHHHHHHHCCCHHHHHHHHCCCHHHHHHH
T ss_conf 8898999992898999999989699999999
No 299
>cd04765 HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=64.16 E-value=5.6 Score=20.71 Aligned_cols=22 Identities=18% Similarity=0.229 Sum_probs=16.3
Q ss_pred CCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 9499999986342999988755
Q gi|254781147|r 35 LTQKEIRNRTGFAQSWISELET 56 (83)
Q Consensus 35 ltq~ela~~~gis~~~is~iE~ 56 (83)
+|..|+|+.+|++.++|.-||.
T Consensus 1 ysIgEva~~~gv~~~tLRywE~ 22 (99)
T cd04765 1 FSIGEVAEILGLPPHVLRYWET 22 (99)
T ss_pred CCHHHHHHHHCCCHHHHHHHHH
T ss_conf 9788999998949999999998
No 300
>pfam00165 HTH_AraC Bacterial regulatory helix-turn-helix proteins, AraC family. In the absence of arabinose, the N-terminal arm of AraC binds to the DNA binding domain (pfam00165) and helps to hold the two DNA binding domains in a relative orientation that favours DNA looping. In the presence of arabinose, the arms bind over the arabinose on the dimerization domain, thus freeing the DNA-binding domains. The freed DNA-binding domains are then able to assume a conformation suitable for binding to the adjacent DNA sites that are utilized when AraC activates transcription, and hence AraC ceases looping the DNA when arabinose is added.
Probab=64.15 E-value=4.4 Score=21.34 Aligned_cols=29 Identities=28% Similarity=0.368 Sum_probs=24.3
Q ss_pred HCCCCHHHHHHHHHH-HHHHHHHHHCCCCC
Q ss_conf 839949999998634-29999887558999
Q gi|254781147|r 32 EAKLTQKEIRNRTGF-AQSWISELETGKST 60 (83)
Q Consensus 32 ~~gltq~ela~~~gi-s~~~is~iE~G~~~ 60 (83)
..+|+..++|..+|+ |+++.++..+-...
T Consensus 6 ~~~~~i~~IA~~~g~~s~~~f~r~fk~~~G 35 (43)
T pfam00165 6 STNWTIADIAEELGFSSQSYFSRLFKKYTG 35 (43)
T ss_pred CCCCCHHHHHHHHCCCCHHHHHHHHHHHHC
T ss_conf 089979999999689976899999999889
No 301
>pfam09339 HTH_IclR IclR helix-turn-helix domain.
Probab=64.11 E-value=6.3 Score=20.38 Aligned_cols=30 Identities=27% Similarity=0.324 Sum_probs=23.8
Q ss_pred HHHH-HHCCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 9999-98399499999986342999988755
Q gi|254781147|r 27 RNIR-KEAKLTQKEIRNRTGFAQSWISELET 56 (83)
Q Consensus 27 r~~R-~~~gltq~ela~~~gis~~~is~iE~ 56 (83)
..+. ....+|..|+|+.+|++++++.++=+
T Consensus 10 ~~~~~~~~~~~l~eia~~~gl~kstv~RlL~ 40 (52)
T pfam09339 10 EALAEAPGGLSLTEIARRTGLPKSTAHRLLQ 40 (52)
T ss_pred HHHHHCCCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 9986289998999999998919999999999
No 302
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=63.79 E-value=10 Score=19.18 Aligned_cols=30 Identities=7% Similarity=-0.041 Sum_probs=25.3
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 999999998399499999986342999988
Q gi|254781147|r 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISE 53 (83)
Q Consensus 24 ~~ir~~R~~~gltq~ela~~~gis~~~is~ 53 (83)
+.+-.++.-.|+|.+|+|+.+|+|.+++-.
T Consensus 112 R~v~~L~~~e~~s~~EIA~~l~is~~tVk~ 141 (160)
T PRK09642 112 RDVVLAHYLEEKSYQEIALQENIEVKTVEM 141 (160)
T ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHH
T ss_conf 999799998299999999998919999999
No 303
>TIGR03454 partition_RepB plasmid partitioning protein RepB. Members of this family are the RepB protein involved in replicon partitioning. RepB is found, in general, as part of a repABC operon in plasmids and small chromosomes, separate from the main chromosome, in various bacteria. This model describes a rather narrow clade of proteins; it should be noted that additional homologs scoring below the trusted cutoff have very similar functions, although they may be named differently.
Probab=63.43 E-value=8.5 Score=19.63 Aligned_cols=50 Identities=10% Similarity=0.181 Sum_probs=34.6
Q ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHH
Q ss_conf 999999999999983994999999863429999887558999448999999999
Q gi|254781147|r 19 RMIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHT 72 (83)
Q Consensus 19 ~~~~g~~ir~~R~~~gltq~ela~~~gis~~~is~iE~G~~~~~~~~l~~la~a 72 (83)
+..|+.++ ++.|++++.++..+|++.+.||++-+=-..+..+.+..|..|
T Consensus 166 rA~fA~~l----~~~g~~r~~I~~aL~vdks~lSrml~Va~~iP~elI~aIGpA 215 (325)
T TIGR03454 166 RALFAQRL----EDRGFDRDTIMAALSVDKTELSRMISVARRIPEELIEAIGPA 215 (325)
T ss_pred HHHHHHHH----HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCHHHHHHHCCC
T ss_conf 99999999----984999999999988899999999999997899999973798
No 304
>COG2826 Tra8 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]
Probab=63.22 E-value=6.9 Score=20.16 Aligned_cols=32 Identities=25% Similarity=0.329 Sum_probs=24.8
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHHH-HHCC
Q ss_conf 99999998399499999986342999988-7558
Q gi|254781147|r 25 NFRNIRKEAKLTQKEIRNRTGFAQSWISE-LETG 57 (83)
Q Consensus 25 ~ir~~R~~~gltq~ela~~~gis~~~is~-iE~G 57 (83)
+|..++ ..|+|..+.|+.+|-+.|+|++ +-+|
T Consensus 15 ~I~~l~-~~~~S~reIA~~LgRh~sTIsRElkRn 47 (318)
T COG2826 15 EIERLL-KAKMSIREIAKQLNRHHSTISRELKRN 47 (318)
T ss_pred HHHHHH-HCCCCHHHHHHHHCCCCCHHHHHHHCC
T ss_conf 999999-859989999998576862042798668
No 305
>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional
Probab=62.86 E-value=12 Score=18.73 Aligned_cols=32 Identities=9% Similarity=0.011 Sum_probs=27.0
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 99999999983994999999863429999887
Q gi|254781147|r 23 VNNFRNIRKEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 23 g~~ir~~R~~~gltq~ela~~~gis~~~is~i 54 (83)
-..|...-.+.+.++.+.|+.+|||++++.+-
T Consensus 593 r~~I~~aL~~~~gN~s~aA~~LGIsR~TLYRK 624 (639)
T PRK11388 593 KQAIINAAQVCGGRIQEMAALLGIGRTTLWRK 624 (639)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHH
T ss_conf 99999999994997999999989899999999
No 306
>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=62.65 E-value=10 Score=19.13 Aligned_cols=28 Identities=36% Similarity=0.452 Sum_probs=22.1
Q ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 99999983994999999863429999887
Q gi|254781147|r 26 FRNIRKEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 26 ir~~R~~~gltq~ela~~~gis~~~is~i 54 (83)
+..+. +.++|..|+|+.+|+|++++++-
T Consensus 13 l~~L~-~~~~~~~eia~~l~is~~~vs~h 40 (78)
T cd00090 13 LRLLL-EGPLTVSELAERLGLSQSTVSRH 40 (78)
T ss_pred HHHHH-HCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 99998-48906999987778487899999
No 307
>PRK09863 putative frv operon regulatory protein; Provisional
Probab=62.54 E-value=8.1 Score=19.76 Aligned_cols=22 Identities=14% Similarity=0.240 Sum_probs=12.6
Q ss_pred HHCCCCHHHHHHHHHHHHHHHH
Q ss_conf 9839949999998634299998
Q gi|254781147|r 31 KEAKLTQKEIRNRTGFAQSWIS 52 (83)
Q Consensus 31 ~~~gltq~ela~~~gis~~~is 52 (83)
++..+|+.|||+.+|||..||.
T Consensus 14 ~~~~lt~~eLA~~L~VS~RTIR 35 (585)
T PRK09863 14 EQQDRSGGELAQQLGVSRRTIV 35 (585)
T ss_pred HCCCCCHHHHHHHCCCCCHHHH
T ss_conf 7599998999987499711789
No 308
>cd04772 HTH_TioE_rpt1 First Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD contains the N-terminal or first repeat (rpt1) of these tandem MerR-like domain proteins.
Probab=62.29 E-value=8.2 Score=19.72 Aligned_cols=24 Identities=8% Similarity=0.165 Sum_probs=20.0
Q ss_pred CCHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf 949999998634299998875589
Q gi|254781147|r 35 LTQKEIRNRTGFAQSWISELETGK 58 (83)
Q Consensus 35 ltq~ela~~~gis~~~is~iE~G~ 58 (83)
++..|+|+.+|+|..+|.-||.-.
T Consensus 1 Yri~ElA~~~Gvs~~tiR~YE~~G 24 (99)
T cd04772 1 YRTVDLARAIGLSPQTVRNYESLG 24 (99)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCC
T ss_conf 978999999896999999999969
No 309
>PRK03837 transcriptional regulator NanR; Provisional
Probab=62.06 E-value=8.6 Score=19.59 Aligned_cols=51 Identities=16% Similarity=0.196 Sum_probs=33.2
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHC--CC-CHHHHHHHHHHHHHHHHHH
Q ss_conf 969888888689899999999999999999983--99-4999999863429999887
Q gi|254781147|r 1 MPRRKRDEPHLSDAILRERMIFVNNFRNIRKEA--KL-TQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 1 Mp~~~~~~p~~~~~~~~~~~~~g~~ir~~R~~~--gl-tq~ela~~~gis~~~is~i 54 (83)
|+.++-..+.+++.+.. .+-..|..-+..- .+ |..+||+..|||++.+..-
T Consensus 5 ~~~~Pi~r~~l~e~V~~---~lr~~I~~g~l~pG~rLp~E~eLae~lgVSRtpVREA 58 (243)
T PRK03837 5 LRSRPLARKKLSEEVEE---RLEQMIRSGEFGPGEQLPSERELMAFFGVGRPSVREA 58 (243)
T ss_pred CCCCCCCCCCHHHHHHH---HHHHHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 78788989989999999---9999998399999497935999999979697899999
No 310
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=61.84 E-value=8.7 Score=19.56 Aligned_cols=27 Identities=26% Similarity=0.302 Sum_probs=22.3
Q ss_pred HHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 9999983994999999863429999887
Q gi|254781147|r 27 RNIRKEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 27 r~~R~~~gltq~ela~~~gis~~~is~i 54 (83)
..+. +..++..|+|+.+|++++++|+-
T Consensus 4 ~~L~-~~~~~~~ela~~l~is~~tvs~H 30 (66)
T smart00418 4 KLLA-EGELCVCELAEILGLSQSTVSHH 30 (66)
T ss_pred HHHH-CCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 8977-39966999999988298888799
No 311
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=61.77 E-value=12 Score=18.78 Aligned_cols=30 Identities=13% Similarity=0.111 Sum_probs=24.8
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 999999983994999999863429999887
Q gi|254781147|r 25 NFRNIRKEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 25 ~ir~~R~~~gltq~ela~~~gis~~~is~i 54 (83)
.+-.+|.-.|+|.+|+|+.+|+|.+++...
T Consensus 144 ~vl~L~~~~g~s~~EIA~~lg~s~~tVk~~ 173 (187)
T PRK09648 144 EILILRVVVGLSAEETAEAVGSTPGAVRVA 173 (187)
T ss_pred HHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 999999984999999999989399999999
No 312
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=61.69 E-value=14 Score=18.27 Aligned_cols=42 Identities=10% Similarity=0.166 Sum_probs=30.9
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 8689899999999999999999983994999999863429999887
Q gi|254781147|r 9 PHLSDAILRERMIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 9 p~~~~~~~~~~~~~g~~ir~~R~~~gltq~ela~~~gis~~~is~i 54 (83)
|.+.....+. -.-+..+++....+..|||+..|||..+|.+=
T Consensus 10 ~~~~~t~ER~----~~Il~~L~~~g~v~v~eLae~~~VS~~TIRRD 51 (269)
T PRK09802 10 KRVTGTSERR----EQIIQRLRQQGSVQVNDLSALYGVSTVTIRND 51 (269)
T ss_pred CCCCCCHHHH----HHHHHHHHHCCCEEHHHHHHHHCCCHHHHHHH
T ss_conf 6767709999----99999999869899999999879698899980
No 313
>PRK09480 slmA nucleoid occlusion protein; Provisional
Probab=61.49 E-value=7.1 Score=20.10 Aligned_cols=42 Identities=10% Similarity=0.145 Sum_probs=30.4
Q ss_pred HHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHH
Q ss_conf 998399499999986342999988755899944899999999
Q gi|254781147|r 30 RKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAH 71 (83)
Q Consensus 30 R~~~gltq~ela~~~gis~~~is~iE~G~~~~~~~~l~~la~ 71 (83)
..-.++|-.++|+++|||.+.+.+...+|...=...+..+.+
T Consensus 26 ~~~~~iTt~~iA~~~gvs~aalYrHF~sK~~i~~~lie~ie~ 67 (194)
T PRK09480 26 PPGERITTAKLAARVGVSEAALYRHFPSKARMFEGLIEFIEE 67 (194)
T ss_pred CCCCCCCHHHHHHHHCCCHHHHHHHCCCHHHHHHHHHHHHHH
T ss_conf 797642299999890997899999758799999999999999
No 314
>PHA01082 putative transcription regulator
Probab=61.38 E-value=9 Score=19.48 Aligned_cols=49 Identities=14% Similarity=0.085 Sum_probs=37.2
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCC-CCHHHHHHHHHH
Q ss_conf 9999999983994999999863429999887558999-448999999999
Q gi|254781147|r 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKST-INIDNMIILAHT 72 (83)
Q Consensus 24 ~~ir~~R~~~gltq~ela~~~gis~~~is~iE~G~~~-~~~~~l~~la~a 72 (83)
.|.--.--+.|+|.+|.|+.|=-|.+++-+|..|+.. |-...|.++-..
T Consensus 20 kNyiFRefeCgLsveeaA~LCfKtVrtVk~WD~G~~IPPeCkRLMRm~~g 69 (133)
T PHA01082 20 KNFVFREFECGLSVEEAAKLCFKTVSEVKQWDAGEKIPPICKRLMRMNKG 69 (133)
T ss_pred CCEEEEEHCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCC
T ss_conf 23240100137639999999999788886304899498799999988517
No 315
>PRK13182 racA polar chromosome segregation protein; Reviewed
Probab=61.32 E-value=8.1 Score=19.76 Aligned_cols=36 Identities=14% Similarity=0.170 Sum_probs=26.6
Q ss_pred HHHHHHHHHHHHHHHHHH-----------HCCCCCCCHHHHHHHHHH
Q ss_conf 999999863429999887-----------558999448999999999
Q gi|254781147|r 37 QKEIRNRTGFAQSWISEL-----------ETGKSTINIDNMIILAHT 72 (83)
Q Consensus 37 q~ela~~~gis~~~is~i-----------E~G~~~~~~~~l~~la~a 72 (83)
-.++|+.+|||+.+|.+| |.|....+-+.+..+.+.
T Consensus 3 T~~vAk~LGVspkTVQRWvKq~ni~~~rNE~GHy~Ft~e~l~~lLk~ 49 (178)
T PRK13182 3 TPFVAKKLGVSPKTVQRWVKQLNLPIERNEYGHYIFTEDDLDQLLKY 49 (178)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCEEECHHHHHHHHHH
T ss_conf 17889993999299999999958995536554433249899999999
No 316
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=60.49 E-value=10 Score=19.17 Aligned_cols=24 Identities=17% Similarity=0.273 Sum_probs=20.9
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 994999999863429999887558
Q gi|254781147|r 34 KLTQKEIRNRTGFAQSWISELETG 57 (83)
Q Consensus 34 gltq~ela~~~gis~~~is~iE~G 57 (83)
.+|++|+|+..|||+-.|.+||+.
T Consensus 278 ~~TL~EIg~~lgvSrERVRQIE~~ 301 (320)
T PRK07921 278 PRTLDQIGKLFGLSRERVRQIERE 301 (320)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 747999998979699999999999
No 317
>PRK09744 DNA-binding transcriptional regulator DicC; Provisional
Probab=60.40 E-value=6.5 Score=20.33 Aligned_cols=25 Identities=12% Similarity=0.270 Sum_probs=20.3
Q ss_pred CHHHHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf 499999986342999988755899944
Q gi|254781147|r 36 TQKEIRNRTGFAQSWISELETGKSTIN 62 (83)
Q Consensus 36 tq~ela~~~gis~~~is~iE~G~~~~~ 62 (83)
|+..+|+.+||+.+.||+| |...|-
T Consensus 12 sk~klA~aLgIs~~aVsqW--ge~IPE 36 (75)
T PRK09744 12 SKTKLANAAGVRLASVAAW--GELVPE 36 (75)
T ss_pred CHHHHHHHHCCCHHHHHHH--HHHCCH
T ss_conf 2999999949987999887--401606
No 318
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=60.21 E-value=7.7 Score=19.87 Aligned_cols=27 Identities=26% Similarity=0.288 Sum_probs=23.0
Q ss_pred HHHCCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 998399499999986342999988755
Q gi|254781147|r 30 RKEAKLTQKEIRNRTGFAQSWISELET 56 (83)
Q Consensus 30 R~~~gltq~ela~~~gis~~~is~iE~ 56 (83)
....|+|-+|+|+.+|+|.+++..+-+
T Consensus 14 ~l~~G~s~~eIA~~L~is~~TV~~~~~ 40 (58)
T smart00421 14 LLAEGLTNKEIAERLGISEKTVKTHLS 40 (58)
T ss_pred HHHHCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 998179999999898978989999999
No 319
>cd04779 HTH_MerR-like_sg4 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 4). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=60.03 E-value=7.4 Score=19.99 Aligned_cols=46 Identities=9% Similarity=0.038 Sum_probs=27.0
Q ss_pred CCHHHHHHHHHHHHHHHHHHHC-----------CCCCCCHHH-----HHHHHHHHCCCHHHH
Q ss_conf 9499999986342999988755-----------899944899-----999999928999996
Q gi|254781147|r 35 LTQKEIRNRTGFAQSWISELET-----------GKSTINIDN-----MIILAHTLDTPLWKL 80 (83)
Q Consensus 35 ltq~ela~~~gis~~~is~iE~-----------G~~~~~~~~-----l~~la~al~i~~~~l 80 (83)
++..|+|+.+|+|..+|.-||. |-+.-+-+. +.+.++.+|.++.+.
T Consensus 1 y~IgelA~~~gvs~~TlRyYe~~GLl~p~R~~~gyR~Y~~~~~~rL~~I~~lr~lg~sL~eI 62 (134)
T cd04779 1 YRIGQLAHLAGVSKRTIDYYTNLGLLTPERSDSNYRYYDETALDRLQLIEHLKGQRLSLAEI 62 (134)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCHHHH
T ss_conf 95889999988688999999977997999699998206999999999999999979989999
No 320
>PRK10365 transcriptional regulatory protein ZraR; Provisional
Probab=59.75 E-value=15 Score=18.19 Aligned_cols=31 Identities=6% Similarity=0.022 Sum_probs=25.8
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 9999999998399499999986342999988
Q gi|254781147|r 23 VNNFRNIRKEAKLTQKEIRNRTGFAQSWISE 53 (83)
Q Consensus 23 g~~ir~~R~~~gltq~ela~~~gis~~~is~ 53 (83)
-..|...-...+..+.+.|+.+|||++++.+
T Consensus 407 r~~I~~aL~~~~gn~~~aA~~LGisR~tLyr 437 (441)
T PRK10365 407 KEVILAALEKTGGNKTEAARQLGITRKTLLA 437 (441)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHCCCHHHHHH
T ss_conf 9999999999399899999997889999999
No 321
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=59.73 E-value=11 Score=18.86 Aligned_cols=34 Identities=9% Similarity=-0.002 Sum_probs=28.6
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999999983994999999863429999887
Q gi|254781147|r 21 IFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 21 ~~g~~ir~~R~~~gltq~ela~~~gis~~~is~i 54 (83)
..-.-+..+++....+-.|||+..|+|..||.+-
T Consensus 6 R~~~Il~~L~~~g~v~v~eLa~~~~VS~~TIRRD 39 (251)
T PRK13509 6 RHQILLDMLAQLGFVTVEKVIERLGISPATARRD 39 (251)
T ss_pred HHHHHHHHHHHCCCEEHHHHHHHHCCCHHHHHHH
T ss_conf 9999999999869898999999989699899983
No 322
>cd04777 HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 1), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=59.56 E-value=7.3 Score=20.02 Aligned_cols=22 Identities=0% Similarity=0.051 Sum_probs=13.9
Q ss_pred CCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 9499999986342999988755
Q gi|254781147|r 35 LTQKEIRNRTGFAQSWISELET 56 (83)
Q Consensus 35 ltq~ela~~~gis~~~is~iE~ 56 (83)
|+..|+|+++|||..+|.-||.
T Consensus 1 m~Ige~Ak~~~vs~~TlRyYe~ 22 (107)
T cd04777 1 MKIGKFAKKNNITIDTVRHYID 22 (107)
T ss_pred CCHHHHHHHHCCCHHHHHHHHH
T ss_conf 9689999996998988899998
No 323
>TIGR02899 spore_safA spore coat assembly protein SafA; InterPro: IPR014248 This entry represents a domain of about 40 residues long which is found in a variety of enzymes involved in bacterial cell wall degradation , and which may have a general peptidoglycan binding function. Proteins containing this domain include SafA of Bacillus subtilis, which is a protein found at the interface of the spore cortex and spore coat, and which is dependent on SpoVID for its localization. This domain is generally found towards the N-terminus of these proteins. The C-terminal region of these proteins are more variable and may contain blocks of 12-residue and 13-residue repeats, tandem LysM domains (IPR002482 from INTERPRO), or an SCP-like domain (IPR014258 from INTERPRO)..
Probab=59.50 E-value=5.5 Score=20.74 Aligned_cols=19 Identities=21% Similarity=0.312 Sum_probs=15.8
Q ss_pred HHHHHHHHHHCCCHHHHCC
Q ss_conf 9999999992899999608
Q gi|254781147|r 64 DNMIILAHTLDTPLWKLLK 82 (83)
Q Consensus 64 ~~l~~la~al~i~~~~l~~ 82 (83)
|+|++||.-|+|.+++|..
T Consensus 5 DtlWkiA~kygV~~~~Li~ 23 (44)
T TIGR02899 5 DTLWKIAKKYGVDLDELIQ 23 (44)
T ss_pred CHHHHHHHHHCCCHHHHHH
T ss_conf 2147778771787678864
No 324
>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family; InterPro: IPR012794 Members of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.; GO: 0003677 DNA binding, 0016563 transcription activator activity, 0045941 positive regulation of transcription, 0046278 protocatechuate metabolic process.
Probab=59.10 E-value=5.7 Score=20.65 Aligned_cols=24 Identities=17% Similarity=0.379 Sum_probs=22.4
Q ss_pred HHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 983994999999863429999887
Q gi|254781147|r 31 KEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 31 ~~~gltq~ela~~~gis~~~is~i 54 (83)
...++|..|+|+++|+++++..++
T Consensus 21 ~~~~ltl~~vA~~TGL~RAaARR~ 44 (252)
T TIGR02431 21 ERPRLTLTDVAEATGLTRAAARRF 44 (252)
T ss_pred CCCCCCHHHHHHHHCCCCHHHHHH
T ss_conf 378989899998758994798889
No 325
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=59.06 E-value=13 Score=18.44 Aligned_cols=33 Identities=12% Similarity=0.159 Sum_probs=27.0
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHH-HHHCC
Q ss_conf 9999999839949999998634299998-87558
Q gi|254781147|r 25 NFRNIRKEAKLTQKEIRNRTGFAQSWIS-ELETG 57 (83)
Q Consensus 25 ~ir~~R~~~gltq~ela~~~gis~~~is-~iE~G 57 (83)
.+-.+|.-.|+|.+|+|+.+|++.+++- ++-++
T Consensus 144 ~vl~Lr~~eglS~~EIAeiLgip~gTVKSRL~RA 177 (217)
T PRK12533 144 EVLVLRELEDMSYREIAAIADVPVGTVMSRLARA 177 (217)
T ss_pred HHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 8999999809999999999894999999999999
No 326
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=58.98 E-value=12 Score=18.81 Aligned_cols=33 Identities=6% Similarity=0.065 Sum_probs=27.6
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 999999999983994999999863429999887
Q gi|254781147|r 22 FVNNFRNIRKEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 22 ~g~~ir~~R~~~gltq~ela~~~gis~~~is~i 54 (83)
.-.-+..+++....+..|||+..|+|..||.+-
T Consensus 7 ~~~Il~~l~~~g~v~v~eLa~~~~VS~~TIRRD 39 (252)
T PRK10906 7 HDAIIELVKQQGYVSTEELVEHFSVSPQTIRRD 39 (252)
T ss_pred HHHHHHHHHHCCCEEHHHHHHHHCCCHHHHHHH
T ss_conf 999999999869899999999879699899882
No 327
>COG1318 Predicted transcriptional regulators [Transcription]
Probab=58.97 E-value=11 Score=18.88 Aligned_cols=32 Identities=22% Similarity=0.305 Sum_probs=28.9
Q ss_pred HHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf 99983994999999863429999887558999
Q gi|254781147|r 29 IRKEAKLTQKEIRNRTGFAQSWISELETGKST 60 (83)
Q Consensus 29 ~R~~~gltq~ela~~~gis~~~is~iE~G~~~ 60 (83)
+|...|+|..+.|+-.|.+.+++.++-.|...
T Consensus 56 arekag~Ti~EIAeelG~TeqTir~hlkgetk 87 (182)
T COG1318 56 AREKAGMTISEIAEELGRTEQTVRNHLKGETK 87 (182)
T ss_pred HHHHCCCCHHHHHHHHCCCHHHHHHHHHCCHH
T ss_conf 99870374999999968779999999751403
No 328
>TIGR00651 pta phosphate acetyltransferase; InterPro: IPR004614 Phosphate acetyltransferase (2.3.1.8 from EC) catalyses the conversion of acetyl-CoA and phosphate to CoA and acetyl phosphate in the last two steps in the conversion of actetae to acetyl-CoA.; GO: 0016407 acetyltransferase activity.
Probab=58.93 E-value=11 Score=19.05 Aligned_cols=37 Identities=16% Similarity=0.372 Sum_probs=30.0
Q ss_pred HHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 99999999999999983994999999863429999887
Q gi|254781147|r 17 RERMIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 17 ~~~~~~g~~ir~~R~~~gltq~ela~~~gis~~~is~i 54 (83)
..++.+.+.+..+||.+|+|.++..+.+ .+..+++-.
T Consensus 61 ~~~E~Y~~~~~e~RK~KG~t~~~A~~~l-~D~~~fa~~ 97 (322)
T TIGR00651 61 PDRESYAERYYELRKHKGVTLAQARKQL-RDESYFATM 97 (322)
T ss_pred HHHHHHHHHHHHHHCCCCCCHHHHHHHH-HCHHHHHHH
T ss_conf 2279999999987415560479999973-045789999
No 329
>TIGR02812 fadR_gamma fatty acid metabolism transcriptional regulator FadR; InterPro: IPR014178 Members of this entry are transcriptional regulators of fatty acid metabolism (FadR), including both biosynthesis and beta-oxidation reactions, which are found exclusively in a subset of Gammaproteobacteria with strictly one copy per genome. Proteins have an N-terminal DNA-binding domain and a less well conserved C-terminal long chain acyl-CoA-binding domain. FadR when expressed in Escherichia coli shows differences in regulatory response and fatty acid binding profiles. All members of this entry are expected to have the same function.; GO: 0000062 acyl-CoA binding, 0003677 DNA binding, 0003700 transcription factor activity, 0019217 regulation of fatty acid metabolic process.
Probab=58.86 E-value=4 Score=21.60 Aligned_cols=17 Identities=18% Similarity=0.429 Sum_probs=14.1
Q ss_pred HHHHHHHHHHHHHHHHH
Q ss_conf 99999863429999887
Q gi|254781147|r 38 KEIRNRTGFAQSWISEL 54 (83)
Q Consensus 38 ~ela~~~gis~~~is~i 54 (83)
.|||+++||+++|+..+
T Consensus 34 RELsElIGVTRTTLREV 50 (275)
T TIGR02812 34 RELSELIGVTRTTLREV 50 (275)
T ss_pred HHHHHHCCCCCCHHHHH
T ss_conf 65754237663037899
No 330
>pfam00196 GerE Bacterial regulatory proteins, luxR family.
Probab=58.79 E-value=8.6 Score=19.60 Aligned_cols=27 Identities=19% Similarity=0.176 Sum_probs=22.9
Q ss_pred HHHCCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 998399499999986342999988755
Q gi|254781147|r 30 RKEAKLTQKEIRNRTGFAQSWISELET 56 (83)
Q Consensus 30 R~~~gltq~ela~~~gis~~~is~iE~ 56 (83)
....|+|-.|+|+.+|+|.+++..+-+
T Consensus 14 ~l~~G~s~~eIA~~L~is~~TV~~h~~ 40 (58)
T pfam00196 14 LLAAGKSNKEIADILGISEKTVKVHRS 40 (58)
T ss_pred HHHHCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 998079999999997888999999999
No 331
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=58.76 E-value=11 Score=18.85 Aligned_cols=25 Identities=12% Similarity=0.239 Sum_probs=21.6
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 3994999999863429999887558
Q gi|254781147|r 33 AKLTQKEIRNRTGFAQSWISELETG 57 (83)
Q Consensus 33 ~gltq~ela~~~gis~~~is~iE~G 57 (83)
.-+|++|+|+..|||+-.|.+||+.
T Consensus 364 ~~~TL~EIG~~lgISRERVRQIE~k 388 (410)
T PRK07598 364 RTYSLAEIGRALDLSRERVRQIEAK 388 (410)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 9668999998979699999999999
No 332
>pfam08220 HTH_DeoR DeoR-like helix-turn-helix domain.
Probab=58.75 E-value=13 Score=18.55 Aligned_cols=30 Identities=13% Similarity=0.266 Sum_probs=26.2
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 999999998399499999986342999988
Q gi|254781147|r 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISE 53 (83)
Q Consensus 24 ~~ir~~R~~~gltq~ela~~~gis~~~is~ 53 (83)
.-+..+......+..|||+..|+|..++.+
T Consensus 4 ~Il~~l~~~~~v~i~~La~~f~VS~~TiRR 33 (57)
T pfam08220 4 QILELLKQQGTLSVEELAELLGVSEMTIRR 33 (57)
T ss_pred HHHHHHHHCCCEEHHHHHHHHCCCHHHHHH
T ss_conf 999999986979799999998959999999
No 333
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=58.62 E-value=12 Score=18.77 Aligned_cols=32 Identities=13% Similarity=0.226 Sum_probs=27.8
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 99999999998399499999986342999988
Q gi|254781147|r 22 FVNNFRNIRKEAKLTQKEIRNRTGFAQSWISE 53 (83)
Q Consensus 22 ~g~~ir~~R~~~gltq~ela~~~gis~~~is~ 53 (83)
.-.-+..++++..++.+|||+..|+|..||.+
T Consensus 7 ~~~Il~~l~~~g~v~v~eLa~~~~VS~~TIRR 38 (253)
T COG1349 7 HQKILELLKEKGKVSVEELAELFGVSEMTIRR 38 (253)
T ss_pred HHHHHHHHHHCCCEEHHHHHHHHCCCHHHHHH
T ss_conf 99999999985969799999885978999986
No 334
>cd04767 HTH_HspR-like_MBC Helix-Turn-Helix DNA binding domain of putative HspR-like transcription regulators. Putative helix-turn-helix (HTH) transcription regulator HspR-like proteins. Unlike the characterized HspR, these proteins have a C-terminal domain with putative metal binding cysteines (MBC). Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind spe
Probab=58.40 E-value=7.8 Score=19.86 Aligned_cols=22 Identities=5% Similarity=-0.076 Sum_probs=13.4
Q ss_pred CCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 9499999986342999988755
Q gi|254781147|r 35 LTQKEIRNRTGFAQSWISELET 56 (83)
Q Consensus 35 ltq~ela~~~gis~~~is~iE~ 56 (83)
++..++|+.+|++..+|.-||+
T Consensus 2 y~Ig~vA~l~gv~~~TLR~YEr 23 (120)
T cd04767 2 YPIGVVAELLNIHPETLRIWER 23 (120)
T ss_pred CCHHHHHHHHCCCHHHHHHHHH
T ss_conf 2489999997868899999998
No 335
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=57.98 E-value=13 Score=18.44 Aligned_cols=23 Identities=22% Similarity=0.224 Sum_probs=20.0
Q ss_pred CCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 94999999863429999887558
Q gi|254781147|r 35 LTQKEIRNRTGFAQSWISELETG 57 (83)
Q Consensus 35 ltq~ela~~~gis~~~is~iE~G 57 (83)
.|++++|+..|||+..|.+||+.
T Consensus 344 ~TL~EIg~~lgISRERVRQIE~r 366 (385)
T PRK07406 344 KTLEEIGQIFNVTRERIRQIEAK 366 (385)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 46999998979599999999999
No 336
>pfam01022 HTH_5 Bacterial regulatory protein, arsR family. Members of this family contains a DNA binding 'helix-turn-helix' motif. This family includes other proteins which are not included in the Prosite definition.
Probab=57.91 E-value=14 Score=18.30 Aligned_cols=28 Identities=25% Similarity=0.270 Sum_probs=22.3
Q ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 99999983994999999863429999887
Q gi|254781147|r 26 FRNIRKEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 26 ir~~R~~~gltq~ela~~~gis~~~is~i 54 (83)
|..+ .+.-++..|+++.+|++++++|+=
T Consensus 8 l~~L-~~~~~~v~el~~~l~~sq~~vS~H 35 (47)
T pfam01022 8 LYLL-SEGELCVCELAEILGLSQSTVSHH 35 (47)
T ss_pred HHHH-HCCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 9999-808996999999989588699999
No 337
>PHA02519 plasmid partition protein SopA; Reviewed
Probab=57.88 E-value=12 Score=18.80 Aligned_cols=56 Identities=13% Similarity=0.183 Sum_probs=38.3
Q ss_pred HHHHHHHHHHH----------HCCCCHHHHHHHHHHHHHHHHHHHCCC----------------CCCCHHHHHHHHHHHC
Q ss_conf 99999999999----------839949999998634299998875589----------------9944899999999928
Q gi|254781147|r 21 IFVNNFRNIRK----------EAKLTQKEIRNRTGFAQSWISELETGK----------------STINIDNMIILAHTLD 74 (83)
Q Consensus 21 ~~g~~ir~~R~----------~~gltq~ela~~~gis~~~is~iE~G~----------------~~~~~~~l~~la~al~ 74 (83)
.+.+.|+.+|. -+.+|-.|+|+.+|||.+++.+.+..- +.-+++.+..+-+.|+
T Consensus 16 ~~~~~~~~~~~~~~~P~~~k~lR~Fs~~E~A~l~gvs~~~lR~~~~~g~~P~p~~~~~gr~~~rr~ytl~~i~~lR~~l~ 95 (387)
T PHA02519 16 EMTQAIAIAQFGDDSPEARAITRRWGITEVADLIGVTPQAIRDAEKSGRLPPPDFETRGRVERRAGYTIDQISHMRDHFG 95 (387)
T ss_pred HHHHHHHHHHHCCCCCHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHC
T ss_conf 99999999972158963312447788899999959998999878756899999768888755334357999999999864
Q ss_pred CC
Q ss_conf 99
Q gi|254781147|r 75 TP 76 (83)
Q Consensus 75 i~ 76 (83)
.+
T Consensus 96 ~~ 97 (387)
T PHA02519 96 NP 97 (387)
T ss_pred CC
T ss_conf 56
No 338
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=57.76 E-value=13 Score=18.59 Aligned_cols=33 Identities=12% Similarity=0.073 Sum_probs=27.5
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 999999999983994999999863429999887
Q gi|254781147|r 22 FVNNFRNIRKEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 22 ~g~~ir~~R~~~gltq~ela~~~gis~~~is~i 54 (83)
.-.-+..+.+....+..|||+..|||..||.+=
T Consensus 7 ~~~Il~~L~~~g~v~v~eLa~~l~VS~~TIRRD 39 (256)
T PRK10434 7 QAAILEYLQKQGKCSVEELAQYFDTTGTTIRKD 39 (256)
T ss_pred HHHHHHHHHHCCCEEHHHHHHHHCCCHHHHHHH
T ss_conf 999999999869799999999879699899984
No 339
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=57.63 E-value=4.5 Score=21.25 Aligned_cols=32 Identities=13% Similarity=0.089 Sum_probs=24.9
Q ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHHH-HHHCC
Q ss_conf 999999839949999998634299998-87558
Q gi|254781147|r 26 FRNIRKEAKLTQKEIRNRTGFAQSWIS-ELETG 57 (83)
Q Consensus 26 ir~~R~~~gltq~ela~~~gis~~~is-~iE~G 57 (83)
+-.++.-.|+|.+|+|+.+|+|.+++- ++-+|
T Consensus 119 vl~L~~~egls~~EIAe~Lgis~gTVKsrl~RA 151 (182)
T PRK12511 119 ALHLVAIEGLSYQEAANVLGIPIGTLMSRIGRA 151 (182)
T ss_pred HEEEEEECCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 112410079999999999893999999999999
No 340
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=56.90 E-value=17 Score=17.78 Aligned_cols=30 Identities=10% Similarity=-0.057 Sum_probs=23.7
Q ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 9999998399499999986342999988755
Q gi|254781147|r 26 FRNIRKEAKLTQKEIRNRTGFAQSWISELET 56 (83)
Q Consensus 26 ir~~R~~~gltq~ela~~~gis~~~is~iE~ 56 (83)
|-.+ .-.|+|.+|+|+.+|+|.++|....+
T Consensus 163 V~~~-~~eg~s~~EIA~~l~is~~tV~~~l~ 192 (209)
T PRK08295 163 VLEL-YLDGKSYQEIAEELNRHVKSIDNALQ 192 (209)
T ss_pred HHHH-HHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 9999-98699999999998929999999999
No 341
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family; InterPro: IPR014325 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 recognized by the major sigma factors , . This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor . The protein appears to include a paralogous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives..
Probab=56.80 E-value=4.1 Score=21.50 Aligned_cols=27 Identities=15% Similarity=0.212 Sum_probs=23.1
Q ss_pred HHHHHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 999998399499999986342999988
Q gi|254781147|r 27 RNIRKEAKLTQKEIRNRTGFAQSWISE 53 (83)
Q Consensus 27 r~~R~~~gltq~ela~~~gis~~~is~ 53 (83)
--+|.--+||-+|+|+.+|||.+++-.
T Consensus 122 vVLRY~eDlSe~~~A~~LG~SvGTVKS 148 (165)
T TIGR02983 122 VVLRYYEDLSEAEVAEVLGISVGTVKS 148 (165)
T ss_pred EEEECCCCCCHHHHHHHHCCCCHHHHH
T ss_conf 232045789868999881999322899
No 342
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=56.56 E-value=18 Score=17.74 Aligned_cols=30 Identities=13% Similarity=0.093 Sum_probs=25.3
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 999999983994999999863429999887
Q gi|254781147|r 25 NFRNIRKEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 25 ~ir~~R~~~gltq~ela~~~gis~~~is~i 54 (83)
.+-.+|.-.|+|-+|+|+.+|+|.+++...
T Consensus 138 ~v~~Lr~~~~ls~~EIA~~l~~s~~tVk~~ 167 (191)
T PRK12520 138 RVFMMREWLELETEEICKELQITATNLWVM 167 (191)
T ss_pred HHHHHHHHHCCCHHHHHHHHCCCHHHHHHH
T ss_conf 999999993899999999989499999999
No 343
>pfam04645 DUF603 Protein of unknown function, DUF603. This family includes several uncharacterized proteins from Borrelia species.
Probab=56.51 E-value=14 Score=18.39 Aligned_cols=40 Identities=18% Similarity=0.350 Sum_probs=28.3
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHH----HHCCCCCC
Q ss_conf 999999999998399499999986342999988----75589994
Q gi|254781147|r 21 IFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISE----LETGKSTI 61 (83)
Q Consensus 21 ~~g~~ir~~R~~~gltq~ela~~~gis~~~is~----iE~G~~~~ 61 (83)
.|-..+-..|+ -.++-.|+|+.+|||+..+++ ||.|..++
T Consensus 7 sfddYv~yF~e-G~L~D~eIA~~LGVsr~nV~kmRqKwes~~dsv 50 (181)
T pfam04645 7 SFDDYVAYFKE-GSLSDAEIAKELGVSRVNVWRMRQKWESGEDSV 50 (181)
T ss_pred HHHHHHHHHHC-CCCCHHHHHHHHCCHHHHHHHHHHHHHHCCCCC
T ss_conf 28999999961-787579999997830999999999998127885
No 344
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=56.42 E-value=10 Score=19.09 Aligned_cols=24 Identities=29% Similarity=0.390 Sum_probs=21.6
Q ss_pred HHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 983994999999863429999887
Q gi|254781147|r 31 KEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 31 ~~~gltq~ela~~~gis~~~is~i 54 (83)
...++|..|+|+.+|++.+++.++
T Consensus 17 ~~~~~sl~eia~~~~l~ksT~~Rl 40 (91)
T smart00346 17 EPGGLTLAELAERLGLSKSTAHRL 40 (91)
T ss_pred CCCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 899989999999989099999999
No 345
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1; InterPro: IPR011745 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 recognized by the major sigma factors , . This entry describes sigma-70 factors in Myxococcus xanthus DK 1622 and in other members of the Mycococcales. Each of the six members in M. xanthusis is encoded near a gene for a predicted serine/threonine kinase. Members of this family show sequence similarity to members of Pfam family IPR007630 from INTERPRO (region 4 of sigma-70 like sigma-factors), a helix-turn-helix family in which trusted and noise cutoffs deliberately are set artificially high and which therefore has many false negatives.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=56.40 E-value=6.9 Score=20.16 Aligned_cols=26 Identities=12% Similarity=-0.008 Sum_probs=21.4
Q ss_pred HHHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 99839949999998634299998875
Q gi|254781147|r 30 RKEAKLTQKEIRNRTGFAQSWISELE 55 (83)
Q Consensus 30 R~~~gltq~ela~~~gis~~~is~iE 55 (83)
=-=.|+|.+++|..-++++||||++=
T Consensus 178 Hfv~~Ls~~r~g~my~~~~STvsR~~ 203 (249)
T TIGR03001 178 HFVEGLSMDRLGAMYQVHRSTVSRWV 203 (249)
T ss_pred HHHCCCCHHHHHHHHCCCCHHHHHHH
T ss_conf 88203329999877457750789999
No 346
>pfam01710 Transposase_14 Transposase. Transposase proteins are necessary for efficient DNA transposition. This family includes insertion sequences from Synechocystis PCC 6803 three of which are characterized as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily.
Probab=56.15 E-value=14 Score=18.32 Aligned_cols=33 Identities=9% Similarity=-0.054 Sum_probs=23.8
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999999983994999999863429999887
Q gi|254781147|r 21 IFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 21 ~~g~~ir~~R~~~gltq~ela~~~gis~~~is~i 54 (83)
.|-+++-.. .+.|.|..+.|..-+||.++|.+|
T Consensus 6 DlR~rVl~~-ve~G~S~~eaA~~F~Is~~Tv~rW 38 (120)
T pfam01710 6 DLRKKVIDY-IESGGSITEASKVFQIGRATIYRW 38 (120)
T ss_pred HHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 999999999-986999999999937029999999
No 347
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=55.69 E-value=18 Score=17.65 Aligned_cols=48 Identities=10% Similarity=-0.036 Sum_probs=36.1
Q ss_pred HHHCCCCHHHHHHHHHHHHHHHHHHHCC----CCCCCHHHHHHHHHHHCCCH
Q ss_conf 9983994999999863429999887558----99944899999999928999
Q gi|254781147|r 30 RKEAKLTQKEIRNRTGFAQSWISELETG----KSTINIDNMIILAHTLDTPL 77 (83)
Q Consensus 30 R~~~gltq~ela~~~gis~~~is~iE~G----~~~~~~~~l~~la~al~i~~ 77 (83)
....|+|-+|.|+++++|..|+..+-+. -.--+.-.|.+++...|+.+
T Consensus 161 lla~G~snkeIA~~L~iS~~TV~~h~~~i~~KLgv~n~~eLv~ya~~~gl~p 212 (216)
T PRK10840 161 LFAEGFLVTEIAKKLNRSIKTISSQKKSAMMKLGVENDIALLNYLSSVTLSP 212 (216)
T ss_pred HHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCC
T ss_conf 9986999999998969899999999999999829998999999999869998
No 348
>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator); InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulphovibrio 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 strain PCC 6803 hypothetical protein slr0846. These are small proteins of 12 to 18 kD which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators..
Probab=55.43 E-value=9 Score=19.49 Aligned_cols=31 Identities=23% Similarity=0.400 Sum_probs=23.6
Q ss_pred HHHHHH--HCCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 999999--8399499999986342999988755
Q gi|254781147|r 26 FRNIRK--EAKLTQKEIRNRTGFAQSWISELET 56 (83)
Q Consensus 26 ir~~R~--~~gltq~ela~~~gis~~~is~iE~ 56 (83)
|.-+++ +.=.+.+|+|++-|||++|+.+|-+
T Consensus 15 ~~LA~~~~~~~v~~~~ia~~~~Is~~yL~K~l~ 47 (133)
T TIGR00738 15 LDLALNADEGPVSVKEIAERQGISRSYLEKVLR 47 (133)
T ss_pred HHHHHCCCCCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 999722688760789999884899879999999
No 349
>PRK10923 glnG nitrogen regulation protein NR(I); Provisional
Probab=55.26 E-value=19 Score=17.61 Aligned_cols=31 Identities=6% Similarity=0.126 Sum_probs=26.2
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999983994999999863429999887
Q gi|254781147|r 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 24 ~~ir~~R~~~gltq~ela~~~gis~~~is~i 54 (83)
..|...-...+..+.+.|+.+||+++++.+-
T Consensus 432 ~~I~~aL~~~~gn~~~aA~~LGisR~TLyrK 462 (469)
T PRK10923 432 TLLTTALRHTQGHKQEAARLLGWGRNTLTRK 462 (469)
T ss_pred HHHHHHHHHHCCCHHHHHHHHCCCHHHHHHH
T ss_conf 9999999990998999999989899999999
No 350
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=54.34 E-value=15 Score=18.12 Aligned_cols=29 Identities=14% Similarity=0.193 Sum_probs=24.7
Q ss_pred HHHHH-HHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 99999-983994999999863429999887
Q gi|254781147|r 26 FRNIR-KEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 26 ir~~R-~~~gltq~ela~~~gis~~~is~i 54 (83)
...+- .+..+|..++|+.++.++|++++.
T Consensus 33 ~~~LL~~~~~~tvdelae~lnr~rStv~rs 62 (126)
T COG3355 33 YKALLEENGPLTVDELAEILNRSRSTVYRS 62 (126)
T ss_pred HHHHHHHCCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 999986469957999999978319999999
No 351
>PRK01905 DNA-binding protein Fis; Provisional
Probab=54.14 E-value=17 Score=17.82 Aligned_cols=31 Identities=10% Similarity=0.032 Sum_probs=26.3
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 9999999998399499999986342999988
Q gi|254781147|r 23 VNNFRNIRKEAKLTQKEIRNRTGFAQSWISE 53 (83)
Q Consensus 23 g~~ir~~R~~~gltq~ela~~~gis~~~is~ 53 (83)
-.-|....+..+..|...|+.+||++.|+.+
T Consensus 39 ~pLi~~vl~~~~gNQ~kAA~~LGinR~TLRk 69 (77)
T PRK01905 39 KPLLEVVMEQAGGNQSLAAEYLGINRNTLRK 69 (77)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHCCCHHHHHH
T ss_conf 9999999998459499999997865888999
No 352
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=53.20 E-value=15 Score=18.15 Aligned_cols=25 Identities=24% Similarity=0.290 Sum_probs=18.5
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 3994999999863429999887558
Q gi|254781147|r 33 AKLTQKEIRNRTGFAQSWISELETG 57 (83)
Q Consensus 33 ~gltq~ela~~~gis~~~is~iE~G 57 (83)
.-+|.+++|+..|||+..|.+||..
T Consensus 354 ~~~TL~eIg~~lgvSrERVRQIE~k 378 (398)
T PRK05901 354 QPKTLDEIGQVYGVTRERIRQIESK 378 (398)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 9603999998979699999999999
No 353
>PRK11361 acetoacetate metabolism regulatory protein AtoC; Provisional
Probab=52.93 E-value=20 Score=17.39 Aligned_cols=32 Identities=3% Similarity=-0.052 Sum_probs=26.4
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 99999999983994999999863429999887
Q gi|254781147|r 23 VNNFRNIRKEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 23 g~~ir~~R~~~gltq~ela~~~gis~~~is~i 54 (83)
-..|...-...+..+.+.|+.+|||++++.+-
T Consensus 419 r~~i~~aL~~~~gn~~~aA~~LGisR~tLyrK 450 (457)
T PRK11361 419 KRIIMEVLEQQEGNRTRTALMLGISRRALMYK 450 (457)
T ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 99999999982998999999989899999999
No 354
>COG3888 Predicted transcriptional regulator [Transcription]
Probab=52.80 E-value=15 Score=18.14 Aligned_cols=24 Identities=29% Similarity=0.371 Sum_probs=20.1
Q ss_pred HHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 983994999999863429999887
Q gi|254781147|r 31 KEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 31 ~~~gltq~ela~~~gis~~~is~i 54 (83)
..-|+.|.|+.+.+|+|.|++|..
T Consensus 17 ~~~GI~Q~eIeel~GlSKStvSEa 40 (321)
T COG3888 17 GPEGIDQTEIEELMGLSKSTVSEA 40 (321)
T ss_pred CCCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 877765878898857456479999
No 355
>COG4496 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=51.63 E-value=21 Score=17.32 Aligned_cols=38 Identities=16% Similarity=0.221 Sum_probs=30.7
Q ss_pred HHHHHHHHHHHH-HHCCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 999999999999-98399499999986342999988755
Q gi|254781147|r 19 RMIFVNNFRNIR-KEAKLTQKEIRNRTGFAQSWISELET 56 (83)
Q Consensus 19 ~~~~g~~ir~~R-~~~gltq~ela~~~gis~~~is~iE~ 56 (83)
-..++++++.++ ...|-|-.++...+|.|..+||++.+
T Consensus 40 iqslaqRlqVa~mL~eg~tY~~I~~eTGaStaTIsRVkR 78 (100)
T COG4496 40 IQSLAQRLQVAKMLKEGRTYRDIEDETGASTATISRVKR 78 (100)
T ss_pred HHHHHHHHHHHHHHHCCCCCCHHHHCCCCCHHHHHHHHH
T ss_conf 999999999999997689722466414840555999999
No 356
>pfam10668 Phage_terminase Phage terminase small subunit. This family of small highly conserved proteins come from a subset of Firmicute species. Its putative function is as a phage terminase small subunit.
Probab=51.45 E-value=9.3 Score=19.38 Aligned_cols=24 Identities=21% Similarity=0.365 Sum_probs=21.2
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 399499999986342999988755
Q gi|254781147|r 33 AKLTQKEIRNRTGFAQSWISELET 56 (83)
Q Consensus 33 ~gltq~ela~~~gis~~~is~iE~ 56 (83)
-.++..++|+.+|++.++|+++.+
T Consensus 21 G~~~l~~IA~~L~vs~~~IrkWKs 44 (60)
T pfam10668 21 GTMKLKDIANKLNVSESQIRKWKS 44 (60)
T ss_pred CCEEHHHHHHHHCCCHHHHHHCCH
T ss_conf 964499999996879888760311
No 357
>TIGR01481 ccpA catabolite control protein A; InterPro: IPR006377 Catabolite control protein A is a LacI family global transcriptional regulator found in Gram-positive bacteria. CcpA is involved in repressing carbohydrate utilization genes [ex: alpha-amylase (amyE), acetyl-coenzyme A synthase (acsA)] and in activating genes involved in transporting excess carbon from the cell [e.g. acetate kinase (ackA), alpha-acetolactate synthase (alsS)]. Additionally, disruption of CcpA in Bacillus megaterium, Staphylococcus xylosus, Lactobacillus casei and Lactocacillus pentosus also decreases growth rate, which suggests CcpA is involved in the regulation of other metabolic pathways.; GO: 0030528 transcription regulator activity, 0045449 regulation of transcription.
Probab=51.19 E-value=3.2 Score=22.14 Aligned_cols=40 Identities=10% Similarity=0.211 Sum_probs=34.8
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHH
Q ss_conf 9949999998634299998875589994489999999992
Q gi|254781147|r 34 KLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTL 73 (83)
Q Consensus 34 gltq~ela~~~gis~~~is~iE~G~~~~~~~~l~~la~al 73 (83)
..|.-|+|.-+|||=.|+||+=||..|..-.|-.|..+..
T Consensus 2 TVTIYDVArEA~VSMATVSRVVNGN~NVKp~TrKKVL~VI 41 (332)
T TIGR01481 2 TVTIYDVAREAGVSMATVSRVVNGNPNVKPATRKKVLEVI 41 (332)
T ss_pred CEEEEEHHHHCCCCCEEEEEEECCCCCCCHHHHHHHHHHH
T ss_conf 5222214652487640564246578997567633599999
No 358
>COG3311 AlpA Predicted transcriptional regulator [Transcription]
Probab=50.48 E-value=16 Score=17.92 Aligned_cols=30 Identities=23% Similarity=0.183 Sum_probs=23.7
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf 399499999986342999988755899944
Q gi|254781147|r 33 AKLTQKEIRNRTGFAQSWISELETGKSTIN 62 (83)
Q Consensus 33 ~gltq~ela~~~gis~~~is~iE~G~~~~~ 62 (83)
+-+...|+++.+|+|+++|.++.+-..-|.
T Consensus 12 r~lrl~ev~~~~GlSrstiYr~i~~~~FPk 41 (70)
T COG3311 12 RLLRLPEVAQLTGLSRSTIYRLIKDGTFPK 41 (70)
T ss_pred HHHHHHHHHHHHCCCHHHHHHHHCCCCCCC
T ss_conf 152089999997766899999980477999
No 359
>PRK13501 transcriptional activator RhaR; Provisional
Probab=50.13 E-value=22 Score=17.12 Aligned_cols=32 Identities=9% Similarity=0.190 Sum_probs=24.7
Q ss_pred HCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCH
Q ss_conf 83994999999863429999887558999448
Q gi|254781147|r 32 EAKLTQKEIRNRTGFAQSWISELETGKSTINI 63 (83)
Q Consensus 32 ~~gltq~ela~~~gis~~~is~iE~G~~~~~~ 63 (83)
...++.+++|+.+++|.++++++-+.....|.
T Consensus 190 ~~~~~l~~lA~~~~lS~~~lsrlFK~~tG~T~ 221 (290)
T PRK13501 190 GAYFDMADFCHKNQLVERSLKQLFRQQTGMSI 221 (290)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHCCCH
T ss_conf 68999999999969899999999999989399
No 360
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=50.12 E-value=22 Score=17.13 Aligned_cols=29 Identities=17% Similarity=0.112 Sum_probs=22.7
Q ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 99999983994999999863429999887
Q gi|254781147|r 26 FRNIRKEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 26 ir~~R~~~gltq~ela~~~gis~~~is~i 54 (83)
+..+.....++.-|+++.+|++++++|+-
T Consensus 20 l~lL~~~gelcV~eL~~~l~~sQs~vS~H 48 (106)
T PRK10141 20 VLLLRESGELCVCDLCTALDQSQPKISRH 48 (106)
T ss_pred HHHHHHCCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 99998749956999998869988899999
No 361
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=49.49 E-value=23 Score=17.06 Aligned_cols=33 Identities=9% Similarity=0.034 Sum_probs=27.5
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 999999999983994999999863429999887
Q gi|254781147|r 22 FVNNFRNIRKEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 22 ~g~~ir~~R~~~gltq~ela~~~gis~~~is~i 54 (83)
.-.-+..+++...++..|||+..|||..+|.+-
T Consensus 6 ~~~Il~~L~~~g~v~v~eLa~~~~VS~~TIRRD 38 (240)
T PRK10411 6 QQAIVDLLLNHTSLTTEALAEQLNVSKETIRRD 38 (240)
T ss_pred HHHHHHHHHHCCCEEHHHHHHHHCCCHHHHHHH
T ss_conf 999999999869799999999889599899982
No 362
>COG2378 Predicted transcriptional regulator [Transcription]
Probab=49.35 E-value=23 Score=17.05 Aligned_cols=36 Identities=11% Similarity=0.080 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 999999999999983994999999863429999887
Q gi|254781147|r 19 RMIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 19 ~~~~g~~ir~~R~~~gltq~ela~~~gis~~~is~i 54 (83)
..-+..-+..++....+|-.++|+..|||..+|.+-
T Consensus 7 a~RL~~ii~~L~~~~~vta~~lA~~~~VS~RTi~RD 42 (311)
T COG2378 7 AERLLQIIQILRAKETVTAAELADEFEVSVRTIYRD 42 (311)
T ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHHCCCHHHHHHH
T ss_conf 999999999998576045999998729889999999
No 363
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=49.34 E-value=15 Score=18.09 Aligned_cols=26 Identities=8% Similarity=0.058 Sum_probs=22.3
Q ss_pred HHCCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 98399499999986342999988755
Q gi|254781147|r 31 KEAKLTQKEIRNRTGFAQSWISELET 56 (83)
Q Consensus 31 ~~~gltq~ela~~~gis~~~is~iE~ 56 (83)
...|+|-+|.|+++++|..|+..+-+
T Consensus 155 l~~G~snkeIA~~L~iS~~TV~~h~~ 180 (204)
T PRK09958 155 ILDGKDNNDIAEKMFISNKTVSTYKS 180 (204)
T ss_pred HHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 98699999999897889999999999
No 364
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=49.29 E-value=16 Score=18.02 Aligned_cols=25 Identities=20% Similarity=0.250 Sum_probs=22.5
Q ss_pred HHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 9983994999999863429999887
Q gi|254781147|r 30 RKEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 30 R~~~gltq~ela~~~gis~~~is~i 54 (83)
....++|..|+|+.+|++++++.++
T Consensus 22 ~~~~~lslsela~~lglpksTv~Rl 46 (264)
T PRK09834 22 RLDGGATVGLLAELTGLHRTTVRRL 46 (264)
T ss_pred HCCCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 1799979999999979099999999
No 365
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=49.12 E-value=10 Score=19.20 Aligned_cols=23 Identities=30% Similarity=0.279 Sum_probs=20.2
Q ss_pred HCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 83994999999863429999887
Q gi|254781147|r 32 EAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 32 ~~gltq~ela~~~gis~~~is~i 54 (83)
..-||..|+++.+|+|.+.+|.-
T Consensus 39 ~~Pmtl~Ei~E~lg~Sks~vS~~ 61 (177)
T COG1510 39 RKPLTLDEIAEALGMSKSNVSMG 61 (177)
T ss_pred CCCCCHHHHHHHHCCCCCHHHHH
T ss_conf 99966999999977780128899
No 366
>TIGR02233 Myxo_sigma_rel Myxococcus probable DNA-binding regulatory protein.
Probab=48.99 E-value=11 Score=18.94 Aligned_cols=34 Identities=12% Similarity=0.193 Sum_probs=27.9
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf 9999999839949999998634299998875589
Q gi|254781147|r 25 NFRNIRKEAKLTQKEIRNRTGFAQSWISELETGK 58 (83)
Q Consensus 25 ~ir~~R~~~gltq~ela~~~gis~~~is~iE~G~ 58 (83)
++=.+--=.|+|.+.+|..-|+++|++|++=.+-
T Consensus 31 ~lLRLH~~~gLsldR~~~lY~~hrStvaR~v~~a 64 (106)
T TIGR02233 31 TLLRLHHVEGLSLDRLGTLYGVHRSTVARWVAGA 64 (106)
T ss_pred HHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHH
T ss_conf 5666776236558999988478861699999999
No 367
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=48.57 E-value=13 Score=18.47 Aligned_cols=24 Identities=21% Similarity=0.295 Sum_probs=19.9
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 994999999863429999887558
Q gi|254781147|r 34 KLTQKEIRNRTGFAQSWISELETG 57 (83)
Q Consensus 34 gltq~ela~~~gis~~~is~iE~G 57 (83)
-.|++++|+..|||+-.|.+||..
T Consensus 326 ~~TLeEIg~~lgvSRERVRQIE~k 349 (368)
T PRK09210 326 TRTLEEVGKVFGVTRERIRQIEAK 349 (368)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 614999998969798999999999
No 368
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=48.51 E-value=24 Score=16.97 Aligned_cols=53 Identities=9% Similarity=0.070 Sum_probs=40.3
Q ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHH
Q ss_conf 9999999999999839949999998634299998875589994489999999992
Q gi|254781147|r 19 RMIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTL 73 (83)
Q Consensus 19 ~~~~g~~ir~~R~~~gltq~ela~~~gis~~~is~iE~G~~~~~~~~l~~la~al 73 (83)
+..-...+++-++...+|.+++|+.+|++.-.+-+|.+=+..+ ...+.+-+.+
T Consensus 8 ~~~Tk~elqan~el~~LS~~~iA~~Ln~t~~~lekil~~tqr~--~dvW~lRd~l 60 (97)
T COG4367 8 KQRTKQELQANFELCPLSDEEIATALNWTEVKLEKILQVTQRP--ADVWRLRDFL 60 (97)
T ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHCC--CHHHHHHHHH
T ss_conf 9988999997544064529999999588799999999885064--2368899999
No 369
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=47.44 E-value=25 Score=16.87 Aligned_cols=27 Identities=4% Similarity=0.080 Sum_probs=21.3
Q ss_pred HHHHHCC--CCHHHHHHHHHHHHHHHHHH
Q ss_conf 9999839--94999999863429999887
Q gi|254781147|r 28 NIRKEAK--LTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 28 ~~R~~~g--ltq~ela~~~gis~~~is~i 54 (83)
.+....+ .|.+++|+.+|+|+..|.+-
T Consensus 11 ll~~~~~~~~SGe~La~~LgiSRtaVwK~ 39 (79)
T COG1654 11 LLLLLTGNFVSGEKLAEELGISRTAVWKH 39 (79)
T ss_pred HHHHCCCCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 99973799666899999978659999999
No 370
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=46.90 E-value=18 Score=17.73 Aligned_cols=28 Identities=14% Similarity=0.202 Sum_probs=23.5
Q ss_pred HHHCCCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 9983994999999863429999887558
Q gi|254781147|r 30 RKEAKLTQKEIRNRTGFAQSWISELETG 57 (83)
Q Consensus 30 R~~~gltq~ela~~~gis~~~is~iE~G 57 (83)
....|+|-+|+|+.+++|..|+..+-+.
T Consensus 148 lia~G~snkeIA~~L~IS~~TVk~h~~~ 175 (196)
T PRK10360 148 KLAQGMAVKEIAAELGLSPKTVHVHRAN 175 (196)
T ss_pred HHHCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 9987999999999969999999999999
No 371
>PRK13503 transcriptional activator RhaS; Provisional
Probab=46.18 E-value=26 Score=16.75 Aligned_cols=38 Identities=0% Similarity=0.055 Sum_probs=27.6
Q ss_pred HHHHHH--HCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCH
Q ss_conf 999999--83994999999863429999887558999448
Q gi|254781147|r 26 FRNIRK--EAKLTQKEIRNRTGFAQSWISELETGKSTINI 63 (83)
Q Consensus 26 ir~~R~--~~gltq~ela~~~gis~~~is~iE~G~~~~~~ 63 (83)
+..+.. ...+|.+++|+.+|+|.++++++-+-....|.
T Consensus 177 ~~yI~~hy~~~isl~~lA~~~~lS~~~l~r~FK~~tG~t~ 216 (278)
T PRK13503 177 LAWLEDHFAEEVNWEAVADQFSLSLRTLHRQLKQQTGLTP 216 (278)
T ss_pred HHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHCCCH
T ss_conf 9999997579999999998979599999999999889389
No 372
>pfam02787 CPSase_L_D3 Carbamoyl-phosphate synthetase large chain, oligomerisation domain. Carbamoyl-phosphate synthase catalyses the ATP-dependent synthesis of carbamyl-phosphate from glutamine or ammonia and bicarbonate. The carbamoyl-phosphate synthase (CPS) enzyme in prokaryotes is a heterodimer of a small and large chain.
Probab=46.14 E-value=19 Score=17.54 Aligned_cols=25 Identities=12% Similarity=0.230 Sum_probs=19.8
Q ss_pred HCCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 8399499999986342999988755
Q gi|254781147|r 32 EAKLTQKEIRNRTGFAQSWISELET 56 (83)
Q Consensus 32 ~~gltq~ela~~~gis~~~is~iE~ 56 (83)
.+|+|.+++.+.++|++=++.++++
T Consensus 21 r~G~sveeI~~~TkID~wFL~~i~~ 45 (122)
T pfam02787 21 RRGYSVEEIHELTKIDPWFLEKIKE 45 (122)
T ss_pred HCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 9599999999988968999999999
No 373
>PRK10403 transcriptional regulator NarP; Provisional
Probab=46.09 E-value=19 Score=17.58 Aligned_cols=26 Identities=12% Similarity=0.081 Sum_probs=22.2
Q ss_pred HHCCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 98399499999986342999988755
Q gi|254781147|r 31 KEAKLTQKEIRNRTGFAQSWISELET 56 (83)
Q Consensus 31 ~~~gltq~ela~~~gis~~~is~iE~ 56 (83)
..+|+|-+|+|+.+++|..|+..+-+
T Consensus 165 la~G~snkeIA~~L~iS~~TV~~h~~ 190 (215)
T PRK10403 165 LAQGLSNKQIASVLNISEQTVKVHIR 190 (215)
T ss_pred HHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 98699999999997982999999999
No 374
>COG2207 AraC AraC-type DNA-binding domain-containing proteins [Transcription]
Probab=45.78 E-value=26 Score=16.71 Aligned_cols=41 Identities=15% Similarity=0.212 Sum_probs=29.4
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCH
Q ss_conf 999999999983994999999863429999887558999448
Q gi|254781147|r 22 FVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINI 63 (83)
Q Consensus 22 ~g~~ir~~R~~~gltq~ela~~~gis~~~is~iE~G~~~~~~ 63 (83)
+...|.. -...+++.+++|..+|+|.+++++.-+.....+.
T Consensus 25 ~~~~i~~-~~~~~~~l~~la~~~g~S~~~l~r~f~~~~g~s~ 65 (127)
T COG2207 25 ALDYIEE-NLAEPLTLEDLARRLGMSRRTLSRLFKKETGTSP 65 (127)
T ss_pred HHHHHHH-CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHCCCH
T ss_conf 9999986-4137999999999979899999999999979799
No 375
>PRK12681 cysB transcriptional regulator CysB; Reviewed
Probab=45.71 E-value=26 Score=16.70 Aligned_cols=30 Identities=20% Similarity=0.094 Sum_probs=22.7
Q ss_pred HHHHHH--HHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 999999--983994999999863429999887
Q gi|254781147|r 25 NFRNIR--KEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 25 ~ir~~R--~~~gltq~ela~~~gis~~~is~i 54 (83)
.||.++ .+.|++..+.|+.+++|++.||+-
T Consensus 5 QLryf~~va~~~~n~t~AA~~L~iSQPavS~q 36 (324)
T PRK12681 5 QLRYIVEVVNHNLNVSATAESLYTSQPGISKQ 36 (324)
T ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 99999999976999999999978977799999
No 376
>pfam09572 RE_XamI XamI restriction endonuclease. This family includes the XamI (recognizes GTCGAC but cleavage site unknown) restriction endonuclease.
Probab=45.69 E-value=26 Score=16.70 Aligned_cols=60 Identities=10% Similarity=0.239 Sum_probs=41.8
Q ss_pred CCHHHHHHHHHHHHHHHHHHH--HCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHH------HHHHHHHH
Q ss_conf 898999999999999999999--8399499999986342999988755899944899------99999992
Q gi|254781147|r 11 LSDAILRERMIFVNNFRNIRK--EAKLTQKEIRNRTGFAQSWISELETGKSTINIDN------MIILAHTL 73 (83)
Q Consensus 11 ~~~~~~~~~~~~g~~ir~~R~--~~gltq~ela~~~gis~~~is~iE~G~~~~~~~~------l~~la~al 73 (83)
.++++++. ....|-.+|. .--++-.+|.-.+|+|.+.+-.+|.|+-.+.... |.++++.+
T Consensus 7 itp~~l~~---~p~~L~~LR~~t~ppia~d~l~~lagvsk~lv~~le~~kl~~~~~~~~l~~~l~ki~~iI 74 (251)
T pfam09572 7 ITPDVLKA---YPLTLPTLRMLTCPPIARDRLVGLAGGSKNLVKSLEPKKLPPKMKADVLDEHLQKVVAVI 74 (251)
T ss_pred CCHHHHHH---CCHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHH
T ss_conf 78899873---804777878613998308787665166678887642278983222436899999999999
No 377
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=45.28 E-value=25 Score=16.81 Aligned_cols=24 Identities=25% Similarity=0.387 Sum_probs=20.7
Q ss_pred HHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 983994999999863429999887
Q gi|254781147|r 31 KEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 31 ~~~gltq~ela~~~gis~~~is~i 54 (83)
...++|..|+|+++|++++++.++
T Consensus 16 ~~~~l~l~ela~~~glpksT~~Rl 39 (246)
T COG1414 16 GPGGLSLAELAERLGLPKSTVHRL 39 (246)
T ss_pred CCCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 888887999999879198899999
No 378
>pfam06056 Terminase_5 Putative ATPase subunit of terminase (gpP-like). 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.
Probab=45.25 E-value=15 Score=18.24 Aligned_cols=28 Identities=11% Similarity=0.018 Sum_probs=23.6
Q ss_pred HHHCCCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 9983994999999863429999887558
Q gi|254781147|r 30 RKEAKLTQKEIRNRTGFAQSWISELETG 57 (83)
Q Consensus 30 R~~~gltq~ela~~~gis~~~is~iE~G 57 (83)
-.-+|++.++.|+.+|++.++|..+-..
T Consensus 9 LY~qg~~~~eIA~~Lg~~~~tVysWk~r 36 (58)
T pfam06056 9 LYWQGYRPAEIAQELGLKARTVYSWKDR 36 (58)
T ss_pred HHHCCCCHHHHHHHHCCCCCHHHHHHHH
T ss_conf 9996898999999978993145658652
No 379
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=45.18 E-value=19 Score=17.51 Aligned_cols=44 Identities=20% Similarity=0.179 Sum_probs=29.2
Q ss_pred HHCCCCHHHHHHHHHHHHHHHHHHHCC----CCCCCHHHHHHHHHHHC
Q ss_conf 983994999999863429999887558----99944899999999928
Q gi|254781147|r 31 KEAKLTQKEIRNRTGFAQSWISELETG----KSTINIDNMIILAHTLD 74 (83)
Q Consensus 31 ~~~gltq~ela~~~gis~~~is~iE~G----~~~~~~~~l~~la~al~ 74 (83)
...|+|-+|.|+.+++|..|+..+-+. -.--+...|..+|...+
T Consensus 161 l~~G~snkeIA~~L~iS~~TV~~h~~~I~~KL~v~nr~elv~~A~~~~ 208 (210)
T PRK09935 161 LANGLSNKEIAEQLLLSNKTISAHKSNIYGKLGLHSIVELIDYAKSHE 208 (210)
T ss_pred HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCC
T ss_conf 986999999998949889999999999999819999999999999859
No 380
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha subunit, Gram-positive type; InterPro: IPR006308 These are the polypeptide chains of DNA polymerase III. Full-length homologs of this protein are restricted to the Gram-positive lineages, including the Mycoplasmas. This protein is designated alpha chain and given the gene symbol polC, but is not a full-length homolog of other polC genes. The N-terminal region of about 200 amino acids is rich in low-complexity sequence and poorly alignable. ; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication, 0005737 cytoplasm.
Probab=44.45 E-value=25 Score=16.88 Aligned_cols=37 Identities=16% Similarity=0.343 Sum_probs=32.1
Q ss_pred HHHHHHHHHHH-HHCCCC-HHHHHHHHHHHHHHHHHHHC
Q ss_conf 99999999999-983994-99999986342999988755
Q gi|254781147|r 20 MIFVNNFRNIR-KEAKLT-QKEIRNRTGFAQSWISELET 56 (83)
Q Consensus 20 ~~~g~~ir~~R-~~~glt-q~ela~~~gis~~~is~iE~ 56 (83)
+.+|..|-.+| .++-++ .+||-+|+|||.+.|-.+..
T Consensus 1210 e~vA~~Iv~ARq~Ek~F~S~eDL~kRtki~~~~iE~l~~ 1248 (1264)
T TIGR01405 1210 ENVAESIVEARQNEKPFLSVEDLKKRTKISKTLIEKLDS 1248 (1264)
T ss_pred HHHHHHHHHHHHCCCCCCCHHHHHHHCCCCHHHHHHHHH
T ss_conf 899999998643178747689876531877779998876
No 381
>TIGR02047 CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional regulator; InterPro: IPR011791 This entry represents the cadmium(II) and/or lead(II) responsive transcriptional activator of the proteobacterial metal efflux system , . This protein is a member of the MerR family of transcriptional activators and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(6-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix ..
Probab=43.49 E-value=13 Score=18.55 Aligned_cols=28 Identities=18% Similarity=0.137 Sum_probs=22.4
Q ss_pred CCHHHHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf 9499999986342999988755899944
Q gi|254781147|r 35 LTQKEIRNRTGFAQSWISELETGKSTIN 62 (83)
Q Consensus 35 ltq~ela~~~gis~~~is~iE~G~~~~~ 62 (83)
|-..|||+++|++..||.-||.-.--|.
T Consensus 1 mkIGeLA~~t~v~v~TIRFYE~~gLLPe 28 (127)
T TIGR02047 1 MKIGELAKKTGVSVETIRFYEKEGLLPE 28 (127)
T ss_pred CCHHHHHHHHCCCCCHHHHHHHCCCCCC
T ss_conf 9413454553344002246441378538
No 382
>PRK09483 response regulator; Provisional
Probab=42.82 E-value=22 Score=17.12 Aligned_cols=45 Identities=9% Similarity=-0.029 Sum_probs=30.5
Q ss_pred HHHCCCCHHHHHHHHHHHHHHHHHHHCC----CCCCCHHHHHHHHHHHC
Q ss_conf 9983994999999863429999887558----99944899999999928
Q gi|254781147|r 30 RKEAKLTQKEIRNRTGFAQSWISELETG----KSTINIDNMIILAHTLD 74 (83)
Q Consensus 30 R~~~gltq~ela~~~gis~~~is~iE~G----~~~~~~~~l~~la~al~ 74 (83)
....|+|-+|.|+.+++|..|+..+-+. -.--+...+..+|.-.|
T Consensus 159 ll~~G~snkeIA~~L~iS~~TV~~h~~~i~~KL~v~~r~el~~~A~~~g 207 (216)
T PRK09483 159 MITKGQKVNEISEQLNLSPKTVNSYRYRMFSKLNISGDVELTHLAIRHG 207 (216)
T ss_pred HHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCC
T ss_conf 9987999999999969899999999999999809999999999999959
No 383
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=42.63 E-value=30 Score=16.42 Aligned_cols=34 Identities=12% Similarity=0.051 Sum_probs=27.9
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHHH-HHHHHHHH
Q ss_conf 99999999999839949999998634-29999887
Q gi|254781147|r 21 IFVNNFRNIRKEAKLTQKEIRNRTGF-AQSWISEL 54 (83)
Q Consensus 21 ~~g~~ir~~R~~~gltq~ela~~~gi-s~~~is~i 54 (83)
.|-..+.....+.|.|..++|...|| +.+.+.+|
T Consensus 11 EfK~~iv~~~~~~g~sv~~vAr~~gv~~~~~l~~W 45 (116)
T COG2963 11 EFKLEAVALYLRGGDTVSEVAREFGIVSATQLYKW 45 (116)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHHHCCCCHHHHHHH
T ss_conf 99999999998178359999999487753789999
No 384
>pfam05732 RepL Firmicute plasmid replication protein (RepL). This family consists of Firmicute RepL proteins which are involved in plasmid replication.
Probab=42.08 E-value=18 Score=17.69 Aligned_cols=22 Identities=27% Similarity=0.385 Sum_probs=18.8
Q ss_pred CCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 3994999999863429999887
Q gi|254781147|r 33 AKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 33 ~gltq~ela~~~gis~~~is~i 54 (83)
.=.||.++|+.+|+|.+++...
T Consensus 74 lI~T~R~lae~~gvs~~TV~~t 95 (165)
T pfam05732 74 LIMTQREIAEETGISLETVRQT 95 (165)
T ss_pred EEEEHHHHHHHHCCCHHHHHHH
T ss_conf 9987899999839529999999
No 385
>TIGR02043 ZntR Zn(II)-responsive transcriptional regulator; InterPro: IPR011788 This entry represents the zinc and cadmium (II) responsive transcriptional activator of the gamma proteobacterial zinc efflux system . This protein is a member of the MerR family of transcriptional activators and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-Cys-X(8-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix . .
Probab=42.05 E-value=18 Score=17.72 Aligned_cols=23 Identities=30% Similarity=0.342 Sum_probs=12.8
Q ss_pred HHHHHHH--HHCCCCHHHHHHHHHH
Q ss_conf 9999999--9839949999998634
Q gi|254781147|r 24 NNFRNIR--KEAKLTQKEIRNRTGF 46 (83)
Q Consensus 24 ~~ir~~R--~~~gltq~ela~~~gi 46 (83)
++||-++ ++.|+|..++++.+.|
T Consensus 46 ~rlRFIl~AK~lGftLdeI~eLLsI 70 (132)
T TIGR02043 46 KRLRFILKAKELGFTLDEIKELLSI 70 (132)
T ss_pred HHHHHHHHHHHHCCCHHHHHHHHCC
T ss_conf 9888999887746878887876312
No 386
>pfam03333 PapB Adhesin biosynthesis transcription regulatory protein. This family includes PapB, DaaA, FanA, FanB, and AfaA.
Probab=41.68 E-value=18 Score=17.64 Aligned_cols=29 Identities=17% Similarity=0.265 Sum_probs=22.8
Q ss_pred HHHHH--HHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 99999--983994999999863429999887
Q gi|254781147|r 26 FRNIR--KEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 26 ir~~R--~~~gltq~ela~~~gis~~~is~i 54 (83)
|.++| .=.|.|++++.++-||++++.|.-
T Consensus 43 I~AL~dylV~G~srkevCe~~~Vn~gyfS~~ 73 (91)
T pfam03333 43 INALRDYLVDGYSRKEVCERHNVNNGYFSIS 73 (91)
T ss_pred HHHHHHHHHCCCCHHHHHHHCCCCHHHHHHH
T ss_conf 9999999876864999998729779999999
No 387
>PRK11202 DNA-binding transcriptional repressor FabR; Provisional
Probab=41.56 E-value=16 Score=17.93 Aligned_cols=49 Identities=12% Similarity=0.182 Sum_probs=31.9
Q ss_pred HHHHHHHHHHHH---CCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHH
Q ss_conf 999999999998---3994999999863429999887558999448999999
Q gi|254781147|r 21 IFVNNFRNIRKE---AKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIIL 69 (83)
Q Consensus 21 ~~g~~ir~~R~~---~gltq~ela~~~gis~~~is~iE~G~~~~~~~~l~~l 69 (83)
.+-.-+..+-.+ .++|..|+|..+||+++++.+...++-..-+..+...
T Consensus 16 lldAAl~~l~~~~gf~~lslreiar~aGv~~~afYrHF~d~e~L~~~lvde~ 67 (203)
T PRK11202 16 LIDAAFSQLSAERSFSSLSLREVAREAGIAPTSFYRHFKDMDELGLTMVDES 67 (203)
T ss_pred HHHHHHHHHHCCCCCCCCCHHHHHHHHCCCCCHHHHHCCCHHHHHHHHHHHH
T ss_conf 9999999986048933067999999848997518887598899999999999
No 388
>PRK11050 manganese transport regulator MntR; Provisional
Probab=41.45 E-value=31 Score=16.31 Aligned_cols=34 Identities=21% Similarity=0.309 Sum_probs=26.5
Q ss_pred HHHHHHHHHHHHCCCC-HHHHHHHHHHHHHHHHHH
Q ss_conf 9999999999983994-999999863429999887
Q gi|254781147|r 21 IFVNNFRNIRKEAKLT-QKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 21 ~~g~~ir~~R~~~glt-q~ela~~~gis~~~is~i 54 (83)
.+-..|-.+-.+.|.. +.|+|+.+|||++++++.
T Consensus 40 DYlE~I~~L~~~~G~aR~~DIA~~LgVs~pSVt~m 74 (155)
T PRK11050 40 DYVELIADLIAEVGEARQVDIAARLGVSQPTVAKM 74 (155)
T ss_pred HHHHHHHHHHHCCCCEEHHHHHHHHCCCCHHHHHH
T ss_conf 99999999998269564999998909993319999
No 389
>PRK00430 fis DNA-binding protein Fis; Provisional
Probab=41.22 E-value=31 Score=16.29 Aligned_cols=31 Identities=6% Similarity=0.009 Sum_probs=26.4
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 9999999998399499999986342999988
Q gi|254781147|r 23 VNNFRNIRKEAKLTQKEIRNRTGFAQSWISE 53 (83)
Q Consensus 23 g~~ir~~R~~~gltq~ela~~~gis~~~is~ 53 (83)
..-|....+..+-.|...|+.+||+++++.+
T Consensus 60 ~pLl~~vL~~t~gNqskAA~~LGInR~TLRk 90 (98)
T PRK00430 60 APLLDMVMQYTRGNQTRAALMLGINRGTLRK 90 (98)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHCCCHHHHHH
T ss_conf 9999999999669599999997877889999
No 390
>PRK09393 ftrA transcriptional activator FtrA; Provisional
Probab=41.15 E-value=31 Score=16.28 Aligned_cols=34 Identities=6% Similarity=-0.008 Sum_probs=27.0
Q ss_pred HHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf 9998399499999986342999988755899944
Q gi|254781147|r 29 IRKEAKLTQKEIRNRTGFAQSWISELETGKSTIN 62 (83)
Q Consensus 29 ~R~~~gltq~ela~~~gis~~~is~iE~G~~~~~ 62 (83)
...+..+|.+++|+.+|+|+.++.+..+.....+
T Consensus 227 ~~l~~~ls~~~lA~~~~~S~R~l~R~Fk~~~G~t 260 (320)
T PRK09393 227 AHLAQPHTVASLAARAAMSPRTFLRRFEAATGMT 260 (320)
T ss_pred HHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHCCC
T ss_conf 6111478899999997879879998997886969
No 391
>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional
Probab=40.72 E-value=32 Score=16.24 Aligned_cols=32 Identities=6% Similarity=-0.025 Sum_probs=27.3
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 99999999983994999999863429999887
Q gi|254781147|r 23 VNNFRNIRKEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 23 g~~ir~~R~~~gltq~ela~~~gis~~~is~i 54 (83)
-+.|...-.+.+.++.+.|+.+||+++++.+.
T Consensus 471 r~lI~~AL~~~~GN~s~AAr~LGIsRstLyRk 502 (510)
T PRK05022 471 RQLIRQALAQHNGNWAAAARALELDRANLHRL 502 (510)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHH
T ss_conf 99999999991998999999979899999999
No 392
>pfam08822 DUF1804 Protein of unknown function (DUF1804). This family of bacterial protein is uncharacterized.
Probab=40.20 E-value=32 Score=16.19 Aligned_cols=34 Identities=15% Similarity=0.131 Sum_probs=27.3
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 9999999998399499999986342999988755
Q gi|254781147|r 23 VNNFRNIRKEAKLTQKEIRNRTGFAQSWISELET 56 (83)
Q Consensus 23 g~~ir~~R~~~gltq~ela~~~gis~~~is~iE~ 56 (83)
-..+|..=.-.++|.+..|..+||+.++..+|.+
T Consensus 8 r~~vR~~Yv~~~~~Le~aA~~~gV~~~TArrWK~ 41 (165)
T pfam08822 8 RDAVRRLYVFDRLTLEVAAAKAGVSYSTARRWKR 41 (165)
T ss_pred HHHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHH
T ss_conf 9999999996678799999880998888999999
No 393
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=39.99 E-value=32 Score=16.17 Aligned_cols=29 Identities=14% Similarity=0.136 Sum_probs=24.3
Q ss_pred HHHHCCCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 99983994999999863429999887558
Q gi|254781147|r 29 IRKEAKLTQKEIRNRTGFAQSWISELETG 57 (83)
Q Consensus 29 ~R~~~gltq~ela~~~gis~~~is~iE~G 57 (83)
.....|+|-+|.|+.+++|.+|+..+-+.
T Consensus 158 ~lla~G~snkeIA~~L~iS~~TVk~h~~~ 186 (211)
T COG2197 158 RLLAEGLSNKEIAEELNLSEKTVKTHVSN 186 (211)
T ss_pred HHHHCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 99987998899999978789899999999
No 394
>PRK10651 transcriptional regulator NarL; Provisional
Probab=39.86 E-value=27 Score=16.68 Aligned_cols=26 Identities=19% Similarity=0.141 Sum_probs=21.9
Q ss_pred HHCCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 98399499999986342999988755
Q gi|254781147|r 31 KEAKLTQKEIRNRTGFAQSWISELET 56 (83)
Q Consensus 31 ~~~gltq~ela~~~gis~~~is~iE~ 56 (83)
...|+|-+|+|+.+++|.+|+..+-+
T Consensus 167 l~~G~snkeIA~~L~iS~~TV~~h~~ 192 (216)
T PRK10651 167 IAQGLSNKMIARRLDITESTVKVHVK 192 (216)
T ss_pred HHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 98599999999996978999999999
No 395
>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=38.88 E-value=34 Score=16.07 Aligned_cols=51 Identities=6% Similarity=-0.040 Sum_probs=38.9
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHH
Q ss_conf 999999999839949999998634299998875589994489999999992
Q gi|254781147|r 23 VNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTL 73 (83)
Q Consensus 23 g~~ir~~R~~~gltq~ela~~~gis~~~is~iE~G~~~~~~~~l~~la~al 73 (83)
+..+-...--.|-|..++|+.+|++.+.|..|...|-..=...+..+.+.+
T Consensus 17 a~~~f~~~G~~g~~~~~Ia~~ag~~k~~i~yyF~~Ke~l~~avl~~~~~~~ 67 (202)
T TIGR03613 17 ALDTFSRFGFHGTSLEQIAELAGVSKTNLLYYFPSKDALYLAVLRQILDIW 67 (202)
T ss_pred HHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 999999849564889999998599888999985899999999999999999
No 396
>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator; InterPro: IPR014290 Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] . FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins , . It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly . The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA . SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA , acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins . Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen . This entry represents proteins belonging to the Rtf2 family of transcriptional regulators and are found, typically, as the first gene of the SUF operon. They are found only in a subset of the genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role..
Probab=38.05 E-value=9.2 Score=19.43 Aligned_cols=35 Identities=17% Similarity=0.227 Sum_probs=28.4
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 99999999998399499999986342999988755
Q gi|254781147|r 22 FVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELET 56 (83)
Q Consensus 22 ~g~~ir~~R~~~gltq~ela~~~gis~~~is~iE~ 56 (83)
+--.+-+.+.+.-+|-+++|+.+|++-.|+|+|=+
T Consensus 13 ~vl~~lA~~~~~~ySAA~lA~~tgL~~pTvsK~Lk 47 (130)
T TIGR02944 13 VVLTVLAQADEQTYSAAELAEQTGLEAPTVSKILK 47 (130)
T ss_pred HHHHHHHCCCCCHHHHHHHHHHCCCCCCHHHHHHH
T ss_conf 99999852899700688878645988604789988
No 397
>TIGR03541 reg_near_HchA LuxR family transcriptional regulatory, chaperone HchA-associated. Members of this protein family belong to the LuxR transcriptional regulator family, and contain both autoinducer binding (pfam03472) and transcriptional regulator (pfam00196) domains. Members, however, occur only in a few members of the Gammaproteobacteria that have the chaperone/aminopeptidase HchA, and are always encoded by the adjacent gene.
Probab=38.00 E-value=32 Score=16.24 Aligned_cols=26 Identities=12% Similarity=0.077 Sum_probs=22.7
Q ss_pred HHCCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 98399499999986342999988755
Q gi|254781147|r 31 KEAKLTQKEIRNRTGFAQSWISELET 56 (83)
Q Consensus 31 ~~~gltq~ela~~~gis~~~is~iE~ 56 (83)
...|.|..|.|..+|||..++..+-+
T Consensus 183 ~A~Gkt~~eIa~iL~iSe~TV~~hl~ 208 (232)
T TIGR03541 183 TALGRRQADIAAILGISERTVENHLR 208 (232)
T ss_pred HHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 98799999999996989999999999
No 398
>TIGR01293 Kv_beta voltage-dependent potassium channel beta subunit; InterPro: IPR005983 Potassium channels are the most diverse group of the ion channel family , . They are important in shaping the action potential, and in neuronal excitability and plasticity . The potassium channel family is composed of several functionally distinct isoforms, which can be broadly separated into 2 groups : the practically non-inactivating 'delayed' group and the rapidly inactivating 'transient' group. These are all highly similar proteins, with only small amino acid changes causing the diversity of the voltage-dependent gating mechanism, channel conductance and toxin binding properties. Each type of K^+ channel is activated by different signals and conditions depending on their type of regulation: some open in response to depolarisation of the plasma membrane; others in response to hyperpolarisation or an increase in intracellular calcium concentration; some can be regulated by binding of a transmitter, together with intracellular kinases; while others are regulated by GTP-binding proteins or other second messengers . In eukaryotic cells, K^+ channels are involved in neural signalling and generation of the cardiac rhythm, act as effectors in signal transduction pathways involving G protein-coupled receptors (GPCRs) and may have a role in target cell lysis by cytotoxic T-lymphocytes . In prokaryotic cells, they play a role in the maintenance of ionic homeostasis . All K^+ channels discovered so far possess a core of alpha subunits, each comprising either one or two copies of a highly conserved pore loop domain (P-domain). The P-domain contains the sequence (T/SxxTxGxG), which has been termed the K^+ selectivity sequence. In families that contain one P-domain, four subunits assemble to form a selective pathway for K^+ across the membrane. However, it remains unclear how the 2 P-domain subunits assemble to form a selective pore. The functional diversity of these families can arise through homo- or hetero-associations of alpha subunits or association with auxiliary cytoplasmic beta subunits. K^+ channel subunits containing one pore domain can be assigned into one of two superfamilies: those that possess six transmembrane (TM) domains and those that possess only two TM domains. The six TM domain superfamily can be further subdivided into conserved gene families: the voltage-gated (Kv) channels; the KCNQ channels (originally known as KvLQT channels); the EAG-like K^+ channels; and three types of calcium (Ca)-activated K^+ channels (BK, IK and SK) , . The 2TM domain family comprises inward-rectifying K^+ channels. In addition, there are K^+ channel alpha-subunits that possess two P-domains. These are usually highly regulated K^+ selective leak channels. The KCNAB family (also known as the Kvbeta family) of voltage-dependent potassium channel beta subunits form complexes with the alpha subunits which can modify the properties of the channel. Four of these soluble beta subunits form a complex with four alpha subunit cytoplasmic (T1) regions. These subunits belong to the family of are NADPH-dependent aldo-keto reductases, and bind NADPH-cofactors in their active sites. Changes in the oxidoreductase activity appear to markedly influence the gating mode of Kv channels, since mutations to the catalytic residues in the active site lessen the inactivating activity of KCNAB . The KCNAB family is further divided into 3 subfamilies: KCNAB1 (Kvbeta1), KCNAB2 (Kvbeta2) and KCNAB3 (Kvbeta3). ; GO: 0005249 voltage-gated potassium channel activity, 0006813 potassium ion transport, 0005737 cytoplasm.
Probab=37.77 E-value=20 Score=17.40 Aligned_cols=50 Identities=18% Similarity=0.248 Sum_probs=36.0
Q ss_pred HHCCCCHHHHHHHHHHHHHHHH---HHHCCCCC-CCHHHHHHHHHHHCCCHHHH
Q ss_conf 9839949999998634299998---87558999-44899999999928999996
Q gi|254781147|r 31 KEAKLTQKEIRNRTGFAQSWIS---ELETGKST-INIDNMIILAHTLDTPLWKL 80 (83)
Q Consensus 31 ~~~gltq~ela~~~gis~~~is---~iE~G~~~-~~~~~l~~la~al~i~~~~l 80 (83)
+.-.|+.+++...+.+|++.-. ++|.|++. -.+..|..||+-|||++.+|
T Consensus 234 K~y~W~~deinrnaalsp~Gsw~K~~~~eGrr~~~rl~dL~a~A~~LGC~~~QL 287 (338)
T TIGR01293 234 KGYQWLKDEINRNAALSPQGSWEKVRSEEGRRQQARLRDLAAIAEKLGCTLTQL 287 (338)
T ss_pred CCHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCHHHH
T ss_conf 200112566533210476765454112110247888898999998718875578
No 399
>pfam07278 DUF1441 Protein of unknown function (DUF1441). This family consists of several hypothetical Enterobacterial proteins of around 160 residues in length. The function of this family is unknown. However, it appears to be distantly related to other HTH families so may act as a transcriptional regulator.
Probab=37.25 E-value=29 Score=16.47 Aligned_cols=25 Identities=20% Similarity=0.284 Sum_probs=19.4
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf 9949999998634299998875589
Q gi|254781147|r 34 KLTQKEIRNRTGFAQSWISELETGK 58 (83)
Q Consensus 34 gltq~ela~~~gis~~~is~iE~G~ 58 (83)
.|+..++|+.+|++++++++=-.|-
T Consensus 1 ~lnI~qlA~~~GlhRqTV~~RL~~~ 25 (152)
T pfam07278 1 KLNINQLAALTGLHRQTVAARLAGV 25 (152)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHCC
T ss_conf 9878999999853299999998459
No 400
>PTZ00298 mevalonate kinase; Provisional
Probab=37.24 E-value=36 Score=15.91 Aligned_cols=37 Identities=11% Similarity=0.103 Sum_probs=31.7
Q ss_pred CHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHC
Q ss_conf 499999986342999988755899944899999999928
Q gi|254781147|r 36 TQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLD 74 (83)
Q Consensus 36 tq~ela~~~gis~~~is~iE~G~~~~~~~~l~~la~al~ 74 (83)
...++++.+..+...+..+ |..+|.++.+..+|+.+|
T Consensus 238 d~~~lG~Lm~~nh~lL~~l--gVS~p~Ld~lv~~a~~~G 274 (328)
T PTZ00298 238 NLFRVGELMNANHDLCQKL--TVSCRELDSIVQTCRTYG 274 (328)
T ss_pred CHHHHHHHHHHHHHHHHHC--CCCCHHHHHHHHHHHHCC
T ss_conf 9999999999999989746--889789999999999769
No 401
>PRK12680 transcriptional regulator CysB-like protein; Reviewed
Probab=37.10 E-value=36 Score=15.90 Aligned_cols=30 Identities=20% Similarity=0.182 Sum_probs=22.8
Q ss_pred HHHHHHH--HCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999--83994999999863429999887
Q gi|254781147|r 25 NFRNIRK--EAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 25 ~ir~~R~--~~gltq~ela~~~gis~~~is~i 54 (83)
.||.+.. +.|++....|+.+++|++.+|+-
T Consensus 5 QLr~f~aVa~~~~n~s~AA~~L~iSQPaVSkq 36 (327)
T PRK12680 5 QLRYLVAIADAELNITLAAARVHATQPGLSKQ 36 (327)
T ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 99999999965899999999978976799999
No 402
>pfam11985 DUF3486 Protein of unknown function (DUF3486). This family of proteins is functionally uncharacterized. This protein is found in bacteria and viruses. Proteins in this family are about 190 amino acids in length.
Probab=37.09 E-value=36 Score=15.90 Aligned_cols=47 Identities=21% Similarity=0.206 Sum_probs=29.6
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHH---------HHHHHHHHHHH
Q ss_conf 96988888868989999999999999999998399499999986---------34299998875
Q gi|254781147|r 1 MPRRKRDEPHLSDAILRERMIFVNNFRNIRKEAKLTQKEIRNRT---------GFAQSWISELE 55 (83)
Q Consensus 1 Mp~~~~~~p~~~~~~~~~~~~~g~~ir~~R~~~gltq~ela~~~---------gis~~~is~iE 55 (83)
||++++-. .++++ +-..|-..-.+.++||.++-+.+ -+|+|.+++|=
T Consensus 1 m~r~SkId-~LP~e-------vr~~L~~~L~e~~~t~~eile~~~~~~~~~g~~iSrSal~RY~ 56 (179)
T pfam11985 1 MGRRSKVD-LLPPE-------VRQWLDRRLREGGFTQYEILEEINQLIDDEGYPISKSALHRYG 56 (179)
T ss_pred CCCCCHHH-HCCHH-------HHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCCHHHHHHHH
T ss_conf 99854586-79899-------9999999988689858999999998878668887588898999
No 403
>PRK07758 hypothetical protein; Provisional
Probab=36.74 E-value=32 Score=16.21 Aligned_cols=40 Identities=18% Similarity=0.310 Sum_probs=33.7
Q ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 9999999999999983994999999863429999887558
Q gi|254781147|r 18 ERMIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETG 57 (83)
Q Consensus 18 ~~~~~g~~ir~~R~~~gltq~ela~~~gis~~~is~iE~G 57 (83)
.+..+..-|..+..-..+|.+|+.+.-||.+..|..+|..
T Consensus 47 RRAL~~~GI~TLedLskytEkELL~LHGmGP~ai~~L~~a 86 (95)
T PRK07758 47 RRALEHHGIHTVEELSKYSEKEILKLHGMGPASLPKLRKA 86 (95)
T ss_pred HHHHHHCCCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHH
T ss_conf 9999982811499998851999999848688889999999
No 404
>pfam10078 DUF2316 Uncharacterized protein conserved in bacteria (DUF2316). Members of this family of hypothetical bacterial proteins have no known function.
Probab=36.40 E-value=37 Score=15.83 Aligned_cols=56 Identities=16% Similarity=0.128 Sum_probs=40.1
Q ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHC
Q ss_conf 999999999999998399499999986342999988755899944899999999928
Q gi|254781147|r 18 ERMIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLD 74 (83)
Q Consensus 18 ~~~~~g~~ir~~R~~~gltq~ela~~~gis~~~is~iE~G~~~~~~~~l~~la~al~ 74 (83)
++..-...+++-....|+|.+++|+.+|+|...+.++-+=+ ...+...+.+-+.|+
T Consensus 7 Q~~~T~~ELqeNf~~~~ls~~~iA~dL~~s~~~ve~vL~m~-~~~i~~vW~lRdyL~ 62 (89)
T pfam10078 7 EMQATRKELQANFELSGLTIEQVAKDLNTTPEKVEALLQLK-QRSIEDVWILRNYLN 62 (89)
T ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHCC-CCCCCHHHHHHHHHH
T ss_conf 99999999999998838989999989499999999999734-677541388999999
No 405
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family; InterPro: IPR014298 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 recognized by the major sigma factors , . This group of sigma factors 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.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=36.35 E-value=23 Score=17.03 Aligned_cols=32 Identities=16% Similarity=0.206 Sum_probs=24.4
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 99999999839949999998634299998875
Q gi|254781147|r 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISELE 55 (83)
Q Consensus 24 ~~ir~~R~~~gltq~ela~~~gis~~~is~iE 55 (83)
+.|-.+|=..||..+|+|+.+|.+.+.|..+-
T Consensus 129 q~viaLrF~~~L~~~EvA~ilGk~~gavk~Lq 160 (171)
T TIGR02952 129 QEVIALRFAQNLPIAEVARILGKTEGAVKALQ 160 (171)
T ss_pred HHHHHHHHCCCCCHHHHHHHHCCCCCHHHHHH
T ss_conf 12033321168838789987268974689999
No 406
>PRK00118 putative DNA-binding protein; Validated
Probab=36.35 E-value=37 Score=15.83 Aligned_cols=31 Identities=6% Similarity=0.040 Sum_probs=24.4
Q ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 9999998399499999986342999988755
Q gi|254781147|r 26 FRNIRKEAKLTQKEIRNRTGFAQSWISELET 56 (83)
Q Consensus 26 ir~~R~~~gltq~ela~~~gis~~~is~iE~ 56 (83)
+-.+=....+|..|.|+..|||++.+...-+
T Consensus 25 ~~~lyy~~DlSl~EIAe~~~iSRQaV~D~ik 55 (105)
T PRK00118 25 YMELYYLDDYSLGEIAEEFNVSRQAVYDNIK 55 (105)
T ss_pred HHHHHHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 9999988549999998996985999999999
No 407
>pfam00325 Crp Bacterial regulatory proteins, crp family.
Probab=36.16 E-value=30 Score=16.36 Aligned_cols=22 Identities=23% Similarity=0.412 Sum_probs=19.0
Q ss_pred CCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 9949999998634299998875
Q gi|254781147|r 34 KLTQKEIRNRTGFAQSWISELE 55 (83)
Q Consensus 34 gltq~ela~~~gis~~~is~iE 55 (83)
-||-.|+|+-+|.+.-++|++-
T Consensus 2 pmsrqdIadylGlt~ETVsR~l 23 (32)
T pfam00325 2 PMSRQEIADYLGLTRETVSRLL 23 (32)
T ss_pred CCCHHHHHHHHCCHHHHHHHHH
T ss_conf 8658899998472599999999
No 408
>pfam02042 RWP-RK RWP-RK domain. This domain is named RWP-RK after a conserved motif at the C terminus of the presumed domain. The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development.
Probab=35.54 E-value=38 Score=15.75 Aligned_cols=29 Identities=17% Similarity=0.288 Sum_probs=21.7
Q ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 99999983994999999863429999887
Q gi|254781147|r 26 FRNIRKEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 26 ir~~R~~~gltq~ela~~~gis~~~is~i 54 (83)
+..++.--.+.+.+.|+.+||+.+.+-++
T Consensus 7 ~~dl~~~F~lpi~~AA~~Lgv~~T~LKk~ 35 (52)
T pfam02042 7 LEDLSKYFHLPIKEAAKELGVCLTVLKKI 35 (52)
T ss_pred HHHHHHHHCCCHHHHHHHHCCCHHHHHHH
T ss_conf 99999981875999999968779999999
No 409
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=35.50 E-value=38 Score=15.74 Aligned_cols=29 Identities=10% Similarity=0.100 Sum_probs=24.0
Q ss_pred HHHH-HHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 9999-9983994999999863429999887
Q gi|254781147|r 26 FRNI-RKEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 26 ir~~-R~~~gltq~ela~~~gis~~~is~i 54 (83)
|..+ ....++|..|+|+.+|++++++.++
T Consensus 31 L~~la~~~~~ltl~eia~~lglpksT~~Rl 60 (271)
T PRK10163 31 LQYLEKSGGSSSVSDISLNLDLPLSTTFRL 60 (271)
T ss_pred HHHHHHCCCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 999974799979999999979199999999
No 410
>COG2452 Predicted site-specific integrase-resolvase [DNA replication, recombination, and repair]
Probab=35.34 E-value=39 Score=15.73 Aligned_cols=23 Identities=22% Similarity=0.085 Sum_probs=18.4
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 99499999986342999988755
Q gi|254781147|r 34 KLTQKEIRNRTGFAQSWISELET 56 (83)
Q Consensus 34 gltq~ela~~~gis~~~is~iE~ 56 (83)
.|+.++.++..|||+.++.+|-+
T Consensus 1 ~m~~~e~~~~lgis~~Tl~rw~r 23 (193)
T COG2452 1 LLRPKEACQLLGISYSTLLRWIR 23 (193)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 98889999983947999999987
No 411
>pfam00392 GntR Bacterial regulatory proteins, gntR family. This family of regulatory proteins consists of the N-terminal HTH region of GntR-like bacterial transcription factors. At the C-terminus there is usually an effector-binding/oligomerisation domain. The GntR-like proteins include the following sub-families: MocR, YtrR, FadR, AraR, HutC and PlmA, DevA, DasR. Many of these proteins have been shown experimentally to be autoregulatory, enabling the prediction of operator sites and the discovery of cis/trans relationships. The DasR regulator has been shown to be a global regulator of primary metabolism and development in Streptomyces coelicolor.
Probab=34.98 E-value=27 Score=16.64 Aligned_cols=22 Identities=23% Similarity=0.442 Sum_probs=17.4
Q ss_pred CCC-CHHHHHHHHHHHHHHHHHH
Q ss_conf 399-4999999863429999887
Q gi|254781147|r 33 AKL-TQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 33 ~gl-tq~ela~~~gis~~~is~i 54 (83)
..+ |..+||+..|+|++++.+-
T Consensus 22 ~~LPs~~~La~~~~vSr~tvr~A 44 (64)
T pfam00392 22 DKLPSERELAAEFGVSRTTVREA 44 (64)
T ss_pred CCCHHHHHHHHHHCCCHHHHHHH
T ss_conf 99847999999979699999999
No 412
>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional
Probab=34.71 E-value=39 Score=15.67 Aligned_cols=29 Identities=10% Similarity=0.320 Sum_probs=21.6
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 999999998399499999986342999988
Q gi|254781147|r 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISE 53 (83)
Q Consensus 24 ~~ir~~R~~~gltq~ela~~~gis~~~is~ 53 (83)
.-|+.+....+ +..++|+.+|||++++.+
T Consensus 471 ~~l~~l~~~~~-~~~kaAk~LGISrttL~~ 499 (513)
T PRK10820 471 SVLTQLYRNYP-STRKLAKRLGVSHTAIAN 499 (513)
T ss_pred HHHHHHHHHCC-CHHHHHHHHCCCHHHHHH
T ss_conf 99999998788-999999997998999999
No 413
>PRK11552 putative DNA-binding transcriptional regulator; Provisional
Probab=34.28 E-value=40 Score=15.63 Aligned_cols=41 Identities=15% Similarity=0.139 Sum_probs=33.0
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHC
Q ss_conf 399499999986342999988755899944899999999928
Q gi|254781147|r 33 AKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLD 74 (83)
Q Consensus 33 ~gltq~ela~~~gis~~~is~iE~G~~~~~~~~l~~la~al~ 74 (83)
.+ |-.++|+.+|++.+.|..|..+|-..=...+..|++...
T Consensus 32 ~a-ttr~Ia~~Ag~~~~~i~yyFg~Ke~Ly~Av~~~ia~~i~ 72 (224)
T PRK11552 32 HA-TTRDIAAQAGQNIAAITYYFGSKEDLYLACAQWIADFIG 72 (224)
T ss_pred CH-HHHHHHHHHCCCHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf 40-099999983999999988738889999999999999999
No 414
>pfam04297 UPF0122 Putative helix-turn-helix protein, YlxM / p13 like. Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13. 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.
Probab=33.95 E-value=41 Score=15.59 Aligned_cols=29 Identities=10% Similarity=0.025 Sum_probs=23.5
Q ss_pred HHHHHHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 99999839949999998634299998875
Q gi|254781147|r 27 RNIRKEAKLTQKEIRNRTGFAQSWISELE 55 (83)
Q Consensus 27 r~~R~~~gltq~ela~~~gis~~~is~iE 55 (83)
-.+=....+|..|.|+..|||++.+...-
T Consensus 26 ~~lyy~eDlSL~EIAe~~~iSRQaV~D~i 54 (101)
T pfam04297 26 FELYYLDDLSLSEIAEEFNVSRQAVYDNI 54 (101)
T ss_pred HHHHHHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 99998763989999988198599999999
No 415
>pfam05043 Mga Mga helix-turn-helix domain. M regulator protein trans-acting positive regulator (Mga) is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions. This domain is found in the centre of the Mga proteins. This family also contains a number of bacterial RofA transcriptional regulators that seem to be largely restricted to streptococci. These proteins have been shown to regulate the expression of important bacterial adhesins. This is presumably a DNA-binding domain.
Probab=33.72 E-value=41 Score=15.57 Aligned_cols=36 Identities=6% Similarity=-0.009 Sum_probs=29.1
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 999999999998399499999986342999988755
Q gi|254781147|r 21 IFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELET 56 (83)
Q Consensus 21 ~~g~~ir~~R~~~gltq~ela~~~gis~~~is~iE~ 56 (83)
..-.-+..+=.....|..++|+...+|.+++.+.-.
T Consensus 17 ~~f~il~~lf~~~~~s~~~~a~~l~iS~sTl~R~ik 52 (87)
T pfam05043 17 LKFQLLKFLFFHEFFSLTSLAQKLFISESTLYRLIK 52 (87)
T ss_pred HHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 299999999818999899999997889999999999
No 416
>pfam09571 RE_XcyI XcyI restriction endonuclease. This family includes the XcyI (recognizes and cleaves C^CCGGG) restriction endonucleases.
Probab=33.58 E-value=19 Score=17.60 Aligned_cols=56 Identities=20% Similarity=0.132 Sum_probs=38.2
Q ss_pred HHHHHHHCCCCHHHHHHH-HHHHHHHHHHHH-CCCCC-CCHHHHHHHHHHHCCCHHHHC
Q ss_conf 999999839949999998-634299998875-58999-448999999999289999960
Q gi|254781147|r 26 FRNIRKEAKLTQKEIRNR-TGFAQSWISELE-TGKST-INIDNMIILAHTLDTPLWKLL 81 (83)
Q Consensus 26 ir~~R~~~gltq~ela~~-~gis~~~is~iE-~G~~~-~~~~~l~~la~al~i~~~~l~ 81 (83)
+-++|.-.|+||+++-.. .|+.....-.+| .|+.+ ..-..+.-+|-+|.-+.+.|+
T Consensus 77 ~GYYRLLlG~SQK~fy~~d~g~g~g~fksmE~kG~i~k~~~p~i~dlc~af~~sas~Ll 135 (318)
T pfam09571 77 IGYYRLLLGYSQKRFYRMDSGLGFGPFKSMEKKGKINKALRPHIPDLCSAFIASASKLL 135 (318)
T ss_pred HHHHHHHHCCCHHHHCCCCCCCCCCCHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHH
T ss_conf 66899985665998646777778761220465176451013320789999999999998
No 417
>COG1339 Transcriptional regulator of a riboflavin/FAD biosynthetic operon [Transcription / Coenzyme metabolism]
Probab=33.18 E-value=25 Score=16.82 Aligned_cols=25 Identities=24% Similarity=0.373 Sum_probs=21.4
Q ss_pred HHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 99983994999999863429999887
Q gi|254781147|r 29 IRKEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 29 ~R~~~gltq~ela~~~gis~~~is~i 54 (83)
.+. -++|..++|+.+|+|.++.+++
T Consensus 15 ~~~-~~~t~~ela~~l~~S~qta~R~ 39 (214)
T COG1339 15 VRG-VKVTSSELAKRLGVSSQTAARK 39 (214)
T ss_pred HCC-CCCCHHHHHHHHCCCCHHHHHH
T ss_conf 037-6020899998857470778899
No 418
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=33.10 E-value=35 Score=16.01 Aligned_cols=41 Identities=15% Similarity=0.068 Sum_probs=29.2
Q ss_pred CCCHHHHHHHHHHHHHHHHHHH-----CC-------C-CCCCHHHHHHHHHHHC
Q ss_conf 9949999998634299998875-----58-------9-9944899999999928
Q gi|254781147|r 34 KLTQKEIRNRTGFAQSWISELE-----TG-------K-STINIDNMIILAHTLD 74 (83)
Q Consensus 34 gltq~ela~~~gis~~~is~iE-----~G-------~-~~~~~~~l~~la~al~ 74 (83)
..++.|+|..+|+|+.+++++- .| + ...+.+.|.+||.-+.
T Consensus 156 ~~~~~elA~~lG~Sretl~R~L~~f~~eGiI~~~~~~i~I~D~~~L~~LA~~~~ 209 (213)
T PRK10402 156 HEKHTQAAEYLGVSYRHLLYVLAQFCQDGYLIKSKRGYLIKNRKQLSGLALELK 209 (213)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCEEEEECHHHHHHHHHHCC
T ss_conf 667999999979889999999999998898897499999957999999986448
No 419
>TIGR02054 MerD mercuric resistence transcriptional repressor protein MerD; InterPro: IPR011797 This entry represents a transcriptional repressor protein of the MerR family whose expression is regulated by the mercury-sensitive transcriptional activator, MerR. MerD has been shown to repress the transcription of the mer operon .; GO: 0003677 DNA binding, 0045892 negative regulation of transcription DNA-dependent, 0046689 response to mercury ion.
Probab=33.07 E-value=20 Score=17.38 Aligned_cols=16 Identities=31% Similarity=0.559 Sum_probs=9.9
Q ss_pred CCCCHHHHHHHHHHHC
Q ss_conf 9944899999999928
Q gi|254781147|r 59 STINIDNMIILAHTLD 74 (83)
Q Consensus 59 ~~~~~~~l~~la~al~ 74 (83)
..+.++.|.++|++||
T Consensus 59 aGIgL~eLARlCraLD 74 (120)
T TIGR02054 59 AGIGLDELARLCRALD 74 (120)
T ss_pred CCCCHHHHHHHHHHHC
T ss_conf 1877888999987406
No 420
>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=32.92 E-value=33 Score=16.16 Aligned_cols=34 Identities=12% Similarity=0.233 Sum_probs=22.6
Q ss_pred HHHHHHHHHH--HHCCC-CHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999999--98399-4999999863429999887
Q gi|254781147|r 21 IFVNNFRNIR--KEAKL-TQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 21 ~~g~~ir~~R--~~~gl-tq~ela~~~gis~~~is~i 54 (83)
.+...|..-. -...+ |..+||+..|+|++++.+.
T Consensus 9 ~i~~~I~~g~~~~G~~LPs~~~La~~~~vSr~tvr~A 45 (66)
T cd07377 9 QLREAILSGELKPGDRLPSERELAEELGVSRTTVREA 45 (66)
T ss_pred HHHHHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 9999998599999199927999999979888999999
No 421
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=32.39 E-value=43 Score=15.44 Aligned_cols=36 Identities=11% Similarity=0.182 Sum_probs=30.5
Q ss_pred HHHHHHHHHHHHCC--CCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 99999999999839--9499999986342999988755
Q gi|254781147|r 21 IFVNNFRNIRKEAK--LTQKEIRNRTGFAQSWISELET 56 (83)
Q Consensus 21 ~~g~~ir~~R~~~g--ltq~ela~~~gis~~~is~iE~ 56 (83)
..++.|-..|++.| -+.+||.+..||..+++-++..
T Consensus 108 ~kA~aIi~yRe~~G~f~sv~dL~~v~GiG~~~~ekl~~ 145 (149)
T COG1555 108 KKAQAIIDYREENGPFKSVDDLAKVKGIGPKTLEKLKD 145 (149)
T ss_pred HHHHHHHHHHHHCCCCCCHHHHCCCCCCCHHHHHHHHH
T ss_conf 99999999999739976578871077778999998775
No 422
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=32.28 E-value=34 Score=16.06 Aligned_cols=21 Identities=24% Similarity=0.499 Sum_probs=17.0
Q ss_pred CC-CHHHHHHHHHHHHHHHHHH
Q ss_conf 99-4999999863429999887
Q gi|254781147|r 34 KL-TQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 34 gl-tq~ela~~~gis~~~is~i 54 (83)
.+ |..+||+..|+|++++.+-
T Consensus 19 ~LPs~~~la~~~~vSr~tvr~A 40 (60)
T smart00345 19 KLPSERELAAQLGVSRTTVREA 40 (60)
T ss_pred CCCCHHHHHHHHCCCHHHHHHH
T ss_conf 8810999999989499999999
No 423
>pfam07506 RepB RepB plasmid partitioning protein. This family includes proteins with sequence similarity to the RepB partitioning protein of the large Ti (tumour-inducing) plasmids of Agrobacterium tumefaciens.
Probab=32.09 E-value=44 Score=15.41 Aligned_cols=25 Identities=20% Similarity=0.266 Sum_probs=22.8
Q ss_pred HHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 9839949999998634299998875
Q gi|254781147|r 31 KEAKLTQKEIRNRTGFAQSWISELE 55 (83)
Q Consensus 31 ~~~gltq~ela~~~gis~~~is~iE 55 (83)
.++|++.+.++..+|++.+++++.-
T Consensus 18 ~~~G~~~~~I~~aL~vd~~~is~~~ 42 (185)
T pfam07506 18 LERGVPRAEIAAALGLDPQTVSKMV 42 (185)
T ss_pred HHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 9869999999999867999999999
No 424
>cd04778 HTH_MerR-like_sg2 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 2). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=31.57 E-value=37 Score=15.85 Aligned_cols=14 Identities=21% Similarity=0.038 Sum_probs=8.6
Q ss_pred HHCCCCHHHHHHHH
Q ss_conf 98399499999986
Q gi|254781147|r 31 KEAKLTQKEIRNRT 44 (83)
Q Consensus 31 ~~~gltq~ela~~~ 44 (83)
..+|+|...+++.+
T Consensus 54 ~~~G~tl~~I~e~l 67 (219)
T cd04778 54 LERGYTLAHIAELL 67 (219)
T ss_pred HHCCCCHHHHHHHH
T ss_conf 98799889999999
No 425
>pfam01978 TrmB Sugar-specific transcriptional regulator TrmB. One member of this family, TrmB, has been shown to be a sugar-specific transcriptional regulator of the trehalose/maltose ABC transporter in Thermococcus litoralis.
Probab=31.57 E-value=45 Score=15.36 Aligned_cols=28 Identities=25% Similarity=0.283 Sum_probs=23.8
Q ss_pred HHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 9999983994999999863429999887
Q gi|254781147|r 27 RNIRKEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 27 r~~R~~~gltq~ela~~~gis~~~is~i 54 (83)
..+-+.-..|-.|+|+.+|++++++..+
T Consensus 15 ~~Ll~~g~~t~~eia~~~~i~r~~vY~~ 42 (68)
T pfam01978 15 LALLKLGPATADEIAEESGVPRSKVYEV 42 (68)
T ss_pred HHHHHCCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 9999819988999999959889899999
No 426
>pfam07750 GcrA GcrA cell cycle regulator. GcrA is a master cell cycle regulator that, together with CtrA (see pfam00072 and pfam00486), is involved in controlling cell cycle 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=31.55 E-value=38 Score=15.74 Aligned_cols=20 Identities=15% Similarity=0.272 Sum_probs=17.4
Q ss_pred HCCCCHHHHHHHHH-HHHHHH
Q ss_conf 83994999999863-429999
Q gi|254781147|r 32 EAKLTQKEIRNRTG-FAQSWI 51 (83)
Q Consensus 32 ~~gltq~ela~~~g-is~~~i 51 (83)
..|+|..|+|+.+| ||++.|
T Consensus 16 ~eGlSaSqIA~~LGgvTRNAV 36 (162)
T pfam07750 16 LEGLSASQIAAQLGGVSRNAV 36 (162)
T ss_pred HCCCCHHHHHHHHCCCCCCCE
T ss_conf 853659999999765540000
No 427
>pfam06970 RepA_N Replication initiator protein A (RepA) N-terminus. This of family of predicted proteins represents the N-terminus (approximately 80 residues) of replication initiator protein A (RepA), a DNA replication initiator in plasmids. Most proteins in this family are bacterial, but archaeal and eukaryotic members are also included.
Probab=31.38 E-value=35 Score=15.98 Aligned_cols=22 Identities=9% Similarity=0.214 Sum_probs=19.1
Q ss_pred CCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 9499999986342999988755
Q gi|254781147|r 35 LTQKEIRNRTGFAQSWISELET 56 (83)
Q Consensus 35 ltq~ela~~~gis~~~is~iE~ 56 (83)
+|.+|+++.+|+|..++.++-+
T Consensus 53 ft~~el~~~L~~s~~~v~k~~k 74 (76)
T pfam06970 53 FTNEELMELLNCSKQKVIKIKK 74 (76)
T ss_pred EEHHHHHHHHCCCHHHHHHHHH
T ss_conf 6499999997878889999996
No 428
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=31.20 E-value=45 Score=15.32 Aligned_cols=30 Identities=23% Similarity=0.328 Sum_probs=23.9
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 999999998399499999986342999988
Q gi|254781147|r 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISE 53 (83)
Q Consensus 24 ~~ir~~R~~~gltq~ela~~~gis~~~is~ 53 (83)
+.|..++...++...|+|+.+|+++++++.
T Consensus 27 ~Il~lL~~k~plNvneiAe~lgLpqst~s~ 56 (308)
T COG4189 27 AILQLLHRKGPLNVNEIAEALGLPQSTMSA 56 (308)
T ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHH
T ss_conf 999999871798789999885886566665
No 429
>TIGR02051 MerR Hg(II)-responsive transcriptional regulator; InterPro: IPR011794 This entry represents the mercury (II) responsive transcriptional activator of the mer organomercurial resistance operon . This protein is a member of the MerR family of transcriptional activators and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(8)-Cys-Pro, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix .; GO: 0003677 DNA binding, 0045340 mercury ion binding, 0045449 regulation of transcription, 0046689 response to mercury ion.
Probab=31.05 E-value=10 Score=19.13 Aligned_cols=21 Identities=19% Similarity=0.222 Sum_probs=14.1
Q ss_pred HHHHHHCCCCHHHHHHHHHHH
Q ss_conf 999998399499999986342
Q gi|254781147|r 27 RNIRKEAKLTQKEIRNRTGFA 47 (83)
Q Consensus 27 r~~R~~~gltq~ela~~~gis 47 (83)
-+.-++.|+|..|++..+++.
T Consensus 49 IKR~QeLGFsL~EI~~LL~l~ 69 (126)
T TIGR02051 49 IKRAQELGFSLEEIGKLLGLV 69 (126)
T ss_pred HHHHHHCCCCHHHHHHHCCCC
T ss_conf 442000379788999870611
No 430
>PRK12679 cbl transcriptional regulator Cbl; Reviewed
Probab=30.91 E-value=46 Score=15.29 Aligned_cols=29 Identities=24% Similarity=0.206 Sum_probs=21.6
Q ss_pred HHHHHH--HHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 999999--98399499999986342999988
Q gi|254781147|r 25 NFRNIR--KEAKLTQKEIRNRTGFAQSWISE 53 (83)
Q Consensus 25 ~ir~~R--~~~gltq~ela~~~gis~~~is~ 53 (83)
.||.++ -+.|+|..+.|+.+++|++.+|+
T Consensus 5 QLr~f~~va~~~~s~t~AAe~L~iSQPavS~ 35 (316)
T PRK12679 5 QLKIIREAARQDYNLTEVANMLFTSQSGVSR 35 (316)
T ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHH
T ss_conf 9999999998689999999997897789999
No 431
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=30.88 E-value=37 Score=15.85 Aligned_cols=21 Identities=10% Similarity=0.226 Sum_probs=18.8
Q ss_pred CCHHHHHHHHHHHHHHHHHHH
Q ss_conf 949999998634299998875
Q gi|254781147|r 35 LTQKEIRNRTGFAQSWISELE 55 (83)
Q Consensus 35 ltq~ela~~~gis~~~is~iE 55 (83)
.|.+++|+..||+++|+.+|-
T Consensus 26 ~~~~eIae~~~Ip~~~L~KIl 46 (141)
T PRK11014 26 TSISEVTEVYGVSRNHMVKII 46 (141)
T ss_pred ECHHHHHHHHCCCHHHHHHHH
T ss_conf 749999998794999999999
No 432
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=30.70 E-value=46 Score=15.27 Aligned_cols=28 Identities=14% Similarity=0.188 Sum_probs=22.6
Q ss_pred HHCCCCHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf 9839949999998634299998875589
Q gi|254781147|r 31 KEAKLTQKEIRNRTGFAQSWISELETGK 58 (83)
Q Consensus 31 ~~~gltq~ela~~~gis~~~is~iE~G~ 58 (83)
.-.||-..++|++.|||+.+|-.|.+..
T Consensus 16 yl~gmk~~dIAeklGvspntiksWKrr~ 43 (279)
T COG5484 16 YLKGMKLKDIAEKLGVSPNTIKSWKRRD 43 (279)
T ss_pred HHHHCCHHHHHHHHCCCHHHHHHHHHHC
T ss_conf 9843419999999689868888778740
No 433
>pfam07453 NUMOD1 NUMOD1 domain. This domain probably represents a DNA-binding helix-turn-helix based on its similarity to other families (Bateman A pers obs).
Probab=30.26 E-value=28 Score=16.54 Aligned_cols=19 Identities=21% Similarity=0.310 Sum_probs=15.4
Q ss_pred CHHHHHHHHHHHHHHHHHH
Q ss_conf 4999999863429999887
Q gi|254781147|r 36 TQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 36 tq~ela~~~gis~~~is~i 54 (83)
|..++|+.+|++.++|+++
T Consensus 18 Si~~aa~~L~i~~~tI~~~ 36 (37)
T pfam07453 18 SIREAARALGISHSTINKY 36 (37)
T ss_pred HHHHHHHHHCCCHHHHHCC
T ss_conf 7999999847646566502
No 434
>PRK12737 gatY tagatose-bisphosphate aldolase; Reviewed
Probab=30.09 E-value=33 Score=16.15 Aligned_cols=39 Identities=26% Similarity=0.411 Sum_probs=28.8
Q ss_pred HHHHHHHH-----HHHHHHHHHCCCCCCCHHHHHHHHHHHCCCH
Q ss_conf 99998634-----2999988755899944899999999928999
Q gi|254781147|r 39 EIRNRTGF-----AQSWISELETGKSTINIDNMIILAHTLDTPL 77 (83)
Q Consensus 39 ela~~~gi-----s~~~is~iE~G~~~~~~~~l~~la~al~i~~ 77 (83)
++.+++|+ +..+.-....|+..+.++.|.+|.++.++|+
T Consensus 162 ~Fv~~TgvD~LAvaiGt~HG~yk~~p~L~~d~L~~I~~~~~iPL 205 (284)
T PRK12737 162 EFVERTGIDSLAVAIGTAHGLYKGEPKLDFDRLEEIREKVSIPL 205 (284)
T ss_pred HHHHHHCCCEEEECCCCCCCCCCCCCCCCHHHHHHHHHHCCCCE
T ss_conf 99999698987000375356759998578999999998639998
No 435
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=30.00 E-value=44 Score=15.40 Aligned_cols=25 Identities=12% Similarity=0.127 Sum_probs=20.5
Q ss_pred HHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 9839949999998634299998875
Q gi|254781147|r 31 KEAKLTQKEIRNRTGFAQSWISELE 55 (83)
Q Consensus 31 ~~~gltq~ela~~~gis~~~is~iE 55 (83)
...-.|..++|+..|+|+.++.+|-
T Consensus 21 ~~~~~~~~~Ia~~~~is~~~l~kIl 45 (153)
T PRK11920 21 DGKLSRIPEIARAYGVSELFLFKIL 45 (153)
T ss_pred CCCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 9997679999988891999999999
No 436
>KOG0774 consensus
Probab=29.66 E-value=20 Score=17.36 Aligned_cols=36 Identities=17% Similarity=0.201 Sum_probs=26.2
Q ss_pred HHHHHHHHCCCCH------------------------HHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf 9999999839949------------------------99999863429999887558999
Q gi|254781147|r 25 NFRNIRKEAKLTQ------------------------KEIRNRTGFAQSWISELETGKST 60 (83)
Q Consensus 25 ~ir~~R~~~gltq------------------------~ela~~~gis~~~is~iE~G~~~ 60 (83)
.+-+.|+.++++. ++||+.|||+.+.+|+|...++.
T Consensus 185 ~ldarRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrI 244 (334)
T KOG0774 185 FLDARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRI 244 (334)
T ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCEEHHHCCCCCCCEE
T ss_conf 998777651644217999999999733799983789999998729340563232245403
No 437
>COG4753 Response regulator containing CheY-like receiver domain and AraC-type DNA-binding domain [Signal transduction mechanisms]
Probab=29.55 E-value=47 Score=15.24 Aligned_cols=32 Identities=13% Similarity=0.141 Sum_probs=25.2
Q ss_pred HHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf 98399499999986342999988755899944
Q gi|254781147|r 31 KEAKLTQKEIRNRTGFAQSWISELETGKSTIN 62 (83)
Q Consensus 31 ~~~gltq~ela~~~gis~~~is~iE~G~~~~~ 62 (83)
-..++|.+++|...++++.|++++-.....-+
T Consensus 385 ~se~LtL~~la~~f~in~~Ylgqlfk~~~~e~ 416 (475)
T COG4753 385 FSENLTLKDLAKVFHINPVYLGQLFKKETGES 416 (475)
T ss_pred HCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCC
T ss_conf 51788799998773708999999999986141
No 438
>PRK04435 hypothetical protein; Provisional
Probab=29.48 E-value=26 Score=16.73 Aligned_cols=29 Identities=10% Similarity=0.114 Sum_probs=23.4
Q ss_pred HHHHCCCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 99983994999999863429999887558
Q gi|254781147|r 29 IRKEAKLTQKEIRNRTGFAQSWISELETG 57 (83)
Q Consensus 29 ~R~~~gltq~ela~~~gis~~~is~iE~G 57 (83)
+...+..|..|..+++|+|+|++.+|.-+
T Consensus 28 L~~g~~~~i~EAvk~vGISRSafYKYKD~ 56 (146)
T PRK04435 28 LKSGKVKSITEAVKQVGISRSAFYKYKDY 56 (146)
T ss_pred HHCCCCCCHHHHHHHHCCCHHHEECCCCC
T ss_conf 97389774999999839652101123662
No 439
>PRK10870 transcriptional repressor MprA; Provisional
Probab=29.41 E-value=41 Score=15.59 Aligned_cols=24 Identities=8% Similarity=0.208 Sum_probs=18.9
Q ss_pred HHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 983994999999863429999887
Q gi|254781147|r 31 KEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 31 ~~~gltq~ela~~~gis~~~is~i 54 (83)
....++..|+|+.+|+|++++.++
T Consensus 68 ~~~~l~PseLa~~l~~s~a~iTr~ 91 (176)
T PRK10870 68 ENHSIQPSELSCALGSSRTNATRI 91 (176)
T ss_pred CCCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 999859899999977871019999
No 440
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=29.33 E-value=49 Score=15.13 Aligned_cols=20 Identities=20% Similarity=0.129 Sum_probs=10.6
Q ss_pred CCHHHHHHHHHHHHHHHHHH
Q ss_conf 94999999863429999887
Q gi|254781147|r 35 LTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 35 ltq~ela~~~gis~~~is~i 54 (83)
.|..|+|+..+++...|++.
T Consensus 183 rtl~Eia~~~~i~~k~i~r~ 202 (310)
T PRK00423 183 RTLDEIAEVSRVSRKEIGRT 202 (310)
T ss_pred CCHHHHHHHHCCCHHHHHHH
T ss_conf 74999999959889999999
No 441
>TIGR01529 argR_whole arginine repressor; InterPro: IPR001669 The arginine dihydrolase (AD) pathway is found in many prokaryotes and some primitive eukaryotes, an example of the latter being Giardia lamblia . The three-enzyme anaerobic pathway breaks down L-arginine to form 1 mol of ATP, carbon dioxide and ammonia. In simpler bacteria, the first enzyme, arginine deiminase, can account for up to 100f total cell protein . Most prokaryotic arginine deiminase pathways are under the control of a repressor gene, termed ArgR . This is a negative regulator, and will only release the arginine deiminase operon for expression in the presence of arginine . The crystal structure of apo-ArgR from Bacillus stearothermophilus has been determined to 2.5A by means of X-ray crystallography . The protein exists as a hexamer of identical subunits, and is shown to have six DNA-binding domains, clustered around a central oligomeric core when bound to arginine. It predominantly interacts with A.T residues in ARG boxes. This hexameric protein binds DNA at its N terminus to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbour-joining tree, some of these paralogous sequences show long branches and differ significantly from the well-conserved C-terminal region. ; GO: 0003700 transcription factor activity, 0006355 regulation of transcription DNA-dependent.
Probab=29.31 E-value=49 Score=15.13 Aligned_cols=32 Identities=25% Similarity=0.234 Sum_probs=23.4
Q ss_pred HHHHHHHHHCCC-CHHHHHHHH-----H-HHHHHHHHHH
Q ss_conf 999999998399-499999986-----3-4299998875
Q gi|254781147|r 24 NNFRNIRKEAKL-TQKEIRNRT-----G-FAQSWISELE 55 (83)
Q Consensus 24 ~~ir~~R~~~gl-tq~ela~~~-----g-is~~~is~iE 55 (83)
+.||.+=.+.++ ||+|+.+.+ . ++|+++||.=
T Consensus 5 ~~Ik~Ii~~e~~~tQ~El~~~L~~~G~~nvTQaTvSRDL 43 (155)
T TIGR01529 5 EAIKEIITEEKISTQEELVALLKKEGVKNVTQATVSRDL 43 (155)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHHHCCCCEECCCCHHHHH
T ss_conf 999999874376798899999986597511234067878
No 442
>pfam01476 LysM LysM domain. The LysM (lysin motif) domain is about 40 residues long. It is found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function. The structure of this domain is known.
Probab=29.29 E-value=31 Score=16.33 Aligned_cols=23 Identities=26% Similarity=0.258 Sum_probs=13.0
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 39949999998634299998875
Q gi|254781147|r 33 AKLTQKEIRNRTGFAQSWISELE 55 (83)
Q Consensus 33 ~gltq~ela~~~gis~~~is~iE 55 (83)
.|=|...+|++-|++...|.++-
T Consensus 5 ~GDtl~~IA~~~~v~~~~i~~~N 27 (43)
T pfam01476 5 KGDTLSSIAKRYGITVEELAELN 27 (43)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 89879999999896899999985
No 443
>COG4977 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]
Probab=29.28 E-value=49 Score=15.12 Aligned_cols=37 Identities=16% Similarity=0.310 Sum_probs=27.4
Q ss_pred HHHHHHH--HHHHCCCCHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf 9999999--999839949999998634299998875589
Q gi|254781147|r 22 FVNNFRN--IRKEAKLTQKEIRNRTGFAQSWISELETGK 58 (83)
Q Consensus 22 ~g~~ir~--~R~~~gltq~ela~~~gis~~~is~iE~G~ 58 (83)
+.+-|.. ...+.-+|.++||+.+|+|+.++.+.....
T Consensus 222 l~~~i~~me~nle~plsl~~LA~~~~~S~R~leRlF~~~ 260 (328)
T COG4977 222 LLRAIELMEANLEEPLSLEELADRAGLSRRQLERLFRAE 260 (328)
T ss_pred HHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 999999999865388689999999687887899999999
No 444
>pfam02082 Rrf2 Transcriptional regulator. This family is related to pfam001022 and other transcription regulation families (personal obs: Yeats C).
Probab=29.23 E-value=39 Score=15.72 Aligned_cols=23 Identities=17% Similarity=0.400 Sum_probs=20.2
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 99499999986342999988755
Q gi|254781147|r 34 KLTQKEIRNRTGFAQSWISELET 56 (83)
Q Consensus 34 gltq~ela~~~gis~~~is~iE~ 56 (83)
-+|-+++|+..|++.+++.++-+
T Consensus 24 ~~s~~~iA~~~~i~~~~l~kil~ 46 (82)
T pfam02082 24 PVTSEEIAERQNISPVYLRKILA 46 (82)
T ss_pred EECHHHHHHHHCCCHHHHHHHHH
T ss_conf 49599999878909999999999
No 445
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=29.18 E-value=49 Score=15.11 Aligned_cols=50 Identities=22% Similarity=0.264 Sum_probs=31.6
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHH--CCC-CHHHHHHHHHHHHHHHHH
Q ss_conf 96988888868989999999999999999998--399-499999986342999988
Q gi|254781147|r 1 MPRRKRDEPHLSDAILRERMIFVNNFRNIRKE--AKL-TQKEIRNRTGFAQSWISE 53 (83)
Q Consensus 1 Mp~~~~~~p~~~~~~~~~~~~~g~~ir~~R~~--~gl-tq~ela~~~gis~~~is~ 53 (83)
||=++...+.+++.+... +-..|..-+.. ..+ +..+||+..|||++.|..
T Consensus 1 ~~f~~i~~~~l~e~V~~~---L~~~I~~G~l~pGd~LPsE~eLA~~lgVSR~~VRE 53 (254)
T PRK09464 1 MAYSKIRQPKLSDVIEQQ---LEFLILEGTLRPGEKLPPERELAKQFDVSRPSLRE 53 (254)
T ss_pred CCCCCCCCCCHHHHHHHH---HHHHHHCCCCCCCCCCCCHHHHHHHHCCCCHHHHH
T ss_conf 999889998899999999---99999849999939693699999986899559999
No 446
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=29.01 E-value=39 Score=15.71 Aligned_cols=23 Identities=22% Similarity=0.452 Sum_probs=20.2
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 99499999986342999988755
Q gi|254781147|r 34 KLTQKEIRNRTGFAQSWISELET 56 (83)
Q Consensus 34 gltq~ela~~~gis~~~is~iE~ 56 (83)
-++..++|+..|||..|+.+|-+
T Consensus 25 ~vsi~eIAe~~~Is~~~LekIl~ 47 (164)
T PRK10857 25 PVPLADISERQGISLSYLEQLFS 47 (164)
T ss_pred EECHHHHHHHHCCCHHHHHHHHH
T ss_conf 09499999887919999999999
No 447
>TIGR02392 rpoH_proteo alternative sigma factor RpoH; InterPro: IPR012759 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 recognized by the major sigma factors , . This entry represents the proteobacterial clade of sigma factors called RpoH. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0008270 zinc ion binding, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent, 0009408 response to heat.
Probab=28.88 E-value=50 Score=15.08 Aligned_cols=30 Identities=27% Similarity=0.416 Sum_probs=25.0
Q ss_pred HHHHHHC-CCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 9999983-994999999863429999887558
Q gi|254781147|r 27 RNIRKEA-KLTQKEIRNRTGFAQSWISELETG 57 (83)
Q Consensus 27 r~~R~~~-gltq~ela~~~gis~~~is~iE~G 57 (83)
|.+. +. +.|..+||..-|||.==|.+||..
T Consensus 238 RwL~-d~~~~TL~~LA~eygvSaERiRQiE~~ 268 (279)
T TIGR02392 238 RWLD-DDGKLTLHELAAEYGVSAERIRQIEKN 268 (279)
T ss_pred HCCC-CCCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 3027-889964789998848746679999999
No 448
>PRK09940 transcriptional regulator YdeO; Provisional
Probab=28.84 E-value=44 Score=15.36 Aligned_cols=32 Identities=19% Similarity=0.156 Sum_probs=22.2
Q ss_pred HHHHHHHH---HHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 99999999---983994999999863429999887
Q gi|254781147|r 23 VNNFRNIR---KEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 23 g~~ir~~R---~~~gltq~ela~~~gis~~~is~i 54 (83)
+..++.+= ..+.|+..++|+.+.+|.+++-+-
T Consensus 136 s~Kv~~II~sDis~~W~L~dIA~~L~mSEStLkRk 170 (253)
T PRK09940 136 SGKVRNIVNMKLAHPWKLKDICDCLYISESLLKKK 170 (253)
T ss_pred HHHHHHHHHCCCCCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 69899999648300460999998874589999999
No 449
>smart00257 LysM Lysin motif.
Probab=28.74 E-value=27 Score=16.65 Aligned_cols=22 Identities=32% Similarity=0.225 Sum_probs=11.8
Q ss_pred CCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 3994999999863429999887
Q gi|254781147|r 33 AKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 33 ~gltq~ela~~~gis~~~is~i 54 (83)
.|=|...+|.+-|++.+.|.++
T Consensus 6 ~GDTl~~IA~~~~v~~~~l~~~ 27 (44)
T smart00257 6 KGDTLSSIARRYGISVSDLLEL 27 (44)
T ss_pred CCCCHHHHHHHHCCCHHHHHHH
T ss_conf 8988999999989689999987
No 450
>PRK13866 plasmid partitioning protein RepB; Provisional
Probab=28.45 E-value=50 Score=15.04 Aligned_cols=43 Identities=12% Similarity=0.046 Sum_probs=31.3
Q ss_pred HHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHH
Q ss_conf 9983994999999863429999887558999448999999999
Q gi|254781147|r 30 RKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHT 72 (83)
Q Consensus 30 R~~~gltq~ela~~~gis~~~is~iE~G~~~~~~~~l~~la~a 72 (83)
.++.|++...+...++++.+.+|++-.=...+..+.+..|..|
T Consensus 175 l~~~g~~r~~i~~aL~~dk~~lS~m~~v~~~iP~~~i~aIG~A 217 (336)
T PRK13866 175 LEDAGFDRATIIAALSTDKADLSRYITVARGIPLNLATQIGPA 217 (336)
T ss_pred HHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCHHHHHHHCCC
T ss_conf 9976998889999967888899999999997899999974788
No 451
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=28.33 E-value=51 Score=15.02 Aligned_cols=30 Identities=27% Similarity=0.249 Sum_probs=21.2
Q ss_pred HHHHHH--HHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 999999--983994999999863429999887
Q gi|254781147|r 25 NFRNIR--KEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 25 ~ir~~R--~~~gltq~ela~~~gis~~~is~i 54 (83)
.|+... ...|.|-...|+.+++|++++|+-
T Consensus 5 qL~~F~~~v~~~~s~t~AA~~L~iSQpavS~~ 36 (308)
T PRK12683 5 QLRIIREAVRQNFNLTEVANALYTSQSGVSKQ 36 (308)
T ss_pred HHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 99999999986899999999978977799999
No 452
>pfam00126 HTH_1 Bacterial regulatory helix-turn-helix protein, lysR family.
Probab=28.08 E-value=44 Score=15.39 Aligned_cols=19 Identities=21% Similarity=0.268 Sum_probs=16.2
Q ss_pred CHHHHHHHHHHHHHHHHHH
Q ss_conf 4999999863429999887
Q gi|254781147|r 36 TQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 36 tq~ela~~~gis~~~is~i 54 (83)
|....|+.+|+|++++|+.
T Consensus 15 s~~~AA~~l~isqs~vs~~ 33 (60)
T pfam00126 15 SFTAAAERLGLSQPAVSRQ 33 (60)
T ss_pred CHHHHHHHHCCCHHHHHHH
T ss_conf 9999999979898899999
No 453
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=28.07 E-value=49 Score=15.11 Aligned_cols=26 Identities=12% Similarity=0.027 Sum_probs=22.1
Q ss_pred HHCCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 98399499999986342999988755
Q gi|254781147|r 31 KEAKLTQKEIRNRTGFAQSWISELET 56 (83)
Q Consensus 31 ~~~gltq~ela~~~gis~~~is~iE~ 56 (83)
...|.|-.|.|.++|||..++.-.-+
T Consensus 191 ~A~GKTs~EIa~IL~ISe~TV~fHl~ 216 (240)
T PRK10188 191 TAEGKTSAEIAMILSISENTVNFHQK 216 (240)
T ss_pred HHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 97799999999883999999999999
No 454
>TIGR02984 Sig-70_plancto1 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1; InterPro: IPR014326 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 recognized by the major sigma factors , . This group of sigma factors are members of the sigma-70 family (IPR014284 from INTERPRO) and are apparently found only in the Planctomycetaceae family including the genus s Gemmata and Pirellula, in which seven sequences are found.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=28.03 E-value=51 Score=14.99 Aligned_cols=32 Identities=19% Similarity=0.173 Sum_probs=27.3
Q ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 99999999983994999999863429999887
Q gi|254781147|r 23 VNNFRNIRKEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 23 g~~ir~~R~~~gltq~ela~~~gis~~~is~i 54 (83)
-..+-.+|.--|||-.|+|+.+|.+...++..
T Consensus 146 ~REvi~LR~~EGLS~~EvA~~Md~~~~av~~l 177 (190)
T TIGR02984 146 YREVILLRHLEGLSFAEVAERMDRSEGAVSML 177 (190)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHCCCHHHHHHH
T ss_conf 58999998760355589998707975898758
No 455
>COG3284 AcoR Transcriptional activator of acetoin/glycerol metabolism [Secondary metabolites biosynthesis, transport, and catabolism / Transcription]
Probab=27.94 E-value=51 Score=14.98 Aligned_cols=34 Identities=12% Similarity=-0.011 Sum_probs=27.5
Q ss_pred HHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 9999999999983994999999863429999887
Q gi|254781147|r 21 IFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 21 ~~g~~ir~~R~~~gltq~ela~~~gis~~~is~i 54 (83)
.....+...-+..+|...+.|+.+||+++|+.+=
T Consensus 565 ~~~~~l~~al~~~~~~is~aa~~lgi~R~T~yrk 598 (606)
T COG3284 565 IEKAALLAALQATNGNISEAARLLGISRSTLYRK 598 (606)
T ss_pred HHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 5799999999980897999999859978889999
No 456
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=27.83 E-value=43 Score=15.46 Aligned_cols=22 Identities=9% Similarity=0.139 Sum_probs=18.7
Q ss_pred CCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 3994999999863429999887
Q gi|254781147|r 33 AKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 33 ~gltq~ela~~~gis~~~is~i 54 (83)
+=-|..+||..+||++.|+++.
T Consensus 34 kLPSvRelA~~~~VNpnTv~ra 55 (125)
T COG1725 34 KLPSVRELAKDLGVNPNTVQRA 55 (125)
T ss_pred CCCCHHHHHHHHCCCHHHHHHH
T ss_conf 8975999999819898899999
No 457
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=27.69 E-value=52 Score=14.95 Aligned_cols=27 Identities=26% Similarity=0.359 Sum_probs=22.7
Q ss_pred HHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 999983994999999863429999887
Q gi|254781147|r 28 NIRKEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 28 ~~R~~~gltq~ela~~~gis~~~is~i 54 (83)
....+-...|.|.|+.+||+.+.+|.+
T Consensus 19 i~~~qp~v~q~eIA~~lgiT~QaVseh 45 (260)
T COG1497 19 IAVRQPRVKQKEIAKKLGITLQAVSEH 45 (260)
T ss_pred HHHHCCCCCHHHHHHHCCCCHHHHHHH
T ss_conf 997588778889998709879999999
No 458
>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR; InterPro: IPR014075 Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] . FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins , . It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly . The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA . SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA , acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins . Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen . This entry represents members of the SufR cyanobacterial protein family of transcriptional regulators that control the SUF system. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus..
Probab=27.31 E-value=53 Score=14.91 Aligned_cols=30 Identities=7% Similarity=0.093 Sum_probs=25.0
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 999999983994999999863429999887
Q gi|254781147|r 25 NFRNIRKEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 25 ~ir~~R~~~gltq~ela~~~gis~~~is~i 54 (83)
.|..+-++-..|-.+||+.++||++.|.+=
T Consensus 6 IL~~LL~~Gq~sA~~lA~~L~iSpQAvRrH 35 (215)
T TIGR02702 6 ILEYLLKEGQASALALAEELAISPQAVRRH 35 (215)
T ss_pred HHHHHHHHHHHHHHHHHHHHCCCHHHHHHH
T ss_conf 999988600488999999727886788765
No 459
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=27.16 E-value=50 Score=15.04 Aligned_cols=28 Identities=7% Similarity=-0.096 Sum_probs=23.8
Q ss_pred HHHCCCCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 9983994999999863429999887558
Q gi|254781147|r 30 RKEAKLTQKEIRNRTGFAQSWISELETG 57 (83)
Q Consensus 30 R~~~gltq~ela~~~gis~~~is~iE~G 57 (83)
....|+|-.|+|+++++|..||+..-..
T Consensus 145 l~a~G~s~~eIA~~L~~S~kTv~thr~~ 172 (205)
T PRK11475 145 FMSRGYSMPQIAEQLERNIKTIRAHKFN 172 (205)
T ss_pred HHHCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 9976999999999978888899999999
No 460
>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family.
Probab=27.05 E-value=45 Score=15.36 Aligned_cols=21 Identities=29% Similarity=0.477 Sum_probs=8.8
Q ss_pred CCHHHHHHHHHHHHHHHHHHH
Q ss_conf 949999998634299998875
Q gi|254781147|r 35 LTQKEIRNRTGFAQSWISELE 55 (83)
Q Consensus 35 ltq~ela~~~gis~~~is~iE 55 (83)
+|.+++|+.+|||+-=|.+||
T Consensus 308 ~TL~eiG~~l~lSRERVRQiE 328 (336)
T TIGR02997 308 LTLAEIGERLNLSRERVRQIE 328 (336)
T ss_pred CCHHHHHHHHCCCHHHHHHHH
T ss_conf 327899988388368888999
No 461
>COG4294 Uve UV damage repair endonuclease [DNA replication, recombination, and repair]
Probab=26.91 E-value=54 Score=14.87 Aligned_cols=40 Identities=20% Similarity=0.360 Sum_probs=30.9
Q ss_pred HHHHHHH-HHHHHHHHHH--HCCCCCCCHHHHHHHHHHHCCCH
Q ss_conf 9999986-3429999887--55899944899999999928999
Q gi|254781147|r 38 KEIRNRT-GFAQSWISEL--ETGKSTINIDNMIILAHTLDTPL 77 (83)
Q Consensus 38 ~ela~~~-gis~~~is~i--E~G~~~~~~~~l~~la~al~i~~ 77 (83)
+++.+-+ .++.+--+++ ||....-|.+.+..+|+.++||+
T Consensus 191 eqf~kni~~LP~~vksRl~LENDd~sYs~eelL~lCek~~iPl 233 (347)
T COG4294 191 EQFIKNIQRLPDSVKSRLTLENDDKSYSTEELLPLCEKLNIPL 233 (347)
T ss_pred HHHHHHHHHCCHHHHHHHEEECCCCCCCHHHHHHHHHHHCCCE
T ss_conf 9999988633888997653306654366999999988738987
No 462
>PRK06801 hypothetical protein; Provisional
Probab=26.88 E-value=39 Score=15.67 Aligned_cols=40 Identities=18% Similarity=0.335 Sum_probs=29.6
Q ss_pred HHHHHHHHH-----HHHHHHHHHCCCCCCCHHHHHHHHHHHCCCH
Q ss_conf 999998634-----2999988755899944899999999928999
Q gi|254781147|r 38 KEIRNRTGF-----AQSWISELETGKSTINIDNMIILAHTLDTPL 77 (83)
Q Consensus 38 ~ela~~~gi-----s~~~is~iE~G~~~~~~~~l~~la~al~i~~ 77 (83)
+++.+.+|+ +..++-....|...+.++.|.+|.++.++|+
T Consensus 162 ~~Fv~~TgvD~LAvaiGn~HG~yk~~p~L~~~~L~~I~~~~~vPL 206 (286)
T PRK06801 162 RDFVDRTGIDALAVAIGNAHGKYKGEPKLDFARLAAIHQQTGLPL 206 (286)
T ss_pred HHHHHHHCCCEEEEECCCCCCCCCCCCCCCHHHHHHHHHHCCCCE
T ss_conf 999998699899752254556768988679999999998529998
No 463
>pfam06323 Phage_antiter_Q Phage antitermination protein Q. This family consists of several phage antitermination protein Q and related bacterial sequences. Phage 82 gene Q encodes a phage-specific positive regulator of late gene expression, thought, by analogy to the corresponding gene of phage lambda, to be a transcription antiterminator.
Probab=26.49 E-value=44 Score=15.39 Aligned_cols=48 Identities=15% Similarity=0.082 Sum_probs=29.6
Q ss_pred HHHHHHHHHH--CCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHC
Q ss_conf 9999999998--399499999986342999988755899944899999999928
Q gi|254781147|r 23 VNNFRNIRKE--AKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLD 74 (83)
Q Consensus 23 g~~ir~~R~~--~gltq~ela~~~gis~~~is~iE~G~~~~~~~~l~~la~al~ 74 (83)
++.++..... .+++..+||..+||+.++.++.-. +---.|..++..||
T Consensus 154 ~Q~vk~~l~~~~~~Y~~~~LA~L~GV~~~nW~~~Y~----~~W~~m~~~~~~LD 203 (230)
T pfam06323 154 AQDVKHELAGRDQDYEYAELASLVGVSKKNWSETYK----AHWLGMKEIFMHLD 203 (230)
T ss_pred HHHHHHHHCCCCCCCCHHHHHHHHCCCHHHHHHHHH----HHHHHHHHHHHHHH
T ss_conf 999999973886345499999982998656636689----99999999999978
No 464
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=26.34 E-value=55 Score=14.81 Aligned_cols=24 Identities=17% Similarity=0.070 Sum_probs=19.0
Q ss_pred HHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 983994999999863429999887
Q gi|254781147|r 31 KEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 31 ~~~gltq~ela~~~gis~~~is~i 54 (83)
-+.|.|-...|+.+++|++++|+-
T Consensus 13 v~~~~Sft~AA~~L~isQ~avS~~ 36 (309)
T PRK12682 13 VRRNLNLTEAAKALHTSQPGVSKA 36 (309)
T ss_pred HHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 986999999999978987899999
No 465
>PRK09195 gatY tagatose-bisphosphate aldolase; Reviewed
Probab=26.09 E-value=41 Score=15.58 Aligned_cols=32 Identities=13% Similarity=0.206 Sum_probs=25.0
Q ss_pred HHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCH
Q ss_conf 42999988755899944899999999928999
Q gi|254781147|r 46 FAQSWISELETGKSTINIDNMIILAHTLDTPL 77 (83)
Q Consensus 46 is~~~is~iE~G~~~~~~~~l~~la~al~i~~ 77 (83)
++..+.-....|...+.++.|..|.+..++|+
T Consensus 174 vaiGt~HG~yk~~p~L~~~~L~~I~~~~~vPL 205 (284)
T PRK09195 174 VAIGTAHGMYKSAPKLDFDRLENIRQWVNIPL 205 (284)
T ss_pred EEECCCCCCCCCCCCCCHHHHHHHHHHHCCCE
T ss_conf 65065455558988459999999999749998
No 466
>cd04334 ProRS-INS INS is an amino acid-editing domain inserted (INS) into the bacterial class II prolyl-tRNA synthetase (ProRS) however, this CD is not exclusively bacterial. It is also found at the N-terminus of the eukaryotic/archaea-like ProRS's of yeasts and single-celled parasites. ProRS catalyzes the attachment of proline to tRNA(Pro); proline is first activated by ATP, and then transferred to the acceptor end of tRNA(Pro). ProRS can inadvertently process noncognate amino acids such as alanine and cysteine, and to avoid such errors, in post-transfer editing, the INS domain deacylates mischarged Ala-tRNA(Pro), thus ensuring the fidelity of translation. Misacylated Cys-tRNA(Pro) is not edited by ProRS. In addition to the INS editing domain, the prokaryote-like ProRS protein contains catalytic and anticodon-binding domains which form a dimeric interface.
Probab=25.92 E-value=42 Score=15.49 Aligned_cols=24 Identities=25% Similarity=0.189 Sum_probs=18.2
Q ss_pred CCCCHHHHHHHHHHHCCCHHHHCC
Q ss_conf 994489999999992899999608
Q gi|254781147|r 59 STINIDNMIILAHTLDTPLWKLLK 82 (83)
Q Consensus 59 ~~~~~~~l~~la~al~i~~~~l~~ 82 (83)
..|...++..+|+.|+++.+++++
T Consensus 31 ~TP~~~TIe~la~fl~v~~~~~iK 54 (160)
T cd04334 31 ATPGQKTIEELAEFLGVPPSQTVK 54 (160)
T ss_pred CCCCCCCHHHHHHHHCCCHHHHEE
T ss_conf 494986399999987969888443
No 467
>cd00118 LysM Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function.
Probab=25.73 E-value=36 Score=15.93 Aligned_cols=25 Identities=20% Similarity=0.170 Sum_probs=13.8
Q ss_pred HCCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 8399499999986342999988755
Q gi|254781147|r 32 EAKLTQKEIRNRTGFAQSWISELET 56 (83)
Q Consensus 32 ~~gltq~ela~~~gis~~~is~iE~ 56 (83)
+.|=|...+|.+-|++...|.++=+
T Consensus 6 ~~GDTl~~Ia~~~~v~~~~l~~~N~ 30 (46)
T cd00118 6 KKGDTLSSIAQRYGISVEELLKLNG 30 (46)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHCC
T ss_conf 9899999999998967999998669
No 468
>PRK10265 chaperone-modulator protein CbpM; Provisional
Probab=25.52 E-value=57 Score=14.72 Aligned_cols=28 Identities=21% Similarity=0.229 Sum_probs=20.7
Q ss_pred CCCHHHHHHHHHHHHHHHHHH-HCCCCCC
Q ss_conf 994999999863429999887-5589994
Q gi|254781147|r 34 KLTQKEIRNRTGFAQSWISEL-ETGKSTI 61 (83)
Q Consensus 34 gltq~ela~~~gis~~~is~i-E~G~~~~ 61 (83)
-+|..|++..+|++...+-.+ |-|-..|
T Consensus 7 t~Tl~Elc~~~gi~~e~l~e~Ve~Gv~eP 35 (101)
T PRK10265 7 TFTITEFCLHTGVSEEELNEIVGLGVIEP 35 (101)
T ss_pred EEEHHHHHHHHCCCHHHHHHHHHHCCCCC
T ss_conf 97699999771989999999999188566
No 469
>COG0856 Orotate phosphoribosyltransferase homologs [Nucleotide transport and metabolism]
Probab=25.33 E-value=57 Score=14.70 Aligned_cols=24 Identities=25% Similarity=0.221 Sum_probs=21.0
Q ss_pred HHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 983994999999863429999887
Q gi|254781147|r 31 KEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 31 ~~~gltq~ela~~~gis~~~is~i 54 (83)
+.+|||-.|.|.-+++|+-+..-+
T Consensus 15 k~~Glt~gEIAdELNvSreTa~WL 38 (203)
T COG0856 15 KSKGLTTGEIADELNVSRETATWL 38 (203)
T ss_pred HHCCCCHHHHHHHHCCHHHHHHHH
T ss_conf 877985777676641048778888
No 470
>PRK12738 kbaY tagatose-bisphosphate aldolase; Reviewed
Probab=25.13 E-value=45 Score=15.34 Aligned_cols=32 Identities=19% Similarity=0.277 Sum_probs=24.8
Q ss_pred HHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCH
Q ss_conf 42999988755899944899999999928999
Q gi|254781147|r 46 FAQSWISELETGKSTINIDNMIILAHTLDTPL 77 (83)
Q Consensus 46 is~~~is~iE~G~~~~~~~~l~~la~al~i~~ 77 (83)
++..++-....+..++.++.|.+|.++.++|+
T Consensus 174 vaiGn~HG~y~~~p~l~~~~L~~I~~~~~iPL 205 (286)
T PRK12738 174 VAIGTAHGLYSKTPKIDFQRLAEIREVVDVPL 205 (286)
T ss_pred HHHCCCCCCCCCCCCCCHHHHHHHHHCCCCCE
T ss_conf 33235467779999478999999973079998
No 471
>TIGR02329 propionate_PrpR propionate catabolism operon regulatory protein PrpR; InterPro: IPR012704 At least five distinct pathways exist for the catabolism of propionate by way of propionyl-CoA. Members of this family represent the transcriptional regulatory protein PrpR which is, in most cases, divergently transcribed from the operon that encodes the genes involved in the methylcitric acid cycle of propionate catabolism. This protein is required for the expression of the proteins involved in this pathway . 2-methylcitric acid, an intermediate in this pathway, has been proposed to be a co-activator of PrpR .; GO: 0000156 two-component response regulator activity, 0003677 DNA binding, 0005524 ATP binding, 0000160 two-component signal transduction system (phosphorelay), 0019629 propionate catabolic process 2-methylcitrate cycle, 0005737 cytoplasm.
Probab=25.10 E-value=58 Score=14.67 Aligned_cols=47 Identities=6% Similarity=0.000 Sum_probs=36.8
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf 68989999999999999999998399499999986342999988755
Q gi|254781147|r 10 HLSDAILRERMIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELET 56 (83)
Q Consensus 10 ~~~~~~~~~~~~~g~~ir~~R~~~gltq~ela~~~gis~~~is~iE~ 56 (83)
+.++.+.......+..++..-+..+=.....|+.+|||++|+.+.-+
T Consensus 611 T~a~~~~~rs~v~a~~~~~aL~~~~G~~~a~a~~LGiSrTTLWRrL~ 657 (658)
T TIGR02329 611 TSADSLRERSRVEALAVRAALERFQGDRAAAAKALGISRTTLWRRLK 657 (658)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHCCCHHHHHHHCCCCHHHHHHHHC
T ss_conf 77477734204335768999987278968998542764245777613
No 472
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=24.92 E-value=59 Score=14.65 Aligned_cols=44 Identities=20% Similarity=0.358 Sum_probs=29.2
Q ss_pred CCCHHHHHHHHHHHHHHHHHHH------------CC-------CCCCCHHHHHHHHHHHCCCH
Q ss_conf 9949999998634299998875------------58-------99944899999999928999
Q gi|254781147|r 34 KLTQKEIRNRTGFAQSWISELE------------TG-------KSTINIDNMIILAHTLDTPL 77 (83)
Q Consensus 34 gltq~ela~~~gis~~~is~iE------------~G-------~~~~~~~~l~~la~al~i~~ 77 (83)
-.|-+++|+..|+|++|+.+|- +| .+.|.--++.-+-++++-++
T Consensus 25 ~~s~~~IA~~~~is~~~L~kil~~L~kaGlV~S~rG~~GGy~Lar~~~~Isl~dVv~ave~~~ 87 (150)
T COG1959 25 PVSSAEIAERQGISPSYLEKILSKLRKAGLVKSVRGKGGGYRLARPPEEITLGDVVRALEGPL 87 (150)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCCCCCEECCCCHHHCCHHHHHHHHCCCC
T ss_conf 464999999989199999999999987798785207998920238979790999999976866
No 473
>PRK11052 malQ 4-alpha-glucanotransferase; Provisional
Probab=24.92 E-value=14 Score=18.30 Aligned_cols=16 Identities=13% Similarity=0.081 Sum_probs=6.4
Q ss_pred CCHHHHHHHHHHHCCC
Q ss_conf 4489999999992899
Q gi|254781147|r 61 INIDNMIILAHTLDTP 76 (83)
Q Consensus 61 ~~~~~l~~la~al~i~ 76 (83)
++-+++..+..+||++
T Consensus 29 vs~~tl~avL~aLG~~ 44 (694)
T PRK11052 29 ISAETKRRLLAAMGYR 44 (694)
T ss_pred CCHHHHHHHHHHCCCC
T ss_conf 8999999999965999
No 474
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=24.85 E-value=59 Score=14.64 Aligned_cols=29 Identities=14% Similarity=0.053 Sum_probs=25.1
Q ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 99999983994999999863429999887
Q gi|254781147|r 26 FRNIRKEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 26 ir~~R~~~gltq~ela~~~gis~~~is~i 54 (83)
+-.+|.-.|++-+|+|+.+|+|..++...
T Consensus 119 v~vLrdv~g~s~~EIA~iLg~s~~avR~~ 147 (289)
T PRK09636 119 AFLLHDVFGVPFDEIASTLGRSEAACRQL 147 (289)
T ss_pred HHHHHHHHCCCHHHHHHHHCCCHHHHHHH
T ss_conf 54049860999999999981799999999
No 475
>PRK10026 arsenate reductase; Provisional
Probab=24.67 E-value=59 Score=14.62 Aligned_cols=40 Identities=15% Similarity=0.326 Sum_probs=25.8
Q ss_pred HHHHHHHHHHHHH-CC---------CCCCCHHHHHHHHHHHCCCHHHHCC
Q ss_conf 8634299998875-58---------9994489999999992899999608
Q gi|254781147|r 43 RTGFAQSWISELE-TG---------KSTINIDNMIILAHTLDTPLWKLLK 82 (83)
Q Consensus 43 ~~gis~~~is~iE-~G---------~~~~~~~~l~~la~al~i~~~~l~~ 82 (83)
+|+-|+.++.-++ +| +..|+.+.|..++..+++++.+|+.
T Consensus 11 rCSKSR~aL~lL~e~g~e~~vv~YLk~p~s~~eL~~l~~~Lg~~~~~liR 60 (141)
T PRK10026 11 ACGTSRNTLEMIRNSGTEPTIIYYLETPPTRDELVKLIADMGISVRALLR 60 (141)
T ss_pred CCHHHHHHHHHHHHCCCCCEEEHHHCCCCCHHHHHHHHHHCCCCHHHHHH
T ss_conf 97889999999998699958715621799999999999985999999987
No 476
>PRK06806 fructose-bisphosphate aldolase; Provisional
Probab=24.65 E-value=43 Score=15.47 Aligned_cols=39 Identities=15% Similarity=0.297 Sum_probs=27.6
Q ss_pred HHHHHHHH-----HHHHHHHHHCCCCCCCHHHHHHHHHHHCCCH
Q ss_conf 99998634-----2999988755899944899999999928999
Q gi|254781147|r 39 EIRNRTGF-----AQSWISELETGKSTINIDNMIILAHTLDTPL 77 (83)
Q Consensus 39 ela~~~gi-----s~~~is~iE~G~~~~~~~~l~~la~al~i~~ 77 (83)
++.+.+|+ +..+.-....|...+.++.|..|.+++++|+
T Consensus 160 ~Fv~~TgvD~LAvaiGt~HG~yk~~p~L~~d~L~~I~~~~~iPL 203 (281)
T PRK06806 160 RFAEETDVDALAVAIGNAHGMYNGDPNLRLDRLQEINDNVHIPL 203 (281)
T ss_pred HHHHHHCCCEEEEECCCCCCCCCCCCCCCHHHHHHHHHHCCCCE
T ss_conf 99998599899874375545658998669999999997289998
No 477
>COG4695 Phage-related protein [Function unknown]
Probab=24.65 E-value=59 Score=14.62 Aligned_cols=44 Identities=11% Similarity=0.124 Sum_probs=36.5
Q ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf 99999999999998399499999986342999988755899944
Q gi|254781147|r 19 RMIFVNNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKSTIN 62 (83)
Q Consensus 19 ~~~~g~~ir~~R~~~gltq~ela~~~gis~~~is~iE~G~~~~~ 62 (83)
...++.+.-.+-+.+++|-.|.|...||+.++|..++.-...-.
T Consensus 262 ~l~~s~~~a~~les~~~~~~~iA~~fgVp~~~i~~~~~~t~s~~ 305 (398)
T COG4695 262 QLSISPCDADLLESRKFTRRDIALAFGVPPSLLGDPGDQTYSNY 305 (398)
T ss_pred HHHCCHHHHHHHHHHHHHHHHHHHHHCCCHHHCCCCCCCCCCCH
T ss_conf 75048878999875132599999983988877278665420148
No 478
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=24.61 E-value=59 Score=14.61 Aligned_cols=24 Identities=13% Similarity=0.012 Sum_probs=18.9
Q ss_pred HHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 983994999999863429999887
Q gi|254781147|r 31 KEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 31 ~~~gltq~ela~~~gis~~~is~i 54 (83)
-+.|.|-...|+.+++|++++|+-
T Consensus 13 a~~~~sft~AA~~L~iSQpavS~~ 36 (313)
T PRK12684 13 VRQNFNLTEAAKALYTSQPGVSKA 36 (313)
T ss_pred HHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 986999999999978977899999
No 479
>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.43 E-value=60 Score=14.59 Aligned_cols=26 Identities=15% Similarity=0.153 Sum_probs=21.7
Q ss_pred HHHHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 99998399499999986342999988
Q gi|254781147|r 28 NIRKEAKLTQKEIRNRTGFAQSWISE 53 (83)
Q Consensus 28 ~~R~~~gltq~ela~~~gis~~~is~ 53 (83)
.+=-...+|..|.|+.-+||++.|..
T Consensus 27 ~lyy~dDlSl~EIAee~~VSRqAIyD 52 (105)
T COG2739 27 ELYYLDDLSLSEIAEEFNVSRQAIYD 52 (105)
T ss_pred HHHHHHHCCHHHHHHHHCCCHHHHHH
T ss_conf 99998116699999995750999999
No 480
>PRK07452 DNA polymerase III subunit delta; Validated
Probab=24.30 E-value=60 Score=14.58 Aligned_cols=53 Identities=17% Similarity=0.198 Sum_probs=29.6
Q ss_pred HHHHHHHH-----HHHHHCCC-CHHHHHHHHHHH-HHHHHHHHCCCCCCCHHHHHHHHHH
Q ss_conf 99999999-----99998399-499999986342-9999887558999448999999999
Q gi|254781147|r 20 MIFVNNFR-----NIRKEAKL-TQKEIRNRTGFA-QSWISELETGKSTINIDNMIILAHT 72 (83)
Q Consensus 20 ~~~g~~ir-----~~R~~~gl-tq~ela~~~gis-~~~is~iE~G~~~~~~~~l~~la~a 72 (83)
..+..++| +...+.|. +++++|+.+|++ +-.+-.+.+..++.+.+.|.++...
T Consensus 237 a~l~~q~r~ll~vk~l~~~G~~~~~~ia~~lgi~~P~r~~~~~~~~~~~s~~~L~~~l~~ 296 (326)
T PRK07452 237 ATLTGQFRTWLWVKLLVESGERDVKVIAKAAGIGNPKRIYFLRKEVQGLSSQQLLKLLPL 296 (326)
T ss_pred HHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCHHHHHHHHHHHCCCHHHHHHHHHH
T ss_conf 999999999999999997489779999998289982789999999867999999999999
No 481
>TIGR02044 CueR Cu(I)-responsive transcriptional regulator; InterPro: IPR011789 This entry represents the copper-, silver- and gold- (I) responsive transcriptional activator of the gamma proteobacterial copper efflux system . This protein is a member of the MerR family of transcriptional activators and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X7-Cys. This family also lacks a conserved cysteine at the N-terminal end of the dimerization helix which is required for the binding of divalent metals such as zinc; here it is replaced by a serine residue .; GO: 0003677 DNA binding, 0005507 copper ion binding, 0016563 transcription activator activity, 0045941 positive regulation of transcription.
Probab=24.12 E-value=61 Score=14.56 Aligned_cols=45 Identities=16% Similarity=0.144 Sum_probs=25.3
Q ss_pred CCHHHHHHHHHHHHHHHHHHHCC-CCC----------------CCHHHHHHHHHHHCCCHHH
Q ss_conf 94999999863429999887558-999----------------4489999999992899999
Q gi|254781147|r 35 LTQKEIRNRTGFAQSWISELETG-KST----------------INIDNMIILAHTLDTPLWK 79 (83)
Q Consensus 35 ltq~ela~~~gis~~~is~iE~G-~~~----------------~~~~~l~~la~al~i~~~~ 79 (83)
|...++|+.+|+|--.|.-||.- -.. +..-+|..=|+.+|=+++|
T Consensus 1 mNIg~~AK~tglssK~IR~YE~kGLi~Pp~Rse~GYR~Y~~~h~~~L~li~raR~~GFSLeE 62 (127)
T TIGR02044 1 MNIGQVAKLTGLSSKSIRYYEEKGLIPPPLRSEGGYRTYTDKHVDELRLISRARSVGFSLEE 62 (127)
T ss_pred CCHHHHHCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCHHH
T ss_conf 97677750147726889887763267998868888856387678888999999871898899
No 482
>PRK13500 transcriptional activator RhaR; Provisional
Probab=24.05 E-value=61 Score=14.55 Aligned_cols=43 Identities=2% Similarity=0.115 Sum_probs=30.0
Q ss_pred HHHHHHHHHH--HCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHH
Q ss_conf 9999999999--839949999998634299998875589994489
Q gi|254781147|r 22 FVNNFRNIRK--EAKLTQKEIRNRTGFAQSWISELETGKSTINID 64 (83)
Q Consensus 22 ~g~~ir~~R~--~~gltq~ela~~~gis~~~is~iE~G~~~~~~~ 64 (83)
+.+-|.++.. ..-++.+++|+..|+|..+++++-+.....|..
T Consensus 208 L~~ll~~l~~~~~ep~~l~~lA~~~~lS~r~L~R~Fk~~tG~Tp~ 252 (312)
T PRK13500 208 LDKLITRLAASLKSPFALDKFCDEASCSERVLRQQFRQQTGMTIN 252 (312)
T ss_pred HHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHCCCHH
T ss_conf 999999999874499989999989788999999999999891999
No 483
>PRK09685 DNA-binding transcriptional activator FeaR; Provisional
Probab=24.05 E-value=61 Score=14.55 Aligned_cols=50 Identities=14% Similarity=0.066 Sum_probs=33.1
Q ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCC-CC----CHHHHHHHHHHH
Q ss_conf 999999998399499999986342999988755899-94----489999999992
Q gi|254781147|r 24 NNFRNIRKEAKLTQKEIRNRTGFAQSWISELETGKS-TI----NIDNMIILAHTL 73 (83)
Q Consensus 24 ~~ir~~R~~~gltq~ela~~~gis~~~is~iE~G~~-~~----~~~~l~~la~al 73 (83)
..|..--..-.+|.+.+|+..|||.+|+.++..+.. .+ .-..|....+.|
T Consensus 205 ~~I~~nL~dp~Ls~~~iA~~~giS~R~L~rlF~~~G~t~~~~I~~~RL~~a~~~L 259 (303)
T PRK09685 205 ALIDQSIQEEILRPEWIAGELGISVRSLYRLFAEQGLVVAQYIRNRRLDRCADDL 259 (303)
T ss_pred HHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHH
T ss_conf 9999863899989999999979999999999998599899999999999999960
No 484
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=23.97 E-value=61 Score=14.54 Aligned_cols=28 Identities=11% Similarity=0.135 Sum_probs=23.7
Q ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 9999998399499999986342999988
Q gi|254781147|r 26 FRNIRKEAKLTQKEIRNRTGFAQSWISE 53 (83)
Q Consensus 26 ir~~R~~~gltq~ela~~~gis~~~is~ 53 (83)
+-.+|.-.||+-+|+|+.+|+|...+..
T Consensus 164 vlvLRdV~g~s~~EiAe~Lg~S~aAVks 191 (341)
T PRK08241 164 VLLLRDVLGWSAAEVAEALGTSTAAVNS 191 (341)
T ss_pred EEEHHHHCCCCHHHHHHHHCCCHHHHHH
T ss_conf 0012975299889999997899999999
No 485
>smart00497 IENR1 Intron encoded nuclease repeat motif. Repeat of unknown function, but possibly DNA-binding via helix-turn-helix motif (Ponting, unpublished).
Probab=23.89 E-value=44 Score=15.40 Aligned_cols=23 Identities=22% Similarity=0.203 Sum_probs=19.9
Q ss_pred CHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf 49999998634299998875589
Q gi|254781147|r 36 TQKEIRNRTGFAQSWISELETGK 58 (83)
Q Consensus 36 tq~ela~~~gis~~~is~iE~G~ 58 (83)
|..|.|+.+|++.++|+++-++.
T Consensus 19 Si~~aak~l~~~~~~I~~~l~~~ 41 (53)
T smart00497 19 SIREAAKYLGISHSSISKYLNTG 41 (53)
T ss_pred HHHHHHHHHCCCCCCHHHHHCCC
T ss_conf 79999998588832388870677
No 486
>TIGR03020 EpsA transcriptional regulator EpsA. Proteins in this family include a C-terminal LuxR transcriptional regulator domain (pfam00196). These proteins are positioned proximal to either EpsH-containing exopolysaccharide biosynthesis operons of the Methylobacillus type, or the associated PEP-CTERM-containing genes.
Probab=23.77 E-value=62 Score=14.52 Aligned_cols=25 Identities=16% Similarity=0.073 Sum_probs=21.8
Q ss_pred HHCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 9839949999998634299998875
Q gi|254781147|r 31 KEAKLTQKEIRNRTGFAQSWISELE 55 (83)
Q Consensus 31 ~~~gltq~ela~~~gis~~~is~iE 55 (83)
...|+|-+|+|..+|||..|+-..-
T Consensus 202 va~G~sn~eIA~~L~iS~~TVk~H~ 226 (247)
T TIGR03020 202 VRDGKTNEEIAAILGISSLTVKNHL 226 (247)
T ss_pred HHCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf 9879999999999497999999999
No 487
>PRK13870 transcriptional regulator TraR; Provisional
Probab=22.81 E-value=64 Score=14.40 Aligned_cols=24 Identities=17% Similarity=0.149 Sum_probs=21.2
Q ss_pred HHCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf 983994999999863429999887
Q gi|254781147|r 31 KEAKLTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 31 ~~~gltq~ela~~~gis~~~is~i 54 (83)
...|.|-.|.|..+|||..++.-.
T Consensus 185 ~A~GKT~~EIA~ILgISe~TV~fH 208 (234)
T PRK13870 185 IAVGMTMEEIADVEGVKYNSVRVK 208 (234)
T ss_pred HHCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 978998999999979889999999
No 488
>TIGR02111 PQQ_syn_pqqC coenzyme PQQ biosynthesis protein C; InterPro: IPR011845 This entry describes the coenzyme PQQ (pyrrolo-quinoline-quinone) biosynthesis protein PqqC. Pyrroloquinoline quinone (PQQ) is the prosthetic group of several bacterial enzymes, including methanol dehydrogenase of methylotrophs and the glucose dehydrogenase of a number of bacteria . PQQC has been found to be required in the synthesis of PQQ but its function is unclear. This entry does not include related proteins likely to be functionally distinct from PqqC, such as homologs found in the Chlamydias.; GO: 0018189 pyrroloquinoline quinone biosynthetic process.
Probab=22.74 E-value=41 Score=15.58 Aligned_cols=59 Identities=8% Similarity=0.034 Sum_probs=34.1
Q ss_pred HHHHHHHHHHHCCCCHHHHHHHHHH-----HHHHHHHHHCCC----CCCCHHHHHHHHHHHCCCHHHH
Q ss_conf 9999999999839949999998634-----299998875589----9944899999999928999996
Q gi|254781147|r 22 FVNNFRNIRKEAKLTQKEIRNRTGF-----AQSWISELETGK----STINIDNMIILAHTLDTPLWKL 80 (83)
Q Consensus 22 ~g~~ir~~R~~~gltq~ela~~~gi-----s~~~is~iE~G~----~~~~~~~l~~la~al~i~~~~l 80 (83)
-|.-+-+.-.+..+=.+|-|-.+.+ -+.++++|+-.. ..=.++.=.+|++++|.+.+.+
T Consensus 39 ~AWv~NRyyYQ~~IP~KDAA~Lar~~D~~~Rr~W~qRi~DhDG~~~~dGGi~rWLrLaeAvGL~r~~v 106 (239)
T TIGR02111 39 QAWVLNRYYYQVNIPLKDAAILARCPDPELRRIWRQRILDHDGEVEEDGGIERWLRLAEAVGLDREYV 106 (239)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHCCCCCHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHCCCCCHHHH
T ss_conf 99998778873258456799860699888899998744204867888742899998763168877874
No 489
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=22.58 E-value=65 Score=14.38 Aligned_cols=44 Identities=11% Similarity=0.093 Sum_probs=29.4
Q ss_pred HHCCCCHHHHHHHHHHHHHHHHHHHC----CCCCCCHHHHHHHHHHHC
Q ss_conf 98399499999986342999988755----899944899999999928
Q gi|254781147|r 31 KEAKLTQKEIRNRTGFAQSWISELET----GKSTINIDNMIILAHTLD 74 (83)
Q Consensus 31 ~~~gltq~ela~~~gis~~~is~iE~----G~~~~~~~~l~~la~al~ 74 (83)
...|+|-+|.|+.+++|..|+..+-. .-.--+...+..+|--.|
T Consensus 153 l~~G~snkeIA~~L~iS~~TV~~h~~~I~~KL~v~~~~elv~~A~~~G 200 (202)
T PRK09390 153 LVAGLSNKVIARDLDISPRTVEVYRANVMTKMQAGSLSELVRMALRAG 200 (202)
T ss_pred HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCC
T ss_conf 983896899999979878899999999999968898899999999859
No 490
>pfam04492 Phage_rep_O Bacteriophage replication protein O. Replication protein O is necessary for the initiation of bacteriophage DNA replication. Protein O interacts with the lambda replication origin, and also with replication protein P to form an oligomer. It is speculated that the N-terminal half interacts with the replication origin while the C terminal half mediates protein-protein interaction.
Probab=22.52 E-value=38 Score=15.80 Aligned_cols=30 Identities=30% Similarity=0.457 Sum_probs=21.4
Q ss_pred HHHHHHHCC-------CCHHHHHHHHHHHHHHHHHHH
Q ss_conf 999999839-------949999998634299998875
Q gi|254781147|r 26 FRNIRKEAK-------LTQKEIRNRTGFAQSWISELE 55 (83)
Q Consensus 26 ir~~R~~~g-------ltq~ela~~~gis~~~is~iE 55 (83)
+-.+|+--| +|-.++++.+|+++..+|+--
T Consensus 39 ~aV~RkTyG~nK~~d~I~~sqi~~mtgi~~~~Vs~a~ 75 (100)
T pfam04492 39 LAVIRKTYGWNKPMDRVTNEQIAELTGLSRTHVSEAK 75 (100)
T ss_pred HHHHHHHCCCCCCHHHHHHHHHHHHHCCCHHHHHHHH
T ss_conf 9999986077850336229999999788854599999
No 491
>pfam03932 CutC CutC family. Copper transport in Escherichia coli is mediated by the products of at least six genes, cutA, cutB, cutC, cutD, cutE, and cutF. A mutation in one or more of these genes results in an increased copper sensitivity. Members of this family are between 200 and 300 amino acids in length are found in both eukaryotes and bacteria.
Probab=22.16 E-value=28 Score=16.56 Aligned_cols=45 Identities=16% Similarity=0.242 Sum_probs=28.6
Q ss_pred HHHHHHHHHHHHH-HHHHCCCCCCCHHHHHHHHHHHCCCHHHHCCC
Q ss_conf 9999863429999-88755899944899999999928999996088
Q gi|254781147|r 39 EIRNRTGFAQSWI-SELETGKSTINIDNMIILAHTLDTPLWKLLKP 83 (83)
Q Consensus 39 ela~~~gis~~~i-s~iE~G~~~~~~~~l~~la~al~i~~~~l~~P 83 (83)
..|+..|.++=-+ +.++-|-..|+...+..+++..++|+.-+..|
T Consensus 14 ~~A~~~GAdRIELCs~L~~GGlTPs~~~i~~~~~~~~ipv~vMIRP 59 (202)
T pfam03932 14 LAAQAGGADRVELCANLAVGGLTPSYGVIKSAAQRAKIPVYVMIRP 59 (202)
T ss_pred HHHHHCCCCEEEECCCCCCCCCCCCHHHHHHHHHHCCCCEEEEEEC
T ss_conf 9999849999986267666897989999999998659974999842
No 492
>PRK13756 tetracycline repressor protein TetR; Provisional
Probab=22.11 E-value=52 Score=14.97 Aligned_cols=41 Identities=12% Similarity=0.200 Sum_probs=28.4
Q ss_pred HHHHHHHHHHHHC--CCCHHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf 9999999999983--9949999998634299998875589994
Q gi|254781147|r 21 IFVNNFRNIRKEA--KLTQKEIRNRTGFAQSWISELETGKSTI 61 (83)
Q Consensus 21 ~~g~~ir~~R~~~--gltq~ela~~~gis~~~is~iE~G~~~~ 61 (83)
++..-++-+..+- ++|...||+.+|++..++..+-.+|...
T Consensus 9 Iv~aAl~Lld~~Gl~alSMRrLA~~LgV~~~sLY~Hv~nK~~L 51 (205)
T PRK13756 9 VINSALELLNEVGIEGLTTRKLAQKLGVEQPTLYWHVKNKRAL 51 (205)
T ss_pred HHHHHHHHHHHCCCCCCCHHHHHHHHCCCCHHHHHHCCCHHHH
T ss_conf 9999999998238000669999999489931789873889999
No 493
>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein; InterPro: IPR010163 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=21.87 E-value=67 Score=14.29 Aligned_cols=31 Identities=23% Similarity=0.235 Sum_probs=25.2
Q ss_pred HHHHHHHHHCC-CCHHHHHHHHHHHHHHHHHH
Q ss_conf 99999999839-94999999863429999887
Q gi|254781147|r 24 NNFRNIRKEAK-LTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 24 ~~ir~~R~~~g-ltq~ela~~~gis~~~is~i 54 (83)
+-|..+-...| .+...+|+.+|.|.+++++.
T Consensus 173 ~vL~~L~~~~Ge~~v~~iA~~lg~s~~T~~~~ 204 (231)
T TIGR01884 173 KVLEALKAEKGEKSVKNIAKKLGKSLSTISRH 204 (231)
T ss_pred HHHHHHHCCCCEECHHHHHHHHCCCHHHHHHH
T ss_conf 99999850788052877998857888799999
No 494
>PRK08610 fructose-bisphosphate aldolase; Reviewed
Probab=21.79 E-value=57 Score=14.71 Aligned_cols=39 Identities=21% Similarity=0.326 Sum_probs=28.0
Q ss_pred HHHHHHHH-----HHHHHHHHHCCCCCCCHHHHHHHHHHHCCCH
Q ss_conf 99998634-----2999988755899944899999999928999
Q gi|254781147|r 39 EIRNRTGF-----AQSWISELETGKSTINIDNMIILAHTLDTPL 77 (83)
Q Consensus 39 ela~~~gi-----s~~~is~iE~G~~~~~~~~l~~la~al~i~~ 77 (83)
++.+.+|+ +..+.-....|...+.++.|.+|.+..++|+
T Consensus 163 ~Fv~~TgvD~LAvaiGt~HG~yk~~p~l~~~~L~~I~~~~~vPL 206 (286)
T PRK08610 163 ELVEKTGIDALAPALGSVHGPYKGEPKLGFKEMEEIGLSTGLPL 206 (286)
T ss_pred HHHHHHCCCEEEEECCCCCCCCCCCCCCCHHHHHHHHHHCCCCE
T ss_conf 99997398667311155446558998778999999985249997
No 495
>PRK05417 glutathione-dependent formaldehyde-activating enzyme; Provisional
Probab=21.45 E-value=69 Score=14.24 Aligned_cols=50 Identities=16% Similarity=0.222 Sum_probs=38.8
Q ss_pred HHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHCCC
Q ss_conf 99998399499999986342999988755899944899999999928999996088
Q gi|254781147|r 28 NIRKEAKLTQKEIRNRTGFAQSWISELETGKSTINIDNMIILAHTLDTPLWKLLKP 83 (83)
Q Consensus 28 ~~R~~~gltq~ela~~~gis~~~is~iE~G~~~~~~~~l~~la~al~i~~~~l~~P 83 (83)
.+-.+.||+.-++|..+ -|-||.|...-.++.+..=.+.+|.+.++.+.|
T Consensus 123 ELs~~~GW~~P~FAaFV------SSIIE~G~~P~~M~~vR~rl~~lGLepYDcLSP 172 (191)
T PRK05417 123 ELSQEQGWSAPGFAAFV------SSIIESGTDPEQMDGIRARLKELGLEPYDCLSP 172 (191)
T ss_pred HHCCCCCCCCCCHHHHH------HHHHHCCCCHHHHHHHHHHHHHCCCCCCCCCCH
T ss_conf 00233588873088899------999866998678489999999849985244798
No 496
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=21.31 E-value=69 Score=14.22 Aligned_cols=34 Identities=15% Similarity=0.283 Sum_probs=24.2
Q ss_pred HHHHHHHHHHHHCC-CCHHHHHHHHHHHHHHHHHH
Q ss_conf 99999999999839-94999999863429999887
Q gi|254781147|r 21 IFVNNFRNIRKEAK-LTQKEIRNRTGFAQSWISEL 54 (83)
Q Consensus 21 ~~g~~ir~~R~~~g-ltq~ela~~~gis~~~is~i 54 (83)
.....|..+-...| ....++|+.++|++++++.+
T Consensus 10 dYL~~Iy~l~~~~~~~~~~diA~~L~Vsp~sVt~m 44 (154)
T COG1321 10 DYLETIYELLEEKGFARTKDIAERLKVSPPSVTEM 44 (154)
T ss_pred HHHHHHHHHHHCCCCCCHHHHHHHHCCCCHHHHHH
T ss_conf 99999999984368751999999858992789999
No 497
>PRK12857 putative aldolase; Reviewed
Probab=21.05 E-value=60 Score=14.60 Aligned_cols=38 Identities=18% Similarity=0.289 Sum_probs=26.1
Q ss_pred HHHHHHH-----HHHHHHHHHCCCCCCCHHHHHHHHHHHCCCH
Q ss_conf 9998634-----2999988755899944899999999928999
Q gi|254781147|r 40 IRNRTGF-----AQSWISELETGKSTINIDNMIILAHTLDTPL 77 (83)
Q Consensus 40 la~~~gi-----s~~~is~iE~G~~~~~~~~l~~la~al~i~~ 77 (83)
+.+.+|+ +..+.-....|...+.++.|.+|.++.++|+
T Consensus 163 Fv~~TgvD~LAvaiGn~HG~yk~~p~L~~~~L~~I~~~~~vPL 205 (284)
T PRK12857 163 FVEETGVDALAIAIGTAHGPYKGVPKLDFDRLAKIRELVNIPL 205 (284)
T ss_pred HHHHHCCCEEEHHHCCCCCCCCCCCCCCHHHHHHHHHHCCCCE
T ss_conf 9998797877012056667768988569999999986169998
No 498
>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD; InterPro: IPR012760 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 recognized by the major sigma factors , . This entry represents the C-terminal region of sigma 70 (RpoD) which contains the well-conserved regions 2, 3 and 4. Region 2 of sigma-70 is the most conserved region of the entire protein. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core-binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime , . The aromatic residues of the recognition helix, found at the C terminus of this domain are thought to mediate strand separation, thereby allowing transcription initiation , . Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme .Region 4 is involved in binding to the -35 promoter element via a helix-turn-helix motif .; GO: 0003677 DNA binding, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=21.05 E-value=49 Score=15.11 Aligned_cols=22 Identities=23% Similarity=0.389 Sum_probs=11.5
Q ss_pred CHHHHHHHHHHHHHHHHHHHCC
Q ss_conf 4999999863429999887558
Q gi|254781147|r 36 TQKEIRNRTGFAQSWISELETG 57 (83)
Q Consensus 36 tq~ela~~~gis~~~is~iE~G 57 (83)
|.+++|+.+|++..-|..|..-
T Consensus 105 t~EelAe~~g~~~~Kv~~i~~~ 126 (240)
T TIGR02393 105 TDEELAERMGLPVEKVREIKKI 126 (240)
T ss_pred CHHHHHHHHCCCHHHHHHHHHH
T ss_conf 8778998708998999999986
No 499
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=20.79 E-value=68 Score=14.27 Aligned_cols=17 Identities=12% Similarity=0.122 Sum_probs=6.7
Q ss_pred CCHHHHHHHHHHHHHHH
Q ss_conf 94999999863429999
Q gi|254781147|r 35 LTQKEIRNRTGFAQSWI 51 (83)
Q Consensus 35 ltq~ela~~~gis~~~i 51 (83)
++..+||+..|||++-|
T Consensus 31 L~e~~Lae~lgVSRtPV 47 (224)
T PRK11534 31 LRMSLLTSRYALGVGPL 47 (224)
T ss_pred CCHHHHHHHHCCCHHHH
T ss_conf 58999999979885899
No 500
>PRK10783 mltD membrane-bound lytic murein transglycosylase D; Provisional
Probab=20.78 E-value=71 Score=14.15 Aligned_cols=53 Identities=11% Similarity=0.121 Sum_probs=41.3
Q ss_pred HHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCC------------------------------CCHHHHHHHHHHHCCCHH
Q ss_conf 99983994999999863429999887558999------------------------------448999999999289999
Q gi|254781147|r 29 IRKEAKLTQKEIRNRTGFAQSWISELETGKST------------------------------INIDNMIILAHTLDTPLW 78 (83)
Q Consensus 29 ~R~~~gltq~ela~~~gis~~~is~iE~G~~~------------------------------~~~~~l~~la~al~i~~~ 78 (83)
.+.+.|=|...+|++.|+|.+.|.++.+-..+ =+=++|..||+-|+|++.
T Consensus 346 y~Vr~GDtL~~IA~ky~vsv~~L~~~N~L~~~~L~~Gq~L~Ip~~~~~~~~~~~~~~~~Y~Vk~GDTL~~IArry~Vsv~ 425 (449)
T PRK10783 346 YKVRSGDTLSGIASRLGVSTKDLQQWNNLRGSTLKVGQSLTIGAGSSAQRLANNSDSITYRVRKGDSLSSIAKRHGVNIK 425 (449)
T ss_pred EEECCCCCHHHHHHHHCCCHHHHHHHCCCCCCCCCCCCEEEECCCCCCCCCCCCCCCEEEEECCCCCHHHHHHHHCCCHH
T ss_conf 88589998999999979799999998399944478998787378875555656789658998999979999999698999
Q ss_pred HHC
Q ss_conf 960
Q gi|254781147|r 79 KLL 81 (83)
Q Consensus 79 ~l~ 81 (83)
+|.
T Consensus 426 ~L~ 428 (449)
T PRK10783 426 DVM 428 (449)
T ss_pred HHH
T ss_conf 999
Done!